An Ontology-Based Method for Semantic Integration of Business Components

Building new business information systems from reusable components is today an approach widely adopted and used. Using this approach in analysis and design phases presents a great interest and requires the use of a particular class of components called Business Components (BC). Business Components are today developed by several manufacturers and are available in many repositories. However, reusing and integrating them in a new Information System requires detection and resolution of semantic conflicts. Moreover, most of integration and semantic conflict resolution systems rely on ontology alignment methods based on domain ontology. This work is positioned at the intersection of two research areas: Integration of reusable Business Components and alignment of ontologies for semantic conflict resolution. Our contribution concerns both the proposal of a BC integration solution based on ontologies alignment and a method for enriching the domain ontology used as a support for alignment.Comment: IEEE New Technologies of Distributed Systems (NOTERE), 2011 11th Annual International Conference; ISSN: 2162-1896 Print ISBN: 978-1-4577-0729-2 INSPEC Accession Number: 12122775 201

Foodborne Staphylococcus Aureus: Identification and Enterotoxin Production in Milk and Cheese.

Onemocnění z potravin (alimentární onemocnění) vyvolaná bakteriemi jsou stále aktuálním tématem v celosvětovém měřítku. Abychom zajistili výrobu zdravotně nezávadných potravin, je potřeba nových poznatků o virulenci patogenů, které by doplnily již známé skutečnosti o jejich růstu a přeživání v potravinách. Také potřebujeme vyvíjet rychlé a citlivé metody na detekci těchto patogenů. Dizertační práce popisuje metodu na detekci S. aureus v potravinách, která je založená na PCR v reálném čase ve spojení s namnožením v selektivním médium. Dále pojednává o vlivu environmentálních faktorů na růst S. aureus a tvorbu enterotoxinů v mléce a sýrech. Vyvinuli jsme rychlou a citlivou metodu na detekci S. aureus v potravinách s použitím selektivního namnožení a PCR v reálném čase. Nově vyvinutá metoda umožnila detekci S. aureus na druhý den od přijetí vzorku. Tato metoda může být použita jako rychlejší, citlivějsí a vysoce specifická alternativní metoda ke konvenční mikrobiologické metodě. Zkoumali jsme vliv tří různých teplot, 8°C, 12°C a 20°C na růst S. aureus a tvorbu enterotoxinu D v pasterizovaném mléce a na růst, expresi genu sed a tvorbu enterotoxinu D v tekutém médiu s extraktem z mozku a srdce (BHI). Experimenty byly prováděny v malých skleněných fermentorech po 6 dní. Genová exprese byla sledována pomocí qRT-PCR a tvorba enterotoxinu D byla měřena pomocí imunologické metody ELISA. Růstová křivka v BHI měla stejný průběh při 20°C a 12°C, ale v při 12°C začal růst se spožděním. Při 8°C nebyl pozorován žádný růst. Růst S. aureus v mléce byl ve srovnání s BHI menší. sed mRNA byla detekována při 20°C po 4 hodinách a při 12°C po 7 hodinách a produkce enterotoxinu se objevila v exponenciální fázi růstu. V mléce se produkce SED při 20°C a při 12°C objevila dříve, ale celkové množství vyprodukovaného SED bylo nižší než v BHI. Při 8°C nebyla pozorována žádná produkce SED stejně jako v BHI. Dále byl zkoumán společný vliv nízké teploty 12°C a přítomnosti kompetitivní doprovodné mikroflóry pocházející ze surového mléka na růst S. aureus a produkci enterotoxinu v pasterizovaném mléce. Byl pozorován inhibiční účinek na růst a produkci enterotoxinů a vliv kompetice byl výraznější než vliv nízké teploty. Produkce enterotoxinu byla nízká a odpovídala růstu. Snížením množství doprovodné mikroflóry a zvýšením inokula došlo pouze k nepatrnému zvýšení produkce enterotoxinu. V další fázi byly dva různé typy sýrů zaočkovány S. aureus za účelem simulace sekundární kontaminace při výrobě sýrů. Vzorky byly odebírány v průběhu 4 týdnů. Kritické faktory jako jsou kompetitivní mikrofóra nebo pH, které jsou zodpovědné za regulaci virulence S. aureus byly sledovány. Snažili jsem se rozlišit situace při kterých: (i) není pozorován růst, ale objevuje se produkce enterotoxinu a (ii) dochází k růstu ale bez produkce enterotoxinu.Foodborne diseases caused by bacteria are an actual issue worldwide. To produce food, which is safe for human consumption, data about food-borne pathogen virulence is required to complement the already existing knowledge about the bacterial growth and survival in food. There is also a growing need for rapid and sensitive methods to detect these pathogens. In this dissertation, the real-time PCR-based method for the detection of S. aureus in food using selective enrichment and the impact of environmental factors on S. aureus growth and enterotoxin production in milk and cheese are described. We developed a rapid and sensitive method for the detection of S. aureus in food using selective enrichment and a new species-specific real-time PCR. The method facilitated the detection of S. aureus on the next day after the sample reception. This method can be used for S. aureus detection as a faster, highly specific, and more sensitive alternative to the microbiological method. We investigated the effect of three different temperatures, 8°C, 12°C and 20°C on S. aureus growth and SED production in pasteurized milk and on growth, sed gene expression and SED production in Brain heart infusion. The experiments were performed in small-scale fermentors for six days and gene expression was followed by qRT-PCR. SED production was measured using Enzyme-Linked ImmunoSorbent Assay (ELISA). In BHI the growth pattern was the same at 20°C and 12°C but delayed in the latter. At 8°C there was no growth. In milk, growth was lower compared to BHI. sed mRNA was detected at 20°C and 12°C after 4 and 7 hours respectively in BHI and the production occurred during the exponential phase of growth. In milk the SED production at 20°C and 12°C occurred earlier in growth but a lower total amount was produced compared to BHI. At 8°C, there was no SED production like in BHI. The combined effect of low temperature, 12°C, and the presence of competing background microflora derived from raw milk on the growth of S. aureus and SED production in pasteurized milk was further investigated. An inhibitory effect on S. aureus growth and enterotoxin production was observed and the impact of competition was greater than the impact of low temperature. The enterotoxin production was low and correlated with the growth. By lowering the amount of competing microflora and increasing the inoculation level of S. aureus, only a slight increase in enterotoxin production occurred. In the next stage, two different cheese matrices were inoculated with S. aureus to simulate a post-contamination scenario in cheese manufacture. Samples were collected over period of 4 weeks. Critical food factors, like competing microflora and pH, which are responsible for down- and up-regulation of the virulence of S. aureus, were monitored. We tried to indentify if there are situations in which: (i) no growth but enterotoxin formation is observed, and (ii) growth and no enterotoxin formation occurs.

