Automatic generation of warehouse mediators using an ontology engine

The Data Foundry research project at LLNL is investigating data warehousing in highly dynamic scientific environments. Specifically, we are developing a data warehouse to aid structural biologists in genetics research. Upon completion, this warehouse will present a uniform view of data obtained from several heterogeneous data sources containing distinct but related data from various genetics domains. Our warehouse uses a mediated data warehouse architecture in which only some data is represented explicitly in the warehouse; remote access is required to obtain the non-materialized data. Mediators are used to convert data from the data source representation to the warehouse representation and make it available to the warehouse. The major challenge we face is reducing the impact of source schema changes on warehouse availability and reliability: based upon previous efforts, we anticipate one source schema modification every 2-4 weeks once all of the desired sources have been integrated. Incorporating these modifications into the mediators using brute force results in an unacceptable amount of warehouse down-time. We believe that extensive use of a carefully designed ontology will allow us to overcome this problem, while providing a useful knowledge base for other applications. In addition to automatically generating the transformation between the data sources and the warehouse, the ontology will be used to guide automatic schema evolution, and provide a high level interface to the warehouse. This paper focuses on the use of the ontology to automatically generate mediators, because reducing the effect of source changes is a critical step in providing reliable access to heterogeneous data sources

Fatigue and fracture assessment of toxic metal replacement coatings for aerospace applications

The use of corrosion resistant and adhesion promoting films and coatings is established industrial practice for many fatigue sensitive components and structures. However, recent environmental legislation restricting the use of a range of toxic heavy metals and their derivative processes, such as chromic acid anodising (CAA), has meant that a number of new coatings systems and pretreatments are currently being developed to replace the traditional processes still in use. Typical of these new systems are the boric–sulphuric acid anodising (BSAA) process, which can be modified to provide excellent adhesive bonding properties, the sulphuric acid anodising process, which includes an additional electrolytic phosphoric acid deoxidising stage (EPAD) to produce a duplex oxide layer, and the recently patented ACDC sulphuric acid anodising process which produces a two layered oxide film which can be tailored to produce different porosity volume fractions within each layer. This communication reports the preliminary findings of a study carried out to assess the fatigue response of Al2618:T6 aluminium alloys to these new processes. In contrast to CAA anodising, the initial results indicate that the EPAD and ACDC processes do not appear to have a significant effect on fatigue

The generalized Robinson-Foulds metric

The Robinson-Foulds (RF) metric is arguably the most widely used measure of phylogenetic tree similarity, despite its well-known shortcomings: For example, moving a single taxon in a tree can result in a tree that has maximum distance to the original one; but the two trees are identical if we remove the single taxon. To this end, we propose a natural extension of the RF metric that does not simply count identical clades but instead, also takes similar clades into consideration. In contrast to previous approaches, our model requires the matching between clades to respect the structure of the two trees, a property that the classical RF metric exhibits, too. We show that computing this generalized RF metric is, unfortunately, NP-hard. We then present a simple Integer Linear Program for its computation, and evaluate it by an all-against-all comparison of 100 trees from a benchmark data set. We find that matchings that respect the tree structure differ significantly from those that do not, underlining the importance of this natural condition.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

Structured Composition of Dataflow and Control-Flow for Reusable and Robust Scientific Workflows

Data-centric scientific workflows are often modeled as dataflow process networks. The simplicity of the dataflow framework facilitates workflow design, analysis, and optimization. However, some workflow tasks are particularly ''control-flow intensive'', e.g., procedures to make workflows more fault-tolerant and adaptive in an unreliable, distributed computing environment. Modeling complex control-flow directly within a dataflow framework often leads to overly complicated workflows that are hard to comprehend, reuse, schedule, and maintain. In this paper, we develop a framework that allows a structured embedding of control-flow intensive subtasks within dataflow process networks. In this way, we can seamlessly handle complex control-flows without sacrificing the benefits of dataflow. We build upon a flexible actor-oriented modeling and design approach and extend it with (actor) frames and (workflow) templates. A frame is a placeholder for an (existing or planned) collection of components with similar function and signature. A template partially specifies the behavior of a subworkflow by leaving ''holes'' (i.e., frames) in the subworkflow definition. Taken together, these abstraction mechanisms facilitate the separation and structured re-combination of control-flow and dataflow in scientific workflow applications. We illustrate our approach with a real-world scientific workflow from the astrophysics domain. This data-intensive workflow requires remote execution and file transfer in a semi-reliable environment. For such work-flows, we propose a 3-layered architecture: The top-level, typically a dataflow process network, includes Generic Data Transfer (GDT) frames and Generic remote eXecution (GX) frames. At the second level, the user can specialize the behavior of these generic components by embedding a suitable template (here: transducer templates for control-flow intensive tasks). At the third level, frames inside the transducer template are specialized by embedding the desired implementation. Our approach yields workflows that are more robust (fault-tolerance strategies can be define by control-flow driven transducer templates) and at the same time more reuseable, since the embedding of frames and templates yields more structured and modular workflows

‘Draw, write and tell’. A literature review and methodological development on the ‘draw and write’ research method.

