Detecting common scientific workflow fragments using templates and execution provenance

Provenance plays a major role when understanding and reusing the methods applied in a scientic experiment, as it provides a record of inputs, the processes carried out and the use and generation of intermediate and nal results. In the specic case of in-silico scientic experiments, a large variety of scientic workflow systems (e.g., Wings, Taverna, Galaxy, Vistrails) have been created to support scientists. All of these systems produce some sort of provenance about the executions of the workflows that encode scientic experiments. However, provenance is normally recorded at a very low level of detail, which complicates the understanding of what happened during execution. In this paper we propose an approach to automatically obtain abstractions from low-level provenance data by finding common workflow fragments on workflow execution provenance and relating them to templates. We have tested our approach with a dataset of workflows published by the Wings workflow system. Our results show that by using these kinds of abstractions we can highlight the most common abstract methods used in the executions of a repository, relating different runs and workflow templates with each other.

Development of One Meter Long Double-Sided CeO2 Buffered Ni-5at.W Templates by Reel-to-Reel Chemical Solution Deposition Route

High performance long-length coated conductors fabricated using various techniques have attracted a lot of interest recently. In this work, a reel-to-reel design for depositing double-sided coatings on long-length flexible metallic tapes via a chemical solution method is proposed and realized. The major achievement of the design is to combine the dip coating and drying processes in order to overcome the technical difficulties of dealing with the wet films on both sides of the tape. We report the successful application of the design to fabricate a one-meter-long double side coated CeO2/Ni-5at%W template. The CeO2 films on both sides exhibit a dense, crack-free morphology, and a high fraction of cube texture on the surface. Homogeneity studies on global texture over the length also reveal that the average full width at half maximum values of the in-plane and out-of-plane orientation on the CeO2 layer are 7.2 ° and 5.8° with standard deviation of 0.26° and 0.34°, respectively, being indicative of the high quality epitaxial growth of the films prepared in the continuous manner. An all chemical solution derived YBCOLow-TFA/Ce0.9La0.1O2 /Gd2Zr2O7/CeO2 structure is obtained on a short sample, demonstrating the possibility of producing long-length texture templates for coated conductors by this low cost deposition route.

RNA polymerase sigma factor determines start-site selection but is not required for upstream promoter element activation on heteroduplex (bubble) templates

Sequence-selective transcription by bacterial RNA polymerase (RNAP) requires σ factor that participates in both promoter recognition and DNA melting. RNAP lacking σ (core enzyme) will initiate RNA synthesis from duplex ends, nicks, gaps, and single-stranded regions. We have used DNA templates containing short regions of heteroduplex (bubbles) to compare initiation in the presence and absence of various σ factors. Using bubble templates containing the σD-dependent flagellin promoter, with or without its associated upstream promoter (UP) element, we demonstrate that UP element stimulation occurs efficiently even in the absence of σ. This supports a model in which the UP element acts primarily through the α subunit of core enzyme to increase the initial association of RNAP with the promoter. Core and holoenzyme do differ substantially in the template positions chosen for initiation: σD restricts initiation to sites 8–9 nucleotides downstream of the conserved −10 element. Remarkably, σA also has a dramatic effect on start-site selection even though the σA holoenzyme is inactive on the corresponding homoduplexes. The start sites chosen by the σA holoenzyme are located 8 nucleotides downstream of sequences on the nontemplate strand that resemble the conserved −10 hexamer recognized by σA. Thus, σA appears to recognize the −10 region even in a single-stranded state. We propose that in addition to its described roles in promoter recognition and start-site melting, σ also localizes the transcription start site.

