Identification of the functional domains of ANT-1, a novel coactivator of the androgen receptor

International Nuclear Information System (INIS)

Fan Shuli; Goto, Kiminobu; Chen Guangchun; Morinaga, Hidetaka; Nomura, Masatoshi; Okabe, Taijiro; Nawata, Hajime; Yanase, Toshihiko

2006-01-01

Previously, we identified a transcriptional coactivator for the activation function-1 (AF-1) domain of the human androgen receptor (AR) and designated it androgen receptor N-terminal domain transactivating protein-1 (ANT-1). This coactivator, which contains multiple tetratricopeptide repeat (TPR) motifs from amino acid (aa) 294, is identical to a component of U5 small nuclear ribonucleoprotein particles and binds specifically to the AR or glucocorticoid receptor. Here, we identified four distinct functional domains. The AR-AF-1-binding domain, which bound to either aa 180-360 or 360-532 in AR-AF-1, clearly overlapped with TAU-1 and TAU-5. This domain and the subnuclear speckle formation domain in ANT-1 were assigned within the TPR motifs, while the transactivating and nuclear localization signal domains resided within the N-terminal sequence. The existence of these functional domains may further support the idea that ANT-1 can function as an AR-AF-1-specific coactivator while mediating a transcription-splicing coupling

Progress report. [Research in theoretical nuclear and subnuclear physics

International Nuclear Information System (INIS)

1997-01-01

Sergei Ananyan has completed one nice piece of nuclear physics on 'Electroweak Processes Involving (0 + 0) Excitations in Nuclei' and has written this work up for publication. He is well into his main thesis problem on weak axial vector exchange currents and already has some very interesting new results. Bryan Barmore is now finishing numerical calculations on the problem of radiating meson fields in relativistic heavy ion collisions. Gary Prezeau has just started on the problem of chiral QHD with vector mesons. Gary should finish his Ph.D. in 1998. A PC has been purchased for the group through CEBAF and they are now tied into the CEBAF computer system., They have organized a Nuclear Theory Study Group in the Department and last year they worked through the books on 'Computational Nuclear Physics.' Next year they will run a series on effective field theories and chiral perturbation theory. Tod Bachman just completed a senior thesis on relativistic Hartree calculations of the newly-found doubly magic nuclei 100 Sn and 132 Sn. The book on 'Theoretical Nuclear and Subnuclear Physics' has now been published by Oxford Press. Also included here is the proposal for renewal of the contract

Paraspeckles. A novel nuclear domain

DEFF Research Database (Denmark)

Fox, Archa H; Lam, Yun Wah; Leung, Anthony K L

2002-01-01

BACKGROUND: The cell nucleus contains distinct classes of subnuclear bodies, including nucleoli, splicing speckles, Cajal bodies, gems, and PML bodies. Many nuclear proteins are known to interact dynamically with one or other of these bodies, and disruption of the specific organization of nuclear...

Glucose effects on long-term memory performance : duration and domain specificity.

OpenAIRE

Owen, Laura; Finnegan, Yvonne; Hu, Henglong; Scholey, Andrew B.; Sünram-Lea, Sandra I.

2010-01-01

Rational; Previous research has suggested that long term- verbal declarative memory is particularly sensitive to enhancement by glucose loading, however investigation of glucose effects on certain memory domains has hitherto been neglected. Therefore domain specificity of glucose effects merits further elucidation. Objectives; The aim of the present research was to provide a more comprehensive investigation of the possible effects of glucose administration on different aspects of memory by i)...

A new baryonic equation of state at sub-nuclear densities for core-collapse simulations

International Nuclear Information System (INIS)

Furusawa, Shun; Yamada, Shoichi; Sumiyoshi, Kohsuke; Suzuki, Hideyuki

2012-01-01

We construct a new equation of state for baryons at sub-nuclear densities for the use in core-collapse simulations of massive stars. The formulation is based on the nuclear statistical equilibrium description and the liquid drop approximation of nuclei. The model free energy to minimize is calculated by using relativistic mean field theory for nucleons and the mass formula for nuclei with atomic number up to ∼ 1000. We have also taken into account the pasta phase. We find that the free energy and other thermodynamical quantities are not very different from those given in the standard EOSs that adopt the single nucleus approximation. On the other hand, the average mass is systematically different, which may have an important effect to the rates of electron captures and coherent neutrino scatterings on nuclei in supernova cores. It is also interesting that the root mean square of the mass number is not very different from the average mass number, since the former is important for the evaluation of coherent scattering rates on nuclei but has been unavailable so far.

A new baryonic equation of state at sub-nuclear densities for core-collapse simulations

Science.gov (United States)

Furusawa, Shun; Yamada, Shoichi; Sumiyoshi, Kohsuke; Suzuki, Hideyuki

2012-11-01

We construct a new equation of state for baryons at sub-nuclear densities for the use in core-collapse simulations of massive stars. The formulation is based on the nuclear statistical equilibrium description and the liquid drop approximation of nuclei. The model free energy to minimize is calculated by using relativistic mean field theory for nucleons and the mass formula for nuclei with atomic number up to ~ 1000. We have also taken into account the pasta phase. We find that the free energy and other thermodynamical quantities are not very different from those given in the standard EOSs that adopt the single nucleus approximation. On the other hand, the average mass is systematically different, which may have an important effect to the rates of electron captures and coherent neutrino scatterings on nuclei in supernova cores. It is also interesting that the root mean square of the mass number is not very different from the average mass number, since the former is important for the evaluation of coherent scattering rates on nuclei but has been unavailable so far.

A new baryonic equation of state at sub-nuclear densities for core-collapse simulations

Energy Technology Data Exchange (ETDEWEB)

Furusawa, Shun; Yamada, Shoichi; Sumiyoshi, Kohsuke; Suzuki, Hideyuki [Department of Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555 (Japan); Department of Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555 (Japan) and Advanced Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555 (Japan); Numazu College of Technology, Ooka 3600, Numazu, Shizuoka 410-8501 (Japan); Faculty of Science and Technology, Tokyo University of Science, Yamazaki 2641, Noda, Chiba 278-8510 (Japan)

2012-11-12

We construct a new equation of state for baryons at sub-nuclear densities for the use in core-collapse simulations of massive stars. The formulation is based on the nuclear statistical equilibrium description and the liquid drop approximation of nuclei. The model free energy to minimize is calculated by using relativistic mean field theory for nucleons and the mass formula for nuclei with atomic number up to {approx} 1000. We have also taken into account the pasta phase. We find that the free energy and other thermodynamical quantities are not very different from those given in the standard EOSs that adopt the single nucleus approximation. On the other hand, the average mass is systematically different, which may have an important effect to the rates of electron captures and coherent neutrino scatterings on nuclei in supernova cores. It is also interesting that the root mean square of the mass number is not very different from the average mass number, since the former is important for the evaluation of coherent scattering rates on nuclei but has been unavailable so far.

Long-term memory consolidation: The role of RNA-binding proteins with prion-like domains.

Science.gov (United States)

Sudhakaran, Indulekha P; Ramaswami, Mani

2017-05-04

Long-term and short-term memories differ primarily in the duration of their retention. At a molecular level, long-term memory (LTM) is distinguished from short-term memory (STM) by its requirement for new gene expression. In addition to transcription (nuclear gene expression) the translation of stored mRNAs is necessary for LTM formation. The mechanisms and functions for temporal and spatial regulation of mRNAs required for LTM is a major contemporary problem, of interest from molecular, cell biological, neurobiological and clinical perspectives. This review discusses primary evidence in support for translational regulatory events involved in LTM and a model in which different phases of translation underlie distinct phases of consolidation of memories. However, it focuses largely on mechanisms of memory persistence and the role of prion-like domains in this defining aspect of long-term memory. We consider primary evidence for the concept that Cytoplasmic Polyadenylation Element Binding (CPEB) protein enables the persistence of formed memories by transforming in prion-like manner from a soluble monomeric state to a self-perpetuating and persistent polymeric translationally active state required for maintaining persistent synaptic plasticity. We further discuss prion-like domains prevalent on several other RNA-binding proteins involved in neuronal translational control underlying LTM. Growing evidence indicates that such RNA regulatory proteins are components of mRNP (RiboNucleoProtein) granules. In these proteins, prion-like domains, being intrinsically disordered, could mediate weak transient interactions that allow the assembly of RNP granules, a source of silenced mRNAs whose translation is necessary for LTM. We consider the structural bases for RNA granules formation as well as functions of disordered domains and discuss how these complicate the interpretation of existing experimental data relevant to general mechanisms by which prion-domain containing RBPs

A comparison of serial order short-term memory effects across verbal and musical domains.

Science.gov (United States)

Gorin, Simon; Mengal, Pierre; Majerus, Steve

2018-04-01

Recent studies suggest that the mechanisms involved in the short-term retention of serial order information may be shared across short-term memory (STM) domains such as verbal and visuospatial STM. Given the intrinsic sequential organization of musical material, the study of STM for musical information may be particularly informative about serial order retention processes and their domain-generality. The present experiment examined serial order STM for verbal and musical sequences in participants with no advanced musical expertise and experienced musicians. Serial order STM for verbal information was assessed via a serial order reconstruction task for digit sequences. In the musical domain, serial order STM was assessed using a novel melodic sequence reconstruction task maximizing the retention of tone order information. We observed that performance for the verbal and musical tasks was characterized by sequence length as well as primacy and recency effects. Serial order errors in both tasks were characterized by similar transposition gradients and ratios of fill-in:infill errors. These effects were observed for both participant groups, although the transposition gradients and ratios of fill-in:infill errors showed additional specificities for musician participants in the musical task. The data support domain-general serial order STM effects but also suggest the existence of additional domain-specific effects. Implications for models of serial order STM in verbal and musical domains are discussed.

Peripheral subnuclear positioning suppresses Tcrb recombination and segregates Tcrb alleles from RAG2.

Science.gov (United States)

Chan, Elizabeth A W; Teng, Grace; Corbett, Elizabeth; Choudhury, Kingshuk Roy; Bassing, Craig H; Schatz, David G; Krangel, Michael S

2013-11-26

Allelic exclusion requires that the two alleles at antigen-receptor loci attempt to recombine variable (V), diversity (D), and joining (J) gene segments [V(D)J recombination] asynchronously in nuclei of developing lymphocytes. It previously was shown that T-cell receptor β (Tcrb) alleles frequently and stochastically associate with the nuclear lamina and pericentromeric heterochromatin in CD4(-)CD8(-) thymocytes. Moreover, rearranged alleles were underrepresented at these locations. Here we used 3D immunofluorescence in situ hybridization to identify recently rearranged Tcrb alleles based on the accumulation of the DNA-repair protein 53BP1. We found that Tcrb alleles recombine asynchronously in double-negative thymocytes and that V(D)J recombination is suppressed on peripheral as compared with central Tcrb alleles. Moreover, the recombination events that did take place at the nuclear periphery preferentially occurred on Tcrb alleles that were partially dissociated from the nuclear lamina. To understand better the mechanism by which V(D)J recombination is suppressed at the nuclear periphery, we evaluated the subnuclear distribution of recombination-activating gene 2 (RAG2) protein. We found that RAG2 abundance was reduced at the nuclear periphery. Moreover, RAG2 was distributed differently from RNA polymerase II and histone H3K4 trimethylation. Our data suggest that the nuclear periphery suppresses V(D)J recombination, at least in part, by segregating Tcrb alleles from RAG proteins.

Involvement of the N-terminal unique domain of Chk tyrosine kinase in Chk-induced tyrosine phosphorylation in the nucleus

International Nuclear Information System (INIS)

Nakayama, Yuji; Kawana, Akiko; Igarashi, Asae; Yamaguchi, Naoto

2006-01-01

Chk tyrosine kinase phosphorylates Src-family kinases and suppresses their kinase activity. We recently showed that Chk localizes to the nucleus as well as the cytoplasm and inhibits cell proliferation. In this study, we explored the role of the N-terminal unique domain of Chk in nuclear localization and Chk-induced tyrosine phosphorylation in the nucleus. In situ binding experiments showed that the N-terminal domain of Chk was associated with the nucleus and the nuclear matrix. The presence of the N-terminal domain of Chk led to a fourfold increase in cell population exhibiting Chk-induced tyrosine phosphorylation in the nucleus. Expression of Chk but not kinase-deficient Chk induced tyrosine phosphorylation of a variety of proteins ranging from 23 kDa to ∼200 kDa, especially in Triton X-100-insoluble fraction that included chromatin and the nuclear matrix. Intriguingly, in situ subnuclear fractionations revealed that Chk induced tyrosine phosphorylation of proteins that were associated with the nuclear matrix. These results suggest that various unidentified substrates of Chk, besides Src-family kinases, may be present in the nucleus. Thus, our findings indicate that the importance of the N-terminal domain to Chk-induced tyrosine phosphorylation in the nucleus, implicating that these nuclear tyrosine-phosphorylated proteins may contribute to inhibition of cell proliferation

Localisation of Neuregulin 1-{beta}3 to different sub-nuclear structures alters gene expression

Energy Technology Data Exchange (ETDEWEB)

Wang, Ming; Trim, Carol M.; Gullick, William J., E-mail: w.j.gullick@kent.ac.uk

2011-02-15

Neuregulins are growth factors that signal via the ErbB3 and ErbB4 receptors. Here we show using immunohistochemistry that they are often expressed in the nucleus of a range of tumour types including soft tissue and breast. The Neuregulin 1 type I-{beta}3 (NRG1-{beta}3) isoform localises to two sub-nuclear compartments in animal cells, nucleoli and spliceosomes. We used NRG1-{beta}3 tagged with photoactivatable GFP and demonstrated that this re-localised from nucleoli to spliceosomes over 90 min. Tyrosine kinase activity was not required for retaining the NRG1-{beta}3 within the nucleus. Mutation of the lysines 14 and 16 or 15 and 16 together prevented nucleolar uptake while four positively charged residues were identified which were required for spliceosome uptake. Molecular modelling suggests that three of these may form a binding site. We showed using a kinome array that NRG1-{beta}3 and a mutant exclusively localising to spliceosomes increased phosphorylation and/or expression of the HER4 and HER2 receptors. Using a transcriptomic analysis the same two constructs induced expression of several messenger RNAs and we confirmed the increased expression at the protein level of the most highly induced, Heat Shock Protein 70B'. These results suggest that Neuregulin activates receptor signalling in spliceosomes leading to altered gene expression.

Localisation of Neuregulin 1-β3 to different sub-nuclear structures alters gene expression

International Nuclear Information System (INIS)

Wang, Ming; Trim, Carol M.; Gullick, William J.

2011-01-01

Neuregulins are growth factors that signal via the ErbB3 and ErbB4 receptors. Here we show using immunohistochemistry that they are often expressed in the nucleus of a range of tumour types including soft tissue and breast. The Neuregulin 1 type I-β3 (NRG1-β3) isoform localises to two sub-nuclear compartments in animal cells, nucleoli and spliceosomes. We used NRG1-β3 tagged with photoactivatable GFP and demonstrated that this re-localised from nucleoli to spliceosomes over 90 min. Tyrosine kinase activity was not required for retaining the NRG1-β3 within the nucleus. Mutation of the lysines 14 and 16 or 15 and 16 together prevented nucleolar uptake while four positively charged residues were identified which were required for spliceosome uptake. Molecular modelling suggests that three of these may form a binding site. We showed using a kinome array that NRG1-β3 and a mutant exclusively localising to spliceosomes increased phosphorylation and/or expression of the HER4 and HER2 receptors. Using a transcriptomic analysis the same two constructs induced expression of several messenger RNAs and we confirmed the increased expression at the protein level of the most highly induced, Heat Shock Protein 70B'. These results suggest that Neuregulin activates receptor signalling in spliceosomes leading to altered gene expression.

Androgen receptor regulates nuclear trafficking and nuclear domain residency of corepressor HDAC7 in a ligand-dependent fashion

International Nuclear Information System (INIS)

Karvonen, Ulla; Jaenne, Olli A.; Palvimo, Jorma J.

2006-01-01

In addition to chromosomal proteins, histone deacetylases (HDACs) target transcription factors in transcriptional repression. Here, we show that the class II HDAC family member HDAC7 is an efficient corepressor of the androgen receptor (AR). HDAC7 resided in the cytoplasm in the absence of AR or a cognate ligand, but hormone-occupancy of AR induced nuclear transfer of HDAC7. Nuclear colocalization pattern of AR and HDAC7 was dependent on the nature of the ligand. In the presence of testosterone, a portion of HDAC7 localized to pearl-like nuclear domains, whereas AR occupied with antagonistic ligands cyproterone acetate- or casodex (bicalutamide) recruited HDAC7 from these domains to colocalize with the receptor in speckles and nucleoplasm in a more complete fashion. Ectopic expression of PML-3 relieved the repressive effect of HDAC7 on AR function by sequestering HDAC7 to PML-3 domains. AR acetylation at Lys630/632/633 was not the target of HDAC7 repression, since repression of AR function was independent of these acetylation sites. Moreover, the deacetylase activity of HDAC7 was in part dispensable in the repression of AR function. In sum, our results identify HDAC7 as a novel AR corepressor whose subcellular and subnuclear compartmentalization can be regulated in an androgen-selective manner

Alanine repeats influence protein localization in splicing speckles and paraspeckles.

Science.gov (United States)

Chang, Shuo-Hsiu; Chang, Wei-Lun; Lu, Chia-Chen; Tarn, Woan-Yuh

2014-12-16

Mammalian splicing regulatory protein RNA-binding motif protein 4 (RBM4) has an alanine repeat-containing C-terminal domain (CAD) that confers both nuclear- and splicing speckle-targeting activities. Alanine-repeat expansion has pathological potential. Here we show that the alanine-repeat tracts influence the subnuclear targeting properties of the RBM4 CAD in cultured human cells. Notably, truncation of the alanine tracts redistributed a portion of RBM4 to paraspeckles. The alanine-deficient CAD was sufficient for paraspeckle targeting. On the other hand, alanine-repeat expansion reduced the mobility of RBM4 and impaired its splicing activity. We further took advantage of the putative coactivator activator (CoAA)-RBM4 conjoined splicing factor, CoAZ, to investigate the function of the CAD in subnuclear targeting. Transiently expressed CoAZ formed discrete nuclear foci that emerged and subsequently separated-fully or partially-from paraspeckles. Alanine-repeat expansion appeared to prevent CoAZ separation from paraspeckles, resulting in their complete colocalization. CoAZ foci were dynamic but, unlike paraspeckles, were resistant to RNase treatment. Our results indicate that the alanine-rich CAD, in conjunction with its conjoined RNA-binding domain(s), differentially influences the subnuclear localization and biogenesis of RBM4 and CoAZ. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Sub-nuclear irradiation, in-vivo microscopy and single-molecule imaging to study a DNA Polymerase

Energy Technology Data Exchange (ETDEWEB)

Soria, G; Mansilla, S; Belluscio, L; Speroni, J; D' Alessio, C; Gottifredi, V [Fundacion Leloir, Buenos Aires (Argentina); Essers, J; Kanaar, R [Erasmus Medical Center, Rotterdam (Netherlands)

2009-07-01

When the DNA is damaged in cells progressing through S phase, replication blockage can be avoided by TLS (Translesion DNA synthesis). This is an auxiliary replication mechanism that relies on the function of specialized polymerases that accomplish DNA damage bypass. An example of a classical TLS polymerase is Pol {eta} ({eta}). The current model implies that Pol {eta} activity is circumscribed to S-phase. Here we perform a systematic characterization of Pol {eta} behaviour after DNA-damage. We show that Pol {eta} is recruited to UV-induced DNA lesions in cells outside S phase including cells permanently arrested in G1. This observation was confirmed by different sub-nuclear damage strategies including global UV irradiation, local UV irradiation and local multi-photon laser irradiation of single nuclei in living cells. By local UV irradiation and alpha particle irradiation we evaluated the potential connection between Pol h recruitment to DNA lesions outside S phase and Homologous recombination repair (HRR) or Nucleotide excision repair (NER). Finally, we employ a single-molecule imaging approach (known as DNA fiber-assay) to determine how Pol h influences the progression of the replication fork. Our data reveals that the re-localization of Pol {eta} to DNA lesions might be temporally and mechanistically uncoupled from replicative DNA synthesis and from DNA damage processing. (authors)

Sub-nuclear irradiation, in-vivo microscopy and single-molecule imaging to study a DNA Polymerase

International Nuclear Information System (INIS)

Soria, G.; Mansilla, S.; Belluscio, L.; Speroni, J.; D'Alessio, C.; Gottifredi, V.; Essers, J.; Kanaar, R.

2009-01-01

When the DNA is damaged in cells progressing through S phase, replication blockage can be avoided by TLS (Translesion DNA synthesis). This is an auxiliary replication mechanism that relies on the function of specialized polymerases that accomplish DNA damage bypass. An example of a classical TLS polymerase is Pol η (eta). The current model implies that Pol η activity is circumscribed to S-phase. Here we perform a systematic characterization of Pol η behaviour after DNA-damage. We show that Pol η is recruited to UV-induced DNA lesions in cells outside S phase including cells permanently arrested in G1. This observation was confirmed by different sub-nuclear damage strategies including global UV irradiation, local UV irradiation and local multi-photon laser irradiation of single nuclei in living cells. By local UV irradiation and alpha particle irradiation we evaluated the potential connection between Pol h recruitment to DNA lesions outside S phase and Homologous recombination repair (HRR) or Nucleotide excision repair (NER). Finally, we employ a single-molecule imaging approach (known as DNA fiber-assay) to determine how Pol h influences the progression of the replication fork. Our data reveals that the re-localization of Pol η to DNA lesions might be temporally and mechanistically uncoupled from replicative DNA synthesis and from DNA damage processing. (authors)

Selective Short-Term Memory Deficits Arise from Impaired Domain-General Semantic Control Mechanisms

Science.gov (United States)

Hoffman, Paul; Jefferies, Elizabeth; Ehsan, Sheeba; Hopper, Samantha; Lambon Ralph, Matthew A.

2009-01-01

Semantic short-term memory (STM) patients have a reduced ability to retain semantic information over brief delays but perform well on other semantic tasks; this pattern suggests damage to a dedicated buffer for semantic information. Alternatively, these difficulties may arise from mild disruption to domain-general semantic processes that have…

Domain-Generality of Timing-Based Serial Order Processes in Short-Term Memory: New Insights from Musical and Verbal Domains.

Directory of Open Access Journals (Sweden)

Simon Gorin

Full Text Available Several models in the verbal domain of short-term memory (STM consider a dissociation between item and order processing. This view is supported by data demonstrating that different types of time-based interference have a greater effect on memory for the order of to-be-remembered items than on memory for the items themselves. The present study investigated the domain-generality of the item versus serial order dissociation by comparing the differential effects of time-based interfering tasks, such as rhythmic interference and articulatory suppression, on item and order processing in verbal and musical STM domains. In Experiment 1, participants had to maintain sequences of verbal or musical information in STM, followed by a probe sequence, this under different conditions of interference (no-interference, rhythmic interference, articulatory suppression. They were required to decide whether all items of the probe list matched those of the memory list (item condition or whether the order of the items in the probe sequence matched the order in the memory list (order condition. In Experiment 2, participants performed a serial order probe recognition task for verbal and musical sequences ensuring sequential maintenance processes, under no-interference or rhythmic interference conditions. For Experiment 1, serial order recognition was not significantly more impacted by interfering tasks than was item recognition, this for both verbal and musical domains. For Experiment 2, we observed selective interference of the rhythmic interference condition on both musical and verbal order STM tasks. Overall, the results suggest a similar and selective sensitivity to time-based interference for serial order STM in verbal and musical domains, but only when the STM tasks ensure sequential maintenance processes.

Domain-Generality of Timing-Based Serial Order Processes in Short-Term Memory: New Insights from Musical and Verbal Domains.

Science.gov (United States)

Gorin, Simon; Kowialiewski, Benjamin; Majerus, Steve

2016-01-01

Several models in the verbal domain of short-term memory (STM) consider a dissociation between item and order processing. This view is supported by data demonstrating that different types of time-based interference have a greater effect on memory for the order of to-be-remembered items than on memory for the items themselves. The present study investigated the domain-generality of the item versus serial order dissociation by comparing the differential effects of time-based interfering tasks, such as rhythmic interference and articulatory suppression, on item and order processing in verbal and musical STM domains. In Experiment 1, participants had to maintain sequences of verbal or musical information in STM, followed by a probe sequence, this under different conditions of interference (no-interference, rhythmic interference, articulatory suppression). They were required to decide whether all items of the probe list matched those of the memory list (item condition) or whether the order of the items in the probe sequence matched the order in the memory list (order condition). In Experiment 2, participants performed a serial order probe recognition task for verbal and musical sequences ensuring sequential maintenance processes, under no-interference or rhythmic interference conditions. For Experiment 1, serial order recognition was not significantly more impacted by interfering tasks than was item recognition, this for both verbal and musical domains. For Experiment 2, we observed selective interference of the rhythmic interference condition on both musical and verbal order STM tasks. Overall, the results suggest a similar and selective sensitivity to time-based interference for serial order STM in verbal and musical domains, but only when the STM tasks ensure sequential maintenance processes.

Glucose effects on long-term memory performance: duration and domain specificity.

Science.gov (United States)

Owen, Lauren; Finnegan, Yvonne; Hu, Henglong; Scholey, Andrew B; Sünram-Lea, Sandra I

2010-08-01

Previous research has suggested that long-term verbal declarative memory is particularly sensitive to enhancement by glucose loading; however, investigation of glucose effects on certain memory domains has hitherto been neglected. Therefore, domain specificity of glucose effects merits further elucidation. The aim of the present research was to provide a more comprehensive investigation of the possible effects of glucose administration on different aspects of memory by 1) contrasting the effect of glucose administration on different memory domains (implicit/explicit memory; verbal/non-verbal memory, and recognition/familiarity processes), 2) investigating whether potential effects on memory domains differ depending on the dose of glucose administered (25 g versus 60 g), 3) exploring the duration of the glucose facilitation effect (assessment of memory performance 35 min and 1 week after encoding). A double-blind between-subjects design was used to test the effects of administration of 25 and 60 g glucose on memory performance. Implicit memory was improved following administration of 60 g of glucose. Glucose supplementation failed to improve face recognition performance but significantly improved performance of word recall and recognition following administration of 60 g of glucose. However, effects were not maintained 1 week following encoding. Improved implicit memory performance following glucose administration has not been reported before. Furthermore, the current data tentatively suggest that level of processing may determine the required glucose dosage to demonstrate memory improvement and that higher dosages may be able to exert effects on memory pertaining to both hippocampal and non-hippocampal brain regions.

Spatio-temporal re-organization of replication foci accompanies replication domain consolidation during human pluripotent stem cell lineage specification

Science.gov (United States)

Wilson, Korey A.; Elefanty, Andrew G.; Stanley, Edouard G.; Gilbert, David M.

2016-01-01

ABSTRACT Lineage specification of both mouse and human pluripotent stem cells (PSCs) is accompanied by spatial consolidation of chromosome domains and temporal consolidation of their replication timing. Replication timing and chromatin organization are both established during G1 phase at the timing decision point (TDP). Here, we have developed live cell imaging tools to track spatio-temporal replication domain consolidation during differentiation. First, we demonstrate that the fluorescence ubiquitination cell cycle indicator (Fucci) system is incapable of demarcating G1/S or G2/M cell cycle transitions. Instead, we employ a combination of fluorescent PCNA to monitor S phase progression, cytokinesis to demarcate mitosis, and fluorescent nucleotides to label early and late replication foci and track their 3D organization into sub-nuclear chromatin compartments throughout all cell cycle transitions. We find that, as human PSCs differentiate, the length of S phase devoted to replication of spatially clustered replication foci increases, coincident with global compartmentalization of domains into temporally clustered blocks of chromatin. Importantly, re-localization and anchorage of domains was completed prior to the onset of S phase, even in the context of an abbreviated PSC G1 phase. This approach can also be employed to investigate cell fate transitions in single PSCs, which could be seen to differentiate preferentially from G1 phase. Together, our results establish real-time, live-cell imaging methods for tracking cell cycle transitions during human PSC differentiation that can be applied to study chromosome domain consolidation and other aspects of lineage specification. PMID:27433885

Long term preservation of scientific data: Lessons from jet and other domains

International Nuclear Information System (INIS)

Layne, R.; Capel, A.; Cook, N.; Wheatley, M.

2012-01-01

Highlights: ► Data from a fusion experiment must be preserved for decades, and will be required beyond the lifetime of the experiment. ► General principles of long-term data preservation have been identified in domains outside fusion. ► Key challenges are media obsolescence, data organisation, and file format obsolescence. ► Data from JET has to date been preserved for almost three decades: the steps taken to achieve this are discussed. ► Recommendations for new devices in planning for the long-term preservation of their data are made. - Abstract: All fusion devices generate large amounts of data, which must remain accessible throughout and beyond the lifetime of the device. This need for long-term data preservation creates major software and hardware challenges. Issues surrounding long-term data preservation will be discussed, and the main challenges in data curation will be outlined. The paper will then review the approaches taken at JET to ensure accessibility of all of JET's data over almost three decades. Using the JET experience and the wider context, the paper will then suggest how new experiments should plan for the long-term preservation of their data.

The C-terminal domain of the Arabidopsis AtMBD7 protein confers strong chromatin binding activity

International Nuclear Information System (INIS)

Zemach, Assaf; Paul, Laju K.; Stambolsky, Perry; Efroni, Idan; Rotter, Varda; Grafi, Gideon

2009-01-01

The Arabidopsis MBD7 (AtMBD7) - a naturally occurring poly MBD protein - was previously found to be functional in binding methylated-CpG dinucleotides in vitro and localized to highly methylated chromocenters in vivo. Furthermore, AtMBD7 has significantly lower mobility within the nucleus conferred by cooperative activity of its three MBD motifs. Here we show that besides the MBD motifs, AtMBD7 possesses a strong chromatin binding domain located at its C-terminus designated sticky-C (StkC). Mutational analysis showed that a glutamic acid residue near the C-terminus is essential though not sufficient for the StkC function. Further analysis demonstrated that this motif can render nuclear proteins highly immobile both in plant and animal cells, without affecting their native subnuclear localization. Thus, the C-terminal, StkC motif plays an important role in fastening AtMBD7 to its chromosomal, CpG-methylated sites. It may be possible to utilize this motif for fastening nuclear proteins to their chromosomal sites both in plant and animal cells for research and gene therapy applications.

The Polyakov, Nambu and Jona-Lasinio model and its applications to describe the sub-nuclear particles

International Nuclear Information System (INIS)

Blanquier, E.

2013-01-01

To study the high energy nuclear physics and the associated phenomenon, as the quark-gluon plasma / hadronic matter phase transition, the Nambu and Jona-Lasinio model (NJL) appears as an interesting alternative to the Quantum Chromodynamics, not solvable at the considered energies. Indeed, the NJL model allows the description of quarks physics, at finite temperatures and densities. Furthermore, in order to try to correct a limitation of the NJL model, i.e. the absence of confinement, it was proposed a coupling of the quarks/antiquarks to a Polyakov loop, forming the PNJL model. The objective of this thesis is to see the possibilities offered by the NJL and PNJL models, to describe relevant sub-nuclear particles (quarks, mesons, diquarks and baryons), to study their interactions, and to proceed to a dynamical study involving these particles. After a recall of the useful tools, we modeled the u, d, s effective quarks and the mesons. Then, we described the baryons as quarks-diquarks bound states. A part of the work concerned the calculations of the cross-sections associated to the possible reactions implying these particles. Then, we incorporated these results in a computer code, in order to study the cooling of a quarks/antiquarks plasma and its hadronization. In this study, each particle evolves in a system in which the temperature and the densities are local parameters. We have two types of interactions: one due to the collisions, and the other is a remote interaction, notably between quarks. Finally, we studied the properties of our approach: qualities, limitations, and possible evolutions. (author)

Short-term memory and working memory in children with blindness: support for a domain general or domain specific system?

Science.gov (United States)

Swanson, H Lee; Luxenberg, Diana

2009-05-01

The study explored the contribution of two component processes (phonological and executive) to blind children's memory performance. Children with blindness and sight were matched on gender, chronological age, and verbal intelligence and compared on measures of short-term memory (STM) and working memory (WM). Although the measures were highly correlated, the results from two experiments indicated that the blind children were superior to sighted children on measures of STM, but not on measures of WM. The results supported the notion that children with blindness have advantages on memory tasks that draw upon resources from the phonological loop. However, comparable performance between the ability groups on WM measures suggests there are domain specific aspects in the executive system.

THE FUNDAMENTAL SOLUTIONS FOR MULTI-TERM MODIFIED POWER LAW WAVE EQUATIONS IN A FINITE DOMAIN.

Science.gov (United States)

Jiang, H; Liu, F; Meerschaert, M M; McGough, R J

2013-01-01

Fractional partial differential equations with more than one fractional derivative term in time, such as the Szabo wave equation, or the power law wave equation, describe important physical phenomena. However, studies of these multi-term time-space or time fractional wave equations are still under development. In this paper, multi-term modified power law wave equations in a finite domain are considered. The multi-term time fractional derivatives are defined in the Caputo sense, whose orders belong to the intervals (1, 2], [2, 3), [2, 4) or (0, n ) ( n > 2), respectively. Analytical solutions of the multi-term modified power law wave equations are derived. These new techniques are based on Luchko's Theorem, a spectral representation of the Laplacian operator, a method of separating variables and fractional derivative techniques. Then these general methods are applied to the special cases of the Szabo wave equation and the power law wave equation. These methods and techniques can also be extended to other kinds of the multi-term time-space fractional models including fractional Laplacian.

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

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

Fractional-Fourier-domain weighted Wigner distribution

NARCIS (Netherlands)

Stankovic, L.; Alieva, T.; Bastiaans, M.J.

2001-01-01

A fractional-Fourier-domain realization of the weighted Wigner distribution (or S-method), producing auto-terms close to the ones in the Wigner distribution itself, but with reduced cross-terms, is presented. The computational cost of this fractional-domain realization is the same as the

Understanding disciplinary vocabularies using a full-text enabled domain-independent term extraction approach.

Science.gov (United States)

Yan, Erjia; Williams, Jake; Chen, Zheng

2017-01-01

Publication metadata help deliver rich analyses of scholarly communication. However, research concepts and ideas are more effectively expressed through unstructured fields such as full texts. Thus, the goals of this paper are to employ a full-text enabled method to extract terms relevant to disciplinary vocabularies, and through them, to understand the relationships between disciplines. This paper uses an efficient, domain-independent term extraction method to extract disciplinary vocabularies from a large multidisciplinary corpus of PLoS ONE publications. It finds a power-law pattern in the frequency distributions of terms present in each discipline, indicating a semantic richness potentially sufficient for further study and advanced analysis. The salient relationships amongst these vocabularies become apparent in application of a principal component analysis. For example, Mathematics and Computer and Information Sciences were found to have similar vocabulary use patterns along with Engineering and Physics; while Chemistry and the Social Sciences were found to exhibit contrasting vocabulary use patterns along with the Earth Sciences and Chemistry. These results have implications to studies of scholarly communication as scholars attempt to identify the epistemological cultures of disciplines, and as a full text-based methodology could lead to machine learning applications in the automated classification of scholarly work according to disciplinary vocabularies.

Work reintegration after long-term sick leave: domains of influence on co-workers' ability to be supportive.

Science.gov (United States)

Petersen, Kirsten Schultz; Labriola, Merete; Nielsen, Claus Vinther; Larsen, Eva Ladekjær

2016-09-01

The purpose of the study is to identify domains of influence on co-workers' ability to be supportive of returning worker during the work reintegration (WR) process. An ethnographic study design was chosen involving fieldwork at four different workplaces, at an emergency care service, a waste disposal company and at two nursing homes. Qualitative methods for inquiry were used including participant observation, individual- and group interviews of 30 participants. Data were coded and analysed according to a grounded theory approach. Four themes were identified related to domains of influence on co-workers' ability to be supportive of returning worker during the WR process: (1) organisation of work and level of interaction; (2) disruption of work routines, (3) relationship with returning worker and (4) attitudes towards sick leave. The WR process after long-term sick leave is not only influenced by the WR's arrangements made, but also by the co-workers' responses to the process. Work arrangements not only affect the returning worker's ability to return-to-work (RTW) successfully, but also the co-workers' ability to be supportive and their ability to take active part in the process. Implications for Rehabilitation The process of WR after long-term sick leave involves interaction with co-workers. Domains of influence is in the co-workers' perspective influencing their ability to be supportive during reintegration of a returning worker. Future WR management could benefit from integrating the conditions for co-worker support. We encourage co-workers to be involved in the RTW planning, monitoring and evaluation with particular focus on how the WR arrangements are influencing their work and their ability to be supportive.

Gait Event Detection in Real-World Environment for Long-Term Applications: Incorporating Domain Knowledge Into Time-Frequency Analysis.

Science.gov (United States)

Khandelwal, Siddhartha; Wickstrom, Nicholas

2016-12-01

Detecting gait events is the key to many gait analysis applications that would benefit from continuous monitoring or long-term analysis. Most gait event detection algorithms using wearable sensors that offer a potential for use in daily living have been developed from data collected in controlled indoor experiments. However, for real-word applications, it is essential that the analysis is carried out in humans' natural environment; that involves different gait speeds, changing walking terrains, varying surface inclinations and regular turns among other factors. Existing domain knowledge in the form of principles or underlying fundamental gait relationships can be utilized to drive and support the data analysis in order to develop robust algorithms that can tackle real-world challenges in gait analysis. This paper presents a novel approach that exhibits how domain knowledge about human gait can be incorporated into time-frequency analysis to detect gait events from long-term accelerometer signals. The accuracy and robustness of the proposed algorithm are validated by experiments done in indoor and outdoor environments with approximately 93 600 gait events in total. The proposed algorithm exhibits consistently high performance scores across all datasets in both, indoor and outdoor environments.

High-resolution whole-genome sequencing reveals that specific chromatin domains from most human chromosomes associate with nucleoli.

Science.gov (United States)

van Koningsbruggen, Silvana; Gierlinski, Marek; Schofield, Pietá; Martin, David; Barton, Geoffey J; Ariyurek, Yavuz; den Dunnen, Johan T; Lamond, Angus I

2010-11-01

The nuclear space is mostly occupied by chromosome territories and nuclear bodies. Although this organization of chromosomes affects gene function, relatively little is known about the role of nuclear bodies in the organization of chromosomal regions. The nucleolus is the best-studied subnuclear structure and forms around the rRNA repeat gene clusters on the acrocentric chromosomes. In addition to rDNA, other chromatin sequences also surround the nucleolar surface and may even loop into the nucleolus. These additional nucleolar-associated domains (NADs) have not been well characterized. We present here a whole-genome, high-resolution analysis of chromatin endogenously associated with nucleoli. We have used a combination of three complementary approaches, namely fluorescence comparative genome hybridization, high-throughput deep DNA sequencing and photoactivation combined with time-lapse fluorescence microscopy. The data show that specific sequences from most human chromosomes, in addition to the rDNA repeat units, associate with nucleoli in a reproducible and heritable manner. NADs have in common a high density of AT-rich sequence elements, low gene density and a statistically significant enrichment in transcriptionally repressed genes. Unexpectedly, both the direct DNA sequencing and fluorescence photoactivation data show that certain chromatin loci can specifically associate with either the nucleolus, or the nuclear envelope.

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.

KEJAHATAN NAMA DOMAIN BERKAITAN DENGAN MEREK

Directory of Open Access Journals (Sweden)

Muhammad Nizar

2018-02-01

Full Text Available Indonesia already has an ITE Law governing domain names in general terms and on certain provisions in chapter VI, but the regulation of domain name crimes is not regulated in the ITE Law as mandated in the academic draft of the ITE Bill. The absence of regulation of domain name norm in the ITE Law creates problems with registrant of domain name (registrant which deliberately register the domain name is bad faith. The characteristic of a crime in a domain name relating to the mark is that the registered domain name has an equation in essence with another party’s well-known brand, the act of doing so by exploiting a reputation for well-known or previously commercially valuable names as domain names for addresses for sites (websites it manages. The Prosecutor may include articles of the KUHP in filing his indictment before the Court during the absence of special regulatory provisions concerning domain name crime.

System Identification A Frequency Domain Approach

CERN Document Server

Pintelon, Rik

2012-01-01

System identification is a general term used to describe mathematical tools and algorithms that build dynamical models from measured data. Used for prediction, control, physical interpretation, and the designing of any electrical systems, they are vital in the fields of electrical, mechanical, civil, and chemical engineering. Focusing mainly on frequency domain techniques, System Identification: A Frequency Domain Approach, Second Edition also studies in detail the similarities and differences with the classical time domain approach. It high??lights many of the important steps in the identi

Word Domain Disambiguation via Word Sense Disambiguation

Energy Technology Data Exchange (ETDEWEB)

Sanfilippo, Antonio P.; Tratz, Stephen C.; Gregory, Michelle L.

2006-06-04

Word subject domains have been widely used to improve the perform-ance of word sense disambiguation al-gorithms. However, comparatively little effort has been devoted so far to the disambiguation of word subject do-mains. The few existing approaches have focused on the development of al-gorithms specific to word domain dis-ambiguation. In this paper we explore an alternative approach where word domain disambiguation is achieved via word sense disambiguation. Our study shows that this approach yields very strong results, suggesting that word domain disambiguation can be ad-dressed in terms of word sense disam-biguation with no need for special purpose algorithms.

The Measurement and Role of Ecological Resilience Systems Theory Across Domain-Specific Outcomes: The Domain-Specific Resilient Systems Scales.

Science.gov (United States)

Maltby, John; Day, Liz; Hall, Sophie S; Chivers, Sally

2017-10-01

Research suggests that trait resilience may be best understood within an ecological resilient systems theory, comprising engineering, ecological, and adaptive capacity resilience. However, there is no evidence as to how this theory translates to specific life domains. Data from two samples (the United States, n = 1,278; the United Kingdom, n = 211) facilitated five studies that introduce the Domain-Specific Resilient Systems Scales for assessing ecological resilient systems theory within work, health, marriage, friendships, and education. The Domain-Specific Resilient Systems Scales are found to predict unique variance in job satisfaction, lower job burnout, quality-of-life following illness, marriage commitment, and educational engagement, while controlling for factors including sex, age, personality, cognitive ability, and trait resilience. The findings also suggest a distinction between the three resilience dimensions in terms of the types of systems to which they contribute. Engineering resilience may contribute most to life domains where an established system needs to be maintained, for example, one's health. Ecological resilience may contribute most to life domains where the system needs sustainability in terms of present and future goal orientation, for example, one's work. Adaptive Capacity may contribute most to life domains where the system needs to be retained, preventing it from reaching a crisis state, for example, work burnout.

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...

Reduced density matrix embedding. General formalism and inter-domain correlation functional.

Science.gov (United States)

Pernal, Katarzyna

2016-08-03

An embedding method for a one-electron reduced density matrix (1-RDM) is proposed. It is based on partitioning of 1-RDM into domains and describing each domain in the effective potential of the other ones. To assure N-representability of the total 1-RDM N-representability and strong-orthogonality conditions are imposed on the domains. The total energy is given as a sum of single-domain energies and domain-domain electron interaction contributions. Higher than two-body inter-domain interaction terms are neglected. The two-body correlation terms are approximated by deriving inter-domain correlation from couplings of density fluctuations of two domains at a time. Unlike in most density embedding methods kinetic energy is treated exactly and it is not required that densities pertaining to the domains are only weakly overlapping. We propose to treat each domain by a corrected perfect-pairing functional. On a few examples it is shown that the embedding reduced density matrix functional method (ERDMF) yields excellent results for molecules that are well described by a single Lewis structure even if strong static intra-domain or dynamic inter-domain correlation effects must be accounted for.

A Unified Framework for Creating Domain Dependent Polarity Lexicons from User Generated Reviews.

Directory of Open Access Journals (Sweden)

Muhammad Zubair Asghar

Full Text Available The exponential increase in the explosion of Web-based user generated reviews has resulted in the emergence of Opinion Mining (OM applications for analyzing the users' opinions toward products, services, and policies. The polarity lexicons often play a pivotal role in the OM, indicating the positivity and negativity of a term along with the numeric score. However, the commonly available domain independent lexicons are not an optimal choice for all of the domains within the OM applications. The aforementioned is due to the fact that the polarity of a term changes from one domain to other and such lexicons do not contain the correct polarity of a term for every domain. In this work, we focus on the problem of adapting a domain dependent polarity lexicon from set of labeled user reviews and domain independent lexicon to propose a unified learning framework based on the information theory concepts that can assign the terms with correct polarity (+ive, -ive scores. The benchmarking on three datasets (car, hotel, and drug reviews shows that our approach improves the performance of the polarity classification by achieving higher accuracy. Moreover, using the derived domain dependent lexicon changed the polarity of terms, and the experimental results show that our approach is more effective than the base line methods.

