DGDFT: A massively parallel method for large scale density functional theory calculations

International Nuclear Information System (INIS)

Hu, Wei; Yang, Chao; Lin, Lin

2015-01-01

We describe a massively parallel implementation of the recently developed discontinuous Galerkin density functional theory (DGDFT) method, for efficient large-scale Kohn-Sham DFT based electronic structure calculations. The DGDFT method uses adaptive local basis (ALB) functions generated on-the-fly during the self-consistent field iteration to represent the solution to the Kohn-Sham equations. The use of the ALB set provides a systematic way to improve the accuracy of the approximation. By using the pole expansion and selected inversion technique to compute electron density, energy, and atomic forces, we can make the computational complexity of DGDFT scale at most quadratically with respect to the number of electrons for both insulating and metallic systems. We show that for the two-dimensional (2D) phosphorene systems studied here, using 37 basis functions per atom allows us to reach an accuracy level of 1.3 × 10 −4 Hartree/atom in terms of the error of energy and 6.2 × 10 −4 Hartree/bohr in terms of the error of atomic force, respectively. DGDFT can achieve 80% parallel efficiency on 128,000 high performance computing cores when it is used to study the electronic structure of 2D phosphorene systems with 3500-14 000 atoms. This high parallel efficiency results from a two-level parallelization scheme that we will describe in detail

DGDFT: A massively parallel method for large scale density functional theory calculations

Energy Technology Data Exchange (ETDEWEB)

Hu, Wei, E-mail: whu@lbl.gov; Yang, Chao, E-mail: cyang@lbl.gov [Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States); Lin, Lin, E-mail: linlin@math.berkeley.edu [Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States); Department of Mathematics, University of California, Berkeley, California 94720 (United States)

2015-09-28

We describe a massively parallel implementation of the recently developed discontinuous Galerkin density functional theory (DGDFT) method, for efficient large-scale Kohn-Sham DFT based electronic structure calculations. The DGDFT method uses adaptive local basis (ALB) functions generated on-the-fly during the self-consistent field iteration to represent the solution to the Kohn-Sham equations. The use of the ALB set provides a systematic way to improve the accuracy of the approximation. By using the pole expansion and selected inversion technique to compute electron density, energy, and atomic forces, we can make the computational complexity of DGDFT scale at most quadratically with respect to the number of electrons for both insulating and metallic systems. We show that for the two-dimensional (2D) phosphorene systems studied here, using 37 basis functions per atom allows us to reach an accuracy level of 1.3 × 10{sup −4} Hartree/atom in terms of the error of energy and 6.2 × 10{sup −4} Hartree/bohr in terms of the error of atomic force, respectively. DGDFT can achieve 80% parallel efficiency on 128,000 high performance computing cores when it is used to study the electronic structure of 2D phosphorene systems with 3500-14 000 atoms. This high parallel efficiency results from a two-level parallelization scheme that we will describe in detail.

Parallel transaction processing in functional languages, towards practical functional databases

NARCIS (Netherlands)

Wevers, L.; Huisman, Marieke; de Keijzer, Ander

2013-01-01

This paper shows how functional languages can be adapted for transaction processing, and discusses the implementation of a parallel runtime system for such functional transaction processing languages. We extend functional languages with current state variables and result state variables to allow the

Calculation of the total electron excitation cross section in the Born approximation using Slater wave functions for the Li (2s yields 2p), Li (2s yields 3p), Na (3s yields 4p), Mg (3p yields 4s), Ca (4s yields 4p) and K (4s yields 4p) excitations. M.S. Thesis

Science.gov (United States)

Simsic, P. L.

1974-01-01

Excitation of neutral atoms by inelastic scattering of incident electrons in gaseous nebulae were investigated using Slater Wave functions to describe the initial and final states of the atom. Total cross sections using the Born Approximation are calculated for: Li(2s yields 2p), Na(3s yields 4p), k(4s yields 4p). The intensity of emitted radiation from gaseous nebulae is also calculated, and Maxwell distribution is employed to average the kinetic energy of electrons.

Phosphatidylinositol-4,5-bisphosphate is required for KCNQ1/KCNE1 channel function but not anterograde trafficking.

Directory of Open Access Journals (Sweden)

Alice A Royal

Full Text Available The slow delayed-rectifier potassium current (IKs is crucial for human cardiac action potential repolarization. The formation of IKs requires co-assembly of the KCNQ1 α-subunit and KCNE1 β-subunit, and mutations in either of these subunits can lead to hereditary long QT syndrome types 1 and 5, respectively. It is widely recognised that the KCNQ1/KCNE1 (Q1/E1 channel requires phosphatidylinositol-4,5-bisphosphate (PIP2 binding for function. We previously identified a cluster of basic residues in the proximal C-terminus of KCNQ1 that form a PIP2/phosphoinositide binding site. Upon charge neutralisation of these residues we found that the channel became more retained in the endoplasmic reticulum, which raised the possibility that channel-phosphoinositide interactions could play a role in channel trafficking. To explore this further we used a chemically induced dimerization (CID system to selectively deplete PIP2 and/or phosphatidylinositol-4-phosphate (PI(4P at the plasma membrane (PM or Golgi, and we subsequently monitored the effects on both channel trafficking and function. The depletion of PIP2 and/or PI(4P at either the PM or Golgi did not alter channel cell-surface expression levels. However, channel function was extremely sensitive to the depletion of PIP2 at the PM, which is in contrast to the response of other cardiac potassium channels tested (Kir2.1 and Kv11.1. Surprisingly, when using the CID system IKs was dramatically reduced even before dimerization was induced, highlighting limitations regarding the utility of this system when studying processes highly sensitive to PIP2 depletion. In conclusion, we identify that the Q1/E1 channel does not require PIP2 or PI(4P for anterograde trafficking, but is heavily reliant on PIP2 for channel function once at the PM.

4P: fast computing of population genetics statistics from large DNA polymorphism panels.

Science.gov (United States)

Benazzo, Andrea; Panziera, Alex; Bertorelle, Giorgio

2015-01-01

Massive DNA sequencing has significantly increased the amount of data available for population genetics and molecular ecology studies. However, the parallel computation of simple statistics within and between populations from large panels of polymorphic sites is not yet available, making the exploratory analyses of a set or subset of data a very laborious task. Here, we present 4P (parallel processing of polymorphism panels), a stand-alone software program for the rapid computation of genetic variation statistics (including the joint frequency spectrum) from millions of DNA variants in multiple individuals and multiple populations. It handles a standard input file format commonly used to store DNA variation from empirical or simulation experiments. The computational performance of 4P was evaluated using large SNP (single nucleotide polymorphism) datasets from human genomes or obtained by simulations. 4P was faster or much faster than other comparable programs, and the impact of parallel computing using multicore computers or servers was evident. 4P is a useful tool for biologists who need a simple and rapid computer program to run exploratory population genetics analyses in large panels of genomic data. It is also particularly suitable to analyze multiple data sets produced in simulation studies. Unix, Windows, and MacOs versions are provided, as well as the source code for easier pipeline implementations.

Density functional theory and parallel processing

International Nuclear Information System (INIS)

Ward, R.C.; Geist, G.A.; Butler, W.H.

1987-01-01

The authors demonstrate a method for obtaining the ground state energies and charge densities of a system of atoms described within density functional theory using simulated annealing on a parallel computer

Functional networks in parallel with cortical development associate with executive functions in children.

Science.gov (United States)

Zhong, Jidan; Rifkin-Graboi, Anne; Ta, Anh Tuan; Yap, Kar Lai; Chuang, Kai-Hsiang; Meaney, Michael J; Qiu, Anqi

2014-07-01

Children begin performing similarly to adults on tasks requiring executive functions in late childhood, a transition that is probably due to neuroanatomical fine-tuning processes, including myelination and synaptic pruning. In parallel to such structural changes in neuroanatomical organization, development of functional organization may also be associated with cognitive behaviors in children. We examined 6- to 10-year-old children's cortical thickness, functional organization, and cognitive performance. We used structural magnetic resonance imaging (MRI) to identify areas with cortical thinning, resting-state fMRI to identify functional organization in parallel to cortical development, and working memory/response inhibition tasks to assess executive functioning. We found that neuroanatomical changes in the form of cortical thinning spread over bilateral frontal, parietal, and occipital regions. These regions were engaged in 3 functional networks: sensorimotor and auditory, executive control, and default mode network. Furthermore, we found that working memory and response inhibition only associated with regional functional connectivity, but not topological organization (i.e., local and global efficiency of information transfer) of these functional networks. Interestingly, functional connections associated with "bottom-up" as opposed to "top-down" processing were more clearly related to children's performance on working memory and response inhibition, implying an important role for brain systems involved in late childhood. © The Author 2013. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Rocket measurement of auroral partial parallel distribution functions

Science.gov (United States)

Lin, C.-A.

1980-01-01

The auroral partial parallel distribution functions are obtained by using the observed energy spectra of electrons. The experiment package was launched by a Nike-Tomahawk rocket from Poker Flat, Alaska over a bright auroral band and covered an altitude range of up to 180 km. Calculated partial distribution functions are presented with emphasis on their slopes. The implications of the slopes are discussed. It should be pointed out that the slope of the partial parallel distribution function obtained from one energy spectra will be changed by superposing another energy spectra on it.

Parallelization of MCNP4 code by using simple FORTRAN algorithms

International Nuclear Information System (INIS)

Yazid, P.I.; Takano, Makoto; Masukawa, Fumihiro; Naito, Yoshitaka.

1993-12-01

Simple FORTRAN algorithms, that rely only on open, close, read and write statements, together with disk files and some UNIX commands have been applied to parallelization of MCNP4. The code, named MCNPNFS, maintains almost all capabilities of MCNP4 in solving shielding problems. It is able to perform parallel computing on a set of any UNIX workstations connected by a network, regardless of the heterogeneity in hardware system, provided that all processors produce a binary file in the same format. Further, it is confirmed that MCNPNFS can be executed also on Monte-4 vector-parallel computer. MCNPNFS has been tested intensively by executing 5 photon-neutron benchmark problems, a spent fuel cask problem and 17 sample problems included in the original code package of MCNP4. Three different workstations, connected by a network, have been used to execute MCNPNFS in parallel. By measuring CPU time, the parallel efficiency is determined to be 58% to 99% and 86% in average. On Monte-4, MCNPNFS has been executed using 4 processors concurrently and has achieved the parallel efficiency of 79% in average. (author)

Comparative Study of Tributyltin Adsorption onto Mesoporous Silica Functionalized with Calix[4]arene, p-tert-Butylcalix[4]arene and p-Sulfonatocalix[4]arene

Directory of Open Access Journals (Sweden)

Sana Alahmadi

2014-04-01

Full Text Available The adsorption of tributyltin (TBT, onto three mesoporous silica adsorbents functionalized with calix[4]arene, p-tert-butylcalix[4]arene and p-sulfonatocalix[4]arene (MCM-TDI-C4, MCM-TDI-PC4 and MCM-TDI-C4S, respectively has been compared. Batch adsorption experiments were carried out and the effect of contact time, initial TBT concentration, pH and temperature were studied. The Koble–Corrigan isotherm was the most suitable for data fitting. Based on a Langmuir isotherm model, the maximum adsorption capacities were 12.1212, 16.4204 and 7.5757 mg/g for MCM-TDI-C4, MCM-TDI-PC4 and MCM-TDI-C4S, respectively. The larger uptake and stronger affinity of MCM-TDI-PC4 than MCM-TDI-C4 and MCM-TDI-C4S probably results from van der Waals interactions and the pore size distribution of MCM-TDI-PC4. Gibbs free energies for the three adsorption processes of TBT presented a negative value, reflecting that TBT/surface interactions are thermodynamic favorable and spontaneous. The interaction processes were accompanied by an increase of entropy value for MCM-TDI-C4 and MCM-TDI-C4S (43.7192 and 120.7609 J/mol K, respectively and a decrease for MCM-TDI-PC4 (−37.4704 J/mol K. It is obviously observed that MCM-TDI-PC4 spontaneously adsorbs TBT driven mainly by enthalpy change, while MCM-TDI-C4 and MCM-TDI-C4S do so driven mainly by entropy changes.

Professional Parallel Programming with C# Master Parallel Extensions with NET 4

CERN Document Server

Hillar, Gastón

2010-01-01

Expert guidance for those programming today's dual-core processors PCs As PC processors explode from one or two to now eight processors, there is an urgent need for programmers to master concurrent programming. This book dives deep into the latest technologies available to programmers for creating professional parallel applications using C#, .NET 4, and Visual Studio 2010. The book covers task-based programming, coordination data structures, PLINQ, thread pools, asynchronous programming model, and more. It also teaches other parallel programming techniques, such as SIMD and vectorization.Teach

Metalate-Mediated Functionalization of P4 by Trapping Anionic [Cp*Fe(CO)2(η1-P4)]− with Lewis Acids

NARCIS (Netherlands)

Borger, Jaap E.; Jongkind, Maarten K.; Ehlers, Andreas W.; Lutz, Martin; Slootweg, J. Chris; Lammertsma, Koop

2017-01-01

The development of selective functionalization strategies ofwhite phosphorus (P4) is important to avoid the current chlori-nated intermediates. The use of transition metals (TMs) couldlead to catalytic procedures, but these are severely hamperedby the high reactivity and unpredictable nature of the

Not all hypochondroplasia families are linked to chromosome 4p16.3

Energy Technology Data Exchange (ETDEWEB)

Rousseau, F.; Munnich, A.; Merrer, M.Le. [INSERM, Paris (France)] [and others

1994-09-01

Achondroplasia (ACH, MIM 100800) and hypochondroplasia (HCH, MIM 146000) are short limb dwarfism with enlarged head sharing some specific radiological features. Inter- and intrafamilial clinical variability and histolopathological aspects of the growth cartilage suggested that ACH and HCH are allelic disorders. Recently, the gene for achondroplasia was mapped to chromosome 4p and no recombinants were found in 9 families with hypochondroplasia between D4S111 and the telomere (Zmax=1.70, {theta}=0). By using an additional polymorphic DNA marker which detects VNTR-like polymorphism at the D4S227 locus and a new microsatellite at locus D4S? (AFM163yc1), we observed recombinant events with markers of the chromosome 4p16.3 in 3/10 hypochondroplasia families, indicating that not all hypochondroplasia families are linked to chromosome 4p. A fibroblast growth factor receptor (FGFR3) expressed in chondrocytes during endochondral ossification which is located in the 2.5 Mb candidate region for achondroplasia was regarded as a good candidate gene. No major rearrangement of the FGFR3 gene was detected by Southern blot analysis using an FGFR3 cDNA probe. Further investigations will be required to conclude as to the possible involvement of this gene in ACH.

Parallel keyed hash function construction based on chaotic maps

International Nuclear Information System (INIS)

Xiao Di; Liao Xiaofeng; Deng Shaojiang

2008-01-01

Recently, a variety of chaos-based hash functions have been proposed. Nevertheless, none of them works efficiently in parallel computing environment. In this Letter, an algorithm for parallel keyed hash function construction is proposed, whose structure can ensure the uniform sensitivity of hash value to the message. By means of the mechanism of both changeable-parameter and self-synchronization, the keystream establishes a close relation with the algorithm key, the content and the order of each message block. The entire message is modulated into the chaotic iteration orbit, and the coarse-graining trajectory is extracted as the hash value. Theoretical analysis and computer simulation indicate that the proposed algorithm can satisfy the performance requirements of hash function. It is simple, efficient, practicable, and reliable. These properties make it a good choice for hash on parallel computing platform

High temporal resolution functional MRI using parallel echo volumar imaging

International Nuclear Information System (INIS)

Rabrait, C.; Ciuciu, P.; Ribes, A.; Poupon, C.; Dehaine-Lambertz, G.; LeBihan, D.; Lethimonnier, F.; Le Roux, P.; Dehaine-Lambertz, G.

2008-01-01

Purpose: To combine parallel imaging with 3D single-shot acquisition (echo volumar imaging, EVI) in order to acquire high temporal resolution volumar functional MRI (fMRI) data. Materials and Methods: An improved EVI sequence was associated with parallel acquisition and field of view reduction in order to acquire a large brain volume in 200 msec. Temporal stability and functional sensitivity were increased through optimization of all imaging parameters and Tikhonov regularization of parallel reconstruction. Two human volunteers were scanned with parallel EVI in a 1.5 T whole-body MR system, while submitted to a slow event-related auditory paradigm. Results: Thanks to parallel acquisition, the EVI volumes display a low level of geometric distortions and signal losses. After removal of low-frequency drifts and physiological artifacts,activations were detected in the temporal lobes of both volunteers and voxel-wise hemodynamic response functions (HRF) could be computed. On these HRF different habituation behaviors in response to sentence repetition could be identified. Conclusion: This work demonstrates the feasibility of high temporal resolution 3D fMRI with parallel EVI. Combined with advanced estimation tools,this acquisition method should prove useful to measure neural activity timing differences or study the nonlinearities and non-stationarities of the BOLD response. (authors)

Parallel sites implicate functional convergence of the hearing gene prestin among echolocating mammals.

Science.gov (United States)

Liu, Zhen; Qi, Fei-Yan; Zhou, Xin; Ren, Hai-Qing; Shi, Peng

2014-09-01

Echolocation is a sensory system whereby certain mammals navigate and forage using sound waves, usually in environments where visibility is limited. Curiously, echolocation has evolved independently in bats and whales, which occupy entirely different environments. Based on this phenotypic convergence, recent studies identified several echolocation-related genes with parallel sites at the protein sequence level among different echolocating mammals, and among these, prestin seems the most promising. Although previous studies analyzed the evolutionary mechanism of prestin, the functional roles of the parallel sites in the evolution of mammalian echolocation are not clear. By functional assays, we show that a key parameter of prestin function, 1/α, is increased in all echolocating mammals and that the N7T parallel substitution accounted for this functional convergence. Moreover, another parameter, V1/2, was shifted toward the depolarization direction in a toothed whale, the bottlenose dolphin (Tursiops truncatus) and a constant-frequency (CF) bat, the Stoliczka's trident bat (Aselliscus stoliczkanus). The parallel site of I384T between toothed whales and CF bats was responsible for this functional convergence. Furthermore, the two parameters (1/α and V1/2) were correlated with mammalian high-frequency hearing, suggesting that the convergent changes of the prestin function in echolocating mammals may play important roles in mammalian echolocation. To our knowledge, these findings present the functional patterns of echolocation-related genes in echolocating mammals for the first time and rigorously demonstrate adaptive parallel evolution at the protein sequence level, paving the way to insights into the molecular mechanism underlying mammalian echolocation. © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Calpain 4 is not necessary for LFA-1-mediated function in CD4+ T cells.

Directory of Open Access Journals (Sweden)

Sarah A Wernimont

2010-05-01

Full Text Available T cell activation and immune synapse formation require the appropriate activation and clustering of the integrin, LFA-1. Previous work has reported that the calpain family of calcium-dependent proteases are important regulators of integrin activation and modulate T cell adhesion and migration. However, these studies have been limited by the use of calpain inhibitors, which have known off-target effects.Here, we used a LoxP/CRE system to specifically deplete calpain 4, a small regulatory calpain subunit required for expression and activity of ubiquitously expressed calpains 1 and 2, in CD4+ T cells. CD4+ and CD8+ T cells developed normally in Capn4(F/F:CD4-CRE mice and had severely diminished expression of Calpain 1 and 2, diminished talin proteolysis and impaired casein degradation. Calpain 4-deficient T cells showed no difference in adhesion or migration on the LFA-1 ligand ICAM-1 compared to control T cells. Moreover, there was no impairment in conjugation between Capn4(F/F:CD4-CRE T cells and antigen presenting cells, and the conjugates were still capable of polarizing LFA-1, PKC-theta and actin to the immune synapse. Furthermore, T cells from Capn4(F/F:CD4-CRE mice showed normal proliferation in response to either anti-CD3/CD28 coated beads or cognate antigen-loaded splenocytes. Finally, there were no differences in the rates of apoptosis following extrinsic and intrinsic apoptotic stimuli.Our findings demonstrate that calpain 4 is not necessary for LFA-1-mediated adhesion, conjugation or migration. These results challenge previous reports that implicate a central role for calpains in the regulation of T cell LFA-1 function.

Unpacking the cognitive map: the parallel map theory of hippocampal function.

Science.gov (United States)

Jacobs, Lucia F; Schenk, Françoise

2003-04-01

In the parallel map theory, the hippocampus encodes space with 2 mapping systems. The bearing map is constructed primarily in the dentate gyrus from directional cues such as stimulus gradients. The sketch map is constructed within the hippocampus proper from positional cues. The integrated map emerges when data from the bearing and sketch maps are combined. Because the component maps work in parallel, the impairment of one can reveal residual learning by the other. Such parallel function may explain paradoxes of spatial learning, such as learning after partial hippocampal lesions, taxonomic and sex differences in spatial learning, and the function of hippocampal neurogenesis. By integrating evidence from physiology to phylogeny, the parallel map theory offers a unified explanation for hippocampal function.

Functional and genetic epidemiological characterisation of the FFAR4 (GPR120) p.R270H variant in the Danish population

DEFF Research Database (Denmark)

Vestmar, Marie Aare; Andersson, Ehm A; Christensen, Charlotte Riis

2016-01-01

. Association with quantitative metabolic traits comprised 8720 non-diabetic individuals. RESULTS: p.R270H showed reduced surface expression of FFAR4. Ligand-independent activity was eliminated and strongly impaired through the Gq and Gi signalling pathways, respectively. The ligand-induced maximal signalling...... reactive protein; hs-CRP) and liver function (alanine aminotransferase) in the Danish population (p>0.05). CONCLUSIONS: We demonstrate that p.R270H of FFAR4 impairs Gq and Gi signalling of FFAR4 in vitro; however, this impaired signalling for p.R270H does not translate into associations with human...

P53 family members modulate the expression of PRODH, but not PRODH2, via intronic p53 response elements.

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Ivan Raimondi

Full Text Available The tumor suppressor p53 was previously shown to markedly up-regulate the expression of the PRODH gene, encoding the proline dehydrogenase (PRODH enzyme, which catalyzes the first step in proline degradation. Also PRODH2, which degrades 4-hydroxy-L-proline, a product of protein (e.g. collagen catabolism, was recently described as a p53 target. Here, we confirmed p53-dependent induction of endogenous PRODH in response to genotoxic damage in cell lines of different histological origin. We established that over-expression of TAp73β or TAp63β is sufficient to induce PRODH expression in p53-null cells and that PRODH expression parallels the modulation of endogenous p73 by genotoxic drugs in several cell lines. The p53, p63, and p73-dependent transcriptional activation was linked to specific intronic response elements (REs, among those predicted by bioinformatics tools and experimentally validated by a yeast-based transactivation assay. p53 occupancy measurements were validated in HCT116 and MCF7 human cell lines. Conversely, PRODH2 was not responsive to p63 nor p73 and, at best, could be considered a weak p53 target. In fact, minimal levels of PRODH2 transcript induction by genotoxic stress was observed exclusively in one of four p53 wild-type cell lines tested. Consistently, all predicted p53 REs in PRODH2 were poor matches to the p53 RE consensus and showed very weak responsiveness, only to p53, in the functional assay. Taken together, our results highlight that PRODH, but not PRODH2, expression is under the control of p53 family members, specifically p53 and p73. This supports a deeper link between proteins of the p53-family and metabolic pathways, as PRODH modulates the balance of proline and glutamate levels and those of their derivative alpha-keto-glutarate (α-KG under normal and pathological (tumor conditions.

Simplifying the parallelization of scientific codes by a function-centric approach in Python

International Nuclear Information System (INIS)

Nilsen, Jon K; Cai Xing; Langtangen, Hans Petter; Hoeyland, Bjoern

2010-01-01

The purpose of this paper is to show how existing scientific software can be parallelized using a separate thin layer of Python code where all parallelization-specific tasks are implemented. We provide specific examples of such a Python code layer, which can act as templates for parallelizing a wide set of serial scientific codes. The use of Python for parallelization is motivated by the fact that the language is well suited for reusing existing serial codes programmed in other languages. The extreme flexibility of Python with regard to handling functions makes it very easy to wrap up decomposed computational tasks of a serial scientific application as Python functions. Many parallelization-specific components can be implemented as generic Python functions, which may take as input those wrapped functions that perform concrete computational tasks. The overall programming effort needed by this parallelization approach is limited, and the resulting parallel Python scripts have a compact and clean structure. The usefulness of the parallelization approach is exemplified by three different classes of application in natural and social sciences.

Bessel functions: parallel display and processing.

Science.gov (United States)

Lohmann, A W; Ojeda-Castañeda, J; Serrano-Heredia, A

1994-01-01

We present an optical setup that converts planar binary curves into two-dimensional amplitude distributions, which are proportional, along one axis, to the Bessel function of order n, whereas along the other axis the order n increases. This Bessel displayer can be used for parallel Bessel transformation of a signal. Experimental verifications are included.

The parallel processing of EGS4 code on distributed memory scalar parallel computer:Intel Paragon XP/S15-256

Energy Technology Data Exchange (ETDEWEB)

Takemiya, Hiroshi; Ohta, Hirofumi; Honma, Ichirou

1996-03-01

The parallelization of Electro-Magnetic Cascade Monte Carlo Simulation Code, EGS4 on distributed memory scalar parallel computer: Intel Paragon XP/S15-256 is described. EGS4 has the feature that calculation time for one incident particle is quite different from each other because of the dynamic generation of secondary particles and different behavior of each particle. Granularity for parallel processing, parallel programming model and the algorithm of parallel random number generation are discussed and two kinds of method, each of which allocates particles dynamically or statically, are used for the purpose of realizing high speed parallel processing of this code. Among four problems chosen for performance evaluation, the speedup factors for three problems have been attained to nearly 100 times with 128 processor. It has been found that when both the calculation time for each incident particles and its dispersion are large, it is preferable to use dynamic particle allocation method which can average the load for each processor. And it has also been found that when they are small, it is preferable to use static particle allocation method which reduces the communication overhead. Moreover, it is pointed out that to get the result accurately, it is necessary to use double precision variables in EGS4 code. Finally, the workflow of program parallelization is analyzed and tools for program parallelization through the experience of the EGS4 parallelization are discussed. (author).

The Parallel System for Integrating Impact Models and Sectors (pSIMS)

Science.gov (United States)

Elliott, Joshua; Kelly, David; Chryssanthacopoulos, James; Glotter, Michael; Jhunjhnuwala, Kanika; Best, Neil; Wilde, Michael; Foster, Ian

2014-01-01

We present a framework for massively parallel climate impact simulations: the parallel System for Integrating Impact Models and Sectors (pSIMS). This framework comprises a) tools for ingesting and converting large amounts of data to a versatile datatype based on a common geospatial grid; b) tools for translating this datatype into custom formats for site-based models; c) a scalable parallel framework for performing large ensemble simulations, using any one of a number of different impacts models, on clusters, supercomputers, distributed grids, or clouds; d) tools and data standards for reformatting outputs to common datatypes for analysis and visualization; and e) methodologies for aggregating these datatypes to arbitrary spatial scales such as administrative and environmental demarcations. By automating many time-consuming and error-prone aspects of large-scale climate impacts studies, pSIMS accelerates computational research, encourages model intercomparison, and enhances reproducibility of simulation results. We present the pSIMS design and use example assessments to demonstrate its multi-model, multi-scale, and multi-sector versatility.

Inactivation of Cytochrome P450 (P450) 3A4 but not P450 3A5 by OSI-930, a Thiophene-Containing Anticancer DrugS⃞

Science.gov (United States)

Lin, Hsia-lien; Zhang, Haoming; Medower, Christine; Johnson, William W.

2011-01-01

An investigational anticancer agent that contains a thiophene moiety, 3-[(quinolin-4-ylmethyl)-amino]-N-[4-trifluoromethox)phenyl] thiophene-2-carboxamide (OSI-930), was tested to investigate its ability to modulate the activities of several cytochrome P450 enzymes. Results showed that OSI-930 inactivated purified, recombinant cytochrome P450 (P450) 3A4 in the reconstituted system in a mechanism-based manner. The inactivation was dependent on cytochrome b5 and required NADPH. Catalase did not protect against the inactivation. No inactivation was observed in studies with human 2B6, 2D6, or 3A5 either in the presence or in the absence of b5. The inactivation of 3A4 by OSI-930 was time- and concentration-dependent. The inactivation of the 7-benzyloxy-4-(trifluoromethyl)coumarin catalytic activity of 3A4 was characterized by a KI of 24 μM and a kinact of 0.04 min−1. This KI is significantly greater than the clinical OSI-930 Cmax of 1.7 μM at the maximum tolerated dose, indicating that clinical drug interactions of OSI-930 via this pathway are not likely. Spectral analysis of the inactivated protein indicated that the decrease in the reduced CO spectrum at 450 nm was comparable to the amount of inactivation, thereby suggesting that the inactivation was primarily due to modification of the heme. High-pressure liquid chromatography (HPLC) analysis with detection at 400 nm showed a loss of heme comparable to the activity loss, but a modified heme was not detected. This result suggests either that the heme must have been modified enough so as not to be observed in a HPLC chromatograph or, possibly, that it was destroyed. The partition ratio for the inactivation of P450 3A4 was approximately 23, suggesting that this P450 3A4-mediated pathway occurs with approximately 4% frequency during the metabolism of OSI-930. Modeling studies on the binding of OSI-930 to the active site of the P450 3A4 indicated that OSI-930 would be oriented properly in the active site for oxidation

Convergent Evolution of Hemoglobin Function in High-Altitude Andean Waterfowl Involves Limited Parallelism at the Molecular Sequence Level.

Directory of Open Access Journals (Sweden)

Chandrasekhar Natarajan

2015-12-01

Full Text Available A fundamental question in evolutionary genetics concerns the extent to which adaptive phenotypic convergence is attributable to convergent or parallel changes at the molecular sequence level. Here we report a comparative analysis of hemoglobin (Hb function in eight phylogenetically replicated pairs of high- and low-altitude waterfowl taxa to test for convergence in the oxygenation properties of Hb, and to assess the extent to which convergence in biochemical phenotype is attributable to repeated amino acid replacements. Functional experiments on native Hb variants and protein engineering experiments based on site-directed mutagenesis revealed the phenotypic effects of specific amino acid replacements that were responsible for convergent increases in Hb-O2 affinity in multiple high-altitude taxa. In six of the eight taxon pairs, high-altitude taxa evolved derived increases in Hb-O2 affinity that were caused by a combination of unique replacements, parallel replacements (involving identical-by-state variants with independent mutational origins in different lineages, and collateral replacements (involving shared, identical-by-descent variants derived via introgressive hybridization. In genome scans of nucleotide differentiation involving high- and low-altitude populations of three separate species, function-altering amino acid polymorphisms in the globin genes emerged as highly significant outliers, providing independent evidence for adaptive divergence in Hb function. The experimental results demonstrate that convergent changes in protein function can occur through multiple historical paths, and can involve multiple possible mutations. Most cases of convergence in Hb function did not involve parallel substitutions and most parallel substitutions did not affect Hb-O2 affinity, indicating that the repeatability of phenotypic evolution does not require parallelism at the molecular level.

Cross sections for electron-impact excitation of krypton from the levels of 4p6, 4p55s, and 4p55p configurations

International Nuclear Information System (INIS)

Zeng Jiaolong; Yuan Jianmin; Wu Jianhua; Jin Fengtao; Zhao Gang

2005-01-01

The electron-impact excitation cross sections at low electron energies have been calculated using a fully relativistic R-matrix method for transitions between levels of 4p 6 , 4p 5 5s, and 4p 5 5p configurations. To ensure the convergence of results, we have paid special attention to the factors that may affect the convergence of cross sections. For examples, we have included extensive configuration interactions in the wave-function expansion of the target states. A large enough R-matrix boundary has been taken to ensure the convergence of atomic wave functions. Contributions to cross sections from a large number of partial waves (up to J=39.5) have been explicitly calculated. The final results are in good agreement with recent experimental data by Jung et al. [Phys. Rev. Lett. 94, 163202 (2005)] after shifting the position of electron energy. The relative difference is about 10% for four transitions out of the metastable levels. The results eliminated the significant discrepancies between theory and experimental work on excitation cross sections out of the metastable levels reported in the literature

Outer membrane protein P4 is not required for virulence in the human challenge model of Haemophilus ducreyi infection.

Science.gov (United States)

Janowicz, Diane M; Zwickl, Beth W; Fortney, Kate R; Katz, Barry P; Bauer, Margaret E

2014-06-24

Bacterial lipoproteins often play important roles in pathogenesis and can stimulate protective immune responses. Such lipoproteins are viable vaccine candidates. Haemophilus ducreyi, which causes the sexually transmitted disease chancroid, expresses a number of lipoproteins during human infection. One such lipoprotein, OmpP4, is homologous to the outer membrane lipoprotein e (P4) of H. influenzae. In H. influenzae, e (P4) stimulates production of bactericidal and protective antibodies and contributes to pathogenesis by facilitating acquisition of the essential nutrients heme and nicotinamide adenine dinucleotide (NAD). Here, we tested the hypothesis that, like its homolog, H. ducreyi OmpP4 contributes to virulence and stimulates production of bactericidal antibodies. We determined that OmpP4 is broadly conserved among clinical isolates of H. ducreyi. We next constructed and characterized an isogenic ompP4 mutant, designated 35000HPompP4, in H. ducreyi strain 35000HP. To test whether OmpP4 was necessary for virulence in humans, eight healthy adults were experimentally infected. Each subject was inoculated with a fixed dose of 35000HP on one arm and three doses of 35000HPompP4 on the other arm. The overall parent and mutant pustule formation rates were 52.4% and 47.6%, respectively (P = 0.74). These results indicate that expression of OmpP4 in not necessary for H. ducreyi to initiate disease or progress to pustule formation in humans. Hyperimmune mouse serum raised against purified, recombinant OmpP4 did not promote bactericidal killing of 35000HP or phagocytosis by J774A.1 mouse macrophages in serum bactericidal and phagocytosis assays, respectively. Our data suggest that, unlike e (P4), H. ducreyi OmpP4 is not a suitable vaccine candidate. OmpP4 may be dispensable for virulence because of redundant mechanisms in H. ducreyi for heme acquisition and NAD utilization.

Multiple roles of the extracellular vestibule amino acid residues in the function of the rat P2X4 receptor.

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Milos B Rokic

Full Text Available The binding of ATP to trimeric P2X receptors (P2XR causes an enlargement of the receptor extracellular vestibule, leading to opening of the cation-selective transmembrane pore, but specific roles of vestibule amino acid residues in receptor activation have not been evaluated systematically. In this study, alanine or cysteine scanning mutagenesis of V47-V61 and F324-N338 sequences of rat P2X4R revealed that V49, Y54, Q55, F324, and G325 mutants were poorly responsive to ATP and trafficking was only affected by the V49 mutation. The Y54F and Y54W mutations, but not the Y54L mutation, rescued receptor function, suggesting that an aromatic residue is important at this position. Furthermore, the Y54A and Y54C receptor function was partially rescued by ivermectin, a positive allosteric modulator of P2X4R, suggesting a rightward shift in the potency of ATP to activate P2X4R. The Q55T, Q55N, Q55E, and Q55K mutations resulted in non-responsive receptors and only the Q55E mutant was ivermectin-sensitive. The F324L, F324Y, and F324W mutations also rescued receptor function partially or completely, ivermectin action on channel gating was preserved in all mutants, and changes in ATP responsiveness correlated with the hydrophobicity and side chain volume of the substituent. The G325P mutant had a normal response to ATP, suggesting that G325 is a flexible hinge. A topological analysis revealed that the G325 and F324 residues disrupt a β-sheet upon ATP binding. These results indicate multiple roles of the extracellular vestibule amino acid residues in the P2X4R function: the V49 residue is important for receptor trafficking to plasma membrane, the Y54 and Q55 residues play a critical role in channel gating and the F324 and G325 residues are critical for vestibule widening.

High temporal resolution magnetic resonance imaging: development of a parallel three dimensional acquisition method for functional neuroimaging

International Nuclear Information System (INIS)

Rabrait, C.

2007-11-01

Echo Planar Imaging is widely used to perform data acquisition in functional neuroimaging. This sequence allows the acquisition of a set of about 30 slices, covering the whole brain, at a spatial resolution ranging from 2 to 4 mm, and a temporal resolution ranging from 1 to 2 s. It is thus well adapted to the mapping of activated brain areas but does not allow precise study of the brain dynamics. Moreover, temporal interpolation is needed in order to correct for inter-slices delays and 2-dimensional acquisition is subject to vascular in flow artifacts. To improve the estimation of the hemodynamic response functions associated with activation, this thesis aimed at developing a 3-dimensional high temporal resolution acquisition method. To do so, Echo Volume Imaging was combined with reduced field-of-view acquisition and parallel imaging. Indeed, E.V.I. allows the acquisition of a whole volume in Fourier space following a single excitation, but it requires very long echo trains. Parallel imaging and field-of-view reduction are used to reduce the echo train durations by a factor of 4, which allows the acquisition of a 3-dimensional brain volume with limited susceptibility-induced distortions and signal losses, in 200 ms. All imaging parameters have been optimized in order to reduce echo train durations and to maximize S.N.R., so that cerebral activation can be detected with a high level of confidence. Robust detection of brain activation was demonstrated with both visual and auditory paradigms. High temporal resolution hemodynamic response functions could be estimated through selective averaging of the response to the different trials of the stimulation. To further improve S.N.R., the matrix inversions required in parallel reconstruction were regularized, and the impact of the level of regularization on activation detection was investigated. Eventually, potential applications of parallel E.V.I. such as the study of non-stationary effects in the B.O.L.D. response

NDL-v2.0: A new version of the numerical differentiation library for parallel architectures

Science.gov (United States)

Hadjidoukas, P. E.; Angelikopoulos, P.; Voglis, C.; Papageorgiou, D. G.; Lagaris, I. E.

2014-07-01

We present a new version of the numerical differentiation library (NDL) used for the numerical estimation of first and second order partial derivatives of a function by finite differencing. In this version we have restructured the serial implementation of the code so as to achieve optimal task-based parallelization. The pure shared-memory parallelization of the library has been based on the lightweight OpenMP tasking model allowing for the full extraction of the available parallelism and efficient scheduling of multiple concurrent library calls. On multicore clusters, parallelism is exploited by means of TORC, an MPI-based multi-threaded tasking library. The new MPI implementation of NDL provides optimal performance in terms of function calls and, furthermore, supports asynchronous execution of multiple library calls within legacy MPI programs. In addition, a Python interface has been implemented for all cases, exporting the functionality of our library to sequential Python codes. Catalog identifier: AEDG_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEDG_v2_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 63036 No. of bytes in distributed program, including test data, etc.: 801872 Distribution format: tar.gz Programming language: ANSI Fortran-77, ANSI C, Python. Computer: Distributed systems (clusters), shared memory systems. Operating system: Linux, Unix. Has the code been vectorized or parallelized?: Yes. RAM: The library uses O(N) internal storage, N being the dimension of the problem. It can use up to O(N2) internal storage for Hessian calculations, if a task throttling factor has not been set by the user. Classification: 4.9, 4.14, 6.5. Catalog identifier of previous version: AEDG_v1_0 Journal reference of previous version: Comput. Phys. Comm. 180

11th International Conference on P2P, Parallel, Grid, Cloud and Internet Computing

CERN Document Server

Barolli, Leonard; Amato, Flora

2017-01-01

P2P, Grid, Cloud and Internet computing technologies have been very fast established as breakthrough paradigms for solving complex problems by enabling aggregation and sharing of an increasing variety of distributed computational resources at large scale. The aim of this volume is to provide latest research findings, innovative research results, methods and development techniques from both theoretical and practical perspectives related to P2P, Grid, Cloud and Internet computing as well as to reveal synergies among such large scale computing paradigms. This proceedings volume presents the results of the 11th International Conference on P2P, Parallel, Grid, Cloud And Internet Computing (3PGCIC-2016), held November 5-7, 2016, at Soonchunhyang University, Asan, Korea.

The Voltage-Gated Potassium Channel Subfamily KQT Member 4 (KCNQ4) Displays Parallel Evolution in Echolocating Bats

Science.gov (United States)

Liu, Yang; Han, Naijian; Franchini, Lucía F.; Xu, Huihui; Pisciottano, Francisco; Elgoyhen, Ana Belén; Rajan, Koilmani Emmanuvel; Zhang, Shuyi

2012-01-01

Bats are the only mammals that use highly developed laryngeal echolocation, a sensory mechanism based on the ability to emit laryngeal sounds and interpret the returning echoes to identify objects. Although this capability allows bats to orientate and hunt in complete darkness, endowing them with great survival advantages, the genetic bases underlying the evolution of bat echolocation are still largely unknown. Echolocation requires high-frequency hearing that in mammals is largely dependent on somatic electromotility of outer hair cells. Then, understanding the molecular evolution of outer hair cell genes might help to unravel the evolutionary history of echolocation. In this work, we analyzed the molecular evolution of two key outer hair cell genes: the voltage-gated potassium channel gene KCNQ4 and CHRNA10, the gene encoding the α10 nicotinic acetylcholine receptor subunit. We reconstructed the phylogeny of bats based on KCNQ4 and CHRNA10 protein and nucleotide sequences. A phylogenetic tree built using KCNQ4 amino acid sequences showed that two paraphyletic clades of laryngeal echolocating bats grouped together, with eight shared substitutions among particular lineages. In addition, our analyses indicated that two of these parallel substitutions, M388I and P406S, were probably fixed under positive selection and could have had a strong functional impact on KCNQ4. Moreover, our results indicated that KCNQ4 evolved under positive selection in the ancestral lineage leading to mammals, suggesting that this gene might have been important for the evolution of mammalian hearing. On the other hand, we found that CHRNA10, a gene that evolved adaptively in the mammalian lineage, was under strong purifying selection in bats. Thus, the CHRNA10 amino acid tree did not show echolocating bat monophyly and reproduced the bat species tree. These results suggest that only a subset of hearing genes could underlie the evolution of echolocation. The present work continues to

A Novel Design of 4-Class BCI Using Two Binary Classifiers and Parallel Mental Tasks

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Tao Geng

2008-01-01

Full Text Available A novel 4-class single-trial brain computer interface (BCI based on two (rather than four or more binary linear discriminant analysis (LDA classifiers is proposed, which is called a “parallel BCI.” Unlike other BCIs where mental tasks are executed and classified in a serial way one after another, the parallel BCI uses properly designed parallel mental tasks that are executed on both sides of the subject body simultaneously, which is the main novelty of the BCI paradigm used in our experiments. Each of the two binary classifiers only classifies the mental tasks executed on one side of the subject body, and the results of the two binary classifiers are combined to give the result of the 4-class BCI. Data was recorded in experiments with both real movement and motor imagery in 3 able-bodied subjects. Artifacts were not detected or removed. Offline analysis has shown that, in some subjects, the parallel BCI can generate a higher accuracy than a conventional 4-class BCI, although both of them have used the same feature selection and classification algorithms.

Human rotavirus strains bearing VP4 gene P[6] allele recovered from asymptomatic or symptomatic infections share similar, if not identical, VP4 neutralization specificities

International Nuclear Information System (INIS)

Hoshino, Yasutaka; Jones, Ronald W.; Ross, Jerri; Santos, Norma; Kapikian, Albert Z.

2003-01-01

A rotavirus VP4 gene P[6] allele has been documented in a number of countries to be characteristically associated with an endemic predominantly asymptomatic infection in neonates in maternity hospital nurseries. The mechanisms underlying the endemicity and asymptomatic nature of such neonatal infections remain unknown. Rotavirus strains sharing this same P genotype, however, have more recently been recovered from an increasing number of symptomatic diarrheal episodes in infants and young children in various parts of the world. Previously, we have shown that an asymptomatic P[6] rotavirus neonatal infection is not associated with a unique VP7 (G) serotype but may occur in conjunction with various G types. Although amino acid sequence comparisons of the VP4 gene between selected 'asymptomatic' and 'symptomatic' P[6] rotavirus strains have been reported and yielded information concerning their VP4 genotypes, serotypic comparisons of the outer capsid spike protein VP4 of such viruses have not been studied systematically by two-way cross-neutralizations. We determined the VP4 neutralization specificities of four asymptomatic and four symptomatic P[6] strains: two each of asymptomatic and symptomatic strains by two-way tests, and two each of additional asymptomatic and symptomatic strains by one-way tests. Both asymptomatic and symptomatic P[6] strains were shown to bear similar, if not identical, VP4 neutralization specificities. Thus, P[6] rotavirus strains causing asymptomatic or symptomatic infections did not appear to belong to unique P (VP4) serotypes. In addition, a close VP4 serotypic relationship between human P[6] rotavirus strains and the porcine P[6] rotavirus Gottfried strain was confirmed

HYPERDIRE. HYPERgeometric functions DIfferential REduction. MATHEMATICA based packages for differential reduction of generalized hypergeometric functions {sub p}F{sub p-1}, F{sub 1}, F{sub 2}, F{sub 3}, F{sub 4}

Energy Technology Data Exchange (ETDEWEB)

Bytev, Vladimir V.; Kalmykov, Mikhail Yu. [Hamburg Univ. (Germany). 2. Inst. fuer Theoretische Physik; Joint Institute for Nuclear Research, Dubna (Russian Federation); Kniehl, Bernd A. [Hamburg Univ. (Germany). 2. Inst. fuer Theoretische Physik

2013-05-15

HYPERDIRE is a project devoted to the creation of a set of Mathematica based programs for the differential reduction of hypergeometric functions. The current version includes two parts: one, pfq, is relevant for manipulations of hypergeometric functions {sub p+1}F{sub p}, and the second one, AppellF1F4, for manipulations with Appell hypergeometric functions F{sub 1}, F{sub 2}, F{sub 3}, F{sub 4} of two variables.

Excitation function measurements of sup 4 sup 0 Ar(p,3n) sup 3 sup 8 K, sup 4 sup 0 Ar(p,2pn) sup 3 sup 8 Cl and sup 4 sup 0 Ar(p,2p) sup 3 sup 9 Cl reactions

CERN Document Server

Nagatsu, K; Suzuki, K

1999-01-01

For the production of sup 3 sup 8 K, excitation functions of the sup 4 sup 0 Ar(p,3n) sup 3 sup 8 K reaction and its accompanying reactions sup 4 sup 0 Ar(p,2pn) sup 3 sup 8 Cl, and sup 4 sup 0 Ar(p,2p) sup 3 sup 9 Cl were measured at the proton energy of 20.5-39.5 MeV to determine the optimum conditions of irradiation. Target cells containing argon gas were prepared using specially developed tools in an argon-replaced glove box. In the sup 4 sup 0 Ar(p,3n) sup 3 sup 8 K, sup 4 sup 0 Ar(p,2pn) sup 3 sup 8 Cl, and sup 4 sup 0 Ar(p,2p) sup 3 sup 9 Cl reactions, the maximum cross sections were 6.7+-0.7, 34+-3.3 and 11+-1.2mbarn at 37.6, 39.5 and 32.0 MeV, respectively, and the saturation thick target yields were calculated to be 560, 2200, and 1300 sup * MBq/mu A, respectively, at an incident energy of 39.5 MeV ( sup * integral yield above 21 MeV).