Oligomerization of activated d- and l-guanosine mononucleotides on templates containing d- and l-deoxycytidylate residues

The oligomerization of activated d- and l- and racemic guanosine-5′-phosphoro-2-methylimidazole on short templates containing d- and l-deoxycytidylate has been studied. Results obtained with d-oligo(dC)s as templates are similar to those previously reported for experiments with a poly(C) template. When one l-dC or two consecutive l-dCs are introduced into a d-template, regiospecific synthesis of 3′-5′ oligo(G)s proceeds to the end of the template, but three consecutive l-dCs block synthesis. Alternating d-,l-oligomers do not facilitate oligomerization of the d-, l-, and racemic 2-guanosine-5′-phosphoro-2-methylimidazole. We suggest that once a “predominately d-metabolism” existed, occasional l-residues in a template would not have led to the termination of self-replication.

Escherichia coli RNA polymerase terminates transcription efficiently at rho-independent terminators on single-stranded DNA templates

Several models have been proposed for the mechanism of transcript termination by Escherichia coli RNA polymerase at rho-independent terminators. Yager and von Hippel (Yager, T. D. & von Hippel, P. H. (1991) Biochemistry 30, 1097–118) postulated that the transcription complex is stabilized by enzyme–nucleic acid interactions and the favorable free energy of a 12-bp RNA–DNA hybrid but is destabilized by the free energy required to maintain an extended transcription bubble. Termination, by their model, is viewed simply as displacement of the RNA transcript from the hybrid helix by reformation of the DNA helix. We have proposed an alternative model where the RNA transcript is stably bound to RNA polymerase primarily through interactions with two single-strand specific RNA-binding sites; termination is triggered by formation of an RNA hairpin that reduces binding of the RNA to one RNA-binding site and, ultimately, leads to its ejection from the complex. To distinguish between these models, we have tested whether E. coli RNA polymerase can terminate transcription at rho-independent terminators on single-stranded DNA. RNA polymerase cannot form a transcription bubble on these templates; thus, the Yager–von Hippel model predicts that intrinsic termination will not occur. We find that transcript elongation on single-stranded DNA templates is hindered somewhat by DNA secondary structure. However, E. coli RNA polymerase efficiently terminates and releases transcripts at several rho-independent terminators on such templates at the same positions as termination occurs on duplex DNAs. Therefore, neither the nontranscribed DNA strand nor the transcription bubble is essential for rho-independent termination by E. coli RNA polymerase.

Rescue of stalled replication forks by RecG: Simultaneous translocation on the leading and lagging strand templates supports an active DNA unwinding model of fork reversal and Holliday junction formation

Modification of damaged replication forks is emerging as a crucial factor for efficient chromosomal duplication and the avoidance of genetic instability. The RecG helicase of Escherichia coli, which is involved in recombination and DNA repair, has been postulated to act on stalled replication forks to promote replication restart via the formation of a four-stranded (Holliday) junction. Here we show that RecG can actively unwind the leading and lagging strand arms of model replication fork structures in vitro. Unwinding is achieved in each case by simultaneous interaction with and translocation along both the leading and lagging strand templates at a fork. Disruption of either of these interactions dramatically inhibits unwinding of the opposing duplex arm. Thus, RecG translocates simultaneously along two DNA strands, one with 5′-3′ and the other with 3′-5′ polarity. The unwinding of both nascent strands at a damaged fork, and their subsequent annealing to form a Holliday junction, may explain the ability of RecG to promote replication restart. Moreover, the preferential binding of partial forks lacking a leading strand suggests that RecG may have the ability to target stalled replication intermediates in vivo in which lagging strand synthesis has continued beyond the leading strand.

Vaccinia virus DNA replication: two hundred base pairs of telomeric sequence confer optimal replication efficiency on minichromosome templates.