Over-expression of SR-cyclophilin, an interaction partner of nuclear pinin, releases SR family splicing factors from nuclear speckles

International Nuclear Information System (INIS)

Lin, C.-L.; Leu, Steve; Lu, M.-C.; Ouyang Pin

2004-01-01

Pre-mRNA splicing takes place within a dynamic ribonucleoprotein particle called the spliceosome and occurs in an ordered pathway. Although it is known that spliceosome consists of five small nuclear RNAs and at least 50 proteins, little is known about how the interaction among the proteins changes during splicing. Here we identify that SR-cyp, a Moca family of nuclear cyclophilin, interacts and colocalizes with nuclear pinin (pnn), a SR-related protein involving in pre-mRNA splicing. Nuclear pnn interacts with SR-cyp via its C-terminal RS domain. Upon SR-cyp over-expression, however, the subnuclear distribution of nuclear pnn is altered, resulting in its redistribution from nuclear speckles to a diffuse nucleoplasmic form. The diffuse subnuclear distribution of nuclear pnn is not due to epitope masking, accelerated protein turnover or post-translational modification. Furthermore, we find that SR-cyp regulates the subnuclear distribution of other SR family proteins, including SC35 and SRm300, in a similar manner as it does on nuclear pnn. This result is significant because it suggests that SR-cyp plays a general role in modulating the distribution pattern of SR-like and SR proteins, similar to that of Clk (cdc2-like kinase)/STY on SR family splicing factors. SR-cyp might direct its effect via either alteration of protein folding/conformation or of protein-protein interaction and thus may add another control level of regulation of SR family proteins and modification of their functions

Identification of structural domains in proteins by a graph heuristic

NARCIS (Netherlands)

Wernisch, Lorenz; Hunting, M.M.G.; Wodak, Shoshana J.

1999-01-01

A novel automatic procedure for identifying domains from protein atomic coordinates is presented. The procedure, termed STRUDL (STRUctural Domain Limits), does not take into account information on secondary structures and handles any number of domains made up of contiguous or non-contiguous chain

Nucleus of the solitary tract in the C57BL/6J mouse: Subnuclear parcellation, chorda tympani nerve projections, and brainstem connections.

Science.gov (United States)

Ganchrow, Donald; Ganchrow, Judith R; Cicchini, Vanessa; Bartel, Dianna L; Kaufman, Daniel; Girard, David; Whitehead, Mark C

2014-05-01

The nucleus of the solitary tract (NST) processes gustatory and related somatosensory information rostrally and general viscerosensory information caudally. To compare its connections with those of other rodents, this study in the C57BL/6J mouse provides a subnuclear cytoarchitectonic parcellation (Nissl stain) of the NST into rostral, intermediate, and caudal divisions. Subnuclei are further characterized by NADPH staining and P2X2 immunoreactivity (IR). Cholera toxin subunit B (CTb) labeling revealed those NST subnuclei receiving chorda tympani nerve (CT) afferents, those connecting with the parabrachial nucleus (PBN) and reticular formation (RF), and those interconnecting NST subnuclei. CT terminals are densest in the rostral central (RC) and medial (M) subnuclei; less dense in the rostral lateral (RL) subnucleus; and sparse in the ventral (V), ventral lateral (VL), and central lateral (CL) subnuclei. CTb injection into the PBN retrogradely labels cells in the aforementioned subnuclei; RC and M providing the largest source of PBN projection neurons. Pontine efferent axons terminate mainly in V and rostral medial (RM) subnuclei. CTb injection into the medullary RF labels cells and axonal endings predominantly in V at rostral and intermediate NST levels. Small CTb injections within the NST label extensive projections from the rostral division to caudal subnuclei. Projections from the caudal division primarily interconnect subnuclei confined to the caudal division of the NST; they also connect with the area postrema. P2X2 -IR identifies probable vagal nerve terminals in the central (Ce) subnucleus in the intermediate/caudal NST. Ce also shows intense NADPH staining and does not project to the PBN. Copyright © 2013 Wiley Periodicals, Inc.

Structural and functional analysis of multi-interface domains.

Directory of Open Access Journals (Sweden)

Liang Zhao

Full Text Available A multi-interface domain is a domain that can shape multiple and distinctive binding sites to contact with many other domains, forming a hub in domain-domain interaction networks. The functions played by the multiple interfaces are usually different, but there is no strict bijection between the functions and interfaces as some subsets of the interfaces play the same function. This work applies graph theory and algorithms to discover fingerprints for the multiple interfaces of a domain and to establish associations between the interfaces and functions, based on a huge set of multi-interface proteins from PDB. We found that about 40% of proteins have the multi-interface property, however the involved multi-interface domains account for only a tiny fraction (1.8% of the total number of domains. The interfaces of these domains are distinguishable in terms of their fingerprints, indicating the functional specificity of the multiple interfaces in a domain. Furthermore, we observed that both cooperative and distinctive structural patterns, which will be useful for protein engineering, exist in the multiple interfaces of a domain.

A Novel Transfer Learning Method Based on Common Space Mapping and Weighted Domain Matching

KAUST Repository

Liang, Ru-Ze; Xie, Wei; Li, Weizhi; Wang, Hongqi; Wang, Jim Jing-Yan; Taylor, Lisa

2017-01-01

In this paper, we propose a novel learning framework for the problem of domain transfer learning. We map the data of two domains to one single common space, and learn a classifier in this common space. Then we adapt the common classifier to the two domains by adding two adaptive functions to it respectively. In the common space, the target domain data points are weighted and matched to the target domain in term of distributions. The weighting terms of source domain data points and the target domain classification responses are also regularized by the local reconstruction coefficients. The novel transfer learning framework is evaluated over some benchmark cross-domain data sets, and it outperforms the existing state-of-the-art transfer learning methods.

A Novel Transfer Learning Method Based on Common Space Mapping and Weighted Domain Matching

KAUST Repository

Liang, Ru-Ze

2017-01-17

In this paper, we propose a novel learning framework for the problem of domain transfer learning. We map the data of two domains to one single common space, and learn a classifier in this common space. Then we adapt the common classifier to the two domains by adding two adaptive functions to it respectively. In the common space, the target domain data points are weighted and matched to the target domain in term of distributions. The weighting terms of source domain data points and the target domain classification responses are also regularized by the local reconstruction coefficients. The novel transfer learning framework is evaluated over some benchmark cross-domain data sets, and it outperforms the existing state-of-the-art transfer learning methods.

Fractional Regularization Term for Variational Image Registration

Directory of Open Access Journals (Sweden)

Rafael Verdú-Monedero

2009-01-01

Full Text Available Image registration is a widely used task of image analysis with applications in many fields. Its classical formulation and current improvements are given in the spatial domain. In this paper a regularization term based on fractional order derivatives is formulated. This term is defined and implemented in the frequency domain by translating the energy functional into the frequency domain and obtaining the Euler-Lagrange equations which minimize it. The new regularization term leads to a simple formulation and design, being applicable to higher dimensions by using the corresponding multidimensional Fourier transform. The proposed regularization term allows for a real gradual transition from a diffusion registration to a curvature registration which is best suited to some applications and it is not possible in the spatial domain. Results with 3D actual images show the validity of this approach.

Comparison of structure, function and regulation of plant cold shock domain proteins to bacterial and animal cold shock domain proteins.

Science.gov (United States)

Chaikam, Vijay; Karlson, Dale T

2010-01-01

The cold shock domain (CSD) is among the most ancient and well conserved nucleic acid binding domains from bacteria to higher animals and plants. The CSD facilitates binding to RNA, ssDNA and dsDNA and most functions attributed to cold shock domain proteins are mediated by this nucleic acid binding activity. In prokaryotes, cold shock domain proteins only contain a single CSD and are termed cold shock proteins (Csps). In animal model systems, various auxiliary domains are present in addition to the CSD and are commonly named Y-box proteins. Similar to animal CSPs, plant CSPs contain auxiliary C-terminal domains in addition to their N-terminal CSD. Cold shock domain proteins have been shown to play important roles in development and stress adaptation in wide variety of organisms. In this review, the structure, function and regulation of plant CSPs are compared and contrasted to the characteristics of bacterial and animal CSPs. [BMB reports 2010; 43(1): 1-8].

Long-term associative learning predicts verbal short-term memory performance

OpenAIRE

Jones, Gary; Macken, Bill

2017-01-01

Studies using tests such as digit span and nonword repetition have implicated short-term memory across a range of developmental domains. Such tests ostensibly assess specialized processes for the short-term manipulation and maintenance of information that are often argued to enable long-term learning. However, there is considerable evidence for an influence of long-term linguistic learning on performance in short-term memory tasks that brings into question the role of a specialized short-term...

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.

Self-consistent field theory simulations of polymers on arbitrary domains

Energy Technology Data Exchange (ETDEWEB)

Ouaknin, Gaddiel, E-mail: gaddielouaknin@umail.ucsb.edu [Department of Mechanical Engineering, University of California, Santa Barbara, CA 93106-5070 (United States); Laachi, Nabil; Delaney, Kris [Materials Research Laboratory, University of California, Santa Barbara, CA 93106-5080 (United States); Fredrickson, Glenn H. [Materials Research Laboratory, University of California, Santa Barbara, CA 93106-5080 (United States); Department of Chemical Engineering, University of California, Santa Barbara, CA 93106-5080 (United States); Department of Materials, University of California, Santa Barbara, CA 93106-5050 (United States); Gibou, Frederic [Department of Mechanical Engineering, University of California, Santa Barbara, CA 93106-5070 (United States); Department of Computer Science, University of California, Santa Barbara, CA 93106-5110 (United States)

2016-12-15

We introduce a framework for simulating the mesoscale self-assembly of block copolymers in arbitrary confined geometries subject to Neumann boundary conditions. We employ a hybrid finite difference/volume approach to discretize the mean-field equations on an irregular domain represented implicitly by a level-set function. The numerical treatment of the Neumann boundary conditions is sharp, i.e. it avoids an artificial smearing in the irregular domain boundary. This strategy enables the study of self-assembly in confined domains and enables the computation of physically meaningful quantities at the domain interface. In addition, we employ adaptive grids encoded with Quad-/Oc-trees in parallel to automatically refine the grid where the statistical fields vary rapidly as well as at the boundary of the confined domain. This approach results in a significant reduction in the number of degrees of freedom and makes the simulations in arbitrary domains using effective boundary conditions computationally efficient in terms of both speed and memory requirement. Finally, in the case of regular periodic domains, where pseudo-spectral approaches are superior to finite differences in terms of CPU time and accuracy, we use the adaptive strategy to store chain propagators, reducing the memory footprint without loss of accuracy in computed physical observables.

Semantic neology in the domain of videogames in Spanish

Directory of Open Access Journals (Sweden)

Inmaculada Álvarez de Mon Rego

2013-04-01

Full Text Available The aim of this paper is to discuss the meaning of five neologisms in the domain of videogames in Spanish: título, aventura, personaje, plataforma, and rol. Our study focuses on a special type of neologism since the Spanish terms we deal with here are not strictly new words; they are what have been called sense neologisms or neosemanticisms, that is, old words taking a new sense in a different domain. These words were identified as new concepts after a process of analysis based on contextual evidence. This study of neology is based on the analysis of a corpus of press articles evaluating videogames published by the Spanish newspaper El País from 1998 to 2008. The analysis of the instances of use of domain specific terms in the corpus revealed that they acquired new senses different to those they have in other domains where they are also used. The paper explains the process of discovering the specialized meaning these words have developed in the domain of videogames and how the analysis of collocational behavior helps in the process of discovering the new sense and in the design of the definition provided.

A thermodynamic definition of protein domains.

Science.gov (United States)

Porter, Lauren L; Rose, George D

2012-06-12

Protein domains are conspicuous structural units in globular proteins, and their identification has been a topic of intense biochemical interest dating back to the earliest crystal structures. Numerous disparate domain identification algorithms have been proposed, all involving some combination of visual intuition and/or structure-based decomposition. Instead, we present a rigorous, thermodynamically-based approach that redefines domains as cooperative chain segments. In greater detail, most small proteins fold with high cooperativity, meaning that the equilibrium population is dominated by completely folded and completely unfolded molecules, with a negligible subpopulation of partially folded intermediates. Here, we redefine structural domains in thermodynamic terms as cooperative folding units, based on m-values, which measure the cooperativity of a protein or its substructures. In our analysis, a domain is equated to a contiguous segment of the folded protein whose m-value is largely unaffected when that segment is excised from its parent structure. Defined in this way, a domain is a self-contained cooperative unit; i.e., its cooperativity depends primarily upon intrasegment interactions, not intersegment interactions. Implementing this concept computationally, the domains in a large representative set of proteins were identified; all exhibit consistency with experimental findings. Specifically, our domain divisions correspond to the experimentally determined equilibrium folding intermediates in a set of nine proteins. The approach was also proofed against a representative set of 71 additional proteins, again with confirmatory results. Our reframed interpretation of a protein domain transforms an indeterminate structural phenomenon into a quantifiable molecular property grounded in solution thermodynamics.

FlexiTerm: a flexible term recognition method

NARCIS (Netherlands)

Spasic, I.; Greenwood, M.; Preece, A.; Francis, N.; Elwyn, G.

2013-01-01

BACKGROUND: The increasing amount of textual information in biomedicine requires effective term recognition methods to identify textual representations of domain-specific concepts as the first step toward automating its semantic interpretation. The dictionary look-up approaches may not always be

The Consequences of Chronic Stereotype Threat: Domain Disidentification and Abandonment

OpenAIRE

Woodcock, Anna; Hernandez, Paul R.; Estrada, Mica; Schultz, P. Wesley

2012-01-01

Stereotype threat impairs performance across many domains. Despite a wealth of research, the long-term consequences of chronic stereotype threat have received little empirical attention. Beyond the immediate impact on performance, the experience of chronic stereotype threat is hypothesized to lead to domain disidentification and eventual domain abandonment. Stereotype threat is 1 explanation why African Americans and Hispanic/Latino(a)s “leak” from each juncture of the academic scientific pip...

GeoSegmenter: A statistically learned Chinese word segmenter for the geoscience domain

Science.gov (United States)

Huang, Lan; Du, Youfu; Chen, Gongyang

2015-03-01

Unlike English, the Chinese language has no space between words. Segmenting texts into words, known as the Chinese word segmentation (CWS) problem, thus becomes a fundamental issue for processing Chinese documents and the first step in many text mining applications, including information retrieval, machine translation and knowledge acquisition. However, for the geoscience subject domain, the CWS problem remains unsolved. Although a generic segmenter can be applied to process geoscience documents, they lack the domain specific knowledge and consequently their segmentation accuracy drops dramatically. This motivated us to develop a segmenter specifically for the geoscience subject domain: the GeoSegmenter. We first proposed a generic two-step framework for domain specific CWS. Following this framework, we built GeoSegmenter using conditional random fields, a principled statistical framework for sequence learning. Specifically, GeoSegmenter first identifies general terms by using a generic baseline segmenter. Then it recognises geoscience terms by learning and applying a model that can transform the initial segmentation into the goal segmentation. Empirical experimental results on geoscience documents and benchmark datasets showed that GeoSegmenter could effectively recognise both geoscience terms and general terms.

Gravitational waves from domain walls and their implications

Directory of Open Access Journals (Sweden)

Kazunori Nakayama

2017-07-01

Full Text Available We evaluate the impact of domain-wall annihilation on the currently ongoing and planned gravitational wave experiments, including a case in which domain walls experience a frictional force due to interactions with the ambient plasma. We show the sensitivity reach in terms of physical parameters, namely, the wall tension and the annihilation temperature. We find that a Higgs portal scalar, which stabilizes the Higgs potential at high energy scales, can form domain walls whose annihilation produces a large amount of gravitational waves within the reach of the advanced LIGO experiment (O5. Domain wall annihilation can also generate baryon asymmetry if the scalar is coupled to either SU(2L gauge fields or the (B−L current. This is a variant of spontaneous baryogenesis, but it naturally avoids the isocurvature constraint due to the scaling behavior of the domain-wall evolution. We delineate the parameter space where the domain-wall baryogenesis works successfully and discuss its implications for the gravitational wave experiments.

The ethnographic method and its relationship with the domain analysis

Directory of Open Access Journals (Sweden)

Manuel Alejandro Romero Quesada

2016-03-01

Full Text Available This paper analyzes the theoretical and conceptual relationship of the ethnographic method with domain analysis. A documentary analysis was performed, exploring the categories of domain analysis and ethnographic method.It was obtained as a result: the analysis of the points of contact between domain analysis and the ethnographic method from an epistemological, methodological and procedural terms. It is concluded that the ethnographic method is an important research tool to scan the turbulent socio-cultural scenarios that occur within discursive communities that constitute the domains of knowledge.

Domain-wall dynamics in glass-coated magnetic microwires

International Nuclear Information System (INIS)

Varga, R.; Zhukov, A.; Usov, N.; Blanco, J.M.; Gonzalez, J.; Zhukova, V.; Vojtanik, P.

2007-01-01

Glass-coated magnetic microwires with positive magnetostriction show peculiar domain structure that consists mostly of one large domain with magnetization-oriented axially. It was shown that small closure domains appear at the end of the microwire in order to decrease the stray fields. As a result of such domain structure, the magnetization reversal in axial direction runs through the depinning of one of such closure domains and subsequent propagation of the corresponding domain wall. Quite unusual domain-wall (DW) dynamics of the DW propagation predicted previously from the theory has been found in such amorphous microwires. In this paper, we are dealing with the DW dynamics of glass-coated microwires with small positive magnetostriction. The DW damping coming from the structural relaxation dominates at low temperatures as a result of the decrease of the mobility of the structural atomic-level defects. Negative critical propagation field points to the possible DW propagation without applied magnetic field. Probable explanation could be in terms of the effective mass of the DW

Domain wall propagation in Fe-rich amorphous microwires

Energy Technology Data Exchange (ETDEWEB)

Panina, L.V. [School of Comp. and Math., Univ. of Plymouth, Drake Circus, PL4 AA, Plymouth (United Kingdom); Ipatov, M.; Zhukova, V. [Dpto. Fisica de Materiales, Fac. Quimicas, UPV/EHU, 20018 San Sebastian (Spain); Zhukov, A., E-mail: arkadi.joukov@ehu.es [Dpto. Fisica de Materiales, Fac. Quimicas, UPV/EHU, 20018 San Sebastian (Spain); IKERBASQUE, Basque Foundation for Science, 48011 Bilbao (Spain)

2012-05-01

The domain wall (DW) propagation in magnetically bistable Fe{sub 74}Si{sub 11}B{sub 13}C{sub 2} amorphous microwires with metallic nucleus diameters of 12-16 {mu}m has been investigated in order to explain high DW velocities observed in Sixtus-Tonks like experiments. In micrometric wires, the boundary between two head-to-head domains is very elongated. The DW mobility normal to the wall surface is reduced by the domain aspect ratio and is in the range of a few m/s/Oe in the linear regime. The experimental results in the viscous regime could be quantitatively explained in terms of the domain length and normal mobility limited by the eddy currents and spin relaxation losses.

A single amino acid difference between the intracellular domains of amyloid precursor protein and amyloid-like precursor protein 2 enables induction of synaptic depression and block of long-term potentiation.

Science.gov (United States)

Trillaud-Doppia, Emilie; Paradis-Isler, Nicolas; Boehm, Jannic

2016-07-01

Alzheimer disease (AD) is initially characterized as a disease of the synapse that affects synaptic transmission and synaptic plasticity. While amyloid-beta and tau have been traditionally implicated in causing AD, recent studies suggest that other factors, such as the intracellular domain of the amyloid-precursor protein (APP-ICD), can also play a role in the development of AD. Here, we show that the expression of APP-ICD induces synaptic depression, while the intracellular domain of its homolog amyloid-like precursor protein 2 (APLP2-ICD) does not. We are able to show that this effect by APP-ICD is due to a single alanine vs. proline difference between APP-ICD and APLP2-ICD. The alanine in APP-ICD and the proline in APLP2-ICD lie directly behind a conserved caspase cleavage site. Inhibition of caspase cleavage of APP-ICD prevents the induction of synaptic depression. Finally, we show that the expression of APP-ICD increases and facilitates long-term depression and blocks induction of long-term potentiation. The block in long-term potentiation can be overcome by mutating the aforementioned alanine in APP-ICD to the proline of APLP2. Based on our results, we propose the emergence of a new APP critical domain for the regulation of synaptic plasticity and in consequence for the development of AD. Copyright © 2016 Elsevier Inc. All rights reserved.

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.

Prospects of particle physics

International Nuclear Information System (INIS)

Meyer-Berkhout, U.

1986-01-01

Remarkable progress has been achieved in the last two decades in the field of particle physics. From the insight gained by the many experimental data, physicists derive a framework picture of matter on the sub-nuclear level, consisting of fundamental components which interact with each other in a defined and quantitatively detectable manner. The data now available allowed a quantum field theory of strong interactions to be set up for the first time, and a unified theory of electromagnetic and weak interaction. Particle physicists today take particular interest in the problem of whether the strong interaction might fit into an extended unified theory. Such a grand unified theory would have a far-reaching impact on the conceptual models both of the cosmic and sub-nuclear dimensions, and possibly lead to observable effects in domains of energy and mass which will be opened up for experiments by the new accelerator generation underway. Current activities throughout the world for constructing or projecting the new high-energy particle accelerators are outlined in the article, together with the prospects expected by particle physicists, and a look back on the history and achievements of this field of science. (orig.) [de

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.

Atomic resolution imaging of ferroelectric domains

International Nuclear Information System (INIS)

Bursill, L.A.

1997-01-01

Electron optical principles involved in obtaining atomic resolution images of ferroelectric domains are reviewed, including the methods available to obtain meaningful interpretation and analysis of the image detail in terms of the atomic structures. Recent work is concerned with establishing the relationship between the essentially static chemical nanodomains and the spatial and temporal fluctuations of the nanoscale polar domains present in the relaxor class of materials, including lead scandium tantalate (PST) and lead magnesium niobate (PMN). Correct interpretation of the images required use of Next Nearest Neighbour Ising model simulations for the chemical domain textures upon which we must superimpose the polar domain textures; an introduction to this work is presented. A thorough analysis of the atomic scale chemical inhomogeneities, based upon the HRTEM results, has lead to an improved formulation of the theory of the dielectric response of PMN and PST, which is capable to predict the observed temperature and frequency dependence. HRTEM may be combined with solid state and statistical physics principles to provide a deeper understanding of structure/property relationships. 15 refs., 6 figs

22nd International Conference on Domain Decomposition Methods

CERN Document Server

Gander, Martin; Halpern, Laurence; Krause, Rolf; Pavarino, Luca

2016-01-01

These are the proceedings of the 22nd International Conference on Domain Decomposition Methods, which was held in Lugano, Switzerland. With 172 participants from over 24 countries, this conference continued a long-standing tradition of internationally oriented meetings on Domain Decomposition Methods. The book features a well-balanced mix of established and new topics, such as the manifold theory of Schwarz Methods, Isogeometric Analysis, Discontinuous Galerkin Methods, exploitation of modern HPC architectures, and industrial applications. As the conference program reflects, the growing capabilities in terms of theory and available hardware allow increasingly complex non-linear and multi-physics simulations, confirming the tremendous potential and flexibility of the domain decomposition concept.

Nuclear and subnuclear geophysics. Neutrinos from the Earth

International Nuclear Information System (INIS)

Fiorentini, G.

2005-01-01

The deepest hole that has ever been dug is about 12 km deep, a mere dent in planetary terms. Geochemists analyze samples from the Earth's crust and from the top of the mantle. Seismology can reconstruct the density profile throughout all Earth, but not its composition. In this respect, our planet is mainly unexplored. Geo-neutrinos, the antineutrinos from the progenies of U, Th and 40 K decays in the Earth, bring to the surface information from the whole planet, concerning its content of radioactive elements. Their detection can shed light on the sources of the terrestrial heat flow, on the present composition and on the origin of the Earth. They represent a new probe of our planet which is becoming practical as a consequence of two fundamental advances that occurred in the last few years: the development of extremely low background neutrino detectors and the progress in understanding neutrino propagation. (author)

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/ .

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...

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.

The dynamic landscape of the cell nucleus.

Science.gov (United States)

Austin, Christopher M; Bellini, Michel

2010-01-01

While the cell nucleus was described for the first time almost two centuries ago, our modern view of the nuclear architecture is primarily based on studies from the last two decades. This surprising late start coincides with the development of new, powerful strategies to probe for the spatial organization of nuclear activities in both fixed and live cells. As a result, three major principles have emerged: first, the nucleus is not just a bag filled with nucleic acids and proteins. Rather, many distinct functional domains, including the chromosomes, resides within the confines of the nuclear envelope. Second, all these nuclear domains are highly dynamic, with molecules exchanging rapidly between them and the surrounding nucleoplasm. Finally, the motion of molecules within the nucleoplasm appears to be mostly driven by random diffusion. Here, the emerging roles of several subnuclear domains are discussed in the context of the dynamic functions of the cell nucleus.

Searching for the Hebb effect in Down syndrome: evidence for a dissociation between verbal short-term memory and domain-general learning of serial order.

Science.gov (United States)

Mosse, E K; Jarrold, C

2010-04-01

The Hebb effect is a form of repetition-driven long-term learning that is thought to provide an analogue for the processes involved in new word learning. Other evidence suggests that verbal short-term memory also constrains now vocabulary acquisition, but if the Hebb effect is independent of short-term memory, then it may be possible to demonstrate its preservation in a sample of individuals with Down syndrome, who typically show a verbal short-term memory deficit alongside surprising relative strengths in vocabulary. In two experiments, individuals both with and without Down syndrome (matched for receptive vocabulary) completed immediate serial recall tasks incorporating a Hebb repetition paradigm in either verbal or visuospatial conditions. Both groups demonstrated equivalent benefit from Hebb repetition, despite individuals with Down syndrome showing significantly lower verbal short-term memory spans. The resultant Hebb effect was equivalent across verbal and visuospatial domains. These studies suggest that the Hebb effect is essentially preserved within Down syndrome, implying that explicit verbal short-term memory is dissociable from potentially more implicit Hebb learning. The relative strength in receptive vocabulary observed in Down syndrome may therefore be supported by largely intact long-term as opposed to short-term serial order learning. This in turn may have implications for teaching methods and interventions that present new phonological material to individuals with Down syndrome.

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.

The consequences of chronic stereotype threat: domain disidentification and abandonment.

Science.gov (United States)

Woodcock, Anna; Hernandez, Paul R; Estrada, Mica; Schultz, P Wesley

2012-10-01

Stereotype threat impairs performance across many domains. Despite a wealth of research, the long-term consequences of chronic stereotype threat have received little empirical attention. Beyond the immediate impact on performance, the experience of chronic stereotype threat is hypothesized to lead to domain disidentification and eventual domain abandonment. Stereotype threat is 1 explanation why African Americans and Hispanic/Latino(a)s "leak" from each juncture of the academic scientific pipeline in disproportionately greater numbers than their White and Asian counterparts. Using structural equation modeling, we tested the stereotype threat-disidentification hypothesis across 3 academic years with a national longitudinal panel of undergraduate minority science students. Experience of stereotype threat was associated with scientific disidentification, which in turn predicted a significant decline in the intention to pursue a scientific career. Race/ethnicity moderated this effect, whereby the effect was evident for Hispanic/Latino(a) students but not for all African American students. We discuss findings in terms of understanding chronic stereotype threat.

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

Concomitant prediction of function and fold at the domain level with GO-based profiles.

Science.gov (United States)

Lopez, Daniel; Pazos, Florencio

2013-01-01

Predicting the function of newly sequenced proteins is crucial due to the pace at which these raw sequences are being obtained. Almost all resources for predicting protein function assign functional terms to whole chains, and do not distinguish which particular domain is responsible for the allocated function. This is not a limitation of the methodologies themselves but it is due to the fact that in the databases of functional annotations these methods use for transferring functional terms to new proteins, these annotations are done on a whole-chain basis. Nevertheless, domains are the basic evolutionary and often functional units of proteins. In many cases, the domains of a protein chain have distinct molecular functions, independent from each other. For that reason resources with functional annotations at the domain level, as well as methodologies for predicting function for individual domains adapted to these resources are required.We present a methodology for predicting the molecular function of individual domains, based on a previously developed database of functional annotations at the domain level. The approach, which we show outperforms a standard method based on sequence searches in assigning function, concomitantly predicts the structural fold of the domains and can give hints on the functionally important residues associated to the predicted function.

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

Resolving the Origin of Pseudo-Single Domain Magnetic Behavior

Science.gov (United States)

Roberts, Andrew P.; Almeida, Trevor P.; Church, Nathan S.; Harrison, Richard J.; Heslop, David; Li, Yiliang; Li, Jinhua; Muxworthy, Adrian R.; Williams, Wyn; Zhao, Xiang

2017-12-01

The term "pseudo-single domain" (PSD) has been used to describe the transitional state in rock magnetism that spans the particle size range between the single domain (SD) and multidomain (MD) states. The particle size range for the stable SD state in the most commonly occurring terrestrial magnetic mineral, magnetite, is so narrow ( 20-75 nm) that it is widely considered that much of the paleomagnetic record of interest is carried by PSD rather than stable SD particles. The PSD concept has, thus, become the dominant explanation for the magnetization associated with a major fraction of particles that record paleomagnetic signals throughout geological time. In this paper, we argue that in contrast to the SD and MD states, the term PSD does not describe the relevant physical processes, which have been documented extensively using three-dimensional micromagnetic modeling and by parallel research in material science and solid-state physics. We also argue that features attributed to PSD behavior can be explained by nucleation of a single magnetic vortex immediately above the maximum stable SD transition size. With increasing particle size, multiple vortices, antivortices, and domain walls can nucleate, which produce variable cancellation of magnetic moments and a gradual transition into the MD state. Thus, while the term PSD describes a well-known transitional state, it fails to describe adequately the physics of the relevant processes. We recommend that use of this term should be discontinued in favor of "vortex state," which spans a range of behaviors associated with magnetic vortices.

Time-domain Green's Function Method for three-dimensional nonlinear subsonic flows

Science.gov (United States)

Tseng, K.; Morino, L.

1978-01-01

The Green's Function Method for linearized 3D unsteady potential flow (embedded in the computer code SOUSSA P) is extended to include the time-domain analysis as well as the nonlinear term retained in the transonic small disturbance equation. The differential-delay equations in time, as obtained by applying the Green's Function Method (in a generalized sense) and the finite-element technique to the transonic equation, are solved directly in the time domain. Comparisons are made with both linearized frequency-domain calculations and existing nonlinear results.

A meta-analysis of work-family conflict and various outcomes with a special emphasis on cross-domain versus matching-domain relations.

Science.gov (United States)

Amstad, Fabienne T; Meier, Laurenz L; Fasel, Ursula; Elfering, Achim; Semmer, Norbert K

2011-04-01

A literature review of studies analyzing work-family conflict and its consequences was conducted, and 427 effect sizes were analyzed meta-analytically. Work-family conflict was analyzed bidirectionally in terms of work interference with family (WIF) and family interference with work (FIW). We assessed 3 categories of potential outcomes: work-related outcomes, family-related outcomes, and domain-unspecific outcomes. Results show that WIF and FIW are consistently related to all 3 types of outcomes. Both types of interrole conflict showed stronger relationships to same-domain outcomes than to cross-domain outcomes. Thus, WIF was more strongly associated with work-related than with family-related outcomes, and FIW was more strongly associated with family-related than with work-related outcomes. In moderator analyses, parenthood could not explain variability in effect sizes. However, time spent at work did moderate the relationships between WIF and family-related outcomes, as well as FIW and domain-unspecific outcomes.

Shape of isolated domains in lithium tantalate single crystals at elevated temperatures

International Nuclear Information System (INIS)

Shur, V. Ya.; Akhmatkhanov, A. R.; Baturin, I. S.; Chezganov, D. S.; Lobov, A. I.; Smirnov, M. M.

2013-01-01

The shape of isolated domains has been investigated in congruent lithium tantalate (CLT) single crystals at elevated temperatures and analyzed in terms of kinetic approach. The obtained temperature dependence of the growing domain shape in CLT including circular shape at temperatures above 190 °C has been attributed to increase of relative input of isotropic ionic conductivity. The observed nonstop wall motion and independent domain growth after merging in CLT as opposed to stoichiometric lithium tantalate have been attributed to difference in wall orientation. The computer simulation has confirmed applicability of the kinetic approach to the domain shape explanation

Protein domain recurrence and order can enhance prediction of protein functions

KAUST Repository

Abdel Messih, Mario A.

2012-09-07

Motivation: Burgeoning sequencing technologies have generated massive amounts of genomic and proteomic data. Annotating the functions of proteins identified in this data has become a big and crucial problem. Various computational methods have been developed to infer the protein functions based on either the sequences or domains of proteins. The existing methods, however, ignore the recurrence and the order of the protein domains in this function inference. Results: We developed two new methods to infer protein functions based on protein domain recurrence and domain order. Our first method, DRDO, calculates the posterior probability of the Gene Ontology terms based on domain recurrence and domain order information, whereas our second method, DRDO-NB, relies on the nave Bayes methodology using the same domain architecture information. Our large-scale benchmark comparisons show strong improvements in the accuracy of the protein function inference achieved by our new methods, demonstrating that domain recurrence and order can provide important information for inference of protein functions. The Author(s) 2012. Published by Oxford University Press.

Going from microscopic to macroscopic on nonuniform growing domains.

Science.gov (United States)

Yates, Christian A; Baker, Ruth E; Erban, Radek; Maini, Philip K

2012-08-01

Throughout development, chemical cues are employed to guide the functional specification of underlying tissues while the spatiotemporal distributions of such chemicals can be influenced by the growth of the tissue itself. These chemicals, termed morphogens, are often modeled using partial differential equations (PDEs). The connection between discrete stochastic and deterministic continuum models of particle migration on growing domains was elucidated by Baker, Yates, and Erban [Bull. Math. Biol. 72, 719 (2010)] in which the migration of individual particles was modeled as an on-lattice position-jump process. We build on this work by incorporating a more physically reasonable description of domain growth. Instead of allowing underlying lattice elements to instantaneously double in size and divide, we allow incremental element growth and splitting upon reaching a predefined threshold size. Such a description of domain growth necessitates a nonuniform partition of the domain. We first demonstrate that an individual-based stochastic model for particle diffusion on such a nonuniform domain partition is equivalent to a PDE model of the same phenomenon on a nongrowing domain, providing the transition rates (which we derive) are chosen correctly and we partition the domain in the correct manner. We extend this analysis to the case where the domain is allowed to change in size, altering the transition rates as necessary. Through application of the master equation formalism we derive a PDE for particle density on this growing domain and corroborate our findings with numerical simulations.

Is Divorce More Painful When Couples Have Children? Evidence From Long-Term Panel Data on Multiple Domains of Well-being.

Science.gov (United States)

Leopold, Thomas; Kalmijn, Matthijs

2016-12-01

Theoretical models of the divorce process suggest that marital breakup is more painful in the presence of children, yet little is known about the role of children as a moderator of divorce effects on adult well-being. The present study addresses this gap of research based on long-term panel data from Germany (SOEP). Following individuals over several years before and after divorce, we investigated whether the impact of divorce on multiple measures of well-being varied by the presence and age of children before marital breakup. Three central findings emerged from the analysis. First, declines in well-being were sharper in the presence of children, and these moderator effects were larger if children were younger. Second, domain-specific measures of well-being revealed gender differences in the moderating role of children. Mothers sustained deeper drops in economic well-being than did fathers; the reverse was true for family well-being. Third, most of these disproportionate declines in the well-being of divorced parents did not persist in the long term given that higher rates of adaptation leveled out the gaps compared with childless divorcees.

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.

Highlights in subnuclear physics

CERN Document Server

Wolf, G

2003-01-01

An overview on new developments in experimental particle and astroparticle physics is presented. This includes observation of CP violation in the B-sector, detection of direct CP violation in the K /sup 0/-system, new measurements on solar neutrinos, cosmic microwave background radiation and properties of the universe, electroweak results from the large colliders and tests of the standard model, measurement of the anomalous magnetic moment of muons, structure of the proton at large energy transfers and virtualities, and heavy ion collisions at very high energies. Finally, the physics reach of TEVATRONII, LHC and TESLA, a linear e/sup +/e/sup -/ collider proposed for the 0.5 1 TeV regime, is briefly reviewed. (93 refs).

Long-term associative learning predicts verbal short-term memory performance.

Science.gov (United States)

Jones, Gary; Macken, Bill

2018-02-01

Studies using tests such as digit span and nonword repetition have implicated short-term memory across a range of developmental domains. Such tests ostensibly assess specialized processes for the short-term manipulation and maintenance of information that are often argued to enable long-term learning. However, there is considerable evidence for an influence of long-term linguistic learning on performance in short-term memory tasks that brings into question the role of a specialized short-term memory system separate from long-term knowledge. Using natural language corpora, we show experimentally and computationally that performance on three widely used measures of short-term memory (digit span, nonword repetition, and sentence recall) can be predicted from simple associative learning operating on the linguistic environment to which a typical child may have been exposed. The findings support the broad view that short-term verbal memory performance reflects the application of long-term language knowledge to the experimental setting.

Domain-specific and domain-general constraints on word and sequence learning.

Science.gov (United States)

Archibald, Lisa M D; Joanisse, Marc F

2013-02-01

The relative influences of language-related and memory-related constraints on the learning of novel words and sequences were examined by comparing individual differences in performance of children with and without specific deficits in either language or working memory. Children recalled lists of words in a Hebbian learning protocol in which occasional lists repeated, yielding improved recall over the course of the task on the repeated lists. The task involved presentation of pictures of common nouns followed immediately by equivalent presentations of the spoken names. The same participants also completed a paired-associate learning task involving word-picture and nonword-picture pairs. Hebbian learning was observed for all groups. Domain-general working memory constrained immediate recall, whereas language abilities impacted recall in the auditory modality only. In addition, working memory constrained paired-associate learning generally, whereas language abilities disproportionately impacted novel word learning. Overall, all of the learning tasks were highly correlated with domain-general working memory. The learning of nonwords was additionally related to general intelligence, phonological short-term memory, language abilities, and implicit learning. The results suggest that distinct associations between language- and memory-related mechanisms support learning of familiar and unfamiliar phonological forms and sequences.

General spectral flow formula for fixed maximal domain

DEFF Research Database (Denmark)

Booss-Bavnbek, Bernhelm; Zhu, Chaofeng

2005-01-01

and symplectic analysis and give a full (and surprisingly short) proof of our General Spectral Flow Formula for the case of fixed maximal domain. As a side result, we establish local stability of weak inner unique continuation property (UCP) and explain its role for parameter dependent spectral theory....... of the resulting continuous family of (unbounded) self-adjoint Fredholm operators in terms of the Maslov index of two related curves of Lagrangian spaces. One curve is given by the varying domains, the other by the Cauchy data spaces. We provide rigorous definitions of the underlying concepts of spectral theory...

NMR and domain wall mobility in intermetallic compounds

International Nuclear Information System (INIS)

Guimaraes, A.P.; Sampaio, L.C.; Cunha, S.F.; Alves, K.M.B.

1991-01-01

The technique of pulsed NMR can be used to study the distribution of hyperfine fields in a magnetic matrix. The dynamics of the domain walls are relevant to the generation of NMR signals. In the present study on the (R x Y 1-x ) Fe 2 intermetallic compounds, the reduction in the signals is associated to increased propagation fields. This indicates that a smaller domain wall mobility is at the origin of these effects. NMR spectra in this system show the importance of direct and indirect (i.e., mediated by Fe atoms) terms in the transferred hyperfine field. (author)

Self-annihilation of inversion domains by high energy defects in III-Nitrides

International Nuclear Information System (INIS)

Koukoula, T.; Kioseoglou, J.; Kehagias, Th.; Komninou, Ph.; Ajagunna, A. O.; Georgakilas, A.

2014-01-01

Low-defect density InN films were grown on Si(111) by molecular beam epitaxy over an ∼1 μm thick GaN/AlN buffer/nucleation layer. Electron microscopy observations revealed the presence of inverse polarity domains propagating across the GaN layer and terminating at the sharp GaN/InN (0001 ¯ ) interface, whereas no inversion domains were detected in InN. The systematic annihilation of GaN inversion domains at the GaN/InN interface is explained in terms of indium incorporation on the Ga-terminated inversion domains forming a metal bonded In-Ga bilayer, a structural instability known as the basal inversion domain boundary, during the initial stages of InN growth on GaN

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....

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

QCD axion dark matter from long-lived domain walls during matter domination

OpenAIRE

Harigaya, Keisuke; Kawasaki, Masahiro

2018-01-01

The domain wall problem of the Peccei–Quinn mechanism can be solved if the Peccei–Quinn symmetry is explicitly broken by a small amount. Domain walls decay into axions, which may account for dark matter of the universe. This scheme is however strongly constrained by overproduction of axions unless the phase of the explicit breaking term is tuned. We investigate the case where the universe is matter-dominated around the temperature of the MeV scale and domain walls decay during this matter dom...

Collision of domain walls in asymptotically anti-de Sitter spacetime

International Nuclear Information System (INIS)

Takamizu, Yu-ichi; Maeda, Kei-ichi

2006-01-01

We study collision of two domain walls in five-dimensional asymptotically anti-de Sitter spacetime. This may provide the reheating mechanism of an ekpyrotic (or cyclic) brane universe, in which two Bogomol'nyi-Prasad-Sommerfield branes collide and evolve into a hot big bang universe. We evaluate a change of scalar field making the domain wall and can investigate the effect of a negative cosmological term in the bulk to the collision process and the evolution of our universe

TRANSIENT ANOMALOUS SUB-DIFFUSION ON BOUNDED DOMAINS

OpenAIRE

MEERSCHAERT, MARK M.; NANE, ERKAN; VELLAISAMY, P.

2012-01-01

This paper develops strong solutions and stochastic solutions for the tempered fractional diffusion equation on bounded domains. First the eigenvalue problem for tempered fractional derivatives is solved. Then a separation of variables, and eigenfunction expansions in time and space, are used to write strong solutions. Finally, stochastic solutions are written in terms of an inverse subordinator.

The Effects of Item Format and Cognitive Domain on Students' Science Performance in TIMSS 2011

Science.gov (United States)

Liou, Pey-Yan; Bulut, Okan

2017-12-01

The purpose of this study was to examine eighth-grade students' science performance in terms of two test design components, item format, and cognitive domain. The portion of Taiwanese data came from the 2011 administration of the Trends in International Mathematics and Science Study (TIMSS), one of the major international large-scale assessments in science. The item difficulty analysis was initially applied to show the proportion of correct items. A regression-based cumulative link mixed modeling (CLMM) approach was further utilized to estimate the impact of item format, cognitive domain, and their interaction on the students' science scores. The results of the proportion-correct statistics showed that constructed-response items were more difficult than multiple-choice items, and that the reasoning cognitive domain items were more difficult compared to the items in the applying and knowing domains. In terms of the CLMM results, students tended to obtain higher scores when answering constructed-response items as well as items in the applying cognitive domain. When the two predictors and the interaction term were included together, the directions and magnitudes of the predictors on student science performance changed substantially. Plausible explanations for the complex nature of the effects of the two test-design predictors on student science performance are discussed. The results provide practical, empirical-based evidence for test developers, teachers, and stakeholders to be aware of the differential function of item format, cognitive domain, and their interaction in students' science performance.

DRO: domain-based route optimization scheme for nested mobile networks

Directory of Open Access Journals (Sweden)

Chuang Ming-Chin

2011-01-01

Full Text Available Abstract The network mobility (NEMO basic support protocol is designed to support NEMO management, and to ensure communication continuity between nodes in mobile networks. However, in nested mobile networks, NEMO suffers from the pinball routing problem, which results in long packet transmission delays. To solve the problem, we propose a domain-based route optimization (DRO scheme that incorporates a domain-based network architecture and ad hoc routing protocols for route optimization. DRO also improves the intra-domain handoff performance, reduces the convergence time during route optimization, and avoids the out-of-sequence packet problem. A detailed performance analysis and simulations were conducted to evaluate the scheme. The results demonstrate that DRO outperforms existing mechanisms in terms of packet transmission delay (i.e., better route-optimization, intra-domain handoff latency, convergence time, and packet tunneling overhead.

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.

Insight into molecular interactions between two PB1 domains

NARCIS (Netherlands)

van Drogen-Petit, A.; Zwahlen, C.; Peter, M.; Bonvin, A.M.J.J.

2004-01-01

Specific protein–protein interactions play crucial roles in the regulation of any biological process. Recently, a new protein–protein interaction domain termed PB1 (Phox and Bem1) was identified, which is conserved throughout evolution and present in diverse proteins functioning in signal

.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...

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.

The pilus usher controls protein interactions via domain masking and is functional as an oligomer.

Science.gov (United States)

Werneburg, Glenn T; Henderson, Nadine S; Portnoy, Erica B; Sarowar, Samema; Hultgren, Scott J; Li, Huilin; Thanassi, David G

2015-07-01

The chaperone-usher (CU) pathway assembles organelles termed pili or fimbriae in Gram-negative bacteria. Type 1 pili expressed by uropathogenic Escherichia coli are prototypical structures assembled by the CU pathway. Biogenesis of pili by the CU pathway requires a periplasmic chaperone and an outer-membrane protein termed the usher (FimD). We show that the FimD C-terminal domains provide the high-affinity substrate-binding site but that these domains are masked in the resting usher. Domain masking requires the FimD plug domain, which serves as a switch controlling usher activation. We demonstrate that usher molecules can act in trans for pilus biogenesis, providing conclusive evidence for a functional usher oligomer. These results reveal mechanisms by which molecular machines such as the usher regulate and harness protein-protein interactions and suggest that ushers may interact in a cooperative manner during pilus assembly in bacteria.