Involvement of Histidine Residue His382 in pH Regulation of MCT4 Activity.

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Shotaro Sasaki

Full Text Available Monocarboxylate transporter 4 (MCT4 is a pH-dependent bi-directional lactate transporter. Transport of lactate via MCT4 is increased by extracellular acidification. We investigated the critical histidine residue involved in pH regulation of MCT4 function. Transport of lactate via MCT4 was measured by using a Xenopus laevis oocyte expression system. MCT4-mediated lactate transport was inhibited by Zn2+ in a pH physiological condition but not in an acidic condition. The histidine modifier DEPC (diethyl pyrocarbonate reduced MCT4 activity but did not completely inactivate MCT4. After treatment with DEPC, pH regulation of MCT4 function was completely knocked out. Inhibitory effects of DEPC were reversed by hydroxylamine and suppressed in the presence of excess lactate and Zn2+. Therefore, we performed an experiment in which the extracellular histidine residue was replaced with alanine. Consequently, the pH regulation of MCT4-H382A function was also knocked out. Our findings demonstrate that the histidine residue His382 in the extracellular loop of the transporter is essential for pH regulation of MCT4-mediated substrate transport activity.

P3T+: A Performance Estimator for Distributed and Parallel Programs

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T. Fahringer

2000-01-01

Full Text Available Developing distributed and parallel programs on today's multiprocessor architectures is still a challenging task. Particular distressing is the lack of effective performance tools that support the programmer in evaluating changes in code, problem and machine sizes, and target architectures. In this paper we introduce P3T+ which is a performance estimator for mostly regular HPF (High Performance Fortran programs but partially covers also message passing programs (MPI. P3T+ is unique by modeling programs, compiler code transformations, and parallel and distributed architectures. It computes at compile-time a variety of performance parameters including work distribution, number of transfers, amount of data transferred, transfer times, computation times, and number of cache misses. Several novel technologies are employed to compute these parameters: loop iteration spaces, array access patterns, and data distributions are modeled by employing highly effective symbolic analysis. Communication is estimated by simulating the behavior of a communication library used by the underlying compiler. Computation times are predicted through pre-measured kernels on every target architecture of interest. We carefully model most critical architecture specific factors such as cache lines sizes, number of cache lines available, startup times, message transfer time per byte, etc. P3T+ has been implemented and is closely integrated with the Vienna High Performance Compiler (VFC to support programmers develop parallel and distributed applications. Experimental results for realistic kernel codes taken from real-world applications are presented to demonstrate both accuracy and usefulness of P3T+.

Implication of Ccr4-Not complex function in mRNA quality control in Saccharomyces cerevisiae

DEFF Research Database (Denmark)

Assenholt, Jannie; Mouaikel, John; Saguez, Cyril

2011-01-01

RNPs are exported to the cytoplasm. The Ccr4-Not complex, which constitutes the major S. cerevisiae cytoplasmic deadenylase, has recently been implied in nuclear exosome–related processes. Consistent with a possible nuclear function of the complex, the deletion or mutation of Ccr4-Not factors also elicits...

Improving the security of a parallel keyed hash function based on chaotic maps

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Xiao Di, E-mail: xiaodi_cqu@hotmail.co [College of Computer Science and Engineering, Chongqing University, Chongqing 400044 (China); Liao Xiaofeng [College of Computer Science and Engineering, Chongqing University, Chongqing 400044 (China); Wang Yong [College of Computer Science and Engineering, Chongqing University, Chongqing 400044 (China)] [College of Economy and Management, Chongqing University of Posts and Telecommunications, Chongqing 400065 (China)

2009-11-23

In this Letter, we analyze the cause of vulnerability of the original parallel keyed hash function based on chaotic maps in detail, and then propose the corresponding enhancement measures. Theoretical analysis and computer simulation indicate that the modified hash function is more secure than the original one. At the same time, it can keep the parallel merit and satisfy the other performance requirements of hash function.

Improving the security of a parallel keyed hash function based on chaotic maps

International Nuclear Information System (INIS)

Xiao Di; Liao Xiaofeng; Wang Yong

2009-01-01

In this Letter, we analyze the cause of vulnerability of the original parallel keyed hash function based on chaotic maps in detail, and then propose the corresponding enhancement measures. Theoretical analysis and computer simulation indicate that the modified hash function is more secure than the original one. At the same time, it can keep the parallel merit and satisfy the other performance requirements of hash function.

A rec(4) dup 4p inherited from a maternal inv(4)(p15q35): case report and review.

Science.gov (United States)

Garcia-Heras, Jaime; Martin, Judith

2002-05-01

A rec(4) dup 4p inherited from a maternal inv(4)(p15q35) was detected in a four-year-old girl with malformations, developmental delay, and behavioral problems that resemble those for trisomy 4p. A review of eight other liveborns with rec(4) dup 4p shows that about 40% of them also have manifestations in common with trisomy 4p, but the rest have a variable spectrum of malformations. Overall, the rec(4) dup 4p phenotype is not specific, and a diagnosis would not have been feasible without cytogenetic studies. This lack of a clinically recognizable phenotype could reflect the effects of the variable sizes of deletions of 4q, molecular differences in the break points, or the known variable expression of trisomy 4p. The fact that 79% of the recombinants in the offspring of inv(4)(p13-p15q35) carriers are rec(4) dup 4p suggests that meiotic recombination favors its generation or that rec(4) dup 4q are more lethal in utero. Copyright 2002 Wiley-Liss, Inc.

Modeling of arylamide helix mimetics in the p53 peptide binding site of hDM2 suggests parallel and anti-parallel conformations are both stable.

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Jonathan C Fuller

Full Text Available The design of novel α-helix mimetic inhibitors of protein-protein interactions is of interest to pharmaceuticals and chemical genetics researchers as these inhibitors provide a chemical scaffold presenting side chains in the same geometry as an α-helix. This conformational arrangement allows the design of high affinity inhibitors mimicking known peptide sequences binding specific protein substrates. We show that GAFF and AutoDock potentials do not properly capture the conformational preferences of α-helix mimetics based on arylamide oligomers and identify alternate parameters matching solution NMR data and suitable for molecular dynamics simulation of arylamide compounds. Results from both docking and molecular dynamics simulations are consistent with the arylamides binding in the p53 peptide binding pocket. Simulations of arylamides in the p53 binding pocket of hDM2 are consistent with binding, exhibiting similar structural dynamics in the pocket as simulations of known hDM2 binders Nutlin-2 and a benzodiazepinedione compound. Arylamide conformations converge towards the same region of the binding pocket on the 20 ns time scale, and most, though not all dihedrals in the binding pocket are well sampled on this timescale. We show that there are two putative classes of binding modes for arylamide compounds supported equally by the modeling evidence. In the first, the arylamide compound lies parallel to the observed p53 helix. In the second class, not previously identified or proposed, the arylamide compound lies anti-parallel to the p53 helix.

Gain-of-function mutant p53 but not p53 deletion promotes head and neck cancer progression in response to oncogenic K-ras

Science.gov (United States)

Acin, Sergio; Li, Zhongyou; Mejia, Olga; Roop, Dennis R; El-Naggar, Adel K; Caulin, Carlos

2015-01-01

Mutations in p53 occur in over 50% of the human head and neck squamous cell carcinomas (SCCHN). The majority of these mutations result in the expression of mutant forms of p53, rather than deletions in the p53 gene. Some p53 mutants are associated with poor prognosis in SCCHN patients. However, the molecular mechanisms that determine the poor outcome of cancers carrying p53 mutations are unknown. Here, we generated a mouse model for SCCHN and found that activation of the endogenous p53 gain-of-function mutation p53R172H, but not deletion of p53, cooperates with oncogenic K-ras during SCCHN initiation, accelerates oral tumour growth, and promotes progression to carcinoma. Mechanistically, expression profiling of the tumours that developed in these mice and studies using cell lines derived from these tumours determined that mutant p53 induces the expression of genes involved in mitosis, including cyclin B1 and cyclin A, and accelerates entry in mitosis. Additionally, we discovered that this oncogenic function of mutant p53 was dependent on K-ras because the expression of cyclin B1 and cyclin A decreased, and entry in mitosis was delayed, after suppressing K-ras expression in oral tumour cells that express p53R172H. The presence of double-strand breaks in the tumours suggests that oncogene-dependent DNA damage resulting from K-ras activation promotes the oncogenic function of mutant p53. Accordingly, DNA damage induced by doxorubicin also induced increased expression of cyclin B1 and cyclin A in cells that express p53R172H. These findings represent strong in vivo evidence for an oncogenic function of endogenous p53 gain-of-function mutations in SCCHN and provide a mechanistic explanation for the genetic interaction between oncogenic K-ras and mutant p53. PMID:21952947

Structural and functional characterization of P4-ATPase lipid flippases

DEFF Research Database (Denmark)

Ulstrup, Jakob

2018-01-01

to its much larger substrate and how the mechanism allowing the transport unfolds. This is one of the central questions in the field known as the “giant substrate problem”. To this date, no structural information of P4-ATPases is available. The focus of this thesis is divided into two projects, both...... focusing on P4-ATPases from the yeast organism Saccharomyces cerevisiae: I. The structural characterization of the flippase Drs2p in complex with its auxiliary subunit Cdc50p. II. Establishing a protocol for obtaining a homogenous sample of the flippase Neo1p suitable for biochemical characterization...... and substrate identification. Part I was performed using X-ray crystallography and single-particle electron microscopy as the main methods. A 3D envelope was obtained by cryo-EM extending to a resolution of 4.4 Å. This envelope reveals the first structural insight of the conformational organization of the Drs2p...

Reversed phase parallel artificial membrane permeation assay for log P measurement

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Zihao Song

2016-03-01

Full Text Available A reversed phase parallel artificial membrane permeation assay (RP-PAMPA was newly invented for log P measurement. An oil/water/oil sandwich was constructed using a conventional PAMPA instrument. 1 % agarose was used to improve the physical stability of the water phase. A linear correlation between log P and the apparent permeability was observed in the -0.24 < log P < 2.85 region (R2 = 0.98. RP-PAMPA was also applied to pKa measurement.

HYPERDIRE. HYPERgeometric functions DIfferential REduction. MATHEMATICA based packages for differential reduction of generalized hypergeometric functions pFp-1, F1, F2, F3, F4

International Nuclear Information System (INIS)

Bytev, Vladimir V.; Kalmykov, Mikhail Yu.; Kniehl, Bernd A.

2013-05-01

HYPERDIRE is a project devoted to the creation of a set of Mathematica based programs for the differential reduction of hypergeometric functions. The current version includes two parts: one, pfq, is relevant for manipulations of hypergeometric functions p+1 F p , and the second one, AppellF1F4, for manipulations with Appell hypergeometric functions F 1 , F 2 , F 3 , F 4 of two variables.

Proteomic analysis reveals a novel function of the kinase Sat4p in Saccharomyces cerevisiae mitochondria.

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Uta Gey

Full Text Available The Saccharomyces cerevisiae kinase Sat4p has been originally identified as a protein involved in salt tolerance and stabilization of plasma membrane transporters, implicating a cytoplasmic localization. Our study revealed an additional mitochondrial (mt localization, suggesting a dual function for Sat4p. While no mt related phenotype was observed in the absence of Sat4p, its overexpression resulted in significant changes of a specific mitochondrial subproteome. As shown by a comparative two dimensional difference gel electrophoresis (2D-DIGE approach combined with mass spectrometry, particularly two groups of proteins were affected: the iron-sulfur containing aconitase-type proteins (Aco1p, Lys4p and the lipoamide-containing subproteome (Lat1p, Kgd2p and Gcv3p. The lipoylation sites of all three proteins could be assigned by nanoLC-MS/MS to Lys75 (Lat1p, Lys114 (Kgd2p and Lys102 (Gcv3p, respectively. Sat4p overexpression resulted in accumulation of the delipoylated protein variants and in reduced levels of aconitase-type proteins, accompanied by a decrease in the activities of the respective enzyme complexes. We propose a regulatory role of Sat4p in the late steps of the maturation of a specific subset of mitochondrial iron-sulfur cluster proteins, including Aco1p and lipoate synthase Lip5p. Impairment of the latter enzyme may account for the observed lipoylation defects.

Dysregulation of the Bmi-1/p16Ink4a pathway provokes an aging-associated decline of submandibular gland function

Science.gov (United States)

Yamakoshi, Kimi; Katano, Satoshi; Iida, Mayu; Kimura, Hiromi; Okuma, Atsushi; Ikemoto-Uezumi, Madoka; Ohtani, Naoko; Hara, Eiji; Maruyama, Mitsuo

2015-01-01

Bmi-1 prevents stem cell aging, at least partly, by blocking expression of the cyclin-dependent kinase inhibitor p16Ink4a. Therefore, dysregulation of the Bmi-1/p16Ink4a pathway is considered key to the loss of tissue homeostasis and development of associated degenerative diseases during aging. However, because Bmi-1 knockout (KO) mice die within 20 weeks after birth, it is difficult to determine exactly where and when dysregulation of the Bmi-1/p16Ink4a pathway occurs during aging in vivo. Using real-time in vivo imaging of p16Ink4a expression in Bmi-1-KO mice, we uncovered a novel function of the Bmi-1/p16Ink4a pathway in controlling homeostasis of the submandibular glands (SMGs), which secrete saliva into the oral cavity. This pathway is dysregulated during aging in vivo, leading to induction of p16Ink4a expression and subsequent declined SMG function. These findings will advance our understanding of the molecular mechanisms underlying the aging-related decline of SMG function and associated salivary gland hypofunction, which is particularly problematic among the elderly. PMID:25832744

P4 ATPases: Flippases in Health and Disease

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Coen C. Paulusma

2013-04-01

Full Text Available P4 ATPases catalyze the translocation of phospholipids from the exoplasmic to the cytosolic leaflet of biological membranes, a process termed “lipid flipping”. Accumulating evidence obtained in lower eukaryotes points to an important role for P4 ATPases in vesicular protein trafficking. The human genome encodes fourteen P4 ATPases (fifteen in mouse of which the cellular and physiological functions are slowly emerging. Thus far, deficiencies of at least two P4 ATPases, ATP8B1 and ATP8A2, are the cause of severe human disease. However, various mouse models and in vitro studies are contributing to our understanding of the cellular and physiological functions of P4-ATPases. This review summarizes current knowledge on the basic function of these phospholipid translocating proteins, their proposed action in intracellular vesicle transport and their physiological role.

Partial monosomy Xq(Xq23 --> qter) and trisomy 4p(4p15.33 --> pter) in a woman with intractable focal epilepsy, borderline intellectual functioning, and dysmorphic features.

Science.gov (United States)

Bartocci, Arnaldo; Striano, Pasquale; Mancardi, Maria Margherita; Fichera, Marco; Castiglia, Lucia; Galesi, Ornella; Michelucci, Roberto; Elia, Maurizio

2008-06-01

Studies of epilepsy associated with chromosomal abnormalities may provide information about clinical and EEG phenotypes and possibly to identify new epilepsy genes. We describe a female patient with intractable focal epilepsy, borderline intellectual functioning, and facial dysmorphisms, in whom genetic study (i.e., karyotype and array-CGH analysis) revealed a distal trisomy 4p and distal monosomy Xq. Although any genetic hypothesis remains speculative, several genes are located in the 4p chromosome segment involved in the rearrangement, some of which may be related to epilepsy.

Highly parallel algorithm for high pT physics at FAIR-CBM

International Nuclear Information System (INIS)

Fueloep, A; Vesztergombi, G

2010-01-01

The limitations of presently available data on p T range are discussed and planned future upgrades are outlined. Special attention is given to the FAIR-CBM experiment as a unique high luminosity facility for future continuation of the measurements at very high p T with emphasis on the so-called mosaic trigger system to use the highly parallel online algorithm.

An approach to multicore parallelism using functional programming: A case study based on Presburger Arithmetic

DEFF Research Database (Denmark)

Dung, Phan Anh; Hansen, Michael Reichhardt

2015-01-01

In this paper we investigate multicore parallelism in the context of functional programming by means of two quantifier-elimination procedures for Presburger Arithmetic: one is based on Cooper’s algorithm and the other is based on the Omega Test. We first develop correct-by-construction prototype...... platform executing on an 8-core machine. A speedup of approximately 4 was obtained for Cooper’s algorithm and a speedup of approximately 6 was obtained for the exact-shadow part of the Omega Test. The considered procedures are complex, memory-intense algorithms on huge formula trees and the case study...... reveals more general applicable techniques and guideline for deriving parallel algorithms from sequential ones in the context of data-intensive tree algorithms. The obtained insights should apply for any strict and impure functional programming language. Furthermore, the results obtained for the exact...

Accelerated cardiovascular magnetic resonance of the mouse heart using self-gated parallel imaging strategies does not compromise accuracy of structural and functional measures

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Dörries Carola

2010-07-01

Full Text Available Abstract Background Self-gated dynamic cardiovascular magnetic resonance (CMR enables non-invasive visualization of the heart and accurate assessment of cardiac function in mouse models of human disease. However, self-gated CMR requires the acquisition of large datasets to ensure accurate and artifact-free reconstruction of cardiac cines and is therefore hampered by long acquisition times putting high demands on the physiological stability of the animal. For this reason, we evaluated the feasibility of accelerating the data collection using the parallel imaging technique SENSE with respect to both anatomical definition and cardiac function quantification. Results Findings obtained from accelerated data sets were compared to fully sampled reference data. Our results revealed only minor differences in image quality of short- and long-axis cardiac cines: small anatomical structures (papillary muscles and the aortic valve and left-ventricular (LV remodeling after myocardial infarction (MI were accurately detected even for 3-fold accelerated data acquisition using a four-element phased array coil. Quantitative analysis of LV cardiac function (end-diastolic volume (EDV, end-systolic volume (ESV, stroke volume (SV, ejection fraction (EF and LV mass in healthy and infarcted animals revealed no substantial deviations from reference (fully sampled data for all investigated acceleration factors with deviations ranging from 2% to 6% in healthy animals and from 2% to 8% in infarcted mice for the highest acceleration factor of 3.0. CNR calculations performed between LV myocardial wall and LV cavity revealed a maximum CNR decrease of 50% for the 3-fold accelerated data acquisition when compared to the fully-sampled acquisition. Conclusions We have demonstrated the feasibility of accelerated self-gated retrospective CMR in mice using the parallel imaging technique SENSE. The proposed method led to considerably reduced acquisition times, while preserving high

Decoding P4-ATPase substrate interactions.

Science.gov (United States)

Roland, Bartholomew P; Graham, Todd R

Cellular membranes display a diversity of functions that are conferred by the unique composition and organization of their proteins and lipids. One important aspect of lipid organization is the asymmetric distribution of phospholipids (PLs) across the plasma membrane. The unequal distribution of key PLs between the cytofacial and exofacial leaflets of the bilayer creates physical surface tension that can be used to bend the membrane; and like Ca 2+ , a chemical gradient that can be used to transduce biochemical signals. PL flippases in the type IV P-type ATPase (P4-ATPase) family are the principle transporters used to set and repair this PL gradient and the asymmetric organization of these membranes are encoded by the substrate specificity of these enzymes. Thus, understanding the mechanisms of P4-ATPase substrate specificity will help reveal their role in membrane organization and cell biology. Further, decoding the structural determinants of substrate specificity provides investigators the opportunity to mutationally tune this specificity to explore the role of particular PL substrates in P4-ATPase cellular functions. This work reviews the role of P4-ATPases in membrane biology, presents our current understanding of P4-ATPase substrate specificity, and discusses how these fundamental aspects of P4-ATPase enzymology may be used to enhance our knowledge of cellular membrane biology.

SAN-b-P4VP block copolymer synthesis by chain extension from RAFT-functional poly(4-vinylpyridine) in solution and in emulsion

NARCIS (Netherlands)

Bozovic, J.S.; Tello Manon, H.M; Meuldijk, J.; Koning, C.E.; Klumperman, B.

2007-01-01

Reversible addition fragmentation chain transfer (RAFT)-mediated polymerization was successfully applied for the synthesis of poly(4-vinylpyridine) (P4VP) polymers of predetermined molar mass and of low polydispersity index. These RAFT end-functionalized polymers were then used as macro-RAFT agents

Luzindole but not 4-phenyl-2- propionamidotetralin (4P-PDOT) diminishes the inhibitory effect of melatonin on murine Colon 38 cancer growth in vitro.

Science.gov (United States)

Winczyk, Katarzyna; Fuss-Chmielewska, Julita; Lawnicka, Hanna; Pawlikowski, Marek; Karasek, Michal

2009-01-01

Our earlier studies have shown that MLT exerts the inhibitory effect on murine cancer via membrane and nuclear receptors. We have found that the antagonist of MT1 receptors does not diminish the antiproliferative effect of MLT on Colon 38 cells, and the contribution of MT2 receptors has been suggested to be responsible. Therefore, in the present study we have examined the influence of the 4-phenyl-2-propionamidotetralin (4P-PDOT), which is a selective antagonist of MT2 membrane receptor, and luzindole - an antagonist of both membrane receptors, on an oncostatic action of MLT. The murine cancer cell line Colon 38 was used in the experiments. In 48 hrs cell culture the effects of MLT, 4P-PDOT and luzindole administered alone and MLT applied jointly with either 4P-PDOT or luzindole were examined. The growth of cancer cells was assessed using the modified colorimetric Mosmann method. Melatonin at both examined concentrations (10-7, 10-9 M) significantly decreased the viability of cancer cells. The selective antagonist of MT2 membrane receptor, namely 4P-PDOT and luzindole applied separately did not have an effect on the growth of Colon 38 cells. The addition of 4P-PDOT to MLT did not change the inhibitory effect of MLT, whereas luzindole given together with MLT diminished, but failed to block totally, the oncostatic properties of MLT. The obtained data and our previous studies conducted on Colon 38 cancer indicate that membrane melatonin receptors are not indispensable to the oncostatic action of melatonin and thus other pathways such as nuclear signaling and receptor-independent mechanism may be also involved.

Interaction of Human Dopa Decarboxylase with L-Dopa: Spectroscopic and Kinetic Studies as a Function of pH

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Riccardo Montioli

2013-01-01

Full Text Available Human Dopa decarboxylase (hDDC, a pyridoxal 5′-phosphate (PLP enzyme, displays maxima at 420 and 335 nm and emits fluorescence at 384 and 504 nm upon excitation at 335 nm and at 504 nm when excited at 420 nm. Absorbance and fluorescence titrations of hDDC-bound coenzyme identify a single pKspec of ~7.2. This pKspec could not represent the ionization of a functional group on the Schiff base but that of an enzymic residue governing the equilibrium between the low- and the high-pH forms of the internal aldimine. During the reaction of hDDC with L-Dopa, monitored by stopped-flow spectrophotometry, a 420 nm band attributed to the 4′-N-protonated external aldimine first appears, and its decrease parallels the emergence of a 390 nm peak, assigned to the 4′-N-unprotonated external aldimine. The pH profile of the spectral change at 390 nm displays a pK of 6.4, a value similar to that (~6.3 observed in both kcat and kcat/Km profiles. This suggests that this pK represents the ESH+ → ES catalytic step. The assignment of the pKs of 7.9 and 8.3 observed on the basic side of kcat and the PLP binding affinity profiles, respectively, is also analyzed and discussed.

CDK2 and PKA mediated-sequential phosphorylation is critical for p19INK4d function in the DNA damage response.

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Mariela C Marazita

Full Text Available DNA damage triggers a phosphorylation-based signaling cascade known as the DNA damage response. p19INK4d, a member of the INK4 family of CDK4/6 inhibitors, has been reported to participate in the DNA damage response promoting DNA repair and cell survival. Here, we provide mechanistic insight into the activation mechanism of p19INK4d linked to the response to DNA damage. Results showed that p19INK4d becomes phosphorylated following UV radiation, β-amyloid peptide and cisplatin treatments. ATM-Chk2/ATR-Chk1 signaling pathways were found to be differentially involved in p19INK4d phosphorylation depending on the type of DNA damage. Two sequential phosphorylation events at serine 76 and threonine 141 were identified using p19INK4d single-point mutants in metabolic labeling assays with (32P-orthophosphate. CDK2 and PKA were found to participate in p19INK4d phosphorylation process and that they would mediate serine 76 and threonine 141 modifications respectively. Nuclear translocation of p19INK4d induced by DNA damage was shown to be dependent on serine 76 phosphorylation. Most importantly, both phosphorylation sites were found to be crucial for p19INK4d function in DNA repair and cell survival. In contrast, serine 76 and threonine 141 were dispensable for CDK4/6 inhibition highlighting the independence of p19INK4d functions, in agreement with our previous findings. These results constitute the first description of the activation mechanism of p19INK4d in response to genotoxic stress and demonstrate the functional relevance of this activation following DNA damage.

P-SPARSLIB: A parallel sparse iterative solution package

Energy Technology Data Exchange (ETDEWEB)

Saad, Y. [Univ. of Minnesota, Minneapolis, MN (United States)

1994-12-31

Iterative methods are gaining popularity in engineering and sciences at a time where the computational environment is changing rapidly. P-SPARSLIB is a project to build a software library for sparse matrix computations on parallel computers. The emphasis is on iterative methods and the use of distributed sparse matrices, an extension of the domain decomposition approach to general sparse matrices. One of the goals of this project is to develop a software package geared towards specific applications. For example, the author will test the performance and usefulness of P-SPARSLIB modules on linear systems arising from CFD applications. Equally important is the goal of portability. In the long run, the author wishes to ensure that this package is portable on a variety of platforms, including SIMD environments and shared memory environments.

Simple Explanation for why Parallel-Propagating Photons do not Gravitationally Attract

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Jensen R.

2015-09-01

Full Text Available In this article it is shown that photons of light, when traveling in parallel, do not attract one another gravitationally. This has been shown previously using general relativity, however here it is only assumed a Newtonian approximation to the gravitational attraction between photons. The explanation for the lack of gravitational attraction is simple: as co-moving objects accelerate in parallel, the flow of time is retarded, as observed by a stationary observer, according to special relativity. Hence so is the tendency for the objects to move toward one another. As the velocity of the objects approach c, the time required for the objects to approach one another approaches infinity, and so there is no gravitational attraction between objects which move parallel at the speed of light.

Prenatal diagnosis and molecular cytogenetic characterization of a de novo proximal interstitial deletion of chromosome 4p (4p15.2→p14).

Science.gov (United States)

Chen, Chih-Ping; Lee, Meng-Ju; Chern, Schu-Rern; Wu, Peih-Shan; Su, Jun-Wei; Chen, Yu-Ting; Lee, Meng-Shan; Wang, Wayseen

2013-10-25

We present prenatal diagnosis of de novo proximal interstitial deletion of chromosome 4p (4p15.2→p14) and molecular cytogenetic characterization of the deletion using uncultured amniocytes. We review the phenotypic abnormalities of previously reported patients with similar proximal interstitial 4p deletions, and we discuss the functions of the genes of RBPJ, CCKAR, STIM2, PCDH7 and ARAP2 that are deleted within this region. © 2013.

Somatotropinomas, but not nonfunctioning pituitary adenomas, maintain a functional apoptotic RET/Pit1/ARF/p53 pathway that is blocked by excess GDNF.

Science.gov (United States)

Diaz-Rodriguez, Esther; Garcia-Rendueles, Angela R; Ibáñez-Costa, Alejandro; Gutierrez-Pascual, Ester; Garcia-Lavandeira, Montserrat; Leal, Alfonso; Japon, Miguel A; Soto, Alfonso; Venegas, Eva; Tinahones, Francisco J; Garcia-Arnes, Juan A; Benito, Pedro; Angeles Galvez, Maria; Jimenez-Reina, Luis; Bernabeu, Ignacio; Dieguez, Carlos; Luque, Raul M; Castaño, Justo P; Alvarez, Clara V

2014-11-01

Acromegaly is caused by somatotroph cell adenomas (somatotropinomas [ACROs]), which secrete GH. Human and rodent somatotroph cells express the RET receptor. In rodents, when normal somatotrophs are deprived of the RET ligand, GDNF (Glial Cell Derived Neurotrophic Factor), RET is processed intracellularly to induce overexpression of Pit1 [Transcription factor (gene : POUF1) essential for transcription of Pituitary hormones GH, PRL and TSHb], which in turn leads to p19Arf/p53-dependent apoptosis. Our purpose was to ascertain whether human ACROs maintain the RET/Pit1/p14ARF/p53/apoptosis pathway, relative to nonfunctioning pituitary adenomas (NFPAs). Apoptosis in the absence and presence of GDNF was studied in primary cultures of 8 ACROs and 3 NFPAs. Parallel protein extracts were analyzed for expression of RET, Pit1, p19Arf, p53, and phospho-Akt. When GDNF deprived, ACRO cells, but not NFPAs, presented marked level of apoptosis that was prevented in the presence of GDNF. Apoptosis was accompanied by RET processing, Pit1 accumulation, and p14ARF and p53 induction. GDNF prevented all these effects via activation of phospho-AKT. Overexpression of human Pit1 (hPit1) directly induced p19Arf/p53 and apoptosis in a pituitary cell line. Using in silico studies, 2 CCAAT/enhancer binding protein alpha (cEBPα) consensus-binding sites were found to be 100% conserved in mouse, rat, and hPit1 promoters. Deletion of 1 cEBPα site prevented the RET-induced increase in hPit1 promoter expression. TaqMan qRT-PCR (real time RT-PCR) for RET, Pit1, Arf, TP53, GDNF, steroidogenic factor 1, and GH was performed in RNA from whole ACRO and NFPA tumors. ACRO but not NFPA adenomas express RET and Pit1. GDNF expression in the tumors was positively correlated with RET and negatively correlated with p53. In conclusion, ACROs maintain an active RET/Pit1/p14Arf/p53/apoptosis pathway that is inhibited by GDNF. Disruption of GDNF's survival function might constitute a new therapeutic route in

Vectorization, parallelization and porting of nuclear codes. Vectorization and parallelization. Progress report fiscal 1999

Energy Technology Data Exchange (ETDEWEB)

Adachi, Masaaki; Ogasawara, Shinobu; Kume, Etsuo [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment; Ishizuki, Shigeru; Nemoto, Toshiyuki; Kawasaki, Nobuo; Kawai, Wataru [Fujitsu Ltd., Tokyo (Japan); Yatake, Yo-ichi [Hitachi Ltd., Tokyo (Japan)

2001-02-01

Several computer codes in the nuclear field have been vectorized, parallelized and trans-ported on the FUJITSU VPP500 system, the AP3000 system, the SX-4 system and the Paragon system at Center for Promotion of Computational Science and Engineering in Japan Atomic Energy Research Institute. We dealt with 18 codes in fiscal 1999. These results are reported in 3 parts, i.e., the vectorization and the parallelization part on vector processors, the parallelization part on scalar processors and the porting part. In this report, we describe the vectorization and parallelization on vector processors. In this vectorization and parallelization on vector processors part, the vectorization of Relativistic Molecular Orbital Calculation code RSCAT, a microscopic transport code for high energy nuclear collisions code JAM, three-dimensional non-steady thermal-fluid analysis code STREAM, Relativistic Density Functional Theory code RDFT and High Speed Three-Dimensional Nodal Diffusion code MOSRA-Light on the VPP500 system and the SX-4 system are described. (author)

Massively Parallel Interrogation of Aptamer Sequence, Structure and Function

Energy Technology Data Exchange (ETDEWEB)

Fischer, N O; Tok, J B; Tarasow, T M

2008-02-08

Optimization of high affinity reagents is a significant bottleneck in medicine and the life sciences. The ability to synthetically create thousands of permutations of a lead high-affinity reagent and survey the properties of individual permutations in parallel could potentially relieve this bottleneck. Aptamers are single stranded oligonucleotides affinity reagents isolated by in vitro selection processes and as a class have been shown to bind a wide variety of target molecules. Methodology/Principal Findings. High density DNA microarray technology was used to synthesize, in situ, arrays of approximately 3,900 aptamer sequence permutations in triplicate. These sequences were interrogated on-chip for their ability to bind the fluorescently-labeled cognate target, immunoglobulin E, resulting in the parallel execution of thousands of experiments. Fluorescence intensity at each array feature was well resolved and shown to be a function of the sequence present. The data demonstrated high intra- and interchip correlation between the same features as well as among the sequence triplicates within a single array. Consistent with aptamer mediated IgE binding, fluorescence intensity correlated strongly with specific aptamer sequences and the concentration of IgE applied to the array. The massively parallel sequence-function analyses provided by this approach confirmed the importance of a consensus sequence found in all 21 of the original IgE aptamer sequences and support a common stem:loop structure as being the secondary structure underlying IgE binding. The microarray application, data and results presented illustrate an efficient, high information content approach to optimizing aptamer function. It also provides a foundation from which to better understand and manipulate this important class of high affinity biomolecules.

Massively parallel interrogation of aptamer sequence, structure and function.

Directory of Open Access Journals (Sweden)

Nicholas O Fischer

Full Text Available BACKGROUND: Optimization of high affinity reagents is a significant bottleneck in medicine and the life sciences. The ability to synthetically create thousands of permutations of a lead high-affinity reagent and survey the properties of individual permutations in parallel could potentially relieve this bottleneck. Aptamers are single stranded oligonucleotides affinity reagents isolated by in vitro selection processes and as a class have been shown to bind a wide variety of target molecules. METHODOLOGY/PRINCIPAL FINDINGS: High density DNA microarray technology was used to synthesize, in situ, arrays of approximately 3,900 aptamer sequence permutations in triplicate. These sequences were interrogated on-chip for their ability to bind the fluorescently-labeled cognate target, immunoglobulin E, resulting in the parallel execution of thousands of experiments. Fluorescence intensity at each array feature was well resolved and shown to be a function of the sequence present. The data demonstrated high intra- and inter-chip correlation between the same features as well as among the sequence triplicates within a single array. Consistent with aptamer mediated IgE binding, fluorescence intensity correlated strongly with specific aptamer sequences and the concentration of IgE applied to the array. CONCLUSION AND SIGNIFICANCE: The massively parallel sequence-function analyses provided by this approach confirmed the importance of a consensus sequence found in all 21 of the original IgE aptamer sequences and support a common stem:loop structure as being the secondary structure underlying IgE binding. The microarray application, data and results presented illustrate an efficient, high information content approach to optimizing aptamer function. It also provides a foundation from which to better understand and manipulate this important class of high affinity biomolecules.

Single to Two Cluster State Transition of Primary Motor Cortex 4-posterior (MI-4p Activities in Humans

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Kazunori Nakada

2015-11-01

Full Text Available The human primary motor cortex has dual representation of the digits, namely, area 4 anterior (MI-4a and area 4 posterior (MI-4p. We have previously demonstrated that activation of these two functional subunits can be identified independently by functional magnetic resonance imaging (fMRI using independent component-cross correlation-sequential epoch (ICS analysis. Subsequent studies in patients with hemiparesis due to subcortical lesions and monoparesis due to peripheral nerve injury demonstrated that MI-4p represents the initiation area of activation, whereas MI-4a is the secondarily activated motor cortex requiring a “long-loop” feedback input from secondary motor systems, likely the cerebellum. A dynamic model of hand motion based on the limit cycle oscillator predicts that the specific pattern of entrainment of neural firing may occur by applying appropriate periodic stimuli. Under normal conditions, such entrainment introduces a single phase-cluster. Under pathological conditions where entrainment stimuli have insufficient strength, the phase cluster splits into two clusters. Observable physiological phenomena of this shift from single cluster to two clusters are: doubling of firing rate of output neurons; or decay in group firing density of the system due to dampening of odd harmonics components. While the former is not testable in humans, the latter can be tested by appropriately designed fMRI experiments, the quantitative index of which is believed to reflect group behavior of neurons functionally localized, e.g., firing density in the dynamic theory. Accordingly, we performed dynamic analysis of MI-4p activation in normal volunteers and paretic patients. The results clearly indicated that MI-4p exhibits a transition from a single to a two phase-cluster state which coincided with loss of MI-4a activation. The study demonstrated that motor dysfunction (hemiparesis in patients with a subcortical infarct is not simply due to afferent

Cryptanalysis on a parallel keyed hash function based on chaotic maps

International Nuclear Information System (INIS)

Guo Wei; Wang Xiaoming; He Dake; Cao Yang

2009-01-01

This Letter analyzes the security of a novel parallel keyed hash function based on chaotic maps, proposed by Xiao et al. to improve the efficiency in parallel computing environment. We show how to devise forgery attacks on Xiao's scheme with differential cryptanalysis and give the experiment results of two kinds of forgery attacks firstly. Furthermore, we discuss the problem of weak keys in the scheme and demonstrate how to utilize weak keys to construct collision.

GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit

Energy Technology Data Exchange (ETDEWEB)

Pronk, Sander [Science for Life Lab., Stockholm (Sweden); KTH Royal Institute of Technology, Stockholm (Sweden); Pall, Szilard [Science for Life Lab., Stockholm (Sweden); KTH Royal Institute of Technology, Stockholm (Sweden); Schulz, Roland [Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Larsson, Per [Univ. of Virginia, Charlottesville, VA (United States); Bjelkmar, Par [Science for Life Lab., Stockholm (Sweden); Stockholm Univ., Stockholm (Sweden); Apostolov, Rossen [Science for Life Lab., Stockholm (Sweden); KTH Royal Institute of Technology, Stockholm (Sweden); Shirts, Michael R. [Univ. of Virginia, Charlottesville, VA (United States); Smith, Jeremy C. [Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Kasson, Peter M. [Univ. of Virginia, Charlottesville, VA (United States); van der Spoel, David [Science for Life Lab., Stockholm (Sweden); Uppsala Univ., Uppsala (Sweden); Hess, Berk [Science for Life Lab., Stockholm (Sweden); KTH Royal Institute of Technology, Stockholm (Sweden); Lindahl, Erik [Science for Life Lab., Stockholm (Sweden); KTH Royal Institute of Technology, Stockholm (Sweden); Stockholm Univ., Stockholm (Sweden)

2013-02-13

In this study, molecular simulation has historically been a low-throughput technique, but faster computers and increasing amounts of genomic and structural data are changing this by enabling large-scale automated simulation of, for instance, many conformers or mutants of biomolecules with or without a range of ligands. At the same time, advances in performance and scaling now make it possible to model complex biomolecular interaction and function in a manner directly testable by experiment. These applications share a need for fast and efficient software that can be deployed on massive scale in clusters, web servers, distributed computing or cloud resources. As a result, we present a range of new simulation algorithms and features developed during the past 4 years, leading up to the GROMACS 4.5 software package. The software now automatically handles wide classes of biomolecules, such as proteins, nucleic acids and lipids, and comes with all commonly used force fields for these molecules built-in. GROMACS supports several implicit solvent models, as well as new free-energy algorithms, and the software now uses multithreading for efficient parallelization even on low-end systems, including windows-based workstations. Together with hand-tuned assembly kernels and state-of-the-art parallelization, this provides extremely high performance and cost efficiency for high-throughput as well as massively parallel simulations.

Relation between hand function and gross motor function in full term infants aged 4 to 8 months

Directory of Open Access Journals (Sweden)

Solange F. Nogueira

2015-02-01

Full Text Available Background: In children, reaching emerges around four months of age, which is followed by rapid changes in hand function and concomitant changes in gross motor function, including the acquisition of independent sitting. Although there is a close functional relationship between these domains, to date they have been investigated separately. Objective: To investigate the longitudinal profile of changes and the relationship between the development of hand function (i.e. reaching for and manipulating an object and gross motor function in 13 normally developing children born at term who were evaluated every 15 days from 4 to 8 months of age. Method: The number of reaches and the period (i.e. time of manipulation to an object were extracted from video synchronized with the Qualisys(r movement analysis system. Gross motor function was measured using the Alberta Infant Motor Scale. ANOVA for repeated measures was used to test the effect of age on the number of reaches, the time of manipulation and gross motor function. Hierarchical regression models were used to test the associations of reaching and manipulation with gross motor function. Results: Results revealed a significant increase in the number of reaches (p<0.001, the time of manipulation (p<0.001 and gross motor function (p<0.001 over time, as well as associations between reaching and gross motor function (R2=0.84; p<0.001 and manipulation and gross motor function (R2=0.13; p=0.02 from 4 to 6 months of age. Associations from 6 to 8 months of age were not significant. Conclusion: The relationship between hand function and gross motor function was not constant, and the age span from 4 to 6 months was a critical period of interdependency of hand function and gross motor function development.

P2X4: A fast and sensitive purinergic receptor

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Jaanus Suurväli

2017-10-01

Full Text Available Extracellular nucleotides have been recognized as important mediators of activation, triggering multiple responses via plasma membrane receptors known as P2 receptors. P2 receptors comprise P2X ionotropic receptors and G protein-coupled P2Y receptors. P2X receptors are expressed in many tissues, where they are involved in a number of functions including synaptic transmission, muscle contraction, platelet aggregation, inflammation, macrophage activation, differentiation and proliferation, neuropathic and inflammatory pain. P2X4 is one of the most sensitive purinergic receptors (at nanomolar ATP concentrations, about one thousand times more than the archetypal P2X7. P2X4 is widely expressed in central and peripheral neurons, in microglia, and also found in various epithelial tissues and endothelial cells. It localizes on the plasma membrane, but also in intracellular compartments. P2X4 is preferentially localized in lysosomes, where it is protected from proteolysis by its glycosylation. High ATP concentration in the lysosomes does not activate P2X4 at low pH; P2X4 gets activated by intra-lysosomal ATP only in its fully dissociated tetra-anionic form, when the pH increases to 7.4. Thus, P2X4 is functioning as a Ca2+-channel after the fusion of late endosomes and lysosomes. P2X4 modulates major neurotransmitter systems and regulates alcohol-induced responses in microglia. P2X4 is one of the key receptors mediating neuropathic pain. However, injury-induced upregulation of P2X4 expression is gender dependent and plays a key role in pain difference between males and females. P2X4 is also involved in inflammation. Extracellular ATP being a pro-inflammatory molecule, P2X4 can trigger inflammation in response to high ATP release. It is therefore involved in multiple pathologies, like post-ischemic inflammation, rheumatoid arthritis, airways inflammation in asthma, neurodegenerative diseases and even metabolic syndrome. Although P2X4 remains poorly

Parallel Implementation of the Discrete Green's Function Formulation of the FDTD Method on a Multicore Central Processing Unit

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T. Stefański

2014-12-01

Full Text Available Parallel implementation of the discrete Green's function formulation of the finite-difference time-domain (DGF-FDTD method was developed on a multicore central processing unit. DGF-FDTD avoids computations of the electromagnetic field in free-space cells and does not require domain termination by absorbing boundary conditions. Computed DGF-FDTD solutions are compatible with the FDTD grid enabling the perfect hybridization of FDTD with the use of time-domain integral equation methods. The developed implementation can be applied to simulations of antenna characteristics. For the sake of example, arrays of Yagi-Uda antennas were simulated with the use of parallel DGF-FDTD. The efficiency of parallel computations was investigated as a function of the number of current elements in the FDTD grid. Although the developed method does not apply the fast Fourier transform for convolution computations, advantages stemming from the application of DGF-FDTD instead of FDTD can be demonstrated for one-dimensional wire antennas when simulation results are post-processed by the near-to-far-field transformation.

The CCR4-NOT complex physically and functionally interacts with TRAMP and the nuclear exosome.

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Nowel Azzouz

Full Text Available BACKGROUND: Ccr4-Not is a highly conserved multi-protein complex consisting in yeast of 9 subunits, including Not5 and the major yeast deadenylase Ccr4. It has been connected functionally in the nucleus to transcription by RNA polymerase II and in the cytoplasm to mRNA degradation. However, there has been no evidence so far that this complex is important for RNA degradation in the nucleus. METHODOLOGY/PRINCIPAL FINDINGS: In this work we point to a new role for the Ccr4-Not complex in nuclear RNA metabolism. We determine the importance of the Ccr4-Not complex for the levels of non-coding nuclear RNAs, such as mis-processed and polyadenylated snoRNAs, whose turnover depends upon the nuclear exosome and TRAMP. Consistently, mutation of both the Ccr4-Not complex and the nuclear exosome results in synthetic slow growth phenotypes. We demonstrate physical interactions between the Ccr4-Not complex and the exosome. First, Not5 co-purifies with the exosome. Second, several exosome subunits co-purify with the Ccr4-Not complex. Third, the Ccr4-Not complex is important for the integrity of large exosome-containing complexes. Finally, we reveal a connection between the Ccr4-Not complex and TRAMP through the association of the Mtr4 helicase with the Ccr4-Not complex and the importance of specific subunits of Ccr4-Not for the association of Mtr4 with the nuclear exosome subunit Rrp6. CONCLUSIONS/SIGNIFICANCE: We propose a model in which the Ccr4-Not complex may provide a platform contributing to dynamic interactions between the nuclear exosome and its co-factor TRAMP. Our findings connect for the first time the different players involved in nuclear and cytoplasmic RNA degradation.

On functional bases of the first-order differential invariants for non-conjugate subgroups of the Poincaré group $P(1,4$

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V.M. Fedorchuk

2008-11-01

Full Text Available It is established which functional bases of the first-order differential invariants of the splitting and non-splitting subgroups of the Poincaré group $P(1,4$ are invariant under the subgroups of the extended Galilei group $widetilde G(1,3 subset P(1,4$. The obtained sets of functional bases are classified according to dimensions.

A hybrid method for the parallel computation of Green's functions

International Nuclear Information System (INIS)

Petersen, Dan Erik; Li Song; Stokbro, Kurt; Sorensen, Hans Henrik B.; Hansen, Per Christian; Skelboe, Stig; Darve, Eric

2009-01-01

Quantum transport models for nanodevices using the non-equilibrium Green's function method require the repeated calculation of the block tridiagonal part of the Green's and lesser Green's function matrices. This problem is related to the calculation of the inverse of a sparse matrix. Because of the large number of times this calculation needs to be performed, this is computationally very expensive even on supercomputers. The classical approach is based on recurrence formulas which cannot be efficiently parallelized. This practically prevents the solution of large problems with hundreds of thousands of atoms. We propose new recurrences for a general class of sparse matrices to calculate Green's and lesser Green's function matrices which extend formulas derived by Takahashi and others. We show that these recurrences may lead to a dramatically reduced computational cost because they only require computing a small number of entries of the inverse matrix. Then, we propose a parallelization strategy for block tridiagonal matrices which involves a combination of Schur complement calculations and cyclic reduction. It achieves good scalability even on problems of modest size.

