A parallel time integrator for noisy nonlinear oscillatory systems

NASA Astrophysics Data System (ADS)

Subber, Waad; Sarkar, Abhijit

2018-06-01

In this paper, we adapt a parallel time integration scheme to track the trajectories of noisy non-linear dynamical systems. Specifically, we formulate a parallel algorithm to generate the sample path of nonlinear oscillator defined by stochastic differential equations (SDEs) using the so-called parareal method for ordinary differential equations (ODEs). The presence of Wiener process in SDEs causes difficulties in the direct application of any numerical integration techniques of ODEs including the parareal algorithm. The parallel implementation of the algorithm involves two SDEs solvers, namely a fine-level scheme to integrate the system in parallel and a coarse-level scheme to generate and correct the required initial conditions to start the fine-level integrators. For the numerical illustration, a randomly excited Duffing oscillator is investigated in order to study the performance of the stochastic parallel algorithm with respect to a range of system parameters. The distributed implementation of the algorithm exploits Massage Passing Interface (MPI).

Variable Swing Optimal Parallel Links - Minimal Power, Maximal Density for Parallel Links

DTIC Science & Technology

2009-01-01

implemented; it allows controlling the transmitter current by a simple design of a differential pair with a 100 ohms termination resistor. Figure 3.4...optimization. Zuber, P., et al. 2005. 0-7695-2288-2. 21. A 36Gb/s ACCI Multi-Channel Bus using a Fully Differential Pulse Receiver. Wilson, Lei Luo

A parallel algorithm for the two-dimensional time fractional diffusion equation with implicit difference method.

PubMed

Gong, Chunye; Bao, Weimin; Tang, Guojian; Jiang, Yuewen; Liu, Jie

2014-01-01

It is very time consuming to solve fractional differential equations. The computational complexity of two-dimensional fractional differential equation (2D-TFDE) with iterative implicit finite difference method is O(M(x)M(y)N(2)). In this paper, we present a parallel algorithm for 2D-TFDE and give an in-depth discussion about this algorithm. A task distribution model and data layout with virtual boundary are designed for this parallel algorithm. The experimental results show that the parallel algorithm compares well with the exact solution. The parallel algorithm on single Intel Xeon X5540 CPU runs 3.16-4.17 times faster than the serial algorithm on single CPU core. The parallel efficiency of 81 processes is up to 88.24% compared with 9 processes on a distributed memory cluster system. We do think that the parallel computing technology will become a very basic method for the computational intensive fractional applications in the near future.

Does Reimportation Reduce Price Differences for Prescription Drugs? Lessons from the European Union

PubMed Central

Kyle, Margaret K; Allsbrook, Jennifer S; Schulman, Kevin A

2008-01-01

Objective To examine the effect of parallel trade on patterns of price dispersion for prescription drugs in the European Union. Data Sources Longitudinal data from an IMS Midas database of prices and units sold for drugs in 36 categories in 30 countries from 1993 through 2004. Study Design The main outcome measures were mean price differentials and other measures of price dispersion within European Union countries compared with within non-European Union countries. Data Collection/Extraction Methods We identified drugs subject to parallel trade using information provided by IMS and by checking membership lists of parallel import trade associations and lists of approved parallel imports. Principal Findings Parallel trade was not associated with substantial reductions in price dispersion in European Union countries. In descriptive and regression analyses, about half of the price differentials exceeded 50 percent in both European Union and non-European Union countries over time, and price distributions among European Union countries did not show a dramatic change concurrent with the adoption of parallel trade. In regression analysis, we found that although price differentials decreased after 1995 in most countries, they decreased less in the European Union than elsewhere. Conclusions Parallel trade for prescription drugs does not automatically reduce international price differences. Future research should explore how other regulatory schemes might lead to different results elsewhere. PMID:18355258

Solving Partial Differential Equations in a data-driven multiprocessor environment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gaudiot, J.L.; Lin, C.M.; Hosseiniyar, M.

1988-12-31

Partial differential equations can be found in a host of engineering and scientific problems. The emergence of new parallel architectures has spurred research in the definition of parallel PDE solvers. Concurrently, highly programmable systems such as data-how architectures have been proposed for the exploitation of large scale parallelism. The implementation of some Partial Differential Equation solvers (such as the Jacobi method) on a tagged token data-flow graph is demonstrated here. Asynchronous methods (chaotic relaxation) are studied and new scheduling approaches (the Token No-Labeling scheme) are introduced in order to support the implementation of the asychronous methods in a data-driven environment.more » New high-level data-flow language program constructs are introduced in order to handle chaotic operations. Finally, the performance of the program graphs is demonstrated by a deterministic simulation of a message passing data-flow multiprocessor. An analysis of the overhead in the data-flow graphs is undertaken to demonstrate the limits of parallel operations in dataflow PDE program graphs.« less

Parallel Gene Expression Differences between Low and High Latitude Populations of Drosophila melanogaster and D. simulans

PubMed Central

Zhao, Li; Wit, Janneke; Svetec, Nicolas; Begun, David J.

2015-01-01

Gene expression variation within species is relatively common, however, the role of natural selection in the maintenance of this variation is poorly understood. Here we investigate low and high latitude populations of Drosophila melanogaster and its sister species, D. simulans, to determine whether the two species show similar patterns of population differentiation, consistent with a role for spatially varying selection in maintaining gene expression variation. We compared at two temperatures the whole male transcriptome of D. melanogaster and D. simulans sampled from Panama City (Panama) and Maine (USA). We observed a significant excess of genes exhibiting differential expression in both species, consistent with parallel adaptation to heterogeneous environments. Moreover, the majority of genes showing parallel expression differentiation showed the same direction of differential expression in the two species and the magnitudes of expression differences between high and low latitude populations were correlated across species, further bolstering the conclusion that parallelism for expression phenotypes results from spatially varying selection. However, the species also exhibited important differences in expression phenotypes. For example, the genomic extent of genotype × environment interaction was much more common in D. melanogaster. Highly differentiated SNPs between low and high latitudes were enriched in the 3’ UTRs and CDS of the geographically differently expressed genes in both species, consistent with an important role for cis-acting variants in driving local adaptation for expression-related phenotypes. PMID:25950438

Parallel Gene Expression Differences between Low and High Latitude Populations of Drosophila melanogaster and D. simulans.

PubMed

Zhao, Li; Wit, Janneke; Svetec, Nicolas; Begun, David J

2015-05-01

Gene expression variation within species is relatively common, however, the role of natural selection in the maintenance of this variation is poorly understood. Here we investigate low and high latitude populations of Drosophila melanogaster and its sister species, D. simulans, to determine whether the two species show similar patterns of population differentiation, consistent with a role for spatially varying selection in maintaining gene expression variation. We compared at two temperatures the whole male transcriptome of D. melanogaster and D. simulans sampled from Panama City (Panama) and Maine (USA). We observed a significant excess of genes exhibiting differential expression in both species, consistent with parallel adaptation to heterogeneous environments. Moreover, the majority of genes showing parallel expression differentiation showed the same direction of differential expression in the two species and the magnitudes of expression differences between high and low latitude populations were correlated across species, further bolstering the conclusion that parallelism for expression phenotypes results from spatially varying selection. However, the species also exhibited important differences in expression phenotypes. For example, the genomic extent of genotype × environment interaction was much more common in D. melanogaster. Highly differentiated SNPs between low and high latitudes were enriched in the 3' UTRs and CDS of the geographically differently expressed genes in both species, consistent with an important role for cis-acting variants in driving local adaptation for expression-related phenotypes.

Complexity of parallel implementation of domain decomposition techniques for elliptic partial differential equations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gropp, W.D.; Keyes, D.E.

1988-03-01

The authors discuss the parallel implementation of preconditioned conjugate gradient (PCG)-based domain decomposition techniques for self-adjoint elliptic partial differential equations in two dimensions on several architectures. The complexity of these methods is described on a variety of message-passing parallel computers as a function of the size of the problem, number of processors and relative communication speeds of the processors. They show that communication startups are very important, and that even the small amount of global communication in these methods can significantly reduce the performance of many message-passing architectures.

Magnetic Properties and Absolute Paleointensity of Upper Oceanic Crust Generated by Superfast Seafloor Spreading, ODP Leg 209.

NASA Astrophysics Data System (ADS)

Herrero-Bervera, E.; Acton, G.

2005-12-01

We investigate the magnetic mineralogy and absolute paleointensity of oceanic basalt samples from Hole 1256D, cored during Ocean Drilling Program (ODP) Leg 206. Hole 1256D is located on the Cocos Plate about 5 km east of the transition zone between marine magnetic anomalies 5Bn.2n and 5Br (~15 Ma). During Leg 206, the hole penetrated 502 m into basalts of the upper oceanic crust that was generated by superfast seafloor spreading (>200 mm/yr) along the East Pacific Rise. Rock magnetic investigations included continuous low field (k-T) thermomagnetic analyses, alternating field (AF) and thermal demagnetization, optical microscopy, saturation isothermal remanent magnetization (SIRM), and magnetic grain size analyses. Following the removal of a drilling overprint, AF and thermal demagnetization paths for most samples decay linearly to the origin on orthogonal vector end point diagrams, suggesting that a stable characteristic remanent magnetization component can be resolved. Optical microscopy and k-T (Curie points) identified titanomagnetites and titanomaghemites as the main magnetic carriers and grain size studies indicate that the carriers are either single domain (SD) and/or pseudosingle domain (PSD) in nature. Using the modified Thellier-Coe double heating method, we determined absolute paleointensity determinations for 51 specimens sampled from different ``stratigraphic'' levels of the core. pTRM checks were performed systematically one temperature step down the last pTRM acquisition in order to document magnetomineralogical changes during heating. The temperature was incremented by steps of 50°C between room temperature and 500°C and every 25-30°C for higher temperatures. The paleointensity determinations were obtained from the slope of the Arai diagrams. Special care was taken to interpret the Arai diagrams within the same range of temperatures lower than 300°C unless a clear and unique slope was present over a higher range of temperatures. Only about 10 percent of the samples yielded acceptable results. The paleofield estimated from these samples ranges between 28 to 16 micro Teslas (i.e., VADM of 6 to 4 x 1022 A/m2), which is concordant with the average paleofield intensity for the period between 0-160 Myr (4 ± 2 x1022 A/m2) and half of the strength of the present field (~8x1022 A/m2).

Cognate effects and cognitive control in patients with parallel and differential bilingual aphasia.

PubMed

Van der Linden, Lize; Verreyt, Nele; De Letter, Miet; Hemelsoet, Dimitri; Mariën, Peter; Santens, Patrick; Stevens, Michaël; Szmalec, Arnaud; Duyck, Wouter

2018-05-01

Until today, there is no satisfying explanation for why one language may recover worse than another in differential bilingual aphasia. One potential explanation that has been largely unexplored is that differential aphasia is the consequence of a loss of language control rather than a loss of linguistic representations. Language control is part of a general control mechanism that also manages non-linguistic cognitive control. If this system is impaired, patients with differential aphasia could still show bilingual language activation, but they may be unable to manage activation in non-target languages, so that performance in another language is hindered. To investigate whether a loss of cognitive control, rather than the loss of word representations in a particular language, might underlie differential aphasia symptoms. We compared the performance of seven bilinguals with differential and eight bilinguals with parallel aphasia with 19 control bilinguals in a lexical decision and a flanker task to assess bilingual language co-activation and non-linguistic control respectively. We found similar cognate effects in the three groups, indicating similar lexical processing across groups. Additionally, we found a larger non-linguistic control congruency effect only for the patients with differential aphasia. The present data indicate preserved language co-activation for patients with parallel as well as differential aphasia. Furthermore, the results suggest a general cognitive control dysfunction, specifically for differential aphasia. Taken together, the results of the current study provide further support for the hypothesis of impaired cognitive control abilities in patients with differential aphasia, which has both theoretical and practical implications. © 2018 Royal College of Speech and Language Therapists.

Parallel architectures for iterative methods on adaptive, block structured grids

NASA Technical Reports Server (NTRS)

Gannon, D.; Vanrosendale, J.

1983-01-01

A parallel computer architecture well suited to the solution of partial differential equations in complicated geometries is proposed. Algorithms for partial differential equations contain a great deal of parallelism. But this parallelism can be difficult to exploit, particularly on complex problems. One approach to extraction of this parallelism is the use of special purpose architectures tuned to a given problem class. The architecture proposed here is tuned to boundary value problems on complex domains. An adaptive elliptic algorithm which maps effectively onto the proposed architecture is considered in detail. Two levels of parallelism are exploited by the proposed architecture. First, by making use of the freedom one has in grid generation, one can construct grids which are locally regular, permitting a one to one mapping of grids to systolic style processor arrays, at least over small regions. All local parallelism can be extracted by this approach. Second, though there may be a regular global structure to the grids constructed, there will be parallelism at this level. One approach to finding and exploiting this parallelism is to use an architecture having a number of processor clusters connected by a switching network. The use of such a network creates a highly flexible architecture which automatically configures to the problem being solved.

Phylogeographic differentiation versus transcriptomic adaptation to warm temperatures in Zostera marina, a globally important seagrass.

PubMed

Jueterbock, A; Franssen, S U; Bergmann, N; Gu, J; Coyer, J A; Reusch, T B H; Bornberg-Bauer, E; Olsen, J L

2016-11-01

Populations distributed across a broad thermal cline are instrumental in addressing adaptation to increasing temperatures under global warming. Using a space-for-time substitution design, we tested for parallel adaptation to warm temperatures along two independent thermal clines in Zostera marina, the most widely distributed seagrass in the temperate Northern Hemisphere. A North-South pair of populations was sampled along the European and North American coasts and exposed to a simulated heatwave in a common-garden mesocosm. Transcriptomic responses under control, heat stress and recovery were recorded in 99 RNAseq libraries with ~13 000 uniquely annotated, expressed genes. We corrected for phylogenetic differentiation among populations to discriminate neutral from adaptive differentiation. The two southern populations recovered faster from heat stress and showed parallel transcriptomic differentiation, as compared with northern populations. Among 2389 differentially expressed genes, 21 exceeded neutral expectations and were likely involved in parallel adaptation to warm temperatures. However, the strongest differentiation following phylogenetic correction was between the three Atlantic populations and the Mediterranean population with 128 of 4711 differentially expressed genes exceeding neutral expectations. Although adaptation to warm temperatures is expected to reduce sensitivity to heatwaves, the continued resistance of seagrass to further anthropogenic stresses may be impaired by heat-induced downregulation of genes related to photosynthesis, pathogen defence and stress tolerance. © 2016 John Wiley & Sons Ltd.

Iterative algorithms for large sparse linear systems on parallel computers

NASA Technical Reports Server (NTRS)

Adams, L. M.

1982-01-01

Algorithms for assembling in parallel the sparse system of linear equations that result from finite difference or finite element discretizations of elliptic partial differential equations, such as those that arise in structural engineering are developed. Parallel linear stationary iterative algorithms and parallel preconditioned conjugate gradient algorithms are developed for solving these systems. In addition, a model for comparing parallel algorithms on array architectures is developed and results of this model for the algorithms are given.

Automatic differentiation for design sensitivity analysis of structural systems using multiple processors

NASA Technical Reports Server (NTRS)

Nguyen, Duc T.; Storaasli, Olaf O.; Qin, Jiangning; Qamar, Ramzi

1994-01-01

An automatic differentiation tool (ADIFOR) is incorporated into a finite element based structural analysis program for shape and non-shape design sensitivity analysis of structural systems. The entire analysis and sensitivity procedures are parallelized and vectorized for high performance computation. Small scale examples to verify the accuracy of the proposed program and a medium scale example to demonstrate the parallel vector performance on multiple CRAY C90 processors are included.

Efficient Implementation of Multigrid Solvers on Message-Passing Parrallel Systems

NASA Technical Reports Server (NTRS)

Lou, John

1994-01-01

We discuss our implementation strategies for finite difference multigrid partial differential equation (PDE) solvers on message-passing systems. Our target parallel architecture is Intel parallel computers: the Delta and Paragon system.

Parallel Geographic Variation in Drosophila melanogaster

PubMed Central

Reinhardt, Josie A.; Kolaczkowski, Bryan; Jones, Corbin D.; Begun, David J.; Kern, Andrew D.

2014-01-01

Drosophila melanogaster, an ancestrally African species, has recently spread throughout the world, associated with human activity. The species has served as the focus of many studies investigating local adaptation relating to latitudinal variation in non-African populations, especially those from the United States and Australia. These studies have documented the existence of shared, genetically determined phenotypic clines for several life history and morphological traits. However, there are no studies designed to formally address the degree of shared latitudinal differentiation at the genomic level. Here we present our comparative analysis of such differentiation. Not surprisingly, we find evidence of substantial, shared selection responses on the two continents, probably resulting from selection on standing ancestral variation. The polymorphic inversion In(3R)P has an important effect on this pattern, but considerable parallelism is also observed across the genome in regions not associated with inversion polymorphism. Interestingly, parallel latitudinal differentiation is observed even for variants that are not particularly strongly differentiated, which suggests that very large numbers of polymorphisms are targets of spatially varying selection in this species. PMID:24610860

Differential Draining of Parallel-Fed Propellant Tanks in Morpheus and Apollo Flight

NASA Technical Reports Server (NTRS)

Hurlbert, Eric; Guardado, Hector; Hernandez, Humberto; Desai, Pooja

2015-01-01

Parallel-fed propellant tanks are an advantageous configuration for many spacecraft. Parallel-fed tanks allow the center of gravity (cg) to be maintained over the engine(s), as opposed to serial-fed propellant tanks which result in a cg shift as propellants are drained from tank one tank first opposite another. Parallel-fed tanks also allow for tank isolation if that is needed. Parallel tanks and feed systems have been used in several past vehicles including the Apollo Lunar Module. The design of the feedsystem connecting the parallel tank is critical to maintain balance in the propellant tanks. The design must account for and minimize the effect of manufacturing variations that could cause delta-p or mass flowrate differences, which would lead to propellant imbalance. Other sources of differential draining will be discussed. Fortunately, physics provides some self-correcting behaviors that tend to equalize any initial imbalance. The question concerning whether or not active control of propellant in each tank is required or can be avoided or not is also important to answer. In order to provide data on parallel-fed tanks and differential draining in flight for cryogenic propellants (as well as any other fluid), a vertical test bed (flying lander) for terrestrial use was employed. The Morpheus vertical test bed is a parallel-fed propellant tank system that uses passive design to keep the propellant tanks balanced. The system is operated in blow down. The Morpheus vehicle was instrumented with a capacitance level sensor in each propellant tank in order to measure the draining of propellants in over 34 tethered and 12 free flights. Morpheus did experience an approximately 20 lb/m imbalance in one pair of tanks. The cause of this imbalance will be discussed. This paper discusses the analysis, design, flight simulation vehicle dynamic modeling, and flight test of the Morpheus parallel-fed propellant. The Apollo LEM data is also examined in this summary report of the flight data.

Parallel Evolution of Copy-Number Variation across Continents in Drosophila melanogaster

PubMed Central

Schrider, Daniel R.; Hahn, Matthew W.; Begun, David J.

2016-01-01

Genetic differentiation across populations that is maintained in the presence of gene flow is a hallmark of spatially varying selection. In Drosophila melanogaster, the latitudinal clines across the eastern coasts of Australia and North America appear to be examples of this type of selection, with recent studies showing that a substantial portion of the D. melanogaster genome exhibits allele frequency differentiation with respect to latitude on both continents. As of yet there has been no genome-wide examination of differentiated copy-number variants (CNVs) in these geographic regions, despite their potential importance for phenotypic variation in Drosophila and other taxa. Here, we present an analysis of geographic variation in CNVs in D. melanogaster. We also present the first genomic analysis of geographic variation for copy-number variation in the sister species, D. simulans, in order to investigate patterns of parallel evolution in these close relatives. In D. melanogaster we find hundreds of CNVs, many of which show parallel patterns of geographic variation on both continents, lending support to the idea that they are influenced by spatially varying selection. These findings support the idea that polymorphic CNVs contribute to local adaptation in D. melanogaster. In contrast, we find very few CNVs in D. simulans that are geographically differentiated in parallel on both continents, consistent with earlier work suggesting that clinal patterns are weaker in this species. PMID:26809315

Oligopeptides of Chorionic Gonadotropin β-Subunit in Induction of T Cell Differentiation into Treg and Th17.

PubMed

Zamorina, S A; Shirshev, S V

2015-11-01

The role of oligopeptides of chorionic gonadotropin β-subunit (LQGV, AQGV, and VLPALP) in induction of differentiation into T-regulatory lymphocytes (Treg) and IL-17-producing lymphocytes (Th17) was studied in an in vitro system. Chorionic gonadotropin and oligopeptides promoted CD4(+) cell differentiation into functionally active Treg (FOXP3(+)GITR(+) and FOXP3(+)CTLA-4(+)), while chorionic gonadotropin and AQGV additionally stimulated IL-10 production by these cells. In parallel, chorionic gonadotropin and oligopeptides prevented CD4(+) cell differentiation into Th17 lymphocytes (ROR-gt(+)IL-17A(+)) and suppressed IL-17A secretion. Hence, oligopeptides of chorionic gonadotropin β-subunit promoted differentiation of CD4(+) cells into Treg and, in parallel, suppress Th17 induction, thus virtually completely reproducing the effects of the hormone, which opens new vista for their use in clinical practice.

DIFFERENTIAL FAULT SENSING CIRCUIT

DOEpatents

Roberts, J.H.

1961-09-01

A differential fault sensing circuit is designed for detecting arcing in high-voltage vacuum tubes arranged in parallel. A circuit is provided which senses differences in voltages appearing between corresponding elements likely to fault. Sensitivity of the circuit is adjusted to some level above which arcing will cause detectable differences in voltage. For particular corresponding elements, a group of pulse transformers are connected in parallel with diodes connected across the secondaries thereof so that only voltage excursions are transmitted to a thyratron which is biased to the sensitivity level mentioned.

Parallel Acquisition of Awareness and Differential Delay Eyeblink Conditioning

ERIC Educational Resources Information Center

Weidemann, Gabrielle; Antees, Cassandra

2012-01-01

There is considerable debate about whether differential delay eyeblink conditioning can be acquired without awareness of the stimulus contingencies. Previous investigations of the relationship between differential-delay eyeblink conditioning and awareness of the stimulus contingencies have assessed awareness after the conditioning session was…

Au Contraire: Differentiation Requires HOPE

ERIC Educational Resources Information Center

Delisle, James R.

2002-01-01

Everybody is doing it: differentiating curriculum to make it deeper, broader, parallel, and more complex. No longer the private property of gifted specialists, differentiation is now a democratic pursuit of classroom teachers, curriculum specialists, and anyone else who subscribes to "Educational Leadership." In an era of competency-based tests…

Protein carboxyl methylation increases in parallel with differentiation of neuroblastoma cells.

PubMed

Kloog, Y; Axelrod, J; Spector, I

1983-02-01

Cells of mouse neuroblastoma clone N1E-115 in the confluent phase of growth can catalyze the formation of endogenous protein carboxyl methyl esters, using a protein carboxyl methylase and membrane-bound methyl acceptor proteins. The enzyme is localized predominantly in the cytosol of the cells and has a molecular weight of about 20,000 daltons. Treatment of the cells with dimethylsulfoxide (DMSO) or hexamethylene-bisacetamide (HMBA), agents that induce morphological and electrophysiological differentiation, results in a marked increase in protein carboxyl methylase activity. Maximal levels are reached 6-7 days after exposure to the agents, a time course that closely parallels the development of electrical excitability mechanisms in these cells. Serum deprivation also causes neurite outgrowth but does not enhance electrical excitability or enzyme activity. The capacity of membrane-bound neuroblastoma protein(s) to be carboxyl methylated is increased by the differentiation procedures that have been examined. However, the increase in methyl acceptor proteins induced by DMSO or HMBA is the largest, and its time course parallels electrophysiological differentiation. In contrast, serum deprivation induced a small increase that reached maximal levels within 24 h. The data suggest that increased protein carboxyl methylation is a developmentally regulated property of neuroblastoma cells and that at least two groups of methyl acceptor proteins are induced during differentiation: a minor group related to morphological differentiation, and a major group that may be related to ionic permeability mechanisms of the excitable membrane.

Parallels between control PDE's (Partial Differential Equations) and systems of ODE's (Ordinary Differential Equations)

NASA Technical Reports Server (NTRS)

Hunt, L. R.; Villarreal, Ramiro

1987-01-01

System theorists understand that the same mathematical objects which determine controllability for nonlinear control systems of ordinary differential equations (ODEs) also determine hypoellipticity for linear partial differentail equations (PDEs). Moreover, almost any study of ODE systems begins with linear systems. It is remarkable that Hormander's paper on hypoellipticity of second order linear p.d.e.'s starts with equations due to Kolmogorov, which are shown to be analogous to the linear PDEs. Eigenvalue placement by state feedback for a controllable linear system can be paralleled for a Kolmogorov equation if an appropriate type of feedback is introduced. Results concerning transformations of nonlinear systems to linear systems are similar to results for transforming a linear PDE to a Kolmogorov equation.

Fast Time and Space Parallel Algorithms for Solution of Parabolic Partial Differential Equations

NASA Technical Reports Server (NTRS)

Fijany, Amir

1993-01-01

In this paper, fast time- and Space -Parallel agorithms for solution of linear parabolic PDEs are developed. It is shown that the seemingly strictly serial iterations of the time-stepping procedure for solution of the problem can be completed decoupled.

Automating the parallel processing of fluid and structural dynamics calculations

NASA Technical Reports Server (NTRS)

Arpasi, Dale J.; Cole, Gary L.

1987-01-01

The NASA Lewis Research Center is actively involved in the development of expert system technology to assist users in applying parallel processing to computational fluid and structural dynamic analysis. The goal of this effort is to eliminate the necessity for the physical scientist to become a computer scientist in order to effectively use the computer as a research tool. Programming and operating software utilities have previously been developed to solve systems of ordinary nonlinear differential equations on parallel scalar processors. Current efforts are aimed at extending these capabilities to systems of partial differential equations, that describe the complex behavior of fluids and structures within aerospace propulsion systems. This paper presents some important considerations in the redesign, in particular, the need for algorithms and software utilities that can automatically identify data flow patterns in the application program and partition and allocate calculations to the parallel processors. A library-oriented multiprocessing concept for integrating the hardware and software functions is described.

Cognate Effects and Cognitive Control in Patients with Parallel and Differential Bilingual Aphasia

ERIC Educational Resources Information Center

Van der Linden, Lize; Verreyt, Nele; De Letter, Miet; Hemelsoet, Dimitri; Mariën, Peter; Santens, Patrick; Stevens, Michaël; Szmalec, Arnaud; Duyck, Wouter

2018-01-01

Background: Until today, there is no satisfying explanation for why one language may recover worse than another in differential bilingual aphasia. One potential explanation that has been largely unexplored is that differential aphasia is the consequence of a loss of language control rather than a loss of linguistic representations. Language…

Partitioning and packing mathematical simulation models for calculation on parallel computers

NASA Technical Reports Server (NTRS)

Arpasi, D. J.; Milner, E. J.

1986-01-01

The development of multiprocessor simulations from a serial set of ordinary differential equations describing a physical system is described. Degrees of parallelism (i.e., coupling between the equations) and their impact on parallel processing are discussed. The problem of identifying computational parallelism within sets of closely coupled equations that require the exchange of current values of variables is described. A technique is presented for identifying this parallelism and for partitioning the equations for parallel solution on a multiprocessor. An algorithm which packs the equations into a minimum number of processors is also described. The results of the packing algorithm when applied to a turbojet engine model are presented in terms of processor utilization.

Increased phospho-AKT is associated with loss of the androgen receptor during the progression of N-methyl-N-nitrosourea-induced prostate carcinogenesis in rats.

PubMed

Liao, Zhiming; Wang, Shihua; Boileau, Thomas W-M; Erdman, John W; Clinton, Steven K

2005-07-01

Characterization of molecular events during N-methyl-N-nitrosourea (MNU)-induced rat prostate carcinogenesis enhances the utility of this model for the preclinical assessment of preventive strategies. Androgen independence is typical of advanced human prostate cancer and may occur through multiple mechanisms including the loss of androgen receptor (AR) expression and the activation of alternative signaling pathways. We examined the interrelationships between AR and p-AKT expression by immunohistochemical staining during MNU-androgen-induced prostate carcinogenesis in male Wistar-Unilever rats. Histone nuclear staining and image analysis was employed to assess parallel changes in chromatin and nuclear structure. The percentage of AR positive nuclei decreased (P < 0.01) as carcinogenesis progressed: hyperplasia (92%), atypical hyperplasia (92%), well-differentiated adenocarcinoma (57%), moderately-differentiated adenocarcinoma (19%), and poorly-differentiated adenocarcinoma (10%). Conversely, p-AKT staining increased significantly during carcinogenesis. Sparse staining was observed in normal tissues (0.2% of epithelial area) and hyperplastic lesions (0.1%), while expression increased significantly (P < 0.001) in atypical hyperplasia (7.6%), well-differentiated adenocarcinoma (16.7%), moderately-differentiated adenocarcinoma (19.6%), and poorly-differentiated adenocarcinoma (17.4%). In parallel, nuclear morphometry revealed increased nuclear size, greater irregularity, and lower DNA compactness as cancers became more poorly differentiated. In the MNU model, the progressive evolution of dominant tumor cell populations showing an increase in p-AKT in parallel with a decline in AR staining suggests that activation of AKT signaling may be one of several mechanisms contributing to androgen insensitivity during prostate cancer progression. Our observations mimic findings suggested by human studies and support the relevance of the MNU model in preclinical studies of preventive strategies. (c) 2005 Wiley-Liss, Inc.

Parallel Evolution of Copy-Number Variation across Continents in Drosophila melanogaster.

PubMed

Schrider, Daniel R; Hahn, Matthew W; Begun, David J

2016-05-01

Genetic differentiation across populations that is maintained in the presence of gene flow is a hallmark of spatially varying selection. In Drosophila melanogaster, the latitudinal clines across the eastern coasts of Australia and North America appear to be examples of this type of selection, with recent studies showing that a substantial portion of the D. melanogaster genome exhibits allele frequency differentiation with respect to latitude on both continents. As of yet there has been no genome-wide examination of differentiated copy-number variants (CNVs) in these geographic regions, despite their potential importance for phenotypic variation in Drosophila and other taxa. Here, we present an analysis of geographic variation in CNVs in D. melanogaster. We also present the first genomic analysis of geographic variation for copy-number variation in the sister species, D. simulans, in order to investigate patterns of parallel evolution in these close relatives. In D. melanogaster we find hundreds of CNVs, many of which show parallel patterns of geographic variation on both continents, lending support to the idea that they are influenced by spatially varying selection. These findings support the idea that polymorphic CNVs contribute to local adaptation in D. melanogaster In contrast, we find very few CNVs in D. simulans that are geographically differentiated in parallel on both continents, consistent with earlier work suggesting that clinal patterns are weaker in this species. © The Author 2016. 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.

Longitudinal trends in climate drive flowering time clines in North American Arabidopsis thaliana.

PubMed

Samis, Karen E; Murren, Courtney J; Bossdorf, Oliver; Donohue, Kathleen; Fenster, Charles B; Malmberg, Russell L; Purugganan, Michael D; Stinchcombe, John R

2012-06-01

Introduced species frequently show geographic differentiation, and when differentiation mirrors the ancestral range, it is often taken as evidence of adaptive evolution. The mouse-ear cress (Arabidopsis thaliana) was introduced to North America from Eurasia 150-200 years ago, providing an opportunity to study parallel adaptation in a genetic model organism. Here, we test for clinal variation in flowering time using 199 North American (NA) accessions of A. thaliana, and evaluate the contributions of major flowering time genes FRI, FLC, and PHYC as well as potential ecological mechanisms underlying differentiation. We find evidence for substantial within population genetic variation in quantitative traits and flowering time, and putatively adaptive longitudinal differentiation, despite low levels of variation at FRI, FLC, and PHYC and genome-wide reductions in population structure relative to Eurasian (EA) samples. The observed longitudinal cline in flowering time in North America is parallel to an EA cline, robust to the effects of population structure, and associated with geographic variation in winter precipitation and temperature. We detected major effects of FRI on quantitative traits associated with reproductive fitness, although the haplotype associated with higher fitness remains rare in North America. Collectively, our results suggest the evolution of parallel flowering time clines through novel genetic mechanisms.

Relationship of Individual and Group Change: Ontogeny and Phylogeny in Biology.

ERIC Educational Resources Information Center

Gould, Steven Jay

1984-01-01

Considers the issue of parallels between ontogeny and phylogeny from an historical perspective. Discusses such parallels in relationship to two ontogenetic principles concerning recapitulation and sequence of stages. Differentiates between Piaget's use of the idea of recapitulation and Haeckel's biogenetic law. (Author/RH)

Some fast elliptic solvers on parallel architectures and their complexities

NASA Technical Reports Server (NTRS)

Gallopoulos, E.; Saad, Y.

1989-01-01

The discretization of separable elliptic partial differential equations leads to linear systems with special block tridiagonal matrices. Several methods are known to solve these systems, the most general of which is the Block Cyclic Reduction (BCR) algorithm which handles equations with nonconstant coefficients. A method was recently proposed to parallelize and vectorize BCR. In this paper, the mapping of BCR on distributed memory architectures is discussed, and its complexity is compared with that of other approaches including the Alternating-Direction method. A fast parallel solver is also described, based on an explicit formula for the solution, which has parallel computational compelxity lower than that of parallel BCR.

Some fast elliptic solvers on parallel architectures and their complexities

NASA Technical Reports Server (NTRS)

Gallopoulos, E.; Saad, Youcef

1989-01-01

The discretization of separable elliptic partial differential equations leads to linear systems with special block triangular matrices. Several methods are known to solve these systems, the most general of which is the Block Cyclic Reduction (BCR) algorithm which handles equations with nonconsistant coefficients. A method was recently proposed to parallelize and vectorize BCR. Here, the mapping of BCR on distributed memory architectures is discussed, and its complexity is compared with that of other approaches, including the Alternating-Direction method. A fast parallel solver is also described, based on an explicit formula for the solution, which has parallel computational complexity lower than that of parallel BCR.

SIAM Conference on Parallel Processing for Scientific Computing, 4th, Chicago, IL, Dec. 11-13, 1989, Proceedings

NASA Technical Reports Server (NTRS)

Dongarra, Jack (Editor); Messina, Paul (Editor); Sorensen, Danny C. (Editor); Voigt, Robert G. (Editor)

1990-01-01

Attention is given to such topics as an evaluation of block algorithm variants in LAPACK and presents a large-grain parallel sparse system solver, a multiprocessor method for the solution of the generalized Eigenvalue problem on an interval, and a parallel QR algorithm for iterative subspace methods on the CM2. A discussion of numerical methods includes the topics of asynchronous numerical solutions of PDEs on parallel computers, parallel homotopy curve tracking on a hypercube, and solving Navier-Stokes equations on the Cedar Multi-Cluster system. A section on differential equations includes a discussion of a six-color procedure for the parallel solution of elliptic systems using the finite quadtree structure, data parallel algorithms for the finite element method, and domain decomposition methods in aerodynamics. Topics dealing with massively parallel computing include hypercube vs. 2-dimensional meshes and massively parallel computation of conservation laws. Performance and tools are also discussed.

Parallelism between gradient temperature raman spectroscopy and differential scanning calorimetry results

USDA-ARS?s Scientific Manuscript database

Temperature dependent Raman spectroscopy (TDR) applies the temperature gradients utilized in differential scanning calorimetry (DSC) to Raman spectroscopy, providing a straightforward technique to identify molecular rearrangements that occur just prior to phase transitions. Herein we apply TDR and D...

Dynamic grid refinement for partial differential equations on parallel computers

NASA Technical Reports Server (NTRS)

Mccormick, S.; Quinlan, D.

1989-01-01

The fast adaptive composite grid method (FAC) is an algorithm that uses various levels of uniform grids to provide adaptive resolution and fast solution of PDEs. An asynchronous version of FAC, called AFAC, that completely eliminates the bottleneck to parallelism is presented. This paper describes the advantage that this algorithm has in adaptive refinement for moving singularities on multiprocessor computers. This work is applicable to the parallel solution of two- and three-dimensional shock tracking problems.

Differential optoacoustic absorption detector

NASA Technical Reports Server (NTRS)

Shumate, M. S. (Inventor)

1978-01-01

A differential optoacoustic absorption detector employed two tapered cells in tandem or in parallel. When operated in tandem, two mirrors were used at one end remote from the source of the beam of light directed into one cell back through the other, and a lens to focus the light beam into the one cell at a principal focus half way between the reflecting mirror. Each cell was tapered to conform to the shape of the beam so that the volume of one was the same as for the other, and the volume of each received maximum illumination. The axes of the cells were placed as close to each other as possible in order to connect a differential pressure detector to the cells with connecting passages of minimum length. An alternative arrangement employed a beam splitter and two lenses to operate the cells in parallel.

Solution of partial differential equations on vector and parallel computers

NASA Technical Reports Server (NTRS)

Ortega, J. M.; Voigt, R. G.

1985-01-01

The present status of numerical methods for partial differential equations on vector and parallel computers was reviewed. The relevant aspects of these computers are discussed and a brief review of their development is included, with particular attention paid to those characteristics that influence algorithm selection. Both direct and iterative methods are given for elliptic equations as well as explicit and implicit methods for initial boundary value problems. The intent is to point out attractive methods as well as areas where this class of computer architecture cannot be fully utilized because of either hardware restrictions or the lack of adequate algorithms. Application areas utilizing these computers are briefly discussed.

Parallel human genome analysis: microarray-based expression monitoring of 1000 genes.

PubMed Central

Schena, M; Shalon, D; Heller, R; Chai, A; Brown, P O; Davis, R W

1996-01-01

Microarrays containing 1046 human cDNAs of unknown sequence were printed on glass with high-speed robotics. These 1.0-cm2 DNA "chips" were used to quantitatively monitor differential expression of the cognate human genes using a highly sensitive two-color hybridization assay. Array elements that displayed differential expression patterns under given experimental conditions were characterized by sequencing. The identification of known and novel heat shock and phorbol ester-regulated genes in human T cells demonstrates the sensitivity of the assay. Parallel gene analysis with microarrays provides a rapid and efficient method for large-scale human gene discovery. Images Fig. 1 Fig. 2 Fig. 3 PMID:8855227

Parallel Calculation of Sensitivity Derivatives for Aircraft Design using Automatic Differentiation

NASA Technical Reports Server (NTRS)

Bischof, c. H.; Green, L. L.; Haigler, K. J.; Knauff, T. L., Jr.

1994-01-01

Sensitivity derivative (SD) calculation via automatic differentiation (AD) typical of that required for the aerodynamic design of a transport-type aircraft is considered. Two ways of computing SD via code generated by the ADIFOR automatic differentiation tool are compared for efficiency and applicability to problems involving large numbers of design variables. A vector implementation on a Cray Y-MP computer is compared with a coarse-grained parallel implementation on an IBM SP1 computer, employing a Fortran M wrapper. The SD are computed for a swept transport wing in turbulent, transonic flow; the number of geometric design variables varies from 1 to 60 with coupling between a wing grid generation program and a state-of-the-art, 3-D computational fluid dynamics program, both augmented for derivative computation via AD. For a small number of design variables, the Cray Y-MP implementation is much faster. As the number of design variables grows, however, the IBM SP1 becomes an attractive alternative in terms of compute speed, job turnaround time, and total memory available for solutions with large numbers of design variables. The coarse-grained parallel implementation also can be moved easily to a network of workstations.

DVS-SOFTWARE: An Effective Tool for Applying Highly Parallelized Hardware To Computational Geophysics

NASA Astrophysics Data System (ADS)

Herrera, I.; Herrera, G. S.

2015-12-01

Most geophysical systems are macroscopic physical systems. The behavior prediction of such systems is carried out by means of computational models whose basic models are partial differential equations (PDEs) [1]. Due to the enormous size of the discretized version of such PDEs it is necessary to apply highly parallelized super-computers. For them, at present, the most efficient software is based on non-overlapping domain decomposition methods (DDM). However, a limiting feature of the present state-of-the-art techniques is due to the kind of discretizations used in them. Recently, I. Herrera and co-workers using 'non-overlapping discretizations' have produced the DVS-Software which overcomes this limitation [2]. The DVS-software can be applied to a great variety of geophysical problems and achieves very high parallel efficiencies (90%, or so [3]). It is therefore very suitable for effectively applying the most advanced parallel supercomputers available at present. In a parallel talk, in this AGU Fall Meeting, Graciela Herrera Z. will present how this software is being applied to advance MOD-FLOW. Key Words: Parallel Software for Geophysics, High Performance Computing, HPC, Parallel Computing, Domain Decomposition Methods (DDM)REFERENCES [1]. Herrera Ismael and George F. Pinder, Mathematical Modelling in Science and Engineering: An axiomatic approach", John Wiley, 243p., 2012. [2]. Herrera, I., de la Cruz L.M. and Rosas-Medina A. "Non Overlapping Discretization Methods for Partial, Differential Equations". NUMER METH PART D E, 30: 1427-1454, 2014, DOI 10.1002/num 21852. (Open source) [3]. Herrera, I., & Contreras Iván "An Innovative Tool for Effectively Applying Highly Parallelized Software To Problems of Elasticity". Geofísica Internacional, 2015 (In press)

Absolute Paleointensity Study of Halawa Excursion (ca. 2.514+/- 0.039 Ma) Recorded on Koolau Volcano at Halawa, Oahu, Hawaii.

NASA Astrophysics Data System (ADS)

Lau, J. K.; Herrero-Bervera, E.

2006-12-01

Absolute Paleointensity determinations coupled with directional analyses and precise 40Ar/39Ar radioisotopic dating, have rendered a record of an excursion of the geomagnetic field providing an insight of the rapid variation of the short-term behavior of the paleomagnetic field. We have sampled a long volcanic section located on the buttressed flank of the Koolau volcano within the Halawa Valley, Oahu, Hawaii and studied 120 m thick sequence of flows providing an excellent candidate for detailed paleomagnetic analysis. At least eight samples collected from each of 28 successive flow-sites were stepwise demagnetized by both alternating field (5mT to 100mT) and thermal (from 28° C to 575-650°C) methods, and the mean directions obtained by principal component analysis. All samples yielded a strong and stable ChRM trending towards the origin based on no less than seven to nine steps, with thermal and AF results agreeing to a very high degree. Low field susceptibility versus temperature (k-T) analyses were conducted for individual lava flows, and the majority of them show reversible curves. Curie point determinations revealed a temperature close to or equal to 580°C, indicative of almost pure magnetite for most of the flows. Magnetic grain sizes analysis indicated SD-PSD sizes. The mean directions of magnetization of the entire section sampled indicate that about 10 m of the section are characterized by excursional directions (5 lava flows). In addition to the directional analyses we performed absolute paleointensity determinations on the 28 lavas sampled. We used the modified Thellier- Coe double heating method to determine paleointensities. pTRM checks were performed systematically one temperature step down the last pTRM acquisition in order to document magnetomineralogical changes during heating. The temperature was incremented by steps of 50° C between room temperature and 500°C and every 25-30° C. The paleointensity determinations were obtained from the slope of the Arai diagrams. Special care was taken to interpret the Arai diagrams within the same range of temperatures lower than 300°C unless a clear and unique slope would be present. Our paleointensity results indicate a near-zero reduced strength of the field during the excursional period ranging from 5 to 9 micro-Tesla but high absolute paleointensity values prior to the excursional lavas The corresponding VGPs are located off the southeast part of Africa, close to Madagascar. The 40Ar/39Ar incremental heating experiments on groundmass from nine flow-sites located at different stratigraphic levels yielded an isochron age of 2.514+/-0.039 Ma indicating that the excursion may correlate with the C2r.2r-l Cryptochron of Cande and Kent [1995].

Spot Reading of the Absolute Paleointensity of the Geomagnetic Field During the Kiaman Superchron: The Exeter Lavas Case

NASA Astrophysics Data System (ADS)

Herrero-Bervera, E.; Fuller, M. D.

2004-12-01

It is well known that Superchrons provide an opportunity to study the geomagnetic field in an extreme state, i.e. when reversals are at their lowest frequency or totally absent. Such Superchrons represent features that may provide constraints for theoretical calculations and numerical models of the geodynamo. Thus, one way to contribute to the understanding of the generation of the paleofield particularly during Superchrons is to determine the absolute paleointensity of rocks formed during those periods of time. We have sampled a member of the Exeter lavas (ca 290.8+/-0.8 Ma, Ar/Ar date) from the large, abandoned quarry in the northeastern slope of the southernmost hill of Killerton Park, 10 km northeast of Exeter where we collected three samples from three different stratigraphic levels. We stepwise demagnetized the samples collected from the three different levels by both alternating field (5mT to 100mT) and thermal (from 28oC to 575-650o C) methods, and the mean directions obtained by principal component analysis (D=198o and I=-25o). All samples yielded a strong and stable ChRM trending towards the origin based on no less than seven to nine steps, with thermal and AF results agreeing to a very high degree. Low field susceptibility versus temperature (k-T) analyses were conducted for individual samples and the majority of them show reversible curves. Curie point determinations revealed a temperature close to or equal to 580o C, indicative of almost pure magnetite for most of the samples. Magnetic grain sizes analysis indicated SD-PSD sizes. We used the modified Thellier-Coe double heating method to determine paleointensities. pTRM checks were performed systematically one temperature step down the last pTRM acquisition in order to document magnetomineralogical changes during heating. The temperature was incremented by steps of 50o C between room temperature and 500oC and every 25-30o C. The paleointensity determinations were obtained from the slope of the Arai diagrams. Special care was taken to interpret the Arai diagrams within the same range of temperatures lower than 300oC unless a clear and unique slope would be present. We were able to obtain paleointensity determinations for the three set of samples. The three independent estimates of paleofield range between 23.5 to 30 uT ( i.e. VADM 5.5 to 9.03 X1022 Am2). The range of these values includes the present dipole moment (i.e. 8X1022 Am2), indicating that the paleofield during the studied period of time was strong, stable and is consistent with available time-averaged intensity and directional data.

Good Questions: Great Ways to Differentiate Mathematics Instruction

ERIC Educational Resources Information Center

Small, Marian

2009-01-01

Using differentiated instruction in the classroom can be a challenge, especially when teaching mathematics. This book cuts through the difficulties with two powerful and universal strategies that teachers can use across all math content: Open Questions and Parallel Tasks. Specific strategies and examples for grades Kindergarten - 8 are organized…

Parallel Algorithm Solves Coupled Differential Equations

NASA Technical Reports Server (NTRS)

Hayashi, A.

1987-01-01

Numerical methods adapted to concurrent processing. Algorithm solves set of coupled partial differential equations by numerical integration. Adapted to run on hypercube computer, algorithm separates problem into smaller problems solved concurrently. Increase in computing speed with concurrent processing over that achievable with conventional sequential processing appreciable, especially for large problems.

Introducing Differential Equations Students to the Fredholm Alternative--In Staggered Doses

ERIC Educational Resources Information Center

Savoye, Philippe

2011-01-01

The development, in an introductory differential equations course, of boundary value problems in parallel with initial value problems and the Fredholm Alternative. Examples are provided of pairs of homogeneous and nonhomogeneous boundary value problems for which existence and uniqueness issues are considered jointly. How this heightens students'…

Promotion of Myogenic Maturation by Timely Application of Electric Field Along the Topographical Alignment.

PubMed

Ko, Ung Hyun; Park, Sukhee; Bang, Hyunseung; Kim, Mina; Shin, Hyunjun; Shin, Jennifer H

2018-05-01

Engineered muscular substitutes can restore the impaired muscle functions when integrated properly into the host tissue. To generate functional muscles with sufficient contractility at the site of transplant, the in vitro construction of fully differentiated muscle fibers would be desired. Many previous reports have identified either topographical alignment or electrical stimulation as an effective tool to promote myogenic differentiation. However, optimization of spatial and temporal arrangement of these two physical cues for better differentiation and maturation of skeletal muscles has not been investigated. In this article, we introduce a novel cell culture system that allows simultaneous application of these two independent directional cues at both orthogonal and parallel arrangements. We then show that the parallel arrangement of the aligned topography and the electric field synergistically facilitates better differentiation and maturation of C2C12, generating myotubes with more fused nuclei. Addition of the electric stimulation at the late stage of myogenic differentiation is found to further improve cell fusion to form multinucleate myotubes through a phosphatidylinositol-3-OH-kinase-dependent pathway. As such, we successfully demonstrated that the combined stimulation of topographical and electrical cues could effectively enhance both myogenic differentiation and maturation in a temporal and orientation-dependent manner, providing the basis for therapeutic strategies for regenerative tissue engineering.

Nuclear translocation of the cytoskeleton-associated protein, smALP, upon induction of skeletal muscle differentiation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cambier, Linda; Pomies, Pascal, E-mail: pascal.pomies@crbm.cnrs.fr

2011-06-17

Highlights: {yields} The cytoskeleton-associated protein, smALP, is expressed in differentiated skeletal muscle. {yields} smALP is translocated from the cytoplasm to the nucleus of C2C12 myoblasts upon induction of myogenesis. {yields} The differentiation-dependent nuclear translocation of smALP occurs in parallel with the nuclear accumulation of myogenin. {yields} The LIM domain of smALP is essential for the nuclear accumulation of the protein. {yields} smALP might act in the nucleus to control some critical aspect of the muscle differentiation process. -- Abstract: The skALP isoform has been shown to play a critical role in actin organization and anchorage within the Z-discs of skeletalmore » muscles, but no data is available on the function of the smALP isoform in skeletal muscle cells. Here, we show that upon induction of differentiation a nuclear translocation of smALP from the cytoplasm to the nucleus of C2C12 myoblasts, concomitant to an up-regulation of the protein expression, occurs in parallel with the nuclear accumulation of myogenin. Moreover, we demonstrate that the LIM domain of smALP is essential for the nuclear translocation of the protein.« less

Nebo: An efficient, parallel, and portable domain-specific language for numerically solving partial differential equations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Earl, Christopher; Might, Matthew; Bagusetty, Abhishek

This study presents Nebo, a declarative domain-specific language embedded in C++ for discretizing partial differential equations for transport phenomena on multiple architectures. Application programmers use Nebo to write code that appears sequential but can be run in parallel, without editing the code. Currently Nebo supports single-thread execution, multi-thread execution, and many-core (GPU-based) execution. With single-thread execution, Nebo performs on par with code written by domain experts. With multi-thread execution, Nebo can linearly scale (with roughly 90% efficiency) up to 12 cores, compared to its single-thread execution. Moreover, Nebo’s many-core execution can be over 140x faster than its single-thread execution.

Nebo: An efficient, parallel, and portable domain-specific language for numerically solving partial differential equations

DOE PAGES

Earl, Christopher; Might, Matthew; Bagusetty, Abhishek; ...

2016-01-26

This study presents Nebo, a declarative domain-specific language embedded in C++ for discretizing partial differential equations for transport phenomena on multiple architectures. Application programmers use Nebo to write code that appears sequential but can be run in parallel, without editing the code. Currently Nebo supports single-thread execution, multi-thread execution, and many-core (GPU-based) execution. With single-thread execution, Nebo performs on par with code written by domain experts. With multi-thread execution, Nebo can linearly scale (with roughly 90% efficiency) up to 12 cores, compared to its single-thread execution. Moreover, Nebo’s many-core execution can be over 140x faster than its single-thread execution.

INSTABILITIES DRIVEN BY THE DRIFT AND TEMPERATURE ANISOTROPY OF ALPHA PARTICLES IN THE SOLAR WIND

DOE Office of Scientific and Technical Information (OSTI.GOV)

Verscharen, Daniel; Bourouaine, Sofiane; Chandran, Benjamin D. G., E-mail: daniel.verscharen@unh.edu, E-mail: s.bourouaine@unh.edu, E-mail: benjamin.chandran@unh.edu

2013-08-20

We investigate the conditions under which parallel-propagating Alfven/ion-cyclotron (A/IC) waves and fast-magnetosonic/whistler (FM/W) waves are driven unstable by the differential flow and temperature anisotropy of alpha particles in the solar wind. We focus on the limit in which w{sub Parallel-To {alpha}} {approx}> 0.25v{sub A}, where w{sub Parallel-To {alpha}} is the parallel alpha-particle thermal speed and v{sub A} is the Alfven speed. We derive analytic expressions for the instability thresholds of these waves, which show, e.g., how the minimum unstable alpha-particle beam speed depends upon w{sub Parallel-To {alpha}}/v{sub A}, the degree of alpha-particle temperature anisotropy, and the alpha-to-proton temperature ratio. Wemore » validate our analytical results using numerical solutions to the full hot-plasma dispersion relation. Consistent with previous work, we find that temperature anisotropy allows A/IC waves and FM/W waves to become unstable at significantly lower values of the alpha-particle beam speed U{sub {alpha}} than in the isotropic-temperature case. Likewise, differential flow lowers the minimum temperature anisotropy needed to excite A/IC or FM/W waves relative to the case in which U{sub {alpha}} = 0. We discuss the relevance of our results to alpha particles in the solar wind near 1 AU.« less

Measuring Differential Delays With Sine-Squared Pulses

NASA Technical Reports Server (NTRS)

Hurst, Robert N.

1994-01-01

Technique for measuring differential delays among red, green, and blue components of video signal transmitted on different parallel channels exploits sine-squared pulses that are parts of standard test signals transmitted during vertical blanking interval of frame period. Technique does not entail expense of test-signal generator. Also applicable to nonvideo signals including sine-squared pulses.

Young and old honey bee (Apis mellifera) larvae differentially prime the developmental maturation of their caregivers

USDA-ARS?s Scientific Manuscript database

In eusocial insects daughters rear the offspring of the queen to adulthood. In the honey bee, Apis mellifera, nurses differentially regulate larval nutrition. Among worker-destined larvae, younger instars receive an unrestricted diet paralleling that of queen larvae in protein composition but with r...

Applications of New Surrogate Global Optimization Algorithms including Efficient Synchronous and Asynchronous Parallelism for Calibration of Expensive Nonlinear Geophysical Simulation Models.

NASA Astrophysics Data System (ADS)

Shoemaker, C. A.; Pang, M.; Akhtar, T.; Bindel, D.

2016-12-01

New parallel surrogate global optimization algorithms are developed and applied to objective functions that are expensive simulations (possibly with multiple local minima). The algorithms can be applied to most geophysical simulations, including those with nonlinear partial differential equations. The optimization does not require simulations be parallelized. Asynchronous (and synchronous) parallel execution is available in the optimization toolbox "pySOT". The parallel algorithms are modified from serial to eliminate fine grained parallelism. The optimization is computed with open source software pySOT, a Surrogate Global Optimization Toolbox that allows user to pick the type of surrogate (or ensembles), the search procedure on surrogate, and the type of parallelism (synchronous or asynchronous). pySOT also allows the user to develop new algorithms by modifying parts of the code. In the applications here, the objective function takes up to 30 minutes for one simulation, and serial optimization can take over 200 hours. Results from Yellowstone (NSF) and NCSS (Singapore) supercomputers are given for groundwater contaminant hydrology simulations with applications to model parameter estimation and decontamination management. All results are compared with alternatives. The first results are for optimization of pumping at many wells to reduce cost for decontamination of groundwater at a superfund site. The optimization runs with up to 128 processors. Superlinear speed up is obtained for up to 16 processors, and efficiency with 64 processors is over 80%. Each evaluation of the objective function requires the solution of nonlinear partial differential equations to describe the impact of spatially distributed pumping and model parameters on model predictions for the spatial and temporal distribution of groundwater contaminants. The second application uses an asynchronous parallel global optimization for groundwater quality model calibration. The time for a single objective function evaluation varies unpredictably, so efficiency is improved with asynchronous parallel calculations to improve load balancing. The third application (done at NCSS) incorporates new global surrogate multi-objective parallel search algorithms into pySOT and applies it to a large watershed calibration problem.

Parallel Element Agglomeration Algebraic Multigrid and Upscaling Library

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barker, Andrew T.; Benson, Thomas R.; Lee, Chak Shing

ParELAG is a parallel C++ library for numerical upscaling of finite element discretizations and element-based algebraic multigrid solvers. It provides optimal complexity algorithms to build multilevel hierarchies and solvers that can be used for solving a wide class of partial differential equations (elliptic, hyperbolic, saddle point problems) on general unstructured meshes. Additionally, a novel multilevel solver for saddle point problems with divergence constraint is implemented.

Negative tunnel magnetoresistance and differential conductance in transport through double quantum dots

NASA Astrophysics Data System (ADS)

Trocha, Piotr; Weymann, Ireneusz; Barnaś, Józef

2009-10-01

Spin-dependent transport through two coupled single-level quantum dots weakly connected to ferromagnetic leads with collinear magnetizations is considered theoretically. Transport characteristics, including the current, linear and nonlinear conductances, and tunnel magnetoresistance are calculated using the real-time diagrammatic technique in the parallel, serial, and intermediate geometries. The effects due to virtual tunneling processes between the two dots via the leads, associated with off-diagonal coupling matrix elements, are also considered. Negative differential conductance and negative tunnel magnetoresistance have been found in the case of serial and intermediate geometries, while no such behavior has been observed for double quantum dots coupled in parallel. It is also shown that transport characteristics strongly depend on the magnitude of the off-diagonal coupling matrix elements.

Differential Scanning Calorimetry Techniques: Applications in Biology and Nanoscience

PubMed Central

Gill, Pooria; Moghadam, Tahereh Tohidi; Ranjbar, Bijan

2010-01-01

This paper reviews the best-known differential scanning calorimetries (DSCs), such as conventional DSC, microelectromechanical systems-DSC, infrared-heated DSC, modulated-temperature DSC, gas flow-modulated DSC, parallel-nano DSC, pressure perturbation calorimetry, self-reference DSC, and high-performance DSC. Also, we describe here the most extensive applications of DSC in biology and nanoscience. PMID:21119929

Querying databases of trajectories of differential equations 2: Index functions

NASA Technical Reports Server (NTRS)

Grossman, Robert

1991-01-01

Suppose that a large number of parameterized trajectories (gamma) of a dynamical system evolving in R sup N are stored in a database. Let eta is contained R sup N denote a parameterized path in Euclidean space, and let parallel to center dot parallel to denote a norm on the space of paths. A data structures and indices for trajectories are defined and algorithms are given to answer queries of the following forms: Query 1. Given a path eta, determine whether eta occurs as a subtrajectory of any trajectory gamma from the database. If so, return the trajectory; otherwise, return null. Query 2. Given a path eta, return the trajectory gamma from the database which minimizes the norm parallel to eta - gamma parallel.

Changes in the distribution of plastids and endoplasmic reticulum during cellular differentiation in root caps of Zea mays

NASA Technical Reports Server (NTRS)

Moore, R.; McClelen, C. E.

1985-01-01

In calyptrogen cells of Zea mays, proplastids are distributed randomly throughout the cell, and the endoplasmic reticulum (ER) is distributed parallel to the cell walls. The differentiation of calyptrogen cells into columella statocytes is characterized by the following sequential events: (1) formation of ER complexes at the distal and proximal ends of the cell, (2) differentiation of proplastids into amyloplasts, (3) sedimentation of amyloplasts onto the distal ER complex, (4) breakdown of the distal ER complex and sedimentation of amyloplasts to the bottom of the cell, and (5) formation of sheets of ER parallel to the longitudinal cell walls. Columella statocytes located in the centre of the cap each possess 4530 +/- 780 micrometers2 of ER surface area, an increase of 670 per cent over that of calyptrogen cells. The differentiation of peripheral cells correlates positively with (1) the ER becoming arranged in concentric sheets, (2) amyloplasts and ER becoming randomly distributed, and (3) a 280 per cent increase in ER surface area over that of columella statocytes. These results are discussed relative to graviperception and mucilage secretion, which are functions of columella and peripheral cells, respectively.

Influence of differentiation on muscarinic receptors in N1E 115 neuroblastoma cells.

PubMed

Buyse, M A; Lefebvre, R A; Fraeyman, N H

1989-01-01

The effect of inducing morphological differentiation in N1E 115 mouse neuroblastoma cells on the number of muscarinic receptors and the ligand binding affinity was investigated using the lipophylic quinuclidinyl benzylate and the hydrophylic N-methylscopolamine as tritiated ligands. Induction of morphological differentiation was accompanied by a two- to three-fold increase of the number of receptors when assayed in a broken cell preparation; the ligand binding affinity was unaffected by differentiation. Using intact cells, this increase was not paralleled by a similar increase in binding sites accessible for N-methylscopolamine, which binds preferentially to extracellular sites.

Massively parallel sparse matrix function calculations with NTPoly

NASA Astrophysics Data System (ADS)

Dawson, William; Nakajima, Takahito

2018-04-01

We present NTPoly, a massively parallel library for computing the functions of sparse, symmetric matrices. The theory of matrix functions is a well developed framework with a wide range of applications including differential equations, graph theory, and electronic structure calculations. One particularly important application area is diagonalization free methods in quantum chemistry. When the input and output of the matrix function are sparse, methods based on polynomial expansions can be used to compute matrix functions in linear time. We present a library based on these methods that can compute a variety of matrix functions. Distributed memory parallelization is based on a communication avoiding sparse matrix multiplication algorithm. OpenMP task parallellization is utilized to implement hybrid parallelization. We describe NTPoly's interface and show how it can be integrated with programs written in many different programming languages. We demonstrate the merits of NTPoly by performing large scale calculations on the K computer.

Implementation of Parallel Dynamic Simulation on Shared-Memory vs. Distributed-Memory Environments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jin, Shuangshuang; Chen, Yousu; Wu, Di

2015-12-09

Power system dynamic simulation computes the system response to a sequence of large disturbance, such as sudden changes in generation or load, or a network short circuit followed by protective branch switching operation. It consists of a large set of differential and algebraic equations, which is computational intensive and challenging to solve using single-processor based dynamic simulation solution. High-performance computing (HPC) based parallel computing is a very promising technology to speed up the computation and facilitate the simulation process. This paper presents two different parallel implementations of power grid dynamic simulation using Open Multi-processing (OpenMP) on shared-memory platform, and Messagemore » Passing Interface (MPI) on distributed-memory clusters, respectively. The difference of the parallel simulation algorithms and architectures of the two HPC technologies are illustrated, and their performances for running parallel dynamic simulation are compared and demonstrated.« less

Parallel adaptive wavelet collocation method for PDEs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nejadmalayeri, Alireza, E-mail: Alireza.Nejadmalayeri@gmail.com; Vezolainen, Alexei, E-mail: Alexei.Vezolainen@Colorado.edu; Brown-Dymkoski, Eric, E-mail: Eric.Browndymkoski@Colorado.edu

2015-10-01

A parallel adaptive wavelet collocation method for solving a large class of Partial Differential Equations is presented. The parallelization is achieved by developing an asynchronous parallel wavelet transform, which allows one to perform parallel wavelet transform and derivative calculations with only one data synchronization at the highest level of resolution. The data are stored using tree-like structure with tree roots starting at a priori defined level of resolution. Both static and dynamic domain partitioning approaches are developed. For the dynamic domain partitioning, trees are considered to be the minimum quanta of data to be migrated between the processes. This allowsmore » fully automated and efficient handling of non-simply connected partitioning of a computational domain. Dynamic load balancing is achieved via domain repartitioning during the grid adaptation step and reassigning trees to the appropriate processes to ensure approximately the same number of grid points on each process. The parallel efficiency of the approach is discussed based on parallel adaptive wavelet-based Coherent Vortex Simulations of homogeneous turbulence with linear forcing at effective non-adaptive resolutions up to 2048{sup 3} using as many as 2048 CPU cores.« less

Turbine airfoil to shroud attachment method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Campbell, Christian X; Kulkarni, Anand A; James, Allister W

2014-12-23

Bi-casting a platform (50) onto an end portion (42) of a turbine airfoil (31) after forming a coating of a fugitive material (56) on the end portion. After bi-casting the platform, the coating is dissolved and removed to relieve differential thermal shrinkage stress between the airfoil and platform. The thickness of the coating is varied around the end portion in proportion to varying amounts of local differential process shrinkage. The coating may be sprayed (76A, 76B) onto the end portion in opposite directions parallel to a chord line (41) of the airfoil or parallel to a mid-platform length (80) ofmore » the platform to form respective layers tapering in thickness from the leading (32) and trailing (34) edges along the suction side (36) of the airfoil.« less

A Scalable Approach for Discovering Conserved Active Subnetworks across Species

PubMed Central

Verfaillie, Catherine M.; Hu, Wei-Shou; Myers, Chad L.

2010-01-01

Overlaying differential changes in gene expression on protein interaction networks has proven to be a useful approach to interpreting the cell's dynamic response to a changing environment. Despite successes in finding active subnetworks in the context of a single species, the idea of overlaying lists of differentially expressed genes on networks has not yet been extended to support the analysis of multiple species' interaction networks. To address this problem, we designed a scalable, cross-species network search algorithm, neXus (Network - cross(X)-species - Search), that discovers conserved, active subnetworks based on parallel differential expression studies in multiple species. Our approach leverages functional linkage networks, which provide more comprehensive coverage of functional relationships than physical interaction networks by combining heterogeneous types of genomic data. We applied our cross-species approach to identify conserved modules that are differentially active in stem cells relative to differentiated cells based on parallel gene expression studies and functional linkage networks from mouse and human. We find hundreds of conserved active subnetworks enriched for stem cell-associated functions such as cell cycle, DNA repair, and chromatin modification processes. Using a variation of this approach, we also find a number of species-specific networks, which likely reflect mechanisms of stem cell function that have diverged between mouse and human. We assess the statistical significance of the subnetworks by comparing them with subnetworks discovered on random permutations of the differential expression data. We also describe several case examples that illustrate the utility of comparative analysis of active subnetworks. PMID:21170309

Optical spatial differentiator based on subwavelength high-contrast gratings

NASA Astrophysics Data System (ADS)

Dong, Zhewei; Si, Jiangnan; Yu, Xuanyi; Deng, Xiaoxu

2018-04-01

An optical spatial differentiator based on subwavelength high-contrast gratings (HCGs) is proposed experimentally. The spatial differentiation property of the subwavelength HCG is analyzed by calculating its spatial spectral transfer function based on the periodic waveguide theory. By employing the FDTD solutions, the performance of the subwavelength HCG spatial differentiator was investigated numerically. The subwavelength HCG differentiator with the thickness at the nanoscale was fabricated on the quartz substrate by electron beam lithography and Bosch deep silicon etching. Observed under an optical microscope with a CCD camera, the spatial differentiation of the incident field profile was obtained by the subwavelength HCG differentiator in transmission without Fourier lens. By projecting the images of slits, letter "X," and a cross on the subwavelength HCG differentiator, edge detections of images were obtained in transmission. With the nanoscale HCG structure and simple optical implementation, the proposed optical spatial differentiator provides the prospects for applications in optical computing systems and parallel data processing.

Unsteady stokes flow of dusty fluid between two parallel plates through porous medium in the presence of magnetic field

NASA Astrophysics Data System (ADS)

Sasikala, R.; Govindarajan, A.; Gayathri, R.

2018-04-01

This paper focus on the result of dust particle between two parallel plates through porous medium in the presence of magnetic field with constant suction in the upper plate and constant injection in the lower plate. The partial differential equations governing the flow are solved by similarity transformation. The velocity of the fluid and the dust particle decreases when there is an increase in the Hartmann number.

A bioconvection model for a squeezing flow of nanofluid between parallel plates in the presence of gyrotactic microorganisms

NASA Astrophysics Data System (ADS)

Bin-Mohsin, Bandar; Ahmed, Naveed; Adnan; Khan, Umar; Tauseef Mohyud-Din, Syed

2017-04-01

This article deals with the bioconvection flow in a parallel-plate channel. The plates are parallel and the flowing fluid is saturated with nanoparticles, and water is considered as a base fluid because microorganisms can survive only in water. A highly nonlinear and coupled system of partial differential equations presenting the model of bioconvection flow between parallel plates is reduced to a nonlinear and coupled system (nondimensional bioconvection flow model) of ordinary differential equations with the help of feasible nondimensional variables. In order to find the convergent solution of the system, a semi-analytical technique is utilized called variation of parameters method (VPM). Numerical solution is also computed and the Runge-Kutta scheme of fourth order is employed for this purpose. Comparison between these solutions has been made on the domain of interest and found to be in excellent agreement. Also, influence of various parameters has been discussed for the nondimensional velocity, temperature, concentration and density of the motile microorganisms both for suction and injection cases. Almost inconsequential influence of thermophoretic and Brownian motion parameters on the temperature field is observed. An interesting variation are inspected for the density of the motile microorganisms due to the varying bioconvection parameter in suction and injection cases. At the end, we make some concluding remarks in the light of this article.

Tie Points Extraction for SAR Images Based on Differential Constraints

NASA Astrophysics Data System (ADS)

Xiong, X.; Jin, G.; Xu, Q.; Zhang, H.

2018-04-01

Automatically extracting tie points (TPs) on large-size synthetic aperture radar (SAR) images is still challenging because the efficiency and correct ratio of the image matching need to be improved. This paper proposes an automatic TPs extraction method based on differential constraints for large-size SAR images obtained from approximately parallel tracks, between which the relative geometric distortions are small in azimuth direction and large in range direction. Image pyramids are built firstly, and then corresponding layers of pyramids are matched from the top to the bottom. In the process, the similarity is measured by the normalized cross correlation (NCC) algorithm, which is calculated from a rectangular window with the long side parallel to the azimuth direction. False matches are removed by the differential constrained random sample consensus (DC-RANSAC) algorithm, which appends strong constraints in azimuth direction and weak constraints in range direction. Matching points in the lower pyramid images are predicted with the local bilinear transformation model in range direction. Experiments performed on ENVISAT ASAR and Chinese airborne SAR images validated the efficiency, correct ratio and accuracy of the proposed method.

Parallel Newton-Krylov-Schwarz algorithms for the transonic full potential equation

NASA Technical Reports Server (NTRS)

Cai, Xiao-Chuan; Gropp, William D.; Keyes, David E.; Melvin, Robin G.; Young, David P.

1996-01-01

We study parallel two-level overlapping Schwarz algorithms for solving nonlinear finite element problems, in particular, for the full potential equation of aerodynamics discretized in two dimensions with bilinear elements. The overall algorithm, Newton-Krylov-Schwarz (NKS), employs an inexact finite-difference Newton method and a Krylov space iterative method, with a two-level overlapping Schwarz method as a preconditioner. We demonstrate that NKS, combined with a density upwinding continuation strategy for problems with weak shocks, is robust and, economical for this class of mixed elliptic-hyperbolic nonlinear partial differential equations, with proper specification of several parameters. We study upwinding parameters, inner convergence tolerance, coarse grid density, subdomain overlap, and the level of fill-in in the incomplete factorization, and report their effect on numerical convergence rate, overall execution time, and parallel efficiency on a distributed-memory parallel computer.

Multithreaded Model for Dynamic Load Balancing Parallel Adaptive PDE Computations

NASA Technical Reports Server (NTRS)

Chrisochoides, Nikos

1995-01-01

We present a multithreaded model for the dynamic load-balancing of numerical, adaptive computations required for the solution of Partial Differential Equations (PDE's) on multiprocessors. Multithreading is used as a means of exploring concurrency in the processor level in order to tolerate synchronization costs inherent to traditional (non-threaded) parallel adaptive PDE solvers. Our preliminary analysis for parallel, adaptive PDE solvers indicates that multithreading can be used an a mechanism to mask overheads required for the dynamic balancing of processor workloads with computations required for the actual numerical solution of the PDE's. Also, multithreading can simplify the implementation of dynamic load-balancing algorithms, a task that is very difficult for traditional data parallel adaptive PDE computations. Unfortunately, multithreading does not always simplify program complexity, often makes code re-usability not an easy task, and increases software complexity.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Connell, Patrick; Frolov, Valeri P.; Kubiznak, David

We obtain and study the equations describing the parallel transport of orthonormal frames along geodesics in a spacetime admitting a nondegenerate, principal, conformal Killing-Yano tensor h. We demonstrate that the operator F, obtained by a projection of h to a subspace orthogonal to the velocity, has in a generic case eigenspaces of dimension not greater than 2. Each of these eigenspaces is independently parallel propagated. This allows one to reduce the parallel transport equations to a set of first order, ordinary, differential equations for the angles of rotation in the 2D eigenspaces. General analysis is illustrated by studying the equationsmore » of the parallel transport in the Kerr-NUT-(A)dS metrics. Examples of three-, four-, and five-dimensional Kerr-NUT-(A)dS are considered, and it is shown that the obtained first order equations can be solved by a separation of variables.« less

The shear-Hall instability in newborn neutron stars

NASA Astrophysics Data System (ADS)

Kondić, T.; Rüdiger, G.; Hollerbach, R.

