Utilizing Structural Knowledge for Information Retrieval in XML Databases

In this paper we address the problem of immediate translation of eXtensible Mark-up Language (XML) information retrieval (IR) queries to relational database expressions and stress the benefits of using an intermediate XML-specific algebra over relational algebra. We show how adding an XML-specific algebra at the logical level of a DBMS enables a level of abstraction from both query languages for information retrieval in XML and the underlying physical storage and manipulation. We picked a region algebra as a basis for defining the structure aware (SA) view on XML in which we can distinguish among different XML entities, such as element nodes, text nodes, words, and determine their containment relation. Region algebras are already well established in semi-structured document processing as shown in an extensive overview of region algebra approaches in this paper. Furthermore, we propose a variant of region algebra that can support ranking operators in an elegant way while staying algebraic. As relevance scores are computed for regions in our region algebra we named it score region algebra (SRA). The benefits of introducing score region algebra are explained on a set of query examples. Besides abstracting from the query language used and the physical implementation, SRA enables a certain degree of abstraction from the retrieval model used and the opportunity to use the query optimization at the logical level of a database. Various retrieval models can be instantiated at the physical level based on the abstract specification of SRA operators. We also discuss numerous region algebra operator properties that provide a firm ground for query rewriting and optimization at the SA level, which is an important premise for the existence of such a logical view on XML

CIRQUID: complex information retrieval queries in a database

The CIRQUID project plans to design and build a DBMS that seemlessly integrates relevance-oriented querying of semi-structured data (XML) with traditional querying of this data. The project is funded by the Netherlands Organisation of Scientific Research

Prediction of Long-Term Benefits of Inhaled Steroids by Phenotypic Markers in Moderate-to-Severe COPD:A Randomized Controlled Trial

BACKGROUND:The decline in lung function can be reduced by long-term inhaled corticosteroid (ICS) treatment in subsets of patients with chronic obstructive pulmonary disease (COPD). We aimed to identify which clinical, physiological and non-invasive inflammatory characteristics predict the benefits of ICS on lung function decline in COPD. METHODS:Analysis was performed in 50 steroid-naive compliant patients with moderate to severe COPD (postbronchodilator forced expiratory volume in one second (FEV1), 30-80% of predicted, compatible with GOLD stages II-III), age 45-75 years, >10 packyears smoking and without asthma. Patients were treated with fluticasone propionate (500 μg bid) or placebo for 2.5 years. Postbronchodilator FEV1, dyspnea and health status were measured every 3 months; lung volumes, airway hyperresponsiveness (PC20), and induced sputum at 0, 6 and 30 months. A linear mixed effect model was used for analysis of this hypothesis generating study. RESULTS:Significant predictors of attenuated FEV1-decline by fluticasone treatment compared to placebo were: fewer packyears smoking, preserved diffusion capacity, limited hyperinflation and lower inflammatory cell counts in induced sputum (p<0.04). CONCLUSIONS:Long-term benefits of ICS on lung function decline in patients with moderate-to-severe COPD are most pronounced in patients with fewer packyears, and less severe emphysema and inflammation. These data generate novel hypotheses on phenotype-driven therapy in COPD. TRIAL REGISTRATION:ClinicalTrials.gov NCT00158847

Susceptibility to chronic mucus hypersecretion, a genome wide association study

Background: Chronic mucus hypersecretion (CMH) is associated with an increased frequency of respiratory infections, excess lung function decline, and increased hospitalisation and mortality rates in the general population. It is associated with smoking, but it is unknown why only a minority of smokers develops CMH. A plausible explanation for this phenomenon is a predisposing genetic constitution. Therefore, we performed a genome wide association (GWA) study of CMH in Caucasian populations. Methods: GWA analysis was performed in the NELSON-study using the Illumina 610 array, followed by replication and meta-analysis in 11 additional cohorts. In total 2,704 subjects with, and 7,624 subjects without CMH were included, all current or former heavy smokers (≥20 pack-years). Additional studies were performed to test the functional relevance of the most significant single nucleotide polymorphism (SNP). Results: A strong association with CMH, consistent across all cohorts, was observed with rs6577641 (p = 4.25x10-6, OR = 1.17), located in intron 9 of the special AT-rich sequence-binding protein 1 locus (SATB1) on chromosome 3. The risk allele (G) was associated with higher mRNA expression of SATB1 (4.3x10 -9) in lung tissue. Presence of CMH was associated with increased SATB1 mRNA expression in bronchial biopsies from COPD patients. SATB1 expression was induced during differentiation of primary human bronchial epithelial cells in culture. Conclusions: Our findings, that SNP rs6577641 is associated with CMH in multiple cohorts and is a cis-eQTL for SATB1, together with our additional observation that SATB1 expression increases during epithelial differentiation provide suggestive evidence that SATB1 is a gene that affects CMH