The language parallel Pascal and other aspects of the massively parallel processor

Science.gov (United States)

Reeves, A. P.; Bruner, J. D.

1982-01-01

A high level language for the Massively Parallel Processor (MPP) was designed. This language, called Parallel Pascal, is described in detail. A description of the language design, a description of the intermediate language, Parallel P-Code, and details for the MPP implementation are included. Formal descriptions of Parallel Pascal and Parallel P-Code are given. A compiler was developed which converts programs in Parallel Pascal into the intermediate Parallel P-Code language. The code generator to complete the compiler for the MPP is being developed independently. A Parallel Pascal to Pascal translator was also developed. The architecture design for a VLSI version of the MPP was completed with a description of fault tolerant interconnection networks. The memory arrangement aspects of the MPP are discussed and a survey of other high level languages is given.

The structure of the Myo4p globular tail and its function in ASH1 mRNA localization.

Science.gov (United States)

Heuck, Alexander; Fetka, Ingrid; Brewer, Daniel N; Hüls, Daniela; Munson, Mary; Jansen, Ralf-Peter; Niessing, Dierk

2010-05-03

Type V myosin (MyoV)-dependent transport of cargo is an essential process in eukaryotes. Studies on yeast and vertebrate MyoV showed that their globular tails mediate binding to the cargo complexes. In Saccharomyces cerevisiae, the MyoV motor Myo4p interacts with She3p to localize asymmetric synthesis of HO 1 (ASH1) mRNA into the bud of dividing cells. A recent study showed that localization of GFP-MS2-tethered ASH1 particles does not require the Myo4p globular tail, challenging the supposed role of this domain. We assessed ASH1 mRNA and Myo4p distribution more directly and found that their localization is impaired in cells expressing globular tail-lacking Myo4p. In vitro studies further show that the globular tail together with a more N-terminal linker region is required for efficient She3p binding. We also determined the x-ray structure of the Myo4p globular tail and identify a conserved surface patch important for She3p binding. The structure shows pronounced similarities to membrane-tethering complexes and indicates that Myo4p may not undergo auto-inhibition of its motor domain.

Jefferson Lab E89-044 experiment: study of the quasi-elastic He3(e,e'p)d reaction in parallel kinematics

International Nuclear Information System (INIS)

Penel-Nottaris, E.

2004-07-01

The Jefferson Lab Hall A E89-044 experiment has measured the He 3 (e,e'p) reaction cross-sections. The extraction of the longitudinal and transverse response functions for the two-body break-up He 3 (e,e'p)d reaction in parallel kinematics allows the study of the bound proton electromagnetic properties inside the He 3 nucleus and the involved nuclear mechanisms beyond plane waves approximations, for missing momenta of 0 and +- 300 MeV/c and transferred momenta from 0.8 to 4.1 GeV 2 . Preliminary cross-sections have been obtained after calibration of the experimental setup by fitting theoretical models averaged over the experimental phase-space using a Monte-Carlo simulation. The 8% systematic error on cross-sections is linked mainly to the absolute normalization of the target density: the elastic scattering data analysis will allow to reduce this error. The preliminary results show some disagreement with theoretical predictions for the forward angles kinematics around 0 MeV/c missing momenta and sensitivity to final state interactions and He 3 waves functions for missing momenta of 300 MeV/c. The longitudinal and transverse separation should constraint theoretical models more strongly. (author)

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit.

Science.gov (United States)

Pronk, Sander; Páll, Szilárd; Schulz, Roland; Larsson, Per; Bjelkmar, Pär; Apostolov, Rossen; Shirts, Michael R; Smith, Jeremy C; Kasson, Peter M; van der Spoel, David; Hess, Berk; Lindahl, Erik

2013-04-01

Molecular simulation has historically been a low-throughput technique, but faster computers and increasing amounts of genomic and structural data are changing this by enabling large-scale automated simulation of, for instance, many conformers or mutants of biomolecules with or without a range of ligands. At the same time, advances in performance and scaling now make it possible to model complex biomolecular interaction and function in a manner directly testable by experiment. These applications share a need for fast and efficient software that can be deployed on massive scale in clusters, web servers, distributed computing or cloud resources. Here, we present a range of new simulation algorithms and features developed during the past 4 years, leading up to the GROMACS 4.5 software package. The software now automatically handles wide classes of biomolecules, such as proteins, nucleic acids and lipids, and comes with all commonly used force fields for these molecules built-in. GROMACS supports several implicit solvent models, as well as new free-energy algorithms, and the software now uses multithreading for efficient parallelization even on low-end systems, including windows-based workstations. Together with hand-tuned assembly kernels and state-of-the-art parallelization, this provides extremely high performance and cost efficiency for high-throughput as well as massively parallel simulations. GROMACS is an open source and free software available from http://www.gromacs.org. Supplementary data are available at Bioinformatics online.

Xyce Parallel Electronic Simulator : users' guide, version 4.1.

Energy Technology Data Exchange (ETDEWEB)

Mei, Ting; Rankin, Eric Lamont; Thornquist, Heidi K.; Santarelli, Keith R.; Fixel, Deborah A.; Coffey, Todd Stirling; Russo, Thomas V.; Schiek, Richard Louis; Keiter, Eric Richard; Pawlowski, Roger Patrick

2009-02-01

This manual describes the use of the Xyce Parallel Electronic Simulator. Xyce has been designed as a SPICE-compatible, high-performance analog circuit simulator, and has been written to support the simulation needs of the Sandia National Laboratories electrical designers. This development has focused on improving capability over the current state-of-the-art in the following areas: (1) Capability to solve extremely large circuit problems by supporting large-scale parallel computing platforms (up to thousands of processors). Note that this includes support for most popular parallel and serial computers. (2) Improved performance for all numerical kernels (e.g., time integrator, nonlinear and linear solvers) through state-of-the-art algorithms and novel techniques. (3) Device models which are specifically tailored to meet Sandia's needs, including some radiation-aware devices (for Sandia users only). (4) Object-oriented code design and implementation using modern coding practices that ensure that the Xyce Parallel Electronic Simulator will be maintainable and extensible far into the future. Xyce is a parallel code in the most general sense of the phrase - a message passing parallel implementation - which allows it to run efficiently on the widest possible number of computing platforms. These include serial, shared-memory and distributed-memory parallel as well as heterogeneous platforms. Careful attention has been paid to the specific nature of circuit-simulation problems to ensure that optimal parallel efficiency is achieved as the number of processors grows. The development of Xyce provides a platform for computational research and development aimed specifically at the needs of the Laboratory. With Xyce, Sandia has an 'in-house' capability with which both new electrical (e.g., device model development) and algorithmic (e.g., faster time-integration methods, parallel solver algorithms) research and development can be performed. As a result, Xyce is a

4-aminopyridine does not enhance flocculus function in tottering, a mouse model of vestibulocerebellar dysfunction and ataxia.

Directory of Open Access Journals (Sweden)

John S Stahl

Full Text Available The potassium channel antagonist 4-aminopyridine (4-AP improves a variety of motor abnormalities associated with disorders of the cerebellum. The most rigorous quantitative data relate to 4-AP's ability to improve eye movement deficits in humans referable to dysfunction of the cerebellar flocculus. Largely based on work in the ataxic mouse mutant tottering (which carries a mutation of the Cacna1a gene of the P/Q voltage-activated calcium channel, 4-AP is hypothesized to function by enhancing excitability or rhythmicity of floccular Purkinje cells. We tested this hypothesis by determining whether systemic or intrafloccular administration of 4-AP would ameliorate the eye movement deficits in tottering that are attributable to flocculus dysfunction, including the reductions in amplitude of the yaw-axis vestibulo-ocular reflex (VOR and vision-enhanced vestibulo-ocular reflex (VVOR, and the optokinetic reflex (OKR about yaw and roll axes. Because tottering's deficits increase with age, both young and elderly mutants were tested to detect any age-dependent 4-AP effects. 4-AP failed to improve VOR, VVOR, and OKR gains during sinusoidal stimuli, although it may have reduced the tendency of the mutants' responses to VOR and VVOR to decline over the course of a one-hour recording session. For constant-velocity optokinetic stimuli, 4-AP generated some enhancement of yaw OKR and upward-directed roll OKR, but the effects were also seen in normal C57BL/6 controls, and thus do not represent a specific reversal of the electrophysiological consequences of the tottering mutation. Data support a possible extra-floccular locus for the effects of 4-AP on habituation and roll OKR. Unilateral intrafloccular 4-AP injections did not affect ocular motility, except to generate mild eye elevations, consistent with reduced floccular output. Because 4-AP did not produce the effects expected if it normalized outputs of floccular Purkinje cells, there is a need for further

Paracrine Apoptotic Effect of p53 Mediated by Tumor Suppressor Par-4

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Ravshan Burikhanov

2014-01-01

Full Text Available The guardian of the genome, p53, is often mutated in cancer and may contribute to therapeutic resistance. Given that p53 is intact and functional in normal tissues, we harnessed its potential to inhibit the growth of p53-deficient cancer cells. Specific activation of p53 in normal fibroblasts selectively induced apoptosis in p53-deficient cancer cells. This paracrine effect was mediated by p53-dependent secretion of the tumor suppressor Par-4. Accordingly, the activation of p53 in normal mice, but not p53−/− or Par-4−/− mice, caused systemic elevation of Par-4, which induced apoptosis of p53-deficient tumor cells. Mechanistically, p53 induced Par-4 secretion by suppressing the expression of its binding partner, UACA, which sequesters Par-4. Thus, normal cells can be empowered by p53 activation to induce Par-4 secretion for the inhibition of therapy-resistant tumors.

Green's function for electrons in a narrow quantum well in a parallel magnetic field

International Nuclear Information System (INIS)

Horing, Norman J. Morgenstern; Glasser, M. Lawrence; Dong Bing

2005-01-01

Electron dynamics in a narrow quantum well in a parallel magnetic field of arbitrary strength are examined here. We derive an explicit analytical closed-form solution for the Green's function of Landau-quantized electrons in skipping states of motion between the narrow well walls coupled with in-plane translational motion and hybridized with the zero-field lowest subband energy eigenstate. Such Landau-quantized modes are not uniformly spaced

EPHA4 is overexpressed but not functionally active in Sezary syndrome

NARCIS (Netherlands)

Hameetman, L; van der Fits, L.; Zoutman, W.H.; Out-Luiting, J.J.; Siegal, G.; de Esch, I.J.P.; Vermeer, M.H.; Tensen, C.P.

2015-01-01

EPHA4 belongs to the largest subfamily of receptor tyrosine kinases. In addition to its function during development, overexpression of EPHA4 in tumors has been correlated with increased proliferation, migration and poor survival. Several genomewide transcription profiling studies have demonstrated

Meiotic and pedigree segregation analyses in carriers of t(4;8)(p16;p23.1) differing in localization of breakpoint positions at 4p subband 4p16.3 and 4p16.1.

Science.gov (United States)

Midro, Alina T; Zollino, Marcella; Wiland, Ewa; Panasiuk, Barbara; Iwanowski, Piotr S; Murdolo, Marina; Śmigiel, Robert; Sąsiadek, Maria; Pilch, Jacek; Kurpisz, Maciej

2016-02-01

The purpose of this study was to compare meiotic segregation in sperm cells from two carriers with t(4;8)(p16;p23.1) reciprocal chromosome translocations (RCTs), differing in localization of the breakpoint positions at the 4p subband-namely, 4p16.3 (carrier 1) and 4p16.1 (carrier 2)-and to compare data of the pedigree analyses performed by direct method. Three-color fluorescent in situ hybridization (FISH) on sperm cells and FISH mapping for the evaluation of the breakpoint positions, data from pedigrees, and direct segregation analysis of the pedigrees were performed. Similar proportions of normal/balanced and unbalanced sperm cells were found in both carriers. The most common was an alternate type of segregation (about 52 % and about 48 %, respectively). Unbalanced adjacent I and adjacent II karyotypes were found in similar proportions about 15 %. The direct segregation analysis (following Stengel-Rutkowski) of the pedigree of carriers of t(4;8)(p16.1;p23.1) was performed and results were compared with the data of the pedigree segregation analysis obtained earlier through the indirect method. The probability of live-born progeny with unbalanced karyotype for carriers of t(4;8)(p16.1;p23.1) was moderately high at 18.8 %-comparable to the value obtained using the indirect method for the same carriership, which was 12 %. This was, however, markedly lower than the value of 41.2 % obtained through the pedigree segregation indirect analysis estimated for carriers of t(4;8)(p16.3;p23.1), perhaps due to the unique composition of genes present within the 4p16.1-4p 16.3 region. Revealed differences in pedigree segregation analysis did not correspond to the very similar profile of meiotic segregation patterns presented by carrier 1 and carrier 2. Most probably, such discordances may be due to differences in embryo survival rates arising from different genetic backgrounds.

[Pay for performance (P4P). Long-term effects and perspectives].

Science.gov (United States)

Schrappe, M; Gültekin, N

2011-02-01

After 10 years of experience and research, a wide array of results on evaluation and long-term effects of pay for performance (P4P) programs have been published. These data do not only give insight into most of the problems of implementation, but also into aspects which, in part, may attenuate the high expectations at the beginning of the discussion. P4P programs exhibit a ceiling effect, some improvements are reversed after incentives are cancelled, and improvements show opportunity costs as absent improvements for indicators, which are not object to financial incentives (in some cases for the same disease). These observations can be explained by the hypothesis that P4P programs have characteristics of fee-for-service reimbursement, if symmetric information is available for insurance and provider. P4P programs are local instruments. While integration of healthcare is considered as an important issue, they should be combined with programs and incentives which foster further vertical and horizontal integration. For Germany, further research in the implementation and effects of P4P programs is necessary.

Parallel Agent-as-a-Service (P-AaaS Based Geospatial Service in the Cloud

Directory of Open Access Journals (Sweden)

Xicheng Tan

2017-04-01

Full Text Available To optimize the efficiency of the geospatial service in the flood response decision making system, a Parallel Agent-as-a-Service (P-AaaS method is proposed and implemented in the cloud. The prototype system and comparisons demonstrate the advantages of our approach over existing methods. The P-AaaS method includes both parallel architecture and a mechanism for adjusting the computational resources—the parallel geocomputing mechanism of the P-AaaS method used to execute a geospatial service and the execution algorithm of the P-AaaS based geospatial service chain, respectively. The P-AaaS based method has the following merits: (1 it inherits the advantages of the AaaS-based method (i.e., avoiding transfer of large volumes of remote sensing data or raster terrain data, agent migration, and intelligent conversion into services to improve domain expert collaboration; (2 it optimizes the low performance and the concurrent geoprocessing capability of the AaaS-based method, which is critical for special applications (e.g., highly concurrent applications and emergency response applications; and (3 it adjusts the computing resources dynamically according to the number and the performance requirements of concurrent requests, which allows the geospatial service chain to support a large number of concurrent requests by scaling up the cloud-based clusters in use and optimizes computing resources and costs by reducing the number of virtual machines (VMs when the number of requests decreases.

Parallelism in matrix computations

CERN Document Server

Gallopoulos, Efstratios; Sameh, Ahmed H

2016-01-01

This book is primarily intended as a research monograph that could also be used in graduate courses for the design of parallel algorithms in matrix computations. It assumes general but not extensive knowledge of numerical linear algebra, parallel architectures, and parallel programming paradigms. The book consists of four parts: (I) Basics; (II) Dense and Special Matrix Computations; (III) Sparse Matrix Computations; and (IV) Matrix functions and characteristics. Part I deals with parallel programming paradigms and fundamental kernels, including reordering schemes for sparse matrices. Part II is devoted to dense matrix computations such as parallel algorithms for solving linear systems, linear least squares, the symmetric algebraic eigenvalue problem, and the singular-value decomposition. It also deals with the development of parallel algorithms for special linear systems such as banded ,Vandermonde ,Toeplitz ,and block Toeplitz systems. Part III addresses sparse matrix computations: (a) the development of pa...

Functional chest pain responds to biofeedback treatment but functional heartburn does not: what is the difference?

Science.gov (United States)

Shapiro, Michael; Shanani, Ram; Taback, Hanna; Abramowich, Dov; Scapa, Eitan; Broide, Efrat

2012-06-01

Patients with functional esophageal disorders represent a challenging treatment group. The purpose of this study was to evaluate the role of biofeedback in the treatment of patients with functional esophageal disorders. In this prospective study, patients with typical/atypical symptoms of gastroesophageal reflux disease underwent upper endoscopy and 24-h pH monitoring. All patients filled out gastroesophageal Reflux Disease Symptom, Hospital Anxiety and Depression, and Symptom Stress Rating questionnaires. Patients with functional heartburn and those with functional chest pain were offered biofeedback treatment. A global assessment questionnaire was filled out at the end of treatment and then 2.8 (range 1-4) years later. From January 2006 to December 2009, 22 patients with functional esophageal diseases were included in the study. Thirteen had functional heartburn and nine had functional chest pain. Six patients from each group received biofeedback treatment. After treatment for 1-4 years, patients with functional chest pain showed significant improvements in symptoms compared with those who were not treated. Patients with functional heartburn showed no improvement. Patients with functional chest pain had a longer time of esophageal acid exposure than those with functional heartburn. Patients with functional chest pain have different central and intraesophageal factors associated with symptom generation in comparison with patients with functional heartburn. Biofeedback is a useful tool in the treatment of patients with functional chest pain, but not for those with functional heartburn.

Functional Parallel Factor Analysis for Functions of One- and Two-dimensional Arguments.

Science.gov (United States)

Choi, Ji Yeh; Hwang, Heungsun; Timmerman, Marieke E

2018-03-01

Parallel factor analysis (PARAFAC) is a useful multivariate method for decomposing three-way data that consist of three different types of entities simultaneously. This method estimates trilinear components, each of which is a low-dimensional representation of a set of entities, often called a mode, to explain the maximum variance of the data. Functional PARAFAC permits the entities in different modes to be smooth functions or curves, varying over a continuum, rather than a collection of unconnected responses. The existing functional PARAFAC methods handle functions of a one-dimensional argument (e.g., time) only. In this paper, we propose a new extension of functional PARAFAC for handling three-way data whose responses are sequenced along both a two-dimensional domain (e.g., a plane with x- and y-axis coordinates) and a one-dimensional argument. Technically, the proposed method combines PARAFAC with basis function expansion approximations, using a set of piecewise quadratic finite element basis functions for estimating two-dimensional smooth functions and a set of one-dimensional basis functions for estimating one-dimensional smooth functions. In a simulation study, the proposed method appeared to outperform the conventional PARAFAC. We apply the method to EEG data to demonstrate its empirical usefulness.

Crossed molecular beam-tunable laser determination of velocity dependence of intramultiplet mixing: K(4p2P1/2)+He →K(4p2P3/2)+He

International Nuclear Information System (INIS)

Anderson, R.W.; Goddard, T.P.; Parravano, C.; Warner, J.

1976-01-01

The velocity dependence of intramultiplet mixing, K(4p 2 P 1 / 2 ) +He→K(4p 2 P 3 / 2 )+He, has been measured over the relative velocity range v=1.3--3.4 km/sec. The cross section appears to fit a linear function Q (v) =A (v-v 0 ), where a=6.3 x 10 -4 A 2 and v 0 = 7.9 x 10 4 cm/sec. The value of A is obtained by normalization to the literature thermal average cross section. The intramultiplet mixing theory of Nikitin is modified to yield Q (v) for the process. The modified theory correctly exhibits detailed balancing, and it is normalized to provide a very good fit to the observed Q (v). The magnitude of the normalization factor, however, is larger than that predicted from recent pseudopotential calculations of the excited state potentials. The temperature dependence of intramultiplet mixing is predicted. The use of laser polarization to determine the m/subj/ dependence of the process K(4p 2 P 3 / 2 +He→K(4p 2 P 1 / 2 )+He and other collision processes of excited 2 P 3 / 2 states is examined

Control rod drop transient analysis with the coupled parallel code pCTF-PARCSv2.7

International Nuclear Information System (INIS)

Ramos, Enrique; Roman, Jose E.; Abarca, Agustín; Miró, Rafael; Bermejo, Juan A.

2016-01-01

Highlights: • An MPI parallel version of the thermal–hydraulic subchannel code COBRA-TF has been developed. • The parallel code has been coupled to the 3D neutron diffusion code PARCSv2.7. • The new codes are validated with a control rod drop transient. - Abstract: In order to reduce the response time when simulating large reactors in detail, a parallel version of the thermal–hydraulic subchannel code COBRA-TF (CTF) has been developed using the standard Message Passing Interface (MPI). The parallelization is oriented to reactor cells, so it is best suited for models consisting of many cells. The generation of the Jacobian matrix is parallelized, in such a way that each processor is in charge of generating the data associated with a subset of cells. Also, the solution of the linear system of equations is done in parallel, using the PETSc toolkit. With the goal of creating a powerful tool to simulate the reactor core behavior during asymmetrical transients, the 3D neutron diffusion code PARCSv2.7 (PARCS) has been coupled with the parallel version of CTF (pCTF) using the Parallel Virtual Machine (PVM) technology. In order to validate the correctness of the parallel coupled code, a control rod drop transient has been simulated comparing the results with the real experimental measures acquired during an NPP real test.

On-line electrochemistry-bioaffinity screening with parallel HR-LC-MS for the generation and characterization of modified p38α kinase inhibitors.

Science.gov (United States)

Falck, David; de Vlieger, Jon S B; Giera, Martin; Honing, Maarten; Irth, Hubertus; Niessen, Wilfried M A; Kool, Jeroen

2012-04-01

In this study, an integrated approach is developed for the formation, identification and biological characterization of electrochemical conversion products of p38α mitogen-activated protein kinase inhibitors. This work demonstrates the hyphenation of an electrochemical reaction cell with a continuous-flow bioaffinity assay and parallel LC-HR-MS. Competition of the formed products with a tracer (SKF-86002) that shows fluorescence enhancement in the orthosteric binding site of the p38α kinase is the readout for bioaffinity. Parallel HR-MS(n) experiments provided information on the identity of binders and non-binders. Finally, the data produced with this on-line system were compared to electrochemical conversion products generated off-line. The electrochemical conversion of 1-{6-chloro-5-[(2R,5S)-4-(4-fluorobenzyl)-2,5-dimethylpiperazine-1-carbonyl]-3aH-indol-3-yl}-2-morpholinoethane-1,2-dione resulted in eight products, three of which showed bioaffinity in the continuous-flow p38α bioaffinity assay used. Electrochemical conversion of BIRB796 resulted, amongst others, in the formation of the reactive quinoneimine structure and its corresponding hydroquinone. Both products were detected in the p38α bioaffinity assay, which indicates binding to the p38α kinase.

Evaluation excitation functions for "2"8Si(n,p)"2"8Al, "3"1P(n,p)"3"1Si, and "1"1"3In(n,γ)"1"1"4"mIn reactions

International Nuclear Information System (INIS)

Zolotarev, K.I.

2014-10-01

Cross section data for "2"8Si(n,p)"2"8Al, "3"1P(n,p)"3"1Si and "1"1"3In(n,γ)"1"1"4"mIn reactions are needed for solving a wide spectrum of scientific and technical tasks. The excitation function of "2"8Si(n,p)"2"8Al reaction refers to the nuclear data involved in fusion reactor design calculations. The "2"8Si(n,p)"2"8Al reaction is interesting also as the monitor reaction for measurements at fusion facilities. Activation detectors on the basis of the 31P(n,p)31Si reaction are commonly used in the reactor dosimetry. The "1"1"3In(n,γ)"1"1"4"mIn reaction is promising regarding reactor dosimetry application for two reasons. First, due to the "1"1"4"mIn decay parameters which are rather suitable for activation measurements. Half-life of "1"1"4"mIn is equal to T_1/_2 = (49.51 ± 0.01) days and gamma spectrum accompanying decay has only one line with energy 190.27 keV and intensity (15.56 ± 0.15)%. Second, the "1"1"3In(n,γ)"1"1"4"mIn reaction rate may be measured by using one activation detector simultaneously with the "1"1"5In(n,γ)"1"1"6"mIn reaction. Preliminary analysis of existing evaluated excitation functions for "2"8Si(n,p)"2"8Al, "3"1P(n,p)"3"1Si and "1"1"3In(n,γ)"1"1"4"mIn reactions show that new evaluations are needed for all above mentioned reactions. This report is devoted to the preparation of the new evaluations of cross sections data and related covariance matrixes of uncertainties for the "2"8Si(n,p)"2"8Al, "3"1P(n,p)"3"1Si and "1"1"3In(n,γ)"1"1"4"mIn reactions.

Parallel computing in plasma physics: Nonlinear instabilities

International Nuclear Information System (INIS)

Pohn, E.; Kamelander, G.; Shoucri, M.

2000-01-01

A Vlasov-Poisson-system is used for studying the time evolution of the charge-separation at a spatial one- as well as a two-dimensional plasma-edge. Ions are advanced in time using the Vlasov-equation. The whole three-dimensional velocity-space is considered leading to very time-consuming four-resp. five-dimensional fully kinetic simulations. In the 1D simulations electrons are assumed to behave adiabatic, i.e. they are Boltzmann-distributed, leading to a nonlinear Poisson-equation. In the 2D simulations a gyro-kinetic approximation is used for the electrons. The plasma is assumed to be initially neutral. The simulations are performed at an equidistant grid. A constant time-step is used for advancing the density-distribution function in time. The time-evolution of the distribution function is performed using a splitting scheme. Each dimension (x, y, υ x , υ y , υ z ) of the phase-space is advanced in time separately. The value of the distribution function for the next time is calculated from the value of an - in general - interstitial point at the present time (fractional shift). One-dimensional cubic-spline interpolation is used for calculating the interstitial function values. After the fractional shifts are performed for each dimension of the phase-space, a whole time-step for advancing the distribution function is finished. Afterwards the charge density is calculated, the Poisson-equation is solved and the electric field is calculated before the next time-step is performed. The fractional shift method sketched above was parallelized for p processors as follows. Considering first the shifts in y-direction, a proper parallelization strategy is to split the grid into p disjoint υ z -slices, which are sub-grids, each containing a different 1/p-th part of the υ z range but the whole range of all other dimensions. Each processor is responsible for performing the y-shifts on a different slice, which can be done in parallel without any communication between

Parallel Wavefront Analysis for a 4D Interferometer

Science.gov (United States)

Rao, Shanti R.

2011-01-01

This software provides a programming interface for automating data collection with a PhaseCam interferometer from 4D Technology, and distributing the image-processing algorithm across a cluster of general-purpose computers. Multiple instances of 4Sight (4D Technology s proprietary software) run on a networked cluster of computers. Each connects to a single server (the controller) and waits for instructions. The controller directs the interferometer to several images, then assigns each image to a different computer for processing. When the image processing is finished, the server directs one of the computers to collate and combine the processed images, saving the resulting measurement in a file on a disk. The available software captures approximately 100 images and analyzes them immediately. This software separates the capture and analysis processes, so that analysis can be done at a different time and faster by running the algorithm in parallel across several processors. The PhaseCam family of interferometers can measure an optical system in milliseconds, but it takes many seconds to process the data so that it is usable. In characterizing an adaptive optics system, like the next generation of astronomical observatories, thousands of measurements are required, and the processing time quickly becomes excessive. A programming interface distributes data processing for a PhaseCam interferometer across a Windows computing cluster. A scriptable controller program coordinates data acquisition from the interferometer, storage on networked hard disks, and parallel processing. Idle time of the interferometer is minimized. This architecture is implemented in Python and JavaScript, and may be altered to fit a customer s needs.

SUN family proteins Sun4p, Uth1p and Sim1p are secreted from Saccharomyces cerevisiae and produced dependently on oxygen level.

Directory of Open Access Journals (Sweden)

Evgeny Kuznetsov

Full Text Available The SUN family is comprised of proteins that are conserved among various yeasts and fungi, but that are absent in mammals and plants. Although the function(s of these proteins are mostly unknown, they have been linked to various, often unrelated cellular processes such as those connected to mitochondrial and cell wall functions. Here we show that three of the four Saccharomyces cerevisiae SUN family proteins, Uth1p, Sim1p and Sun4p, are efficiently secreted out of the cells in different growth phases and their production is affected by the level of oxygen. The Uth1p, Sim1p, Sun4p and Nca3p are mostly synthesized during the growth phase of both yeast liquid cultures and colonies. Culture transition to slow-growing or stationary phases is linked with a decreased cellular concentration of Sim1p and Sun4p and with their efficient release from the cells. In contrast, Uth1p is released mainly from growing cells. The synthesis of Uth1p and Sim1p, but not of Sun4p, is repressed by anoxia. All four proteins confer cell sensitivity to zymolyase. In addition, Uth1p affects cell sensitivity to compounds influencing cell wall composition and integrity (such as Calcofluor white and Congo red differently when growing on fermentative versus respiratory carbon sources. In contrast, Uth1p is essential for cell resistance to boric acids irrespective of carbon source. In summary, our novel findings support the hypothesis that SUN family proteins are involved in the remodeling of the yeast cell wall during the various phases of yeast culture development and under various environmental conditions. The finding that Uth1p is involved in cell sensitivity to boric acid, i.e. to a compound that is commonly used as an important antifungal in mycoses, opens up new possibilities of investigating the mechanisms of boric acid's action.

Parallel processor for fast event analysis

International Nuclear Information System (INIS)

Hensley, D.C.

1983-01-01

Current maximum data rates from the Spin Spectrometer of approx. 5000 events/s (up to 1.3 MBytes/s) and minimum analysis requiring at least 3000 operations/event require a CPU cycle time near 70 ns. In order to achieve an effective cycle time of 70 ns, a parallel processing device is proposed where up to 4 independent processors will be implemented in parallel. The individual processors are designed around the Am2910 Microsequencer, the AM29116 μP, and the Am29517 Multiplier. Satellite histogramming in a mass memory system will be managed by a commercial 16-bit μP system

Pi-pi Stacking Mediated Cooperative Mechanism for Human Cytochrome P450 3A4

Directory of Open Access Journals (Sweden)

Botao Fa

2015-04-01

Full Text Available Human Cytochrome P450 3A4 (CYP3A4 is an important member of the cytochrome P450 superfamily with responsibility for metabolizing ~50% of clinical drugs. Experimental evidence showed that CYP3A4 can adopt multiple substrates in its active site to form a cooperative binding model, accelerating substrate metabolism efficiency. In the current study, we constructed both normal and cooperative binding models of human CYP3A4 with antifungal drug ketoconazoles (KLN. Molecular dynamics simulation and free energy calculation were then carried out to study the cooperative binding mechanism. Our simulation showed that the second KLN in the cooperative binding model had a positive impact on the first one binding in the active site by two significant pi-pi stacking interactions. The first one was formed by Phe215, functioning to position the first KLN in a favorable orientation in the active site for further metabolism reactions. The second one was contributed by Phe304. This pi-pi stacking was enhanced in the cooperative binding model by the parallel conformation between the aromatic rings in Phe304 and the dioxolan moiety of the first KLN. These findings can provide an atomic insight into the cooperative binding in CYP3A4, revealing a novel pi-pi stacking mechanism for drug-drug interactions.

Automatic Parallelization Tool: Classification of Program Code for Parallel Computing

Directory of Open Access Journals (Sweden)

Mustafa Basthikodi

2016-04-01

Full Text Available Performance growth of single-core processors has come to a halt in the past decade, but was re-enabled by the introduction of parallelism in processors. Multicore frameworks along with Graphical Processing Units empowered to enhance parallelism broadly. Couples of compilers are updated to developing challenges forsynchronization and threading issues. Appropriate program and algorithm classifications will have advantage to a great extent to the group of software engineers to get opportunities for effective parallelization. In present work we investigated current species for classification of algorithms, in that related work on classification is discussed along with the comparison of issues that challenges the classification. The set of algorithms are chosen which matches the structure with different issues and perform given task. We have tested these algorithms utilizing existing automatic species extraction toolsalong with Bones compiler. We have added functionalities to existing tool, providing a more detailed characterization. The contributions of our work include support for pointer arithmetic, conditional and incremental statements, user defined types, constants and mathematical functions. With this, we can retain significant data which is not captured by original speciesof algorithms. We executed new theories into the device, empowering automatic characterization of program code.

Parallelization for X-ray crystal structural analysis program

Energy Technology Data Exchange (ETDEWEB)

Watanabe, Hiroshi [Japan Atomic Energy Research Inst., Tokyo (Japan); Minami, Masayuki; Yamamoto, Akiji

1997-10-01

In this report we study vectorization and parallelization for X-ray crystal structural analysis program. The target machine is NEC SX-4 which is a distributed/shared memory type vector parallel supercomputer. X-ray crystal structural analysis is surveyed, and a new multi-dimensional discrete Fourier transform method is proposed. The new method is designed to have a very long vector length, so that it enables to obtain the 12.0 times higher performance result that the original code. Besides the above-mentioned vectorization, the parallelization by micro-task functions on SX-4 reaches 13.7 times acceleration in the part of multi-dimensional discrete Fourier transform with 14 CPUs, and 3.0 times acceleration in the whole program. Totally 35.9 times acceleration to the original 1CPU scalar version is achieved with vectorization and parallelization on SX-4. (author)

Administering truncated receive functions in a parallel messaging interface

Science.gov (United States)

Archer, Charles J; Blocksome, Michael A; Ratterman, Joseph D; Smith, Brian E

2014-12-09

Administering truncated receive functions in a parallel messaging interface (`PMI`) of a parallel computer comprising a plurality of compute nodes coupled for data communications through the PMI and through a data communications network, including: sending, through the PMI on a source compute node, a quantity of data from the source compute node to a destination compute node; specifying, by an application on the destination compute node, a portion of the quantity of data to be received by the application on the destination compute node and a portion of the quantity of data to be discarded; receiving, by the PMI on the destination compute node, all of the quantity of data; providing, by the PMI on the destination compute node to the application on the destination compute node, only the portion of the quantity of data to be received by the application; and discarding, by the PMI on the destination compute node, the portion of the quantity of data to be discarded.

A hybrid method for the parallel computation of Green's functions

DEFF Research Database (Denmark)

Petersen, Dan Erik; Li, Song; Stokbro, Kurt

2009-01-01

of the large number of times this calculation needs to be performed, this is computationally very expensive even on supercomputers. The classical approach is based on recurrence formulas which cannot be efficiently parallelized. This practically prevents the solution of large problems with hundreds...... of thousands of atoms. We propose new recurrences for a general class of sparse matrices to calculate Green's and lesser Green's function matrices which extend formulas derived by Takahashi and others. We show that these recurrences may lead to a dramatically reduced computational cost because they only...... require computing a small number of entries of the inverse matrix. Then. we propose a parallelization strategy for block tridiagonal matrices which involves a combination of Schur complement calculations and cyclic reduction. It achieves good scalability even on problems of modest size....

Parallel computing works

Energy Technology Data Exchange (ETDEWEB)

1991-10-23

An account of the Caltech Concurrent Computation Program (C{sup 3}P), a five year project that focused on answering the question: Can parallel computers be used to do large-scale scientific computations '' As the title indicates, the question is answered in the affirmative, by implementing numerous scientific applications on real parallel computers and doing computations that produced new scientific results. In the process of doing so, C{sup 3}P helped design and build several new computers, designed and implemented basic system software, developed algorithms for frequently used mathematical computations on massively parallel machines, devised performance models and measured the performance of many computers, and created a high performance computing facility based exclusively on parallel computers. While the initial focus of C{sup 3}P was the hypercube architecture developed by C. Seitz, many of the methods developed and lessons learned have been applied successfully on other massively parallel architectures.

Compiling the functional data-parallel language SaC for Microgrids of Self-Adaptive Virtual Processors

NARCIS (Netherlands)

Grelck, C.; Herhut, S.; Jesshope, C.; Joslin, C.; Lankamp, M.; Scholz, S.-B.; Shafarenko, A.

2009-01-01

We present preliminary results from compiling the high-level, functional and data-parallel programming language SaC into a novel multi-core design: Microgrids of Self-Adaptive Virtual Processors (SVPs). The side-effect free nature of SaC in conjunction with its data-parallel foundation make it an

High temporal resolution magnetic resonance imaging: development of a parallel three dimensional acquisition method for functional neuroimaging; Imagerie par resonance magnetique a haute resolution temporelle: developpement d'une methode d'acquisition parallele tridimensionnelle pour l'imagerie fonctionnelle cerebrale

Energy Technology Data Exchange (ETDEWEB)

Rabrait, C

2007-11-15

Echo Planar Imaging is widely used to perform data acquisition in functional neuroimaging. This sequence allows the acquisition of a set of about 30 slices, covering the whole brain, at a spatial resolution ranging from 2 to 4 mm, and a temporal resolution ranging from 1 to 2 s. It is thus well adapted to the mapping of activated brain areas but does not allow precise study of the brain dynamics. Moreover, temporal interpolation is needed in order to correct for inter-slices delays and 2-dimensional acquisition is subject to vascular in flow artifacts. To improve the estimation of the hemodynamic response functions associated with activation, this thesis aimed at developing a 3-dimensional high temporal resolution acquisition method. To do so, Echo Volume Imaging was combined with reduced field-of-view acquisition and parallel imaging. Indeed, E.V.I. allows the acquisition of a whole volume in Fourier space following a single excitation, but it requires very long echo trains. Parallel imaging and field-of-view reduction are used to reduce the echo train durations by a factor of 4, which allows the acquisition of a 3-dimensional brain volume with limited susceptibility-induced distortions and signal losses, in 200 ms. All imaging parameters have been optimized in order to reduce echo train durations and to maximize S.N.R., so that cerebral activation can be detected with a high level of confidence. Robust detection of brain activation was demonstrated with both visual and auditory paradigms. High temporal resolution hemodynamic response functions could be estimated through selective averaging of the response to the different trials of the stimulation. To further improve S.N.R., the matrix inversions required in parallel reconstruction were regularized, and the impact of the level of regularization on activation detection was investigated. Eventually, potential applications of parallel E.V.I. such as the study of non-stationary effects in the B.O.L.D. response

Antidepressants inhibit P2X4 receptor function: a possible involvement in neuropathic pain relief

Directory of Open Access Journals (Sweden)

Tozaki-Saitoh Hidetoshi

2009-04-01

Full Text Available Abstract Background Neuropathic pain is characterized by pain hypersensitivity to innocuous stimuli (tactile allodynia that is nearly always resistant to known treatments such as non-steroidal anti-inflammatory drugs or even opioids. It has been reported that some antidepressants are effective for treating neuropathic pain. However, the underlying molecular mechanisms are not well understood. We have recently demonstrated that blocking P2X4 receptors in the spinal cord reverses tactile allodynia after peripheral nerve injury in rats, implying that P2X4 receptors are a key molecule in neuropathic pain. We investigated a possible role of antidepressants as inhibitors of P2X4 receptors and analysed their analgesic mechanism using an animal model of neuropathic pain. Results Antidepressants strongly inhibited ATP-mediated Ca2+ responses in P2X4 receptor-expressing 1321N1 cells, which are known to have no endogenous ATP receptors. Paroxetine exhibited the most powerful inhibition of calcium influx via rat and human P2X4 receptors, with IC50 values of 2.45 μM and 1.87 μM, respectively. Intrathecal administration of paroxetine produced a striking antiallodynic effect in an animal model of neuropathic pain. Co-administration of WAY100635, ketanserin or ondansetron with paroxetine induced no significant change in the antiallodynic effect of paroxetine. Furthermore, the antiallodynic effect of paroxetine was observed even in rats that had received intrathecal pretreatment with 5,7-dihydroxytryptamine, which dramatically depletes spinal 5-hydroxytryptamine. Conclusion These results suggest that paroxetine acts as a potent analgesic in the spinal cord via a mechanism independent of its inhibitory effect on serotonin transporters. Powerful inhibition on P2X4 receptors may underlie the analgesic effect of paroxetine, and it is possible that some antidepressants clinically used in patients with neuropathic pain show antiallodynic effects, at least in part

MR-sialography: optimisation and evaluation of an ultra-fast sequence in parallel acquisition technique and different functional conditions of salivary glands; MR-Sialographie: Optimierung und Bewertung ultraschneller Sequenzen mit paralleler Bildgebung und oraler Stimulation

Energy Technology Data Exchange (ETDEWEB)

Habermann, C.R.; Cramer, M.C.; Aldefeld, D.; Weiss, F.; Kaul, M.G.; Adam, G. [Radiologisches Zentrum, Klinik und Poliklinik fuer Diagnostische und Interventionelle Radiologie, Universitaetsklinikum Hamburg-Eppendorf (Germany); Graessner, J. [Siemens Medical Systems, Hamburg (Germany); Reitmeier, F.; Jaehne, M. [Kopf- und Hautzentrum, Klinik und Poliklinik fuer Hals-, Nasen- und Ohrenheilkunde, Universitaetsklinikum Hamburg-Eppendorf (Germany); Petersen, K.U. [Zentrum fuer Psychosoziale Medizin, Klinik und Poliklinik fuer Psychiatrie und Psychotherapie, Universitaetsklinikum Hamburg-Eppendorf (Germany)

2005-04-01

Purpose: To optimise a fast sequence for MR-sialography and to compare a parallel and non-parallel acquisition technique. Additionally, the effect of oral stimulation regarding the image quality was evaluated. Material and Methods: All examinations were performed by using a 1.5-T superconducting system. After developing a sufficient sequence for MR-sialography, a single-shot turbo-spin-echo sequence (ss-TSE) with an acquisition time of 2.8 sec was used in transverse and oblique sagittal orientation in 27 healthy volunteers. All images were performed with and without parallel imaging technique. The assessment of the ductal system of the submandibular and parotid gland was performed using a 1 to 5 visual scale for each side separately. Images were evaluated by four independent experienced radiologists. For statistical evaluation, an ANOVA with post-hoc comparisons was used with an overall two-tailed significance level of P=.05. For evaluation of interobserver variability, an intraclass correlation was computed and correlation >.08 was determined to indicate a high correlation. Results: All parts of salivary excretal ducts could be visualised in all volunteers, with an overall rating for all ducts of 2.26 (SD{+-}1.09). Between the four observers a high correlation could be obtained with an intraclass correlation of 0.9475. A significant influence regarding the slice angulations could not be obtained (p=0.74). In all healthy volunteers the visibility of excretory ducts improved significantly after oral application of a Sialogogum (p<0.001; {eta}{sup 2}=0.049). The use of a parallel imaging technique did not lead to an improvement of visualisation, showing a significant loss of image quality compared to an acquistion technique without parallel imaging (p<0.001; {eta}{sup 2}=0.013). Conclusion: The optimised ss-TSE MR-sialography seems to be a fast and sufficient technique for visualisation of excretory ducts of the main salivary glands, with no elaborate post

Parallel Execution of Functional Mock-up Units in Buildings Modeling

Energy Technology Data Exchange (ETDEWEB)

Ozmen, Ozgur [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Nutaro, James J. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); New, Joshua Ryan [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

2016-06-30

A Functional Mock-up Interface (FMI) defines a standardized interface to be used in computer simulations to develop complex cyber-physical systems. FMI implementation by a software modeling tool enables the creation of a simulation model that can be interconnected, or the creation of a software library called a Functional Mock-up Unit (FMU). This report describes an FMU wrapper implementation that imports FMUs into a C++ environment and uses an Euler solver that executes FMUs in parallel using Open Multi-Processing (OpenMP). The purpose of this report is to elucidate the runtime performance of the solver when a multi-component system is imported as a single FMU (for the whole system) or as multiple FMUs (for different groups of components as sub-systems). This performance comparison is conducted using two test cases: (1) a simple, multi-tank problem; and (2) a more realistic use case based on the Modelica Buildings Library. In both test cases, the performance gains are promising when each FMU consists of a large number of states and state events that are wrapped in a single FMU. Load balancing is demonstrated to be a critical factor in speeding up parallel execution of multiple FMUs.

The STAPL pView

KAUST Repository

Buss, Antal

2011-01-01

The Standard Template Adaptive Parallel Library (STAPL) is a C++ parallel programming library that provides a collection of distributed data structures (pContainers) and parallel algorithms (pAlgorithms) and a generic methodology for extending them to provide customized functionality. STAPL algorithms are written in terms of pViews, which provide a generic access interface to pContainer data by abstracting common data structure concepts. Briefly, pViews allow the same pContainer to present multiple interfaces, e.g., enabling the same pMatrix to be \\'viewed\\' (or used) as a row-major or column-major matrix, or even as a vector. In this paper, we describe the stapl pView concept and its properties. pViews generalize the iterator concept and enable parallelism by providing random access to, and an ADT for, collections of elements. We illustrate how pViews provide support for managing the tradeoff between expressivity and performance and examine the performance overhead incurred when using pViews. © 2011 Springer-Verlag Berlin Heidelberg.

Parallel Alterations of Functional Connectivity during Execution and Imagination after Motor Imagery Learning

Science.gov (United States)

Zhang, Rushao; Hui, Mingqi; Long, Zhiying; Zhao, Xiaojie; Yao, Li

2012-01-01

Background Neural substrates underlying motor learning have been widely investigated with neuroimaging technologies. Investigations have illustrated the critical regions of motor learning and further revealed parallel alterations of functional activation during imagination and execution after learning. However, little is known about the functional connectivity associated with motor learning, especially motor imagery learning, although benefits from functional connectivity analysis attract more attention to the related explorations. We explored whether motor imagery (MI) and motor execution (ME) shared parallel alterations of functional connectivity after MI learning. Methodology/Principal Findings Graph theory analysis, which is widely used in functional connectivity exploration, was performed on the functional magnetic resonance imaging (fMRI) data of MI and ME tasks before and after 14 days of consecutive MI learning. The control group had no learning. Two measures, connectivity degree and interregional connectivity, were calculated and further assessed at a statistical level. Two interesting results were obtained: (1) The connectivity degree of the right posterior parietal lobe decreased in both MI and ME tasks after MI learning in the experimental group; (2) The parallel alterations of interregional connectivity related to the right posterior parietal lobe occurred in the supplementary motor area for both tasks. Conclusions/Significance These computational results may provide the following insights: (1) The establishment of motor schema through MI learning may induce the significant decrease of connectivity degree in the posterior parietal lobe; (2) The decreased interregional connectivity between the supplementary motor area and the right posterior parietal lobe in post-test implicates the dissociation between motor learning and task performing. These findings and explanations further revealed the neural substrates underpinning MI learning and supported that

Common variations in 4p locus are related to male completed suicide.