2011-11-01

Aims: In the first few minutes of a newborn neutron star's life the Hall effect and differential rotation may both be important. We demonstrate that these two ingredients are sufficient for generating a "shear-Hall instability" and for studying its excitation conditions, growth rates, and characteristic magnetic field patterns. Methods: We numerically solve the induction equation in a spherical shell, with a kinematically prescribed differential rotation profile Ω(s), where s is the cylindrical radius. The Hall term is linearized about an imposed uniform axial field. The linear stability of individual azimuthal modes, both axisymmetric and non-axisymmetric, is then investigated. Results: For the shear-Hall instability to occur, the axial field must be parallel to the rotation axis if Ω(s) decreases outward, whereas if Ω(s) increases outward it must be anti-parallel. The instability draws its energy from the differential rotation, and occurs on the short rotational timescale rather than on the much longer Hall timescale. It operates most efficiently if the Hall time is comparable to the diffusion time. Depending on the precise field strengths B0, either axisymmetric or non-axisymmetric modes may be the most unstable. Conclusions: Even if the differential rotation in newborn neutron stars is quenched within minutes, the shear-Hall instability may nevertheless amplify any seed magnetic fields by many orders of magnitude.

Concept for a Differential Lock and Traction Control Model in Automobiles

NASA Astrophysics Data System (ADS)

Shukul, A. K.; Hansra, S. K.

2014-01-01

The automobile is a complex integration of electronics and mechanical components. One of the major components is the differential which is limited due to its shortcomings. The paper proposes a concept of a cost effective differential lock and traction for passenger cars to sports utility vehicles alike, employing a parallel braking mechanism coming into action based on the relative speeds of the wheels driven by the differential. The paper highlights the employment of minimum number of components unlike the already existing systems. The system was designed numerically for the traction control and differential lock for the world's cheapest car. The paper manages to come up with all the system parameters and component costing making it a cost effective system.

Series and parallel arc-fault circuit interrupter tests.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnson, Jay Dean; Fresquez, Armando J.; Gudgel, Bob

2013-07-01

While the 2011 National Electrical Codeª (NEC) only requires series arc-fault protection, some arc-fault circuit interrupter (AFCI) manufacturers are designing products to detect and mitigate both series and parallel arc-faults. Sandia National Laboratories (SNL) has extensively investigated the electrical differences of series and parallel arc-faults and has offered possible classification and mitigation solutions. As part of this effort, Sandia National Laboratories has collaborated with MidNite Solar to create and test a 24-string combiner box with an AFCI which detects, differentiates, and de-energizes series and parallel arc-faults. In the case of the MidNite AFCI prototype, series arc-faults are mitigated by openingmore » the PV strings, whereas parallel arc-faults are mitigated by shorting the array. A range of different experimental series and parallel arc-fault tests with the MidNite combiner box were performed at the Distributed Energy Technologies Laboratory (DETL) at SNL in Albuquerque, NM. In all the tests, the prototype de-energized the arc-faults in the time period required by the arc-fault circuit interrupt testing standard, UL 1699B. The experimental tests confirm series and parallel arc-faults can be successfully mitigated with a combiner box-integrated solution.« less

MPF: A portable message passing facility for shared memory multiprocessors

NASA Technical Reports Server (NTRS)

Malony, Allen D.; Reed, Daniel A.; Mcguire, Patrick J.

1987-01-01

The design, implementation, and performance evaluation of a message passing facility (MPF) for shared memory multiprocessors are presented. The MPF is based on a message passing model conceptually similar to conversations. Participants (parallel processors) can enter or leave a conversation at any time. The message passing primitives for this model are implemented as a portable library of C function calls. The MPF is currently operational on a Sequent Balance 21000, and several parallel applications were developed and tested. Several simple benchmark programs are presented to establish interprocess communication performance for common patterns of interprocess communication. Finally, performance figures are presented for two parallel applications, linear systems solution, and iterative solution of partial differential equations.

Differentiating social and personal power: opposite effects on stereotyping, but parallel effects on behavioral approach tendencies.

PubMed

Lammers, Joris; Stoker, Janka I; Stapel, Diederik A

2009-12-01

How does power affect behavior? We posit that this depends on the type of power. We distinguish between social power (power over other people) and personal power (freedom from other people) and argue that these two types of power have opposite associations with independence and interdependence. We propose that when the distinction between independence and interdependence is relevant, social power and personal power will have opposite effects; however, they will have parallel effects when the distinction is irrelevant. In two studies (an experimental study and a large field study), we demonstrate this by showing that social power and personal power have opposite effects on stereotyping, but parallel effects on behavioral approach.

Two improved coherent optical feedback systems for optical information processing

NASA Technical Reports Server (NTRS)

Lee, S. H.; Bartholomew, B.; Cederquist, J.

1976-01-01

Coherent optical feedback systems are Fabry-Perot interferometers modified to perform optical information processing. Two new systems based on plane parallel and confocal Fabry-Perot interferometers are introduced. The plane parallel system can be used for contrast control, intensity level selection, and image thresholding. The confocal system can be used for image restoration and solving partial differential equations. These devices are simpler and less expensive than previous systems. Experimental results are presented to demonstrate their potential for optical information processing.

Morphology of poly-p-xylylene crystallized during polymerization.

NASA Technical Reports Server (NTRS)

Kubo, S.; Wunderlich, B.

1971-01-01

The morphology of as-polymerized poly-p-xylylene grown between -17 and 30 C is found to consist of lame llar alpha crystals oriented with the (010) plane parallel to the support surface. The crystallinity decreases with decreasing polymerization temperature. Spherulitic and nonspherulitic portions of the polymer film consist of folded chain lamellas with the chain axis parallel to the support surface. The results were obtained by small- and wide-angle X-ray measurements, electron and optical microscopy, and differential thermal analysis.

Parallel ridge pattern on dermoscopy: observation in non-melanoma cases*

PubMed Central

Fracaroli, Tainá Scalfoni; Lavorato, Fernanda Guedes; Maceira, Juan Piñeiro; Barcaui, Carlos

2013-01-01

The acral melanoma is the most prevalent type of melanoma in the non-Caucasian population, and dermoscopy is a useful tool for earlier diagnosis and differentiation from benign lesions. The dermoscopic pattern often associated with melanoma on the volar skin is the parallel ridge, with 99% specificity according to the literature. However, this pattern can also occur in several benign acral lesions, so it is important to make a good interpretation of this pattern, along with the clinical history and evolution. PMID:24068145

Xyce parallel electronic simulator users guide, version 6.1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Keiter, Eric R; Mei, Ting; Russo, Thomas V.

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; Capability to solve extremely large circuit problems by supporting large-scale parallel computing 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 developmore » 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 radiationaware devices (for Sandia users only); and 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.« less

Xyce parallel electronic simulator users' guide, Version 6.0.1.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Keiter, Eric R; Mei, Ting; Russo, Thomas V.

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: Capability to solve extremely large circuit problems by supporting large-scale parallel computing 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 developmore » new types of analysis without requiring the implementation of analysis-specific device models. Device models that are specifically tailored to meet Sandias needs, including some radiationaware 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.« less

Xyce parallel electronic simulator users guide, version 6.0.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Keiter, Eric R; Mei, Ting; Russo, Thomas V.

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: Capability to solve extremely large circuit problems by supporting large-scale parallel computing 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 developmore » new types of analysis without requiring the implementation of analysis-specific device models. Device models that are specifically tailored to meet Sandias needs, including some radiationaware 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.« less

Parallel Optimization of 3D Cardiac Electrophysiological Model Using GPU

PubMed Central

Xia, Yong; Zhang, Henggui

2015-01-01

Large-scale 3D virtual heart model simulations are highly demanding in computational resources. This imposes a big challenge to the traditional computation resources based on CPU environment, which already cannot meet the requirement of the whole computation demands or are not easily available due to expensive costs. GPU as a parallel computing environment therefore provides an alternative to solve the large-scale computational problems of whole heart modeling. In this study, using a 3D sheep atrial model as a test bed, we developed a GPU-based simulation algorithm to simulate the conduction of electrical excitation waves in the 3D atria. In the GPU algorithm, a multicellular tissue model was split into two components: one is the single cell model (ordinary differential equation) and the other is the diffusion term of the monodomain model (partial differential equation). Such a decoupling enabled realization of the GPU parallel algorithm. Furthermore, several optimization strategies were proposed based on the features of the virtual heart model, which enabled a 200-fold speedup as compared to a CPU implementation. In conclusion, an optimized GPU algorithm has been developed that provides an economic and powerful platform for 3D whole heart simulations. PMID:26581957

Parallel Optimization of 3D Cardiac Electrophysiological Model Using GPU.

PubMed

Xia, Yong; Wang, Kuanquan; Zhang, Henggui

2015-01-01

Large-scale 3D virtual heart model simulations are highly demanding in computational resources. This imposes a big challenge to the traditional computation resources based on CPU environment, which already cannot meet the requirement of the whole computation demands or are not easily available due to expensive costs. GPU as a parallel computing environment therefore provides an alternative to solve the large-scale computational problems of whole heart modeling. In this study, using a 3D sheep atrial model as a test bed, we developed a GPU-based simulation algorithm to simulate the conduction of electrical excitation waves in the 3D atria. In the GPU algorithm, a multicellular tissue model was split into two components: one is the single cell model (ordinary differential equation) and the other is the diffusion term of the monodomain model (partial differential equation). Such a decoupling enabled realization of the GPU parallel algorithm. Furthermore, several optimization strategies were proposed based on the features of the virtual heart model, which enabled a 200-fold speedup as compared to a CPU implementation. In conclusion, an optimized GPU algorithm has been developed that provides an economic and powerful platform for 3D whole heart simulations.

The Refinement-Tree Partition for Parallel Solution of Partial Differential Equations

PubMed Central

Mitchell, William F.

1998-01-01

Dynamic load balancing is considered in the context of adaptive multilevel methods for partial differential equations on distributed memory multiprocessors. An approach that periodically repartitions the grid is taken. The important properties of a partitioning algorithm are presented and discussed in this context. A partitioning algorithm based on the refinement tree of the adaptive grid is presented and analyzed in terms of these properties. Theoretical and numerical results are given. PMID:28009355

The Refinement-Tree Partition for Parallel Solution of Partial Differential Equations.

PubMed

Mitchell, William F

1998-01-01

Dynamic load balancing is considered in the context of adaptive multilevel methods for partial differential equations on distributed memory multiprocessors. An approach that periodically repartitions the grid is taken. The important properties of a partitioning algorithm are presented and discussed in this context. A partitioning algorithm based on the refinement tree of the adaptive grid is presented and analyzed in terms of these properties. Theoretical and numerical results are given.

Linear and nonlinear stability of the Blasius boundary layer

NASA Technical Reports Server (NTRS)

Bertolotti, F. P.; Herbert, TH.; Spalart, P. R.

1992-01-01

Two new techniques for the study of the linear and nonlinear instability in growing boundary layers are presented. The first technique employs partial differential equations of parabolic type exploiting the slow change of the mean flow, disturbance velocity profiles, wavelengths, and growth rates in the streamwise direction. The second technique solves the Navier-Stokes equation for spatially evolving disturbances using buffer zones adjacent to the inflow and outflow boundaries. Results of both techniques are in excellent agreement. The linear and nonlinear development of Tollmien-Schlichting (TS) waves in the Blasius boundary layer is investigated with both techniques and with a local procedure based on a system of ordinary differential equations. The results are compared with previous work and the effects of non-parallelism and nonlinearity are clarified. The effect of nonparallelism is confirmed to be weak and, consequently, not responsible for the discrepancies between measurements and theoretical results for parallel flow.

Kinetic theory for electrostatic waves due to transverse velocity shears

NASA Technical Reports Server (NTRS)

Ganguli, G.; Lee, Y. C.; Palmadesso, P. J.

1988-01-01

A kinetic theory in the form of an integral equation is provided to study the electrostatic oscillations in a collisionless plasma immersed in a uniform magnetic field and a nonuniform transverse electric field. In the low temperature limit the dispersion differential equation is recovered for the transverse Kelvin-Helmholtz modes for arbitrary values of K parallel, where K parallel is the component of the wave vector in the direction of the external magnetic field assumed in the z direction. For higher temperatures the ion-cyclotron-like modes described earlier in the literature by Ganguli, Lee and Plamadesso are recovered. In this article, the integral equation is reduced to a second-order differential equation and a study is made of the kinetic Kelvin-Helmholtz and ion-cyclotron-like modes that constitute the two branches of oscillation in a magnetized plasma including a transverse inhomogeneous dc electric field.

Labeled trees and the efficient computation of derivations

NASA Technical Reports Server (NTRS)

Grossman, Robert; Larson, Richard G.

1989-01-01

The effective parallel symbolic computation of operators under composition is discussed. Examples include differential operators under composition and vector fields under the Lie bracket. Data structures consisting of formal linear combinations of rooted labeled trees are discussed. A multiplication on rooted labeled trees is defined, thereby making the set of these data structures into an associative algebra. An algebra homomorphism is defined from the original algebra of operators into this algebra of trees. An algebra homomorphism from the algebra of trees into the algebra of differential operators is then described. The cancellation which occurs when noncommuting operators are expressed in terms of commuting ones occurs naturally when the operators are represented using this data structure. This leads to an algorithm which, for operators which are derivations, speeds up the computation exponentially in the degree of the operator. It is shown that the algebra of trees leads naturally to a parallel version of the algorithm.

Discrete sensitivity derivatives of the Navier-Stokes equations with a parallel Krylov solver

NASA Technical Reports Server (NTRS)

Ajmani, Kumud; Taylor, Arthur C., III

1994-01-01

This paper solves an 'incremental' form of the sensitivity equations derived by differentiating the discretized thin-layer Navier Stokes equations with respect to certain design variables of interest. The equations are solved with a parallel, preconditioned Generalized Minimal RESidual (GMRES) solver on a distributed-memory architecture. The 'serial' sensitivity analysis code is parallelized by using the Single Program Multiple Data (SPMD) programming model, domain decomposition techniques, and message-passing tools. Sensitivity derivatives are computed for low and high Reynolds number flows over a NACA 1406 airfoil on a 32-processor Intel Hypercube, and found to be identical to those computed on a single-processor Cray Y-MP. It is estimated that the parallel sensitivity analysis code has to be run on 40-50 processors of the Intel Hypercube in order to match the single-processor processing time of a Cray Y-MP.

Parallel Selection Revealed by Population Sequencing in Chicken.

PubMed

Qanbari, Saber; Seidel, Michael; Strom, Tim-Mathias; Mayer, Klaus F X; Preisinger, Ruedi; Simianer, Henner

2015-11-13

Human-driven selection during domestication and subsequent breed formation has likely left detectable signatures within the genome of modern chicken. The elucidation of these signatures of selection is of interest from the perspective of evolutionary biology, and for identifying genes relevant to domestication and improvement that ultimately may help to further genetically improve this economically important animal. We used whole genome sequence data from 50 hens of commercial white (WL) and brown (BL) egg-laying chicken along with pool sequences of three meat-type chicken to perform a systematic screening of past selection in modern chicken. Evidence of positive selection was investigated in two steps. First, we explored evidence of parallel fixation in regions with overlapping elevated allele frequencies in replicated populations of layers and broilers, suggestive of selection during domestication or preimprovement ages. We confirmed parallel fixation in BCDO2 and TSHR genes and found four candidates including AGTR2, a gene heavily involved in "Ascites" in commercial birds. Next, we explored differentiated loci between layers and broilers suggestive of selection during improvement in chicken. This analysis revealed evidence of parallel differentiation in genes relevant to appearance and production traits exemplified with the candidate gene OPG, implicated in Osteoporosis, a disorder related to overconsumption of calcium in egg-laying hens. Our results illustrate the potential for population genetic techniques to identify genomic regions relevant to the phenotypes of importance to breeders. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Cell growth and differentiation on feeder layers is predicted to be influenced by bioreactor geometry.

PubMed

Peng, C A; Palsson, B Ø

1996-06-05

Tissue function is comprised of a complex interplay between biological and physicochemical rate processes. The design of bioreactors for tissue engineering must account for these processes simultaneously in order to obtain a bioreactor that provides a uniform environment for tissue growth and development. In the present study we consider the effects of fluid flow and mass transfer on the growth of a tissue in a parallel-plate bioreactor configuration. The parenchymal cells grow on a preformed stromal (feeder) layer that secretes a growth factor that stimulates parenchymal stem cell replication and differentiation. The biological dynamics are described by a unilineage model that describes the replication and differentiation of the tissue stem cell. The physicochemical rates are described by the Navier-Stokes and convective-diffusion equations. The model equations are solved by a finite element method. Two dimensionless groups govern the behavior of the solution. One is the Graetz number (Gz) that describes the relative rates of convection and diffusion, and the other a new dimensionless ratio (designated by P) that describes the interplay of the growth factor production, diffusion, and stimulation. Four geometries (slab, gondola, diamond, and radial shapes) for the parallel-plate bioreactor are analyzed. The uniformity of cell growth is measured by a two-dimensional coefficient of variance. The concentration distribution of the stroma-derived growth factor was computed first based on fluid flow and bioreactor geometry. Then the concomitant cell density distribution was obtained by integrating the calculated growth factor concentration with the parenchymal cell growth and unilineage differentiation process. The spatiotemporal cell growth patterns in four different bioreactor configurations were investigated under a variety of combinations of Gz (10(-1), 10(0), and 10(1)) and P(10(-2), 10(-1), 10(0), 10(1), and 10(2)). The results indicate high cell density and uniformity can be achieved for parameter values of P = 0.01, ..., 0.1 and Gz = 0.1, ..., 1.0. Among the four geometries investigated the radial-flow-type bioreactor provides the most uniform environment in which parenchymal cells can grow and differentiate ex vivo due to the absence of walls that are parallel to the flow paths creating slow flowing regions.

Multirate Integration Properties of Waveform Relaxation with Applications to Circuit Simulation and Parallel Computation

DTIC Science & Technology

1985-11-18

Greenberg and K. Sakallah at Digital Equipment Corporation, and C-F. Chen, L Nagel, and P. ,. Subrahmanyam at AT&T Bell Laboratories, both for providing...Circuit Theory McGraw-Hill, 1969. [37] R. Courant and D. Hilbert , Partial Differential Equations, Vol. 2 of Methods of Mathematical Physics...McGraw-Hill, N.Y., 1965. Page 161 [44) R. Courant and D. Hilbert , Partial Differential Equations, Vol. 2 of Methods of Mathematical Physics

Xyce Parallel Electronic Simulator Users' Guide Version 6.8

DOE Office of Scientific and Technical Information (OSTI.GOV)

Keiter, Eric R.; Aadithya, Karthik Venkatraman; Mei, Ting

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 onemore » 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.« less

New technologies for advanced three-dimensional optimum shape design in aeronautics

NASA Astrophysics Data System (ADS)

Dervieux, Alain; Lanteri, Stéphane; Malé, Jean-Michel; Marco, Nathalie; Rostaing-Schmidt, Nicole; Stoufflet, Bruno

1999-05-01

The analysis of complex flows around realistic aircraft geometries is becoming more and more predictive. In order to obtain this result, the complexity of flow analysis codes has been constantly increasing, involving more refined fluid models and sophisticated numerical methods. These codes can only run on top computers, exhausting their memory and CPU capabilities. It is, therefore, difficult to introduce best analysis codes in a shape optimization loop: most previous works in the optimum shape design field used only simplified analysis codes. Moreover, as the most popular optimization methods are the gradient-based ones, the more complex the flow solver, the more difficult it is to compute the sensitivity code. However, emerging technologies are contributing to make such an ambitious project, of including a state-of-the-art flow analysis code into an optimisation loop, feasible. Among those technologies, there are three important issues that this paper wishes to address: shape parametrization, automated differentiation and parallel computing. Shape parametrization allows faster optimization by reducing the number of design variable; in this work, it relies on a hierarchical multilevel approach. The sensitivity code can be obtained using automated differentiation. The automated approach is based on software manipulation tools, which allow the differentiation to be quick and the resulting differentiated code to be rather fast and reliable. In addition, the parallel algorithms implemented in this work allow the resulting optimization software to run on increasingly larger geometries. Copyright

Increasing morphological complexity in multiple parallel lineages of the Crustacea

PubMed Central

Adamowicz, Sarah J.; Purvis, Andy; Wills, Matthew A.

2008-01-01

The prospect of finding macroevolutionary trends and rules in the history of life is tremendously appealing, but very few pervasive trends have been found. Here, we demonstrate a parallel increase in the morphological complexity of most of the deep lineages within a major clade. We focus on the Crustacea, measuring the morphological differentiation of limbs. First, we show a clear trend of increasing complexity among 66 free-living, ordinal-level taxa from the Phanerozoic fossil record. We next demonstrate that this trend is pervasive, occurring in 10 or 11 of 12 matched-pair comparisons (across five morphological diversity indices) between extinct Paleozoic and related Recent taxa. This clearly differentiates the pattern from the effects of lineage sorting. Furthermore, newly appearing taxa tend to have had more types of limbs and a higher degree of limb differentiation than the contemporaneous average, whereas those going extinct showed higher-than-average limb redundancy. Patterns of contemporary species diversity partially reflect the paleontological trend. These results provide a rare demonstration of a large-scale and probably driven trend occurring across multiple independent lineages and influencing both the form and number of species through deep time and in the present day. PMID:18347335

Quaking Is a Key Regulator of Endothelial Cell Differentiation, Neovascularization, and Angiogenesis

PubMed Central

Cochrane, Amy; Kelaini, Sophia; Tsifaki, Marianna; Bojdo, James; Vilà‐González, Marta; Drehmer, Daiana; Caines, Rachel; Magee, Corey; Eleftheriadou, Magdalini; Hu, Yanhua; Grieve, David; Stitt, Alan W.; Zeng, Lingfang; Xu, Qingbo

2017-01-01

Abstract The capability to derive endothelial cell (ECs) from induced pluripotent stem cells (iPSCs) holds huge therapeutic potential for cardiovascular disease. This study elucidates the precise role of the RNA‐binding protein Quaking isoform 5 (QKI‐5) during EC differentiation from both mouse and human iPSCs (hiPSCs) and dissects how RNA‐binding proteins can improve differentiation efficiency toward cell therapy for important vascular diseases. iPSCs represent an attractive cellular approach for regenerative medicine today as they can be used to generate patient‐specific therapeutic cells toward autologous cell therapy. In this study, using the model of iPSCs differentiation toward ECs, the QKI‐5 was found to be an important regulator of STAT3 stabilization and vascular endothelial growth factor receptor 2 (VEGFR2) activation during the EC differentiation process. QKI‐5 was induced during EC differentiation, resulting in stabilization of STAT3 expression and modulation of VEGFR2 transcriptional activation as well as VEGF secretion through direct binding to the 3′ UTR of STAT3. Importantly, mouse iPS‐ECs overexpressing QKI‐5 significantly improved angiogenesis and neovascularization and blood flow recovery in experimental hind limb ischemia. Notably, hiPSCs overexpressing QKI‐5, induced angiogenesis on Matrigel plug assays in vivo only 7 days after subcutaneous injection in SCID mice. These results highlight a clear functional benefit of QKI‐5 in neovascularization, blood flow recovery, and angiogenesis. Thus, they provide support to the growing consensus that elucidation of the molecular mechanisms underlying EC differentiation will ultimately advance stem cell regenerative therapy and eventually make the treatment of cardiovascular disease a reality. The RNA binding protein QKI‐5 is induced during EC differentiation from iPSCs. RNA binding protein QKI‐5 was induced during EC differentiation in parallel with the EC marker CD144. Immunofluorescence staining showing that QKI‐5 is localized in the nucleus and stained in parallel with CD144 in differentiated ECs (scale bar = 50 µm). stem cells 2017 Stem Cells 2017;35:952–966 PMID:28207177

Reconstructing human pancreatic differentiation by mapping specific cell populations during development.

PubMed

Ramond, Cyrille; Glaser, Nicolas; Berthault, Claire; Ameri, Jacqueline; Kirkegaard, Jeannette Schlichting; Hansson, Mattias; Honoré, Christian; Semb, Henrik; Scharfmann, Raphaël

2017-07-21

Information remains scarce on human development compared to animal models. Here, we reconstructed human fetal pancreatic differentiation using cell surface markers. We demonstrate that at 7weeks of development, the glycoprotein 2 (GP2) marks a multipotent cell population that will differentiate into the acinar, ductal or endocrine lineages. Development towards the acinar lineage is paralleled by an increase in GP2 expression. Conversely, a subset of the GP2 + population undergoes endocrine differentiation by down-regulating GP2 and CD142 and turning on NEUROG3 , a marker of endocrine differentiation. Endocrine maturation progresses by up-regulating SUSD2 and lowering ECAD levels. Finally, in vitro differentiation of pancreatic endocrine cells derived from human pluripotent stem cells mimics key in vivo events. Our work paves the way to extend our understanding of the origin of mature human pancreatic cell types and how such lineage decisions are regulated.

Parallel processing of general and specific threat during early stages of perception

PubMed Central

2016-01-01

Differential processing of threat can consummate as early as 100 ms post-stimulus. Moreover, early perception not only differentiates threat from non-threat stimuli but also distinguishes among discrete threat subtypes (e.g. fear, disgust and anger). Combining spatial-frequency-filtered images of fear, disgust and neutral scenes with high-density event-related potentials and intracranial source estimation, we investigated the neural underpinnings of general and specific threat processing in early stages of perception. Conveyed in low spatial frequencies, fear and disgust images evoked convergent visual responses with similarly enhanced N1 potentials and dorsal visual (middle temporal gyrus) cortical activity (relative to neutral cues; peaking at 156 ms). Nevertheless, conveyed in high spatial frequencies, fear and disgust elicited divergent visual responses, with fear enhancing and disgust suppressing P1 potentials and ventral visual (occipital fusiform) cortical activity (peaking at 121 ms). Therefore, general and specific threat processing operates in parallel in early perception, with the ventral visual pathway engaged in specific processing of discrete threats and the dorsal visual pathway in general threat processing. Furthermore, selectively tuned to distinctive spatial-frequency channels and visual pathways, these parallel processes underpin dimensional and categorical threat characterization, promoting efficient threat response. These findings thus lend support to hybrid models of emotion. PMID:26412811

Assessment of phytoplankton class abundance using fluorescence excitation-emission matrix by parallel factor analysis and nonnegative least squares

NASA Astrophysics Data System (ADS)

Su, Rongguo; Chen, Xiaona; Wu, Zhenzhen; Yao, Peng; Shi, Xiaoyong

2015-07-01

The feasibility of using fluorescence excitation-emission matrix (EEM) along with parallel factor analysis (PARAFAC) and nonnegative least squares (NNLS) method for the differentiation of phytoplankton taxonomic groups was investigated. Forty-one phytoplankton species belonging to 28 genera of five divisions were studied. First, the PARAFAC model was applied to EEMs, and 15 fluorescence components were generated. Second, 15 fluorescence components were found to have a strong discriminating capability based on Bayesian discriminant analysis (BDA). Third, all spectra of the fluorescence component compositions for the 41 phytoplankton species were spectrographically sorted into 61 reference spectra using hierarchical cluster analysis (HCA), and then, the reference spectra were used to establish a database. Finally, the phytoplankton taxonomic groups was differentiated by the reference spectra database using the NNLS method. The five phytoplankton groups were differentiated with the correct discrimination ratios (CDRs) of 100% for single-species samples at the division level. The CDRs for the mixtures were above 91% for the dominant phytoplankton species and above 73% for the subdominant phytoplankton species. Sixteen of the 85 field samples collected from the Changjiang River estuary were analyzed by both HPLC-CHEMTAX and the fluorometric technique developed. The results of both methods reveal that Bacillariophyta was the dominant algal group in these 16 samples and that the subdominant algal groups comprised Dinophyta, Chlorophyta and Cryptophyta. The differentiation results by the fluorometric technique were in good agreement with those from HPLC-CHEMTAX. The results indicate that the fluorometric technique could differentiate algal taxonomic groups accurately at the division level.

Introduction to Numerical Methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schoonover, Joseph A.

2016-06-14

These are slides for a lecture for the Parallel Computing Summer Research Internship at the National Security Education Center. This gives an introduction to numerical methods. Repetitive algorithms are used to obtain approximate solutions to mathematical problems, using sorting, searching, root finding, optimization, interpolation, extrapolation, least squares regresion, Eigenvalue problems, ordinary differential equations, and partial differential equations. Many equations are shown. Discretizations allow us to approximate solutions to mathematical models of physical systems using a repetitive algorithm and introduce errors that can lead to numerical instabilities if we are not careful.

Cloning of Trametes versicolar genes induced by nitrogen starvation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Trudel, P.; Courchesne, D.; Roy, C.

1988-06-01

We have screened a genomic library of Trametes versicolar for genes whose expression is associated with nitrogen starvation, which has been shown to induce ligninolytic activity. Using two different approaches based on differential expression, we isolated 29 clones. These were shown by restriction mapping and cross-hybridization to code for 11 distinct differentially expressed genes. Northern analysis of the kinetics of expression of these genes revealed that at least four of them have kinetics of induction that parallel kinetics of induction of ligninolytic activity.

Plasmonic Nanoholes in a Multi-Channel Microarray Format for Parallel Kinetic Assays and Differential Sensing

PubMed Central

Im, Hyungsoon; Lesuffleur, Antoine; Lindquist, Nathan C.; Oh, Sang-Hyun

2009-01-01

We present nanohole arrays in a gold film integrated with a 6-channel microfluidic chip for parallel measurements of molecular binding kinetics. Surface plasmon resonance effects in the nanohole arrays enable real-time label-free measurements of molecular binding events in each channel, while adjacent negative reference channels can record measurement artifacts such as bulk solution index changes, temperature variations, or changing light absorption in the liquid. Using this platform, streptavidin-biotin specific binding kinetics are measured at various concentrations with negative controls. A high-density microarray of 252 biosensing pixels is also demonstrated with a packing density of 106 sensing elements/cm2, which can potentially be coupled with a massively parallel array of microfluidic channels for protein microarray applications. PMID:19284776

Differential clinical efficacy of anti-CD4 monoclonal antibodies in rat adjuvant arthritis is paralleled by differential influence on NF-κB binding activity and TNF-α secretion of T cells

PubMed Central

Pohlers, Dirk; Schmidt-Weber, Carsten B; Franch, Angels; Kuhlmann, Jürgen; Bräuer, Rolf; Emmrich, Frank; Kinne, Raimund W

2002-01-01

The aim of this study was to analyze the differential effects of three anti-CD4 monoclonal antibodies (mAbs) (with distinct epitope specifities) in the treatment of rat adjuvant arthritis (AA) and on T-cell function and signal transduction. Rat AA was preventively treated by intraperitoneal injection of the anti-CD4 mAbs W3/25, OX35, and RIB5/2 (on days -1, 0, 3, and 6, i.e. 1 day before AA induction, on the day of induction [day 0], and thereafter). The effects on T-cell reactivity in vivo (delayed-type hypersensitivity), ex vivo (ConA-induced proliferation), and in vitro (mixed lymphocyte culture) were assessed. The in vitro effects of anti-CD4 preincubation on T-cell receptor (TCR)/CD3-induced cytokine production and signal transduction were also analyzed. While preventive treatment with OX35 and W3/25 significantly ameliorated AA from the onset, treatment with RIB5/2 even accelerated the onset of AA by approximately 2 days (day 10), and ameliorated the arthritis only in the late phase (day 27). Differential clinical effects at the onset of AA were paralleled by a differential influence of the mAbs on T-cell functions, i.e. in comparison with OX35 and W3/25, the 'accelerating' mAb RIB5/2 failed to increase the delayed-type hypersentivity (DTH) to Mycobacterium tuberculosis, increased the in vitro tumor necrosis factor (TNF)-α secretion, and more strongly induced NF-κB binding activity after anti-CD4 preincubation and subsequent TCR/CD3-stimulation. Depending on their epitope specificity, different anti-CD4 mAbs differentially influence individual proinflammatory functions of T cells. This fine regulation may explain the differential efficacy in the treatment of AA and may contribute to the understanding of such treatments in other immunopathologies. PMID:12010568

Xyce™ Parallel Electronic Simulator Users' Guide, Version 6.5.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Keiter, Eric R.; Aadithya, Karthik V.; Mei, Ting

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: Capability to solve extremely large circuit problems by supporting large-scale parallel computing 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 developmore » 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. The information herein is subject to change without notice. Copyright © 2002-2016 Sandia Corporation. All rights reserved.« less

Evaluation of a new parallel numerical parameter optimization algorithm for a dynamical system

NASA Astrophysics Data System (ADS)

Duran, Ahmet; Tuncel, Mehmet

2016-10-01

It is important to have a scalable parallel numerical parameter optimization algorithm for a dynamical system used in financial applications where time limitation is crucial. We use Message Passing Interface parallel programming and present such a new parallel algorithm for parameter estimation. For example, we apply the algorithm to the asset flow differential equations that have been developed and analyzed since 1989 (see [3-6] and references contained therein). We achieved speed-up for some time series to run up to 512 cores (see [10]). Unlike [10], we consider more extensive financial market situations, for example, in presence of low volatility, high volatility and stock market price at a discount/premium to its net asset value with varying magnitude, in this work. Moreover, we evaluated the convergence of the model parameter vector, the nonlinear least squares error and maximum improvement factor to quantify the success of the optimization process depending on the number of initial parameter vectors.

Multigrid methods with space–time concurrency

DOE PAGES

Falgout, R. D.; Friedhoff, S.; Kolev, Tz. V.; ...

2017-10-06

Here, we consider the comparison of multigrid methods for parabolic partial differential equations that allow space–time concurrency. With current trends in computer architectures leading towards systems with more, but not faster, processors, space–time concurrency is crucial for speeding up time-integration simulations. In contrast, traditional time-integration techniques impose serious limitations on parallel performance due to the sequential nature of the time-stepping approach, allowing spatial concurrency only. This paper considers the three basic options of multigrid algorithms on space–time grids that allow parallelism in space and time: coarsening in space and time, semicoarsening in the spatial dimensions, and semicoarsening in the temporalmore » dimension. We develop parallel software and performance models to study the three methods at scales of up to 16K cores and introduce an extension of one of them for handling multistep time integration. We then discuss advantages and disadvantages of the different approaches and their benefit compared to traditional space-parallel algorithms with sequential time stepping on modern architectures.« less

Increasing the reach of forensic genetics with massively parallel sequencing.

PubMed

Budowle, Bruce; Schmedes, Sarah E; Wendt, Frank R

2017-09-01

The field of forensic genetics has made great strides in the analysis of biological evidence related to criminal and civil matters. More so, the discipline has set a standard of performance and quality in the forensic sciences. The advent of massively parallel sequencing will allow the field to expand its capabilities substantially. This review describes the salient features of massively parallel sequencing and how it can impact forensic genetics. The features of this technology offer increased number and types of genetic markers that can be analyzed, higher throughput of samples, and the capability of targeting different organisms, all by one unifying methodology. While there are many applications, three are described where massively parallel sequencing will have immediate impact: molecular autopsy, microbial forensics and differentiation of monozygotic twins. The intent of this review is to expose the forensic science community to the potential enhancements that have or are soon to arrive and demonstrate the continued expansion the field of forensic genetics and its service in the investigation of legal matters.

Parallel Fortran-MPI software for numerical inversion of the Laplace transform and its application to oscillatory water levels in groundwater environments

USGS Publications Warehouse

Zhan, X.

2005-01-01

A parallel Fortran-MPI (Message Passing Interface) software for numerical inversion of the Laplace transform based on a Fourier series method is developed to meet the need of solving intensive computational problems involving oscillatory water level's response to hydraulic tests in a groundwater environment. The software is a parallel version of ACM (The Association for Computing Machinery) Transactions on Mathematical Software (TOMS) Algorithm 796. Running 38 test examples indicated that implementation of MPI techniques with distributed memory architecture speedups the processing and improves the efficiency. Applications to oscillatory water levels in a well during aquifer tests are presented to illustrate how this package can be applied to solve complicated environmental problems involved in differential and integral equations. The package is free and is easy to use for people with little or no previous experience in using MPI but who wish to get off to a quick start in parallel computing. ?? 2004 Elsevier Ltd. All rights reserved.

Multigrid methods with space–time concurrency

DOE Office of Scientific and Technical Information (OSTI.GOV)

Falgout, R. D.; Friedhoff, S.; Kolev, Tz. V.

Here, we consider the comparison of multigrid methods for parabolic partial differential equations that allow space–time concurrency. With current trends in computer architectures leading towards systems with more, but not faster, processors, space–time concurrency is crucial for speeding up time-integration simulations. In contrast, traditional time-integration techniques impose serious limitations on parallel performance due to the sequential nature of the time-stepping approach, allowing spatial concurrency only. This paper considers the three basic options of multigrid algorithms on space–time grids that allow parallelism in space and time: coarsening in space and time, semicoarsening in the spatial dimensions, and semicoarsening in the temporalmore » dimension. We develop parallel software and performance models to study the three methods at scales of up to 16K cores and introduce an extension of one of them for handling multistep time integration. We then discuss advantages and disadvantages of the different approaches and their benefit compared to traditional space-parallel algorithms with sequential time stepping on modern architectures.« less

ANNarchy: a code generation approach to neural simulations on parallel hardware

PubMed Central

Vitay, Julien; Dinkelbach, Helge Ü.; Hamker, Fred H.

2015-01-01

Many modern neural simulators focus on the simulation of networks of spiking neurons on parallel hardware. Another important framework in computational neuroscience, rate-coded neural networks, is mostly difficult or impossible to implement using these simulators. We present here the ANNarchy (Artificial Neural Networks architect) neural simulator, which allows to easily define and simulate rate-coded and spiking networks, as well as combinations of both. The interface in Python has been designed to be close to the PyNN interface, while the definition of neuron and synapse models can be specified using an equation-oriented mathematical description similar to the Brian neural simulator. This information is used to generate C++ code that will efficiently perform the simulation on the chosen parallel hardware (multi-core system or graphical processing unit). Several numerical methods are available to transform ordinary differential equations into an efficient C++code. We compare the parallel performance of the simulator to existing solutions. PMID:26283957

PIXIE3D: A Parallel, Implicit, eXtended MHD 3D Code

NASA Astrophysics Data System (ADS)

Chacon, Luis

2006-10-01

We report on the development of PIXIE3D, a 3D parallel, fully implicit Newton-Krylov extended MHD code in general curvilinear geometry. PIXIE3D employs a second-order, finite-volume-based spatial discretization that satisfies remarkable properties such as being conservative, solenoidal in the magnetic field to machine precision, non-dissipative, and linearly and nonlinearly stable in the absence of physical dissipation. PIXIE3D employs fully-implicit Newton-Krylov methods for the time advance. Currently, second-order implicit schemes such as Crank-Nicolson and BDF2 (2^nd order backward differentiation formula) are available. PIXIE3D is fully parallel (employs PETSc for parallelism), and exhibits excellent parallel scalability. A parallel, scalable, MG preconditioning strategy, based on physics-based preconditioning ideas, has been developed for resistive MHD, and is currently being extended to Hall MHD. In this poster, we will report on progress in the algorithmic formulation for extended MHD, as well as the the serial and parallel performance of PIXIE3D in a variety of problems and geometries. L. Chac'on, Comput. Phys. Comm., 163 (3), 143-171 (2004) L. Chac'on et al., J. Comput. Phys. 178 (1), 15- 36 (2002); J. Comput. Phys., 188 (2), 573-592 (2003) L. Chac'on, 32nd EPS Conf. Plasma Physics, Tarragona, Spain, 2005 L. Chac'on et al., 33rd EPS Conf. Plasma Physics, Rome, Italy, 2006

Arkas: Rapid reproducible RNAseq analysis

PubMed Central

Colombo, Anthony R.; J. Triche Jr, Timothy; Ramsingh, Giridharan

2017-01-01

The recently introduced Kallisto pseudoaligner has radically simplified the quantification of transcripts in RNA-sequencing experiments.  We offer cloud-scale RNAseq pipelines Arkas-Quantification, and Arkas-Analysis available within Illumina’s BaseSpace cloud application platform which expedites Kallisto preparatory routines, reliably calculates differential expression, and performs gene-set enrichment of REACTOME pathways .  Due to inherit inefficiencies of scale, Illumina's BaseSpace computing platform offers a massively parallel distributive environment improving data management services and data importing.   Arkas-Quantification deploys Kallisto for parallel cloud computations and is conveniently integrated downstream from the BaseSpace Sequence Read Archive (SRA) import/conversion application titled SRA Import.  Arkas-Analysis annotates the Kallisto results by extracting structured information directly from source FASTA files with per-contig metadata, calculates the differential expression and gene-set enrichment analysis on both coding genes and transcripts. The Arkas cloud pipeline supports ENSEMBL transcriptomes and can be used downstream from the SRA Import facilitating raw sequencing importing, SRA FASTQ conversion, RNA quantification and analysis steps. PMID:28868134

Multiscale Simulations of Magnetic Island Coalescence

NASA Technical Reports Server (NTRS)

Dorelli, John C.

2010-01-01

We describe a new interactive parallel Adaptive Mesh Refinement (AMR) framework written in the Python programming language. This new framework, PyAMR, hides the details of parallel AMR data structures and algorithms (e.g., domain decomposition, grid partition, and inter-process communication), allowing the user to focus on the development of algorithms for advancing the solution of a systems of partial differential equations on a single uniform mesh. We demonstrate the use of PyAMR by simulating the pairwise coalescence of magnetic islands using the resistive Hall MHD equations. Techniques for coupling different physics models on different levels of the AMR grid hierarchy are discussed.

In-memory integration of existing software components for parallel adaptive unstructured mesh workflows

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smith, Cameron W.; Granzow, Brian; Diamond, Gerrett

Unstructured mesh methods, like finite elements and finite volumes, support the effective analysis of complex physical behaviors modeled by partial differential equations over general threedimensional domains. The most reliable and efficient methods apply adaptive procedures with a-posteriori error estimators that indicate where and how the mesh is to be modified. Although adaptive meshes can have two to three orders of magnitude fewer elements than a more uniform mesh for the same level of accuracy, there are many complex simulations where the meshes required are so large that they can only be solved on massively parallel systems.

In-memory integration of existing software components for parallel adaptive unstructured mesh workflows

DOE PAGES

Smith, Cameron W.; Granzow, Brian; Diamond, Gerrett; ...

2017-01-01

Unstructured mesh methods, like finite elements and finite volumes, support the effective analysis of complex physical behaviors modeled by partial differential equations over general threedimensional domains. The most reliable and efficient methods apply adaptive procedures with a-posteriori error estimators that indicate where and how the mesh is to be modified. Although adaptive meshes can have two to three orders of magnitude fewer elements than a more uniform mesh for the same level of accuracy, there are many complex simulations where the meshes required are so large that they can only be solved on massively parallel systems.

Arcmancer: Geodesics and polarized radiative transfer library

NASA Astrophysics Data System (ADS)

Pihajoki, Pauli; Mannerkoski, Matias; Nättilä, Joonas; Johansson, Peter H.

2018-05-01

Arcmancer computes geodesics and performs polarized radiative transfer in user-specified spacetimes. The library supports Riemannian and semi-Riemannian spaces of any dimension and metric; it also supports multiple simultaneous coordinate charts, embedded geometric shapes, local coordinate systems, and automatic parallel propagation. Arcmancer can be used to solve various problems in numerical geometry, such as solving the curve equation of motion using adaptive integration with configurable tolerances and differential equations along precomputed curves. It also provides support for curves with an arbitrary acceleration term and generic tools for generating ray initial conditions and performing parallel computation over the image, among other tools.

Computational Challenges of 3D Radiative Transfer in Atmospheric Models

NASA Astrophysics Data System (ADS)

Jakub, Fabian; Bernhard, Mayer

2017-04-01

The computation of radiative heating and cooling rates is one of the most expensive components in todays atmospheric models. The high computational cost stems not only from the laborious integration over a wide range of the electromagnetic spectrum but also from the fact that solving the integro-differential radiative transfer equation for monochromatic light is already rather involved. This lead to the advent of numerous approximations and parameterizations to reduce the cost of the solver. One of the most prominent one is the so called independent pixel approximations (IPA) where horizontal energy transfer is neglected whatsoever and radiation may only propagate in the vertical direction (1D). Recent studies implicate that the IPA introduces significant errors in high resolution simulations and affects the evolution and development of convective systems. However, using fully 3D solvers such as for example MonteCarlo methods is not even on state of the art supercomputers feasible. The parallelization of atmospheric models is often realized by a horizontal domain decomposition, and hence, horizontal transfer of energy necessitates communication. E.g. a cloud's shadow at a low zenith angle will cast a long shadow and potentially needs to communication through a multitude of processors. Especially light in the solar spectral range may travel long distances through the atmosphere. Concerning highly parallel simulations, it is vital that 3D radiative transfer solvers put a special emphasis on parallel scalability. We will present an introduction to intricacies computing 3D radiative heating and cooling rates as well as report on the parallel performance of the TenStream solver. The TenStream is a 3D radiative transfer solver using the PETSc framework to iteratively solve a set of partial differential equation. We investigate two matrix preconditioners, (a) geometric algebraic multigrid preconditioning(MG+GAMG) and (b) block Jacobi incomplete LU (ILU) factorization. The TenStream solver is tested for up to 4096 cores and shows a parallel scaling efficiency of 80-90% on various supercomputers.

The end of gonad-centric sex determination in mammals

PubMed Central

Arnold, Arthur P.

2011-01-01

The 20th century theory of mammalian sex determination states that the embryo is sexually indifferent until the differentiation of gonads, after which sex differences in phenotype are caused by differential effects of gonadal hormones. That theory is inadequate because some sex differences precede differentiation of the gonads and/or are determined by non-gonadal effects of the sexual inequality in number and type of sex chromosomes. A general theory of sex determination is proposed, which recognizes multiple parallel primary sex-determining pathways initiated by genes or factors encoded by the sex chromosomes. The separate sex-specific pathways interact to synergize with or antagonize each other, enhancing or reducing sex differences in phenotype. PMID:22078126

Comment on Schuster's Technique for Focusing the Prism Spectrometer.

ERIC Educational Resources Information Center

Beynon, John

1991-01-01

Discussed is the physics that underpins Schuster's technique for obtaining a parallel light beam for use in various prism and grating experiments. Basic physics concepts using geometrical optics of prism, together with elementary differential calculus are explained as well as the mechanics of Schuster's technique. (KR)

Extendability of parallel sections in vector bundles

NASA Astrophysics Data System (ADS)

Kirschner, Tim

2016-01-01

I address the following question: Given a differentiable manifold M, what are the open subsets U of M such that, for all vector bundles E over M and all linear connections ∇ on E, any ∇-parallel section in E defined on U extends to a ∇-parallel section in E defined on M? For simply connected manifolds M (among others) I describe the entirety of all such sets U which are, in addition, the complement of a C1 submanifold, boundary allowed, of M. This delivers a partial positive answer to a problem posed by Antonio J. Di Scala and Gianni Manno (2014). Furthermore, in case M is an open submanifold of Rn, n ≥ 2, I prove that the complement of U in M, not required to be a submanifold now, can have arbitrarily large n-dimensional Lebesgue measure.

Reconstructing human pancreatic differentiation by mapping specific cell populations during development

PubMed Central

Ramond, Cyrille; Glaser, Nicolas; Berthault, Claire; Ameri, Jacqueline; Kirkegaard, Jeannette Schlichting; Hansson, Mattias; Honoré, Christian; Semb, Henrik; Scharfmann, Raphaël

2017-01-01

Information remains scarce on human development compared to animal models. Here, we reconstructed human fetal pancreatic differentiation using cell surface markers. We demonstrate that at 7weeks of development, the glycoprotein 2 (GP2) marks a multipotent cell population that will differentiate into the acinar, ductal or endocrine lineages. Development towards the acinar lineage is paralleled by an increase in GP2 expression. Conversely, a subset of the GP2+ population undergoes endocrine differentiation by down-regulating GP2 and CD142 and turning on NEUROG3, a marker of endocrine differentiation. Endocrine maturation progresses by up-regulating SUSD2 and lowering ECAD levels. Finally, in vitro differentiation of pancreatic endocrine cells derived from human pluripotent stem cells mimics key in vivo events. Our work paves the way to extend our understanding of the origin of mature human pancreatic cell types and how such lineage decisions are regulated. DOI: http://dx.doi.org/10.7554/eLife.27564.001 PMID:28731406

Accelerating the Gillespie Exact Stochastic Simulation Algorithm using hybrid parallel execution on graphics processing units.

PubMed

Komarov, Ivan; D'Souza, Roshan M

2012-01-01

The Gillespie Stochastic Simulation Algorithm (GSSA) and its variants are cornerstone techniques to simulate reaction kinetics in situations where the concentration of the reactant is too low to allow deterministic techniques such as differential equations. The inherent limitations of the GSSA include the time required for executing a single run and the need for multiple runs for parameter sweep exercises due to the stochastic nature of the simulation. Even very efficient variants of GSSA are prohibitively expensive to compute and perform parameter sweeps. Here we present a novel variant of the exact GSSA that is amenable to acceleration by using graphics processing units (GPUs). We parallelize the execution of a single realization across threads in a warp (fine-grained parallelism). A warp is a collection of threads that are executed synchronously on a single multi-processor. Warps executing in parallel on different multi-processors (coarse-grained parallelism) simultaneously generate multiple trajectories. Novel data-structures and algorithms reduce memory traffic, which is the bottleneck in computing the GSSA. Our benchmarks show an 8×-120× performance gain over various state-of-the-art serial algorithms when simulating different types of models.

Toward an automated parallel computing environment for geosciences

NASA Astrophysics Data System (ADS)

Zhang, Huai; Liu, Mian; Shi, Yaolin; Yuen, David A.; Yan, Zhenzhen; Liang, Guoping

2007-08-01

Software for geodynamic modeling has not kept up with the fast growing computing hardware and network resources. In the past decade supercomputing power has become available to most researchers in the form of affordable Beowulf clusters and other parallel computer platforms. However, to take full advantage of such computing power requires developing parallel algorithms and associated software, a task that is often too daunting for geoscience modelers whose main expertise is in geosciences. We introduce here an automated parallel computing environment built on open-source algorithms and libraries. Users interact with this computing environment by specifying the partial differential equations, solvers, and model-specific properties using an English-like modeling language in the input files. The system then automatically generates the finite element codes that can be run on distributed or shared memory parallel machines. This system is dynamic and flexible, allowing users to address different problems in geosciences. It is capable of providing web-based services, enabling users to generate source codes online. This unique feature will facilitate high-performance computing to be integrated with distributed data grids in the emerging cyber-infrastructures for geosciences. In this paper we discuss the principles of this automated modeling environment and provide examples to demonstrate its versatility.

Differential encoding of spatial information among retinal on cone bipolar cells

PubMed Central

Purgert, Robert J.

2015-01-01

The retina is the first stage of visual processing. It encodes elemental features of visual scenes. Distinct cone bipolar cells provide the substrate for this to occur. They encode visual information, such as color and luminance, a principle known as parallel processing. Few studies have directly examined whether different forms of spatial information are processed in parallel among cone bipolar cells. To address this issue, we examined the spatial information encoded by mouse ON cone bipolar cells, the subpopulation excited by increments in illumination. Two types of spatial processing were identified. We found that ON cone bipolar cells with axons ramifying in the central inner plexiform layer were tuned to preferentially encode small stimuli. By contrast, ON cone bipolar cells with axons ramifying in the proximal inner plexiform layer, nearest the ganglion cell layer, were tuned to encode both small and large stimuli. This dichotomy in spatial tuning is attributable to amacrine cells providing stronger inhibition to central ON cone bipolar cells compared with proximal ON cone bipolar cells. Furthermore, background illumination altered this difference in spatial tuning. It became less pronounced in bright light, as amacrine cell-driven inhibition became pervasive among all ON cone bipolar cells. These results suggest that differential amacrine cell input determined the distinct spatial encoding properties among ON cone bipolar cells. These findings enhance the known parallel processing capacity of the retina. PMID:26203104

On a model of three-dimensional bursting and its parallel implementation

NASA Astrophysics Data System (ADS)

Tabik, S.; Romero, L. F.; Garzón, E. M.; Ramos, J. I.

2008-04-01

A mathematical model for the simulation of three-dimensional bursting phenomena and its parallel implementation are presented. The model consists of four nonlinearly coupled partial differential equations that include fast and slow variables, and exhibits bursting in the absence of diffusion. The differential equations have been discretized by means of a second-order accurate in both space and time, linearly-implicit finite difference method in equally-spaced grids. The resulting system of linear algebraic equations at each time level has been solved by means of the Preconditioned Conjugate Gradient (PCG) method. Three different parallel implementations of the proposed mathematical model have been developed; two of these implementations, i.e., the MPI and the PETSc codes, are based on a message passing paradigm, while the third one, i.e., the OpenMP code, is based on a shared space address paradigm. These three implementations are evaluated on two current high performance parallel architectures, i.e., a dual-processor cluster and a Shared Distributed Memory (SDM) system. A novel representation of the results that emphasizes the most relevant factors that affect the performance of the paralled implementations, is proposed. The comparative analysis of the computational results shows that the MPI and the OpenMP implementations are about twice more efficient than the PETSc code on the SDM system. It is also shown that, for the conditions reported here, the nonlinear dynamics of the three-dimensional bursting phenomena exhibits three stages characterized by asynchronous, synchronous and then asynchronous oscillations, before a quiescent state is reached. It is also shown that the fast system reaches steady state in much less time than the slow variables.

Differentiating Categories and Dimensions: Evaluating the Robustness of Taxometric Analyses

ERIC Educational Resources Information Center

Ruscio, John; Kaczetow, Walter

2009-01-01

Interest in modeling the structure of latent variables is gaining momentum, and many simulation studies suggest that taxometric analysis can validly assess the relative fit of categorical and dimensional models. The generation and parallel analysis of categorical and dimensional comparison data sets reduces the subjectivity required to interpret…

Documenting Reproduction and Inequality: Revisiting Jean Anyon's "Social Class and School Knowledge"

ERIC Educational Resources Information Center

Luke, Allan

2010-01-01

Jean Anyon's (1981) "Social Class and School Knowledge" was a landmark work in North American educational research. It provided a richly detailed qualitative description of differential, social class-based constructions of knowledge and epistemological stance. This essay situates Anyon's work in two parallel traditions of critical educational…

Analysis of a Delayed Delta Modulator.

DTIC Science & Technology

1983-05-01

parallels that of Janardhanan [10] for DPCM with matched integra- tion of stationary first-order Gauss-Markov input. In Subsection A the limiting...181, 1978. [10] JANARDHANAN , E., "Differential PCM -ystems", IEEE Trans. Conmmun., vol. Com-27, pp. 82-93, 1979. [111 KANTOROVICI, L.V. and KRYLOV, V.I

Differential Geometry and Lie Groups for Physicists

NASA Astrophysics Data System (ADS)

Fecko, Marián.

2006-10-01

Introduction; 1. The concept of a manifold; 2. Vector and tensor fields; 3. Mappings of tensors induced by mappings of manifolds; 4. Lie derivative; 5. Exterior algebra; 6. Differential calculus of forms; 7. Integral calculus of forms; 8. Particular cases and applications of Stoke's Theorem; 9. Poincaré Lemma and cohomologies; 10. Lie Groups - basic facts; 11. Differential geometry of Lie Groups; 12. Representations of Lie Groups and Lie Algebras; 13. Actions of Lie Groups and Lie Algebras on manifolds; 14. Hamiltonian mechanics and symplectic manifolds; 15. Parallel transport and linear connection on M; 16. Field theory and the language of forms; 17. Differential geometry on TM and T*M; 18. Hamiltonian and Lagrangian equations; 19. Linear connection and the frame bundle; 20. Connection on a principal G-bundle; 21. Gauge theories and connections; 22. Spinor fields and Dirac operator; Appendices; Bibliography; Index.

Differential Geometry and Lie Groups for Physicists

NASA Astrophysics Data System (ADS)

Fecko, Marián.

2011-03-01

Introduction; 1. The concept of a manifold; 2. Vector and tensor fields; 3. Mappings of tensors induced by mappings of manifolds; 4. Lie derivative; 5. Exterior algebra; 6. Differential calculus of forms; 7. Integral calculus of forms; 8. Particular cases and applications of Stoke's Theorem; 9. Poincaré Lemma and cohomologies; 10. Lie Groups - basic facts; 11. Differential geometry of Lie Groups; 12. Representations of Lie Groups and Lie Algebras; 13. Actions of Lie Groups and Lie Algebras on manifolds; 14. Hamiltonian mechanics and symplectic manifolds; 15. Parallel transport and linear connection on M; 16. Field theory and the language of forms; 17. Differential geometry on TM and T*M; 18. Hamiltonian and Lagrangian equations; 19. Linear connection and the frame bundle; 20. Connection on a principal G-bundle; 21. Gauge theories and connections; 22. Spinor fields and Dirac operator; Appendices; Bibliography; Index.

Volcanic Record of the Halawa Excursion (ca 2.514+/-0.039 Ma), Koolau Volcano, Oahu Hawaii, USA: Full Vector Analyses

NASA Astrophysics Data System (ADS)

Lau, J.; Herrero-Bervera, E.

2007-05-01

New paleomagnetic measurements (directions and paleointensity determinations), coupled with precise 40Ar/39Ar radioisotopic dating, are revolutionizing our understanding of the geodynamo by providing detailed terrestrial lava records of the short-term behavior of the paleomagnetic field. As part of an investigation of the evolution of Koolau Volcano (one of the volcanoes comprising Oahu Island) and the short-term behavior of the geomagnetic field, we have sampled a long volcanic section located on the buttressed flank of the volcano within Halawa Valley. Prior paleomagnetic and K-Ar investigations of the Koolau (Volcano) Series revealed excursional directions (Site F of Doell and Dalrymple, 1973). The alkaline composition of lava flows, easy access, and close geographical proximity to K-Ar dated lava flows made this newly studied 120 m thick sequence of flows in Halawa valley an excellent candidate for detailed paleomagnetic analysis. At least eight samples collected from each of 28 successive flow-sites were stepwise demagnetized by both alternating field (5mT to 100mT) and thermal (from 28° C to 575-650°C) methods, and the mean directions obtained by principal component analysis. All samples yielded a strong and stable ChRM trending towards the origin based on no less than seven to nine steps, with thermal and AF results agreeing to a very high degree. Low field susceptibility versus temperature (k-T) analyses were conducted for individual lava flows, and the majority of them show reversible curves. Curie point determinations revealed a temperature close to or equal to 580°C, indicative of almost pure magnetite for most of the flows. Magnetic grain sizes analysis indicated SD-PSD sizes. The mean directions of magnetization of the entire section sampled indicate that about 10 m of the section are characterized by excursional directions (5 lava flows). In addition to the directional analyses we performed absolute paleointensity determinations on the 28 lavas sampled. We used the modified Thellier-Coe double heating method to determine paleointensities. pTRM checks were performed systematically one temperature step down the last pTRM acquisition in order to document magnetomineralogical changes during heating. The temperature was incremented by steps of 50°C between room temperature and 500°C and every 25-30°C. The paleointensity determinations were obtained from the slope of the Arai diagrams. Special care was taken to interpret the Arai diagrams within the same range of temperatures lower than 300°C unless a clear and unique slope would be present. Our paleointensity results indicate a near-zero reduced strength of the field during the excursional period ranging from 5 to 9 micro-Tesla. The corresponding VGPs are located off the southeast part of Africa, close to Madagascar. 40Ar/39Ar incremental heating experiments on groundmass from nine flow-sites located at different stratigraphic levels yielded isochron ages ranging from 2.64+/-0.25 to 2.40+/-0.46 Ma indicating that the excursion may correlate with the C2r.2r-l Cryptochron of Cande and Kent [1995]. This is potentially the first terrestrial record of the ca. 2.514 +/- 0.039 Ma Cryptochron, a finding that will place important constraints on evolution of the entire Koolau shield edifice also.

Full Vector Analyses of Cryptochron C2r.2r-l (ca. 2.42-2.44 Ma) Recorded on Koolau Volcano at Halawa, Oahu, Hawaii: Evidence From Directions, Absolute Paleointensity Determinations and 40Ar/39Ar Studies.

NASA Astrophysics Data System (ADS)

Browne, E. J.; Herrero-Bervera, E.; Singer, B.

2005-12-01

New paleomagnetic measurements (directions and paleointensity determinations), coupled with precise 40Ar/39Ar radioisotopic dating, are revolutionizing our understanding of the geodynamo by providing detailed terrestrial lava records of the short-term behavior of the paleomagnetic field. As part of an investigation of the evolution of Koolau Volcano (one of the volcanoes comprising Oahu Island) and the short-term behavior of the geomagnetic field, we have sampled a long volcanic section located on the buttressed flank of the volcano within Halawa Valley. Prior paleomagnetic and K-Ar investigations of the Koolau (Volcano) Series revealed excursional directions (Site F of Doell and Dalrymple, 1973). The alkaline composition of lava flows, easy access, and close geographical proximity to K-Ar dated lava flows made this newly studied 120 m thick sequence of flows in Halawa valley an excellent candidate for detailed paleomagnetic analysis. At least eight samples collected from each of 28 successive flow-sites were stepwise demagnetized by both alternating field (5mT to 100mT) and thermal (from 28o C to 575-650oC) methods, and the mean directions obtained by principal component analysis. All samples yielded a strong and stable ChRM trending towards the origin based on no less than seven to nine steps, with thermal and AF results agreeing to a very high degree. Low field susceptibility versus temperature (k-T) analyses were conducted for individual lava flows, and the majority of them show reversible curves. Curie point determinations revealed a temperature close to or equal to 580oC, indicative of almost pure magnetite for most of the flows. Magnetic grain sizes analysis indicated SD-PSD sizes. The mean directions of magnetization of the entire section sampled indicate that about 10 m of the section are characterized by excursional directions (5 lava flows). In addition to the directional analyses we performed absolute paleointensity determinations on the 28 lavas sampled. We used the modified Thellier-Coe double heating method to determine paleointensities. pTRM checks were performed systematically one temperature step down the last pTRM acquisition in order to document magnetomineralogical changes during heating. The temperature was incremented by steps of 50o C between room temperature and 500oC and every 25-30o C. The paleointensity determinations were obtained from the slope of the Arai diagrams. Special care was taken to interpret the Arai diagrams within the same range of temperatures lower than 300oC unless a clear and unique slope would be present. Our paleointensity results indicate a near-zero reduced strength of the field during the excursional period ranging from 5 to 9 micro-Tesla. The corresponding VGPs are located off the southeast part of Africa, close to Madagascar. Initial 40Ar/39Ar incremental heating experiments on groundmass from nine flow-sites located at different stratigraphic levels yielded isochron ages ranging from 2.64+/-0.25 to 2.40+/-0.46 Ma indicating that the excursion may correlate with the C2r.2r-l Cryptochron of Cande and Kent [1995]. this is potentially the first terrestrial record of the ca. 2.4 Ma Cryptochron, a finding that will place important constraints on evolution of the entire Koolau shield edifice also.

Geomagnetic Field Inclinations and Absolute Paleointensities for a 350 kyr Time gap From the 350m Core of the Kalihi Scientific Drilling Project Recovered From the Ko'olau Volcano, O'ahu, Hawai'i

NASA Astrophysics Data System (ADS)

Herrero-Bervera, E.; Garcia, M. O.; Valet, J.; Haskins, E.

2002-12-01

In order to investigate the volcanic evolution of the Ko'olau Volcano, O'ahu, Hawai'i and the geomagnetic field behavior recorded by the lavas, a paleomagnetic and rock magnetic was conducted on a 350 m thick sequence of flows from the Kalihi Scientific Drilling Project. This drill core records geomagnetic field inclination for the period approximately between 2.75 to 3.1 Ma. The core extends deeper stratigraphically any surface exposures of the volcano and the rocks obtained have experienced less tropical weathering than surface rocks. Previous published work on Ko'olau has indicated that the volcano was formed during the Matuyama Chron (Doell and Dalrymple, 1973, GSA Bull, 84, 127-42). We drilled multiple one-inch long samples from each of the 103 flows in the drill core section. The paleomagnetic results of all the specimens were stepwise demagnetized by alternating fields from 5-100mT. Companion specimens from the same core were demagnetized at 15 temperature steps. In both cases the demagnetization diagrams obtained with each technique showed a stable and unambiguous characteristic direction of remanence (ChRM). The ChRM calculated using principal component analysis for the demagnetization diagrams with a well-defined component trending towards the origin. No bias or systematic departure from the origin was accepted and in all cases the ChRM relies on a minimum of seven successive directions isolated during demagnetization. In addtion, low-field susceptibility versus temperature (k-T) and SIRM experiments were performed on a dozen or so flows at different levels of the core. As a result of such tests, we were able to identify magnetite and and in few instances a low-temperature mineral phase (300-400 oC), reflecting the presence of titanomagnetite with low Ti content as suggested by its large susceptibility. We used the modified Thellier-Coe double heating method to determine paleointensities. pTRM checks were performed systematically one temperature step down the last pTRM acquisition in order to document magnetomineralogical changes during heating. We were able to obtain paleointensity determination for 25 lavas (out of 103 flows) which represent about 25 percent success rate. The analyses reveals two instances of near-zero and two instances of low negative inclination (reversed polarity, 7.5 uT of low paleointensity) within an otherwise normal polarity. In particular, flow units 34-50 record a horizontal inclination and may be associated with the top of the Kaena Subchron. This interpretation is supported also by two Ar-Ar age determinations for flow 14 (2.89+/-0.12 Ma) and flow 66 (3.06+/-0.15 Ma old), and subaerial lavas at several localities where the Reunion II Subchron (ca. 2.11 to 2.15 Ma) is recorded and which previous results were reported by Herrero-Bervera et al (2002, PEPI, 129, 83-98). Our findings lead us to conclude that the growth of the Ko'olau Volcano was concomitant with respect to the youngest exposed lavas of the Wai'anae Volcano and both were forming during the Kaena Subchron.

Population annealing with weighted averages: A Monte Carlo method for rough free-energy landscapes

NASA Astrophysics Data System (ADS)

Machta, J.

2010-08-01

The population annealing algorithm introduced by Hukushima and Iba is described. Population annealing combines simulated annealing and Boltzmann weighted differential reproduction within a population of replicas to sample equilibrium states. Population annealing gives direct access to the free energy. It is shown that unbiased measurements of observables can be obtained by weighted averages over many runs with weight factors related to the free-energy estimate from the run. Population annealing is well suited to parallelization and may be a useful alternative to parallel tempering for systems with rough free-energy landscapes such as spin glasses. The method is demonstrated for spin glasses.

Serial multiplier arrays for parallel computation

NASA Technical Reports Server (NTRS)

Winters, Kel

1990-01-01

Arrays of systolic serial-parallel multiplier elements are proposed as an alternative to conventional SIMD mesh serial adder arrays for applications that are multiplication intensive and require few stored operands. The design and operation of a number of multiplier and array configurations featuring locality of connection, modularity, and regularity of structure are discussed. A design methodology combining top-down and bottom-up techniques is described to facilitate development of custom high-performance CMOS multiplier element arrays as well as rapid synthesis of simulation models and semicustom prototype CMOS components. Finally, a differential version of NORA dynamic circuits requiring a single-phase uncomplemented clock signal introduced for this application.

An interfering Go/No-go task does not affect accuracy in a Concealed Information Test.

PubMed

Ambach, Wolfgang; Stark, Rudolf; Peper, Martin; Vaitl, Dieter

2008-04-01

Following the idea that response inhibition processes play a central role in concealing information, the present study investigated the influence of a Go/No-go task as an interfering mental activity, performed parallel to the Concealed Information Test (CIT), on the detectability of concealed information. 40 undergraduate students participated in a mock-crime experiment and simultaneously performed a CIT and a Go/No-go task. Electrodermal activity (EDA), respiration line length (RLL), heart rate (HR) and finger pulse waveform length (FPWL) were registered. Reaction times were recorded as behavioral measures in the Go/No-go task as well as in the CIT. As a within-subject control condition, the CIT was also applied without an additional task. The parallel task did not influence the mean differences of the physiological measures of the mock-crime-related probe and the irrelevant items. This finding might possibly be due to the fact that the applied parallel task induced a tonic rather than a phasic mental activity, which did not influence differential responding to CIT items. No physiological evidence for an interaction between the parallel task and sub-processes of deception (e.g. inhibition) was found. Subjects' performance in the Go/No-go parallel task did not contribute to the detection of concealed information. Generalizability needs further investigations of different variations of the parallel task.

An object-oriented approach for parallel self adaptive mesh refinement on block structured grids

NASA Technical Reports Server (NTRS)

Lemke, Max; Witsch, Kristian; Quinlan, Daniel

1993-01-01

Self-adaptive mesh refinement dynamically matches the computational demands of a solver for partial differential equations to the activity in the application's domain. In this paper we present two C++ class libraries, P++ and AMR++, which significantly simplify the development of sophisticated adaptive mesh refinement codes on (massively) parallel distributed memory architectures. The development is based on our previous research in this area. The C++ class libraries provide abstractions to separate the issues of developing parallel adaptive mesh refinement applications into those of parallelism, abstracted by P++, and adaptive mesh refinement, abstracted by AMR++. P++ is a parallel array class library to permit efficient development of architecture independent codes for structured grid applications, and AMR++ provides support for self-adaptive mesh refinement on block-structured grids of rectangular non-overlapping blocks. Using these libraries, the application programmers' work is greatly simplified to primarily specifying the serial single grid application and obtaining the parallel and self-adaptive mesh refinement code with minimal effort. Initial results for simple singular perturbation problems solved by self-adaptive multilevel techniques (FAC, AFAC), being implemented on the basis of prototypes of the P++/AMR++ environment, are presented. Singular perturbation problems frequently arise in large applications, e.g. in the area of computational fluid dynamics. They usually have solutions with layers which require adaptive mesh refinement and fast basic solvers in order to be resolved efficiently.

Mesenchymal stem cells and myoblast differentiation under HGF and IGF-1 stimulation for 3D skeletal muscle tissue engineering.

