Visual exploration and retrieval of XML document collections with the generic system X2

This article reports on the XML retrieval system X2 which has been developed at the University of Munich over the last five years. In a typical session with X2, the user first browses a structural summary of the XML database in order to select interesting elements and keywords occurring in documents. Using this intermediate result, queries combining structure and textual references are composed semiautomatically. After query evaluation, the full set of answers is presented in a visual and structured way. X2 largely exploits the structure found in documents, queries and answers to enable new interactive visualization and exploration techniques that support mixed IR and database-oriented querying, thus bridging the gap between these three views on the data to be retrieved. Another salient characteristic of X2 which distinguishes it from other visual query systems for XML is that it supports various degrees of detailedness in the presentation of answers, as well as techniques for dynamically reordering and grouping retrieved elements once the complete answer set has been computed

Bacterial Biofilms in Drinking Water Systems: Protecting Patient Health at the Alberta Children’s Hospital

When we hear of bacterial contaminated drinking water, we generally think of microscopic organisms swimming freely throughout the system. Although bacteria are found in this free living form, or planktonically, the majority of microorganisms in natural environments are in fact found growing on a surface. These surface adhered bacteria are called biofilms and can be found anywhere, ranging from implanted medical devices to drinking water pipes. Drinking water system operators use the multiple barrier approach to ensure the microbiological safety of the water. The approach includes primary treatment of the source water with chlorine or UV light; secondary chlorine treatment throughout distribution systems; and routine testing for indicator organisms, such as Escherichia coli. Thus, the presence of indicator organisms signifies that there has been a failure in the treatment process or a contamination in the water system. Regardless of chemical or irradiation treatment, normal flora biofilms continue to grow in these systems. It is theorized that these resident flora biofilms may incorporate and shield pathogenic organisms from chlorine disinfection. The Alberta Children’s Hospital (ACH) water system has a unique design, engineered to reduce bacterial contamination and biofilm growth. This project, done in collaboration with Alberta Health Services and the ACH, aims to evaluate bacterial survival after exposure to low levels of chlorine. It is hypothesized that the chlorine levels maintained in our water systems for secondary treatment may be insufficient to disinfect biofilm growth. Eight isolates were obtained directly from chlorinated water systems, including the ACH. These isolates were tested both planktonically and as biofilms, grown using the Calgary Biofilm Device, under a range of chlorine concentrations. Minimum inhibitory concentration (MIC) and minimum biofilm eradication concentration (MBEC) assays have shown that biofilms can be 2-20 times more resistant to chlorine disinfection when compared to their more vulnerable planktonic counterparts

In vitro antimicrobial susceptibility of single and mixed populations in cystic fibrosis: the role of novel microorganisms

Pseudomonas aeruginosa is the dominant pathogen associated with bacterial infections occurring in Cystic Fibrosis (CF) patients, resulting in 80% of mortality in adults. However, pulmonary infection has recently been defined as polymicrobial, involving classical and other unusual bacteria, which may play a crucial role when associated with the conventional ones. This work aims to evaluate the susceptibility patterns of mono and dual-species biofilms encompassing traditional and emerging microorganisms from CF. The traditional pathogen, P. aeruginosa PA14, and two novel microorganisms, Inquilinus limosus M53 and Dolosigranulum pigrum CIP104051 were used to form single and dual-species biofilms. These were developed on the Calgary Biofilm Device and their susceptibility profiles were estimated against eight antibiotics (tobramycin, gentamicin, levofloxacin, ciprofloxacin, clindamycin, cefotaxime, chloramphenicol and rifampicin), by measuring the minimum inhibitory concentrations (MIC) and minimum biofilm eradication concentration (MBEC). Data showed that most antibiotics were effective in inhibiting planktonic bacterial growth at low concentrations, mainly in mono-populations. Single biofilms involving novel bacteria were more sensitive to virtually all antibiotics than P. aeruginosa. However, when in mixed biofilms, those organisms acted synergistically with P. aeruginosa, attaining additional antibiotic resistance and requiring higher doses of antibiotics to eradicate them. From these results, it can be concluded that the presence of unusual bacteria and their complex interactions with conventional organisms might not be ignored in order to develop more suitable therapy strategies to combat CF.PhD Grant (SFRH/BD/47613/2008

Causes of the Violation of Integrity Constraints for Supporting the Quality of Databases

