Search and Result Presentation in Scientific Workflow Repositories

We study the problem of searching a repository of complex hierarchical workflows whose component modules, both composite and atomic, have been annotated with keywords. Since keyword search does not use the graph structure of a workflow, we develop a model of workflows using context-free bag grammars. We then give efficient polynomial-time algorithms that, given a workflow and a keyword query, determine whether some execution of the workflow matches the query. Based on these algorithms we develop a search and ranking solution that efficiently retrieves the top-k grammars from a repository. Finally, we propose a novel result presentation method for grammars matching a keyword query, based on representative parse-trees. The effectiveness of our approach is validated through an extensive experimental evaluation

Answering Regular Path Queries on Workflow Provenance

This paper proposes a novel approach for efficiently evaluating regular path queries over provenance graphs of workflows that may include recursion. The approach assumes that an execution g of a workflow G is labeled with query-agnostic reachability labels using an existing technique. At query time, given g, G and a regular path query R, the approach decomposes R into a set of subqueries R1, ..., Rk that are safe for G. For each safe subquery Ri, G is rewritten so that, using the reachability labels of nodes in g, whether or not there is a path which matches Ri between two nodes can be decided in constant time. The results of each safe subquery are then composed, possibly with some small unsafe remainder, to produce an answer to R. The approach results in an algorithm that significantly reduces the number of subqueries k over existing techniques by increasing their size and complexity, and that evaluates each subquery in time bounded by its input and output size. Experimental results demonstrate the benefit of this approach

Humidity's influence on visible region refractive index structure parameter Cn2C_n^2

In the infrared and visible bandpass, optical propagation theory conventionally assumes that humidity does not contribute to the effects of atmospheric turbulence on optical beams. While this assumption may be reasonable for dry locations, we demonstrate in this paper that there is an unequivocal effect due to the pre sence of humidity upon the strength of turbulence parameter, $C_n^2$, from data collected in the Chesapeake Bay area over 100-m length horizontal propagation paths. We describe and apply a novel technique, Hilbert Phase Analysis, to the relative humidity, temperature and $C_n^2$ data to show the contribution of the re levant climate variable to $C_n^2$ as a function of time.Comment: 16 pages, 7 figures, 2 tables, submitted to Applied Optic

EST analysis of gene expression in early cleavage-stage sea urchin embryos

A set of 956 expressed sequence tags derived from 7-hour (mid-cleavage) sea urchin embryos was analyzed to assess biosynthetic functions and to illuminate the structure of the message population at this stage. About a quarter of the expressed sequence tags represented repetitive sequence transcripts typical of early embryos, or ribosomal and mitochondrial RNAs, while a majority of the remainder contained significant open reading frames. A total of 232 sequences, including 153 different proteins, produced significant matches when compared against GenBank. The majority of these identified sequences represented ‘housekeeping’ proteins, i.e., cytoskeletal proteins, metabolic enzymes, transporters and proteins involved in cell division. The most interesting finds were components of signaling systems and transcription factors not previously reported in early sea urchin embryos, including components of Notch and TGF signal transduction pathways. As expected from earlier kinetic analyses of the embryo mRNA populations, no very prevalent protein-coding species were encountered; the most highly represented such sequences were cDNAs encoding cyclins A and B. The frequency of occurrence of all sequences within the database was used to construct a sequence prevalence distribution. The result, confirming earlier mRNA population analyses, indicated that the poly(A) RNA of the early embryo consists mainly of a very complex set of low-copy-number transcripts

Search and Result Presentation in Scientific Workflow Repositories

We study the problem of searching a repository of complex hierarchical workflows whose component modules, both composite and atomic, have been annotated with keywords. Since keyword search does not use the graph structure of a workflow, we develop a model of workflows using context-free bag grammars. We then give efficient polynomial-time algorithms that, given a workflow and a keyword query, determine whether some execution of the workflow matches the query. Based on these algorithms we develop a search and ranking solution that efficiently retrieves the top-k grammars from a repository. Finally, we propose a novel result presentation method for grammars matching a keyword query, based on representative parse-trees. The effectiveness of ou

Deposition And Drying Dynamics Of Liquid Crystal Droplets

Drop drying and deposition phenomena reveal a rich interplay of fundamental science and engineering, give rise to fascinating everyday effects (coffee rings), and influence technologies ranging from printing to genotyping. Here we investigate evaporation dynamics, morphology, and deposition patterns of drying lyotropic chromonic liquid crystal droplets. These drops differ from typical evaporating colloidal drops primarily due to their concentration-dependent isotropic, nematic, and columnar phases. Phase separation occurs during evaporation, and in the process creates surface tension gradients and significant density and viscosity variation within the droplet. As a result, the drying multiphase drops exhibit different convective currents, drop morphologies, and deposition patterns (coffee-rings)

Exploring the feasibility of a community-based strength training program for older people with depressive symptoms and its impact on depressive symptoms