PubMed

Witt, R; Weigand, A; Boos, A M; Cai, A; Dippold, D; Boccaccini, A R; Schubert, D W; Hardt, M; Lange, C; Arkudas, A; Horch, R E; Beier, J P

2017-02-28

Volumetric muscle loss caused by trauma or after tumour surgery exceeds the natural regeneration capacity of skeletal muscle. Hence, the future goal of tissue engineering (TE) is the replacement and repair of lost muscle tissue by newly generating skeletal muscle combining different cell sources, such as myoblasts and mesenchymal stem cells (MSCs), within a three-dimensional matrix. Latest research showed that seeding skeletal muscle cells on aligned constructs enhance the formation of myotubes as well as cell alignment and may provide a further step towards the clinical application of engineered skeletal muscle. In this study the myogenic differentiation potential of MSCs upon co-cultivation with myoblasts and under stimulation with hepatocyte growth factor (HGF) and insulin-like growth factor-1 (IGF-1) was evaluated. We further analysed the behaviour of MSC-myoblast co-cultures in different 3D matrices. Primary rat myoblasts and rat MSCs were mono- and co-cultivated for 2, 7 or 14 days. The effect of different concentrations of HGF and IGF-1 alone, as well as in combination, on myogenic differentiation was analysed using microscopy, multicolour flow cytometry and real-time PCR. Furthermore, the influence of different three-dimensional culture models, such as fibrin, fibrin-collagen-I gels and parallel aligned electrospun poly-ε-caprolacton collagen-I nanofibers, on myogenic differentiation was analysed. MSCs could be successfully differentiated into the myogenic lineage both in mono- and in co-cultures independent of HGF and IGF-1 stimulation by expressing desmin, myocyte enhancer factor 2, myosin heavy chain 2 and alpha-sarcomeric actinin. An increased expression of different myogenic key markers could be observed under HGF and IGF-1 stimulation. Even though, stimulation with HGF/IGF-1 does not seem essential for sufficient myogenic differentiation. Three-dimensional cultivation in fibrin-collagen-I gels induced higher levels of myogenic differentiation compared with two-dimensional experiments. Cultivation on poly-ε-caprolacton-collagen-I nanofibers induced parallel alignment of cells and positive expression of desmin. In this study, we were able to myogenically differentiate MSC upon mono- and co-cultivation with myoblasts. The addition of HGF/IGF-1 might not be essential for achieving successful myogenic differentiation. Furthermore, with the development of a biocompatible nanofiber scaffold we established the basis for further experiments aiming at the generation of functional muscle tissue.

An Artificial Neural Networks Method for Solving Partial Differential Equations

NASA Astrophysics Data System (ADS)

Alharbi, Abir

2010-09-01

While there already exists many analytical and numerical techniques for solving PDEs, this paper introduces an approach using artificial neural networks. The approach consists of a technique developed by combining the standard numerical method, finite-difference, with the Hopfield neural network. The method is denoted Hopfield-finite-difference (HFD). The architecture of the nets, energy function, updating equations, and algorithms are developed for the method. The HFD method has been used successfully to approximate the solution of classical PDEs, such as the Wave, Heat, Poisson and the Diffusion equations, and on a system of PDEs. The software Matlab is used to obtain the results in both tabular and graphical form. The results are similar in terms of accuracy to those obtained by standard numerical methods. In terms of speed, the parallel nature of the Hopfield nets methods makes them easier to implement on fast parallel computers while some numerical methods need extra effort for parallelization.

Experiments with a Parallel Multi-Objective Evolutionary Algorithm for Scheduling

NASA Technical Reports Server (NTRS)

Brown, Matthew; Johnston, Mark D.

2013-01-01

Evolutionary multi-objective algorithms have great potential for scheduling in those situations where tradeoffs among competing objectives represent a key requirement. One challenge, however, is runtime performance, as a consequence of evolving not just a single schedule, but an entire population, while attempting to sample the Pareto frontier as accurately and uniformly as possible. The growing availability of multi-core processors in end user workstations, and even laptops, has raised the question of the extent to which such hardware can be used to speed up evolutionary algorithms. In this paper we report on early experiments in parallelizing a Generalized Differential Evolution (GDE) algorithm for scheduling long-range activities on NASA's Deep Space Network. Initial results show that significant speedups can be achieved, but that performance does not necessarily improve as more cores are utilized. We describe our preliminary results and some initial suggestions from parallelizing the GDE algorithm. Directions for future work are outlined.

Efficient parallel architecture for highly coupled real-time linear system applications

NASA Technical Reports Server (NTRS)

Carroll, Chester C.; Homaifar, Abdollah; Barua, Soumavo

1988-01-01

A systematic procedure is developed for exploiting the parallel constructs of computation in a highly coupled, linear system application. An overall top-down design approach is adopted. Differential equations governing the application under consideration are partitioned into subtasks on the basis of a data flow analysis. The interconnected task units constitute a task graph which has to be computed in every update interval. Multiprocessing concepts utilizing parallel integration algorithms are then applied for efficient task graph execution. A simple scheduling routine is developed to handle task allocation while in the multiprocessor mode. Results of simulation and scheduling are compared on the basis of standard performance indices. Processor timing diagrams are developed on the basis of program output accruing to an optimal set of processors. Basic architectural attributes for implementing the system are discussed together with suggestions for processing element design. Emphasis is placed on flexible architectures capable of accommodating widely varying application specifics.

Evaluation of massively parallel sequencing for forensic DNA methylation profiling.

PubMed

Richards, Rebecca; Patel, Jayshree; Stevenson, Kate; Harbison, SallyAnn

2018-05-11

Epigenetics is an emerging area of interest in forensic science. DNA methylation, a type of epigenetic modification, can be applied to chronological age estimation, identical twin differentiation and body fluid identification. However, there is not yet an agreed, established methodology for targeted detection and analysis of DNA methylation markers in forensic research. Recently a massively parallel sequencing-based approach has been suggested. The use of massively parallel sequencing is well established in clinical epigenetics and is emerging as a new technology in the forensic field. This review investigates the potential benefits, limitations and considerations of this technique for the analysis of DNA methylation in a forensic context. The importance of a robust protocol, regardless of the methodology used, that minimises potential sources of bias is highlighted. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Acoustooptic linear algebra processors - Architectures, algorithms, and applications

NASA Technical Reports Server (NTRS)

Casasent, D.

1984-01-01

Architectures, algorithms, and applications for systolic processors are described with attention to the realization of parallel algorithms on various optical systolic array processors. Systolic processors for matrices with special structure and matrices of general structure, and the realization of matrix-vector, matrix-matrix, and triple-matrix products and such architectures are described. Parallel algorithms for direct and indirect solutions to systems of linear algebraic equations and their implementation on optical systolic processors are detailed with attention to the pipelining and flow of data and operations. Parallel algorithms and their optical realization for LU and QR matrix decomposition are specifically detailed. These represent the fundamental operations necessary in the implementation of least squares, eigenvalue, and SVD solutions. Specific applications (e.g., the solution of partial differential equations, adaptive noise cancellation, and optimal control) are described to typify the use of matrix processors in modern advanced signal processing.

Parallel O(N) Stokes’ solver towards scalable Brownian dynamics of hydrodynamically interacting objects in general geometries

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, Xujun; Li, Jiyuan; Jiang, Xikai

An efficient parallel Stokes’s solver is developed towards the complete inclusion of hydrodynamic interactions of Brownian particles in any geometry. A Langevin description of the particle dynamics is adopted, where the long-range interactions are included using a Green’s function formalism. We present a scalable parallel computational approach, where the general geometry Stokeslet is calculated following a matrix-free algorithm using the General geometry Ewald-like method. Our approach employs a highly-efficient iterative finite element Stokes’ solver for the accurate treatment of long-range hydrodynamic interactions within arbitrary confined geometries. A combination of mid-point time integration of the Brownian stochastic differential equation, the parallelmore » Stokes’ solver, and a Chebyshev polynomial approximation for the fluctuation-dissipation theorem result in an O(N) parallel algorithm. We also illustrate the new algorithm in the context of the dynamics of confined polymer solutions in equilibrium and non-equilibrium conditions. Our method is extended to treat suspended finite size particles of arbitrary shape in any geometry using an Immersed Boundary approach.« less

Domain decomposition methods for the parallel computation of reacting flows

NASA Technical Reports Server (NTRS)

Keyes, David E.

1988-01-01

Domain decomposition is a natural route to parallel computing for partial differential equation solvers. Subdomains of which the original domain of definition is comprised are assigned to independent processors at the price of periodic coordination between processors to compute global parameters and maintain the requisite degree of continuity of the solution at the subdomain interfaces. In the domain-decomposed solution of steady multidimensional systems of PDEs by finite difference methods using a pseudo-transient version of Newton iteration, the only portion of the computation which generally stands in the way of efficient parallelization is the solution of the large, sparse linear systems arising at each Newton step. For some Jacobian matrices drawn from an actual two-dimensional reacting flow problem, comparisons are made between relaxation-based linear solvers and also preconditioned iterative methods of Conjugate Gradient and Chebyshev type, focusing attention on both iteration count and global inner product count. The generalized minimum residual method with block-ILU preconditioning is judged the best serial method among those considered, and parallel numerical experiments on the Encore Multimax demonstrate for it approximately 10-fold speedup on 16 processors.

Evolution method and ``differential hierarchy'' of colored knot polynomials

NASA Astrophysics Data System (ADS)

Mironov, A.; Morozov, A.; Morozov, And.

2013-10-01

We consider braids with repeating patterns inside arbitrary knots which provides a multi-parametric family of knots, depending on the "evolution" parameter, which controls the number of repetitions. The dependence of knot (super)polynomials on such evolution parameters is very easy to find. We apply this evolution method to study of the families of knots and links which include the cases with just two parallel and anti-parallel strands in the braid, like the ordinary twist and 2-strand torus knots/links and counter-oriented 2-strand links. When the answers were available before, they are immediately reproduced, and an essentially new example is added of the "double braid", which is a combination of parallel and anti-parallel 2-strand braids. This study helps us to reveal with the full clarity and partly investigate a mysterious hierarchical structure of the colored HOMFLY polynomials, at least, in (anti)symmetric representations, which extends the original observation for the figure-eight knot to many (presumably all) knots. We demonstrate that this structure is typically respected by the t-deformation to the superpolynomials.

Parallel O(N) Stokes’ solver towards scalable Brownian dynamics of hydrodynamically interacting objects in general geometries

DOE PAGES

Zhao, Xujun; Li, Jiyuan; Jiang, Xikai; ...

2017-06-29

An efficient parallel Stokes’s solver is developed towards the complete inclusion of hydrodynamic interactions of Brownian particles in any geometry. A Langevin description of the particle dynamics is adopted, where the long-range interactions are included using a Green’s function formalism. We present a scalable parallel computational approach, where the general geometry Stokeslet is calculated following a matrix-free algorithm using the General geometry Ewald-like method. Our approach employs a highly-efficient iterative finite element Stokes’ solver for the accurate treatment of long-range hydrodynamic interactions within arbitrary confined geometries. A combination of mid-point time integration of the Brownian stochastic differential equation, the parallelmore » Stokes’ solver, and a Chebyshev polynomial approximation for the fluctuation-dissipation theorem result in an O(N) parallel algorithm. We also illustrate the new algorithm in the context of the dynamics of confined polymer solutions in equilibrium and non-equilibrium conditions. Our method is extended to treat suspended finite size particles of arbitrary shape in any geometry using an Immersed Boundary approach.« less

Twostep-by-twostep PIRK-type PC methods with continuous output formulas

NASA Astrophysics Data System (ADS)

Cong, Nguyen Huu; Xuan, Le Ngoc

2008-11-01

This paper deals with parallel predictor-corrector (PC) iteration methods based on collocation Runge-Kutta (RK) corrector methods with continuous output formulas for solving nonstiff initial-value problems (IVPs) for systems of first-order differential equations. At nth step, the continuous output formulas are used not only for predicting the stage values in the PC iteration methods but also for calculating the step values at (n+2)th step. In this case, the integration processes can be proceeded twostep-by-twostep. The resulting twostep-by-twostep (TBT) parallel-iterated RK-type (PIRK-type) methods with continuous output formulas (twostep-by-twostep PIRKC methods or TBTPIRKC methods) give us a faster integration process. Fixed stepsize applications of these TBTPIRKC methods to a few widely-used test problems reveal that the new PC methods are much more efficient when compared with the well-known parallel-iterated RK methods (PIRK methods), parallel-iterated RK-type PC methods with continuous output formulas (PIRKC methods) and sequential explicit RK codes DOPRI5 and DOP853 available from the literature.

Glycolysis, but not Mitochondria, responsible for intracellular ATP distribution in cortical area of podocytes.

PubMed

Ozawa, Shota; Ueda, Shuko; Imamura, Hiromi; Mori, Kiyoshi; Asanuma, Katsuhiko; Yanagita, Motoko; Nakagawa, Takahiko

2015-12-18

Differentiated podocytes, a type of renal glomerular cells, require substantial levels of energy to maintain glomerular physiology. Mitochondria and glycolysis are two major producers of ATP, but the precise roles of each in podocytes remain unknown. This study evaluated the roles of mitochondria and glycolysis in differentiated and differentiating podocytes. Mitochondria in differentiated podocytes are located in the central part of cell body while blocking mitochondria had minor effects on cell shape and migratory ability. In contrast, blocking glycolysis significantly reduced the formation of lamellipodia, a cortical area of these cells, decreased the cell migratory ability and induced the apoptosis. Consistently, the local ATP production in lamellipodia was predominantly regulated by glycolysis. In turn, synaptopodin expression was ameliorated by blocking either mitochondrial respiration or glycolysis. Similar to differentiated podocytes, the differentiating podocytes utilized the glycolysis for regulating apoptosis and lamellipodia formation while synaptopodin expression was likely involved in both mitochondrial OXPHOS and glycolysis. Finally, adult mouse podocytes have most of mitochondria predominantly in the center of the cytosol whereas phosphofructokinase, a rate limiting enzyme for glycolysis, was expressed in foot processes. These data suggest that mitochondria and glycolysis play parallel but distinct roles in differentiated and differentiating podocytes.

Glycolysis, but not Mitochondria, responsible for intracellular ATP distribution in cortical area of podocytes

PubMed Central

Ozawa, Shota; Ueda, Shuko; Imamura, Hiromi; Mori, Kiyoshi; Asanuma, Katsuhiko; Yanagita, Motoko; Nakagawa, Takahiko

2015-01-01

Differentiated podocytes, a type of renal glomerular cells, require substantial levels of energy to maintain glomerular physiology. Mitochondria and glycolysis are two major producers of ATP, but the precise roles of each in podocytes remain unknown. This study evaluated the roles of mitochondria and glycolysis in differentiated and differentiating podocytes. Mitochondria in differentiated podocytes are located in the central part of cell body while blocking mitochondria had minor effects on cell shape and migratory ability. In contrast, blocking glycolysis significantly reduced the formation of lamellipodia, a cortical area of these cells, decreased the cell migratory ability and induced the apoptosis. Consistently, the local ATP production in lamellipodia was predominantly regulated by glycolysis. In turn, synaptopodin expression was ameliorated by blocking either mitochondrial respiration or glycolysis. Similar to differentiated podocytes, the differentiating podocytes utilized the glycolysis for regulating apoptosis and lamellipodia formation while synaptopodin expression was likely involved in both mitochondrial OXPHOS and glycolysis. Finally, adult mouse podocytes have most of mitochondria predominantly in the center of the cytosol whereas phosphofructokinase, a rate limiting enzyme for glycolysis, was expressed in foot processes. These data suggest that mitochondria and glycolysis play parallel but distinct roles in differentiated and differentiating podocytes. PMID:26677804

Carpet: Adaptive Mesh Refinement for the Cactus Framework

NASA Astrophysics Data System (ADS)

Schnetter, Erik; Hawley, Scott; Hawke, Ian

2016-11-01

Carpet is an adaptive mesh refinement and multi-patch driver for the Cactus Framework (ascl:1102.013). Cactus is a software framework for solving time-dependent partial differential equations on block-structured grids, and Carpet acts as driver layer providing adaptive mesh refinement, multi-patch capability, as well as parallelization and efficient I/O.

Parallel changes in genital morphology delineate cryptic diversification of planktonic nudibranchs

PubMed Central

Churchill, Celia K. C.; Alejandrino, Alvin; Valdés, Ángel; Ó Foighil, Diarmaid

2013-01-01

The relative roles of geographical and non-geographical barriers in the genesis of genetic isolation are highly debated in evolutionary biology, yet knowing how speciation occurs is essential to our understanding of biodiversity. In the open ocean, differentiating between the two is particularly difficult, because of the high levels of gene flow found in pelagic communities. Here, we use molecular phylogenetics to test the hypothesis that geography is the primary isolating mechanism in a clade of pelagic nudibranchs, Glaucinae. Our results contradict allopatric expectations: the cosmopolitan Glaucus atlanticus is panmictic, whereas the Indo-Pacific Glaucus marginatus contains two pairs of cryptic species with overlapping distributions. Within the G. marginatus species complex, a parallel reproductive change has occurred in each cryptic species pair: the loss of a bursa copulatrix. Available G. marginatus data are most consistent with non-geographical speciation events, but we cannot rule out the possibility of allopatric speciation, followed by iterative range extension and secondary overlap. Irrespective of ancestral range distributions, our results implicate a central role for reproductive character differentiation in glaucinin speciation—a novel result in a planktonic system. PMID:23825213

A domain-specific compiler for a parallel multiresolution adaptive numerical simulation environment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rajbhandari, Samyam; Kim, Jinsung; Krishnamoorthy, Sriram

This paper describes the design and implementation of a layered domain-specific compiler to support MADNESS---Multiresolution ADaptive Numerical Environment for Scientific Simulation. MADNESS is a high-level software environment for the solution of integral and differential equations in many dimensions, using adaptive and fast harmonic analysis methods with guaranteed precision. MADNESS uses k-d trees to represent spatial functions and implements operators like addition, multiplication, differentiation, and integration on the numerical representation of functions. The MADNESS runtime system provides global namespace support and a task-based execution model including futures. MADNESS is currently deployed on massively parallel supercomputers and has enabled many science advances.more » Due to the highly irregular and statically unpredictable structure of the k-d trees representing the spatial functions encountered in MADNESS applications, only purely runtime approaches to optimization have previously been implemented in the MADNESS framework. This paper describes a layered domain-specific compiler developed to address some performance bottlenecks in MADNESS. The newly developed static compile-time optimizations, in conjunction with the MADNESS runtime support, enable significant performance improvement for the MADNESS framework.« less

Refraction of high frequency noise in an arbitrary jet flow

NASA Technical Reports Server (NTRS)

Khavaran, Abbas; Krejsa, Eugene A.

1994-01-01

Refraction of high frequency noise by mean flow gradients in a jet is studied using the ray-tracing methods of geometrical acoustics. Both the two-dimensional (2D) and three-dimensional (3D) formulations are considered. In the former case, the mean flow is assumed parallel and the governing propagation equations are described by a system of four first order ordinary differential equations. The 3D formulation, on the other hand, accounts for the jet spreading as well as the axial flow development. In this case, a system of six first order differential equations are solved to trace a ray from its source location to an observer in the far field. For subsonic jets with a small spreading angle both methods lead to similar results outside the zone of silence. However, with increasing jet speed the two prediction models diverge to the point where the parallel flow assumption is no longer justified. The Doppler factor of supersonic jets as influenced by the refraction effects is discussed and compared with the conventional modified Doppler factor.

Spatial and temporal accuracy of asynchrony-tolerant finite difference schemes for partial differential equations at extreme scales

NASA Astrophysics Data System (ADS)

Kumari, Komal; Donzis, Diego

2017-11-01

Highly resolved computational simulations on massively parallel machines are critical in understanding the physics of a vast number of complex phenomena in nature governed by partial differential equations. Simulations at extreme levels of parallelism present many challenges with communication between processing elements (PEs) being a major bottleneck. In order to fully exploit the computational power of exascale machines one needs to devise numerical schemes that relax global synchronizations across PEs. This asynchronous computations, however, have a degrading effect on the accuracy of standard numerical schemes.We have developed asynchrony-tolerant (AT) schemes that maintain order of accuracy despite relaxed communications. We show, analytically and numerically, that these schemes retain their numerical properties with multi-step higher order temporal Runge-Kutta schemes. We also show that for a range of optimized parameters,the computation time and error for AT schemes is less than their synchronous counterpart. Stability of the AT schemes which depends upon history and random nature of delays, are also discussed. Support from NSF is gratefully acknowledged.

Modification of the parallel scattering mean free path of cosmic rays in the presence of adiabatic focusing

DOE Office of Scientific and Technical Information (OSTI.GOV)

He, H.-Q.; Schlickeiser, R., E-mail: hqhe@mail.iggcas.ac.cn, E-mail: rsch@tp4.rub.de

The cosmic ray mean free path in a large-scale nonuniform guide magnetic field with superposed magnetostatic turbulence is calculated to clarify some conflicting results in the literature. A new, exact integro-differential equation for the cosmic-ray anisotropy is derived from the Fokker-Planck transport equation. A perturbation analysis of this integro-differential equation leads to an analytical expression for the cosmic ray anisotropy and the focused transport equation for the isotropic part of the cosmic ray distribution function. The derived parallel spatial diffusion coefficient and the associated cosmic ray mean free path include the effect of adiabatic focusing and reduce to the standardmore » forms in the limit of a uniform guide magnetic field. For the illustrative case of isotropic pitch angle scattering, the derived mean free path agrees with the earlier expressions of Beeck and Wibberenz, Bieber and Burger, Kota, and Litvinenko, but disagrees with the result of Shalchi. The disagreement with the expression of Shalchi is particularly strong in the limit of strong adiabatic focusing.« less

Radiative transfer in a sphere illuminated by a parallel beam - An integral equation approach. [in planetary atmosphere

NASA Technical Reports Server (NTRS)

Shia, R.-L.; Yung, Y. L.

1986-01-01

The problem of multiple scattering of nonpolarized light in a planetary body of arbitrary shape illuminated by a parallel beam is formulated using the integral equation approach. There exists a simple functional whose stationarity condition is equivalent to solving the equation of radiative transfer and whose value at the stationary point is proportional to the differential cross section. The analysis reveals a direct relation between the microscopic symmetry of the phase function for each scattering event and the macroscopic symmetry of the differential cross section for the entire planetary body, and the interconnection of these symmetry relations and the variational principle. The case of a homogeneous sphere containing isotropic scatterers is investigated in detail. It is shown that the solution can be expanded in a multipole series such that the general spherical problem is reduced to solving a set of decoupled integral equations in one dimension. Computations have been performed for a range of parameters of interest, and illustrative examples of applications to planetary problems as provided.

Dax1 and Nanog act in parallel to stabilize mouse embryonic stem cells and induced pluripotency

PubMed Central

Zhang, Junlei; Liu, Gaoke; Ruan, Yan; Wang, Jiali; Zhao, Ke; Wan, Ying; Liu, Bing; Zheng, Hongting; Peng, Tao; Wu, Wei; He, Ping; Hu, Fu-Quan; Jian, Rui

2014-01-01

Nanog expression is heterogeneous and dynamic in embryonic stem cells (ESCs). However, the mechanism for stabilizing pluripotency during the transitions between Nanoghigh and Nanoglow states is not well understood. Here we report that Dax1 acts in parallel with Nanog to regulate mouse ESC (mESCs) identity. Dax1 stable knockdown mESCs are predisposed towards differentiation but do not lose pluripotency, whereas Dax1 overexpression supports LIF-independent self-renewal. Although partially complementary, Dax1 and Nanog function independently and cannot replace one another. They are both required for full reprogramming to induce pluripotency. Importantly, Dax1 is indispensable for self-renewal of Nanoglow mESCs. Moreover, we report that Dax1 prevents extra-embryonic endoderm (ExEn) commitment by directly repressing Gata6 transcription. Dax1 may also mediate inhibition of trophectoderm differentiation independent or as a downstream effector of Oct4. These findings establish a basal role of Dax1 in maintaining pluripotency during the state transition of mESCs and somatic cell reprogramming. PMID:25284313

Parallels between Global Transcriptional Programs of Polarizing Caco-2 Intestinal Epithelial Cells In Vitro and Gene Expression Programs in Normal Colon and Colon Cancer

PubMed Central

Sääf, Annika M.; Halbleib, Jennifer M.; Chen, Xin; Yuen, Siu Tsan; Leung, Suet Yi

2007-01-01

Posttranslational mechanisms are implicated in the development of epithelial cell polarity, but little is known about the patterns of gene expression and transcriptional regulation during this process. We characterized temporal patterns of gene expression during cell–cell adhesion-initiated polarization of cultured human Caco-2 cells, which develop structural and functional polarity resembling enterocytes in vivo. A distinctive switch in gene expression patterns occurred upon formation of cell–cell contacts. Comparison to gene expression patterns in normal human colon and colon tumors revealed that the pattern in proliferating, nonpolarized Caco-2 cells paralleled patterns seen in human colon cancer in vivo, including expression of genes involved in cell proliferation. The pattern switched in polarized Caco-2 cells to one more closely resembling that in normal colon tissue, indicating that regulation of transcription underlying Caco-2 cell polarization is similar to that during enterocyte differentiation in vivo. Surprisingly, the temporal program of gene expression in polarizing Caco-2 cells involved changes in signaling pathways (e.g., Wnt, Hh, BMP, FGF) in patterns similar to those during migration and differentiation of intestinal epithelial cells in vivo, despite the absence of morphogen gradients and interactions with stromal cells characteristic of enterocyte differentiation in situ. The full data set is available at http://microarray-pubs.stanford.edu/CACO2. PMID:17699589

SAChES: Scalable Adaptive Chain-Ensemble Sampling.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Swiler, Laura Painton; Ray, Jaideep; Ebeida, Mohamed Salah

We present the development of a parallel Markov Chain Monte Carlo (MCMC) method called SAChES, Scalable Adaptive Chain-Ensemble Sampling. This capability is targed to Bayesian calibration of com- putationally expensive simulation models. SAChES involves a hybrid of two methods: Differential Evo- lution Monte Carlo followed by Adaptive Metropolis. Both methods involve parallel chains. Differential evolution allows one to explore high-dimensional parameter spaces using loosely coupled (i.e., largely asynchronous) chains. Loose coupling allows the use of large chain ensembles, with far more chains than the number of parameters to explore. This reduces per-chain sampling burden, enables high-dimensional inversions and the usemore » of computationally expensive forward models. The large number of chains can also ameliorate the impact of silent-errors, which may affect only a few chains. The chain ensemble can also be sampled to provide an initial condition when an aberrant chain is re-spawned. Adaptive Metropolis takes the best points from the differential evolution and efficiently hones in on the poste- rior density. The multitude of chains in SAChES is leveraged to (1) enable efficient exploration of the parameter space; and (2) ensure robustness to silent errors which may be unavoidable in extreme-scale computational platforms of the future. This report outlines SAChES, describes four papers that are the result of the project, and discusses some additional results.« less

Biophysical regulation of stem cell differentiation.

PubMed

Govey, Peter M; Loiselle, Alayna E; Donahue, Henry J

2013-06-01

Bone adaptation to its mechanical environment, from embryonic through adult life, is thought to be the product of increased osteoblastic differentiation from mesenchymal stem cells. In parallel with tissue-scale loading, these heterogeneous populations of multipotent stem cells are subject to a variety of biophysical cues within their native microenvironments. Bone marrow-derived mesenchymal stem cells-the most broadly studied source of osteoblastic progenitors-undergo osteoblastic differentiation in vitro in response to biophysical signals, including hydrostatic pressure, fluid flow and accompanying shear stress, substrate strain and stiffness, substrate topography, and electromagnetic fields. Furthermore, stem cells may be subject to indirect regulation by mechano-sensing osteocytes positioned to more readily detect these same loading-induced signals within the bone matrix. Such paracrine and juxtacrine regulation of differentiation by osteocytes occurs in vitro. Further studies are needed to confirm both direct and indirect mechanisms of biophysical regulation within the in vivo stem cell niche.

Investigation of electrophoretic exclusion method for the concentration and differentiation of proteins.

PubMed

Meighan, Michelle M; Vasquez, Jared; Dziubcynski, Luke; Hews, Sarah; Hayes, Mark A

2011-01-01

This work presents a technique termed as "electrophoretic exclusion" that is capable of differentiation and concentration of proteins in bulk solution. In this method, a hydrodynamic flow is countered by the electrophoretic velocity to prevent a species from entering into a channel. The separation can be controlled by changing the flow rate or applied electric potential in order to exclude a certain species selectively while allowing others to pass through the capillary. The exclusion of various proteins is investigated using a flow-injection regime of the method. Concentration of myoglobin of up to 1200 times the background concentration in 60 s was demonstrated. Additionally, negatively charged myoglobin was separated from a solution containing negatively charged allophycocyanin. Cationic cytochrome c was also differentiated from a solution with allophycocyanin. The ability to differentially transport species in bulk solution enables parallel and serial separation modes not available with other separations schemes.

A Performance Comparison of the Parallel Preconditioners for Iterative Methods for Large Sparse Linear Systems Arising from Partial Differential Equations on Structured Grids

NASA Astrophysics Data System (ADS)

Ma, Sangback

In this paper we compare various parallel preconditioners such as Point-SSOR (Symmetric Successive OverRelaxation), ILU(0) (Incomplete LU) in the Wavefront ordering, ILU(0) in the Multi-color ordering, Multi-Color Block SOR (Successive OverRelaxation), SPAI (SParse Approximate Inverse) and pARMS (Parallel Algebraic Recursive Multilevel Solver) for solving large sparse linear systems arising from two-dimensional PDE (Partial Differential Equation)s on structured grids. Point-SSOR is well-known, and ILU(0) is one of the most popular preconditioner, but it is inherently serial. ILU(0) in the Wavefront ordering maximizes the parallelism in the natural order, but the lengths of the wave-fronts are often nonuniform. ILU(0) in the Multi-color ordering is a simple way of achieving a parallelism of the order N, where N is the order of the matrix, but its convergence rate often deteriorates as compared to that of natural ordering. We have chosen the Multi-Color Block SOR preconditioner combined with direct sparse matrix solver, since for the Laplacian matrix the SOR method is known to have a nondeteriorating rate of convergence when used with the Multi-Color ordering. By using block version we expect to minimize the interprocessor communications. SPAI computes the sparse approximate inverse directly by least squares method. Finally, ARMS is a preconditioner recursively exploiting the concept of independent sets and pARMS is the parallel version of ARMS. Experiments were conducted for the Finite Difference and Finite Element discretizations of five two-dimensional PDEs with large meshsizes up to a million on an IBM p595 machine with distributed memory. Our matrices are real positive, i. e., their real parts of the eigenvalues are positive. We have used GMRES(m) as our outer iterative method, so that the convergence of GMRES(m) for our test matrices are mathematically guaranteed. Interprocessor communications were done using MPI (Message Passing Interface) primitives. The results show that in general ILU(0) in the Multi-Color ordering ahd ILU(0) in the Wavefront ordering outperform the other methods but for symmetric and nearly symmetric 5-point matrices Multi-Color Block SOR gives the best performance, except for a few cases with a small number of processors.

Differential interferometry for measurement of density fluctuations and fluctuation-induced transport (invited)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lin, L.; Ding, W. X.; Brower, D. L.

2010-10-15

Differential interferometry employs two parallel laser beams with a small spatial offset (less than beam width) and frequency difference (1-2 MHz) using common optics and a single mixer for a heterodyne detection. The differential approach allows measurement of the electron density gradient, its fluctuations, as well as the equilibrium density distribution. This novel interferometry technique is immune to fringe skip errors and is particularly useful in harsh plasma environments. Accurate calibration of the beam spatial offset, accomplished by use of a rotating dielectric wedge, is required to enable broad application of this approach. Differential interferometry has been successfully used onmore » the Madison Symmetric Torus reversed-field pinch plasma to directly measure fluctuation-induced transport along with equilibrium density profile evolution during pellet injection. In addition, by combining differential and conventional interferometry, both linear and nonlinear terms of the electron density fluctuation energy equation can be determined, thereby allowing quantitative investigation of the origin of the density fluctuations. The concept, calibration, and application of differential interferometry are presented.« less

Differential capacitance probe for process control involving aqueous dielectric fluids

DOEpatents

Svoboda, John M.; Morrison, John L.

2002-10-08

A differential capacitance probe device for process control involving aqueous dielectric fluids is disclosed. The device contains a pair of matched capacitor probes configured in parallel, one immersed in a sealed container of reference fluid, and the other immersed in the process fluid. The sealed container holding the reference fluid is also immersed in the process fluid, hence both probes are operated at the same temperature. Signal conditioning measures the difference in capacitance between the reference probe and the process probe. The resulting signal is a control error signal that can be used to control the process.

Inter-laboratory evaluation of the EUROFORGEN Global ancestry-informative SNP panel by massively parallel sequencing using the Ion PGM™.

PubMed

Eduardoff, M; Gross, T E; Santos, C; de la Puente, M; Ballard, D; Strobl, C; Børsting, C; Morling, N; Fusco, L; Hussing, C; Egyed, B; Souto, L; Uacyisrael, J; Syndercombe Court, D; Carracedo, Á; Lareu, M V; Schneider, P M; Parson, W; Phillips, C; Parson, W; Phillips, C

2016-07-01

The EUROFORGEN Global ancestry-informative SNP (AIM-SNPs) panel is a forensic multiplex of 128 markers designed to differentiate an individual's ancestry from amongst the five continental population groups of Africa, Europe, East Asia, Native America, and Oceania. A custom multiplex of AmpliSeq™ PCR primers was designed for the Global AIM-SNPs to perform massively parallel sequencing using the Ion PGM™ system. This study assessed individual SNP genotyping precision using the Ion PGM™, the forensic sensitivity of the multiplex using dilution series, degraded DNA plus simple mixtures, and the ancestry differentiation power of the final panel design, which required substitution of three original ancestry-informative SNPs with alternatives. Fourteen populations that had not been previously analyzed were genotyped using the custom multiplex and these studies allowed assessment of genotyping performance by comparison of data across five laboratories. Results indicate a low level of genotyping error can still occur from sequence misalignment caused by homopolymeric tracts close to the target SNP, despite careful scrutiny of candidate SNPs at the design stage. Such sequence misalignment required the exclusion of component SNP rs2080161 from the Global AIM-SNPs panel. However, the overall genotyping precision and sensitivity of this custom multiplex indicates the Ion PGM™ assay for the Global AIM-SNPs is highly suitable for forensic ancestry analysis with massively parallel sequencing. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Modified Chebyshev Picard Iteration for Efficient Numerical Integration of Ordinary Differential Equations

NASA Astrophysics Data System (ADS)

Macomber, B.; Woollands, R. M.; Probe, A.; Younes, A.; Bai, X.; Junkins, J.

2013-09-01

Modified Chebyshev Picard Iteration (MCPI) is an iterative numerical method for approximating solutions of linear or non-linear Ordinary Differential Equations (ODEs) to obtain time histories of system state trajectories. Unlike other step-by-step differential equation solvers, the Runge-Kutta family of numerical integrators for example, MCPI approximates long arcs of the state trajectory with an iterative path approximation approach, and is ideally suited to parallel computation. Orthogonal Chebyshev Polynomials are used as basis functions during each path iteration; the integrations of the Picard iteration are then done analytically. Due to the orthogonality of the Chebyshev basis functions, the least square approximations are computed without matrix inversion; the coefficients are computed robustly from discrete inner products. As a consequence of discrete sampling and weighting adopted for the inner product definition, Runge phenomena errors are minimized near the ends of the approximation intervals. The MCPI algorithm utilizes a vector-matrix framework for computational efficiency. Additionally, all Chebyshev coefficients and integrand function evaluations are independent, meaning they can be simultaneously computed in parallel for further decreased computational cost. Over an order of magnitude speedup from traditional methods is achieved in serial processing, and an additional order of magnitude is achievable in parallel architectures. This paper presents a new MCPI library, a modular toolset designed to allow MCPI to be easily applied to a wide variety of ODE systems. Library users will not have to concern themselves with the underlying mathematics behind the MCPI method. Inputs are the boundary conditions of the dynamical system, the integrand function governing system behavior, and the desired time interval of integration, and the output is a time history of the system states over the interval of interest. Examples from the field of astrodynamics are presented to compare the output from the MCPI library to current state-of-practice numerical integration methods. It is shown that MCPI is capable of out-performing the state-of-practice in terms of computational cost and accuracy.

Parallel/Vector Integration Methods for Dynamical Astronomy

NASA Astrophysics Data System (ADS)

Fukushima, Toshio

1999-01-01

This paper reviews three recent works on the numerical methods to integrate ordinary differential equations (ODE), which are specially designed for parallel, vector, and/or multi-processor-unit(PU) computers. The first is the Picard-Chebyshev method (Fukushima, 1997a). It obtains a global solution of ODE in the form of Chebyshev polynomial of large (> 1000) degree by applying the Picard iteration repeatedly. The iteration converges for smooth problems and/or perturbed dynamics. The method runs around 100-1000 times faster in the vector mode than in the scalar mode of a certain computer with vector processors (Fukushima, 1997b). The second is a parallelization of a symplectic integrator (Saha et al., 1997). It regards the implicit midpoint rules covering thousands of timesteps as large-scale nonlinear equations and solves them by the fixed-point iteration. The method is applicable to Hamiltonian systems and is expected to lead an acceleration factor of around 50 in parallel computers with more than 1000 PUs. The last is a parallelization of the extrapolation method (Ito and Fukushima, 1997). It performs trial integrations in parallel. Also the trial integrations are further accelerated by balancing computational load among PUs by the technique of folding. The method is all-purpose and achieves an acceleration factor of around 3.5 by using several PUs. Finally, we give a perspective on the parallelization of some implicit integrators which require multiple corrections in solving implicit formulas like the implicit Hermitian integrators (Makino and Aarseth, 1992), (Hut et al., 1995) or the implicit symmetric multistep methods (Fukushima, 1998), (Fukushima, 1999).

Optimization of differentiation time of mesenchymal-stem-cell to tenocyte under a cyclic stretching with a microgrooved culture membrane and selected measurement cells.

PubMed

Morita, Yasuyuki; Yamashita, Takahiro; Toku, Toku; Ju, Yang

2018-01-01

There is a need for efficient stem cell-to-tenocyte differentiation techniques for tendon tissue engineering. More than 1 week is required for tenogenic differentiation with chemical stimuli, including co-culturing. Research has begun to examine the utility of mechanical stimuli, which reduces the differentiation time to several days. However, the precise length of time required to differentiate human bone marrow-derived mesenchymal stem cells (hBMSCs) into tenocytes has not been clarified. Understanding the precise time required is important for future tissue engineering projects. Therefore, in this study, a method was developed to more precisely determine the length of time required to differentiate hBMSCs into tenocytes with cyclic stretching stimulus. First, it had to be determined how stretching stimulation affected the cells. Microgrooved culture membranes were used to suppress cell orientation behavior. Then, only cells oriented parallel to the microgrooves were selected and evaluated for protein synthesis levels for differentiation. The results revealed that growing cells on the microgrooved membrane and selecting optimally-oriented cells for measurement improved the accuracy of the differentiation evaluation, and that hBMSCs differentiated into tenocytes in approximately 10 h. The differentiation time corresponded to the time required for cellular cytoskeleton reorganization and cellular morphology alterations. This suggests that cells, when subjected to mechanical stimulus, secrete mRNAs and proteins for both cytoskeleton reorganization and differentiation.

Accelerating population balance-Monte Carlo simulation for coagulation dynamics from the Markov jump model, stochastic algorithm and GPU parallel computing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Zuwei; Zhao, Haibo, E-mail: klinsmannzhb@163.com; Zheng, Chuguang

2015-01-15

This paper proposes a comprehensive framework for accelerating population balance-Monte Carlo (PBMC) simulation of particle coagulation dynamics. By combining Markov jump model, weighted majorant kernel and GPU (graphics processing unit) parallel computing, a significant gain in computational efficiency is achieved. The Markov jump model constructs a coagulation-rule matrix of differentially-weighted simulation particles, so as to capture the time evolution of particle size distribution with low statistical noise over the full size range and as far as possible to reduce the number of time loopings. Here three coagulation rules are highlighted and it is found that constructing appropriate coagulation rule providesmore » a route to attain the compromise between accuracy and cost of PBMC methods. Further, in order to avoid double looping over all simulation particles when considering the two-particle events (typically, particle coagulation), the weighted majorant kernel is introduced to estimate the maximum coagulation rates being used for acceptance–rejection processes by single-looping over all particles, and meanwhile the mean time-step of coagulation event is estimated by summing the coagulation kernels of rejected and accepted particle pairs. The computational load of these fast differentially-weighted PBMC simulations (based on the Markov jump model) is reduced greatly to be proportional to the number of simulation particles in a zero-dimensional system (single cell). Finally, for a spatially inhomogeneous multi-dimensional (multi-cell) simulation, the proposed fast PBMC is performed in each cell, and multiple cells are parallel processed by multi-cores on a GPU that can implement the massively threaded data-parallel tasks to obtain remarkable speedup ratio (comparing with CPU computation, the speedup ratio of GPU parallel computing is as high as 200 in a case of 100 cells with 10 000 simulation particles per cell). These accelerating approaches of PBMC are demonstrated in a physically realistic Brownian coagulation case. The computational accuracy is validated with benchmark solution of discrete-sectional method. The simulation results show that the comprehensive approach can attain very favorable improvement in cost without sacrificing computational accuracy.« less

NASA Research For Instrument Approaches To Closely Spaced Parallel Runways

NASA Technical Reports Server (NTRS)

Elliott, Dawn M.; Perry, R. Brad

2000-01-01

Within the NASA Aviation Systems Capacity Program, the Terminal Area Productivity (TAP) Project is addressing airport capacity enhancements during instrument meteorological condition (IMC). The Airborne Information for Lateral Spacing (AILS) research within TAP has focused on an airborne centered approach for independent instrument approaches to closely spaced parallel runways using Differential Global Positioning System (DGPS) and Automatic Dependent Surveillance-Broadcast (ADS-B) technologies. NASA Langley Research Center (LaRC), working in partnership with Honeywell, Inc., completed in AILS simulation study, flight test, and demonstration in 1999 examining normal approaches and potential collision scenarios to runways with separation distances of 3,400 and 2,500 feet. The results of the flight test and demonstration validate the simulation study.

Interlayer tunneling in double-layer quantum hall pseudoferromagnets.

PubMed

Balents, L; Radzihovsky, L

2001-02-26

We show that the interlayer tunneling I-V in double-layer quantum Hall states displays a rich behavior which depends on the relative magnitude of sample size, voltage length scale, current screening, disorder, and thermal lengths. For weak tunneling, we predict a negative differential conductance of a power-law shape crossing over to a sharp zero-bias peak. An in-plane magnetic field splits this zero-bias peak, leading instead to a "derivative" feature at V(B)(B(parallel)) = 2 pi Planck's over 2 pi upsilon B(parallel)d/e phi(0), which gives a direct measurement of the dispersion of the Goldstone mode corresponding to the spontaneous symmetry breaking of the double-layer Hall state.

PFLOTRAN User Manual: A Massively Parallel Reactive Flow and Transport Model for Describing Surface and Subsurface Processes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lichtner, Peter C.; Hammond, Glenn E.; Lu, Chuan

PFLOTRAN solves a system of generally nonlinear partial differential equations describing multi-phase, multicomponent and multiscale reactive flow and transport in porous materials. The code is designed to run on massively parallel computing architectures as well as workstations and laptops (e.g. Hammond et al., 2011). Parallelization is achieved through domain decomposition using the PETSc (Portable Extensible Toolkit for Scientific Computation) libraries for the parallelization framework (Balay et al., 1997). PFLOTRAN has been developed from the ground up for parallel scalability and has been run on up to 218 processor cores with problem sizes up to 2 billion degrees of freedom. Writtenmore » in object oriented Fortran 90, the code requires the latest compilers compatible with Fortran 2003. At the time of this writing this requires gcc 4.7.x, Intel 12.1.x and PGC compilers. As a requirement of running problems with a large number of degrees of freedom, PFLOTRAN allows reading input data that is too large to fit into memory allotted to a single processor core. The current limitation to the problem size PFLOTRAN can handle is the limitation of the HDF5 file format used for parallel IO to 32 bit integers. Noting that 2 32 = 4; 294; 967; 296, this gives an estimate of the maximum problem size that can be currently run with PFLOTRAN. Hopefully this limitation will be remedied in the near future.« less

Children's Use of Evaluative Devices in Spoken and Written Narratives

ERIC Educational Resources Information Center

Drijbooms, Elise; Groen, Margriet A.; Verhoeven, Ludo

2017-01-01

This study investigated the development of evaluation in narratives from middle to late childhood, within the context of differentiating between spoken and written modalities. Two parallel forms of a picture story were used to elicit spoken and written narratives from fourth- and sixth-graders. It was expected that, in addition to an increase of…

DOE Office of Scientific and Technical Information (OSTI.GOV)

Libregts, Sten F.W.M.; Nolte, Martijn A., E-mail: m.nolte@sanquin.nl

Quiescence, self-renewal, lineage commitment and differentiation of hematopoietic stem cells (HSCs) towards fully mature blood cells are a complex process that involves both intrinsic and extrinsic signals. During steady-state conditions, most hematopoietic signals are provided by various resident cells inside the bone marrow (BM), which establish the HSC micro-environment. However, upon infection, the hematopoietic process is also affected by pathogens and activated immune cells, which illustrates an effective feedback mechanism to hematopoietic stem and progenitor cells (HSPCs) via immune-mediated signals. Here, we review the impact of pathogen-associated molecular patterns (PAMPs), damage-associated molecular patterns (DAMPs), costimulatory molecules and pro-inflammatory cytokines onmore » the quiescence, proliferation and differentiation of HSCs and more committed progenitors. As modulation of HSPC function via these immune-mediated signals holds an interesting parallel with the “three-signal-model” described for the activation and differentiation of naïve T-cells, we propose a novel “three-signal” concept for immune-driven hematopoiesis. In this model, the recognition of PAMPs and DAMPs will activate HSCs and induce proliferation, while costimulatory molecules and pro-inflammatory cytokines confer a second and third signal, respectively, which further regulate expansion, lineage commitment and differentiation of HSPCs. We review the impact of inflammatory stress on hematopoiesis along these three signals and we discuss whether they act independently from each other or that concurrence of these signals is important for an adequate response of HSPCs upon infection. - Highlights: • Inflammation and infection have a direct impact on hematopoiesis in the bone marrow. • We draw a striking parallel between immune-driven hematopoiesis and T cell activation. • We review how PAMPs and DAMPs, costimulation and cytokines influence HSPC function.« less

a Non-Overlapping Discretization Method for Partial Differential Equations

NASA Astrophysics Data System (ADS)

Rosas-Medina, A.; Herrera, I.

2013-05-01

Mathematical models of many systems of interest, including very important continuous systems of Engineering and Science, lead to a great variety of partial differential equations whose solution methods are based on the computational processing of large-scale algebraic systems. Furthermore, the incredible expansion experienced by the existing computational hardware and software has made amenable to effective treatment problems of an ever increasing diversity and complexity, posed by engineering and scientific applications. The emergence of parallel computing prompted on the part of the computational-modeling community a continued and systematic effort with the purpose of harnessing it for the endeavor of solving boundary-value problems (BVPs) of partial differential equations. Very early after such an effort began, it was recognized that domain decomposition methods (DDM) were the most effective technique for applying parallel computing to the solution of partial differential equations, since such an approach drastically simplifies the coordination of the many processors that carry out the different tasks and also reduces very much the requirements of information-transmission between them. Ideally, DDMs intend producing algorithms that fulfill the DDM-paradigm; i.e., such that "the global solution is obtained by solving local problems defined separately in each subdomain of the coarse-mesh -or domain-decomposition-". Stated in a simplistic manner, the basic idea is that, when the DDM-paradigm is satisfied, full parallelization can be achieved by assigning each subdomain to a different processor. When intensive DDM research began much attention was given to overlapping DDMs, but soon after attention shifted to non-overlapping DDMs. This evolution seems natural when the DDM-paradigm is taken into account: it is easier to uncouple the local problems when the subdomains are separated. However, an important limitation of non-overlapping domain decompositions, as that concept is usually understood today, is that interface nodes are shared by two or more subdomains of the coarse-mesh and, therefore, even non-overlapping DDMs are actually overlapping when seen from the perspective of the nodes used in the discretization. In this talk we present and discuss a discretization method in which the nodes used are non-overlapping, in the sense that each one of them belongs to one and only one subdomain of the coarse-mesh.

Impact of equalizing currents on losses and torque ripples in electrical machines with fractional slot concentrated windings

NASA Astrophysics Data System (ADS)

Toporkov, D. M.; Vialcev, G. B.

2017-10-01

The implementation of parallel branches is a commonly used manufacturing method of the realizing of fractional slot concentrated windings in electrical machines. If the rotor eccentricity is enabled in a machine with parallel branches, the equalizing currents can arise. The simulation approach of the equalizing currents in parallel branches of an electrical machine winding based on magnetic field calculation by using Finite Elements Method is discussed in the paper. The high accuracy of the model is provided by the dynamic improvement of the inductances in the differential equation system describing a machine. The pre-computed table flux linkage functions are used for that. The functions are the dependences of the flux linkage of parallel branches on the branches currents and rotor position angle. The functions permit to calculate self-inductances and mutual inductances by partial derivative. The calculated results obtained for the electric machine specimen are presented. The results received show that the adverse combination of design solutions and the rotor eccentricity leads to a high value of the equalizing currents and windings heating. Additional torque ripples also arise. The additional ripples harmonic content is not similar to the cogging torque or ripples caused by the rotor eccentricity.

Automatic partitioning of unstructured meshes for the parallel solution of problems in computational mechanics

NASA Technical Reports Server (NTRS)

Farhat, Charbel; Lesoinne, Michel

1993-01-01

Most of the recently proposed computational methods for solving partial differential equations on multiprocessor architectures stem from the 'divide and conquer' paradigm and involve some form of domain decomposition. For those methods which also require grids of points or patches of elements, it is often necessary to explicitly partition the underlying mesh, especially when working with local memory parallel processors. In this paper, a family of cost-effective algorithms for the automatic partitioning of arbitrary two- and three-dimensional finite element and finite difference meshes is presented and discussed in view of a domain decomposed solution procedure and parallel processing. The influence of the algorithmic aspects of a solution method (implicit/explicit computations), and the architectural specifics of a multiprocessor (SIMD/MIMD, startup/transmission time), on the design of a mesh partitioning algorithm are discussed. The impact of the partitioning strategy on load balancing, operation count, operator conditioning, rate of convergence and processor mapping is also addressed. Finally, the proposed mesh decomposition algorithms are demonstrated with realistic examples of finite element, finite volume, and finite difference meshes associated with the parallel solution of solid and fluid mechanics problems on the iPSC/2 and iPSC/860 multiprocessors.

Genomics of parallel adaptation at two timescales in Drosophila

PubMed Central

Begun, David J.

2017-01-01

Two interesting unanswered questions are the extent to which both the broad patterns and genetic details of adaptive divergence are repeatable across species, and the timescales over which parallel adaptation may be observed. Drosophila melanogaster is a key model system for population and evolutionary genomics. Findings from genetics and genomics suggest that recent adaptation to latitudinal environmental variation (on the timescale of hundreds or thousands of years) associated with Out-of-Africa colonization plays an important role in maintaining biological variation in the species. Additionally, studies of interspecific differences between D. melanogaster and its sister species D. simulans have revealed that a substantial proportion of proteins and amino acid residues exhibit adaptive divergence on a roughly few million years long timescale. Here we use population genomic approaches to attack the problem of parallelism between D. melanogaster and a highly diverged conger, D. hydei, on two timescales. D. hydei, a member of the repleta group of Drosophila, is similar to D. melanogaster, in that it too appears to be a recently cosmopolitan species and recent colonizer of high latitude environments. We observed parallelism both for genes exhibiting latitudinal allele frequency differentiation within species and for genes exhibiting recurrent adaptive protein divergence between species. Greater parallelism was observed for long-term adaptive protein evolution and this parallelism includes not only the specific genes/proteins that exhibit adaptive evolution, but extends even to the magnitudes of the selective effects on interspecific protein differences. Thus, despite the roughly 50 million years of time separating D. melanogaster and D. hydei, and despite their considerably divergent biology, they exhibit substantial parallelism, suggesting the existence of a fundamental predictability of adaptive evolution in the genus. PMID:28968391

On the costs of parallel processing in dual-task performance: The case of lexical processing in word production.

PubMed

Paucke, Madlen; Oppermann, Frank; Koch, Iring; Jescheniak, Jörg D

2015-12-01

Previous dual-task picture-naming studies suggest that lexical processes require capacity-limited processes and prevent other tasks to be carried out in parallel. However, studies involving the processing of multiple pictures suggest that parallel lexical processing is possible. The present study investigated the specific costs that may arise when such parallel processing occurs. We used a novel dual-task paradigm by presenting 2 visual objects associated with different tasks and manipulating between-task similarity. With high similarity, a picture-naming task (T1) was combined with a phoneme-decision task (T2), so that lexical processes were shared across tasks. With low similarity, picture-naming was combined with a size-decision T2 (nonshared lexical processes). In Experiment 1, we found that a manipulation of lexical processes (lexical frequency of T1 object name) showed an additive propagation with low between-task similarity and an overadditive propagation with high between-task similarity. Experiment 2 replicated this differential forward propagation of the lexical effect and showed that it disappeared with longer stimulus onset asynchronies. Moreover, both experiments showed backward crosstalk, indexed as worse T1 performance with high between-task similarity compared with low similarity. Together, these findings suggest that conditions of high between-task similarity can lead to parallel lexical processing in both tasks, which, however, does not result in benefits but rather in extra performance costs. These costs can be attributed to crosstalk based on the dual-task binding problem arising from parallel processing. Hence, the present study reveals that capacity-limited lexical processing can run in parallel across dual tasks but only at the expense of extraordinary high costs. (c) 2015 APA, all rights reserved).

Aztec user`s guide. Version 1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hutchinson, S.A.; Shadid, J.N.; Tuminaro, R.S.

1995-10-01

Aztec is an iterative library that greatly simplifies the parallelization process when solving the linear systems of equations Ax = b where A is a user supplied n x n sparse matrix, b is a user supplied vector of length n and x is a vector of length n to be computed. Aztec is intended as a software tool for users who want to avoid cumbersome parallel programming details but who have large sparse linear systems which require an efficiently utilized parallel processing system. A collection of data transformation tools are provided that allow for easy creation of distributed sparsemore » unstructured matrices for parallel solution. Once the distributed matrix is created, computation can be performed on any of the parallel machines running Aztec: nCUBE 2, IBM SP2 and Intel Paragon, MPI platforms as well as standard serial and vector platforms. Aztec includes a number of Krylov iterative methods such as conjugate gradient (CG), generalized minimum residual (GMRES) and stabilized biconjugate gradient (BICGSTAB) to solve systems of equations. These Krylov methods are used in conjunction with various preconditioners such as polynomial or domain decomposition methods using LU or incomplete LU factorizations within subdomains. Although the matrix A can be general, the package has been designed for matrices arising from the approximation of partial differential equations (PDEs). In particular, the Aztec package is oriented toward systems arising from PDE applications.« less

Process for hydraulically mining coal. [28 claims

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shoji, K.; Sieling, R.E.; Taylor, J.T.

The invention is a method for the hydraulic mining of coal of varying hardness. It is described in particular as to coal of the type occurring in the Balmer seam in British Columbia. By the method at least two parallel spaced entries are driven upward through a seam of coal. Monitors are positioned in each entry. Each monitor is horizontally and vertically pivotable, and has nozzle means from which a jet of water under a pressure of about 1900 to 2200 psi is emitted. The high pressure jet cuts the coal, which is then fed to a machine that breaksmore » and crushes the coal into sizes wherein the resultant coal/water slurry will flow down a sloped flume into a dewatering station. The method further embodies differentially retreating along adjacent parallel entries by increments of desirably at least about 40 feet each. By the different retreat system, as a panel of coal is hydraulically mined in one entry, the monitor and associated equipment in a second adjacent parallel entry are moved back the desired increment to the next working position (retreated). When the panel of coal in the first entry is mined, the monitor is retreated in the same manner and hydraulic mining commences in the second adjacent parallel entry. The operation is thus alternated along the length of the parallel entries. 28 claims, 4 figures.« less

Parallel Computation of Flow in Heterogeneous Media Modelled by Mixed Finite Elements

NASA Astrophysics Data System (ADS)

Cliffe, K. A.; Graham, I. G.; Scheichl, R.; Stals, L.

2000-11-01

In this paper we describe a fast parallel method for solving highly ill-conditioned saddle-point systems arising from mixed finite element simulations of stochastic partial differential equations (PDEs) modelling flow in heterogeneous media. Each realisation of these stochastic PDEs requires the solution of the linear first-order velocity-pressure system comprising Darcy's law coupled with an incompressibility constraint. The chief difficulty is that the permeability may be highly variable, especially when the statistical model has a large variance and a small correlation length. For reasonable accuracy, the discretisation has to be extremely fine. We solve these problems by first reducing the saddle-point formulation to a symmetric positive definite (SPD) problem using a suitable basis for the space of divergence-free velocities. The reduced problem is solved using parallel conjugate gradients preconditioned with an algebraically determined additive Schwarz domain decomposition preconditioner. The result is a solver which exhibits a good degree of robustness with respect to the mesh size as well as to the variance and to physically relevant values of the correlation length of the underlying permeability field. Numerical experiments exhibit almost optimal levels of parallel efficiency. The domain decomposition solver (DOUG, http://www.maths.bath.ac.uk/~parsoft) used here not only is applicable to this problem but can be used to solve general unstructured finite element systems on a wide range of parallel architectures.

Joint carrier phase and frequency-offset estimation with parallel implementation for dual-polarization coherent receiver.

PubMed

Lu, Jianing; Li, Xiang; Fu, Songnian; Luo, Ming; Xiang, Meng; Zhou, Huibin; Tang, Ming; Liu, Deming

2017-03-06

We present dual-polarization complex-weighted, decision-aided, maximum-likelihood algorithm with superscalar parallelization (SSP-DP-CW-DA-ML) for joint carrier phase and frequency-offset estimation (FOE) in coherent optical receivers. By pre-compensation of the phase offset between signals in dual polarizations, the performance can be substantially improved. Meanwhile, with the help of modified SSP-based parallel implementation, the acquisition time of FO and the required number of training symbols are reduced by transferring the complex weights of the filters between adjacent buffers, where differential coding/decoding is not required. Simulation results show that the laser linewidth tolerance of our proposed algorithm is comparable to traditional blind phase search (BPS), while a complete FOE range of ± symbol rate/2 can be achieved. Finally, performance of our proposed algorithm is experimentally verified under the scenario of back-to-back (B2B) transmission using 10 Gbaud DP-16/32-QAM formats.

Thermal spin filtering effect and giant magnetoresistance of half-metallic graphene nanoribbon co-doped with non-metallic Nitrogen and Boron

NASA Astrophysics Data System (ADS)

Huang, Hai; Zheng, Anmin; Gao, Guoying; Yao, Kailun

2018-03-01

Ab initio calculations based on density functional theory and non-equilibrium Green's function are performed to investigate the thermal spin transport properties of single-hydrogen-saturated zigzag graphene nanoribbon co-doped with non-metallic Nitrogen and Boron in parallel and anti-parallel spin configurations. The results show that the doped graphene nanoribbon is a full half-metal. The two-probe system based on the doped graphene nanoribbon exhibits various excellent spin transport properties, including the spin-filtering effect, the spin Seebeck effect, the single-spin negative differential thermal resistance effect and the sign-reversible giant magnetoresistance feature. Excellently, the spin-filtering efficiency can reach nearly 100% in the parallel configuration and the magnetoresistance ratio can be up to -1.5 × 1010% by modulating the electrode temperature and temperature gradient. Our findings indicate that the metal-free doped graphene nanoribbon would be a promising candidate for spin caloritronic applications.

Uniaxial cyclic strain enhances adipose-derived stem cell fusion with skeletal myocytes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Andersen, Jens Isak; Juhl, Morten; Nielsen, Thøger

2014-07-25

Highlights: • Uniaxial cyclic tensile strain (CTS) applied to ASCs alone or in coculture with myogenic precursors. • CTS promoted the formation of a highly ordered array of parallel ASCs. • Without biochemical supplements, CTS did not support advanced myogenic differentiation of ASCs. • Mechanical stimulation of cocultures boosted fusion of ASCs with skeletal myoblasts. - Abstract: Although adult muscle tissue possesses an exceptional capacity for regeneration, in the case of large defects, the restoration to original state is not possible. A well-known source for the de novo regeneration is the adipose-derived stem cells (ASCs), which can be readily isolatedmore » and have been shown to have a broad differentiation and regenerative potential. In this work, we employed uniaxial cyclic tensile strain (CTS), to mechanically stimulate human ASCs to participate in the formation skeletal myotubes in an in vitro model of myogenesis. The application of CTS for 48 h resulted in the formation of a highly ordered array of parallel ASCs, but failed to support skeletal muscle terminal differentiation. When the same stimulation paradigm was applied to cocultures with mouse skeletal muscle myoblasts, the percentage of ASCs contributing to the formation of myotubes significantly exceeded the levels reported in the literature hitherto. In perspective, the mechanical strain may be used to increase the efficiency of incorporation of ASCs in the skeletal muscles, which could be found useful in diverse traumatic or pathologic scenarios.« less

Survey of the status of finite element methods for partial differential equations

NASA Technical Reports Server (NTRS)

Temam, Roger

1986-01-01

The finite element methods (FEM) have proved to be a powerful technique for the solution of boundary value problems associated with partial differential equations of either elliptic, parabolic, or hyperbolic type. They also have a good potential for utilization on parallel computers particularly in relation to the concept of domain decomposition. This report is intended as an introduction to the FEM for the nonspecialist. It contains a survey which is totally nonexhaustive, and it also contains as an illustration, a report on some new results concerning two specific applications, namely a free boundary fluid-structure interaction problem and the Euler equations for inviscid flows.

Volcanic rocks and processes of the Mid-Atlantic Ridge rift valley near 36 ° 49′ N

USGS Publications Warehouse

Hekinian, R.; Moore, J.G.; Bryan, W.B.

1976-01-01

The above relations indicate that the diverse lava types were erupted from a shallow, zoned magma chamber from fissures distributed over the width of the inner rift valley and elongate parallel to it. Differentiation was accomplished by cooling and crystallization of plagioclase, olivine, and clinopyroxene toward the margins of the chamber. The centrally located hills were built by the piling up of frequent eruption of mainly primitive lavas which also are the youngest flows. In contrast smaller and less frequent eruptions of more differentiated lavas were exposed on both sides of the rift valley axis.

Efficient spin-filter and negative differential resistance behaviors in FeN4 embedded graphene nanoribbon device

NASA Astrophysics Data System (ADS)

Liu, N.; Liu, J. B.; Yao, K. L.; Ni, Y.; Wang, S. L.

2016-03-01

In this paper, we propose a new device of spintronics by embedding two FeN4 molecules into armchair graphene nanoribbon and sandwiching them between N-doped graphene nanoribbon electrodes. Our first-principle quantum transport calculations show that the device is a perfect spin filter with high spin-polarizations both in parallel configuration (PC) and antiparallel configuration (APC). Moreover, negative differential resistance phenomena are obtained for the spin-down current in PC, and the spin-up and spin-down currents in APC. These transport properties are explained by the bias-dependent evolution of molecular orbitals and the transmission spectra.

Time-partitioning simulation models for calculation on parallel computers

NASA Technical Reports Server (NTRS)

Milner, Edward J.; Blech, Richard A.; Chima, Rodrick V.

1987-01-01

A technique allowing time-staggered solution of partial differential equations is presented in this report. Using this technique, called time-partitioning, simulation execution speedup is proportional to the number of processors used because all processors operate simultaneously, with each updating of the solution grid at a different time point. The technique is limited by neither the number of processors available nor by the dimension of the solution grid. Time-partitioning was used to obtain the flow pattern through a cascade of airfoils, modeled by the Euler partial differential equations. An execution speedup factor of 1.77 was achieved using a two processor Cray X-MP/24 computer.

Regulated expression of the MRP8 and MRP14 genes during terminal differentiation of human promyelocytic leukemic HL-60 cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Warner-Bartnicki, A.L.; Murao, S.; Collart, F.R.

1992-02-14

The calcium-binding proteins MRP8 and MRP14 are induced during monomyelocytic cell maturation and may mediate the growth arrest in differentiating HL-60 cells. We determined the levels of a protein complex (PC) containing MRP8 and MRP14 and investigated the mechanism by which the genes encoding these proteins are regulated in HL-60 cells treated with the differentiation-inducing agent mycophenolic acid. Elevated levels of the PC were found to directly parallel gains in the steady-state levels of MRP8 and MRP14 mRNA. Transcription studies with the use of nuclear run-on experiments revealed increased transcription initiation at the MRP8 and MRP14 promoters after MPA treatment.more » 1{alpha},25-Dihydroxyvitamin D{sub 3}, which induces HL-60 cell differentiation by another mechanism, was also found to increase transcription initiation at the MRP8 and MRP14 promoters, suggesting that this initiation is the major control of MRP8 and MRP14 gene expression during terminal differentiation of human promyelocytic cells.« less

Structural organization of parallel information processing within the tectofugal visual system of the pigeon.

PubMed

Hellmann, B; Güntürkün, O

2001-01-01

Visual information processing within the ascending tectofugal pathway to the forebrain undergoes essential rearrangements between the mesencephalic tectum opticum and the diencephalic nucleus rotundus of birds. The outer tectal layers constitute a two-dimensional map of the visual surrounding, whereas nucleus rotundus is characterized by functional domains in which different visual features such as movement, color, or luminance are processed in parallel. Morphologic correlates of this reorganization were investigated by means of focal injections of the neuronal tracer choleratoxin subunit B into different regions of the nuclei rotundus and triangularis of the pigeon. Dependent on the thalamic injection site, variations in the retrograde labeling pattern of ascending tectal efferents were observed. All rotundal projecting neurons were located within the deep tectal layer 13. Five different cell populations were distinguished that could be differentiated according to their dendritic ramifications within different retinorecipient laminae and their axons projecting to different subcomponents of the nucleus rotundus. Because retinorecipient tectal layers differ in their input from distinct classes of retinal ganglion cells, each tectorotundal cell type probably processes different aspects of the visual surrounding. Therefore, the differential input/output connections of the five tectorotundal cell groups might constitute the structural basis for spatially segregated parallel information processing of different stimulus aspects within the tectofugal visual system. Because two of five rotundal projecting cell groups additionally exhibited quantitative shifts along the dorsoventral extension of the tectum, data also indicate visual field-dependent alterations in information processing for particular visual features. Copyright 2001 Wiley-Liss, Inc.

Seamless Transfer or Crooked Seams? The Differentiated Outcomes of Associate's Degree Types Completing the Baccalaureate Degree

ERIC Educational Resources Information Center

Thomas, John Phillip

2012-01-01

In this study academic outcomes for Associate of Applied Science and Associate of Applied Arts degree students who transferred to a large public midwestern research university were examined. A group with transcripted technical credits of 16 hours at transfer were compared and contrasted with a peer group of college-parallel associate's degree…

Software for the Parallel Solution of Systems of Ordinary Differential Equations

DTIC Science & Technology

1991-02-01

x real g (ndim) , x (O:nmax*maxnp) , yin (1) real vout (flout) , left , right equivalence # (n,vin(l)),(ndimc,vin(2)),(ninc, vin ( 3 )) # ’ (noutc,vin(4...ninc, vin ( 3 )) #, (noutc,vin(4)) , (m,vin(5)), (mp,vin(6)) #, (h,vin(7)), (left,vin(8)), (right,vin(9)) #, (g(1) ,vin(10)) #,(x(O),vin(10+ndim

Development of a Novel Screening Method for the Isolation of “Cronobacter” spp. (Enterobacter sakazakii)▿

PubMed Central

Iversen, Carol; Druggan, Patrick; Schumacher, Sandra; Lehner, Angelika; Feer, Claudia; Gschwend, Karl; Joosten, Han; Stephan, Roger

2008-01-01

A differential medium, “Cronobacter” screening broth, has been designed to complement agars based on hydrolysis of chromogenic α-glucopyranoside substrates. The broth was evaluated using 329 Enterobacteriaceae strains (229 target isolates), spiked/naturally contaminated samples, and a parallel comparison with current methods for raw materials, line/end products, and factory environment samples. PMID:18310415

Retinoic acid downregulates Rae1 leading to APC(Cdh1) activation and neuroblastoma SH-SY5Y differentiation.

PubMed

Cuende, J; Moreno, S; Bolaños, J P; Almeida, A

2008-05-22

In neuroblastoma cells, retinoic acid induces cell cycle arrest and differentiation through degradation of the F-box protein, Skp2, and stabilization of cyclin-dependent kinase inhibitor, p27. However, the mechanism responsible for retinoic acid-mediated Skp2 destabilization is unknown. Since Skp2 is degraded by anaphase-promoting complex (APC)(Cdh1), here we studied whether retinoic acid promotes differentiation of human SH-SY5Y neuroblastoma cells by modulating Cdh1. We found that retinoic acid induced the nuclear accumulation of Cdh1 that paralleled Skp2 destabilization and p27 accumulation. The mRNA and protein abundance of Rae1-a nuclear export factor that limits APC(Cdh1) activity in mitosis-decreased upon retinoic acid-induced inhibition of neuroblastoma cell proliferation. Furthermore, either Rae1 overexpression or Cdh1 inhibition promoted Skp2 accumulation, p27 destabilization and prevented retinoic acid-induced cell cycle arrest and differentiation. Conversely, inhibition of Rae1 accelerated retinoic acid-induced differentiation. Thus, retinoic acid downregulates Rae1, hence facilitating APC(Cdh1)-mediated Skp2 degradation leading to the arrest of cell cycle progression and neuroblastoma differentiation.

Using Hadoop MapReduce for Parallel Genetic Algorithms: A Comparison of the Global, Grid and Island Models.

PubMed

Ferrucci, Filomena; Salza, Pasquale; Sarro, Federica

2017-06-29

The need to improve the scalability of Genetic Algorithms (GAs) has motivated the research on Parallel Genetic Algorithms (PGAs), and different technologies and approaches have been used. Hadoop MapReduce represents one of the most mature technologies to develop parallel algorithms. Based on the fact that parallel algorithms introduce communication overhead, the aim of the present work is to understand if, and possibly when, the parallel GAs solutions using Hadoop MapReduce show better performance than sequential versions in terms of execution time. Moreover, we are interested in understanding which PGA model can be most effective among the global, grid, and island models. We empirically assessed the performance of these three parallel models with respect to a sequential GA on a software engineering problem, evaluating the execution time and the achieved speedup. We also analysed the behaviour of the parallel models in relation to the overhead produced by the use of Hadoop MapReduce and the GAs' computational effort, which gives a more machine-independent measure of these algorithms. We exploited three problem instances to differentiate the computation load and three cluster configurations based on 2, 4, and 8 parallel nodes. Moreover, we estimated the costs of the execution of the experimentation on a potential cloud infrastructure, based on the pricing of the major commercial cloud providers. The empirical study revealed that the use of PGA based on the island model outperforms the other parallel models and the sequential GA for all the considered instances and clusters. Using 2, 4, and 8 nodes, the island model achieves an average speedup over the three datasets of 1.8, 3.4, and 7.0 times, respectively. Hadoop MapReduce has a set of different constraints that need to be considered during the design and the implementation of parallel algorithms. The overhead of data store (i.e., HDFS) accesses, communication, and latency requires solutions that reduce data store operations. For this reason, the island model is more suitable for PGAs than the global and grid model, also in terms of costs when executed on a commercial cloud provider.

Proteolipidic Composition of Exosomes Changes during Reticulocyte Maturation*

PubMed Central

Carayon, Kévin; Chaoui, Karima; Ronzier, Elsa; Lazar, Ikrame; Bertrand-Michel, Justine; Roques, Véronique; Balor, Stéphanie; Terce, François; Lopez, André; Salomé, Laurence; Joly, Etienne

2011-01-01

During the orchestrated process leading to mature erythrocytes, reticulocytes must synthesize large amounts of hemoglobin, while eliminating numerous cellular components. Exosomes are small secreted vesicles that play an important role in this process of specific elimination. To understand the mechanisms of proteolipidic sorting leading to their biogenesis, we have explored changes in the composition of exosomes released by reticulocytes during their differentiation, in parallel to their physical properties. By combining proteomic and lipidomic approaches, we found dramatic alterations in the composition of the exosomes retrieved over the course of a 7-day in vitro differentiation protocol. Our data support a previously proposed model, whereby in reticulocytes the biogenesis of exosomes involves several distinct mechanisms for the preferential recruitment of particular proteins and lipids and suggest that the respective prominence of those pathways changes over the course of the differentiation process. PMID:21828046

Detecting free-mass common-mode motion induced by incident gravitational waves

NASA Astrophysics Data System (ADS)

Tobar, Michael Edmund; Suzuki, Toshikazu; Kuroda, Kazuaki

1999-05-01

In this paper we show that information on both the differential and common mode free-mass response to a gravitational wave can provide important information on discriminating the direction of the gravitational wave source and between different theories of gravitation. The conventional Michelson interferometer scheme only measures the differential free-mass response. By changing the orientation of the beam splitter, it is possible to configure the detector so it is sensitive to the common-mode of the free-mass motion. The proposed interferometer is an adaptation of the Fox-Smith interferometer. A major limitation to the new scheme is its enhanced sensitivity to laser frequency fluctuations over the conventional, and we propose a method of cancelling these fluctuations. The configuration could be used in parallel to the conventional differential detection scheme with a significant sensitivity and bandwidth.