[EN] The quality of the information provided by databases can be captured by integrity constraints. Thus, violated cases of constraints may serve as a basis for measuring the quality of given database states. A quality metric with the potential of more accuracy is obtained by measuring the causes, i.e., data that are responsible for constraint violations. Such measures also serve for controlling quality impairment across updates.Partially supported by FEDER and the Spanish grants TIN2009-14460-C03 and TIN2010-17139Decker, H. (2011). Causes of the Violation of Integrity Constraints for Supporting the Quality of Databases. Lecture Notes in Computer Science. 6786:283-292. https://doi.org/10.1007/978-3-642-21934-4_24S2832926786Ceri, S., Gottlob, G., Tanca, L.: What you always wanted to know about Datalog (and never dared to ask). TKDE 1(1), 146–166 (1989)Christiansen, H., Martinenghi, D.: On simplification of database integrity constraints. Fundam. Inform. 71(4), 371–417 (2006)Decker, H.: Answers that Have Integrity in Databases that Violate Constraints. Presented at the ICALP Workshop SDKB 2010, to appear in the Post-Workshop Proceedings of SDKB (2011)Decker, H.: Toward a uniform cause-based approach to inconsistency-tolerant database semantics. In: Meersman, R., Dillon, T., Herrero, P. (eds.) OTM 2010. LNCS, vol. 6427, pp. 983–998. Springer, Heidelberg (2010)Decker, H.: Quantifying the Quality of Stored Data by Measuring their Integrity. In: Proc. DIWT 2009, Workshop SMM, pp. 823–828. IEEE, Los Alamitos (2009)Decker, H., Martinenghi, D.: Inconsistency-tolerant Integrity Checking. TKDE 23(2), 218–234 (2011)Decker, H., Martinenghi, D.: Modeling, measuring and monitoring the quality of information. In: Heuser, C.A., Pernul, G. (eds.) ER 2009. LNCS, vol. 5833, pp. 212–221. Springer, Heidelberg (2009)Grant, J., Hunter, A.: Measuring inconsistency in knowledgebases. J. Intelligent Information Systems 27(2), 159–184 (2006)Ramakrishnan, R., Gehrke, J.: Database Management Systems. McGraw-Hill, New York (2003

Eliminating Recursion from Monadic Datalog Programs on Trees

We study the problem of eliminating recursion from monadic datalog programs on trees with an infinite set of labels. We show that the boundedness problem, i.e., determining whether a datalog program is equivalent to some nonrecursive one is undecidable but the decidability is regained if the descendant relation is disallowed. Under similar restrictions we obtain decidability of the problem of equivalence to a given nonrecursive program. We investigate the connection between these two problems in more detail

Tert-butyl benzoquinone: mechanism of biofilm eradication and potential for use as a topical antibiofilm agent

Objectives: Tert-butyl benzoquinone (TBBQ) is the oxidation product of tert-butyl hydroquinone (TBHQ), an antimicrobial food additive with >40 years of safe use. TBBQ displays potent activity against Staphylococcus aureus biofilms in vitro. Here, we report on studies to further explore the action of TBBQ on staphylococcal biofilms, and provide a preliminary preclinical assessment of its potential for use as a topical treatment for staphylococcal infections involving a biofilm component. Methods: The antibacterial properties of TBBQ were assessed against staphylococci growing in planktonic culture and as biofilms in the Calgary Biofilm Device. Established assays were employed to measure the effects of TBBQ on biofilm structure and bacterial membranes, and to assess resistance potential. A living skin equivalent was used to evaluate the effects of TBBQ on human skin. Results: TBBQ eradicated biofilms of S. aureus and other staphylococcal species at concentrations ≤64 mg/L. In contrast to other redox-active agents exhibiting activity against biofilms, TBBQ did not cause substantial destructuring of the biofilm matrix; instead, the antibiofilm activity of the compound was attributed to its ability to kill slow- and non-growing cells via membrane perturbation. TBBQ acted synergistically with gentamicin, did not damage a living skin equivalent following topical application, and exhibited low resistance potential. Conclusions: The ability of TBBQ to eradicate biofilms appears to result from its ability to kill bacteria regardless of growth state. Preliminary evaluation suggests that TBBQ represents a promising candidate for development as a topical antistaphylococcal biofilm agent

New potential carbon emission reduction enterprises in China: deep geological storage of CO2 emitted through industrial usage of coal in China