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

The profile of the domain walls in amorphous glass-covered microwires

Energy Technology Data Exchange (ETDEWEB)

Beck, F.; Rigue, J.N. [Universidade Federal de Santa Maria, Campus Cachoeira do Sul, RS (Brazil); Carara, M., E-mail: carara@smail.ufsm.br [Departamento de Física, Universidade Federal de Santa Maria, Santa Maria, RS (Brazil)

2017-08-01

Highlights: • Glass-covered microwires with positive magnetostriction were studied. • The single domain wall dynamics was studied under different conditions. • We have evaluated the profile and shape of the moving domain walls. • The domain wall evolves from a bell shape to a parabolic one when a current is applied. - Abstract: We have studied the domain wall dynamics in Joule-annealed amorphous glass-covered microwires with positive magnetostriction in the presence of an electric current, in order to evaluate the profile and shape of the moving domain wall. Such microwires are known to present magnetic bi-stability when axially magnetized. The single domain wall dynamics was evaluated under different conditions, under an axially applied stress and an electric current. We have observed the well known increasing of the domain wall damping with the applied stress due to the increase in the magnetoelastic anisotropy and, when the current is applied, depending on the current intensity and direction, a modification on the axial domain wall damping. When the orthogonal motion of the domain wall is considered, we have observed that the associated velocity present a smaller dependence on the applied current intensity. It was observed a modification on both the domain wall shape and length. In a general way, the domain wall evolves from a bell shape to a parabolic shape as the current intensity is increased. The results were explained in terms of the change in the magnetic energy promoted by the additional Oersted field.

Modeling Network Traffic in Wavelet Domain

Directory of Open Access Journals (Sweden)

Sheng Ma

2004-12-01

Full Text Available This work discovers that although network traffic has the complicated short- and long-range temporal dependence, the corresponding wavelet coefficients are no longer long-range dependent. Therefore, a "short-range" dependent process can be used to model network traffic in the wavelet domain. Both independent and Markov models are investigated. Theoretical analysis shows that the independent wavelet model is sufficiently accurate in terms of the buffer overflow probability for Fractional Gaussian Noise traffic. Any model, which captures additional correlations in the wavelet domain, only improves the performance marginally. The independent wavelet model is then used as a unified approach to model network traffic including VBR MPEG video and Ethernet data. The computational complexity is O(N for developing such wavelet models and generating synthesized traffic of length N, which is among the lowest attained.

Organization of functional domains in the docking protein p130Cas

International Nuclear Information System (INIS)

Nasertorabi, Fariborz; Garcia-Guzman, Miguel; Briknarova, Klara; Larsen, Elise; Havert, Marnie L.; Vuori, Kristiina; Ely, Kathryn R.

2004-01-01

The docking protein p130Cas becomes phosphorylated upon cell adhesion to extracellular matrix proteins, and is thought to play an essential role in cell transformation. Cas transmits signals through interactions with the Src-homology 3 (SH3) and Src-homology 2 domains of FAK or v-Crk signaling molecules, or with 14-3-3 protein, as well as phosphatases PTP1B and PTP-PEST. The large (130 kDa), multi-domain Cas molecule contains an SH3 domain, a Src-binding domain, a serine-rich protein interaction region, and a C-terminal region that participates in protein interactions implicated in antiestrogen resistance in breast cancer. In this study, as part of a long-term goal to examine the protein interactions of Cas by X-ray crystallography and nuclear magnetic resonance spectroscopy, molecular constructs were designed to express two adjacent domains, the serine-rich domain and the Src-binding domain, that each participate in intermolecular contacts dependent on protein phosphorylation. The protein products are soluble, homogeneous, monodisperse, and highly suitable for structural studies to define the role of Cas in integrin-mediated cell signaling

A convergent overlapping domain decomposition method for total variation minimization

KAUST Repository

Fornasier, Massimo; Langer, Andreas; Schö nlieb, Carola-Bibiane

2010-01-01

In this paper we are concerned with the analysis of convergent sequential and parallel overlapping domain decomposition methods for the minimization of functionals formed by a discrepancy term with respect to the data and a total variation

Perturbative evolution of particle orbits around Kerr black holes: time-domain calculation

Energy Technology Data Exchange (ETDEWEB)

Lopez-Aleman, Ramon [Physical Sciences Department, University of Puerto Rico-Rio Piedras, San Juan, PR 00931 (Puerto Rico); Khanna, Gaurav [Natural Science Division, Long Island University, Southampton, NY 11968 (United States); Pullin, Jorge [Department of Physics and Astronomy, Louisiana State University, 202 Nicholson Hall, Baton Rouge, LA 70803-4001 (United States)

2003-07-21

We consider the problem of the gravitational waves produced by a particle of negligible mass orbiting a Kerr black hole. We treat the Teukolsky perturbation equation in the time domain numerically as a 2 + 1 partial differential equation. We model the particle by smearing the singularities in the source term by the use of narrow Gaussian distributions. We have been able to reproduce earlier results for equatorial circular orbits that were computed using the frequency-domain formalism. The time-domain approach is however geared for a more general evolution, for instance of nearly geodesic orbits under the effects of radiation reaction.

Perturbative evolution of particle orbits around Kerr black holes: time-domain calculation

International Nuclear Information System (INIS)

Lopez-Aleman, Ramon; Khanna, Gaurav; Pullin, Jorge

2003-01-01

We consider the problem of the gravitational waves produced by a particle of negligible mass orbiting a Kerr black hole. We treat the Teukolsky perturbation equation in the time domain numerically as a 2 + 1 partial differential equation. We model the particle by smearing the singularities in the source term by the use of narrow Gaussian distributions. We have been able to reproduce earlier results for equatorial circular orbits that were computed using the frequency-domain formalism. The time-domain approach is however geared for a more general evolution, for instance of nearly geodesic orbits under the effects of radiation reaction

[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.

Current-induced domain wall motion in nanoscale ferromagnetic elements

Energy Technology Data Exchange (ETDEWEB)

Malinowski, G [Laboratoire de Physique des Solides, CNRS, Universite Paris-sud 11, 91405 Orsay Cedex (France); Boulle, O [SPINTEC, CEA/CNRS/UJF/GINP, INAC, 38054 Grenoble Cedex 9 (France); Klaeui, M, E-mail: Klaeui@uni-mainz.de [SwissFEL, Paul Scherrer Institut, 5232 Villigen PSI (Switzerland); Laboratory of Nanomagnetism and Spin Dynamics, Ecole Polytechnique Federale de Lausanne (EPFL), 1015 Lausanne (Switzerland)

2011-09-28

We review the details of domain wall (DW) propagation due to spin-polarized currents that could potentially be used in magnetic data storage devices based on domains and DWs. We discuss briefly the basics of the underlying spin torque effect and show how the two torques arising from the interaction between the spin-polarized charge carriers and the magnetization lead to complex dynamics of a spin texture such as a DW. By direct imaging we show how confined DWs in nanowires can be displaced using currents in in-plane soft-magnetic materials, and that when using short pulses, fast velocities can be attained. For high-anisotropy out-of-plane magnetized wires with narrow DWs we present approaches to deducing the torque terms and show that in these materials potentially more efficient domain wall motion could be achieved.

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

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.

Conceptual model of the globalization for domain-specific languages

NARCIS (Netherlands)

Clark, T.; van den Brand, M.; Combemale, B.; Rumpe, B.; Combemale, B.

2015-01-01

Domain Specific Languages (DSL) have received some prominence recently. Designing a DSL and all their tools is still cumbersome and lots of work. Engineering of DSLs is still at infancy, not even the terms have been coined and agreed on. In particular globalization and all its consequences need to

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.)

Gimme Context – towards New Domain-Specific Collocational Dictionaries

Directory of Open Access Journals (Sweden)

Sylvana Krausse

2011-04-01

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

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

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.

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.

Study of stratified dielectric slab medium structures using pseudo-spectral time domain (PSTD) algorithm

DEFF Research Database (Denmark)

Tong, M.S.; Lu, Y.; Chen, Y.

2005-01-01

-layer structures are analyzed. Results show that this method matches satisfactorily the Nyquist sampling theorem in terms of spatial discretization. By comparing the given results, it is found that the PSTD method outperforms the finite-difference time-domain (FDTD) method in general, especially in terms...

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.

Evidence of benzenoid domains in nanographenes.

Science.gov (United States)

Baldoni, Matteo; Mercuri, Francesco

2015-01-21

Calculations based on density functional theory demonstrate the occurrence of local deformations of the perfect honeycomb lattice in nanographenes to form arrangements, with triangular symmetry, composed of six-membered ring patterns. The formation of these locally regular superstructures, which can be considered as benzenoid-like domains on the 2D graphene lattice, is ascribed to the gain in resonance energy deriving from aromaticity. The relationship between the atomic morphology of nanographenes and details of the relaxed structure is rationalized in terms of Clar's theory of the aromatic sextet and by extending concepts borrowed from valence bond theory to 2D carbon nanostructures. Namely, two regular arrangements can be evidenced, defined as Clar (fully benzenoid) and Kekulé domains, which correspond to two different regular bond patterns in sets of adjacent six-membered rings. Our findings are compatible with recent experiments and have potentially relevant consequences in the development of novel electronic devices based on graphene materials.

From Microscopic to Macroscopic Descriptions of Cell Migration on Growing Domains

KAUST Repository

Baker, Ruth E.; Yates, Christian A.; Erban, Radek

2009-01-01

are studied, and correspondence with a macroscopic-level PDE describing the evolution of cell density is demonstrated. The individual-based models are formulated in terms of random walkers on a lattice. Domain growth provides an extra mathematical challenge

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.

Restoration in multi-domain GMPLS-based networks

DEFF Research Database (Denmark)

Manolova, Anna; Ruepp, Sarah Renée; Dittmann, Lars

2011-01-01

In this paper, we evaluate the efficiency of using restoration mechanisms in a dynamic multi-domain GMPLS network. Major challenges and solutions are introduced and two well-known restoration schemes (End-to-End and Local-to-End) are evaluated. Additionally, new restoration mechanisms are introdu......In this paper, we evaluate the efficiency of using restoration mechanisms in a dynamic multi-domain GMPLS network. Major challenges and solutions are introduced and two well-known restoration schemes (End-to-End and Local-to-End) are evaluated. Additionally, new restoration mechanisms...... are introduced: one based on the position of a failed link, called Location-Based, and another based on minimizing the additional resources consumed during restoration, called Shortest-New. A complete set of simulations in different network scenarios show where each mechanism is more efficient in terms, such as...

A Time Domain Waveform for Testing General Relativity

International Nuclear Information System (INIS)

Huwyler, Cédric; Jetzer, Philippe; Porter, Edward K

2015-01-01

Gravitational-wave parameter estimation is only as good as the theory the waveform generation models are based upon. It is therefore crucial to test General Relativity (GR) once data becomes available. Many previous works, such as studies connected with the ppE framework by Yunes and Pretorius, rely on the stationary phase approximation (SPA) to model deviations from GR in the frequency domain. As Fast Fourier Transform algorithms have become considerably faster and in order to circumvent possible problems with the SPA, we test GR with corrected time domain waveforms instead of SPA waveforms. Since a considerable amount of work has been done already in the field using SPA waveforms, we establish a connection between leading-order-corrected waveforms in time and frequency domain, concentrating on phase-only corrected terms. In a Markov Chain Monte Carlo study, whose results are preliminary and will only be available later, we will assess the ability of the eLISA detector to measure deviations from GR for signals coming from supermassive black hole inspirals using these corrected waveforms. (paper)

Frequency-domain waveform inversion using the phase derivative

KAUST Repository

Choi, Yun Seok

2013-09-26

Phase wrapping in the frequency domain or cycle skipping in the time domain is the major cause of the local minima problem in the waveform inversion when the starting model is far from the true model. Since the phase derivative does not suffer from the wrapping effect, its inversion has the potential of providing a robust and reliable inversion result. We propose a new waveform inversion algorithm using the phase derivative in the frequency domain along with the exponential damping term to attenuate reflections. We estimate the phase derivative, or what we refer to as the instantaneous traveltime, by taking the derivative of the Fourier-transformed wavefield with respect to the angular frequency, dividing it by the wavefield itself and taking the imaginary part. The objective function is constructed using the phase derivative and the gradient of the objective function is computed using the back-propagation algorithm. Numerical examples show that our inversion algorithm with a strong damping generates a tomographic result even for a high ‘single’ frequency, which can be a good initial model for full waveform inversion and migration.

Performance of Downlink Frequency Domain Packet Scheduling for the UTRAN Long Term Evolution

DEFF Research Database (Denmark)

Pokhariyal, Akhilesh; Kolding, Troels E.; Mogensen, Preben

2006-01-01

-blind, but time-opportunistic scheduling, FDPS shows gain in both average system capacity and cell-edge data rates on the order of 40%. However, FDPS performance is shown to depend significantly on the frequency-domain scheduling resolution as well as the accuracy of the channel state reports. Assuming Typical...... Urban channel profile, studies show that the scheduling resolution should preferably be as low as 375 kHz to yield significant FDPS gain and the std. of the error of radio state reports need to be kept within 1.5-2 dB....

Influence of boundary geometry in domain wall propagation in magnetic films with asymmetric holes: Micromagnetic calculations

International Nuclear Information System (INIS)

Alija, A; Sobrado, I; Rodriguez-RodrIguez, G; Velez, M; Alameda, J M; MartIn, J I; Parrondo, J M R

2010-01-01

Micromagnetic simulations have been performed in uniaxial magnetic films with 2D array of asymmetric arrow shape holes. In order to understand the asymmetric pinning potential created by the holes, different boundary geometries conditions are used on the simulations. The depinning fields for forward and backward domain wall propagation have been calculated by the analysis of the energy landscapes as a function of the domain wall position. Domain wall depinning occurs preferentially at the free ends of the domain wall at the film boundaries. We have found that the domain wall propagation is different at the top/bottom boundaries of the simulated film which can be understood in terms of the magnetostatic energy and the chirality of the domain wall.

A Domain-Specific Risk-Taking (DOSPERT scale for adult populations

Directory of Open Access Journals (Sweden)

Ann-Renée Blais

2006-07-01

Full Text Available This paper proposes a revised version of the original Domain-Specific Risk-Taking (DOSPERT scale developed by Weber, Blais, and Betz (2002 that is shorter and applicable to a {broader range of ages, cultures, and educational levels}. It also provides a French translation of the revised scale. Using multilevel modeling, we investigated the risk-return relationship between apparent risk taking and risk perception in 5 risk domains. The results replicate previously noted differences in reported degree of risk taking and risk perception at the mean level of analysis. The multilevel modeling shows, more interestingly, that within-participants variation in risk taking across the 5 content domains of the scale was about 7 times as large as between-participants variation. We discuss the implications of our findings in terms of the person-situation debate related to risk attitude

Induced motion of domain walls in multiferroics with quadratic interaction

Energy Technology Data Exchange (ETDEWEB)

Gerasimchuk, Victor S., E-mail: viktor.gera@gmail.com [National Technical University of Ukraine “Kyiv Polytechnic Institute”, Peremohy Avenue 37, 03056 Kiev (Ukraine); Shitov, Anatoliy A., E-mail: shitov@mail.ru [Donbass National Academy of Civil Engineering, Derzhavina Street 2, 86123 Makeevka, Donetsk Region (Ukraine)

2013-10-15

We theoretically study the dynamics of 180-degree domain wall of the ab-type in magnetic materials with quadratic magnetoelectric interaction in external alternating magnetic and electric fields. The features of the oscillatory and translational motions of the domain walls and stripe structures depending on the parameters of external fields and characteristics of the multiferroics are discussed. The possibility of the domain walls drift in a purely electric field is established. - Highlights: • We study DW and stripe DS in multiferroics with quadratic magnetoelectric interaction. • We build up the theory of oscillatory and translational (drift) DW and DS motion. • DW motion can be caused by crossed alternating electric and magnetic fields. • DW motion can be caused by alternating “pure” electric field. • DW drift velocity is formed by the AFM and Dzyaloshinskii interaction terms.

Identifying APT Malware Domain Based on Mobile DNS Logging

Directory of Open Access Journals (Sweden)

Weina Niu

2017-01-01

Full Text Available Advanced Persistent Threat (APT is a serious threat against sensitive information. Current detection approaches are time-consuming since they detect APT attack by in-depth analysis of massive amounts of data after data breaches. Specifically, APT attackers make use of DNS to locate their command and control (C&C servers and victims’ machines. In this paper, we propose an efficient approach to detect APT malware C&C domain with high accuracy by analyzing DNS logs. We first extract 15 features from DNS logs of mobile devices. According to Alexa ranking and the VirusTotal’s judgement result, we give each domain a score. Then, we select the most normal domains by the score metric. Finally, we utilize our anomaly detection algorithm, called Global Abnormal Forest (GAF, to identify malware C&C domains. We conduct a performance analysis to demonstrate that our approach is more efficient than other existing works in terms of calculation efficiency and recognition accuracy. Compared with Local Outlier Factor (LOF, k-Nearest Neighbor (KNN, and Isolation Forest (iForest, our approach obtains more than 99% F-M and R for the detection of C&C domains. Our approach not only can reduce data volume that needs to be recorded and analyzed but also can be applicable to unsupervised learning.

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.

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.

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.

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...

Atomic resolution structure of the E. coli YajR transporter YAM domain

Energy Technology Data Exchange (ETDEWEB)

Jiang, Daohua [National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101 (China); School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074 (China); Zhao, Yan [National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101 (China); School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027 (China); Fan, Junping; Liu, Xuehui; Wu, Yan; Feng, Wei [National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101 (China); Zhang, Xuejun C., E-mail: zhangc@ibp.ac.cn [National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101 (China)

2014-07-25

Highlights: • We report the crystal structure of the YAM domain of YajR transporter at 1.07 Å. • The YAM dimerization is related to the halogen-dependent high thermal stability. • A belt of poly-pentagonal water molecules was observed in the dimer interface. - Abstract: YajR is an Escherichia coli transporter that belongs to the major facilitator superfamily. Unlike most MFS transporters, YajR contains a carboxyl terminal, cytosolic domain of 67 amino acid residues termed YAM domain. Although it is speculated that the function of this small soluble domain is to regulate the conformational change of the 12-helix transmembrane domain, its precise regulatory role remains unclear. Here, we report the crystal structure of the YAM domain at 1.07-Å resolution, along with its structure determined using nuclear magnetic resonance. Detailed analysis of the high resolution structure revealed a symmetrical dimer in which a belt of well-ordered poly-pentagonal water molecules is embedded. A mutagenesis experiment and a thermal stability assay were used to analyze the putative role of this dimerization in response to changes in halogen concentration.

The use of typed lambda calculus for comprehension and construction of simulation models in the domain of ecology

Science.gov (United States)

Uschold, Michael

1992-01-01

We are concerned with two important issues in simulation modelling: model comprehension and model construction. Model comprehension is limited because many important choices taken during the modelling process are not documented. This makes it difficult for models to be modified or used by others. A key factor hindering model construction is the vast modelling search space which must be navigated. This is exacerbated by the fact that many modellers are unfamiliar with the terms and concepts catered to by current tools. The root of both problems is the lack of facilities for representing or reasoning about domain concepts in current simulation technology. The basis for our achievements in both of these areas is the development of a language with two distinct levels; one for representing domain information, and the other for representing the simulation model. Of equal importance, is the fact that we make formal connections between these two levels. The domain we are concerned with is ecological modelling. This language, called Elklogic, is based on the typed lambda calculus. Important features include a rich type structure, the use of various higher order functions, and semantics. This enables complex expressions to be constructed from relatively few primitives. The meaning of each expression can be determined in terms of the domain, the simulation model, or the relationship between the two. We describe a novel representation for sets and substructure, and a variety of other general concepts that are especially useful in the ecological domain. We use the type structure in a novel way: for controlling the modelling search space, rather than a proof search space. We facilitate model comprehension by representing modelling decisions that are embodied in the simulation model. We represent the simulation model separately from, but in terms of a domain mode. The explicit links between the two models constitute the modelling decisions. The semantics of Elklogic enables

N=1 domain wall solutions of massive type II supergravity as generalized geometries

International Nuclear Information System (INIS)

Louis, J.

2006-05-01

We study N=1 domain wall solutions of type IIB supergravity compactified on a Calabi-Yau manifold in the presence of RR and NS electric and magnetic fluxes. We show that the dynamics of the scalar fields along the direction transverse to the domain wall is described by gradient flow equations controlled by a superpotential W. We then provide a geometrical interpretation of the gradient flow equations in terms of the mirror symmetric compactification of type IIA. They correspond to a set of generalized Hitchin flow equations of a manifold with SU(3) x SU(3)structure which is fibered over the direction transverse to the domain wall. (Orig.)

Chasing probabilities — Signaling negative and positive prediction errors across domains

DEFF Research Database (Denmark)

Meder, David; Madsen, Kristoffer H; Hulme, Oliver

2016-01-01

of the two. We acquired functional MRI data while volunteers performed four probabilistic reversal learning tasks which differed in terms of outcome valence (reward-seeking versus punishment-avoidance) and domain (abstract symbols versus facial expressions) of outcomes. We found that ventral striatum...

Short-term versus long-term heart rate variability in ischemic cardiomyopathy risk stratification

Directory of Open Access Journals (Sweden)

Andreas eVoss

2013-12-01

Full Text Available In industrialized countries with aging populations, heart failure affects 0.3%-2% of the general population. The investigation of 24h-ECG recordings revealed the potential of nonlinear indices of heart rate variability (HRV for enhanced risk stratification in patients with ischemic heart failure (IHF. However, long-term analyses are time-consuming, expensive and delay the initial diagnosis. The objective of this study was to investigate whether 30min short-term HRV analysis is sufficient for comparable risk stratification in IHF in comparison to 24h-HRV analysis. From 256 IHF patients (221 at low risk (IHFLR and 35 at high risk (IHFHR a 24h beat-to-beat time series b the first 30min segment c the 30min most stationary day segment and d the 30min most stationary night segment were investigated. We calculated linear (time and frequency domain and nonlinear HRV analysis indices. Optimal parameter sets for risk stratification in IHF were determined for 24 hours and for each 30min segment by applying discriminant analysis on significant clinical and non-clinical indices. Long- and short-term HRV indices from frequency domain and particularly from nonlinear dynamics revealed high univariate significances (p

Stable multi-domain spectral penalty methods for fractional partial differential equations

Science.gov (United States)

Xu, Qinwu; Hesthaven, Jan S.

2014-01-01

We propose stable multi-domain spectral penalty methods suitable for solving fractional partial differential equations with fractional derivatives of any order. First, a high order discretization is proposed to approximate fractional derivatives of any order on any given grids based on orthogonal polynomials. The approximation order is analyzed and verified through numerical examples. Based on the discrete fractional derivative, we introduce stable multi-domain spectral penalty methods for solving fractional advection and diffusion equations. The equations are discretized in each sub-domain separately and the global schemes are obtained by weakly imposed boundary and interface conditions through a penalty term. Stability of the schemes are analyzed and numerical examples based on both uniform and nonuniform grids are considered to highlight the flexibility and high accuracy of the proposed schemes.

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

Theoretical nuclear and subnuclear physics

CERN Document Server

Walecka, John Dirk

1995-01-01

This comprehensive text expertly details the numerous theoretical techniques central to the discipline of nuclear physics. It is based on lecture notes from a three-lecture series given at CEBAF (the Continuous Electron Beam Accelerator Facility), where John Dirk Walecka at the time was Scientific Director: "Graduate Quantum Mechanics", "Advanced Quantum Mechanics and Field Theory" and "Special Topics in Nuclear Physics". The primary goal of this text is pedagogical; providing a clear, logical, in-depth, and unifying treatment of many diverse aspects of modern nuclear theory ranging from the non-relativistic many-body problem to the standard model of the strong, electromagnetic, and weak interactions. Four key topics are emphasised in this text: basic nuclear structure, the relativistic nuclear many-body problem, strong-coupling QCD, and electroweak interactions with nuclei. The text is designed to provide graduate students with a basic level of understanding of modern nuclear physics so that they in turn can...

Periodic domain inversion in x-cut single-crystal lithium niobate thin film

Energy Technology Data Exchange (ETDEWEB)

Mackwitz, P., E-mail: peterm@mail.upb.de; Rüsing, M.; Berth, G.; Zrenner, A. [Department Physik, Universität Paderborn, 33095 Paderborn (Germany); Center for Optoelectronics and Photonics Paderborn, 33095 Paderborn (Germany); Widhalm, A.; Müller, K. [Department Physik, Universität Paderborn, 33095 Paderborn (Germany)

2016-04-11

We report the fabrication of periodically poled domain patterns in x-cut lithium niobate thin-film. Here, thin films on insulator have drawn particular attention due to their intrinsic waveguiding properties offering high mode confinement and smaller devices compared to in-diffused waveguides in bulk material. In contrast to z-cut thin film lithium niobate, the x-cut geometry does not require back electrodes for poling. Further, the x-cut geometry grants direct access to the largest nonlinear and electro-optical tensor element, which overall promises smaller devices. The domain inversion was realized via electric field poling utilizing deposited aluminum top electrodes on a stack of LN thin film/SiO{sub 2} layer/Bulk LN, which were patterned by optical lithography. The periodic domain inversion was verified by non-invasive confocal second harmonic microscopy. Our results show domain patterns in accordance to the electrode mask layout. The second harmonic signatures can be interpreted in terms of spatially, overlapping domain filaments which start their growth on the +z side.

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.

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.

Ratchet Effects and Domain Wall Energy Landscapes in Amorphous Magnetic Films with 2D Arrays of Asymmetric Holes

Science.gov (United States)

Martin, J. I.; Alija, A.; Sobrado, I.; Perez-Junquera, A.; Rodriguez-Rodriguez, G.; Velez, M.; Alameda, J. M.; Marconi, V. I.; Kolton, A. B.; Parrondo, J. M. R.

2009-03-01

The driven motion of domain walls in extended magnetic films patterned with 2D arrays of asymmetric holes has been found to be subject to two different crossed ratchet effects [1] which results in an inversion of the sign of domain wall motion rectification as a function of the applied magnetic field. This effect can be understood in terms of the competition between drive, elasticity and asymmetric pinning as revealed by a simple 4̂-model. In order to optimize the asymmetric hole design, the relevant energy landscapes for domain wall motion across the array of asymmetric holes have been calculated by micromagnetic simulations as a function of array geometrical characteristics. The effects of a transverse magnetic field on these two crossed ratchet effects will also be discussed in terms of the decrease in domain wall energy per unit area and of the modifications in the magnetostatic barriers for domain wall pinning at the asymmetric inclusions. Work supported by Spanish MICINN.[1] A. Perez-Junquera et al, Phys. Rev. Lett. 100 (2008) 037203

Around and beyond 53BP1 Nuclear Bodies.

Science.gov (United States)

Fernandez-Vidal, Anne; Vignard, Julien; Mirey, Gladys

2017-12-05

Within the nucleus, sub-nuclear domains define territories where specific functions occur. Nuclear bodies (NBs) are dynamic structures that concentrate nuclear factors and that can be observed microscopically. Recently, NBs containing the p53 binding protein 1 (53BP1), a key component of the DNA damage response, were defined. Interestingly, 53BP1 NBs are visualized during G1 phase, in daughter cells, while DNA damage was generated in mother cells and not properly processed. Unlike most NBs involved in transcriptional processes, replication has proven to be key for 53BP1 NBs, with replication stress leading to the formation of these large chromatin domains in daughter cells. In this review, we expose the composition and organization of 53BP1 NBs and focus on recent findings regarding their regulation and dynamics. We then concentrate on the importance of the replication stress, examine the relation of 53BP1 NBs with DNA damage and discuss their dysfunction.

Around and beyond 53BP1 Nuclear Bodies

Directory of Open Access Journals (Sweden)

Anne Fernandez-Vidal

2017-12-01

Full Text Available Within the nucleus, sub-nuclear domains define territories where specific functions occur. Nuclear bodies (NBs are dynamic structures that concentrate nuclear factors and that can be observed microscopically. Recently, NBs containing the p53 binding protein 1 (53BP1, a key component of the DNA damage response, were defined. Interestingly, 53BP1 NBs are visualized during G1 phase, in daughter cells, while DNA damage was generated in mother cells and not properly processed. Unlike most NBs involved in transcriptional processes, replication has proven to be key for 53BP1 NBs, with replication stress leading to the formation of these large chromatin domains in daughter cells. In this review, we expose the composition and organization of 53BP1 NBs and focus on recent findings regarding their regulation and dynamics. We then concentrate on the importance of the replication stress, examine the relation of 53BP1 NBs with DNA damage and discuss their dysfunction.

Time-domain analytic Solutions of two-wire transmission line excited by a plane-wave field

Institute of Scientific and Technical Information of China (English)

Ni Gu-Yan; Yan Li; Yuan Nai-Chang

2008-01-01

This paper reports that an analytic method is used to calculate the load responses of the two-wire transmission line excited by a plane-wave directly in the time domain.By the frequency-domain Baum-Liu-Tesche(BLT)equation,the time-domain analytic solutions are obtained and expressed in an infinite geometric series.Moreover,it is shown that there exist only finite nonzero terms in the infinite geometric series if the time variate is at a finite interval.In other word.the time-domain analytic solutions are expanded in a finite geometric series indeed if the time variate is at a finite interval.The computed results are subsequently compared with transient responses obtained by using the frequency-domain BLT equation via a fast Fourier transform,and the agreement is excellent.

Perturbation on diffusion problems in domain with interfaces

International Nuclear Information System (INIS)

Watson, F.V.

1985-01-01

A perturbative type algorithm for the solution of linear diffusion equation at two dimensions, in domain with interfaces is presented. The perturbative scheme should be assembled in the weak formulation of diffusion equation, even if the strong solution exists, and when it is taken in terms superiors to first order, it should be calculated analytically, in one of the dimensions to avoid problems of slow convergence. (M.C.K.) [pt

Thickness-dependent a_1/a_2 domain evolution in ferroelectric PbTiO_3 films

International Nuclear Information System (INIS)

Li, S.; Zhu, Y.L.; Tang, Y.L.; Liu, Y.; Zhang, S.R.; Wang, Y.J.; Ma, X.L.

2017-01-01

Ferroelectric a_1/a_2 domain structure has great potentials in high dielectric capacitors and tunable microwave devices. Understanding its structure is crucial to better control the domain configurations for future applications. In this paper, PbTiO_3 thin films with variant thicknesses are deposited on (110)-oriented GdScO_3 substrates by Pulsed Laser Deposition (PLD) and investigated by using conventional transmission electron microscopy (TEM) and Cs-corrected Scanning TEM. Contrast analysis and electron diffractions reveal that PbTiO_3 films are domain oriented consisting of a_1/a_2 and a/c domain structure. The a_1/a_2 domains are found to distribute periodically and its width increases with increasing film thickness following square root rule. Cs-corrected STEM imaging demonstrates that the domain walls of a_1/a_2 domain structure have the rotation characteristic of 90° ferroelastic domain wall. The interchange of a_1/a_2 domains induces the formation of vertex domains composed of two 90° and one 180° domain walls. Strains are mainly concentrated on the domain walls. The formation of this complex domain configuration is discussed in terms of the effect of the misfit strain, film thickness and cooling rate. These results provide novel information about a_1/a_2 domain structures and are expected to shed some light on modulating a_1/a_2 ferroelectric domain patterns in the design of ferroelectric-based devices.

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.

Comparative structure-function characterization of the saposin-like domains from potato, barley, cardoon and Arabidopsis aspartic proteases.

Science.gov (United States)

Bryksa, Brian C; Grahame, Douglas A; Yada, Rickey Y

2017-05-01

The present study characterized the aspartic protease saposin-like domains of four plant species, Solanum tuberosum (potato), Hordeum vulgare L. (barley), Cynara cardunculus L. (cardoon; artichoke thistle) and Arabidopsis thaliana, in terms of bilayer disruption and fusion, and structure pH-dependence. Comparison of the recombinant saposin-like domains revealed that each induced leakage of bilayer vesicles composed of a simple phospholipid mixture with relative rates Arabidopsis>barley>cardoon>potato. When compared for leakage of bilayer composed of a vacuole-like phospholipid mixture, leakage was approximately five times higher for potato saposin-like domain compared to the others. In terms of fusogenic activity, distinctions between particle size profiles were noted among the four proteins, particularly for potato saposin-like domain. Bilayer fusion assays in reducing conditions resulted in altered fusion profiles except in the case of cardoon saposin-like domain which was virtually unchanged. Secondary structure profiles were similar across all four proteins under different pH conditions, although cardoon saposin-like domain appeared to have higher overall helix structure. Furthermore, increases in Trp emission upon protein-bilayer interactions suggested that protein structure rearrangements equilibrated with half-times ranging from 52 to 120s, with cardoon saposin-like domain significantly slower than the other three species. Overall, the present findings serve as a foundation for future studies seeking to delineate protein structural features and motifs in protein-bilayer interactions based upon variability in plant aspartic protease saposin-like domain structures. Copyright © 2017 Elsevier B.V. All rights reserved.

Time space domain decomposition methods for reactive transport - Application to CO2 geological storage

International Nuclear Information System (INIS)

Haeberlein, F.

2011-01-01

Reactive transport modelling is a basic tool to model chemical reactions and flow processes in porous media. A totally reduced multi-species reactive transport model including kinetic and equilibrium reactions is presented. A structured numerical formulation is developed and different numerical approaches are proposed. Domain decomposition methods offer the possibility to split large problems into smaller subproblems that can be treated in parallel. The class of Schwarz-type domain decomposition methods that have proved to be high-performing algorithms in many fields of applications is presented with a special emphasis on the geometrical viewpoint. Numerical issues for the realisation of geometrical domain decomposition methods and transmission conditions in the context of finite volumes are discussed. We propose and validate numerically a hybrid finite volume scheme for advection-diffusion processes that is particularly well-suited for the use in a domain decomposition context. Optimised Schwarz waveform relaxation methods are studied in detail on a theoretical and numerical level for a two species coupled reactive transport system with linear and nonlinear coupling terms. Well-posedness and convergence results are developed and the influence of the coupling term on the convergence behaviour of the Schwarz algorithm is studied. Finally, we apply a Schwarz waveform relaxation method on the presented multi-species reactive transport system. (author)

RADIANCE DOMAIN COMPOSITING FOR HIGH DYNAMIC RANGE IMAGING

Directory of Open Access Journals (Sweden)

M.R. Renu

2013-02-01

Full Text Available High dynamic range imaging aims at creating an image with a range of intensity variations larger than the range supported by a camera sensor. Most commonly used methods combine multiple exposure low dynamic range (LDR images, to obtain the high dynamic range (HDR image. Available methods typically neglect the noise term while finding appropriate weighting functions to estimate the camera response function as well as the radiance map. We look at the HDR imaging problem in a denoising frame work and aim at reconstructing a low noise radiance map from noisy low dynamic range images, which is tone mapped to get the LDR equivalent of the HDR image. We propose a maximum aposteriori probability (MAP based reconstruction of the HDR image using Gibb’s prior to model the radiance map, with total variation (TV as the prior to avoid unnecessary smoothing of the radiance field. To make the computation with TV prior efficient, we extend the majorize-minimize method of upper bounding the total variation by a quadratic function to our case which has a nonlinear term arising from the camera response function. A theoretical justification for doing radiance domain denoising as opposed to image domain denoising is also provided.

METHOD OF RARE TERM CONTRASTIVE EXTRACTION FROM NATURAL LANGUAGE TEXTS

Directory of Open Access Journals (Sweden)

I. A. Bessmertny

2017-01-01

Full Text Available The paper considers a problem of automatic domain term extraction from documents corpus by means of a contrast collection. Existing contrastive methods successfully extract often used terms but mishandle rare terms. This could yield poorness of the resulting thesaurus. Assessment of point-wise mutual information is one of the known statistical methods of term extraction and it finds rare terms successfully. Although, it extracts many false terms at that. The proposed approach consists of point-wise mutual information application for rare terms extraction and filtering of candidates by criterion of joint occurrence with the other candidates. We build “documents-by-terms” matrix that is subjected to singular value decomposition to eliminate noise and reveal strong interconnections. Then we pass on to the resulting matrix “terms-by-terms” that reproduces strength of interconnections between words. This approach was approved on a documents collection from “Geology” domain with the use of contrast documents from such topics as “Politics”, “Culture”, “Economics” and “Accidents” on some Internet resources. The experimental results demonstrate operability of this method for rare terms extraction.

Development of source term PIRT of Fukushima Daiichi NPPs accident

International Nuclear Information System (INIS)

Suehiro, S.; Okamoto, K.

2017-01-01

The severe accident evaluation committee of AESJ (Atomic Energy Society of Japan) developed the thermal hydraulic PIRT (Phenomena Identification and Ranking Table) and the source term PIRT based on findings during the Fukushima Daiichi NPPs accident. These PIRTs aimed to explore the debris distribution and the current condition in the NPPs with high accuracy and to extract higher priority from the aspect of the sophistication of the analytical technology to predict the severe accident phenomena by the code. The source term PIRT was divided into 3 phases for the time domain and 9 categories for the spatial domain. The 68 phenomena were extracted and the importance from viewpoint of the source term was ranked through brainstorming and discussion. This paper describes the developed source term PIRT list and summarized the high ranked phenomena in each phase. (author)

General spectral flow formula for fixed maximal domain

DEFF Research Database (Denmark)

Booss-Bavnbek, Bernhelm; Zhu, Chaofeng

2005-01-01

of the resulting continuous family of (unbounded) self-adjoint Fredholm operators in terms of the Maslov index of two related curves of Lagrangian spaces. One curve is given by the varying domains, the other by the Cauchy data spaces. We provide rigorous definitions of the underlying concepts of spectral theory......We consider a continuous curve of linear elliptic formally self-adjoint differential operators of first order with smooth coefficients over a compact Riemannian manifold with boundary together with a continuous curve of global elliptic boundary value problems. We express the spectral flow...... and symplectic analysis and give a full (and surprisingly short) proof of our General Spectral Flow Formula for the case of fixed maximal domain. As a side result, we establish local stability of weak inner unique continuation property (UCP) and explain its role for parameter dependent spectral theory....

Age related differences in individual quality of life domains in youth with type 1 diabetes

Directory of Open Access Journals (Sweden)

Lett Syretta

2004-09-01

Full Text Available Abstract Background Investigating individual, as opposed to predetermined, quality of life domains may yield important information about quality of life. This study investigated the individual quality of life domains nominated by youth with type 1 diabetes. Methods Eighty young people attending a diabetes summer camp completed the Schedule for the Evaluation of Individual Quality of Life-Direct Weighting interview, which allows respondents to nominate and evaluate their own quality of life domains. Results The most frequently nominated life domains were 'family', 'friends', 'diabetes', 'school', and 'health' respectively; ranked in terms of importance, domains were 'religion', 'family', 'diabetes', 'health', and 'the golden rule'; ranked in order of satisfaction, domains were 'camp', 'religion', 'pets', and 'family' and 'a special person' were tied for fifth. Respondent age was significantly positively associated with the importance of 'friends', and a significantly negatively associated with the importance of 'family'. Nearly all respondents nominated a quality of life domain relating to physical status, however, the specific physical status domain and the rationale for its nomination varied. Some respondents nominated 'diabetes' as a domain and emphasized diabetes 'self-care behaviors' in order to avoid negative health consequences such as hospitalization. Other respondents nominated 'health' and focused more generally on 'living well with diabetes'. In an ANOVA with physical status domain as the independent variable and age as the dependent variable, participants who nominated 'diabetes' were younger (M = 12.9 years than those who nominated 'health' (M = 15.9 years. In a second ANOVA, with rationale for nomination the physical status domain as the independent variable, and age as the dependent variable, those who emphasized 'self care behaviors' were younger (M = 11.8 years than those who emphasized 'living well with diabetes' (M = 14.6 years

Nonlinear system identification NARMAX methods in the time, frequency, and spatio-temporal domains

CERN Document Server

Billings, Stephen A

2013-01-01

Nonlinear System Identification: NARMAX Methods in the Time, Frequency, and Spatio-Temporal Domains describes a comprehensive framework for the identification and analysis of nonlinear dynamic systems in the time, frequency, and spatio-temporal domains. This book is written with an emphasis on making the algorithms accessible so that they can be applied and used in practice. Includes coverage of: The NARMAX (nonlinear autoregressive moving average with exogenous inputs) modelThe orthogonal least squares algorithm that allows models to be built term by

Joint time-frequency domain proportional fair scheduler with HARQ for 3GPP LTE systems

OpenAIRE

Beh, KC; Doufexi, A; Armour, SMD

2008-01-01

This paper explores the potential gain of joint diversity in both frequency domain and time domain which can be exploited to achieve spectral efficiency gains whilst simultaneously facilitating QoS/ fairness in an OFDMA system particularly in 3GPP Long Term Evolution (LTE)). The performance of several joint time-frequency schedulers is investigated. Simulation results show that joint time frequency schedulers achieve significantly superior performance compared to a more conventional time doma...

A feature dictionary supporting a multi-domain medical knowledge base.

Science.gov (United States)

Naeymi-Rad, F

1989-01-01

Because different terminology is used by physicians of different specialties in different locations to refer to the same feature (signs, symptoms, test results), it is essential that our knowledge development tools provide a means to access a common pool of terms. This paper discusses the design of an online medical dictionary that provides a solution to this problem for developers of multi-domain knowledge bases for MEDAS (Medical Emergency Decision Assistance System). Our Feature Dictionary supports phrase equivalents for features, feature interactions, feature classifications, and translations to the binary features generated by the expert during knowledge creation. It is also used in the conversion of a domain knowledge to the database used by the MEDAS inference diagnostic sessions. The Feature Dictionary also provides capabilities for complex queries across multiple domains using the supported relations. The Feature Dictionary supports three methods for feature representation: (1) for binary features, (2) for continuous valued features, and (3) for derived features.

Performance of synthetic antiferromagnetic racetrack memory: domain wall versus skyrmion

International Nuclear Information System (INIS)

Tomasello, R; Puliafito, V; Martinez, E; Manchon, A; Ricci, M; Carpentieri, M; Finocchio, G

2017-01-01

A storage scheme based on racetrack memory, where the information can be coded in a domain or a skyrmion, seems to be an alternative to conventional hard disk drive for high density storage. Here, we perform a full micromagnetic study of the performance of synthetic antiferromagnetic (SAF) racetrack memory in terms of velocity and sensitivity to defects by using experimental parameters. We find that, to stabilize a SAF skyrmion, the Dzyaloshinskii–Moriya interaction in the top and the bottom ferromagnet should have an opposite sign. The velocity of SAF skyrmions and SAF Néel domain walls are of the same order and can reach values larger than 1200 m s −1 if a spin–orbit torque from the spin-Hall effect with opposite sign is applied to both ferromagnets. The presence of disordered anisotropy in the form of randomly distributed grains introduces a threshold current for both SAF skyrmions and SAF domain walls motions. (paper)

Performance of synthetic antiferromagnetic racetrack memory: domain wall versus skyrmion

KAUST Repository

Tomasello, R

2017-06-20

A storage scheme based on racetrack memory, where the information can be coded in a domain or a skyrmion, seems to be an alternative to conventional hard disk drive for high density storage. Here, we perform a full micromagnetic study of the performance of synthetic antiferromagnetic (SAF) racetrack memory in terms of velocity and sensitivity to defects by using experimental parameters. We find that, to stabilize a SAF skyrmion, the Dzyaloshinskii–Moriya interaction in the top and the bottom ferromagnet should have an opposite sign. The velocity of SAF skyrmions and SAF Néel domain walls are of the same order and can reach values larger than 1200 m s−1 if a spin–orbit torque from the spin-Hall effect with opposite sign is applied to both ferromagnets. The presence of disordered anisotropy in the form of randomly distributed grains introduces a threshold current for both SAF skyrmions and SAF domain walls motions.

A Domain-Specific Terminology for Retinopathy of Prematurity and Its Applications in Clinical Settings.

Science.gov (United States)

Zhang, Yinsheng; Zhang, Guoming

2018-01-01

A terminology (or coding system) is a formal set of controlled vocabulary in a specific domain. With a well-defined terminology, each concept in the target domain is assigned with a unique code, which can be identified and processed across different medical systems in an unambiguous way. Though there are lots of well-known biomedical terminologies, there is currently no domain-specific terminology for ROP (retinopathy of prematurity). Based on a collection of historical ROP patients' data in the electronic medical record system, we extracted the most frequent terms in the domain and organized them into a hierarchical coding system-ROP Minimal Standard Terminology, which contains 62 core concepts in 4 categories. This terminology has been successfully used to provide highly structured and semantic-rich clinical data in several ROP-related applications.

A Domain-Specific Terminology for Retinopathy of Prematurity and Its Applications in Clinical Settings

Directory of Open Access Journals (Sweden)

Yinsheng Zhang

2018-01-01

Full Text Available A terminology (or coding system is a formal set of controlled vocabulary in a specific domain. With a well-defined terminology, each concept in the target domain is assigned with a unique code, which can be identified and processed across different medical systems in an unambiguous way. Though there are lots of well-known biomedical terminologies, there is currently no domain-specific terminology for ROP (retinopathy of prematurity. Based on a collection of historical ROP patients’ data in the electronic medical record system, we extracted the most frequent terms in the domain and organized them into a hierarchical coding system—ROP Minimal Standard Terminology, which contains 62 core concepts in 4 categories. This terminology has been successfully used to provide highly structured and semantic-rich clinical data in several ROP-related applications.

Time-domain analytic solutions of two-wire transmission line excited by a plane-wave field

International Nuclear Information System (INIS)

Ni Guyan; Yan Li; Yuan Naichang

2008-01-01

This paper reports that an analytic method is used to calculate the load responses of the two-wire transmission line excited by a plane-wave directly in the time domain. By the frequency-domain Baum–Liu–Tesche (BLT) equation, the time-domain analytic solutions are obtained and expressed in an infinite geometric series. Moreover, it is shown that there exist only finite nonzero terms in the infinite geometric series if the time variate is at a finite interval. In other word, the time-domain analytic solutions are expanded in a finite geometric series indeed if the time variate is at a finite interval. The computed results are subsequently compared with transient responses obtained by using the frequency-domain BLT equation via a fast Fourier transform, and the agreement is excellent. (the physics of elementary particles and fields)

Influence of social relationship domains and their combinations on incident dementia: a prospective cohort study.