Shift-connected SIMD array architectures for digital optical computing systems, with algorithms for numerical transforms and partial differential equations

NASA Astrophysics Data System (ADS)

Drabik, Timothy J.; Lee, Sing H.

1986-11-01

The intrinsic parallelism characteristics of easily realizable optical SIMD arrays prompt their present consideration in the implementation of highly structured algorithms for the numerical solution of multidimensional partial differential equations and the computation of fast numerical transforms. Attention is given to a system, comprising several spatial light modulators (SLMs), an optical read/write memory, and a functional block, which performs simple, space-invariant shifts on images with sufficient flexibility to implement the fastest known methods for partial differential equations as well as a wide variety of numerical transforms in two or more dimensions. Either fixed or floating-point arithmetic may be used. A performance projection of more than 1 billion floating point operations/sec using SLMs with 1000 x 1000-resolution and operating at 1-MHz frame rates is made.

Thyroid nodules and thyroid autoimmunity in the context of environmental pollution.

PubMed

Benvenga, Salvatore; Antonelli, Alessandro; Vita, Roberto

2015-12-01

Evidence suggests that in most industrialized countries autoimmune disorders, including chronic lymphocytic thyroiditis, are increasing. This increase parallels the one regarding differentiated thyroid cancer, the increment of which is mainly due to the papillary histotype. A number of studies have pointed to an association between chronic lymphocytic thyroiditis and differentiated thyroid cancer. The upward trend of these two thyroid diseases is sustained by certain environmental factors, such as polluting substances acting as endocrine disrupting chemicals. Herein we will review the experimental and clinical literature that highlights the effects of environmental and occupational exposure to polluting chemicals in the development of autoimmune thyroid disease or differentiated thyroid cancer. Stakeholders, starting from policymarkers, should become more sensitive to the consequences for the thyroid resulting from exposure to EDC. Indeed, the economic burden resulting from such consequences has not been quantified thus far.

Parallel Dynamics Simulation Using a Krylov-Schwarz Linear Solution Scheme

DOE PAGES

Abhyankar, Shrirang; Constantinescu, Emil M.; Smith, Barry F.; ...

2016-11-07

Fast dynamics simulation of large-scale power systems is a computational challenge because of the need to solve a large set of stiff, nonlinear differential-algebraic equations at every time step. The main bottleneck in dynamic simulations is the solution of a linear system during each nonlinear iteration of Newton’s method. In this paper, we present a parallel Krylov- Schwarz linear solution scheme that uses the Krylov subspacebased iterative linear solver GMRES with an overlapping restricted additive Schwarz preconditioner. As a result, performance tests of the proposed Krylov-Schwarz scheme for several large test cases ranging from 2,000 to 20,000 buses, including amore » real utility network, show good scalability on different computing architectures.« less

Paralleling power MOSFETs in their active region: Extended range of passively forced current sharing

NASA Technical Reports Server (NTRS)

Niedra, Janis M.

1989-01-01

A simple passive circuit that improves current balance in parallelled power MOSFETs that are not precisely matched and that are operated in their active region from a common gate drive are exhibited. A nonlinear circuit consisting of diodes and resistors generates the differential gate potential required to correct for unbalance while maintaining low losses over a range of current. Also application of a thin tape wound magnetic core to effect dynamic current balance is reviewed, and a simple theory is presented showing that for operation in the active region the branch currents tend to revert to their normal unbalanced values even if the core is not driven into saturation. Results of several comparative experiments are given.

Parallel Dynamics Simulation Using a Krylov-Schwarz Linear Solution Scheme

DOE Office of Scientific and Technical Information (OSTI.GOV)

Abhyankar, Shrirang; Constantinescu, Emil M.; Smith, Barry F.

Fast dynamics simulation of large-scale power systems is a computational challenge because of the need to solve a large set of stiff, nonlinear differential-algebraic equations at every time step. The main bottleneck in dynamic simulations is the solution of a linear system during each nonlinear iteration of Newton’s method. In this paper, we present a parallel Krylov- Schwarz linear solution scheme that uses the Krylov subspacebased iterative linear solver GMRES with an overlapping restricted additive Schwarz preconditioner. As a result, performance tests of the proposed Krylov-Schwarz scheme for several large test cases ranging from 2,000 to 20,000 buses, including amore » real utility network, show good scalability on different computing architectures.« less

Pre-metatarsal skeletal development in tissue culture at unit- and microgravity

NASA Technical Reports Server (NTRS)

Klement, B. J.; Spooner, B. S.

1994-01-01

Explant organ culture was used to demonstrate that isolated embryonic mouse pre-metatarsal mesenchyme is capable of undergoing a series of differentiative and morphogenetic developmental events. Mesenchyme differentiation into chondrocytes, and concurrent morphogenetic patterning of the cartilage tissue, and terminal chondrocyte differentiation with subsequent matrix mineralization show that cultured tissue closely parallels in vivo development. Whole mount alizarin red staining of the cultured tissue demonstrates that the extracellular matrix around the hypertrophied chondrocytes is competent to support mineralization. Intensely stained mineralized bands are similar to those formed in pre-metatarsals developing in vivo. We have adapted the culture strategy for experimentation in a reduced gravity environment on the Space Shuttle. Spaceflight culture of pre-metatarsals, which have already initiated chondrogenesis and morphogenetic patterning, results in an increase in cartilage rod size and maintenance of rod shape, compared to controls. Older pre-metatarsal tissue, already terminally differentiated to hypertrophied cartilage, maintained rod structure and cartilage phenotype during spaceflight culture.

Constraint treatment techniques and parallel algorithms for multibody dynamic analysis. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Chiou, Jin-Chern

1990-01-01

Computational procedures for kinematic and dynamic analysis of three-dimensional multibody dynamic (MBD) systems are developed from the differential-algebraic equations (DAE's) viewpoint. Constraint violations during the time integration process are minimized and penalty constraint stabilization techniques and partitioning schemes are developed. The governing equations of motion, a two-stage staggered explicit-implicit numerical algorithm, are treated which takes advantage of a partitioned solution procedure. A robust and parallelizable integration algorithm is developed. This algorithm uses a two-stage staggered central difference algorithm to integrate the translational coordinates and the angular velocities. The angular orientations of bodies in MBD systems are then obtained by using an implicit algorithm via the kinematic relationship between Euler parameters and angular velocities. It is shown that the combination of the present solution procedures yields a computationally more accurate solution. To speed up the computational procedures, parallel implementation of the present constraint treatment techniques, the two-stage staggered explicit-implicit numerical algorithm was efficiently carried out. The DAE's and the constraint treatment techniques were transformed into arrowhead matrices to which Schur complement form was derived. By fully exploiting the sparse matrix structural analysis techniques, a parallel preconditioned conjugate gradient numerical algorithm is used to solve the systems equations written in Schur complement form. A software testbed was designed and implemented in both sequential and parallel computers. This testbed was used to demonstrate the robustness and efficiency of the constraint treatment techniques, the accuracy of the two-stage staggered explicit-implicit numerical algorithm, and the speed up of the Schur-complement-based parallel preconditioned conjugate gradient algorithm on a parallel computer.

Real-time simultaneous and proportional myoelectric control using intramuscular EMG

PubMed Central

Kuiken, Todd A; Hargrove, Levi J

2014-01-01

Objective Myoelectric prostheses use electromyographic (EMG) signals to control movement of prosthetic joints. Clinically available myoelectric control strategies do not allow simultaneous movement of multiple degrees of freedom (DOFs); however, the use of implantable devices that record intramuscular EMG signals could overcome this constraint. The objective of this study was to evaluate the real-time simultaneous control of three DOFs (wrist rotation, wrist flexion/extension, and hand open/close) using intramuscular EMG. Approach We evaluated task performance of five able-bodied subjects in a virtual environment using two control strategies with fine-wire EMG: (i) parallel dual-site differential control, which enabled simultaneous control of three DOFs and (ii) pattern recognition control, which required sequential control of DOFs. Main Results Over the course of the experiment, subjects using parallel dual-site control demonstrated increased use of simultaneous control and improved performance in a Fitts' Law test. By the end of the experiment, performance using parallel dual-site control was significantly better (up to a 25% increase in throughput) than when using sequential pattern recognition control for tasks requiring multiple DOFs. The learning trends with parallel dual-site control suggested that further improvements in performance metrics were possible. Subjects occasionally experienced difficulty in performing isolated single-DOF movements with parallel dual-site control but were able to accomplish related Fitts' Law tasks with high levels of path efficiency. Significance These results suggest that intramuscular EMG, used in a parallel dual-site configuration, can provide simultaneous control of a multi-DOF prosthetic wrist and hand and may outperform current methods that enforce sequential control. PMID:25394366

Real-time simultaneous and proportional myoelectric control using intramuscular EMG

NASA Astrophysics Data System (ADS)

Smith, Lauren H.; Kuiken, Todd A.; Hargrove, Levi J.

2014-12-01

Objective. Myoelectric prostheses use electromyographic (EMG) signals to control movement of prosthetic joints. Clinically available myoelectric control strategies do not allow simultaneous movement of multiple degrees of freedom (DOFs); however, the use of implantable devices that record intramuscular EMG signals could overcome this constraint. The objective of this study was to evaluate the real-time simultaneous control of three DOFs (wrist rotation, wrist flexion/extension, and hand open/close) using intramuscular EMG. Approach. We evaluated task performance of five able-bodied subjects in a virtual environment using two control strategies with fine-wire EMG: (i) parallel dual-site differential control, which enabled simultaneous control of three DOFs and (ii) pattern recognition control, which required sequential control of DOFs. Main results. Over the course of the experiment, subjects using parallel dual-site control demonstrated increased use of simultaneous control and improved performance in a Fitts’ Law test. By the end of the experiment, performance using parallel dual-site control was significantly better (up to a 25% increase in throughput) than when using sequential pattern recognition control for tasks requiring multiple DOFs. The learning trends with parallel dual-site control suggested that further improvements in performance metrics were possible. Subjects occasionally experienced difficulty in performing isolated single-DOF movements with parallel dual-site control but were able to accomplish related Fitts’ Law tasks with high levels of path efficiency. Significance. These results suggest that intramuscular EMG, used in a parallel dual-site configuration, can provide simultaneous control of a multi-DOF prosthetic wrist and hand and may outperform current methods that enforce sequential control.

What Multilevel Parallel Programs do when you are not Watching: A Performance Analysis Case Study Comparing MPI/OpenMP, MLP, and Nested OpenMP

NASA Technical Reports Server (NTRS)

Jost, Gabriele; Labarta, Jesus; Gimenez, Judit

2004-01-01

With the current trend in parallel computer architectures towards clusters of shared memory symmetric multi-processors, parallel programming techniques have evolved that support parallelism beyond a single level. When comparing the performance of applications based on different programming paradigms, it is important to differentiate between the influence of the programming model itself and other factors, such as implementation specific behavior of the operating system (OS) or architectural issues. Rewriting-a large scientific application in order to employ a new programming paradigms is usually a time consuming and error prone task. Before embarking on such an endeavor it is important to determine that there is really a gain that would not be possible with the current implementation. A detailed performance analysis is crucial to clarify these issues. The multilevel programming paradigms considered in this study are hybrid MPI/OpenMP, MLP, and nested OpenMP. The hybrid MPI/OpenMP approach is based on using MPI [7] for the coarse grained parallelization and OpenMP [9] for fine grained loop level parallelism. The MPI programming paradigm assumes a private address space for each process. Data is transferred by explicitly exchanging messages via calls to the MPI library. This model was originally designed for distributed memory architectures but is also suitable for shared memory systems. The second paradigm under consideration is MLP which was developed by Taft. The approach is similar to MPi/OpenMP, using a mix of coarse grain process level parallelization and loop level OpenMP parallelization. As it is the case with MPI, a private address space is assumed for each process. The MLP approach was developed for ccNUMA architectures and explicitly takes advantage of the availability of shared memory. A shared memory arena which is accessible by all processes is required. Communication is done by reading from and writing to the shared memory.

Identifying the "Subnormal" Child in an Age of Expansion of Special Education and Child Science in the Netherlands (c.1945-1965)

ERIC Educational Resources Information Center

Bakker, Nelleke

2015-01-01

Between c.1945 and 1965 across the West special education has grown and differentiated substantially. In the Netherlands this expansion ran parallel to the academic recognition and rapid development of the study of learning disabilities. How are these two processes related? This article argues that in this country child science and special…

PETSc Users Manual Revision 3.7

DOE Office of Scientific and Technical Information (OSTI.GOV)

Balay, Satish; Abhyankar, S.; Adams, M.

This manual describes the use of PETSc for the numerical solution of partial differential equations and related problems on high-performance computers. The Portable, Extensible Toolkit for Scientific Computation (PETSc) is a suite of data structures and routines that provide the building blocks for the implementation of large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all message-passing communication.

PETSc Users Manual Revision 3.8

DOE Office of Scientific and Technical Information (OSTI.GOV)

Balay, S.; Abhyankar, S.; Adams, M.

This manual describes the use of PETSc for the numerical solution of partial differential equations and related problems on high-performance computers. The Portable, Extensible Toolkit for Scientific Computation (PETSc) is a suite of data structures and routines that provide the building blocks for the implementation of large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all message-passing communication.

Differentiation of mesenchymal stem cells into neuronal cells on fetal bovine acellular dermal matrix as a tissue engineered nerve scaffold

PubMed Central

Feng, Yuping; Wang, Jiao; Ling, Shixin; Li, Zhuo; Li, Mingsheng; Li, Qiongyi; Ma, Zongren; Yu, Sijiu

2014-01-01

The purpose of this study was to assess fetal bovine acellular dermal matrix as a scaffold for supporting the differentiation of bone marrow mesenchymal stem cells into neural cells following induction with neural differentiation medium. We performed long-term, continuous observation of cell morphology, growth, differentiation, and neuronal development using several microscopy techniques in conjunction with immunohistochemistry. We examined specific neuronal proteins and Nissl bodies involved in the differentiation process in order to determine the neuronal differentiation of bone marrow mesenchymal stem cells. The results show that bone marrow mesenchymal stem cells that differentiate on fetal bovine acellular dermal matrix display neuronal morphology with unipolar and bi/multipolar neurite elongations that express neuronal-specific proteins, including βIII tubulin. The bone marrow mesenchymal stem cells grown on fetal bovine acellular dermal matrix and induced for long periods of time with neural differentiation medium differentiated into a multilayered neural network-like structure with long nerve fibers that was composed of several parallel microfibers and neuronal cells, forming a complete neural circuit with dendrite-dendrite to axon-dendrite to dendrite-axon synapses. In addition, growth cones with filopodia were observed using scanning electron microscopy. Paraffin sectioning showed differentiated bone marrow mesenchymal stem cells with the typical features of neuronal phenotype, such as a large, round nucleus and a cytoplasm full of Nissl bodies. The data suggest that the biological scaffold fetal bovine acellular dermal matrix is capable of supporting human bone marrow mesenchymal stem cell differentiation into functional neurons and the subsequent formation of tissue engineered nerve. PMID:25598779

A Parallel Compact Multi-Dimensional Numerical Algorithm with Aeroacoustics Applications

NASA Technical Reports Server (NTRS)

Povitsky, Alex; Morris, Philip J.

1999-01-01

In this study we propose a novel method to parallelize high-order compact numerical algorithms for the solution of three-dimensional PDEs (Partial Differential Equations) in a space-time domain. For this numerical integration most of the computer time is spent in computation of spatial derivatives at each stage of the Runge-Kutta temporal update. The most efficient direct method to compute spatial derivatives on a serial computer is a version of Gaussian elimination for narrow linear banded systems known as the Thomas algorithm. In a straightforward pipelined implementation of the Thomas algorithm processors are idle due to the forward and backward recurrences of the Thomas algorithm. To utilize processors during this time, we propose to use them for either non-local data independent computations, solving lines in the next spatial direction, or local data-dependent computations by the Runge-Kutta method. To achieve this goal, control of processor communication and computations by a static schedule is adopted. Thus, our parallel code is driven by a communication and computation schedule instead of the usual "creative, programming" approach. The obtained parallelization speed-up of the novel algorithm is about twice as much as that for the standard pipelined algorithm and close to that for the explicit DRP algorithm.

Micro-differential scanning calorimeter for liquid biological samples

DOE PAGES

Wang, Shuyu; Yu, Shifeng; Siedler, Michael S.; ...

2016-10-20

Here, we developed an ultrasensitive micro-DSC (differential scanning calorimeter) for liquid protein sample characterization. Our design integrated vanadium oxide thermistors and flexible polymer substrates with microfluidics chambers to achieve a high sensitivity (6 V/W), low thermal conductivity (0.7 mW/K), high power resolutions (40 nW), and well-defined liquid volume (1 μl) calorimeter sensor in a compact and cost-effective way. Furthermore, we demonstrated the performance of the sensor with lysozyme unfolding. The measured transition temperature and enthalpy change were in accordance with the previous literature data. This micro-DSC could potentially raise the prospect of high-throughput biochemical measurement by parallel operation with miniaturizedmore » sample consumption.« less

Simple two-electrode biosignal amplifier.

PubMed

Dobrev, D; Neycheva, T; Mudrov, N

2005-11-01

A simple, cost effective circuit for a two-electrode non-differential biopotential amplifier is proposed. It uses a 'virtual ground' transimpedance amplifier and a parallel RC network for input common mode current equalisation, while the signal input impedance preserves its high value. With this innovative interface circuit, a simple non-inverting amplifier fully emulates high CMRR differential. The amplifier equivalent CMRR (typical range from 70-100 dB) is equal to the open loop gain of the operational amplifier used in the transimpedance interface stage. The circuit has very simple structure and utilises a small number of popular components. The amplifier is intended for use in various two-electrode applications, such as Holter-type monitors, defibrillators, ECG monitors, biotelemetry devices etc.

Differential high-speed digital micromirror device based fluorescence speckle confocal microscopy.

PubMed

Jiang, Shihong; Walker, John

2010-01-20

We report a differential fluorescence speckle confocal microscope that acquires an image in a fraction of a second by exploiting the very high frame rate of modern digital micromirror devices (DMDs). The DMD projects a sequence of predefined binary speckle patterns to the sample and modulates the intensity of the returning fluorescent light simultaneously. The fluorescent light reflecting from the DMD's "on" and "off" pixels is modulated by correlated speckle and anticorrelated speckle, respectively, to form two images on two CCD cameras in parallel. The sum of the two images recovers a widefield image, but their difference gives a near-confocal image in real time. Experimental results for both low and high numerical apertures are shown.

Astigmatism error modification for absolute shape reconstruction using Fourier transform method

NASA Astrophysics Data System (ADS)

He, Yuhang; Li, Qiang; Gao, Bo; Liu, Ang; Xu, Kaiyuan; Wei, Xiaohong; Chai, Liqun

2014-12-01

A method is proposed to modify astigmatism errors in absolute shape reconstruction of optical plane using Fourier transform method. If a transmission and reflection flat are used in an absolute test, two translation measurements lead to obtain the absolute shapes by making use of the characteristic relationship between the differential and original shapes in spatial frequency domain. However, because the translation device cannot guarantee the test and reference flats rigidly parallel to each other after the translations, a tilt error exists in the obtained differential data, which caused power and astigmatism errors in the reconstructed shapes. In order to modify the astigmatism errors, a rotation measurement is added. Based on the rotation invariability of the form of Zernike polynomial in circular domain, the astigmatism terms are calculated by solving polynomial coefficient equations related to the rotation differential data, and subsequently the astigmatism terms including error are modified. Computer simulation proves the validity of the proposed method.

Ion mobility sensor system

DOEpatents

Xu, Jun; Watson, David B.; Whitten, William B.

2013-01-22

An ion mobility sensor system including an ion mobility spectrometer and a differential mobility spectrometer coupled to the ion mobility spectrometer. The ion mobility spectrometer has a first chamber having first end and a second end extending along a first direction, and a first electrode system that generates a constant electric field parallel to the first direction. The differential mobility spectrometer includes a second chamber having a third end and a fourth end configured such that a fluid may flow in a second direction from the third end to the fourth end, and a second electrode system that generates an asymmetric electric field within an interior of the second chamber. Additionally, the ion mobility spectrometer and the differential mobility spectrometer form an interface region. Also, the first end and the third end are positioned facing one another so that the constant electric field enters the third end and overlaps the fluid flowing in the second direction.

Differential optical shadow sensor for sub-nanometer displacement measurement and its application to drag-free satellites.

PubMed

Zoellner, Andreas; Tan, Si; Saraf, Shailendhar; Alfauwaz, Abdul; DeBra, Dan; Buchman, Sasha; Lipa, John A

2017-10-16

We present a method for 3D sub-nanometer displacement measurement using a set of differential optical shadow sensors. It is based on using pairs of collimated beams on opposite sides of an object that are partially blocked by it. Applied to a sphere, our 3-axis sensor module consists of 8 parallel beam-detector sets for redundancy. The sphere blocks half of each beam's power in the nominal centered position, and any displacement can be measured by the differential optical power changes amongst the pairs of detectors. We have experimentally demonstrated a displacement sensitivity of 0.87nm/Hz at 1 Hz and 0.39nm/Hz at 10 Hz. We describe the application of the module to the inertial sensor of a drag-free satellite, which can potentially be used for navigation, geodesy and fundamental science experiments as well as ground based applications.

Low Differential Pressure Generator

NASA Technical Reports Server (NTRS)

Stout, Stephen J. (Inventor); Deyoe, Richard T. (Inventor)

1997-01-01

A method and apparatus for evaluating low differential pressure transducers includes a pressure generator in the form of a piston-cylinder assembly having a piston that may be manually positioned precisely within the cylinder to change the volume and thus the pressure at respective sides of the piston. At one side of the piston the cylinder communicates with a first chamber and at the other side of the piston the cylinder communicates with a second chamber, the first and second chambers being formed within a common tank by a partition wall. The chambers each communicate with the transducer to be evaluated and a standard pre-calibrated transducer the transducers being connected fluidly in parallel so that a pressure differential between air in the two chambers resulting from movement of the piston within the cylinder is communicated to both the transducer to be evaluated and the standard transducer, and the outputs of the transducers is observed and recorded.

Solar wind helium ions - Observations of the Helios solar probes between 0.3 and 1 AU

NASA Technical Reports Server (NTRS)

Marsch, E.; Rosenbauer, H.; Schwenn, R.; Muehlhaeuser, K.-H.; Neubauer, F. M.

1982-01-01

A Helios solar probe survey of solar wind helium ion velocity distributions and derived parameters between 0.3 and 1 AU is presented. Distributions in high-speed wind are found to generally have small total anisotropies, with some indication that, in the core part, the temperatures are greater parallel rather than perpendicular to the magnetic field. The anisotropy tends to increase with heliocentric radial distance, and the average dependence of helium ion temperatures on radial distance from the sun is described by a power law. Differential ion speeds with values of more than 150 km/sec are observed near perihelion, or 0.3 AU. The role of Coulomb collisions in limiting differential ion speeds and the ion temperature ratio is investigated, and it is found that collisions play a distinct role in low-speed wind, by limiting both differential ion velocity and temperature.

PetIGA: A framework for high-performance isogeometric analysis

DOE PAGES

Dalcin, Lisandro; Collier, Nathaniel; Vignal, Philippe; ...

2016-05-25

We present PetIGA, a code framework to approximate the solution of partial differential equations using isogeometric analysis. PetIGA can be used to assemble matrices and vectors which come from a Galerkin weak form, discretized with Non-Uniform Rational B-spline basis functions. We base our framework on PETSc, a high-performance library for the scalable solution of partial differential equations, which simplifies the development of large-scale scientific codes, provides a rich environment for prototyping, and separates parallelism from algorithm choice. We describe the implementation of PetIGA, and exemplify its use by solving a model nonlinear problem. To illustrate the robustness and flexibility ofmore » PetIGA, we solve some challenging nonlinear partial differential equations that include problems in both solid and fluid mechanics. Lastly, we show strong scaling results on up to 4096 cores, which confirm the suitability of PetIGA for large scale simulations.« less

Standing chromosomal variation in Lake Whitefish species pairs: the role of historical contingency and relevance for speciation.

PubMed

Dion-Côté, Anne-Marie; Symonová, Radka; Lamaze, Fabien C; Pelikánová, Šárka; Ráb, Petr; Bernatchez, Louis

2017-01-01

The role of chromosome changes in speciation remains a debated topic, although demographic conditions associated with divergence should promote their appearance. We tested a potential relationship between chromosome changes and speciation by studying two Lake Whitefish (Coregonus clupeaformis) lineages that recently colonized postglacial lakes following allopatry. A dwarf limnetic species evolved repeatedly from the normal benthic species, becoming reproductively isolated. Lake Whitefish hybrids experience mitotic and meiotic instability, which may result from structurally divergent chromosomes. Motivated by this observation, we test the hypothesis that chromosome organization differs between Lake Whitefish species pairs using cytogenetics. While chromosome and fundamental numbers are conserved between the species (2n = 80, NF = 98), we observe extensive polymorphism of subtle karyotype traits. We describe intrachromosomal differences associated with heterochromatin and repetitive DNA, and test for parallelism among three sympatric species pairs. Multivariate analyses support the hypothesis that differentiation at the level of subchromosomal markers mostly appeared during allopatry. Yet we find no evidence for parallelism between species pairs among lakes, consistent with colonization effect or postcolonization differentiation. The reported intrachromosomal polymorphisms do not appear to play a central role in driving adaptive divergence between normal and dwarf Lake Whitefish. We discuss how chromosomal differentiation in the Lake Whitefish system may contribute to the destabilization of mitotic and meiotic chromosome segregation in hybrids, as documented previously. The chromosome structures detected here are still difficult to sequence and assemble, demonstrating the value of cytogenetics as a complementary approach to understand the genomic bases of speciation. © 2016 John Wiley & Sons Ltd.

Conjunctive search for one and two identical targets.

PubMed

Ward, R; McClelland, J L

1989-11-01

The assumptions of feature integration theory as a blind, serial, self-terminating search (SSTS) mechanism are extended to displays containing 2 identical targets. The SSTS predicts no differences in negative-response displays, which require an exhaustive search of the display. Quantitative predictions are confirmed for the positive responses, but not for the negatives, suggesting that the SSTS model is incorrect. Two possible explanations for the results in the negative conditions, differential search rates and early quitting in the negatives, are rejected. It is suggested that using any self-terminating search mechanism will lead to difficulty in interpreting the results, including accounts for which the search is parallel over small groups of items. A resource-limited parallel model, which is based on the diffusion model of Ratcliff (1978), appears to fit the data well.

Seq-ing answers: uncovering the unexpected in global gene regulation.

PubMed

Otto, George Maxwell; Brar, Gloria Ann

2018-04-19

The development of techniques for measuring gene expression globally has greatly expanded our understanding of gene regulatory mechanisms in depth and scale. We can now quantify every intermediate and transition in the canonical pathway of gene expression-from DNA to mRNA to protein-genome-wide. Employing such measurements in parallel can produce rich datasets, but extracting the most information requires careful experimental design and analysis. Here, we argue for the value of genome-wide studies that measure multiple outputs of gene expression over many timepoints during the course of a natural developmental process. We discuss our findings from a highly parallel gene expression dataset of meiotic differentiation, and those of others, to illustrate how leveraging these features can provide new and surprising insight into fundamental mechanisms of gene regulation.

Large tuning of birefringence in two strip silicon waveguides via optomechanical motion.

PubMed

Ma, Jing; Povinelli, Michelle L

2009-09-28

We present an optomechanical method to tune phase and group birefringence in parallel silicon strip waveguides. We first calculate the deformation of suspended, parallel strip waveguides due to optical forces. We optimize the frequency and polarization of the pump light to obtain a 9 nm deformation for an optical power of 20 mW. Widely tunable phase and group birefringence can be achieved by varying the pump power, with maximum values of 0.026 and 0.13, respectively. The giant phase birefringence allows linear to circular polarization conversion within 30 microm for a pump power of 67 mW. The group birefringence gives a tunable differential group delay of 6fs between orthogonal polarizations. We also evaluate the tuning performance of waveguides with different cross sections.

Survey of new vector computers: The CRAY 1S from CRAY research; the CYBER 205 from CDC and the parallel computer from ICL - architecture and programming

NASA Technical Reports Server (NTRS)

Gentzsch, W.

1982-01-01

Problems which can arise with vector and parallel computers are discussed in a user oriented context. Emphasis is placed on the algorithms used and the programming techniques adopted. Three recently developed supercomputers are examined and typical application examples are given in CRAY FORTRAN, CYBER 205 FORTRAN and DAP (distributed array processor) FORTRAN. The systems performance is compared. The addition of parts of two N x N arrays is considered. The influence of the architecture on the algorithms and programming language is demonstrated. Numerical analysis of magnetohydrodynamic differential equations by an explicit difference method is illustrated, showing very good results for all three systems. The prognosis for supercomputer development is assessed.

Photon escape probabilities in a semi-infinite plane-parallel medium. [from electron plasma surrounding galactic X-ray sources

NASA Technical Reports Server (NTRS)

Williams, A. C.; Elsner, R. F.; Weisskopf, M. C.; Darbro, W.

1984-01-01

It is shown in this work how to obtain the probabilities of photons escaping from a cold electron plasma environment after having undergone an arbitrary number of scatterings. This is done by retaining the exact differential cross section for Thomson scattering as opposed to using its polarization and angle averaged form. The results are given in the form of recursion relations. The geometry used is the semi-infinite plane-parallel geometry witlh a photon source located on a plane at an arbitrary optical depth below the surface. Analytical expressions are given for the probabilities which are accurate over a wide range of initial optical depth. These results can be used to model compact X-ray galactic sources which are surrounded by an electron-rich plasma.

Solving the Cauchy-Riemann equations on parallel computers

NASA Technical Reports Server (NTRS)

Fatoohi, Raad A.; Grosch, Chester E.

1987-01-01

Discussed is the implementation of a single algorithm on three parallel-vector computers. The algorithm is a relaxation scheme for the solution of the Cauchy-Riemann equations; a set of coupled first order partial differential equations. The computers were chosen so as to encompass a variety of architectures. They are: the MPP, and SIMD machine with 16K bit serial processors; FLEX/32, an MIMD machine with 20 processors; and CRAY/2, an MIMD machine with four vector processors. The machine architectures are briefly described. The implementation of the algorithm is discussed in relation to these architectures and measures of the performance on each machine are given. Simple performance models are used to describe the performance. These models highlight the bottlenecks and limiting factors for this algorithm on these architectures. Conclusions are presented.

Implementation of a partitioned algorithm for simulation of large CSI problems

NASA Technical Reports Server (NTRS)

Alvin, Kenneth F.; Park, K. C.

1991-01-01

The implementation of a partitioned numerical algorithm for determining the dynamic response of coupled structure/controller/estimator finite-dimensional systems is reviewed. The partitioned approach leads to a set of coupled first and second-order linear differential equations which are numerically integrated with extrapolation and implicit step methods. The present software implementation, ACSIS, utilizes parallel processing techniques at various levels to optimize performance on a shared-memory concurrent/vector processing system. A general procedure for the design of controller and filter gains is also implemented, which utilizes the vibration characteristics of the structure to be solved. Also presented are: example problems; a user's guide to the software; the procedures and algorithm scripts; a stability analysis for the algorithm; and the source code for the parallel implementation.

The HOX genes are expressed, in vivo, in human tooth germs: in vitro cAMP exposure of dental pulp cells results in parallel HOX network activation and neuronal differentiation.

PubMed

D'Antò, Vincenzo; Cantile, Monica; D'Armiento, Maria; Schiavo, Giulia; Spagnuolo, Gianrico; Terracciano, Luigi; Vecchione, Raffaela; Cillo, Clemente

2006-03-01

Homeobox-containing genes play a crucial role in odontogenesis. After the detection of Dlx and Msx genes in overlapping domains along maxillary and mandibular processes, a homeobox odontogenic code has been proposed to explain the interaction between different homeobox genes during dental lamina patterning. No role has so far been assigned to the Hox gene network in the homeobox odontogenic code due to studies on specific Hox genes and evolutionary considerations. Despite its involvement in early patterning during embryonal development, the HOX gene network, the most repeat-poor regions of the human genome, controls the phenotype identity of adult eukaryotic cells. Here, according to our results, the HOX gene network appears to be active in human tooth germs between 18 and 24 weeks of development. The immunohistochemical localization of specific HOX proteins mostly concerns the epithelial tooth germ compartment. Furthermore, only a few genes of the network are active in embryonal retromolar tissues, as well as in ectomesenchymal dental pulp cells (DPC) grown in vitro from adult human molar. Exposure of DPCs to cAMP induces the expression of from three to nine total HOX genes of the network in parallel with phenotype modifications with traits of neuronal differentiation. Our observations suggest that: (i) by combining its component genes, the HOX gene network determines the phenotype identity of epithelial and ectomesenchymal cells interacting in the generation of human tooth germ; (ii) cAMP treatment activates the HOX network and induces, in parallel, a neuronal-like phenotype in human primary ectomesenchymal dental pulp cells. 2005 Wiley-Liss, Inc.

Parallel multiscale simulations of a brain aneurysm

PubMed Central

Grinberg, Leopold; Fedosov, Dmitry A.; Karniadakis, George Em

2012-01-01

Cardiovascular pathologies, such as a brain aneurysm, are affected by the global blood circulation as well as by the local microrheology. Hence, developing computational models for such cases requires the coupling of disparate spatial and temporal scales often governed by diverse mathematical descriptions, e.g., by partial differential equations (continuum) and ordinary differential equations for discrete particles (atomistic). However, interfacing atomistic-based with continuum-based domain discretizations is a challenging problem that requires both mathematical and computational advances. We present here a hybrid methodology that enabled us to perform the first multi-scale simulations of platelet depositions on the wall of a brain aneurysm. The large scale flow features in the intracranial network are accurately resolved by using the high-order spectral element Navier-Stokes solver εκ αr. The blood rheology inside the aneurysm is modeled using a coarse-grained stochastic molecular dynamics approach (the dissipative particle dynamics method) implemented in the parallel code LAMMPS. The continuum and atomistic domains overlap with interface conditions provided by effective forces computed adaptively to ensure continuity of states across the interface boundary. A two-way interaction is allowed with the time-evolving boundary of the (deposited) platelet clusters tracked by an immersed boundary method. The corresponding heterogeneous solvers ( εκ αr and LAMMPS) are linked together by a computational multilevel message passing interface that facilitates modularity and high parallel efficiency. Results of multiscale simulations of clot formation inside the aneurysm in a patient-specific arterial tree are presented. We also discuss the computational challenges involved and present scalability results of our coupled solver on up to 300K computer processors. Validation of such coupled atomistic-continuum models is a main open issue that has to be addressed in future work. PMID:23734066

Parallel multiscale simulations of a brain aneurysm.

PubMed

Grinberg, Leopold; Fedosov, Dmitry A; Karniadakis, George Em

2013-07-01

Cardiovascular pathologies, such as a brain aneurysm, are affected by the global blood circulation as well as by the local microrheology. Hence, developing computational models for such cases requires the coupling of disparate spatial and temporal scales often governed by diverse mathematical descriptions, e.g., by partial differential equations (continuum) and ordinary differential equations for discrete particles (atomistic). However, interfacing atomistic-based with continuum-based domain discretizations is a challenging problem that requires both mathematical and computational advances. We present here a hybrid methodology that enabled us to perform the first multi-scale simulations of platelet depositions on the wall of a brain aneurysm. The large scale flow features in the intracranial network are accurately resolved by using the high-order spectral element Navier-Stokes solver εκ αr . The blood rheology inside the aneurysm is modeled using a coarse-grained stochastic molecular dynamics approach (the dissipative particle dynamics method) implemented in the parallel code LAMMPS. The continuum and atomistic domains overlap with interface conditions provided by effective forces computed adaptively to ensure continuity of states across the interface boundary. A two-way interaction is allowed with the time-evolving boundary of the (deposited) platelet clusters tracked by an immersed boundary method. The corresponding heterogeneous solvers ( εκ αr and LAMMPS) are linked together by a computational multilevel message passing interface that facilitates modularity and high parallel efficiency. Results of multiscale simulations of clot formation inside the aneurysm in a patient-specific arterial tree are presented. We also discuss the computational challenges involved and present scalability results of our coupled solver on up to 300K computer processors. Validation of such coupled atomistic-continuum models is a main open issue that has to be addressed in future work.

Parallel multiscale simulations of a brain aneurysm

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grinberg, Leopold; Fedosov, Dmitry A.; Karniadakis, George Em, E-mail: george_karniadakis@brown.edu

2013-07-01

Cardiovascular pathologies, such as a brain aneurysm, are affected by the global blood circulation as well as by the local microrheology. Hence, developing computational models for such cases requires the coupling of disparate spatial and temporal scales often governed by diverse mathematical descriptions, e.g., by partial differential equations (continuum) and ordinary differential equations for discrete particles (atomistic). However, interfacing atomistic-based with continuum-based domain discretizations is a challenging problem that requires both mathematical and computational advances. We present here a hybrid methodology that enabled us to perform the first multiscale simulations of platelet depositions on the wall of a brain aneurysm.more » The large scale flow features in the intracranial network are accurately resolved by using the high-order spectral element Navier–Stokes solver NεκTαr. The blood rheology inside the aneurysm is modeled using a coarse-grained stochastic molecular dynamics approach (the dissipative particle dynamics method) implemented in the parallel code LAMMPS. The continuum and atomistic domains overlap with interface conditions provided by effective forces computed adaptively to ensure continuity of states across the interface boundary. A two-way interaction is allowed with the time-evolving boundary of the (deposited) platelet clusters tracked by an immersed boundary method. The corresponding heterogeneous solvers (NεκTαr and LAMMPS) are linked together by a computational multilevel message passing interface that facilitates modularity and high parallel efficiency. Results of multiscale simulations of clot formation inside the aneurysm in a patient-specific arterial tree are presented. We also discuss the computational challenges involved and present scalability results of our coupled solver on up to 300 K computer processors. Validation of such coupled atomistic-continuum models is a main open issue that has to be addressed in future work.« less

Removal of suspended solids and turbidity from marble processing wastewaters by electrocoagulation: comparison of electrode materials and electrode connection systems.

PubMed

Solak, Murat; Kiliç, Mehmet; Hüseyin, Yazici; Sencan, Aziz

2009-12-15

In this study, removal of suspended solids (SS) and turbidity from marble processing wastewaters by electrocoagulation (EC) process were investigated by using aluminium (Al) and iron (Fe) electrodes which were run in serial and parallel connection systems. To remove these pollutants from the marble processing wastewater, an EC reactor including monopolar electrodes (Al/Fe) in parallel and serial connection system, was utilized. Optimization of differential operation parameters such as pH, current density, and electrolysis time on SS and turbidity removal were determined in this way. EC process with monopolar Al electrodes in parallel and serial connections carried out at the optimum conditions where the pH value was 9, current density was approximately 15 A/m(2), and electrolysis time was 2 min resulted in 100% SS removal. Removal efficiencies of EC process for SS with monopolar Fe electrodes in parallel and serial connection were found to be 99.86% and 99.94%, respectively. Optimum parameters for monopolar Fe electrodes in both of the connection types were found to be for pH value as 8, for electrolysis time as 2 min. The optimum current density value for Fe electrodes used in serial and parallel connections was also obtained at 10 and 20 A/m(2), respectively. Based on the results obtained, it was found that EC process running with each type of the electrodes and the connections was highly effective for the removal of SS and turbidity from marble processing wastewaters, and that operating costs with monopolar Al electrodes in parallel connection were the cheapest than that of the serial connection and all the configurations for Fe electrode.

Preliminary archeointensity results from well-dated ceramics from ancient Bactria (Uzbekistan, Central Asia)

NASA Astrophysics Data System (ADS)

Gomez-Paccard, M.; Beamud, E.; Martínez-Ferreras, V.; Gurt-Esparraguera, J. M.

2017-12-01

Improving geomagnetic field reconstructions clearly poses a high-priority challenge in Earth Sciences today. A better characterization of the variation of the geomagnetic field strength at centennial to millennial time scales is particularly crucial to disentangle the long-term evolution of the Earth's dipole moment, a global characteristic of our planet. Here we present new high-quality archeointensities for Central Asia, a vast and rather poorly known region in terms of geomagnetic field intensity fluctuations. These new data are obtained from the study of 26 pottery fragments from Termez, a great urban and Buddhist religious center in ancient Bactria (south Uzbekistan) during the Kushan period. The samples have been collected in several sectors related to different stages of the occupation as demonstrated by 14C analysis: 1) two sectors in the alluvial plain (AC2 and AC1), dated to the Greco-Bactrian (from the 3rd to the 1st centuries BC) and the nomadic Yuezhi (≈1st century AD) periods respectively; 2) sector RC at the Tchingiz Tepe fortress, dated to the Kushan and Kushano-Sassanian periods (from the 2nd to the 4th centuries AD). The classical Thellier method including regular partial thermoremanent magnetization (pTRM) checks and TRM anisotropy and cooling rate corrections has been used for archeointensity determination. The new data obtained shed new light on the past fluctuation of geomagnetic field strength in Central Asia. In addition, a critical revision of archeointensity data from Central Asia is presented. Selected high-quality archeointensities are finally compared with regional and global geomagnetic field reconstructions.

On the suitability of the Thellier method of palaeointensity determinations on pseudo-single-domain and multidomain grains

NASA Astrophysics Data System (ADS)

Shcherbakov, V. P.; Shcherbakova, V. V.

2001-07-01

We report an experimental and theoretical study of non-linear Arai-Nagata diagrams for samples containing pseudo-single-domain (PSD) and multidomain (MD) magnetite. Our aim is to reveal the physical reasons for the deviation of these plots from ideal straight lines. Contrary to expectations, the concavity of the Arai-Nagata diagrams is not related to the two most noticeable violations of the Thellier laws documented for non-single-domain particles: the tail of partial thermoremanence and the dependence of the magnitude of pTRM on the thermal history of the sample. Indeed, the contributions from these two factors mutually cancel each other. Phenomenologically, the non-linear Arai-Nagata plots occur because samples during low-temperature stages of the Thellier procedure lose too much remanence and recover too little of it. The excessive loss of the previously imparted total TRM is due at least partly to some partial demagnetization of high-temperature TRM components and to progressive stabilization of domain structure during the repetitive heatings to moderate temperatures that form the basis of the Thellier procedure. For natural MD samples a linear fit to the low-temperature data points on the Arai-Nagata plots leads to a palaeointensity overestimated by as much as 60 per cent. The samples containing hydrothermally grown or crushed and sieved MD magnetite provide low-temperature apparent palaeointensities two to three times larger than the correct value. For small PSD samples the overestimate is less than 10-20 per cent and, in general, PSD samples can be used for the palaeointensity determinations.

Effects of titanomagnetite reordering processes on thermal demagnetization and paleointensity experiments

NASA Astrophysics Data System (ADS)

Bowles, Julie A.; Jackson, Mike J.

2016-12-01

Titanomagnetite (Fe3-xTixO4, 0 ≤ x ≤ 1) is a common, naturally occurring magnetic mineral critical to many paleomagnetic studies. Underlying most interpretations is the assumption that, lacking chemical alteration, Curie temperature (Tc) remains constant. However, recent work has demonstrated that Tc of many natural titanomagnetites varies strongly as a function of thermal history, independent of chemical alteration. This is inferred to arise from reordering of cations and/or vacancies in the crystal structure, and changes occur at temperatures and times relevant to standard paleomagnetic thermal treatments. Because changes take place at T < Tc, they have the potential to dramatically affect thermal remanence acquisition or demagnetization, impacting interpretation of paleomagnetic results. Here we have modeled the effects of reordering on standard thermal demagnetization and paleointensity experiments. Results suggest that Tc changes during laboratory heating make it impossible to accurately measure the unblocking temperature spectrum without modifying it. Samples with a starting Tc0 less than the closure temperature (Tclose) for the reordering process will develop a high-temperature "tail" that did not exist prior to heating. Samples with a starting Tc0 > Tclose will have their original Tb spectrum truncated at T ≈ Tclose. Predicted behavior during Thellier-type paleointensity experiments results in only modest deviations in NRM-lost or pTRM*-gained from the nonreordering case. Much larger deviations are predicted for pTRM checks. Compared to paleointensity results from titanomagnetite-bearing pyroclastic deposits, modeled nonideal behavior occurs in the same temperature intervals, but is much more systematic. Reordering is likely one contributing factor to failure of paleointensity experiments.

Geomagnetic paleointensity between 1300 and 1750 A.D. derived from a bread oven floor sequence in Lübeck, Germany

NASA Astrophysics Data System (ADS)

Schnepp, Elisabeth; Lanos, Philippe; Chauvin, Annick

2009-08-01

Geomagnetic paleointensities have been determined from a single archaeological site in Lübeck, Germany, where a sequence of 25 bread oven floors has been preserved in a bakery from medieval times until today. Age dating confines the time interval from about 1300 A.D. to about 1750 A.D. Paleomagnetic directions have been published from each oven floor and are updated here. The specimens have very stable directions and no or only weak secondary components. The oven floor material was characterized rock magnetically using Thellier viscosity indices, median destructive field values, Curie point determinations, and hysteresis measurements. Magnetic carriers are mixtures of SD, PSD, and minor MD magnetite and/or maghemite together with small amounts of hematite. Paleointensity was measured from selected specimens with the double-heating Thellier method including pTRM checks and determination of TRM anisotropy tensors. Corrections for anisotropy as well as for cooling rate turned out to be unnecessary. Ninety-two percent of the Thellier experiments passed the assigned acceptance criteria and provided four to six reliable paleointensity estimates per oven floor. Mean paleointensity values derived from 22 oven floors show maxima in the 15th and early 17th centuries A.D., followed by a decrease of paleointensity of about 20% until 1750 A.D. Together with the directions the record represents about 450 years of full vector secular variation. The results compare well with historical models of the Earth's magnetic field as well as with a selected high-quality paleointensity data set for western and central Europe.

Nanoparticle-mediated intracellular lipid accumulation during C2C12 cell differentiation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tsukahara, Tamotsu, E-mail: ttamotsu@shinshu-u.ac.jp; Haniu, Hisao, E-mail: hhaniu@shinshu-u.ac.jp

2011-03-25

Research highlights: {yields} HTT2800 has a significant effect on intracellular lipid accumulation. {yields} HTT2800 reduced muscle-specific genes and led to the emergence of adipocyte-related genes. {yields} HT2800 converts the differentiation pathway of C2C12 myoblasts to that of adipoblast-like cells. -- Abstract: In this report, we sought to elucidate whether multiwall carbon nanotubes are involved in the modulation of the proliferation and differentiation of the skeletal muscle cell line C2C12. Skeletal muscle is a major mass peripheral tissue that accounts for 40% of total body weight and 50% of energy consumption. We focused on the differentiation pathway of myoblasts after exposuremore » to a vapor-grown carbon fiber, HTT2800, which is one of the most highly purified carbon nanotubes. This treatment leads in parallel to the expression of a typical adipose differentiation program. We found that HTT2800 stimulated intracellular lipid accumulation in C2C12 cells. We have also shown by quantified PCR analysis that the expression of adipose-related genes was markedly upregulated during HTT2800 exposure. Taken together, these results suggest that HTT2800 specifically converts the differentiation pathway of C2C12 myoblasts to that of adipoblast-like cells.« less

The Parker-Sochacki Method--A Powerful New Method for Solving Systems of Differential Equations

NASA Astrophysics Data System (ADS)

Rudmin, Joseph W.

2001-04-01

The Parker-Sochacki Method--A Powerful New Method for Solving Systems of Differential Equations Joseph W. Rudmin (Physics Dept, James Madison University) A new system of solving systems of differential equations will be presented, which has been developed by J. Edgar Parker and James Sochacki, of the James Madison University Mathematics Department. The method produces MacClaurin Series solutions to systems of differential equations, with the coefficients in either algebraic or numerical form. The method yields high-degree solutions: 20th degree is easily obtainable. It is conceptually simple, fast, and extremely general. It has been applied to over a hundred systems of differential equations, some of which were previously unsolved, and has yet to fail to solve any system for which the MacClaurin series converges. The method is non-recursive: each coefficient in the series is calculated just once, in closed form, and its accuracy is limited only by the digital accuracy of the computer. Although the original differential equations may include any mathematical functions, the computational method includes ONLY the operations of addition, subtraction, and multiplication. Furthermore, it is perfectly suited to parallel -processing computer languages. Those who learn this system will never use Runge-Kutta or predictor-corrector methods again. Examples will be presented, including the classical many-body problem.

Marker-free detection of progenitor cell differentiation by analysis of Brownian motion in micro-wells.

PubMed

Sekhavati, Farzad; Endele, Max; Rappl, Susanne; Marel, Anna-Kristina; Schroeder, Timm; Rädler, Joachim O

2015-02-01

The kinetics of stem and progenitor cell differentiation at the single-cell level provides essential clues to the complexity of the underlying decision-making circuits. In many hematopoietic progenitor cells, differentiation is accompanied by the expression of lineage-specific markers and by a transition from a non-adherent to an adherent state. Here, using the granulocyte-macrophage progenitor (GMP) as a model, we introduce a label-free approach that allows one to follow the course of this transition in hundreds of single cells in parallel. We trap single cells in patterned arrays of micro-wells and use phase-contrast time-lapse movies to distinguish non-adherent from adherent cells by an analysis of Brownian motion. This approach allowed us to observe the kinetics of induced differentiation of primary bone-marrow-derived GMPs into macrophages. The time lapse started 2 hours after addition of the cytokine M-CSF, and nearly 80% of the population had accomplished the transition within the first 20 h. The analysis of Brownian motion proved to be a sensitive and robust tool for monitoring the transition, and thus provides a high-throughput method for the study of cell differentiation at the single-cell level.

Parallel Syndromes: Two Dimensions of Narcissism and the Facets of Psychopathic Personality in Criminally-Involved Individuals

PubMed Central

2012-01-01

Little research has examined different dimensions of narcissism that may parallel psychopathy facets in criminally-involved individuals. The present study examined the pattern of relationships between grandiose and vulnerable narcissism, assessed using the Narcissistic Personality Inventory-16 and the Hypersensitive Narcissism Scale, respectively, and the four facets of psychopathy (interpersonal, affective, lifestyle, and antisocial) assessed via the Psychopathy Checklist: Screening Version (PCL:SV). As predicted, grandiose and vulnerable narcissism showed differential relationships to psychopathy facets, with grandiose narcissism relating positively to the interpersonal facet of psychopathy and vulnerable narcissism relating positively to the lifestyle facet of psychopathy. Paralleling existing psychopathy research, vulnerable narcissism showed stronger associations than grandiose narcissism to 1) other forms of psychopathology, including internalizing and substance use disorders, and 2) self- and other-directed aggression, measured using the Life History of Aggression and the Forms of Aggression Questionnaire. Grandiose narcissism was nonetheless associated with social dysfunction marked by a manipulative and deceitful interpersonal style and unprovoked aggression. Potentially important implications for uncovering etiological pathways and developing treatment interventions for these disorders in externalizing adults are discussed. PMID:22448731

Proton core-beam system in the expanding solar wind: Hybrid simulations

NASA Astrophysics Data System (ADS)

Hellinger, Petr; Trávníček, Pavel M.

2011-11-01

Results of a two-dimensional hybrid expanding box simulation of a proton beam-core system in the solar wind are presented. The expansion with a strictly radial magnetic field leads to a decrease of the ratio between the proton perpendicular and parallel temperatures as well as to an increase of the ratio between the beam-core differential velocity and the local Alfvén velocity creating a free energy for many different instabilities. The system is indeed most of the time marginally stable with respect to the parallel magnetosonic, oblique Alfvén, proton cyclotron and parallel fire hose instabilities which determine the system evolution counteracting some effects of the expansion and interacting with each other. Nonlinear evolution of these instabilities leads to large modifications of the proton velocity distribution function. The beam and core protons are slowed with respect to each other and heated, and at later stages of the evolution the two populations are not clearly distinguishable. On the macroscopic level the instabilities cause large departures from the double adiabatic prediction leading to an efficient isotropization of effective proton temperatures in agreement with Helios observations.

Summer Proceedings 2016: The Center for Computing Research at Sandia National Laboratories

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carleton, James Brian; Parks, Michael L.

Solving sparse linear systems from the discretization of elliptic partial differential equations (PDEs) is an important building block in many engineering applications. Sparse direct solvers can solve general linear systems, but are usually slower and use much more memory than effective iterative solvers. To overcome these two disadvantages, a hierarchical solver (LoRaSp) based on H2-matrices was introduced in [22]. Here, we have developed a parallel version of the algorithm in LoRaSp to solve large sparse matrices on distributed memory machines. On a single processor, the factorization time of our parallel solver scales almost linearly with the problem size for three-dimensionalmore » problems, as opposed to the quadratic scalability of many existing sparse direct solvers. Moreover, our solver leads to almost constant numbers of iterations, when used as a preconditioner for Poisson problems. On more than one processor, our algorithm has significant speedups compared to sequential runs. With this parallel algorithm, we are able to solve large problems much faster than many existing packages as demonstrated by the numerical experiments.« less

Importance of ERK activation in As2O3-induced differentiation and promyelocytic leukemia nuclear bodies formation in neuroblastoma cells.

PubMed

Petit, A; Delaune, A; Falluel-Morel, A; Goullé, J-P; Vannier, J-P; Dubus, I; Vasse, M

2013-11-01

Neuroblastoma malignant cell growth is dependent on their undifferentiated status. Arsenic trioxide (As2O3) induces neuroblastoma cell differentiation in vitro, but its mechanisms still remains unknown. We used three human neuroblastoma cell lines (SH-SY5Y, IGR-N-91, LAN-1) that differ from their MYCN and p53 status to explore the intracellular events activated by As2O3 and involved in neurite outgrowth, a morphological marker of differentiation. As2O3 (2μM) induced neurite outgrowth in all cell lines, which was dependent on ERK activation but independent on MYCN status. This process was induced either by a sustained (3 days) or a transient (2h) incubation with As2O3, indicating that very early events trigger the induction of differentiation. In parallel, As2O3 induced a rapid assembly of promyelocytic leukemia nuclear bodies (PML-NB) in an ERK-dependent manner. In conclusion, mechanisms leading to neuroblastoma cell differentiation in response to As2O3 appear to involve the ERK pathway activation and PML-NB formation, which are observed in response to other differentiating molecules such as retinoic acid derivates. This open new perspectives based on the use of treatment combinations to potentiate the differentiating effects of each drug alone and reduce their adverse side effects. Copyright © 2013 Elsevier Ltd. All rights reserved.

Parameterized spectral distributions for meson production in proton-proton collisions

NASA Technical Reports Server (NTRS)

Schneider, John P.; Norbury, John W.; Cucinotta, Francis A.

1995-01-01

Accurate semiempirical parameterizations of the energy-differential cross sections for charged pion and kaon production from proton-proton collisions are presented at energies relevant to cosmic rays. The parameterizations, which depend on both the outgoing meson parallel momentum and the incident proton kinetic energy, are able to be reduced to very simple analytical formulas suitable for cosmic ray transport through spacecraft walls, interstellar space, the atmosphere, and meteorites.

Prediction of Crack Growth Aqueous Environments.

DTIC Science & Technology

1983-06-01

one- dimensional one. The mathematical model for the electrical representation shown in Figure 1 requires solutions to a set of differential equations ... equation (5) is equivalent to that at a plane-parallel electrode. That is, it contains the info~rmation that would be available if it were possible to...concentration, and A" expresses the electrode electrolyte area per unit length that is actively engaged in reaction. The other parameters in equation (7

Development of fast parallel multi-technique scanning X-ray imaging at Synchrotron Soleil

NASA Astrophysics Data System (ADS)

Medjoubi, K.; Leclercq, N.; Langlois, F.; Buteau, A.; Lé, S.; Poirier, S.; Mercère, P.; Kewish, C. M.; Somogyi, A.

2013-10-01

A fast multimodal scanning X-ray imaging scheme is prototyped at Soleil Synchrotron. It permits the simultaneous acquisition of complementary information on the sample structure, composition and chemistry by measuring transmission, differential phase contrast, small-angle scattering, and X-ray fluorescence by dedicated detectors with ms dwell time per pixel. The results of the proof of principle experiments are presented in this paper.

A high-order time-parallel scheme for solving wave propagation problems via the direct construction of an approximate time-evolution operator

DOE Office of Scientific and Technical Information (OSTI.GOV)

Haut, T. S.; Babb, T.; Martinsson, P. G.

2015-06-16

Our manuscript demonstrates a technique for efficiently solving the classical wave equation, the shallow water equations, and, more generally, equations of the form ∂u/∂t=Lu∂u/∂t=Lu, where LL is a skew-Hermitian differential operator. The idea is to explicitly construct an approximation to the time-evolution operator exp(τL)exp(τL) for a relatively large time-step ττ. Recently developed techniques for approximating oscillatory scalar functions by rational functions, and accelerated algorithms for computing functions of discretized differential operators are exploited. Principal advantages of the proposed method include: stability even for large time-steps, the possibility to parallelize in time over many characteristic wavelengths and large speed-ups over existingmore » methods in situations where simulation over long times are required. Numerical examples involving the 2D rotating shallow water equations and the 2D wave equation in an inhomogenous medium are presented, and the method is compared to the 4th order Runge–Kutta (RK4) method and to the use of Chebyshev polynomials. The new method achieved high accuracy over long-time intervals, and with speeds that are orders of magnitude faster than both RK4 and the use of Chebyshev polynomials.« less

Parallel Patterns of Host-Specific Morphology and Genetic Admixture in Sister Lineages of a Commensal Barnacle.

PubMed

Ewers-Saucedo, Christine; Chan, Benny K K; Zardus, John D; Wares, John P

2017-06-01

Symbiotic relationships are often species specific, allowing symbionts to adapt to their host environments. Host generalists, on the other hand, have to cope with diverse environments. One coping strategy is phenotypic plasticity, defined by the presence of host-specific phenotypes in the absence of genetic differentiation. Recent work indicates that such host-specific phenotypic plasticity is present in the West Pacific lineage of the commensal barnacle Chelonibia testudinaria (Linnaeus, 1758). We investigated genetic and morphological host-specific structure in the genetically distinct Atlantic sister lineage of C. testudinaria. We collected adult C. testudinaria from loggerhead sea turtles, horseshoe crabs, and blue crabs along the eastern U.S. coast between Delaware and Florida and in the Gulf of Mexico off Mississippi. We find that shell morphology, especially shell thickness, is host specific and comparable in similar host species between the Atlantic and West Pacific lineages. We did not detect significant genetic differentiation related to host species when analyzing data from 11 nuclear microsatellite loci and mitochondrial sequence data, which is comparable to findings for the Pacific lineage. The most parsimonious explanation for these parallel patterns between distinct lineages of C. testudinaria is that C. testudinaria maintained phenotypic plasticity since the lineages diverged 4-5 mya.

Application of a hybrid MPI/OpenMP approach for parallel groundwater model calibration using multi-core computers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tang, Guoping; D'Azevedo, Ed F; Zhang, Fan

2010-01-01

Calibration of groundwater models involves hundreds to thousands of forward solutions, each of which may solve many transient coupled nonlinear partial differential equations, resulting in a computationally intensive problem. We describe a hybrid MPI/OpenMP approach to exploit two levels of parallelisms in software and hardware to reduce calibration time on multi-core computers. HydroGeoChem 5.0 (HGC5) is parallelized using OpenMP for direct solutions for a reactive transport model application, and a field-scale coupled flow and transport model application. In the reactive transport model, a single parallelizable loop is identified to account for over 97% of the total computational time using GPROF.more » Addition of a few lines of OpenMP compiler directives to the loop yields a speedup of about 10 on a 16-core compute node. For the field-scale model, parallelizable loops in 14 of 174 HGC5 subroutines that require 99% of the execution time are identified. As these loops are parallelized incrementally, the scalability is found to be limited by a loop where Cray PAT detects over 90% cache missing rates. With this loop rewritten, similar speedup as the first application is achieved. The OpenMP-parallelized code can be run efficiently on multiple workstations in a network or multiple compute nodes on a cluster as slaves using parallel PEST to speedup model calibration. To run calibration on clusters as a single task, the Levenberg Marquardt algorithm is added to HGC5 with the Jacobian calculation and lambda search parallelized using MPI. With this hybrid approach, 100 200 compute cores are used to reduce the calibration time from weeks to a few hours for these two applications. This approach is applicable to most of the existing groundwater model codes for many applications.« less

Hepatocellular differentiation status is characterized by distinct subnuclear localization and form of the chanzyme TRPM7.

PubMed

Ogunrinde, Adenike; Pereira, Robyn D; Beaton, Natalie; Lam, D Hung; Whetstone, Christiane; Hill, Ceredwyn E

The channel-kinase TRPM7 is important for the survival, proliferation, and differentiation, of many cell types. Both plasma membrane channel activity and kinase function are implicated in these roles. Channel activity is greater in less differentiated hepatoma cells compared with non-dividing, terminally differentiated adult hepatocytes, suggesting differences in protein expression and/or localization. We used electrophysiological and immunofluorescence approaches to establish whether hepatocellular differentiation is associated with altered TRPM7 expression. Mean outward current decreased by 44% in WIF-B hepatoma cells incubated with the established hepatic differentiating factors oncostatin M/dexamethasone for 1-8 days. Pre-incubation with pyridone 6, a pan-JAK inhibitor, blocked the current reduction. An antibody targeted to the C-terminus of TRPM7 labelled the cytoplasm in WIF-B cells and intact rat liver. Significant label also localized to the nuclear envelope (NE), with relatively more detected in adult hepatocytes compared with WIF-B cells. Hepatoma cells also exhibited nucleoplasmic labelling with intense signal in the nucleolus. The endogenous labelling pattern closely resembles that of HEK293T cells heterologously expressing a TRPM7 kinase construct containing a putative nucleolar localization sequence. These results suggest that TRPM7 form and distribution between the plasma membrane and nucleus, rather than expression, is altered in parallel with differentiation status in rat hepatic cells. Copyright © 2017 International Society of Differentiation. Published by Elsevier B.V. All rights reserved.

A reconstruction method for cone-beam differential x-ray phase-contrast computed tomography.

PubMed

Fu, Jian; Velroyen, Astrid; Tan, Renbo; Zhang, Junwei; Chen, Liyuan; Tapfer, Arne; Bech, Martin; Pfeiffer, Franz

2012-09-10

Most existing differential phase-contrast computed tomography (DPC-CT) approaches are based on three kinds of scanning geometries, described by parallel-beam, fan-beam and cone-beam. Due to the potential of compact imaging systems with magnified spatial resolution, cone-beam DPC-CT has attracted significant interest. In this paper, we report a reconstruction method based on a back-projection filtration (BPF) algorithm for cone-beam DPC-CT. Due to the differential nature of phase contrast projections, the algorithm restrains from differentiation of the projection data prior to back-projection, unlike BPF algorithms commonly used for absorption-based CT data. This work comprises a numerical study of the algorithm and its experimental verification using a dataset measured with a three-grating interferometer and a micro-focus x-ray tube source. Moreover, the numerical simulation and experimental results demonstrate that the proposed method can deal with several classes of truncated cone-beam datasets. We believe that this feature is of particular interest for future medical cone-beam phase-contrast CT imaging applications.

Concurrent generation of functional smooth muscle and endothelial cells via a vascular progenitor.

PubMed

Marchand, Melanie; Anderson, Erica K; Phadnis, Smruti M; Longaker, Michael T; Cooke, John P; Chen, Bertha; Reijo Pera, Renee A

2014-01-01

Smooth muscle cells (SMCs) and endothelial cells (ECs) are typically derived separately, with low efficiencies, from human pluripotent stem cells (hPSCs). The concurrent generation of these cell types might lead to potential applications in regenerative medicine to model, elucidate, and eventually treat vascular diseases. Here we report a robust two-step protocol that can be used to simultaneously generate large numbers of functional SMCs and ECs from a common proliferative vascular progenitor population via a two-dimensional culture system. We show here that coculturing hPSCs with OP9 cells in media supplemented with vascular endothelial growth factor, basic fibroblast growth factor, and bone morphogenetic protein 4 yields a higher percentage of CD31(+)CD34(+) cells on day 8 of differentiation. Upon exposure to endothelial differentiation media and SM differentiation media, these vascular progenitors were able to differentiate and mature into functional endothelial cells and smooth muscle cells, respectively. Furthermore, we were able to expand the intermediate population more than a billion fold to generate sufficient numbers of ECs and SMCs in parallel for potential therapeutic transplantations.

A numerical differentiation library exploiting parallel architectures

NASA Astrophysics Data System (ADS)

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

2009-08-01

We present a software library for numerically estimating first and second order partial derivatives of a function by finite differencing. Various truncation schemes are offered resulting in corresponding formulas that are accurate to order O(h), O(h), and O(h), h being the differencing step. The derivatives are calculated via forward, backward and central differences. Care has been taken that only feasible points are used in the case where bound constraints are imposed on the variables. The Hessian may be approximated either from function or from gradient values. There are three versions of the software: a sequential version, an OpenMP version for shared memory architectures and an MPI version for distributed systems (clusters). The parallel versions exploit the multiprocessing capability offered by computer clusters, as well as modern multi-core systems and due to the independent character of the derivative computation, the speedup scales almost linearly with the number of available processors/cores. Program summaryProgram title: NDL (Numerical Differentiation Library) Catalogue identifier: AEDG_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEDG_v1_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.: 73 030 No. of bytes in distributed program, including test data, etc.: 630 876 Distribution format: tar.gz Programming language: ANSI FORTRAN-77, ANSI C, MPI, OPENMP Computer: Distributed systems (clusters), shared memory systems Operating system: Linux, Solaris Has the code been vectorised or parallelized?: Yes RAM: The library uses O(N) internal storage, N being the dimension of the problem Classification: 4.9, 4.14, 6.5 Nature of problem: The numerical estimation of derivatives at several accuracy levels is a common requirement in many computational tasks, such as optimization, solution of nonlinear systems, etc. The parallel implementation that exploits systems with multiple CPUs is very important for large scale and computationally expensive problems. Solution method: Finite differencing is used with carefully chosen step that minimizes the sum of the truncation and round-off errors. The parallel versions employ both OpenMP and MPI libraries. Restrictions: The library uses only double precision arithmetic. Unusual features: The software takes into account bound constraints, in the sense that only feasible points are used to evaluate the derivatives, and given the level of the desired accuracy, the proper formula is automatically employed. Running time: Running time depends on the function's complexity. The test run took 15 ms for the serial distribution, 0.6 s for the OpenMP and 4.2 s for the MPI parallel distribution on 2 processors.

Xyce Parallel Electronic Simulator Users' Guide Version 6.7.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Keiter, Eric R.; Aadithya, Karthik Venkatraman; Mei, Ting

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: 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 tomore » 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. The information herein is subject to change without notice. Copyright c 2002-2017 Sandia Corporation. All rights reserved. Trademarks Xyce TM Electronic Simulator and Xyce TM are trademarks of Sandia Corporation. Orcad, Orcad Capture, PSpice and Probe are registered trademarks of Cadence Design Systems, Inc. Microsoft, Windows and Windows 7 are registered trademarks of Microsoft Corporation. Medici, DaVinci and Taurus are registered trademarks of Synopsys Corporation. Amtec and TecPlot are trademarks of Amtec Engineering, Inc. All other trademarks are property of their respective owners. Contacts World Wide Web http://xyce.sandia.gov https://info.sandia.gov/xyce (Sandia only) Email xyce@sandia.gov (outside Sandia) xyce-sandia@sandia.gov (Sandia only) Bug Reports (Sandia only) http://joseki-vm.sandia.gov/bugzilla http://morannon.sandia.gov/bugzilla« less

The differential emission measure of nested hot and cool magnetic loops

NASA Technical Reports Server (NTRS)

Van Hoven, G.; Mok, Y.

1993-01-01

The detailed thermal structure of the magnetized solar transition region, as measured by its differential emission measure (DEM(T)), is poorly known. Building on the fact that the solar surface is strongly magnetized and thereby structured, proposals have been made that envision a significant lower-temperature contribution to the energy balance from (ion) heat flux across an arcade of different temperature loops. In this paper, we describe a self-consistent 2D MHD simulation, which includes the full thermal effects of parallel stability and anisotropic conduction, of a nested-loop model of the thermal and magnetic structure of the transition region. We then demonstrate that the predicted DEM agrees with observations in the conceptually elusive T less than 10 exp 5 K regime.

The role of nonlinear critical layers in boundary layer transition

NASA Technical Reports Server (NTRS)

Goldstein, M.E.

1995-01-01

Asymptotic methods are used to describe the nonlinear self-interaction between pairs of oblique instability modes that eventually develops when initially linear spatially growing instability waves evolve downstream in nominally two-dimensional laminar boundary layers. The first nonlinear reaction takes place locally within a so-called 'critical layer', with the flow outside this layer consisting of a locally parallel mean flow plus a pair of oblique instability waves - which may or may not be accompanied by an associated plane wave. The amplitudes of these waves, which are completely determined by nonlinear effects within the critical layer, satisfy either a single integro-differential equation or a pair of integro-differential equations with quadratic to quartic-type nonlinearities. The physical implications of these equations are discussed.

Neural differentiation of lexico-syntactic categories or semantic features? event-related potential evidence for both.

PubMed

Kellenbach, Marion L; Wijers, Albertus A; Hovius, Marjolijn; Mulder, Juul; Mulder, Gijsbertus

2002-05-15

Event-related potentials (ERPs) were used to investigate whether processing differences between nouns and verbs can be accounted for by the differential salience of visual-perceptual and motor attributes in their semantic specifications. Three subclasses of nouns and verbs were selected, which differed in their semantic attribute composition (abstract, high visual, high visual and motor). Single visual word presentation with a recognition memory task was used. While multiple robust and parallel ERP effects were observed for both grammatical class and attribute type, there were no interactions between these. This pattern of effects provides support for lexical-semantic knowledge being organized in a manner that takes account both of category-based (grammatical class) and attribute-based distinctions.

Efficient spin-filtering, magnetoresistance and negative differential resistance effects of a one-dimensional single-molecule magnet Mn(dmit)2-based device with graphene nanoribbon electrodes

NASA Astrophysics Data System (ADS)

Liu, N.; Liu, J. B.; Yao, K. L.

2017-12-01

We present first-principle spin-dependent quantum transport calculations in a molecular device constructed by one single-molecule magnet Mn(dmit)2 and two graphene nanoribbon electrodes. Our results show that the device could generate perfect spin-filtering performance in a certain bias range both in the parallel configuration (PC) and the antiparallel configuration (APC). At the same time, a magnetoresistance effect, up to a high value of 103%, can be realized. Moreover, visible negative differential resistance phenomenon is obtained for the spin-up current of the PC. These results suggest that our one-dimensional molecular device is a promising candidate for multi-functional spintronics devices.

Smart Cameras for Remote Science Survey

NASA Technical Reports Server (NTRS)

Thompson, David R.; Abbey, William; Allwood, Abigail; Bekker, Dmitriy; Bornstein, Benjamin; Cabrol, Nathalie A.; Castano, Rebecca; Estlin, Tara; Fuchs, Thomas; Wagstaff, Kiri L.