Science.gov (United States)

Must, Anne; Kõks, Sulev; Vasar, Eero; Tasa, Gunnar; Lang, Aavo; Maron, Eduard; Väli, Marika

2009-01-01

Suicidal behavior is a multifactorial phenomenon, with a significant genetic predisposition. To assess the contribution of genes in the 4p region to suicide risk, we genotyped 36 single nucleotide polymorphisms from a 49Mb region on the chromosome arm 4p11-16 in a total of 288 male suicide victims and 327 healthy male volunteers. The nonsynonymous variants rs1383180 in EVC gene, rs6811863 in TBC1D1 gene, rs362272 in HTT gene, and rs734312 in WFS1 gene were associated to the male completed suicide. However, only EVC polymorphism remained significant after correcting for multiple comparisons (P < .05 after 10 K permutations). The function of these genes is not clear yet. WFS1 and HTT are related to the unfolded protein response and endoplasmic reticulum stress, and TBC1D1 is a GTPase activator. EVC is a protein with transmembrane and leucine zipper domains, its function has not been elucidated yet. Further studies are required in order to reveal the role of these four polymorphisms in the pathoetiology of suicide.

Peripheral Blood CD4 T-Cell and Plasmacytoid Dendritic Cell (pDC) Reactivity to Herpes Simplex Virus 2 and pDC Number Do Not Correlate with the Clinical or Virologic Severity of Recurrent Genital Herpes

Science.gov (United States)

Moss, Nicholas J.; Magaret, Amalia; Laing, Kerry J.; Kask, Angela Shaulov; Wang, Minna; Mark, Karen E.; Schiffer, Joshua T.; Wald, Anna

2012-01-01

Leukocytes participate in the immune control of herpes simplex virus (HSV). Data from HIV coinfections, germ line mutations, and case reports suggest involvement of CD4 T cells and plasmacytoid dendritic cells (pDC). We investigated the relationships between these cells and recurrent genital herpes disease severity in the general population. Circulating CD4 T-cell responses to HSV-2 were measured in specimens from 67 immunocompetent individuals with measured genital lesion and HSV shedding rates. Similarly, pDC number and functional responses to HSV-2 were analyzed in 40 persons. CD4 responses and pDC concentrations and responses ranged as much as 100-fold between persons while displaying moderate within-person consistency over time. No correlations were observed between these immune response parameters and genital HSV-2 severity. Cytomegalovirus (CMV) coinfection was not correlated with differences in HSV-2-specific CD4 T-cell responses. The CD4 T-cell response to HSV-2 was much more polyfunctional than was the response to CMV. These data suggest that other immune cell subsets with alternate phenotypes or anatomical locations may be responsible for genital herpes control in chronically infected individuals. PMID:22761381

Prion protein (PrP) gene-knockout cell lines: insight into functions of the PrP

OpenAIRE

Sakudo, Akikazu; Onodera, Takashi

2015-01-01

Elucidation of prion protein (PrP) functions is crucial to fully understand prion diseases. A major approach to studying PrP functions is the use of PrP gene-knockout (Prnp ?/?) mice. So far, six types of Prnp ?/? mice have been generated, demonstrating the promiscuous functions of PrP. Recently, other PrP family members, such as Doppel and Shadoo, have been found. However, information obtained from comparative studies of structural and functional analyses of these PrP family proteins do not ...

Effects of prostratin on Cyclin T1/P-TEFb function and the gene expression profile in primary resting CD4+ T cells

Directory of Open Access Journals (Sweden)

Rice Andrew P

2006-10-01

Full Text Available Abstract Background The latent reservoir of human immunodeficiency virus type 1 (HIV-1 in resting CD4+ T cells is a major obstacle to the clearance of infection by highly active antiretroviral therapy (HAART. Recent studies have focused on searches for adjuvant therapies to activate this reservoir under conditions of HAART. Prostratin, a non tumor-promoting phorbol ester, is a candidate for such a strategy. Prostratin has been shown to reactivate latent HIV-1 and Tat-mediated transactivation may play an important role in this process. We examined resting CD4+ T cells from healthy donors to determine if prostratin induces Cyclin T1/P-TEFb, a cellular kinase composed of Cyclin T1 and Cyclin-dependent kinase-9 (CDK9 that mediates Tat function. We also examined effects of prostratin on Cyclin T2a, an alternative regulatory subunit for CDK9, and 7SK snRNA and the HEXIM1 protein, two factors that associate with P-TEFb and repress its kinase activity. Results Prostratin up-regulated Cyclin T1 protein expression, modestly induced CDK9 protein expression, and did not affect Cyclin T2a protein expression. Although the kinase activity of CDK9 in vitro was up-regulated by prostratin, we observed a large increase in the association of 7SK snRNA and the HEXIM1 protein with CDK9. Using HIV-1 reporter viruses with and without a functional Tat protein, we found that prostratin stimulation of HIV-1 gene expression appears to require a functional Tat protein. Microarray analyses were performed and several genes related to HIV biology, including APOBEC3B, DEFA1, and S100 calcium-binding protein genes, were found to be regulated by prostratin. Conclusion Prostratin induces Cyclin T1 expression and P-TEFb function and this is likely to be involved in prostratin reactivation of latent HIV-1 proviruses. The large increase in association of 7SK and HEXIM1 with P-TEFb following prostratin treatment may reflect a requirement in CD4+ T cells for a precise balance between

Parallel computations

CERN Document Server

1982-01-01

Parallel Computations focuses on parallel computation, with emphasis on algorithms used in a variety of numerical and physical applications and for many different types of parallel computers. Topics covered range from vectorization of fast Fourier transforms (FFTs) and of the incomplete Cholesky conjugate gradient (ICCG) algorithm on the Cray-1 to calculation of table lookups and piecewise functions. Single tridiagonal linear systems and vectorized computation of reactive flow are also discussed.Comprised of 13 chapters, this volume begins by classifying parallel computers and describing techn

Origin of the p-type character of AuCl3 functionalized carbon nanotubes

KAUST Repository

Murat, Altynbek

2014-02-13

The microscopic origin of the p-type character of AuCl3 functionalized carbon nanotubes (CNTs) is investigated using first-principles self-interaction corrected density functional theory (DFT). Recent DFT calculations suggest that the p-type character of AuCl3 functionalized CNTs is due to the Cl atoms adsorbed on the CNTs. We test this hypothesis and show that adsorbed Cl atoms only lead to a p-type character for very specific concentrations and arrangements of the Cl atoms, which furthermore are not the lowest energy configurations. We therefore investigate alternative mechanisms and conclude that the p-type character is due to the adsorption of AuCl4 molecules. The unraveling of the exact nature of the p-doping adsorbates is a key step for further development of AuCl3 functionalized CNTs in water sensor applications. © 2014 American Chemical Society.

P4-ATPases

DEFF Research Database (Denmark)

Lopez Marques, Rosa Laura; Theorin, Lisa; Palmgren, Michael Broberg

2014-01-01

) comprises lipid flippases that catalyze the translocation of phospholipids from the exoplasmic to the cytosolic leaflet of cell membranes. While initially characterized as aminophospholipid translocases, recent studies of individual P4-ATPase family members from fungi, plants, and animals show that P4......Cellular membranes, notably eukaryotic plasma membranes, are equipped with special proteins that actively translocate lipids from one leaflet to the other and thereby help generate membrane lipid asymmetry. Among these ATP-driven transporters, the P4 subfamily of P-type ATPases (P4-ATPases...... to include the regulation of membrane traffic, cytoskeletal dynamics, cell division, lipid metabolism, and lipid signaling. In this review, we will summarize the basic features of P4-ATPases and the physiological implications of their lipid transport activity in the cell....

Inactivation of p16INK4a, with retention of pRB and p53/p21cip1 function, in human MRC5 fibroblasts that overcome a telomere-independent crisis during immortalization.

Science.gov (United States)

Taylor, Lisa M; James, Alexander; Schuller, Christine E; Brce, Jesena; Lock, Richard B; Mackenzie, Karen L

2004-10-15

Recent investigations, including our own, have shown that specific strains of fibroblasts expressing telomerase reverse transcriptase (hTERT) have an extended lifespan, but are not immortal. We previously demonstrated that hTERT-transduced MRC5 fetal lung fibroblasts (MRC5hTERTs) bypassed senescence but eventually succumbed to a second mortality barrier (crisis). In the present study, 67 MRC5hTERT clones were established by limiting dilution of a mass culture. Whereas 39/67 clones had an extended lifespan, all 39 extended lifespan clones underwent crisis. 11 of 39 clones escaped crisis and were immortalized. There was no apparent relationship between the fate of clones at crisis and the level of telomerase activity. Telomeres were hyperextended in the majority of the clones analyzed. There was no difference in telomere length of pre-crisis compared with post-crisis and immortal clones, indicating that hyperextended telomeres were conducive for immortalization and confirming that crisis was independent of telomere length. Immortalization of MRC5hTERT cells was associated with repression of the cyclin-dependent kinase inhibitor p16INK4a and up-regulation of pRB. However, the regulation of pRB phosphorylation and the response of the p53/p21cip1/waf1 pathway were normal in immortal cells subject to genotoxic stress. Overexpression of oncogenic ras failed to de-repress p16INK4a in immortal cells. Furthermore, expression of ras enforced senescent-like growth arrest in p16INK4a-positive, but not p16INK4a-negative MRC5hTERT cells. Immortal cells expressing ras formed small, infrequent colonies in soft agarose, but were non-tumorigenic. Overall, these results implicate the inactivation of p16INK4a as a critical event for overcoming telomere-independent crisis, immortalizing MRC5 fibroblasts and overcoming ras-induced premature senescence.

[Pay for performance in dental care: A systematic narrative review of quality P4P models in dental care].

Science.gov (United States)

Chenot, Regine

2017-11-01

Pay for performance (P4P) links reimbursement to the achievement of quality objectives. Experiences with P4P instruments and studies on their effects are available for the inpatient sector. A systematic narrative review brings together findings concerning the use and the effects of P4P, especially in dental care. A systematic literature search in PubMed and the Cochrane Library for reimbursement models using quality indicators provided 77 publications. Inclusion criteria were: year of publication not older than 2007, dental sector, models of quality-oriented remuneration, quality of care, quality indicators. 27 publications met the inclusion criteria and were evaluated with regard to the instruments and effects of P4P. The database search was supplemented by a free search on the Internet as well as a search in indicator databases and portals. The results of the included studies were extracted and summarized narratively. 27 studies were included in the review. Performance-oriented remuneration is an instrument of quality competition. In principle, P4P is embedded in an existing remuneration system, i.e., it does not occur in isolation. In the United States, England and Scandinavia, models are currently being tested for quality-oriented remuneration in dental care, based on quality indicators. The studies identified by the literature search are very heterogeneous and do not yield comparable endpoints. Difficulties are seen in the reproducibility of the quality of dental care with regard to certain characteristics which still have to be defined as quality-promoting properties. Risk selection cannot be ruled out, which may have an impact on structural quality (access to care, coordination). There were no long-term effects of P4P on the quality of care. In the short and medium term, adverse effects on the participants' motivation as well as shifting effects towards the private sector are described. A prerequisite for the functioning of P4P is the definition of clear

A study of objective functions for organs with parallel and serial architecture

International Nuclear Information System (INIS)

Stavrev, P.V.; Stavreva, N.A.; Round, W.H.

1997-01-01

An objective function analysis when target volumes are deliberately enlarged to account for tumour mobility and consecutive uncertainty in the tumour position in external beam radiotherapy has been carried out. The dose distribution inside the tumour is assumed to have logarithmic dependence on the tumour cell density which assures an iso-local tumour control probability. The normal tissue immediately surrounding the tumour is irradiated homogeneously at a dose level equal to the dose D(R)) delivered at the edge of the tumour The normal tissue in the high dose field is modelled as being organized in identical functional subunits (FSUs) composed of a relatively large number of cells. Two types of organs - having serial and parallel architecture are considered. Implicit averaging over intrapatient normal tissue radiosensitivity variations is done. A function describing the normal tissue survival probability S 0 is constructed. The objective function is given as a product of the total tumour control probability (TCP) and the normal tissue survival probability S 0 . The values of the dose D(R)) which result in a maximum of the objective function are obtained for different combinations of tumour and normal tissue parameters, such as tumour and normal tissue radiosensitivities, number of cells constituting a normal tissue functional unit, total number of normal cells under high dose (D(R)) exposure and functional reserve for organs having parallel architecture. The corresponding TCP and S 0 values are computed and discussed. (authors)

MnTM-4-PyP modulates endogenous antioxidant responses and protects primary cortical neurons against oxidative stress.

Science.gov (United States)

Cheng, Kuo-Yuan; Guo, Fei; Lu, Jia-Qi; Cao, Yuan-Zhao; Wang, Tian-Chang; Yang, Qi; Xia, Qing

2015-05-01

Oxidative stress is a direct cause of injury in various neural diseases. Manganese porphyrins (MnPs), a large category of superoxide dismutase (SOD) mimics, shown universally to have effects in numerous neural disease models in vivo. Given their complex intracellular redox activities, detailed mechanisms underlying the biomedical efficacies are not fully elucidated. This study sought to investigate the regulation of endogenous antioxidant systems by a MnP (MnTM-4-PyP) and its role in the protection against neural oxidative stress. Primary cortical neurons were treated with MnTM-4-PyP prior to hydrogen peroxide-induced oxidative stress. MnTM-4-PyP increased cell viability, reduced intracellular level of reactive oxygen species, inhibited mitochondrial apoptotic pathway, and ameliorated endoplasmic reticulum function. The protein levels and activities of endogenous SODs were elevated, but not those of catalase. SOD2 transcription was promoted in a transcription factor-specific manner. Additionally, we found FOXO3A and Sirt3 levels also increased. These effects were not observed with MnTM-4-PyP alone. Induction of various levels of endogenous antioxidant responses by MnTM-4-PyP has indispensable functions in its protection for cortical neurons against hydrogen peroxide-induced oxidative stress. © 2014 John Wiley & Sons Ltd.

p63 expression confers significantly better survival outcomes in high-risk diffuse large B-cell lymphoma and demonstrates p53-like and p53-independent tumor suppressor function

DEFF Research Database (Denmark)

Xu-Monette, Zijun Y; Zhang, Shanxiang; Li, Xin

2016-01-01

with a pan-p63-monoclonal antibody and correlated it with other clinicopathologic factors and clinical outcomes. p63 expression was observed in 42.5% of DLBCL, did not correlate with p53 levels, but correlated with p21, MDM2, p16INK4A, Ki-67, Bcl-6, IRF4/MUM-1 and CD30 expression, REL gains, and BCL6...... was likely due to the association of p63 expression with high-risk IPI, and potential presence of ∆Np63 isoform in TP63 rearranged patients (a mere speculation). Gene expression profiling suggested that p63 has both overlapping and distinct functions compared with p53, and that p63 and mutated p53 antagonize...

MR-sialography: optimisation and evaluation of an ultra-fast sequence in parallel acquisition technique and different functional conditions of salivary glands

International Nuclear Information System (INIS)

Habermann, C.R.; Cramer, M.C.; Aldefeld, D.; Weiss, F.; Kaul, M.G.; Adam, G.; Graessner, J.; Reitmeier, F.; Jaehne, M.; Petersen, K.U.

2005-01-01

Purpose: To optimise a fast sequence for MR-sialography and to compare a parallel and non-parallel acquisition technique. Additionally, the effect of oral stimulation regarding the image quality was evaluated. Material and Methods: All examinations were performed by using a 1.5-T superconducting system. After developing a sufficient sequence for MR-sialography, a single-shot turbo-spin-echo sequence (ss-TSE) with an acquisition time of 2.8 sec was used in transverse and oblique sagittal orientation in 27 healthy volunteers. All images were performed with and without parallel imaging technique. The assessment of the ductal system of the submandibular and parotid gland was performed using a 1 to 5 visual scale for each side separately. Images were evaluated by four independent experienced radiologists. For statistical evaluation, an ANOVA with post-hoc comparisons was used with an overall two-tailed significance level of P=.05. For evaluation of interobserver variability, an intraclass correlation was computed and correlation >.08 was determined to indicate a high correlation. Results: All parts of salivary excretal ducts could be visualised in all volunteers, with an overall rating for all ducts of 2.26 (SD±1.09). Between the four observers a high correlation could be obtained with an intraclass correlation of 0.9475. A significant influence regarding the slice angulations could not be obtained (p=0.74). In all healthy volunteers the visibility of excretory ducts improved significantly after oral application of a Sialogogum (p 2 =0.049). The use of a parallel imaging technique did not lead to an improvement of visualisation, showing a significant loss of image quality compared to an acquistion technique without parallel imaging (p 2 =0.013). Conclusion: The optimised ss-TSE MR-sialography seems to be a fast and sufficient technique for visualisation of excretory ducts of the main salivary glands, with no elaborate post-processing needed. To improve results of MR

Time-dependent density-functional theory in massively parallel computer architectures: the OCTOPUS project.

Science.gov (United States)

Andrade, Xavier; Alberdi-Rodriguez, Joseba; Strubbe, David A; Oliveira, Micael J T; Nogueira, Fernando; Castro, Alberto; Muguerza, Javier; Arruabarrena, Agustin; Louie, Steven G; Aspuru-Guzik, Alán; Rubio, Angel; Marques, Miguel A L

2012-06-13

Octopus is a general-purpose density-functional theory (DFT) code, with a particular emphasis on the time-dependent version of DFT (TDDFT). In this paper we present the ongoing efforts to achieve the parallelization of octopus. We focus on the real-time variant of TDDFT, where the time-dependent Kohn-Sham equations are directly propagated in time. This approach has great potential for execution in massively parallel systems such as modern supercomputers with thousands of processors and graphics processing units (GPUs). For harvesting the potential of conventional supercomputers, the main strategy is a multi-level parallelization scheme that combines the inherent scalability of real-time TDDFT with a real-space grid domain-partitioning approach. A scalable Poisson solver is critical for the efficiency of this scheme. For GPUs, we show how using blocks of Kohn-Sham states provides the required level of data parallelism and that this strategy is also applicable for code optimization on standard processors. Our results show that real-time TDDFT, as implemented in octopus, can be the method of choice for studying the excited states of large molecular systems in modern parallel architectures.

Time-dependent density-functional theory in massively parallel computer architectures: the octopus project

Science.gov (United States)

Andrade, Xavier; Alberdi-Rodriguez, Joseba; Strubbe, David A.; Oliveira, Micael J. T.; Nogueira, Fernando; Castro, Alberto; Muguerza, Javier; Arruabarrena, Agustin; Louie, Steven G.; Aspuru-Guzik, Alán; Rubio, Angel; Marques, Miguel A. L.

2012-06-01

Octopus is a general-purpose density-functional theory (DFT) code, with a particular emphasis on the time-dependent version of DFT (TDDFT). In this paper we present the ongoing efforts to achieve the parallelization of octopus. We focus on the real-time variant of TDDFT, where the time-dependent Kohn-Sham equations are directly propagated in time. This approach has great potential for execution in massively parallel systems such as modern supercomputers with thousands of processors and graphics processing units (GPUs). For harvesting the potential of conventional supercomputers, the main strategy is a multi-level parallelization scheme that combines the inherent scalability of real-time TDDFT with a real-space grid domain-partitioning approach. A scalable Poisson solver is critical for the efficiency of this scheme. For GPUs, we show how using blocks of Kohn-Sham states provides the required level of data parallelism and that this strategy is also applicable for code optimization on standard processors. Our results show that real-time TDDFT, as implemented in octopus, can be the method of choice for studying the excited states of large molecular systems in modern parallel architectures.

Time-dependent density-functional theory in massively parallel computer architectures: the octopus project

International Nuclear Information System (INIS)

Andrade, Xavier; Aspuru-Guzik, Alán; Alberdi-Rodriguez, Joseba; Rubio, Angel; Strubbe, David A; Louie, Steven G; Oliveira, Micael J T; Nogueira, Fernando; Castro, Alberto; Muguerza, Javier; Arruabarrena, Agustin; Marques, Miguel A L

2012-01-01

Octopus is a general-purpose density-functional theory (DFT) code, with a particular emphasis on the time-dependent version of DFT (TDDFT). In this paper we present the ongoing efforts to achieve the parallelization of octopus. We focus on the real-time variant of TDDFT, where the time-dependent Kohn-Sham equations are directly propagated in time. This approach has great potential for execution in massively parallel systems such as modern supercomputers with thousands of processors and graphics processing units (GPUs). For harvesting the potential of conventional supercomputers, the main strategy is a multi-level parallelization scheme that combines the inherent scalability of real-time TDDFT with a real-space grid domain-partitioning approach. A scalable Poisson solver is critical for the efficiency of this scheme. For GPUs, we show how using blocks of Kohn-Sham states provides the required level of data parallelism and that this strategy is also applicable for code optimization on standard processors. Our results show that real-time TDDFT, as implemented in octopus, can be the method of choice for studying the excited states of large molecular systems in modern parallel architectures. (topical review)

Systematic approach for deriving feasible mappings of parallel algorithms to parallel computing platforms

NARCIS (Netherlands)

Arkin, Ethem; Tekinerdogan, Bedir; Imre, Kayhan M.

2017-01-01

<p>The need for high-performance computing together with the increasing trend from single processor to parallel computer architectures has leveraged the adoption of parallel computing. To benefit from parallel computing power, usually parallel algorithms are defined that can be mapped and executed

The 4s24p3-4s4p4 transition in AsI-like AgXV

International Nuclear Information System (INIS)

Dong Chenzhong; Zhao Jinbao

1992-01-01

Some terms of the 4s 4p 4 configuration in RuXII, RhXIII and PdXIV ions can be improved and all the energy values of the configuration in AgXV can be predicted theoretically by means of a configuration-interaction ab initio analysis for the level structure of the 4s 4p 4 configuration along the AsI sequence of KrIV-AgXV ions. Calculations of the wavelengths and oscillator strenghts are presented for the 4s 2 4p 3 -4s 4p 4 transition in AgXV. (orig.)

The Effects of Stress and Executive Functions on Decision Making in an Executive Parallel Task

OpenAIRE

McGuigan, Brian

2016-01-01

The aim of this study was to investigate the effects of acute stress on parallel task performance with the Game of Dice Task (GDT) to measure decision making and the Stroop test.  Two previous studies have found that the combination of stress and a parallel task with the GDT and an executive functions task preserved performance on the GDT for a stress group compared to a control group.  The purpose of this study was to create and use a new parallel task with the GDT and the stroop test to elu...

Novel protective role of endogenous cardiac myocyte P2X4 receptors in heart failure.

Science.gov (United States)

Yang, Tiehong; Shen, Jian-bing; Yang, Ronghua; Redden, John; Dodge-Kafka, Kimberly; Grady, James; Jacobson, Kenneth A; Liang, Bruce T

2014-05-01

Heart failure (HF), despite continuing progress, remains a leading cause of mortality and morbidity. P2X4 receptors (P2X4R) have emerged as potentially important molecules in regulating cardiac function and as potential targets for HF therapy. Transgenic P2X4R overexpression can protect against HF, but this does not explain the role of native cardiac P2X4R. Our goal is to define the physiological role of endogenous cardiac myocyte P2X4R under basal conditions and during HF induced by myocardial infarction or pressure overload. Mice established with conditional cardiac-specific P2X4R knockout were subjected to left anterior descending coronary artery ligation-induced postinfarct or transverse aorta constriction-induced pressure overload HF. Knockout cardiac myocytes did not show P2X4R by immunoblotting or by any response to the P2X4R-specific allosteric enhancer ivermectin. Knockout hearts showed normal basal cardiac function but depressed contractile performance in postinfarct and pressure overload models of HF by in vivo echocardiography and ex vivo isolated working heart parameters. P2X4R coimmunoprecipitated and colocalized with nitric oxide synthase 3 (eNOS) in wild-type cardiac myocytes. Mice with cardiac-specific P2X4R overexpression had increased S-nitrosylation, cyclic GMP, NO formation, and were protected from postinfarct and pressure overload HF. Inhibitor of eNOS, L-N(5)-(1-iminoethyl)ornithine hydrochloride, blocked the salutary effect of cardiac P2X4R overexpression in postinfarct and pressure overload HF as did eNOS knockout. This study establishes a new protective role for endogenous cardiac myocyte P2X4R in HF and is the first to demonstrate a physical interaction between the myocyte receptor and eNOS, a mediator of HF protection. © 2014 American Heart Association, Inc.

SYNTHESIS OF TETRA-p-PROPENYLTETRAESTERCALIX[4]ARENE AND TETRA-p-PROPENYLTETRACARBOXYLICACIDCALIX[4]ARENE FROM p-t-BUTYLPHENOL

Directory of Open Access Journals (Sweden)

Triana Kusumaningsih

2010-06-01

Full Text Available A research has been conducted to synthesize tetra-p-propenyltetraestercalix[4]arene and tetra-p-propenyltetracarboxylicacidcalix[4] arene using p-t-butylphenol as a starting material. The synthesis was carried out in following stages, i.e (1 synthesis of p-t-butylcalix[4]arene from p-t-butylphenol, (2 debutylation of p-t-butylcalix[4]arene, (3 tetraallilation of 25,26,27,28-tetrahydroxycalix[4]arene with NaH and allilbromida in dry tetrahydrofuran, (4 Claissen rearrangement of 25,26,27,28-tetrapropenyloxycalix[4]arene, (5 esterification of tetra-p-propenyltetrahydroxycalix[4]arene, (6 hydrolisis of tetra-p-propenyltetraestercalix[4]arene. The all structures of products were observed by means of melting point, FTIR, and 1H-NMR spectrometers. Tetra-p-propenyltetraestercalix[4]arene compound was obtained as yellow liquid product in 55.08% yield. Tetra-p-propenyltetracarboxylicacidcalix[4]arene compound was obtained as white solid product with the melting point 135-137 °C at decomposed and in 70.05% yield.   Keywords: calix[4]arene, Claissen rearrangement, esterification, hydrolisis

Stimulation of Eryptosis by Combretastatin A4 Phosphate Disodium (CA4P

Directory of Open Access Journals (Sweden)

Elena Signoretto

2016-03-01

Full Text Available Background/Aims: Combretastatin A4 phosphate disodium (CA4P is utilized for the treatment of malignancy. The substance has previously been shown to trigger suicidal cell death or apoptosis. Similar to apoptosis of nucleated cells, erythrocytes may enter suicidal death or eryptosis, characterized by cell shrinkage and cell membrane scrambling with phosphatidylserine translocation to the erythrocyte surface. Stimulators of eryptosis include increase of cytosolic Ca2+ activity ([Ca2+]i, ceramide, oxidative stress and ATP depletion. The present study explored, whether CA4P induces eryptosis and, if so, to gain insight into mechanisms involved. Methods: Flow cytometry has been employed to estimate phosphatidylserine exposure at the cell surface from annexin-V-binding, cell volume from forward scatter, [Ca2+]i from Fluo3-fluorescence, reactive oxygen species (ROS abundance from DCF fluorescence, glutathione (GSH abundance from CMF fluorescence and ceramide abundance from fluorescent antibodies. In addition cytosolic ATP levels were quantified utilizing a luciferin-luciferase-based assay and hemolysis was estimated from hemoglobin concentration in the supernatant. Results: A 48 hours exposure of human erythrocytes to CA4P (≥ 50 µM significantly increased the percentage of annexin-V-binding cells and significantly decreased forward scatter. CA4P did not appreciably increase hemolysis. Hundred µM CA4P significantly increased Fluo3-fluorescence. The effect of CA4P (100 µM on annexin-V-binding was significantly blunted, but not abolished, by removal of extracellular Ca2+. CA4P (≥ 50 µM significantly decreased GSH abundance and ATP levels but did not significantly increase ROS or ceramide. Conclusions: CA4P triggers cell shrinkage and phospholipid scrambling of the erythrocyte cell membrane, an effect at least in part due to entry of extracellular Ca2+ and energy depletion.

Towards the structure of yeast and mammalian P4-ATPases

DEFF Research Database (Denmark)

Lyons, Joseph; Laban, Milena; Mikkelsen, Stine

2017-01-01

P4-ATPases are members of the P-type ATPase superfamily that drive the inward translocation (flipping) of lipids within the membrane. These lipid flippase largely function as binary complexes with an auxiliary protein from the CDC50 family. The bulk of our knowledge has derived genetic and bioche......P4-ATPases are members of the P-type ATPase superfamily that drive the inward translocation (flipping) of lipids within the membrane. These lipid flippase largely function as binary complexes with an auxiliary protein from the CDC50 family. The bulk of our knowledge has derived genetic...... a basis for the analysis of reported mutagenesis data, we aim to solve the first molecular structures of the PS transporting P4-ATPases using electron microscopy. To date, negative stain EM analysis, on detergent, amphipol and saposin-lipoprotein nanoparticle (Salipro) reconstituted of both Drs2p/CDC50p...... and bATP8A2/CDC50A, has yielded comparable low-resolution envelopes of these two transporters, highlighting the bulk architecture of the complex. Current efforts and progress on the functional characterization and cryo-EM analysis of both lipid transporters reconstituted in Salipro are described...

Alignment of Ar+ [3P]4p2P03/2 satellite state from the polarization analysis of fluorescent radiation after photoionization

International Nuclear Information System (INIS)

Yenen, O.; McLaughlin, K.W.; Jaecks, D.H.

1997-01-01

The measurement of the polarization of radiation from satellite states of Ar + formed after the photoionization of Ar provides detailed information about the nature of doubly excited states, magnetic sublevel cross sections and partial wave ratios of the photo-ejected electrons. Since the formation of these satellite states is a weak process, it is necessary to use a high flux beam of incoming photons. In addition, in order to resolve the many narrow doubly excited Ar resonances, the incoming photons must have a high resolution. The characteristics of the beam line 9.0.1 of the Advanced Light Source fulfill these requirements. The authors determined the polarization of 4765 Angstrom fluorescence from the Ar + [ 3 P] 4p 2 P 3/2 0 satellite state formed after photoionization of Ar by photons from the 9.0.1 beam line of ALS in the 35.620-38.261 eV energy range using a resolution of approximately 12,700. This is accomplished by measuring the intensities of the fluorescent light polarized parallel (I parallel) and perpendicular (I perpendicular) to the polarization axis of the incident synchrotron radiation using a Sterling Optics 105MB polarizing filter. The optical system placed at 90 degrees with respect to the polarization axis of the incident light had a narrow band interference filter (δλ=0.3 nm) to isolate the fluorescent radiation

Parallel 4-dimensional cellular automaton track finder for the CBM experiment

Energy Technology Data Exchange (ETDEWEB)

Akishina, Valentina [Goethe-Universitaet Frankfurt am Main, Frankfurt am Main (Germany); Frankfurt Institute for Advanced Studies, Frankfurt am Main (Germany); GSI Helmholtzzentrum fuer Schwerionenforschung GmbH, Darmstadt (Germany); JINR Joint Institute for Nuclear Research, Dubna (Russian Federation); Kisel, Ivan [Goethe-Universitaet Frankfurt am Main, Frankfurt am Main (Germany); Frankfurt Institute for Advanced Studies, Frankfurt am Main (Germany); GSI Helmholtzzentrum fuer Schwerionenforschung GmbH, Darmstadt (Germany); Collaboration: CBM-Collaboration

2016-07-01

The CBM experiment at FAIR will focus on the measurement of rare probes at interaction rates up to 10 MHz. The beam will provide free stream of particles, so that information about different collisions may overlap in time. It requires the full online event reconstruction not only in space, but also in time, so-called 4D (4-dimensional) event building. This is a task of the First-Level Event Selection (FLES) package. The FLES reconstruction package consists of several modules: track finding, track fitting, short-lived particles finding, event building and selection. The Silicon Tracking System (STS) time measurement information was included into the Cellular Automaton (CA) track finder algorithm. The 4D track finder algorithm speed (8.5 ms per event in a time-slice) and efficiency is comparable with the event-based analysis. The CA track finder was fully parallelised inside the time-slice. The parallel version achieves a speed-up factor of 10.6 while parallelising between 10 Intel Xeon physical cores with a hyper-threading. The first version of event building based on 4D track finder was implemented.

A massively-parallel electronic-structure calculations based on real-space density functional theory

International Nuclear Information System (INIS)

Iwata, Jun-Ichi; Takahashi, Daisuke; Oshiyama, Atsushi; Boku, Taisuke; Shiraishi, Kenji; Okada, Susumu; Yabana, Kazuhiro

2010-01-01

Based on the real-space finite-difference method, we have developed a first-principles density functional program that efficiently performs large-scale calculations on massively-parallel computers. In addition to efficient parallel implementation, we also implemented several computational improvements, substantially reducing the computational costs of O(N 3 ) operations such as the Gram-Schmidt procedure and subspace diagonalization. Using the program on a massively-parallel computer cluster with a theoretical peak performance of several TFLOPS, we perform electronic-structure calculations for a system consisting of over 10,000 Si atoms, and obtain a self-consistent electronic-structure in a few hundred hours. We analyze in detail the costs of the program in terms of computation and of inter-node communications to clarify the efficiency, the applicability, and the possibility for further improvements.

The role of crowding in parallel search: Peripheral pooling is not responsible for logarithmic efficiency in parallel search.

Science.gov (United States)

Madison, Anna; Lleras, Alejandro; Buetti, Simona

2018-02-01

Recent results from our laboratory showed that, in fixed-target parallel search tasks, reaction times increase in a logarithmic fashion with set size, and the slope of this logarithmic function is modulated by lure-target similarity. These results were interpreted as being consistent with a processing architecture where early vision (stage one) processes elements in the display in exhaustive fashion with unlimited capacity and with a limitation in resolution. Here, we evaluate the contribution of crowding to our recent logarithmic search slope findings, considering the possibility that peripheral pooling of features (as observed in crowding) may be responsible for logarithmic efficiency. Factors known to affect the strength of crowding were varied, specifically: item spacing and similarity. The results from three experiments converge on the same pattern of results: reaction times increased logarithmically with set size and were modulated by lure-target similarity even when crowding was minimized within displays through an inter-item spacing manipulation. Furthermore, we found logarithmic search efficiencies were overall improved in displays where crowding was minimized compared to displays where crowding was possible. The findings from these three experiments suggest logarithmic efficiency in efficient search is not the result peripheral pooling of features. That said, the presence of crowding does tend to reduce search efficiency, even in "pop-out" search situations.

Helios, and not FoxP3, is the marker of activated Tregs expressing GARP/LAP.

Science.gov (United States)

Elkord, Eyad; Abd Al Samid, May; Chaudhary, Belal

2015-08-21

Regulatory T cells (Tregs) are key players of immune regulation/dysregulation both in physiological and pathophysiological settings. Despite significant advances in understanding Treg function, there is still a pressing need to define reliable and specific markers that can distinguish different Treg subpopulations. Herein we show for the first time that markers of activated Tregs [latency associated peptide (LAP) and glycoprotein A repetitions predominant (GARP, or LRRC32)] are expressed on CD4+FoxP3- T cells expressing Helios (FoxP3-Helios+) in the steady state. Following TCR activation, GARP/LAP are up-regulated on CD4+Helios+ T cells regardless of FoxP3 expression (FoxP3+/-Helios+). We show that CD4+GARP+/-LAP+ Tregs make IL-10 immunosuppressive cytokine but not IFN-γ effector cytokine. Further characterization of FoxP3/Helios subpopulations showed that FoxP3+Helios+ Tregs proliferate in vitro significantly less than FoxP3+Helios- Tregs upon TCR stimulation. Unlike FoxP3+Helios- Tregs, FoxP3+Helios+ Tregs secrete IL-10 but not IFN-γ or IL-2, confirming they are bona fide Tregs with immunosuppressive characteristics. Taken together, Helios, and not FoxP3, is the marker of activated Tregs expressing GARP/LAP, and FoxP3+Helios+ Tregs have more suppressive characteristics, compared with FoxP3+Helios- Tregs. Our work implies that therapeutic modalities for treating autoimmune and inflammatory diseases, allergies and graft rejection should be designed to induce and/or expand FoxP3+Helios+ Tregs, while therapies against cancers or infectious diseases should avoid such expansion/induction.

Parallelization and automatic data distribution for nuclear reactor simulations

Energy Technology Data Exchange (ETDEWEB)

Liebrock, L.M. [Liebrock-Hicks Research, Calumet, MI (United States)

1997-07-01

Detailed attempts at realistic nuclear reactor simulations currently take many times real time to execute on high performance workstations. Even the fastest sequential machine can not run these simulations fast enough to ensure that the best corrective measure is used during a nuclear accident to prevent a minor malfunction from becoming a major catastrophe. Since sequential computers have nearly reached the speed of light barrier, these simulations will have to be run in parallel to make significant improvements in speed. In physical reactor plants, parallelism abounds. Fluids flow, controls change, and reactions occur in parallel with only adjacent components directly affecting each other. These do not occur in the sequentialized manner, with global instantaneous effects, that is often used in simulators. Development of parallel algorithms that more closely approximate the real-world operation of a reactor may, in addition to speeding up the simulations, actually improve the accuracy and reliability of the predictions generated. Three types of parallel architecture (shared memory machines, distributed memory multicomputers, and distributed networks) are briefly reviewed as targets for parallelization of nuclear reactor simulation. Various parallelization models (loop-based model, shared memory model, functional model, data parallel model, and a combined functional and data parallel model) are discussed along with their advantages and disadvantages for nuclear reactor simulation. A variety of tools are introduced for each of the models. Emphasis is placed on the data parallel model as the primary focus for two-phase flow simulation. Tools to support data parallel programming for multiple component applications and special parallelization considerations are also discussed.

Parallelization and automatic data distribution for nuclear reactor simulations

International Nuclear Information System (INIS)

Liebrock, L.M.

1997-01-01

Detailed attempts at realistic nuclear reactor simulations currently take many times real time to execute on high performance workstations. Even the fastest sequential machine can not run these simulations fast enough to ensure that the best corrective measure is used during a nuclear accident to prevent a minor malfunction from becoming a major catastrophe. Since sequential computers have nearly reached the speed of light barrier, these simulations will have to be run in parallel to make significant improvements in speed. In physical reactor plants, parallelism abounds. Fluids flow, controls change, and reactions occur in parallel with only adjacent components directly affecting each other. These do not occur in the sequentialized manner, with global instantaneous effects, that is often used in simulators. Development of parallel algorithms that more closely approximate the real-world operation of a reactor may, in addition to speeding up the simulations, actually improve the accuracy and reliability of the predictions generated. Three types of parallel architecture (shared memory machines, distributed memory multicomputers, and distributed networks) are briefly reviewed as targets for parallelization of nuclear reactor simulation. Various parallelization models (loop-based model, shared memory model, functional model, data parallel model, and a combined functional and data parallel model) are discussed along with their advantages and disadvantages for nuclear reactor simulation. A variety of tools are introduced for each of the models. Emphasis is placed on the data parallel model as the primary focus for two-phase flow simulation. Tools to support data parallel programming for multiple component applications and special parallelization considerations are also discussed

Population inversion and gain calculations for 4p54d-4p55p and 4p55s - 4p55p Kr-like transitions in Y IV, Zr V, Nb VI and Mo VII

International Nuclear Information System (INIS)

Fournier, K.B.; Goldstein, W.H.; Stutman, D.; Finkenthal, M.; Soukhanovskii, V.; May, M.J.

1999-01-01

We present calculations of the quasi-steady state gain coefficient for the 4p 5 4d 1 P-4p 5 5p 1/2[1/2] 0 transition in Kr-like Y IV, Zr V, Nb VI and Mo VII ions. Gain coefficients which can lead to FUV-VUV (∝260 to 60 nm) lasing are found in all ions. Large gain coefficients are found for each ion at temperatures in excess of the ion's equilibrium temperature; realizing lasing in these systems will require a transient excitation mechanism. The density at which the maximal gain coefficient obtains increases for increasing ionization state. The 4p 5 5s 1/2[1/2] 1 -4p 5 5p 1/2[1/2] 0 and 4p 5 5s 3/2[3/2] 1 -4p 5 5p 1/2[1/2] 0 transitions also show population inversion and modest gain coefficients. Attractive features of these ions as potential lasents are the large ratio between the energy of the lasing transition and the excitation energy of the upper level of the lasing transition as well as the case with which they are produced in a low temperature, table-top scale plasma source. (orig.)

4p16.1-p15.31 duplication and 4p terminal deletion in a 3-years old Chinese girl: Array-CGH, genotype-phenotype and neurological characterization.

Science.gov (United States)

Piccione, Maria; Salzano, Emanuela; Vecchio, Davide; Ferrara, Dante; Malacarne, Michela; Pierluigi, Mauro; Ferrara, Ines; Corsello, Giovanni

2015-07-01

Microscopically chromosome rearrangements of the short arm of chromosome 4 include the two known clinical entities: partial trisomy 4p and deletions of the Wolf-Hirschhorn critical regions 1 and 2 (WHSCR-1 and WHSCR-2, respectively), which cause cranio-facial anomalies, congenital malformations and developmental delay/intellectual disability. We report on clinical findings detected in a Chinese patient with a de novo 4p16.1-p15.32 duplication in association with a subtle 4p terminal deletion of 6 Mb in size. This unusual chromosome imbalance resulted in WHS classical phenotype, while clinical manifestations of 4p trisomy were practically absent. This observation suggests the hypothesis that haploinsufficiency of sensitive dosage genes with regulatory function placed in WHS critical region, is more pathogenic than concomitant 4p duplicated segment. Additionally clinical findings in our patient confirm a variable penetrance of major malformations and neurological features in Chinese children despite of WHS critical region's deletion. Copyright © 2015 European Paediatric Neurology Society. Published by Elsevier Ltd. All rights reserved.

Vector Green's function algorithm for radiative transfer in plane-parallel atmosphere

International Nuclear Information System (INIS)

Qin Yi; Box, Michael A.

2006-01-01

Green's function is a widely used approach for boundary value problems. In problems related to radiative transfer, Green's function has been found to be useful in land, ocean and atmosphere remote sensing. It is also a key element in higher order perturbation theory. This paper presents an explicit expression of the Green's function, in terms of the source and radiation field variables, for a plane-parallel atmosphere with either vacuum boundaries or a reflecting (BRDF) surface. Full polarization state is considered but the algorithm has been developed in such way that it can be easily reduced to solve scalar radiative transfer problems, which makes it possible to implement a single set of code for computing both the scalar and the vector Green's function

Phosphatidylinositol 4-kinases: Function, structure, and inhibition

International Nuclear Information System (INIS)

Boura, Evzen; Nencka, Radim

2015-01-01

The phosphatidylinositol 4-kinases (PI4Ks) synthesize phosphatidylinositol 4-phosphate (PI4P), a key member of the phosphoinositide family. PI4P defines the membranes of Golgi and trans-Golgi network (TGN) and regulates trafficking to and from the Golgi. Humans have two type II PI4Ks (α and β) and two type III enzymes (α and β). Recently, the crystal structures were solved for both type II and type III kinase revealing atomic details of their function. Importantly, the type III PI4Ks are hijacked by +RNA viruses to create so-called membranous web, an extensively phosphorylated and modified membrane system dedicated to their replication. Therefore, selective and potent inhibitors of PI4Ks have been developed as potential antiviral agents. Here we focus on the structure and function of PI4Ks and their potential in human medicine

Phosphatidylinositol 4-kinases: Function, structure, and inhibition

Energy Technology Data Exchange (ETDEWEB)

Boura, Evzen, E-mail: boura@uochb.cas.cz; Nencka, Radim, E-mail: nencka@uochb.cas.cz

2015-10-01

The phosphatidylinositol 4-kinases (PI4Ks) synthesize phosphatidylinositol 4-phosphate (PI4P), a key member of the phosphoinositide family. PI4P defines the membranes of Golgi and trans-Golgi network (TGN) and regulates trafficking to and from the Golgi. Humans have two type II PI4Ks (α and β) and two type III enzymes (α and β). Recently, the crystal structures were solved for both type II and type III kinase revealing atomic details of their function. Importantly, the type III PI4Ks are hijacked by +RNA viruses to create so-called membranous web, an extensively phosphorylated and modified membrane system dedicated to their replication. Therefore, selective and potent inhibitors of PI4Ks have been developed as potential antiviral agents. Here we focus on the structure and function of PI4Ks and their potential in human medicine.

Nematic-smectic A and nematic-solid transitions of parallel hard spherocylinders from density functional theory

NARCIS (Netherlands)

University Utrecht

1992-01-01

A simple density functional theory for the various liquid-crystalline phases of parallel hard spherocylinders is formulated on the basis of Pynn's ansatz for the direct correlation function of the spherocylinders. Fair agreement with the computer simulations is found.

Parallelization of a blind deconvolution algorithm

Science.gov (United States)

Matson, Charles L.; Borelli, Kathy J.

2006-09-01

Often it is of interest to deblur imagery in order to obtain higher-resolution images. Deblurring requires knowledge of the blurring function - information that is often not available separately from the blurred imagery. Blind deconvolution algorithms overcome this problem by jointly estimating both the high-resolution image and the blurring function from the blurred imagery. Because blind deconvolution algorithms are iterative in nature, they can take minutes to days to deblur an image depending how many frames of data are used for the deblurring and the platforms on which the algorithms are executed. Here we present our progress in parallelizing a blind deconvolution algorithm to increase its execution speed. This progress includes sub-frame parallelization and a code structure that is not specialized to a specific computer hardware architecture.

The Not5 subunit of the ccr4-not complex connects transcription and translation.

Directory of Open Access Journals (Sweden)

Zoltan Villanyi

2014-10-01

Full Text Available Recent studies have suggested that a sub-complex of RNA polymerase II composed of Rpb4 and Rpb7 couples the nuclear and cytoplasmic stages of gene expression by associating with newly made mRNAs in the nucleus, and contributing to their translation and degradation in the cytoplasm. Here we show by yeast two hybrid and co-immunoprecipitation experiments, followed by ribosome fractionation and fluorescent microscopy, that a subunit of the Ccr4-Not complex, Not5, is essential in the nucleus for the cytoplasmic functions of Rpb4. Not5 interacts with Rpb4; it is required for the presence of Rpb4 in polysomes, for interaction of Rpb4 with the translation initiation factor eIF3 and for association of Rpb4 with mRNAs. We find that Rpb7 presence in the cytoplasm and polysomes is much less significant than that of Rpb4, and that it does not depend upon Not5. Hence Not5-dependence unlinks the cytoplasmic functions of Rpb4 and Rpb7. We additionally determine with RNA immunoprecipitation and native gel analysis that Not5 is needed in the cytoplasm for the co-translational assembly of RNA polymerase II. This stems from the importance of Not5 for the association of the R2TP Hsp90 co-chaperone with polysomes translating RPB1 mRNA to protect newly synthesized Rpb1 from aggregation. Hence taken together our results show that Not5 interconnects translation and transcription.