Science.gov (United States)

Saito, Tami; Murata, Chiyoe; Saito, Masashige; Takeda, Tokunori; Kondo, Katsunori

2018-01-01

Social relationships consist of mutually related but distinct dimensions. It remains unclear how these domains independently contribute to incident dementia. This large-scale, prospective cohort study examines associations between the social relationship domains as well as their combinations and incident dementia among community-dwelling older adults. We analysed data from 13 984 community-dwelling adults aged 65+ without long-term care needs living in Aichi prefecture in Japan. Incident dementia was assessed based on the Long-term Care Insurance records, followed for 3436 days from the baseline survey conducted in 2003. Three social relationships domains (social support, social networks and social activities) were further divided into a total of eight subdomains. A social relationship diversity score was calculated using the social relationship domains which were significantly related to incident dementia. A Cox proportional hazards model showed that being married, exchanging support with family members, having contact with friends, participating in community groups and engaging in paid work were related to a lower likelihood of developing incident dementia, controlling for covariates and other social relationship domains. The diversity scores, ranging from 0 to 5, were linearly associated with incident dementia (psocial relationship subdomains which were negatively related to incident dementia, suggesting that dementia may potentially be prevented by enhancing these social relationships. Future studies should examine independent pathways between each social relationship domain and incident dementia. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Economic terms and beyond how researchers in specialised varieties of English can benefit from focusing on terms

CERN Document Server

Resche, Catherine

2013-01-01

This book, which is aimed at researchers in specialised varieties of English, provides an illustration of how linguists can use terms, i.e. the expression of concepts in specialised fields, as entry points to explore any specialised domain, whether academic or professional, and to get acquainted with its history, its culture, and the evolution of the ideas that have nurtured it. Choosing the field of economics as an example, the author approaches terms from a diachronic, descriptive and contextual perspective, focusing on neonyms, metaphorical, ambiguous or indeterminate terms, as well as inte

Domain wall network as QCD vacuum and the chromomagnetic trap formation under extreme conditions

International Nuclear Information System (INIS)

Nedelko, Sergei N.; Voronin, Vladimir E.

2015-01-01

The ensemble of Euclidean gluon field configurations represented by the domain wall network is considered. A single domain wall is given by the sine-Gordon kink for the angle between chromomagnetic and chromoelectric components of the gauge field. The domain wall separates the regions with Abelian self-dual and anti-self-dual fields. The network of the domain wall defects is introduced as a combination of multiplicative and additive superpositions of kinks. The character of the spectrum and eigenmodes of color-charged fluctuations in the presence of the domain wall network is discussed. Conditions for the formation of a stable thick domain wall junction (the chromomagnetic trap) during heavy-ion collisions are discussed, and the spectrum of color-charged quasi-particles inside the trap is evaluated. An important observation is the existence of the critical size L c of a single trap stable against gluon tachyonic modes. The size L c is related to the value of gluon condensate left angle g 2 F 2 right angle. The growth of large lumps of merged chromomagnetic traps and the concept of the confinement-deconfinement transition in terms of the ensemble of domain wall networks are outlined. (orig.)

Flavor Mixing, CP-Violation and the Masses of the Light Quarks

CERN Document Server

Fritzsch, Harald

1998-01-01

The observed hierarchy of the quark masses is interpreted as a signal for an underlying ``subnuclear democracy'' as the relevant symmetry of the quark mass terms. A simple breaking of the symmetry leads to a mixing between the second and the third family, in agreement with observation. Introducing the mixing between the first and the second family, one finds an interesting pattern of maximal CP--violation as well as a complete determination of the elements of the CKM matrix and of the unitarity triangle.

Flavor mixing, CP-violation and the masses of the light quarks

International Nuclear Information System (INIS)

Fritzsch, H.

1998-01-01

The observed hierarchy of the quark masses is interpreted as a signal for an underlying ''subnuclear democracy'' as the relevant symmetry of the quark mass terms. A simple breaking of the symmetry leads to a mixing between the second and the third family, in agreement with observation. Introducing the mixing between the first and the second family, one finds an interesting pattern of maximal CP-violation as well as a complete determination of the elements of the CKM matrix and of the unitarity triangle. (orig.)

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.

Legal Challenges Related to the Regulation of a Domain Name System

Directory of Open Access Journals (Sweden)

Marius Kalinauskas

2012-12-01

Full Text Available Purpose—to review and analyse the problematic aspects related to domain name allocation and further usage processes, highlighting legal regulation of a domain name system.Design/methodology/approach—based on the comparison analysis of scientific literature, authors discuss problematic issues related to the legal regulation of domain name allocation and usage processes, analyse practical approaches and collision cases in the context of a domain name system. The authors examine the positive and negative aspects of a domain naming system and conflicting regulatory specifics. This paper describes the development of institutional bodies responsible for DNS management, supervision approaches and inner functionality policies.Findings—the authors examine domain naming system models and dispute resolution mechanisms, their evolution in the context of Internet development and the structural changes of the Internet governance institutions. The authors analyse tendencies related to DNS regulation and the possible effect of new regulation models in practice, while reflecting interests of stakeholders in the subject field.Research limitations/implications—agreements on the registration of domain names are based on self-regulation principles. A number of different interests may collide when speaking about domain name registration or usage and this issue becomes a major challenge to scientists and lawyers who are seeking an optimal domain-naming regulatory mechanism. The article does not address trademark conflicts within domain names in this respect. This should be considered as an object for separate study, which requires deeper analysis.Practical implications—the authors review key aspects of the domain name system and describe tendencies for the regulatory models.Value—the article emphasizes potential domain naming conflicts and disputes concerning the usage of common terms and phrases in order to manipulate information for illicit purposes. The

Legal Challenges Related to the Regulation of a Domain Name System

Directory of Open Access Journals (Sweden)

Marius Kalinauskas

2013-02-01

Full Text Available Purpose—to review and analyse the problematic aspects related to domain name allocation and further usage processes, highlighting legal regulation of a domain name system. Design/methodology/approach—based on the comparison analysis of scientific literature, authors discuss problematic issues related to the legal regulation of domain name allocation and usage processes, analyse practical approaches and collision cases in the context of a domain name system. The authors examine the positive and negative aspects of a domain naming system and conflicting regulatory specifics. This paper describes the development of institutional bodies responsible for DNS management, supervision approaches and inner functionality policies. Findings—the authors examine domain naming system models and dispute resolution mechanisms, their evolution in the context of Internet development and the structural changes of the Internet governance institutions. The authors analyse tendencies related to DNS regulation and the possible effect of new regulation models in practice, while reflecting interests of stakeholders in the subject field. Research limitations/implications—agreements on the registration of domain names are based on self-regulation principles. A number of different interests may collide when speaking about domain name registration or usage and this issue becomes a major challenge to scientists and lawyers who are seeking an optimal domain-naming regulatory mechanism. The article does not address trademark conflicts within domain names in this respect. This should be considered as an object for separate study, which requires deeper analysis. Practical implications—the authors review key aspects of the domain name system and describe tendencies for the regulatory models. Value—the article emphasizes potential domain naming conflicts and disputes concerning the usage of common terms and phrases in order to manipulate information for illicit purposes

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'.

Domains and facets: hierarchical personality assessment using the revised NEO personality inventory.

Science.gov (United States)

Costa, P T; McCrae, R R

1995-02-01

Personality traits are organized hierarchically, with narrow, specific traits combining to define broad, global factors. The Revised NEO Personality Inventory (NEO-PI-R; Costa & McCrae, 1992c) assesses personality at both levels, with six specific facet scales in each of five broad domains. This article describes conceptual issues in specifying facets of a domain and reports evidence on the validity of NEO-PI-R facet scales. Facet analysis-the interpretation of a scale in terms of the specific facets with which it correlates-is illustrated using alternative measures of the five-factor model and occupational scales. Finally, the hierarchical interpretation of personality profiles is discussed. Interpretation on the domain level yields a rapid understanding of the individual interpretation of specific facet scales gives a more detailed assessment.

The study of co-citation analysis and knowledge structure on healthcare domain

Science.gov (United States)

Chu, Kuo-Chung; Liu, Wen-I.; Tsai, Ming-Yu

2012-11-01

With the prevalence of Internet and digital archives, the online e-journal database facilitates scholars to search literature in a research domain, or to cross-search an inter-disciplined field; the key literature can be efficiently traced out. This study intends to build a Web-based citation analysis system, which consists of four modules, they are: 1) literature search module; (2) statistics module; (3) articles analysis module; and (4) co-citation analysis module. The system focuses on PubMed Central dataset that has 170,000 records. In a research domain, a specific keyword searches in terms of authors, journals, and core issues. In addition, we use data mining techniques for co-citation analysis. The results assist researchers with in-depth understanding of the domain knowledge. Having an automated system for co-citation analysis, it helps to understand changes, trends, and knowledge structure of research domain. For the best of our knowledge, the proposed system differentiates from existing online electronic retrieval database analysis function. Perhaps, the proposed system is going to be a value-added database of healthcare domain, and hope to contribute the researchers.

The role of glycosylation and domain interactions in the thermal stability of human angiotensin-converting enzyme.

Science.gov (United States)

O'Neill, Hester G; Redelinghuys, Pierre; Schwager, Sylva L U; Sturrock, Edward D

2008-09-01

The N and C domains of somatic angiotensin-converting enzyme (sACE) differ in terms of their substrate specificity, inhibitor profiling, chloride dependency and thermal stability. The C domain is thermally less stable than sACE or the N domain. Since both domains are heavily glycosylated, the effect of glycosylation on their thermal stability was investigated by assessing their catalytic and physicochemical properties. Testis ACE (tACE) expressed in mammalian cells, mammalian cells in the presence of a glucosidase inhibitor and insect cells yielded proteins with altered catalytic and physicochemical properties, indicating that the more complex glycans confer greater thermal stabilization. Furthermore, a decrease in tACE and N-domain N-glycans using site-directed mutagenesis decreased their thermal stability, suggesting that certain N-glycans have an important effect on the protein's thermodynamic properties. Evaluation of the thermal stability of sACE domain swopover and domain duplication mutants, together with sACE expressed in insect cells, showed that the C domain contained in sACE is less dependent on glycosylation for thermal stabilization than a single C domain, indicating that stabilizing interactions between the two domains contribute to the thermal stability of sACE and are decreased in a C-domain-duplicating mutant.

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.

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

Domain wall kinetics of lithium niobate single crystals near the hexagonal corner

Energy Technology Data Exchange (ETDEWEB)

Choi, Ju Won [Department of Physics and Photon Science, Gwangju Institute of Science and Technology (GIST), 1 Oryong-dong, Buk-gu, Gwangju 500-712 (Korea, Republic of); Ko, Do-Kyeong [Department of Physics and Photon Science, Gwangju Institute of Science and Technology (GIST), 1 Oryong-dong, Buk-gu, Gwangju 500-712 (Korea, Republic of); Advanced Photonics Research Institute, GIST, 1 Oryong-dong, Buk-gu, Gwangju 500-712 (Korea, Republic of); Yu, Nan Ei, E-mail: neyu@gist.ac.kr, E-mail: jhro@pnu.edu [Advanced Photonics Research Institute, GIST, 1 Oryong-dong, Buk-gu, Gwangju 500-712 (Korea, Republic of); Kitamura, Kenji [National Institute for Materials Science, Tsukuba, Ibaraki 305-0044 (Japan); Ro, Jung Hoon, E-mail: neyu@gist.ac.kr, E-mail: jhro@pnu.edu [Department of Biomedical Engineering, School of Medicine, Pusan National University, Busan 602-739 (Korea, Republic of)

2015-03-09

A mesospheric approach based on a simple microscopic 2D Ising model in a hexagonal lattice plane is proposed to explain macroscopic “asymmetric in-out domain wall motion” observation in the (0001) plane of MgO-doped stoichiometric lithium niobate. Under application of an electric field that was higher than the conventional coercive field (E{sub c}) to the ferroelectric crystal, a natural hexagonal domain was obtained with walls that were parallel to the Y-axis of the crystal. When a fraction of the coercive field of around 0.1E{sub c} is applied in the reverse direction, this hexagonal domain is shrunk (moved inward) from the corner site into a shape with a corner angle of around 150° and 15° wall slopes to the Y-axis. A flipped electric field of 0.15E{sub c} is then applied to recover the natural hexagonal shape, and the 150° corner shape changes into a flat wall with 30° slope (moved outward). The differences in corner domain shapes between inward and outward domain motion were analyzed theoretically in terms of corner and wall site energies, which are described using the domain corner angle and wall slope with respect to the crystal Y-axis, respectively. In the inward domain wall motion case, the energy levels of the evolving 150° domain corner and 15° slope walls are most competitive, and could co-exist. In the outward case, the energy levels of corners with angles >180° are highly stable when compared with the possible domain walls; only a flat wall with 30° slope to the Y-axis is possible during outward motion.

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.

Mutations of amino acids in the DNA-recognition domain of Epstein-Barr virus ZEBRA protein alter its sub-nuclear localization and affect formation of replication compartments

International Nuclear Information System (INIS)

Park, Richard; Heston, Lee; Shedd, Duane; Delecluse, Henri-Jacques; Miller, George

2008-01-01

foci. The speckled appearance of R179A and Y180E was more regular and clearly defined in EBV-positive than in EBV-negative 293 cells. The Y180E late-mutant induced EA-D, but prevented EA-D from localizing to globular replication compartments. These results show that individual amino acids within the basic domain influence localization of the ZEBRA protein and its capacity to induce EA-D to become located in mature viral replication compartments. Furthermore, these mutant ZEBRA proteins delineate several stages in the processes of nuclear re-organization which accompany lytic EBV replication

Hebb learning, verbal short-term memory, and the acquisition of phonological forms in children.

Science.gov (United States)

Mosse, Emma K; Jarrold, Christopher

2008-04-01

Recent work using the Hebb effect as a marker for implicit long-term acquisition of serial order has demonstrated a functional equivalence across verbal and visuospatial short-term memory. The current study extends this observation to a sample of five- to six-year-olds using verbal and spatial immediate serial recall and also correlates the magnitude of Hebb learning with explicit measures of word and nonword paired-associate learning. Comparable Hebb effects were observed in both domains, but only nonword learning was significantly related to the magnitude of Hebb learning. Nonword learning was also independently related to individuals' general level of verbal serial recall. This suggests that vocabulary acquisition depends on both a domain-specific short-term memory system and a domain-general process of learning through repetition.

The corkscrew instability of a Freedericksz domain wall in a nematic liquid crystal

CERN Document Server

Munoz, A D L; Müller, M; Schoepf, W; Rehberg, I

2003-01-01

A liquid crystal with slightly positive dielectric anisotropy is investigated in the planar configuration. This system allows for competition between electroconvection and the homogeneous Freedericksz transition, leading to a rather complicated bifurcation scenario. We report measurements of a novel instability leading to the 'corkscrew' pattern. This state is closely connected to the Freedericksz state as it manifests itself as a regular modulation along a Freedericksz domain wall, although its frequency dependence indicates that electroconvection must play a crucial role. It can be understood in terms of a pitchfork bifurcation from a straight domain wall. Quantitative characterization is performed in terms of amplitude, wavelength and relaxation time. Its wavelength is of the order of the probe thickness, while its ondulation amplitude is an order of magnitude smaller. The relaxation time is comparable to the one obtained for electroconvection.

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,

PENGATURAN PASSING OFF DALAM PENGGUNAAN DOMAIN NAME TERKAIT DENGAN MEREK

Directory of Open Access Journals (Sweden)

Herti Yunita Putri

2016-09-01

Full Text Available In cyber world we often hear about domain name’s term. Domain name is a unique name to identify the server computer’s name like a web server or email server on a computer network or Internet. Passing off also make causes confusion in using merk from a famous brand or merk on the goods and services. Selected domain name in the internet media often creates the similar domain name with the other parties. This similar domain name are often used by people who are not responsible to take advantages of the domain name for themself. This can be caused by the presence of competition from Internet media business. This things called passing off. This research is a normative juridical research with a qualitative analysis. The legal materials include primary legal, secondary law and tertiary legal materials. Collection technique applied is literary study. Legal materials were analyzed to see the argument implementation of the definition of merk, the definition of domain name, definition of passing off, passing off in use related by merk and domain name and the rules of law in Indonesia related by merk, domain name and passing off. Big wishes in the future it can assist as a basic reference and legal considerations which are useful in Indonesian law practice. There are two passing off related to the merk and domain name, called Crybersquatting and Tiposquatting. Domain name rules are not regulated clearly in merk regulation named Act No. 15 of 2001. It regulated in PP 24 Year 1993 about The Class List of Goods or Services In Merk, Telecommunications are included in the goods or services in merk. Domain name are regulated in UDRP (Uniform Dispute Resolution Policy with competent institutions called ICANN (Internet Corporation for Assigned Names and Numbers. Dalam dunia maya (cyber world, kita sering mendengar istilah domain name. Domain name adalah nama unik yang diberikan untuk mengidentifikasi nama server komputer seperti web server atau email server di

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

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.

An Evaluation of the Performance Diagnostic Checklist-Human Services (PDC-HS) Across Domains.

Science.gov (United States)

Wilder, David A; Lipschultz, Joshua; Gehrman, Chana

2018-06-01

The Performance Diagnostic Checklist-Human Services (PDC-HS) is an informant-based tool designed to assess the environmental variables that contribute to poor employee performance in human service settings. Although the PDC-HS has been shown to effectively identify variables contributing to problematic performance, interventions based on only two of the four PDC-HS domains have been evaluated to date. In addition, the extent to which PDC-HS-indicated interventions are more effective than nonindicated interventions for two domains remains unclear. In the current study, we administered the PDC-HS to supervisors to assess the variables contributing to infrequent teaching of verbal operants and use of a timer by therapists at a center-based autism treatment program. Each of the four PDC-HS domains was identified as contributing to poor performance for at least one therapist. We then evaluated PDC-HS-indicated interventions for each domain. In addition, to assess the predictive validity of the tool, we evaluated various nonindicated interventions prior to implementing a PDC-HS-indicated intervention for two of the four domains. Results suggest that the PDC-HS-indicated interventions were effective across all four domains and were more effective than the nonindicated interventions for the two domains for which they were evaluated. Results are discussed in terms of the utility of the PDC-HS to identify appropriate interventions to manage therapist performance in human service settings.

Subnuclear foci quantification using high-throughput 3D image cytometry

Science.gov (United States)

Wadduwage, Dushan N.; Parrish, Marcus; Choi, Heejin; Engelward, Bevin P.; Matsudaira, Paul; So, Peter T. C.

2015-07-01

Ionising radiation causes various types of DNA damages including double strand breaks (DSBs). DSBs are often recognized by DNA repair protein ATM which forms gamma-H2AX foci at the site of the DSBs that can be visualized using immunohistochemistry. However most of such experiments are of low throughput in terms of imaging and image analysis techniques. Most of the studies still use manual counting or classification. Hence they are limited to counting a low number of foci per cell (5 foci per nucleus) as the quantification process is extremely labour intensive. Therefore we have developed a high throughput instrumentation and computational pipeline specialized for gamma-H2AX foci quantification. A population of cells with highly clustered foci inside nuclei were imaged, in 3D with submicron resolution, using an in-house developed high throughput image cytometer. Imaging speeds as high as 800 cells/second in 3D were achieved by using HiLo wide-field depth resolved imaging and a remote z-scanning technique. Then the number of foci per cell nucleus were quantified using a 3D extended maxima transform based algorithm. Our results suggests that while most of the other 2D imaging and manual quantification studies can count only up to about 5 foci per nucleus our method is capable of counting more than 100. Moreover we show that 3D analysis is significantly superior compared to the 2D techniques.

Structural matching of ferroelectric domains and associated distortion in potassium titanyl phosphate crystals

CERN Document Server

Pernot-Rejmankova, P; Cloetens, P; Lyford, T; Baruchel, J

2003-01-01

The surface deformation and atomic-level distortions associated with crystal structural matching at ferroelectric inversion domain walls are investigated in periodically poled potassium titanyl phosphate (KTP) crystals. A deformation, of the order of 10 sup - sup 8 m in scale and having the periodicity of the domains, is observed at the surfaces by optical interferometry. It is discussed in terms of the piezoelectric effect. The matching of the crystal structures at the domain walls is studied by combining the hard x-ray Fresnel phase-imaging technique with Bragg diffraction imaging methods ('Bragg-Fresnel imaging') and using synchrotron radiation. Quantitative analysis of the contrast of the Bragg-Fresnel images recorded as a function of the propagation distance is demonstrated to allow the determination of how the domains are matched at the atomic (unit cell) level, even though the spatial resolution of the images is on the scale of micrometres. The atom P(1) is determined as the linking atom for connecting...

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

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

Crystal Structure of the FERM Domain of Focal Adhesion Kinase

International Nuclear Information System (INIS)

Ceccarelli, D.; Song, H.; Poy, F.; Schaller, M.; Eck, M.

2006-01-01

Focal adhesion kinase (FAK) is a non-receptor tyrosine kinase that localizes to focal adhesions in adherent cells. Through phosphorylation of proteins assembled at the cytoplasmic tails of integrins, FAK promotes signaling events that modulate cellular growth, survival, and migration. The amino-terminal region of FAK contains a region of sequence homology with band 4.1 and ezrin/radixin/moesin (ERM) proteins termed a FERM domain. FERM domains are found in a variety of signaling and cytoskeletal proteins and are thought to mediate intermolecular interactions with partner proteins and phospholipids at the plasma membrane and intramolecular regulatory interactions. Here we report two crystal structures of an NH2-terminal fragment of avian FAK containing the FERM domain and a portion of the regulatory linker that connects the FERM and kinase domains. The tertiary folds of the three subdomains (F1, F2, and F3) are similar to those of known FERM structures despite low sequence conservation. Differences in the sequence and relative orientation of the F3 subdomain alters the nature of the interdomain interface, and the phosphoinositide binding site found in ERM family FERM domains is not present in FAK. A putative protein interaction site on the F3 lobe is masked by the proximal region of the linker. Additionally, in one structure the adjacent Src SH3 and SH2 binding sites in the linker associate with the surfaces of the F3 and F1 lobes, respectively. These structural features suggest the possibility that protein interactions of the FAK FERM domain can be regulated by binding of Src kinases to the linker segment

Identification and Characterisation CRN Effectors in Phytophthora capsici Shows Modularity and Functional Diversity.

Directory of Open Access Journals (Sweden)

Remco Stam

Full Text Available Phytophthora species secrete a large array of effectors during infection of their host plants. The Crinkler (CRN gene family encodes a ubiquitous but understudied class of effectors with possible but as of yet unknown roles in infection. To appreciate CRN effector function in Phytophthora, we devised a simple Crn gene identification and annotation pipeline to improve effector prediction rates. We predicted 84 full-length CRN coding genes and assessed CRN effector domain diversity in sequenced Oomycete genomes. These analyses revealed evidence of CRN domain innovation in Phytophthora and expansion in the Peronosporales. We performed gene expression analyses to validate and define two classes of CRN effectors, each possibly contributing to infection at different stages. CRN localisation studies revealed that P. capsici CRN effector domains target the nucleus and accumulate in specific sub-nuclear compartments. Phenotypic analyses showed that few CRN domains induce necrosis when expressed in planta and that one cell death inducing effector, enhances P. capsici virulence on Nicotiana benthamiana. These results suggest that the CRN protein family form an important class of intracellular effectors that target the host nucleus during infection. These results combined with domain expansion in hemi-biotrophic and necrotrophic pathogens, suggests specific contributions to pathogen lifestyles. This work will bolster CRN identification efforts in other sequenced oomycete species and set the stage for future functional studies towards understanding CRN effector functions.

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...

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

From Microscopic to Macroscopic Descriptions of Cell Migration on Growing Domains

KAUST Repository

Baker, Ruth E.

2009-10-28

Cell migration and growth are essential components of the development of multicellular organisms. The role of various cues in directing cell migration is widespread, in particular, the role of signals in the environment in the control of cell motility and directional guidance. In many cases, especially in developmental biology, growth of the domain also plays a large role in the distribution of cells and, in some cases, cell or signal distribution may actually drive domain growth. There is an almost ubiquitous use of partial differential equations (PDEs) for modelling the time evolution of cellular density and environmental cues. In the last 20 years, a lot of attention has been devoted to connecting macroscopic PDEs with more detailed microscopic models of cellular motility, including models of directional sensing and signal transduction pathways. However, domain growth is largely omitted in the literature. In this paper, individual-based models describing cell movement and domain growth are studied, and correspondence with a macroscopic-level PDE describing the evolution of cell density is demonstrated. The individual-based models are formulated in terms of random walkers on a lattice. Domain growth provides an extra mathematical challenge by making the lattice size variable over time. A reaction-diffusion master equation formalism is generalised to the case of growing lattices and used in the derivation of the macroscopic PDEs. © 2009 Society for Mathematical Biology.

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

Advances in spectral inversion of time-domain induced polarization

DEFF Research Database (Denmark)

Fiandaca, Gianluca; Auken, Esben; Christiansen, Anders Vest

The extraction of spectral information in the inversion process of time-domain (TD) induced polarization (IP) data is changing the use of the TDIP method. Data interpretation is evolving from a qualitative description of the subsurface, able only to discriminate the presence of contrasts in charg......The extraction of spectral information in the inversion process of time-domain (TD) induced polarization (IP) data is changing the use of the TDIP method. Data interpretation is evolving from a qualitative description of the subsurface, able only to discriminate the presence of contrasts...... in chargeability parameters, towards a quantitative analysis of the investigated media, which allows for detailed soil- and rock-type characterization. In this work a review of the recent advances in spectral inversion of TDIP data is presented, in terms of: supported IP parameterizations; modelling of transmitter...

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.

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/.

Superdiffusive motion of membrane-targeting C2 domains

Science.gov (United States)

Campagnola, Grace; Nepal, Kanti; Schroder, Bryce W.; Peersen, Olve B.; Krapf, Diego

2015-12-01

Membrane-targeting domains play crucial roles in the recruitment of signalling molecules to the plasma membrane. For most peripheral proteins, the protein-to-membrane interaction is transient. After proteins dissociate from the membrane they have been observed to rebind following brief excursions in the bulk solution. Such membrane hops can have broad implications for the efficiency of reactions on membranes. We study the diffusion of membrane-targeting C2 domains using single-molecule tracking in supported lipid bilayers. The ensemble-averaged mean square displacement (MSD) exhibits superdiffusive behaviour. However, traditional time-averaged MSD analysis of individual trajectories remains linear and does not reveal superdiffusion. Our observations are explained in terms of bulk excursions that introduce jumps with a heavy-tail distribution. These hopping events allow proteins to explore large areas in a short time. The experimental results are shown to be consistent with analytical models of bulk-mediated diffusion and numerical simulations.

Understanding Engagement with the Privacy Domain Through Design Research.

OpenAIRE

Vasalou, A.; Oostveen, A.; Bowers, Christopher; Beale, R.

2015-01-01

This paper reports findings from participatory design research aimed at uncovering how technological interventions can engage users in the domain of privacy. Our work was undertaken in the context of a new design concept “Privacy Trends” whose aspiration is to foster technology users’ digital literacy regarding ongoing privacy risks and elucidate how such risks fit within existing social, organizational and political systems, leading to a longer term privacy concern. Our study reveals two cha...

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.

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.

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.

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.

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.

Structure of Pseudoknot PK26 Shows 3D Domain Swapping in an RNA

Science.gov (United States)

Lietzke, Susan E; Barnes, Cindy L.

1998-01-01

3D domain swapping provides a facile pathway for the evolution of oligomeric proteins and allosteric mechanisms and a means for using monomer-oligomer equilibria to regulate biological activity. The term "3D domain swapping" describes the exchange of identical domains between two protein monomers to create an oligomer. 3D domain swapping has, so far, only been recognized in proteins. In this study, the structure of the pseudoknot PK26 is reported and it is a clear example of 3D domain swapping in RNA. PK26 was chosen for study because RNA pseudoknots are required structures in several biological processes and they arise frequently in in vitro selection experiments directed against protein targets. PK26 specifically inhibits HIV-1 reverse transcriptase with nanomolar affinity. We have now determined the 3.1 A resolution crystal structure of PK26 and find that it forms a 3D domain swapped dimer. PK26 shows extensive base pairing between and within strands. Formation of the dimer requires the linker region between the pseudoknot folds to adopt a unique conformation that allows a base within a helical stem to skip one base in the stacking register. Rearrangement of the linker would permit a monomeric pseudoknot to form. This structure shows how RNA can use 3D domain swapping to build large scale oligomers like the putative hexamer in the packaging RNA of bacteriophage Phi29.

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.

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.

Temporal grouping effects in musical short-term memory.

Science.gov (United States)

Gorin, Simon; Mengal, Pierre; Majerus, Steve

2018-07-01

Recent theoretical accounts of verbal and visuo-spatial short-term memory (STM) have proposed the existence of domain-general mechanisms for the maintenance of serial order information. These accounts are based on the observation of similar behavioural effects across several modalities, such as temporal grouping effects. Across two experiments, the present study aimed at extending these findings, by exploring a STM modality that has received little interest so far, STM for musical information. Given its inherent rhythmic, temporal and serial organisation, the musical domain is of interest for investigating serial order STM processes such as temporal grouping. In Experiment 1, the data did not allow to determine the presence or the absence of temporal grouping effects. In Experiment 2, we observed that temporal grouping of tone sequences during encoding improves short-term recognition for serially presented probe tones. Furthermore, the serial position curves included micro-primacy and micro-recency effects, which are the hallmark characteristic of temporal grouping. Our results suggest that the encoding of serial order information in musical STM may be supported by temporal positional coding mechanisms similar to those reported in the verbal domain.

Changement climatique et domaines skiables: simulation en Savoie et Haute-Savoie à l’horizon 2015

Directory of Open Access Journals (Sweden)

Jean-Christophe Loubier

2007-03-01

Full Text Available Les domaines skiables et le changement climatique posent des questions importantes et nouvelles pour les espaces montagnards. Dans les hautes vallées où ces domaines sont souvent le moteur principal du développement local, on peut s'interroger sur la pérennité du modèle économique de l'or blanc à moyen terme quand les modèles de simulation du climat tablent sur une élévation de la température moyenne comprise entre 1,5° et 5° en 2100. Nous avons tenté de simuler les effets du changement climatique à l'horizon 2015, sur les domaines skiables de Savoie et Haute Savoie.

Short-term memory stores organized by information domain.

Science.gov (United States)

Noyce, Abigail L; Cestero, Nishmar; Shinn-Cunningham, Barbara G; Somers, David C

2016-04-01

Vision and audition have complementary affinities, with vision excelling in spatial resolution and audition excelling in temporal resolution. Here, we investigated the relationships among the visual and auditory modalities and spatial and temporal short-term memory (STM) using change detection tasks. We created short sequences of visual or auditory items, such that each item within a sequence arose at a unique spatial location at a unique time. On each trial, two successive sequences were presented; subjects attended to either space (the sequence of locations) or time (the sequence of inter item intervals) and reported whether the patterns of locations or intervals were identical. Each subject completed blocks of unimodal trials (both sequences presented in the same modality) and crossmodal trials (Sequence 1 visual, Sequence 2 auditory, or vice versa) for both spatial and temporal tasks. We found a strong interaction between modality and task: Spatial performance was best on unimodal visual trials, whereas temporal performance was best on unimodal auditory trials. The order of modalities on crossmodal trials also mattered, suggesting that perceptual fidelity at encoding is critical to STM. Critically, no cost was attributable to crossmodal comparison: In both tasks, performance on crossmodal trials was as good as or better than on the weaker unimodal trials. STM representations of space and time can guide change detection in either the visual or the auditory modality, suggesting that the temporal or spatial organization of STM may supersede sensory-specific organization.

Short-term memory stores organized by information domain

Science.gov (United States)

Noyce, Abigail L.; Cestero, Nishmar; Shinn-Cunningham, Barbara G.; Somers, David C.

2016-01-01

Vision and audition have complementary affinities, with vision excelling in spatial resolution and audition excelling in temporal resolution. Here, we investigate the relationships among visual and auditory modalities and spatial and temporal short-term memory (STM) using change detection tasks. We created short sequences of visual or auditory items, such that each item within a sequence arose at a unique spatial location at a unique time. On each trial, two successive sequences were presented; subjects attended to either space (the sequence of locations), or time (the sequence of inter-item intervals), and reported whether the patterns of locations or intervals were identical. Each subject completed blocks of unimodal trials (both sequences presented in the same modality) and crossmodal trials (sequence 1 visual and sequence 2 auditory, or vice versa) for both spatial and temporal tasks. We found a strong interaction between modality and task: spatial performance was best on unimodal visual trials, while temporal performance was best on unimodal auditory trials. The order of modalities on crossmodal trials also mattered, suggesting that perceptual fidelity at encoding is critical to STM. Critically, there was no cost attributable to crossmodal comparison: in both tasks, performance on crossmodal trials was as good or better than on the weaker unimodal trials. STM representations of space and time can guide change detection in either the visual or the auditory modality, suggesting that temporal or spatial organization of STM may supersede sensory-specific organization. PMID:26791231

Assessing Data Quality in Emergent Domains of Earth Sciences

Science.gov (United States)

Darch, P. T.; Borgman, C.

2016-12-01

As earth scientists seek to study known phenomena in new ways, and to study new phenomena, they often develop new technologies and new methods such as embedded network sensing, or reapply extant technologies, such as seafloor drilling. Emergent domains are often highly multidisciplinary as researchers from many backgrounds converge on new research questions. They may adapt existing methods, or develop methods de novo. As a result, emerging domains tend to be methodologically heterogeneous. As these domains mature, pressure to standardize methods increases. Standardization promotes trust, reliability, accuracy, and reproducibility, and simplifies data management. However, for standardization to occur, researchers must be able to assess which of the competing methods produces the highest quality data. The exploratory nature of emerging domains discourages standardization. Because competing methods originate in different disciplinary backgrounds, their scientific credibility is difficult to compare. Instead of direct comparison, researchers attempt to conduct meta-analyses. Scientists compare datasets produced by different methods to assess their consistency and efficiency. This paper presents findings from a long-term qualitative case study of research on the deep subseafloor biosphere, an emergent domain. A diverse community converged on the study of microbes in the seafloor and those microbes' interactions with the physical environments they inhabit. Data on this problem are scarce, leading to calls for standardization as a means to acquire and analyze greater volumes of data. Lacking consistent methods, scientists attempted to conduct meta-analyses to determine the most promising methods on which to standardize. Among the factors that inhibited meta-analyses were disparate approaches to metadata and to curating data. Datasets may be deposited in a variety of databases or kept on individual scientists' servers. Associated metadata may be inconsistent or hard to

Label-free imaging of mammalian cell nucleoli by Raman microspectroscopy.

Science.gov (United States)

Schulze, H Georg; Konorov, Stanislav O; Piret, James M; Blades, Michael W; Turner, Robin F B

2013-06-21

The nucleolus is a prominent subnuclear structure whose major function is the transcription and assembly of ribosome subunits. The size of the nucleolus varies with the cell cycle, proliferation rate and stress. Changes in nucleolar size, number, chemical composition, and shape can be used to characterize malignant cells. We used spontaneous Raman microscopy as a label-free technique to examine nucleolar spatial and chemical features. Raman images of the 1003 cm(-1) phenylalanine band revealed large, well-defined subnuclear protein structures in MFC-7 breast cancer cells. The 783 cm(-1) images showed that nucleic acids were similarly distributed, but varied more in intensity, forming observable high-intensity regions. High subnuclear RNA concentrations were observed within some of these regions as shown by 809 cm(-1) Raman band images. Principal component analyses of sub-images and library spectra validated the subnuclear presence of RNA. They also revealed that an actin-like protein covaried with DNA within the nucleolus, a combination that accounted for 64% or more of the spectral variance. Embryonic stem cells are another rapidly proliferating cell type, but their nucleoli were not as large or well defined. Estimating the size of the larger MCF-7 nucleolus was used to show the utility of Raman microscopy for morphometric analyses. It was concluded that imaging based on Raman microscopy provides a promising new method for the study of nucleolar function and organization, in the evaluation of drug and experimental effects on the nucleolus, and in clinical diagnostics and prognostics.

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...

Remotely Piloted Aircraft and War in the Public Relations Domain

Science.gov (United States)

2014-10-01

the terms as they appear in quoted texts. 2. Peter Kreeft, Socratic Logic: A Logic Text Using Socratic Method , Platonic Questions, and Aristotelian...Ronald Brooks.22 This method of refuting an argu- ment reflects option C (above), demonstrating that the conclusion does not follow from the premises...and War in the Public Relations Domain Feature tional Security Assistance Force (ISAF) met to discuss methods of elim- inating civilian casualties in

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.

Polycomb domain formation depends on short and long distance regulatory cues.

Directory of Open Access Journals (Sweden)

Bernd Schuettengruber

Full Text Available BACKGROUND: Polycomb group (PcG proteins dynamically define cellular identities through the epigenetic repression of key developmental genes. In Drosophila, cis-regulatory regions termed PcG response elements (PREs act as nucleation sites for PcG proteins to create large repressive PcG domains that are marked by trimethylation of lysine 27 on histone H3 (H3K27me3. In addition to an action in cis, PREs can interact over long distances, thereby enhancing PcG dependent silencing. How PcG domains are established, which factors limit their propagation in cis, and how long range interactions of PREs in trans affect the chromatin structure is largely unknown. PRINCIPAL FINDINGS: We demonstrate that the insertion of a PRE-containing transgene in the Drosophila genome generates an artificial PcG domain and we analyze its organization by quantitative ChIP and ChIP-on-chip experiments. Intriguingly, a boundary element and known insulator proteins do not necessarily interfere with spreading of H3K27me3. Instead, domain borders correlate with the presence of promoter regions bound by RNA Polymerase II and active chromatin marks. In contrast, genes that are silent during early fly development get included within the PcG domain and this incorporation interferes with gene activation at later developmental stages. Moreover, trans-interaction of the transgenic PRE with its homologous endogenous PRE results in increased PcG binding, correlating with reinforced silencing of genes within the domain borders. CONCLUSIONS: Our results suggest that higher-order organization of PcG-bound chromatin can stabilize gene silencing within PcG domains. Further we propose that multi-protein complexes associated with active promoters are able to define the limits of PcG domains. Future work aimed to pinpoint the factors providing this barrier function will be required to understand the precise molecular mechanism by which active promoter regions can act as boundaries to stop

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)

Unstructured characteristic method embedded with variational nodal method using domain decomposition techniques

Energy Technology Data Exchange (ETDEWEB)

Girardi, E.; Ruggieri, J.M. [CEA Cadarache (DER/SPRC/LEPH), 13 - Saint-Paul-lez-Durance (France). Dept. d' Etudes des Reacteurs; Santandrea, S. [CEA Saclay, Dept. Modelisation de Systemes et Structures DM2S/SERMA/LENR, 91 - Gif sur Yvette (France)

2005-07-01

This paper describes a recently-developed extension of our 'Multi-methods,multi-domains' (MM-MD) method for the solution of the multigroup transport equation. Based on a domain decomposition technique, our approach allows us to treat the one-group equation by cooperatively employing several numerical methods together. In this work, we describe the coupling between the Method of Characteristics (integro-differential equation, unstructured meshes) with the Variational Nodal Method (even parity equation, cartesian meshes). Then, the coupling method is applied to the benchmark model of the Phebus experimental facility (Cea Cadarache). Our domain decomposition method give us the capability to employ a very fine mesh in describing a particular fuel bundle with an appropriate numerical method (MOC), while using a much large mesh size in the rest of the core, in conjunction with a coarse-mesh method (VNM). This application shows the benefits of our MM-MD approach, in terms of accuracy and computing time: the domain decomposition method allows us to reduce the Cpu time, while preserving a good accuracy of the neutronic indicators: reactivity, core-to-bundle power coupling coefficient and flux error. (authors)

Unstructured characteristic method embedded with variational nodal method using domain decomposition techniques

International Nuclear Information System (INIS)

Girardi, E.; Ruggieri, J.M.

2005-01-01

This paper describes a recently-developed extension of our 'Multi-methods,multi-domains' (MM-MD) method for the solution of the multigroup transport equation. Based on a domain decomposition technique, our approach allows us to treat the one-group equation by cooperatively employing several numerical methods together. In this work, we describe the coupling between the Method of Characteristics (integro-differential equation, unstructured meshes) with the Variational Nodal Method (even parity equation, cartesian meshes). Then, the coupling method is applied to the benchmark model of the Phebus experimental facility (Cea Cadarache). Our domain decomposition method give us the capability to employ a very fine mesh in describing a particular fuel bundle with an appropriate numerical method (MOC), while using a much large mesh size in the rest of the core, in conjunction with a coarse-mesh method (VNM). This application shows the benefits of our MM-MD approach, in terms of accuracy and computing time: the domain decomposition method allows us to reduce the Cpu time, while preserving a good accuracy of the neutronic indicators: reactivity, core-to-bundle power coupling coefficient and flux error. (authors)

Time domain electromagnetic metal detectors

International Nuclear Information System (INIS)

Hoekstra, P.

1996-01-01

This presentation focuses on illustrating by case histories the range of applications and limitations of time domain electromagnetic (TDEM) systems for buried metal detection. Advantages claimed for TDEM metal detectors are: independent of instrument response (Geonics EM61) to surrounding soil and rock type; simple anomaly shape; mitigation of interference by ambient electromagnetic noise; and responsive to both ferrous and non-ferrous metallic targets. The data in all case histories to be presented were acquired with the Geonics EM61 TDEM system. Case histories are a test bed site on Molokai, Hawaii; Fort Monroe, Virginia; and USDOE, Rocky Flats Plant. The present limitations of this technology are: discrimination capabilities in terms of type of ordnance, and depth of burial is limited, and ability of resolving targets with small metallic ambient needs to be improved

Unbound motion on a Schwarzschild background: Practical approaches to frequency domain computations

Science.gov (United States)

Hopper, Seth

2018-03-01

Gravitational perturbations due to a point particle moving on a static black hole background are naturally described in Regge-Wheeler gauge. The first-order field equations reduce to a single master wave equation for each radiative mode. The master function satisfying this wave equation is a linear combination of the metric perturbation amplitudes with a source term arising from the stress-energy tensor of the point particle. The original master functions were found by Regge and Wheeler (odd parity) and Zerilli (even parity). Subsequent work by Moncrief and then Cunningham, Price and Moncrief introduced new master variables which allow time domain reconstruction of the metric perturbation amplitudes. Here, I explore the relationship between these different functions and develop a general procedure for deriving new higher-order master functions from ones already known. The benefit of higher-order functions is that their source terms always converge faster at large distance than their lower-order counterparts. This makes for a dramatic improvement in both the speed and accuracy of frequency domain codes when analyzing unbound motion.

Domain Wall Motion in Magnetic Nanostrips under the Influence of Rashba Field

Directory of Open Access Journals (Sweden)

Vito Puliafito

2012-01-01

Full Text Available Spin-orbit Rashba effect applies a torque on the magnetization of a ferromagnetic nanostrip in the case of structural inversion asymmetry, also affecting the steady domain wall motion induced by a spin-polarized current. This influence is here analytically studied in the framework of the extended Landau-Lifshitz-Gilbert equation, including the Rashba effect as an additive term of the effective field. Results of previous micromagnetic simulations and experiments have shown that this field yields an increased value of the Walker breakdown current together with an enlargement of the domain wall width. In order to analytically describe these results, the standard travelling wave ansatz for the steady domain wall motion is here adopted. Results of our investigations reveal the impossibility to reproduce, at the same time, the previous features and suggest the need of a more sophisticated model whose development requires, in turn, additional information to be extracted from ad hoc micromagnetic simulations.

Monte Carlo Simulation of Ferroelectric Domain Structure and Applied Field Response in Two Dimensions

Energy Technology Data Exchange (ETDEWEB)

Potter, Jr., B.G.; Tikare, V.; Tuttle, B.A.

1999-06-30

A 2-D, lattice-Monte Carlo approach was developed to simulate ferroelectric domain structure. The model currently utilizes a Hamiltonian for the total energy based only upon electrostatic terms involving dipole-dipole interactions, local polarization gradients and the influence of applied electric fields. The impact of boundary conditions on the domain configurations obtained was also examined. In general, the model exhibits domain structure characteristics consistent with those observed in a tetragonally distorted ferroelectric. The model was also extended to enable the simulation of ferroelectric hysteresis behavior. Simulated hysteresis loops were found to be very similar in appearance to those observed experimentally in actual materials. This qualitative agreement between the simulated hysteresis loop characteristics and real ferroelectric behavior was also confirmed in simulations run over a range of simulation temperatures and applied field frequencies.

Ligand binding by PDZ domains

DEFF Research Database (Denmark)

Chi, Celestine N.; Bach, Anders; Strømgaard, Kristian

2012-01-01

, for example, are particularly rich in these domains. The general function of PDZ domains is to bring proteins together within the appropriate cellular compartment, thereby facilitating scaffolding, signaling, and trafficking events. The many functions of PDZ domains under normal physiological as well...... as pathological conditions have been reviewed recently. In this review, we focus on the molecular details of how PDZ domains bind their protein ligands and their potential as drug targets in this context....