BACKGROUND: Depression is a disabling, prevalent condition. Physical activity programs may assist depression management in older people, ameliorate co-morbid conditions and reduce the need for antidepressants. The UPLIFT pilot study assessed the feasibility of older depressed people attending a community-based progressive resistance training (PRT) program. The study also aimed to determine whether PRT improves depressive status in older depressed patients. METHODS: A randomised controlled trial was conducted. People aged ≥ 65 years with depressive symptoms were recruited via general practices. Following baseline assessment, subjects were randomly allocated to attend a local PRT program three times per week for 10 weeks or a brief advice control group. Follow-up assessment of depressive status, physical and psychological health, functional and quality of life status occurred post intervention and at six months. RESULTS: Three hundred and forty six people responded to the study invitation, of whom 22% had depressive symptoms (Geriatric Depression Scale, GDS-30 score ≥ 11). Thirty two people entered the trial. There were no significant group differences on the GDS at follow-up. At six months there was a trend for the PRT intervention group to have lower GDS scores than the comparison group, but this finding did not reach significance (p = 0.08). More of the PRT group (57%) had a reduction in depressive symptoms post program, compared to 44% of the control group. It was not possible to discern which specific components of the program influenced its impact, but in post hoc analyses, improvement in depressive status appeared to be associated with the number of exercise sessions completed (r = -0.8, p < 0.01). CONCLUSION: The UPLIFT pilot study confirmed that older people with depression can be successfully recruited to a community based PRT program. The program can be offered by existing community-based facilities, enabling its ongoing implementation for the potential benefit of other older people

A zebrafish model of conditional targeted podocyte ablation and regeneration

Podocytes are specialized cells that contribute critically to the normal structure and function of the glomerular filtration barrier. Their depletion plays an important role in the pathogenesis of glomerulosclerosis. Here, we report generation of a genetic model of conditional podocyte ablation and regeneration in zebrafish using a bacterial nitroreductase strategy to convert a prodrug, Metronidazole, into a cytotoxic metabolite. A transgenic zebrafish line was generated that expresses a green fluorescence protein (GFP) and the nitroreductase fusion protein under the control of the podocin promoter Tg(podocin:nitroreductase-GFP). Treatment of these transgenic zebrafish with Metronidazole results in podocyte apoptosis, a loss of nephrin and podocin expression, foot process effacement, and a leaky glomerular filtration barrier. Following Metronidazole washout, proliferating cells were detected in the glomeruli of recovering transgenic fish with a restoration of nitroreductase-GFP fluorescence, nephrin and podocin expression, a reestablishment of normal foot process architecture and glomerular barrier function. Thus, our studies show that zebrafish podocytes are capable of regenerating following depletion and establish the Tg(podocin:NTR-GFP) fish as a new model to study podocyte injury and repair

Blade-Tip Vortex Noise Mitigation Traded-Off against Aerodynamic Design for Propellers of Future Electric Aircraft

We study noise generation at the blade tips of propellers designed for future electric aircraft propulsion and, furthermore, analyze the interrelationship between noise mitigation and aerodynamics improvement in terms of propeller geometric designs. Classical propellers with three or six blades and a conceptual propeller with three joined dual-blades are compared to understand the effects of blade tip vortices on the noise generation and aerodynamics. The dual blade of the conceptual propeller is constructed by joining the tips of two sub-blades. These propellers are designed to operate under the same freestream flow conditions and similar electric power consumption. The Improved Delayed Detached Eddy Simulation (IDDES) is adopted for the flow simulation to identify high-resolution time-dependent noise sources around the blade tips. The acoustic computations use a time-domain method based on the convective Ffowcs Williams–Hawkings (FW-H) equation. The thrust of the 3-blade conceptual propeller is\ua04%\ua0larger than the 3-blade classical propeller and\ua08%\ua0more than the 6-blade one, given that they have similar efficiencies. Blade tip vortices are found emitting broadband noise. Since the classical and conceptual 3-blade propellers have different geometries, especially at the blade tips, they introduce deviations in the vortex development. However, the differences are small regarding the broadband noise generation. As compared to the 6-blade classical propeller, both 3-blade propellers produce much larger noise. The reason is that the increased number of blades leads to the reduced strength of tip vortices. The findings indicate that the noise mitigation through the modification of the blade design and number can be traded-off by the changed aerodynamic performance

Physical Constraints and Functional Characteristics of Transcription Factor-DNA Interaction

We study theoretical ``design principles'' for transcription factor-DNA interaction in bacteria, focusing particularly on the statistical interaction of the transcription factors (TF's) with the genomic background (i.e., the genome without the target sites). We introduce and motivate the concept of `programmability', i.e. the ability to set the threshold concentration for TF binding over a wide range merely by mutating the binding sequence of a target site. This functional demand, together with physical constraints arising from the thermodynamics and kinetics of TF-DNA interaction, leads us to a narrow range of ``optimal'' interaction parameters. We find that this parameter set agrees well with experimental data for the interaction parameters of a few exemplary prokaryotic TF's. This indicates that TF-DNA interaction is indeed programmable. We suggest further experiments to test whether this is a general feature for a large class of TF's.Comment: 9 pages, 4 figures; revised version as published in PNA