2012-01-01

Communication with remote exploration spacecraft is often intermittent and bandwidth is highly constrained. Future missions could use onboard science data understanding to prioritize downlink of critical features [1], draft summary maps of visited terrain [2], or identify targets of opportunity for followup measurements [3]. We describe a generic approach to classify geologic surfaces for autonomous science operations, suitable for parallelized implementations in FPGA hardware. We map these surfaces with texture channels - distinctive numerical signatures that differentiate properties such as roughness, pavement coatings, regolith characteristics, sedimentary fabrics and differential outcrop weathering. This work describes our basic image analysis approach and reports an initial performance evaluation using surface images from the Mars Exploration Rovers. Future work will incorporate these methods into camera hardware for real-time processing.

Final Report, DE-FG01-06ER25718 Domain Decomposition and Parallel Computing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Widlund, Olof B.

2015-06-09

The goal of this project is to develop and improve domain decomposition algorithms for a variety of partial differential equations such as those of linear elasticity and electro-magnetics.These iterative methods are designed for massively parallel computing systems and allow the fast solution of the very large systems of algebraic equations that arise in large scale and complicated simulations. A special emphasis is placed on problems arising from Maxwell's equation. The approximate solvers, the preconditioners, are combined with the conjugate gradient method and must always include a solver of a coarse model in order to have a performance which is independentmore » of the number of processors used in the computer simulation. A recent development allows for an adaptive construction of this coarse component of the preconditioner.« less

Analogies between oscillation and rotation of bodies induced or influenced by vortex shedding

NASA Astrophysics Data System (ADS)

Lugt, H. J.

Vortex-induced or vortex-influenced rotation and oscillation of bodies in a parallel flow are discussed. A steady flow occurs if the body axis is parallel to the flow or if the axis of rotation is perpendicular to the flow. Flows around an oscillating body are quasi-steady only if the Strougal number is much smaller than unity. The connection between rotation and oscillation is demonstrated in terms of the autorotation of a Lanchester propeller, and conditions for stable autorotation are defined. The Riabouchinsky curve is shown to be typical of forces and torques on bodies with vortical wakes, including situations with fixed body axes perpendicular to the flow. A differential equation is formulated for rotational and oscillating bodies that shed vortices by extending the pendulum equation to include vortical effects expressed as a fifth-order polynomial.

A dynamic system with digital lock-in-photon-counting for pharmacokinetic diffuse fluorescence tomography

NASA Astrophysics Data System (ADS)

Yin, Guoyan; Zhang, Limin; Zhang, Yanqi; Liu, Han; Du, Wenwen; Ma, Wenjuan; Zhao, Huijuan; Gao, Feng

2018-02-01

Pharmacokinetic diffuse fluorescence tomography (DFT) can describe the metabolic processes of fluorescent agents in biomedical tissue and provide helpful information for tumor differentiation. In this paper, a dynamic DFT system was developed by employing digital lock-in-photon-counting with square wave modulation, which predominates in ultra-high sensitivity and measurement parallelism. In this system, 16 frequency-encoded laser diodes (LDs) driven by self-designed light source system were distributed evenly in the imaging plane and irradiated simultaneously. Meanwhile, 16 detection fibers collected emission light in parallel by the digital lock-in-photon-counting module. The fundamental performances of the proposed system were assessed with phantom experiments in terms of stability, linearity, anti-crosstalk as well as images reconstruction. The results validated the availability of the proposed dynamic DFT system.

MOOSE: A parallel computational framework for coupled systems of nonlinear equations.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Derek Gaston; Chris Newman; Glen Hansen

Systems of coupled, nonlinear partial differential equations (PDEs) often arise in simulation of nuclear processes. MOOSE: Multiphysics Object Oriented Simulation Environment, a parallel computational framework targeted at the solution of such systems, is presented. As opposed to traditional data-flow oriented computational frameworks, MOOSE is instead founded on the mathematical principle of Jacobian-free Newton-Krylov (JFNK) solution methods. Utilizing the mathematical structure present in JFNK, physics expressions are modularized into `Kernels,'' allowing for rapid production of new simulation tools. In addition, systems are solved implicitly and fully coupled, employing physics based preconditioning, which provides great flexibility even with large variance in timemore » scales. A summary of the mathematics, an overview of the structure of MOOSE, and several representative solutions from applications built on the framework are presented.« less

Parallel block schemes for large scale least squares computations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Golub, G.H.; Plemmons, R.J.; Sameh, A.

1986-04-01

Large scale least squares computations arise in a variety of scientific and engineering problems, including geodetic adjustments and surveys, medical image analysis, molecular structures, partial differential equations and substructuring methods in structural engineering. In each of these problems, matrices often arise which possess a block structure which reflects the local connection nature of the underlying physical problem. For example, such super-large nonlinear least squares computations arise in geodesy. Here the coordinates of positions are calculated by iteratively solving overdetermined systems of nonlinear equations by the Gauss-Newton method. The US National Geodetic Survey will complete this year (1986) the readjustment ofmore » the North American Datum, a problem which involves over 540 thousand unknowns and over 6.5 million observations (equations). The observation matrix for these least squares computations has a block angular form with 161 diagnonal blocks, each containing 3 to 4 thousand unknowns. In this paper parallel schemes are suggested for the orthogonal factorization of matrices in block angular form and for the associated backsubstitution phase of the least squares computations. In addition, a parallel scheme for the calculation of certain elements of the covariance matrix for such problems is described. It is shown that these algorithms are ideally suited for multiprocessors with three levels of parallelism such as the Cedar system at the University of Illinois. 20 refs., 7 figs.« less

Kranc: a Mathematica package to generate numerical codes for tensorial evolution equations

NASA Astrophysics Data System (ADS)

Husa, Sascha; Hinder, Ian; Lechner, Christiane

2006-06-01

We present a suite of Mathematica-based computer-algebra packages, termed "Kranc", which comprise a toolbox to convert certain (tensorial) systems of partial differential evolution equations to parallelized C or Fortran code for solving initial boundary value problems. Kranc can be used as a "rapid prototyping" system for physicists or mathematicians handling very complicated systems of partial differential equations, but through integration into the Cactus computational toolkit we can also produce efficient parallelized production codes. Our work is motivated by the field of numerical relativity, where Kranc is used as a research tool by the authors. In this paper we describe the design and implementation of both the Mathematica packages and the resulting code, we discuss some example applications, and provide results on the performance of an example numerical code for the Einstein equations. Program summaryTitle of program: Kranc Catalogue identifier: ADXS_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXS_v1_0 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Distribution format: tar.gz Computer for which the program is designed and others on which it has been tested: General computers which run Mathematica (for code generation) and Cactus (for numerical simulations), tested under Linux Programming language used: Mathematica, C, Fortran 90 Memory required to execute with typical data: This depends on the number of variables and gridsize, the included ADM example requires 4308 KB Has the code been vectorized or parallelized: The code is parallelized based on the Cactus framework. Number of bytes in distributed program, including test data, etc.: 1 578 142 Number of lines in distributed program, including test data, etc.: 11 711 Nature of physical problem: Solution of partial differential equations in three space dimensions, which are formulated as an initial value problem. In particular, the program is geared towards handling very complex tensorial equations as they appear, e.g., in numerical relativity. The worked out examples comprise the Klein-Gordon equations, the Maxwell equations, and the ADM formulation of the Einstein equations. Method of solution: The method of numerical solution is finite differencing and method of lines time integration, the numerical code is generated through a high level Mathematica interface. Restrictions on the complexity of the program: Typical numerical relativity applications will contain up to several dozen evolution variables and thousands of source terms, Cactus applications have shown scaling up to several thousand processors and grid sizes exceeding 500 3. Typical running time: This depends on the number of variables and the grid size: the included ADM example takes approximately 100 seconds on a 1600 MHz Intel Pentium M processor. Unusual features of the program: based on Mathematica and Cactus

Computational Fluid Dynamic Solutions of Optimized Heat Shields Designed for Earth Entry

DTIC Science & Technology

2010-01-01

domain ρ = Density (kg/m3) σ = Stefan Boltzmann constant τ = Shear stress tensor τT−V = T-V relaxation time τe−V = e-V relaxation time xi φ = Sweep angle...Vehicle DES = Differential evolutionary Scheme DOR = Design Optimization Tools DPLR = Data Parallel Line Relaxation GSLR = Gauss- Seidel Line... Stefan - Boltzmann constant. This model provides accurate heating predictions, especially for the non-ablating heat-shields explored in this work. Various

Quantitation of a slide test (Monotest) for infectious mononucleosis

PubMed Central

Carter, P. Kenneth; Schoen, Irwin; Miyahira, Teru

1970-01-01

A slide test for infectious mononucleosis using formalinized horse erythrocytes (Monotest2) was quantitated and compared with standard differential heterophile (Davidsohn) titres performed on the same specimens. The Monotest titre parallels the standard presumptive heterophile (antisheep cell) titre in the degree of elevation, with a ratio of Monotest to heterophile titre of approximately 1 to 56. The simplicity of the quantitative slide test recommends it as a routine test for infectious mononucleosis. PMID:5530641

GPU-accelerated adjoint algorithmic differentiation

NASA Astrophysics Data System (ADS)

Gremse, Felix; Höfter, Andreas; Razik, Lukas; Kiessling, Fabian; Naumann, Uwe

2016-03-01

Many scientific problems such as classifier training or medical image reconstruction can be expressed as minimization of differentiable real-valued cost functions and solved with iterative gradient-based methods. Adjoint algorithmic differentiation (AAD) enables automated computation of gradients of such cost functions implemented as computer programs. To backpropagate adjoint derivatives, excessive memory is potentially required to store the intermediate partial derivatives on a dedicated data structure, referred to as the ;tape;. Parallelization is difficult because threads need to synchronize their accesses during taping and backpropagation. This situation is aggravated for many-core architectures, such as Graphics Processing Units (GPUs), because of the large number of light-weight threads and the limited memory size in general as well as per thread. We show how these limitations can be mediated if the cost function is expressed using GPU-accelerated vector and matrix operations which are recognized as intrinsic functions by our AAD software. We compare this approach with naive and vectorized implementations for CPUs. We use four increasingly complex cost functions to evaluate the performance with respect to memory consumption and gradient computation times. Using vectorization, CPU and GPU memory consumption could be substantially reduced compared to the naive reference implementation, in some cases even by an order of complexity. The vectorization allowed usage of optimized parallel libraries during forward and reverse passes which resulted in high speedups for the vectorized CPU version compared to the naive reference implementation. The GPU version achieved an additional speedup of 7.5 ± 4.4, showing that the processing power of GPUs can be utilized for AAD using this concept. Furthermore, we show how this software can be systematically extended for more complex problems such as nonlinear absorption reconstruction for fluorescence-mediated tomography.

GPU-Accelerated Adjoint Algorithmic Differentiation.

PubMed

Gremse, Felix; Höfter, Andreas; Razik, Lukas; Kiessling, Fabian; Naumann, Uwe

2016-03-01

Many scientific problems such as classifier training or medical image reconstruction can be expressed as minimization of differentiable real-valued cost functions and solved with iterative gradient-based methods. Adjoint algorithmic differentiation (AAD) enables automated computation of gradients of such cost functions implemented as computer programs. To backpropagate adjoint derivatives, excessive memory is potentially required to store the intermediate partial derivatives on a dedicated data structure, referred to as the "tape". Parallelization is difficult because threads need to synchronize their accesses during taping and backpropagation. This situation is aggravated for many-core architectures, such as Graphics Processing Units (GPUs), because of the large number of light-weight threads and the limited memory size in general as well as per thread. We show how these limitations can be mediated if the cost function is expressed using GPU-accelerated vector and matrix operations which are recognized as intrinsic functions by our AAD software. We compare this approach with naive and vectorized implementations for CPUs. We use four increasingly complex cost functions to evaluate the performance with respect to memory consumption and gradient computation times. Using vectorization, CPU and GPU memory consumption could be substantially reduced compared to the naive reference implementation, in some cases even by an order of complexity. The vectorization allowed usage of optimized parallel libraries during forward and reverse passes which resulted in high speedups for the vectorized CPU version compared to the naive reference implementation. The GPU version achieved an additional speedup of 7.5 ± 4.4, showing that the processing power of GPUs can be utilized for AAD using this concept. Furthermore, we show how this software can be systematically extended for more complex problems such as nonlinear absorption reconstruction for fluorescence-mediated tomography.

GPU-Accelerated Adjoint Algorithmic Differentiation

PubMed Central

Gremse, Felix; Höfter, Andreas; Razik, Lukas; Kiessling, Fabian; Naumann, Uwe

2015-01-01

Many scientific problems such as classifier training or medical image reconstruction can be expressed as minimization of differentiable real-valued cost functions and solved with iterative gradient-based methods. Adjoint algorithmic differentiation (AAD) enables automated computation of gradients of such cost functions implemented as computer programs. To backpropagate adjoint derivatives, excessive memory is potentially required to store the intermediate partial derivatives on a dedicated data structure, referred to as the “tape”. Parallelization is difficult because threads need to synchronize their accesses during taping and backpropagation. This situation is aggravated for many-core architectures, such as Graphics Processing Units (GPUs), because of the large number of light-weight threads and the limited memory size in general as well as per thread. We show how these limitations can be mediated if the cost function is expressed using GPU-accelerated vector and matrix operations which are recognized as intrinsic functions by our AAD software. We compare this approach with naive and vectorized implementations for CPUs. We use four increasingly complex cost functions to evaluate the performance with respect to memory consumption and gradient computation times. Using vectorization, CPU and GPU memory consumption could be substantially reduced compared to the naive reference implementation, in some cases even by an order of complexity. The vectorization allowed usage of optimized parallel libraries during forward and reverse passes which resulted in high speedups for the vectorized CPU version compared to the naive reference implementation. The GPU version achieved an additional speedup of 7.5 ± 4.4, showing that the processing power of GPUs can be utilized for AAD using this concept. Furthermore, we show how this software can be systematically extended for more complex problems such as nonlinear absorption reconstruction for fluorescence-mediated tomography. PMID:26941443

Train stimulation of parallel fibre to Purkinje cell inputs reveals two populations of synaptic responses with different receptor signatures

PubMed Central

Devi, Suma Priya Sudarsana; Howe, James R.

2016-01-01

Key points Purkinje cells of the cerebellum receive ∼180,000 parallel fibre synapses, which have often been viewed as a homogeneous synaptic population and studied using single action potentials.Many parallel fibre synapses might be silent, however, and granule cells in vivo fire in bursts. Here, we used trains of stimuli to study parallel fibre inputs to Purkinje cells in rat cerebellar slices.Analysis of train EPSCs revealed two synaptic components, phase 1 and 2. Phase 1 is initially large and saturates rapidly, whereas phase 2 is initially small and facilitates throughout the train. The two components have a heterogeneous distribution at dendritic sites and different pharmacological profiles.The differential sensitivity of phase 1 and phase 2 to inhibition by pentobarbital and NBQX mirrors the differential sensitivity of AMPA receptors associated with the transmembrane AMPA receptor regulatory protein, γ‐2, gating in the low‐ and high‐open probability modes, respectively. Abstract Cerebellar granule cells fire in bursts, and their parallel fibre axons (PFs) form ∼180,000 excitatory synapses onto the dendritic tree of a Purkinje cell. As many as 85% of these synapses have been proposed to be silent, but most are labelled for AMPA receptors. Here, we studied PF to Purkinje cell synapses using trains of 100 Hz stimulation in rat cerebellar slices. The PF train EPSC consisted of two components that were present in variable proportions at different dendritic sites: one, with large initial EPSC amplitude, saturated after three stimuli and dominated the early phase of the train EPSC; and the other, with small initial amplitude, increased steadily throughout the train of 10 stimuli and dominated the late phase of the train EPSC. The two phases also displayed different pharmacological profiles. Phase 2 was less sensitive to inhibition by NBQX but more sensitive to block by pentobarbital than phase 1. Comparison of synaptic results with fast glutamate applications to recombinant receptors suggests that the high‐open‐probability gating mode of AMPA receptors containing the auxiliary subunit transmembrane AMPA receptor regulatory protein γ‐2 makes a substantial contribution to phase 2. We argue that the two synaptic components arise from AMPA receptors with different functional signatures and synaptic distributions. Comparisons of voltage‐ and current‐clamp responses obtained from the same Purkinje cells indicate that phase 1 of the EPSC arises from synapses ideally suited to transmit short bursts of action potentials, whereas phase 2 is likely to arise from low‐release‐probability or ‘silent’ synapses that are recruited during longer bursts. PMID:27094216

Modeling evolution of the mind and cultures: emotional Sapir-Whorf hypothesis

NASA Astrophysics Data System (ADS)

Perlovsky, Leonid I.

2009-05-01

Evolution of cultures is ultimately determined by mechanisms of the human mind. The paper discusses the mechanisms of evolution of language from primordial undifferentiated animal cries to contemporary conceptual contents. In parallel with differentiation of conceptual contents, the conceptual contents were differentiated from emotional contents of languages. The paper suggests the neural brain mechanisms involved in these processes. Experimental evidence and theoretical arguments are discussed, including mathematical approaches to cognition and language: modeling fields theory, the knowledge instinct, and the dual model connecting language and cognition. Mathematical results are related to cognitive science, linguistics, and psychology. The paper gives an initial mathematical formulation and mean-field equations for the hierarchical dynamics of both the human mind and culture. In the mind heterarchy operation of the knowledge instinct manifests through mechanisms of differentiation and synthesis. The emotional contents of language are related to language grammar. The conclusion is an emotional version of Sapir-Whorf hypothesis. Cultural advantages of "conceptual" pragmatic cultures, in which emotionality of language is diminished and differentiation overtakes synthesis resulting in fast evolution at the price of self doubts and internal crises are compared to those of traditional cultures where differentiation lags behind synthesis, resulting in cultural stability at the price of stagnation. Multi-language, multi-ethnic society might combine the benefits of stability and fast differentiation. Unsolved problems and future theoretical and experimental directions are discussed.

The Effects of Topographical Patterns and Sizes on Neural Stem Cell Behavior

PubMed Central

Qi, Lin; Li, Ning; Huang, Rong; Song, Qin; Wang, Long; Zhang, Qi; Su, Ruigong; Kong, Tao; Tang, Mingliang; Cheng, Guosheng

2013-01-01

Engineered topographical manipulation, a paralleling approach with conventional biochemical cues, has recently attracted the growing interests in utilizations to control stem cell fate. In this study, effects of topological parameters, pattern and size are emphasized on the proliferation and differentiation of adult neural stem cells (ANSCs). We fabricate micro-scale topographical Si wafers with two different feature sizes. These topographical patterns present linear micro-pattern (LMP), circular micro-pattern (CMP) and dot micro-pattern (DMP). The results show that the three topography substrates are suitable for ANSC growth, while they all depress ANSC proliferation when compared to non-patterned substrates (control). Meanwhile, LMP and CMP with two feature sizes can both significantly enhance ANSC differentiation to neurons compared to control. The smaller the feature size is, the better upregulation applies to ANSC for the differentiated neurons. The underlying mechanisms of topography-enhanced neuronal differentiation are further revealed by directing suppression of mitogen-activated protein kinase/extracellular signaling-regulated kinase (MAPK/Erk) signaling pathway in ANSC using U0126, known to inhibit the activation of Erk. The statistical results suggest MAPK/Erk pathway is partially involved in topography-induced differentiation. These observations provide a better understanding on the different roles of topographical cues on stem cell behavior, especially on the selective differentiation, and facilitate to advance the field of stem cell therapy. PMID:23527077

The aryl hydrocarbon receptor (AHR) transcription factor regulates megakaryocytic polyploidization

PubMed Central

Lindsey, Stephan; T. Papoutsakis, Eleftherios

2012-01-01

Summary We propose that the aryl hydrocarbon receptor (AHR) is a novel transcriptional regulator of megakaryopoietic polyploidization. Functional evidence was obtained that AHR impacts in vivo megakaryocytic differentiation and maturation; compared to wild-type mice, AHR-null mice had lower platelet counts, fewer numbers of newly synthesized platelets, increased bleeding times and lower-ploidy megakaryocytes (Mks). AHR mRNA increased 3·6-fold during ex vivo megakaryocytic differentiation, but reduced or remained constant during parallel isogenic granulocytic or erythroid differentiation. We interrogated the role of AHR in megakaryopoiesis using a validated Mk model of megakaryopoiesis, the human megakaryoblastic leukaemia CHRF cell line. Upon CHRF Mk differentiation, AHR mRNA and protein levels increased, AHR protein shifted from the cytoplasm to the nucleus and AHR binding to its consensus DNA binding sequence increased. Protein and mRNA levels of the AHR transcriptional target HES1 also increased. Mk differentiation of CHRF cells where AHR or HES1 was knocked-down using RNAi resulted in lower ploidy distributions and cells that were incapable of reaching ploidy classes ≥16n. AHR knockdown also resulted in increased DNA synthesis of lower ploidy cells, without impacting apoptosis. Together, these data support a role for AHR in Mk polyploidization and in vivo platelet function, and warrant further detailed investigations. PMID:21226706

Decreased RB1 mRNA, Protein, and Activity Reflect Obesity-Induced Altered Adipogenic Capacity in Human Adipose Tissue

PubMed Central

Moreno-Navarrete, José María; Petrov, Petar; Serrano, Marta; Ortega, Francisco; García-Ruiz, Estefanía; Oliver, Paula; Ribot, Joan; Ricart, Wifredo; Palou, Andreu; Bonet, Mª Luisa; Fernández-Real, José Manuel

2013-01-01

Retinoblastoma (Rb1) has been described as an essential player in white adipocyte differentiation in mice. No studies have been reported thus far in human adipose tissue or human adipocytes. We aimed to investigate the possible role and regulation of RB1 in adipose tissue in obesity using human samples and animal and cell models. Adipose RB1 (mRNA, protein, and activity) was negatively associated with BMI and insulin resistance (HOMA-IR) while positively associated with the expression of adipogenic genes (PPARγ and IRS1) in both visceral and subcutaneous human adipose tissue. BMI increase was the main contributor to adipose RB1 downregulation. In rats, adipose Rb1 gene expression and activity decreased in parallel to dietary-induced weight gain and returned to baseline with weight loss. RB1 gene and protein expression and activity increased significantly during human adipocyte differentiation. In fully differentiated adipocytes, transient knockdown of Rb1 led to loss of the adipogenic phenotype. In conclusion, Rb1 seems to play a permissive role for human adipose tissue function, being downregulated in obesity and increased during differentiation of human adipocytes. Rb1 knockdown findings further implicate Rb1 as necessary for maintenance of adipogenic characteristics in fully differentiated adipocytes. PMID:23315497

Proteomic changes during intestinal cell maturation in vivo

PubMed Central

Chang, Jinsook; Chance, Mark R.; Nicholas, Courtney; Ahmed, Naseem; Guilmeau, Sandra; Flandez, Marta; Wang, Donghai; Byun, Do-Sun; Nasser, Shannon; Albanese, Joseph M.; Corner, Georgia A.; Heerdt, Barbara G.; Wilson, Andrew J.; Augenlicht, Leonard H.; Mariadason, John M.

2008-01-01

Intestinal epithelial cells undergo progressive cell maturation as they migrate along the crypt-villus axis. To determine molecular signatures that define this process, proteins differentially expressed between the crypt and villus were identified by 2D-DIGE and MALDI-MS. Forty-six differentially expressed proteins were identified, several of which were validated by immunohistochemistry. Proteins upregulated in the villus were enriched for those involved in brush border assembly and lipid uptake, established features of differentiated intestinal epithelial cells. Multiple proteins involved in glycolysis were also upregulated in the villus, suggesting increased glycolysis is a feature of intestinal cell differentiation. Conversely, proteins involved in nucleotide metabolism, and protein processing and folding were increased in the crypt, consistent with functions associated with cell proliferation. Three novel paneth cell markers, AGR2, HSPA5 and RRBP1 were also identified. Notably, significant correlation was observed between overall proteomic changes and corresponding gene expression changes along the crypt-villus axis, indicating intestinal cell maturation is primarily regulated at the transcriptional level. This proteomic profiling analysis identified several novel proteins and functional processes differentially induced during intestinal cell maturation in vivo. Integration of proteomic, immunohistochemical, and parallel gene expression datasets demonstrate the coordinated manner in which intestinal cell maturation is regulated. PMID:18824147

The aryl hydrocarbon receptor (AHR) transcription factor regulates megakaryocytic polyploidization.

PubMed

Lindsey, Stephan; Papoutsakis, Eleftherios T

2011-02-01

We propose that the aryl hydrocarbon receptor (AHR) is a novel transcriptional regulator of megakaryopoietic polyploidization. Functional evidence was obtained that AHR impacts in vivo megakaryocytic differentiation and maturation; compared to wild-type mice, AHR-null mice had lower platelet counts, fewer numbers of newly synthesized platelets, increased bleeding times and lower-ploidy megakaryocytes (Mks). AHR mRNA increased 3·6-fold during ex vivo megakaryocytic differentiation, but reduced or remained constant during parallel isogenic granulocytic or erythroid differentiation. We interrogated the role of AHR in megakaryopoiesis using a validated Mk model of megakaryopoiesis, the human megakaryoblastic leukaemia CHRF cell line. Upon CHRF Mk differentiation, AHR mRNA and protein levels increased, AHR protein shifted from the cytoplasm to the nucleus and AHR binding to its consensus DNA binding sequence increased. Protein and mRNA levels of the AHR transcriptional target HES1 also increased. Mk differentiation of CHRF cells where AHR or HES1 was knocked-down using RNAi resulted in lower ploidy distributions and cells that were incapable of reaching ploidy classes ≥16n. AHR knockdown also resulted in increased DNA synthesis of lower ploidy cells, without impacting apoptosis. Together, these data support a role for AHR in Mk polyploidization and in vivo platelet function, and warrant further detailed investigations. © 2011 Blackwell Publishing Ltd.

Drosophila sessile hemocyte clusters are true hematopoietic tissues that regulate larval blood cell differentiation

PubMed Central

Leitão, Alexandre B; Sucena, Élio

2015-01-01

Virtually all species of coelomate animals contain blood cells that display a division of labor necessary for homeostasis. This functional partition depends upon the balance between proliferation and differentiation mostly accomplished in the hematopoietic organs. In Drosophila melanogaster, the lymph gland produces plasmatocytes and crystal cells that are not released until pupariation. Yet, throughout larval development, both hemocyte types increase in numbers. Mature plasmatocytes can proliferate but it is not known if crystal cell numbers increase by self-renewal or by de novo differentiation. We show that new crystal cells in third instar larvae originate through a Notch-dependent process of plasmatocyte transdifferentiation. This process occurs in the sessile clusters and is contingent upon the integrity of these structures. The existence of this hematopoietic tissue, relying on structure-dependent signaling events to promote blood homeostasis, creates a new paradigm for addressing outstanding questions in Drosophila hematopoiesis and establishing further parallels with vertebrate systems. DOI: http://dx.doi.org/10.7554/eLife.06166.001 PMID:25650737

Multi Sensor Fusion Using Fitness Adaptive Differential Evolution

NASA Astrophysics Data System (ADS)

Giri, Ritwik; Ghosh, Arnob; Chowdhury, Aritra; Das, Swagatam

The rising popularity of multi-source, multi-sensor networks supports real-life applications calls for an efficient and intelligent approach to information fusion. Traditional optimization techniques often fail to meet the demands. The evolutionary approach provides a valuable alternative due to its inherent parallel nature and its ability to deal with difficult problems. We present a new evolutionary approach based on a modified version of Differential Evolution (DE), called Fitness Adaptive Differential Evolution (FiADE). FiADE treats sensors in the network as distributed intelligent agents with various degrees of autonomy. Existing approaches based on intelligent agents cannot completely answer the question of how their agents could coordinate their decisions in a complex environment. The proposed approach is formulated to produce good result for the problems that are high-dimensional, highly nonlinear, and random. The proposed approach gives better result in case of optimal allocation of sensors. The performance of the proposed approach is compared with an evolutionary algorithm coordination generalized particle model (C-GPM).

Period of vibration of axially vibrating truly nonlinear rod

NASA Astrophysics Data System (ADS)

Cveticanin, L.

2016-07-01

In this paper the axial vibration of a muscle whose fibers are parallel to the direction of muscle compression is investigated. The model is a clamped-free rod with a strongly nonlinear elastic property. Axial vibration is described by a nonlinear partial differential equation. A solution of the equation is constructed for special initial conditions by using the method of separation of variables. The partial differential equation is separated into two uncoupled strongly nonlinear second order differential equations. Both equations, with displacement function and with time function are exactly determined. Exact solutions are given in the form of inverse incomplete and inverse complete Beta function. Using boundary and initial conditions, the frequency of vibration is obtained. It has to be mentioned that the determined frequency represents the exact analytic description for the axially vibrating truly nonlinear clamped-free rod. The procedure suggested in this paper is applied for calculation of the frequency of the longissimus dorsi muscle of a cow. The influence of elasticity order and elasticity coefficient on the frequency property is tested.

SiGN-SSM: open source parallel software for estimating gene networks with state space models.

PubMed

Tamada, Yoshinori; Yamaguchi, Rui; Imoto, Seiya; Hirose, Osamu; Yoshida, Ryo; Nagasaki, Masao; Miyano, Satoru

2011-04-15

SiGN-SSM is an open-source gene network estimation software able to run in parallel on PCs and massively parallel supercomputers. The software estimates a state space model (SSM), that is a statistical dynamic model suitable for analyzing short time and/or replicated time series gene expression profiles. SiGN-SSM implements a novel parameter constraint effective to stabilize the estimated models. Also, by using a supercomputer, it is able to determine the gene network structure by a statistical permutation test in a practical time. SiGN-SSM is applicable not only to analyzing temporal regulatory dependencies between genes, but also to extracting the differentially regulated genes from time series expression profiles. SiGN-SSM is distributed under GNU Affero General Public Licence (GNU AGPL) version 3 and can be downloaded at http://sign.hgc.jp/signssm/. The pre-compiled binaries for some architectures are available in addition to the source code. The pre-installed binaries are also available on the Human Genome Center supercomputer system. The online manual and the supplementary information of SiGN-SSM is available on our web site. tamada@ims.u-tokyo.ac.jp.

Comparison of adult age differences in verbal and visuo-spatial memory: the importance of 'pure', parallel and validated measures.

PubMed

Kemps, Eva; Newson, Rachel

2006-04-01

The study compared age-related decrements in verbal and visuo-spatial memory across a broad elderly adult age range. Twenty-four young (18-25 years), 24 young-old (65-74 years), 24 middle-old (75-84 years) and 24 old-old (85-93 years) adults completed parallel recall and recognition measures of verbal and visuo-spatial memory from the Doors and People Test (Baddeley, Emslie & Nimmo-Smith, 1994). These constituted 'pure' and validated indices of either verbal or visuo-spatial memory. Verbal and visuo-spatial memory declined similarly with age, with a steeper decline in recall than recognition. Unlike recognition memory, recall performance also showed a heightened decline after the age of 85. Age-associated memory loss in both modalities was largely due to working memory and executive function. Processing speed and sensory functioning (vision, hearing) made minor contributions to memory performance and age differences in it. Together, these findings demonstrate common, rather than differential, age-related effects on verbal and visuo-spatial memory. They also emphasize the importance of using 'pure', parallel and validated measures of verbal and visuo-spatial memory in memory ageing research.

Optimizing ion channel models using a parallel genetic algorithm on graphical processors.

PubMed

Ben-Shalom, Roy; Aviv, Amit; Razon, Benjamin; Korngreen, Alon

2012-01-01

We have recently shown that we can semi-automatically constrain models of voltage-gated ion channels by combining a stochastic search algorithm with ionic currents measured using multiple voltage-clamp protocols. Although numerically successful, this approach is highly demanding computationally, with optimization on a high performance Linux cluster typically lasting several days. To solve this computational bottleneck we converted our optimization algorithm for work on a graphical processing unit (GPU) using NVIDIA's CUDA. Parallelizing the process on a Fermi graphic computing engine from NVIDIA increased the speed ∼180 times over an application running on an 80 node Linux cluster, considerably reducing simulation times. This application allows users to optimize models for ion channel kinetics on a single, inexpensive, desktop "super computer," greatly reducing the time and cost of building models relevant to neuronal physiology. We also demonstrate that the point of algorithm parallelization is crucial to its performance. We substantially reduced computing time by solving the ODEs (Ordinary Differential Equations) so as to massively reduce memory transfers to and from the GPU. This approach may be applied to speed up other data intensive applications requiring iterative solutions of ODEs. Copyright © 2012 Elsevier B.V. All rights reserved.

Massive Exploration of Perturbed Conditions of the Blood Coagulation Cascade through GPU Parallelization

PubMed Central

Cazzaniga, Paolo; Nobile, Marco S.; Besozzi, Daniela; Bellini, Matteo; Mauri, Giancarlo

2014-01-01

The introduction of general-purpose Graphics Processing Units (GPUs) is boosting scientific applications in Bioinformatics, Systems Biology, and Computational Biology. In these fields, the use of high-performance computing solutions is motivated by the need of performing large numbers of in silico analysis to study the behavior of biological systems in different conditions, which necessitate a computing power that usually overtakes the capability of standard desktop computers. In this work we present coagSODA, a CUDA-powered computational tool that was purposely developed for the analysis of a large mechanistic model of the blood coagulation cascade (BCC), defined according to both mass-action kinetics and Hill functions. coagSODA allows the execution of parallel simulations of the dynamics of the BCC by automatically deriving the system of ordinary differential equations and then exploiting the numerical integration algorithm LSODA. We present the biological results achieved with a massive exploration of perturbed conditions of the BCC, carried out with one-dimensional and bi-dimensional parameter sweep analysis, and show that GPU-accelerated parallel simulations of this model can increase the computational performances up to a 181× speedup compared to the corresponding sequential simulations. PMID:25025072

Development of the auto-steering software and equipment technology (ASSET)

NASA Astrophysics Data System (ADS)

McKay, Mark D.; Anderson, Matthew O.; Wadsworth, Derek C.

2003-09-01

The Idaho National Engineering and Environmental Laboratory (INEEL), through collaboration with INSAT Co., has developed a low cost robotic auto-steering system for parallel contour swathing. The capability to perform parallel contour swathing while minimizing "skip" and "overlap" is a necessity for cost-effective crop management within precision agriculture. Current methods for performing parallel contour swathing consist of using a Differential Global Position System (DGPS) coupled with a light bar system to prompt an operator where to steer. The complexity of operating heavy equipment, ensuring proper chemical mixture and application, and steering to a light bar indicator can be overwhelming to an operator. To simplify these tasks, an inexpensive robotic steering system has been developed and tested on several farming implements. This development leveraged research conducted by the INEEL and Utah State University. The INEEL-INSAT Auto-Steering Software and Equipment Technology provides the following: 1) the ability to drive in a straight line within +/- 2 feet while traveling at least 15 mph, 2) interfaces to a Real Time Kinematic (RTK) DGPS and sub-meter DGPS, 3) safety features such as Emergency-stop, steering wheel deactivation, computer watchdog deactivation, etc., and 4) a low-cost, field-ready system that is easily adapted to other systems.

Parallel diversifications of Cremastosperma and Mosannona (Annonaceae), tropical rainforest trees tracking Neogene upheaval of South America

PubMed Central

Maas, Paul J. M.; Melchers-Sharrott, Heleen

2018-01-01

Much of the immense present day biological diversity of Neotropical rainforests originated from the Miocene onwards, a period of geological and ecological upheaval in South America. We assess the impact of the Andean orogeny, drainage of Lake Pebas and closure of the Panama isthmus on two clades of tropical trees (Cremastosperma, ca 31 spp.; and Mosannona, ca 14 spp.; both Annonaceae). Phylogenetic inference revealed similar patterns of geographically restricted clades and molecular dating showed diversifications in the different areas occurred in parallel, with timing consistent with Andean vicariance and Central American geodispersal. Ecological niche modelling approaches show phylogenetically conserved niche differentiation, particularly within Cremastosperma. Niche similarity and recent common ancestry of Amazon and Guianan Mosannona species contrast with dissimilar niches and more distant ancestry of Amazon, Venezuelan and Guianan species of Cremastosperma, suggesting that this element of the similar patterns of disjunct distributions in the two genera is instead a biogeographic parallelism, with differing origins. The results provide further independent evidence for the importance of the Andean orogeny, the drainage of Lake Pebas, and the formation of links between South and Central America in the evolutionary history of Neotropical lowland rainforest trees. PMID:29410860

Parallel diversifications of Cremastosperma and Mosannona (Annonaceae), tropical rainforest trees tracking Neogene upheaval of South America.

PubMed

Pirie, Michael D; Maas, Paul J M; Wilschut, Rutger A; Melchers-Sharrott, Heleen; Chatrou, Lars W

2018-01-01

Much of the immense present day biological diversity of Neotropical rainforests originated from the Miocene onwards, a period of geological and ecological upheaval in South America. We assess the impact of the Andean orogeny, drainage of Lake Pebas and closure of the Panama isthmus on two clades of tropical trees ( Cremastosperma , ca 31 spp.; and Mosannona , ca 14 spp.; both Annonaceae). Phylogenetic inference revealed similar patterns of geographically restricted clades and molecular dating showed diversifications in the different areas occurred in parallel, with timing consistent with Andean vicariance and Central American geodispersal. Ecological niche modelling approaches show phylogenetically conserved niche differentiation, particularly within Cremastosperma . Niche similarity and recent common ancestry of Amazon and Guianan Mosannona species contrast with dissimilar niches and more distant ancestry of Amazon, Venezuelan and Guianan species of Cremastosperma , suggesting that this element of the similar patterns of disjunct distributions in the two genera is instead a biogeographic parallelism, with differing origins. The results provide further independent evidence for the importance of the Andean orogeny, the drainage of Lake Pebas, and the formation of links between South and Central America in the evolutionary history of Neotropical lowland rainforest trees.

The electrical MHD and Hall current impact on micropolar nanofluid flow between rotating parallel plates

NASA Astrophysics Data System (ADS)

Shah, Zahir; Islam, Saeed; Gul, Taza; Bonyah, Ebenezer; Altaf Khan, Muhammad

2018-06-01

The current research aims to examine the combined effect of magnetic and electric field on micropolar nanofluid between two parallel plates in a rotating system. The nanofluid flow between two parallel plates is taken under the influence of Hall current. The flow of micropolar nanofluid has been assumed in steady state. The rudimentary governing equations have been changed to a set of differential nonlinear and coupled equations using suitable similarity variables. An optimal approach has been used to acquire the solution of the modelled problems. The convergence of the method has been shown numerically. The impact of the Skin friction on velocity profile, Nusslet number on temperature profile and Sherwood number on concentration profile have been studied. The influences of the Hall currents, rotation, Brownian motion and thermophoresis analysis of micropolar nanofluid have been mainly focused in this work. Moreover, for comprehension the physical presentation of the embedded parameters that is, coupling parameter N1 , viscosity parameter Re , spin gradient viscosity parameter N2 , rotating parameter Kr , Micropolar fluid constant N3 , magnetic parameter M , Prandtl number Pr , Thermophoretic parameter Nt , Brownian motion parameter Nb , and Schmidt number Sc have been plotted and deliberated graphically.

Proceedings: Sisal `93

DOE Office of Scientific and Technical Information (OSTI.GOV)

Feo, J.T.

1993-10-01

This report contain papers on: Programmability and performance issues; The case of an iterative partial differential equation solver; Implementing the kernal of the Australian Region Weather Prediction Model in Sisal; Even and quarter-even prime length symmetric FFTs and their Sisal Implementations; Top-down thread generation for Sisal; Overlapping communications and computations on NUMA architechtures; Compiling technique based on dataflow analysis for funtional programming language Valid; Copy elimination for true multidimensional arrays in Sisal 2.0; Increasing parallelism for an optimization that reduces copying in IF2 graphs; Caching in on Sisal; Cache performance of Sisal Vs. FORTRAN; FFT algorithms on a shared-memory multiprocessor;more » A parallel implementation of nonnumeric search problems in Sisal; Computer vision algorithms in Sisal; Compilation of Sisal for a high-performance data driven vector processor; Sisal on distributed memory machines; A virtual shared addressing system for distributed memory Sisal; Developing a high-performance FFT algorithm in Sisal for a vector supercomputer; Implementation issues for IF2 on a static data-flow architechture; and Systematic control of parallelism in array-based data-flow computation. Selected papers have been indexed separately for inclusion in the Energy Science and Technology Database.« less

Parallel high-precision orbit propagation using the modified Picard-Chebyshev method

NASA Astrophysics Data System (ADS)

Koblick, Darin C.

2012-03-01

The modified Picard-Chebyshev method, when run in parallel, is thought to be more accurate and faster than the most efficient sequential numerical integration techniques when applied to orbit propagation problems. Previous experiments have shown that the modified Picard-Chebyshev method can have up to a one order magnitude speedup over the 12th order Runge-Kutta-Nystrom method. For this study, the evaluation of the accuracy and computational time of the modified Picard-Chebyshev method, using the Java Astrodynamics Toolkit high-precision force model, is conducted to assess its runtime performance. Simulation results of the modified Picard-Chebyshev method, implemented in MATLAB and the MATLAB Parallel Computing Toolbox, are compared against the most efficient first and second order Ordinary Differential Equation (ODE) solvers. A total of six processors were used to assess the runtime performance of the modified Picard-Chebyshev method. It was found that for all orbit propagation test cases, where the gravity model was simulated to be of higher degree and order (above 225 to increase computational overhead), the modified Picard-Chebyshev method was faster, by as much as a factor of two, than the other ODE solvers which were tested.

Penetration and differentiation of cephalic neural crest-derived cells in the developing mouse telencephalon.

PubMed

Yamanishi, Emiko; Takahashi, Masanori; Saga, Yumiko; Osumi, Noriko

2012-12-01

Neural crest (NC) cells originate from the neural folds and migrate into the various embryonic regions where they differentiate into multiple cell types. A population of cephalic neural crest-derived cells (NCDCs) penetrates back into the developing forebrain to differentiate into microvascular pericytes, but little is known about when and how cephalic NCDCs invade the telencephalon and differentiate into pericytes. Using a transgenic mouse line in which NCDCs are genetically labeled with enhanced green fluorescent protein (EGFP), we observed that NCDCs started to invade the telencephalon together with endothelial cells from embryonic day (E) 9.5. A majority of NCDCs located in the telencephalon expressed pericyte markers, that is, PDGFRβ and NG2, and differentiated into pericytes around E11.5. Surprisingly, many of the NC-derived pericytes express p75, an undifferentiated NCDC marker at E11.5, as well as NCDCs in the mesenchyme. At the same time, a minor population of NCDCs that located separately from blood vessels in the telencephalon were NG2-negative and some of these NCDCs also expressed p75. Proliferation and differentiation of pericytes appeared to occur in a specific mesenchymal region where blood vessels penetrated into the telencephalon. These results indicate that (i) NCDCs penetrate back into the telencephalon in parallel with angiogenesis, (ii) many NC-derived pericytes may be still in pre-mature states even though after differentiation into pericytes in the early developing stages, (iii) a small minority of NCDCs may retain undifferentiated states in the developing telencephalon, and (iv) a majority of NCDCs proliferate and differentiate into pericytes in the mesenchyme around the telencephalon. © 2012 The Authors Development, Growth & Differentiation © 2012 Japanese Society of Developmental Biologists.

Massively Parallel Rogue Cell Detection Using Serial Time-Encoded Amplified Microscopy of Inertially Ordered Cells in High-Throughput Flow

DTIC Science & Technology

2012-08-01

techniques and STEAM imager. It couples the high-speed capability of the STEAM imager and differential phase contrast imaging of DIC / Nomarski microscopy...On 10 TPE chips, we obtained 9 homogenous and strong bonds, the failed bond being due to operator error and presence of air bubbles in the TPE...instruments, structural dynamics, and microelectromechanical systems (MEMS) via laser-scanning surface vibrometry , and observation of biomechanical motility

Systematic generation of multibody equations of motion suitable for recursive and parallel manipulation

NASA Technical Reports Server (NTRS)

Nikravesh, Parviz E.; Gim, Gwanghum; Arabyan, Ara; Rein, Udo

1989-01-01

The formulation of a method known as the joint coordinate method for automatic generation of the equations of motion for multibody systems is summarized. For systems containing open or closed kinematic loops, the equations of motion can be reduced systematically to a minimum number of second order differential equations. The application of recursive and nonrecursive algorithms to this formulation, computational considerations and the feasibility of implementing this formulation on multiprocessor computers are discussed.

Identification of a Genomic Signature Predicting for Recurrence in Early Stage Ovarian Cancer

DTIC Science & Technology

2015-12-01

early stage ovarian cancer to help researchers worldwide identify biomarkers that can aid early detection and inform novel targets for therapy. This...to detect differentially expressed genes after transformation using Voom. When using the top 5 genes to build the classifier, it predicted...to analyze expression of micro-RNA in these samples. Thus, at the end of the third year of funding we started a parallel analysis of RNAseq, DNA- CNV

Differential gene expression revealed with RNA-Seq and parallel genotype selection of the ornithine decarboxylase gene in fish inhabiting polluted areas.

PubMed

Vega-Retter, C; Rojas-Hernandez, N; Vila, I; Espejo, R; Loyola, D E; Copaja, S; Briones, M; Nolte, A W; Véliz, D

2018-03-19

How organisms adapt to unfavorable environmental conditions by means of plasticity or selection of favorable genetic variants is a central issue in evolutionary biology. In the Maipo River basin, the fish Basilichthys microlepidotus inhabits polluted and non-polluted areas. Previous studies have suggested that directional selection drives genomic divergence between these areas in 4% of Amplified Fragment Length Polymorphism (AFLP) loci, but the underlying genes and functions remain unknown. We hypothesized that B. microlepidotus in this basin has plastic and/or genetic responses to these conditions. Using RNA-Seq, we identified differentially expressed genes in individuals from two polluted sites compared with fish inhabiting non-polluted sites. In one polluted site, the main upregulated genes were related to cellular proliferation as well as suppression and progression of tumors, while biological processes and molecular functions involved in apoptotic processes were overrepresented in the upregulated genes of the second polluted site. The ornithine decarboxylase gene (related to tumor promotion and progression), which was overexpressed in both polluted sites, was sequenced, and a parallel pattern of a heterozygote deficiency and increase of the same homozygote genotype in both polluted sites compared with fish inhabiting the non-polluted sites was detected. These results suggest the occurrence of both a plastic response in gene expression and an interplay between phenotypic change and genotypic selection in the face of anthropogenic pollution.

Cloud-Scale Genomic Signals Processing for Robust Large-Scale Cancer Genomic Microarray Data Analysis.

PubMed

Harvey, Benjamin Simeon; Ji, Soo-Yeon

2017-01-01

As microarray data available to scientists continues to increase in size and complexity, it has become overwhelmingly important to find multiple ways to bring forth oncological inference to the bioinformatics community through the analysis of large-scale cancer genomic (LSCG) DNA and mRNA microarray data that is useful to scientists. Though there have been many attempts to elucidate the issue of bringing forth biological interpretation by means of wavelet preprocessing and classification, there has not been a research effort that focuses on a cloud-scale distributed parallel (CSDP) separable 1-D wavelet decomposition technique for denoising through differential expression thresholding and classification of LSCG microarray data. This research presents a novel methodology that utilizes a CSDP separable 1-D method for wavelet-based transformation in order to initialize a threshold which will retain significantly expressed genes through the denoising process for robust classification of cancer patients. Additionally, the overall study was implemented and encompassed within CSDP environment. The utilization of cloud computing and wavelet-based thresholding for denoising was used for the classification of samples within the Global Cancer Map, Cancer Cell Line Encyclopedia, and The Cancer Genome Atlas. The results proved that separable 1-D parallel distributed wavelet denoising in the cloud and differential expression thresholding increased the computational performance and enabled the generation of higher quality LSCG microarray datasets, which led to more accurate classification results.

Implicit solution of Navier-Stokes equations on staggered curvilinear grids using a Newton-Krylov method with a novel analytical Jacobian.

NASA Astrophysics Data System (ADS)

Borazjani, Iman; Asgharzadeh, Hafez

2015-11-01

Flow simulations involving complex geometries and moving boundaries suffer from time-step size restriction and low convergence rates with explicit and semi-implicit schemes. Implicit schemes can be used to overcome these restrictions. However, implementing implicit solver for nonlinear equations including Navier-Stokes is not straightforward. Newton-Krylov subspace methods (NKMs) are one of the most advanced iterative methods to solve non-linear equations such as implicit descritization of the Navier-Stokes equation. The efficiency of NKMs massively depends on the Jacobian formation method, e.g., automatic differentiation is very expensive, and matrix-free methods slow down as the mesh is refined. Analytical Jacobian is inexpensive method, but derivation of analytical Jacobian for Navier-Stokes equation on staggered grid is challenging. The NKM with a novel analytical Jacobian was developed and validated against Taylor-Green vortex and pulsatile flow in a 90 degree bend. The developed method successfully handled the complex geometries such as an intracranial aneurysm with multiple overset grids, and immersed boundaries. It is shown that the NKM with an analytical Jacobian is 3 to 25 times faster than the fixed-point implicit Runge-Kutta method, and more than 100 times faster than automatic differentiation depending on the grid (size) and the flow problem. The developed methods are fully parallelized with parallel efficiency of 80-90% on the problems tested.

[Role of CD2-associated protein in podocyte differentiation.].

PubMed

Jiang, Hua-Jun; Chang, Ying; Zhu, Zhong-Hua; Liu, Jian-She; Deng, An-Guo; Zhang, Chun

2008-02-25

To study the cellular changes and the potential role of CD2-associated protein (CD2AP) in podocyte differentiation, conditionally immortalized murine podocyte cell line was cultured in RPMI 1640 medium under permissive condition at 33 °C. After transfection with CD2AP small interfering RNA (siRNA) the cells were shifted to non-permissive condition at 37 °C. Simultaneously, untransfected cells were taken as differentiation control. The podocyte proliferation rate was determined by MTT method. The expressions of CD2AP, WT1, synaptopodin and nephrin mRNAs were examined by RT-PCR. CD2AP, WT1 and nephrin protein expressions were examined by Western blot. The distribution of CD2AP, nephrin, F-actin and tubulin in differentiated and undifferentiated podocytes was detected by laser scanning confocal microscopy. The results showed: (1) CD2AP, WT1 and nephrin were stably expressed in differentiated and undifferentiated podocytes while synaptopodin was only expressed in differentiated podocytes. (2) CD2AP and nephrin mRNA and protein expressions were up-regulated during podocyte differentiation (P<0.05). (3) CD2AP and tubulin were distributed in the cytoplasm and perinulcear region in undifferentiated podocytes, and F-actin was predominantly localized to a cortical belt and paralleled to the cell axis. Under differentiation condition, CD2AP distribution profile was presented as peripheral accumulation, tubulin took on fascicular style and F-actin extended into foot processes in podocytes. CD2AP colocalized with nephrin and F-actin in undifferentiated podocytes. (4) After transfection with CD2AP siRNA, the expression of CD2AP was partially inhibited and cell growth was arrested; Synaptopodin, the differentiation podocyte marker, was apparently down-regulated; The differentiation of podocytes was delayed. The results demonstrate that podocyte differentiation is accompanied by cytoskeleton rearrangement and cell morphology change. CD2AP might play an essential role in podocyte differentiation.

Microelectromechanical filter formed from parallel-connected lattice networks of contour-mode resonators

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wojciechowski, Kenneth E; Olsson, III, Roy H; Ziaei-Moayyed, Maryam

2013-07-30

A microelectromechanical (MEM) filter is disclosed which has a plurality of lattice networks formed on a substrate and electrically connected together in parallel. Each lattice network has a series resonant frequency and a shunt resonant frequency provided by one or more contour-mode resonators in the lattice network. Different types of contour-mode resonators including single input, single output resonators, differential resonators, balun resonators, and ring resonators can be used in MEM filter. The MEM filter can have a center frequency in the range of 10 MHz-10 GHz, with a filter bandwidth of up to about 1% when all of the latticemore » networks have the same series resonant frequency and the same shunt resonant frequency. The filter bandwidth can be increased up to about 5% by using unique series and shunt resonant frequencies for the lattice networks.« less

Laser-induced free-free transitions in elastic electron scattering from CO2

NASA Astrophysics Data System (ADS)

Musa, Mohamed; MacDonald, Amy; Tidswell, Lisa; Holmes, Jim; St. Francis Xavier Laser Scattering Lab Team

2011-03-01

This report presents measurements of laser-induced free-free transitions of electrons scattered from CO2 molecules in the ground electronic state at incident electron energies of 3.8 and 5.8 eV under pulsed CO2 laser field. The differential cross section of free-free transitions involving absorption and emission of up to two photons were measured at various scattering angles with the polarization of the laser either parallel with or perpendicular to the the momentum change vector of the scattered electrons. The results of the parallel geometry are found to be in qualitative agreement with the predictions of the Kroll-Watson approximation within the experimental uncertainty whereas those of the perpendicular geometry show marked discrepancy with the Kroll-Watson predictions. This work was supported by the Natural Sciences and Engineering Research Council of Canada and the St. Francis Xavier University Council for Research.

Acceleration of the Particle Swarm Optimization for Peierls-Nabarro modeling of dislocations in conventional and high-entropy alloys

NASA Astrophysics Data System (ADS)

Pei, Zongrui; Eisenbach, Markus

2017-06-01

Dislocations are among the most important defects in determining the mechanical properties of both conventional alloys and high-entropy alloys. The Peierls-Nabarro model supplies an efficient pathway to their geometries and mobility. The difficulty in solving the integro-differential Peierls-Nabarro equation is how to effectively avoid the local minima in the energy landscape of a dislocation core. Among the other methods to optimize the dislocation core structures, we choose the algorithm of Particle Swarm Optimization, an algorithm that simulates the social behaviors of organisms. By employing more particles (bigger swarm) and more iterative steps (allowing them to explore for longer time), the local minima can be effectively avoided. But this would require more computational cost. The advantage of this algorithm is that it is readily parallelized in modern high computing architecture. We demonstrate the performance of our parallelized algorithm scales linearly with the number of employed cores.

Satellite Angular Rate Estimation From Vector Measurements

NASA Technical Reports Server (NTRS)

Azor, Ruth; Bar-Itzhack, Itzhack Y.; Harman, Richard R.

1996-01-01

This paper presents an algorithm for estimating the angular rate vector of a satellite which is based on the time derivatives of vector measurements expressed in a reference and body coordinate. The computed derivatives are fed into a spacial Kalman filter which yields an estimate of the spacecraft angular velocity. The filter, named Extended Interlaced Kalman Filter (EIKF), is an extension of the Kalman filter which, although being linear, estimates the state of a nonlinear dynamic system. It consists of two or three parallel Kalman filters whose individual estimates are fed to one another and are considered as known inputs by the other parallel filter(s). The nonlinear dynamics stem from the nonlinear differential equation that describes the rotation of a three dimensional body. Initial results, using simulated data, and real Rossi X ray Timing Explorer (RXTE) data indicate that the algorithm is efficient and robust.

Asynchronous multilevel adaptive methods for solving partial differential equations on multiprocessors - Performance results

NASA Technical Reports Server (NTRS)

Mccormick, S.; Quinlan, D.

1989-01-01

The fast adaptive composite grid method (FAC) is an algorithm that uses various levels of uniform grids (global and local) to provide adaptive resolution and fast solution of PDEs. Like all such methods, it offers parallelism by using possibly many disconnected patches per level, but is hindered by the need to handle these levels sequentially. The finest levels must therefore wait for processing to be essentially completed on all the coarser ones. A recently developed asynchronous version of FAC, called AFAC, completely eliminates this bottleneck to parallelism. This paper describes timing results for AFAC, coupled with a simple load balancing scheme, applied to the solution of elliptic PDEs on an Intel iPSC hypercube. These tests include performance of certain processes necessary in adaptive methods, including moving grids and changing refinement. A companion paper reports on numerical and analytical results for estimating convergence factors of AFAC applied to very large scale examples.

Nonlocal stability analysis of the MHD Kelvin-Helmholtz instability in a compressible plasma. [solar wind-magnetosphere interaction

NASA Technical Reports Server (NTRS)

Miura, A.; Pritchett, P. L.

1982-01-01

A general stability analysis is given of the Kevin-Helmholtz instability, for the case of sheared MHD flow of finite thickness in a compressible plasma which allows for the arbitrary orientation of the magnetic field, velocity flow, and wave vector in the plane perpendicular to the velocity gradient. The stability problem is reduced to the solution of a single second-order differential equation including a gravitational term to represent the coupling between the Kelvin-Helmholtz mode and the interchange mode. Compressibility and a magnetic field component parallel to the flow are found to be stabilizing effects, with destabilization of only the fast magnetosonic mode in the transverse case, and the presence of both Alfven and slow magnetosonic components in the parallel case. Analysis results are used in a discussion of the stability of sheared plasma flow at the magnetopause boundary and in the solar wind.

Comparison of the efficacy of nickel-titanium rotary systems with or without the retreatment instruments in the removal of gutta-percha in the apical third

PubMed Central

2014-01-01

Background The purpose of this study was to compare the efficacy of nickel-titanium rotary systems with or without the retreatment instruments in the removal of gutta-percha from the apical third. Methods The systems compared were as follows: ProTaper Universal (PT), ProTaper Universal Retreatment (PTr), Mtwo (M2) and Mtwo Retreatment (M2r). Sixty extracted mandibular incisors were treated with a crown-down technique and filled with gutta-percha and sealer. The apical diameter was standardized in 0.30 mm, 1 mm from the apex. The teeth were distributed into 4 experimental groups: PT, PTr, M2 and M2r. In PTr and M2r groups, filling materials were removed by PTr/M2r followed by root canals preparation up to a PT F4/M2 40; in groups PT/M2, the filling materials were removed and the root canals were prepared by PT up to a PT F4/M2 up to a M2 40. The roots were split and photomicrographing. The percentage of clean area in the apical 5 mm was calculated using software. Data were analyzed with the Kruskal-Wallis test. Results Remaining material was found in all hemisections and there was no statistically significant difference between the groups (p = 0.09). Considering the surface of the canal walls of all teeth, the mean of the percentage of clean area was 54%. Conclusions Considering the applied methodology, remaining filling material was found in all hemisections, regardless of the retreatment technique and PT or M2 were as effective as PTr/PT or M2r/M2. PMID:25128277

Physical basis of the Thellier-Thellier and related paleointensity methods

NASA Astrophysics Data System (ADS)

Dunlop, David J.

2011-08-01

Émile and Odette Thellier produced the first reliable determinations of paleointensity following an experimental protocol used earlier by Johann Koenigsberger. Although Koenigsberger did groundbreaking work on thermoremanent magnetization (TRM), it was the Thelliers who formulated the fundamental idea of partial TRMs as building blocks for TRM. In his 1938 doctoral thesis and a series of short notes, Émile Thellier minutely examined the data on TRM and partial TRM, ultimately establishing for bricks and other baked clays his laws of pTRM reciprocity, independence and additivity. In 1946 he speculated that blocking represents "…immobilization of elementary magnetic moments below a temperature Θ … Θ will vary at each point in the body, perhaps with the dimensions and the shape of the crystalline grains … One can thus explain thermoremanence by the progressive fixing, in the course of cooling, of moments which find themselves held fast when they pass through their individual temperature Θ." Thellier thus established the physical basis of TRM blocking and recognized the essential role of grain size and shape. In 1949 Louis Néel quantified these concepts in terms of the properties of single-domain grains. Today the Thellier-Thellier method remains the benchmark of reliable paleointensity data. The challenge has been the non-ideality of real geological and archeological materials: TRM carriers larger than single-domain size and physicochemical alteration during heating. The Thelliers avoided these problems by using bricks and pottery previously fired under conditions similar to those in laboratory heatings, eschewing volcanic and other rocks. But despite their problems, we have to deal with the material nature provides. This paper provides insights into the physics underlying the Thellier-Thellier method and check procedures that detect non-ideal behavior, as well as reviewing recent advances in paleointensity methodology.

Some observations aimed at improving the success rate of paleointensity experiments for lava flows (Invited)

NASA Astrophysics Data System (ADS)

Valet, J. M.; Herrero-Bervera, E.

2009-12-01

Emile Thellier did not believe to the possibility of obtaining reliable determinations of absolute paleointensity from lava flows and defended that only archeomagnetic material was suitable. Many protocols have been proposed over the past fifty years to defend that this assertion was not really justified. We have performed paleointensity studies on contemporaneous flows in Hawaii and in the Canaries. To those we have added determinations obtained from relatively recent flows at Santorini. The hawaiian flows that are dominated by pure magnetite with a narrow distribution of grain sizes provide by far the most accurate determinations of paleointensity. Such characteristics are simply derived from the spectrum of unbloking temperatures. Thus the evolution of the TRM upon thermal demagnetization appears to be a very important feature for successfull paleointensity experiments. The existence of a sharp decrease of the magnetization before reaching the unique Curie temperature of the rock is conclusively a very appropriate condition for obtaining suitable field determinations. Of course, these characteristics are only valid if the pTRM checks do not deviate from the original TRM. In this respect, we have noticed that deviations larger than 5% are frequently associated with significant deviations from the expected field intensity. The results from the Canary islands are also consistent with this observation despite the presence of a larger amount of titanium. Overall, these conclusions make sense when faced to Thellier’s statement regarding the success of archeomagnetic material. Indeed, the features that have been outlined above are typical of the characteristics found in archeological materials which have been largely oxidized during cooling and are dominated by a single magnetic mineral with a tiny distribution of grain sizes.

Progress toward a general species concept.

PubMed

Hausdorf, Bernhard

2011-04-01

New insights in the speciation process and the nature of "species" that accumulated in the past decade demand adjustments of the species concept. The standing of some of the most broadly accepted or most innovative species concepts in the light of the growing evidence that reproductive barriers are semipermeable to gene flow, that species can differentiate despite ongoing interbreeding, that a single species can originate polyphyletically by parallel evolution, and that uniparental organisms are organised in units that resemble species of biparental organisms is discussed. As a synthesis of ideas in existing concepts and the new insights, a generalization of the genic concept is proposed that defines species as groups of individuals that are reciprocally characterized by features that would have negative fitness effects in other groups and that cannot be regularly exchanged between groups upon contact. The benefits of this differential fitness species concept are that it classifies groups that keep differentiated and keep on differentiating despite interbreeding as species, that it is not restricted to specific mutations or mechanisms causing speciation, and that it can be applied to the whole spectrum of organisms from uni- to biparentals. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ghafarian, M.; Ariaei, A., E-mail: ariaei@eng.ui.ac.ir

The free vibration analysis of a multiple rotating nanobeams' system applying the nonlocal Eringen elasticity theory is presented. Multiple nanobeams' systems are of great importance in nano-optomechanical applications. At nanoscale, the nonlocal effects become non-negligible. According to the nonlocal Euler-Bernoulli beam theory, the governing partial differential equations are derived by incorporating the nonlocal scale effects. Assuming a structure of n parallel nanobeams, the vibration of the system is described by a coupled set of n partial differential equations. The method involves a change of variables to uncouple the equations and the differential transform method as an efficient mathematical technique tomore » solve the nonlocal governing differential equations. Then a number of parametric studies are conducted to assess the effect of the nonlocal scaling parameter, rotational speed, boundary conditions, hub radius, and the stiffness coefficients of the elastic interlayer media on the vibration behavior of the coupled rotating multiple-carbon-nanotube-beam system. It is revealed that the bending vibration of the system is significantly influenced by the rotational speed, elastic mediums, and the nonlocal scaling parameters. This model is validated by comparing the results with those available in the literature. The natural frequencies are in a reasonably good agreement with the reported results.« less

Gravitropism in cut flower stalks of snapdragon

NASA Astrophysics Data System (ADS)

Philosoph-Hadas, S.; Friedman, H.; Meir, S.; Berkovitz-SimanTov, R.; Rosenberger, I.; Halevy, A. H.; Kaufman, P. B.; Balk, P.; Woltering, E. J.

The negative gravitropic response of cut flower stalks is a complex multistep process that requires the participation of various cellular components acting in succession or in parallel. The process was particularly characterized in snapdragon (Antirrhinum majus L.) spikes with regard to (1) gravity stimulus perception associated with amyloplast reorientation; (2) stimulus transduction mediated through differential changes in the level, action and related genes of auxin and ethylene and their possible interaction; (3) stimulus response associated with differential growth leading to stalk curvature; (4) involvement of cytosolic calcium and actin cytoskeleton. Results show that the gravity-induced amyloplast reorientation, differential over-expression of two early auxin responsive genes and asymmetrical distribution of free IAA are early events in the bending process. These precede the asymmetrical ethylene production and differential stem growth, which was derived from initial shrinkage of the upper stem side and a subsequent elongation of the lower stem side. Results obtained with various calcium- and cytoskeleton-related agents indicate that cytosolic calcium and actin filaments may play essential roles in gravitropism-related processes of cut flower stalks. Therefore, modulators of these two physiological mediators may serve as means for controlling any undesired gravitropic bending.

Efficient parallel simulation of CO2 geologic sequestration insaline aquifers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Keni; Doughty, Christine; Wu, Yu-Shu

2007-01-01

An efficient parallel simulator for large-scale, long-termCO2 geologic sequestration in saline aquifers has been developed. Theparallel simulator is a three-dimensional, fully implicit model thatsolves large, sparse linear systems arising from discretization of thepartial differential equations for mass and energy balance in porous andfractured media. The simulator is based on the ECO2N module of the TOUGH2code and inherits all the process capabilities of the single-CPU TOUGH2code, including a comprehensive description of the thermodynamics andthermophysical properties of H2O-NaCl- CO2 mixtures, modeling singleand/or two-phase isothermal or non-isothermal flow processes, two-phasemixtures, fluid phases appearing or disappearing, as well as saltprecipitation or dissolution. The newmore » parallel simulator uses MPI forparallel implementation, the METIS software package for simulation domainpartitioning, and the iterative parallel linear solver package Aztec forsolving linear equations by multiple processors. In addition, theparallel simulator has been implemented with an efficient communicationscheme. Test examples show that a linear or super-linear speedup can beobtained on Linux clusters as well as on supercomputers. Because of thesignificant improvement in both simulation time and memory requirement,the new simulator provides a powerful tool for tackling larger scale andmore complex problems than can be solved by single-CPU codes. Ahigh-resolution simulation example is presented that models buoyantconvection, induced by a small increase in brine density caused bydissolution of CO2.« less

Sequential or parallel decomposed processing of two-digit numbers? Evidence from eye-tracking.

PubMed

Moeller, Korbinian; Fischer, Martin H; Nuerk, Hans-Christoph; Willmes, Klaus

2009-02-01

While reaction time data have shown that decomposed processing of two-digit numbers occurs, there is little evidence about how decomposed processing functions. Poltrock and Schwartz (1984) argued that multi-digit numbers are compared in a sequential digit-by-digit fashion starting at the leftmost digit pair. In contrast, Nuerk and Willmes (2005) favoured parallel processing of the digits constituting a number. These models (i.e., sequential decomposition, parallel decomposition) make different predictions regarding the fixation pattern in a two-digit number magnitude comparison task and can therefore be differentiated by eye fixation data. We tested these models by evaluating participants' eye fixation behaviour while selecting the larger of two numbers. The stimulus set consisted of within-decade comparisons (e.g., 53_57) and between-decade comparisons (e.g., 42_57). The between-decade comparisons were further divided into compatible and incompatible trials (cf. Nuerk, Weger, & Willmes, 2001) and trials with different decade and unit distances. The observed fixation pattern implies that the comparison of two-digit numbers is not executed by sequentially comparing decade and unit digits as proposed by Poltrock and Schwartz (1984) but rather in a decomposed but parallel fashion. Moreover, the present fixation data provide first evidence that digit processing in multi-digit numbers is not a pure bottom-up effect, but is also influenced by top-down factors. Finally, implications for multi-digit number processing beyond the range of two-digit numbers are discussed.

Parallel basal ganglia circuits for voluntary and automatic behaviour to reach rewards

PubMed Central

Hikosaka, Okihide

2015-01-01

The basal ganglia control body movements, value processing and decision-making. Many studies have shown that the inputs and outputs of each basal ganglia structure are topographically organized, which suggests that the basal ganglia consist of separate circuits that serve distinct functions. A notable example is the circuits that originate from the rostral (head) and caudal (tail) regions of the caudate nucleus, both of which target the superior colliculus. These two caudate regions encode the reward values of visual objects differently: flexible (short-term) values by the caudate head and stable (long-term) values by the caudate tail. These value signals in the caudate guide the orienting of gaze differently: voluntary saccades by the caudate head circuit and automatic saccades by the caudate tail circuit. Moreover, separate groups of dopamine neurons innervate the caudate head and tail and may selectively guide the flexible and stable learning/memory in the caudate regions. Studies focusing on manual handling of objects also suggest that rostrocaudally separated circuits in the basal ganglia control the action differently. These results suggest that the basal ganglia contain parallel circuits for two steps of goal-directed behaviour: finding valuable objects and manipulating the valuable objects. These parallel circuits may underlie voluntary behaviour and automatic skills, enabling animals (including humans) to adapt to both volatile and stable environments. This understanding of the functions and mechanisms of the basal ganglia parallel circuits may inform the differential diagnosis and treatment of basal ganglia disorders. PMID:25981958

jInv: A Modular and Scalable Framework for Electromagnetic Inverse Problems

NASA Astrophysics Data System (ADS)

Belliveau, P. T.; Haber, E.

2016-12-01

Inversion is a key tool in the interpretation of geophysical electromagnetic (EM) data. Three-dimensional (3D) EM inversion is very computationally expensive and practical software for inverting large 3D EM surveys must be able to take advantage of high performance computing (HPC) resources. It has traditionally been difficult to achieve those goals in a high level dynamic programming environment that allows rapid development and testing of new algorithms, which is important in a research setting. With those goals in mind, we have developed jInv, a framework for PDE constrained parameter estimation problems. jInv provides optimization and regularization routines, a framework for user defined forward problems, and interfaces to several direct and iterative solvers for sparse linear systems. The forward modeling framework provides finite volume discretizations of differential operators on rectangular tensor product meshes and tetrahedral unstructured meshes that can be used to easily construct forward modeling and sensitivity routines for forward problems described by partial differential equations. jInv is written in the emerging programming language Julia. Julia is a dynamic language targeted at the computational science community with a focus on high performance and native support for parallel programming. We have developed frequency and time-domain EM forward modeling and sensitivity routines for jInv. We will illustrate its capabilities and performance with two synthetic time-domain EM inversion examples. First, in airborne surveys, which use many sources, we achieve distributed memory parallelism by decoupling the forward and inverse meshes and performing forward modeling for each source on small, locally refined meshes. Secondly, we invert grounded source time-domain data from a gradient array style induced polarization survey using a novel time-stepping technique that allows us to compute data from different time-steps in parallel. These examples both show that it is possible to invert large scale 3D time-domain EM datasets within a modular, extensible framework written in a high-level, easy to use programming language.

High-Resolution DCE-MRI of the Pituitary Gland Using Radial k-Space Acquisition with Compressed Sensing Reconstruction.

PubMed

Rossi Espagnet, M C; Bangiyev, L; Haber, M; Block, K T; Babb, J; Ruggiero, V; Boada, F; Gonen, O; Fatterpekar, G M

2015-08-01

The pituitary gland is located outside of the blood-brain barrier. Dynamic T1 weighted contrast enhanced sequence is considered to be the gold standard to evaluate this region. However, it does not allow assessment of intrinsic permeability properties of the gland. Our aim was to demonstrate the utility of radial volumetric interpolated brain examination with the golden-angle radial sparse parallel technique to evaluate permeability characteristics of the individual components (anterior and posterior gland and the median eminence) of the pituitary gland and areas of differential enhancement and to optimize the study acquisition time. A retrospective study was performed in 52 patients (group 1, 25 patients with normal pituitary glands; and group 2, 27 patients with a known diagnosis of microadenoma). Radial volumetric interpolated brain examination sequences with golden-angle radial sparse parallel technique were evaluated with an ROI-based method to obtain signal-time curves and permeability measures of individual normal structures within the pituitary gland and areas of differential enhancement. Statistical analyses were performed to assess differences in the permeability parameters of these individual regions and optimize the study acquisition time. Signal-time curves from the posterior pituitary gland and median eminence demonstrated a faster wash-in and time of maximum enhancement with a lower peak of enhancement compared with the anterior pituitary gland (P < .005). Time-optimization analysis demonstrated that 120 seconds is ideal for dynamic pituitary gland evaluation. In the absence of a clinical history, differences in the signal-time curves allow easy distinction between a simple cyst and a microadenoma. This retrospective study confirms the ability of the golden-angle radial sparse parallel technique to evaluate the permeability characteristics of the pituitary gland and establishes 120 seconds as the ideal acquisition time for dynamic pituitary gland imaging. © 2015 by American Journal of Neuroradiology.