An Ontology-Based Knowledge Modelling for a Sustainability Assessment Domain

Directory of Open Access Journals (Sweden)

Agnieszka Konys

2018-01-01

Full Text Available Sustainability assessment has received more and more attention from researchers and it offers a large number of opportunities to measure and evaluate the level of its accomplishment. However, proper selection of a particular sustainability assessment approach, reflecting problem properties and the evaluator’s preferences, is a complex and important issue. Due to an existing number of different approaches dedicated to assessing, supporting, or measuring the level of sustainability and their structure oriented on the particular domain usage, problems with accurate matching frequently occur. On the other hand, the efficiency of sustainability assessment depends on the available knowledge of the ongoing capabilities. Additionally, actual research trends confirm that knowledge engineering gives a method to handle domain knowledge practically and effectively. Unfortunately, literature studies confirm that there is a lack of knowledge systematization in the sustainability assessment domain, however. The practical application of knowledge-based mechanisms may cover this gap. In this paper, we provide formal, practical and technological guidance to a knowledge management-based approach to sustainability assessment. We propose ontology as a form of knowledge conceptualization and using knowledge engineering, we make gathered knowledge publicly available and reusable, especially in terms of interoperability of collected knowledge.

A kingdom-specific protein domain HMM library for improved annotation of fungal genomes

Directory of Open Access Journals (Sweden)

Oliver Stephen G

2007-04-01

Full Text Available Abstract Background Pfam is a general-purpose database of protein domain alignments and profile Hidden Markov Models (HMMs, which is very popular for the annotation of sequence data produced by genome sequencing projects. Pfam provides models that are often very general in terms of the taxa that they cover and it has previously been suggested that such general models may lack some of the specificity or selectivity that would be provided by kingdom-specific models. Results Here we present a general approach to create domain libraries of HMMs for sub-taxa of a kingdom. Taking fungal species as an example, we construct a domain library of HMMs (called Fungal Pfam or FPfam using sequences from 30 genomes, consisting of 24 species from the ascomycetes group and two basidiomycetes, Ustilago maydis, a fungal pathogen of maize, and the white rot fungus Phanerochaete chrysosporium. In addition, we include the Microsporidion Encephalitozoon cuniculi, an obligate intracellular parasite, and two non-fungal species, the oomycetes Phytophthora sojae and Phytophthora ramorum, both plant pathogens. We evaluate the performance in terms of coverage against the original 30 genomes used in training FPfam and against five more recently sequenced fungal genomes that can be considered as an independent test set. We show that kingdom-specific models such as FPfam can find instances of both novel and well characterized domains, increases overall coverage and detects more domains per sequence with typically higher bitscores than Pfam for the same domain families. An evaluation of the effect of changing E-values on the coverage shows that the performance of FPfam is consistent over the range of E-values applied. Conclusion Kingdom-specific models are shown to provide improved coverage. However, as the models become more specific, some sequences found by Pfam may be missed by the models in FPfam and some of the families represented in the test set are not present in FPfam

Primordial domains in the depleted upper mantle identified by noble gases in MORBs

Science.gov (United States)

Tucker, J.; Mukhopadhyay, S.; Langmuir, C. H.; Hamelin, C.; Fuentes, J.

2017-12-01

The distribution of noble gas isotopic compositions in the mantle provides important constraints on the large-scale mantle evolution, as noble gases can trace the interaction between degassed, or processed, mantle domains and undegassed, or primitive, mantle domains. Data from the radiogenic He, Ne, Ar and Xe isotopic systems have shown that plume-related lavas sample relatively undegassed mantle domains, and the recent identification of isotopic anomalies in the short-lived I-Xe and Hf-W isotopic systems in plume-related lavas further suggests that these domains may be ancient, dating back to Earth's accretion. However, little is known about the potential variability of the heavy noble gas systems and the distribution of undegassed domains in the ambient upper mantle not influenced by plumes. Here, we present new high-precision He, Ne, Ar, and Xe isotopic data for a series of MORBs from a depleted section of the subtropical north Mid-Atlantic Ridge, distant from any known plume influence. Some samples have extremely low (unradiogenic) 4He/3He, 21Ne/22Ne, 40Ar/36Ar, and 129Xe/130Xe ratios, including some of the lowest values ever determined for MORBs. Such unradiogenic compositions are reminiscent of OIBs and plume-influenced E-MORBs, suggesting the presence of a relatively undegassed or primitive reservoir in the source of these depleted MORBs. The He, Ne, and Ar isotopic systems are sensitive to the long-term degassing history, suggesting that this domain in the MORB source is ancient. The 129Xe/130Xe ratio is sensitive to degassing only during the first 100 Ma of Earth history, suggesting that some of the isotopic character of these samples has been preserved since Earth's accretion. Together, these observations suggest that primordial or undegassed material is not only sampled in plumes-related lavas, but also normal, depleted MORBs. Along with data from E-MORBs in the southern EPR (Kurz et al., 2005), southern MAR (Sarda et al., 2000), and equatorial MAR

Polar Domain Discovery with Sparkler

Science.gov (United States)

Duerr, R.; Khalsa, S. J. S.; Mattmann, C. A.; Ottilingam, N. K.; Singh, K.; Lopez, L. A.

2017-12-01

The scientific web is vast and ever growing. It encompasses millions of textual, scientific and multimedia documents describing research in a multitude of scientific streams. Most of these documents are hidden behind forms which require user action to retrieve and thus can't be directly accessed by content crawlers. These documents are hosted on web servers across the world, most often on outdated hardware and network infrastructure. Hence it is difficult and time-consuming to aggregate documents from the scientific web, especially those relevant to a specific domain. Thus generating meaningful domain-specific insights is currently difficult. We present an automated discovery system (Figure 1) using Sparkler, an open-source, extensible, horizontally scalable crawler which facilitates high throughput and focused crawling of documents pertinent to a particular domain such as information about polar regions. With this set of highly domain relevant documents, we show that it is possible to answer analytical questions about that domain. Our domain discovery algorithm leverages prior domain knowledge to reach out to commercial/scientific search engines to generate seed URLs. Subject matter experts then annotate these seed URLs manually on a scale from highly relevant to irrelevant. We leverage this annotated dataset to train a machine learning model which predicts the `domain relevance' of a given document. We extend Sparkler with this model to focus crawling on documents relevant to that domain. Sparkler avoids disruption of service by 1) partitioning URLs by hostname such that every node gets a different host to crawl and by 2) inserting delays between subsequent requests. With an NSF-funded supercomputer Wrangler, we scaled our domain discovery pipeline to crawl about 200k polar specific documents from the scientific web, within a day.

Blocking-resistant communication through domain fronting

Directory of Open Access Journals (Sweden)

Fifield David

2015-06-01

Full Text Available We describe “domain fronting,” a versatile censorship circumvention technique that hides the remote endpoint of a communication. Domain fronting works at the application layer, using HTTPS, to communicate with a forbidden host while appearing to communicate with some other host, permitted by the censor. The key idea is the use of different domain names at different layers of communication. One domain appears on the “outside” of an HTTPS request—in the DNS request and TLS Server Name Indication—while another domain appears on the “inside”—in the HTTP Host header, invisible to the censor under HTTPS encryption. A censor, unable to distinguish fronted and nonfronted traffic to a domain, must choose between allowing circumvention traffic and blocking the domain entirely, which results in expensive collateral damage. Domain fronting is easy to deploy and use and does not require special cooperation by network intermediaries. We identify a number of hard-to-block web services, such as content delivery networks, that support domain-fronted connections and are useful for censorship circumvention. Domain fronting, in various forms, is now a circumvention workhorse. We describe several months of deployment experience in the Tor, Lantern, and Psiphon circumvention systems, whose domain-fronting transports now connect thousands of users daily and transfer many terabytes per month.

SH3 Domains Differentially Stimulate Distinct Dynamin I Assembly Modes and G Domain Activity.

Directory of Open Access Journals (Sweden)

Sai Krishnan

Full Text Available Dynamin I is a highly regulated GTPase enzyme enriched in nerve terminals which mediates vesicle fission during synaptic vesicle endocytosis. One regulatory mechanism involves its interactions with proteins containing Src homology 3 (SH3 domains. At least 30 SH3 domain-containing proteins bind dynamin at its proline-rich domain (PRD. Those that stimulate dynamin activity act by promoting its oligomerisation. We undertook a systematic parallel screening of 13 glutathione-S-transferase (GST-tagged endocytosis-related SH3 domains on dynamin binding, GTPase activity and oligomerisation. No correlation was found between dynamin binding and their potency to stimulate GTPase activity. There was limited correlation between the extent of their ability to stimulate dynamin activity and the level of oligomerisation, indicating an as yet uncharacterised allosteric coupling of the PRD and G domain. We examined the two variants, dynamin Iab and Ibb, which differ in the alternately splice middle domain α2 helix. They responded differently to the panel of SH3s, with the extent of stimulation between the splice variants varying greatly between the SH3s. This study reveals that SH3 binding can act as a heterotropic allosteric regulator of the G domain via the middle domain α2 helix, suggesting an involvement of this helix in communicating the PRD-mediated allostery. This indicates that SH3 binding both stabilises multiple conformations of the tetrameric building block of dynamin, and promotes assembly of dynamin-SH3 complexes with distinct rates of GTP hydrolysis.

Domain wall motions in perpendicularly magnetized CoFe/Pd multilayer nanowire

DEFF Research Database (Denmark)

Meng, Zhaoliang; Kumar, Manoj; Qiu, Jinjun

2014-01-01

Current-induced domain wall (DW) motion is investigated in a 600nm wide nanowire using multilayer film with a structure of Ta(5nm)/Pd(5nm)/[CoFe(0.4nm)/Pd(1.2nm)]15/Ta(5nm) in terms of anomalous Hall effect measurements. It is found that motion of DWs can be driven by a current density as low as 1...

An ontological approach to domain engineering

NARCIS (Netherlands)

Falbo, R.A.; Guizzardi, G.; Duarte, K.

2002-01-01

Domain engineering aims to support systematic reuse, focusing on modeling common knowledge in a problem domain. Ontologies have also been pointed as holding great promise for software reuse. In this paper, we present ODE (Ontology-based Domain Engineering), an ontological approach for domain

Ferroelectric negative capacitance domain dynamics

Science.gov (United States)

Hoffmann, Michael; Khan, Asif Islam; Serrao, Claudy; Lu, Zhongyuan; Salahuddin, Sayeef; Pešić, Milan; Slesazeck, Stefan; Schroeder, Uwe; Mikolajick, Thomas

2018-05-01

Transient negative capacitance effects in epitaxial ferroelectric Pb(Zr0.2Ti0.8)O3 capacitors are investigated with a focus on the dynamical switching behavior governed by domain nucleation and growth. Voltage pulses are applied to a series connection of the ferroelectric capacitor and a resistor to directly measure the ferroelectric negative capacitance during switching. A time-dependent Ginzburg-Landau approach is used to investigate the underlying domain dynamics. The transient negative capacitance is shown to originate from reverse domain nucleation and unrestricted domain growth. However, with the onset of domain coalescence, the capacitance becomes positive again. The persistence of the negative capacitance state is therefore limited by the speed of domain wall motion. By changing the applied electric field, capacitor area or external resistance, this domain wall velocity can be varied predictably over several orders of magnitude. Additionally, detailed insights into the intrinsic material properties of the ferroelectric are obtainable through these measurements. A new method for reliable extraction of the average negative capacitance of the ferroelectric is presented. Furthermore, a simple analytical model is developed, which accurately describes the negative capacitance transient time as a function of the material properties and the experimental boundary conditions.

Functional domains of plant chimeric calcium/calmodulin-dependent protein kinase: regulation by autoinhibitory and visinin-like domains

Science.gov (United States)

Ramachandiran, S.; Takezawa, D.; Wang, W.; Poovaiah, B. W.

1997-01-01

A novel calcium-binding calcium/calmodulin-dependent protein kinase (CCaMK) with a catalytic domain, calmodulin-binding domain, and a neural visinin-like domain was cloned and characterized from plants [Patil et al., (1995) Proc. Natl. Acad. Sci. USA 92, 4797-4801; Takezawa et al. (1996) J. Biol. Chem. 271, 8126-8132]. The mechanisms of CCaMK activation by calcium and calcium/calmodulin were investigated using various deletion mutants. The use of deletion mutants of CCaMK lacking either one, two, or all three calcium-binding EF hands indicated that all three calcium-binding sites in the visinin-like domain were crucial for the full calcium/calmodulin-dependent kinase activity. As each calcium-binding EF hand was deleted, there was a gradual reduction in calcium/calmodulin-dependent kinase activity from 100 to 4%. Another mutant (amino acids 1-322) which lacks both the visinin-like domain containing three EF hands and the calmodulin-binding domain was constitutively active, indicating the presence of an autoinhibitory domain around the calmodulin-binding domain. By using various synthetic peptides and the constitutively active mutant, we have shown that CCaMK contains an autoinhibitory domain within the residues 322-340 which overlaps its calmodulin-binding domain. Kinetic studies with both ATP and the GS peptide substrate suggest that the autoinhibitory domain of CCaMK interacts only with the peptide substrate binding motif of the catalytic domain, but not with the ATP-binding motif.

Summarization by domain ontology navigation

DEFF Research Database (Denmark)

Andreasen, Troels; Bulskov, Henrik

2013-01-01

of the subject. In between these two extremes, conceptual summaries encompass selected concepts derived using background knowledge. We address in this paper an approach where conceptual summaries are provided through a conceptualization as given by an ontology. The ontology guiding the summarization can...... be a simple taxonomy or a generative domain ontology. A domain ontology can be provided by a preanalysis of a domain corpus and can be used to condense improved summaries that better reflects the conceptualization of a given domain....

Accurate characterization of 3D diffraction gratings using time domain discontinuous Galerkin method with exact absorbing boundary conditions

KAUST Repository

Sirenko, Kostyantyn

2013-07-01

Exact absorbing and periodic boundary conditions allow to truncate grating problems\\' infinite physical domains without introducing any errors. This work presents exact absorbing boundary conditions for 3D diffraction gratings and describes their discretization within a high-order time-domain discontinuous Galerkin finite element method (TD-DG-FEM). The error introduced by the boundary condition discretization matches that of the TD-DG-FEM; this results in an optimal solver in terms of accuracy and computation time. Numerical results demonstrate the superiority of this solver over TD-DG-FEM with perfectly matched layers (PML)-based domain truncation. © 2013 IEEE.

Controller design for flexible, distributed parameter mechanical arms via combined state space and frequency domain techniques

Science.gov (United States)

Book, W. J.; Majett, M.

1982-01-01

The potential benefits of the ability to control more flexible mechanical arms are discussed. A justification is made in terms of speed of movement. A new controller design procedure is then developed to provide this capability. It uses both a frequency domain representation and a state variable representation of the arm model. The frequency domain model is used to update the modal state variable model to insure decoupled states. The technique is applied to a simple example with encouraging results.

Ferroelectric domain continuity over grain boundaries

DEFF Research Database (Denmark)

Mantri, Sukriti; Oddershede, Jette; Damjanovic, Dragan

2017-01-01

Formation and mobility of domain walls in ferroelectric materials is responsible for many of their electrical and mechanical properties. Domain wall continuity across grain boundaries has been observed since the 1950's and is speculated to affect the grain boundary-domain interactions, thereby...... impacting macroscopic ferroelectric properties in polycrystalline systems. However detailed studies of such correlated domain structures across grain boundaries are limited. In this work, we have developed the mathematical requirements for domain wall plane matching at grain boundaries of any given...... orientation. We have also incorporated the effect of grain boundary ferroelectric polarization charge created when any two domains meet at the grain boundary plane. The probability of domain wall continuity for three specific grain misorientations is studied. Use of this knowledge to optimize processing...

Usability engineering: domain analysis activities for augmented-reality systems

Science.gov (United States)

Gabbard, Joseph; Swan, J. E., II; Hix, Deborah; Lanzagorta, Marco O.; Livingston, Mark; Brown, Dennis B.; Julier, Simon J.

2002-05-01

This paper discusses our usability engineering process for the Battlefield Augmented Reality System (BARS). Usability engineering is a structured, iterative, stepwise development process. Like the related disciplines of software and systems engineering, usability engineering is a combination of management principals and techniques, formal and semi- formal evaluation techniques, and computerized tools. BARS is an outdoor augmented reality system that displays heads- up battlefield intelligence information to a dismounted warrior. The paper discusses our general usability engineering process. We originally developed the process in the context of virtual reality applications, but in this work we are adapting the procedures to an augmented reality system. The focus of this paper is our work on domain analysis, the first activity of the usability engineering process. We describe our plans for and our progress to date on our domain analysis for BARS. We give results in terms of a specific urban battlefield use case we have designed.

Domain-specific languages in perspective

NARCIS (Netherlands)

J. Heering (Jan); M. Mernik (Marjan)

2007-01-01

textabstractDomain-specific languages (DSLs) are languages tailored to a specific application domain. They offer substantial gains in expressiveness and ease of use compared with general-purpose languages in their domain of application. Although the use of DSLs is by no means new, it is receiving

Detecting atypical examples of known domain types by sequence similarity searching: the SBASE domain library approach.

Science.gov (United States)

Dhir, Somdutta; Pacurar, Mircea; Franklin, Dino; Gáspári, Zoltán; Kertész-Farkas, Attila; Kocsor, András; Eisenhaber, Frank; Pongor, Sándor

2010-11-01

SBASE is a project initiated to detect known domain types and predicting domain architectures using sequence similarity searching (Simon et al., Protein Seq Data Anal, 5: 39-42, 1992, Pongor et al, Nucl. Acids. Res. 21:3111-3115, 1992). The current approach uses a curated collection of domain sequences - the SBASE domain library - and standard similarity search algorithms, followed by postprocessing which is based on a simple statistics of the domain similarity network (http://hydra.icgeb.trieste.it/sbase/). It is especially useful in detecting rare, atypical examples of known domain types which are sometimes missed even by more sophisticated methodologies. This approach does not require multiple alignment or machine learning techniques, and can be a useful complement to other domain detection methodologies. This article gives an overview of the project history as well as of the concepts and principles developed within this the project.

EH domain of EHD1

Energy Technology Data Exchange (ETDEWEB)

Kieken, Fabien; Jovic, Marko; Naslavsky, Naava; Caplan, Steve, E-mail: scaplan@unmc.edu; Sorgen, Paul L. [University of Nebraska Medical Center, Department of Biochemistry and Molecular Biology and Eppley Cancer Center (United States)], E-mail: psorgen@unmc.edu

2007-12-15

EHD1 is a member of the mammalian C-terminal Eps15 homology domain (EH) containing protein family, and regulates the recycling of various receptors from the endocytic recycling compartment to the plasma membrane. The EH domain of EHD1 binds to proteins containing either an Asn-Pro-Phe or Asp-Pro-Phe motif, and plays an important role in the subcellular localization and function of EHD1. Thus far, the structures of five N-terminal EH domains from other proteins have been solved, but to date, the structure of the EH domains from the four C-terminal EHD family paralogs remains unknown. In this study, we have assigned the 133 C-terminal residues of EHD1, which includes the EH domain, and solved its solution structure. While the overall structure resembles that of the second of the three N-terminal Eps15 EH domains, potentially significant differences in surface charge and the structure of the tripeptide-binding pocket are discussed.

EH domain of EHD1

International Nuclear Information System (INIS)

Kieken, Fabien; Jovic, Marko; Naslavsky, Naava; Caplan, Steve; Sorgen, Paul L.

2007-01-01

EHD1 is a member of the mammalian C-terminal Eps15 homology domain (EH) containing protein family, and regulates the recycling of various receptors from the endocytic recycling compartment to the plasma membrane. The EH domain of EHD1 binds to proteins containing either an Asn-Pro-Phe or Asp-Pro-Phe motif, and plays an important role in the subcellular localization and function of EHD1. Thus far, the structures of five N-terminal EH domains from other proteins have been solved, but to date, the structure of the EH domains from the four C-terminal EHD family paralogs remains unknown. In this study, we have assigned the 133 C-terminal residues of EHD1, which includes the EH domain, and solved its solution structure. While the overall structure resembles that of the second of the three N-terminal Eps15 EH domains, potentially significant differences in surface charge and the structure of the tripeptide-binding pocket are discussed

Relationship of work-family conflict with burnout and marital satisfaction: cross-domain or source attribution relations?

Directory of Open Access Journals (Sweden)

Razieh Bagherzadeh

2016-03-01

Conclusion: In terms of practical implication, to avoid creating disadvantages of WIF and FIW,facilitation in two domains of improving work and family conditions can be a useful means to prevent WFC and its consequences.

"Journal of Documentary Reproduction", 1938-1942: Domain as Reflected in Characteristics of Authorship and Citation.

Science.gov (United States)

Walker, Thomas D.

1997-01-01

Places the "Journal of Documentary Reproduction", published by the American Library Association, in an historical context and defines its domain in terms of the characteristics of its contributors. Authorship characteristics include occupation, institutional affiliation, geographic distribution, and gender. (Author/LRW)

Lesion insertion in the projection domain: Methods and initial results

International Nuclear Information System (INIS)

Chen, Baiyu; Leng, Shuai; Yu, Lifeng; Yu, Zhicong; Ma, Chi; McCollough, Cynthia

2015-01-01

Purpose: To perform task-based image quality assessment in CT, it is desirable to have a large number of realistic patient images with known diagnostic truth. One effective way of achieving this objective is to create hybrid images that combine patient images with inserted lesions. Because conventional hybrid images generated in the image domain fails to reflect the impact of scan and reconstruction parameters on lesion appearance, this study explored a projection-domain approach. Methods: Lesions were segmented from patient images and forward projected to acquire lesion projections. The forward-projection geometry was designed according to a commercial CT scanner and accommodated both axial and helical modes with various focal spot movement patterns. The energy employed by the commercial CT scanner for beam hardening correction was measured and used for the forward projection. The lesion projections were inserted into patient projections decoded from commercial CT projection data. The combined projections were formatted to match those of commercial CT raw data, loaded onto a commercial CT scanner, and reconstructed to create the hybrid images. Two validations were performed. First, to validate the accuracy of the forward-projection geometry, images were reconstructed from the forward projections of a virtual ACR phantom and compared to physically acquired ACR phantom images in terms of CT number accuracy and high-contrast resolution. Second, to validate the realism of the lesion in hybrid images, liver lesions were segmented from patient images and inserted back into the same patients, each at a new location specified by a radiologist. The inserted lesions were compared to the original lesions and visually assessed for realism by two experienced radiologists in a blinded fashion. Results: For the validation of the forward-projection geometry, the images reconstructed from the forward projections of the virtual ACR phantom were consistent with the images physically

Lesion insertion in the projection domain: Methods and initial results

Energy Technology Data Exchange (ETDEWEB)

Chen, Baiyu; Leng, Shuai; Yu, Lifeng; Yu, Zhicong; Ma, Chi; McCollough, Cynthia, E-mail: mccollough.cynthia@mayo.edu [Department of Radiology, Mayo Clinic, Rochester, Minnesota 55905 (United States)

2015-12-15

Purpose: To perform task-based image quality assessment in CT, it is desirable to have a large number of realistic patient images with known diagnostic truth. One effective way of achieving this objective is to create hybrid images that combine patient images with inserted lesions. Because conventional hybrid images generated in the image domain fails to reflect the impact of scan and reconstruction parameters on lesion appearance, this study explored a projection-domain approach. Methods: Lesions were segmented from patient images and forward projected to acquire lesion projections. The forward-projection geometry was designed according to a commercial CT scanner and accommodated both axial and helical modes with various focal spot movement patterns. The energy employed by the commercial CT scanner for beam hardening correction was measured and used for the forward projection. The lesion projections were inserted into patient projections decoded from commercial CT projection data. The combined projections were formatted to match those of commercial CT raw data, loaded onto a commercial CT scanner, and reconstructed to create the hybrid images. Two validations were performed. First, to validate the accuracy of the forward-projection geometry, images were reconstructed from the forward projections of a virtual ACR phantom and compared to physically acquired ACR phantom images in terms of CT number accuracy and high-contrast resolution. Second, to validate the realism of the lesion in hybrid images, liver lesions were segmented from patient images and inserted back into the same patients, each at a new location specified by a radiologist. The inserted lesions were compared to the original lesions and visually assessed for realism by two experienced radiologists in a blinded fashion. Results: For the validation of the forward-projection geometry, the images reconstructed from the forward projections of the virtual ACR phantom were consistent with the images physically

Lesion insertion in the projection domain: Methods and initial results.

Science.gov (United States)

Chen, Baiyu; Leng, Shuai; Yu, Lifeng; Yu, Zhicong; Ma, Chi; McCollough, Cynthia

2015-12-01

To perform task-based image quality assessment in CT, it is desirable to have a large number of realistic patient images with known diagnostic truth. One effective way of achieving this objective is to create hybrid images that combine patient images with inserted lesions. Because conventional hybrid images generated in the image domain fails to reflect the impact of scan and reconstruction parameters on lesion appearance, this study explored a projection-domain approach. Lesions were segmented from patient images and forward projected to acquire lesion projections. The forward-projection geometry was designed according to a commercial CT scanner and accommodated both axial and helical modes with various focal spot movement patterns. The energy employed by the commercial CT scanner for beam hardening correction was measured and used for the forward projection. The lesion projections were inserted into patient projections decoded from commercial CT projection data. The combined projections were formatted to match those of commercial CT raw data, loaded onto a commercial CT scanner, and reconstructed to create the hybrid images. Two validations were performed. First, to validate the accuracy of the forward-projection geometry, images were reconstructed from the forward projections of a virtual ACR phantom and compared to physically acquired ACR phantom images in terms of CT number accuracy and high-contrast resolution. Second, to validate the realism of the lesion in hybrid images, liver lesions were segmented from patient images and inserted back into the same patients, each at a new location specified by a radiologist. The inserted lesions were compared to the original lesions and visually assessed for realism by two experienced radiologists in a blinded fashion. For the validation of the forward-projection geometry, the images reconstructed from the forward projections of the virtual ACR phantom were consistent with the images physically acquired for the ACR

Exact solutions of linear reaction-diffusion processes on a uniformly growing domain: criteria for successful colonization.

Directory of Open Access Journals (Sweden)

Matthew J Simpson

Full Text Available Many processes during embryonic development involve transport and reaction of molecules, or transport and proliferation of cells, within growing tissues. Mathematical models of such processes usually take the form of a reaction-diffusion partial differential equation (PDE on a growing domain. Previous analyses of such models have mainly involved solving the PDEs numerically. Here, we present a framework for calculating the exact solution of a linear reaction-diffusion PDE on a growing domain. We derive an exact solution for a general class of one-dimensional linear reaction-diffusion process on 0domain. Comparing our exact solutions with numerical approximations confirms the veracity of the method. Furthermore, our examples illustrate a delicate interplay between: (i the rate at which the domain elongates, (ii the diffusivity associated with the spreading density profile, (iii the reaction rate, and (iv the initial condition. Altering the balance between these four features leads to different outcomes in terms of whether an initial profile, located near x = 0, eventually overcomes the domain growth and colonizes the entire length of the domain by reaching the boundary where x = L(t.

Role of SUMO in RNF4-mediated promyelocytic leukemia protein (PML) degradation: sumoylation of PML and phospho-switch control of its SUMO binding domain dissected in living cells.

Science.gov (United States)

Percherancier, Yann; Germain-Desprez, Delphine; Galisson, Frédéric; Mascle, Xavier H; Dianoux, Laurent; Estephan, Patricia; Chelbi-Alix, Mounira K; Aubry, Muriel

2009-06-12

Promyelocytic leukemia protein (PML) is a tumor suppressor acting as the organizer of subnuclear structures called PML nuclear bodies (NBs). Both covalent modification of PML by the small ubiquitin-like modifier (SUMO) and non-covalent binding of SUMO to the PML SUMO binding domain (SBD) are necessary for PML NB formation and maturation. PML sumoylation and proteasome-dependent degradation induced by the E3 ubiquitin ligase, RNF4, are enhanced by the acute promyelocytic leukemia therapeutic agent, arsenic trioxide (As2O3). Here, we established a novel bioluminescence resonance energy transfer (BRET) assay to dissect and monitor PML/SUMO interactions dynamically in living cells upon addition of therapeutic agents. Using this sensitive and quantitative SUMO BRET assay that distinguishes PML sumoylation from SBD-mediated PML/SUMO non-covalent interactions, we probed the respective roles of covalent and non-covalent PML/SUMO interactions in PML degradation and interaction with RNF4. We found that, although dispensable for As2O3-enhanced PML sumoylation and RNF4 interaction, PML SBD core sequence was required for As2O3- and RNF4-induced PML degradation. As confirmed with a phosphomimetic mutant, phosphorylation of a stretch of serine residues, contained within PML SBD was needed for PML interaction with SUMO-modified protein partners and thus for NB maturation. However, mutation of these serine residues did not impair As2O3- and RNF4-induced PML degradation, contrasting with the known role of these phosphoserine residues for casein kinase 2-promoted PML degradation. Altogether, these data suggest a model whereby sumoylation- and SBD-dependent PML oligomerization within NBs is sufficient for RNF4-mediated PML degradation and does not require the phosphorylation-dependent association of PML with other sumoylated partners.

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

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Zhao-Qing Wang

2014-01-01

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

Structure and dynamics of the human pleckstrin DEP domain: distinct molecular features of a novel DEP domain subfamily.

Science.gov (United States)

Civera, Concepcion; Simon, Bernd; Stier, Gunter; Sattler, Michael; Macias, Maria J

2005-02-01

Pleckstrin1 is a major substrate for protein kinase C in platelets and leukocytes, and comprises a central DEP (disheveled, Egl-10, pleckstrin) domain, which is flanked by two PH (pleckstrin homology) domains. DEP domains display a unique alpha/beta fold and have been implicated in membrane binding utilizing different mechanisms. Using multiple sequence alignments and phylogenetic tree reconstructions, we find that 6 subfamilies of the DEP domain exist, of which pleckstrin represents a novel and distinct subfamily. To clarify structural determinants of the DEP fold and to gain further insight into the role of the DEP domain, we determined the three-dimensional structure of the pleckstrin DEP domain using heteronuclear NMR spectroscopy. Pleckstrin DEP shares main structural features with the DEP domains of disheveled and Epac, which belong to different DEP subfamilies. However, the pleckstrin DEP fold is distinct from these structures and contains an additional, short helix alpha4 inserted in the beta4-beta5 loop that exhibits increased backbone mobility as judged by NMR relaxation measurements. Based on sequence conservation, the helix alpha4 may also be present in the DEP domains of regulator of G-protein signaling (RGS) proteins, which are members of the same DEP subfamily. In pleckstrin, the DEP domain is surrounded by two PH domains. Structural analysis and charge complementarity suggest that the DEP domain may interact with the N-terminal PH domain in pleckstrin. Phosphorylation of the PH-DEP linker, which is required for pleckstrin function, could regulate such an intramolecular interaction. This suggests a role of the pleckstrin DEP domain in intramolecular domain interactions, which is distinct from the functions of other DEP domain subfamilies found so far.

Ferromagnetic and twin domains in LCMO manganites

International Nuclear Information System (INIS)

Jung, G.; Markovich, V.; Mogilyanski, D.; Beek, C. van der; Mukovskii, Y.M.

2005-01-01

Ferromagnetic and twin domains in lightly Ca-doped La 1-x Ca x MnO 3 single crystals have been visualized and investigated by means of the magneto-optical technique. Both types of domains became visible below the Curie temperature. The dominant structures seen in applied magnetic field are associated with magneto-crystalline anisotropy and twin domains. In a marked difference to the twin domains which appear only in applied magnetic field, ferromagnetic domains show up in zero applied field and are characterized by oppositely oriented spontaneous magnetization in adjacent domains. Ferromagnetic domains take form of almost periodic, corrugated strip-like structures. The corrugation of the ferromagnetic domain pattern is enforced by the underlying twin domains

Presynaptic protein synthesis required for NT-3-induced long-term synaptic modulation

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Je H

2011-01-01

Full Text Available Abstract Background Neurotrophins elicit both acute and long-term modulation of synaptic transmission and plasticity. Previously, we demonstrated that the long-term synaptic modulation requires the endocytosis of neurotrophin-receptor complex, the activation of PI3K and Akt, and mTOR mediated protein synthesis. However, it is unclear whether the long-term synaptic modulation by neurotrophins depends on protein synthesis in pre- or post-synaptic cells. Results Here we have developed an inducible protein translation blocker, in which the kinase domain of protein kinase R (PKR is fused with bacterial gyrase B domain (GyrB-PKR, which could be dimerized upon treatment with a cell permeable drug, coumermycin. By genetically targeting GyrB-PKR to specific cell types, we show that NT-3 induced long-term synaptic modulation requires presynaptic, but not postsynaptic protein synthesis. Conclusions Our results provide mechanistic insights into the cell-specific requirement for protein synthesis in the long-term synaptic modulation by neurotrophins. The GyrB-PKR system may be useful tool to study protein synthesis in a cell-specific manner.

Dynamic Hippocampal and Prefrontal Contributions to Memory Processes and Representations Blur the Boundaries of Traditional Cognitive Domains

OpenAIRE

Rachael D. Rubin; Hillary Schwarb; Heather D. Lucas; Michael R. Dulas; Neal J. Cohen

2017-01-01

The hippocampus has long been known to be a critical component of the memory system involved in the formation and use of long-term declarative memory. However, recent findings have revealed that the reach of hippocampal contributions extends to a variety of domains and tasks that require the flexible use of cognitive and social behavior, including domains traditionally linked to prefrontal cortex (PFC), such as decision-making. In addition, the prefrontal cortex (PFC) has gained traction as a...

Exact solutions of linear reaction-diffusion processes on a uniformly growing domain: criteria for successful colonization.

Science.gov (United States)

Simpson, Matthew J

2015-01-01

Many processes during embryonic development involve transport and reaction of molecules, or transport and proliferation of cells, within growing tissues. Mathematical models of such processes usually take the form of a reaction-diffusion partial differential equation (PDE) on a growing domain. Previous analyses of such models have mainly involved solving the PDEs numerically. Here, we present a framework for calculating the exact solution of a linear reaction-diffusion PDE on a growing domain. We derive an exact solution for a general class of one-dimensional linear reaction-diffusion process on 0exact solutions with numerical approximations confirms the veracity of the method. Furthermore, our examples illustrate a delicate interplay between: (i) the rate at which the domain elongates, (ii) the diffusivity associated with the spreading density profile, (iii) the reaction rate, and (iv) the initial condition. Altering the balance between these four features leads to different outcomes in terms of whether an initial profile, located near x = 0, eventually overcomes the domain growth and colonizes the entire length of the domain by reaching the boundary where x = L(t).

Investigating domain-general short-term memory for order versus specific item memory in developmental dyslexia

OpenAIRE

Hachmann, Wibke Maria

2012-01-01

Recent findings suggest that people with dyslexia experience difficulties with the learning of serial order information during the transition from short- to long-term memory. At the same time, models of short-term memory increasingly incorporate a distinction of order and item processing. This work aims to investigate whether serial order processing deficiencies in dyslexia can be traced back to a selective impairment of short-term memory for serial order, and whether this impairment also aff...

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.

From Meaning Well to Doing Well: Ethical Expertise in the GIS Domain

Science.gov (United States)

Huff, Chuck

2014-01-01

There is evidence to support the idea that moral action can be thought of in terms of expertise in a domain. This paper reviews work on the development of moral expertise across five levels, from novice to expertise. It addresses the role of habit in expertise and self-regulation strategies that signal when habitual action is not working and that…

Domain-Specific Control of Selective Attention

Science.gov (United States)

Lin, Szu-Hung; Yeh, Yei-Yu

2014-01-01

Previous research has shown that loading information on working memory affects selective attention. However, whether the load effect on selective attention is domain-general or domain-specific remains unresolved. The domain-general effect refers to the findings that load in one content (e.g. phonological) domain in working memory influences processing in another content (e.g., visuospatial) domain. Attentional control supervises selection regardless of information domain. The domain-specific effect refers to the constraint of influence only when maintenance and processing operate in the same domain. Selective attention operates in a specific content domain. This study is designed to resolve this controversy. Across three experiments, we manipulated the type of representation maintained in working memory and the type of representation upon which the participants must exert control to resolve conflict and select a target into the focus of attention. In Experiments 1a and 1b, participants maintained digits and nonverbalized objects, respectively, in working memory while selecting a target in a letter array. In Experiment 2, we presented auditory digits with a letter flanker task to exclude the involvement of resource competition within the same input modality. In Experiments 3a and 3b, we replaced the letter flanker task with an object flanker task while manipulating the memory load on object and digit representation, respectively. The results consistently showed that memory load modulated distractibility only when the stimuli of the two tasks were represented in the same domain. The magnitude of distractor interference was larger under high load than under low load, reflecting a lower efficacy of information prioritization. When the stimuli of the two tasks were represented in different domains, memory load did not modulate distractibility. Control of processing priority in selective attention demands domain-specific resources. PMID:24866977

The development of global and domain-specific self-esteem from age 13 to 31.

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von Soest, Tilmann; Wichstrøm, Lars; Kvalem, Ingela Lundin

2016-04-01

This study examines the development of global self-esteem and self-esteem in 6 specific domains across adolescence and young adulthood. Using a cohort-sequential design, we analyzed longitudinal data on 3,116 Norwegian men and women from 13 to 31 years of age by means of growth curve modeling. Questionnaire data provided information on global self-esteem and self-esteem in social, academic, athletic, and appearance domains. Data on important life outcomes was provided by register linkages. Results showed increasing levels of global self-esteem and self-esteem in most domains with increasing age. Being male, higher parental education, and reported higher levels of parental care were related to higher levels of global self-esteem and self-esteem in several domains. Self-esteem in the appearance domain showed high and stable correlations with global self-esteem, whereas in social domains, correlations with global self-esteem increased over age, with a particularly steep increase for romantic appeal self-esteem. As to the prospective relationship between self-esteem and important life outcomes, results showed that participants high in academic self-esteem attained higher education levels and higher income, but most of the relationship was explained by covariates such as parents' socioeconomic status and school grades. Low global self-esteem predicted later prescription of antidepressants, even after controlling for covariates. This study is the first to provide a comprehensive picture of the development of global and domain-specific self-esteem throughout adolescence and young adulthood using long-term longitudinal data. The results underscore the importance of examining development of self-esteem in specific domains in addition to global self-esteem. (c) 2016 APA, all rights reserved).

Domain wall engineering through exchange bias

International Nuclear Information System (INIS)

Albisetti, E.; Petti, D.

2016-01-01

The control of the structure and position of magnetic domain walls is at the basis of the development of different magnetic devices and architectures. Several nanofabrication techniques have been proposed to geometrically confine and shape domain wall structures; however, a fine tuning of the position and micromagnetic configuration is hardly achieved, especially in continuous films. This work shows that, by controlling the unidirectional anisotropy of a continuous ferromagnetic film through exchange bias, domain walls whose spin arrangement is generally not favored by dipolar and exchange interactions can be created. Micromagnetic simulations reveal that the domain wall width, position and profile can be tuned by establishing an abrupt change in the direction and magnitude of the exchange bias field set in the system. - Highlights: • Micromagnetic simulations study domain walls in exchange biased thin films. • Novel domain wall configurations can be stabilized via exchange bias. • Domain walls nucleate at the boundary of regions with different exchange bias. • Domain wall width and spin profile are controlled by tuning the exchange bias.

Frequency Domain Image Filtering Using CUDA

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Muhammad Awais Rajput

2014-10-01

Full Text Available In this paper, we investigate the implementation of image filtering in frequency domain using NVIDIA?s CUDA (Compute Unified Device Architecture. In contrast to signal and image filtering in spatial domain which uses convolution operations and hence is more compute-intensive for filters having larger spatial extent, the frequency domain filtering uses FFT (Fast Fourier Transform which is much faster and significantly reduces the computational complexity of the filtering. We implement the frequency domain filtering on CPU and GPU respectively and analyze the speed-up obtained from the CUDA?s parallel processing paradigm. In order to demonstrate the efficiency of frequency domain filtering on CUDA, we implement three frequency domain filters, i.e., Butterworth, low-pass and Gaussian for processing different sizes of images on CPU and GPU respectively and perform the GPU vs. CPU benchmarks. The results presented in this paper show that the frequency domain filtering with CUDA achieves significant speed-up over the CPU processing in frequency domain with the same level of (output image quality on both the processing architectures

Frequency domain image filtering using cuda

International Nuclear Information System (INIS)

Rajput, M.A.; Khan, U.A.

2014-01-01

In this paper, we investigate the implementation of image filtering in frequency domain using NVIDIA's CUDA (Compute Unified Device Architecture). In contrast to signal and image filtering in spatial domain which uses convolution operations and hence is more compute-intensive for filters having larger spatial extent, the frequency domain filtering uses FFT (Fast Fourier Transform) which is much faster and significantly reduces the computational complexity of the filtering. We implement the frequency domain filtering on CPU and GPU respectively and analyze the speed-up obtained from the CUDA's parallel processing paradigm. In order to demonstrate the efficiency of frequency domain filtering on CUDA, we implement three frequency domain filters, i.e., Butter worth, low-pass and Gaussian for processing different sizes of images on CPU and GPU respectively and perform the GPU vs. CPU benchmarks. The results presented in this paper show that the frequency domain filtering with CUDA achieves significant speed-up over the CPU processing in frequency domain with the same level of (output) image quality on both the processing architectures. (author)

Schrödinger's kittens and the search for reality

CERN Document Server

Gribbin, John

1995-01-01

Following on from his bestseller, SCHRODINGER'S CAT, John Gribbin presents the recent dramatic improvements in experimental techniques that have enabled physicists to formulate and test new theories about the nature of light. He describes these theories not in terms of hard-to-imagine entities like spinning subnuclear particles, but in terms of the fate of two small cats, separated at a tender age and carried to opposite ends of the universe. In this way Gribbin introduces the reader to such new developments as quantum cryptography, through which unbreakable codes can be made, and goes on to possible future developments such as the idea that the 'entanglement' of quantum particles could be a way to build a STAR TREK style teleportation machine.

Individual globular domains and domain unfolding visualized in overstretched titin molecules with atomic force microscopy.

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Zsolt Mártonfalvi

Full Text Available Titin is a giant elastomeric protein responsible for the generation of passive muscle force. Mechanical force unfolds titin's globular domains, but the exact structure of the overstretched titin molecule is not known. Here we analyzed, by using high-resolution atomic force microscopy, the structure of titin molecules overstretched with receding meniscus. The axial contour of the molecules was interrupted by topographical gaps with a mean width of 27.7 nm that corresponds well to the length of an unfolded globular (immunoglobulin and fibronectin domain. The wide gap-width distribution suggests, however, that additional mechanisms such as partial domain unfolding and the unfolding of neighboring domain multimers may also be present. In the folded regions we resolved globules with an average spacing of 5.9 nm, which is consistent with a titin chain composed globular domains with extended interdomain linker regions. Topographical analysis allowed us to allocate the most distal unfolded titin region to the kinase domain, suggesting that this domain systematically unfolds when the molecule is exposed to overstretching forces. The observations support the prediction that upon the action of stretching forces the N-terminal ß-sheet of the titin kinase unfolds, thus exposing the enzyme's ATP-binding site and hence contributing to the molecule's mechanosensory function.

Quantifying information transfer by protein domains: Analysis of the Fyn SH2 domain structure

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Serrano Luis

2008-10-01

Full Text Available Abstract Background Efficient communication between distant sites within a protein is essential for cooperative biological response. Although often associated with large allosteric movements, more subtle changes in protein dynamics can also induce long-range correlations. However, an appropriate formalism that directly relates protein structural dynamics to information exchange between functional sites is still lacking. Results Here we introduce a method to analyze protein dynamics within the framework of information theory and show that signal transduction within proteins can be considered as a particular instance of communication over a noisy channel. In particular, we analyze the conformational correlations between protein residues and apply the concept of mutual information to quantify information exchange. Mapping out changes of mutual information on the protein structure then allows visualizing how distal communication is achieved. We illustrate the approach by analyzing information transfer by the SH2 domain of Fyn tyrosine kinase, obtained from Monte Carlo dynamics simulations. Our analysis reveals that the Fyn SH2 domain forms a noisy communication channel that couples residues located in the phosphopeptide and specificity binding sites and a number of residues at the other side of the domain near the linkers that connect the SH2 domain to the SH3 and kinase domains. We find that for this particular domain, communication is affected by a series of contiguous residues that connect distal sites by crossing the core of the SH2 domain. Conclusion As a result, our method provides a means to directly map the exchange of biological information on the structure of protein domains, making it clear how binding triggers conformational changes in the protein structure. As such it provides a structural road, next to the existing attempts at sequence level, to predict long-range interactions within protein structures.

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.

Phylogeny of the TRAF/MATH domain.

Science.gov (United States)

Zapata, Juan M; Martínez-García, Vanesa; Lefebvre, Sophie

2007-01-01

The TNF-receptor associated factor (TRAF) domain (TD), also known as the meprin and TRAF-C homology (MATH) domain is a fold of seven anti-parallel p-helices that participates in protein-protein interactions. This fold is broadly represented among eukaryotes, where it is found associated with a discrete set of protein-domains. Virtually all protein families encompassing a TRAF/MATH domain seem to be involved in the regulation of protein processing and ubiquitination, strongly suggesting a parallel evolution of the TRAF/MATH domain and certain proteolysis pathways in eukaryotes. The restricted number of living organisms for which we have information of their genetic and protein make-up limits the scope and analysis of the MATH domain in evolution. However, the available information allows us to get a glimpse on the origins, distribution and evolution of the TRAF/MATH domain, which will be overviewed in this chapter.