Prion protein (PrP) gene-knockout cell lines: insight into functions of the PrP

Science.gov (United States)

Sakudo, Akikazu; Onodera, Takashi

2015-01-01

Elucidation of prion protein (PrP) functions is crucial to fully understand prion diseases. A major approach to studying PrP functions is the use of PrP gene-knockout (Prnp−/−) mice. So far, six types of Prnp−/− mice have been generated, demonstrating the promiscuous functions of PrP. Recently, other PrP family members, such as Doppel and Shadoo, have been found. However, information obtained from comparative studies of structural and functional analyses of these PrP family proteins do not fully reveal PrP functions. Recently, varieties of Prnp−/− cell lines established from Prnp−/− mice have contributed to the analysis of PrP functions. In this mini-review, we focus on Prnp−/− cell lines and summarize currently available Prnp−/− cell lines and their characterizations. In addition, we introduce the recent advances in the methodology of cell line generation with knockout or knockdown of the PrP gene. We also discuss how these cell lines have provided valuable insights into PrP functions and show future perspectives. PMID:25642423

Expression of p16(INK4A) gene in human pituitary tumours.

Science.gov (United States)

Machiavelli, Gloria; Cotignola, Javier; Danilowicz, Karina; Carbonara, Carolina; Paes de Lima, Andrea; Basso, Armando; Bruno, Oscar Domingo; Szijan, Irene

2008-01-01

Pituitary adenomas comprise 10-15% of primary intracranial tumours but the mechanisms leading to tumour development are yet to be clearly established. The retinoblastoma pathway, which regulates the progression through the cell cycle, is often deregulated in different types of tumours. We studied the cyclin-dependent kinase inhibitor p16(INK4A) gene expression at mRNA level in human pituitary adenomas. Forty-six tumour specimens of different subtypes, 21 clinically non-functioning, 12 growth hormone-secreting, 6 prolactin-secreting, 6 adrenocorticotropin-secreting, and 1 thyrotropin-secreting tumours were studied. All clinically non-functioning and most of the hormone-secreting tumours were macroadenomas (38/46). The RT-PCR assay and electrophoresis of the PCR-products showed that p16(INK4A) mRNA was undetectable in: 62% of non-functioning, 8% of growth hormone-secreting, 17% of prolactin-secreting and 17% of adrenocorticotropin-secreting adenomas. Forty percent of all macroadenomas and 25% of microadenomas had negative p16(INK4A) mRNA, the latter results suggest that the absence of p16(INK4A) product might be an early event in tumours with no expression of this suppressor gene. Within the non-functioning adenomas 63% were "null cell" and 37% were positive for some hormone, both subgroups showed similar percentage of cases with absence of p16(INK4A) mRNA. Our results show that clinically non-functioning macroadenomas have impaired p16(INK4A) expression in a clearly higher proportion than any other pituitary tumour subtype investigated. Other regulatory pathways may be implicated in the development of tumours with positive p16(INK4A) expression.

Computational cost of isogeometric multi-frontal solvers on parallel distributed memory machines

KAUST Repository

Woźniak, Maciej

2015-02-01

This paper derives theoretical estimates of the computational cost for isogeometric multi-frontal direct solver executed on parallel distributed memory machines. We show theoretically that for the Cp-1 global continuity of the isogeometric solution, both the computational cost and the communication cost of a direct solver are of order O(log(N)p2) for the one dimensional (1D) case, O(Np2) for the two dimensional (2D) case, and O(N4/3p2) for the three dimensional (3D) case, where N is the number of degrees of freedom and p is the polynomial order of the B-spline basis functions. The theoretical estimates are verified by numerical experiments performed with three parallel multi-frontal direct solvers: MUMPS, PaStiX and SuperLU, available through PETIGA toolkit built on top of PETSc. Numerical results confirm these theoretical estimates both in terms of p and N. For a given problem size, the strong efficiency rapidly decreases as the number of processors increases, becoming about 20% for 256 processors for a 3D example with 1283 unknowns and linear B-splines with C0 global continuity, and 15% for a 3D example with 643 unknowns and quartic B-splines with C3 global continuity. At the same time, one cannot arbitrarily increase the problem size, since the memory required by higher order continuity spaces is large, quickly consuming all the available memory resources even in the parallel distributed memory version. Numerical results also suggest that the use of distributed parallel machines is highly beneficial when solving higher order continuity spaces, although the number of processors that one can efficiently employ is somehow limited.

From functional programming to multicore parallelism: A case study based on Presburger Arithmetic

DEFF Research Database (Denmark)

Dung, Phan Anh; Hansen, Michael Reichhardt

2011-01-01

, we are interested in using PA in connection with the Duration Calculus Model Checker (DCMC) [5]. There are effective decision procedures for PA including Cooper’s algorithm and the Omega Test; however, their complexity is extremely high with doubly exponential lower bound and triply exponential upper...... bound [7]. We investigate these decision procedures in the context of multicore parallelism with the hope of exploiting multicore powers. Unfortunately, we are not aware of any prior parallelism research related to decision procedures for PA. The closest work is the preliminary results on parallelism...

Copper Selenidophosphates Cu4P2Se6, Cu4P3Se4, Cu4P4Se3, and CuP2Se, Featuring Zero-, One-, and Two-Dimensional Anions.

Science.gov (United States)

Kuhn, Alexander; Schoop, Leslie M; Eger, Roland; Moudrakovski, Igor; Schwarzmüller, Stefan; Duppel, Viola; Kremer, Reinhard K; Oeckler, Oliver; Lotsch, Bettina V

2016-08-15

Five new compounds in the Cu/P/Se phase diagram have been synthesized, and their crystal structures have been determined. The crystal structures of these compounds comprise four previously unreported zero-, one-, and two-dimensional selenidophosphate anions containing low-valent phosphorus. In addition to two new modifications of Cu4P2Se6 featuring the well-known hexaselenidohypodiphosphate(IV) ion, there are three copper selenidophosphates with low-valent P: Cu4P3Se4 contains two different new anions, (i) a monomeric (zero-dimensional) selenidophosphate anion [P2Se4](4-) and (ii) a one-dimensional selenidophosphate anion [Formula: see text], which is related to the well-known gray-Se-like [Formula: see text] Zintl anion. Cu4P4Se3 contains one-dimensional [Formula: see text] polyanions, whereas CuP2Se contains the 2D selenidophosphate [Formula: see text] polyanion. It consists of charge-neutral CuP2Se layers separated by a van der Waals gap which is very rare for a Zintl-type phase. Hence, besides black P, CuP2Se constitutes a new possible source of 2D oxidized phosphorus containing layers for intercalation or exfoliation experiments. Additionally, the electronic structures and some fundamental physical properties of the new compounds are reported. All compounds are semiconducting with indirect band gaps of the orders of around 1 eV. The phases reported here add to the structural diversity of chalcogenido phosphates. The structural variety of this family of compounds may translate into a variety of tunable physical properties.

Parallel paving: An algorithm for generating distributed, adaptive, all-quadrilateral meshes on parallel computers

Energy Technology Data Exchange (ETDEWEB)

Lober, R.R.; Tautges, T.J.; Vaughan, C.T.

1997-03-01

Paving is an automated mesh generation algorithm which produces all-quadrilateral elements. It can additionally generate these elements in varying sizes such that the resulting mesh adapts to a function distribution, such as an error function. While powerful, conventional paving is a very serial algorithm in its operation. Parallel paving is the extension of serial paving into parallel environments to perform the same meshing functions as conventional paving only on distributed, discretized models. This extension allows large, adaptive, parallel finite element simulations to take advantage of paving`s meshing capabilities for h-remap remeshing. A significantly modified version of the CUBIT mesh generation code has been developed to host the parallel paving algorithm and demonstrate its capabilities on both two dimensional and three dimensional surface geometries and compare the resulting parallel produced meshes to conventionally paved meshes for mesh quality and algorithm performance. Sandia`s {open_quotes}tiling{close_quotes} dynamic load balancing code has also been extended to work with the paving algorithm to retain parallel efficiency as subdomains undergo iterative mesh refinement.

Quantification of PRL/Stat5 signaling with a novel pGL4-CISH reporter.

Science.gov (United States)

Fang, Feng; Antico, Giovanni; Zheng, Jiamao; Clevenger, Charles V

2008-02-06

Elevations of serum prolactin (PRL) are associated with an increased risk for breast cancer. PRL signaling through its prolactin receptor (PRLr) involves the Jak2/Stat5 pathway. Luciferase-based reporter assays have been widely used to evaluate the activity of this pathway. However, the existing reporters are often not sensitive enough to monitor the effect of PRL in this pathway. In this study, a new biologically relevant reporter, pGL4-CISH, was generated to study the PRL/Jak2/Stat5 signaling pathway. The sensitivity of pGL4-CISH to detect PRL was superior to that of several other commonly utilized Stat5-responsive reporters. Interestingly, the enhanced function pGL4-CISH was restricted to the estrogen receptor positive (ER+) human breast cancer cell lines T47D and MCF7, but not in the ER-MDA-231, BT-474, or MCF10A cell lines. Overexpression of Stat5 further enhanced the effect of PRL on pGL4-CISH. These studies demonstrate that pGL4-CISH is a novel and sensitive reporter for assessing the activity of the PRL/Stat5 signaling pathway in the ER+ human breast cancer cells.

Xyce Parallel Electronic Simulator : reference guide, version 4.1.

Energy Technology Data Exchange (ETDEWEB)

Mei, Ting; Rankin, Eric Lamont; Thornquist, Heidi K.; Santarelli, Keith R.; Fixel, Deborah A.; Coffey, Todd Stirling; Russo, Thomas V.; Schiek, Richard Louis; Keiter, Eric Richard; Pawlowski, Roger Patrick

2009-02-01

This document is a reference guide to the Xyce Parallel Electronic Simulator, and is a companion document to the Xyce Users Guide. The focus of this document is (to the extent possible) exhaustively list device parameters, solver options, parser options, and other usage details of Xyce. This document is not intended to be a tutorial. Users who are new to circuit simulation are better served by the Xyce Users Guide.

Model-driven product line engineering for mapping parallel algorithms to parallel computing platforms

NARCIS (Netherlands)

Arkin, Ethem; Tekinerdogan, Bedir

2016-01-01

<p>Mapping parallel algorithms to parallel computing platforms requires several activities such as the analysis of the parallel algorithm, the definition of the logical configuration of the platform, the mapping of the algorithm to the logical configuration platform and the implementation of the

PROBING VERY BRIGHT END OF GALAXY LUMINOSITY FUNCTION AT z ∼> 7 USING HUBBLE SPACE TELESCOPE PURE PARALLEL OBSERVATIONS

International Nuclear Information System (INIS)

Yan Haojing; Yan Lin; Zamojski, Michel A.; Windhorst, Rogier A.; McCarthy, Patrick J.; Fan Xiaohui; Dave, Romeel; Roettgering, Huub J. A.; Koekemoer, Anton M.; Robertson, Brant E.; Cai Zheng

2011-01-01

We report the first results from the Hubble Infrared Pure Parallel Imaging Extragalactic Survey, which utilizes the pure parallel orbits of the Hubble Space Telescope to do deep imaging along a large number of random sightlines. To date, our analysis includes 26 widely separated fields observed by the Wide Field Camera 3, which amounts to 122.8 arcmin 2 in total area. We have found three bright Y 098 -dropouts, which are candidate galaxies at z ∼> 7.4. One of these objects shows an indication of peculiar variability and its nature is uncertain. The other two objects are among the brightest candidate galaxies at these redshifts known to date (L>2L*). Such very luminous objects could be the progenitors of the high-mass Lyman break galaxies observed at lower redshifts (up to z ∼ 5). While our sample is still limited in size, it is much less subject to the uncertainty caused by 'cosmic variance' than other samples because it is derived using fields along many random sightlines. We find that the existence of the brightest candidate at z ∼ 7.4 is not well explained by the current luminosity function (LF) estimates at z ∼ 8. However, its inferred surface density could be explained by the prediction from the LFs at z ∼ 7 if it belongs to the high-redshift tail of the galaxy population at z ∼ 7.

4s24p3--4s4p4 and 4s24p3--4s2fp25s transitions in Y VII, Zr VIII, Nb IX, and MoX

International Nuclear Information System (INIS)

Reader, J.; Acquista, N.

1981-01-01

Spectra of ionized Y, Zr, Nb, and Mo have been observed in sliding-spark and triggered-spark discharges on 10.7-m normal- and grazing-incidence spectrographs at the National Bureau of Standards in Washington, D. C. From these observations the 4s 2 4p 3 --4s4p 4 transitions in Y VII, Zr VIII, Nb IX, and Mo X have been identified. The 4s 2 4p 3 --4s 2 4p 2 5s transitions in Y VII-Mo X, previously identified by Rahimullah et al. [Phys. Scr. 14, 221--223 (1976); 18, 96--106 (1978)], have been confirmed. In Y VII the 4s 2 4p 3 --4s 2 4p 2 6s and 4s4p 4 --4p 5 transition also have been found. The parameters obtained from least-squares fits to the energy levels are compared with Hartree--Fock calculations. Preliminary values of the ionization energies have been determined as 110.02 +- 0.15 eV for Y VII, 133.7 +- 0.5 eV for Zr VIII, 159.2 +- 0.7 eV for Nb IX, and 186.4 +- 1.2 eV for Mo X

Molecular and clinical description of a girl with a 46,X,t(Y;4)(q11.2;p16)/45,X,der(4)t(Y;4)(q11.2;p16) karyotype and a small cryptic 4p subtelomeric deletion.

Science.gov (United States)

Zahed, Laila; Sismani, Carolina; Ioannides, M; Saleh, Monzer; Koumbaris, G; Kenj, Mazen; Abdallah, Amal; Ayyache, Maya; Patsalis, Philippos

2008-04-01

We report on a 13-year-old female with short stature, minimal axillary and pubic hair, no breast development, absence of uterus and ovaries, with the following karyotype on lymphocyte cultures: 46,X,t(Y;4)(q11.2;p16)[40]/45,X,der(4)t(Y;4)(q11.2;p16)[10]. Loss of the small derivative Y chromosome in 20% of the cells was also confirmed in skin fibroblast cultures. FISH analyses using Y centromere, SRY, subtelomere XpYp/XqYq, Y and 4 painting probes, confirmed the cytogenetic findings. High-resolution STS analyses using 40 markers covering the Y chromosome did not identify any deletion on the Y. However, de novo absence of the 4p subtelomeric region was noted by FISH, although this deletion was not revealed by Array-CGH at 1 Mb resolution, the last array clone being 0.35 or 1 Mb distal to the 4p FISH probe. The female phenotype of this patient must be due to the loss of the derivative Y chromosomes in some of her cells, especially the gonads, while the 4p subtelomeric deletion does not seem to contribute to her phenotype. Copyright 2008 Wiley-Liss, Inc.

Organotin(IV Derivatives of 2-Acetylpyridine-N(4-Phenylthiosemicarbazone, HAP4P, and 2-Hydroxyacetophenone-N(4-Phenylthiosemicarbazone, H2DAP4P: Crystal and Molecular Structure of [SnMe2(DAP4P] and [SnBu2(DAP4P

Directory of Open Access Journals (Sweden)

Sousa Gerimário F. de

2001-01-01

Full Text Available The reactions of 2-acetylpyridine-N(4-phenylthiosemicarbazone, HAP4P, and 2-hydroxyacetophenone-N(4-phenylthiosemicarbazone, H2DAP4P, with R4-mSnXm (m = 2, 3; R = Me, nBu, Ph and X = Cl, Br led to the formation of hexa- and penta-coordinated organotin(IV complexes, which were studied by microanalysis, IR, ¹H-NMR and Mössbauer spectroscopies. The molecular structures of [SnMe2(DAP4P] and [Sn nBu2(DAP4P] were determined by single-crystal X-ray diffraction studies. In the compounds [SnClMe2(AP4P] and [SnBrMe2(AP4P], the deprotonated ligand AP4P- is N,N,S-bonded to the Sn(IV atoms, which exhibit strongly distorted octahedral coordination. The structures of [SnMe2(DAP4P] and [Sn nBu2(DAP4P] revealed that the DAP4P2- anion acts as a O,N,S-tridentate ligand. In these cases, the Sn(IV atoms adopt a strongly distorted trigonal bipyramidal configuration where the azomethine N and the two C atoms are on the equatorial plane while the O and the S atoms occupy the axial positions.

Development of massively parallel quantum chemistry program SMASH

International Nuclear Information System (INIS)

Ishimura, Kazuya

2015-01-01

A massively parallel program for quantum chemistry calculations SMASH was released under the Apache License 2.0 in September 2014. The SMASH program is written in the Fortran90/95 language with MPI and OpenMP standards for parallelization. Frequently used routines, such as one- and two-electron integral calculations, are modularized to make program developments simple. The speed-up of the B3LYP energy calculation for (C 150 H 30 ) 2 with the cc-pVDZ basis set (4500 basis functions) was 50,499 on 98,304 cores of the K computer

Nuclear receptors of the NR4a family are not required for the development and function of follicular T helper cells.

Science.gov (United States)

Ma, Weiwei; Zhao, Ruozhu; Yang, Runqing; Liu, Bo; Chen, Xin; Wu, Longyan; Qi, Hai

2015-10-01

Follicular T helper (Tfh) cells promote germinal center (GC) reaction and high-affinity antibody production. The molecular mechanisms that regulate development and function of Tfh cells are not fully understood. Here we report that ligand-independent nuclear receptors of the Nr4a family are highly expressed in Tfh cells. In a well-established adoptive transfer model, enforced expression of Nr4a receptors reduces helper T cell expansion but apparently increased the T cell capacity to promote the GC response. On the other hand, deletion of all Nr4a receptors in T cells did not significantly affect expansion or differentiation of Tfh cells or the development of GC reaction. These findings suggest that Nr4a receptors may promote but are not necessary for Tfh development or function in vivo. Copyright © 2015 Elsevier B.V. All rights reserved.

Saccharomyces cerevisiae Linker Histone Hho1p Functionally Interacts with Core Histone H4 and Negatively Regulates the Establishment of Transcriptionally Silent Chromatin*

OpenAIRE

Yu, Qun; Kuzmiak, Holly; Zou, Yanfei; Olsen, Lars; Defossez, Pierre-Antoine; Bi, Xin

2009-01-01

Saccharomyces cerevisiae linker histone Hho1p is not essential for cell viability, and very little is known about its function in vivo. We show that deletion of HHO1 (hho1Δ) suppresses the defect in transcriptional silencing caused by a mutation in the globular domain of histone H4. hho1Δ also suppresses the reduction in HML silencing by the deletion of SIR1 that is involved in the establishment of silent chromatin at HML. We further show that hho1Δ suppresses chan...

Hal2p functions in Bdf1p-involved salt stress response in Saccharomyces cerevisiae.

Directory of Open Access Journals (Sweden)

Lei Chen

Full Text Available The Saccharomyces cerevisiae Bdf1p associates with the basal transcription complexes TFIID and acts as a transcriptional regulator. Lack of Bdf1p is salt sensitive and displays abnormal mitochondrial function. The nucleotidase Hal2p detoxifies the toxic compound 3' -phosphoadenosine-5'-phosphate (pAp, which blocks the biosynthesis of methionine. Hal2p is also a target of high concentration of Na(+. Here, we reported that HAL2 overexpression recovered the salt stress sensitivity of bdf1Δ. Further evidence demonstrated that HAL2 expression was regulated indirectly by Bdf1p. The salt stress response mechanisms mediated by Bdf1p and Hal2p were different. Unlike hal2Δ, high Na(+ or Li(+ stress did not cause pAp accumulation in bdf1Δ and methionine supplementation did not recover its salt sensitivity. HAL2 overexpression in bdf1Δ reduced ROS level and improved mitochondrial function, but not respiration. Further analyses suggested that autophagy was apparently defective in bdf1Δ, and autophagy stimulated by Hal2p may play an important role in recovering mitochondrial functions and Na(+ sensitivity of bdf1Δ. Our findings shed new light towards our understanding about the molecular mechanism of Bdf1p-involved salt stress response in budding yeast.

Parallel tempering in full QCD with Wilson fermions

International Nuclear Information System (INIS)

Ilgenfritz, E.-M.; Kerler, W.; Mueller-Preussker, M.; Stueben, H.

2002-01-01

We study the performance of QCD simulations with dynamical Wilson fermions by combining the hybrid Monte Carlo algorithm with parallel tempering on 10 4 and 12 4 lattices. In order to compare tempered with standard simulations, covariance matrices between subensembles have to be formulated and evaluated using the general properties of autocorrelations of the parallel tempering algorithm. We find that rendering the hopping parameter κ dynamical does not lead to an essential improvement. We point out possible reasons for this observation and discuss more suitable ways of applying parallel tempering to QCD

Storing files in a parallel computing system based on user-specified parser function

Science.gov (United States)

Faibish, Sorin; Bent, John M; Tzelnic, Percy; Grider, Gary; Manzanares, Adam; Torres, Aaron

2014-10-21

Techniques are provided for storing files in a parallel computing system based on a user-specified parser function. A plurality of files generated by a distributed application in a parallel computing system are stored by obtaining a parser from the distributed application for processing the plurality of files prior to storage; and storing one or more of the plurality of files in one or more storage nodes of the parallel computing system based on the processing by the parser. The plurality of files comprise one or more of a plurality of complete files and a plurality of sub-files. The parser can optionally store only those files that satisfy one or more semantic requirements of the parser. The parser can also extract metadata from one or more of the files and the extracted metadata can be stored with one or more of the plurality of files and used for searching for files.

Regulatory Mechanisms in the P4-ATPase Complex

DEFF Research Database (Denmark)

Costa, Sara

. The functionality on the P4-ATPase complex is essential for several cellular processes, such as vesicle-mediated transport. However, the specific role of flippase activity in vesicle biogenesis and the regulatory mechanism behind this process is still poorly understood. In these studies, we identified...... affordable alternative using a microscope-based cytometer. This system can simultaneously provide information on flippase activity and expression levels. Taken together, the findings described in this thesis provide new tools for P4-ATPase characterization and valuable insights into the regulation...

Stampi: a message passing library for distributed parallel computing. User's guide

International Nuclear Information System (INIS)

Imamura, Toshiyuki; Koide, Hiroshi; Takemiya, Hiroshi

1998-11-01

A new message passing library, Stampi, has been developed to realize a computation with different kind of parallel computers arbitrarily and making MPI (Message Passing Interface) as an unique interface for communication. Stampi is based on MPI2 specification. It realizes dynamic process creation to different machines and communication between spawned one within the scope of MPI semantics. Vender implemented MPI as a closed system in one parallel machine and did not support both functions; process creation and communication to external machines. Stampi supports both functions and enables us distributed parallel computing. Currently Stampi has been implemented on COMPACS (COMplex PArallel Computer System) introduced in CCSE, five parallel computers and one graphic workstation, and any communication on them can be processed on. (author)

The Fortran-P Translator: Towards Automatic Translation of Fortran 77 Programs for Massively Parallel Processors

Directory of Open Access Journals (Sweden)

Matthew O'keefe

1995-01-01

Full Text Available Massively parallel processors (MPPs hold the promise of extremely high performance that, if realized, could be used to study problems of unprecedented size and complexity. One of the primary stumbling blocks to this promise has been the lack of tools to translate application codes to MPP form. In this article we show how applications codes written in a subset of Fortran 77, called Fortran-P, can be translated to achieve good performance on several massively parallel machines. This subset can express codes that are self-similar, where the algorithm applied to the global data domain is also applied to each subdomain. We have found many codes that match the Fortran-P programming style and have converted them using our tools. We believe a self-similar coding style will accomplish what a vectorizable style has accomplished for vector machines by allowing the construction of robust, user-friendly, automatic translation systems that increase programmer productivity and generate fast, efficient code for MPPs.

Wolf-Hirschhorn Syndrome with Epibulbar Dermoid: An Unusual Association in a Patient with 4p Deletion and Functional Xp Disomy.

Science.gov (United States)

Bragagnolo, Silvia; Colovati, Mileny E S; Guilherme, Roberta S; Dantas, Anelisa G; de Souza, Malú Zamariolli; de Soares, Maria F; Melaragno, Maria I; Perez, Ana B

2016-01-01

Wolf-Hirschhorn syndrome (WHS) is a contiguous gene and multiple malformation syndrome that results from a deletion in the 4p16.3 region. We describe here a 6-month-old girl that presented with WHS features but also displayed unusual findings, such as epibulbar dermoid in the left eye, ear tags, and left microtia. Although on G-banding her karyotype appeared to be normal, chromosomal microarray analysis revealed an ∼13-Mb 4p16.3p15.33 deletion and an ∼9-Mb Xp22.33p22.31 duplication, resulting from a balanced maternal t(X;4)(p22.31;p15.33) translocation. The patient presented with functional Xp disomy due to an unbalanced X-autosome translocation, a rare cytogenetic finding in females with unbalanced rearrangements. Sequencing of both chromosome breakpoints detected no gene disruption. To the best of our knowledge, this is the first patient described in the literature with WHS and epibulbar dermoid, a typical characteristic of the oculoauriculovertebral spectrum (OAVS). Our data suggest that possible candidate genes for OAVS may have been deleted along with the WHS critical region. © 2016 S. Karger AG, Basel.

Oxothiomolybdenum derivatives of the superlacunary crown heteropolyanion {P8W48}: structure of [K4{Mo4O4S4(H2O)3(OH)2}2(WO2)(P8W48O184)]30– and studies in solution.

Science.gov (United States)

Korenev, Vladimir S; Floquet, Sébastien; Marrot, Jérôme; Haouas, Mohamed; Mbomekallé, Israël-Martyr; Taulelle, Francis; Sokolov, Maxim N; Fedin, Vladimir P; Cadot, Emmanuel

2012-02-20

Reaction of the cyclic lacunary [H(7)P(8)W(48)O(184)](33-) anion (noted P(8)W(48)) with the [Mo(2)S(2)O(2)(H(2)O)(6)](2+) oxothiocation led to two compounds, namely, [K(4){Mo(4)O(4)S(4)(H(2)O)(3)(OH)(2)}(2)(WO(2))(P(8)W(48)O(184))](30-) (denoted 1) and [{Mo(4)O(4)S(4)(H(2)O)(3)(OH)(2)}(2)(P(8)W(48)O(184))](36-) (denoted 2), which were characterized in the solid state and solution. In the solid state, the structure of [K(4){Mo(4)O(4)S(4)(H(2)O)(3)(OH)(2)}(2)(WO(2))(P(8)W(48)O(184))](30-) reveals the presence of two disordered {Mo(4)O(4)S(4)(H(2)O)(3)(OH)(2)}(2+) "handles" connected on both sides of the P(8)W(48) ring. Such a disorder is consistent with the presence of two geometrical isomers where the relative disposition of the two {Mo(4)O(4)S(4)(H(2)O)(3)(OH)(2)}(2+) handles are arranged in a perpendicular or parallel mode. Such an interpretation is fully supported by (31)P and (183)W NMR solution studies. The relative stability of both geometrical isomers appears to be dependent upon the nature of the internal alkali cations, i.e., Na(+) vs K(+), and increased lability of the two {Mo(4)O(4)S(4)(H(2)O)(3)(OH)(2)}(2+) handles, compared to the oxo analogous, was clearly identified by significant broadening of the (31)P and (183)W NMR lines. Solution studies carried out by UV-vis spectroscopy showed that formation of the adduct [{Mo(4)O(4)S(4)(H(2)O)(3)(OH)(2)}(2)(P(8)W(48)O(184))](36-) occurs in the 1.5-4.7 pH range and corresponds to a fast and quantitative condensation process. Furthermore, (31)P NMR titrations in solution reveal formation of the "monohandle" derivative [{Mo(4)O(4)S(4)(H(2)O)(3)(OH)(2)}(P(8)W(48)O(184))](38-) as an intermediate prior to formation of the "bishandle" derivatives. Furthermore, the electrochemical behavior of [{Mo(4)O(4)S(4)(H(2)O)(3)(OH)(2)}(2)(P(8)W(48)O(184))](36-) was studied in aqueous medium and compared with the parent anion P(8)W(48).

P-gp activity is a critical resistance factor against AVE9633 and DM4 cytotoxicity in leukaemia cell lines, but not a major mechanism of chemoresistance in cells from acute myeloid leukaemia patients

International Nuclear Information System (INIS)

Tang, Ruoping; Legrand, Ollivier; Marie, Jean-Pierre; Cohen, Simy; Perrot, Jean-Yves; Faussat, Anne-Marie; Zuany-Amorim, Claudia; Marjanovic, Zora; Morjani, Hamid; Fava, Fanny; Corre, Elise

2009-01-01

AVE9633 is a new immunoconjugate comprising a humanized monoclonal antibody, anti-CD33 antigen, linked through a disulfide bond to the maytansine derivative DM4, a cytotoxic agent and potent tubulin inhibitor. It is undergoing a phase I clinical trial. Chemoresistance to anti-mitotic agents has been shown to be related, in part, to overexpression of ABC proteins. The aim of the present study was to investigate the potential roles of P-gp, MRP1 and BCRP in cytotoxicity in AVE9633-induced acute myeloid leukaemia (AML). This study used AML cell lines expressing different levels of P-gp, MRP1 or BCRP proteins and twenty-five samples from AML patients. Expression and functionality of the transporter protein were analyzed by flow cytometry. The cytotoxicity of the drug was evaluated by MTT and apoptosis assays. P-gp activity, but not MRP1 and BCRP, attenuated AVE9633 and DM4 cytotoxicity in myeloid cell lines. Zosuquidar, a potent specific P-gp inhibitor, restored the sensitivity of cells expressing P-gp to both AVE9633 and DM4. However, the data from AML patients show that 10/25 samples of AML cells (40%) were resistant to AVE9633 or DM4 (IC 50 > 500 nM), and this was not related to P-gp activity (p-Value: 0.7). Zosuquidar also failed to re-establish drug sensitivity. Furthermore, this resistance was not correlated with CD33 expression (p-Value: 0.6) in those cells. P-gp activity is not a crucial mechanism of chemoresistance to AVE9633. For patients whose resistance to conventional anthracycline AML regimens is related to ABC protein expression, a combination with AVE9633 could be beneficial. Other mechanisms such as microtubule alteration could play an important role in chemoresistance to AVE9633

Nonclassical states of light with a smooth P function

Science.gov (United States)

Damanet, François; Kübler, Jonas; Martin, John; Braun, Daniel

2018-02-01

There is a common understanding in quantum optics that nonclassical states of light are states that do not have a positive semidefinite and sufficiently regular Glauber-Sudarshan P function. Almost all known nonclassical states have P functions that are highly irregular, which makes working with them difficult and direct experimental reconstruction impossible. Here we introduce classes of nonclassical states with regular, non-positive-definite P functions. They are constructed by "puncturing" regular smooth positive P functions with negative Dirac-δ peaks or other sufficiently narrow smooth negative functions. We determine the parameter ranges for which such punctures are possible without losing the positivity of the state, the regimes yielding antibunching of light, and the expressions of the Wigner functions for all investigated punctured states. Finally, we propose some possible experimental realizations of such states.

CD4 T cell knockout does not protect against kidney injury and worsens cancer.

Science.gov (United States)

Ravichandran, Kameswaran; Wang, Qian; Ozkok, Abdullah; Jani, Alkesh; Li, Howard; He, Zhibin; Ljubanovic, Danica; Weiser-Evans, Mary C; Nemenoff, Raphael A; Edelstein, Charles L

2016-04-01

Most previous studies of cisplatin-induced acute kidney injury (AKI) have been in models of acute, high-dose cisplatin administration that leads to mortality in non-tumor-bearing mice. The aim of the study was to determine whether CD4 T cell knockout protects against AKI and cancer in a clinically relevant model of low-dose cisplatin-induced AKI in mice with cancer. Kidney function, serum neutrophil gelatinase-associated lipocalin (NGAL), acute tubular necrosis (ATN), and tubular apoptosis score were the same in wild-type and CD4 -/- mice with AKI. The lack of protection against AKI in CD4 -/- mice was associated with an increase in extracellular signal-regulated kinase (ERK), p38, CXCL1, and TNF-α, mediators of AKI and fibrosis, in both cisplatin-treated CD4 -/- mice and wild-type mice. The lack of protection was independent of the presence of cancer or not. Tumor size was double, and cisplatin had an impaired therapeutic effect on the tumors in CD4 -/- vs. wild-type mice. Mice depleted of CD4 T cells using the GK1.5 antibody were not protected against AKI and had larger tumors and lesser response to cisplatin. In summary, in a clinically relevant model of cisplatin-induced AKI in mice with cancer, (1) CD4 -/- mice were not protected against AKI; (2) ERK, p38, CXCL1, and TNF-α, known mediators of AKI, and interstitial fibrosis were increased in CD4 -/- kidneys; and (3) CD4 -/- mice had faster tumor growth and an impaired therapeutic effect of cisplatin on the tumors. The data warns against the use of CD4 T cell inhibition to attenuate cisplatin-induced AKI in patients with cancer. A clinically relevant low-dose cisplatin model of AKI in mice with cancer was used. CD4 -/- mice were not functionally or histologically protected against AKI. CD4 -/- mice had faster tumor growth. CD4 -/- mice had an impaired therapeutic effect of cisplatin on the tumors. Mice depleted of CD4 T cells were not protected against AKI and had larger tumors.

Interaction of integrin β4 with S1P receptors in S1P- and HGF-induced endothelial barrier enhancement.

Science.gov (United States)

Ni, Xiuqin; Epshtein, Yulia; Chen, Weiguo; Zhou, Tingting; Xie, Lishi; Garcia, Joe G N; Jacobson, Jeffrey R

2014-06-01

We previously reported sphingosine 1-phosphate (S1P) and hepatocyte growth factor (HGF) augment endothelial cell (EC) barrier function and attenuate murine acute lung inury (ALI). While the mechanisms underlying these effects are not fully understood, S1P and HGF both transactivate the S1P receptor, S1PR1 and integrin β4 (ITGB4) at membrane caveolin-enriched microdomains (CEMs). In the current study, we investigated the roles of S1PR2 and S1PR3 in S1P/HGF-mediated EC signaling and their associations with ITGB4. Our studies confirmed ITGB4 and S1PR2/3 are recruited to CEMs in human lung EC in response to either S1P (1 µM, 5 min) or HGF (25 ng/ml, 5 min). Co-immunoprecipitation experiments identified an S1P/HGF-mediated interaction of ITGB4 with both S1PR2 and S1PR3. We then employed an in situ proximity ligation assay (PLA) to confirm a direct ITGB4-S1PR3 association induced by S1P/HGF although a direct association was not detectable between S1PR2 and ITGB4. S1PR1 knockdown (siRNA), however, abrogated S1P/HGF-induced ITGB4-S1PR2 associations while there was no effect on ITGB4-S1PR3 associations. Moreover, PLA confirmed a direct association between S1PR1 and S1PR2 induced by S1P and HGF. Finally, silencing of S1PR2 significantly attenuated S1P/HGF-induced EC barrier enhancement as measured by transendothelial resistance while silencing of S1PR3 significantly augmented S1P/HGF-induced barrier enhancement. These results confirm an important role for S1PR2 and S1PR3 in S1P/HGF-mediated EC barrier responses that are associated with their complex formation with ITGB4. Our findings elucidate novel mechanisms of EC barrier regulation that may ultimately lead to new therapeutic targets for disorders characterized by increased vascular permeability including ALI. © 2013 Wiley Periodicals, Inc.

Characterization of a parallel-stranded DNA hairpin

International Nuclear Information System (INIS)

Germann, M.W.; Vogel, H.J.; Pon, R.T.; van de Sande, J.H.

1989-01-01

Recently, the authors have shown that synthetic DNA containing homooligomeric A-T base pairs can form a parallel-stranded intramolecular hairpin structure. In the present study, they have employed NMR and optical spectroscopy to investigate the structure of the parallel-stranded (PS) DNA hairpin 3'-d(T) 8 C 4 (A) 8 -3' and the related antiparallel (APS) hair 5'-d(T) 8 C 4 (A) 8 -3'. The parallel orientation of the strands in the PS oligonucleotide is achieved by introducing a 5'-5' phosphodiester linkage in the hairpin loop. Ultraviolet spectroscopic and fluorescence data of drug binding are consistent with the formation of PS and APS structures, respectively, in these two hairpins. Vacuum circular dichroism measurements in combination with theoretical CD calculations indicate that the PS structure forms a right-handed helix. 31 P NMR measurements indicate that the conformation of the phosphodiester backbone of the PS structure is not drastically different from that of the APS control. The presence of slowly exchanging imino protons at 14 ppm and the observation of nuclear Overhauser enhancement between imino protons and the AH-2 protons demonstrate that similar base pairing and base stacking between T and A residues occur in both hairpins. On the basis of NOESY measurements, they find that the orientation of the bases is in the anti region and that the sugar puckering is in the 2'-endo range. The results indicate a B-like conformation for each of the strands in the stem part of the PS hairpin and reverse Watson-Crick base pairing between the T and A residues. These data are consistent with a previously calculated structure for parallel-stranded DNA

Isotope shift of 40,42,44,48Ca in the 4s 2S1/2 → 4p 2P3/2 transition

Science.gov (United States)

Gorges, C.; Blaum, K.; Frömmgen, N.; Geppert, Ch; Hammen, M.; Kaufmann, S.; Krämer, J.; Krieger, A.; Neugart, R.; Sánchez, R.; Nörtershäuser, W.

2015-12-01

We report on improved isotope shift measurements of the isotopes {}{40,42,{44,48}}Ca in the 4{{s}}{ }2{{{S}}}1/2\\to 4{{p}}{ }2{{{P}}}3/2 (D2) transition using collinear laser spectroscopy. Accurately known isotope shifts in the 4{{s}}{ }2{{{S}}}1/2\\to 4{{p}}{ }2{{{P}}}1/2(D1) transition were used to calibrate the ion beam energy with an uncertainty of {{Δ }}U≈ +/- 0.25 {{V}}. The accuracy in the D2 transition was improved by a factor of 5-10. A King-plot analysis of the two transitions revealed that the field shift factor in the D2 line is about 1.8(13)% larger than in the D1 transition which is ascribed to relativistic contributions of the 4{{{p}}}1/2 wave function.

Quantification of PRL/Stat5 signaling with a novel pGL4-CISH reporter

Directory of Open Access Journals (Sweden)

Zheng Jiamao

2008-02-01

Full Text Available Abstract Background Elevations of serum prolactin (PRL are associated with an increased risk for breast cancer. PRL signaling through its prolactin receptor (PRLr involves the Jak2/Stat5 pathway. Luciferase-based reporter assays have been widely used to evaluate the activity of this pathway. However, the existing reporters are often not sensitive enough to monitor the effect of PRL in this pathway. Results In this study, a new biologically relevant reporter, pGL4-CISH, was generated to study the PRL/Jak2/Stat5 signaling pathway. The sensitivity of pGL4-CISH to detect PRL was superior to that of several other commonly utilized Stat5-responsive reporters. Interestingly, the enhanced function pGL4-CISH was restricted to the estrogen receptor positive (ER+ human breast cancer cell lines T47D and MCF7, but not in the ER-MDA-231, BT-474, or MCF10A cell lines. Overexpression of Stat5 further enhanced the effect of PRL on pGL4-CISH. Conclusion These studies demonstrate that pGL4-CISH is a novel and sensitive reporter for assessing the activity of the PRL/Stat5 signaling pathway in the ER+ human breast cancer cells.

Evidence that kidney function but not type 2 diabetes determines retinol-binding protein 4 serum levels

DEFF Research Database (Denmark)

Henze, Andrea; Frey, Simone K; Raila, Jens

2008-01-01

It has been suggested that retinol-binding protein 4 (RBP4) links adiposity, insulin resistance, and type 2 diabetes. However, circulating RBP4 levels are also affected by kidney function. Therefore, the aim of this study was to test whether RBP4 serum levels are primarily associated with kidney...... function or type 2 diabetes....

Parallel algorithms for continuum dynamics

International Nuclear Information System (INIS)

Hicks, D.L.; Liebrock, L.M.

1987-01-01

Simply porting existing parallel programs to a new parallel processor may not achieve the full speedup possible; to achieve the maximum efficiency may require redesigning the parallel algorithms for the specific architecture. The authors discuss here parallel algorithms that were developed first for the HEP processor and then ported to the CRAY X-MP/4, the ELXSI/10, and the Intel iPSC/32. Focus is mainly on the most recent parallel processing results produced, i.e., those on the Intel Hypercube. The applications are simulations of continuum dynamics in which the momentum and stress gradients are important. Examples of these are inertial confinement fusion experiments, severe breaks in the coolant system of a reactor, weapons physics, shock-wave physics. Speedup efficiencies on the Intel iPSC Hypercube are very sensitive to the ratio of communication to computation. Great care must be taken in designing algorithms for this machine to avoid global communication. This is much more critical on the iPSC than it was on the three previous parallel processors

Interactive effects of pH and metals on mitochondrial functions of intertidal bivalves Crassostrea virginica and Mercenaria mercenaria

International Nuclear Information System (INIS)

Ivanina, Anna V.; Sokolova, Inna M.

2013-01-01

Highlights: •Interactive effects of trace metals Cd and Cu and pH were studied in mitochondria of clams and oysters. •Mitochondrial respiration and membrane potential of bivalves were robust to pH variation (6.6–7.8). •Elevated levels of Cd and Cu inhibited mitochondrial respiration in the pH-dependent manner but did not affect the membrane potential. •Negative effects of Cd and Cd on mitochondrial respiration were alleviated at low pH (7.0 and below). •Moderate acidosis may protect molluscan mitochondria from metal toxicity. -- Abstract: Intertidal bivalves experience broad fluctuations of environmental temperature, pH and oxygen content which could change their intracellular pH. They are also exposed to trace metals such as cadmium (Cd) and copper (Cu) that accumulate in their tissues and may negatively affect mitochondrial functions and bioenergetics. We determined the interactive effects of pH and trace metals (25 μM Cd or Cu) on mitochondrial functions (including respiration and membrane potentials in both ADP-stimulated (state 3) and resting (state 4) states) of two common marine bivalves, the hard clams (Mercenaria mercenaria) and eastern oysters (Crassostrea virginica). In the absence of the trace metals, mitochondrial functions of C. virginica and M. mercenaria were insensitive to pH in a broad physiologically relevant range (6.6–7.8). Mitochondrial respiration was generally suppressed by 25 μM Cd or Cu (with the stronger effects observed for ADP-stimulated compared to the resting respiration) while the mitochondrial membrane potential was unaffected. pH modulated the effects of Cu and Cd on mitochondrial respiration of the bivalves. In oysters, Cu suppressed ADP-stimulated mitochondrial respiration at high and low pH values (6.6 and 7.8, respectively), but had no effect in the intermediate pH range (7.0–7.4). In clams, the negative effect of Cu on ADP-stimulated respiration was only observed at extremely high pH (7.8). A decrease in p

Interactive effects of pH and metals on mitochondrial functions of intertidal bivalves Crassostrea virginica and Mercenaria mercenaria

Energy Technology Data Exchange (ETDEWEB)

Ivanina, Anna V.; Sokolova, Inna M., E-mail: isokolov@uncc.edu

2013-11-15

Highlights: •Interactive effects of trace metals Cd and Cu and pH were studied in mitochondria of clams and oysters. •Mitochondrial respiration and membrane potential of bivalves were robust to pH variation (6.6–7.8). •Elevated levels of Cd and Cu inhibited mitochondrial respiration in the pH-dependent manner but did not affect the membrane potential. •Negative effects of Cd and Cd on mitochondrial respiration were alleviated at low pH (7.0 and below). •Moderate acidosis may protect molluscan mitochondria from metal toxicity. -- Abstract: Intertidal bivalves experience broad fluctuations of environmental temperature, pH and oxygen content which could change their intracellular pH. They are also exposed to trace metals such as cadmium (Cd) and copper (Cu) that accumulate in their tissues and may negatively affect mitochondrial functions and bioenergetics. We determined the interactive effects of pH and trace metals (25 μM Cd or Cu) on mitochondrial functions (including respiration and membrane potentials in both ADP-stimulated (state 3) and resting (state 4) states) of two common marine bivalves, the hard clams (Mercenaria mercenaria) and eastern oysters (Crassostrea virginica). In the absence of the trace metals, mitochondrial functions of C. virginica and M. mercenaria were insensitive to pH in a broad physiologically relevant range (6.6–7.8). Mitochondrial respiration was generally suppressed by 25 μM Cd or Cu (with the stronger effects observed for ADP-stimulated compared to the resting respiration) while the mitochondrial membrane potential was unaffected. pH modulated the effects of Cu and Cd on mitochondrial respiration of the bivalves. In oysters, Cu suppressed ADP-stimulated mitochondrial respiration at high and low pH values (6.6 and 7.8, respectively), but had no effect in the intermediate pH range (7.0–7.4). In clams, the negative effect of Cu on ADP-stimulated respiration was only observed at extremely high pH (7.8). A decrease in p

Introduction to parallel programming

CERN Document Server

Brawer, Steven

1989-01-01

Introduction to Parallel Programming focuses on the techniques, processes, methodologies, and approaches involved in parallel programming. The book first offers information on Fortran, hardware and operating system models, and processes, shared memory, and simple parallel programs. Discussions focus on processes and processors, joining processes, shared memory, time-sharing with multiple processors, hardware, loops, passing arguments in function/subroutine calls, program structure, and arithmetic expressions. The text then elaborates on basic parallel programming techniques, barriers and race

Topology in SU(2) lattice gauge theory and parallelization of functional magnetic resonance imaging

Energy Technology Data Exchange (ETDEWEB)

Solbrig, Stefan

2008-07-01

In this thesis, I discuss topological properties of quenched SU(2) lattice gauge fields. In particular, clusters of topological charge density exhibit a power-law. The exponent of that power-law can be used to validate models for lattice gauge fields. Instead of working with fixed cutoffs of the topological charge density, using the notion of a ''watermark'' is more convenient. Furthermore, I discuss how a parallel computer, originally designed for lattice gauge field simulations, can be used for functional magnetic resonance imaging. Multi parameter fits can be parallelized to achieve almost real-time evaluation of fMRI data. (orig.)

