Improving Prolog Programs: Refactoring for Prolog

Refactoring is an established technique from the OO-community to restructure code: it aims at improving software readability, maintainability and extensibility. Although refactoring is not tied to the OO-paradigm in particular, its ideas have not been applied to Logic Programming until now. This paper applies the ideas of refactoring to Prolog programs. A catalogue is presented listing refactorings classified according to scope. Some of the refactorings have been adapted from the OO-paradigm, while others have been specifically designed for Prolog. Also the discrepancy between intended and operational semantics in Prolog is addressed by some of the refactorings. In addition, ViPReSS, a semi-automatic refactoring browser, is discussed and the experience with applying \vipress to a large Prolog legacy system is reported. Our main conclusion is that refactoring is not only a viable technique in Prolog but also a rather desirable one.Comment: To appear in ICLP 200

Adjuvant formulation for veterinary vaccines: Montanide™ Gel safety profile

AbstractSelecting the adjuvant is one of the key for the success of the vaccine in the field. Selecting a flexible adjuvant that will fit with several vaccines dedicated to one or more animal species is a source of economical efficiency. Frequently the safety or efficacy obtained with one model is different from another: there are few adjuvants fitting with the expectation of more than one animal species. Montanide™ Gel an innovative polymeric adjuvant have been tested in several animals. Our studies demonstrated the ability to use this adjuvant in dogs, cattle and pig vaccines. Three trials were performed to validate Montanide™ Gel ability to be used in cattle, pigs and dogs. Respectively, vaccines were formulated with ovalbumin in cattle, Pasteurella Multocida anatoxin and Bordetella bronchiseptica cell walls for pig and finally with parvovirus associated to two leptospira valence for dog model. All antigenic media used in the three trials were inactivated. In all trial, safety was followed through behaviour and temperature measurement as well as histology studies.Montanide™ Gel adjuvant can be used associated with a wide range of antigenic media. Nevertheless, the uses of such adjuvant need validation in avian and fish vaccines

Villa Sint Gertrudis te Landen (Landen, provincie Vlaams-Brabant). Studieopdracht naar een archeologische evaluatie en waardering

In opdracht van het agentschap Onroerend Erfgoed evalueerde Condor Archaeological Research bvba van januari 2012 tot oktober 2012 de erfgoedwaarde van de site die bekend staat als Villa Sint-Gertrudis te Landen, provincie Vlaams-Brabant. Ten oosten hiervan werd in 2010 een soortgelijke studie uitgevoerd naar twee mottes, een bron en de Sint-Gertrudiskerk, waaruit bleek dat in het in dit rapport beschreven gebied van circa 23 ha mogelijk de restanten van een Romeinse villa en bijhorende off site fenomenen aanwezig waren. In dit rapport worden de resultaten van de studieopdracht beschreven en wordt het gebied gewaardeerd volgens de beschermingscriteria opgesteld door het agentschap Onroerend Erfgoed. Behalve enkele losse vondsten waarvan het onduidelijk is of deze door bemesting van op grote afstand, dan wel lokaal vanuit de onmiddellijke omgeving van het plangebied afkomstig zijn, zijn er tijdens dit onderzoek geen archeologische vindplaatsen vastgesteld. De verwachtte villa blijkt, met een vrij grote zekerheid, niet aanwezig te zijn binnen de grenzen van het plangebied. Er werd dus ook niet aanbevolen dit gebied in aanmerking te nemen voor archeologische bescherming

Freezing-induced self-assembly of amphiphilic molecules

The self-assembly of amphiphilic molecules usually takes place in a liquid phase, near room temperature. Here, using small angle X-ray scattering (SAXS) experiments performed in real time, we show that freezing of aqueous solutions of copolymer amphiphilic molecules can induce self-assembly below 0{\deg}C.Comment: 10 pages, 3 figure

Kesselberg te Leuven/Holsbeek (Leuven en Holsbeek, provincie Vlaams-Brabant). Studieopdracht naar een archeologische evaluatie en waardering

