Towards Intelligent Databases

This article is a presentation of the objectives and techniques of deductive databases. The deductive approach to databases aims at extending with intensional definitions other database paradigms that describe applications extensionaUy. We first show how constructive specifications can be expressed with deduction rules, and how normative conditions can be defined using integrity constraints. We outline the principles of bottom-up and top-down query answering procedures and present the techniques used for integrity checking. We then argue that it is often desirable to manage with a database system not only database applications, but also specifications of system components. We present such meta-level specifications and discuss their advantages over conventional approaches

Asymptotics of the solutions of the stochastic lattice wave equation

We consider the long time limit theorems for the solutions of a discrete wave equation with a weak stochastic forcing. The multiplicative noise conserves the energy and the momentum. We obtain a time-inhomogeneous Ornstein-Uhlenbeck equation for the limit wave function that holds both for square integrable and statistically homogeneous initial data. The limit is understood in the point-wise sense in the former case, and in the weak sense in the latter. On the other hand, the weak limit for square integrable initial data is deterministic

Long time, large scale limit of the Wigner transform for a system of linear oscillators in one dimension

We consider the long time, large scale behavior of the Wigner transform W_\eps(t,x,k) of the wave function corresponding to a discrete wave equation on a 1-d integer lattice, with a weak multiplicative noise. This model has been introduced in Basile, Bernardin, and Olla to describe a system of interacting linear oscillators with a weak noise that conserves locally the kinetic energy and the momentum. The kinetic limit for the Wigner transform has been shown in Basile, Olla, and Spohn. In the present paper we prove that in the unpinned case there exists $\gamma_0>0$ such that for any $\gamma\in(0,\gamma_0]$ the weak limit of W_\eps(t/\eps^{3/2\gamma},x/\eps^{\gamma},k), as \eps\ll1, satisfies a one dimensional fractional heat equation $\partial_t W(t,x)=-\hat c(-\partial_x^2)^{3/4}W(t,x)$ with $\hat c>0$. In the pinned case an analogous result can be claimed for W_\eps(t/\eps^{2\gamma},x/\eps^{\gamma},k) but the limit satisfies then the usual heat equation

A hierarchical model of transcriptional dynamics allows robust estimation of transcription rates in populations of single cells with variable gene copy number

Motivation: cis-regulatory DNA sequence elements, such as enhancers and silencers, function to control the spatial and temporal expression of their target genes. Although the overall levels of gene expression in large cell populations seem to be precisely controlled, transcription of individual genes in single cells is extremely variable in real time. It is, therefore, important to understand how these cis-regulatory elements function to dynamically control transcription at single-cell resolution. Recently, statistical methods have been proposed to back calculate the rates involved in mRNA transcription using parameter estimation of a mathematical model of transcription and translation. However, a major complication in these approaches is that some of the parameters, particularly those corresponding to the gene copy number and transcription rate, cannot be distinguished; therefore, these methods cannot be used when the copy number is unknown. Results: Here, we develop a hierarchical Bayesian model to estimate biokinetic parameters from live cell enhancer–promoter reporter measurements performed on a population of single cells. This allows us to investigate transcriptional dynamics when the copy number is variable across the population. We validate our method using synthetic data and then apply it to quantify the function of two known developmental enhancers in real time and in single cells

Cut Points and Diffusions in Random Environment

In this article we investigate the asymptotic behavior of a new class of multi-dimensional diffusions in random environment. We introduce cut times in the spirit of the work done by Bolthausen, Sznitman and Zeitouni, see [4], in the discrete setting providing a decoupling effect in the process. This allows us to take advantage of an ergodic structure to derive a strong law of large numbers with possibly vanishing limiting velocity and a central limit theorem under the quenched measure.Comment: 44 pages; accepted for publication in "Journal of Theoretical Probability

Modelling expected physical impacts and human casualties from explosive volcanic eruptions

A multi-hazard, multi-vulnerability impact model has been developed for application to European volcanoes that could significantly damage human settlements. This impact model is based on volcanological analyses of the potential hazards and hazard intensities coupled with engineering analyses of the vulnerability to these hazards of residential buildings in four European locations threatened by explosive volcanic eruptions. For a given case study site, inputs to the model are population data, building characteristics, volcano scenarios as a series of hazard intensities, and scenarios such as the time of eruption or the percentage of the population which has been evacuated. Outputs are the rates of fatalities, seriously injured casualties, and destroyed buildings for a given scenario. These results are displayed in a GIS, thereby presenting risk maps which are easy to use for presenting to public officials, the media, and the public. Technical limitations of the model are discussed and future planned developments are considered. This work contributes to the EU-funded project EXPLORIS (Explosive Eruption Risk and Decision Support for EU Populations Threatened by Volcanoes, EVR1-2001-00047). </p><p style='line-height: 20px;'>&nbsp;</p

Neurotransmitter uptake of synaptic vesicles studied by X-ray diffraction

The size, polydispersity, and electron density profile of synaptic vesicles (SVs) can be studied by small-angle X-ray scattering (SAXS), i.e. by X-ray diffraction from purified SV suspensions in solution. Here we show that size and shape transformations, as they appear in the functional context of these important synaptic organelles, can also be monitored by SAXS. In particular, we have investigated the active uptake of neurotransmitters, and find a mean vesicle radius increase of about 12% after the uptake of glutamate, which indicates an unusually large extensibility of the vesicle surface, likely to be accompanied by conformational changes of membrane proteins and rearrangements of the bilayer. Changes in the electron density profile (EDP) give first indications for such a rearrangement. Details of the protein structure are screened, however, by SVs polydispersity. To overcome the limitations of large ensemble averages and heterogeneous structures, we therefore propose serial X-ray diffraction by single free electron laser pulses. Using simulated data for realistic parameters, we show that this is in principle feasible, and that even spatial distances between vesicle proteins could be assessed by this approach

Reconstitution of SNARE proteins into solid-supported lipid bilayer stacks and X-ray structure analysis.

SNAREs are known as an important family of proteins mediating vesicle fusion. For various biophysical studies, they have been reconstituted into supported single bilayers via proteoliposome adsorption and rupture. In this study we extended this method to the reconstitution of SNAREs into supported multilamellar lipid membranes, i.e. oriented multibilayer stacks, as an ideal model system for X-ray structure analysis (X-ray reflectivity and diffraction). The reconstitution was implemented through a pathway of proteomicelle, proteoliposome and multibilayer. To monitor the structural evolution in each step, we used small-angle X-ray scattering for the proteomicelles and proteoliposomes, followed by X-ray reflectivity and grazing-incidence small-angle scattering for the multibilayers. Results show that SNAREs can be successfully reconstituted into supported multibilayers, with high enough orientational alignment for the application of surface sensitive X-ray characterizations. Based on this protocol, we then investigated the effect of SNAREs on the structure and phase diagram of the lipid membranes. Beyond this application, this reconstitution protocol could also be useful for X-ray analysis of many further membrane proteins