Dynamic Hippocampal and Prefrontal Contributions to Memory Processes and Representations Blur the Boundaries of Traditional Cognitive Domains.

Science.gov (United States)

Rubin, Rachael D; Schwarb, Hillary; Lucas, Heather D; Dulas, Michael R; Cohen, Neal J

2017-07-12

The hippocampus has long been known to be a critical component of the memory system involved in the formation and use of long-term declarative memory. However, recent findings have revealed that the reach of hippocampal contributions extends to a variety of domains and tasks that require the flexible use of cognitive and social behavior, including domains traditionally linked to prefrontal cortex (PFC), such as decision-making. In addition, the prefrontal cortex (PFC) has gained traction as a necessary part of the memory system. These findings challenge the conventional characterizations of hippocampus and PFC as being circumscribed to traditional cognitive domains. Here, we emphasize that the ability to parsimoniously account for the breadth of hippocampal and PFC contributions to behavior, in terms of memory function and beyond, requires theoretical advances in our understanding of their characteristic processing features and mental representations. Notably, several literatures exist that touch upon this issue, but have remained disjointed because of methodological differences that necessarily limit the scope of inquiry, as well as the somewhat artificial boundaries that have been historically imposed between domains of cognition. In particular, this article focuses on the contribution of relational memory theory as an example of a framework that describes both the representations and processes supported by the hippocampus, and further elucidates the role of the hippocampal-PFC network to a variety of behaviors.

Dynamic Hippocampal and Prefrontal Contributions to Memory Processes and Representations Blur the Boundaries of Traditional Cognitive Domains

Directory of Open Access Journals (Sweden)

Rachael D. Rubin

2017-07-01

Full Text Available The hippocampus has long been known to be a critical component of the memory system involved in the formation and use of long-term declarative memory. However, recent findings have revealed that the reach of hippocampal contributions extends to a variety of domains and tasks that require the flexible use of cognitive and social behavior, including domains traditionally linked to prefrontal cortex (PFC, such as decision-making. In addition, the prefrontal cortex (PFC has gained traction as a necessary part of the memory system. These findings challenge the conventional characterizations of hippocampus and PFC as being circumscribed to traditional cognitive domains. Here, we emphasize that the ability to parsimoniously account for the breadth of hippocampal and PFC contributions to behavior, in terms of memory function and beyond, requires theoretical advances in our understanding of their characteristic processing features and mental representations. Notably, several literatures exist that touch upon this issue, but have remained disjointed because of methodological differences that necessarily limit the scope of inquiry, as well as the somewhat artificial boundaries that have been historically imposed between domains of cognition. In particular, this article focuses on the contribution of relational memory theory as an example of a framework that describes both the representations and processes supported by the hippocampus, and further elucidates the role of the hippocampal–PFC network to a variety of behaviors.

Domain-based small molecule binding site annotation

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Dumontier Michel

2006-03-01

focusing on protein domain-small molecule interactions, SMID is able to cluster similar interactions and detect subtle binding patterns that would not otherwise be obvious. Using SMID-BLAST, small molecule targets can be predicted for any protein sequence, with the only limitation being that the small molecule must exist in the PDB. Validation results and specific examples within illustrate that SMID-BLAST has a high degree of accuracy in terms of predicting both the small molecule ligand and binding site residue positions for a query protein.

A micromagnetic study of domain structure modeling

International Nuclear Information System (INIS)

Matsuo, Tetsuji; Mimuro, Naoki; Shimasaki, Masaaki

2008-01-01

To develop a mesoscopic model for magnetic-domain behavior, a domain structure model (DSM) was examined and compared with a micromagnetic simulation. The domain structure of this model is given by several domains with uniform magnetization vectors and domain walls. The directions of magnetization vectors and the locations of domain walls are determined so as to minimize the magnetic total energy of the magnetic material. The DSM was modified to improve its representation capability for domain behavior. The domain wall energy is multiplied by a vanishing factor to represent the disappearance of magnetic domain. The sequential quadratic programming procedure is divided into two steps to improve an energy minimization process. A comparison with micromagnetic simulation shows that the modified DSM improves the representation accuracy of the magnetization process

Texture of lipid bilayer domains

DEFF Research Database (Denmark)

Jensen, Uffe Bernchou; Brewer, Jonathan R.; Midtiby, Henrik Skov

2009-01-01

We investigate the texture of gel (g) domains in binary lipid membranes composed of the phospholipids DPPC and DOPC. Lateral organization of lipid bilayer membranes is a topic of fundamental and biological importance. Whereas questions related to size and composition of fluid membrane domain...... are well studied, the possibility of texture in gel domains has so far not been examined. When using polarized light for two-photon excitation of the fluorescent lipid probe Laurdan, the emission intensity is highly sensitive to the angle between the polarization and the tilt orientation of lipid acyl...... chains. By imaging the intensity variations as a function of the polarization angle, we map the lateral variations of the lipid tilt within domains. Results reveal that gel domains are composed of subdomains with different lipid tilt directions. We have applied a Fourier decomposition method...

On the structure of order domains

DEFF Research Database (Denmark)

Geil, Olav; Pellikaan, Ruud

2002-01-01

The notion of an order domain is generalized. The behaviour of an order domain by taking a subalgebra, the extension of scalars, and the tensor product is studied. The relation of an order domain with valuation theory, Gröbner algebras, and graded structures is given. The theory of Gröbner bases...... for order domains is developed and used to show that the factor ring theorem and its converse, the presentation theorem, hold. The dimension of an order domain is related to the rank of its value semigroup....

Stabilization of the solution of a two-dimensional system of Navier-Stokes equations in an unbounded domain with several exits to infinity

International Nuclear Information System (INIS)

Khisamutdinova, N A

2003-01-01

The behaviour as t→∞ of the solution of the mixed problem for the system of Navier-Stokes equations with a Dirichlet condition at the boundary is studied in an unbounded two-dimensional domain with several exits to infinity. A class of domains is distinguished in which an estimate characterizing the decay of solutions in terms of the geometry of the domain is proved for exponentially decreasing initial velocities. A similar estimate of the solution of the first mixed problem for the heat equation is sharp in a broad class of domains with several exits to infinity

Hybrid meshes and domain decomposition for the modeling of oil reservoirs; Maillages hybrides et decomposition de domaine pour la modelisation des reservoirs petroliers

Energy Technology Data Exchange (ETDEWEB)

Gaiffe, St

2000-03-23

In this thesis, we are interested in the modeling of fluid flow through porous media with 2-D and 3-D unstructured meshes, and in the use of domain decomposition methods. The behavior of flow through porous media is strongly influenced by heterogeneities: either large-scale lithological discontinuities or quite localized phenomena such as fluid flow in the neighbourhood of wells. In these two typical cases, an accurate consideration of the singularities requires the use of adapted meshes. After having shown the limits of classic meshes we present the future prospects offered by hybrid and flexible meshes. Next, we consider the generalization possibilities of the numerical schemes traditionally used in reservoir simulation and we draw two available approaches: mixed finite elements and U-finite volumes. The investigated phenomena being also characterized by different time-scales, special treatments in terms of time discretization on various parts of the domain are required. We think that the combination of domain decomposition methods with operator splitting techniques may provide a promising approach to obtain high flexibility for a local tune-steps management. Consequently, we develop a new numerical scheme for linear parabolic equations which allows to get a higher flexibility in the local space and time steps management. To conclude, a priori estimates and error estimates on the two variables of interest, namely the pressure and the velocity are proposed. (author)

(Br-SCMM) Brazilian Smart City Maturity Model: A Perspective from the Health Domain.

Science.gov (United States)

Afonso, Ricardo Alexandre; dos Santos Brito, Kellyton; Holanda do Nascimento, Clóvis; Campos da Costa, Luciana; Álvaro, Alexandre; Cardoso Garcia, Vinicius

2015-01-01

The term definition "Smart City" still allows various interpretations, and this causes some difficulty in establishing parameters to measure how smart the cities can be. This paper presents a Maturity Model that uses a set of minimum domains and indicators that aim to encourage cities of different sizes to identify their potential and improve processes and public policies.

Ranking Medical Terms to Support Expansion of Lay Language Resources for Patient Comprehension of Electronic Health Record Notes: Adapted Distant Supervision Approach.

Science.gov (United States)

Chen, Jinying; Jagannatha, Abhyuday N; Fodeh, Samah J; Yu, Hong

2017-10-31

Medical terms are a major obstacle for patients to comprehend their electronic health record (EHR) notes. Clinical natural language processing (NLP) systems that link EHR terms to lay terms or definitions allow patients to easily access helpful information when reading through their EHR notes, and have shown to improve patient EHR comprehension. However, high-quality lay language resources for EHR terms are very limited in the public domain. Because expanding and curating such a resource is a costly process, it is beneficial and even necessary to identify terms important for patient EHR comprehension first. We aimed to develop an NLP system, called adapted distant supervision (ADS), to rank candidate terms mined from EHR corpora. We will give EHR terms ranked as high by ADS a higher priority for lay language annotation-that is, creating lay definitions for these terms. Adapted distant supervision uses distant supervision from consumer health vocabulary and transfer learning to adapt itself to solve the problem of ranking EHR terms in the target domain. We investigated 2 state-of-the-art transfer learning algorithms (ie, feature space augmentation and supervised distant supervision) and designed 5 types of learning features, including distributed word representations learned from large EHR data for ADS. For evaluating ADS, we asked domain experts to annotate 6038 candidate terms as important or nonimportant for EHR comprehension. We then randomly divided these data into the target-domain training data (1000 examples) and the evaluation data (5038 examples). We compared ADS with 2 strong baselines, including standard supervised learning, on the evaluation data. The ADS system using feature space augmentation achieved the best average precision, 0.850, on the evaluation set when using 1000 target-domain training examples. The ADS system using supervised distant supervision achieved the best average precision, 0.819, on the evaluation set when using only 100 target-domain

Multiple graph regularized protein domain ranking.

Science.gov (United States)

Wang, Jim Jing-Yan; Bensmail, Halima; Gao, Xin

2012-11-19

Protein domain ranking is a fundamental task in structural biology. Most protein domain ranking methods rely on the pairwise comparison of protein domains while neglecting the global manifold structure of the protein domain database. Recently, graph regularized ranking that exploits the global structure of the graph defined by the pairwise similarities has been proposed. However, the existing graph regularized ranking methods are very sensitive to the choice of the graph model and parameters, and this remains a difficult problem for most of the protein domain ranking methods. To tackle this problem, we have developed the Multiple Graph regularized Ranking algorithm, MultiG-Rank. Instead of using a single graph to regularize the ranking scores, MultiG-Rank approximates the intrinsic manifold of protein domain distribution by combining multiple initial graphs for the regularization. Graph weights are learned with ranking scores jointly and automatically, by alternately minimizing an objective function in an iterative algorithm. Experimental results on a subset of the ASTRAL SCOP protein domain database demonstrate that MultiG-Rank achieves a better ranking performance than single graph regularized ranking methods and pairwise similarity based ranking methods. The problem of graph model and parameter selection in graph regularized protein domain ranking can be solved effectively by combining multiple graphs. This aspect of generalization introduces a new frontier in applying multiple graphs to solving protein domain ranking applications.

On the asymptotic of solutions of elliptic boundary value problems in domains with edges

International Nuclear Information System (INIS)

Nkemzi, B.

2005-10-01

Solutions of elliptic boundary value problems in three-dimensional domains with edges may exhibit singularities. The usual procedure to study these singularities is by the application of the classical Mellin transformation or continuous Fourier transformation. In this paper, we show how the asymptotic behavior of solutions of elliptic boundary value problems in general three-dimensional domains with straight edges can be investigated by means of discrete Fourier transformation. We apply this approach to time-harmonic Maxwell's equations and prove that the singular solutions can fully be described in terms of Fourier series. The representation here can easily be used to approximate three-dimensional stress intensity factors associated with edge singularities. (author)

Robust exponential stability and domains of attraction in a class of interval neural networks

International Nuclear Information System (INIS)

Yang Xiaofan; Liao Xiaofeng; Bai Sen; Evans, David J

2005-01-01

This paper addresses robust exponential stability as well as domains of attraction in a class of interval neural networks. A sufficient condition for an equilibrium point to be exponentially stable is established. And an estimate on the domains of attraction of exponentially stable equilibrium points is presented. Both the condition and the estimate are formulated in terms of the parameter intervals, the neurons' activation functions and the equilibrium point. Hence, they are easily checkable. In addition, our results neither depend on monotonicity of the activation functions nor on coupling conditions between the neurons. Consequently, these results are of practical importance in evaluating the performance of interval associative memory networks

Diagrammatic Representations in Domain-Specific Languages

OpenAIRE

Tourlas, Konstantinos

2002-01-01

One emerging approach to reducing the labour and costs of software development favours the specialisation of techniques to particular application domains. The rationale is that programs within a given domain often share enough common features and assumptions to enable the incorporation of substantial support mechanisms into domain-specific programming languages and associated tools. Instead of being machine-oriented, algorithmic implementations, programs in many domain-speci...

Domain wall networks on solitons

International Nuclear Information System (INIS)

Sutcliffe, Paul

2003-01-01

Domain wall networks on the surface of a soliton are studied in a simple theory. It consists of two complex scalar fields, in 3+1 dimensions, with a global U(1)xZ n symmetry, where n>2. Solutions are computed numerically in which one of the fields forms a Q ball and the other field forms a network of domain walls localized on the surface of the Q ball. Examples are presented in which the domain walls lie along the edges of a spherical polyhedron, forming junctions at its vertices. It is explained why only a small restricted class of polyhedra can arise as domain wall networks

Traditions in spider monkeys are biased towards the social domain.

Directory of Open Access Journals (Sweden)

Claire J Santorelli

Full Text Available Cross-site comparison studies of behavioral variation can provide evidence for traditions in wild species once ecological and genetic factors are excluded as causes for cross-site differences. These studies ensure behavior variants are considered within the context of a species' ecology and evolutionary adaptations. We examined wide-scale geographic variation in the behavior of spider monkeys (Ateles geoffroyi across five long-term field sites in Central America using a well established ethnographic cross-site survey method. Spider monkeys possess a relatively rare social system with a high degree of fission-fusion dynamics, also typical of chimpanzees (Pan troglodytes and humans (Homo sapiens. From the initial 62 behaviors surveyed 65% failed to meet the necessary criteria for traditions. The remaining 22 behaviors showed cross-site variation in occurrence ranging from absent through to customary, representing to our knowledge, the first documented cases of traditions in this taxon and only the second case of multiple traditions in a New World monkey species. Of the 22 behavioral variants recorded across all sites, on average 57% occurred in the social domain, 19% in food-related domains and 24% in other domains. This social bias contrasts with the food-related bias reported in great ape cross-site comparison studies and has implications for the evolution of human culture. No pattern of geographical radiation was found in relation to distance across sites. Our findings promote A. geoffroyi as a model species to investigate traditions with field and captive based experiments and emphasize the importance of the social domain for the study of animal traditions.

Towards Domain-specific Flow-based Languages

DEFF Research Database (Denmark)

Zarrin, Bahram; Baumeister, Hubert; Sarjoughian, Hessam S.

2018-01-01

describe their problems and solutions, instead of using general purpose programming languages. The goal of these languages is to improve the productivity and efficiency of the development and simulation of concurrent scientific models and systems. Moreover, they help to expose parallelism and to specify...... the concurrency within a component or across different independent components. In this paper, we introduce the concept of domain-specific flowbased languages which allows domain experts to use flow-based languages adapted to a particular problem domain. Flow-based programming is used to support concurrency, while......Due to the significant growth of the demand for data-intensive computing, in addition to the emergence of new parallel and distributed computing technologies, scientists and domain experts are leveraging languages specialized for their problem domain, i.e., domain-specific languages, to help them...

Initial boundary value problems of nonlinear wave equations in an exterior domain

International Nuclear Information System (INIS)

Chen Yunmei.

1987-06-01

In this paper, we investigate the existence and uniqueness of the global solutions to the initial boundary value problems of nonlinear wave equations in an exterior domain. When the space dimension n >= 3, the unique global solution of the above problem is obtained for small initial data, even if the nonlinear term is fully nonlinear and contains the unknown function itself. (author). 10 refs

Improving the Effectiveness of Speaker Verification Domain Adaptation With Inadequate In-Domain Data

Science.gov (United States)

2017-08-20

M speakers. We seek a probabilistic solution to domain adap- tation, and so we encode knowledge of the out-of-domain data in prior distributions...the VB solution from (16)-(21) becomes: µ =αȳ + (1− α)µout, (24) Σa =α ( 1 NT NT∑ n=1 〈ynyTn 〉 − ȳȳT ) + (1− α) Σouta (25) + α (1− α) ( ȳ − µout...non- English languages and from unseen channels. An inadequate in-domain set was provided, which consisted of 2272 samples from 1164 speakers, and

The SPOR Domain, a Widely Conserved Peptidoglycan Binding Domain That Targets Proteins to the Site of Cell Division.

Science.gov (United States)

Yahashiri, Atsushi; Jorgenson, Matthew A; Weiss, David S

2017-07-15

Sporulation-related repeat (SPOR) domains are small peptidoglycan (PG) binding domains found in thousands of bacterial proteins. The name "SPOR domain" stems from the fact that several early examples came from proteins involved in sporulation, but SPOR domain proteins are quite diverse and contribute to a variety of processes that involve remodeling of the PG sacculus, especially with respect to cell division. SPOR domains target proteins to the division site by binding to regions of PG devoid of stem peptides ("denuded" glycans), which in turn are enriched in septal PG by the intense, localized activity of cell wall amidases involved in daughter cell separation. This targeting mechanism sets SPOR domain proteins apart from most other septal ring proteins, which localize via protein-protein interactions. In addition to SPOR domains, bacteria contain several other PG-binding domains that can exploit features of the cell wall to target proteins to specific subcellular sites. Copyright © 2017 American Society for Microbiology.

Self-Assembly of Narrowly Dispersed Brush Diblock Copolymers with Domain Spacing more than 100 nm

Science.gov (United States)

Gu, Weiyin; Sveinbjornsson, Benjamin; Hong, Sung Woo; Grubbs, Robert; Russell, Thomas

2012-02-01

Self-assembled structures of high molecular weight (MW), narrow molecular weight distribution brush block copolymers containing polylactic acid (PLA) and polystyrene (PS) side chains with similar MWs were studied in both the melt and thin films. The polynorbornene-backbone-based brush diblock copolymers containing approximately equal volume fractions of each block self-assembled into highly ordered lamellae with domain spacing over 100 nm, as revealed by SAXS, GISAXS and AFM. The domain size increased approximately linearly with backbone length, which indicated an extended conformation of the backbone in the ordered state. The length of side chains also played a significant role in terms of controlling the domain size. As the degree of polymerization (DP) increased, the symmetric brush diblock copolymers with longer side chains tended to form larger lamellar microdomains in comparison to those that have the same DP but shorter side chains.

THE FUNDAMENTAL SOLUTIONS FOR MULTI-TERM MODIFIED POWER LAW WAVE EQUATIONS IN A FINITE DOMAIN

OpenAIRE

Jiang, H.; Liu, F.; Meerschaert, M. M.; McGough, R. J.

2013-01-01

Fractional partial differential equations with more than one fractional derivative term in time, such as the Szabo wave equation, or the power law wave equation, describe important physical phenomena. However, studies of these multi-term time-space or time fractional wave equations are still under development.

Frequency-domain and time-domain methods for feedback nonlinear systems and applications to chaos control

International Nuclear Information System (INIS)

Duan Zhisheng; Wang Jinzhi; Yang Ying; Huang Lin

2009-01-01

This paper surveys frequency-domain and time-domain methods for feedback nonlinear systems and their possible applications to chaos control, coupled systems and complex dynamical networks. The absolute stability of Lur'e systems with single equilibrium and global properties of a class of pendulum-like systems with multi-equilibria are discussed. Time-domain and frequency-domain criteria for the convergence of solutions are presented. Some latest results on analysis and control of nonlinear systems with multiple equilibria and applications to chaos control are reviewed. Finally, new chaotic oscillating phenomena are shown in a pendulum-like system and a new nonlinear system with an attraction/repulsion function.

Multiple graph regularized protein domain ranking

KAUST Repository

Wang, Jim Jing-Yan

2012-11-19

Background: Protein domain ranking is a fundamental task in structural biology. Most protein domain ranking methods rely on the pairwise comparison of protein domains while neglecting the global manifold structure of the protein domain database. Recently, graph regularized ranking that exploits the global structure of the graph defined by the pairwise similarities has been proposed. However, the existing graph regularized ranking methods are very sensitive to the choice of the graph model and parameters, and this remains a difficult problem for most of the protein domain ranking methods.Results: To tackle this problem, we have developed the Multiple Graph regularized Ranking algorithm, MultiG-Rank. Instead of using a single graph to regularize the ranking scores, MultiG-Rank approximates the intrinsic manifold of protein domain distribution by combining multiple initial graphs for the regularization. Graph weights are learned with ranking scores jointly and automatically, by alternately minimizing an objective function in an iterative algorithm. Experimental results on a subset of the ASTRAL SCOP protein domain database demonstrate that MultiG-Rank achieves a better ranking performance than single graph regularized ranking methods and pairwise similarity based ranking methods.Conclusion: The problem of graph model and parameter selection in graph regularized protein domain ranking can be solved effectively by combining multiple graphs. This aspect of generalization introduces a new frontier in applying multiple graphs to solving protein domain ranking applications. 2012 Wang et al; licensee BioMed Central Ltd.

Multiple graph regularized protein domain ranking

KAUST Repository

Wang, Jim Jing-Yan; Bensmail, Halima; Gao, Xin

2012-01-01

Background: Protein domain ranking is a fundamental task in structural biology. Most protein domain ranking methods rely on the pairwise comparison of protein domains while neglecting the global manifold structure of the protein domain database. Recently, graph regularized ranking that exploits the global structure of the graph defined by the pairwise similarities has been proposed. However, the existing graph regularized ranking methods are very sensitive to the choice of the graph model and parameters, and this remains a difficult problem for most of the protein domain ranking methods.Results: To tackle this problem, we have developed the Multiple Graph regularized Ranking algorithm, MultiG-Rank. Instead of using a single graph to regularize the ranking scores, MultiG-Rank approximates the intrinsic manifold of protein domain distribution by combining multiple initial graphs for the regularization. Graph weights are learned with ranking scores jointly and automatically, by alternately minimizing an objective function in an iterative algorithm. Experimental results on a subset of the ASTRAL SCOP protein domain database demonstrate that MultiG-Rank achieves a better ranking performance than single graph regularized ranking methods and pairwise similarity based ranking methods.Conclusion: The problem of graph model and parameter selection in graph regularized protein domain ranking can be solved effectively by combining multiple graphs. This aspect of generalization introduces a new frontier in applying multiple graphs to solving protein domain ranking applications. 2012 Wang et al; licensee BioMed Central Ltd.

Multiple graph regularized protein domain ranking

Directory of Open Access Journals (Sweden)

Wang Jim

2012-11-01

Full Text Available Abstract Background Protein domain ranking is a fundamental task in structural biology. Most protein domain ranking methods rely on the pairwise comparison of protein domains while neglecting the global manifold structure of the protein domain database. Recently, graph regularized ranking that exploits the global structure of the graph defined by the pairwise similarities has been proposed. However, the existing graph regularized ranking methods are very sensitive to the choice of the graph model and parameters, and this remains a difficult problem for most of the protein domain ranking methods. Results To tackle this problem, we have developed the Multiple Graph regularized Ranking algorithm, MultiG-Rank. Instead of using a single graph to regularize the ranking scores, MultiG-Rank approximates the intrinsic manifold of protein domain distribution by combining multiple initial graphs for the regularization. Graph weights are learned with ranking scores jointly and automatically, by alternately minimizing an objective function in an iterative algorithm. Experimental results on a subset of the ASTRAL SCOP protein domain database demonstrate that MultiG-Rank achieves a better ranking performance than single graph regularized ranking methods and pairwise similarity based ranking methods. Conclusion The problem of graph model and parameter selection in graph regularized protein domain ranking can be solved effectively by combining multiple graphs. This aspect of generalization introduces a new frontier in applying multiple graphs to solving protein domain ranking applications.

Simulation of two-phase flows by domain decomposition

International Nuclear Information System (INIS)

Dao, T.H.

2013-01-01

This thesis deals with numerical simulations of compressible fluid flows by implicit finite volume methods. Firstly, we studied and implemented an implicit version of the Roe scheme for compressible single-phase and two-phase flows. Thanks to Newton method for solving nonlinear systems, our schemes are conservative. Unfortunately, the resolution of nonlinear systems is very expensive. It is therefore essential to use an efficient algorithm to solve these systems. For large size matrices, we often use iterative methods whose convergence depends on the spectrum. We have studied the spectrum of the linear system and proposed a strategy, called Scaling, to improve the condition number of the matrix. Combined with the classical ILU pre-conditioner, our strategy has reduced significantly the GMRES iterations for local systems and the computation time. We also show some satisfactory results for low Mach-number flows using the implicit centered scheme. We then studied and implemented a domain decomposition method for compressible fluid flows. We have proposed a new interface variable which makes the Schur complement method easy to build and allows us to treat diffusion terms. Using GMRES iterative solver rather than Richardson for the interface system also provides a better performance compared to other methods. We can also decompose the computational domain into any number of sub-domains. Moreover, the Scaling strategy for the interface system has improved the condition number of the matrix and reduced the number of GMRES iterations. In comparison with the classical distributed computing, we have shown that our method is more robust and efficient. (author) [fr

Fusion protein based on Grb2-SH2 domain for cancer therapy

International Nuclear Information System (INIS)

Saito, Yuriko; Furukawa, Takako; Arano, Yasushi; Fujibayashi, Yasuhisa; Saga, Tsuneo

2010-01-01

Research highlights: → Grb2 mediates EGFR signaling through binding to phosphorylate EGFR with SH2 domain. → We generated fusion proteins containing 1 or 2 SH2 domains of Grb2 added with TAT. → The one with 2 SH2 domains (TSSF) interfered ERK phosphorylation. → TSSF significantly delayed the growth of EGFR overexpressing tumor in a mouse model. -- Abstract: Epidermal growth factor receptor (EGFR) is one of the very attractive targets for cancer therapy. In this study, we generated fusion proteins containing one or two Src-homology 2 (SH2) domains of growth factor receptor bound protein 2 (Grb2), which bind to phosphorylated EGFR, added with HIV-1 transactivating transcription for cell membrane penetration (termed TSF and TSSF, respectively). We examined if they can interfere Grb2-mediated signaling pathway and suppress tumor growth as expected from the lack of SH3 domain, which is necessary to intermediate EGFR-Grb2 cell signaling, in the fusion proteins. The transduction efficiency of TSSF was similar to that of TSF, but the binding activity of TSSF to EGFR was higher than that of TSF. Treatment of EGFR-overexpressing cells showed that TSSF decreased p42-ERK phosphorylation, while TSF did not. Both the proteins delayed cell growth but did not induce cell death in culture. TSSF also significantly suppressed tumor growth in vivo under consecutive administration. In conclusion, TSSF showed an ability to inhibit EGFR-Grb2 signaling and could have a potential to treat EGFR-activated cancer.

Anisotropy of domain wall resistance

Science.gov (United States)

Viret; Samson; Warin; Marty; Ott; Sondergard; Klein; Fermon

2000-10-30

The resistive effect of domain walls in FePd films with perpendicular anisotropy was studied experimentally as a function of field and temperature. The films were grown directly on MgO substrates, which induces an unusual virgin magnetic configuration composed of 60 nm wide parallel stripe domains. This allowed us to carry out the first measurements of the anisotropy of domain wall resistivity in the two configurations of current perpendicular and parallel to the walls. At 18 K, we find 8.2% and 1.3% for the domain wall magnetoresistance normalized to the wall width (8 nm) in these two respective configurations. These values are consistent with the predictions of Levy and Zhang.

Formation of nucleoplasmic protein aggregates impairs nuclear function in response to SiO2 nanoparticles

International Nuclear Information System (INIS)

Chen Min; Mikecz, Anna von

2005-01-01

Despite of their exponentially growing use, little is known about cell biological effects of nanoparticles. Here, we report uptake of silica (SiO 2 ) nanoparticles to the cell nucleus where they induce aberrant clusters of topoisomerase I (topo I) in the nucleoplasm that additionally contain signature proteins of nuclear domains, and protein aggregation such as ubiquitin, proteasomes, cellular glutamine repeat (polyQ) proteins, and huntingtin. Formation of intranuclear protein aggregates (1) inhibits replication, transcription, and cell proliferation; (2) does not significantly alter proteasomal activity or cell viability; and (3) is reversible by Congo red and trehalose. Since SiO 2 nanoparticles trigger a subnuclear pathology resembling the one occurring in expanded polyglutamine neurodegenerative disorders, we suggest that integrity of the functional architecture of the cell nucleus should be used as a read out for cytotoxicity and considered in the development of safe nanotechnology

Human-computer interface incorporating personal and application domains

Science.gov (United States)

Anderson, Thomas G [Albuquerque, NM

2011-03-29

The present invention provides a human-computer interface. The interface includes provision of an application domain, for example corresponding to a three-dimensional application. The user is allowed to navigate and interact with the application domain. The interface also includes a personal domain, offering the user controls and interaction distinct from the application domain. The separation into two domains allows the most suitable interface methods in each: for example, three-dimensional navigation in the application domain, and two- or three-dimensional controls in the personal domain. Transitions between the application domain and the personal domain are under control of the user, and the transition method is substantially independent of the navigation in the application domain. For example, the user can fly through a three-dimensional application domain, and always move to the personal domain by moving a cursor near one extreme of the display.

Non-slipping domains of a pulled spool

International Nuclear Information System (INIS)

Wagner, Clemens; Vaterlaus, Andreas

2014-01-01

We have investigated the pulled spool by considering pulling angles up to 360 ∘ . Our focus was on downward pulling forces with pulling angles in the range of 180 ∘ to 360 ∘ . In this range we have found a domain of pulling angles where the spool never starts to slip independent of the strength of the pulling force. The size of the domain depends on the static friction coefficient and on the moment of inertia of the spool. The non-slipping domain is mainly formed around the critical angle where the static friction force becomes zero. For low static friction the non-slipping domain decays into two different domains. We have determined the limiting angles of the non-slipping domains and explored the transitions from a single domain to two separated domains in parameter space. (paper)

The domain walls of gauged maximal supergravities and their M-theory origin

International Nuclear Information System (INIS)

Bergshoe, Eric; Nielsen, Mikkel; Roest, Diederik

2004-01-01

We consider gauged maximal supergravities with CSO(p,q,r) gauge groups and their relation to the branes of string and M-theory. The gauge groups are characterised by n mass parameters, where n is the transverse dimension of the brane. We give the scalar potentials and construct the corresponding domain wall solutions. In addition, we show the higher-dimensional origin of the domain walls in terms of (distributions of) branes. We put particular emphasis on the CSO(p,q,r) gauged supergravities in D = 9 and D = 8, which are related to the D7-brane and D6-brane, respectively. In these cases, twisted and group manifold reductions are shown to play a crucial role. We also discuss salient features of the corresponding brane distributions. (author)

Image-domain full waveform inversion

KAUST Repository

Zhang, Sanzong

2013-08-20

The main difficulty with the data-domain full waveform inversion (FWI) is that it tends to get stuck in the local minima associated with the waveform misfit function. This is because the waveform misfit function is highly nonlinear with respect to changes in velocity model. To reduce this nonlinearity, we define the image-domain objective function to minimize the difference of the suboffset-domain common image gathers (CIGs) obtained by migrating the observed data and the calculated data. The derivation shows that the gradient of this new objective function is the combination of the gradient of the conventional FWI and the image-domain differential semblance optimization (DSO). Compared to the conventional FWI, the imagedomain FWI is immune to cycle skipping problems by smearing the nonzero suboffset images along wavepath. It also can avoid the edge effects and the gradient artifacts that are inherent in DSO due to the falsely over-penalized focused images. This is achieved by subtracting the focused image associated with the calculated data from the unfocused image associated with the observed data in the image-domain misfit function. The numerical results of the Marmousi model show that image-domain FWI is less sensitive the initial model than the conventional FWI. © 2013 SEG.

Image-domain full waveform inversion

KAUST Repository

Zhang, Sanzong; Schuster, Gerard T.

2013-01-01

The main difficulty with the data-domain full waveform inversion (FWI) is that it tends to get stuck in the local minima associated with the waveform misfit function. This is because the waveform misfit function is highly nonlinear with respect to changes in velocity model. To reduce this nonlinearity, we define the image-domain objective function to minimize the difference of the suboffset-domain common image gathers (CIGs) obtained by migrating the observed data and the calculated data. The derivation shows that the gradient of this new objective function is the combination of the gradient of the conventional FWI and the image-domain differential semblance optimization (DSO). Compared to the conventional FWI, the imagedomain FWI is immune to cycle skipping problems by smearing the nonzero suboffset images along wavepath. It also can avoid the edge effects and the gradient artifacts that are inherent in DSO due to the falsely over-penalized focused images. This is achieved by subtracting the focused image associated with the calculated data from the unfocused image associated with the observed data in the image-domain misfit function. The numerical results of the Marmousi model show that image-domain FWI is less sensitive the initial model than the conventional FWI. © 2013 SEG.

Sub-nuclear distribution and mobility of nuclear proteins involved in histone acetylation and pre-mRNA splicing

International Nuclear Information System (INIS)

Kruhlak, Michael John

2001-01-01

The mitotic relationship between levels of highly acetylated chromatin, chromatin condensation, and HAT/HDAC organization was examined. HATs and HDACs were found to dissociate from chromosomes along with a loss of highly acetylated histones in condensed chromatin in mitosis. We demonstrate that, rather than being enzymatically inactivated, HAT and HDAC activities are decreased in mitosis because the enzymes are sequestered to a non-chromatin domain. Highly acetylated histone species reappear coincident with the reassociation of HATs and HDACs in late telophase/early interphase and before reinitiation of transcription. We propose that HATs and HDACs are spatially regulated through the cell cycle and that this regulation influences which chromatin domains are available for acetylation and deacetylation. We examined the movement of a splicing factor, ASF, green fluorescent fusion protein (ASF:GFP) using timelapse microscopy and the technique fluorescence recovery after photobleaching (FRAP). We found that ASF:GFP moves significantly slower than free diffusion when it is associated with speckles and, surprisingly, also when it is dispersed in the nucleoplasm. The mobility of ASF is consistent with frequent but transient interactions with relatively immobile nuclear binding sites. This mobility is slightly increased in the presence of transcription inhibitors and the ASF molecules further enrich in speckles. We propose that the nonrandom organization of splicing factors reflects spatial differences in the concentration of relatively immobile binding sites. Through a careful analysis of HDAC4 expression we found that HDAC4-containing MAD bodies are not a consistent component of the interphase nucleus. By comparing MAD bodies to PML bodies we found that the assembly, maintenance and distribution of PML bodies is regulated. We investigated the involvement of chromatin condensation in establishing mitotic transcription repression, by analyzing transcriptional activity in

The influence of boundary conditions on domain structure stability in spin wave approximation

International Nuclear Information System (INIS)

Wachinewski, A.

1974-01-01

Instead of the usually used Born-Karman cyclic conditions, boundary conditions which take into account the situation of the boundary lattice sites lying on the crystal's surface are assumed. It is shown that the particular choice of the boundary conditions secures the stability of domain structure in ferromagnet (positive spin wave energies), without including the Winter term in Hamiltonian. (author)

Generic domain models in software engineering

Science.gov (United States)

Maiden, Neil

1992-01-01

This paper outlines three research directions related to domain-specific software development: (1) reuse of generic models for domain-specific software development; (2) empirical evidence to determine these generic models, namely elicitation of mental knowledge schema possessed by expert software developers; and (3) exploitation of generic domain models to assist modelling of specific applications. It focuses on knowledge acquisition for domain-specific software development, with emphasis on tool support for the most important phases of software development.

Interaction Between the Biotin Carboxyl Carrier Domain and the Biotin Carboxylase Domain in Pyruvate Carboxylase from Rhizobium etli†

Science.gov (United States)

Lietzan, Adam D.; Menefee, Ann L.; Zeczycki, Tonya N.; Kumar, Sudhanshu; Attwood, Paul V.; Wallace, John C.; Cleland, W. Wallace; Maurice, Martin St.

2011-01-01

Pyruvate carboxylase (PC) catalyzes the ATP-dependent carboxylation of pyruvate to oxaloacetate, an important anaplerotic reaction in mammalian tissues. To effect catalysis, the tethered biotin of PC must gain access to active sites in both the biotin carboxylase domain and the carboxyl transferase domain. Previous studies have demonstrated that a mutation of threonine 882 to alanine in PC from Rhizobium etli renders the carboxyl transferase domain inactive and favors the positioning of biotin in the biotin carboxylase domain. We report the 2.4 Å resolution X-ray crystal structure of the Rhizobium etli PC T882A mutant which reveals the first high-resolution description of the domain interaction between the biotin carboxyl carrier protein domain and the biotin carboxylase domain. The overall quaternary arrangement of Rhizobium etli PC remains highly asymmetrical and is independent of the presence of allosteric activator. While biotin is observed in the biotin carboxylase domain, its access to the active site is precluded by the interaction between Arg353 and Glu248, revealing a mechanism for regulating carboxybiotin access to the BC domain active site. The binding location for the biotin carboxyl carrier protein domain demonstrates that tethered biotin cannot bind in the biotin carboxylase domain active site in the same orientation as free biotin, helping to explain the difference in catalysis observed between tethered biotin and free biotin substrates in biotin carboxylase enzymes. Electron density located in the biotin carboxylase domain active site is assigned to phosphonoacetate, offering a probable location for the putative carboxyphosphate intermediate formed during biotin carboxylation. The insights gained from the T882A Rhizobium etli PC crystal structure provide a new series of catalytic snapshots in PC and offer a revised perspective on catalysis in the biotin-dependent enzyme family. PMID:21958016

Perceived Interpersonal Discrimination and Older Women’s Mental Health: Accumulation Across Domains, Attributions, and Time

Science.gov (United States)

Bécares, Laia; Zhang, Nan

2018-01-01

Abstract Experiencing discrimination is associated with poor mental health, but how cumulative experiences of perceived interpersonal discrimination across attributes, domains, and time are associated with mental disorders is still unknown. Using data from the Study of Women’s Health Across the Nation (1996–2008), we applied latent class analysis and generalized linear models to estimate the association between cumulative exposure to perceived interpersonal discrimination and older women’s mental health. We found 4 classes of perceived interpersonal discrimination, ranging from cumulative exposure to discrimination over attributes, domains, and time to none or minimal reports of discrimination. Women who experienced cumulative perceived interpersonal discrimination over time and across attributes and domains had the highest risk of depression (Center for Epidemiologic Studies Depression Scale score ≥16) compared with women in all other classes. This was true for all women regardless of race/ethnicity, although the type and severity of perceived discrimination differed across racial/ethnic groups. Cumulative exposure to perceived interpersonal discrimination across attributes, domains, and time has an incremental negative long-term association with mental health. Studies that examine exposure to perceived discrimination due to a single attribute in 1 domain or at 1 point in time underestimate the magnitude and complexity of discrimination and its association with health. PMID:29036550

Using context to improve protein domain identification

Directory of Open Access Journals (Sweden)

Llinás Manuel

2011-03-01

Full Text Available Abstract Background Identifying domains in protein sequences is an important step in protein structural and functional annotation. Existing domain recognition methods typically evaluate each domain prediction independently of the rest. However, the majority of proteins are multidomain, and pairwise domain co-occurrences are highly specific and non-transitive. Results Here, we demonstrate how to exploit domain co-occurrence to boost weak domain predictions that appear in previously observed combinations, while penalizing higher confidence domains if such combinations have never been observed. Our framework, Domain Prediction Using Context (dPUC, incorporates pairwise "context" scores between domains, along with traditional domain scores and thresholds, and improves domain prediction across a variety of organisms from bacteria to protozoa and metazoa. Among the genomes we tested, dPUC is most successful at improving predictions for the poorly-annotated malaria parasite Plasmodium falciparum, for which over 38% of the genome is currently unannotated. Our approach enables high-confidence annotations in this organism and the identification of orthologs to many core machinery proteins conserved in all eukaryotes, including those involved in ribosomal assembly and other RNA processing events, which surprisingly had not been previously known. Conclusions Overall, our results demonstrate that this new context-based approach will provide significant improvements in domain and function prediction, especially for poorly understood genomes for which the need for additional annotations is greatest. Source code for the algorithm is available under a GPL open source license at http://compbio.cs.princeton.edu/dpuc/. Pre-computed results for our test organisms and a web server are also available at that location.

Classical solutions of mixed problems for quasilinear first order PFDEs on a cylindrical domain

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Wojciech Czernous

2014-01-01

Full Text Available We abandon the setting of the domain as a Cartesian product of real intervals, customary for first order PFDEs (partial functional differential equations with initial boundary conditions. We give a new set of conditions on the possibly unbounded domain \\(\\Omega\\ with Lipschitz differentiable boundary. Well-posedness is then reliant on a variant of the normal vector condition. There is a neighbourhood of \\(\\partial\\Omega\\ with the property that if a characteristic trajectory has a point therein, then its every earlier point lies there as well. With local assumptions on coefficients and on the free term, we prove existence and Lipschitz dependence on data of classical solutions on \\((0,c\\times\\Omega\\ to the initial boundary value problem, for small \\(c\\. Regularity of solutions matches this domain, and the proof uses the Banach fixed-point theorem. Our general model of functional dependence covers problems with deviating arguments and integro-differential equations.

A Domain Standard for Land Administration

NARCIS (Netherlands)

Lemmen, C.; Van Oosterom, P.; Van der Molen, P.

2013-01-01

This paper presents the design of a Domain Model for Land Administration (LA). As a result a formal International Standard is available: ISO 19152 Geographic Information – Land Administration Domain Model (LADM) (ISO, 2012). Domain specific standardisation is needed to capture the semantics of the

Teachers’ Professional Development in Context-based Chemistry Education : Strategies to Support Teachers in Developing Domain-specific Expertise

NARCIS (Netherlands)

Dolfing, R.

2013-01-01

The international trend of redesigning science curricula in terms of meaningful context-based programmes, involves a tremendous change in teachers’ practices. The successful implementation of such new curricula requires that teachers develop new domain-specific expertise in teaching innovative

Conservation of the human integrin-type beta-propeller domain in bacteria.

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Bhanupratap Chouhan

Full Text Available Integrins are heterodimeric cell-surface receptors with key functions in cell-cell and cell-matrix adhesion. Integrin α and β subunits are present throughout the metazoans, but it is unclear whether the subunits predate the origin of multicellular organisms. Several component domains have been detected in bacteria, one of which, a specific 7-bladed β-propeller domain, is a unique feature of the integrin α subunits. Here, we describe a structure-derived motif, which incorporates key features of each blade from the X-ray structures of human αIIbβ3 and αVβ3, includes elements of the FG-GAP/Cage and Ca(2+-binding motifs, and is specific only for the metazoan integrin domains. Separately, we searched for the metazoan integrin type β-propeller domains among all available sequences from bacteria and unicellular eukaryotic organisms, which must incorporate seven repeats, corresponding to the seven blades of the β-propeller domain, and so that the newly found structure-derived motif would exist in every repeat. As the result, among 47 available genomes of unicellular eukaryotes we could not find a single instance of seven repeats with the motif. Several sequences contained three repeats, a predicted transmembrane segment, and a short cytoplasmic motif associated with some integrins, but otherwise differ from the metazoan integrin α subunits. Among the available bacterial sequences, we found five examples containing seven sequential metazoan integrin-specific motifs within the seven repeats. The motifs differ in having one Ca(2+-binding site per repeat, whereas metazoan integrins have three or four sites. The bacterial sequences are more conserved in terms of motif conservation and loop length, suggesting that the structure is more regular and compact than those example structures from human integrins. Although the bacterial examples are not full-length integrins, the full-length metazoan-type 7-bladed β-propeller domains are present, and

Memory for serial order across domains: An overview of the literature and directions for future research.

Science.gov (United States)

Hurlstone, Mark J; Hitch, Graham J; Baddeley, Alan D

2014-03-01

From vocabulary learning to imitating sequences of motor actions, the ability to plan, represent, and recall a novel sequence of items in the correct order is fundamental for many verbal and nonverbal higher level cognitive activities. Here we review phenomena of serial order documented across the verbal, visual, and spatial short-term memory domains and interpret them with reference to the principles of serial order and ancillary assumptions instantiated in contemporary computational theories of memory for serial order. We propose that functional similarities across domains buttress the notion that verbal, visual, and spatial sequences are planned and controlled by a competitive queuing (CQ) mechanism in which items are simultaneously active in parallel and the strongest item is chosen for output. Within the verbal short-term memory CQ system, evidence suggests that serial order is represented via a primacy gradient, position marking, response suppression, and cumulative matching. Evidence further indicates that output interference operates during recall and that item similarity effects manifest during both serial order encoding and retrieval. By contrast, the principles underlying the representation of serial order in the visual and spatial CQ systems are unclear, largely because the relevant studies have yet to be performed. In the spatial domain, there is some evidence for a primacy gradient and position marking, whereas in the visual domain there is no direct evidence for either of the principles of serial order. We conclude by proposing some directions for future research designed to bridge this and other theoretical gaps in the literature.