Topology in SU(2) lattice gauge theory and parallelization of functional magnetic resonance imaging

International Nuclear Information System (INIS)

Solbrig, Stefan

2008-01-01

In this thesis, I discuss topological properties of quenched SU(2) lattice gauge fields. In particular, clusters of topological charge density exhibit a power-law. The exponent of that power-law can be used to validate models for lattice gauge fields. Instead of working with fixed cutoffs of the topological charge density, using the notion of a ''watermark'' is more convenient. Furthermore, I discuss how a parallel computer, originally designed for lattice gauge field simulations, can be used for functional magnetic resonance imaging. Multi parameter fits can be parallelized to achieve almost real-time evaluation of fMRI data. (orig.)

PPADS: an antagonist at endothelial P2Y-purinoceptors but not P2U-purinoceptors.

Science.gov (United States)

Brown, C; Tanna, B; Boarder, M R

1995-11-01

1. Bovine aortic endothelial (BAE) cells contain two co-existing receptors for extracellular ATP, the P2Y and P2U-purinoceptors. Here we have determined whether the proposed P2X-purinoceptor antagonist, pyridoxalphosphate-6-azophenyl-2', 4'-disulphonic acid (PPADS) could distinguish between these two receptor subtypes. 2. Cells labelled with myo-[2-3H]-inositol were stimulated with increasing concentrations of either the P2Y-agonist, 2MeSATP, or the P2U-agonist, UTP in the absence or presence of 30 microM PPADS. The accumulation of total [3H]-inositol (poly)phosphates mediated by 2MeSATP was markedly attenuated by PPADS, whereas the response to UTP was not significantly affected. 3. Stimulation of BAE cells with increasing concentrations of ATP showed a reduced response in the presence of 10 microM PPADS, but this effect of the antagonist was not significant. By contrast, inhibition of the response to ADP was profound and highly significant. 4. These observations show that PPADS is not a selective P2X-purinoceptor antagonist, but is able to distinguish between P2Y- and P2YU-purinoceptors in BAE cells, and indicate that this compound may provide a useful tool in the study of multiple subtypes of P2-purinoceptors. Furthermore the results are consistent with the hypothesis that ATP interacts with both receptor subtypes, but that the action of ADP is primarily at the P2Y-purinoceptor in these endothelial cells.

Development of massively parallel quantum chemistry program SMASH

Energy Technology Data Exchange (ETDEWEB)

Ishimura, Kazuya [Department of Theoretical and Computational Molecular Science, Institute for Molecular Science 38 Nishigo-Naka, Myodaiji, Okazaki, Aichi 444-8585 (Japan)

2015-12-31

A massively parallel program for quantum chemistry calculations SMASH was released under the Apache License 2.0 in September 2014. The SMASH program is written in the Fortran90/95 language with MPI and OpenMP standards for parallelization. Frequently used routines, such as one- and two-electron integral calculations, are modularized to make program developments simple. The speed-up of the B3LYP energy calculation for (C{sub 150}H{sub 30}){sub 2} with the cc-pVDZ basis set (4500 basis functions) was 50,499 on 98,304 cores of the K computer.

Transfer function modeling of parallel connected two three-phase induction motor implementation using LabView platform

DEFF Research Database (Denmark)

Gunabalan, R.; Sanjeevikumar, P.; Blaabjerg, Frede

2015-01-01

This paper presents the transfer function modeling and stability analysis of two induction motors of same ratings and parameters connected in parallel. The induction motors are controlled by a single inverter and the entire drive system is modeled using transfer function in LabView. Further...

Antigenic and functional characterization of p57 produced by Renibacterium salmoninarum

Science.gov (United States)

Weins, G.; Chien, M.S.; Winton, J.R.; Kaatari, S.L.

1999-01-01

Renibacterium salmoninarum, the causative agent of bacterial kidney disease, produces large quantities of a 57-58 kDa protein (p57) during growth in broth culture and during infection of salmonid fish. Biological activities of secreted p57 include agglutination of salrnonid leucocytes and rabbit erythrocytes. We define the location of epitopes on p57 recognized by agglutination-blocking monoclonal antibodies (MAbs) 4Cl1, 4H8 and 4D3, and demonstrate that the majority of secreted p57 is a nlonomer that retains salrnonid leucocyte agglutinat~ng activity. The 3 MAbs bound a recombinant, amino-terminal fragment of p57 (211 aa) but not a carboxy-terminal fragment (315 aa) demonstrating that the neutralizing epitopes are located within the amino-terminal portion of p57. When combinations of the MAbs were used in an antigen capture ELISA. the epitopes recognized by the 3 MAbs were shown to be sterically separate. However, when the same MAb was used as both the coating and detection MAb, binding of the biotinylated detection MAb was not observed. These data indicate that the epitopes recognized by the 3 agglutination-blocking antibodies are functionally available only once per molecule and that native p57 exists as a monomer Similar ELISA results were obtained when kidney tissues from 3 naturally infected chinook salmon were assayed. Finally, a p57 monomer was purified using anion exchange and size exclusion chromatography that retained in vitro agglutinating activity. A model in which p57 is released from R. salmoninarum as a biologically active monomer during infection of salmonid fish is proposed.

Plant P4-ATPases: lipid translocators with a role in membrane traficking

DEFF Research Database (Denmark)

Lopez Marques, Rosa Laura

a large family of membrane proteins involved in pumping different physiologically-relevant substrates across biological membranes [4]. The members of the P4 subfamily (also known as flippases) catalyze the energy-driven translocation of lipids necessary for establishing transbilayer lipid asymmetry [5......], a feature necessary for correct functioning of the cells [6,7]. Deletion of one or more P4-ATPase genes causes defects in vesicle budding in various organisms [8-10] and some members of the yeast family have been shown to interact with the vesiculation machinery [11,12]. Thus, unraveling the key features...... of P4-ATPase functioning is crucial to understand the mechanisms underlying the whole secretory and endocytic pathways. In the model plant Arabidopsis, 12 members of the P4-ATPase family have been described (ALA1-ALA12, for Aminophospholipid ATPase) [4]. In the past years, we have characterized several...

Nucleus-associated phosphorylation of Ins(1,4,5)P3 to InsP6 in Dictyostelium

NARCIS (Netherlands)

Kaay, Jeroen van der; Wesseling, Jelle; Haastert, Peter J.M. van

1995-01-01

Although many cells contain large amounts of InsP(6), its metabolism and function is still largely unknown. In Dictyostelium lysates, the formation of InsP(6) by sequential phosphorylation of inositol via Ins(3,4,6)P-3 has been described [Stevens and Irvine (1990) Nature (London) 346, 580-583]; the

Computational cost estimates for parallel shared memory isogeometric multi-frontal solvers

KAUST Repository

Woźniak, Maciej; Kuźnik, Krzysztof M.; Paszyński, Maciej R.; Calo, Victor M.; Pardo, D.

2014-01-01

In this paper we present computational cost estimates for parallel shared memory isogeometric multi-frontal solvers. The estimates show that the ideal isogeometric shared memory parallel direct solver scales as O( p2log(N/p)) for one dimensional problems, O(Np2) for two dimensional problems, and O(N4/3p2) for three dimensional problems, where N is the number of degrees of freedom, and p is the polynomial order of approximation. The computational costs of the shared memory parallel isogeometric direct solver are compared with those corresponding to the sequential isogeometric direct solver, being the latest equal to O(N p2) for the one dimensional case, O(N1.5p3) for the two dimensional case, and O(N2p3) for the three dimensional case. The shared memory version significantly reduces both the scalability in terms of N and p. Theoretical estimates are compared with numerical experiments performed with linear, quadratic, cubic, quartic, and quintic B-splines, in one and two spatial dimensions. © 2014 Elsevier Ltd. All rights reserved.

Computational cost estimates for parallel shared memory isogeometric multi-frontal solvers

KAUST Repository

Woźniak, Maciej

2014-06-01

In this paper we present computational cost estimates for parallel shared memory isogeometric multi-frontal solvers. The estimates show that the ideal isogeometric shared memory parallel direct solver scales as O( p2log(N/p)) for one dimensional problems, O(Np2) for two dimensional problems, and O(N4/3p2) for three dimensional problems, where N is the number of degrees of freedom, and p is the polynomial order of approximation. The computational costs of the shared memory parallel isogeometric direct solver are compared with those corresponding to the sequential isogeometric direct solver, being the latest equal to O(N p2) for the one dimensional case, O(N1.5p3) for the two dimensional case, and O(N2p3) for the three dimensional case. The shared memory version significantly reduces both the scalability in terms of N and p. Theoretical estimates are compared with numerical experiments performed with linear, quadratic, cubic, quartic, and quintic B-splines, in one and two spatial dimensions. © 2014 Elsevier Ltd. All rights reserved.

Why not make a PC cluster of your own? 5. AppleSeed: A Parallel Macintosh Cluster for Scientific Computing

Science.gov (United States)

Decyk, Viktor K.; Dauger, Dean E.

We have constructed a parallel cluster consisting of Apple Macintosh G4 computers running both Classic Mac OS as well as the Unix-based Mac OS X, and have achieved very good performance on numerically intensive, parallel plasma particle-in-cell simulations. Unlike other Unix-based clusters, no special expertise in operating systems is required to build and run the cluster. This enables us to move parallel computing from the realm of experts to the mainstream of computing.

The anti-hypercholesterolemic effect of low p53 expression protects vascular endothelial function in mice.

Directory of Open Access Journals (Sweden)

Francois Leblond

Full Text Available To demonstrate that p53 modulates endothelial function and the stress response to a high-fat western diet (WD.Three-month old p53+/+ wild type (WT and p53+/- male mice were fed a regular or WD for 3 months. Plasma levels of total cholesterol (TC and LDL-cholesterol were significantly elevated (p<0.05 in WD-fed WT (from 2.1±0.2 mmol/L to 3.1±0.2, and from 0.64±0.09 mmol/L to 1.25±0.11, respectively but not in p53+/- mice. The lack of cholesterol accumulation in WD-fed p53+/- mice was associated with high bile acid plasma concentrations (p53+/- =  4.7±0.9 vs. WT =  3.3±0.2 μmol/L, p<0.05 concomitant with an increased hepatic 7-alpha-hydroxylase mRNA expression. While the WD did not affect aortic endothelial relaxant function in p53+/- mice (WD =  83±5 and RD =  82±4% relaxation, it increased the maximal response to acetylcholine in WT mice (WD =  87±2 vs. RD =  62±5% relaxation, p<0.05 to levels of p53+/-. In WT mice, the rise in TC associated with higher (p<0.05 plasma levels of pro-inflammatory keratinocyte-derived chemokine, and an over-activation (p<0.05 of the relaxant non-nitric oxide/non-prostacyclin endothelial pathway. It is likely that in WT mice, activations of these pathways are adaptive and contributed to maintain endothelial function, while the WD neither promoted inflammation nor affected endothelial function in p53+/- mice.Our data demonstrate that low endogenous p53 expression prevents the rise in circulating levels of cholesterol when fed a WD. Consequently, the endothelial stress of hypercholesterolemia is absent in young p53+/- mice as evidenced by the absence of endothelial adaptive pathway over-activation to minimize stress-related damage.

Polymer Concentration-Controlled Substrate Specificity in Solvolysis of p-Nitrophenyl Alkanoates Catalyzed by 4-(Dialkylamino)pyridine- Functionalized Polymer in Aqueous Methanol Solution

National Research Council Canada - National Science Library

Wang, Guang-Jia

1996-01-01

The substrate specificity in solvolysis reactions of p-nitrophenyl alkanoates 2 (n=2-18) catalyzed by 4-(dialkylamino)pyridine-functionalized polymer 1 can be controlled by the concentration of 1 in 1...

Parallelizing AT with MatlabMPI

International Nuclear Information System (INIS)

2011-01-01

The Accelerator Toolbox (AT) is a high-level collection of tools and scripts specifically oriented toward solving problems dealing with computational accelerator physics. It is integrated into the MATLAB environment, which provides an accessible, intuitive interface for accelerator physicists, allowing researchers to focus the majority of their efforts on simulations and calculations, rather than programming and debugging difficulties. Efforts toward parallelization of AT have been put in place to upgrade its performance to modern standards of computing. We utilized the packages MatlabMPI and pMatlab, which were developed by MIT Lincoln Laboratory, to set up a message-passing environment that could be called within MATLAB, which set up the necessary pre-requisites for multithread processing capabilities. On local quad-core CPUs, we were able to demonstrate processor efficiencies of roughly 95% and speed increases of nearly 380%. By exploiting the efficacy of modern-day parallel computing, we were able to demonstrate incredibly efficient speed increments per processor in AT's beam-tracking functions. Extrapolating from prediction, we can expect to reduce week-long computation runtimes to less than 15 minutes. This is a huge performance improvement and has enormous implications for the future computing power of the accelerator physics group at SSRL. However, one of the downfalls of parringpass is its current lack of transparency; the pMatlab and MatlabMPI packages must first be well-understood by the user before the system can be configured to run the scripts. In addition, the instantiation of argument parameters requires internal modification of the source code. Thus, parringpass, cannot be directly run from the MATLAB command line, which detracts from its flexibility and user-friendliness. Future work in AT's parallelization will focus on development of external functions and scripts that can be called from within MATLAB and configured on multiple nodes, while

Searching for globally optimal functional forms for interatomic potentials using genetic programming with parallel tempering.

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Slepoy, A; Peters, M D; Thompson, A P

2007-11-30

Molecular dynamics and other molecular simulation methods rely on a potential energy function, based only on the relative coordinates of the atomic nuclei. Such a function, called a force field, approximately represents the electronic structure interactions of a condensed matter system. Developing such approximate functions and fitting their parameters remains an arduous, time-consuming process, relying on expert physical intuition. To address this problem, a functional programming methodology was developed that may enable automated discovery of entirely new force-field functional forms, while simultaneously fitting parameter values. The method uses a combination of genetic programming, Metropolis Monte Carlo importance sampling and parallel tempering, to efficiently search a large space of candidate functional forms and parameters. The methodology was tested using a nontrivial problem with a well-defined globally optimal solution: a small set of atomic configurations was generated and the energy of each configuration was calculated using the Lennard-Jones pair potential. Starting with a population of random functions, our fully automated, massively parallel implementation of the method reproducibly discovered the original Lennard-Jones pair potential by searching for several hours on 100 processors, sampling only a minuscule portion of the total search space. This result indicates that, with further improvement, the method may be suitable for unsupervised development of more accurate force fields with completely new functional forms. Copyright (c) 2007 Wiley Periodicals, Inc.

Probing Very Bright End of Galaxy Luminosity Function at z >~ 7 Using Hubble Space Telescope Pure Parallel Observations

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Yan, Haojing; Yan, Lin; Zamojski, Michel A.; Windhorst, Rogier A.; McCarthy, Patrick J.; Fan, Xiaohui; Röttgering, Huub J. A.; Koekemoer, Anton M.; Robertson, Brant E.; Davé, Romeel; Cai, Zheng

2011-02-01

We report the first results from the Hubble Infrared Pure Parallel Imaging Extragalactic Survey, which utilizes the pure parallel orbits of the Hubble Space Telescope to do deep imaging along a large number of random sightlines. To date, our analysis includes 26 widely separated fields observed by the Wide Field Camera 3, which amounts to 122.8 arcmin2 in total area. We have found three bright Y 098-dropouts, which are candidate galaxies at z >~ 7.4. One of these objects shows an indication of peculiar variability and its nature is uncertain. The other two objects are among the brightest candidate galaxies at these redshifts known to date (L>2L*). Such very luminous objects could be the progenitors of the high-mass Lyman break galaxies observed at lower redshifts (up to z ~ 5). While our sample is still limited in size, it is much less subject to the uncertainty caused by "cosmic variance" than other samples because it is derived using fields along many random sightlines. We find that the existence of the brightest candidate at z ≈ 7.4 is not well explained by the current luminosity function (LF) estimates at z ≈ 8. However, its inferred surface density could be explained by the prediction from the LFs at z ≈ 7 if it belongs to the high-redshift tail of the galaxy population at z ≈ 7. Based on observations made with the NASA/ESA Hubble Space Telescope, obtained at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-26555. These observations are associated with programs 11700 and 11702.

Parallel integer sorting with medium and fine-scale parallelism

Science.gov (United States)

Dagum, Leonardo

1993-01-01

Two new parallel integer sorting algorithms, queue-sort and barrel-sort, are presented and analyzed in detail. These algorithms do not have optimal parallel complexity, yet they show very good performance in practice. Queue-sort designed for fine-scale parallel architectures which allow the queueing of multiple messages to the same destination. Barrel-sort is designed for medium-scale parallel architectures with a high message passing overhead. The performance results from the implementation of queue-sort on a Connection Machine CM-2 and barrel-sort on a 128 processor iPSC/860 are given. The two implementations are found to be comparable in performance but not as good as a fully vectorized bucket sort on the Cray YMP.

Effect of Potential Range in Pressure-Temperature Behavior in Isotropic-Nematic Transition of 4-4´-Bis(EthyloxyAzoxybenzene (P-Azoxyphenetole, Pap, 4-Pentyl-4´-Cyanobiphenyl (5cb, P-Methoxybenzydidene-P-N-Butylaniline (Mbba and P–Ethoxybenzylidene–P–N-Butylaniline (Ebba

Directory of Open Access Journals (Sweden)

García-Sánchez E.

2011-04-01

Full Text Available In this work we employed the Density Functional Theory (IPCM model to calculate molecular volume and k, and the perturbation theory proposed by García-Sánchez et al. (2002 to predict phase diagram and experimental behavior pressure-temperature for isotropic-nematic transition of 4-4´-bis(ethyloxyazoxybenzene (p-azoxyphenetole, PAP, 4-pentyl-4´-cyanobiphenyl (5CB, p-methoxybenzydidene-p-n-butylaniline (MBBA and p–ethoxybenzylidene–p–n-butylaniline (EBBA at 1 atm. If during the theoretical prediction bigger potential values of potential range of square well (l > k are considered in the theoretical model, it is possible to get better prediction of the experimental behavior. The above mentioned is according with the theoretical formulation of the Second Order Perturbation Theory since Ponce-Renon approximation is included.

P53 function influences the effect of fractionated radiotherapy on glioblastoma tumors

International Nuclear Information System (INIS)

Haas-Kogan, Daphne A.; Kogan, Scott S.; Yount, Garret; Hsu, Jennie; Haas, Martin; Deen, Dennis F.; Israel, Mark A.

1999-01-01

Purpose: Glioblastoma multiforme brain tumors (GM) are treated with a spectrum of fractionation regimens based on the clinical and anatomical characteristics of the tumor but rarely based on the molecular characteristics of the individual neoplasm. This study tests the hypothesis that the response of cell lines derived from GM to fractionated radiotherapy depends on the function of wild-type p53 (wt p53), a tumor suppressor gene frequently mutated in GM tumors. Methods and Materials: Isogenic derivatives of glioblastoma cells differing only in p53 function were prepared using a retroviral vector expressing a dominant negative mutant of p53 (mt p53). Radiation survival in vitro was quantitated using linear quadratic and repair-saturation mathematical models. Apoptosis was assayed by a terminal deoxynucleotide transferase-labeling technique and chromatin morphology. Results: We have previously reported the generation of isogenic GM cell lines differing only in p53 function. U87-175.4, lacking wt p53 function, had a significantly lower α/β value than U87-LUX.8, expressing functional wt p53, leading us to hypothesize that fractionated irradiation would preferentially spare GM cells harboring mt p53 compared with those expressing functional, wt p53. Survival curves following either 2.0 Gy or 3.5 Gy/fraction demonstrated that lack of functional wt p53 was associated with resistance to fractionated irradiation. Radiation-induced apoptosis could not account for the observed differences in clonogenic survival. Rather, our data suggested that a deficit in the G1-checkpoint contributed to increased resistance to fractionated irradiation of cells expressing mutant p53. Conclusions: The effect of fractionated radiotherapy in GM may depend on the function of the tumor suppressor gene p53. A potential clinical consequence of these findings is that hyperfractionation regimens may provide a therapeutic advantage specifically for tumors expressing wt p53 whereas a radiotherapy

Parallel and non-parallel laminar mixed convection flow in an inclined tube: The effect of the boundary conditions

International Nuclear Information System (INIS)

Barletta, A.

2008-01-01

The necessary condition for the onset of parallel flow in the fully developed region of an inclined duct is applied to the case of a circular tube. Parallel flow in inclined ducts is an uncommon regime, since in most cases buoyancy tends to produce the onset of secondary flow. The present study shows how proper thermal boundary conditions may preserve parallel flow regime. Mixed convection flow is studied for a special non-axisymmetric thermal boundary condition that, with a proper choice of a switch parameter, may be compatible with parallel flow. More precisely, a circumferentially variable heat flux distribution is prescribed on the tube wall, expressed as a sinusoidal function of the azimuthal coordinate θ with period 2π. A π/2 rotation in the position of the maximum heat flux, achieved by setting the switch parameter, may allow or not the existence of parallel flow. Two cases are considered corresponding to parallel and non-parallel flow. In the first case, the governing balance equations allow a simple analytical solution. On the contrary, in the second case, the local balance equations are solved numerically by employing a finite element method

N-Heterocyclic Carbene Capture by Cytochrome P450 3A4

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Jennings, Gareth K.; Ritchie, Caroline M.; Shock, Lisa S.; Lyons, Charles E.

2016-01-01

Cytochrome P450 3A4 (CYP3A4) is the dominant P450 enzyme involved in human drug metabolism, and its inhibition may result in adverse interactions or, conversely, favorably reduce the systemic elimination rates of poorly bioavailable drugs. Herein we describe a spectroscopic investigation of the interaction of CYP3A4 with N-methylritonavir, an analog of ritonavir, widely used as a pharmacoenhancer. In contrast to ritonavir, the binding affinity of N-methylritonavir for CYP3A4 is pH-dependent. At pH UV-visible spectroscopy binding studies with molecular fragments narrows the source of this pH dependence to its N-methylthiazolium fragment. The C2 proton of this group is acidic, and variable-pH resonance Raman spectroscopy tentatively assigns it a pKa of 7.4. Hence, this fragment of N-methylritonavir is expected to be readily deprotonated under physiologic conditions to yield a thiazol-2-ylidene, which is an N-heterocyclic carbene that has high-affinity for and is presumed to be subsequently captured by the heme iron. This mechanism is supported by time-dependent density functional theory with an active site model that accurately reproduces distinguishing features of the experimental UV-visible spectra of N-methylritonavir bound to CYP3A4. Finally, density functional theory calculations support that this novel interaction is as strong as the tightest-binding azaheterocycles found in P450 inhibitors and could offer new avenues for inhibitor development. PMID:27126611

Parallel transport of long mean-free-path plasma along open magnetic field lines: Parallel heat flux

International Nuclear Information System (INIS)

Guo Zehua; Tang Xianzhu

2012-01-01

In a long mean-free-path plasma where temperature anisotropy can be sustained, the parallel heat flux has two components with one associated with the parallel thermal energy and the other the perpendicular thermal energy. Due to the large deviation of the distribution function from local Maxwellian in an open field line plasma with low collisionality, the conventional perturbative calculation of the parallel heat flux closure in its local or non-local form is no longer applicable. Here, a non-perturbative calculation is presented for a collisionless plasma in a two-dimensional flux expander bounded by absorbing walls. Specifically, closures of previously unfamiliar form are obtained for ions and electrons, which relate two distinct components of the species parallel heat flux to the lower order fluid moments such as density, parallel flow, parallel and perpendicular temperatures, and the field quantities such as the magnetic field strength and the electrostatic potential. The plasma source and boundary condition at the absorbing wall enter explicitly in the closure calculation. Although the closure calculation does not take into account wave-particle interactions, the results based on passing orbits from steady-state collisionless drift-kinetic equation show remarkable agreement with fully kinetic-Maxwell simulations. As an example of the physical implications of the theory, the parallel heat flux closures are found to predict a surprising observation in the kinetic-Maxwell simulation of the 2D magnetic flux expander problem, where the parallel heat flux of the parallel thermal energy flows from low to high parallel temperature region.

Muscle enzyme release does not predict muscle function impairment after triathlon.

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Margaritis, I; Tessier, F; Verdera, F; Bermon, S; Marconnet, P

1999-06-01

We sought to determine the effects of a long distance triathlon (4 km swim, 120 km bike-ride, and 30 km run) on the four-day kinetics of the biochemical markers of muscle damage, and whether they were quantitatively linked with muscle function impairment and soreness. Data were collected from 2 days before until 4 days after the completion of the race. Twelve triathletes performed the triathlon and five did not. Maximal voluntary contraction (MVC), muscle soreness (DOMS) and total serum CK, CK-MB, LDH, AST and ALT activities were assessed. Significant changes after triathlon completion were found for all muscle damage indirect markers over time (p triathlon. Long distance triathlon race caused muscle damage, but extent, as well as muscle recovery cannot be evaluated by the magnitude of changes in serum enzyme activities. Muscle enzyme release cannot be used to predict the magnitude of the muscle function impairment caused by muscle damage.

Simulation of Different Truncated p16INK4a Forms and In Silico Study of Interaction with Cdk4

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Najmeh Fahham

2009-01-01

Full Text Available Protein-protein interactions studies can greatly increase the amount of structural and functional information pertaining to biologically active molecules and processes. The information obtained from such studies can lead to design and application of new modification in order to obtain a desired bioactivity. Many application packages and servers performing docking, such as HEX, DOT, AUTODOCK, and ZDOCK are now available for predicting the lowest free energy state of a protein complex. In this study, we have focused on cyclin-dependent kinase 4 (Cdk4, a key molecule in the regulation of cell cycle progression at the G1-S phase restriction point and p16INK4a, a tumor suppressor which inhibits Cdk4 activity. Truncated structures were created to find the more critical regions of p16 for interaction. The tertiary structures were determined by ProSAL, GENO3D Web Server. We evaluated their interactions with Cdk4 using two docking systems, HEX 4.5 and DOT 1. Calculations were performed on a high-speed computer. Minimizations and visualizations were carried out by PdbViewer 3.7. Considering shape and shape/electrostatic total energy, structures containing ANK II, III and IV motifs that lack the N-terminal region of the full length p16 molecule showed the best fi t complexes among the p16 truncated forms. The free energies were compatible with that of p16 full length original form, the full length. It seems that the N-terminal of the molecule is not crucial for the interaction since the truncated structure containing only this region did not show a good total energy.

Buffer capacity of 4% succinylated gelatin does not provide any advantages over acidic 6% hydroxyethyl starch 130/0.4 for acid-base balance during experimental mixed acidaemia in a porcine model.

Science.gov (United States)

Esche, V; Russ, M; Melzer, S; Grossmann, B; Boemke, W; Unger, J K

2008-11-01

Four percent gelatine is an alkaline compound due to NH2 groups, whereas 6% hydroxyethyl starch 130/0.4 (HES130) has acidic features. We investigated whether these solutions lead to differences in acid-base balance in pigs during acidaemia and correction of pH. Anaesthetized pigs were randomized to HES130 or gelatine infusion (n = 5 per group). Animals received acid infusion (0.4 M solution of lactic acid and HCl diluted in normal saline) and low tidal volume ventilation (6-7 mL kg(-1), PaCO2 of 80-85 mmHg, pH 7.19-7.24). Measurements were made before and after induction of acidaemia, before and after correction of pH with haemofiltration (continuous venovenous haemofiltration) and tris-hydroxymethylaminomethane infusion. We measured parameters describing acid-base balance according to Stewart's approach, ketone body formation, oxygen delivery, haemodynamics, diuresis and urinary pH. Acid-base balance did not differ significantly between the groups. In HES130-treated pigs, the haemodilution-based drop of haemoglobin (1.4 +/- 1.0 g dL(-1), median +/- SD) was paralleled by an increase in the cardiac output (0.5 +/- 0.4 L min(-1). Lacking increases in cardiac output, gelatine-treated pigs demonstrated a reduction in oxygen delivery (149.4 +/- 106.0 mL min(-1)). Tris-hydroxymethylaminomethane volumes required for pH titration to desired values were significantly higher in the gelatine group (0.7 +/- 0.1 mL kg(-1) h(-1) vs. HES130: 0.5 +/- 0.2 mL kg(-1) h(-1)). The buffer capacity of gelatine did not lead to favourable differences in acid-base balance in comparison to HES130.

Topology in SU(2) lattice gauge theory and parallelization of functional magnetic resonance imaging

Energy Technology Data Exchange (ETDEWEB)

Solbrig, Stefan

2008-07-01

In this thesis, I discuss topological properties of quenched SU(2) lattice gauge fields. In particular, clusters of topological charge density exhibit a power-law. The exponent of that power-law can be used to validate models for lattice gauge fields. Instead of working with fixed cutoffs of the topological charge density, using the notion of a ''watermark'' is more convenient. Furthermore, I discuss how a parallel computer, originally designed for lattice gauge field simulations, can be used for functional magnetic resonance imaging. Multi parameter fits can be parallelized to achieve almost real-time evaluation of fMRI data. (orig.)

Relation between hand function and gross motor function in full term infants aged 4 to 8 months

Science.gov (United States)

Nogueira, Solange F.; Figueiredo, Elyonara M.; Gonçalves, Rejane V.; Mancini, Marisa C.

2015-01-01

Background: In children, reaching emerges around four months of age, which is followed by rapid changes in hand function and concomitant changes in gross motor function, including the acquisition of independent sitting. Although there is a close functional relationship between these domains, to date they have been investigated separately. Objective: To investigate the longitudinal profile of changes and the relationship between the development of hand function (i.e. reaching for and manipulating an object) and gross motor function in 13 normally developing children born at term who were evaluated every 15 days from 4 to 8 months of age. Method: The number of reaches and the period (i.e. time) of manipulation to an object were extracted from video synchronized with the Qualisys(r) movement analysis system. Gross motor function was measured using the Alberta Infant Motor Scale. ANOVA for repeated measures was used to test the effect of age on the number of reaches, the time of manipulation and gross motor function. Hierarchical regression models were used to test the associations of reaching and manipulation with gross motor function. Results: Results revealed a significant increase in the number of reaches (pgross motor function (pgross motor function (R2=0.84; pgross motor function (R2=0.13; p=0.02) from 4 to 6 months of age. Associations from 6 to 8 months of age were not significant. Conclusion: The relationship between hand function and gross motor function was not constant, and the age span from 4 to 6 months was a critical period of interdependency of hand function and gross motor function development. PMID:25714437

Thymic irradiation inhibits the rapid recovery of TH1 but not TH2-like functions of CD4+ T cells after total lymphoid irradiation

International Nuclear Information System (INIS)

Bass, H.; Adkins, B.; Strober, S.

1991-01-01

Four to six weeks after total lymphoid irradiation (TLI), there is a selective deficit in the CD4+ T cells which secrete IL-2, proliferate in the MLR, and induce GVHD (Th1-like functions). A similar deficit in CD4+ T cells which secrete IL-4 and help antibody responses (Th2-like functions) is not observed. In the present study, shielding of the thymus with lead during TLI increased the Th1-like functions of CD4+ cells. Mice without thymus shields showed a marked selective reduction in the medullary stromal cells identified with the monoclonal antibody, MD1, and the severe reduction was prevented with thymus shields. Thus, shielding the thymus prevents the depletion of thymic medullary stromal cells and allows for a rapid recovery of Th1-like functions in the mouse spleen after TLI. Th2-like functions recover rapidly after TLI whether or not the thymus is irradiated

Oral prednisolone for 4 days does not increase exercise tolerance in men with COPD

DEFF Research Database (Denmark)

Karlsson, S L; Backer, V; Godtfredsen, Nina Skavlan

2018-01-01

One of the primary objectives in management of chronic obstructive pulmonary disease (COPD) is preventing decrease in lung function and reducing the annual number of acute exacerbations of COPD (AECOPD). An oral course of systemic corticosteroids is a commonly used treatment in AECOPD. We...... hypothesize that this treatment also increases exercise performance and decreases muscle fatigue. In a randomized double-blinded, parallel, placebo-controlled trial, we investigated 14 men (8 on prednisolone 37.5 mg vs. 6 on placebo) with severe and very severe COPD. For 5 consecutive days, the patients...... out after 40 minutes of cycling at 40% of maximal effort. No differences between groups were found for TTE, lung function or maximal inspiratory or expiratory pressure, however, patients on prednisolone showed significant increased MVC: median 5.15 [3.35; 9.15] against placebo: -2 [-5.57; 3.95] ( p...

The role of Bh4 in parallel evolution of hull colour in domesticated and weedy rice.

Science.gov (United States)

Vigueira, C C; Li, W; Olsen, K M

2013-08-01

The two independent domestication events in the genus Oryza that led to African and Asian rice offer an extremely useful system for studying the genetic basis of parallel evolution. This system is also characterized by parallel de-domestication events, with two genetically distinct weedy rice biotypes in the US derived from the Asian domesticate. One important trait that has been altered by rice domestication and de-domestication is hull colour. The wild progenitors of the two cultivated rice species have predominantly black-coloured hulls, as does one of the two U.S. weed biotypes; both cultivated species and one of the US weedy biotypes are characterized by straw-coloured hulls. Using Black hull 4 (Bh4) as a hull colour candidate gene, we examined DNA sequence variation at this locus to study the parallel evolution of hull colour variation in the domesticated and weedy rice system. We find that independent Bh4-coding mutations have arisen in African and Asian rice that are correlated with the straw hull phenotype, suggesting that the same gene is responsible for parallel trait evolution. For the U.S. weeds, Bh4 haplotype sequences support current hypotheses on the phylogenetic relationship between the two biotypes and domesticated Asian rice; straw hull weeds are most similar to indica crops, and black hull weeds are most similar to aus crops. Tests for selection indicate that Asian crops and straw hull weeds deviate from neutrality at this gene, suggesting possible selection on Bh4 during both rice domestication and de-domestication. © 2013 The Authors. Journal of Evolutionary Biology © 2013 European Society For Evolutionary Biology.

A parallel buffer tree

DEFF Research Database (Denmark)

Sitchinava, Nodar; Zeh, Norbert

2012-01-01

We present the parallel buffer tree, a parallel external memory (PEM) data structure for batched search problems. This data structure is a non-trivial extension of Arge's sequential buffer tree to a private-cache multiprocessor environment and reduces the number of I/O operations by the number of...... in the optimal OhOf(psortN + K/PB) parallel I/O complexity, where K is the size of the output reported in the process and psortN is the parallel I/O complexity of sorting N elements using P processors....

An efficient parallel algorithm for the calculation of canonical MP2 energies.

Science.gov (United States)

Baker, Jon; Pulay, Peter

2002-09-01

We present the parallel version of a previous serial algorithm for the efficient calculation of canonical MP2 energies (Pulay, P.; Saebo, S.; Wolinski, K. Chem Phys Lett 2001, 344, 543). It is based on the Saebo-Almlöf direct-integral transformation, coupled with an efficient prescreening of the AO integrals. The parallel algorithm avoids synchronization delays by spawning a second set of slaves during the bin-sort prior to the second half-transformation. Results are presented for systems with up to 2000 basis functions. MP2 energies for molecules with 400-500 basis functions can be routinely calculated to microhartree accuracy on a small number of processors (6-8) in a matter of minutes with modern PC-based parallel computers. Copyright 2002 Wiley Periodicals, Inc. J Comput Chem 23: 1150-1156, 2002

A theoretical survey of 4s-4p and 4p-4d transitions in nickel-like ions through Sn XXIII

International Nuclear Information System (INIS)

Wyart, J.F.

1987-01-01

The predictions of 4s-4p and 4p-4d transitions derived from Slater-Condon type calculations of 3d 9 4s, -4p and -4d configurations in the sequence Zn III-Se VII have been recently confirmed experimentally through Mo XV. These new data are used here to refine the predictions in the sequence Mo XV-Sn XXIII. The radial parameters involved in the three configurations are determined in generalized least-squares fits using all known levels in the sequence. (orig.)

The chromatin remodelling factor BRG1 is a novel binding partner of the tumor suppressor p16INK4a

Directory of Open Access Journals (Sweden)

Mann Graham J

2009-01-01

Full Text Available Abstract Background CDKN2A/p16INK4a is frequently altered in human cancers and it is the most important melanoma susceptibility gene identified to date. p16INK4a inhibits pRb phosphorylation and induces cell cycle arrest, which is considered its main tumour suppressor function. Nevertheless, additional activities may contribute to the tumour suppressor role of p16INK4a and could help explain its specific association with melanoma predisposition. To identify such functions we conducted a yeast-two-hybrid screen for novel p16INK4a binding partners. Results We now report that p16INK4a interacts with the chromatin remodelling factor BRG1. We investigated the cooperative roles of p16INK4a and BRG1 using a panel of cell lines and a melanoma cell model with inducible p16INK4a expression and BRG1 silencing. We found evidence that BRG1 is not required for p16INK4a-induced cell cycle inhibition and propose that the p16INK4a-BRG1 complex regulates BRG1 chromatin remodelling activity. Importantly, we found frequent loss of BRG1 expression in primary and metastatic melanomas, implicating this novel p16INK4a binding partner as an important tumour suppressor in melanoma. Conclusion This data adds to the increasing evidence implicating the SWI/SNF chromatin remodelling complex in tumour development and the association of p16INK4a with chromatin remodelling highlights potentially new functions that may be important in melanoma predisposition and chemoresistance.

Inactivation of p15INK4b in chronic arsenic poisoning cases

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Aihua Zhang

2014-01-01

Full Text Available Arsenic exposure from burning high arsenic-containing coal has been associated with human skin lesion and cancer. However, the mechanisms of arsenic-related carcinogenesis are not fully understood. Inactivation of critical tumor suppression genes by epigenetic regulation or genetic modification might contribute to arsenic-induced carcinogenicity. This study aims to clarify the correlation between arsenic pollution and functional defect of p15INK4b gene in arsenic exposure residents from a region of Guizhou Province, China. To this end, 103 arsenic exposure residents and 105 control subjects were recruited in this study. The results showed that the exposure group exhibited higher levels of urinary and hair arsenic compared with the control group (55.28 vs 28.87 μg/L, 5.16 vs 1.36 μg/g. Subjects with higher arsenic concentrations are more likely to have p15INK4b methylation and gene deletion (χ2 = 4.28, P = 0.04 and χ2 = 4.31, P = 0.04. We also found that the degree of p15INK4b hypermethylation and gene deletion occurred at higher incidence in the poisoning cases with skin cancer (3.7% and 14.81% in non-skin cancer group, 41.18% and 47.06 in skin cancer group, and were significantly associated with the stage of skin lesions (χ2 = 12.82, P < 0.01 and χ2 = 7.835, P = 0.005. These observations indicate that inactivation of p15INK4b through genetic alteration or epigenetic modification is a common event that is associated with arsenic exposure and the development of arsenicosis.

Energy level properties of 4p64d3, 4p64d24f, and 4p54d4 configurations of the W35+ ion

International Nuclear Information System (INIS)

Bogdanovich, P.; Kisielius, R.

2014-01-01

The ab initio quasirelativistic Hartree–Fock method developed specifically for the calculation of spectroscopic parameters of heavy atoms and highly charged ions was used to derive spectral data for the multicharged tungsten ion W 35+ . The configuration interaction method was applied to include the electron-correlation effects. The relativistic effects were taken into account in the Breit–Pauli approximation for quasirelativistic Hartree–Fock radial orbitals. The energy level spectra, radiative lifetimes τ, and Lande g-factors have been calculated for the 4p 6 4d 3 , 4p 6 4d 2 4f, and 4p 5 4d 4 configurations of the W 35+ ion

A Green's function method for two-dimensional reactive solute transport in a parallel fracture-matrix system

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Chen, Kewei; Zhan, Hongbin

2018-06-01

The reactive solute transport in a single fracture bounded by upper and lower matrixes is a classical problem that captures the dominant factors affecting transport behavior beyond pore scale. A parallel fracture-matrix system which considers the interaction among multiple paralleled fractures is an extension to a single fracture-matrix system. The existing analytical or semi-analytical solution for solute transport in a parallel fracture-matrix simplifies the problem to various degrees, such as neglecting the transverse dispersion in the fracture and/or the longitudinal diffusion in the matrix. The difficulty of solving the full two-dimensional (2-D) problem lies in the calculation of the mass exchange between the fracture and matrix. In this study, we propose an innovative Green's function approach to address the 2-D reactive solute transport in a parallel fracture-matrix system. The flux at the interface is calculated numerically. It is found that the transverse dispersion in the fracture can be safely neglected due to the small scale of fracture aperture. However, neglecting the longitudinal matrix diffusion would overestimate the concentration profile near the solute entrance face and underestimate the concentration profile at the far side. The error caused by neglecting the longitudinal matrix diffusion decreases with increasing Peclet number. The longitudinal matrix diffusion does not have obvious influence on the concentration profile in long-term. The developed model is applied to a non-aqueous-phase-liquid (DNAPL) contamination field case in New Haven Arkose of Connecticut in USA to estimate the Trichloroethylene (TCE) behavior over 40 years. The ratio of TCE mass stored in the matrix and the injected TCE mass increases above 90% in less than 10 years.

Poly[diaqua(μ-4,4′-bipyridine-κ2N:N′[μ-2,2′-(p-phenylenedioxydiacetato-κ2O:O′]cadmium

Directory of Open Access Journals (Sweden)

Guang-Yin Wang

2011-09-01

Full Text Available In the title compound, [Cd(C10H8O6(C10H8N2(H2O2]n, the CdII ion has inversion symmetry and is coordinated by O atoms from two water molecules and two bridging 2,2′-(μ-p-phenylenedioxydiacetate ligands and two N atoms from two 4,4′-bipyridine ligands, giving a slightly distorted octahedral geometry. The diacetate and 4,4′-bipyridine ligands also lie across inversion centers. The bridging ligands form layers parallel to (11overline{1}, with adjacent layers interconnected via O—H...O hydrogen bonds between the coordinated water molecules and the carboxylate O atoms, giving a three-dimensional supramolecular architecture.

Why the nth-root function is not a rational function

Science.gov (United States)

Dobbs, David E.

2017-11-01

The set of functions ? is linearly independent over ? (with respect to any open subinterval of (0, ∞)). The titular result is a corollary for any integer n ≥ 2 (and the domain [0, ∞)). Some more accessible proofs of that result are also given. Let F be a finite field of characteristic p and cardinality pk. Then the pth-root function F → F is a polynomial function of degree at most pk - 2 if pk ≠ 2 (resp., the identity function if pk = 2). Also, for any integer n ≥ 2, every element of F has an nth root in F if and only if, for each prime number q dividing n, q is not a factor of pk - 1. Various parts of this note could find classroom use in courses at various levels, on precalculus, calculus or abstract algebra. A final section addresses educational benefits of such coverage and offers some recommendations to practitioners.

The STAPL Parallel Graph Library

KAUST Repository

Harshvardhan,

2013-01-01

This paper describes the stapl Parallel Graph Library, a high-level framework that abstracts the user from data-distribution and parallelism details and allows them to concentrate on parallel graph algorithm development. It includes a customizable distributed graph container and a collection of commonly used parallel graph algorithms. The library introduces pGraph pViews that separate algorithm design from the container implementation. It supports three graph processing algorithmic paradigms, level-synchronous, asynchronous and coarse-grained, and provides common graph algorithms based on them. Experimental results demonstrate improved scalability in performance and data size over existing graph libraries on more than 16,000 cores and on internet-scale graphs containing over 16 billion vertices and 250 billion edges. © Springer-Verlag Berlin Heidelberg 2013.

Parallel β-Sheet Structure of Alanine Tetrapeptide in the Solid State As Studied by Solid-State NMR Spectroscopy.

Science.gov (United States)

Asakura, Tetsuo; Horiguchi, Kumiko; Aoki, Akihiro; Tasei, Yugo; Naito, Akira

2016-09-01

The structural analysis of alanine oligopeptides is important for understanding the crystalline region in silks from spiders and wild silkworms and also the mechanism of cellular toxicity of human diseases arising from expansion in polyalanine sequences. The atomic-level structures of alanine tripeptide and tetrapeptide with antiparallel β-sheet structures (AP-Ala3 and AP-Ala4, respectively) together with alanine tripeptide with parallel β-sheet structures (P-Ala3) have been determined, but alanine tetrapeptide with a parallel β-sheet structure (P-Ala4) has not been reported yet. In this article, first, we established the preparation protocol of P-Ala4 from more stable AP-Ala4. Second, complete assignments of the (13)C, (15)N, and (1)H solid-state NMR spectra were performed with (13)C- and (15)N-labeled Ala4 samples using several solid-state NMR techniques. Then, the structural constraints were obtained, for example, the amide proton peaks of P-Ala4 in the (1)H double-quantum magic-angle spinning NMR spectrum were heavily overlapped and observed at about 7.4 ppm, which was a much higher field than that of 8.7-9.1 ppm observed for AP-Ala4, indicating that the intermolecular hydrogen-bond lengths across strands (N-H···O═C) were considerably longer for P-Ala4, that is, 2.21-2.34 Å, than those reported for AP-Ala4, that is, 1.8-1.9 Å. The structural model was proposed for P-Ala4 by NMR results and MD calculations.

The Glasgow Parallel Reduction Machine: Programming Shared-memory Many-core Systems using Parallel Task Composition

Directory of Open Access Journals (Sweden)

Ashkan Tousimojarad

2013-12-01

Full Text Available We present the Glasgow Parallel Reduction Machine (GPRM, a novel, flexible framework for parallel task-composition based many-core programming. We allow the programmer to structure programs into task code, written as C++ classes, and communication code, written in a restricted subset of C++ with functional semantics and parallel evaluation. In this paper we discuss the GPRM, the virtual machine framework that enables the parallel task composition approach. We focus the discussion on GPIR, the functional language used as the intermediate representation of the bytecode running on the GPRM. Using examples in this language we show the flexibility and power of our task composition framework. We demonstrate the potential using an implementation of a merge sort algorithm on a 64-core Tilera processor, as well as on a conventional Intel quad-core processor and an AMD 48-core processor system. We also compare our framework with OpenMP tasks in a parallel pointer chasing algorithm running on the Tilera processor. Our results show that the GPRM programs outperform the corresponding OpenMP codes on all test platforms, and can greatly facilitate writing of parallel programs, in particular non-data parallel algorithms such as reductions.

Parallel External Memory Graph Algorithms

DEFF Research Database (Denmark)

Arge, Lars Allan; Goodrich, Michael T.; Sitchinava, Nodari

2010-01-01

In this paper, we study parallel I/O efficient graph algorithms in the Parallel External Memory (PEM) model, one o f the private-cache chip multiprocessor (CMP) models. We study the fundamental problem of list ranking which leads to efficient solutions to problems on trees, such as computing lowest...... an optimal speedup of ¿(P) in parallel I/O complexity and parallel computation time, compared to the single-processor external memory counterparts....

