FireWorks: a dynamic workflow system designed for high‐throughput applications

This paper introduces FireWorks, a workflow software for running high‐throughput calculation workflows at supercomputing centers. FireWorks has been used to complete over 50 million CPU‐hours worth of computational chemistry and materials science calculations at the National Energy Research Supercomputing Center. It has been designed to serve the demanding high‐throughput computing needs of these applications, with extensive support for (i) concurrent execution through job packing, (ii) failure detection and correction, (iii) provenance and reporting for long‐running projects, (iv) automated duplicate detection, and (v) dynamic workflows (i.e., modifying the workflow graph during runtime). We have found that these features are highly relevant to enabling modern data‐driven and high‐throughput science applications, and we discuss our implementation strategy that rests on Python and NoSQL databases (MongoDB). Finally, we present performance data and limitations of our approach along with planned future work. Copyright © 2015 John Wiley & Sons, Ltd.     

Photoelectrochemical treatment of the dye reactive red 198 using DSA electrodes

The study of the oxidation of the dye reactive red 198 on Ti/Ru_0.3Ti_0.7O₂ electrode is presented. Three different techniques were employed: photocatalytic (interaction of UV radiation and electrode surface), electrochemical (application of a constant current) and photoelectrochemical (simultaneous application of a constant current and UV radiation). The effect of temperature (20–45 °C) and current density (5–89 mA cm⁻²) were investigated. No significant temperature effect was observed for the three techniques used. It was observed that at low current densities (5–30 mA cm⁻²) the photoelectrochemical (PhEC) rate of colour and TOC removal is simply the sum of the photocatalytic (PC) and electrochemical (EC) rates. However, as the current density increases, the rate of PhEC removal is much greater. This phenomenon is interpreted as being due to the increased production of O₂, which goes on to interact with the UV radiation and cause the oxidation of the dye.     

A new phage display system to construct multicombinatorial libraries of very large antibody repertoires

We present an easy and efficient technique for the construction of large phage-displayed antibody (Ab) repertoires through the recombination of two separate heavy (VH) and light (VL) chain gene libraries. Here, the system has been applied to the display of a chimpanzee anti-HIV gp160 Ab. The process, which makes use of lambda phage att recombination sites, leads to the irreversible physical association between plasmid and phagemid vectors carrying, respectively, VL and VH sequences. The heat-inducible expression of the Int recombinase allows perfect control of recombination. Selection of the recombinant phagemid is made possible by the assembly, in vivo, of a genetic marker (chloramphenicol resistance) created only after the correct recombination event. Theoretically, all possible associations between the VL and VH sequences should be obtained, and it should be possible to generate multicombinatorial libraries of close to 10(12) clones.     

The elimination of selenium(IV) from aqueous solution by precipitation with sodium sulfide

In this study, the removal/precipitation of selenium with sodium sulfide from initially weakly acidic sulfate solutions containing 300 mg/L of selenium(IV) at 23 °C was studied. The results showed that, below a pH of approximately 7.0, the precipitation reaction was complete at a sulfide to selenium ratio above 1.8 and less than 11 with less than 0.005 mg/L of soluble selenium remaining in solution. When the pH rose between 7.0 and 9.5 the precipitation of selenium was incomplete. Above pH 9.5 the solution turned dark red but no precipitation was apparent. The precipitation reaction started as soon as the sodium sulfide was added in the selenium-bearing solution and was completed in less than 10 min. The orange "selenium sulfide" precipitates, characterized using X-ray diffraction, scanning electron microscopy and chemical analysis, were crystalline in the form of aggregated dense particles with their sulfur/selenium molar ratio varying from 1.7 to 2.3. The precipitate was deduced to be a Se-S solid solution consisting of ring molecules of the following Se(n)S(8-n) formula, where n = 2.5-3. Long term leachability tests (>2 month equilibration) under ambient conditions at pH 7 showed the produced precipitate to be essentially insoluble (<0.005 mg/L).     