High-Resolution DCE-MRI of the Pituitary Gland Using Radial k-Space Acquisition with Compressed Sensing Reconstruction

PubMed Central

Rossi Espagnet, M.C.; Bangiyev, L.; Haber, M.; Block, K.T.; Babb, J.; Ruggiero, V.; Boada, F.; Gonen, O.; Fatterpekar, G.M.

2015-01-01

BACKGROUNDANDPURPOSE The pituitary gland is located outside of the blood-brain barrier. Dynamic T1 weighted contrast enhanced sequence is considered to be the gold standard to evaluate this region. However, it does not allow assessment of intrinsic permeability properties of the gland. Our aim was to demonstrate the utility of radial volumetric interpolated brain examination with the golden-angle radial sparse parallel technique to evaluate permeability characteristics of the individual components (anterior and posterior gland and the median eminence) of the pituitary gland and areas of differential enhancement and to optimize the study acquisition time. MATERIALS AND METHODS A retrospective study was performed in 52 patients (group 1, 25 patients with normal pituitary glands; and group 2, 27 patients with a known diagnosis of microadenoma). Radial volumetric interpolated brain examination sequences with golden-angle radial sparse parallel technique were evaluated with an ROI-based method to obtain signal-time curves and permeability measures of individual normal structures within the pituitary gland and areas of differential enhancement. Statistical analyses were performed to assess differences in the permeability parameters of these individual regions and optimize the study acquisition time. RESULTS Signal-time curves from the posterior pituitary gland and median eminence demonstrated a faster wash-in and time of maximum enhancement with a lower peak of enhancement compared with the anterior pituitary gland (P < .005). Time-optimization analysis demonstrated that 120 seconds is ideal for dynamic pituitary gland evaluation. In the absence of a clinical history, differences in the signal-time curves allow easy distinction between a simple cyst and a microadenoma. CONCLUSIONS This retrospective study confirms the ability of the golden-angle radial sparse parallel technique to evaluate the permeability characteristics of the pituitary gland and establishes 120 seconds as the ideal acquisition time for dynamic pituitary gland imaging. PMID:25953760

Parallel evolution of storage roots in morning glories (Convolvulaceae).

PubMed

Eserman, Lauren A; Jarret, Robert L; Leebens-Mack, James H

2018-05-29

Storage roots are an ecologically and agriculturally important plant trait that have evolved numerous times in angiosperms. Storage roots primarily function to store carbohydrates underground as reserves for perennial species. In morning glories, storage roots are well characterized in the crop species sweetpotato, where starch accumulates in storage roots. This starch-storage tissue proliferates, and roots thicken to accommodate the additional tissue. In morning glories, storage roots have evolved numerous times. The primary goal of this study is to understand whether this was through parallel evolution, where species use a common genetic mechanism to achieve storage root formation, or through convergent evolution, where storage roots in distantly related species are formed using a different set of genes. Pairs of species where one forms storage roots and the other does not were sampled from two tribes in the morning glory family, the Ipomoeeae and Merremieae. Root anatomy in storage roots and fine roots was examined. Furthermore, we sequenced total mRNA from storage roots and fine roots in these species and analyzed differential gene expression. Anatomical results reveal that storage roots of species in the Ipomoeeae tribe, such as sweetpotato, accumulate starch similar to species in the Merremieae tribe but differ in vascular tissue organization. In both storage root forming species, more genes were found to be upregulated in storage roots compared to fine roots. Further, we find that fifty-seven orthologous genes were differentially expressed between storage roots and fine roots in both storage root forming species. These genes are primarily involved in starch biosynthesis, regulation of starch biosynthesis, and transcription factor activity. Taken together, these results demonstrate that storage roots of species from both morning glory tribes are anatomically different but utilize a common core set of genes in storage root formation. This is consistent with a pattern of parallel evolution, thus highlighting the importance of examining anatomy together with gene expression to understand the evolutionary origins of ecologically and economically important plant traits.

Intrinsic Deregulation of Vascular Smooth Muscle and Myofibroblast Differentiation in Mesenchymal Stromal Cells from Patients with Systemic Sclerosis.

PubMed

Hegner, Björn; Schaub, Theres; Catar, Rusan; Kusch, Angelika; Wagner, Philine; Essin, Kirill; Lange, Claudia; Riemekasten, Gabriela; Dragun, Duska

2016-01-01

Obliterative vasculopathy and fibrosis are hallmarks of systemic sclerosis (SSc), a severe systemic autoimmune disease. Bone marrow-derived mesenchymal stromal cells (MSCs) from SSc patients may harbor disease-specific abnormalities. We hypothesized disturbed vascular smooth muscle cell (VSMC) differentiation with increased propensity towards myofibroblast differentiation in response to SSc-microenvironment defining growth factors and determined responsible mechanisms. We studied responses of multipotent MSCs from SSc-patients (SSc-MSCs) and healthy controls (H-MSCs) to long-term exposure to CTGF, b-FGF, PDGF-BB or TGF-β1. Differentiation towards VSMC and myofibroblast lineages was analyzed on phenotypic, biochemical, and functional levels. Intracellular signaling studies included analysis of TGF-β receptor regulation, SMAD, AKT, ERK1/2 and autocrine loops. VSMC differentiation towards both, contractile and synthetic VSMC phenotypes in response to CTGF and b-FGF was disturbed in SSc-MSCs. H-MSCs and SSc-MSCs responded equally to PDGF-BB with prototypic fibroblastic differentiation. TGF-β1 initiated myofibroblast differentiation in both cell types, yet with striking phenotypic and functional differences: In relation to H-MSC-derived myofibroblasts induced by TGF-β1, those obtained from SSc-MSCs expressed more contractile proteins, migrated towards TGF-β1, had low proliferative capacity, and secreted higher amounts of collagen paralleled by reduced MMP expression. Higher levels of TGF-β receptor 1 and enhanced canonical and noncanonical TGF-β signaling in SSc-MSCs accompanied aberrant differentiation response of SSc-MSCs in comparison to H-MSCs. Deregulated VSMC differentiation with a shift towards myofibroblast differentiation expands the concept of disturbed endogenous regenerative capacity of MSCs from SSc patients. Disease related intrinsic hyperresponsiveness to TGF-β1 with increased collagen production may represent one responsible mechanism. Better understanding of repair barriers and harnessing beneficial differentiation processes in MSCs could widen options of autologous MSC application in SSc patients.

Lipidomic profiling of patient-specific iPSC-derived hepatocyte-like cells

PubMed Central

Viiri, Leena E.; Vihervaara, Terhi; Koistinen, Kaisa M.; Hilvo, Mika; Ekroos, Kim; Käkelä, Reijo; Aalto-Setälä, Katriina

2017-01-01

ABSTRACT Hepatocyte-like cells (HLCs) differentiated from human induced pluripotent stem cells (iPSCs) offer an alternative model to primary human hepatocytes to study lipid aberrations. However, the detailed lipid profile of HLCs is yet unknown. In the current study, functional HLCs were differentiated from iPSCs generated from dermal fibroblasts of three individuals by a three-step protocol through the definitive endoderm (DE) stage. In parallel, detailed lipidomic analyses as well as gene expression profiling of a set of lipid-metabolism-related genes were performed during the entire differentiation process from iPSCs to HLCs. Additionally, fatty acid (FA) composition of the cell culture media at different stages was determined. Our results show that major alterations in the molecular species of lipids occurring during DE and early hepatic differentiation stages mainly mirror the quality and quantity of the FAs supplied in culture medium at each stage. Polyunsaturated phospholipids and sphingolipids with a very long FA were produced in the cells at a later stage of differentiation. This work uncovers the previously unknown lipid composition of iPSC-HLCs and its alterations during the differentiation in conjunction with the expression of key lipid-associated genes. Together with biochemical, functional and gene expression measurements, the lipidomic analyses allowed us to improve our understanding of the concerted influence of the exogenous metabolite supply and cellular biosynthesis essential for iPSC-HLC differentiation and function. Importantly, the study describes in detail a cell model that can be applied in exploring, for example, the lipid metabolism involved in the development of fatty liver disease or atherosclerosis. PMID:28733363

Methylmercury exposure causes a persistent inhibition of myogenin expression and C2C12 myoblast differentiation.

PubMed

Prince, Lisa M; Rand, Matthew D

2018-01-15

Methylmercury (MeHg) is a ubiquitous environmental toxicant, best known for its selective targeting of the developing nervous system. MeHg exposure has been shown to cause motor deficits such as impaired gait and coordination, muscle weakness, and muscle atrophy, which have been associated with disruption of motor neurons. However, recent studies have suggested that muscle may also be a target of MeHg toxicity, both in the context of developmental myogenic events and of low-level chronic exposures affecting muscle wasting in aging. We therefore investigated the effects of MeHg on myotube formation, using the C2C12 mouse myoblast model. We found that MeHg inhibits both differentiation and fusion, in a concentration-dependent manner. Furthermore, MeHg specifically and persistently inhibits myogenin (MyoG), a transcription factor involved in myocyte differentiation, within the first six hours of exposure. MeHg-induced reduction in MyoG expression is contemporaneous with a reduction of a number of factors involved in mitochondrial biogenesis and mtDNA transcription and translation, which may implicate a role for mitochondria in mediating MeHg-induced change in the differentiation program. Unexpectedly, inhibition of myoblast differentiation with MeHg parallels inhibition of Notch receptor signaling. Our research establishes muscle cell differentiation as a target for MeHg toxicity, which may contribute to the underlying etiology of motor deficits with MeHg toxicity. Copyright © 2017 Elsevier B.V. All rights reserved.

Elevated α-synuclein caused by SNCA gene triplication impairs neuronal differentiation and maturation in Parkinson's patient-derived induced pluripotent stem cells

PubMed Central

Oliveira, L M A; Falomir-Lockhart, L J; Botelho, M G; Lin, K-H; Wales, P; Koch, J C; Gerhardt, E; Taschenberger, H; Outeiro, T F; Lingor, P; Schüle, B; Arndt-Jovin, D J; Jovin, T M

2015-01-01

We have assessed the impact of α-synuclein overexpression on the differentiation potential and phenotypic signatures of two neural-committed induced pluripotent stem cell lines derived from a Parkinson's disease patient with a triplication of the human SNCA genomic locus. In parallel, comparative studies were performed on two control lines derived from healthy individuals and lines generated from the patient iPS-derived neuroprogenitor lines infected with a lentivirus incorporating a small hairpin RNA to knock down the SNCA mRNA. The SNCA triplication lines exhibited a reduced capacity to differentiate into dopaminergic or GABAergic neurons and decreased neurite outgrowth and lower neuronal activity compared with control cultures. This delayed maturation phenotype was confirmed by gene expression profiling, which revealed a significant reduction in mRNA for genes implicated in neuronal differentiation such as delta-like homolog 1 (DLK1), gamma-aminobutyric acid type B receptor subunit 2 (GABABR2), nuclear receptor related 1 protein (NURR1), G-protein-regulated inward-rectifier potassium channel 2 (GIRK-2) and tyrosine hydroxylase (TH). The differentiated patient cells also demonstrated increased autophagic flux when stressed with chloroquine. We conclude that a two-fold overexpression of α-synuclein caused by a triplication of the SNCA gene is sufficient to impair the differentiation of neuronal progenitor cells, a finding with implications for adult neurogenesis and Parkinson's disease progression, particularly in the context of bioenergetic dysfunction. PMID:26610207

Regulated expression of the MRP8 and MRP14 genes in human promyelocytic leukemic HL-60 cell treated with the differentiation-inducing agents mycophenolic acid and 1{alpha},25-Dihydroxyvitamin D{sub 3}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Warner-Bartnicki, A.L.; Murao, S.; Collart, F.R.

1992-12-31

The calcium-binding proteins MRP8 and MEP14 are present in mature monomyelocytic cells and are induced during differentiation. Previous studies have demonstrated that the proteins may mediate the growth arrest in differentiating HL-60 cells. We determined the levels of a protein complex (PC) containing MRP8 and MRP14 and investigated the mechanism by which the genes encoding these proteins are regulated in HL-60 cells treated with the differentiation-inducing agent mycophenorc acid (MPA)While the PC was barely detectable in untreated cells, MPA treatment resulted in elevated levels of the PC which were maximal at 3-4 d, and were found to directly parallel gainsmore » in the steady-state levels of MRP8 and MRP14 MRNA. Transcription studies with the use of nuclear run-on experiments revealed increased transcription initiation at the MRP8 and MRP14 promoters after MPA treatment. 1{alpha},25-Dihydroxyvitamin D{sub 3}, which induces HL-60 cell differentiation by another mechanism, was also found to increase transcription initiation at the MRP8 and MRP14 promoters. Our results suggest that this initiation is the major control of maturation agent-mediated increases in MRP8 and MRPl4 gene expression, and support a role for the PC in terminal differentiation of human monomyelocytic cells.« less

Mom, dad, I'm straight: the coming out of gender ideologies in adolescent sexual-identity development.

PubMed

Striepe, Meg I; Tolman, Deborah L

2003-12-01

Little attention has been given to how femininity and masculinity ideologies impact sexual-identity development. Differentiating violations of conventional femininity and masculinity ideologies as part of an overt process of sexual-identity development in sexual-minority adolescents suggested the possibility of a parallel process among heterosexual adolescents. Based on feminist theory and analysis of heterosexual adolescents narratives about relationships, the importance of negotiating femininity and masculinity ideologies as part of sexual-identity development for all adolescents is described.

Computer-aided mechanogenesis of skeletal muscle organs from single cells in vitro

NASA Technical Reports Server (NTRS)

Vanderburgh, Herman H.; Swasdison, Somporn; Karlisch, Patricia

1991-01-01

Complex mechanical forces generated in the growing embryo play an important role in organogenesis. Computerized application of similar forces to differentiating skeletal muscle myoblasts in vitro generate three dimensional artificial muscle organs. These organs contain parallel networks of long unbranched myofibers organized into fascicle-like structures. Tendon development is initiated and the muscles are capable of performing directed, functional work. Kinetically engineered organs provide a new method for studying the growth and development of normal and diseased skeletal muscle.

Computer aided mechanogenesis of skeletal muscle organs from single cells in vitro

NASA Technical Reports Server (NTRS)

Vandenburgh, Herman H.; Swasdison, Somporn; Karlisch, Patricia

1990-01-01

Complex mechanical forces generated in the growing embryo play an important role in organogenesis. Computerized application of similar forces to differentiating skeletal muscle myoblasts in vitro generate three dimensional artificial muscle organs. These organs contain parallel networks of long unbranched myofibers organized into fascicle-like structures. Tendon development is initiated and the muscles are capable of performing directed, functional work. Kinetically engineered organs provide a new method for studying the growth and development of normal and diseased skeletal muscle.

Time-Parallel Solutions to Ordinary Differential Equations on GPUs with a New Functional Optimization Approach Related to the Sobolev Gradient Method

DTIC Science & Technology

2012-10-01

black and approximations in cyan and magenta. The second ODE is the pendulum equation, given by: This ODE was also implemented using Crank...The drawback of approaches like the one proposed can be observed with a very simple example. Suppose vector is found by applying 4 linear...public release; distribution unlimited Figure 2. A phase space plot of the Pendulum example. Fine solution (black) contains 32768 time steps

CosApps: Simulate gravitational lensing through ray tracing and shear calculation

NASA Astrophysics Data System (ADS)

Coss, David

2017-12-01

Cosmology Applications (CosApps) provides tools to simulate gravitational lensing using two different techniques, ray tracing and shear calculation. The tool ray_trace_ellipse calculates deflection angles on a grid for light passing a deflecting mass distribution. Using MPI, ray_trace_ellipse may calculate deflection in parallel across network connected computers, such as cluster. The program physcalc calculates the gravitational lensing shear using the relationship of convergence and shear, described by a set of coupled partial differential equations.

Modulation of Stem Cells Differentiation and Myostatin as an Approach to Counteract Fibrosis in Muscle Dystrophy and Regeneration after Injury

DTIC Science & Technology

2008-03-01

well as the other parallel work with bone marrow cells [ 22 ], the effects were comparatively short- lived, since in our case, the considerable...comparison of myogenic, fibrogenic and adipogenic potential of stem cells from intact and regenerating muscle from mdx, wt and Mst(-/-) mice; b) effects on...sections (not shown). Figure 3. The stem cell nature of Wt MDSC and response to paracrine effects is evidenced by their conversion into SMC when

MADNESS: A Multiresolution, Adaptive Numerical Environment for Scientific Simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harrison, Robert J.; Beylkin, Gregory; Bischoff, Florian A.

2016-01-01

MADNESS (multiresolution adaptive numerical environment for scientific simulation) is a high-level software environment for solving integral and differential equations in many dimensions that uses adaptive and fast harmonic analysis methods with guaranteed precision based on multiresolution analysis and separated representations. Underpinning the numerical capabilities is a powerful petascale parallel programming environment that aims to increase both programmer productivity and code scalability. This paper describes the features and capabilities of MADNESS and briefly discusses some current applications in chemistry and several areas of physics.

Comparison of Implicit Collocation Methods for the Heat Equation

NASA Technical Reports Server (NTRS)

Kouatchou, Jules; Jezequel, Fabienne; Zukor, Dorothy (Technical Monitor)

2001-01-01

We combine a high-order compact finite difference scheme to approximate spatial derivatives arid collocation techniques for the time component to numerically solve the two dimensional heat equation. We use two approaches to implement the collocation methods. The first one is based on an explicit computation of the coefficients of polynomials and the second one relies on differential quadrature. We compare them by studying their merits and analyzing their numerical performance. All our computations, based on parallel algorithms, are carried out on the CRAY SV1.

Interaction of non-radially symmetric camphor particles

NASA Astrophysics Data System (ADS)

Ei, Shin-Ichiro; Kitahata, Hiroyuki; Koyano, Yuki; Nagayama, Masaharu

2018-03-01

In this study, the interaction between two non-radially symmetric camphor particles is theoretically investigated and the equation describing the motion is derived as an ordinary differential system for the locations and the rotations. In particular, slightly modified non-radially symmetric cases from radial symmetry are extensively investigated and explicit motions are obtained. For example, it is theoretically shown that elliptically deformed camphor particles interact so as to be parallel with major axes. Such predicted motions are also checked by real experiments and numerical simulations.

A Metric to Quantify Shared Visual Attention in Two-Person Teams

NASA Technical Reports Server (NTRS)

Gontar, Patrick; Mulligan, Jeffrey B.

2015-01-01

Critical tasks in high-risk environments are often performed by teams, the members of which must work together efficiently. In some situations, the team members may have to work together to solve a particular problem, while in others it may be better for them to divide the work into separate tasks that can be completed in parallel. We hypothesize that these two team strategies can be differentiated on the basis of shared visual attention, measured by gaze tracking.

Implementation of a Pseudo-Bending Seismic Travel-Time Calculator in a Distributed Parallel Computing Environment

DTIC Science & Technology

2008-09-01

algorithms that have been proposed to accomplish it fall into three broad categories. Eikonal solvers (e.g., Vidale, 1988, 1990; Podvin and Lecomte, 1991...difference eikonal solvers, the FMM algorithm works by following a wavefront as it moves across a volume of grid points, updating the travel times in...the grid according to the eikonal differential equation, using a second-order finite-difference scheme. We chose to use FMM for our comparison because

The Mendeleev Crater chain: A description and discussion of origin

NASA Technical Reports Server (NTRS)

Eppler, D.; Heiken, G.

1974-01-01

A 113-kilometer-long crater chain on the floor of Mendeleev Crater is the best morphological example of several similar chains on the lunar far side. Age relationships relative to Mendeleev Crater indicate that it is a younger feature that may have developed over a fault parallel to the lunar grid system. The dumbbell shape of the chain may be related to a differential stress along a fault crossing the floor that resulted in varying resistance to magma invasion.

PLC-beta2 monitors the drug-induced release of differentiation blockade in tumoral myeloid precursors.

PubMed

Brugnoli, Federica; Bovolenta, Matteo; Benedusi, Mascia; Miscia, Sebastianó; Capitani, Silvano; Bertagnolo, Valeria

2006-05-01

The differentiation therapy in treatment of acute promyelocytic leukemia (APL), based on the administration of all-trans retinoic acid (ATRA), is currently flanked with the use of As2O3, a safe and effective agent for patients showing a resistance to ATRA treatment. A synergy between ATRA and As3O3 was also reported in inducing granulocytic differentiation of APL-derived cells. We have demonstrated that phospholipase C-beta2 (PLC-beta2), highly expressed in neutrophils and nearly absent in tumoral promyelocytes, largely increases during ATRA treatment of APL-derived cells and strongly correlates with the responsiveness of APL patients to ATRA-based differentiating therapies. Here we report that, in APL-derived cells, low doses of As3O3 induce a slight increase of PLC-beta2 together with a moderate maturation, and cooperate with ATRA to provoke a significant increase of PLC-beta2 expression. Remarkably, the amounts of PLC-beta2 draw a parallel with the differentiation levels reached by both ATRA-responsive and -resistant cells treated with ATRA/As2O3 combinations. PLC-beta2 is not necessary for the progression of tumoral promyelocytes along the granulocytic lineage and is unable to overcome the differentiation block or to potentiate the agonist-induced maturation. On the other hand, since its expression closely correlates with the differentiation level reached by APL-derived cells induced to maturate by drugs presently employed in APL therapies, PLC-beta2 represents indeed a specific marker to test the ability of differentiation agents to induce the release of the maturation blockade of tumoral myeloid precursors.

Generation and evolution of anisotropic turbulence and related energy transfer in a multi-species solar wind

NASA Astrophysics Data System (ADS)

Maneva, Yana; Poedts, Stefaan

2017-04-01

The electromagnetic fluctuations in the solar wind represent a zoo of plasma waves with different properties, whose wavelengths range from largest fluid scales to the smallest dissipation scales. By nature the power spectrum of the magnetic fluctuations is anisotropic with different spectral slopes in parallel and perpendicular directions with respect to the background magnetic field. Furthermore, the magnetic field power spectra steepen as one moves from the inertial to the dissipation range and we observe multiple spectral breaks with different slopes in parallel and perpendicular direction at the ion scales and beyond. The turbulent dissipation of magnetic field fluctuations at the sub-ion scales is believed to go into local ion heating and acceleration, so that the spectral breaks are typically associated with particle energization. The gained energy can be in the form of anisotropic heating, formation of non-thermal features in the particle velocity distributions functions, and redistribution of the differential acceleration between the different ion populations. To study the relation between the evolution of the anisotropic turbulent spectra and the particle heating at the ion and sub-ion scales we perform a series of 2.5D hybrid simulations in a collisionless drifting proton-alpha plasma. We neglect the fast electron dynamics and treat the electrons as an isothermal fluid electrons, whereas the protons and a minor population of alpha particles are evolved in a fully kinetic manner. We start with a given wave spectrum and study the evolution of the magnetic field spectral slopes as a function of the parallel and perpendicular wave¬numbers. Simultaneously, we track the particle response and the energy exchange between the parallel and perpendicular scales. We observe anisotropic behavior of the turbulent power spectra with steeper slopes along the dominant energy-containing direction. This means that for parallel and quasi-parallel waves we have steeper spectral slope in parallel direction, whereas for highly oblique waves the dissipation occurs predominantly in perpendicular direction and the spectral slopes are steeper across the background magnetic field. The value of the spectral slopes depends on the angle of propagation, the spectral range, as well as the plasma properties. In general the dissipation is stronger at small scales and the corresponding spectral slopes there are steeper. For parallel and quasi-parallel propagation the prevailing energy cascade remains along the magnetic field, whereas for initially isotropic oblique turbulence the cascade develops mainly in perpendicular direction.

The Bone Morphogenetic Protein Type Ib Receptor Is a Major Mediator of Glial Differentiation and Cell Survival in Adult Hippocampal Progenitor Cell Culture

PubMed Central

Brederlau, A.; Faigle, R.; Elmi, M.; Zarebski, A.; Sjöberg, S.; Fujii, M.; Miyazono, K.; Funa, K.

2004-01-01

Bone morphogenetic proteins (BMPs) act as growth regulators and inducers of differentiation. They transduce their signal via three different type I receptors, termed activin receptor-like kinase 2 (Alk2), Alk3, or bone morphogenetic protein receptor Ia (BMPRIa) and Alk6 or BMPRIb. Little is known about functional differences between the three type I receptors. Here, we have investigated consequences of constitutively active (ca) and dominant negative (dn) type I receptor overexpression in adult-derived hippocampal progenitor cells (AHPs). The dn receptors have a nonfunctional intracellular but functional extracellular domain. They thus trap BMPs that are endogenously produced by AHPs. We found that effects obtained by overexpression of dnAlk2 and dnAlk6 were similar, suggesting similar ligand binding patterns for these receptors. Thus, cell survival was decreased, glial fibrillary acidic protein (GFAP) expression was reduced, whereas the number of oligodendrocytes increased. No effect on neuronal differentiation was seen. Whereas the expression of Alk2 and Alk3 mRNA remained unchanged, the Alk6 mRNA was induced after impaired BMP signaling. After dnAlk3 overexpression, cell survival and astroglial differentiation increased in parallel to augmented Alk6 receptor signaling. We conclude that endogenous BMPs mediate cell survival, astroglial differentiation and the suppression of oligodendrocytic cell fate mainly via the Alk6 receptor in AHP culture. PMID:15194807

Stem Cell Differentiation Toward the Myogenic Lineage for Muscle Tissue Regeneration: A Focus on Muscular Dystrophy.

PubMed

Ostrovidov, Serge; Shi, Xuetao; Sadeghian, Ramin Banan; Salehi, Sahar; Fujie, Toshinori; Bae, Hojae; Ramalingam, Murugan; Khademhosseini, Ali

2015-12-01

Skeletal muscle tissue engineering is one of the important ways for regenerating functionally defective muscles. Among the myopathies, the Duchenne muscular dystrophy (DMD) is a progressive disease due to mutations of the dystrophin gene leading to progressive myofiber degeneration with severe symptoms. Although current therapies in muscular dystrophy are still very challenging, important progress has been made in materials science and in cellular technologies with the use of stem cells. It is therefore useful to review these advances and the results obtained in a clinical point of view. This article focuses on the differentiation of stem cells into myoblasts, and their application in muscular dystrophy. After an overview of the different stem cells that can be induced to differentiate into the myogenic lineage, we introduce scaffolding materials used for muscular tissue engineering. We then described some widely used methods to differentiate different types of stem cell into myoblasts. We highlight recent insights obtained in therapies for muscular dystrophy. Finally, we conclude with a discussion on stem cell technology. We discussed in parallel the benefits brought by the evolution of the materials and by the expansion of cell sources which can differentiate into myoblasts. We also discussed on future challenges for clinical applications and how to accelerate the translation from the research to the clinic in the frame of DMD.

Secretome of Differentiated PC12 Cells Enhances Neuronal Differentiation in Human Mesenchymal Stem Cells Via NGF-Like Mechanism.

PubMed

Srivastava, A; Singh, S; Pandey, A; Kumar, D; Rajpurohit, C S; Khanna, V K; Pant, A B

2018-03-12

The secretome-mediated responses over cellular physiology are well documented. Stem cells have been ruling the field of secretomics and its role in regenerative medicine since the past few years. However, the mechanistic aspects of secretome-mediated responses and the role of other cells in this area remain somewhat elusive. Here, we investigate the effects of secretome-enriched conditioned medium (CM) of neuronally differentiated PC12 cells on the neuronal differentiation of human mesenchymal stem cells (hMSCs). The exposure to CM at a ratio of 1:1 (CM: conditioned medium of PC12 cells) led to neuronal induction in hMSCs. This neuronal induction was compared with a parallel group of cells exposed to nerve growth factor (NGF). There was a marked increase in neurite length and expression of neuronal markers (β-III tubulin, neurofilament-M (NF-M), synaptophysin, NeuN in exposed hMSCs). Experimental group co-exposed to NGF and CM showed an additive response via MAPK signaling and directed the cells particularly towards cholinergic lineage. The ability of CM to enhance the neuronal properties of stem cells could aid in their rapid differentiation into neuronal subtypes in case of stem cell transplantation for neuronal injuries, thus broadening the scope of non-stem cell-based applications in the area of secretomics.

PML–RARA-RXR Oligomers Mediate Retinoid and Rexinoid/cAMP Cross-Talk in Acute Promyelocytic Leukemia Cell Differentiation

PubMed Central

Kamashev, Dmitrii; Vitoux, Dominique; de Thé, Hugues

2004-01-01

PML–RARA was proposed to initiate acute promyelocytic leukemia (APL) through PML–RARA homodimer–triggered repression. Here, we examined the nature of the PML–RARA protein complex and of its DNA targets in APL cells. Using a selection/amplification approach, we demonstrate that PML–RARA targets consist of two AGGTCA elements in an astonishing variety of orientations and spacings, pointing to highly relaxed structural constrains for DNA binding and identifying a major gain of function of this oncogene. PML–RARA-specific response elements were identified, which all conveyed a major transcriptional response to RA only in APL cells. In these cells, we demonstrate that PML–RARA oligomers are complexed to RXR. Directly probing PML–RARA function in APL cells, we found that the differentiation enhancer cyclic AMP (cAMP) boosted transcriptional activation by RA. cAMP also reversed the normal silencing (subordination) of the transactivating function of RXR when bound to RARA or PML–RARA, demonstrating that the alternate rexinoid/cAMP-triggered APL differentiation pathway also activates PML–RARA targets. Finally, cAMP restored both RA-triggered differentiation and PML–RARA transcriptional activation in mutant RA-resistant APL cells. Collectively, our findings directly demonstrate that APL cell differentiation parallels transcriptional activation through PML–RARA-RXR oligomers and that those are functionally targeted by cAMP, identifying this agent as another oncogene-targeted therapy. PMID:15096541

Loss of end-differentiated β-cell phenotype following pancreatic islet transplantation.

PubMed

Anderson, S J; White, M G; Armour, S L; Maheshwari, R; Tiniakos, D; Muller, Y D; Berishvili, E; Berney, T; Shaw, J A M

2018-03-01

Replacement of pancreatic β-cells through deceased donor islet transplantation is a proven therapy for preventing recurrent life-threatening hypoglycemia in type 1 diabetes. Although near-normal glucose levels and insulin independence can be maintained for many years following successful islet transplantation, restoration of normal functional β-cell mass has remained elusive. It has recently been proposed that dedifferentiation/plasticity towards other endocrine phenotypes may play an important role in stress-induced β-cell dysfunction in type 2 diabetes. Here we report loss of end-differentiated β-cell phenotype in 2 intraportal islet allotransplant recipients. Despite excellent graft function and sustained insulin independence, all examined insulin-positive cells had lost expression of the end-differentiation marker, urocortin-3, or appeared to co-express the α-cell marker, glucagon. In contrast, no insulin + /urocortin-3 - cells were seen in nondiabetic deceased donor control pancreatic islets. Loss of end-differentiated phenotype may facilitate β-cell survival during the stresses associated with islet isolation and culture, in addition to sustained hypoxia following engraftment. As further refinements in islet isolation and culture are made in parallel with exploration of alternative β-cell sources, graft sites, and ultimately fully vascularized bioengineered insulin-secreting microtissues, differentiation status immunostaining provides a novel tool to assess whether fully mature β-cell phenotype has been maintained. © 2017 The American Society of Transplantation and the American Society of Transplant Surgeons.

On Improving Efficiency of Differential Evolution for Aerodynamic Shape Optimization Applications

NASA Technical Reports Server (NTRS)

Madavan, Nateri K.

2004-01-01

Differential Evolution (DE) is a simple and robust evolutionary strategy that has been proven effective in determining the global optimum for several difficult optimization problems. Although DE offers several advantages over traditional optimization approaches, its use in applications such as aerodynamic shape optimization where the objective function evaluations are computationally expensive is limited by the large number of function evaluations often required. In this paper various approaches for improving the efficiency of DE are reviewed and discussed. These approaches are implemented in a DE-based aerodynamic shape optimization method that uses a Navier-Stokes solver for the objective function evaluations. Parallelization techniques on distributed computers are used to reduce turnaround times. Results are presented for the inverse design of a turbine airfoil. The efficiency improvements achieved by the different approaches are evaluated and compared.

Multiple Differential-Amplifier MMICs Embedded in Waveguides

NASA Technical Reports Server (NTRS)

Kangaslahti, Pekka; Schlecht, Erich

2010-01-01

Compact amplifier assemblies of a type now being developed for operation at frequencies of hundreds of gigahertz comprise multiple amplifier units in parallel arrangements to increase power and/or cascade arrangements to increase gains. Each amplifier unit is a monolithic microwave integrated circuit (MMIC) implementation of a pair of amplifiers in differential (in contradistinction to single-ended) configuration. Heretofore, in cascading amplifiers to increase gain, it has been common practice to interconnect the amplifiers by use of wires and/or thin films on substrates. This practice has not yielded satisfactory results at frequencies greater than 200 Hz, in each case, for either or both of two reasons: Wire bonds introduce large discontinuities. Because the interconnections are typically tens of wavelengths long, any impedance mismatches give rise to ripples in the gain-vs.-frequency response, which degrade the performance of the cascade.

Evolution of vertebrate sex chromosomes and dosage compensation.

PubMed

Graves, Jennifer A Marshall

2016-01-01

Differentiated sex chromosomes in mammals and other vertebrates evolved independently but in strikingly similar ways. Vertebrates with differentiated sex chromosomes share the problems of the unequal expression of the genes borne on sex chromosomes, both between the sexes and with respect to autosomes. Dosage compensation of genes on sex chromosomes is surprisingly variable - and can even be absent - in different vertebrate groups. Systems that compensate for different gene dosages include a wide range of global, regional and gene-by-gene processes that differ in their extent and their molecular mechanisms. However, many elements of these control systems are similar across distant phylogenetic divisions and show parallels to other gene silencing systems. These dosage systems cannot be identical by descent but were probably constructed from elements of ancient silencing mechanisms that are ubiquitous among vertebrates and shared throughout eukaryotes.

Identifying miRNA-mediated signaling subpathways by integrating paired miRNA/mRNA expression data with pathway topology.

PubMed

Vrahatis, Aristidis G; Dimitrakopoulos, Georgios N; Tsakalidis, Athanasios K; Bezerianos, Anastasios

2015-01-01

In the road for network medicine the newly emerged systems-level subpathway-based analysis methods offer new disease genes, drug targets and network-based biomarkers. In parallel, paired miRNA/mRNA expression data enable simultaneously monitoring of the micronome effect upon the signaling pathways. Towards this orientation, we present a methodological pipeline for the identification of differentially expressed subpathways along with their miRNA regulators by using KEGG signaling pathway maps, miRNA-target interactions and expression profiles from paired miRNA/mRNA experiments. Our pipeline offered new biological insights on a real application of paired miRNA/mRNA expression profiles with respect to the dynamic changes from colostrum to mature milk whey; several literature supported genes and miRNAs were recontextualized through miRNA-mediated differentially expressed subpathways.

Genetic analysis of rock hole and domestic Aedes aegypti on the Caribbean island of Anguilla.

PubMed

Wallis, G P; Tabachnick, W J

1990-12-01

Genetic variation was characterized at 11 enzyme coding loci in Aedes aegypti collected from 3 rock hole and 4 domestic sites on the island of Anguilla, West Indies. The pattern of gene frequency variation suggests that these mosquito samples do not constitute a single panmictic population, but there are no large consistent differences between rock hole and domestic forms to parallel the East African sylvan-domestic dichotomy. With the exception of one of the domestic populations, two loci did however show some gene frequency differences consistent with genetic differentiation between the 2 habitat types. We conclude that whereas there may be some degree of differentiation between the 2 habitat types, local eradication attempts and sporadic gene flow cause temporal and spatial volatility that is sufficient to swamp these differences.

The application of UV LEDs for differential optical absorption spectroscopy

NASA Astrophysics Data System (ADS)

Geiko, Pavel P.; Smirnov, Sergey S.; Samokhvalov, Ignatii V.

2018-04-01

Modern UV LEDs represent a potentially very advantageous alternative to thermal light sources, in particular xenon arc lamps, which are the most common light sources in trace gas-analyzers. So, the light-emitting diodes are very attractive for use of as light sources for Long Path Differential Optical Absorption Spectroscopy (DOAS) measurements of trace gases in the open atmosphere. Recent developments in fibre-coupling telescope technology and the availability of ultraviolet light emitting diodes have now allowed us to construct a portable, long path DOAS instrument for use at remote locations and specifically for measuring degassing from active volcanic systems. First of all, we are talking about the measurement of sulphur dioxide, carbon disulphide and, oxides of chlorine and bromine. The parallel measurements of sulfur dioxide using a certified gas analyzer, were conducted and showed good correlation.

Large Negative Differential of Heat Generation in a Two-Level Quantum Dot Coupled to Ferromagnetic Leads

NASA Astrophysics Data System (ADS)

Peng, Ya-Jing; Zheng, Jun; Chi, Feng

2015-12-01

Heat current exchanged between a two-level quantum dot (QD) and a phonon reservoir coupled to it is studied within the nonequilibrium Green's function method. We consider that the QD is connected to the left and right ferromagnetic leads. It is found that the negative differential of the heat generation (NDHG) phenomenon, i.e., the intensity of the heat generation decreases with increasing bias voltage, is obviously enhanced as compared to that in single-level QD system. The NDHG can emerge in the absence of the negative differential conductance of the electric current, and occurs in different bias voltage regions when the magnetic moments of the two leads are arranged in parallel or antiparallel configurations. The characteristics of the found phenomena can be understood by examining the change of the electron number on the dot. Supported by the National Natural Science Foundation of China under Grant No. 61274101 and the Liaoning Excellent Talents Programand (LJQ2013118), the Foundation of State Key Laboratory of Explosion Science and Technology of Beijing Institute of Technology (KFJJ14-08M)

Discussion summary: Fictitious domain methods

NASA Technical Reports Server (NTRS)

Glowinski, Rowland; Rodrigue, Garry

1991-01-01

Fictitious Domain methods are constructed in the following manner: Suppose a partial differential equation is to be solved on an open bounded set, Omega, in 2-D or 3-D. Let R be a rectangle domain containing the closure of Omega. The partial differential equation is first solved on R. Using the solution on R, the solution of the equation on Omega is then recovered by some procedure. The advantage of the fictitious domain method is that in many cases the solution of a partial differential equation on a rectangular region is easier to compute than on a nonrectangular region. Fictitious domain methods for solving elliptic PDEs on general regions are also very efficient when used on a parallel computer. The reason is that one can use the many domain decomposition methods that are available for solving the PDE on the fictitious rectangular region. The discussion on fictitious domain methods began with a talk by R. Glowinski in which he gave some examples of a variational approach to ficititious domain methods for solving the Helmholtz and Navier-Stokes equations.

Receptor for advanced glycation end-products is a marker of type I lung alveolar cells.

PubMed

Shirasawa, Madoka; Fujiwara, Naoyuki; Hirabayashi, Susumu; Ohno, Hideki; Iida, Junko; Makita, Koshi; Hata, Yutaka

2004-02-01

Lung alveolar epithelial cells are comprised of type I (ATI) and type II (ATII) cells. ATI cells are polarized, although they have very flat morphology. The identification of marker proteins for apical and basolateral membranes of ATI cells is important to investigate into the differentiation of ATI cells. In this paper, we characterized receptor for advanced glycation end-products (RAGE) as a marker for ATI cells. RAGE was localized on basolateral membranes of ATI cells in the immunoelectron microscopy and its expression was enhanced in a parallel manner to the differentiation of ATI cells in vivo and in primary cultures of ATII cells. RAGE and T1 alpha, a well-known ATI marker protein, were targeted to basolateral and apical membranes, respectively, when expressed in polarized Madine Darby canine kidney cells. Moreover, RAGE was expressed in ATI cells after T1 alpha in vivo and in ex in vivo organ cultures. In conclusion, RAGE is a marker for basolateral membranes of well-differentiated ATI cells. ATI cells require some signal provided by the in vivo environment to express RAGE.

Differential involvement of forearm muscles in ALS does not relate to sonographic structural nerve alterations.

PubMed

Schreiber, Stefanie; Schreiber, Frank; Debska-Vielhaber, Grazyna; Garz, Cornelia; Hensiek, Nathalie; Machts, Judith; Abdulla, Susanne; Dengler, Reinhard; Petri, Susanne; Nestor, Peter J; Vielhaber, Stefan

2018-07-01

We aimed to assess whether differential peripheral nerve involvement parallels dissociated forearm muscle weakness in amyotrophic lateral sclerosis (ALS). The analysis comprised 41 ALS patients and 18 age-, sex-, height- and weight-matched healthy controls. Strength of finger-extension and -flexion was measured using the Medical Research Council (MRC) scale. Radial, median and ulnar nerve sonographic cross-sectional area (CSA) and echogenicity, expressed by the hypoechoic fraction (HF), were determined. In ALS, finger extensors were significantly weaker than finger flexors. Sonographic evaluation revealed peripheral nerve atrophy, affecting various nerve segments in ALS. HF was unaltered. This systematic study confirmed a long-observed physical examination finding in ALS - weakness in finger-extension out of proportion to finger-flexion. This phenomenon was not related to any particular sonographic pattern of upper limb peripheral nerve alteration. In ALS, dissociated forearm muscle weakness could aid in the disease's diagnosis. Nerve ultrasound did not provide additional information on the differential involvement of finger-extension and finger-flexion strength. Copyright © 2018 International Federation of Clinical Neurophysiology. Published by Elsevier B.V. All rights reserved.

Mushroom body defect is required in parallel to Netrin for midline axon guidance in Drosophila

PubMed Central

Cate, Marie-Sophie; Gajendra, Sangeetha; Alsbury, Samantha; Raabe, Thomas; Tear, Guy; Mitchell, Kevin J.

2016-01-01

The outgrowth of many neurons within the central nervous system is initially directed towards or away from the cells lying at the midline. Recent genetic evidence suggests that a simple model of differential sensitivity to the conserved Netrin attractants and Slit repellents is insufficient to explain the guidance of all axons at the midline. In the Drosophila embryonic ventral nerve cord, many axons still cross the midline in the absence of the Netrin genes (NetA and NetB) or their receptor frazzled. Here we show that mutation of mushroom body defect (mud) dramatically enhances the phenotype of Netrin or frazzled mutants, resulting in many more axons failing to cross the midline, although mutations in mud alone have little effect. This suggests that mud, which encodes a microtubule-binding coiled-coil protein homologous to NuMA and LIN-5, is an essential component of a Netrin-independent pathway that acts in parallel to promote midline crossing. We demonstrate that this novel role of Mud in axon guidance is independent of its previously described role in neural precursor development. These studies identify a parallel pathway controlling midline guidance in Drosophila and highlight a novel role for Mud potentially acting downstream of Frizzled to aid axon guidance. PMID:26893348

A Comparison of PETSC Library and HPF Implementations of an Archetypal PDE Computation

NASA Technical Reports Server (NTRS)

Hayder, M. Ehtesham; Keyes, David E.; Mehrotra, Piyush

1997-01-01

Two paradigms for distributed-memory parallel computation that free the application programmer from the details of message passing are compared for an archetypal structured scientific computation a nonlinear, structured-grid partial differential equation boundary value problem using the same algorithm on the same hardware. Both paradigms, parallel libraries represented by Argonne's PETSC, and parallel languages represented by the Portland Group's HPF, are found to be easy to use for this problem class, and both are reasonably effective in exploiting concurrency after a short learning curve. The level of involvement required by the application programmer under either paradigm includes specification of the data partitioning (corresponding to a geometrically simple decomposition of the domain of the PDE). Programming in SPAM style for the PETSC library requires writing the routines that discretize the PDE and its Jacobian, managing subdomain-to-processor mappings (affine global- to-local index mappings), and interfacing to library solver routines. Programming for HPF requires a complete sequential implementation of the same algorithm, introducing concurrency through subdomain blocking (an effort similar to the index mapping), and modest experimentation with rewriting loops to elucidate to the compiler the latent concurrency. Correctness and scalability are cross-validated on up to 32 nodes of an IBM SP2.

A parallel domain decomposition-based implicit method for the Cahn–Hilliard–Cook phase-field equation in 3D

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zheng, Xiang; Yang, Chao; State Key Laboratory of Computer Science, Chinese Academy of Sciences, Beijing 100190

2015-03-15

We present a numerical algorithm for simulating the spinodal decomposition described by the three dimensional Cahn–Hilliard–Cook (CHC) equation, which is a fourth-order stochastic partial differential equation with a noise term. The equation is discretized in space and time based on a fully implicit, cell-centered finite difference scheme, with an adaptive time-stepping strategy designed to accelerate the progress to equilibrium. At each time step, a parallel Newton–Krylov–Schwarz algorithm is used to solve the nonlinear system. We discuss various numerical and computational challenges associated with the method. The numerical scheme is validated by a comparison with an explicit scheme of high accuracymore » (and unreasonably high cost). We present steady state solutions of the CHC equation in two and three dimensions. The effect of the thermal fluctuation on the spinodal decomposition process is studied. We show that the existence of the thermal fluctuation accelerates the spinodal decomposition process and that the final steady morphology is sensitive to the stochastic noise. We also show the evolution of the energies and statistical moments. In terms of the parallel performance, it is found that the implicit domain decomposition approach scales well on supercomputers with a large number of processors.« less

Range-wide parallel climate-associated genomic clines in Atlantic salmon

PubMed Central

Stanley, Ryan R. E.; Wringe, Brendan F.; Guijarro-Sabaniel, Javier; Bourret, Vincent; Bernatchez, Louis; Bentzen, Paul; Beiko, Robert G.; Gilbey, John; Clément, Marie; Bradbury, Ian R.

2017-01-01

Clinal variation across replicated environmental gradients can reveal evidence of local adaptation, providing insight into the demographic and evolutionary processes that shape intraspecific diversity. Using 1773 genome-wide single nucleotide polymorphisms we evaluated latitudinal variation in allele frequency for 134 populations of North American and European Atlantic salmon (Salmo salar). We detected 84 (4.74%) and 195 (11%) loci showing clinal patterns in North America and Europe, respectively, with 12 clinal loci in common between continents. Clinal single nucleotide polymorphisms were evenly distributed across the salmon genome and logistic regression revealed significant associations with latitude and seasonal temperatures, particularly average spring temperature in both continents. Loci displaying parallel clines were associated with several metabolic and immune functions, suggesting a potential basis for climate-associated adaptive differentiation. These climate-based clines collectively suggest evidence of large-scale environmental associated differences on either side of the North Atlantic. Our results support patterns of parallel evolution on both sides of the North Atlantic, with evidence of both similar and divergent underlying genetic architecture. The identification of climate-associated genomic clines illuminates the role of selection and demographic processes on intraspecific diversity in this species and provides a context in which to evaluate the impacts of climate change. PMID:29291123

Spermatogenesis in Animals as Revealed by Electron Microscopy

PubMed Central

Yasuzumi, G.; Tanaka, Hiroaki

1958-01-01

This paper reports an electron microscope study of typical and atypical spermatogenesis in the pond snail, Cipangopaludina malteata. In the typical spermatid the nucleus undergoes profound changes as development proceeds, affecting both its form and internal fine structure. A large number of roughly parallel, dense filaments, arranged along the long axis of the nucleus, fuse with each other to form in the end the homogeneous helical body characteristic of the head of the adult spermatozoa. The nebenkern is apparently mitochondrial in nature and, in its early development, is similar to that of insects except that it appears as a double structure from the beginning. As differentiation proceeds, the mitochondria lose their membranes, and the residual, now denuded cristae, reorganize to give a parallel radial arrangement. In the last stages of development, the nebenkern derivations become applied to the sheath of the middle piece in a compact helical fashion. In the development of the atypical spermatozoa, the nucleus fails to differentiate and simply shrinks in volume until only a remnant, devoid of DNA, is left. The cytoplasm shows numerous vesicles containing small Feulgen-positive bodies, 80 to 130 mµ in diameter. These vesicles plus contents increase in number as spermatogenesis proceeds. The "head" structure of the atypical spermatozoa consists of a bundle (7 to 17) of tail flagella, each with a centriole at its anterior end. The end-piece of the atypical form appears brush-like and is made up of the free ends of the several flagella. PMID:13587559

A survey of cellulose microfibril patterns in dividing, expanding, and differentiating cells of Arabidopsis thaliana.

PubMed

Fujita, Miki; Wasteneys, Geoffrey O

2014-05-01

Cellulose microfibrils are critical for plant cell specialization and function. Recent advances in live cell imaging of fluorescently tagged cellulose synthases to track cellulose synthesis have greatly advanced our understanding of cellulose biosynthesis. Nevertheless, cellulose deposition patterns remain poorly described in many cell types, including those in the process of division or differentiation. In this study, we used field emission scanning electron microscopy analysis of cryo-planed tissues to determine the arrangement of cellulose microfibrils in various faces of cells undergoing cytokinesis or specialized development, including cell types in which cellulose cannot be imaged by conventional approaches. In dividing cells, we detected microfibrillar meshworks in the cell plates, consistent with the concentration at the cell plate of cellulose synthase complexes, as detected by fluorescently tagged CesA6. We also observed a loss of parallel cellulose microfibril orientation in walls of the mother cell during cytokinesis, which corresponded with the loss of fluorescently tagged cellulose synthase complexes from these surfaces. In recently formed guard cells, microfibrils were randomly organized and only formed a highly ordered circumferential pattern after pore formation. In pit fields, cellulose microfibrils were arranged in circular patterns around plasmodesmata. Microfibrils were random in most cotyledon cells except the epidermis and were parallel to the growth axis in trichomes. Deposition of cellulose microfibrils was spatially delineated in metaxylem and protoxylem cells of the inflorescence stem, supporting recent studies on microtubule exclusion mechanisms.

Becoming organisms: the organisation of development and the development of organisation.

PubMed

de la Rosa, Laura Nuño

2010-01-01

Despite the radical importance of embryology in the development of organicism, developmental biology remains philosophically underexplored as a theoretical and empirical resource to clarify the nature of organisms. This paper discusses how embryology can help develop the organisational definition of the organism as a differentiated, functionally integrated, and autonomous system. I distinguish two conceptions of development in the organisational tradition that yield two different conceptions of the organism: the life-history view claims that organisms can be considered as such during their whole ontogeny; the constitutive view distinguishes two periods in the life history, a period of generation and a period of self-maintenance of a constitutive organisation. Arguing in favour of the constitutive view, it will be claimed that the organisational criteria for the definition of organism (i.e., differentiation, functional integration, and autonomy) can only be applied to the developmental system when it has entered the period of self-maintenance of a constitutive organisation. Under the light of current research in developmental biology, it is possible to make explicit how organisms come to be as organisms. To this end, I explore key ontogenetic events that help us clarify the core aspects of animal organisation and allow us to identify the developmental stage that marks the ontological transition between an organism in potency and an organism in actuality. The structure of this ontogenetic unfolding parallels the conceptual structure of the very notion of organism; the generation of the being of a particular organism parallels its definition.

Monitoring the Wet-Heat Inactivation Dynamics of Single Spores of Bacillus Species by Using Raman Tweezers, Differential Interference Contrast Microscopy, and Nucleic Acid Dye Fluorescence Microscopy▿

PubMed Central

Zhang, Pengfei; Kong, Lingbo; Wang, Guiwen; Setlow, Peter; Li, Yong-qing

2011-01-01

Dynamic processes during wet-heat treatment of individual spores of Bacillus cereus, Bacillus megaterium, and Bacillus subtilis at 80 to 90°C were investigated using dual-trap Raman spectroscopy, differential interference contrast (DIC) microscopy, and nucleic acid stain (SYTO 16) fluorescence microscopy. During spore wet-heat treatment, while the spores' 1:1 chelate of Ca2+ with dipicolinic acid (CaDPA) was released rapidly at a highly variable time Tlag, the levels of spore nucleic acids remained nearly unchanged, and the Tlag times for individual spores from the same preparation were increased somewhat as spore levels of CaDPA increased. The brightness of the spores' DIC image decreased by ∼50% in parallel with CaDPA release, and there was no spore cortex hydrolysis observed. The lateral diameters of the spores' DIC image and SYTO 16 fluorescence image also decreased in parallel with CaDPA release. The SYTO 16 fluorescence intensity began to increase during wet-heat treatment at a time before Tlag and reached maximum at a time slightly later than Trelease. However, the fluorescence intensities of wet-heat-inactivated spores were ∼15-fold lower than those of nutrient-germinated spores, and this low SYTO 16 fluorescence intensity may be due in part to the low permeability of the dormant spores' inner membranes to SYTO 16 and in part to nucleic acid denaturation during the wet-heat treatment. PMID:21602365

Xenopus Bicaudal-C Is Required for the Differentiation of the Amphibian Pronephros

PubMed Central

Tran, Uyen; Mary Pickney, L.; Duygu Özpolat, B.; Wessely, Oliver

2007-01-01

The RNA-binding molecule Bicaudal-C regulates embryonic development in Drosophila and Xenopus. Interestingly, mouse mutants of Bicaudal-C do not show early patterning defects, but instead develop polycystic kidney disease (PKD). To further investigate the molecular mechanism of Bicaudal-C in kidney development, we analyzed its function in the developing amphibian pronephros. Bicaudal-C mRNA was present in the epithelial structures of the Xenopus pronephros, the tubules and the duct, but not the glomus. Inhibition of the translation of endogenous Bicaudal-C with antisense morpholino oligomers (xBic-C-MO) led to a PKD-like phenotype in Xenopus. Embryos lacking Bicaudal-C developed generalized edemas and dilated pronephric tubules and ducts. This phenotype was caused by impaired differentiation of the pronephros. Molecular markers specifically expressed in the late distal tubule were absent in xBic-C-MO-injected embryos. Furthermore, Bicaudal-C was not required for primary cilia formation, an important organelle affected in PKD. These data support the idea that Bicaudal-C functions downstream or parallel of a cilia-regulated signaling pathway. This pathway is required for terminal differentiation of the late distal tubule of the Xenopus pronephros and regulates renal epithelial cell differentiation, which - when disrupted - results in PKD. PMID:17521625

Resolving quandaries: basaloid adenoid cystic carcinoma or breast cylindroma? The role of massively parallel sequencing.

PubMed

Fusco, Nicola; Colombo, Pierre-Emmanuel; Martelotto, Luciano G; De Filippo, Maria R; Piscuoglio, Salvatore; Ng, Charlotte K Y; Lim, Raymond S; Jacot, William; Vincent-Salomon, Anne; Reis-Filho, Jorge S; Weigelt, Britta

2016-01-01

The aims of this study were to perform a whole-exome sequencing analysis of a breast cylindroma and to investigate the role of molecular analyses in the differentiation between breast cylindroma, a benign tumour that displays MYB expression, and CYLD gene mutations, and its main differential diagnosis, the breast solid-basaloid adenoid cystic carcinoma, a malignant tumour that is characterized by the presence of the MYB-NFIB fusion gene and MYB overexpression. A 66-year-old female underwent quadrantectomy after an irregular dense shadow was discovered in the right breast at the screening mammogram. Histologically, the tumour displayed features suggestive of a solid-basaloid variant of adenoid cystic carcinoma with a differential diagnosis of cylindroma. Fluorescence in situ hybridization, reverse transcription-polymerase chain reaction, immunohistochemistry and whole-exome sequencing revealed absence of the MYB-NFIB fusion gene, low levels of MYB protein expression and a clonal somatic CYLD splice site mutation associated with loss of heterozygosity of the wild-type allele. The results of the histological, immunohistochemical and molecular analyses were consistent with a diagnosis of breast cylindroma, providing a proof-of-principle that the integration of histopathological and molecular approaches can help to differentiate between a low-malignant potential and a benign breast tumour of triple-negative phenotype. © 2015 John Wiley & Sons Ltd.

Superelement model based parallel algorithm for vehicle dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Agrawal, O.P.; Danhof, K.J.; Kumar, R.

1994-05-01

This paper presents a superelement model based parallel algorithm for a planar vehicle dynamics. The vehicle model is made up of a chassis and two suspension systems each of which consists of an axle-wheel assembly and two trailing arms. In this model, the chassis is treated as a Cartesian element and each suspension system is treated as a superelement. The parameters associated with the superelements are computed using an inverse dynamics technique. Suspension shock absorbers and the tires are modeled by nonlinear springs and dampers. The Euler-Lagrange approach is used to develop the system equations of motion. This leads tomore » a system of differential and algebraic equations in which the constraints internal to superelements appear only explicitly. The above formulation is implemented on a multiprocessor machine. The numerical flow chart is divided into modules and the computation of several modules is performed in parallel to gain computational efficiency. In this implementation, the master (parent processor) creates a pool of slaves (child processors) at the beginning of the program. The slaves remain in the pool until they are needed to perform certain tasks. Upon completion of a particular task, a slave returns to the pool. This improves the overall response time of the algorithm. The formulation presented is general which makes it attractive for a general purpose code development. Speedups obtained in the different modules of the dynamic analysis computation are also presented. Results show that the superelement model based parallel algorithm can significantly reduce the vehicle dynamics simulation time. 52 refs.« less

Aerodynamic Shape Optimization of Supersonic Aircraft Configurations via an Adjoint Formulation on Parallel Computers

NASA Technical Reports Server (NTRS)

Reuther, James; Alonso, Juan Jose; Rimlinger, Mark J.; Jameson, Antony

1996-01-01

This work describes the application of a control theory-based aerodynamic shape optimization method to the problem of supersonic aircraft design. The design process is greatly accelerated through the use of both control theory and a parallel implementation on distributed memory computers. Control theory is employed to derive the adjoint differential equations whose solution allows for the evaluation of design gradient information at a fraction of the computational cost required by previous design methods. The resulting problem is then implemented on parallel distributed memory architectures using a domain decomposition approach, an optimized communication schedule, and the MPI (Message Passing Interface) Standard for portability and efficiency. The final result achieves very rapid aerodynamic design based on higher order computational fluid dynamics methods (CFD). In our earlier studies, the serial implementation of this design method was shown to be effective for the optimization of airfoils, wings, wing-bodies, and complex aircraft configurations using both the potential equation and the Euler equations. In our most recent paper, the Euler method was extended to treat complete aircraft configurations via a new multiblock implementation. Furthermore, during the same conference, we also presented preliminary results demonstrating that this basic methodology could be ported to distributed memory parallel computing architectures. In this paper, our concern will be to demonstrate that the combined power of these new technologies can be used routinely in an industrial design environment by applying it to the case study of the design of typical supersonic transport configurations. A particular difficulty of this test case is posed by the propulsion/airframe integration.

Parallel Evolution of Cold Tolerance within Drosophila melanogaster

PubMed Central

Braun, Dylan T.; Lack, Justin B.

2017-01-01

Drosophila melanogaster originated in tropical Africa before expanding into strikingly different temperate climates in Eurasia and beyond. Here, we find elevated cold tolerance in three distinct geographic regions: beyond the well-studied non-African case, we show that populations from the highlands of Ethiopia and South Africa have significantly increased cold tolerance as well. We observe greater cold tolerance in outbred versus inbred flies, but only in populations with higher inversion frequencies. Each cold-adapted population shows lower inversion frequencies than a closely-related warm-adapted population, suggesting that inversion frequencies may decrease with altitude in addition to latitude. Using the FST-based “Population Branch Excess” statistic (PBE), we found only limited evidence for parallel genetic differentiation at the scale of ∼4 kb windows, specifically between Ethiopian and South African cold-adapted populations. And yet, when we looked for single nucleotide polymorphisms (SNPs) with codirectional frequency change in two or three cold-adapted populations, strong genomic enrichments were observed from all comparisons. These findings could reflect an important role for selection on standing genetic variation leading to “soft sweeps”. One SNP showed sufficient codirectional frequency change in all cold-adapted populations to achieve experiment-wide significance: an intronic variant in the synaptic gene Prosap. Another codirectional outlier SNP, at senseless-2, had a strong association with our cold trait measurements, but in the opposite direction as predicted. More generally, proteins involved in neurotransmission were enriched as potential targets of parallel adaptation. The ability to study cold tolerance evolution in a parallel framework will enhance this classic study system for climate adaptation. PMID:27777283

Signal processing method of the diameter measurement system based on CCD parallel light projection method

NASA Astrophysics Data System (ADS)

Song, Qing; Zhu, Sijia; Yan, Han; Wu, Wenqian

2008-03-01

Parallel light projection method for the diameter measurement is to project the workpiece to be measured on the photosensitive units of CCD, but the original signal output from CCD cannot be directly used for counting or measurement. The weak signal with high-frequency noise should be filtered and amplified firstly. This paper introduces RC low-pass filter and multiple feed-back second-order low-pass filter with infinite gain. Additionally there is always dispersion on the light band and the output signal has a transition between the irradiant area and the shadow, because of the instability of the light source intensity and the imperfection of the light system adjustment. To obtain exactly the shadow size related to the workpiece diameter, binary-value processing is necessary to achieve a square wave. Comparison method and differential method can be adopted for binary-value processing. There are two ways to decide the threshold value when using voltage comparator: the fixed level method and the floated level method. The latter has a high accuracy. Deferential method is to output two spike pulses with opposite pole by the rising edge and the failing edge of the video signal related to the differential circuit firstly, then the rising edge of the signal output from the differential circuit is acquired by half-wave rectifying circuit. After traveling through the zero passing comparator and the maintain- resistance edge trigger, the square wave which indicates the measured size is acquired at last. And then it is used for filling through standard pulses and for counting through the counter. Data acquisition and information processing is accomplished by the computer and the control software. This paper will introduce in detail the design and analysis of the filter circuit, binary-value processing circuit and the interface circuit towards the computer.

The regulation of mitochondrial transcription factor A (Tfam) expression during skeletal muscle cell differentiation.

PubMed

Collu-Marchese, Melania; Shuen, Michael; Pauly, Marion; Saleem, Ayesha; Hood, David A

2015-05-19

The ATP demand required for muscle development is accommodated by elevations in mitochondrial biogenesis, through the co-ordinated activities of the nuclear and mitochondrial genomes. The most important transcriptional activator of the mitochondrial genome is mitochondrial transcription factor A (Tfam); however, the regulation of Tfam expression during muscle differentiation is not known. Thus, we measured Tfam mRNA levels, mRNA stability, protein expression and localization and Tfam transcription during the progression of muscle differentiation. Parallel 2-fold increases in Tfam protein and mRNA were observed, corresponding with 2-3-fold increases in mitochondrial content. Transcriptional activity of a 2051 bp promoter increased during this differentiation period and this was accompanied by a 3-fold greater Tfam mRNA stabilization. Interestingly, truncations of the promoter at 1706 bp, 978 bp and 393 bp promoter all exhibited 2-3-fold higher transcriptional activity than the 2051 bp construct, indicating the presence of negative regulatory elements within the distal 350 bp of the promoter. Activation of AMP kinase augmented Tfam transcription within the proximal promoter, suggesting the presence of binding sites for transcription factors that are responsive to cellular energy state. During differentiation, the accumulating Tfam protein was progressively distributed to the mitochondrial matrix where it augmented the expression of mtDNA and COX (cytochrome c oxidase) subunit I, an mtDNA gene product. Our data suggest that, during muscle differentiation, Tfam protein levels are regulated by the availability of Tfam mRNA, which is controlled by both transcription and mRNA stability. Changes in energy state and Tfam localization also affect Tfam expression and action in differentiating myotubes. © 2015 Authors.

A model of early human embryonic stem cell differentiation reveals inter- and intracellular changes on transition to squamous epithelium.

PubMed

Galat, Vasiliy; Malchenko, Sergey; Galat, Yekaterina; Ishkin, Alex; Nikolsky, Yuri; Kosak, Steven T; Soares, Bento Marcelo; Iannaccone, Philip; Crispino, John D; Hendrix, Mary J C

2012-05-20

The molecular events leading to human embryonic stem cell (hESC) differentiation are the subject of considerable scrutiny. Here, we characterize an in vitro model that permits analysis of the earliest steps in the transition of hESC colonies to squamous epithelium on basic fibroblast growth factor withdrawal. A set of markers (GSC, CK18, Gata4, Eomes, and Sox17) point to a mesendodermal nature of the epithelial cells with subsequent commitment to definitive endoderm (Sox17, Cdx2, nestin, and Islet1). We assayed alterations in the transcriptome in parallel with the distribution of immunohistochemical markers. Our results indicate that the alterations of tight junctions in pluripotent culture precede the beginning of differentiation. We defined this cell population as "specified," as it is committed toward differentiation. The transitional zone between "specified" pluripotent and differentiated cells displays significant up-regulation of keratin-18 (CK18) along with a decrease in the functional activity of gap junctions and the down-regulation of 2 gap junction proteins, connexin 43 (Cx43) and connexin 45 (Cx45), which is coincidental with substantial elevation of intracellular Ca2+ levels. These findings reveal a set of cellular changes that may represent the earliest markers of in vitro hESC transition to an epithelial phenotype, before the induction of gene expression networks that guide hESC differentiation. Moreover, we hypothesize that these events may be common during the primary steps of hESC commitment to functionally varied epithelial tissue derivatives of different embryological origins.

A Model of Early Human Embryonic Stem Cell Differentiation Reveals Inter- and Intracellular Changes on Transition to Squamous Epithelium

PubMed Central

Malchenko, Sergey; Galat, Yekaterina; Ishkin, Alex; Nikolsky, Yuri; Kosak, Steven T.; Soares, Bento Marcelo; Iannaccone, Philip; Crispino, John D.; Hendrix, Mary J.C.

2012-01-01

The molecular events leading to human embryonic stem cell (hESC) differentiation are the subject of considerable scrutiny. Here, we characterize an in vitro model that permits analysis of the earliest steps in the transition of hESC colonies to squamous epithelium on basic fibroblast growth factor withdrawal. A set of markers (GSC, CK18, Gata4, Eomes, and Sox17) point to a mesendodermal nature of the epithelial cells with subsequent commitment to definitive endoderm (Sox17, Cdx2, nestin, and Islet1). We assayed alterations in the transcriptome in parallel with the distribution of immunohistochemical markers. Our results indicate that the alterations of tight junctions in pluripotent culture precede the beginning of differentiation. We defined this cell population as “specified,” as it is committed toward differentiation. The transitional zone between “specified” pluripotent and differentiated cells displays significant up-regulation of keratin-18 (CK18) along with a decrease in the functional activity of gap junctions and the down-regulation of 2 gap junction proteins, connexin 43 (Cx43) and connexin 45 (Cx45), which is coincidental with substantial elevation of intracellular Ca2+ levels. These findings reveal a set of cellular changes that may represent the earliest markers of in vitro hESC transition to an epithelial phenotype, before the induction of gene expression networks that guide hESC differentiation. Moreover, we hypothesize that these events may be common during the primary steps of hESC commitment to functionally varied epithelial tissue derivatives of different embryological origins. PMID:21861759

Tracing the first step to speciation: ecological and genetic differentiation of a salamander population in a small forest.

PubMed

Steinfartz, Sebastian; Weitere, Markus; Tautz, Diethard

2007-11-01

Mechanisms and processes of ecologically driven adaptive speciation are best studied in natural situations where the splitting process is still occurring, i.e. before complete reproductive isolation is achieved. Here, we present a case of an early stage of adaptive differentiation under sympatric conditions in the fire salamander, Salamandra salamandra, that allows inferring the underlying processes for the split. Larvae of S. salamandra normally mature in small streams until metamorphosis, but in an old, continuous forest area near Bonn (the Kottenforst), we found salamander larvae not only in small streams but also in shallow ponds, which are ecologically very different from small streams. Common-environment experiments with larvae from both habitat types reveal specific adaptations to these different ecological conditions. Mitochondrial and microsatellite analyses show that the two ecologically differentiated groups also show signs of genetic differentiation. A parallel analysis of animals from a neighbouring much larger forest area (the Eifel), in which larvae mature only in streams, shows no signs of genetic differentiation, indicating that gene flow between ecologically similar types can occur over large distances. Hence, geographical factors cannot explain the differential larval habitat adaptations in the Kottenforst, in particular since adult life and mating of S. salamandra is strictly terrestrial and not associated with larval habitats. We propose therefore that the evolution of these adaptations was coupled with the evolution of cues for assortative mating which would be in line with models of sympatric speciation that suggest a co-evolution of habitat adaptations and associated mating signals.

Temperature gradient affects differentiation of gene expression and SNP allele frequencies in the dominant Lake Baikal zooplankton species.

PubMed

Bowman, Larry L; Kondrateva, Elizaveta S; Timofeyev, Maxim A; Yampolsky, Lev Y

2018-06-01

Local adaptation and phenotypic plasticity are main mechanisms of organisms' resilience in changing environments. Both are affected by gene flow and are expected to be weak in zooplankton populations inhabiting large continuous water bodies and strongly affected by currents. Lake Baikal, the deepest and one of the coldest lakes on Earth, experienced epilimnion temperature increase during the last 100 years, exposing Baikal's zooplankton to novel selective pressures. We obtained a partial transcriptome of Epischura baikalensis (Copepoda: Calanoida), the dominant component of Baikal's zooplankton, and estimated SNP allele frequencies and transcript abundances in samples from regions of Baikal that differ in multiyear average surface temperatures. The strongest signal in both SNP and transcript abundance differentiation is the SW-NE gradient along the 600+ km long axis of the lake, suggesting isolation by distance. SNP differentiation is stronger for nonsynonymous than synonymous SNPs and is paralleled by differential survival during a laboratory exposure to increased temperature, indicating directional selection operating on the temperature gradient. Transcript abundance, generally collinear with the SNP differentiation, shows samples from the warmest, less deep location clustering together with the southernmost samples. Differential expression is more frequent among transcripts orthologous to candidate thermal response genes previously identified in model arthropods, including genes encoding cytoskeleton proteins, heat-shock proteins, proteases, enzymes of central energy metabolism, lipid and antioxidant pathways. We conclude that the pivotal endemic zooplankton species in Lake Baikal exists under temperature-mediated selection and possesses both genetic variation and plasticity to respond to novel temperature-related environmental pressures. © 2018 John Wiley & Sons Ltd.

Ontogeny of surface markers on functionally distinct T cell subsets in the chicken.

PubMed

Traill, K N; Böck, G; Boyd, R L; Ratheiser, K; Wick, G

1984-01-01

Three subsets of chicken peripheral T cells (T1, T2 and T3) have been identified in peripheral blood of adult chickens on the basis of fluorescence intensity after staining with certain xenogeneic anti-thymus cell sera (from turkeys and rabbits). They differentiate between 3-10 weeks of age in parallel with development of responsiveness to the mitogens concanavalin A (Con A), phytohemagglutinin (PHA) and pokeweed mitogen (PWM). Functional tests on the T subsets, sorted with a fluorescence-activated cell sorter, have shown that T2, 3 cells respond to Con A, PHA and PWM and are capable of eliciting a graft-vs.-host reaction (GvHR). In contrast, although T1 cells respond to Con A, they respond poorly to PHA and not at all to PWM or in GvHR. There was some indication of cooperation between T1 and T2,3 cells for the PHA response. Parallels between these chicken subsets and helper and suppressor/cytotoxic subsets in mammalian systems are discussed.