Vaccinia virus is a complex DNA virus that exhibits significant genetic and physical autonomy from the host cell. Most if not all of the functions involved in replication and transcription of the 192-kb genome are virally encoded. Although significant progress has been made in identifying trans-acting factors involved in DNA synthesis, the mechanism of genome replication has remained poorly understood. The genome is a linear duplex with covalently closed hairpin termini, and it has been presumed that sequences and/or structures within these termini are important for the initiation of genome replication. In this report we describe the construction of minichromosomes containing a central plasmid insert flanked by hairpin termini derived from the viral genome and their use as replication templates. When replication of these minichromosomes was compared with a control substrate containing synthetic hairpin termini, specificity for viral telomeres was apparent. Inclusion of > or = 200 bp from the viral telomere was sufficient to confer optimal replication efficiency, whereas 65-bp telomeres were not effective. Chimeric 200-bp telomeres containing the 65-bp terminal element and 135 bp of ectopic sequence also failed to confer efficient replication, providing additional evidence that telomere function is sequence-specific. Replication of these exogenous templates was dependent upon the viral replication machinery, was temporally coincident with viral replication, and generated covalently closed minichromosome products. These data provide compelling evidence for specificity in template recognition and utilization in vaccinia virus-infected cells.

Homologous recombination promoted by reverse transcriptase during copying of two distinct RNA templates.

Retroviruses are known to mutate at high rates. An important source of genetic variability is recombination taking place during reverse transcription of internal regions of the two genomic RNAs. We have designed an in vitro model system, involving genetic markers carried on two RNA templates, to allow a search for individual recombination events and to score their frequency of occurrence. We show that Moloney murine leukemia virus reverse transcriptase alone promotes homologous recombination efficiently. While RNA concentration has little effect on recombination frequency, there is a clear correlation between the amount of reverse transcriptase used in the assay and the extent of recombination observed. Under conditions mimicking the in vivo situation, a rate compatible with ex vivo estimates has been obtained.

Deformable templates for plaque thickness estimation of intravascular ultrasound sequences

Comunicación presentada en el VII Symposium Nacional de Reconocimiento de Formas y Análisis de Imágenes, SNRFAI, Barcelona, abril 1997.

Deformable templates for tracking and analysis of intravascular ultrasound sequences

Deformable Template models are first applied to track the inner wall of coronary arteries in intravascular ultrasound sequences, mainly in the assistance to angioplasty surgery. A circular template is used for initializing an elliptical deformable model to track wall deformation when inflating a balloon placed at the tip of the catheter. We define a new energy function for driving the behavior of the template and we test its robustness both in real and synthetic images. Finally we introduce a framework for learning and recognizing spatio-temporal geometric constraints based on Principal Component Analysis (eigenconstraints).

Magnetization reversal of ferromagnetic nanowires studied by magnetic force microscopy

The magnetization reversal of two-dimensional arrays of parallel ferromagnetic Fe nanowires embedded in nanoporous alumina templates has been studied. By combining bulk magnetization measurements (superconducting quantum interference device magnetometry) with field-dependent magnetic force microscopy (MFM), we have been able to decompose the macroscopic hysteresis loop in terms of the irreversible magnetic responses of individual nanowires. The latter are found to behave as monodomain ferromagnetic needles, with hysteresis loops displaced (asymmetric) as a consequence of the strong dipolar interactions between them. The application of field-dependent MFM provides a microscopic method to obtain the hysteresis curve of the array, by simply registering the fraction of up and down magnetized wires as a function of applied field. The observed deviations from the rectangular shape of the macroscopic hysteresis loop of the array can be ascribed to the spatial variation of the dipolar field through the inhomogeneously filled membrane. The system studied proves to be an excellent example of the two-dimensional classical Preisach model, well known from the field of hysteresis modeling and micromagnetism.

Electrocatalytic activity of Ni-doped nanoporous carbons in the electrooxidation of propargyl alcohol