Deep geological storage of carbon dioxide (CO2) could offer an essential solution to mitigate greenhouse gas emissions from the continued use of fossil fuels. Currently, CO2 capture is both costly and energy intensive; it represents about 60% of the cost of the total carbon capture and storage (CCS) chain which is causing a bottleneck in advancement of CCS in China. This paper proposes capturing CO2 from coal chemical plants where the CO2 is high purity and relatively cheap to collect, thus offering an early opportunity for industrial-scale full-chain CCS implementation. The total amount of high concentration CO2 that will be emitted (or is being emitted) by the coal chemical factories approved by the National Development and Reform Commission described in this paper is 42 million tonnes. If all eight projects could utilize CCS, it would be of great significance for mitigating greenhouse gas emissions in China. Basins which may provide storage sites for captured CO2 in North China are characterized by large sedimentary thicknesses and several sets of reservoir-caprock strata. Some oil fields are nearing depletion and a sub-set of these are potentially suitable for CO2 enhanced oil recovery (EOR) and CCS demonstration but all these still require detailed geological characterization. The short distance between the high concentration CO2 sources and potential storage sites should reduce transport costs and complications. The authors believe these high purity sources coupled with EOR or aquifer storage could offer China an opportunity to lead development in this globally beneficial CCS optio

Evaluation of Differentiated Human Bronchial Epithelial Cell Culture Systems for Asthma Research

The aim of the current study was to evaluate primary (human bronchial epithelial cells, HBEC) and non-primary (Calu-3, BEAS-2B, BEAS-2B R1) bronchial epithelial cell culture systems as air-liquid interface- (ALI-) differentiated models for asthma research. Ability to differentiate into goblet (MUC5AC+) and ciliated (β-Tubulin IV+) cells was evaluated by confocal imaging and qPCR. Expression of tight junction/adhesion proteins (ZO-1, E-Cadherin) and development of transepithelial electrical resistance (TEER) were assessed. Primary cells showed localised MUC5AC, β-Tubulin IV, ZO-1, and E-Cadherin and developed TEER with, however, a large degree of inter- and intradonor variation. Calu-3 cells developed a more reproducible TEER and a phenotype similar to primary cells although with diffuse β-Tubulin IV staining. BEAS-2B cells did not differentiate or develop tight junctions. These data highlight the challenges in working with primary cell models and the need for careful characterisation and selection of systems to answer specific research questions

GenoMetric Query Language: A novel approach to large-scale genomic data management

Motivation: Improvement of sequencing technologies and data processing pipelines is rapidly providing sequencing data, with associated high-level features, of many individual genomes in multiple biological and clinical conditions. They allow for data-driven genomic, transcriptomic and epigenomic characterizations, but require state-of-the-art ‘big data’ computing strategies, with abstraction levels beyond available tool capabilities. Results: We propose a high-level, declarative GenoMetric Query Language (GMQL) and a toolkit for its use. GMQL operates downstream of raw data preprocessing pipelines and supports queries over thousands of heterogeneous datasets and samples; as such it is key to genomic ‘big data’ analysis. GMQL leverages a simple data model that provides both abstractions of genomic region data and associated experimental, biological and clinical metadata and interoperability between many data formats. Based on Hadoop framework and Apache Pig platform, GMQL ensures high scalability, expressivity, flexibility and simplicity of use, as demonstrated by several biological query examples on ENCODE and TCGA datasets. Availability and implementation: The GMQL toolkit is freely available for non-commercial use at http://www.bioinformatics.deib.polimi.it/GMQL/. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online

Development and initial application of δ18Op to understand phosphorus cycling in river, lake and groundwater ecosystems.

Variation in the stable isotope composition of oxygen within dissolved phosphate (δ18Op) represents a novel and potentially powerful environmental tracer. In freshwater, marine and terrestrial ecosystems, δ18Op can act as an inherent label for the sources of phosphorus and the extent to which phosphorus from different sources is metabolised. This paper focuses on the methodological development and initial application of δ18Op across a range of freshwater ecosystems. Initially, we report modifications to the analytical protocol for δ18Op that are designed to minimise incorporation of contaminant oxygen in the final silver phosphate precipitate prior to pyrolysis. This is critical given the range of possible sources of contaminant oxygen within freshwater matrices. Subsequently, we consider the potential utility of δ18Op through application of the technique within a range of freshwater ecosystems in England, UK. Firstly, we characterise δ18Op in river water and effluents from Sewage Treatment Works (STW), and examine the opportunity to use the 18Op of STW effluents to trace the entry and downstream fate of phosphorus from these point sources in rivers. Secondly, we analyse δ18Op to gain insights into variations in the sources and biological cycling of phosphorus in a seasonally stratified lake ecosystem. Thirdly, we characterise δ18Op in shallow and deep groundwater samples, considering whether δ18Op might provide evidence for variation in source and extent of metabolism for phosphorus in groundwater ecosystems. Taken together, these data extend the catalogue of δ18Op in freshwater ecosystems, and further the scope of δ18Op as a tool to better understand phosphorus biogeochemistry