SQL Query Completion for Data Exploration

Within the big data tsunami, relational databases and SQL are still there and remain mandatory in most of cases for accessing data. On the one hand, SQL is easy-to-use by non specialists and allows to identify pertinent initial data at the very beginning of the data exploration process. On the other hand, it is not always so easy to formulate SQL queries: nowadays, it is more and more frequent to have several databases available for one application domain, some of them with hundreds of tables and/or attributes. Identifying the pertinent conditions to select the desired data, or even identifying relevant attributes is far from trivial. To make it easier to write SQL queries, we propose the notion of SQL query completion: given a query, it suggests additional conditions to be added to its WHERE clause. This completion is semantic, as it relies on the data from the database, unlike current completion tools that are mostly syntactic. Since the process can be repeated over and over again -- until the data analyst reaches her data of interest --, SQL query completion facilitates the exploration of databases. SQL query completion has been implemented in a SQL editor on top of a database management system. For the evaluation, two questions need to be studied: first, does the completion speed up the writing of SQL queries? Second , is the completion easily adopted by users? A thorough experiment has been conducted on a group of 70 computer science students divided in two groups (one with the completion and the other one without) to answer those questions. The results are positive and very promising

Assessing microbial life in extreme subglacial Lake Vostok, East Antarctica from accretion ice-lake water boundary samples

第3回極域科学シンポジウム/第34回極域生物シンポジウム 11月27日（火） 統計数理研究所 ３階セミナー

RQL : un langage " à la SQL " pour découvrir des règles à partir des données

National audienceRQL (pour Rule Query Language) est un langage de requêtes " à la SQL " qui étend et généralise les dépendances fonctionnelles 1 à de nouvelles catégories de règles. RQL apporte aux analystes de données un outil pratique pour découvrir les implications logiques entre attributs d'une base de données. Ces implications peuvent mettre en évidence des problèmes de qualité de données ou de nouvelles corrélations inattendues entre les attributs. Le traitement de ces requêtes RQL est basé sur une technique de réécriture qui délègue un maximum de calculs au SGBD sous-jacent. Cette contribution vise à renforcer le lien entre la fouille de données et les bases de données et de faciliter l'utilisation de techniques de fouille par des analystes ou des étudiants habitués au SQL

Increasing the stability of sacB transcript improves levansucrase production in Bacillus subtilis.

Aims: To develop a strategy to increase the stability of transcripts of structural genes expressed under the control of sacR, the leader region of Bacillus subtilis levansucrase gene. Methods and Results: Insertion of Shine Dalgarno like sequences in the 5'-untranslated sacR region controlling the expression of sacB. Depending on the number of stabilizing sequences inserted and the position of these sequences with respect to the translation start codon, it was observed that the mRNA stability and the final protein production could be increased or decreased. Conclusions: This mRNA stabilization can be used to increase exocellular protein production in the degU32 (Hy) mutant. Significance and Impact of the Study: This approach can be applied to the expression of heterologous genes of biotechnological interest

Autogenous modulation of the Bacillus subtilis sacB-levB-yveA levansucrase operon by levB transcript.

Silencing of levB, the second structural gene of the tricistronic levansucrase operon encoding the endolevanase LevB, decreases the level of levansucrase expression. Conversely, independent expression of levB greatly stimulates operon expression in Bacillus subtilis. This autogenous effect is mediated by the levB transcript, which carries an internal sequence (5'-AAAGCAGGCAA-3') involved in the enhancing effect. In vitro, the levB transcript displays an affinity to the N-terminal fragment of SacY (KD 0.2 µM), the regulatory protein that prevents transcription termination of levansucrase operon. This positive feed back loop leads to an increase in the operon expression when B. subtilis is growing in the presence of high sucrose concentrations. Under these conditions, extracellular levan synthesized by the fructosyl polymerase activity of levansucrase can be degraded mainly into levanbiose by the action of LevB. Levanbiose is neither taken up nor metabolized by the bacteria. This work modifies the present view of the status of levansucrase in B. subtilis physiology

Temporal sampling helps unravel the genetic structure of naturally occurring populations of a phytoparasitic nematode. 2. Separating the relative effects of gene flow and genetic drift