A wearable microwave antenna array for time-domain breast tumor screening

OpenAIRE

Porter, Emily; Bahrami, Hadi; Santorelli, Adam; Gosselin, Benoit; Rusch, Leslie; Popovic, Milica

2016-01-01

In this work, we present a clinical prototype with a wearable patient interface for microwave breast cancer detection. The long-term aim of the prototype is a breast health monitoring application. The system operates using multistatic time-domain pulsed radar, with 16 flexible antennas embedded into a bra. Unlike the previously reported, table-based prototype with a rigid cup-like holder, the wearable one requires no immersion medium and enables simple localization of breast surface. In compa...

Cross-Genome Comparisons of Newly Identified Domains in Mycoplasma gallisepticum and Domain Architectures with Other Mycoplasma species

Directory of Open Access Journals (Sweden)

Chandra Sekhar Reddy Chilamakuri

2011-01-01

Full Text Available Accurate functional annotation of protein sequences is hampered by important factors such as the failure of sequence search methods to identify relationships and the inherent diversity in function of proteins related at low sequence similarities. Earlier, we had employed intermediate sequence search approach to establish new domain relationships in the unassigned regions of gene products at the whole genome level by taking Mycoplasma gallisepticum as a specific example and established new domain relationships. In this paper, we report a detailed comparison of the conservation status of the domain and domain architectures of the gene products that bear our newly predicted domains amongst 14 other Mycoplasma genomes and reported the probable implications for the organisms. Some of the domain associations, observed in Mycoplasma that afflict humans and other non-human primates, are involved in regulation of solute transport and DNA binding suggesting specific modes of host-pathogen interactions.

When Do Adolescents Accept or Defy to Maternal Prohibitions? The Role of Social Domain and Communication Style.

Science.gov (United States)

Van Petegem, Stijn; Vansteenkiste, Maarten; Soenens, Bart; Zimmermann, Grégoire; Antonietti, Jean-Philippe; Baudat, Sophie; Audenaert, Elien

2017-05-01

Drawing upon both Social-Cognitive Domain Theory and Self-Determination Theory, the goal of the present multi-informant study was to test whether the correlates of maternal prohibitions depend on what is prohibited (i.e., the content of the social domain involved), thereby contrasting moral with friendship prohibitions, as well on how the prohibition is communicated, thereby contrasting an autonomy-supportive with a controlling communication style. In a sample of adolescents (N = 196; mean age = 13.9 years; 63 % female) and their mothers (N = 185; mean age = 44 years), we first examined mean-level differences between the two domains in terms of mothers' degree and style of prohibition, as well as on a number of developmental outcomes (i.e., adolescents' legitimacy perceptions, internalization, and oppositional defiance). Both adolescents and mothers reported more maternal involvement in the moral domain (e.g., higher scores for degree of prohibition and controlling communication style). In addition, adolescents reported greater perceived legitimacy and less oppositional defiance in the moral domain (as compared to the friendships domain). Second, we tested whether associations between degree and style of prohibition and the developmental outcomes were moderated by social domain. Whereas associations between degree of prohibition and developmental outcomes either were non-significant or moderated by domain, the associations with communication style were more domain-invariant, with an autonomy-supportive style generally yielding an adaptive pattern of correlates and with a controlling style relating to maladaptive outcomes. The discussion focuses on similarities and differences in the characteristics and correlates of both types of prohibitions.

Domain-General Factors Influencing Numerical and Arithmetic Processing

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André Knops

2017-12-01

Full Text Available This special issue contains 18 articles that address the question how numerical processes interact with domain-general factors. We start the editorial with a discussion of how to define domain-general versus domain-specific factors and then discuss the contributions to this special issue grouped into two core numerical domains that are subject to domain-general influences (see Figure 1. The first group of contributions addresses the question how numbers interact with spatial factors. The second group of contributions is concerned with factors that determine and predict arithmetic understanding, performance and development. This special issue shows that domain-general (Table 1a as well as domain-specific (Table 1b abilities influence numerical and arithmetic performance virtually at all levels and make it clear that for the field of numerical cognition a sole focus on one or several domain-specific factors like the approximate number system or spatial-numerical associations is not sufficient. Vice versa, in most studies that included domain-general and domain-specific variables, domain-specific numerical variables predicted arithmetic performance above and beyond domain-general variables. Therefore, a sole focus on domain-general aspects such as, for example, working memory, to explain, predict and foster arithmetic learning is also not sufficient. Based on the articles in this special issue we conclude that both domain-general and domain-specific factors contribute to numerical cognition. But the how, why and when of their contribution still needs to be better understood. We hope that this special issue may be helpful to readers in constraining future theory and model building about the interplay of domain-specific and domain-general factors.

Novel Burst Suppression Segmentation in the Joint Time-Frequency Domain for EEG in Treatment of Status Epilepticus

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Jaeyun Lee

2016-01-01

Full Text Available We developed a method to distinguish bursts and suppressions for EEG burst suppression from the treatments of status epilepticus, employing the joint time-frequency domain. We obtained the feature used in the proposed method from the joint use of the time and frequency domains, and we estimated the decision as to whether the measured EEG was a burst segment or suppression segment by the maximum likelihood estimation. We evaluated the performance of the proposed method in terms of its accordance with the visual scores and estimation of the burst suppression ratio. The accuracy was higher than the sole use of the time or frequency domains, as well as conventional methods conducted in the time domain. In addition, probabilistic modeling provided a more simplified optimization than conventional methods. Burst suppression quantification necessitated precise burst suppression segmentation with an easy optimization; therefore, the excellent discrimination and the easy optimization of burst suppression by the proposed method appear to be beneficial.

Policy legitimacy - The key to long term Management of Radioactive Waste

International Nuclear Information System (INIS)

Atherton, E.; Dalton, J.; Wild, D.

2003-01-01

Experience in the UK has shown that the central theme of delivering a solution is contingent on building a broad base of support for the long term management project. This is multi-layered, both in terms of local, regional and national political actors, but also across societal groups. Legitimacy is the key to success and needs to be understood in three main domains - equity, competence and economics. Finding the appropriate balance is essential for progress in the long term. (authors)

Source terms for analysis of accidents at a high level waste repository

International Nuclear Information System (INIS)

Mubayi, V.; Davis, R.E.; Youngblood, R.

1989-01-01

This paper describes an approach to identifying source terms from possible accidents during the preclosure phase of a high-level nuclear waste repository. A review of the literature on repository safety analyses indicated that source term estimation is in a preliminary stage, largely based on judgement-based scoping analyses. The approach developed here was to partition the accident space into domains defined by certain threshold values of temperature and impact energy density which may arise in potential accidents and specify release fractions of various radionuclides, present in the waste form, in each domain. Along with a more quantitative understanding of accident phenomenology, this approach should help in achieving a clearer perspective on scenarios important to preclosure safety assessments of geologic repositories. 18 refs., 3 tabs

Global existence of solutions for semilinear damped wave equation in 2-D exterior domain

Science.gov (United States)

Ikehata, Ryo

We consider a mixed problem of a damped wave equation utt-Δ u+ ut=| u| p in the two dimensional exterior domain case. Small global in time solutions can be constructed in the case when the power p on the nonlinear term | u| p satisfies p ∗=2Japon. 55 (2002) 33) plays an effective role.

Structure of neutron stars

International Nuclear Information System (INIS)

Cheong, C.K.

1974-01-01

Structure of neutron stars consisting of a cold and catalyzed superdense matter were investigated by integrating the equations for hydrostatic equilibrium based on the General Relativity theory. The equations of state were obtained with the help of semiempirical nuclear mass formulae. A large phase transition was found between the nuclear and subnuclear density regions. The density phase transition points were calculated as 6.2 x 10 11 and 3.8 x 10 13 g/cm 3 . Due to such a large phase transition, the equation of state practically consists of two parts: The nuclear and subnuclear phases wich are in contact under the thermodynamical equilibrium at the corresponding pressure. Some macroscopic properties of neutron stars are discussed. (Author) [pt

The X chromosome in space.

Science.gov (United States)

Jégu, Teddy; Aeby, Eric; Lee, Jeannie T

2017-06-01

Extensive 3D folding is required to package a genome into the tiny nuclear space, and this packaging must be compatible with proper gene expression. Thus, in the well-hierarchized nucleus, chromosomes occupy discrete territories and adopt specific 3D organizational structures that facilitate interactions between regulatory elements for gene expression. The mammalian X chromosome exemplifies this structure-function relationship. Recent studies have shown that, upon X-chromosome inactivation, active and inactive X chromosomes localize to different subnuclear positions and adopt distinct chromosomal architectures that reflect their activity states. Here, we review the roles of long non-coding RNAs, chromosomal organizational structures and the subnuclear localization of chromosomes as they relate to X-linked gene expression.

In vitro guanine nucleotide exchange activity of DHR-2/DOCKER/CZH2 domains.

Science.gov (United States)

Côté, Jean-François; Vuori, Kristiina

2006-01-01

Rho family GTPases regulate a large variety of biological processes, including the reorganization of the actin cytoskeleton. Like other members of the Ras superfamily of small GTP-binding proteins, Rho GTPases cycle between a GDP-bound (inactive) and a GTP-bound (active) state, and, when active, the GTPases relay extracellular signals to a large number of downstream effectors. Guanine nucleotide exchange factors (GEFs) promote the exchange of GDP for GTP on Rho GTPases, thereby activating them. Most Rho-GEFs mediate their effects through their signature domain known as the Dbl Homology-Pleckstrin Homology (DH-PH) module. Recently, we and others identified a family of evolutionarily conserved, DOCK180-related proteins that also display GEF activity toward Rho GTPases. The DOCK180-family of proteins lacks the canonical DH-PH module. Instead, they rely on a novel domain, termed DHR-2, DOCKER, or CZH2, to exchange GDP for GTP on Rho targets. In this chapter, the experimental approach that we used to uncover the exchange activity of the DHR-2 domain of DOCK180-related proteins will be described.

Distractibility during Retrieval of Long-Term Memory: Domain-General Interference, Neural Networks and Increased Susceptibility in Normal Aging

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Peter Edward Wais

2014-04-01

Full Text Available The mere presence of irrelevant external stimuli results in interference with the fidelity of details retrieved from long-term memory (LTM. Recent studies suggest that distractibility during LTM retrieval occurs when the focus of resource-limited, top-down mechanisms that guide the selection of relevant mnemonic details is disrupted by representations of external distractors. We review findings from four studies that reveal distractibility during episodic retrieval. The approach cued participants to recall previously studied visual details when their eyes were closed, or were open and irrelevant visual information was present. The results showed a negative impact of the distractors on the fidelity of details retrieved from LTM. An fMRI experiment using the same paradigm replicated the behavioral results and found that diminished episodic memory was associated with the disruption of functional connectivity in whole-brain networks. Specifically, network connectivity supported recollection of details based on visual imagery when eyes were closed, but connectivity declined in the presence of visual distractors. Another experiment using auditory distractors found equivalent effects for auditory and visual distraction during cued recall, suggesting that the negative impact of distractibility is a domain-general phenomenon in LTM. Comparisons between older and younger adults revealed an aging-related increase in the negative impact of distractibility on retrieval of LTM. Finally, a new study that compared categorization abilities between younger and older adults suggests a cause underlying age-related decline of visual details in LTM. The sum of our findings suggests that cognitive control resources, although limited, have the capability to resolve interference from distractors during tasks of moderate effort, but these resources are overwhelmed when additional processes associated with episodic retrieval, or categorization of complex prototypes, are

Evolution of Parallel Spindles Like genes in plants and highlight of unique domain architecture#

Directory of Open Access Journals (Sweden)

Consiglio Federica M

2011-03-01

Full Text Available Abstract Background Polyploidy has long been recognized as playing an important role in plant evolution. In flowering plants, the major route of polyploidization is suggested to be sexual through gametes with somatic chromosome number (2n. Parallel Spindle1 gene in Arabidopsis thaliana (AtPS1 was recently demonstrated to control spindle orientation in the 2nd division of meiosis and, when mutated, to induce 2n pollen. Interestingly, AtPS1 encodes a protein with a FHA domain and PINc domain putatively involved in RNA decay (i.e. Nonsense Mediated mRNA Decay. In potato, 2n pollen depending on parallel spindles was described long time ago but the responsible gene has never been isolated. The knowledge derived from AtPS1 as well as the availability of genome sequences makes it possible to isolate potato PSLike (PSL and to highlight the evolution of PSL family in plants. Results Our work leading to the first characterization of PSLs in potato showed a greater PSL complexity in this species respect to Arabidopsis thaliana. Indeed, a genomic PSL locus and seven cDNAs affected by alternative splicing have been cloned. In addition, the occurrence of at least two other PSL loci in potato was suggested by the sequence comparison of alternatively spliced transcripts. Phylogenetic analysis on 20 Viridaeplantae showed the wide distribution of PSLs throughout the species and the occurrence of multiple copies only in potato and soybean. The analysis of PSLFHA and PSLPINc domains evidenced that, in terms of secondary structure, a major degree of variability occurred in PINc domain respect to FHA. In terms of specific active sites, both domains showed diversification among plant species that could be related to a functional diversification among PSL genes. In addition, some specific active sites were strongly conserved among plants as supported by sequence alignment and by evidence of negative selection evaluated as difference between non-synonymous and

Compensating for Incomplete Domain Knowledge

National Research Council Canada - National Science Library

Scott, Lynn M; Drezner, Steve; Rue, Rachel; Reyes, Jesse

2007-01-01

.... First, many senior leader positions require experience in more than one functional or operational domain, but it is difficult to develop a corps of senior leaders with all the required combinations of domain knowledge...

Long-term Associations Between Physical Frailty and Performance in Specific Cognitive Domains.

Science.gov (United States)

Bunce, David; Batterham, Philip J; Mackinnon, Andrew J

2018-02-01

No longitudinal epidemiological research has reported associations between physical frailty and performance in specific cognitive domains. Our aim was to investigate whether such associations existed in the absence of accompanying neurodegenerative disorders such as mild cognitive impairment (MCI) and dementia. We addressed this issue in a population-based sample of 896 adults aged 70 years and older over 4 waves of data covering a 12-year period. Physical frailty was assessed and a cognitive battery included measures of processing speed, verbal fluency, face and word recognition, episodic memory and simple and choice reaction time (RT). Latent growth models showed frailty was associated with poorer baseline performance in processing speed, verbal fluency, simple and choice RT, and choice intraindividual RT variability. However, no significant effects of frailty on slopes of cognition were observed, suggesting that frailty was not associated with cognitive decline. Importantly, when the models took possible dementia into account, significant effects were retained suggesting that differences were not associated with dementia-related neurodegenerative disorders. The findings suggest that frailty-related cognitive deficits may exist independently of mechanisms underpinning neurodegenerative disorders such as MCI and dementia. If confirmed, this finding suggests a new avenue for preventative and therapeutic interventions in clinical and public health contexts for older adults. © The Author(s) 2018. Published by Oxford University Press on behalf of The Gerontological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Heliborne time domain electromagnetic system

International Nuclear Information System (INIS)

Bhattacharya, S.

2009-01-01

Atomic Minerals Directorate (AMD), are using heliborne and ground time domain electromagnetic (TDEM) system for the exploration of deep seated unconformity type uranium deposits. Uranium has been explored in various parts of the world like Athabasca basin using time domain electromagnetic system. AMD has identified some areas in India where such deposits are available. Apart from uranium exploration, the TDEM systems are used for the exploration of deep seated minerals like diamonds. Bhabha Atomic Research Centre (BARC) is involved in the indigenous design of the heliborne time domain system since this system is useful for DAE and also it has a scope of wide application. In this paper we discuss about the principle of time domain electromagnetic systems, their capabilities and the development and problems of such system for various other mineral exploration. (author)

Evolutionary dynamics of protein domain architecture in plants

Directory of Open Access Journals (Sweden)

Zhang Xue-Cheng

2012-01-01

Full Text Available Abstract Background Protein domains are the structural, functional and evolutionary units of the protein. Protein domain architectures are the linear arrangements of domain(s in individual proteins. Although the evolutionary history of protein domain architecture has been extensively studied in microorganisms, the evolutionary dynamics of domain architecture in the plant kingdom remains largely undefined. To address this question, we analyzed the lineage-based protein domain architecture content in 14 completed green plant genomes. Results Our analyses show that all 14 plant genomes maintain similar distributions of species-specific, single-domain, and multi-domain architectures. Approximately 65% of plant domain architectures are universally present in all plant lineages, while the remaining architectures are lineage-specific. Clear examples are seen of both the loss and gain of specific protein architectures in higher plants. There has been a dynamic, lineage-wise expansion of domain architectures during plant evolution. The data suggest that this expansion can be largely explained by changes in nuclear ploidy resulting from rounds of whole genome duplications. Indeed, there has been a decrease in the number of unique domain architectures when the genomes were normalized into a presumed ancestral genome that has not undergone whole genome duplications. Conclusions Our data show the conservation of universal domain architectures in all available plant genomes, indicating the presence of an evolutionarily conserved, core set of protein components. However, the occurrence of lineage-specific domain architectures indicates that domain architecture diversity has been maintained beyond these core components in plant genomes. Although several features of genome-wide domain architecture content are conserved in plants, the data clearly demonstrate lineage-wise, progressive changes and expansions of individual protein domain architectures, reinforcing

Mesoscale organization of domains in the plasma membrane - beyond the lipid raft.

Science.gov (United States)

Lu, Stella M; Fairn, Gregory D

2018-04-01

The plasma membrane is compartmentalized into several distinct regions or domains, which show a broad diversity in both size and lifetime. The segregation of lipids and membrane proteins is thought to be driven by the lipid composition itself, lipid-protein interactions and diffusional barriers. With regards to the lipid composition, the immiscibility of certain classes of lipids underlies the "lipid raft" concept of plasmalemmal compartmentalization. Historically, lipid rafts have been described as cholesterol and (glyco)sphingolipid-rich regions of the plasma membrane that exist as a liquid-ordered phase that are resistant to extraction with non-ionic detergents. Over the years the interest in lipid rafts grew as did the challenges with studying these nanodomains. The term lipid raft has fallen out of favor with many scientists and instead the terms "membrane raft" or "membrane nanodomain" are preferred as they connote the heterogeneity and dynamic nature of the lipid-protein assemblies. In this article, we will discuss the classical lipid raft hypothesis and its limitations. This review will also discuss alternative models of lipid-protein interactions, annular lipid shells, and larger membrane clusters. We will also discuss the mesoscale organization of plasmalemmal domains including visible structures such as clathrin-coated pits and caveolae.

On Domain Registries and Website Content

DEFF Research Database (Denmark)

Schwemer, Sebastian Felix

2018-01-01

such as Internet access service providers, hosting platforms, and websites that link to content. This article shows that in recent years, however, that the (secondary) liability of domain registries and registrars, and more specifically country code top-level domain registries (ccTLDs) for website content, has...... been tested in several EU Member States. The article investigates tendencies in the national lower-court jurisprudence and explores to what extent the liability exemption regime of the E-Commerce Directive applies to domain registries. The analysis concludes that whereas domain registries fall under...

Entropy based classifier for cross-domain opinion mining

Directory of Open Access Journals (Sweden)

Jyoti S. Deshmukh

2018-01-01

Full Text Available In recent years, the growth of social network has increased the interest of people in analyzing reviews and opinions for products before they buy them. Consequently, this has given rise to the domain adaptation as a prominent area of research in sentiment analysis. A classifier trained from one domain often gives poor results on data from another domain. Expression of sentiment is different in every domain. The labeling cost of each domain separately is very high as well as time consuming. Therefore, this study has proposed an approach that extracts and classifies opinion words from one domain called source domain and predicts opinion words of another domain called target domain using a semi-supervised approach, which combines modified maximum entropy and bipartite graph clustering. A comparison of opinion classification on reviews on four different product domains is presented. The results demonstrate that the proposed method performs relatively well in comparison to the other methods. Comparison of SentiWordNet of domain-specific and domain-independent words reveals that on an average 72.6% and 88.4% words, respectively, are correctly classified.

Trusted Domain

DEFF Research Database (Denmark)

Hjorth, Theis Solberg; Torbensen, Rune

2012-01-01

remote access via IP-based devices such as smartphones. The Trusted Domain platform fits existing legacy technologies by managing their interoperability and access controls, and it seeks to avoid the security issues of relying on third-party servers outside the home. It is a distributed system...... of wireless standards, limited resources of embedded systems, etc. Taking these challenges into account, we present a Trusted Domain home automation platform, which dynamically and securely connects heterogeneous networks of Short-Range Wireless devices via simple non-expert user. interactions, and allows......In the digital age of home automation and with the proliferation of mobile Internet access, the intelligent home and its devices should be accessible at any time from anywhere. There are many challenges such as security, privacy, ease of configuration, incompatible legacy devices, a wealth...

Database Concepts in a Domain Ontology

Directory of Open Access Journals (Sweden)

Gorskis Henrihs

2017-12-01

Full Text Available There are multiple approaches for mapping from a domain ontology to a database in the task of ontology-based data access. For that purpose, external mapping documents are most commonly used. These documents describe how the data necessary for the description of ontology individuals and other values, are to be obtained from the database. The present paper investigates the use of special database concepts. These concepts are not separated from the domain ontology; they are mixed with domain concepts to form a combined application ontology. By creating natural relationships between database concepts and domain concepts, mapping can be implemented more easily and with a specific purpose. The paper also investigates how the use of such database concepts in addition to domain concepts impacts ontology building and data retrieval.

Separating Cognitive and Content Domains in Mathematical Competence

Science.gov (United States)

Harks, Birgit; Klieme, Eckhard; Hartig, Johannes; Leiss, Dominik

2014-01-01

The present study investigates the empirical separability of mathematical (a) content domains, (b) cognitive domains, and (c) content-specific cognitive domains. There were 122 items representing two content domains (linear equations vs. theorem of Pythagoras) combined with two cognitive domains (modeling competence vs. technical competence)…

Domains and naïve theories.

Science.gov (United States)

Gelman, Susan A; Noles, Nicholaus S

2011-09-01

Human cognition entails domain-specific cognitive processes that influence memory, attention, categorization, problem-solving, reasoning, and knowledge organization. This article examines domain-specific causal theories, which are of particular interest for permitting an examination of how knowledge structures change over time. We first describe the properties of commonsense theories, and how commonsense theories differ from scientific theories, illustrating with children's classification of biological and nonbiological kinds. We next consider the implications of domain-specificity for broader issues regarding cognitive development and conceptual change. We then examine the extent to which domain-specific theories interact, and how people reconcile competing causal frameworks. Future directions for research include examining how different content domains interact, the nature of theory change, the role of context (including culture, language, and social interaction) in inducing different frameworks, and the neural bases for domain-specific reasoning. WIREs Cogni Sci 2011 2 490-502 DOI: 10.1002/wcs.124 This article is categorized under: Psychology > Reasoning and Decision Making. Copyright © 2010 John Wiley & Sons, Ltd.

Hydrophobic interaction between the SH2 domain and the kinase domain is required for the activation of Csk.

Science.gov (United States)

Mikkola, Esa T; Gahmberg, Carl G

2010-06-18

The protein tyrosine kinase C-terminal Src kinase (Csk) is activated by the engagement of its Src homology (SH) 2 domain. However, the molecular mechanism required for this is not completely understood. The crystal structure of the active Csk indicates that Csk could be activated by contact between the SH2 domain and the beta3-alphaC loop in the N-terminal lobe of the kinase domain. To study the importance of this interaction for the SH2-domain-mediated activation of Csk, we mutated the amino acid residues forming the contacts between the SH2 domain and the beta3-alphaC loop. The mutation of the beta3-alphaC loop Ala228 to glycine and of the SH2 domain Tyr116, Tyr133, Leu138, and Leu149 to alanine resulted in the inability of the SH2 domain ligand to activate Csk. Furthermore, the overexpressed Csk mutants A228G, Y133A/Y116A, L138A, and L149A were unable to efficiently inactivate endogenous Src in human embryonic kidney 293 cells. The results suggest that the SH2-domain-mediated activation of Csk is dependent on the binding of the beta3-alphaC loop Ala228 to the hydrophobic pocket formed by the side chains of Tyr116, Tyr133, Leu138, and Leu149 on the surface of the SH2 domain. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

Domain Discretization and Circle Packings

DEFF Research Database (Denmark)

Dias, Kealey

A circle packing is a configuration of circles which are tangent with one another in a prescribed pattern determined by a combinatorial triangulation, where the configuration fills a planar domain or a two-dimensional surface. The vertices in the triangulation correspond to centers of circles...... to domain discretization problems such as triangulation and unstructured mesh generation techniques. We wish to ask ourselves the question: given a cloud of points in the plane (we restrict ourselves to planar domains), is it possible to construct a circle packing preserving the positions of the vertices...... and constrained meshes having predefined vertices as constraints. A standard method of two-dimensional mesh generation involves conformal mapping of the surface or domain to standardized shapes, such as a disk. Since circle packing is a new technique for constructing discrete conformal mappings, it is possible...

FY1995 ultrafast photonic devices using dielectric domain superlattice; 1995 nendo yudentai domain chokoshi wo mochiita chokosoku photonic device

Energy Technology Data Exchange (ETDEWEB)

NONE

1997-03-31

All optical wavelength conversion around 1550nm is of great importance for the wavelength division multiplexing optical communication system. A dielectric domain superlattice, which has a periodically domain inverted structure, has a wide potential for the various nonlinear interactions such as second harmonic generation (SHG) and difference frequency generation (DFG). The purpose of our research is to establish the theoretical bases and fabrication processes of the guided-wave wavelength converter based on the DFG by domain-inverted LiTaO{sub 3}. We have investigated basic characteristics of guided-wave DFG devices and developed the domain-inversion process by an electric field poling utilizing a liquid electrolyte consisting of LiCI in deionized water as a electrode for applying the electric field to LiTaO{sub 3} substrate. By controlling the injection current for the domain inversion precisely, we fabricated successfully uniform domain-inverted structures. 0.5mm-thick domain-inverted LiTaO{sub 3} of 7.8, 17.2 and 21.3 {mu}m periods and 0.5 duty ratio were obtained by optimizing electrode structure and the domain-inversion process. Waveguide structures can increase the conversion efficiency of DFG by several orders of magnitude over bulk interactions. We have also developed waveguide fabrication process for the domain-inverted LiTaO{sub 3} substrate. Low loss proton-exchanged waveguides were formed by annealed proton exchange technique without a degradation of the domain inversion structure. Domain-controlled nonlinear optics by designing the ferroelectric domain structure of LiTaO{sub 3} and LiNbO{sub 3} make it possible to extend all the spectral range from ultra-violet to far-infrared and THz wave region. (NEDO)

Mechanistic insights into phosphoprotein-binding FHA domains.

Science.gov (United States)

Liang, Xiangyang; Van Doren, Steven R

2008-08-01

[Structure: see text]. FHA domains are protein modules that switch signals in diverse biological pathways by monitoring the phosphorylation of threonine residues of target proteins. As part of the effort to gain insight into cellular avoidance of cancer, FHA domains involved in the cellular response to DNA damage have been especially well-characterized. The complete protein where the FHA domain resides and the interaction partners determine the nature of the signaling. Thus, a key biochemical question is how do FHA domains pick out their partners from among thousands of alternatives in the cell? This Account discusses the structure, affinity, and specificity of FHA domains and the formation of their functional structure. Although FHA domains share sequence identity at only five loop residues, they all fold into a beta-sandwich of two beta-sheets. The conserved arginine and serine of the recognition loops recognize the phosphorylation of the threonine targeted. Side chains emanating from loops that join beta-strand 4 with 5, 6 with 7, or 10 with 11 make specific contacts with amino acids of the ligand that tailor sequence preferences. Many FHA domains choose a partner in extended conformation, somewhat according to the residue three after the phosphothreonine in sequence (pT + 3 position). One group of FHA domains chooses a short carboxylate-containing side chain at pT + 3. Another group chooses a long, branched aliphatic side chain. A third group prefers other hydrophobic or uncharged polar side chains at pT + 3. However, another FHA domain instead chooses on the basis of pT - 2, pT - 3, and pT + 1 positions. An FHA domain from a marker of human cancer instead chooses a much longer protein fragment that adds a beta-strand to its beta-sheet and that presents hydrophobic residues from a novel helix to the usual recognition surface. This novel recognition site and more remote sites for the binding of other types of protein partners were predicted for the entire family

Classification of domains of closed operators

International Nuclear Information System (INIS)

Lassner, G.; Timmermann, W.

1975-01-01

The structure of domains of determining closed operators in the Hilbert space by means of sequence spaces is investigated. The final classification provides three classes of these domains. Necessary and sufficient conditions of equivalence of these domains are obtained in the form of equivalency of corresponding sequences of natural numbers. Connection with the perturbation theory is mentioned [ru

The dynamics of the asymmetric motion of domain walls of sandwich domain structure in a Fe-based amorphous ribbon

Energy Technology Data Exchange (ETDEWEB)

Zhmetko, D.N., E-mail: sergey.zhmetko@gmail.com [Department of Physics, Zaporizhzhya National University, 66 Zhukovsky Street, 69063 Zaporizhzhya (Ukraine); Zhmetko, S.D. [Department of Physics, Zaporizhzhya National University, 66 Zhukovsky Street, 69063 Zaporizhzhya (Ukraine); Troschenkov, Y.N. [Institute for Magnetism, 36-b Vernadsky Boulevard, 03142 Kyiv (Ukraine); Matsura, A.V. [Department of Physics, Zaporizhzhya National University, 66 Zhukovsky Street, 69063 Zaporizhzhya (Ukraine)

2013-08-15

The frequency dependence of asymmetry of the domain walls velocity relative to the middle plane of amorphous ribbon is investigated. An additional pressure of the same direction acting on each domain wall caused by dependence of eddy current damping on the coordinate of the domain wall is revealed. The microscopic mechanisms of this additional pressure are considered. - Highlights: ► Additional pressure on the domain wall, caused by inhomogeneity of its damping. ► Asymmetry of the coordinate of the nucleation of domain walls and their damping. ► Connection between the components of additional pressure and its direction. ► Interaction of domain walls with the surface defects of the amorphous ribbon.

The dynamics of the asymmetric motion of domain walls of sandwich domain structure in a Fe-based amorphous ribbon

International Nuclear Information System (INIS)

Zhmetko, D.N.; Zhmetko, S.D.; Troschenkov, Y.N.; Matsura, A.V.

2013-01-01

The frequency dependence of asymmetry of the domain walls velocity relative to the middle plane of amorphous ribbon is investigated. An additional pressure of the same direction acting on each domain wall caused by dependence of eddy current damping on the coordinate of the domain wall is revealed. The microscopic mechanisms of this additional pressure are considered. - Highlights: ► Additional pressure on the domain wall, caused by inhomogeneity of its damping. ► Asymmetry of the coordinate of the nucleation of domain walls and their damping. ► Connection between the components of additional pressure and its direction. ► Interaction of domain walls with the surface defects of the amorphous ribbon

N-Terminal Domains in Two-Domain Proteins Are Biased to Be Shorter and Predicted to Fold Faster Than Their C-Terminal Counterparts

Directory of Open Access Journals (Sweden)

Etai Jacob

2013-04-01

Full Text Available Computational analysis of proteomes in all kingdoms of life reveals a strong tendency for N-terminal domains in two-domain proteins to have shorter sequences than their neighboring C-terminal domains. Given that folding rates are affected by chain length, we asked whether the tendency for N-terminal domains to be shorter than their neighboring C-terminal domains reflects selection for faster-folding N-terminal domains. Calculations of absolute contact order, another predictor of folding rate, provide additional evidence that N-terminal domains tend to fold faster than their neighboring C-terminal domains. A possible explanation for this bias, which is more pronounced in prokaryotes than in eukaryotes, is that faster folding of N-terminal domains reduces the risk for protein aggregation during folding by preventing formation of nonnative interdomain interactions. This explanation is supported by our finding that two-domain proteins with a shorter N-terminal domain are much more abundant than those with a shorter C-terminal domain.

Selective Targeting of SH2 Domain-Phosphotyrosine Interactions of Src Family Tyrosine Kinases with Monobodies.

Science.gov (United States)

Kükenshöner, Tim; Schmit, Nadine Eliane; Bouda, Emilie; Sha, Fern; Pojer, Florence; Koide, Akiko; Seeliger, Markus; Koide, Shohei; Hantschel, Oliver

2017-05-05

The binding of Src-homology 2 (SH2) domains to phosphotyrosine (pY) sites is critical for the autoinhibition and substrate recognition of the eight Src family kinases (SFKs). The high sequence conservation of the 120 human SH2 domains poses a significant challenge to selectively perturb the interactions of even the SFK SH2 family against the rest of the SH2 domains. We have developed synthetic binding proteins, termed monobodies, for six of the SFK SH2 domains with nanomolar affinity. Most of these monobodies competed with pY ligand binding and showed strong selectivity for either the SrcA (Yes, Src, Fyn, Fgr) or SrcB subgroup (Lck, Lyn, Blk, Hck). Interactome analysis of intracellularly expressed monobodies revealed that they bind SFKs but no other SH2-containing proteins. Three crystal structures of monobody-SH2 complexes unveiled different and only partly overlapping binding modes, which rationalized the observed selectivity and enabled structure-based mutagenesis to modulate inhibition mode and selectivity. In line with the critical roles of SFK SH2 domains in kinase autoinhibition and T-cell receptor signaling, monobodies binding the Src and Hck SH2 domains selectively activated respective recombinant kinases, whereas an Lck SH2-binding monobody inhibited proximal signaling events downstream of the T-cell receptor complex. Our results show that SFK SH2 domains can be targeted with unprecedented potency and selectivity using monobodies. They are excellent tools for dissecting SFK functions in normal development and signaling and to interfere with aberrant SFK signaling networks in cancer cells. Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.

PML-associated repressor of transcription (PAROT), a novel KRAB-zinc finger repressor, is regulated through association with PML nuclear bodies

International Nuclear Information System (INIS)

Fleischer, Sandra; Wiemann, Stefan; Will, Hans; Hofmann, Thomas G.

2006-01-01

Promyelocytic leukemia nuclear bodies (PML-NBs) are implicated in transcriptional regulation. Here we identify a novel transcriptional repressor, PML-associated repressor of transcription (PAROT), which is regulated in its repressor activity through recruitment to PML-NBs. PAROT is a Krueppel-associated box ( KRAB) zinc-finger (ZNF) protein, which comprises an amino terminal KRAB-A and KRAB-B box, a linker domain and 8 tandemly repeated C 2 H 2 -ZNF motifs at its carboxy terminus. Consistent with its domain structure, when tethered to DNA, PAROT represses transcription, and this is partially released by the HDAC inhibitor trichostatin A. PAROT colocalizes with members of the heterochromatin protein 1 (HP1) family and with transcriptional intermediary factor-1β/KRAB-associated protein 1 (TIF-1β/KAP1), a transcriptional corepressor for the KRAB-ZNF family. Interestingly, PML isoform IV, in contrast to PML-III, efficiently recruits PAROT and TIF-1β from heterochromatin to PML-NBs. PML-NB recruitment of PAROT partially releases its transcriptional repressor activity, indicating that PAROT can be regulated through subnuclear compartmentalization. Taken together, our data identify a novel transcriptional repressor and provide evidence for its regulation through association with PML-NBs

Layered and Laterally Constrained 2D Inversion of Time Domain Induced Polarization Data

DEFF Research Database (Denmark)

Fiandaca, Gianluca; Ramm, James; Auken, Esben

description of the transmitter waveform and of the receiver transfer function allowing for a quantitative interpretation of the parameters. The code has been optimized for parallel computation and the inversion time is comparable to codes inverting just for direct current resistivity. The new inversion......In a sedimentary environment, quasi-layered models often represent the actual geology more accurately than smooth minimum-structure models. We have developed a new layered and laterally constrained inversion algorithm for time domain induced polarization data. The algorithm is based on the time...... transform of a complex resistivity forward response and the inversion extracts the spectral information of the time domain measures in terms of the Cole-Cole parameters. The developed forward code and inversion algorithm use the full time decay of the induced polarization response, together with an accurate...

Differences between time domain and Fourier domain optical coherence tomography in imaging tissues.

Science.gov (United States)

Gao, W; Wu, X

2017-11-01

It has been numerously demonstrated that both time domain and Fourier domain optical coherence tomography (OCT) can generate high-resolution depth-resolved images of living tissues and cells. In this work, we compare the common points and differences between two methods when the continuous and random properties of live tissue are taken into account. It is found that when relationships that exist between the scattered light and tissue structures are taken into account, spectral interference measurements in Fourier domain OCT (FDOCT) is more advantageous than interference fringe envelope measurements in time domain OCT (TDOCT) in the cases where continuous property of tissue is taken into account. It is also demonstrated that when random property of tissue is taken into account FDOCT measures the Fourier transform of the spatial correlation function of the refractive index and speckle phenomena will limit the effective limiting imaging resolution in both TDOCT and FDOCT. Finally, the effective limiting resolution of both TDOCT and FDOCT are given which can be used to estimate the effective limiting resolution in various practical applications. © 2017 The Authors Journal of Microscopy © 2017 Royal Microscopical Society.

Cooperative interactions between paired domain and homeodomain.

Science.gov (United States)

Jun, S; Desplan, C

1996-09-01

The Pax proteins are a family of transcriptional regulators involved in many developmental processes in all higher eukaryotes. They are characterized by the presence of a paired domain (PD), a bipartite DNA binding domain composed of two helix-turn-helix (HTH) motifs,the PAI and RED domains. The PD is also often associated with a homeodomain (HD) which is itself able to form homo- and hetero-dimers on DNA. Many of these proteins therefore contain three HTH motifs each able to recognize DNA. However, all PDs recognize highly related DNA sequences, and most HDs also recognize almost identical sites. We show here that different Pax proteins use multiple combinations of their HTHs to recognize several types of target sites. For instance, the Drosophila Paired protein can bind, in vitro, exclusively through its PAI domain, or through a dimer of its HD, or through cooperative interaction between PAI domain and HD. However, prd function in vivo requires the synergistic action of both the PAI domain and the HD. Pax proteins with only a PD appear to require both PAI and RED domains, while a Pax-6 isoform and a new Pax protein, Lune, may rely on the RED domain and HD. We propose a model by which Pax proteins recognize different target genes in vivo through various combinations of their DNA binding domains, thus expanding their recognition repertoire.

A photoaffinity scan maps regions of the p85 SH2 domain involved in phosphoprotein binding.

Science.gov (United States)

Williams, K P; Shoelson, S E

1993-03-15

Src homology 2 (SH2) domains are modular phosphotyrosine binding pockets found within a wide variety of cytoplasmic signaling molecules. Here we develop a new approach to analyzing protein-protein interfaces termed photoaffinity scanning, and apply the method to map regions of the phosphatidylinositol 3-kinase p85 SH2 domain that participate in phospho-protein binding. Each residue except phosphotyrosine (pY) within a tightly binding, IRS-1-derived phosphopeptide (GNGDpYMPMSPKS) was substituted with the photoactive amino acid, benzoylphenylalanine (Bpa). Whereas most substitutions had little effect on binding affinity, Bpa substitution of either Met (+1 and +3 with respect to pY) reduced affinity 50-100-fold to confirm their importance in the pYMXM recognition motif. In three cases photolysis of SH2 domain/Bpa phosphopeptide complexes led to cross-linking of > 50% of the SH2 domain; cross-link positions were identified by microsequence, amino acid composition, and electrospray mass spectrometric analyses. Bpa-1 cross-links within alpha-helix I, whereas Bpa+1 and Bpa+4 cross-link the SH2 domain within the flexible loop C-terminal to alpha-helix II. Moreover, cross-linking at any position prevents SH2 domain cleavage at a trypsin-sensitive site within the flexible loop between beta-strands 1 and 2. Therefore, at least three distinct SH2 regions in addition to the beta-sheet participate in phosphoprotein binding; the loop cross-linked by phosphopeptide residues C-terminal to pY appears to confer specificity to the phosphoprotein/SH2 domain interaction.

Thermal Loss of High-Q Antennas in Time Domain vs. Frequency Domain Solver

DEFF Research Database (Denmark)

Bahramzy, Pevand; Pedersen, Gert Frølund

2014-01-01

High-Q structures pose great challenges to their loss simulations in Time Domain Solvers (TDS). Therefore, in this work the thermal loss of high-Q antennas is calculated both in TDS and Frequency Domain Solver (FDS), which are then compared with each other and with the actual measurements....... The thermal loss calculation in FDS is shown to be more accurate for high-Q antennas....

Numerical electromagnetic frequency domain analysis with discrete exterior calculus

Science.gov (United States)

Chen, Shu C.; Chew, Weng Cho

2017-12-01

In this paper, we perform a numerical analysis in frequency domain for various electromagnetic problems based on discrete exterior calculus (DEC) with an arbitrary 2-D triangular or 3-D tetrahedral mesh. We formulate the governing equations in terms of DEC for 3-D and 2-D inhomogeneous structures, and also show that the charge continuity relation is naturally satisfied. Then we introduce a general construction for signed dual volume to incorporate material information and take into account the case when circumcenters fall outside triangles or tetrahedrons, which may lead to negative dual volume without Delaunay triangulation. Then we examine the boundary terms induced by the dual mesh and provide a systematical treatment of various boundary conditions, including perfect magnetic conductor (PMC), perfect electric conductor (PEC), Dirichlet, periodic, and absorbing boundary conditions (ABC) within this method. An excellent agreement is achieved through the numerical calculation of several problems, including homogeneous waveguides, microstructured fibers, photonic crystals, scattering by a 2-D PEC, and resonant cavities.

Protein domain analysis of genomic sequence data reveals regulation of LRR related domains in plant transpiration in Ficus.

Science.gov (United States)

Lang, Tiange; Yin, Kangquan; Liu, Jinyu; Cao, Kunfang; Cannon, Charles H; Du, Fang K

2014-01-01

Predicting protein domains is essential for understanding a protein's function at the molecular level. However, up till now, there has been no direct and straightforward method for predicting protein domains in species without a reference genome sequence. In this study, we developed a functionality with a set of programs that can predict protein domains directly from genomic sequence data without a reference genome. Using whole genome sequence data, the programming functionality mainly comprised DNA assembly in combination with next-generation sequencing (NGS) assembly methods and traditional methods, peptide prediction and protein domain prediction. The proposed new functionality avoids problems associated with de novo assembly due to micro reads and small single repeats. Furthermore, we applied our functionality for the prediction of leucine rich repeat (LRR) domains in four species of Ficus with no reference genome, based on NGS genomic data. We found that the LRRNT_2 and LRR_8 domains are related to plant transpiration efficiency, as indicated by the stomata index, in the four species of Ficus. The programming functionality established in this study provides new insights for protein domain prediction, which is particularly timely in the current age of NGS data expansion.

Rating knowledge sharing in cross-domain collaborative filtering.

Science.gov (United States)

Li, Bin; Zhu, Xingquan; Li, Ruijiang; Zhang, Chengqi

2015-05-01

Cross-domain collaborative filtering (CF) aims to share common rating knowledge across multiple related CF domains to boost the CF performance. In this paper, we view CF domains as a 2-D site-time coordinate system, on which multiple related domains, such as similar recommender sites or successive time-slices, can share group-level rating patterns. We propose a unified framework for cross-domain CF over the site-time coordinate system by sharing group-level rating patterns and imposing user/item dependence across domains. A generative model, say ratings over site-time (ROST), which can generate and predict ratings for multiple related CF domains, is developed as the basic model for the framework. We further introduce cross-domain user/item dependence into ROST and extend it to two real-world cross-domain CF scenarios: 1) ROST (sites) for alleviating rating sparsity in the target domain, where multiple similar sites are viewed as related CF domains and some items in the target domain depend on their correspondences in the related ones; and 2) ROST (time) for modeling user-interest drift over time, where a series of time-slices are viewed as related CF domains and a user at current time-slice depends on herself in the previous time-slice. All these ROST models are instances of the proposed unified framework. The experimental results show that ROST (sites) can effectively alleviate the sparsity problem to improve rating prediction performance and ROST (time) can clearly track and visualize user-interest drift over time.

Modelling DNA origami self-assembly at the domain level

Energy Technology Data Exchange (ETDEWEB)

Dannenberg, Frits; Kwiatkowska, Marta [Department of Computer Science, University of Oxford, Wolfson Building, Parks Road, Oxford OX1 3QD (United Kingdom); Dunn, Katherine E. [Department of Physics, University of Oxford, Clarendon Laboratory, Parks Road, Oxford OX1 3PU (United Kingdom); Department of Electronics, University of York, York YO10 5DD (United Kingdom); Bath, Jonathan; Turberfield, Andrew J. [Department of Physics, University of Oxford, Clarendon Laboratory, Parks Road, Oxford OX1 3PU (United Kingdom); Ouldridge, Thomas E. [Department of Physics, University of Oxford, Rudolf Peierls Centre for Theoretical Physics, 1 Keble Road, Oxford OX1 3NP (United Kingdom); Department of Mathematics, Imperial College, 180 Queen’s Gate, London SW7 2AZ (United Kingdom)

2015-10-28

We present a modelling framework, and basic model parameterization, for the study of DNA origami folding at the level of DNA domains. Our approach is explicitly kinetic and does not assume a specific folding pathway. The binding of each staple is associated with a free-energy change that depends on staple sequence, the possibility of coaxial stacking with neighbouring domains, and the entropic cost of constraining the scaffold by inserting staple crossovers. A rigorous thermodynamic model is difficult to implement as a result of the complex, multiply connected geometry of the scaffold: we present a solution to this problem for planar origami. Coaxial stacking of helices and entropic terms, particularly when loop closure exponents are taken to be larger than those for ideal chains, introduce interactions between staples. These cooperative interactions lead to the prediction of sharp assembly transitions with notable hysteresis that are consistent with experimental observations. We show that the model reproduces the experimentally observed consequences of reducing staple concentration, accelerated cooling, and absent staples. We also present a simpler methodology that gives consistent results and can be used to study a wider range of systems including non-planar origami.