The creative research method ‘draw and write’ has been used in health, social care and education research for several decades. A literature search of studies utilising this method was conducted during the planning stages of a study exploring primary school children’s perceptions of infant feeding. A review of this literature noted a range of benefits of ‘draw and write’ in enabling child participation. However, it also identified that the method has been used inconsistently and found that there are issues for researchers in relation to interpretation of creative work and analysis of data. As a result of this, an improvement on this method, entitled ‘draw, write and tell’, was developed in an attempt to provide a more child-orientated and consistent approach to data collection, interpretation and analysis. This article identifies the issues relating to ‘draw and write’ and describes the development and application of ‘draw, write and tell’ as a case study, noting its limitations and benefit

Tracking Multiple Topics for Finding Interesting Articles

We introduce multiple topic tracking (MTT) for iScore to better recommend news articles for users with multiple interests and to address changes in user interests over time. As an extension of the basic Rocchio algorithm, traditional topic detection and tracking, and single-pass clustering, MTT maintains multiple interest profiles to identify interesting articles for a specific user given user-feedback. Focusing on only interesting topics enables iScore to discard useless profiles to address changes in user interests and to achieve a balance between resource consumption and classification accuracy. iScore is able to achieve higher quality results than traditional methods such as the Rocchio algorithm. We identify several operating parameters that work well for MTT. Using the same parameters, we show that MTT alone yields high quality results for recommending interesting articles from several corpora. The inclusion of MTT improves iScore's performance by 25% in recommending news articles from the Yahoo! News RSS feeds and the TREC11 adaptive filter article collection. And through a small user study, we show that iScore can still perform well when only provided with little user feedback

An X-ray photoelectron spectroscopy investigation of chromium conversion coatings and chromium compounds

Hexavalent and trivalent chromium based conversion coatings on zinc electrodeposited steel have been investigated using X-ray photoelectron spectroscopy (XPS) with the aim of elucidating their film chemistry. Furthermore, a monochromatic Al Kα X-ray source was utilised and the spectra produced evaluated using curve fitting software to elucidate oxidation state information. In addition, a number of chromium compounds were investigated and used to complement the curve fitting analysis for the conversion coatings. High resolution Cr2p spectra from chromium compounds exhibited multiplet splitting for Cr2O3. Additional satellite emissions can also be observed for Cr2O3 and Cr(OH)3. Curve fitting of hexavalent chromium conversion coating (CCC) 2p3/2 spectra contained both Cr(VI) and Cr(III) species with the content of the former slightly higher when the X-ray beam take-off angle (TOA) was reduced to determine more surface specific information. The Cr(III) content was determined to be mainly composed of Cr(OH)3 with some Cr2O3. In comparison, trivalent CCCs were largely composed of Cr2O3 as opposed to Cr(OH)3. Survey scans of both coatings revealed that the trivalent CCCs had a higher relative zinc content

Acetyl-CoA synthetase 2 promotes acetate utilization and maintains cancer cell growth under metabolic stress

A functional genomics study revealed that the activity of acetyl-CoA synthetase 2 (ACSS2) contributes to cancer cell growth under low-oxygen and lipid-depleted conditions. Comparative metabolomics and lipidomics demonstrated that acetate is used as a nutritional source by cancer cells in an ACSS2-dependent manner, and supplied a significant fraction of the carbon within the fatty acid and phospholipid pools. ACSS2 expression is upregulated under metabolically stressed conditions and ACSS2 silencing reduced the growth of tumor xenografts. ACSS2 exhibits copy-number gain in human breast tumors, and ACSS2 expression correlates with disease progression. These results signify a critical role for acetate consumption in the production of lipid biomass within the harsh tumor microenvironment

Notes on the ecology of Ethiopian Bush-crow Zavattariornis stresemanni

We used the focal sampling method to conduct a behavioural study of the endemic Ethiopian Bush-crow Zavattariornis stresemanni in the Yabelo-Mega area of southern Ethiopia. We found that feeding rates were lower in areas with low sward height and low numbers of trees. This was particularly concerning given the degradation of natural habitat in this area