International audienceStudying wild pathogen populations in natural ecosystems offers the opportunity to better understand the evolutionary dynamics of biotic diseases in crops and to enhance pest control strategies. We used simulations and genetic markers to investigate the spatial and temporal population genetic structure of wild populations of the beet cyst nematode Heterodera schachtii on a wild host plant species, the sea beet (Beta vulgaris spp. maritima), the wild ancestor of cultivated beets. Our analysis of the variation of eight microsatellite loci across four study sites showed that (i) wild H. schachtii populations displayed fine-scaled genetic structure with no evidence of substantial levels of gene flow beyond the scale of the host plant, and comparisons with simulations indicated that (ii) genetic drift substantially affected the residual signals of isolation-by-distance processes, leading to departures from migration–drift equilibrium. In contrast to what can be suspected for (crop) field populations, this showed that wild cyst nematodes have very low dispersal capabilities and are strongly disconnected from each other. Our results provide some key elements for designing pest control strategies , such as decreasing passive dispersal events to limit the spread of virulence among field nematode populations

New antibiotic molecules: bypassing the membrane barrier of gram negative bacteria increases the activity of peptide deformylase inhibitors

International audienceBACKGROUND : Multi-drug resistant (MDR) bacteria have become a major concern in hospitals worldwide and urgently require the development of new antibacterial molecules. Peptide deformylase is an intracellular target now well-recognized for the design of new antibiotics. The bacterial susceptibility to such a cytoplasmic target primarily depends on the capacity of the compound to reach and accumulate in the cytosol. METHODOLOGY/PRINCIPAL FINDINGS : To determine the respective involvement of penetration (influx) and pumping out (efflux) mechanisms to peptide deformylase inhibitors (PDF-I) activity, the potency of various series was determined using various genetic contexts (efflux overproducers or efflux-deleted strains) and membrane permeabilizers. Depending on the structure of the tested molecules, two behaviors could be observed: (i) for actinonin the first PDF-I characterized, the AcrAB efflux system was the main parameter involved in the bacterial susceptibility, and (ii), for the latest PDF-Is such as the derivatives of 2-(5-bromo-1H-indol-3-yl)-N-hydroxyacetamide, the penetration through the membrane was a important limiting step CONCLUSIONS/SIGNIFICANCE : Our results clearly show that the bacterial membrane plays a key role in modulating the antibacterial activity of PDF-Is. The bacterial susceptibility for these new antibacterial molecules can be improved by two unrelated ways in MDR strains: by collapsing the Acr efflux activity or by increasing the uptake rate through the bacterial membrane. The efficiency of the second method is associated with the nature of the compound

Combining Logic and Probabilities for Discovering Mappings between Taxonomies

Abstract. In this paper, we investigate a principled approach for defining and discovering probabilistic mappings between two taxonomies. First, we compare two ways of modeling probabilistic mappings which are compatible with the logical constraints declared in each taxonomy. Then we describe a generate and test algorithm which minimizes the number of calls to the probability estimator for determining those mappings whose probability exceeds a certain threshold. Finally, we provide an experimental analysis of this approach

Erythromycin degradation by an esterase in enzymatic membrane reactors

1 Introduction Pharmaceuticals products (PPs) and endocrine disrupting chemicals (EDCs) as well as their transformation products have been detected in almost all effluents from sewage facilities, in surface water, in groundwater, adsorbed on sediments and even in drinking water [1,2]. Ecotoxicity studies have demonstrated that pharmaceutical pollutants could affect the growth, reproduction and behavior of birds, fishes, invertebrates, plants and bacteria [3,4]. Some recently published studies report that the presence of low concentrations of antibiotics in the wastewaters may develop antibiotic resistance in the whole environment [5, 6]. As previously reported by Demarche et al. [7], the use of enzymes might be beneficial to enhance or complement conventional wastewater treatments. As far as enzymes are relatively expensive the reuse of the biocatalyst appears to be essential to ensure the economic and industrial viability of the process. Enzymatic membrane reactors appear to be an interesting alternative since they enable to couple reaction and separation [8]. In fact, in such enzymatic reactors, the substrate is continuously brought in contact with the biocatalyst, which is retained by the membrane, either freely circulating with the retentate or fixed on or within the membrane and the reaction products are recovered in the permeate. This work describes the study of erythromycin degradation by an EreB esterase in free and immobilized forms. It focuses on the comparison between 3 different enzymatic membrane reactors for erythromycin degradation by esterase EreB. In the first configuration the free biocatalyst was confined in the reaction media by a ceramic membrane. In the two other cases, the enzyme was immobilized in the membrane either covalently grafted or adsorbed. Please click Additional Files below to see the full abstract