Turbine blade tip flow discouragers

DOEpatents

Bunker, Ronald Scott

2000-01-01

A turbine assembly comprises a plurality of rotating blade portions in a spaced relation with a stationery shroud. The rotating blade portions comprise a root section, a tip portion and an airfoil. The tip portion has a pressure side wall and a suction side wall. A number of flow discouragers are disposed on the blade tip portion. In one embodiment, the flow discouragers extend circumferentially from the pressure side wall to the suction side wall so as to be aligned generally parallel to the direction of rotation. In an alternative embodiment, the flow discouragers extend circumferentially from the pressure side wall to the suction side wall so as to be aligned at an angle in the range between about 0.degree. to about 60.degree. with respect to a reference axis aligned generally parallel to the direction of rotation. The flow discouragers increase the flow resistance and thus reduce the flow of hot gas flow leakage for a given pressure differential across the blade tip portion so as to improve overall turbine efficiency.

A set of parallel, implicit methods for a reconstructed discontinuous Galerkin method for compressible flows on 3D hybrid grids

DOE PAGES

Xia, Yidong; Luo, Hong; Frisbey, Megan; ...

2014-07-01

A set of implicit methods are proposed for a third-order hierarchical WENO reconstructed discontinuous Galerkin method for compressible flows on 3D hybrid grids. An attractive feature in these methods are the application of the Jacobian matrix based on the P1 element approximation, resulting in a huge reduction of memory requirement compared with DG (P2). Also, three approaches -- analytical derivation, divided differencing, and automatic differentiation (AD) are presented to construct the Jacobian matrix respectively, where the AD approach shows the best robustness. A variety of compressible flow problems are computed to demonstrate the fast convergence property of the implemented flowmore » solver. Furthermore, an SPMD (single program, multiple data) programming paradigm based on MPI is proposed to achieve parallelism. The numerical results on complex geometries indicate that this low-storage implicit method can provide a viable and attractive DG solution for complicated flows of practical importance.« less

An Implicit Solver on A Parallel Block-Structured Adaptive Mesh Grid for FLASH

NASA Astrophysics Data System (ADS)

Lee, D.; Gopal, S.; Mohapatra, P.

2012-07-01

We introduce a fully implicit solver for FLASH based on a Jacobian-Free Newton-Krylov (JFNK) approach with an appropriate preconditioner. The main goal of developing this JFNK-type implicit solver is to provide efficient high-order numerical algorithms and methodology for simulating stiff systems of differential equations on large-scale parallel computer architectures. A large number of natural problems in nonlinear physics involve a wide range of spatial and time scales of interest. A system that encompasses such a wide magnitude of scales is described as "stiff." A stiff system can arise in many different fields of physics, including fluid dynamics/aerodynamics, laboratory/space plasma physics, low Mach number flows, reactive flows, radiation hydrodynamics, and geophysical flows. One of the big challenges in solving such a stiff system using current-day computational resources lies in resolving time and length scales varying by several orders of magnitude. We introduce FLASH's preliminary implementation of a time-accurate JFNK-based implicit solver in the framework of FLASH's unsplit hydro solver.

Acceleration of the Particle Swarm Optimization for Peierls–Nabarro modeling of dislocations in conventional and high-entropy alloys

DOE PAGES

Pei, Zongrui; Max-Planck-Inst. fur Eisenforschung, Duseldorf; Eisenbach, Markus

2017-02-06

Dislocations are among the most important defects in determining the mechanical properties of both conventional alloys and high-entropy alloys. The Peierls-Nabarro model supplies an efficient pathway to their geometries and mobility. The difficulty in solving the integro-differential Peierls-Nabarro equation is how to effectively avoid the local minima in the energy landscape of a dislocation core. Among the other methods to optimize the dislocation core structures, we choose the algorithm of Particle Swarm Optimization, an algorithm that simulates the social behaviors of organisms. By employing more particles (bigger swarm) and more iterative steps (allowing them to explore for longer time), themore » local minima can be effectively avoided. But this would require more computational cost. The advantage of this algorithm is that it is readily parallelized in modern high computing architecture. We demonstrate the performance of our parallelized algorithm scales linearly with the number of employed cores.« less

A solution to neural field equations by a recurrent neural network method

NASA Astrophysics Data System (ADS)

Alharbi, Abir

2012-09-01

Neural field equations (NFE) are used to model the activity of neurons in the brain, it is introduced from a single neuron 'integrate-and-fire model' starting point. The neural continuum is spatially discretized for numerical studies, and the governing equations are modeled as a system of ordinary differential equations. In this article the recurrent neural network approach is used to solve this system of ODEs. This consists of a technique developed by combining the standard numerical method of finite-differences with the Hopfield neural network. The architecture of the net, energy function, updating equations, and algorithms are developed for the NFE model. A Hopfield Neural Network is then designed to minimize the energy function modeling the NFE. Results obtained from the Hopfield-finite-differences net show excellent performance in terms of accuracy and speed. The parallelism nature of the Hopfield approaches may make them easier to implement on fast parallel computers and give them the speed advantage over the traditional methods.

Final Report: Subcontract B623868 Algebraic Multigrid solvers for coupled PDE systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brannick, J.

The Pennsylvania State University (“Subcontractor”) continued to work on the design of algebraic multigrid solvers for coupled systems of partial differential equations (PDEs) arising in numerical modeling of various applications, with a main focus on solving the Dirac equation arising in Quantum Chromodynamics (QCD). The goal of the proposed work was to develop combined geometric and algebraic multilevel solvers that are robust and lend themselves to efficient implementation on massively parallel heterogeneous computers for these QCD systems. The research in these areas built on previous works, focusing on the following three topics: (1) the development of parallel full-multigrid (PFMG) andmore » non-Galerkin coarsening techniques in this frame work for solving the Wilson Dirac system; (2) the use of these same Wilson MG solvers for preconditioning the Overlap and Domain Wall formulations of the Dirac equation; and (3) the design and analysis of algebraic coarsening algorithms for coupled PDE systems including Stokes equation, Maxwell equation and linear elasticity.« less

Clinical implications of parallel visual pathways.

PubMed

Bassi, C J; Lehmkuhle, S

1990-02-01

Visual information travels from the retina to visual cortical areas along at least two parallel pathways. In this paper, anatomical and physiological evidence is presented to demonstrate the existence of, and trace these two pathways throughout the visual systems of the cat, primate, and human. Physiological and behavioral experiments are discussed which establish that these two pathways are differentially sensitive to stimuli that vary in spatial and temporal frequency. One pathway (M-pathway) is more sensitive to coarse visual form that is modulated or moving at fast rates, whereas the other pathway (P-pathway) is more sensitive to spatial detail that is stationary or moving at slow rates. This difference between the M- and P-pathways is related to some spatial and temporal effects observed in humans. Furthermore, evidence is presented that certain diseases selectively comprise the functioning of M- or P-pathways (i.e., glaucoma, Alzheimer's disease, and anisometropic amblyopia), and some of the spatial and temporal deficits observed in these patients are presented within the context of the dysfunction of the M- or P-pathway.

Pyrolysis kinetics of algal consortia grown using swine manure wastewater.

PubMed

Sharara, Mahmoud A; Holeman, Nathan; Sadaka, Sammy S; Costello, Thomas A

2014-10-01

In this study, pyrolysis kinetics of periphytic microalgae consortia grown using swine manure slurry in two seasonal climatic patterns in northwest Arkansas were investigated. Four heating rates (5, 10, 20 and 40 °C min(-1)) were used to determine the pyrolysis kinetics. Differences in proximate, ultimate, and heating value analyses reflected variability in growing substrate conditions, i.e., flocculant use, manure slurry dilution, and differences in diurnal solar radiation and air temperature regimes. Peak decomposition temperature in algal harvests varied with changing the heating rate. Analyzing pyrolysis kinetics using differential and integral isoconversional methods (Friedman, Flynn-Wall-Ozawa, and Kissinger-Akahira-Sunose) showed strong dependency of apparent activation energy on the degree of conversion suggesting parallel reaction scheme. Consequently, the weight loss data in each thermogravimetric test was modeled using independent parallel reactions (IPR). The quality of fit (QOF) for the model ranged between 2.09% and 3.31% indicating a good agreement with the experimental data. Copyright © 2014 Elsevier Ltd. All rights reserved.

Π4U: A high performance computing framework for Bayesian uncertainty quantification of complex models

NASA Astrophysics Data System (ADS)

Hadjidoukas, P. E.; Angelikopoulos, P.; Papadimitriou, C.; Koumoutsakos, P.

2015-03-01

We present Π4U, an extensible framework, for non-intrusive Bayesian Uncertainty Quantification and Propagation (UQ+P) of complex and computationally demanding physical models, that can exploit massively parallel computer architectures. The framework incorporates Laplace asymptotic approximations as well as stochastic algorithms, along with distributed numerical differentiation and task-based parallelism for heterogeneous clusters. Sampling is based on the Transitional Markov Chain Monte Carlo (TMCMC) algorithm and its variants. The optimization tasks associated with the asymptotic approximations are treated via the Covariance Matrix Adaptation Evolution Strategy (CMA-ES). A modified subset simulation method is used for posterior reliability measurements of rare events. The framework accommodates scheduling of multiple physical model evaluations based on an adaptive load balancing library and shows excellent scalability. In addition to the software framework, we also provide guidelines as to the applicability and efficiency of Bayesian tools when applied to computationally demanding physical models. Theoretical and computational developments are demonstrated with applications drawn from molecular dynamics, structural dynamics and granular flow.

On Improving Efficiency of Differential Evolution for Aerodynamic Shape Optimization Applications

NASA Technical Reports Server (NTRS)

Madavan, Nateri K.

2004-01-01

Differential Evolution (DE) is a simple and robust evolutionary strategy that has been provEn effective in determining the global optimum for several difficult optimization problems. Although DE offers several advantages over traditional optimization approaches, its use in applications such as aerodynamic shape optimization where the objective function evaluations are computationally expensive is limited by the large number of function evaluations often required. In this paper various approaches for improving the efficiency of DE are reviewed and discussed. Several approaches that have proven effective for other evolutionary algorithms are modified and implemented in a DE-based aerodynamic shape optimization method that uses a Navier-Stokes solver for the objective function evaluations. Parallelization techniques on distributed computers are used to reduce turnaround times. Results are presented for standard test optimization problems and for the inverse design of a turbine airfoil. The efficiency improvements achieved by the different approaches are evaluated and compared.

Analog-to-digital conversion techniques for precision photometry

NASA Technical Reports Server (NTRS)

Opal, Chet B.

1988-01-01

Three types of analog-to-digital converters are described: parallel, successive-approximation, and integrating. The functioning of comparators and sample-and-hold amplifiers is explained. Differential and integral linearity are defined, and good and bad examples are illustrated. The applicability and relative advantages of the three types of converters for precision astronomical photometric measurements are discussed. For most measurements, integral linearity is more important than differential linearity. Successive-approximation converters should be used with multielement solid state detectors because of their high speed, but dual slope integrating converters may be superior for use with single element solid state detectors where speed of digitization is not a factor. In all cases, the input signal should be tailored so that they occupy the upper part of the converter's dynamic range; this can be achieved by providing adjustable gain, or better by varying the integration time of the observation if possible.

Endochondral bone formation in embryonic mouse pre-metatarsals

NASA Technical Reports Server (NTRS)

Klement, B. J.; Spooner, B. S.

1992-01-01

Long term exposure to a reduced gravitational environment has a deleterious effect on bone. The developmental events which occur prior to initial bone deposition will provide insight into the regulation of mature bone physiology. We have characterized a system in which the events preceding bone formation take place in an isolated in vitro organ culture environment. We show that cultured pre-metatarsal tissue parallels development of pre-metatarsal tissue in the embryo. Both undergo mesenchyme differentiation and morphogenesis to form a cartilage rod, which resembles the future bone, followed by terminal chondrocyte differentiation in a definite morphogenetic pattern. These sequential steps occur prior to osteoblast maturation and bone matrix deposition in the developing organism. Alkaline phosphatase (ALP) activity is a distinctive enzymatic marker for mineralizing tissues. We have measured this activity throughout pre-metatarsal development and show (a) where in the tissue it is predominantly found, and (b) that this is indeed the mineralizing isoform of the enzyme.

Aerodynamic Shape Optimization Using Hybridized Differential Evolution

NASA Technical Reports Server (NTRS)

Madavan, Nateri K.

2003-01-01

An aerodynamic shape optimization method that uses an evolutionary algorithm known at Differential Evolution (DE) in conjunction with various hybridization strategies is described. DE is a simple and robust evolutionary strategy that has been proven effective in determining the global optimum for several difficult optimization problems. Various hybridization strategies for DE are explored, including the use of neural networks as well as traditional local search methods. A Navier-Stokes solver is used to evaluate the various intermediate designs and provide inputs to the hybrid DE optimizer. The method is implemented on distributed parallel computers so that new designs can be obtained within reasonable turnaround times. Results are presented for the inverse design of a turbine airfoil from a modern jet engine. (The final paper will include at least one other aerodynamic design application). The capability of the method to search large design spaces and obtain the optimal airfoils in an automatic fashion is demonstrated.

[The "athlete's heart": structure, function and differential diagnosis].

PubMed

Carro, Amelia; Carro, Fernando; del Valle, Miguel Enrique

2011-10-22

Long-term, intense sport activity induces morphologic and functional adaptations on cardiovascular system. The magnitude of these changes is determined by various factors, creating a specific condition: the "Athlete's Heart" (AH). It is important to distinguish this entity from other cardiomyopathies, taking into account that the differential diagnosis can be challenging. There has been an increase in the number of people practicing sports, which goes in parallel with the increase in the prevalence of AH. However, the proportion of asymptomatic subjects affected by cardiovascular diseases taking part on competitive sports, is also growing. We revise the main characteristics of AH, as well as the key points to distinguish AH from pathologic conditions. A delicate characterization as AH or cardiomyopathy would help to settle appropriate measures to lower the risk of sports-related sudden cardiac death. Copyright © 2010 Elsevier España, S.L. All rights reserved.

Exploiting single-cell variability to infer the dynamics of immune responses

NASA Astrophysics Data System (ADS)

Höfer, Thomas

Cell division, differentiation, migration and death determine the dynamics of immune responses. These processes are regulated by a multitude of biochemical signals which, at present, cannot faithfully be reconstituted outside the living organism. However, quantitative measurements in living organisms have been limited. In recent years experimental techniques for the ``fate mapping'' of single immune cells have been developed that allow performing parallel single-cell experiments in an experimental animal. The resulting data are more informative about underlying biological processes than traditional measurements. I will show how the theory of stochastic dynamical systems can be used to infer the topology and dynamics of cell differentiation pathways from such data. The focus will be on joint theoretical and experimental work addressing: (i) the development of immune cells during hematopoiesis, and (ii) T cell responses to diverse pathogens. I will discuss questions on the nature of cellular variability that are posed by these new findings.

Optimal matrix rigidity for stress fiber polarization in stem cells

PubMed Central

Rehfeldt, F.; Brown, A. E. X.; Discher, D. E.; Safran, S. A.

2010-01-01

The shape and differentiation of human mesenchymal stem cells is especially sensitive to the rigidity of their environment; the physical mechanisms involved are unknown. A theoretical model and experiments demonstrate here that the polarization/alignment of stress-fibers within stem cells is a non-monotonic function of matrix rigidity. We treat the cell as an active elastic inclusion in a surrounding matrix whose polarizability, unlike dead matter, depends on the feedback of cellular forces that develop in response to matrix stresses. The theory correctly predicts the monotonic increase of the cellular forces with the matrix rigidity and the alignment of stress-fibers parallel to the long axis of cells. We show that the anisotropy of this alignment depends non-monotonically on matrix rigidity and demonstrate it experimentally by quantifying the orientational distribution of stress-fibers in stem cells. These findings offer a first physical insight for the dependence of stem cell differentiation on tissue elasticity. PMID:20563235

Modeling of outgassing and matrix decomposition in carbon-phenolic composites

NASA Technical Reports Server (NTRS)

Mcmanus, Hugh L.

1994-01-01

Work done in the period Jan. - June 1994 is summarized. Two threads of research have been followed. First, the thermodynamics approach was used to model the chemical and mechanical responses of composites exposed to high temperatures. The thermodynamics approach lends itself easily to the usage of variational principles. This thermodynamic-variational approach has been applied to the transpiration cooling problem. The second thread is the development of a better algorithm to solve the governing equations resulting from the modeling. Explicit finite difference method is explored for solving the governing nonlinear, partial differential equations. The method allows detailed material models to be included and solution on massively parallel supercomputers. To demonstrate the feasibility of the explicit scheme in solving nonlinear partial differential equations, a transpiration cooling problem was solved. Some interesting transient behaviors were captured such as stress waves and small spatial oscillations of transient pressure distribution.

Epigenetic developmental programs and adipogenesis: implications for psychotropic induced obesity.

PubMed

Chase, Kayla; Sharma, Rajiv P

2013-11-01

Psychotropic agents are notorious for their ability to increase fat mass in psychiatric patients. The two determinants of fat mass are the production of newly differentiated adipocytes (adipogenesis), and the volume of lipid accumulation. Epigenetic programs have a prominent role in cell fate commitments and differentiation required for adipogenesis. In parallel, epigenetic effects on energy metabolism are well supported by several genetic models. Consequently, a variety of psychotropics, often prescribed in combinations and for long periods, may utilize a common epigenetic effector path causing an increase in adipogenesis or reduction in energy metabolism. In particular, the recent discovery that G protein coupled signaling cascades can directly modify epigenetic regulatory enzymes implicates surface receptor activity by psychotropic medications. The potential therapeutic implications are also suggested by the effects of the clinically approved antidepressant tranylcypromine, also a histone demethylase inhibitor, which has impressive therapeutic effects on metabolism in the obese phenotype.

Tracking modern human population history from linguistic and cranial phenotype

PubMed Central

Reyes-Centeno, Hugo; Harvati, Katerina; Jäger, Gerhard

2016-01-01

Languages and genes arguably follow parallel evolutionary trajectories, descending from a common source and subsequently differentiating. However, although common ancestry is established within language families, it remains controversial whether language preserves a deep historical signal. To address this question, we evaluate the association between linguistic and geographic distances across 265 language families, as well as between linguistic, geographic, and cranial distances among eleven populations from Africa, Asia, and Australia. We take advantage of differential population history signals reflected by human cranial anatomy, where temporal bone shape reliably tracks deep population history and neutral genetic changes, while facial shape is more strongly associated with recent environmental effects. We show that linguistic distances are strongly geographically patterned, even within widely dispersed groups. However, they are correlated predominantly with facial, rather than temporal bone, morphology, suggesting that variation in vocabulary likely tracks relatively recent events and possibly population contact. PMID:27833101

A mixed finite difference/Galerkin method for three-dimensional Rayleigh-Benard convection

NASA Technical Reports Server (NTRS)

Buell, Jeffrey C.

1988-01-01

A fast and accurate numerical method, for nonlinear conservation equation systems whose solutions are periodic in two of the three spatial dimensions, is presently implemented for the case of Rayleigh-Benard convection between two rigid parallel plates in the parameter region where steady, three-dimensional convection is known to be stable. High-order streamfunctions secure the reduction of the system of five partial differential equations to a system of only three. Numerical experiments are presented which verify both the expected convergence rates and the absolute accuracy of the method.

Massively Parallel Rogue Cell Detection using Serial Time-Encoded Amplified Microscopy of Inertially Ordered Cells in High Throughput Flow

DTIC Science & Technology

2013-06-01

couples  the  high-­‐speed  capability  of  the   STEAM  imager  and  differential  phase... air  bubbles  in  the  TPE  mix.  Moreover,  TPE  chips  were  also  successfully  sealed  to  other  substrates...dynamics,  and  microelectromechanical  systems  (MEMS)  via  laser-­‐scanning  surface   vibrometry ,  and   observation

MADNESS: A Multiresolution, Adaptive Numerical Environment for Scientific Simulation

DOE PAGES

Harrison, Robert J.; Beylkin, Gregory; Bischoff, Florian A.; ...

2016-01-01

We present MADNESS (multiresolution adaptive numerical environment for scientific simulation) that is a high-level software environment for solving integral and differential equations in many dimensions that uses adaptive and fast harmonic analysis methods with guaranteed precision that are based on multiresolution analysis and separated representations. Underpinning the numerical capabilities is a powerful petascale parallel programming environment that aims to increase both programmer productivity and code scalability. This paper describes the features and capabilities of MADNESS and briefly discusses some current applications in chemistry and several areas of physics.

Right/left assignment in drift chambers and proportional multiwire chambers (PWC's) using induced signals

DOEpatents

Walenta, Albert H.

1979-01-01

Improved multiwire chamber having means for resolving the left/right ambiguity in the location of an ionizing event. The chamber includes a plurality of spaced parallel anode wires positioned between spaced planar cathodes. Associated with each of the anode wires are a pair of localizing wires, one positioned on either side of the anode wire. The localizing wires are connected to a differential amplifier whose output polarity is determined by whether the ionizing event occurs to the right or left of the anode wire.

Stability of an oscillating boundary layer

NASA Technical Reports Server (NTRS)

Levchenko, V. Y.; Solovyev, A. S.

1985-01-01

Levchenko and Solov'ev (1972, 1974) have developed a stability theory for space periodic flows, assuming that the Floquet theory is applicable to partial differential equations. In the present paper, this approach is extended to unsteady periodic flows. A complete unsteady formulation of the stability problem is obtained, and the stability characteristics over an oscillating period are determined from the solution of the problem. Calculations carried out for an oscillating incompressible boundary layer on a plate showed that the boundary layer flow may be regarded as a locally parallel flow.

Computer program for the load and trajectory analysis of two DOF bodies connected by an elastic tether: Users manual

NASA Technical Reports Server (NTRS)

Doyle, G. R., Jr.; Burbick, J. W.

1973-01-01

The derivation of the differential equations of motion of a 3 Degrees of Freedom body joined to a 3 Degrees of Freedom body by an elastic tether. The tether is represented by a spring and dashpot in parallel. A computer program which integrates the equations of motion is also described. Although the derivation of the equations of motions are for a general system, the computer program is written for defining loads in large boosters recovered by parachutes.

Testing the Multispecimen Absolute Paleointensity Method with Archaeological Baked Clays and Bricks: New Data for Central Europe

NASA Astrophysics Data System (ADS)

Schnepp, Elisabeth; Leonhardt, Roman

2014-05-01

The domain-state corrected multiple-specimen paleointensity determination technique (MSP-DSC, Fabian & Leonhardt, EPSL 297, 84, 2010) has been tested for archaeological baked clays and bricks. The following procedure was applied: (1) Exclusion of secondary overprints using alternating field (AF) or thermal demagnetization and assignment of characteristic remanent magnetization (ChRM) direction. (2) Determination of magneto mineralogical alteration using anhysteretic remanent magnetization (ARM) or temperature dependence of susceptibility. (3) Measurement of ARM anisotropy tensor, calculation of the ancient magnetic field direction. (4) Sister specimens were subjected to the MSP-DSC technique aligned (anti-)parallel to the ancient magnetic field direction. (5) Several checks were applied in order to exclude data points from further evaluation: (a) The accuracy of orientation (< 10°), (b) absence of secondary components (< 10°), (c) use of a considerable NRM fraction (20 to 80%), (d) weak alteration (smaller than for domain state change) and finally (e) domain state correction was applied. Bricks and baked clays from archaeological sites with ages between 645 BC and 2003 AD have been subjected to MSP-DSC absolute paleointensity (PI) determination. Aims of study are to check precision and reliability of the method. The obtained PI values are compared with direct field observation, the IGRF, the GUFM1 or Thellier results. The Thellier experiments often show curved lines and pTRM checks fail for higher temperatures. Nevertheless in the low temperature range straight lines have been obtained but they provide scattered paleointensity values. Mean paleointensites have relative errors often exceeding 10%, which are not considered as high quality PI estimates. MSP-DSC experiments for the structures older than 300 years are still under progress. The paleointensities obtained from the MSP-DSC experiments for the young materials (after 1700 AD) have small relative errors of a few or even less than one per cent, although the data points are scattered in some cases. For these sites comparison with the historical field values shows very good agreement. Small deviations could be explained by the higher cooling rates used in the laboratory. These young structures were made of bricks and the unweathered baked clay of the 2003 experimental kiln was like brick, either. The sites provided much material so that tests were done to investigate the MSP-DSC methodology further. For example it was tested, if different NRM deblocking fractions have influence on the paleointensity estimate. It seems that use of fractions lower than 20% of the NRM can lead to an underestimation of PI. Although MSP-DSC experiments carried out on different blocks of the same structure can provide very similar results, the use of several fragments from at least five different units (potshards, bricks, in situ burnt blocks or rocks) of the same structure is recommended in or to obtain a reliable estimate of the experimental errors. Five data points may define already a well constraint straight line, but for a better precision 15 (< 2%) data points may be required. For the young structures the MSP-DSC method provided reliable PI estimates which have been included into the archaeointensity data base

Archaeomagnetic Records from Early Bronze to Iron Age Mediterranean Settlements

NASA Astrophysics Data System (ADS)

Ertepinar, Pinar; Hammond, Megan; Hill, Mimi; Biggin, Andy; Langereis, Cor; Yener, Aslihan; Akar, Murat; Greaves, Alan; Gates, Mary; Harrison, Timothy; Özgen, Ilknur

2017-04-01

Recent studies on the geomagnetic field variations over the Middle East have started to take particular attention due to the presence of numerous high intensity periods proposed by various authors. Considering the recent volume of papers focused on archaeomagnetism in this region, the lack of published work centered in Turkey and Cyprus is surprising since both regions have a long cultural heritage and history of trade and immigration from neighboring countries. Here we present a large dataset of directions and intensities from seven archaeological sites in the Mediterranean with 21 subsets of directional and 40 subsets of intensity data covering a long sequence of levels from 3300 to 700 BCE. The sample sets are composed of both ex-situ potsherds and in-situ features such as mud-bricks, basalts and an ash layer. The results from the rock magnetic experiments run on at least three samples from each set indicate that the magnetic mineral assemblage is composed mostly of pseudo-single domain grain magnetite or titano-magnetite with various Ti content. The majority of the demagnetization diagrams are single component and 14 out of 21 sets have a well-defined characteristic remanent magnetization direction. The directional results show a swing of 37.6° in declination and 26.9° in inclination within an age interval of 2000 years. The archaeointensity experiments involved both microwave and thermal methods. To avoid the anisotropy effects, the applied field is either set parallel to the samples NRM or the angle between the pTRM acquired at the last step used for the best-fit segment and the applied field direction, γ, was checked and found to be less than 7.5°. For the samples that are measured in random directions with respect to their NRM, prior to the intensity experiments, the anisotropy of magnetic susceptibility was individually measured and the anisotropy degree is found to be less than 2.5%. For all the potsherds, one or two samples from each set are subjected to cooling rate experiment since the rest failed to meet alteration criteria. The measured cooling rate factor is applied to the whole group of the same type. The effect of cooling rate on mud-bricks was found to be minimal. In general, the directional results are in agreement with the global field models except for two data points, one that plots 10° shallower and to the west and the other, also shallower, by 20°. Both are highly coherent with previous data from Turkey. The archaeointensity values spanning 2200 to 700 BCE are in the range of 6.54×1022 to 17.44×1022 Am2. The measured intensities are much higher than the field models but mostly in agreement with the data in the literature. Recently published archaeointensity values from neighboring countries suggest that there was a period of relatively high field intensity at 1000 BCE, the geographic extent of which has been the subject of much debate. This study potentially extends the geographic range of this intensity high.

Mechanisms mediating parallel action monitoring in fronto-striatal circuits.

PubMed

Beste, Christian; Ness, Vanessa; Lukas, Carsten; Hoffmann, Rainer; Stüwe, Sven; Falkenstein, Michael; Saft, Carsten

2012-08-01

Flexible response adaptation and the control of conflicting information play a pivotal role in daily life. Yet, little is known about the neuronal mechanisms mediating parallel control of these processes. We examined these mechanisms using a multi-methodological approach that integrated data from event-related potentials (ERPs) with structural MRI data and source localisation using sLORETA. Moreover, we calculated evoked wavelet oscillations. We applied this multi-methodological approach in healthy subjects and patients in a prodromal phase of a major basal ganglia disorder (i.e., Huntington's disease), to directly focus on fronto-striatal networks. Behavioural data indicated, especially the parallel execution of conflict monitoring and flexible response adaptation was modulated across the examined cohorts. When both processes do not co-incide a high integrity of fronto-striatal loops seems to be dispensable. The neurophysiological data suggests that conflict monitoring (reflected by the N2 ERP) and working memory processes (reflected by the P3 ERP) differentially contribute to this pattern of results. Flexible response adaptation under the constraint of high conflict processing affected the N2 and P3 ERP, as well as their delta frequency band oscillations. Yet, modulatory effects were strongest for the N2 ERP and evoked wavelet oscillations in this time range. The N2 ERPs were localized in the anterior cingulate cortex (BA32, BA24). Modulations of the P3 ERP were localized in parietal areas (BA7). In addition, MRI-determined caudate head volume predicted modulations in conflict monitoring, but not working memory processes. The results show how parallel conflict monitoring and flexible adaptation of action is mediated via fronto-striatal networks. While both, response monitoring and working memory processes seem to play a role, especially response selection processes and ACC-basal ganglia networks seem to be the driving force in mediating parallel conflict monitoring and flexible adaptation of actions. Copyright © 2012 Elsevier Inc. All rights reserved.

Field-Programmable Gate Array Computer in Structural Analysis: An Initial Exploration

NASA Technical Reports Server (NTRS)

Singleterry, Robert C., Jr.; Sobieszczanski-Sobieski, Jaroslaw; Brown, Samuel

2002-01-01

This paper reports on an initial assessment of using a Field-Programmable Gate Array (FPGA) computational device as a new tool for solving structural mechanics problems. A FPGA is an assemblage of binary gates arranged in logical blocks that are interconnected via software in a manner dependent on the algorithm being implemented and can be reprogrammed thousands of times per second. In effect, this creates a computer specialized for the problem that automatically exploits all the potential for parallel computing intrinsic in an algorithm. This inherent parallelism is the most important feature of the FPGA computational environment. It is therefore important that if a problem offers a choice of different solution algorithms, an algorithm of a higher degree of inherent parallelism should be selected. It is found that in structural analysis, an 'analog computer' style of programming, which solves problems by direct simulation of the terms in the governing differential equations, yields a more favorable solution algorithm than current solution methods. This style of programming is facilitated by a 'drag-and-drop' graphic programming language that is supplied with the particular type of FPGA computer reported in this paper. Simple examples in structural dynamics and statics illustrate the solution approach used. The FPGA system also allows linear scalability in computing capability. As the problem grows, the number of FPGA chips can be increased with no loss of computing efficiency due to data flow or algorithmic latency that occurs when a single problem is distributed among many conventional processors that operate in parallel. This initial assessment finds the FPGA hardware and software to be in their infancy in regard to the user conveniences; however, they have enormous potential for shrinking the elapsed time of structural analysis solutions if programmed with algorithms that exhibit inherent parallelism and linear scalability. This potential warrants further development of FPGA-tailored algorithms for structural analysis.

Seismic anisotropy in the Hellenic subduction zone: Effects of slab segmentation and subslab mantle flow

NASA Astrophysics Data System (ADS)

Evangelidis, C. P.

2017-12-01

The segmentation and differentiation of subducting slabs have considerable effects on mantle convection and tectonics. The Hellenic subduction zone is a complex convergent margin with strong curvature and fast slab rollback. The upper mantle seismic anisotropy in the region is studied focusing at its western and eastern edges in order to explore the effects of possible slab segmentation on mantle flow and fabrics. Complementary to new SKS shear-wave splitting measurements in regions not adequately sampled so far, the source-side splitting technique is applied to constrain the depth of anisotropy and to densify measurements. In the western Hellenic arc, a trench-normal subslab anisotropy is observed near the trench. In the forearc domain, source-side and SKS measurements reveal a trench-parallel pattern. This indicates subslab trench-parallel mantle flow, associated with return flow due to the fast slab rollback. The passage from continental to oceanic subduction in the western Hellenic zone is illustrated by a forearc transitional anisotropy pattern. This indicates subslab mantle flow parallel to a NE-SW smooth ramp that possibly connects the two subducted slabs. A young tear fault initiated at the Kefalonia Transform Fault is likely not entirely developed, as this trench-parallel anisotropy pattern is observed along the entire western Hellenic subduction system, even following this horizontal offset between the two slabs. At the eastern side of the Hellenic subduction zone, subslab source-side anisotropy measurements show a general trench-normal pattern. These are associated with mantle flow through a possible ongoing tearing of the oceanic lithosphere in the area. Although the exact geometry of this slab tear is relatively unknown, SKS trench-parallel measurements imply that the tear has not reached the surface yet. Further exploration of the Hellenic subduction system is necessary; denser seismic networks should be deployed at both its edges in order to achieve a more definite image of the structure and geodynamics of this area.

A comparative study of proliferation and osteogenic differentiation of adipose-derived stem cells on akermanite and beta-TCP ceramics.

PubMed

Liu, Qihai; Cen, Lian; Yin, Shuo; Chen, Lei; Liu, Guangpeng; Chang, Jiang; Cui, Lei

2008-12-01

This study investigated the in vitro effects of akermanite, a new kind of Ca-, Mg-, Si-containing bioceramic, on the attachment, proliferation and osteogenic differentiation of human adipose-derived stem cells (hASCs). Parallel comparison of the cellular behaviors of hASCs on the akermanite was made with those on beta-tricalcium phosphate (beta-TCP). Scanning electron microscope (SEM) observation and fluorescent DiO labeling were carried out to reveal the attachment and growth of hASCs on the two ceramic surfaces, while the quantitative assay of cell proliferation with time was detected by DNA assay. Osteogenic differentiation of hASCs cultured on the akermanite and beta-TCP was assayed by ALP expression and osteocalcin (OCN) deposition, which was further confirmed by Real-time PCR analysis for markers of osteogenic differentiation. It was shown that hASCs attached and spread well on the akermanite as those on beta-TCP, and similar proliferation behaviors of hASCs were observed on the two ceramics. Both of them exhibited good compatibility to hASCs with only minor cytotoxicity as compared with the tissue culture plates. Interestingly, the osteogenic differentiation of hASCs could be enhanced on the akermanite compared with that on the beta-TCP when the culture time was extended to approximately 10 days. Thus, it can be ascertained that akermanite ceramics may serve as a potential scaffold for bone tissue engineering.

Gene expression profiling in multipotent DFAT cells derived from mature adipocytes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ono, Hiromasa; Database Center for Life Science; Oki, Yoshinao

2011-04-15

Highlights: {yields} Adipocyte dedifferentiation is evident in a significant decrease in typical genes. {yields} Cell proliferation is strongly related to adipocyte dedifferentiation. {yields} Dedifferentiated adipocytes express several lineage-specific genes. {yields} Comparative analyses using publicly available datasets boost the interpretation. -- Abstract: Cellular dedifferentiation signifies the withdrawal of cells from a specific differentiated state to a stem cell-like undifferentiated state. However, the mechanism of dedifferentiation remains obscure. Here we performed comparative transcriptome analyses during dedifferentiation in mature adipocytes (MAs) to identify the transcriptional signatures of multipotent dedifferentiated fat (DFAT) cells derived from MAs. Using microarray systems, we explored similarly expressed asmore » well as significantly differentially expressed genes in MAs during dedifferentiation. This analysis revealed significant changes in gene expression during this process, including a significant reduction in expression of genes for lipid metabolism concomitantly with a significant increase in expression of genes for cell movement, cell migration, tissue developmental processes, cell growth, cell proliferation, cell morphogenesis, altered cell shape, and cell differentiation. Our observations indicate that the transcriptional signatures of DFAT cells derived from MAs are summarized in terms of a significant decrease in functional phenotype-related genes and a parallel increase in cell proliferation, altered cell morphology, and regulation of the differentiation of related genes. A better understanding of the mechanisms involved in dedifferentiation may enable scientists to control and possibly alter the plasticity of the differentiated state, which may lead to benefits not only in stem cell research but also in regenerative medicine.« less

Loss of lysophosphatidic acid receptor LPA1 alters oligodendrocyte differentiation and myelination in the mouse cerebral cortex.

PubMed

García-Díaz, Beatriz; Riquelme, Raquel; Varela-Nieto, Isabel; Jiménez, Antonio Jesús; de Diego, Isabel; Gómez-Conde, Ana Isabel; Matas-Rico, Elisa; Aguirre, José Ángel; Chun, Jerold; Pedraza, Carmen; Santín, Luis Javier; Fernández, Oscar; Rodríguez de Fonseca, Fernando; Estivill-Torrús, Guillermo

2015-11-01

Lysophosphatidic acid (LPA) is an intercellular signaling lipid that regulates multiple cellular functions, acting through specific G-protein coupled receptors (LPA(1-6)). Our previous studies using viable Malaga variant maLPA1-null mice demonstrated the requirement of the LPA1 receptor for normal proliferation, differentiation, and survival of the neuronal precursors. In the cerebral cortex LPA1 is expressed extensively in differentiating oligodendrocytes, in parallel with myelination. Although exogenous LPA-induced effects have been investigated in myelinating cells, the in vivo contribution of LPA1 to normal myelination remains to be demonstrated. This study identified a relevant in vivo role for LPA1 as a regulator of cortical myelination. Immunochemical analysis in adult maLPA1-null mice demonstrated a reduction in the steady-state levels of the myelin proteins MBP, PLP/DM20, and CNPase in the cerebral cortex. The myelin defects were confirmed using magnetic resonance spectroscopy and electron microscopy. Stereological analysis limited the defects to adult differentiating oligodendrocytes, without variation in the NG2+ precursor cells. Finally, a possible mechanism involving oligodendrocyte survival was demonstrated by the impaired intracellular transport of the PLP/DM20 myelin protein which was accompanied by cellular loss, suggesting stress-induced apoptosis. These findings describe a previously uncharacterized in vivo functional role for LPA1 in the regulation of oligodendrocyte differentiation and myelination in the CNS, underlining the importance of the maLPA1-null mouse as a model for the study of demyelinating diseases.

Population genetic structure of a widespread coniferous tree, Taxodium distichum [L.] Rich. (Cupressaceae), in the Mississippi River Alluvial Valley and Florida

USGS Publications Warehouse

Tanaka, Ayako; Ohtani, Masato; Suyama, Yoshihisa; Inomata, Nobuyuki; Tsumura, Yoshihiko; Middleton, Beth A.; Tachida, Hidenori; Kusumi, Junko

2012-01-01

Studies of genetic variation can elucidate the structure of present and past populations as well as the genetic basis of the phenotypic variability of species. Taxodium distichum is a coniferous tree dominant in lowland river flood plains and swamps of the southeastern USA which exhibits morphological variability and adaption to stressful habitats. This study provides a survey of the Mississippi River Alluvial Valley (MAV) and Florida to elucidate their population structure and the extent of genetic differentiation between the two regions and sympatric varieties, including bald cypress (var. distichum) and pond cypress (var. imbricatum). We determined the genotypes of 12 simple sequence repeat loci totaling 444 adult individuals from 18 natural populations. Bayesian clustering analysis revealed high levels of differentiation between the MAV and the Florida regions. Within the MAV region, there was a significant correlation between genetic and geographical distances. In addition, we found that there was almost no genetic differentiation between the varieties. Most genetic variation was found within individuals (76.73 %), 1.67 % among individuals within population, 15.36 % among populations within the regions, and 9.23 % between regions within the variety. Our results suggest that (1) the populations of the MAV and the Florida regions are divided into two major genetic groups, which might originate from different glacial refugia, and (2) the patterns of genetic differentiation and phenotypic differentiation were not parallel in this species.

Parallel hyperbolic PDE simulation on clusters: Cell versus GPU

NASA Astrophysics Data System (ADS)

Rostrup, Scott; De Sterck, Hans

2010-12-01

Increasingly, high-performance computing is looking towards data-parallel computational devices to enhance computational performance. Two technologies that have received significant attention are IBM's Cell Processor and NVIDIA's CUDA programming model for graphics processing unit (GPU) computing. In this paper we investigate the acceleration of parallel hyperbolic partial differential equation simulation on structured grids with explicit time integration on clusters with Cell and GPU backends. The message passing interface (MPI) is used for communication between nodes at the coarsest level of parallelism. Optimizations of the simulation code at the several finer levels of parallelism that the data-parallel devices provide are described in terms of data layout, data flow and data-parallel instructions. Optimized Cell and GPU performance are compared with reference code performance on a single x86 central processing unit (CPU) core in single and double precision. We further compare the CPU, Cell and GPU platforms on a chip-to-chip basis, and compare performance on single cluster nodes with two CPUs, two Cell processors or two GPUs in a shared memory configuration (without MPI). We finally compare performance on clusters with 32 CPUs, 32 Cell processors, and 32 GPUs using MPI. Our GPU cluster results use NVIDIA Tesla GPUs with GT200 architecture, but some preliminary results on recently introduced NVIDIA GPUs with the next-generation Fermi architecture are also included. This paper provides computational scientists and engineers who are considering porting their codes to accelerator environments with insight into how structured grid based explicit algorithms can be optimized for clusters with Cell and GPU accelerators. It also provides insight into the speed-up that may be gained on current and future accelerator architectures for this class of applications. Program summaryProgram title: SWsolver Catalogue identifier: AEGY_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGY_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GPL v3 No. of lines in distributed program, including test data, etc.: 59 168 No. of bytes in distributed program, including test data, etc.: 453 409 Distribution format: tar.gz Programming language: C, CUDA Computer: Parallel Computing Clusters. Individual compute nodes may consist of x86 CPU, Cell processor, or x86 CPU with attached NVIDIA GPU accelerator. Operating system: Linux Has the code been vectorised or parallelized?: Yes. Tested on 1-128 x86 CPU cores, 1-32 Cell Processors, and 1-32 NVIDIA GPUs. RAM: Tested on Problems requiring up to 4 GB per compute node. Classification: 12 External routines: MPI, CUDA, IBM Cell SDK Nature of problem: MPI-parallel simulation of Shallow Water equations using high-resolution 2D hyperbolic equation solver on regular Cartesian grids for x86 CPU, Cell Processor, and NVIDIA GPU using CUDA. Solution method: SWsolver provides 3 implementations of a high-resolution 2D Shallow Water equation solver on regular Cartesian grids, for CPU, Cell Processor, and NVIDIA GPU. Each implementation uses MPI to divide work across a parallel computing cluster. Additional comments: Sub-program numdiff is used for the test run.

The Transcriptomes of Two Heritable Cell Types Illuminate the Circuit Governing Their Differentiation

PubMed Central

Homann, Oliver R.; Hernday, Aaron D.; Monighetti, Cinna K.; De La Vega, Francisco M.; Johnson, Alexander D.

2010-01-01

The differentiation of cells into distinct cell types, each of which is heritable for many generations, underlies many biological phenomena. White and opaque cells of the fungal pathogen Candida albicans are two such heritable cell types, each thought to be adapted to unique niches within their human host. To systematically investigate their differences, we performed strand-specific, massively-parallel sequencing of RNA from C. albicans white and opaque cells. With these data we first annotated the C. albicans transcriptome, finding hundreds of novel differentially-expressed transcripts. Using the new annotation, we compared differences in transcript abundance between the two cell types with the genomic regions bound by a master regulator of the white-opaque switch (Wor1). We found that the revised transcriptional landscape considerably alters our understanding of the circuit governing differentiation. In particular, we can now resolve the poor concordance between binding of a master regulator and the differential expression of adjacent genes, a discrepancy observed in several other studies of cell differentiation. More than one third of the Wor1-bound differentially-expressed transcripts were previously unannotated, which explains the formerly puzzling presence of Wor1 at these positions along the genome. Many of these newly identified Wor1-regulated genes are non-coding and transcribed antisense to coding transcripts. We also find that 5′ and 3′ UTRs of mRNAs in the circuit are unusually long and that 5′ UTRs often differ in length between cell-types, suggesting UTRs encode important regulatory information and that use of alternative promoters is widespread. Further analysis revealed that the revised Wor1 circuit bears several striking similarities to the Oct4 circuit that specifies the pluripotency of mammalian embryonic stem cells. Additional characteristics shared with the Oct4 circuit suggest a set of general hallmarks characteristic of heritable differentiation states in eukaryotes. PMID:20808890

TIA: algorithms for development of identity-linked SNP islands for analysis by massively parallel DNA sequencing.

PubMed

Farris, M Heath; Scott, Andrew R; Texter, Pamela A; Bartlett, Marta; Coleman, Patricia; Masters, David

2018-04-11

Single nucleotide polymorphisms (SNPs) located within the human genome have been shown to have utility as markers of identity in the differentiation of DNA from individual contributors. Massively parallel DNA sequencing (MPS) technologies and human genome SNP databases allow for the design of suites of identity-linked target regions, amenable to sequencing in a multiplexed and massively parallel manner. Therefore, tools are needed for leveraging the genotypic information found within SNP databases for the discovery of genomic targets that can be evaluated on MPS platforms. The SNP island target identification algorithm (TIA) was developed as a user-tunable system to leverage SNP information within databases. Using data within the 1000 Genomes Project SNP database, human genome regions were identified that contain globally ubiquitous identity-linked SNPs and that were responsive to targeted resequencing on MPS platforms. Algorithmic filters were used to exclude target regions that did not conform to user-tunable SNP island target characteristics. To validate the accuracy of TIA for discovering these identity-linked SNP islands within the human genome, SNP island target regions were amplified from 70 contributor genomic DNA samples using the polymerase chain reaction. Multiplexed amplicons were sequenced using the Illumina MiSeq platform, and the resulting sequences were analyzed for SNP variations. 166 putative identity-linked SNPs were targeted in the identified genomic regions. Of the 309 SNPs that provided discerning power across individual SNP profiles, 74 previously undefined SNPs were identified during evaluation of targets from individual genomes. Overall, DNA samples of 70 individuals were uniquely identified using a subset of the suite of identity-linked SNP islands. TIA offers a tunable genome search tool for the discovery of targeted genomic regions that are scalable in the population frequency and numbers of SNPs contained within the SNP island regions. It also allows the definition of sequence length and sequence variability of the target region as well as the less variable flanking regions for tailoring to MPS platforms. As shown in this study, TIA can be used to discover identity-linked SNP islands within the human genome, useful for differentiating individuals by targeted resequencing on MPS technologies.

Substrate topography: A valuable in vitro tool, but a clinical red herring for in vivo tenogenesis.

PubMed

English, Andrew; Azeem, Ayesha; Spanoudes, Kyriakos; Jones, Eleanor; Tripathi, Bhawana; Basu, Nandita; McNamara, Karrina; Tofail, Syed A M; Rooney, Niall; Riley, Graham; O'Riordan, Alan; Cross, Graham; Hutmacher, Dietmar; Biggs, Manus; Pandit, Abhay; Zeugolis, Dimitrios I

2015-11-01

Controlling the cell-substrate interactions at the bio-interface is becoming an inherent element in the design of implantable devices. Modulation of cellular adhesion in vitro, through topographical cues, is a well-documented process that offers control over subsequent cellular functions. However, it is still unclear whether surface topography can be translated into a clinically functional response in vivo at the tissue/device interface. Herein, we demonstrated that anisotropic substrates with a groove depth of ∼317nm and ∼1988nm promoted human tenocyte alignment parallel to the underlying topography in vitro. However, the rigid poly(lactic-co-glycolic acid) substrates used in this study upregulated the expression of chondrogenic and osteogenic genes, indicating possible tenocyte trans-differentiation. Of significant importance is that none of the topographies assessed (∼37nm, ∼317nm and ∼1988nm groove depth) induced extracellular matrix orientation parallel to the substrate orientation in a rat patellar tendon model. These data indicate that two-dimensional imprinting technologies are useful tools for in vitro cell phenotype maintenance, rather than for organised neotissue formation in vivo, should multifactorial approaches that consider both surface topography and substrate rigidity be established. Herein, we ventured to assess the influence of parallel groves, ranging from nano- to micro-level, on tenocytes response in vitro and on host response using a tendon and a subcutaneous model. In vitro analysis indicates that anisotropically ordered micro-scale grooves, as opposed to nano-scale grooves, maintain physiological cell morphology. The rather rigid PLGA substrates appeared to induce trans-differentiation towards chondrogenic and/or steogenic lineage, as evidence by TILDA gene analysis. In vivo data in both tendon and subcutaneous models indicate that none of the substrates induced bidirectional host cell and tissue growth. Collective, these observations indicate that two-dimensional imprinting technologies are useful tools for in vitro cell phenotype maintenance, rather than for directional neotissue formation, should multifactorial approaches that consider both surface topography and substrate rigidity be established. Copyright © 2015 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Smart photodetector arrays for error control in page-oriented optical memory

NASA Astrophysics Data System (ADS)

Schaffer, Maureen Elizabeth

1998-12-01

Page-oriented optical memories (POMs) have been proposed to meet high speed, high capacity storage requirements for input/output intensive computer applications. This technology offers the capability for storage and retrieval of optical data in two-dimensional pages resulting in high throughput data rates. Since currently measured raw bit error rates for these systems fall several orders of magnitude short of industry requirements for binary data storage, powerful error control codes must be adopted. These codes must be designed to take advantage of the two-dimensional memory output. In addition, POMs require an optoelectronic interface to transfer the optical data pages to one or more electronic host systems. Conventional charge coupled device (CCD) arrays can receive optical data in parallel, but the relatively slow serial electronic output of these devices creates a system bottleneck thereby eliminating the POM advantage of high transfer rates. Also, CCD arrays are "unintelligent" interfaces in that they offer little data processing capabilities. The optical data page can be received by two-dimensional arrays of "smart" photo-detector elements that replace conventional CCD arrays. These smart photodetector arrays (SPAs) can perform fast parallel data decoding and error control, thereby providing an efficient optoelectronic interface between the memory and the electronic computer. This approach optimizes the computer memory system by combining the massive parallelism and high speed of optics with the diverse functionality, low cost, and local interconnection efficiency of electronics. In this dissertation we examine the design of smart photodetector arrays for use as the optoelectronic interface for page-oriented optical memory. We review options and technologies for SPA fabrication, develop SPA requirements, and determine SPA scalability constraints with respect to pixel complexity, electrical power dissipation, and optical power limits. Next, we examine data modulation and error correction coding for the purpose of error control in the POM system. These techniques are adapted, where possible, for 2D data and evaluated as to their suitability for a SPA implementation in terms of BER, code rate, decoder time and pixel complexity. Our analysis shows that differential data modulation combined with relatively simple block codes known as array codes provide a powerful means to achieve the desired data transfer rates while reducing error rates to industry requirements. Finally, we demonstrate the first smart photodetector array designed to perform parallel error correction on an entire page of data and satisfy the sustained data rates of page-oriented optical memories. Our implementation integrates a monolithic PN photodiode array and differential input receiver for optoelectronic signal conversion with a cluster error correction code using 0.35-mum CMOS. This approach provides high sensitivity, low electrical power dissipation, and fast parallel correction of 2 x 2-bit cluster errors in an 8 x 8 bit code block to achieve corrected output data rates scalable to 102 Gbps in the current technology increasing to 1.88 Tbps in 0.1-mum CMOS.

Fear-potentiated startle processing in humans: Parallel fMRI and orbicularis EMG assessment during cue conditioning and extinction.

PubMed

Lindner, Katja; Neubert, Jörg; Pfannmöller, Jörg; Lotze, Martin; Hamm, Alfons O; Wendt, Julia

2015-12-01

Studying neural networks and behavioral indices such as potentiated startle responses during fear conditioning has a long tradition in both animal and human research. However, most of the studies in humans do not link startle potentiation and neural activity during fear acquisition and extinction. Therefore, we examined startle blink responses measured with electromyography (EMG) and brain activity measured with functional MRI simultaneously during differential conditioning. Furthermore, we combined these behavioral fear indices with brain network activity by analyzing the brain activity evoked by the startle probe stimulus presented during conditioned visual threat and safety cues as well as in the absence of visual stimulation. In line with previous research, we found a fear-induced potentiation of the startle blink responses when elicited during a conditioned threat stimulus and a rapid decline of amygdala activity after an initial differentiation of threat and safety cues in early acquisition trials. Increased activation during processing of threat cues was also found in the anterior insula, the anterior cingulate cortex (ACC), and the periaqueductal gray (PAG). More importantly, our results depict an increase of brain activity to probes presented during threatening in comparison to safety cues indicating an involvement of the anterior insula, the ACC, the thalamus, and the PAG in fear-potentiated startle processing during early extinction trials. Our study underlines that parallel assessment of fear-potentiated startle in fMRI paradigms can provide a helpful method to investigate common and distinct processing pathways in humans and animals and, thus, contributes to translational research. Copyright © 2015 Elsevier B.V. All rights reserved.

Transcriptional analysis of the Arabidopsis ovule by massively parallel signature sequencing

PubMed Central

Sánchez-León, Nidia; Arteaga-Vázquez, Mario; Alvarez-Mejía, César; Mendiola-Soto, Javier; Durán-Figueroa, Noé; Rodríguez-Leal, Daniel; Rodríguez-Arévalo, Isaac; García-Campayo, Vicenta; García-Aguilar, Marcelina; Olmedo-Monfil, Vianey; Arteaga-Sánchez, Mario; Martínez de la Vega, Octavio; Nobuta, Kan; Vemaraju, Kalyan; Meyers, Blake C.; Vielle-Calzada, Jean-Philippe

2012-01-01

The life cycle of flowering plants alternates between a predominant sporophytic (diploid) and an ephemeral gametophytic (haploid) generation that only occurs in reproductive organs. In Arabidopsis thaliana, the female gametophyte is deeply embedded within the ovule, complicating the study of the genetic and molecular interactions involved in the sporophytic to gametophytic transition. Massively parallel signature sequencing (MPSS) was used to conduct a quantitative large-scale transcriptional analysis of the fully differentiated Arabidopsis ovule prior to fertilization. The expression of 9775 genes was quantified in wild-type ovules, additionally detecting >2200 new transcripts mapping to antisense or intergenic regions. A quantitative comparison of global expression in wild-type and sporocyteless (spl) individuals resulted in 1301 genes showing 25-fold reduced or null activity in ovules lacking a female gametophyte, including those encoding 92 signalling proteins, 75 transcription factors, and 72 RNA-binding proteins not reported in previous studies based on microarray profiling. A combination of independent genetic and molecular strategies confirmed the differential expression of 28 of them, showing that they are either preferentially active in the female gametophyte, or dependent on the presence of a female gametophyte to be expressed in sporophytic cells of the ovule. Among 18 genes encoding pentatricopeptide-repeat proteins (PPRs) that show transcriptional activity in wild-type but not spl ovules, CIHUATEOTL (At4g38150) is specifically expressed in the female gametophyte and necessary for female gametogenesis. These results expand the nature of the transcriptional universe present in the ovule of Arabidopsis, and offer a large-scale quantitative reference of global expression for future genomic and developmental studies. PMID:22442422

Transcriptional analysis of the Arabidopsis ovule by massively parallel signature sequencing.

PubMed

Sánchez-León, Nidia; Arteaga-Vázquez, Mario; Alvarez-Mejía, César; Mendiola-Soto, Javier; Durán-Figueroa, Noé; Rodríguez-Leal, Daniel; Rodríguez-Arévalo, Isaac; García-Campayo, Vicenta; García-Aguilar, Marcelina; Olmedo-Monfil, Vianey; Arteaga-Sánchez, Mario; de la Vega, Octavio Martínez; Nobuta, Kan; Vemaraju, Kalyan; Meyers, Blake C; Vielle-Calzada, Jean-Philippe

2012-06-01

The life cycle of flowering plants alternates between a predominant sporophytic (diploid) and an ephemeral gametophytic (haploid) generation that only occurs in reproductive organs. In Arabidopsis thaliana, the female gametophyte is deeply embedded within the ovule, complicating the study of the genetic and molecular interactions involved in the sporophytic to gametophytic transition. Massively parallel signature sequencing (MPSS) was used to conduct a quantitative large-scale transcriptional analysis of the fully differentiated Arabidopsis ovule prior to fertilization. The expression of 9775 genes was quantified in wild-type ovules, additionally detecting >2200 new transcripts mapping to antisense or intergenic regions. A quantitative comparison of global expression in wild-type and sporocyteless (spl) individuals resulted in 1301 genes showing 25-fold reduced or null activity in ovules lacking a female gametophyte, including those encoding 92 signalling proteins, 75 transcription factors, and 72 RNA-binding proteins not reported in previous studies based on microarray profiling. A combination of independent genetic and molecular strategies confirmed the differential expression of 28 of them, showing that they are either preferentially active in the female gametophyte, or dependent on the presence of a female gametophyte to be expressed in sporophytic cells of the ovule. Among 18 genes encoding pentatricopeptide-repeat proteins (PPRs) that show transcriptional activity in wild-type but not spl ovules, CIHUATEOTL (At4g38150) is specifically expressed in the female gametophyte and necessary for female gametogenesis. These results expand the nature of the transcriptional universe present in the ovule of Arabidopsis, and offer a large-scale quantitative reference of global expression for future genomic and developmental studies.

Effects of flow configuration on bone tissue engineering using human mesenchymal stem cells in 3D chitosan composite scaffolds.

PubMed

Sellgren, Katelyn L; Ma, Teng

2015-08-01

Perfusion bioreactor plays important role in supporting 3D bone construct development. Scaffolds of chitosan composites have been studied to support bone tissue regeneration from osteogenic progenitor cells including human mesenchymal stem cells (hMSC). In this study, porous scaffolds of hydroxyapatite (H), chitosan (C), and gelatin (G) were fabricated by phase-separation and press-fitted in the perfusion bioreactor system where media flow is configured either parallel or transverse with respect to the scaffolds to investigate the impact of flow configuration on hMSC proliferation and osteogenic differentiation. The in vitro results showed that the interstitial flow in the transverse flow (TF) constructs reduced cell growth during the first week of culture but improved spatial cell distribution and early onset of osteogenic differentiation measured by alkaline phosphatase and expression of osteogenic genes. After 14 days of bioreactor culture, the TF constructs have comparable cell number but higher expression of bone markers genes and proteins compared to the parallel flow constructs. To evaluate ectopic bone formation, the HCG constructs seeded with hMSCs pre-cultured under two flow configurations for 7 days were implanted in CD-1 nude mice. While Masson's Trichrom staining revealed bone formation in both constructs, the TF constructs have improved spatial cell and osteoid distribution throughout the 2.0 mm constructs. The results highlight the divergent effects of media flow over the course of construct development and suggest that the flow configuration is an important parameter regulating the cellular events leading to bone construct formation in the HCG scaffolds. © 2014 Wiley Periodicals, Inc.

Transmission between Archaic and Modern Human Ancestors during the Evolution of the Oncogenic Human Papillomavirus 16.

PubMed

Pimenoff, Ville N; de Oliveira, Cristina Mendes; Bravo, Ignacio G

2017-01-01

Every human suffers through life a number of papillomaviruses (PVs) infections, most of them asymptomatic. A notable exception are persistent infections by Human papillomavirus 16 (HPV16), the most oncogenic infectious agent for humans and responsible for most infection-driven anogenital cancers. Oncogenic potential is not homogeneous among HPV16 lineages, and genetic variation within HPV16 exhibits some geographic structure. However, an in-depth analysis of the HPV16 evolutionary history was still wanting. We have analyzed extant HPV16 diversity and compared the evolutionary and phylogeographical patterns of humans and of HPV16. We show that codivergence with modern humans explains at most 30% of the present viral geographical distribution. The most explanatory scenario suggests that ancestral HPV16 already infected ancestral human populations and that viral lineages co-diverged with the hosts in parallel with the split between archaic Neanderthal-Denisovans and ancestral modern human populations, generating the ancestral HPV16A and HPV16BCD viral lineages, respectively. We propose that after out-of-Africa migration of modern human ancestors, sexual transmission between human populations introduced HPV16A into modern human ancestor populations. We hypothesize that differential coevolution of HPV16 lineages with different but closely related ancestral human populations and subsequent host-switch events in parallel with introgression of archaic alleles into the genomes of modern human ancestors may be largely responsible for the present-day differential prevalence and association with cancers for HPV16 variants. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Numerical Nuclear Second Derivatives on a Computing Grid: Enabling and Accelerating Frequency Calculations on Complex Molecular Systems.

PubMed

Yang, Tzuhsiung; Berry, John F

2018-06-04

The computation of nuclear second derivatives of energy, or the nuclear Hessian, is an essential routine in quantum chemical investigations of ground and transition states, thermodynamic calculations, and molecular vibrations. Analytic nuclear Hessian computations require the resolution of costly coupled-perturbed self-consistent field (CP-SCF) equations, while numerical differentiation of analytic first derivatives has an unfavorable 6 N ( N = number of atoms) prefactor. Herein, we present a new method in which grid computing is used to accelerate and/or enable the evaluation of the nuclear Hessian via numerical differentiation: NUMFREQ@Grid. Nuclear Hessians were successfully evaluated by NUMFREQ@Grid at the DFT level as well as using RIJCOSX-ZORA-MP2 or RIJCOSX-ZORA-B2PLYP for a set of linear polyacenes with systematically increasing size. For the larger members of this group, NUMFREQ@Grid was found to outperform the wall clock time of analytic Hessian evaluation; at the MP2 or B2LYP levels, these Hessians cannot even be evaluated analytically. We also evaluated a 156-atom catalytically relevant open-shell transition metal complex and found that NUMFREQ@Grid is faster (7.7 times shorter wall clock time) and less demanding (4.4 times less memory requirement) than an analytic Hessian. Capitalizing on the capabilities of parallel grid computing, NUMFREQ@Grid can outperform analytic methods in terms of wall time, memory requirements, and treatable system size. The NUMFREQ@Grid method presented herein demonstrates how grid computing can be used to facilitate embarrassingly parallel computational procedures and is a pioneer for future implementations.

Wound-Healing Studies in Cornea and Skin: Parallels, Differences and Opportunities

PubMed Central

Bukowiecki, Anne; Hos, Deniz; Cursiefen, Claus; Eming, Sabine A.

2017-01-01

The cornea and the skin are both organs that provide the outer barrier of the body. Both tissues have developed intrinsic mechanisms that protect the organism from a wide range of external threats, but at the same time also enable rapid restoration of tissue integrity and organ-specific function. The easy accessibility makes the skin an attractive model system to study tissue damage and repair. Findings from skin research have contributed to unravelling novel fundamental principles in regenerative biology and the repair of other epithelial-mesenchymal tissues, such as the cornea. Following barrier disruption, the influx of inflammatory cells, myofibroblast differentiation, extracellular matrix synthesis and scar formation present parallel repair mechanisms in cornea and skin wound healing. Yet, capillary sprouting, while pivotal in proper skin wound healing, is a process that is rather associated with pathological repair of the cornea. Understanding the parallels and differences of the cellular and molecular networks that coordinate the wound healing response in skin and cornea are likely of mutual importance for both organs with regard to the development of regenerative therapies and understanding of the disease pathologies that affect epithelial-mesenchymal interactions. Here, we review the principal events in corneal wound healing and the mechanisms to restore corneal transparency and barrier function. We also refer to skin repair mechanisms and their potential implications for regenerative processes in the cornea. PMID:28604651

Preliminary Diffusive Clearance of Silicon Nanopore Membranes in a Parallel Plate Configuration for Renal Replacement Therapy

PubMed Central

Kim, Steven; Heller, James; Iqbal, Zohora; Kant, Rishi; Kim, Eun Jung; Durack, Jeremy; Saeed, Maythem; Do, Loi; Hetts, Steven; Wilson, Mark; Brakeman, Paul; Fissell, William H.; Roy, Shuvo

2015-01-01

Silicon nanopore membranes (SNM) with compact geometry and uniform pore size distribution have demonstrated a remarkable capacity for hemofiltration. These advantages could potentially be used for hemodialysis. Here we present an initial evaluation of the SNM’s mechanical robustness, diffusive clearance, and hemocompatibility in a parallel plate configuration. Mechanical robustness of the SNM was demonstrated by exposing membranes to high flows (200ml/min) and pressures (1,448mmHg). Diffusive clearance was performed in an albumin solution and whole blood with blood and dialysate flow rates of 25ml/min. Hemocompatibility was evaluated using scanning electron microscopy and immunohistochemistry after 4-hours in an extra-corporeal porcine model. The pressure drop across the flow cell was 4.6mmHg at 200ml/min. Mechanical testing showed that SNM could withstand up to 775.7mmHg without fracture. Urea clearance did not show an appreciable decline in blood versus albumin solution. Extra-corporeal studies showed blood was successfully driven via the arterial-venous pressure differential without thrombus formation. Bare silicon showed increased cell adhesion with a 4.1 fold increase and 1.8 fold increase over polyethylene-glycol (PEG)-coated surfaces for tissue plasminogen factor (t-PA) and platelet adhesion (CD-41), respectively. These initial results warrant further design and development of a fully scaled SNM-based parallel plate dialyzer for renal replacement therapy. PMID:26692401

DOMAIN DECOMPOSITION METHOD APPLIED TO A FLOW PROBLEM Norberto C. Vera Guzmán Institute of Geophysics, UNAM

NASA Astrophysics Data System (ADS)

Vera, N. C.; GMMC

2013-05-01

In this paper we present the results of macrohybrid mixed Darcian flow in porous media in a general three-dimensional domain. The global problem is solved as a set of local subproblems which are posed using a domain decomposition method. Unknown fields of local problems, velocity and pressure are approximated using mixed finite elements. For this application, a general three-dimensional domain is considered which is discretized using tetrahedra. The discrete domain is decomposed into subdomains and reformulated the original problem as a set of subproblems, communicated through their interfaces. To solve this set of subproblems, we use finite element mixed and parallel computing. The parallelization of a problem using this methodology can, in principle, to fully exploit a computer equipment and also provides results in less time, two very important elements in modeling. Referencias G.Alduncin and N.Vera-Guzmán Parallel proximal-point algorithms for mixed _nite element models of _ow in the subsurface, Commun. Numer. Meth. Engng 2004; 20:83-104 (DOI: 10.1002/cnm.647) Z. Chen, G.Huan and Y. Ma Computational Methods for Multiphase Flows in Porous Media, SIAM, Society for Industrial and Applied Mathematics, Philadelphia, 2006. A. Quarteroni and A. Valli, Numerical Approximation of Partial Differential Equations, Springer-Verlag, Berlin, 1994. Brezzi F, Fortin M. Mixed and Hybrid Finite Element Methods. Springer: New York, 1991.

Parallel tagged next-generation sequencing on pooled samples - a new approach for population genetics in ecology and conservation.

PubMed

Zavodna, Monika; Grueber, Catherine E; Gemmell, Neil J

2013-01-01

Next-generation sequencing (NGS) on pooled samples has already been broadly applied in human medical diagnostics and plant and animal breeding. However, thus far it has been only sparingly employed in ecology and conservation, where it may serve as a useful diagnostic tool for rapid assessment of species genetic diversity and structure at the population level. Here we undertake a comprehensive evaluation of the accuracy, practicality and limitations of parallel tagged amplicon NGS on pooled population samples for estimating species population diversity and structure. We obtained 16S and Cyt b data from 20 populations of Leiopelma hochstetteri, a frog species of conservation concern in New Zealand, using two approaches - parallel tagged NGS on pooled population samples and individual Sanger sequenced samples. Data from each approach were then used to estimate two standard population genetic parameters, nucleotide diversity (π) and population differentiation (FST), that enable population genetic inference in a species conservation context. We found a positive correlation between our two approaches for population genetic estimates, showing that the pooled population NGS approach is a reliable, rapid and appropriate method for population genetic inference in an ecological and conservation context. Our experimental design also allowed us to identify both the strengths and weaknesses of the pooled population NGS approach and outline some guidelines and suggestions that might be considered when planning future projects.

High performance computing aspects of a dimension independent semi-Lagrangian discontinuous Galerkin code

NASA Astrophysics Data System (ADS)

Einkemmer, Lukas

2016-05-01

The recently developed semi-Lagrangian discontinuous Galerkin approach is used to discretize hyperbolic partial differential equations (usually first order equations). Since these methods are conservative, local in space, and able to limit numerical diffusion, they are considered a promising alternative to more traditional semi-Lagrangian schemes (which are usually based on polynomial or spline interpolation). In this paper, we consider a parallel implementation of a semi-Lagrangian discontinuous Galerkin method for distributed memory systems (so-called clusters). Both strong and weak scaling studies are performed on the Vienna Scientific Cluster 2 (VSC-2). In the case of weak scaling we observe a parallel efficiency above 0.8 for both two and four dimensional problems and up to 8192 cores. Strong scaling results show good scalability to at least 512 cores (we consider problems that can be run on a single processor in reasonable time). In addition, we study the scaling of a two dimensional Vlasov-Poisson solver that is implemented using the framework provided. All of the simulations are conducted in the context of worst case communication overhead; i.e., in a setting where the CFL (Courant-Friedrichs-Lewy) number increases linearly with the problem size. The framework introduced in this paper facilitates a dimension independent implementation of scientific codes (based on C++ templates) using both an MPI and a hybrid approach to parallelization. We describe the essential ingredients of our implementation.

Wound-Healing Studies in Cornea and Skin: Parallels, Differences and Opportunities.

PubMed

Bukowiecki, Anne; Hos, Deniz; Cursiefen, Claus; Eming, Sabine A

2017-06-12

The cornea and the skin are both organs that provide the outer barrier of the body. Both tissues have developed intrinsic mechanisms that protect the organism from a wide range of external threats, but at the same time also enable rapid restoration of tissue integrity and organ-specific function. The easy accessibility makes the skin an attractive model system to study tissue damage and repair. Findings from skin research have contributed to unravelling novel fundamental principles in regenerative biology and the repair of other epithelial-mesenchymal tissues, such as the cornea. Following barrier disruption, the influx of inflammatory cells, myofibroblast differentiation, extracellular matrix synthesis and scar formation present parallel repair mechanisms in cornea and skin wound healing. Yet, capillary sprouting, while pivotal in proper skin wound healing, is a process that is rather associated with pathological repair of the cornea. Understanding the parallels and differences of the cellular and molecular networks that coordinate the wound healing response in skin and cornea are likely of mutual importance for both organs with regard to the development of regenerative therapies and understanding of the disease pathologies that affect epithelial-mesenchymal interactions. Here, we review the principal events in corneal wound healing and the mechanisms to restore corneal transparency and barrier function. We also refer to skin repair mechanisms and their potential implications for regenerative processes in the cornea.

R-spondin 2 facilitates differentiation of proliferating chondrocytes into hypertrophic chondrocytes by enhancing Wnt/β-catenin signaling in endochondral ossification

DOE Office of Scientific and Technical Information (OSTI.GOV)

Takegami, Yasuhiko; Department of Orthopaedic Surgery, Nagoya University School of Medicine, Nagoya; Ohkawara, Bisei

Endochondral ossification is a crucial process for longitudinal growth of bones. Differentiating chondrocytes in growth cartilage form four sequential zones of proliferation, alignment into column, hypertrophy, and substitution of chondrocytes with osteoblasts. Wnt/β-catenin signaling is essential for differentiation of proliferating chondrocytes into hypertrophic chondrocytes in growth cartilage. R-spondin 2 (Rspo2), a member of R-spondin family, is an agonist for Wnt signaling, but its role in chondrocyte differentiation remains unknown. Here we report that growth cartilage of Rspo2-knockout mice shows a decreased amount of β-catenin and increased amounts collagen type II (CII) and Sox9 in the abnormally extended proliferating zone. Inmore » contrast, expression of collagen type X (CX) in the hypertrophic zone remains unchanged. Differentiating chondrogenic ATDC5 cells, mimicking proliferating chondrocytes, upregulate Rspo2 and its putative receptor, Lgr5, in parallel. Addition of recombinant human Rspo2 to differentiating ATDC5 cells decreases expressions of Col2a1, Sox9, and Acan, as well as production of proteoglycans. In contrast, lentivirus-mediated knockdown of Rspo2 has the opposite effect. The effect of Rspo2 on chondrogenic differentiation is mediated by Wnt/β-catenin signaling, and not by Wnt/PCP or Wnt/Ca{sup 2+} signaling. We propose that Rspo2 activates Wnt/β-catenin signaling to reduce Col2a1 and Sox9 and to facilitate differentiation of proliferating chondrocytes into hypertrophic chondrocytes in growth cartilage. - Highlights: • Rspo2 is a secreted activator of Wnt, and its knockout shows extended proliferating chondrocytes in endochondral ossification. • In proliferating chondrocytes of Rspo2-knockout mice, Sox9 and collagen type 2 are increased and β-catenin is decreased. • Rspo2 and its receptor Lgr5, as well as Sox9 and collagen type 2, are expressed in differentiating ATDC5 chondrogenic cells. • In ATDC5 cells, Rspo2 decreases expressions of Sox9, collagen type 2, and aggrecan through Wnt/β-catenin signaling. • We propose that Rspo2 activates Wnt/β-catenin to facilitate chondrocyte differentiation in endochondral ossification.« less

Neoclassical, semi-collisional tearing mode theory in an axisymmetric torus

NASA Astrophysics Data System (ADS)

Connor, J. W.; Hastie, R. J.; Helander, P.