Diagnostic applications of next generation sequencing: working towards quality standards

Over the past 6 years, next generation sequencing (NGS) has been established as a valuable high-throughput method for research in molecular genetics and has successfully been employed in the identification of rare and common genetic variations. All major NGS technology companies providing commercially available instruments (Roche 454, Illumina, Life Technologies) have recently marketed bench top sequencing instruments with lower throughput and shorter run times, thereby broadening the applications of NGS and opening the technology to the potential use for clinical diagnostics. Although the high expectations regarding the discovery of new diagnostic targets and an overall reduction of cost have been achieved, technological challenges in instrument handling, robustness of the chemistry and data analysis need to be overcome. To facilitate the implementation of NGS as a routine method in molecular diagnostics, consistent quality standards need to be developed. Here the authors give an overview of the current standards in protocols and workflows and discuss possible approaches to define quality criteria for NGS in molecular genetic diagnostics

Domain-mediated interactions for protein subfamily identification

Within a protein family, proteins with the same domain often exhibit different cellular functions, despite the shared evolutionary history and molecular function of the domain. We hypothesized that domain-mediated interactions (DMIs) may categorize a protein family into subfamilies because the diversified functions of a single domain often depend on interacting partners of domains. Here we systematically identified DMI subfamilies, in which proteins share domains with DMI partners, as well as with various functional and physical interaction networks in individual species. In humans, DMI subfamily members are associated with similar diseases, including cancers, and are frequently co-associated with the same diseases. DMI information relates to the functional and evolutionary subdivisions of human kinases. In yeast, DMI subfamilies contain proteins with similar phenotypic outcomes from specific chemical treatments. Therefore, the systematic investigation here provides insights into the diverse functions of subfamilies derived from a protein family with a link-centric approach and suggests a useful resource for annotating the functions and phenotypic outcomes of proteins.11Ysciescopu