Functional rescue of mutant ABCA1 proteins by sodium 4-phenylbutyrate.

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Sorrenson, Brie; Suetani, Rachel J; Williams, Michael J A; Bickley, Vivienne M; George, Peter M; Jones, Gregory T; McCormick, Sally P A

2013-01-01

Mutations in the ATP-binding cassette transporter A1 (ABCA1) are a major cause of decreased HDL cholesterol (HDL-C), which infers an increased risk of cardiovascular disease (CVD). Many ABCA1 mutants show impaired localization to the plasma membrane. The aim of this study was to investigate whether the chemical chaperone, sodium 4-phenylbutyrate (4-PBA) could improve cellular localization and function of ABCA1 mutants. Nine different ABCA1 mutants (p.A594T, p.I659V, p.R1068H, p.T1512M, p.Y1767D, p.N1800H, p.R2004K, p.A2028V, p.Q2239N) expressed in HEK293 cells, displaying different degrees of mislocalization to the plasma membrane and discrete impacts on cholesterol efflux, were subject to treatment with 4-PBA. Treatment restored localization to the plasma membrane and increased cholesterol efflux function for the majority of mutants. Treatment with 4-PBA also increased ABCA1 protein expression in all transfected cell lines. In fibroblast cells obtained from low HDL-C subjects expressing two of the ABCA1 mutants (p.R1068H and p.N1800H), 4-PBA increased cholesterol efflux without any increase in ABCA1 expression. Our study is the first to investigate the effect of the chemical chaperone, 4-PBA on ABCA1 and shows that it is capable of restoring plasma membrane localization and enhancing the cholesterol efflux function of mutant ABCA1s both in vitro and ex vivo. These results suggest 4-PBA may warrant further investigation as a potential therapy for increasing cholesterol efflux and HDL-C levels.

A point mutation of human p53, which was not detected as a mutation by a yeast functional assay, led to apoptosis but not p21Waf1/Cip1/Sdi1 expression in response to ionizing radiation in a human osteosarcoma cell line, Saos-2

International Nuclear Information System (INIS)

Okaichi, Kumio; Wang Lihong; Sasaki, Ji-ichiro; Saya, Hideyuki; Tada, Mitsuhiro; Okumura, Yutaka

1999-01-01

Purpose: The 123A point mutation of p53 showed increased radiosensitivity, whereas other mutations (143A, 175H, and 273H) were not affected. To determine the reason for increased radiosensitivity of the 123A mutation, the response of the transformant of 123A mutation to ionizing radiation (IR) was examined and compared to those of transformants with the wild type p53 or other point mutations (143A, 175H, and 273H). Methods and Materials: Stable transformants with a mutant or wild type p53 made by introducing cDNA into the human osteosarcoma cell line, Saos-2, which lacks an endogenous p53 were used. The transcriptional activity of mutant p53 was examined using a yeast functional assay. The transformants were examined for the accumulation of p53, the induction of p21 Waf1/Cip1/Sdi1 (hereafter referred to as p21), and the other response of p53-responsive genes (MDM2, Bax, and Bcl-2) by Western blotting. Apoptosis was analyzed by detection of DNA fragmentation. Results: The 123A point mutation of p53 was detected as a wild type in the yeast functional assay. The 123A mutant accumulated p53 in response to IR. The 123A mutant did not induce p21, but normally responded to MDM2, Bax, and Bcl-2. The 123A mutant entered apoptosis earlier than the wild type p53 transformant, and induced Fas at earlier in response to IR. Conclusion: The 123A mutant led to apoptosis, but not p21 expression in response to IR. The occurrence of apoptosis, but not induction of p21, corresponded to the radiosensitivity in the transformant. The early occurrence of apoptosis in 123A transformants may depend on the early induction of Fas

Electronic structure and physical properties of the spinel-type phase of BeP2N4 from all-electron density functional calculations

International Nuclear Information System (INIS)

Ching, W. Y.; Aryal, Sitram; Rulis, Paul; Schnick, Wolfgang

2011-01-01

Using density-functional-theory-based ab initio methods, the electronic structure and physical properties of the newly synthesized nitride BeP 2 N 4 with a phenakite-type structure and the predicted high-pressure spinel phase of BeP 2 N 4 are studied in detail. It is shown that both polymorphs are wide band-gap semiconductors with relatively small electron effective masses at the conduction-band minima. The spinel-type phase is more covalently bonded due to the increased number of P-N bonds for P at the octahedral sites. Calculations of mechanical properties indicate that the spinel-type polymorph is a promising superhard material with notably large bulk, shear, and Young's moduli. Also calculated are the Be K, P K, P L 3 , and N K edges of the electron energy-loss near-edge structure for both phases. They show marked differences because of the different local environments of the atoms in the two crystalline polymorphs. These differences will be very useful for the experimental identification of the products of high-pressure syntheses targeting the predicted spinel-type phase of BeP 2 N 4 .

Solid energy calibration standards for P K-edge XANES: electronic structure analysis of PPh4Br.

Science.gov (United States)

Blake, Anastasia V; Wei, Haochuan; Donahue, Courtney M; Lee, Kyounghoon; Keith, Jason M; Daly, Scott R

2018-03-01

P K-edge X-ray absorption near-edge structure (XANES) spectroscopy is a powerful method for analyzing the electronic structure of organic and inorganic phosphorus compounds. Like all XANES experiments, P K-edge XANES requires well defined and readily accessible calibration standards for energy referencing so that spectra collected at different beamlines or under different conditions can be compared. This is especially true for ligand K-edge X-ray absorption spectroscopy, which has well established energy calibration standards for Cl (Cs 2 CuCl 4 ) and S (Na 2 S 2 O 3 ·5H 2 O), but not neighboring P. This paper presents a review of common P K-edge XANES energy calibration standards and analysis of PPh 4 Br as a potential alternative. The P K-edge XANES region of commercially available PPh 4 Br revealed a single, highly resolved pre-edge feature with a maximum at 2146.96 eV. PPh 4 Br also showed no evidence of photodecomposition when repeatedly scanned over the course of several days. In contrast, we found that PPh 3 rapidly decomposes under identical conditions. Density functional theory calculations performed on PPh 3 and PPh 4 + revealed large differences in the molecular orbital energies that were ascribed to differences in the phosphorus oxidation state (III versus V) and molecular charge (neutral versus +1). Time-dependent density functional theory calculations corroborated the experimental data and allowed the spectral features to be assigned. The first pre-edge feature in the P K-edge XANES spectrum of PPh 4 Br was assigned to P 1s → P-C π* transitions, whereas those at higher energy were P 1s → P-C σ*. Overall, the analysis suggests that PPh 4 Br is an excellent alternative to other solid energy calibration standards commonly used in P K-edge XANES experiments.

Left Ventricular Function Evaluation on a 3T MR Scanner with Parallel RF Transmission Technique: Prospective Comparison of Cine Sequences Acquired before and after Gadolinium Injection.

Science.gov (United States)

Caspar, Thibault; Schultz, Anthony; Schaeffer, Mickaël; Labani, Aïssam; Jeung, Mi-Young; Jurgens, Paul Thomas; El Ghannudi, Soraya; Roy, Catherine; Ohana, Mickaël

To compare cine MR b-TFE sequences acquired before and after gadolinium injection, on a 3T scanner with a parallel RF transmission technique in order to potentially improve scanning time efficiency when evaluating LV function. 25 consecutive patients scheduled for a cardiac MRI were prospectively included and had their b-TFE cine sequences acquired before and right after gadobutrol injection. Images were assessed qualitatively (overall image quality, LV edge sharpness, artifacts and LV wall motion) and quantitatively with measurement of LVEF, LV mass, and telediastolic volume and contrast-to-noise ratio (CNR) between the myocardium and the cardiac chamber. Statistical analysis was conducted using a Bayesian paradigm. No difference was found before or after injection for the LVEF, LV mass and telediastolic volume evaluations. Overall image quality and CNR were significantly lower after injection (estimated coefficient cine after > cine before gadolinium: -1.75 CI = [-3.78;-0.0305], prob(coef>0) = 0% and -0.23 CI = [-0.49;0.04], prob(coef>0) = 4%) respectively), but this decrease did not affect the visual assessment of LV wall motion (cine after > cine before gadolinium: -1.46 CI = [-4.72;1.13], prob(coef>0) = 15%). In 3T cardiac MRI acquired with parallel RF transmission technique, qualitative and quantitative assessment of LV function can reliably be performed with cine sequences acquired after gadolinium injection, despite a significant decrease in the CNR and the overall image quality.

High-speed parallel solution of the neutron diffusion equation with the hierarchical domain decomposition boundary element method incorporating parallel communications

International Nuclear Information System (INIS)

Tsuji, Masashi; Chiba, Gou

2000-01-01

A hierarchical domain decomposition boundary element method (HDD-BEM) for solving the multiregion neutron diffusion equation (NDE) has been fully parallelized, both for numerical computations and for data communications, to accomplish a high parallel efficiency on distributed memory message passing parallel computers. Data exchanges between node processors that are repeated during iteration processes of HDD-BEM are implemented, without any intervention of the host processor that was used to supervise parallel processing in the conventional parallelized HDD-BEM (P-HDD-BEM). Thus, the parallel processing can be executed with only cooperative operations of node processors. The communication overhead was even the dominant time consuming part in the conventional P-HDD-BEM, and the parallelization efficiency decreased steeply with the increase of the number of processors. With the parallel data communication, the efficiency is affected only by the number of boundary elements assigned to decomposed subregions, and the communication overhead can be drastically reduced. This feature can be particularly advantageous in the analysis of three-dimensional problems where a large number of processors are required. The proposed P-HDD-BEM offers a promising solution to the deterioration problem of parallel efficiency and opens a new path to parallel computations of NDEs on distributed memory message passing parallel computers. (author)

Mapping the involvement of BA 4a and 4p during Motor Imagery.

Science.gov (United States)

Sharma, Nikhil; Jones, P S; Carpenter, T A; Baron, Jean-Claude

2008-05-15

Motor Imagery (MI) is an attractive but intriguing means to access the motor network. There are marked inconsistencies in the functional imaging literature regarding the degree, extent and distribution of the primary motor cortex (BA 4) involvement during MI as compared to Executed Movement (EM), which may in part be related to the diverse role of BA 4 and its two subdivisions (i.e., 4a and 4p) in motor processes as well as to methodological issues. Here we used fMRI with monitoring of compliance to show that in healthy volunteers optimally screened for their ability to perform MI the contralateral BA 4 is involved during MI of a finger opposition sequence (2, 3, 4, 5; paced at 1 Hz), albeit less than during EM of the same sequence, and in a location sparing the hand area. Furthermore, both 4a and 4p subdivisions were found to be involved in MI, but the relative involvement of BA 4p appeared more robust and closer to that seen with EM. We suggest that during MI the role of BA 4 and its subdivisions may be non-executive, perhaps related to spatial encoding, though clearly further studies are needed. Finally, we report a similar hemispheric activation balance within BA 4 with both tasks, which extends the commonalities between EM and MI.

Quasirelativistic calculation of 4s24p5, 4s24p44d and 4s4p6 configuration spectroscopic parameters for the W39+ ion

International Nuclear Information System (INIS)

Bogdanovich, P; Karpuškienė, R; Kisielius, R

2015-01-01

The ab initio quasirelativistic Hartree–Fock method developed specifically for the calculation of spectral parameters of heavy atoms and highly charged ions is used to derive spectral data for the 4s 2 4p 5 , 4s 2 4p 4 4d and 4s4p 6 configurations of the multicharged tungsten ion W 39+ . The relativistic effects are taken into account in the Breit–Pauli approximation for the quasirelativistic Hartree–Fock radial orbitals. The configuration interaction method is applied to include the electron correlation effects. Produced data are compared with existing experimental measurements and theoretical calculations. (paper)

Reliability allocation problem in a series-parallel system

International Nuclear Information System (INIS)

Yalaoui, Alice; Chu, Chengbin; Chatelet, Eric

2005-01-01

In order to improve system reliability, designers may introduce in a system different technologies in parallel. When each technology is composed of components in series, the configuration belongs to the series-parallel systems. This type of system has not been studied as much as the parallel-series architecture. There exist no methods dedicated to the reliability allocation in series-parallel systems with different technologies. We propose in this paper theoretical and practical results for the allocation problem in a series-parallel system. Two resolution approaches are developed. Firstly, a one stage problem is studied and the results are exploited for the multi-stages problem. A theoretical condition for obtaining the optimal allocation is developed. Since this condition is too restrictive, we secondly propose an alternative approach based on an approximated function and the results of the one-stage study. This second approach is applied to numerical examples

De novo case of a partial trisomy 4p and a partial monosomy 8p.

Science.gov (United States)

Skrlec, Ivana; Wagner, Jasenka; Pubeljić, Silvija; Heffer, Marija; Stipoljev, Feodora

2014-03-01

The extent of clinical expression in cases of segmental aneuploidy often varies depending on the size of the chromosomal region involved. Here we present clinical and cytogenetic findings in a 5-month old boy with a duplication of a chromosomal segment 4p16.1-->4pter and a deletion of a chromosomal segment 8p23.1-->8pter. His karyotype was determined by applying classical GTG banding and FISH method (WHCR region, centromere 4, centromere 8, telomere 8p) as 46,XY,der(8)t(4;8)(p16.1;p23.1).ish der(8)t(4;8)(D8S504-,WHCR+,D8Z2+)dn. Parents are not related and have normal karyotypes, indicating de novo origin. We have compared similarity of the clinical features in our proband to other patients carrying only a duplication of the distal part of 4p or a deletion of distal part of 8p or similar combination described in the literature.

General upper bounds on the runtime of parallel evolutionary algorithms.

Science.gov (United States)

Lässig, Jörg; Sudholt, Dirk

2014-01-01

We present a general method for analyzing the runtime of parallel evolutionary algorithms with spatially structured populations. Based on the fitness-level method, it yields upper bounds on the expected parallel runtime. This allows for a rigorous estimate of the speedup gained by parallelization. Tailored results are given for common migration topologies: ring graphs, torus graphs, hypercubes, and the complete graph. Example applications for pseudo-Boolean optimization show that our method is easy to apply and that it gives powerful results. In our examples the performance guarantees improve with the density of the topology. Surprisingly, even sparse topologies such as ring graphs lead to a significant speedup for many functions while not increasing the total number of function evaluations by more than a constant factor. We also identify which number of processors lead to the best guaranteed speedups, thus giving hints on how to parameterize parallel evolutionary algorithms.

[Recombinant chromosome 4 with partial 4p deletion and 4q duplication inherited from paternal pericentric inversion].

Science.gov (United States)

Mun, Se Jin; Cho, Eun Hae; Chey, Myoung-Jae; Shim, Gyu-Hong; Shin, Bo-Moon; Lee, Rae-Kyung; Ko, Ji-Kyung; Yoo, Soo Jin

2010-02-01

Pericentric inversion of chromosome 4 can give rise to 2 alternate recombinant (rec) chromosomesby duplication or deletion of 4p. The deletion of distal 4p manifests as Wolf-Hirschhorn syndrome (WHS). Here, we report the molecular cytogenetic findings and clinical manifestations observed in an infant with 46,XX,rec(4)dup(4q)inv(4)(p16q31.3)pat. The infant was delivered by Cesarean section at the 33rd week of gestation because pleural effusion and polyhydramnios were detected on ultrasonography. At birth, the infant showed no malformation or dysfunction, except for a preauricular skin tag. Array comparative genomic hybridization analysis of neonatal peripheral blood samples showed a gain of 38 Mb on 4q31.3-qter and a loss of 3 Mb on 4p16.3, and these results were consistent with WHS. At the last follow-up at 8 months of age (corrected age, 6 months), the infant had not achieved complete head control.

Functional ablation of pRb activates Cdk2 and causes antiestrogen resistance in human breast cancer cells.

Directory of Open Access Journals (Sweden)

Hemant Varma

2007-12-01

Full Text Available Estrogens are required for the proliferation of hormone dependent breast cancer cells, making estrogen receptor (ER positive tumors amenable to endocrine therapies such as antiestrogens. However, resistance to these agents remains a significant cause of treatment failure. We previously demonstrated that inactivation of the retinoblastoma protein (pRb family tumor suppressors causes antiestrogen resistance in MCF-7 cells, a widely studied model of estrogen responsive human breast cancers. In this study, we investigate the mechanism by which pRb inactivation leads to antiestrogen resistance. Cdk4 and cdk2 are two key cell cycle regulators that can phosphorylate and inactivate pRb, therefore we tested whether these kinases are required in cells lacking pRb function. pRb family members were inactivated in MCF-7 cells by expressing polyomavirus large tumor antigen (PyLT, and cdk activity was inhibited using the cdk inhibitors p16(INK4A and p21(Waf1/Cip1. Cdk4 activity was no longer required in cells lacking functional pRb, while cdk2 activity was required for proliferation in both the presence and absence of pRb function. Using inducible PyLT cell lines, we further demonstrated that pRb inactivation leads to increased cyclin A expression, cdk2 activation and proliferation in antiestrogen arrested cells. These results demonstrate that antiestrogens do not inhibit cdk2 activity or proliferation of MCF-7 cells in the absence of pRb family function, and suggest that antiestrogen resistant breast cancer cells resulting from pRb pathway inactivation would be susceptible to therapies that target cdk2.

Vector Green's function algorithm for radiative transfer in plane-parallel atmosphere

Energy Technology Data Exchange (ETDEWEB)

Qin Yi [School of Physics, University of New South Wales (Australia)]. E-mail: yi.qin@csiro.au; Box, Michael A. [School of Physics, University of New South Wales (Australia)

2006-01-15

Green's function is a widely used approach for boundary value problems. In problems related to radiative transfer, Green's function has been found to be useful in land, ocean and atmosphere remote sensing. It is also a key element in higher order perturbation theory. This paper presents an explicit expression of the Green's function, in terms of the source and radiation field variables, for a plane-parallel atmosphere with either vacuum boundaries or a reflecting (BRDF) surface. Full polarization state is considered but the algorithm has been developed in such way that it can be easily reduced to solve scalar radiative transfer problems, which makes it possible to implement a single set of code for computing both the scalar and the vector Green's function.

Parallel Fixed Point Implementation of a Radial Basis Function Network in an FPGA

Directory of Open Access Journals (Sweden)

Alisson C. D. de Souza

2014-09-01

Full Text Available This paper proposes a parallel fixed point radial basis function (RBF artificial neural network (ANN, implemented in a field programmable gate array (FPGA trained online with a least mean square (LMS algorithm. The processing time and occupied area were analyzed for various fixed point formats. The problems of precision of the ANN response for nonlinear classification using the XOR gate and interpolation using the sine function were also analyzed in a hardware implementation. The entire project was developed using the System Generator platform (Xilinx, with a Virtex-6 xc6vcx240t-1ff1156 as the target FPGA.

Ion channel regulation by phosphoinositides analyzed with VSPs – PI(4,5P2 affinity, phosphoinositide selectivity, and PI(4,5P2 pool accessibility

Directory of Open Access Journals (Sweden)

Alexandra eRjasanow

2015-06-01

Full Text Available The activity of many proteins depends on the phosphoinositide (PI content of the membrane. E.g., dynamic changes of the concentration of PI(4,5P2 are cellular signals that regulate ion channels. The susceptibility of a channel to such dynamics depends on its affinity for PI(4,5P2. Yet, measuring affinities for endogenous PIs has not been possible directly, but has relied largely on the response to soluble analogs, which may not quantitatively reflect binding to native lipids.Voltage-sensitive phosphatases (VSPs turn over PI(4,5P2 to PI(4P when activated by depolarization. In combination with voltage-clamp electrophysiology VSPs are useful tools for rapid and reversible depletion of PI(4,5P2. Because cellular PI(4,5P2 is resynthesized rapidly, steady state PI(4,5P2 changes with the degree of VSP activation and thus depends on membrane potential.Here we show that titration of endogenous PI(4,5P2 with Ci-VSP allows for the quantification of relative PI(4,5P2 affinities of ion channels. The sensitivity of inward rectifier and voltage-gated K+ channels to Ci-VSP allowed for comparison of PI(4,5P2 affinities within and across channel subfamilies and detected changes of affinity in mutant channels. The results also reveal that VSPs are useful only for PI effectors with high binding specificity among PI isoforms, because PI(4,5P2 depletion occurs at constant overall PI level. Thus, Kir6.2, a channel activated by PI(4,5P2 and PI(4P was insensitive to VSP.Surprisingly, despite comparable PI(4,5P2 affinity as determined by Ci-VSP, the Kv7 and Kir channel families strongly differed in their sensitivity to receptor-mediated depletion of PI(4,5P2. While Kv7 members were highly sensitive to activation of PLC by Gq-coupled receptors, Kir channels were insensitive even when PI(4,5P2 affinity was lowered by mutation. We hypothesize that different channels may be associated with distinct pools of PI(4,5P2 that differ in their accessibility to PLC and VSPs.

Radiative lifetimes and two-body collisional deactivation rate constants in argon for Kr(4p 55p) and Kr(4p 55p') states

International Nuclear Information System (INIS)

Chang, R.S.F.; Horiguchi, H.; Setser, D.W.

1980-01-01

The radiative lifetimes and collisional deactivation rate constants, in argon, of eight Kr(4p 5 [ 2 P/sub 1/2/]5p and [ 2 P/sub 3/2/]5p) levels have been measured by a time-resolved laser-induced fluorescence technique in a flowing afterglow apparatus. The measured radiative lifetimes are compared with other experimental values and with theoretical calculations. Radiative branching ratios of these excited states also were measured in order to assign the absolute transition probabilities of the Kr(5p,5p'--5s, 5s') transition array from the radiative lifetimes. In addition to the total deactivation rate constants, product states from two-body collisions between Kr(5p and 5p') atoms and ground state argon atoms were identified from the laser-induced emission spectra, and product formation rate constants were assigned. Two-body intermultiplet transfer from Kr(4p 5 [ 2 P/sub 1/2/]5p) to the Kr(4p 5 [ 2 P/sub 3/2/]4d) levels occurs with ease. Intermultiplet transfer from the lowest level in the (4p 5 5p) configuration to the Kr(4p 5 5s and 5s') manifold was fast despite the large energy defect. However, this was the only Kr(5p) level that gave appreciable transfer to the Kr(5s or 5s') manifold. Generally the favored product states are within a few kT of the entrance channel

A program system for ab initio MO calculations on vector and parallel processing machines. Pt. 1

International Nuclear Information System (INIS)

Ernenwein, R.; Rohmer, M.M.; Benard, M.

1990-01-01

We present a program system for ab initio molecular orbital calculations on vector and parallel computers. The present article is devoted to the computation of one- and two-electron integrals over contracted Gaussian basis sets involving s-, p-, d- and f-type functions. The McMurchie and Davidson (MMD) algorithm has been implemented and parallelized by distributing over a limited number of logical tasks the calculation of the 55 relevant classes of integrals. All sections of the MMD algorithm have been efficiently vectorized, leading to a scalar/vector ratio of 5.8. Different algorithms are proposed and compared for an optimal vectorization of the contraction of the 'intermediate integrals' generated by the MMD formalism. Advantage is taken of the dynamic storage allocation for tuning the length of the vector loops (i.e. the size of the vectorization buffer) as a function of (i) the total memory available for the job, (ii) the number of logical tasks defined by the user (≤13), and (iii) the storage requested by each specific class of integrals. Test calculations carried out on a CRAY-2 computer show that the average number of finite integrals computed over a (s, p, d, f) CGTO basis set is about 1180000 per second and per processor. The combination of vectorization and parallelism on this 4-processor machine reduces the CPU time by a factor larger than 20 with respect to the scalar and sequential performance. (orig.)

Sparse BLIP: BLind Iterative Parallel imaging reconstruction using compressed sensing.

Science.gov (United States)

She, Huajun; Chen, Rong-Rong; Liang, Dong; DiBella, Edward V R; Ying, Leslie

2014-02-01

To develop a sensitivity-based parallel imaging reconstruction method to reconstruct iteratively both the coil sensitivities and MR image simultaneously based on their prior information. Parallel magnetic resonance imaging reconstruction problem can be formulated as a multichannel sampling problem where solutions are sought analytically. However, the channel functions given by the coil sensitivities in parallel imaging are not known exactly and the estimation error usually leads to artifacts. In this study, we propose a new reconstruction algorithm, termed Sparse BLind Iterative Parallel, for blind iterative parallel imaging reconstruction using compressed sensing. The proposed algorithm reconstructs both the sensitivity functions and the image simultaneously from undersampled data. It enforces the sparseness constraint in the image as done in compressed sensing, but is different from compressed sensing in that the sensing matrix is unknown and additional constraint is enforced on the sensitivities as well. Both phantom and in vivo imaging experiments were carried out with retrospective undersampling to evaluate the performance of the proposed method. Experiments show improvement in Sparse BLind Iterative Parallel reconstruction when compared with Sparse SENSE, JSENSE, IRGN-TV, and L1-SPIRiT reconstructions with the same number of measurements. The proposed Sparse BLind Iterative Parallel algorithm reduces the reconstruction errors when compared to the state-of-the-art parallel imaging methods. Copyright © 2013 Wiley Periodicals, Inc.

The 4p5rd10 and 4d86p configurations of Te VIII

International Nuclear Information System (INIS)

Churilov, S.S.; Rossijskaya Akademiya Nauk, Troitsk; Joshi, Y.N.; Kildiyarova, R.R.

1998-01-01

The spectrum of tellurium was photographed in the 100-500 A region on a variety of grazing incidence spectrographs using a triggered spark source. The analysis of the lines in the 117-216 A region has lead to establishing 42 out of 45 levels of the 4d 8 6p configuration of Te VIII. Four levels of the 4d 8 4f configuration were confirmed and their level values revised, and an additional 4d 8 4f level was established. The 4p 5 4d 10 levels reported earlier were found to be erroneous and new values have been found for them. Eighty seven (87) new lines have been classified in the (4d 9 + 4d 8 5s)-(4d 8 4f + 4p 5 4d 10 + 4d 8 6p) transition array. Hartree-Fock with relativistic corrections (HFR) and parametric least-squares-fitted (lSF) calculations were carried out to interpret the present analysis adequately. (orig.)

Integrated variable projection approach (IVAPA) for parallel magnetic resonance imaging.

Science.gov (United States)

Zhang, Qiao; Sheng, Jinhua

2012-10-01

Parallel magnetic resonance imaging (pMRI) is a fast method which requires algorithms for the reconstructing image from a small number of measured k-space lines. The accurate estimation of the coil sensitivity functions is still a challenging problem in parallel imaging. The joint estimation of the coil sensitivity functions and the desired image has recently been proposed to improve the situation by iteratively optimizing both the coil sensitivity functions and the image reconstruction. It regards both the coil sensitivities and the desired images as unknowns to be solved for jointly. In this paper, we propose an integrated variable projection approach (IVAPA) for pMRI, which integrates two individual processing steps (coil sensitivity estimation and image reconstruction) into a single processing step to improve the accuracy of the coil sensitivity estimation using the variable projection approach. The method is demonstrated to be able to give an optimal solution with considerably reduced artifacts for high reduction factors and a low number of auto-calibration signal (ACS) lines, and our implementation has a fast convergence rate. The performance of the proposed method is evaluated using a set of in vivo experiment data. Copyright © 2012 Elsevier Ltd. All rights reserved.

Parallelization for first principles electronic state calculation program

International Nuclear Information System (INIS)

Watanabe, Hiroshi; Oguchi, Tamio.

1997-03-01

In this report we study the parallelization for First principles electronic state calculation program. The target machines are NEC SX-4 for shared memory type parallelization and FUJITSU VPP300 for distributed memory type parallelization. The features of each parallel machine are surveyed, and the parallelization methods suitable for each are proposed. It is shown that 1.60 times acceleration is achieved with 2 CPU parallelization by SX-4 and 4.97 times acceleration is achieved with 12 PE parallelization by VPP 300. (author)

About Parallel Programming: Paradigms, Parallel Execution and Collaborative Systems

Directory of Open Access Journals (Sweden)

Loredana MOCEAN

2009-01-01

Full Text Available In the last years, there were made efforts for delineation of a stabile and unitary frame, where the problems of logical parallel processing must find solutions at least at the level of imperative languages. The results obtained by now are not at the level of the made efforts. This paper wants to be a little contribution at these efforts. We propose an overview in parallel programming, parallel execution and collaborative systems.

Anti-vascular agent Combretastatin A-4-P modulates Hypoxia Inducible Factor-1 and gene expression

Directory of Open Access Journals (Sweden)

Currie Margaret J

2006-12-01

Full Text Available Abstract Background A functional vascular network is essential for the survival, growth and spread of solid tumours, making blood vessels a key target for therapeutic strategies. Combretastatin A-4 phosphate (CA-4-P is a tubulin-depolymerising agent in Phase II clinical trials as a vascular disrupting agent. Not much is known of the molecular effect of CA-4-P under tumour conditions. The tumour microenvironment differs markedly from that in normal tissue, specifically with respect to oxygenation (hypoxia. Gene regulation under tumour conditions is governed by hypoxia inducible factor 1 (HIF-1, controlling angiogenic and metastatic pathways. Methods We investigated the effect of CA-4-P on factors of the upstream and downstream signalling pathway of HIF-1 in vitro. Results CA-4-P treatment under hypoxia tended to reduce HIF-1 accumulation in a concentration-dependent manner, an effect which was more prominent in endothelial cells than in cancer cell lines. Conversely, CA-4-P increased HIF-1 accumulation under aerobic conditions in vitro. At these concentrations of CA-4-P under aerobic conditions, nuclear factor κB was activated via the small GTPase RhoA, and expression of the HIF-1 downstream angiogenic effector gene, vascular endothelial growth factor (VEGF-A, was increased. Conclusion Our findings advance the understanding of signal transduction pathways involved in the actions of the anti-vascular agent CA-4-P.

Xyce Parallel Electronic Simulator Users Guide Version 6.4

Energy Technology Data Exchange (ETDEWEB)

Keiter, Eric R. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Mei, Ting [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Russo, Thomas V. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Schiek, Richard [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Sholander, Peter E. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Thornquist, Heidi K. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Verley, Jason [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Baur, David Gregory [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

2015-12-01

This manual describes the use of the Xyce Parallel Electronic Simulator. Xyce has been de- signed as a SPICE-compatible, high-performance analog circuit simulator, and has been written to support the simulation needs of the Sandia National Laboratories electrical designers. This development has focused on improving capability over the current state-of-the-art in the following areas: Capability to solve extremely large circuit problems by supporting large-scale parallel com- puting platforms (up to thousands of processors). This includes support for most popular parallel and serial computers. A differential-algebraic-equation (DAE) formulation, which better isolates the device model package from solver algorithms. This allows one to develop new types of analysis without requiring the implementation of analysis-specific device models. Device models that are specifically tailored to meet Sandia's needs, including some radiation- aware devices (for Sandia users only). Object-oriented code design and implementation using modern coding practices. Xyce is a parallel code in the most general sense of the phrase -- a message passing parallel implementation -- which allows it to run efficiently a wide range of computing platforms. These include serial, shared-memory and distributed-memory parallel platforms. Attention has been paid to the specific nature of circuit-simulation problems to ensure that optimal parallel efficiency is achieved as the number of processors grows. Trademarks The information herein is subject to change without notice. Copyright c 2002-2015 Sandia Corporation. All rights reserved. Xyce TM Electronic Simulator and Xyce TM are trademarks of Sandia Corporation. Portions of the Xyce TM code are: Copyright c 2002, The Regents of the University of California. Produced at the Lawrence Livermore National Laboratory. Written by Alan Hindmarsh, Allan Taylor, Radu Serban. UCRL-CODE-2002-59 All rights reserved. Orcad, Orcad Capture, PSpice and Probe are

Inclusive dielectron cross sections in p+p and p+d interactions at beam energies from 1.04 to 4.88 GeV

International Nuclear Information System (INIS)

Wilson, W.K.; Beedoe, S.; Carroll, J.; Igo, G.; Seidl, P.; Toy, M.; Bossingham, R.; Gong, W.G.; Heilbronn, L.; Huang, H.Z.; Krebs, G.; Letessier-Selvon, A.; Magestro, D.; Matis, H.S.; Miller, J.; Naudet, C.; Porter, R.J.; Roche, G.; Schroeder, L.S.; Yegneswaran, A.; Bougteb, M.; Manso, F.; Prunet, M.; Roche, G.; Hallman, T.; Madansky, L.; Welsh, R.C.; Kirk, P.; Wang, Z.F.

1998-01-01

Measurements of dielectron production in p+p and p+d collisions with beam kinetic energies from 1.04 to 4.88 GeV are presented. The differential cross section is presented as a function of invariant pair mass, transverse momentum, and rapidity. The shapes of the mass spectra and their evolution with beam energy provide information about the relative importance of the various dielectron production mechanisms in this energy regime. The p+d to p+p ratio of the dielectron yield is also presented as a function of invariant pair mass, transverse momentum, and rapidity. The shapes of the transverse momentum and rapidity spectra from the p+d and p+p systems are found to be similar to one another for each of the beam energies studied. The beam energy dependence of the integrated cross sections is also presented. copyright 1998 The American Physical Society

Identification of the interleukin 4 receptor alpha gene as a direct target for p73.

Science.gov (United States)

Sasaki, Yasushi; Mita, Hiroaki; Toyota, Minoru; Ishida, Setsuko; Morimoto, Ichiro; Yamashita, Toshiharu; Tanaka, Toshihiro; Imai, Kohzoh; Nakamura, Yusuke; Tokino, Takashi

2003-12-01

p73 has a high degree of structural homology to p53 and can activate transcription of p53-responsive genes. However, analysis of p73-deficient mice revealed a marked divergence in the physiological activities of p53 family genes and distinguishes p73 from p53. Mice deficient for p73 exhibit profound defects, including hippocampal dysgenesis, chronic infection, and inflammation, as well as abnormalities in pheromone sensory pathways. p73 plays important roles in neurogenesis, sensory pathways, and homeostatic regulation. Here, we found that the interleukin 4 receptor alpha (IL-4Ralpha) gene is up-regulated by p73 but not significantly by p53 in several human cancer cell lines. IL-4Ralphatranscription is also activated in response to cisplatin, a DNA-damaging agent known to induce p73. By using small interference RNA designed to target p73, we demonstrated that silencing endogenous p73 abrogates the induction of the IL-4Ralpha gene after cisplatin treatment. Furthermore, we identified a p73-binding site in the first intron of the IL-4Ralpha gene that can directly interact with the p73 protein in vivo. This p73-binding site consists of eight copies of a 10-bp consensus p53-binding motif and is a functional response element that is relatively specific for p73 among the p53 family. p73beta promoted localized nucleosomal acetylation through recruitment of coactivator p300, indicating that p73 regulates transcription of IL-4Ralpha through the unique p73-binding site. We also found that p73beta-transfected tumor cells are sensitive to IL-4-mediated apoptosis. Our data suggest that IL-4Ralpha could mediate, in part, certain immune responses and p73-dependent cell death.

A Parallel Butterfly Algorithm

KAUST Repository

Poulson, Jack; Demanet, Laurent; Maxwell, Nicholas; Ying, Lexing

2014-01-01

The butterfly algorithm is a fast algorithm which approximately evaluates a discrete analogue of the integral transform (Equation Presented.) at large numbers of target points when the kernel, K(x, y), is approximately low-rank when restricted to subdomains satisfying a certain simple geometric condition. In d dimensions with O(Nd) quasi-uniformly distributed source and target points, when each appropriate submatrix of K is approximately rank-r, the running time of the algorithm is at most O(r2Nd logN). A parallelization of the butterfly algorithm is introduced which, assuming a message latency of α and per-process inverse bandwidth of β, executes in at most (Equation Presented.) time using p processes. This parallel algorithm was then instantiated in the form of the open-source DistButterfly library for the special case where K(x, y) = exp(iΦ(x, y)), where Φ(x, y) is a black-box, sufficiently smooth, real-valued phase function. Experiments on Blue Gene/Q demonstrate impressive strong-scaling results for important classes of phase functions. Using quasi-uniform sources, hyperbolic Radon transforms, and an analogue of a three-dimensional generalized Radon transform were, respectively, observed to strong-scale from 1-node/16-cores up to 1024-nodes/16,384-cores with greater than 90% and 82% efficiency, respectively. © 2014 Society for Industrial and Applied Mathematics.

A Parallel Butterfly Algorithm

KAUST Repository

Poulson, Jack

2014-02-04

The butterfly algorithm is a fast algorithm which approximately evaluates a discrete analogue of the integral transform (Equation Presented.) at large numbers of target points when the kernel, K(x, y), is approximately low-rank when restricted to subdomains satisfying a certain simple geometric condition. In d dimensions with O(Nd) quasi-uniformly distributed source and target points, when each appropriate submatrix of K is approximately rank-r, the running time of the algorithm is at most O(r2Nd logN). A parallelization of the butterfly algorithm is introduced which, assuming a message latency of α and per-process inverse bandwidth of β, executes in at most (Equation Presented.) time using p processes. This parallel algorithm was then instantiated in the form of the open-source DistButterfly library for the special case where K(x, y) = exp(iΦ(x, y)), where Φ(x, y) is a black-box, sufficiently smooth, real-valued phase function. Experiments on Blue Gene/Q demonstrate impressive strong-scaling results for important classes of phase functions. Using quasi-uniform sources, hyperbolic Radon transforms, and an analogue of a three-dimensional generalized Radon transform were, respectively, observed to strong-scale from 1-node/16-cores up to 1024-nodes/16,384-cores with greater than 90% and 82% efficiency, respectively. © 2014 Society for Industrial and Applied Mathematics.

First principles electronic structure and optical properties of the Zintl compound Eu3In2P4

KAUST Repository

Singh, Nirpendra; Schwingenschlö gl, Udo

2011-01-01

We have performed full-potential calculations of the electronic structure and optical properties of the newly found Zintl compound Eu3In 2P4. Eu3In2P4 turns out to be a small gap semiconductor with an energy gap of 0.42 eV, which is in agreement with the experimental value of 0.452 eV. The peaks of the optical spectra originate mainly from transitions between occupied Eu 4f states in the valence band and unoccupied Eu 5d states in the conduction band. A considerable anisotropy is observed for the parallel and perpendicular components in the frequency dependent optical spectra. The spectral features are explained in terms of the band structure. © 2011 Elsevier B.V. All rights reserved.

First principles electronic structure and optical properties of the Zintl compound Eu3In2P4

KAUST Repository

Singh, Nirpendra

2011-05-01

We have performed full-potential calculations of the electronic structure and optical properties of the newly found Zintl compound Eu3In 2P4. Eu3In2P4 turns out to be a small gap semiconductor with an energy gap of 0.42 eV, which is in agreement with the experimental value of 0.452 eV. The peaks of the optical spectra originate mainly from transitions between occupied Eu 4f states in the valence band and unoccupied Eu 5d states in the conduction band. A considerable anisotropy is observed for the parallel and perpendicular components in the frequency dependent optical spectra. The spectral features are explained in terms of the band structure. © 2011 Elsevier B.V. All rights reserved.

Parallel family trees for transfer matrices in the Potts model

Science.gov (United States)

Navarro, Cristobal A.; Canfora, Fabrizio; Hitschfeld, Nancy; Navarro, Gonzalo

2015-02-01

The computational cost of transfer matrix methods for the Potts model is related to the question in how many ways can two layers of a lattice be connected? Answering the question leads to the generation of a combinatorial set of lattice configurations. This set defines the configuration space of the problem, and the smaller it is, the faster the transfer matrix can be computed. The configuration space of generic (q , v) transfer matrix methods for strips is in the order of the Catalan numbers, which grows asymptotically as O(4m) where m is the width of the strip. Other transfer matrix methods with a smaller configuration space indeed exist but they make assumptions on the temperature, number of spin states, or restrict the structure of the lattice. In this paper we propose a parallel algorithm that uses a sub-Catalan configuration space of O(3m) to build the generic (q , v) transfer matrix in a compressed form. The improvement is achieved by grouping the original set of Catalan configurations into a forest of family trees, in such a way that the solution to the problem is now computed by solving the root node of each family. As a result, the algorithm becomes exponentially faster than the Catalan approach while still highly parallel. The resulting matrix is stored in a compressed form using O(3m ×4m) of space, making numerical evaluation and decompression to be faster than evaluating the matrix in its O(4m ×4m) uncompressed form. Experimental results for different sizes of strip lattices show that the parallel family trees (PFT) strategy indeed runs exponentially faster than the Catalan Parallel Method (CPM), especially when dealing with dense transfer matrices. In terms of parallel performance, we report strong-scaling speedups of up to 5.7 × when running on an 8-core shared memory machine and 28 × for a 32-core cluster. The best balance of speedup and efficiency for the multi-core machine was achieved when using p = 4 processors, while for the cluster

Concurrent particle-in-cell plasma simulation on a multi-transputer parallel computer

International Nuclear Information System (INIS)

Khare, A.N.; Jethra, A.; Patel, Kartik

1992-01-01

This report describes the parallelization of a Particle-in-Cell (PIC) plasma simulation code on a multi-transputer parallel computer. The algorithm used in the parallelization of the PIC method is described. The decomposition schemes related to the distribution of the particles among the processors are discussed. The implementation of the algorithm on a transputer network connected as a torus is presented. The solutions of the problems related to global communication of data are presented in the form of a set of generalized communication functions. The performance of the program as a function of data size and the number of transputers show that the implementation is scalable and represents an effective way of achieving high performance at acceptable cost. (author). 11 refs., 4 figs., 2 tabs., appendices

Processing data communications events by awakening threads in parallel active messaging interface of a parallel computer

Science.gov (United States)

Archer, Charles J.; Blocksome, Michael A.; Ratterman, Joseph D.; Smith, Brian E.

2016-03-15

Processing data communications events in a parallel active messaging interface (`PAMI`) of a parallel computer that includes compute nodes that execute a parallel application, with the PAMI including data communications endpoints, and the endpoints are coupled for data communications through the PAMI and through other data communications resources, including determining by an advance function that there are no actionable data communications events pending for its context, placing by the advance function its thread of execution into a wait state, waiting for a subsequent data communications event for the context; responsive to occurrence of a subsequent data communications event for the context, awakening by the thread from the wait state; and processing by the advance function the subsequent data communications event now pending for the context.

A simple approach to design chitosan functionalized Fe3O4 nanoparticles for pH responsive delivery of doxorubicin for cancer therapy

Science.gov (United States)

Adimoolam, Mahesh G.; Amreddy, Narsireddy; Nalam, Madhusudana Rao; Sunkara, Manorama V.

2018-02-01

The use of magnetic nanoparticles (MNPs) in cancer therapy offer many advantages due to their unique size, physical and biocompatible properties. In this study we have developed a formulation, comprising of anti-cancer drug doxorubicin (Dox) conjugated to iron oxide nanoparticles via a pH sensitive imine linker. Different amounts of chitosan functionalized superparamagnetic iron oxide nanoparticles (Fe3O4-CHI) were synthesized in-situ by a simple hydrolysis method at room temperature. The synthesized nanoparticles were well characterized by TEM, Zeta Potential, TOC, XPS, TGA and VSM for their physicochemical properties. Dox was conjugated to the Fe3O4-CHI nanoparticles via a glutaraldehyde cross linker with the imine (sbnd Cdbnd Nsbnd) bond, which is sensitive to cleavage in the pH range of 4.4-6.4. The synthesized Fe3O4-Dox nanoparticles exhibited enhanced drug release in lower pH conditions which mimics the tumor microenvironment or intracellular organelles such as endosomes/lysosomes. The cell uptake and therapeutic efficacy of Fe3O4-Dox nanoparticles carried out in ovarian cancer cell (SK-OV-3) and breast cancer cell line (MCF7) showed improved therapeutic efficacy of Dox by nearly four-fold with Fe3O4-Dox nanoparticles.

Stampi: a message passing library for distributed parallel computing. User's guide, second edition

International Nuclear Information System (INIS)

Imamura, Toshiyuki; Koide, Hiroshi; Takemiya, Hiroshi

2000-02-01

A new message passing library, Stampi, has been developed to realize a computation with different kind of parallel computers arbitrarily and making MPI (Message Passing Interface) as an unique interface for communication. Stampi is based on the MPI2 specification, and it realizes dynamic process creation to different machines and communication between spawned one within the scope of MPI semantics. Main features of Stampi are summarized as follows: (i) an automatic switch function between external- and internal communications, (ii) a message routing/relaying with a routing module, (iii) a dynamic process creation, (iv) a support of two types of connection, Master/Slave and Client/Server, (v) a support of a communication with Java applets. Indeed vendors implemented MPI libraries as a closed system in one parallel machine or their systems, and did not support both functions; process creation and communication to external machines. Stampi supports both functions and enables us distributed parallel computing. Currently Stampi has been implemented on COMPACS (COMplex PArallel Computer System) introduced in CCSE, five parallel computers and one graphic workstation, moreover on eight kinds of parallel machines, totally fourteen systems. Stampi provides us MPI communication functionality on them. This report describes mainly the usage of Stampi. (author)

Quadrupole and monopole generalized oscillator strength for 2p-3p, 2p-4p transition of neon atomic in the velocity formulation

International Nuclear Information System (INIS)

Gomis, L; Diedhiou, I; Tall, M S; Diallo, S; Diatta, C S; Niassy, B

2007-01-01

The quadrupole and monopole generalized oscillator strengths (GOS) as a function of momentum transfer are calculated for the 2p-3p and 2p-4p transitions of the neon atom using the analytical Hartree-Fock (HF) wavefunctions for the ground-state and the wavefunctions for the excited states which are obtained numerically from the modified HF Slater equation. Calculations are carried out by using the HF method and random phase approximation with exchange in the velocity formulation. The positions and the number of the extrema in the GOS have received particular attention in the evaluation. Our calculated monopole GOS of 2p-3p transition in velocity form reveals one maximum located between the experimental and theoretical results of other authors. The disagreement between our first maximum of the quadrupole GOS 2p-3p transition with the experimental and other theoretical ones is unimportant. The extrema of the monopole and quadrupole GOS of 2p-4p transition are given in this paper. The results of velocity form study also show that the electron correlation effects are important around the maxima and are found to influence the positions of the extrema insignificantly

CCHCR1 interacts with EDC4, suggesting its localization in P-bodies

Energy Technology Data Exchange (ETDEWEB)

Ling, Y.H.; Wong, C.C. [School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong (China); Li, K.W. [Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, 1081 HV Amsterdam (Netherlands); Chan, K.M. [School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong (China); Boukamp, P. [Division of Genetics of Skin Carcinogenesis, A110 German Cancer Research Center, Im Neuenheimer Feld 280, D-69120 Heidelberg (Germany); Liu, W.K., E-mail: ken-liu@cuhk.edu.hk [School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong (China)

2014-09-10

Coiled‐coil alpha‐helical rod protein 1 (CCHCR1) is suggested as a candidate biomarker for psoriasis for more than a decade but its function remains poorly understood because of the inconsistent findings in the literature. CCHCR1 protein is suggested to be localized in the cytoplasm, nucleus, mitochondria, or centrosome and to regulate various cellular functions, including steroidogenesis, proliferation, differentiation, and cytoskeleton organization. In this study, we attempted to find a consensus between these findings by identifying the interaction partners of CCHCR1 using co-immunoprecipiation with a stable cell line expressing EGFP-tagged CCHCR1. Out of more than 100 co-immunoprecipitants identified by liquid chromatography-tandem mass spectrometry (LC-MS/MS), the enhancer of mRNA-decapping protein 4 (EDC4), which is a processing body (P-body) component, was particularly found to be the major interacting partner of CCHCR1. Confocal imaging confirmed the localization of CCHCR1 in P-bodies and its N-terminus is required for this subcellular localization, suggesting that CCHCR1 is a novel P-body component. As P-bodies are the site for mRNA metabolism, our findings provide a molecular basis for the function of CCHCR1, any disruption of which may affect the transcriptome of the cell, and causing abnormal cell functions. - Highlights: • We identified CCHCR1 as a novel P-body component. • We identified EDC4 as the major interacting partner of CCHCR1. • N-terminus of CCHCR1 protein is required for its P-bodies localization.