2017-12-01

A set of layer equations for determining the stability of semi-collisional tearing modes in an axisymmetric torus, incorporating neoclassical physics, in the small ion Larmor radius limit, is provided. These can be used as an inner layer module for inclusion in numerical codes that asymptotically match the layer to toroidal calculations of the tearing mode stability index, \\prime $ . They are more complete than in earlier work and comprise equations for the perturbed electron density and temperature, the ion temperature, Ampère's law and the vorticity equation, amounting to a twelvth-order set of radial differential equations. While the toroidal geometry is kept quite general when treating the classical and Pfirsch-Schlüter transport, parallel bootstrap current and semi-collisional physics, it is assumed that the fraction of trapped particles is small for the banana regime contribution. This is to justify the use of a model collision term when acting on the localised (in velocity space) solutions that remain after the Spitzer solutions have been exploited to account for the bulk of the passing distributions. In this respect, unlike standard neoclassical transport theory, the calculation involves the second Spitzer solution connected with a parallel temperature gradient, because this stability problem involves parallel temperature gradients that cannot occur in equilibrium toroidal transport theory. Furthermore, a calculation of the linearised neoclassical radial transport of toroidal momentum for general geometry is required to complete the vorticity equation. The solutions of the resulting set of equations do not match properly to the ideal magnetohydrodynamic (MHD) equations at large distances from the layer, and a further, intermediate layer involving ion corrections to the electrical conductivity and ion parallel thermal transport is invoked to achieve this matching and allow one to correctly calculate the layer \\prime $ .

A Dynamic Finite Element Method for Simulating the Physics of Faults Systems

NASA Astrophysics Data System (ADS)

Saez, E.; Mora, P.; Gross, L.; Weatherley, D.

2004-12-01

We introduce a dynamic Finite Element method using a novel high level scripting language to describe the physical equations, boundary conditions and time integration scheme. The library we use is the parallel Finley library: a finite element kernel library, designed for solving large-scale problems. It is incorporated as a differential equation solver into a more general library called escript, based on the scripting language Python. This library has been developed to facilitate the rapid development of 3D parallel codes, and is optimised for the Australian Computational Earth Systems Simulator Major National Research Facility (ACcESS MNRF) supercomputer, a 208 processor SGI Altix with a peak performance of 1.1 TFlops. Using the scripting approach we obtain a parallel FE code able to take advantage of the computational efficiency of the Altix 3700. We consider faults as material discontinuities (the displacement, velocity, and acceleration fields are discontinuous at the fault), with elastic behavior. The stress continuity at the fault is achieved naturally through the expression of the fault interactions in the weak formulation. The elasticity problem is solved explicitly in time, using the Saint Verlat scheme. Finally, we specify a suitable frictional constitutive relation and numerical scheme to simulate fault behaviour. Our model is based on previous work on modelling fault friction and multi-fault systems using lattice solid-like models. We adapt the 2D model for simulating the dynamics of parallel fault systems described to the Finite-Element method. The approach uses a frictional relation along faults that is slip and slip-rate dependent, and the numerical integration approach introduced by Mora and Place in the lattice solid model. In order to illustrate the new Finite Element model, single and multi-fault simulation examples are presented.

Facilitating arrhythmia simulation: the method of quantitative cellular automata modeling and parallel running

PubMed Central

Zhu, Hao; Sun, Yan; Rajagopal, Gunaretnam; Mondry, Adrian; Dhar, Pawan

2004-01-01

Background Many arrhythmias are triggered by abnormal electrical activity at the ionic channel and cell level, and then evolve spatio-temporally within the heart. To understand arrhythmias better and to diagnose them more precisely by their ECG waveforms, a whole-heart model is required to explore the association between the massively parallel activities at the channel/cell level and the integrative electrophysiological phenomena at organ level. Methods We have developed a method to build large-scale electrophysiological models by using extended cellular automata, and to run such models on a cluster of shared memory machines. We describe here the method, including the extension of a language-based cellular automaton to implement quantitative computing, the building of a whole-heart model with Visible Human Project data, the parallelization of the model on a cluster of shared memory computers with OpenMP and MPI hybrid programming, and a simulation algorithm that links cellular activity with the ECG. Results We demonstrate that electrical activities at channel, cell, and organ levels can be traced and captured conveniently in our extended cellular automaton system. Examples of some ECG waveforms simulated with a 2-D slice are given to support the ECG simulation algorithm. A performance evaluation of the 3-D model on a four-node cluster is also given. Conclusions Quantitative multicellular modeling with extended cellular automata is a highly efficient and widely applicable method to weave experimental data at different levels into computational models. This process can be used to investigate complex and collective biological activities that can be described neither by their governing differentiation equations nor by discrete parallel computation. Transparent cluster computing is a convenient and effective method to make time-consuming simulation feasible. Arrhythmias, as a typical case, can be effectively simulated with the methods described. PMID:15339335

Advancing MODFLOW Applying the Derived Vector Space Method

NASA Astrophysics Data System (ADS)

Herrera, G. S.; Herrera, I.; Lemus-García, M.; Hernandez-Garcia, G. D.

2015-12-01

The most effective domain decomposition methods (DDM) are non-overlapping DDMs. Recently a new approach, the DVS-framework, based on an innovative discretization method that uses a non-overlapping system of nodes (the derived-nodes), was introduced and developed by I. Herrera et al. [1, 2]. Using the DVS-approach a group of four algorithms, referred to as the 'DVS-algorithms', which fulfill the DDM-paradigm (i.e. the solution of global problems is obtained by resolution of local problems exclusively) has been derived. Such procedures are applicable to any boundary-value problem, or system of such equations, for which a standard discretization method is available and then software with a high degree of parallelization can be constructed. In a parallel talk, in this AGU Fall Meeting, Ismael Herrera will introduce the general DVS methodology. The application of the DVS-algorithms has been demonstrated in the solution of several boundary values problems of interest in Geophysics. Numerical examples for a single-equation, for the cases of symmetric, non-symmetric and indefinite problems were demonstrated before [1,2]. For these problems DVS-algorithms exhibited significantly improved numerical performance with respect to standard versions of DDM algorithms. In view of these results our research group is in the process of applying the DVS method to a widely used simulator for the first time, here we present the advances of the application of this method for the parallelization of MODFLOW. Efficiency results for a group of tests will be presented. References [1] I. Herrera, L.M. de la Cruz and A. Rosas-Medina. Non overlapping discretization methods for partial differential equations, Numer Meth Part D E, (2013). [2] Herrera, I., & Contreras Iván "An Innovative Tool for Effectively Applying Highly Parallelized Software To Problems of Elasticity". Geofísica Internacional, 2015 (In press)

A simple hyperbolic model for communication in parallel processing environments

NASA Technical Reports Server (NTRS)

Stoica, Ion; Sultan, Florin; Keyes, David

1994-01-01

We introduce a model for communication costs in parallel processing environments called the 'hyperbolic model,' which generalizes two-parameter dedicated-link models in an analytically simple way. Dedicated interprocessor links parameterized by a latency and a transfer rate that are independent of load are assumed by many existing communication models; such models are unrealistic for workstation networks. The communication system is modeled as a directed communication graph in which terminal nodes represent the application processes that initiate the sending and receiving of the information and in which internal nodes, called communication blocks (CBs), reflect the layered structure of the underlying communication architecture. The direction of graph edges specifies the flow of the information carried through messages. Each CB is characterized by a two-parameter hyperbolic function of the message size that represents the service time needed for processing the message. The parameters are evaluated in the limits of very large and very small messages. Rules are given for reducing a communication graph consisting of many to an equivalent two-parameter form, while maintaining an approximation for the service time that is exact in both large and small limits. The model is validated on a dedicated Ethernet network of workstations by experiments with communication subprograms arising in scientific applications, for which a tight fit of the model predictions with actual measurements of the communication and synchronization time between end processes is demonstrated. The model is then used to evaluate the performance of two simple parallel scientific applications from partial differential equations: domain decomposition and time-parallel multigrid. In an appropriate limit, we also show the compatibility of the hyperbolic model with the recently proposed LogP model.

Aerodynamic Shape Optimization of Supersonic Aircraft Configurations via an Adjoint Formulation on Parallel Computers

NASA Technical Reports Server (NTRS)

Reuther, James; Alonso, Juan Jose; Rimlinger, Mark J.; Jameson, Antony

1996-01-01

This work describes the application of a control theory-based aerodynamic shape optimization method to the problem of supersonic aircraft design. The design process is greatly accelerated through the use of both control theory and a parallel implementation on distributed memory computers. Control theory is employed to derive the adjoint differential equations whose solution allows for the evaluation of design gradient information at a fraction of the computational cost required by previous design methods (13, 12, 44, 38). The resulting problem is then implemented on parallel distributed memory architectures using a domain decomposition approach, an optimized communication schedule, and the MPI (Message Passing Interface) Standard for portability and efficiency. The final result achieves very rapid aerodynamic design based on higher order computational fluid dynamics methods (CFD). In our earlier studies, the serial implementation of this design method (19, 20, 21, 23, 39, 25, 40, 41, 42, 43, 9) was shown to be effective for the optimization of airfoils, wings, wing-bodies, and complex aircraft configurations using both the potential equation and the Euler equations (39, 25). In our most recent paper, the Euler method was extended to treat complete aircraft configurations via a new multiblock implementation. Furthermore, during the same conference, we also presented preliminary results demonstrating that the basic methodology could be ported to distributed memory parallel computing architectures [241. In this paper, our concem will be to demonstrate that the combined power of these new technologies can be used routinely in an industrial design environment by applying it to the case study of the design of typical supersonic transport configurations. A particular difficulty of this test case is posed by the propulsion/airframe integration.

Wnt3a induces the expression of acetylcholinesterase during osteoblast differentiation via the Runx2 transcription factor.

PubMed

Xu, Miranda L; Bi, Cathy W C; Liu, Etta Y L; Dong, Tina T X; Tsim, Karl W K

2017-07-28

Acetylcholinesterase (AChE) hydrolyzes acetylcholine to terminate cholinergic transmission in neurons. Apart from this AChE activity, emerging evidence suggests that AChE could also function in other, non-neuronal cells. For instance, in bone, AChE exists as a proline-rich membrane anchor (PRiMA)-linked globular form in osteoblasts, in which it is proposed to play a noncholinergic role in differentiation. However, this hypothesis is untested. Here, we found that in cultured rat osteoblasts, AChE expression was increased in parallel with osteoblastic differentiation. Because several lines of evidence indicate that AChE activity in osteoblast could be triggered by Wnt/β-catenin signaling, we added recombinant human Wnt3a to cultured osteoblasts and found that this addition induced expression of the ACHE gene and protein product. This Wnt3a-induced AChE expression was blocked by the Wnt-signaling inhibitor Dickkopf protein-1 (DKK-1). We hypothesized that the Runt-related transcription factor 2 (Runx2), a downstream transcription factor in Wnt/β-catenin signaling, is involved in AChE regulation in osteoblasts, confirmed by the identification of a Runx2-binding site in the ACHE gene promoter, further corroborated by ChIP. Of note, Runx2 overexpression in osteoblasts induced AChE expression and activity of the ACHE promoter tagged with the luciferase gene. Moreover, deletion of the Runx2-binding site in the ACHE promoter reduced its activity during osteoblastic differentiation, and addition of 5-azacytidine and trichostatin A to differentiating osteoblasts affected AChE expression, suggesting epigenetic regulation of the ACHE gene. We conclude that AChE plays a role in osteoblastic differentiation and is regulated by both Wnt3a and Runx2. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Altered MENIN expression disrupts the MAFA differentiation pathway in insulinoma.

PubMed

Hamze, Z; Vercherat, C; Bernigaud-Lacheretz, A; Bazzi, W; Bonnavion, R; Lu, J; Calender, A; Pouponnot, C; Bertolino, P; Roche, C; Stein, R; Scoazec, J Y; Zhang, C X; Cordier-Bussat, M

2013-12-01

The protein MENIN is the product of the multiple endocrine neoplasia type I (MEN1) gene. Altered MENIN expression is one of the few events that are clearly associated with foregut neuroendocrine tumours (NETs), classical oncogenes or tumour suppressors being not involved. One of the current challenges is to understand how alteration of MENIN expression contributes to the development of these tumours. We hypothesised that MENIN might regulate factors maintaining endocrine-differentiated functions. We chose the insulinoma model, a paradigmatic example of well-differentiated pancreatic NETs, to study whether MENIN interferes with the expression of v-MAF musculoaponeurotic fibrosarcoma oncogene homologue A (MAFA), a master glucose-dependent transcription factor in differentiated β-cells. Immunohistochemical analysis of a series of human insulinomas revealed a correlated decrease in both MENIN and MAFA. Decreased MAFA expression resulting from targeted Men1 ablation was also consistently observed in mouse insulinomas. In vitro analyses using insulinoma cell lines showed that MENIN regulated MAFA protein and mRNA levels, and bound to Mafa promoter sequences. MENIN knockdown concomitantly decreased mRNA expression of both Mafa and β-cell differentiation markers (Ins1/2, Gck, Slc2a2 and Pdx1) and, in parallel, increased the proliferation rate of tumours as measured by bromodeoxyuridine incorporation. Interestingly, MAFA knockdown alone also increased proliferation rate but did not affect the expression of candidate proliferation genes regulated by MENIN. Finally, MENIN variants with missense mutations detected in patients with MEN1 lost the WT MENIN properties to regulate MAFA. Together, our findings unveil a previously unsuspected MENIN/MAFA connection regarding control of the β-cell differentiation/proliferation balance, which could contribute to tumorigenesis.

Antitumor activity of ethanol extract from Hippophae rhamnoides L. leaves towards human acute myeloid leukemia cells in vitro.

PubMed

Zhamanbaeva, G T; Murzakhmetova, M K; Tuleukhanov, S T; Danilenko, M P

2014-12-01

We studied the effects of ethanol extract from Hippophae rhamnoides L. leaves on the growth and differentiation of human acute myeloid leukemia cells (KG-1a, HL60, and U937). The extract of Hippophae rhamnoides L. leaves inhibited cell growth depending on the cell strain and extract dose. In a high concentration (100 μg/ml), the extract also exhibited a cytotoxic effect on HL60 cells. Hippophae rhamnoides L. leaves extract did not affect cell differentiation and did not modify the differentiating effect of calcitriol, active vitamin D metabolite. Inhibition of cell proliferation was paralleled by paradoxical accumulation of phase S cells (synthetic phase) with a reciprocal decrease in the count of G1 cells (presynthetic phase). The extract in a concentration of 100 μg/ml induced the appearance of cells with a subdiploid DNA content (sub-G1 phase cells), which indicated induction of apoptosis. The antiproliferative effect of Hippophae rhamnoides L. extract on acute myeloid leukemia cells was at least partially determined by activation of the S phase checkpoint, which probably led to deceleration of the cell cycle and apoptosis induction.

Optical coherence tomography in differential diagnosis of skin pathology

NASA Astrophysics Data System (ADS)

Gladkova, Natalia D.; Petrova, Galina P.; Derpaluk, Elena; Nikulin, Nikolai K.; Snopova, Ludmila; Chumakov, Yuri; Feldchtein, Felix I.; Gelikonov, Valentin M.; Gelikonov, Grigory V.; Kuranov, Roman V.

2000-05-01

The capabilities of optical coherence tomography (OCT) for imaging in vivo of optical patterns of pathomorphological processes in the skin and use of their optical patterns in clinical practice for differential diagnosis of dermatoses are presented. Images of skin tissue 0.8 - 1.5 mm deep were acquired with a resolution of 5, 12 and 20 micrometer using three compact fiber OCT devices developed at the Institute of Applied Physics RAS. The acquisition time of images of skin regions 2 - 6 mm in length was 2 - 4 s. The OCT capabilities were analyzed based on the study of 50 patients with different dermatoses. OCT images were interpreted by comparing with parallel histology. It is shown that OCT can detect in vivo optical patterns of morphological alterations in such general papulous dermatoses as lichen ruber planus and psoriasis, a capability that can be used in differential diagnosis of these diseases. Most informative are OCT images obtained with a resolution of 5 micrometer. The results of our study demonstrate the practical importance of OCT imaging for diagnosis of different dermatoses. OCT is noninvasive and, therefore, makes it possible to perform frequent multifocal examination of skin without any adverse effects.

A microRNA-mRNA expression network during oral siphon regeneration in Ciona.

PubMed

Spina, Elijah J; Guzman, Elmer; Zhou, Hongjun; Kosik, Kenneth S; Smith, William C

2017-05-15

Here we present a parallel study of mRNA and microRNA expression during oral siphon (OS) regeneration in Ciona robusta , and the derived network of their interactions. In the process of identifying 248 mRNAs and 15 microRNAs as differentially expressed, we also identified 57 novel microRNAs, several of which are among the most highly differentially expressed. Analysis of functional categories identified enriched transcripts related to stress responses and apoptosis at the wound healing stage, signaling pathways including Wnt and TGFβ during early regrowth, and negative regulation of extracellular proteases in late stage regeneration. Consistent with the expression results, we found that inhibition of TGFβ signaling blocked OS regeneration. A correlation network was subsequently inferred for all predicted microRNA-mRNA target pairs expressed during regeneration. Network-based clustering associated transcripts into 22 non-overlapping groups, the functional analysis of which showed enrichment of stress response, signaling pathway and extracellular protease categories that could be related to specific microRNAs. Predicted targets of the miR-9 cluster suggest a role in regulating differentiation and the proliferative state of neural progenitors through regulation of the cytoskeleton and cell cycle. © 2017. Published by The Company of Biologists Ltd.

csaw: a Bioconductor package for differential binding analysis of ChIP-seq data using sliding windows

PubMed Central

Lun, Aaron T.L.; Smyth, Gordon K.

2016-01-01

Chromatin immunoprecipitation with massively parallel sequencing (ChIP-seq) is widely used to identify binding sites for a target protein in the genome. An important scientific application is to identify changes in protein binding between different treatment conditions, i.e. to detect differential binding. This can reveal potential mechanisms through which changes in binding may contribute to the treatment effect. The csaw package provides a framework for the de novo detection of differentially bound genomic regions. It uses a window-based strategy to summarize read counts across the genome. It exploits existing statistical software to test for significant differences in each window. Finally, it clusters windows into regions for output and controls the false discovery rate properly over all detected regions. The csaw package can handle arbitrarily complex experimental designs involving biological replicates. It can be applied to both transcription factor and histone mark datasets, and, more generally, to any type of sequencing data measuring genomic coverage. csaw performs favorably against existing methods for de novo DB analyses on both simulated and real data. csaw is implemented as a R software package and is freely available from the open-source Bioconductor project. PMID:26578583

A microRNA-mRNA expression network during oral siphon regeneration in Ciona

PubMed Central

Spina, Elijah J.; Guzman, Elmer; Zhou, Hongjun; Kosik, Kenneth S.

2017-01-01

Here we present a parallel study of mRNA and microRNA expression during oral siphon (OS) regeneration in Ciona robusta, and the derived network of their interactions. In the process of identifying 248 mRNAs and 15 microRNAs as differentially expressed, we also identified 57 novel microRNAs, several of which are among the most highly differentially expressed. Analysis of functional categories identified enriched transcripts related to stress responses and apoptosis at the wound healing stage, signaling pathways including Wnt and TGFβ during early regrowth, and negative regulation of extracellular proteases in late stage regeneration. Consistent with the expression results, we found that inhibition of TGFβ signaling blocked OS regeneration. A correlation network was subsequently inferred for all predicted microRNA-mRNA target pairs expressed during regeneration. Network-based clustering associated transcripts into 22 non-overlapping groups, the functional analysis of which showed enrichment of stress response, signaling pathway and extracellular protease categories that could be related to specific microRNAs. Predicted targets of the miR-9 cluster suggest a role in regulating differentiation and the proliferative state of neural progenitors through regulation of the cytoskeleton and cell cycle. PMID:28432214

Los Años de la Crisis: an examination of change in differential infant mortality risk within Mexico.

PubMed

Frank, R; Finch, Brian Karl

2004-08-01

The main aim of the present analysis is to test the possibility that the period of economic hardship characterizing Mexico over the decade 1986-1996 has negatively influenced infant health outcomes. Data on births from two installments of the Encuesta Nacional de la Dinámica Demográfica, a nationally representative demographic survey, are used to determine whether a reduction in mortality differentials has paralleled the overall drop in the national infant mortality rate. The findings indicate that the decrease observed in the overall infant mortality rate has been matched by decreases in several disparities at the same time that it has been marred by increases in others. The data support the possibility that where you live has become an increasingly salient factor in determining the odds of infant mortality. High parity, low education and unemployment status have also become more salient factors in predicting post neonatal infant mortality risk in the more recent period as compared to the earlier period. As Mexico's infant mortality rate begins to stabilize in the near future, this research highlights the need to re-focus our research efforts on the causes and consequences of differential mortality trends.

Lens fibre cell differentiation and organelle loss: many paths lead to clarity

PubMed Central

Wride, Michael A.

2011-01-01

The programmed removal of organelles from differentiating lens fibre cells contributes towards lens transparency through formation of an organelle-free zone (OFZ). Disruptions in OFZ formation are accompanied by the persistence of organelles in lens fibre cells and can contribute towards cataract. A great deal of work has gone into elucidating the nature of the mechanisms and signalling pathways involved. It is apparent that multiple, parallel and redundant pathways are involved in this process and that these pathways form interacting networks. Furthermore, it is possible that the pathways can functionally compensate for each other, for example in mouse knockout studies. This makes sense given the importance of lens clarity in an evolutionary context. Apoptosis signalling and proteolytic pathways have been implicated in both lens fibre cell differentiation and organelle loss, including the Bcl-2 and inhibitor of apoptosis families, tumour necrosis factors, p53 and its regulators (such as Mdm2) and proteolytic enzymes, including caspases, cathepsins, calpains and the ubiquitin–proteasome pathway. Ongoing approaches being used to dissect the molecular pathways involved, such as transgenics, lens-specific gene deletion and zebrafish mutants, are discussed here. Finally, some of the remaining unresolved issues and potential areas for future studies are highlighted. PMID:21402582

Bioactive glass ions as strong enhancers of osteogenic differentiation in human adipose stem cells.

PubMed

Ojansivu, Miina; Vanhatupa, Sari; Björkvik, Leena; Häkkänen, Heikki; Kellomäki, Minna; Autio, Reija; Ihalainen, Janne A; Hupa, Leena; Miettinen, Susanna

2015-07-01

Bioactive glasses are known for their ability to induce osteogenic differentiation of stem cells. To elucidate the mechanism of the osteoinductivity in more detail, we studied whether ionic extracts prepared from a commercial glass S53P4 and from three experimental glasses (2-06, 1-06 and 3-06) are alone sufficient to induce osteogenic differentiation of human adipose stem cells. Cells were cultured using basic medium or osteogenic medium as extract basis. Our results indicate that cells stay viable in all the glass extracts for the whole culturing period, 14 days. At 14 days the mineralization in osteogenic medium extracts was excessive compared to the control. Parallel to the increased mineralization we observed a decrease in the cell amount. Raman and Laser Induced Breakdown Spectroscopy analyses confirmed that the mineral consisted of calcium phosphates. Consistently, the osteogenic medium extracts also increased osteocalcin production and collagen Type-I accumulation in the extracellular matrix at 13 days. Of the four osteogenic medium extracts, 2-06 and 3-06 induced the best responses of osteogenesis. However, regardless of the enhanced mineral formation, alkaline phosphatase activity was not promoted by the extracts. The osteogenic medium extracts could potentially provide a fast and effective way to differentiate human adipose stem cells in vitro. Copyright © 2015 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Effects of Maternal Dietary Restriction of Vitamin B-6 on Neocortex Development in Rats

NASA Astrophysics Data System (ADS)

Groziak, Susan Marie

The aim of this investigation was to quantitate the effects of a dietary restriction in Vitamin B-6 during gestation or gestation and lactation on neurogenesis, neuron longevity and neuron differentiation in the neocortex of rats. Sprague Dawley female rats were fed, ad libitum, a Vitamin B-6 free diet (AIN 76) supplemented with 0.0 or 0.6 mg pyridoxine (PN)/kg diet during gestation followed by a control level of 7.0 mg PN/kg diet during lactation, or were fed the Vitamin B-6 free diet supplemented with 0.6 or 7.0 mg PN/kg diet throughout gestation and lactation. The neocortex of progeny of these animals were examined at 30 days of age employing light and electron microscopy. Analyses of neurogenesis, neuron longevity and differentiation of neurons (size of somata, dendritic arborization and spine density in Golgi Cox preparations, and synaptic density in E.M. preparations) were conducted. Each of the Vitamin B-6 restricted treatments adversely affected neurogenesis, neuron longevity and neuron differentiation. The degree of adverse effects paralleled the severity (dose or duration) of the restriction imposed. Expressed as percentage reduction from control values, the findings indicated that neuron longevity and differentiation of neurons in the neocortex were more severely affected than neurogenesis by a maternal dietary restriction in Vitamin B-6.

DEMONSTRATION OF ACID PHOSPHATASE-CONTAINING GRANULES AND CYTOPLASMIC BODIES IN THE EPITHELIUM OF FOETAL RAT DUODENUM DURING CERTAIN STAGES OF DIFFERENTIATION

PubMed Central

Behnke, O.

1963-01-01

Dense cytoplasmic bodies surrounded by one or two unit membranes and containing mitochondria, vesicles, ribosomes, rough and smooth surfaced endoplasmic reticulum, and lamellated membranes (myelin figures) have been observed in the differentiating mucosa of the duodenum of rat foetuses by electron microscopy. Generally, the cytoplasmic components in the bodies seem to be in varying stages of disintegration. The bodies are found in greatest number on the 17th and 18th day of gestation, i.e. at the onset of differentiation. At this period of development the epithelium is stratified, and the villus formation is initiated by invagination of the epithelium by buds of mesenchyme followed by a splitting of the epithelium along the sides of the invaginations. When the villi have formed, the stratified epithelium has changed to the simple columnar type and the dense bodies have largely disappeared. Simultaneously, the lumen has widened considerably. In a parallel study with the light microscope, frozen sections incubated for the demonstration of acid phosphatase activity revealed the reaction product to be localized in bodies of the same size and distribution as the dense bodies found by electron microscopy. Hence, it seems that the bodies are altered and enlarged lysosomes (cytolysomes) active during the intensive differentiative events in the small intestine during the last part of intra-uterine life. PMID:14079488

Histological and transcriptomic effects of 17α-methyltestosterone on zebrafish gonad development.

PubMed

Lee, Stephanie Ling Jie; Horsfield, Julia A; Black, Michael A; Rutherford, Kim; Fisher, Amanda; Gemmell, Neil J

2017-07-24

Sex hormones play important roles in teleost ovarian and testicular development. In zebrafish, ovarian differentiation appears to be dictated by an oocyte-derived signal via Cyp19a1a aromatase-mediated estrogen production. Androgens and aromatase inhibitors can induce female-to-male sex reversal, however, the mechanisms underlying gonadal masculinisation are poorly understood. We used histological analyses together with RNA sequencing to characterise zebrafish gonadal transcriptomes and investigate the effects of 17α-methyltestosterone on gonadal differentiation. At a morphological level, 17α-methyltestosterone (MT) masculinised gonads and accelerated spermatogenesis, and these changes were paralleled in masculinisation and de-feminisation of gonadal transcriptomes. MT treatment upregulated expression of genes involved in male sex determination and differentiation (amh, dmrt1, gsdf and wt1a) and those involved in 11-oxygenated androgen production (cyp11c1 and hsd11b2). It also repressed expression of ovarian development and folliculogenesis genes (bmp15, gdf9, figla, zp2.1 and zp3b). Furthermore, MT treatment altered epigenetic modification of histones in zebrafish gonads. Contrary to expectations, higher levels of cyp19a1a or foxl2 expression in control ovaries compared to MT-treated testes and control testes were not statistically significant during early gonad development (40 dpf). Our study suggests that both androgen production and aromatase inhibition are important for androgen-induced gonadal masculinisation and natural testicular differentiation in zebrafish.

IFN-α regulates Blimp-1 expression via miR-23a and miR-125b in both monocytes-derived DC and pDC.

PubMed

Parlato, Stefania; Bruni, Roberto; Fragapane, Paola; Salerno, Debora; Marcantonio, Cinzia; Borghi, Paola; Tataseo, Paola; Ciccaglione, Anna Rita; Presutti, Carlo; Romagnoli, Giulia; Bozzoni, Irene; Belardelli, Filippo; Gabriele, Lucia

2013-01-01

Type I interferon (IFN-I) have emerged as crucial mediators of cellular signals controlling DC differentiation and function. Human DC differentiated from monocytes in the presence of IFN-α (IFN-α DC) show a partially mature phenotype and a special capability of stimulating CD4+ T cell and cross-priming CD8+ T cells. Likewise, plasmacytoid DC (pDC) are blood DC highly specialized in the production of IFN-α in response to viruses and other danger signals, whose functional features may be shaped by IFN-I. Here, we investigated the molecular mechanisms stimulated by IFN-α in driving human monocyte-derived DC differentiation and performed parallel studies on peripheral unstimulated and IFN-α-treated pDC. A specific miRNA signature was induced in IFN-α DC and selected miRNAs, among which miR-23a and miR-125b, proved to be negatively associated with up-modulation of Blimp-1 occurring during IFN-α-driven DC differentiation. Of note, monocyte-derived IFN-α DC and in vitro IFN-α-treated pDC shared a restricted pattern of miRNAs regulating Blimp-1 expression as well as some similar phenotypic, molecular and functional hallmarks, supporting the existence of a potential relationship between these DC populations. On the whole, these data uncover a new role of Blimp-1 in human DC differentiation driven by IFN-α and identify Blimp-1 as an IFN-α-mediated key regulator potentially accounting for shared functional features between IFN-α DC and pDC.

IFN-α Regulates Blimp-1 Expression via miR-23a and miR-125b in Both Monocytes-Derived DC and pDC

PubMed Central

Parlato, Stefania; Salerno, Debora; Marcantonio, Cinzia; Borghi, Paola; Tataseo, Paola; Ciccaglione, Anna Rita; Presutti, Carlo; Romagnoli, Giulia; Bozzoni, Irene; Belardelli, Filippo; Gabriele, Lucia

2013-01-01

Type I interferon (IFN-I) have emerged as crucial mediators of cellular signals controlling DC differentiation and function. Human DC differentiated from monocytes in the presence of IFN-α (IFN-α DC) show a partially mature phenotype and a special capability of stimulating CD4+ T cell and cross-priming CD8+ T cells. Likewise, plasmacytoid DC (pDC) are blood DC highly specialized in the production of IFN-α in response to viruses and other danger signals, whose functional features may be shaped by IFN-I. Here, we investigated the molecular mechanisms stimulated by IFN-α in driving human monocyte-derived DC differentiation and performed parallel studies on peripheral unstimulated and IFN-α-treated pDC. A specific miRNA signature was induced in IFN-α DC and selected miRNAs, among which miR-23a and miR-125b, proved to be negatively associated with up-modulation of Blimp-1 occurring during IFN-α-driven DC differentiation. Of note, monocyte-derived IFN-α DC and in vitro IFN-α-treated pDC shared a restricted pattern of miRNAs regulating Blimp-1 expression as well as some similar phenotypic, molecular and functional hallmarks, supporting the existence of a potential relationship between these DC populations. On the whole, these data uncover a new role of Blimp-1 in human DC differentiation driven by IFN-α and identify Blimp-1 as an IFN-α-mediated key regulator potentially accounting for shared functional features between IFN-α DC and pDC. PMID:23977359

Genome-wide DNase hypersensitivity, and occupancy of RUNX2 and CTCF reveal a highly dynamic gene regulome during MC3T3 pre-osteoblast differentiation.

PubMed

Tai, Phillip W L; Wu, Hai; van Wijnen, André J; Stein, Gary S; Stein, Janet L; Lian, Jane B

2017-01-01

The ability to discover regulatory sequences that control bone-related genes during development has been greatly improved by massively parallel sequencing methodologies. To expand our understanding of cis-regulatory regions critical to the control of gene expression during osteoblastogenesis, we probed the presence of open chromatin states across the osteoblast genome using global DNase hypersensitivity (DHS) mapping. Our profiling of MC3T3 mouse pre-osteoblasts during differentiation has identified more than 224,000 unique DHS sites. Approximately 65% of these sites are dynamic during temporal stages of osteoblastogenesis, and a majority of them are located within non-promoter (intergenic and intronic) regions. Nearly half of all DHS sites (both constitutive and dynamic) overlap binding events of the bone-essential RUNX2 and/or the chromatin-related CTCF transcription factors. This finding reinforces the role of these regulatory proteins as essential components of the bone gene regulome. We observe a reduction in chromatin accessibility throughout the genome between pre-osteoblast and early osteoblasts. Our analysis also defined a class of differentially expressed genes that harbor DHS peaks centered within 1 kb downstream of transcriptional end sites (TES). These DHSs at the 3'-flanks of genes exhibit dynamic changes during differentiation that may impact regulation of the osteoblast genome. Taken together, the distribution of DHS regions within non-promoter locations harboring osteoblast and chromatin related transcription factor binding motifs, reflect novel cis-regulatory requirements to support temporal gene expression in differentiating osteoblasts.

Analysis of MYB oncogene in transformed adenoid cystic carcinomas reveals distinct pathways of tumor progression.

PubMed

Costa, Ana F; Altemani, Albina; García-Inclán, Cristina; Fresno, Florentino; Suárez, Carlos; Llorente, José L; Hermsen, Mario

2014-06-01

Adenoid cystic carcinomas can occasionally undergo dedifferentiation, a phenomenon also referred to as high-grade transformation. However, cases of adenoid cystic carcinomas have been described showing transformation to adenocarcinomas that are not poorly differentiated, indicating that high-grade transformation may not necessarily reflect a more advanced stage of tumor progression, but rather a transformation to another histological form, which may encompass a wide spectrum of carcinomas in terms of aggressiveness. The aim of this study was to gain more insight in the biology of this pathological phenomenon by means of genetic profiling of both histological components. Using microarray comparative genomic hybridization, we compared the genome-wide DNA copy-number changes of the conventional and transformed area of eight adenoid cystic carcinomas with high-grade transformation, comprising four with transformation into moderately differentiated adenocarcinomas and four into poorly differentiated carcinomas. In general, the poorly differentiated carcinoma cases showed a higher total number of copy-number changes than the moderately differentiated adenocarcinoma cases, and this correlated with a worse clinical course. Special attention was given to chromosomal translocation and protein expression of MYB, recently being considered to be an early and major oncogenic event in adenoid cystic carcinomas. Our data showed that the process of high-grade transformation is not always accompanied by an accumulation of genetic alterations; both conventional and transformed components harbored unique genetic alterations, which indicate a parallel progression. Our data further demonstrated that the MYB/NFIB translocation is not necessarily an early event or fundamental for the progression to adenoid cystic carcinoma with high-grade transformation.

Mechanical stimuli differentially control stem cell behavior: morphology, proliferation, and differentiation

PubMed Central

Maul, Timothy M.; Chew, Douglas W.; Nieponice, Alejandro

2011-01-01

Mesenchymal stem cell (MSC) therapy has demonstrated applications in vascular regenerative medicine. Although blood vessels exist in a mechanically dynamic environment, there has been no rigorous, systematic analysis of mechanical stimulation on stem cell differentiation. We hypothesize that mechanical stimuli, relevant to the vasculature, can differentiate MSCs toward smooth muscle (SMCs) and endothelial cells (ECs). This was tested using a unique experimental platform to differentially apply various mechanical stimuli in parallel. Three forces, cyclic stretch, cyclic pressure, and laminar shear stress, were applied independently to mimic several vascular physiologic conditions. Experiments were conducted using subconfluent MSCs for 5 days and demonstrated significant effects on morphology and proliferation depending upon the type, magnitude, frequency, and duration of applied stimulation. We have defined thresholds of cyclic stretch that potentiate SMC protein expression, but did not find EC protein expression under any condition tested. However, a second set of experiments performed at confluence and aimed to elicit the temporal gene expression response of a select magnitude of each stimulus revealed that EC gene expression can be increased with cyclic pressure and shear stress in a cell-contact-dependent manner. Further, these MSCs also appear to express genes from multiple lineages simultaneously which may warrant further investigation into post-transcriptional mechanisms for controlling protein expression. To our knowledge, this is the first systematic examination of the effects of mechanical stimulation on MSCs and has implications for the understanding of stem cell biology, as well as potential bioreactor designs for tissue engineering and cell therapy applications. PMID:21253809

PETSc Users Manual Revision 3.3

DOE Office of Scientific and Technical Information (OSTI.GOV)

Balay, S.; Brown, J.; Buschelman, K.

This manual describes the use of PETSc for the numerical solution of partial differential equations and related problems on high-performance computers. The Portable, Extensible Toolkit for Scientific Computation (PETSc) is a suite of data structures and routines that provide the building blocks for the implementation of large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all message-passing communication. PETSc includes an expanding suite of parallel linear, nonlinear equation solvers and time integrators that may be used in application codes written in Fortran, C, C++, Python, and MATLAB (sequential). PETSc provides many of the mechanisms neededmore » within parallel application codes, such as parallel matrix and vector assembly routines. The library is organized hierarchically, enabling users to employ the level of abstraction that is most appropriate for a particular problem. By using techniques of object-oriented programming, PETSc provides enormous flexibility for users. PETSc is a sophisticated set of software tools; as such, for some users it initially has a much steeper learning curve than a simple subroutine library. In particular, for individuals without some computer science background, experience programming in C, C++ or Fortran and experience using a debugger such as gdb or dbx, it may require a significant amount of time to take full advantage of the features that enable efficient software use. However, the power of the PETSc design and the algorithms it incorporates may make the efficient implementation of many application codes simpler than “rolling them” yourself; For many tasks a package such as MATLAB is often the best tool; PETSc is not intended for the classes of problems for which effective MATLAB code can be written. PETSc also has a MATLAB interface, so portions of your code can be written in MATLAB to “try out” the PETSc solvers. The resulting code will not be scalable however because currently MATLAB is inherently not scalable; and PETSc should not be used to attempt to provide a “parallel linear solver” in an otherwise sequential code. Certainly all parts of a previously sequential code need not be parallelized but the matrix generation portion must be parallelized to expect any kind of reasonable performance. Do not expect to generate your matrix sequentially and then “use PETSc” to solve the linear system in parallel. Since PETSc is under continued development, small changes in usage and calling sequences of routines will occur. PETSc is supported; see the web site http://www.mcs.anl.gov/petsc for information on contacting support. A http://www.mcs.anl.gov/petsc/publications may be found a list of publications and web sites that feature work involving PETSc. We welcome any reports of corrections for this document.« less

PETSc Users Manual Revision 3.4

DOE Office of Scientific and Technical Information (OSTI.GOV)

Balay, S.; Brown, J.; Buschelman, K.

This manual describes the use of PETSc for the numerical solution of partial differential equations and related problems on high-performance computers. The Portable, Extensible Toolkit for Scientific Computation (PETSc) is a suite of data structures and routines that provide the building blocks for the implementation of large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all message-passing communication. PETSc includes an expanding suite of parallel linear, nonlinear equation solvers and time integrators that may be used in application codes written in Fortran, C, C++, Python, and MATLAB (sequential). PETSc provides many of the mechanisms neededmore » within parallel application codes, such as parallel matrix and vector assembly routines. The library is organized hierarchically, enabling users to employ the level of abstraction that is most appropriate for a particular problem. By using techniques of object-oriented programming, PETSc provides enormous flexibility for users. PETSc is a sophisticated set of software tools; as such, for some users it initially has a much steeper learning curve than a simple subroutine library. In particular, for individuals without some computer science background, experience programming in C, C++ or Fortran and experience using a debugger such as gdb or dbx, it may require a significant amount of time to take full advantage of the features that enable efficient software use. However, the power of the PETSc design and the algorithms it incorporates may make the efficient implementation of many application codes simpler than “rolling them” yourself; For many tasks a package such as MATLAB is often the best tool; PETSc is not intended for the classes of problems for which effective MATLAB code can be written. PETSc also has a MATLAB interface, so portions of your code can be written in MATLAB to “try out” the PETSc solvers. The resulting code will not be scalable however because currently MATLAB is inherently not scalable; and PETSc should not be used to attempt to provide a “parallel linear solver” in an otherwise sequential code. Certainly all parts of a previously sequential code need not be parallelized but the matrix generation portion must be parallelized to expect any kind of reasonable performance. Do not expect to generate your matrix sequentially and then “use PETSc” to solve the linear system in parallel. Since PETSc is under continued development, small changes in usage and calling sequences of routines will occur. PETSc is supported; see the web site http://www.mcs.anl.gov/petsc for information on contacting support. A http://www.mcs.anl.gov/petsc/publications may be found a list of publications and web sites that feature work involving PETSc. We welcome any reports of corrections for this document.« less

PETSc Users Manual Revision 3.5

DOE Office of Scientific and Technical Information (OSTI.GOV)

Balay, S.; Abhyankar, S.; Adams, M.

This manual describes the use of PETSc for the numerical solution of partial differential equations and related problems on high-performance computers. The Portable, Extensible Toolkit for Scientific Computation (PETSc) is a suite of data structures and routines that provide the building blocks for the implementation of large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all message-passing communication. PETSc includes an expanding suite of parallel linear, nonlinear equation solvers and time integrators that may be used in application codes written in Fortran, C, C++, Python, and MATLAB (sequential). PETSc provides many of the mechanisms neededmore » within parallel application codes, such as parallel matrix and vector assembly routines. The library is organized hierarchically, enabling users to employ the level of abstraction that is most appropriate for a particular problem. By using techniques of object-oriented programming, PETSc provides enormous flexibility for users. PETSc is a sophisticated set of software tools; as such, for some users it initially has a much steeper learning curve than a simple subroutine library. In particular, for individuals without some computer science background, experience programming in C, C++ or Fortran and experience using a debugger such as gdb or dbx, it may require a significant amount of time to take full advantage of the features that enable efficient software use. However, the power of the PETSc design and the algorithms it incorporates may make the efficient implementation of many application codes simpler than “rolling them” yourself. ;For many tasks a package such as MATLAB is often the best tool; PETSc is not intended for the classes of problems for which effective MATLAB code can be written. PETSc also has a MATLAB interface, so portions of your code can be written in MATLAB to “try out” the PETSc solvers. The resulting code will not be scalable however because currently MATLAB is inherently not scalable; and PETSc should not be used to attempt to provide a “parallel linear solver” in an otherwise sequential code. Certainly all parts of a previously sequential code need not be parallelized but the matrix generation portion must be parallelized to expect any kind of reasonable performance. Do not expect to generate your matrix sequentially and then “use PETSc” to solve the linear system in parallel. Since PETSc is under continued development, small changes in usage and calling sequences of routines will occur. PETSc is supported; see the web site http://www.mcs.anl.gov/petsc for information on contacting support. A http://www.mcs.anl.gov/petsc/publications may be found a list of publications and web sites that feature work involving PETSc. We welcome any reports of corrections for this document.« less

Xyce Parallel Electronic Simulator Users Guide Version 6.2.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Keiter, Eric R.; Mei, Ting; Russo, Thomas V.

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 onemore » 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 2002-2014 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 registered trademarks of Cadence Design Systems, Inc. Microsoft, Windows and Windows 7 are registered trademarks of Microsoft Corporation. Medici, DaVinci and Taurus are registered trademarks of Synopsys Corporation. Amtec and TecPlot are trademarks of Amtec Engineering, Inc. Xyce 's expression library is based on that inside Spice 3F5 developed by the EECS Department at the University of California. The EKV3 MOSFET model was developed by the EKV Team of the Electronics Laboratory-TUC of the Technical University of Crete. All other trademarks are property of their respective owners. Contacts Bug Reports (Sandia only) http://joseki.sandia.gov/bugzilla http://charleston.sandia.gov/bugzilla World Wide Web http://xyce.sandia.gov http://charleston.sandia.gov/xyce (Sandia only) Email xyce@sandia.gov (outside Sandia) xyce-sandia@sandia.gov (Sandia only)« less

Xyce Parallel Electronic Simulator Users Guide Version 6.4

DOE Office of Scientific and Technical Information (OSTI.GOV)

Keiter, Eric R.; Mei, Ting; Russo, Thomas V.

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 onemore » 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 registered trademarks of Cadence Design Systems, Inc. Microsoft, Windows and Windows 7 are registered trademarks of Microsoft Corporation. Medici, DaVinci and Taurus are registered trademarks of Synopsys Corporation. Amtec and TecPlot are trademarks of Amtec Engineering, Inc. Xyce 's expression library is based on that inside Spice 3F5 developed by the EECS Department at the University of California. The EKV3 MOSFET model was developed by the EKV Team of the Electronics Laboratory-TUC of the Technical University of Crete. All other trademarks are property of their respective owners. Contacts Bug Reports (Sandia only) http://joseki.sandia.gov/bugzilla http://charleston.sandia.gov/bugzilla World Wide Web http://xyce.sandia.gov http://charleston.sandia.gov/xyce (Sandia only) Email xyce@sandia.gov (outside Sandia) xyce-sandia@sandia.gov (Sandia only)« less

Quantitative phase imaging for enhanced assessment of optomechanical cancer cell properties

NASA Astrophysics Data System (ADS)

Kastl, Lena; Kemper, Björn; Schnekenburger, Jürgen

2018-02-01

Optical cell stretching provides label-free investigations of cells by measuring their biomechanical properties based on deformability determination in a fiber optical two-beam trap. However, the stretching forces in this two-beam laser trap depend on the optical properties of the investigated specimen. Therefore, we characterized in parallel four cancer cell lines with varying degree of differentiation utilizing quantitative phase imaging (QPI) and optical cell stretching. The QPI data allowed enhanced assessment of the mechanical cell properties measured with the optical cell stretcher and demonstrates the high potential of cell phenotyping when both techniques are combined.

Informatics for RNA Sequencing: A Web Resource for Analysis on the Cloud

PubMed Central

Griffith, Malachi; Walker, Jason R.; Spies, Nicholas C.; Ainscough, Benjamin J.; Griffith, Obi L.

2015-01-01

Massively parallel RNA sequencing (RNA-seq) has rapidly become the assay of choice for interrogating RNA transcript abundance and diversity. This article provides a detailed introduction to fundamental RNA-seq molecular biology and informatics concepts. We make available open-access RNA-seq tutorials that cover cloud computing, tool installation, relevant file formats, reference genomes, transcriptome annotations, quality-control strategies, expression, differential expression, and alternative splicing analysis methods. These tutorials and additional training resources are accompanied by complete analysis pipelines and test datasets made available without encumbrance at www.rnaseq.wiki. PMID:26248053

Preliminary Work in Atmospheric Turbulence Profiles with the Differential Multi-image Motion Monitor

DTIC Science & Technology

2016-09-01

Center Pacific’s (SSC Pacific) Optical Channel Characterization in Maritime Atmospheres (OCCIMA) Python code is demonstrated with examples that match...OCCIMA) Python code, show how to model the DM3 and anisoplanitic jitter measurements, and finally demonstrate how the turbulence strength profile... python modules. 0.0 0.5 1.0 1.5 2.0 Separation at target plane (m) 2.1 2.2 2.3 2.4 2.5 2.6 2.7 2.8 2.9 3.0 A ni so pl an at ic jit te r( λ /D ) Parallel

A Clinician's Approach to Clinical Ethical Reasoning

PubMed Central

Kaldjian, Lauris C; Weir, Robert F; Duffy, Thomas P

2005-01-01

We offer a systematic strategy that situates clinical ethical reasoning within the paradigm of clinical reasoning. The trajectory of this strategy parallels clinical reasoning: a plain statement of the initial problem, careful gathering of data, a differential diagnostic assessment, and articulation and confirmation of a justified plan. This approach pays special attention to the goals of medical care, because so much depends on whether or not physician and patient share the same goals. This approach also addresses the heterogeneity of clinical problems that at first appear ethical and acknowledges the ethical pluralism that pervades clinical ethics. PMID:15836537

Spin-polarized transport properties of a pyridinium-based molecular spintronics device

NASA Astrophysics Data System (ADS)

Zhang, J.; Xu, B.; Qin, Z.

2018-05-01

By applying a first-principles approach based on non-equilibrium Green's functions combined with density functional theory, the transport properties of a pyridinium-based "radical-π-radical" molecular spintronics device are investigated. The obvious negative differential resistance (NDR) and spin current polarization (SCP) effect, and abnormal magnetoresistance (MR) are obtained. Orbital reconstruction is responsible for novel transport properties such as that the MR increases with bias and then decreases and that the NDR being present for both parallel and antiparallel magnetization configurations, which may have future applications in the field of molecular spintronics.

Higher-order continuation for the determination of robot workspace boundaries

NASA Astrophysics Data System (ADS)

Hentz, Gauthier; Charpentier, Isabelle; Renaud, Pierre

2016-02-01

In the medical and surgical fields, robotics may be of great interest for safer and more accurate procedures. Space constraints for a robotic assistant are however strict. Therefore, roboticists study non-conventional mechanisms with advantageous size/workspace ratios. The determination of mechanism workspace, and primarily its boundaries, is thus of major importance. This Note builds on boundary equation definition, continuation and automatic differentiation to propose a general, accurate, fast and automated method for the determination of mechanism workspace. The method is illustrated with a planar RRR mechanism and a three-dimensional Orthoglide parallel mechanism.

Gravitation. [Book on general relativity

NASA Technical Reports Server (NTRS)

Misner, C. W.; Thorne, K. S.; Wheeler, J. A.

1973-01-01

This textbook on gravitation physics (Einstein's general relativity or geometrodynamics) is designed for a rigorous full-year course at the graduate level. The material is presented in two parallel tracks in an attempt to divide key physical ideas from more complex enrichment material to be selected at the discretion of the reader or teacher. The full book is intended to provide competence relative to the laws of physics in flat space-time, Einstein's geometric framework for physics, applications with pulsars and neutron stars, cosmology, the Schwarzschild geometry and gravitational collapse, gravitational waves, experimental tests of Einstein's theory, and mathematical concepts of differential geometry.

[Kraepelin's basic nosologic postulates. An attempt at a critical evaluation of the later works of Kraepelin].

PubMed

Hoff, P

1988-01-01

This study discusses three important papers by Emil Kraepelin, published between 1918 and 1920. Kraepelin supports--in accordance with his teacher Wilhelm Wundt--the view of psychophysical parallelism as a basic principle of dealing with the questions of mental illness. Kraepelin is often called a nosologist; but one must not forget that Kraepelins nosology was not a static one, nor did he vote in favor of any kind of dogmatism. Only when Kraepelin's basic positions are reflected in a differentiated way, his enormous influence on very different parts of psychiatry as science can be understood.

Accelerating finite-rate chemical kinetics with coprocessors: Comparing vectorization methods on GPUs, MICs, and CPUs

NASA Astrophysics Data System (ADS)

Stone, Christopher P.; Alferman, Andrew T.; Niemeyer, Kyle E.

2018-05-01

Accurate and efficient methods for solving stiff ordinary differential equations (ODEs) are a critical component of turbulent combustion simulations with finite-rate chemistry. The ODEs governing the chemical kinetics at each mesh point are decoupled by operator-splitting allowing each to be solved concurrently. An efficient ODE solver must then take into account the available thread and instruction-level parallelism of the underlying hardware, especially on many-core coprocessors, as well as the numerical efficiency. A stiff Rosenbrock and a nonstiff Runge-Kutta ODE solver are both implemented using the single instruction, multiple thread (SIMT) and single instruction, multiple data (SIMD) paradigms within OpenCL. Both methods solve multiple ODEs concurrently within the same instruction stream. The performance of these parallel implementations was measured on three chemical kinetic models of increasing size across several multicore and many-core platforms. Two separate benchmarks were conducted to clearly determine any performance advantage offered by either method. The first benchmark measured the run-time of evaluating the right-hand-side source terms in parallel and the second benchmark integrated a series of constant-pressure, homogeneous reactors using the Rosenbrock and Runge-Kutta solvers. The right-hand-side evaluations with SIMD parallelism on the host multicore Xeon CPU and many-core Xeon Phi co-processor performed approximately three times faster than the baseline multithreaded C++ code. The SIMT parallel model on the host and Phi was 13%-35% slower than the baseline while the SIMT model on the NVIDIA Kepler GPU provided approximately the same performance as the SIMD model on the Phi. The runtimes for both ODE solvers decreased significantly with the SIMD implementations on the host CPU (2.5-2.7 ×) and Xeon Phi coprocessor (4.7-4.9 ×) compared to the baseline parallel code. The SIMT implementations on the GPU ran 1.5-1.6 times faster than the baseline multithreaded CPU code; however, this was significantly slower than the SIMD versions on the host CPU or the Xeon Phi. The performance difference between the three platforms was attributed to thread divergence caused by the adaptive step-sizes within the ODE integrators. Analysis showed that the wider vector width of the GPU incurs a higher level of divergence than the narrower Sandy Bridge or Xeon Phi. The significant performance improvement provided by the SIMD parallel strategy motivates further research into more ODE solver methods that are both SIMD-friendly and computationally efficient.

Some operational tools for solving fractional and higher integer order differential equations: A survey on their mutual relations

NASA Astrophysics Data System (ADS)

Kiryakova, Virginia S.

2012-11-01

The Laplace Transform (LT) serves as a basis of the Operational Calculus (OC), widely explored by engineers and applied scientists in solving mathematical models for their practical needs. This transform is closely related to the exponential and trigonometric functions (exp, cos, sin) and to the classical differentiation and integration operators, reducing them to simple algebraic operations. Thus, the classical LT and the OC give useful tool to handle differential equations and systems with constant coefficients. Several generalizations of the LT have been introduced to allow solving, in a similar way, of differential equations with variable coefficients and of higher integer orders, as well as of fractional (arbitrary non-integer) orders. Note that fractional order mathematical models are recently widely used to describe better various systems and phenomena of the real world. This paper surveys briefly some of our results on classes of such integral transforms, that can be obtained from the LT by means of "transmutations" which are operators of the generalized fractional calculus (GFC). On the list of these Laplace-type integral transforms, we consider the Borel-Dzrbashjan, Meijer, Krätzel, Obrechkoff, generalized Obrechkoff (multi-index Borel-Dzrbashjan) transforms, etc. All of them are G- and H-integral transforms of convolutional type, having as kernels Meijer's G- or Fox's H-functions. Besides, some special functions (also being G- and H-functions), among them - the generalized Bessel-type and Mittag-Leffler (M-L) type functions, are generating Gel'fond-Leontiev (G-L) operators of generalized differentiation and integration, which happen to be also operators of GFC. Our integral transforms have operational properties analogous to those of the LT - they do algebrize the G-L generalized integrations and differentiations, and thus can serve for solving wide classes of differential equations with variable coefficients of arbitrary, including non-integer order. Throughout the survey, we illustrate the parallels in the relationships: Laplace type integral transforms - special functions as kernels - operators of generalized integration and differentiation generated by special functions - special functions as solutions of related differential equations. The role of the so-called Special Functions of Fractional Calculus is emphasized.

Neural Differentiation of Embryonic Stem Cells In Vitro: A Road Map to Neurogenesis in the Embryo

PubMed Central

Abranches, Elsa; Silva, Margarida; Pradier, Laurent; Schulz, Herbert; Hummel, Oliver; Henrique, Domingos; Bekman, Evguenia

2009-01-01

Background The in vitro generation of neurons from embryonic stem (ES) cells is a promising approach to produce cells suitable for neural tissue repair and cell-based replacement therapies of the nervous system. Available methods to promote ES cell differentiation towards neural lineages attempt to replicate, in different ways, the multistep process of embryonic neural development. However, to achieve this aim in an efficient and reproducible way, a better knowledge of the cellular and molecular events that are involved in the process, from the initial specification of neuroepithelial progenitors to their terminal differentiation into neurons and glial cells, is required. Methodology/Principal Findings In this work, we characterize the main stages and transitions that occur when ES cells are driven into a neural fate, using an adherent monolayer culture system. We established improved conditions to routinely produce highly homogeneous cultures of neuroepithelial progenitors, which organize into neural tube-like rosettes when they acquire competence for neuronal production. Within rosettes, neuroepithelial progenitors display morphological and functional characteristics of their embryonic counterparts, namely, apico-basal polarity, active Notch signalling, and proper timing of production of neurons and glia. In order to characterize the global gene activity correlated with each particular stage of neural development, the full transcriptome of different cell populations that arise during the in vitro differentiation protocol was determined by microarray analysis. By using embryo-oriented criteria to cluster the differentially expressed genes, we define five gene expression signatures that correlate with successive stages in the path from ES cells to neurons. These include a gene signature for a primitive ectoderm-like stage that appears after ES cells enter differentiation, and three gene signatures for subsequent stages of neural progenitor development, from an early stage that follows neural induction to a final stage preceding terminal differentiation. Conclusions/Significance Overall, our work confirms and extends the cellular and molecular parallels between monolayer ES cell neural differentiation and embryonic neural development, revealing in addition novel aspects of the genetic network underlying the multistep process that leads from uncommitted cells to differentiated neurons. PMID:19621087

A Theoretical Study of Cold Air Damming.

NASA Astrophysics Data System (ADS)

Xu, Qin

1990-12-01

The dynamics of cold air damming are examined analytically with a two-layer steady state model. The upper layer is a warm and saturated cross-mountain (easterly or southeasterly onshore) flow. The lower layer is a cold mountain-parallel (northerly) jet trapped on the windward (eastern) side of the mountain. The interface between the two layers represents a coastal front-a sloping inversion layer coupling the trapped cold dome with the warm onshore flow above through pressure continuity.An analytical expression is obtained for the inviscid upper-layer flow with hydrostatic and moist adiabatic approximations. Blackadar's PBL parameterization of eddy viscosity is used in the lower-layer equations. Solutions for the mountain-parallel jet and its associated secondary transverse circulation are obtained by expanding asymptotically upon a small parameter proportional to the square root of the inertial aspect ratio-the ratio between the mountain height and the radius of inertial oscillation. The geometric shape of the sloping interface is solved numerically from a differential-integral equation derived from the pressure continuity condition imposed at the interface.The observed flow structures and force balances of cold air damming events are produced qualitatively by the model. In the cold dome the mountain-parallel jet is controlled by the competition between the mountain-parallel pressure gradient and friction: the jet is stronger with smoother surfaces, higher mountains, and faster mountain-normal geostrophic winds. In the mountain-normal direction the vertically averaged force balance in the cold dome is nearly geostrophic and controls the geometric shape of the cold dome. The basic mountain-normal pressure gradient generated in the cold dome by the negative buoyancy distribution tends to flatten the sloping interface and expand the cold dome upstream against the mountain-normal pressure gradient (produced by the upper-layer onshore wind) and Coriolis force (induced by the lower-layer mountain-parallel jet). It is found that the interface slope increases and the cold dome shrinks as the Froude number and/or upstream mountain-parallel geostrophic wind increase, or as the Rossby number, upper-layer depth, and/or surface roughness length decrease, and vice versa. The cold dome will either vanish or not be in a steady state if the Froude number is large enough or the roughness length gets too small. The theoretical findings are explained physically based on detailed analyses of the force balance along the inversion interface.

Basic research needed for stimulating the development of behavioral technologies

PubMed Central

Mace, F. Charles

1994-01-01

The costs of disconnection between the basic and applied sectors of behavior analysis are reviewed, and some solutions to these problems are proposed. Central to these solutions are collaborations between basic and applied behavioral scientists in programmatic research that addresses the behavioral basis and solution of human behavior problems. This kind of collaboration parallels the deliberate interactions between basic and applied researchers that have proven to be so profitable in other scientific fields, such as medicine. Basic research questions of particular relevance to the development of behavioral technologies are posed in the following areas: response allocation, resistance to change, countercontrol, formation and differentiation/discrimination of stimulus and response classes, analysis of low-rate behavior, and rule-governed behavior. Three interrelated strategies to build connections between the basic and applied analysis of behavior are identified: (a) the development of nonhuman animal models of human behavior problems using operations that parallel plausible human circumstances, (b) replication of the modeled relations with human subjects in the operant laboratory, and (c) tests of the generality of the model with actual human problems in natural settings. PMID:16812734

Effects of symmetry and spin configuration on spin-dependent transport properties of iron-phthalocyanine-based devices

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cui, Li-Ling; School of Science, Hunan University of Technology, Zhuzhou 412007; Yang, Bing-Chu, E-mail: bingchuyang@csu.edu.cn

2014-07-21

Spin-dependent transport properties of nanodevices constructed by iron-phthalocyanine (FePc) molecule sandwiched between two zigzag graphene nanoribbon electrodes are studied using first-principles quantum transport calculations. The effects of the symmetry and spin configuration of electrodes have been taken into account. It is found that large magnetoresistance, large spin polarization, dual spin-filtering, and negative differential resistance (NDR) can coexist in these devices. Our results show that 5Z-FePc system presents well conductive ability in both parallel (P) and anti-parallel (AP) configurations. For 6Z-FePc-P system, spin filtering effect and large spin polarization can be found. A dual spin filtering and NDR can also bemore » shown in 6Z-FePc-AP. Our studies indicate that the dual spin filtering effect depends on the orbitals symmetry of the energy bands and spin mismatching of the electrodes. And all the effects would open up possibilities for their applications in spin-valve, spin-filter as well as effective spin diode devices.« less

Geometry of matrix product states: Metric, parallel transport, and curvature

DOE Office of Scientific and Technical Information (OSTI.GOV)

Haegeman, Jutho, E-mail: jutho.haegeman@gmail.com; Verstraete, Frank; Faculty of Physics and Astronomy, University of Ghent, Krijgslaan 281 S9, 9000 Gent

2014-02-15

We study the geometric properties of the manifold of states described as (uniform) matrix product states. Due to the parameter redundancy in the matrix product state representation, matrix product states have the mathematical structure of a (principal) fiber bundle. The total space or bundle space corresponds to the parameter space, i.e., the space of tensors associated to every physical site. The base manifold is embedded in Hilbert space and can be given the structure of a Kähler manifold by inducing the Hilbert space metric. Our main interest is in the states living in the tangent space to the base manifold,more » which have recently been shown to be interesting in relation to time dependence and elementary excitations. By lifting these tangent vectors to the (tangent space) of the bundle space using a well-chosen prescription (a principal bundle connection), we can define and efficiently compute an inverse metric, and introduce differential geometric concepts such as parallel transport (related to the Levi-Civita connection) and the Riemann curvature tensor.« less

Scalable Nonlinear Solvers for Fully Implicit Coupled Nuclear Fuel Modeling. Final Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cai, Xiao-Chuan; Keyes, David; Yang, Chao

2014-09-29

The focus of the project is on the development and customization of some highly scalable domain decomposition based preconditioning techniques for the numerical solution of nonlinear, coupled systems of partial differential equations (PDEs) arising from nuclear fuel simulations. These high-order PDEs represent multiple interacting physical fields (for example, heat conduction, oxygen transport, solid deformation), each is modeled by a certain type of Cahn-Hilliard and/or Allen-Cahn equations. Most existing approaches involve a careful splitting of the fields and the use of field-by-field iterations to obtain a solution of the coupled problem. Such approaches have many advantages such as ease of implementationmore » since only single field solvers are needed, but also exhibit disadvantages. For example, certain nonlinear interactions between the fields may not be fully captured, and for unsteady problems, stable time integration schemes are difficult to design. In addition, when implemented on large scale parallel computers, the sequential nature of the field-by-field iterations substantially reduces the parallel efficiency. To overcome the disadvantages, fully coupled approaches have been investigated in order to obtain full physics simulations.« less

A 32-bit Ultrafast Parallel Correlator using Resonant Tunneling Devices

NASA Technical Reports Server (NTRS)

Kulkarni, Shriram; Mazumder, Pinaki; Haddad, George I.

1995-01-01

An ultrafast 32-bit pipeline correlator has been implemented using resonant tunneling diodes (RTD) and hetero-junction bipolar transistors (HBT). The negative differential resistance (NDR) characteristics of RTD's is the basis of logic gates with the self-latching property that eliminates pipeline area and delay overheads which limit throughput in conventional technologies. The circuit topology also allows threshold logic functions such as minority/majority to be implemented in a compact manner resulting in reduction of the overall complexity and delay of arbitrary logic circuits. The parallel correlator is an essential component in code division multi-access (CDMA) transceivers used for the continuous calculation of correlation between an incoming data stream and a PN sequence. Simulation results show that a nano-pipelined correlator can provide and effective throughput of one 32-bit correlation every 100 picoseconds, using minimal hardware, with a power dissipation of 1.5 watts. RTD plus HBT based logic gates have been fabricated and the RTD plus HBT based correlator is compared with state of the art complementary metal oxide semiconductor (CMOS) implementations.

Comparison of language used and patterns of communication in interprofessional and multidisciplinary teams.

PubMed

Sheehan, D; Robertson, L; Ormond, T

2007-02-01

Can the language used and the patterns of communication differentiate a multidisciplinary team from an interprofessional team? This research question arose from an unexpected outcome of a study that investigated clinical reasoning of health professional team members in the elder care wards of two different hospitals. The issue at stake was the apparent disparity in the way in which the two teams communicated. To further explore this, the original transcribed interview data was analysed from a symbolic interactionist perspective in order that the language and communication patterns between the two teams could be identified and compared. Differences appeared to parallel the distinctions between multidisciplinary and interprofessional teams as reported in the literature. Our observations were that an interprofessional team was characterized by its use of inclusive language, continual sharing of information between team members and a collaborative working approach. In the multidisciplinary team, the members worked in parallel, drawing information from one another but did not have a common understanding of issues that could influence intervention. The implications of these communication differences for team members, team leaders and future research are then discussed.

Bone-Inspired Spatially Specific Piezoelectricity Induces Bone Regeneration

PubMed Central

Yu, Peng; Ning, Chengyun; Zhang, Yu; Tan, Guoxin; Lin, Zefeng; Liu, Shaoxiang; Wang, Xiaolan; Yang, Haoqi; Li, Kang; Yi, Xin; Zhu, Ye; Mao, Chuanbin

2017-01-01

The extracellular matrix of bone can be pictured as a material made of parallel interspersed domains of fibrous piezoelectric collagenous materials and non-piezoelectric non-collagenous materials. To mimic this feature for enhanced bone regeneration, a material made of two parallel interspersed domains, with higher and lower piezoelectricity, respectively, is constructed to form microscale piezoelectric zones (MPZs). The MPZs are produced using a versatile and effective laser-irradiation technique in which K0.5Na0.5NbO3 (KNN) ceramics are selectively irradiated to achieve microzone phase transitions. The phase structure of the laser-irradiated microzones is changed from a mixture of orthorhombic and tetragonal phases (with higher piezoelectricity) to a tetragonal dominant phase (with lower piezoelectricity). The microzoned piezoelectricity distribution results in spatially specific surface charge distribution, enabling the MPZs to bear bone-like microscale electric cues. Hence, the MPZs induce osteogenic differentiation of stem cells in vitro and bone regeneration in vivo even without being seeded with stem cells. The concept of mimicking the spatially specific piezoelectricity in bone will facilitate future research on the rational design of tissue regenerative materials. PMID:28900517

Comparison of global brain gene expression profiles between inbred long-sleep and inbred short-sleep mice by high-density gene array hybridization.

PubMed

Xu, Y; Ehringer, M; Yang, F; Sikela, J M

2001-06-01

Inbred long-sleep (ILS) and short-sleep (ISS) mice show significant central nervous system-mediated differences in sleep time for sedative dose of ethanol and are frequently used as a rodent model for ethanol sensitivity. In this study, we have used complementary DNA (cDNA) array hybridization methodology to identify genes that are differentially expressed between the brains of ILS and ISS mice. To carry out this analysis, we used both the gene discovery array (GDA) and the Mouse GEM 1 Microarray. GDA consists of 18,378 nonredundant mouse cDNA clones on a single nylon filter. Complex probes were prepared from total brain mRNA of ILS or ISS mice by using reverse transcription and 33P labeling. The labeled probes were hybridized in parallel to the gene array filters. Data from GDA experiments were analyzed with SQL-Plus and Oracle 8. The GEM microarray includes 8,730 sequence-verified clones on a glass chip. Two fluorescently labeled probes were used to hybridize a microarray simultaneously. Data from GEM experiments were analyzed by using the GEMTools software package (Incyte). Differentially expressed genes identified from each method were confirmed by relative quantitative reverse transcription-polymerase chain reaction (RT-PCR). A total of 41 genes or expressed sequence tags (ESTs) display significant expression level differences between brains of ILS and ISS mice after GDA, GEM1 hybridization, and quantitative RT-PCR confirmation. Among them, 18 clones were expressed higher in ILS mice, and 23 clones were expressed higher in ISS mice. The individual gene or EST's function and mapping information have been analyzed. This study identified 41 genes that are differentially expressed between brains of ILS and ISS mice. Some of them may have biological relevance in mediation of phenotypic variation between ILS and ISS mice for ethanol sensitivity. This study also demonstrates that parallel gene expression comparison with high-density cDNA arrays is a rapid and efficient way to discover potential genes and pathways involved in alcoholism and alcohol-related physiologic processes.

Synthetic osteogenic extracellular matrix formed by coated silicon dioxide nanosprings

PubMed Central

2012-01-01

Background The design of biomimetic materials that parallel the morphology and biology of extracellular matrixes is key to the ability to grow functional tissues in vitro and to enhance the integration of biomaterial implants into existing tissues in vivo. Special attention has been put into mimicking the nanostructures of the extracellular matrix of bone, as there is a need to find biomaterials that can enhance the bonding between orthopedic devices and this tissue. Methods We have tested the ability of normal human osteoblasts to propagate and differentiate on silicon dioxide nanosprings, which can be easily grown on practically any surface. In addition, we tested different metals and metal alloys as coats for the nanosprings in tissue culture experiments with bone cells. Results Normal human osteoblasts grown on coated nanosprings exhibited an enhanced rate of propagation, differentiation into bone forming cells and mineralization. While osteoblasts did not attach effectively to bare nanowires grown on glass, these cells propagated successfully on nanosprings coated with titanium oxide and gold. We observed a 270 fold increase in the division rate of osteoblasts when grow on titanium/gold coated nanosprings. This effect was shown to be dependent on the nanosprings, as the coating by themselves did not alter the growth rate of osteoblast. We also observed that titanium/zinc/gold coated nanosprings increased the levels of osteoblast production of alkaline phosphatase seven folds. This result indicates that osteoblasts grown on this metal alloy coated nanosprings are differentiating to mature bone making cells. Consistent with this hypothesis, we showed that osteoblasts grown on the same metal alloy coated nanosprings have an enhanced ability to deposit calcium salt. Conclusion We have established that metal/metal alloy coated silicon dioxide nanosprings can be used as a biomimetic material paralleling the morphology and biology of osteogenic extracellular matrix. The coated nanosprings enhance normal human osteoblasts cellular behaviors needed for improving osseointegration of orthopedic materials. Thus, metal-coated nanosprings represent a novel biomaterial that could be exploited for improving success rates of orthopedic implant procedures. PMID:22284364