Qualitative Effects of Knowledge Rules in Probabilistic Data Integration

One of the problems in data integration is data overlap: the fact that different data sources have data on the same real world entities. Much development time in data integration projects is devoted to entity resolution. Often advanced similarity measurement techniques are used to remove semantic duplicates from the integration result or solve other semantic conflicts, but it proofs impossible to get rid of all semantic problems in data integration. An often-used rule of thumb states that about 90% of the development effort is devoted to solving the remaining 10% hard cases. In an attempt to significantly decrease human effort at data integration time, we have proposed an approach that stores any remaining semantic uncertainty and conflicts in a probabilistic database enabling it to already be meaningfully used. The main development effort in our approach is devoted to defining and tuning knowledge rules and thresholds. Rules and thresholds directly impact the size and quality of the integration result. We measure integration quality indirectly by measuring the quality of answers to queries on the integrated data set in an information retrieval-like way. The main contribution of this report is an experimental investigation of the effects and sensitivity of rule definition and threshold tuning on the integration quality. This proves that our approach indeed reduces development effort — and not merely shifts the effort to rule definition and threshold tuning — by showing that setting rough safe thresholds and defining only a few rules suffices to produce a ‘good enough’ integration that can be meaningfully used

Membrane glycomics reveal heterogeneity and quantitative distribution of cell surface sialylation.

Given that unnatural sugar expression is metabolically achieved, the kinetics and disposition of incorporation can lend insight into the temporal and localization preferences of sialylation across the cell surface. However, common detection schemes lack the ability to detail the molecular diversity and distribution of target moieties. Here we employed a mass spectrometric approach to trace the placement of azido sialic acids on membrane glycoconjugates, which revealed substantial variations in incorporation efficiencies between N-/O-glycans, glycosites, and glycosphingolipids. To further explore the propensity for sialylation, we subsequently mapped the native glycome of model epithelial cell surfaces and illustrate that while glycosylation sites span broadly across the extracellular region, a higher number of heterogeneous glycoforms occur on sialylated sites closest to the transmembrane domain. Beyond imaging techniques, this integrative approach provides unprecedented details about the frequency and structure-specific distribution of cell surface sialylation, a critical feature that regulates cellular interactions and homeostatic pathways

Populous: A tool for populating ontology templates

We present Populous, a tool for gathering content with which to populate an ontology. Domain experts need to add content, that is often repetitive in its form, but without having to tackle the underlying ontological representation. Populous presents users with a table based form in which columns are constrained to take values from particular ontologies; the user can select a concept from an ontology via its meaningful label to give a value for a given entity attribute. Populated tables are mapped to patterns that can then be used to automatically generate the ontology's content. Populous's contribution is in the knowledge gathering stage of ontology development. It separates knowledge gathering from the conceptualisation and also separates the user from the standard ontology authoring environments. As a result, Populous can allow knowledge to be gathered in a straight-forward manner that can then be used to do mass production of ontology content.Comment: in Adrian Paschke, Albert Burger begin_of_the_skype_highlighting end_of_the_skype_highlighting, Andrea Splendiani, M. Scott Marshall, Paolo Romano: Proceedings of the 3rd International Workshop on Semantic Web Applications and Tools for the Life Sciences, Berlin,Germany, December 8-10, 201

Ontologies and Information Extraction

This report argues that, even in the simplest cases, IE is an ontology-driven process. It is not a mere text filtering method based on simple pattern matching and keywords, because the extracted pieces of texts are interpreted with respect to a predefined partial domain model. This report shows that depending on the nature and the depth of the interpretation to be done for extracting the information, more or less knowledge must be involved. This report is mainly illustrated in biology, a domain in which there are critical needs for content-based exploration of the scientific literature and which becomes a major application domain for IE