Modelling DNA origami self-assembly at the domain level

International Nuclear Information System (INIS)

Dannenberg, Frits; Kwiatkowska, Marta; Dunn, Katherine E.; Bath, Jonathan; Turberfield, Andrew J.; Ouldridge, Thomas E.

2015-01-01

We present a modelling framework, and basic model parameterization, for the study of DNA origami folding at the level of DNA domains. Our approach is explicitly kinetic and does not assume a specific folding pathway. The binding of each staple is associated with a free-energy change that depends on staple sequence, the possibility of coaxial stacking with neighbouring domains, and the entropic cost of constraining the scaffold by inserting staple crossovers. A rigorous thermodynamic model is difficult to implement as a result of the complex, multiply connected geometry of the scaffold: we present a solution to this problem for planar origami. Coaxial stacking of helices and entropic terms, particularly when loop closure exponents are taken to be larger than those for ideal chains, introduce interactions between staples. These cooperative interactions lead to the prediction of sharp assembly transitions with notable hysteresis that are consistent with experimental observations. We show that the model reproduces the experimentally observed consequences of reducing staple concentration, accelerated cooling, and absent staples. We also present a simpler methodology that gives consistent results and can be used to study a wider range of systems including non-planar origami

Modelling DNA origami self-assembly at the domain level

Science.gov (United States)

Dannenberg, Frits; Dunn, Katherine E.; Bath, Jonathan; Kwiatkowska, Marta; Turberfield, Andrew J.; Ouldridge, Thomas E.

2015-10-01

We present a modelling framework, and basic model parameterization, for the study of DNA origami folding at the level of DNA domains. Our approach is explicitly kinetic and does not assume a specific folding pathway. The binding of each staple is associated with a free-energy change that depends on staple sequence, the possibility of coaxial stacking with neighbouring domains, and the entropic cost of constraining the scaffold by inserting staple crossovers. A rigorous thermodynamic model is difficult to implement as a result of the complex, multiply connected geometry of the scaffold: we present a solution to this problem for planar origami. Coaxial stacking of helices and entropic terms, particularly when loop closure exponents are taken to be larger than those for ideal chains, introduce interactions between staples. These cooperative interactions lead to the prediction of sharp assembly transitions with notable hysteresis that are consistent with experimental observations. We show that the model reproduces the experimentally observed consequences of reducing staple concentration, accelerated cooling, and absent staples. We also present a simpler methodology that gives consistent results and can be used to study a wider range of systems including non-planar origami.

Engaging Students to Learn through the Affective Domain: A New Framework for Teaching in the Geosciences

Science.gov (United States)

van der Hoeven Kraft, Katrien J.; Srogi, LeeAnn; Husman, Jenefer; Semken, Steven; Fuhrman, Miriam

2011-01-01

To motivate student learning, the affective domain--emotion, attitude, and motivation--must be engaged. We propose a model that is specific to the geosciences with theoretical components of motivation and emotion from the field of educational psychology, and a term we are proposing, "connections with Earth" based on research in the…

Stability equation and two-component Eigenmode for domain walls in scalar potential model

International Nuclear Information System (INIS)

Dias, G.S.; Graca, E.L.; Rodrigues, R. de Lima

2002-08-01

Supersymmetric quantum mechanics involving a two-component representation and two-component eigenfunctions is applied to obtain the stability equation associated to a potential model formulated in terms of two coupled real scalar fields. We investigate the question of stability by introducing an operator technique for the Bogomol'nyi-Prasad-Sommerfield (BPS) and non-BPS states on two domain walls in a scalar potential model with minimal N 1-supersymmetry. (author)

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

Enhanced spin transfer torque effect for transverse domain walls in cylindrical nanowires

Science.gov (United States)

Franchin, Matteo; Knittel, Andreas; Albert, Maximilian; Chernyshenko, Dmitri S.; Fischbacher, Thomas; Prabhakar, Anil; Fangohr, Hans

2011-09-01

Recent studies have predicted extraordinary properties for transverse domain walls in cylindrical nanowires: zero depinning current, the absence of the Walker breakdown, and applications as domain wall oscillators. In order to reliably control the domain wall motion, it is important to understand how they interact with pinning centers, which may be engineered, for example, through modulations in the nanowire geometry (such as notches or extrusions) or in the magnetic properties of the material. In this paper we study the motion and depinning of transverse domain walls through pinning centers in ferromagnetic cylindrical nanowires. We use (i) magnetic fields and (ii) spin-polarized currents to drive the domain walls along the wire. The pinning centers are modelled as a section of the nanowire which exhibits a uniaxial crystal anisotropy where the anisotropy easy axis and the wire axis enclose a variable angle θP. Using (i) magnetic fields, we find that the minimum and the maximum fields required to push the domain wall through the pinning center differ by 30%. On the contrary, using (ii) spin-polarized currents, we find variations of a factor 130 between the minimum value of the depinning current density (observed for θP=0∘, i.e., anisotropy axis pointing parallel to the wire axis) and the maximum value (for θP=90∘, i.e., anisotropy axis perpendicular to the wire axis). We study the depinning current density as a function of the height of the energy barrier of the pinning center using numerical and analytical methods. We find that for an industry standard energy barrier of 40kBT, a depinning current of about 5μA (corresponding to a current density of 6×1010A/m2 in a nanowire of 10nm diameter) is sufficient to depin the domain wall. We reveal and explain the mechanism that leads to these unusually low depinning currents. One requirement for this depinning mechanism is for the domain wall to be able to rotate around its own axis. With the right barrier design

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.

Distinct roles for the IIId2 sub-domain in pestivirus and picornavirus internal ribosome entry sites.

Science.gov (United States)

Willcocks, Margaret M; Zaini, Salmah; Chamond, Nathalie; Ulryck, Nathalie; Allouche, Delphine; Rajagopalan, Noemie; Davids, Nana A; Fahnøe, Ulrik; Hadsbjerg, Johanne; Rasmussen, Thomas Bruun; Roberts, Lisa O; Sargueil, Bruno; Belsham, Graham J; Locker, Nicolas

2017-12-15

Viral internal ribosomes entry site (IRES) elements coordinate the recruitment of the host translation machinery to direct the initiation of viral protein synthesis. Within hepatitis C virus (HCV)-like IRES elements, the sub-domain IIId(1) is crucial for recruiting the 40S ribosomal subunit. However, some HCV-like IRES elements possess an additional sub-domain, termed IIId2, whose function remains unclear. Herein, we show that IIId2 sub-domains from divergent viruses have different functions. The IIId2 sub-domain present in Seneca valley virus (SVV), a picornavirus, is dispensable for IRES activity, while the IIId2 sub-domains of two pestiviruses, classical swine fever virus (CSFV) and border disease virus (BDV), are required for 80S ribosomes assembly and IRES activity. Unlike in SVV, the deletion of IIId2 from the CSFV and BDV IRES elements impairs initiation of translation by inhibiting the assembly of 80S ribosomes. Consequently, this negatively affects the replication of CSFV and BDV. Finally, we show that the SVV IIId2 sub-domain is required for efficient viral RNA synthesis and growth of SVV, but not for IRES function. This study sheds light on the molecular evolution of viruses by clearly demonstrating that conserved RNA structures, within distantly related RNA viruses, have acquired different roles in the virus life cycles. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Domain engineering of the metastable domains in the 4f-uniaxial-ferromagnet CeRu2Ga2B

Science.gov (United States)

Wulferding, D.; Kim, H.; Yang, I.; Jeong, J.; Barros, K.; Kato, Y.; Martin, I.; Ayala-Valenzuela, O. E.; Lee, M.; Choi, H. C.; Ronning, F.; Civale, L.; Baumbach, R. E.; Bauer, E. D.; Thompson, J. D.; Movshovich, R.; Kim, Jeehoon

2017-04-01

In search of novel, improved materials for magnetic data storage and spintronic devices, compounds that allow a tailoring of magnetic domain shapes and sizes are essential. Good candidates are materials with intrinsic anisotropies or competing interactions, as they are prone to host various domain phases that can be easily and precisely selected by external tuning parameters such as temperature and magnetic field. Here, we utilize vector magnetic fields to visualize directly the magnetic anisotropy in the uniaxial ferromagnet CeRu2Ga2B. We demonstrate a feasible control both globally and locally of domain shapes and sizes by the external field as well as a smooth transition from single stripe to bubble domains, which opens the door to future applications based on magnetic domain tailoring.

The SH2 Domain Interaction Landscape

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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.

Wavelet Domain Radiofrequency Pulse Design Applied to Magnetic Resonance Imaging.

Directory of Open Access Journals (Sweden)

Andrew M Huettner

Full Text Available A new method for designing radiofrequency (RF pulses with numerical optimization in the wavelet domain is presented. Numerical optimization may yield solutions that might otherwise have not been discovered with analytic techniques alone. Further, processing in the wavelet domain reduces the number of unknowns through compression properties inherent in wavelet transforms, providing a more tractable optimization problem. This algorithm is demonstrated with simultaneous multi-slice (SMS spin echo refocusing pulses because reduced peak RF power is necessary for SMS diffusion imaging with high acceleration factors. An iterative, nonlinear, constrained numerical minimization algorithm was developed to generate an optimized RF pulse waveform. Wavelet domain coefficients were modulated while iteratively running a Bloch equation simulator to generate the intermediate slice profile of the net magnetization. The algorithm minimizes the L2-norm of the slice profile with additional terms to penalize rejection band ripple and maximize the net transverse magnetization across each slice. Simulations and human brain imaging were used to demonstrate a new RF pulse design that yields an optimized slice profile and reduced peak energy deposition when applied to a multiband single-shot echo planar diffusion acquisition. This method may be used to optimize factors such as magnitude and phase spectral profiles and peak RF pulse power for multiband simultaneous multi-slice (SMS acquisitions. Wavelet-based RF pulse optimization provides a useful design method to achieve a pulse waveform with beneficial amplitude reduction while preserving appropriate magnetization response for magnetic resonance imaging.

Waggawagga-CLI: A command-line tool for predicting stable single α-helices (SAH-domains, and the SAH-domain distribution across eukaryotes.

Directory of Open Access Journals (Sweden)

Dominic Simm

Full Text Available Stable single-alpha helices (SAH-domains function as rigid connectors and constant force springs between structural domains, and can provide contact surfaces for protein-protein and protein-RNA interactions. SAH-domains mainly consist of charged amino acids and are monomeric and stable in polar solutions, characteristics which distinguish them from coiled-coil domains and intrinsically disordered regions. Although the number of reported SAH-domains is steadily increasing, genome-wide analyses of SAH-domains in eukaryotic genomes are still missing. Here, we present Waggawagga-CLI, a command-line tool for predicting and analysing SAH-domains in protein sequence datasets. Using Waggawagga-CLI we predicted SAH-domains in 24 datasets from eukaryotes across the tree of life. SAH-domains were predicted in 0.5 to 3.5% of the protein-coding content per species. SAH-domains are particularly present in longer proteins supporting their function as structural building block in multi-domain proteins. In human, SAH-domains are mainly used as alternative building blocks not being present in all transcripts of a gene. Gene ontology analysis showed that yeast proteins with SAH-domains are particular enriched in macromolecular complex subunit organization, cellular component biogenesis and RNA metabolic processes, and that they have a strong nuclear and ribonucleoprotein complex localization and function in ribosome and nucleic acid binding. Human proteins with SAH-domains have roles in all types of RNA processing and cytoskeleton organization, and are predicted to function in RNA binding, protein binding involved in cell and cell-cell adhesion, and cytoskeletal protein binding. Waggawagga-CLI allows the user to adjust the stabilizing and destabilizing contribution of amino acid interactions in i,i+3 and i,i+4 spacings, and provides extensive flexibility for user-designed analyses.

Functional anthology of intrinsic disorder. 2. Cellular components, domains, technical terms, developmental processes, and coding sequence diversities correlated with long disordered regions.

Science.gov (United States)

Vucetic, Slobodan; Xie, Hongbo; Iakoucheva, Lilia M; Oldfield, Christopher J; Dunker, A Keith; Obradovic, Zoran; Uversky, Vladimir N

2007-05-01

Biologically active proteins without stable ordered structure (i.e., intrinsically disordered proteins) are attracting increased attention. Functional repertoires of ordered and disordered proteins are very different, and the ability to differentiate whether a given function is associated with intrinsic disorder or with a well-folded protein is crucial for modern protein science. However, there is a large gap between the number of proteins experimentally confirmed to be disordered and their actual number in nature. As a result, studies of functional properties of confirmed disordered proteins, while helpful in revealing the functional diversity of protein disorder, provide only a limited view. To overcome this problem, a bioinformatics approach for comprehensive study of functional roles of protein disorder was proposed in the first paper of this series (Xie, H.; Vucetic, S.; Iakoucheva, L. M.; Oldfield, C. J.; Dunker, A. K.; Obradovic, Z.; Uversky, V. N. Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regions. J. Proteome Res. 2007, 5, 1882-1898). Applying this novel approach to Swiss-Prot sequences and functional keywords, we found over 238 and 302 keywords to be strongly positively or negatively correlated, respectively, with long intrinsically disordered regions. This paper describes approximately 90 Swiss-Prot keywords attributed to the cellular components, domains, technical terms, developmental processes, and coding sequence diversities possessing strong positive and negative correlation with long disordered regions.

Functional Anthology of Intrinsic Disorder. II. Cellular Components, Domains, Technical Terms, Developmental Processes and Coding Sequence Diversities Correlated with Long Disordered Regions

Science.gov (United States)

Vucetic, Slobodan; Xie, Hongbo; Iakoucheva, Lilia M.; Oldfield, Christopher J.; Dunker, A. Keith; Obradovic, Zoran; Uversky, Vladimir N.

2008-01-01

Biologically active proteins without stable ordered structure (i.e., intrinsically disordered proteins) are attracting increased attention. Functional repertoires of ordered and disordered proteins are very different, and the ability to differentiate whether a given function is associated with intrinsic disorder or with a well-folded protein is crucial for modern protein science. However, there is a large gap between the number of proteins experimentally confirmed to be disordered and their actual number in nature. As a result, studies of functional properties of confirmed disordered proteins, while helpful in revealing the functional diversity of protein disorder, provide only a limited view. To overcome this problem, a bioinformatics approach for comprehensive study of functional roles of protein disorder was proposed in the first paper of this series (Xie H., Vucetic S., Iakoucheva L.M., Oldfield C.J., Dunker A.K., Obradovic Z., Uversky V.N. (2006) Functional anthology of intrinsic disorder. I. Biological processes and functions of proteins with long disordered regions. J. Proteome Res.). Applying this novel approach to Swiss-Prot sequences and functional keywords, we found over 238 and 302 keywords to be strongly positively or negatively correlated, respectively, with long intrinsically disordered regions. This paper describes ~90 Swiss-Prot keywords attributed to the cellular components, domains, technical terms, developmental processes and coding sequence diversities possessing strong positive and negative correlation with long disordered regions. PMID:17391015

Neutron dosimetry at a high-energy electron-positron collider

Science.gov (United States)

Bedogni, Roberto

Electron-positron colliders with energy of hundreds of MeV per beam have been employed for studies in the domain of nuclear and sub-nuclear physics. The typical structure of such a collider includes an LINAC, able to produce both types of particles, an accumulator ring and a main ring, whose diameter ranges from several tens to hundred meters and allows circulating particle currents of several amperes per beam. As a consequence of the interaction of the primary particles with targets, shutters, structures and barriers, a complex radiation environment is produced. This paper addresses the neutron dosimetry issues associated with the operation of such accelerators, referring in particular to the DAΦ NE complex, operative since 1997 at INFN-Frascati National Laboratory (Italy). Special attention is given to the active and passive techniques used for the spectrometric and dosimetric characterization of the workplace neutron fields, for radiation protection dosimetry purposes.

PUBLIC DOMAIN PROTECTION. USES AND REUSES OF PUBLIC DOMAIN WORKS

Directory of Open Access Journals (Sweden)

Monica Adriana LUPAȘCU

2015-07-01

Full Text Available This study tries to highlight the necessity of an awareness of the right of access to the public domain, particularly using the example of works whose protection period has expired, as well as the ones which the law considers to be excluded from protection. Such works are used not only by large libraries from around the world, but also by rights holders, via different means of use, including incorporations into original works or adaptations. However, the reuse that follows these uses often only remains at the level of concept, as the notion of the public’s right of access to public domain works is not substantiated, nor is the notion of the correct or legal use of such works.

Crystal structure of the N domain of human somatic angiotensin I-converting enzyme provides a structural basis for domain-specific inhibitor design.

Science.gov (United States)

Corradi, Hazel R; Schwager, Sylva L U; Nchinda, Aloysius T; Sturrock, Edward D; Acharya, K Ravi

2006-03-31

Human somatic angiotensin I-converting enzyme (sACE) is a key regulator of blood pressure and an important drug target for combating cardiovascular and renal disease. sACE comprises two homologous metallopeptidase domains, N and C, joined by an inter-domain linker. Both domains are capable of cleaving the two hemoregulatory peptides angiotensin I and bradykinin, but differ in their affinities for a range of other substrates and inhibitors. Previously we determined the structure of testis ACE (C domain); here we present the crystal structure of the N domain of sACE (both in the presence and absence of the antihypertensive drug lisinopril) in order to aid the understanding of how these two domains differ in specificity and function. In addition, the structure of most of the inter-domain linker allows us to propose relative domain positions for sACE that may contribute to the domain cooperativity. The structure now provides a platform for the design of "domain-specific" second-generation ACE inhibitors.

Domain-Specific Thesaurus as a Tool for Information Retrieval and Collection of Knowledge

Directory of Open Access Journals (Sweden)

Vladimir N. Boikov

2013-01-01

Full Text Available This paper reports basic approaches to constructive creation of an open resource named ”Domain-specified thesaurus of poetics”, which is one of the levels of an information-analytical system of the Russian poetry (IAS RP. The poetics is a group of disciplines focused on a comprehensive theoretical and historical study of poetry. IAS RP will be used as a tool for a wide range of studies allowing to determine the characteristic features of the analyzed works of poetry. Consequently, the thesaurus is the knowledge base from which one can borrow input data for training the system. The aim of our research requires a specific approach to formating the knowledge base. Thesaurus is a web-based resource which includes a domain-specific directory, information retrieval tools and tools for further analyzes. The study of glossary consisting of three thousand terms and a set of semantic fields is reviewed in this paper. Rdf-graph of the domain-specified thesaurus of poetics is presented, containing 9 types of objects and different kinds of relationships among them. Wiki-tecnologies are used for implementing a resource which allows to store data in Semantic Web formats.

Crystal structure of the Ig1 domain of the neural cell adhesion molecule NCAM2 displays domain swapping

DEFF Research Database (Denmark)

Rasmussen, Kim Krighaar; Kulahin, Nikolaj; Kristensen, Ole

2008-01-01

The crystal structure of the first immunoglobulin (Ig1) domain of neural cell adhesion molecule 2 (NCAM2/OCAM/RNCAM) is presented at a resolution of 2.7 A. NCAM2 is a member of the immunoglobulin superfamily of cell adhesion molecules (IgCAMs). In the structure, two Ig domains interact by domain...

Big domains are novel Ca²+-binding modules: evidences from big domains of Leptospira immunoglobulin-like (Lig) proteins.

Science.gov (United States)

Raman, Rajeev; Rajanikanth, V; Palaniappan, Raghavan U M; Lin, Yi-Pin; He, Hongxuan; McDonough, Sean P; Sharma, Yogendra; Chang, Yung-Fu

2010-12-29

Many bacterial surface exposed proteins mediate the host-pathogen interaction more effectively in the presence of Ca²+. Leptospiral immunoglobulin-like (Lig) proteins, LigA and LigB, are surface exposed proteins containing Bacterial immunoglobulin like (Big) domains. The function of proteins which contain Big fold is not known. Based on the possible similarities of immunoglobulin and βγ-crystallin folds, we here explore the important question whether Ca²+ binds to a Big domains, which would provide a novel functional role of the proteins containing Big fold. We selected six individual Big domains for this study (three from the conserved part of LigA and LigB, denoted as Lig A3, Lig A4, and LigBCon5; two from the variable region of LigA, i.e., 9(th) (Lig A9) and 10(th) repeats (Lig A10); and one from the variable region of LigB, i.e., LigBCen2. We have also studied the conserved region covering the three and six repeats (LigBCon1-3 and LigCon). All these proteins bind the calcium-mimic dye Stains-all. All the selected four domains bind Ca²+ with dissociation constants of 2-4 µM. Lig A9 and Lig A10 domains fold well with moderate thermal stability, have β-sheet conformation and form homodimers. Fluorescence spectra of Big domains show a specific doublet (at 317 and 330 nm), probably due to Trp interaction with a Phe residue. Equilibrium unfolding of selected Big domains is similar and follows a two-state model, suggesting the similarity in their fold. We demonstrate that the Lig are Ca²+-binding proteins, with Big domains harbouring the binding motif. We conclude that despite differences in sequence, a Big motif binds Ca²+. This work thus sets up a strong possibility for classifying the proteins containing Big domains as a novel family of Ca²+-binding proteins. Since Big domain is a part of many proteins in bacterial kingdom, we suggest a possible function these proteins via Ca²+ binding.

Domains in Ferroic Crystals and Thin Films

CERN Document Server

Tagantsev, Alexander K; Fousek, Jan

2010-01-01

Domains in Ferroic Crystals and Thin Films presents experimental findings and theoretical understanding of ferroic (non-magnetic) domains developed during the past 60 years. It addresses the situation by looking specifically at bulk crystals and thin films, with a particular focus on recently-developed microelectronic applications and methods for observation of domains with techniques such as scanning force microscopy, polarized light microscopy, scanning optical microscopy, electron microscopy, and surface decorating techniques. Domains in Ferroic Crystals and Thin Films covers a large area of material properties and effects connected with static and dynamic properties of domains, which are extremely relevant to materials referred to as ferroics. In most solid state physics books, one large group of ferroics is customarily covered: those in which magnetic properties play a dominant role. Numerous books are specifically devoted to magnetic ferroics and cover a wide spectrum of magnetic domain phenomena. In co...

Bilingual Dictionaries for Communication in the Domain of Economics: Function-Based Translation Dictionaries

DEFF Research Database (Denmark)

Nielsen, Sandro

2015-01-01

With their focus on terms, bilingual dictionaries are important tools for translating texts on economics. The most common type is the multi-fi eld dictionary covering several related subject fi elds; however, multi-fi eld dictionaries treat one or few fi elds extensively thereby neglecting other fi...... elds in contrast to single-fi eld and sub-fi eld dictionaries. Furthermore, recent research shows that economic translation is not limited to terms so lexicographers who identify and analyse the needs of translators, usage situations and stages in translating economic texts will have a sound basis...... for designing their lexicographic tools. The function theory allows lexicographers to study these basics so that they can offer translation tools to the domain of economics. Dictionaries should include data about terms, their grammatical properties, and their combinatorial potential as well as language...

Wavefield extrapolation in pseudodepth domain

KAUST Repository

Ma, Xuxin

2013-02-01

Wavefields are commonly computed in the Cartesian coordinate frame. Its efficiency is inherently limited due to spatial oversampling in deep layers, where the velocity is high and wavelengths are long. To alleviate this computational waste due to uneven wavelength sampling, we convert the vertical axis of the conventional domain from depth to vertical time or pseudodepth. This creates a nonorthognal Riemannian coordinate system. Isotropic and anisotropic wavefields can be extrapolated in the new coordinate frame with improved efficiency and good consistency with Cartesian domain extrapolation results. Prestack depth migrations are also evaluated based on the wavefield extrapolation in the pseudodepth domain.© 2013 Society of Exploration Geophysicists. All rights reserved.

Structural domain walls in polar hexagonal manganites

Science.gov (United States)

Kumagai, Yu

2014-03-01

The domain structure in the multiferroic hexagonal manganites is currently intensely investigated, motivated by the observation of intriguing sixfold topological defects at their meeting points [Choi, T. et al,. Nature Mater. 9, 253 (2010).] and nanoscale electrical conductivity at the domain walls [Wu, W. et al., Phys. Rev. Lett. 108, 077203 (2012).; Meier, D. et al., Nature Mater. 11, 284 (2012).], as well as reports of coupling between ferroelectricity, magnetism and structural antiphase domains [Geng, Y. et al., Nano Lett. 12, 6055 (2012).]. The detailed structure of the domain walls, as well as the origin of such couplings, however, was previously not fully understood. In the present study, we have used first-principles density functional theory to calculate the structure and properties of the low-energy structural domain walls in the hexagonal manganites [Kumagai, Y. and Spaldin, N. A., Nature Commun. 4, 1540 (2013).]. We find that the lowest energy domain walls are atomically sharp, with {210}orientation, explaining the orientation of recently observed stripe domains and suggesting their topological protection [Chae, S. C. et al., Phys. Rev. Lett. 108, 167603 (2012).]. We also explain why ferroelectric domain walls are always simultaneously antiphase walls, propose a mechanism for ferroelectric switching through domain-wall motion, and suggest an atomistic structure for the cores of the sixfold topological defects. This work was supported by ETH Zurich, the European Research Council FP7 Advanced Grants program me (grant number 291151), the JSPS Postdoctoral Fellowships for Research Abroad, and the MEXT Elements Strategy Initiative to Form Core Research Center TIES.

Visualizing the Knowledge Domain of Nanoparticle Drug Delivery Technologies: A Scientometric Review

Directory of Open Access Journals (Sweden)

Yen-Chun Lee

2016-01-01

Full Text Available The scientific literature of nanoparticle drug delivery technologies (NDDT between 2005 and 2014 was reviewed. The visualized co-citation network of its knowledge domain was characterized in terms of thematic concentrations of co-cited references and emerging trends of surging keywords and citations to references through a scientometric review. The combined dataset of 25,171 bibliographic records were constructed through topic search and citation expansion to ensure adequate coverage of the field. While research in gold nanoparticle and magnetic nanoparticle remains the two most prominent knowledge domains in the NDDT field, research related to clinical and therapeutic applications has experienced a considerable growth. In particular, clinical and therapeutic developments in NDDT have demonstrated profound connections with the mesoporous silica nanoparticle research and microcrystal research. A rapid adaptation of mesoporous silica-based nanomaterials and rare earth fluoride nano-/microcrystal in NDDT is evident. Innovative strategies have been employed to exploit the multicomponent, chemical synthesis, surface modification, and controlled release imparting functionalized targeting capabilities. This study not only facilitated the connection of authors and research themes in the NDDT community, but also demonstrated how research interests and trends evolve over time, which greatly contributes to our understanding of the NDDT knowledge domains.

Comparison of the landslide susceptibility models in Taipei Water Source Domain, Taiwan

Science.gov (United States)

WU, C. Y.; Yeh, Y. C.; Chou, T. H.

2017-12-01

Taipei Water Source Domain, locating at the southeast of Taipei Metropolis, is the main source of water resource in this region. Recently, the downstream turbidity often soared significantly during the typhoon period because of the upstream landslides. The landslide susceptibilities should be analysed to assess the influence zones caused by different rainfall events, and to ensure the abilities of this domain to serve enough and quality water resource. Generally, the landslide susceptibility models can be established based on either a long-term landslide inventory or a specified landslide event. Sometimes, there is no long-term landslide inventory in some areas. Thus, the event-based landslide susceptibility models are established widely. However, the inventory-based and event-based landslide susceptibility models may result in dissimilar susceptibility maps in the same area. So the purposes of this study were to compare the landslide susceptibility maps derived from the inventory-based and event-based models, and to interpret how to select a representative event to be included in the susceptibility model. The landslide inventory from Typhoon Tim in July, 1994 and Typhoon Soudelor in August, 2015 was collected, and used to establish the inventory-based landslide susceptibility model. The landslides caused by Typhoon Nari and rainfall data were used to establish the event-based model. The results indicated the high susceptibility slope-units were located at middle upstream Nan-Shih Stream basin.

Domain-orientation dependence of levitation force in seeded melt grown single-domain YBa2Cu3Ox

International Nuclear Information System (INIS)

Shi, D.; Qu, D.; Sagar, S.; Lahiri, K.

1997-01-01

Domain-orientation dependence of levitation force has been determined for single-domain YBa 2 Cu 3 O x . The single-domain material is obtained from a seeded melt growth process. The levitation force has been found to reach a maximum as the c axis of the domain is parallel to the direction of the force. The levitation force decreases in a cosine law fashion as the angle θ (the angle between the direction of the force and the c axis) increases from 0 degree to 60 degree. A maximum anisotropy of levitation force of 2.29 has been found. A physical model is proposed to explain the observed orientation dependence. copyright 1997 American Institute of Physics

GUM2DFT—a software tool for uncertainty evaluation of transient signals in the frequency domain

International Nuclear Information System (INIS)

Eichstädt, S; Wilkens, V

2016-01-01

The Fourier transform and its counterpart for discrete time signals, the discrete Fourier transform (DFT), are common tools in measurement science and application. Although almost every scientific software package offers ready-to-use implementations of the DFT, the propagation of uncertainties in line with the guide to the expression of uncertainty in measurement (GUM) is typically neglected. This is of particular importance in dynamic metrology, when input estimation is carried out by deconvolution in the frequency domain. To this end, we present the new open-source software tool GUM2DFT, which utilizes closed formulas for the efficient propagation of uncertainties for the application of the DFT, inverse DFT and input estimation in the frequency domain. It handles different frequency domain representations, accounts for autocorrelation and takes advantage of the symmetry inherent in the DFT result for real-valued time domain signals. All tools are presented in terms of examples which form part of the software package. GUM2DFT will foster GUM-compliant evaluation of uncertainty in a DFT-based analysis and enable metrologists to include uncertainty evaluations in their routine work. (paper)

A Reaction-Diffusion Model for Synapse Growth and Long-Term Memory

Science.gov (United States)

Liu, Kang; Lisman, John; Hagan, Michael

Memory storage involves strengthening of synaptic transmission known as long-term potentiation (LTP). The late phase of LTP is associated with structural processes that enlarge the synapse. Yet, synapses must be stable, despite continual subunit turnover, over the lifetime of an encoded memory. These considerations suggest that synapses are variable-size stable structure (VSSS), meaning they can switch between multiple metastable structures with different sizes. The mechanisms underlying VSSS are poorly understood. While experiments and theory have suggested that the interplay between diffusion and receptor-scaffold interactions can lead to a preferred stable size for synaptic domains, such a mechanism cannot explain how synapses adopt widely different sizes. Here we develop a minimal reaction-diffusion model of VSSS for synapse growth, incorporating the recent observation from super-resolution microscopy that neural activity can build compositional heterogeneities within synaptic domains. We find that introducing such heterogeneities can change the stable domain size in a controlled manner. We discuss a potential connection between this model and experimental data on synapse sizes, and how it provides a possible mechanism to structurally encode graded long-term memory. We acknowledge the support from NSF INSPIRE Award number IOS-1526941 (KL, MFH, JL) and the Brandeis Center for Bioinspired Soft Materials, an NSF MRSEC, DMR- 1420382 (MFH).

Membrane-sculpting BAR domains generate stable lipid microdomains

DEFF Research Database (Denmark)

Zhao, Hongxia; Michelot, Alphée; Koskela, Essi V.

2013-01-01

Bin-Amphiphysin-Rvs (BAR) domain proteins are central regulators of many cellular processes involving membrane dynamics. BAR domains sculpt phosphoinositide-rich membranes to generate membrane protrusions or invaginations. Here, we report that, in addition to regulating membrane geometry, BAR...... domains can generate extremely stable lipid microdomains by "freezing" phosphoinositide dynamics. This is a general feature of BAR domains, because the yeast endocytic BAR and Fes/CIP4 homology BAR (F-BAR) domains, the inverse BAR domain of Pinkbar, and the eisosomal BAR protein Lsp1 induced...... phosphoinositide clustering and halted lipid diffusion, despite differences in mechanisms of membrane interactions. Lsp1 displays comparable low diffusion rates in vitro and in vivo, suggesting that BAR domain proteins also generate stable phosphoinositide microdomains in cells. These results uncover a conserved...

Short-Term Lifestyle Strategies for Sustaining Cognitive Status

Directory of Open Access Journals (Sweden)

Elizabeth P. Howard

2016-01-01

Full Text Available Cognitive decline impacts older adults, particularly their independence. The goal of this project was to increase understanding of how short-term, everyday lifestyle options, including physical activity, help an older adult sustain cognitive independence. Using a secondary analysis of lifestyle choices, we drew on a dataset of 4,620 community-dwelling elders in the US, assessed at baseline and one year later using 2 valid and reliable tools, the interRAI Community Health Assessment and the interRAI Wellness tool. Decline or no decline on the Cognitive Performance Scale was the dependent variable. We examined sustaining one’s status on this measure over a one-year period in relation to key dimensions of wellness through intellectual, physical, emotional, social, and spiritual variables. Engaging in physical activity, formal exercise, and specific recreational activities had a favorable effect on short-term cognitive decline. Involvement with computers, crossword puzzles, handicrafts, and formal education courses also were protective factors. The physical and intellectual domains of wellness are prominent aspects in protection from cognitive decline. Inherent in these two domains are mutable factors suitable for targeted efforts to promote older adult health and well-being.

Short-Term Lifestyle Strategies for Sustaining Cognitive Status

Science.gov (United States)

Morris, John N.; Steel, Knight; Strout, Kelley A.; Fries, Brant E.; Moore, Alice; Garms-Homolová, Vjenka

2016-01-01

Cognitive decline impacts older adults, particularly their independence. The goal of this project was to increase understanding of how short-term, everyday lifestyle options, including physical activity, help an older adult sustain cognitive independence. Using a secondary analysis of lifestyle choices, we drew on a dataset of 4,620 community-dwelling elders in the US, assessed at baseline and one year later using 2 valid and reliable tools, the interRAI Community Health Assessment and the interRAI Wellness tool. Decline or no decline on the Cognitive Performance Scale was the dependent variable. We examined sustaining one's status on this measure over a one-year period in relation to key dimensions of wellness through intellectual, physical, emotional, social, and spiritual variables. Engaging in physical activity, formal exercise, and specific recreational activities had a favorable effect on short-term cognitive decline. Involvement with computers, crossword puzzles, handicrafts, and formal education courses also were protective factors. The physical and intellectual domains of wellness are prominent aspects in protection from cognitive decline. Inherent in these two domains are mutable factors suitable for targeted efforts to promote older adult health and well-being. PMID:27891520

Molecular Details of Olfactomedin Domains Provide Pathway to Structure-Function Studies.

Directory of Open Access Journals (Sweden)

Shannon E Hill

Full Text Available Olfactomedin (OLF domains are found within extracellular, multidomain proteins in numerous tissues of multicellular organisms. Even though these proteins have been implicated in human disorders ranging from cancers to attention deficit disorder to glaucoma, little is known about their structure(s and function(s. Here we biophysically, biochemically, and structurally characterize OLF domains from H. sapiens olfactomedin-1 (npoh-OLF, also called noelin, pancortin, OLFM1, and hOlfA, and M. musculus gliomedin (glio-OLF, also called collomin, collmin, and CRG-L2, and compare them with available structures of myocilin (myoc-OLF recently reported by us and R. norvegicus glio-OLF and M. musculus latrophilin-3 (lat3-OLF by others. Although the five-bladed β-propeller architecture remains unchanged, numerous physicochemical characteristics differ among these OLF domains. First, npoh-OLF and glio-OLF exhibit prominent, yet distinct, positive surface charges and copurify with polynucleotides. Second, whereas npoh-OLF and myoc-OLF exhibit thermal stabilities typical of human proteins near 55°C, and most myoc-OLF variants are destabilized and highly prone to aggregation, glio-OLF is nearly 20°C more stable and significantly more resistant to chemical denaturation. Phylogenetically, glio-OLF is most similar to primitive OLFs, and structurally, glio-OLF is missing distinguishing features seen in OLFs such as the disulfide bond formed by N- and C- terminal cysteines, the sequestered Ca2+ ion within the propeller central hydrophilic cavity, and a key loop-stabilizing cation-π interaction on the top face of npoh-OLF and myoc-OLF. While deciphering the explicit biological functions, ligands, and binding partners for OLF domains will likely continue to be a challenging long-term experimental pursuit, we used structural insights gained here to generate a new antibody selective for myoc-OLF over npoh-OLF and glio-OLF as a first step in overcoming the impasse in

Taxonomies of Educational Objective Domain

OpenAIRE

Eman Ghanem Nayef; Nik Rosila Nik Yaacob; Hairul Nizam Ismail

2013-01-01

This paper highlights an effort to study the educational objective domain taxonomies including Bloom’s taxonomy, Lorin Anderson’s taxonomy, and Wilson’s taxonomy. In this study a comparison among these three taxonomies have been done. Results show that Bloom’s taxonomy is more suitable as an analysis tool to Educational Objective domain.

Latent domain models for statistical machine translation

NARCIS (Netherlands)

Hoàng, C.

2017-01-01

A data-driven approach to model translation suffers from the data mismatch problem and demands domain adaptation techniques. Given parallel training data originating from a specific domain, training an MT system on the data would result in a rather suboptimal translation for other domains. But does

Second-harmonic imaging of ferroelectric domain walls

DEFF Research Database (Denmark)

Bozhevolnyi, Sergey I.; Hvam, Jørn Märcher; Pedersen, Kjeld

1998-01-01

configurations are presented. The SH generation enhancement is found especially pronounced for the polarization of the SH radiation being perpendicular to the domain walls. The origin and selection rules for the contrast in SH images of domain walls are discussed. The results obtained suggest that the domain...

Self-assembled domain structures: From micro- to nanoscale

Directory of Open Access Journals (Sweden)

Vladimir Shur

2015-06-01

Full Text Available The recent achievements in studying the self-assembled evolution of micro- and nanoscale domain structures in uniaxial single crystalline ferroelectrics lithium niobate and lithium tantalate have been reviewed. The results obtained by visualization of static domain patterns and kinetics of the domain structure by different methods from common optical microscopy to more sophisticated scanning probe microscopy, scanning electron microscopy and confocal Raman microscopy, have been discussed. The kinetic approach based on various nucleation processes similar to the first-order phase transition was used for explanation of the domain structure evolution scenarios. The main mechanisms of self-assembling for nonequilibrium switching conditions caused by screening ineffectiveness including correlated nucleation, domain growth anisotropy, and domain–domain interaction have been considered. The formation of variety of self-assembled domain patterns such as fractal-type, finger and web structures, broad domain boundaries, and dendrites have been revealed at each of all five stages of domain structure evolution during polarization reversal. The possible applications of self-assembling for micro- and nanodomain engineering were reviewed briefly. The review covers mostly the results published by our research group.

Domain Adaptation of Translation Models for Multilingual Applications

Science.gov (United States)

2009-04-01

employed. In the past two years, domain adaptation for NLP tasks has become an active research area [3, 38, 25, 23]. New domain adaptation tasks have...and unlabeled data in the target domain and learn a mixture model to adapt from the source domain. Other NLP tasks where domain adaptation has been...evaluation forum, http://www.clef-campaign.org. [13] K. Darwish and D. Oard, CLIR experiments at maryland for TREC-2002: Evidence combination for arabic

Domain Endurants: An Analysis and Description Process Model

DEFF Research Database (Denmark)

Bjørner, Dines

2014-01-01

We present a summary, Sect. 2, of a structure of domain analysis and description concepts: techniques and tools. And we link, in Sect. 3, these concepts, embodied in domain analysis prompts and domain description prompts, in a model of how a diligent domain analyser cum describer would use them. We...

The Distributed-SDF Domain

DEFF Research Database (Denmark)

Cuadrado, Daniel Lázaro; Ravn, Anders Peter; Koch, Peter

2005-01-01

The purpose of the Distributed-SDF domain for Ptolemy II is to allow distributed simulation of SDF models. It builds on top of the existing SDF domain by extending it. From the user’s point of view, using the Distributed-SDF director is sufficient to run the distributed version. It provides optio...... distributed nature. First of all, known memory bounds of the JVM can be overcome. Second, it yields smaller simulation times, mainly for models with high degree of parallelism and granularity....

Changepoint detection in base-resolution methylome data reveals a robust signature of methylated domain landscape.

Science.gov (United States)

Yokoyama, Takao; Miura, Fumihito; Araki, Hiromitsu; Okamura, Kohji; Ito, Takashi

2015-08-12

Base-resolution methylome data generated by whole-genome bisulfite sequencing (WGBS) is often used to segment the genome into domains with distinct methylation levels. However, most segmentation methods include many parameters to be carefully tuned and/or fail to exploit the unsurpassed resolution of the data. Furthermore, there is no simple method that displays the composition of the domains to grasp global trends in each methylome. We propose to use changepoint detection for domain demarcation based on base-resolution methylome data. While the proposed method segments the methylome in a largely comparable manner to conventional approaches, it has only a single parameter to be tuned. Furthermore, it fully exploits the base-resolution of the data to enable simultaneous detection of methylation changes in even contrasting size ranges, such as focal hypermethylation and global hypomethylation in cancer methylomes. We also propose a simple plot termed methylated domain landscape (MDL) that globally displays the size, the methylation level and the number of the domains thus defined, thereby enabling one to intuitively grasp trends in each methylome. Since the pattern of MDL often reflects cell lineages and is largely unaffected by data size, it can serve as a novel signature of methylome. Changepoint detection in base-resolution methylome data followed by MDL plotting provides a novel method for methylome characterization and will facilitate global comparison among various WGBS data differing in size and even species origin.

Domain similarity based orthology detection.

Science.gov (United States)

Bitard-Feildel, Tristan; Kemena, Carsten; Greenwood, Jenny M; Bornberg-Bauer, Erich

2015-05-13

Orthologous protein detection software mostly uses pairwise comparisons of amino-acid sequences to assert whether two proteins are orthologous or not. Accordingly, when the number of sequences for comparison increases, the number of comparisons to compute grows in a quadratic order. A current challenge of bioinformatic research, especially when taking into account the increasing number of sequenced organisms available, is to make this ever-growing number of comparisons computationally feasible in a reasonable amount of time. We propose to speed up the detection of orthologous proteins by using strings of domains to characterize the proteins. We present two new protein similarity measures, a cosine and a maximal weight matching score based on domain content similarity, and new software, named porthoDom. The qualities of the cosine and the maximal weight matching similarity measures are compared against curated datasets. The measures show that domain content similarities are able to correctly group proteins into their families. Accordingly, the cosine similarity measure is used inside porthoDom, the wrapper developed for proteinortho. porthoDom makes use of domain content similarity measures to group proteins together before searching for orthologs. By using domains instead of amino acid sequences, the reduction of the search space decreases the computational complexity of an all-against-all sequence comparison. We demonstrate that representing and comparing proteins as strings of discrete domains, i.e. as a concatenation of their unique identifiers, allows a drastic simplification of search space. porthoDom has the advantage of speeding up orthology detection while maintaining a degree of accuracy similar to proteinortho. The implementation of porthoDom is released using python and C++ languages and is available under the GNU GPL licence 3 at http://www.bornberglab.org/pages/porthoda .

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.

Effective Domain Partitioning for Multi-Clock Domain IP Core Wrapper Design under Power Constraints

Science.gov (United States)

Yu, Thomas Edison; Yoneda, Tomokazu; Zhao, Danella; Fujiwara, Hideo

The rapid advancement of VLSI technology has made it possible for chip designers and manufacturers to embed the components of a whole system onto a single chip, called System-on-Chip or SoC. SoCs make use of pre-designed modules, called IP-cores, which provide faster design time and quicker time-to-market. Furthermore, SoCs that operate at multiple clock domains and very low power requirements are being utilized in the latest communications, networking and signal processing devices. As a result, the testing of SoCs and multi-clock domain embedded cores under power constraints has been rapidly gaining importance. In this research, a novel method for designing power-aware test wrappers for embedded cores with multiple clock domains is presented. By effectively partitioning the various clock domains, we are able to increase the solution space of possible test schedules for the core. Since previous methods were limited to concurrently testing all the clock domains, we effectively remove this limitation by making use of bandwidth conversion, multiple shift frequencies and properly gating the clock signals to control the shift activity of various core logic elements. The combination of the above techniques gains us greater flexibility when determining an optimal test schedule under very tight power constraints. Furthermore, since it is computationally intensive to search the entire expanded solution space for the possible test schedules, we propose a heuristic 3-D bin packing algorithm to determine the optimal wrapper architecture and test schedule while minimizing the test time under power and bandwidth constraints.

Domain Adaptation for Opinion Classification: A Self-Training Approach

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Yu, Ning

2013-03-01

Full Text Available Domain transfer is a widely recognized problem for machine learning algorithms because models built upon one data domain generally do not perform well in another data domain. This is especially a challenge for tasks such as opinion classification, which often has to deal with insufficient quantities of labeled data. This study investigates the feasibility of self-training in dealing with the domain transfer problem in opinion classification via leveraging labeled data in non-target data domain(s and unlabeled data in the target-domain. Specifically, self-training is evaluated for effectiveness in sparse data situations and feasibility for domain adaptation in opinion classification. Three types of Web content are tested: edited news articles, semi-structured movie reviews, and the informal and unstructured content of the blogosphere. Findings of this study suggest that, when there are limited labeled data, self-training is a promising approach for opinion classification, although the contributions vary across data domains. Significant improvement was demonstrated for the most challenging data domain-the blogosphere-when a domain transfer-based self-training strategy was implemented.