Theobromine consumption does not improve fasting and postprandial vascular function in overweight and obese subjects.

Science.gov (United States)

Smolders, Lotte; Mensink, Ronald P; van den Driessche, Jose J; Joris, Peter J; Plat, Jogchum

2018-01-12

Theobromine, a component of cocoa, may favorably affect conventional lipid-related cardiovascular risk markers, but effects on flow-mediated dilation (FMD) and other vascular function markers are not known. To evaluate the effects of 4-week theobromine consumption (500 mg/day) on fasting and postprandial vascular function markers. In a randomized, double-blind crossover study, 44 apparently healthy overweight (N = 30) and obese (N = 14) men and women with low HDL-C concentrations, consumed daily 500 mg theobromine or placebo for 4 weeks. After 4 weeks, FMD, peripheral arterial tonometry (PAT), augmentation index (AIx), pulse wave velocity (PWV), blood pressure (BP) and retinal microvasculature measurements were performed. These measurements were carried out under fasting conditions and 2.5 h after a high-fat mixed meal challenge. 4-week theobromine consumption did not change fasting vascular function markers, except for a decrease in central AIx (cAIx, - 1.7 pp, P = 0.037) and a trend towards smaller venular calibers (- 2 µm, P = 0.074). Consuming a high-fat mixed meal decreased FMD (0.89 pp, P = 0.002), reactive hyperemia index (RHI, - 0.30, P Theobromine did not modify these postprandial effects, but increased postprandially the brachial artery diameter (0.03 cm, P = 0.015), and decreased the cAIx corrected for a HR of 75 (cAIx75, - 5.0 pp, P = 0.004) and peripheral AIx (pAIx, - 6.3 pp, P = 0.017). Theobromine consumption did not improve fasting and postprandial endothelial function, but increased postprandial peripheral arterial diameters and decreased the AIx. These findings do not suggest that theobromine alone contributes to the proposed cardioprotective effects of cocoa. This trial was registered on clinicaltrials.gov under study number NCT02209025.

Experiment E89-044 of quasi-elastic diffusion ³He(e,e'p) at Jefferson Laboratory: Analyze cross sections of the two body breakup in parallel kinematics; Experience E89-044 de diffusion quasi-elastique ³he(e,e'p) au Jefferson Laboratory : analyse des sections efficaces de desintegration a deux corps en cinematique parallele

Energy Technology Data Exchange (ETDEWEB)

Penel-Nottaris, Emilie [Univ. Joseph Fourier Grenoble (France)

2004-07-01

The Jefferson Lab Hall A experiment has measured the ³He(e,e'p) reaction cross sections. The separation of the longitudinal and transverse response functions for the two-body breakup reaction in parallel kinematics allows to study the bound proton electromagnetic properties in the 3He nucleus and the involved nuclear mechanisms beyond impulse approximation. Preliminary cross sections show some disagreement with theoretical predictions for the forward angles kinematics around 0 MeV/c missing momenta, and sensitivity to final state interactions and ³He wave functions for missing momenta of 300 MeV/c.

Parallel computing for data science with examples in R, C++ and CUDA

CERN Document Server

Matloff, Norman

2015-01-01

Parallel Computing for Data Science: With Examples in R, C++ and CUDA is one of the first parallel computing books to concentrate exclusively on parallel data structures, algorithms, software tools, and applications in data science. It includes examples not only from the classic ""n observations, p variables"" matrix format but also from time series, network graph models, and numerous other structures common in data science. The examples illustrate the range of issues encountered in parallel programming.With the main focus on computation, the book shows how to compute on three types of platfor

The effect of heat on Na+/H+ antiport function and survival in mammalian cells

International Nuclear Information System (INIS)

Liu, F.-F.; Diep, Kim; Tannock, Ian F.; Hill, Richard P.

1996-01-01

Purpose: Because intracellular pH (pH i ) is a determinant of thermosensitivity, it is important to understand the relationship between heat cytotoxicity and the mechanisms responsible for pH i regulation, such as the Na + /H + antiport. The objective of this study is to elucidate the relationship between heat damage and Na + /H + antiport activity. Methods and Materials: Various cell lines, EMT6, RIF-1, and its thermoresistant variant TR-4, and CCL39, and its variant that lacks the Na + /H + antiport (PS120), were all heated using a water bath. Parallel assessments of antiport function and pH i were made using the fluorescent dye 2,7-biscarboxyethyl-5(6)-carboxyfluorescein (BCECF). Results: Exposure of EMT6 cells to 43-46 deg. C for 30-60 min caused progressive decline in antiport activity, in parallel with cytotoxicity. When the same degree of cytotoxicity was induced by ionizing radiation, no alteration in Na + /H + antiport function was observed. Despite a 10-fold lower survival in RIF-1 compared to TR-4 cells after heating, there was no difference in the thermosensitivity of their antiports. Antiport activity in the TR-4 cells, however, was higher than that of RIF-1 cells both before and during heating. Intracellular pH for TR-4 cells decreased minimally during heating, in contrast to a decline of 1 pH unit in RIF-1 cells despite similar relative levels of antiport activity, suggesting that in this pair of cell lines, antiport activity does not play a major pH i regulatory role. PS120 and CCL39 cells had similar survival levels when heated at pH e 7.2 in the presence of NaHCO 3 , which allows function of the other major regulator of pH i , the Na + -dependent HCO 3 - /Cl - exchanger. This occurred despite a drop in pH i in the PS120 cells during heating. A reduced survival was observed, however, in PS120 cells after 43 deg. C for 30-60 min at either pH e 6.5 or pH e 7.2 in the absence of NaHCO 3 . Intracellular pH for both lines decreased with increasing

Data communications in a parallel active messaging interface of a parallel computer

Science.gov (United States)

Archer, Charles J; Blocksome, Michael A; Ratterman, Joseph D; Smith, Brian E

2013-11-12

Data communications in a parallel active messaging interface (`PAMI`) of a parallel computer composed of compute nodes that execute a parallel application, each compute node including application processors that execute the parallel application and at least one management processor dedicated to gathering information regarding data communications. The PAMI is composed of data communications endpoints, each endpoint composed of a specification of data communications parameters for a thread of execution on a compute node, including specifications of a client, a context, and a task, the compute nodes and the endpoints coupled for data communications through the PAMI and through data communications resources. Embodiments function by gathering call site statistics describing data communications resulting from execution of data communications instructions and identifying in dependence upon the call cite statistics a data communications algorithm for use in executing a data communications instruction at a call site in the parallel application.

2D parallel interpenetration of [M2(bpp)4X4] [M, Fe(II)/Co(II); bpp, 4,4'-trimethylenedipyridine; X, SCN-, SeCN- and N3-] complexes: Pseudohalide-dependent conformation of bpp

International Nuclear Information System (INIS)

Manna, Subal Chandra; Jana, Atish Dipankar; Rosair, Georgina M.; Drew, Michael G.B.; Mostafa, Golam; Ray Chaudhuri, Nirmalendu

2008-01-01

Three coordination complexes of Co(II)/Fe(II) with 4,4'-trimethylenedipyridine (bpp) and pseudohalides (SCN - , SeCN - and N 3 - ) have been synthesized. The complexes have been characterized by X-ray single crystal structure determination. They are isomorphous having 2D layers in which two independent wavy nets display parallel interwoven structures. Pseudohalide binds metal centers through N terminal and occupies the trans axial positions of the octahedral metal coordination environment. Pseudohalide remains pendant on both sides of the polymeric layer and help the stacking through hydrogen bonding. The conformation of bpp in the interpenetrated nets is observed to be dependent on the choice of pseudohalide. - Graphical abstract: Complexes of [M 2 (bpp) 4 X 4 ] [M, Fe(II)/Co(II); bpp, 4,4'-trimethylenedipyridine; X, SCN - , SeCN - and N3 - ] have been synthesized. The structural analysis reveals undulated 2D network with (4,4) net topology adopting two different conformations of bpp alternately. Two such networks undergo parallel interpenetration. Pseudohalides are observed to help in stacking the interpenetrated nets through hydrogen bonding

Parallel Branch-and-Bound Methods for the Job Shop Scheduling

DEFF Research Database (Denmark)

Clausen, Jens; Perregaard, Michael

1998-01-01

Job-shop scheduling (JSS) problems are among the more difficult to solve in the class of NP-complete problems. The only successful approach has been branch-and-bound based algorithms, but such algorithms depend heavily on good bound functions. Much work has been done to identify such functions...... for the JSS problem, but with limited success. Even with recent methods, it is still not possible to solve problems substantially larger than 10 machines and 10 jobs. In the current study, we focus on parallel methods for solving JSS problems. We implement two different parallel branch-and-bound algorithms...

Enhanced Reactive Oxygen Species Production, Acidic Cytosolic pH and Upregulated Na+/H+ Exchanger (NHE) in Dicer Deficient CD4+ T Cells.

Science.gov (United States)

Singh, Yogesh; Zhou, Yuetao; Zhang, Shaqiu; Abdelazeem, Khalid N M; Elvira, Bernat; Salker, Madhuri S; Lang, Florian

2017-01-01

MicroRNAs (miRNAs) negatively regulate gene expression at a post-transcriptional level. Dicer, a cytoplasmic RNase III enzyme, is required for the maturation of miRNAs from precursor miRNAs. Dicer, therefore, is a critical enzyme involved in the biogenesis and processing of miRNAs. Several biological processes are controlled by miRNAs, including the regulation of T cell development and function. T cells generate reactive oxygen species (ROS) with parallel H+ extrusion accomplished by the Na+/H+-exchanger 1 (NHE1). The present study explored whether ROS production, as well as NHE1 expression and function are sensitive to the lack of Dicer (miRNAs deficient) and could be modified by individual miRNAs. CD4+ T cells were isolated from CD4 specific Dicer deficient (DicerΔ/Δ) mice and the respective control mice (Dicerfl/fl). Transcript and protein levels were quantified with RT-PCR and Western blotting, respectively. For determination of intracellular pH (pHi) cells were incubated with the pH sensitive dye bis-(2-carboxyethyl)-5-(and-6)-carboxyfluorescein (BCECF) and Na+/H+ exchanger (NHE) activity was calculated from re-alkalinization after an ammonium pulse. Changes in cell volume were measured using the forward scatter in flow cytometry, and ROS production utilizing 2',7' -dichlorofluorescin diacetate (DCFDA) fluorescence. Transfection of miRNA-control and mimics in T cells was performed using DharmaFECT3 reagent. ROS production, cytosolic H+ concentration, NHE1 transcript and protein levels, NHE activity, and cell volume were all significantly higher in CD4+ T cells from DicerΔ/Δ mice than in CD4+ T cells from Dicerfl/fl mice. Furthermore, individual miR-200b and miR-15b modify pHi and NHE activity in Dicerfl/fl and DicerΔ/Δ CD4+ T cells, respectively. Lack of Dicer leads to oxidative stress, cytosolic acidification, upregulated NHE1 expression and activity as well as swelling of CD4+ T cells, functions all reversed by miR-15b or miR-200b. © 2017 The Author

An Introductory Review of Parallel Independent Component Analysis (p-ICA and a Guide to Applying p-ICA to Genetic Data and Imaging Phenotypes to Identify Disease-Associated Biological Pathways and Systems in Common Complex Disorders

Directory of Open Access Journals (Sweden)

Godfrey D Pearlson

2015-09-01

Full Text Available Complex inherited phenotypes, including those for many common medical and psychiatric diseases, are most likely underpinned by multiple genes contributing to interlocking molecular biological processes, along with environmental factors (Owen et al., 2010. Despite this, genotyping strategies for complex, inherited, disease-related phenotypes mostly employ univariate analyses, e.g. genome wide association (GWA. Such procedures most often identify isolated risk-related SNPs or loci, not the underlying biological pathways necessary to help guide the development of novel treatment approaches. This article focuses on the multivariate analysis strategy of parallel (i.e. simultaneous combination of SNP and neuroimage information independent component analysis (p-ICA, which typically yields large clusters of functionally related SNPs statistically correlated with phenotype components, whose overall molecular biologic relevance is inferred subsequently using annotation software suites. Because this is a novel approach, whose details are relatively new to the field we summarize its underlying principles and address conceptual questions regarding interpretation of resulting data and provide practical illustrations of the method.

Deletion of the pH sensor GPR4 decreases renal acid excretion.

Science.gov (United States)

Sun, Xuming; Yang, Li V; Tiegs, Brian C; Arend, Lois J; McGraw, Dennis W; Penn, Raymond B; Petrovic, Snezana

2010-10-01

Proton receptors are G protein-coupled receptors that accept protons as ligands and function as pH sensors. One of the proton receptors, GPR4, is relatively abundant in the kidney, but its potential role in acid-base homeostasis is unknown. In this study, we examined the distribution of GPR4 in the kidney, its function in kidney epithelial cells, and the effects of its deletion on acid-base homeostasis. We observed GPR4 expression in the kidney cortex, in the outer and inner medulla, in isolated kidney collecting ducts, and in cultured outer and inner medullary collecting duct cells (mOMCD1 and mIMCD3). Cultured mOMCD1 cells exhibited pH-dependent accumulation of intracellular cAMP, characteristic of GPR4 activation; GPR4 knockdown attenuated this accumulation. In vivo, deletion of GPR4 decreased net acid secretion by the kidney and resulted in a nongap metabolic acidosis, indicating that GPR4 is required to maintain acid-base homeostasis. Collectively, these findings suggest that GPR4 is a pH sensor with an important role in regulating acid secretion in the kidney collecting duct.

Collision broadening and shift of the potassium 4p-ns and 4p-nd lines by argon

International Nuclear Information System (INIS)

Hohimer, J.P.; Gee, J.

1982-01-01

A two-step laser excitation technique was used to investigate the collisional broadening and shift of excited-state potassium transitions. Measurements were also made to determine that the broadening and shift constants were unaffected by optical pumping and saturation effects. Values for the argon collisional-broadening and shift constants for the potassium 4p-ns (n = 8--11) and 4p-nd (n = 6--9) transitions were determined from line-shape measurements. The values of these constants (in units of 10 -9 rad s -1 atom -1 cm 3 at 110 0 C) and their one-sigma statistical uncertainties are (4P/sub 1/2/-8S/sub 1/2/): γ = 17.03 +- 0.15, β = -14.58 +- 0.29; (4P/sub 3/2/-8S/sub 1/2/): γ = 17.45 +- 0.24, β = -14.71 +- 0.30; (4P/sub 1/2/-9S/sub 1/2/): γ = 17.29 +- 0.15, β = -24.16 +- 0.15; (4P/sub 3/2/-9S/sub 1/2/): γ = 17.35 +- 0.12, β = -24.16 +- 0.09; (4P/sub 1/2/-10S/sub 1/2/): γ = 15.62 +- 0.07, β = -29.49 +- 0.22; (4P/sub 3/2/-10S/sub 1/2/): γ = 15.80 +- 0.11, β = -29.86 +- 0.27; (4P/sub 1/2/-11S/sub 1/2/): γ = 12.69 +- 0.09, β = -33.66 +- 0.11; (4P/sub 3/2/-11S/sub 1/2/): γ = 12.85 +- 0.17, β = -35.10 +- 0.23; (4P/sub 1/2/-6D/sub 3/2/): γ = 13.75 +- 0.27, β = -8.28 +- 0.16; (4P/sub 3/2/-6D/sub 5/2/): γ = 15.15 +- 0.41, β = -8.96 +- 0.10; (4P/sub 1/2/-7D/sub 3/2/): γ = 18.60 +- 0.21, β = -16.00 +- 0.18; (4P/sub 3/2/-7D/sub 5/2/): γ = 19.64 +- 0.25, β = -15.16 +- 0.21; (4P/sub 1/2/-8D/sub 3/2/): γ = 19.94 +- 0.09, β = -24.14 +- 0.22; (4P/sub 3/2/-8D/sub 5/2/): γ = 19.80 +- 0.06, β = -24.16 +- 0.18; (4P/sub 1/2/-9D/sub 3/2/): γ = 17.40 +- 0.13, β = -30.17 +- 0.28; (4P/sub 3/2/-9D/sub 5/2/): γ = 17.50 +- 0.27, β = -29.47 +- 0.12. The overall accuracy of these measurements is estimated to be about 5%

Modulation transfer function assessment in parallel beam and fan beam collimators with square and cylindrical holes.

Science.gov (United States)

Khorshidi, Abdollah; Ashoor, Mansour

2014-05-01

This study investigates modulation transfer function (MTF) in parallel beam (PB) and fan beam (FB) collimators using the Monte Carlo method with full width at half maximum (FWHM), square and circular-shaped holes, and scatter and penetration (S + P) components. A regulation similar to the lead-to-air ratio was used for both collimators to estimate output data. The hole pattern was designed to compare FB by PB parameters. The radioactive source in air and in a water phantom placed in front of the collimators was simulated using MCNP5 code. The test results indicated that the square holes in PB (PBs) had better FWHM than did the cylindrical (PBc) holes. In contrast, the cylindrical holes in the FB (FBc) had better FWHM than the square holes. In general, the resolution of FBc was better than that of the PBc in air and scatter mediums. The S + P decreased for all collimators as the distance from the source to the collimator surface (z) increased. The FBc had a lower S + P than FBs, but PBc had a higher S + P than PBs. Of the FB and PB collimators with the identical hole shapes, PBs had a smaller S + P than FBs, and FBc had a smaller S + P than PBc. The MTF value for the FB was greater than for the PB and had increased spatial frequency; the FBc had higher MTF than the FBs and PB collimators. Estimating the FB using PB parameters and diverse hole shapes may be useful in collimator design to improve the resolution and efficiency of SPECT images.

Apical membrane P2Y4 purinergic receptor controls K+ secretion by strial marginal cell epithelium

Directory of Open Access Journals (Sweden)

Scofield Margaret A

2005-11-01

Full Text Available Abstract Background It was previously shown that K+ secretion by strial marginal cell epithelium is under the control of G-protein coupled receptors of the P2Y family in the apical membrane. Receptor activation by uracil nucleotides (P2Y2, P2Y4 or P2Y6 leads to a decrease in the electrogenic K+ secretion. The present study was conducted to determine the subtype of the functional purinergic receptor in gerbil stria vascularis, to test if receptor activation leads to elevation of intracellular [Ca2+] and to test if the response to these receptors undergoes desensitization. Results The transepithelial short circuit current (Isc represents electrogenic K+ secretion and was found to be decreased by uridine 5'-triphosphate (UTP, adenosine 5'-triphosphate (ATP and diadenosine tetraphosphate (Ap4A but not uridine 5'-diphosphate (UDP at the apical membrane of marginal cells of the gerbil stria vascularis. The potencies of these agonists were consistent with rodent P2Y4 and P2Y2 but not P2Y6 receptors. Activation caused a biphasic increase in intracellular [Ca2+] that could be partially blocked by 2-aminoethoxy-diphenyl borate (2-APB, an inhibitor of the IP3 receptor and store-operated channels. Suramin (100 μM did not inhibit the effect of UTP (1 μM. The ineffectiveness of suramin at the concentration used was consistent with P2Y4 but not P2Y2. Transcripts for both P2Y2 and P2Y4 were found in the stria vascularis. Sustained exposure to ATP or UTP for 15 min caused a depression of Isc that appeared to have two components but with apparently no chronic desensitization. Conclusion The results support the conclusion that regulation of K+ secretion across strial marginal cell epithelium occurs by P2Y4 receptors at the apical membrane. The apparent lack of desensitization of the response is consistent with two processes: a rapid-onset phosphorylation of KCNE1 channel subunit and a slower-onset of regulation by depletion of plasma membrane PIP2.

Resonance parallel viscosity in the banana regime in poloidally rotating tokamak plasmas

International Nuclear Information System (INIS)

Shaing, K.C.; Hsu, C.T.; Dominguez, N.

1994-01-01

Parallel viscosity in the banana regime in a poloidally (ExB) rotating tokamak plasma is calculated to include the effects of orbit squeezing and to allow the poloidal ExB Mach number M p to have a value of order unity. Here, E is the electric field and B is the magnetic field. The effects of orbit squeezing not only modify the size of the particle orbit, but also change the fraction of poloidally trapped particles. Resonance between the particle parallel (to B) speed u and the poloidal component of the ExB velocity can only occur for those particles with energy (v/v t ) 2 >M 2 p (with v the particle speed and v t the thermal speed). Thus, the resonance parallel plasma viscosity in the banana regime decreases exponentially with M 2 p when M 2 p ≥1, and has a local maximum of M 2 p ∼1

All-polymer organic semiconductor laser chips: Parallel fabrication and encapsulation

DEFF Research Database (Denmark)

Vannahme, Christoph; Klinkhammer, Sönke; Christiansen, Mads Brøkner

2010-01-01

Organic semiconductor lasers are of particular interest as tunable visible laser light sources. For bringing those to market encapsulation is needed to ensure practicable lifetimes. Additionally, fabrication technologies suitable for mass production must be used. We introduce all-polymer chips...... comprising encapsulated distributed feedback organic semiconductor lasers. Several chips are fabricated in parallel by thermal nanoimprint of the feedback grating on 4? wafer scale out of poly(methyl methacrylate) (PMMA) and cyclic olefin copolymer (COC). The lasers consisting of the organic semiconductor...... tris(8- hydroxyquinoline) aluminum (Alq3) doped with the laser dye 4-dicyanomethylene-2- methyl-6-(p-dimethylaminostyril)-4H-pyrane (DCM) are hermetically sealed by thermally bonding a polymer lid. The organic thin film is placed in a basin within the substrate and is not in direct contact to the lid...

The 4p-5d, 6d and 4p-6s, 7s transitions of Mo IX

International Nuclear Information System (INIS)

Khatoon, S.; Chaghtai, M.S.Z.; Rahimullah, K.

1979-01-01

The transitions 4p-5d, 6d and 4p-6s, 7s have been studied for the first time in Mo IX. The authors have identified 42 4p-5d, 36 4p-6d, 22 4p-6s and 22 4p-7s transitions, establishing 16 4p 3 5d, 14 4p 3 6d and all the ten 4p 3 6s, 7s levels of the spectrum concerned. The ionization energy is estimated to be (1 323 700 +- 700)cm -1 or (164.11 +- 0.09)eV. The spectrum was recorded in sliding and open spark discharges with a 5 m grazing incidence spectrograph of Lund University (Sweden) from about 40 A to 440 A. (Auth.)

Transcriptional Activation Domains of the Candida albicans Gcn4p and Gal4p Homologs▿ †

OpenAIRE

Martchenko, Mikhail; Levitin, Anastasia; Whiteway, Malcolm

2006-01-01

Many putative transcription factors in the pathogenic fungus Candida albicans contain sequence similarity to well-defined transcriptional regulators in the budding yeast Saccharomyces cerevisiae, but this sequence similarity is often limited to the DNA binding domains of the molecules. The Gcn4p and Gal4p proteins of Saccharomyces cerevisiae are highly studied and well-understood eukaryotic transcription factors of the basic leucine zipper (Gcn4p) and C6 zinc cluster (Gal4p) families; C. albi...

Paleointensity determinations during the Akaroa polarity reversal, New Zealand: New input from the multispecimen parallel differential pTRM method

Science.gov (United States)

Camps, P.; Fanjat, G.; Poidras, T.; Hoffman, K. A.; Carvallo, C.; kennedy, B.

2011-12-01

We resampled two polarity reversals of late Miocene age (~ 9 Ma) recorded successively in the Akaroa volcano (Hoffman, 1986, Nature). Our main objective was to check old paleointensity determinations (Sherwood & Shaw, 1986, J. Geomag. Geoelec.) that yielded stronger values during the transitional period than during stable periods that preceded and followed the reversals. This observation is opposite to what is generally observed. An increase in intensity during the reversal would provide an extreme example of increasing secular variation. However, the experimental method used for determining the paleointensity, method of Shaw, is strongly questioned by the scientific community. A check of these data by the conventional Thellier method was required. Unfortunately, among the 72 sampled flows, only 4 yielded rock magnetic properties well suited for Thellier determinations. In most of the flows, the presence of large Multi-Domain grains of Ti-magnetite, which are frequently associated with Ti-maghemite, precludes any Thellier paleointensity determinations. We implement the domain-state independent paleointensity method (the multispecimen parallel differential pTRM, Dekkers & Bohnel, 2006, EPSL; Fabian & Leonhardt, 2010, EPSL) for 16 lava flows in which the MD Ti-magnetite are not oxidized. Thellier paleointensities obtained do not confirm the Sherwood results but show more scattered values of the intensity even during the stable periods of the field. To complete the data, multispecimen mesearements are being to be done.

Alignment of Ar{sup +} [{sup 3}P]4p{sup 2}P{sup 0}{sub 3/2} satellite state from the polarization analysis of fluorescent radiation after photoionization

Energy Technology Data Exchange (ETDEWEB)

Yenen, O.; McLaughlin, K.W.; Jaecks, D.H. [Univ. of Nebraska, Lincoln, NE (United States)] [and others

1997-04-01

The measurement of the polarization of radiation from satellite states of Ar{sup +} formed after the photoionization of Ar provides detailed information about the nature of doubly excited states, magnetic sublevel cross sections and partial wave ratios of the photo-ejected electrons. Since the formation of these satellite states is a weak process, it is necessary to use a high flux beam of incoming photons. In addition, in order to resolve the many narrow doubly excited Ar resonances, the incoming photons must have a high resolution. The characteristics of the beam line 9.0.1 of the Advanced Light Source fulfill these requirements. The authors determined the polarization of 4765 {Angstrom} fluorescence from the Ar{sup +} [{sup 3}P] 4p {sup 2}P{sub 3/2}{sup 0} satellite state formed after photoionization of Ar by photons from the 9.0.1 beam line of ALS in the 35.620-38.261 eV energy range using a resolution of approximately 12,700. This is accomplished by measuring the intensities of the fluorescent light polarized parallel (I{parallel}) and perpendicular (I{perpendicular}) to the polarization axis of the incident synchrotron radiation using a Sterling Optics 105MB polarizing filter. The optical system placed at 90{degrees} with respect to the polarization axis of the incident light had a narrow band interference filter ({delta}{lambda}=0.3 nm) to isolate the fluorescent radiation.

ATP/P2X7 axis modulates myeloid-derived suppressor cell functions in neuroblastoma microenvironment.

Science.gov (United States)

Bianchi, G; Vuerich, M; Pellegatti, P; Marimpietri, D; Emionite, L; Marigo, I; Bronte, V; Di Virgilio, F; Pistoia, V; Raffaghello, L

2014-03-20

Tumor microenvironment of solid tumors is characterized by a strikingly high concentration of adenosine and ATP. Physiological significance of this biochemical feature is unknown, but it has been suggested that it may affect infiltrating immune cell responses and tumor progression. There is increasing awareness that many of the effects of extracellular ATP on tumor and inflammatory cells are mediated by the P2X7 receptor (P2X7R). Aim of this study was to investigate whether: (i) extracellular ATP is a component of neuroblastoma (NB) microenvironment, (ii) myeloid-derived suppressor cells (MDSCs) express functional P2X7R and (iii) the ATP/P2X7R axis modulates MDSC functions. Our results show that extracellular ATP was detected in NB microenvironment in amounts that increased in parallel with tumor progression. The percentage of CD11b(+)/Gr-1(+) cells was higher in NB-bearing mice compared with healthy animals. Within the CD11b/Gr-1(+) population, monocytic MDSCs (M-MDSCs) produced higher levels of reactive oxygen species (ROS), arginase-1 (ARG-1), transforming growth factor-β1 (TGF-β1) and stimulated more potently in vivo tumor growth, as compared with granulocytic MDSCs (G-MDSCs). P2X7R of M-MDSCs was localized at the plasma membrane, coupled to increased functionality, upregulation of ARG-1, TGF-β1 and ROS. Quite surprisingly, the P2X7R in primary MDSCs as well as in the MSC-1 and MSC-2 lines was uncoupled from cytotoxicity. This study describes a novel scenario in which MDSC immunosuppressive functions are modulated by the ATP-enriched tumor microenvironment.

La{sub 3}Cu{sub 4}P{sub 4}O{sub 2} and La{sub 5}Cu{sub 4}P{sub 4}O{sub 4}Cl{sub 2}. Synthesis, structure and {sup 31}P solid state NMR spectroscopy

Energy Technology Data Exchange (ETDEWEB)

Bartsch, Timo; Eul, Matthias; Poettgen, Rainer [Muenster Univ. (Germany). Inst. fuer Anorganische und Analytische Chemie; Benndorf, Christopher; Eckert, Hellmut [Muenster Univ. (Germany). Inst. fuer Physikalische Chemie; Sao Paulo Univ., Sao Carlos, SP (Brazil). Inst. of Physics

2016-04-01

The phosphide oxides La{sub 3}Cu{sub 4}P{sub 4}O{sub 2} and La{sub 5}Cu{sub 4}P{sub 4}O{sub 4}Cl{sub 2} were synthesized from lanthanum, copper(I) oxide, red phosphorus, and lanthanum(III) chloride through a ceramic technique. Single crystals can be grown in a NaCl/KCl flux. Both structures were refined from single crystal X-ray diffractometer data: I4/mmm, a = 403.89(4), c = 2681.7(3) pm, wR2 = 0.0660, 269 F{sup 2} values, 19 variables for La{sub 3}Cu{sub 4}P{sub 4}O{sub 2} and a = 407.52(5), c = 4056.8(7) pm, wR2 = 0.0905, 426 F{sup 2} values, 27 variables for La{sub 5}Cu{sub 4}P{sub 4}O{sub 4}Cl{sub 2}. Refinement of the occupancy parameters revealed full occupancy for the oxygen sites in both compounds. The structures are composed of cationic (La{sub 2}O{sub 2}){sup 2+} layers and covalently bonded (Cu{sub 4}P{sub 4}){sup 5-} polyanionic layers with metallic characteristics, and an additional La{sup 3+} between two adjacent (Cu{sub 4}P{sub 4}){sup 5-} layers. The structure of La{sub 5}Cu{sub 4}P{sub 4}O{sub 4}Cl{sub 2} comprises two additional LaOCl slabs per unit cell. Temperature-dependent magnetic susceptibility studies revealed Pauli paramagnetism. The phosphide substructure of La{sub 3}Cu{sub 4}P{sub 4}O{sub 2} was studied by {sup 31}P solid state NMR spectroscopy. By using a suitable dipolar re-coupling approach the two distinct resonances belonging to the P{sub 2}{sup 4-} and the P{sup 3-} units could be identified.

Expression of the p16{sup INK4a} tumor suppressor gene in rodent lung tumors

Energy Technology Data Exchange (ETDEWEB)

Swafford, D.S.; Tesfaigzi, J.; Belinsky, S.A.

1995-12-01

Aberrations on the short arm of chromosome 9 are among the earliest genetic changes in human cancer. p16{sup INK4a} is a candidate tumor suppressor gene that lies within human 9p21, a chromosome region associated with frequent loss of heterozygosity in human lung tumors. The p16{sup INK4a} protein functions as an inhibitor of cyclin D{sub 1}-dependent kinases that phosphorylate the retinoblastoma (Rb) tumor suppressor gene product enabling cell-cycle progression. Thus, overexpression of cyclin D{sub 1}, mutation of cyclin-dependent kinase genes, or loss of p16{sup INK4a} function, can all result in functional inactivation of Rb. Inactivation of Rb by mutation or deletion can result in an increase in p16{sup INK4a} transcription, suggesting that an increased p16{sup INK4a} expression in a tumor cell signals dysfunction of the pathway. The p16{sup (INK4a)} gene, unlike some tumor suppressor genes, is rarely inactivated by mutation. Instead, the expression of this gene is suppressed in some human cancers by hypermethylation of the CpG island within the first exon or by homozygous deletion: 686. Chromosome losses have been observed at 9p21 syntenic loci in tumors of the mouse and rat, two species often used as animal models for pulmonary carcinogenesis. Expression of p16{sup INK4a} is lost in some mouse tumor cell lines, often due to homozygous deletion. These observations indicate that p16{sup INK4a} dysfunction may play a role in the development of neoplasia in rodents as well as humans. The purpose of the current investigation was to define the extent to which p16{sup INK4a} dysfunction contributes to the development of rodent lung tumors and to determine the mechanism of inactivation of the gene. There is no evidence to suggest a loss of function of the p16{sup INK4a} tumor suppressor gene in these primary murine lung tumors by mutation, deletion, or methylation.

Significance of lymphadenectomy with splenectomy in radical surgery for advanced (pT3/pT4) remnant gastric cancer.

Science.gov (United States)

Sugita, Hiroki; Oda, Eri; Hirota, Masahiko; Ishikawa, Shinji; Tomiyasu, Shinjiro; Tanaka, Hiroshi; Arita, Tetsumasa; Yagi, Yasushi; Baba, Hideo

2016-04-01

To date, the optimal surgical strategy for remnant gastric cancer has not been determined. The purpose of this study was to clarify the significance of lymphadenectomy with splenectomy in remnant gastric cancer surgery. This retrospective cohort study was conducted at the Kumamoto Regional Medical Center. The primary endpoint was overall survival after surgery. We retrospectively analyzed the clinicopathologic features, surgical treatments, and long-term prognosis of remnant gastric cancer patients treated with total gastrectomy. A total of 80 patients with gastric cancer in the remnant stomach after distal gastrectomy and who underwent total gastrectomy were enrolled in the study. Splenectomy was performed in 38 patients. Lymph node metastasis in the splenic hilum was not observed in the patients with pT1/pT2 tumors, whereas nodal metastasis at the splenic hilum was detected in 30.4% of the patients with pT3/pT4 tumors. The survival rate of the patients with pT3/pT4 tumors who underwent splenectomy was significantly higher than that of the patients who did not undergo splenectomy, although there was no difference in the patients with pT1/pT2 tumors. Among the patients classified as R0, the survival rate of the patients with pT3/pT4 tumors who underwent splenectomy was significantly higher than that of the patients who did not undergo splenectomy. Lymphadenectomy with splenectomy in radical surgery is beneficial for patients with advanced (pT3/pT4) remnant gastric cancer. Copyright © 2016 Elsevier Inc. All rights reserved.

Parallel computing solution of Boltzmann neutron transport equation

International Nuclear Information System (INIS)

Ansah-Narh, T.

2010-01-01

The focus of the research was on developing parallel computing algorithm for solving Eigen-values of the Boltzmam Neutron Transport Equation (BNTE) in a slab geometry using multi-grid approach. In response to the problem of slow execution of serial computing when solving large problems, such as BNTE, the study was focused on the design of parallel computing systems which was an evolution of serial computing that used multiple processing elements simultaneously to solve complex physical and mathematical problems. Finite element method (FEM) was used for the spatial discretization scheme, while angular discretization was accomplished by expanding the angular dependence in terms of Legendre polynomials. The eigenvalues representing the multiplication factors in the BNTE were determined by the power method. MATLAB Compiler Version 4.1 (R2009a) was used to compile the MATLAB codes of BNTE. The implemented parallel algorithms were enabled with matlabpool, a Parallel Computing Toolbox function. The option UseParallel was set to 'always' and the default value of the option was 'never'. When those conditions held, the solvers computed estimated gradients in parallel. The parallel computing system was used to handle all the bottlenecks in the matrix generated from the finite element scheme and each domain of the power method generated. The parallel algorithm was implemented on a Symmetric Multi Processor (SMP) cluster machine, which had Intel 32 bit quad-core x 86 processors. Convergence rates and timings for the algorithm on the SMP cluster machine were obtained. Numerical experiments indicated the designed parallel algorithm could reach perfect speedup and had good stability and scalability. (au)

Functional characterization of a cadmium resistance operon in Staphylococcus aureus ATCC12600: CadC does not function as a repressor.

Science.gov (United States)

Hoogewerf, Arlene J; Dyk, Lisa A Van; Buit, Tyler S; Roukema, David; Resseguie, Emily; Plaisier, Christina; Le, Nga; Heeringa, Lee; Griend, Douglas A Vander

2015-02-01

Sequencing of a cadmium resistance operon from a Staphylococcus aureus ATCC12600 plasmid revealed that it is identical to a cadCA operon found in MRSA strains. Compared to plasmid-cured and cadC-mutant strains, cadC-positive ATCC12600 cells had increased resistance to cadmium (1 mg ml(-1) cadmium sulfate) and zinc (4 mg ml(-1) zinc sulfate), but not to other metal ions. After growth in media containing 20 µg ml(-1) cadmium sulfate, cadC-mutant cells contained more intracellular cadmium than cadC-positive ATCC12600 cells, suggesting that cadC absence results in impaired cadmium efflux. Electrophoretic mobility shift assays were performed with CadC proteins encoded by the S. aureus ATCC12600 plasmid and by the cadC gene of pI258, which is known to act as a transcriptional repressor and shares only 47% protein sequence identity with ATCC12600 CadC. Mobility shifts occurred when pI258 CadC protein was incubated with the promoter DNA-regions from the pI258 and S. aureus ATCC12600 cadCA operons, but did not occur with S. aureus ATCC12600 CadC protein, indicating that the ATCC12600 CadC protein does not interact with promoter region DNA. This cadCA operon, found in MRSA strains and previously functionally uncharacterized, increases resistance to cadmium and zinc by an efflux mechanism, and CadC does not function as a transcriptional repressor. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Velocity auto-correlation and hot-electron diffusion constant in GaAs and InP

International Nuclear Information System (INIS)

Deb Roy, M.

1982-01-01

Auto-correlation functions of the fluctuations in the electron velocities transverse and parallel to the applied electric field are calculated by the Monte Carlo method for GaAs and InP at three different values of field strength which are around three times the threshold field for negative differential mobility in each case. From these the frequency-dependent diffusion coefficients transverse and parallel to the applied field and the figure of merit for noise performance when used in a microwave amplifying device are determined. The results indicate that the transverse auto-correlation function Csub(t)(s) falls nearly exponentially to zero with increasing interval s while the parallel function Csub(p)(s) falls sharply, attains a minimum and then rises towards zero. In each case a higher field gives a higher rate of fall and makes the correlation functions zero within a shorter interval. The transverses diffusion coefficient falls monotonically with the frequency but the parallel diffusion coefficient generally starts with a low value at low frequencies, rises to a maximum and then falls. InP, with a larger separation between the central and the satellite valleys, has a higher value of the low frequency transverse diffusion coefficient and a lower value of its parallel counterpart. The noise performance of microwave semiconductor amplifying devices depends mainly on the low frequency parallel diffusion constant and consequently devices made out of materials like InP with a large separation between valleys are likely to have better noise characteristics. (orig.)

Application of Parallel Hierarchical Matrices in Spatial Statistics and Parameter Identification

KAUST Repository

Litvinenko, Alexander

2018-04-20

Parallel H-matrices in spatial statistics 1. Motivation: improve statistical model 2. Tools: Hierarchical matrices [Hackbusch 1999] 3. Matern covariance function and joint Gaussian likelihood 4. Identification of unknown parameters via maximizing Gaussian log-likelihood 5. Implementation with HLIBPro

Prenatal Diagnosis of 4p and 4q Subtelomeric Microdeletion in De Novo Ring Chromosome 4

Directory of Open Access Journals (Sweden)

Halit Akbas

2013-01-01

Full Text Available Ring chromosomes are unusual abnormalities that are observed in prenatal diagnosis. A 23-year-old patient (gravida 1, para 0 referred for amniocentesis due to abnormal maternal serum screening result in the 16th week of second pregnancy. Cytogenetic analysis of cultured amniyotic fluid cells revealed out ring chromosome 4. Both maternal and paternal karyotypes were normal. Terminal deletion was observed in both 4p and 4q arms of ring chromosome 4 by fluorescence in situ hybridization (FISH. However deletion was not observed in the WHS critical region of both normal and ring chromosome 4 by an additional FISH study. These results were confirmed by means of array-CGH showing terminal deletions on 4p16.3 (130 kb and 4q35.2 (2.449 Mb. In the 21th week of pregnancy, no gross anomalia, except two weeks symmetric growth retardation, was present in the fetal ultrasonographic examination. According to our review of literature, this is the first prenatal case with 4p and 4q subtelomeric deletion of ring chromosome 4 without the involvement of WHS critical region. Our report describes the prenatal case with a ring chromosome 4 abnormality completely characterized by array-CGH which provided complementary data for genetic counseling of prenatal diagnosis.

Prenatal diagnosis of 4p and 4q subtelomeric microdeletion in de novo ring chromosome 4.

Science.gov (United States)

Akbas, Halit; Cine, Naci; Erdemoglu, Mahmut; Atay, Ahmet Engin; Simsek, Selda; Turkyilmaz, Aysegul; Fidanboy, Mehmet

2013-01-01

Ring chromosomes are unusual abnormalities that are observed in prenatal diagnosis. A 23-year-old patient (gravida 1, para 0) referred for amniocentesis due to abnormal maternal serum screening result in the 16th week of second pregnancy. Cytogenetic analysis of cultured amniyotic fluid cells revealed out ring chromosome 4. Both maternal and paternal karyotypes were normal. Terminal deletion was observed in both 4p and 4q arms of ring chromosome 4 by fluorescence in situ hybridization (FISH). However deletion was not observed in the WHS critical region of both normal and ring chromosome 4 by an additional FISH study. These results were confirmed by means of array-CGH showing terminal deletions on 4p16.3 (130 kb) and 4q35.2 (2.449 Mb). In the 21th week of pregnancy, no gross anomalia, except two weeks symmetric growth retardation, was present in the fetal ultrasonographic examination. According to our review of literature, this is the first prenatal case with 4p and 4q subtelomeric deletion of ring chromosome 4 without the involvement of WHS critical region. Our report describes the prenatal case with a ring chromosome 4 abnormality completely characterized by array-CGH which provided complementary data for genetic counseling of prenatal diagnosis.

Acute Malaria Induces PD1+CTLA4+ Effector T Cells with Cell-Extrinsic Suppressor Function.

Directory of Open Access Journals (Sweden)

Maria Sophia Mackroth

2016-11-01

Full Text Available In acute Plasmodium falciparum (P. falciparum malaria, the pro- and anti-inflammatory immune pathways must be delicately balanced so that the parasitemia is controlled without inducing immunopathology. An important mechanism to fine-tune T cell responses in the periphery is the induction of coinhibitory receptors such as CTLA4 and PD1. However, their role in acute infections such as P. falciparum malaria remains poorly understood. To test whether coinhibitory receptors modulate CD4+ T cell functions in malaria, blood samples were obtained from patients with acute P. falciparum malaria treated in Germany. Flow cytometric analysis showed a more frequent expression of CTLA4 and PD1 on CD4+ T cells of malaria patients than of healthy control subjects. In vitro stimulation with P. falciparum-infected red blood cells revealed a distinct population of PD1+CTLA4+CD4+ T cells that simultaneously produced IFNγ and IL10. This antigen-specific cytokine production was enhanced by blocking PD1/PDL1 and CTLA4. PD1+CTLA4+CD4+ T cells were further isolated based on surface expression of PD1 and their inhibitory function investigated in-vitro. Isolated PD1+CTLA4+CD4+ T cells suppressed the proliferation of the total CD4+ population in response to anti-CD3/28 and plasmodial antigens in a cell-extrinsic manner. The response to other specific antigens was not suppressed. Thus, acute P. falciparum malaria induces P. falciparum-specific PD1+CTLA4+CD4+ Teffector cells that coproduce IFNγ and IL10, and inhibit other CD4+ T cells. Transient induction of regulatory Teffector cells may be an important mechanism that controls T cell responses and might prevent severe inflammation in patients with malaria and potentially other acute infections.

Trisomy 12p and monosomy 4p: phenotype-genotype correlation.

Science.gov (United States)

Benussi, Daniela Gambel; Costa, Paola; Zollino, Marcella; Murdolo, Marina; Petix, Vincenzo; Carrozzi, Marco; Pecile, Vanna

2009-04-01

4p Monosomy and 12p trisomy have been discussed and redefined along with recently reviewed chromosomal syndromes. 12p Trisomy syndrome is characterized by normal or increased birth weight, developmental delay with early hypotonia, psychomotor delay, and typical facial appearance. Most likely, the observed phenotypic variability depends on the type and extent of the associated partial monosomy. Partial deletions of the short arm of one chromosome 4 cause the Wolf-Hirschhorn syndrome (WHS). Affected patients present Greek helmet face, growth and mental retardation, hypotonia, and seizures. The combination of these characteristics constitutes the phenotypic core of WHS. We present a clinical and molecular cytogenetic characterization of a 4-year old mentally retarded girl with macrosomy, facial dysmorphisms, and epilepsy, in whom an unbalanced t(4;12)(p16.3;p13.3) translocation was detected, giving rise to partial 4p monosomy and partial 12p trisomy. Because the patient shows most of the phenotypic characteristics of 12p trisomy, this case could contribute to a better definition of the duplicate critical region that determines the phenotype of the 12p trisomy syndrome.

Real-time SHVC software decoding with multi-threaded parallel processing