Herein, we explore the immobilization of nickel on various carbon supports and their application as electrocatalysts for the oxidation of propargyl alcohol in alkaline medium. In comparison with massive and nanoparticulated nickel electrode systems, Ni-doped nanoporous carbons provided similar propargyl alcohol conversions for very low metallic contents. Nanoparticulated Ni on various carbon supports gave rise to the highest electrocatalytic activity in terms of product selectivity, with a clear dependence on Ni content. The results point to the importance of controlling the dispersion of the Ni phase within the carbon matrix for a full exploitation of the electroactive area of the metal. Additionally, a change in the mechanism of the propargyl alcohol electrooxidation was noted, which seems to be related to the physicochemical properties of the carbon support as well. Thus, the stereoselectivity of the electrooxidative reaction can be controlled by the active nickel content immobilized on the anode, with a preferential oxidation to (Z)-3-(2-propynoxy)-2-propenoic acid with high Ni-loading, and to propiolic acid with low loading of active Ni sites. Moreover, the formation of (E)-3-(2-propynoxy)-2-propenoic acid was discriminatory irrespective of the experimental conditions and Ni loadings on the carbon matrixes.

Preparation of high metal content nanoporous carbon

Activated carbons with high metal content have been prepared by the pyrolysis of ethylene tar with dissolved metal acetylacetonates (Ti, V, Fe, Co, Ni and Cu) and subsequent activation with KOH of the pitch obtained in pyrolysis. These metal compounds decompose during the pyrolysis of ethylene tar yielding metal nanoparticles formed by metal and/or oxide which are homogeneously distributed in the pitch and remain in the activated carbon, so that the concentration of metal is, in most cases, 4–5 times higher than in the pristine ethylene tar. Since KOH is an effective activating agent, all activated carbons combine a high porosity development with a high metal content. In some of the carbons, such as P2FeA (3.3% Fe, pore volume 1.84 cm3/g, BET surface area 3270 m2/g), there is even an increase in the pore volume when compared to the activated carbon prepared in the same way without metal, in spite of the fact that the metal increases the weight of carbon without contributing to the adsorptive capacity. It seems that iron, on the one hand modifies the pyrolysis to give a pitch with larger mesophase content and on the other hand it locally catalyzes carbon gasification with the CO2 produced along the synthesis of the carbon. In addition to its influence on activation, iron promotes the formation of graphitic carbon fibers.

New insights on electrochemical hydrogen storage in nanoporous carbons by in situ Raman spectroscopy

In situ Raman spectroscopy was exploited to analyze the interaction between carbon and hydrogen during electrochemical hydrogen storage at cathodic conditions. Two different activated carbons were used and characterized by different electrochemical techniques in two electrolytes (6 M KOH and 0.5 M Na2SO4). The in situ Raman spectra collected showed that, in addition to the D and G bands associated to the graphitic carbons, two bands appear simultaneously at about 1110 and 1500 cm−1 under cathodic conditions, and then they disappear when the potential increases to more positive values. This indicates that carbon–hydrogen bonds are formed reversibly in both electrolytes during cathodic conditions. Comparing the two activated carbons, it was confirmed that, in both electrolytes, the hydrogenation of carbon atoms is produced more easily for the sample with lower amount of surface oxygen groups. In KOH medium, for the two samples, the formation of carbon–hydrogen bonds proceeds at more positive potential with respect to the thermodynamic potential value for hydrogen evolution. Furthermore, changes in the shape of the D band (due to an intensity increase of the D1 band) during the formation of carbon–hydrogen bonds suggest that hydrogenation of the carbon atoms increases the number of edge planes.

Potentiostatic Reversible Photoelectrochromism: An Effect Appearing in Nanoporous TiO2/Ni(OH)2 Thin Films

In the field of energy saving, finding composite materials with the ability of coloring upon both illumination and change of the applied electrode potential keeps on being an important goal. In this context, chemical bath deposition of Ni(OH)2 into nanoporous TiO2 thin films supported on conducting glass leads to electrodes showing both conventional electrochromic behavior (from colorless to dark brown and vice versa) together with photochromism at constant applied potential. The latter phenomenon, reported here for the first time, is characterized by fast and reversible coloration upon UV illumination. The bleaching kinetics shows first order behavior with respect to the NiIII centers in the film, and an order 1.2 with respect to electrons in the TiO2 film. From a more applied point of view, this study opens up the possibility of having two-mode smart windows showing not only conventional electrochromism but also reversible darkening upon illumination.