Thresholds of Endoglin Expression in Endothelial Cells Explains Vascular Etiology in Hereditary Hemorrhagic Telangiectasia Type 1

Hereditary Hemorrhagic Telangiectasia type 1 (HHT1) is an autosomal dominant inherited disease characterized by arteriovenous malformations and hemorrhage. HHT1 is caused by mutations in ENDOGLIN, which encodes an ancillary receptor for Transforming Growth Factor-β/Bone Morphogenetic Protein-9 expressed in all vascular endothelial cells. Haploinsufficiency is widely accepted as the underlying mechanism for HHT1. However, it remains intriguing that only some, but not all, vascular beds are affected, as these causal gene mutations are present in vasculature throughout the body. Here, we have examined the endoglin expression levels in the blood vessels of multiple organs in mice and in humans. We found a positive correlation between low basal levels of endoglin and the general prevalence of clinical manifestations in selected organs. Endoglin was found to be particularly low in the skin, the earliest site of vascular lesions in HHT1, and even undetectable in the arteries and capillaries of heterozygous endoglin mice. Endoglin levels did not appear to be associated with organ-specific vascular functions. Instead, our data revealed a critical endoglin threshold compatible with the haploinsufficiency model, below which endothelial cells independent of their tissue of origin exhibited abnormal responses to Vascular Endothelial Growth Factor. Our results support the development of drugs promoting endoglin expression as potentially protective.     

Sharing intelligence: Decision-making interactions between users and software in maestro

By combining the best of automated and human decision-making in scheduling, many advantages can accrue. The joint performance of the user and system is potentially much better than either alone. Features of the MAESTRO scheduling system serve to illustrate concepts of user/software cooperation. MAESTRO may be operated at a user-determinable and dynamic level of autonomy. Because the system allows so much flexibility in the allocation of decision-making responsibilities, and provides users with a wealth of information and other support for their own decision-making, better overall schedules may result.     

GaAs/Ge tandem-cell space concentrator development

GaAs/Ge monolithic tandem two-junction concentrators are being developed by optimizing separate one-junction GaAs and Ge cells that simulate the GaAs top cell and Ge bottom cell of the tandem. Separation allows easier analysis of the tandem's top and bottom cells than if these two junctions were in series. The best GaAs top cell has an independently measured AM1.5D efficiency of 28.7% at 200 suns and 25°C (24.5% AM0 at 170 suns), a record for a monolithic cell without a prismatic cover. The Ge bottom cells have a GaAs optical filter (but no GaAs junction) to replicate the spectrum that the Ge cell sees when incorporated into a tandem. The best Ge-under-GaAs bottom cell efficiency is 4.6% AM0 at 103 suns. Evidence that the 900-1800-nm response seen from the Ge bottom cell is due to a p-n junction in the Ge and not a GaAs/Ge heterojunction is presented     

Decomposition applied to layered manufacturing using critical points

Slicing represents an important step in all rapid prototyping processes. This paper proposes the use of critical points for adaptive local slicing for strataconception in particular and rapid prototyping technologies in general. The context of using critical points in rapid prototyping to optimise usual slicing is presented. Its definition on both surfaces and triangular meshings is given and extended to other geometric entities, such as edges, facets and faces. Finally, this new slicing approach is compared with the usual one on a few models manufactured through the stratoconception process.     

Zn speciation in the organic horizon of a contaminated soil by micro-X-ray fluorescence, micro- and powder-EXAFS spectroscopy, and isotopic dilution

Soils that have been acutely contaminated by heavy metals show distinct characteristics, such as colonization by metal-tolerant plant species and topsoil enrichment in weakly degraded plant debris, because biodegradation processes are strongly inhibited by contamination. Such an organic topsoil, located downwind of an active zinc smelter and extremely rich in Zn (approximately 2%, dry weight), was investigated by X-ray diffraction, synchrotron-based X-ray microfluorescence, and powder- and micro-extended X-ray absorption fine structure (EXAFS) spectroscopy for Zn speciation and by isotopic dilution for Zn lability. EXAFS spectra recorded on size fractions and on selected spots of thin sections were analyzed by principal component analysis and linear combination fits. Although Zn primary minerals (franklinite, sphalerite, and willemite) are still present (approximately 15% of total Zn) in the bulk soil, Zn was found to be predominantly speciated as Zn-organic matter complexes (approximately 45%), outer-sphere complexes (approximately 20%), Zn-sorbed phosphate (approximately 10%), and Zn-sorbed iron oxyhydroxides (approximately 10%). The bioaccumulated Zn fraction is likely complexed to soil organic matter after the plants' death. The proportion of labile Zn ranges from 54 to 92%, depending on the soil fraction, in agreement with the high proportion of organically bound Zn. Despite its marked lability, Zn seems to be retained in the topsoil thanks to the huge content of organic matter, which confers to this horizon a high sorption capacity. The speciation of Zn in this organic soil horizon is compared with that found in other types of soils.