In opdracht van het agentschap Onroerend Erfgoed evalueerde Condor Archaeological Research bvba tussen januari 2012 en februari 2013 de archeologische site van de Kesselberg te Leuven en Holsbeek (prov. Vlaams-Brabant) in functie van de mogelijke opmaak van een archeologisch beschermingsdossier. Door de jarenlange prospecties van A. Boschmans en de opgravingen in 1959 door J. Mertens (Nationale Dienst voor Opgravingen) stond de Kesselberg reeds lang bekend als een archeologisch waardevolle zone met o.a. de aanwezigheid van een versterking uit de ijzertijd, verschillende oudere vondsten en de mogelijke aanwezigheid van kasteel Kesselstein, dat teruggaat tot de 11e eeuw. Vandaag bestaat het gebied van circa 20 ha voornamelijk uit bos met hier en daar een stuk open weiland. Enkele percelen zijn bebouwd. In het voorliggend rapport worden de resultaten van de studieopdracht beschreven. Tussen het begin van de 20e eeuw en het midden van de jaren 70 is meer dan anderhalve hectare van de Kesselberg weggegraven. Met dank aan Boschmans zijn er rijke archeologische gegevens bekend over het afgegraven gedeelte, maar zeer veel relicten zijn zeker ook ongedocumenteerd verdwenen. Tot in het midden van de jaren 70 liep over de Kesselberg een groot en intens gebruikt motorcross parcours. Veldwaarnemingen en geofysisch onderzoek brachten de resten van die diepe verstoringen aan het licht en ook van oudere gebouwen. Volgens het proefsleuvenonderzoek, waarbij verschillende grondsporen zijn vastgesteld, hadden deze verstoringen en de natuurlijke erosie in sommige zones al bij al toch nog betrekkelijk weinig impact. Grote delen van het terrein bleken nog onverstoord of zwak verstoord. In dit gebied is dus zeker nog heel wat informatie aanwezig die beter inzicht kan geven over de voormalige nederzetting(en). De studie beveelt aan deze resten te beschermen zodat verdere degradatie van de archeologische waarden wordt tegengegaan

Compositionality, stochasticity and cooperativity in dynamic models of gene regulation

We present an approach for constructing dynamic models for the simulation of gene regulatory networks from simple computational elements. Each element is called a ``gene gate'' and defines an input/output-relationship corresponding to the binding and production of transcription factors. The proposed reaction kinetics of the gene gates can be mapped onto stochastic processes and the standard ode-description. While the ode-approach requires fixing the system's topology before its correct implementation, expressing them in stochastic pi-calculus leads to a fully compositional scheme: network elements become autonomous and only the input/output relationships fix their wiring. The modularity of our approach allows to pass easily from a basic first-level description to refined models which capture more details of the biological system. As an illustrative application we present the stochastic repressilator, an artificial cellular clock, which oscillates readily without any cooperative effects.Comment: 15 pages, 8 figures. Accepted by the HFSP journal (13/09/07

On Distributive Subalgebras of Qualitative Spatial and Temporal Calculi

Qualitative calculi play a central role in representing and reasoning about qualitative spatial and temporal knowledge. This paper studies distributive subalgebras of qualitative calculi, which are subalgebras in which (weak) composition distributives over nonempty intersections. It has been proven for RCC5 and RCC8 that path consistent constraint network over a distributive subalgebra is always minimal and globally consistent (in the sense of strong $n$-consistency) in a qualitative sense. The well-known subclass of convex interval relations provides one such an example of distributive subalgebras. This paper first gives a characterisation of distributive subalgebras, which states that the intersection of a set of $n\geq 3$ relations in the subalgebra is nonempty if and only if the intersection of every two of these relations is nonempty. We further compute and generate all maximal distributive subalgebras for Point Algebra, Interval Algebra, RCC5 and RCC8, Cardinal Relation Algebra, and Rectangle Algebra. Lastly, we establish two nice properties which will play an important role in efficient reasoning with constraint networks involving a large number of variables.Comment: Adding proof of Theorem 2 to appendi

Quantitative Stability of Linear Infinite Inequality Systems under Block Perturbations with Applications to Convex Systems

The original motivation for this paper was to provide an efficient quantitative analysis of convex infinite (or semi-infinite) inequality systems whose decision variables run over general infinite-dimensional (resp. finite-dimensional) Banach spaces and that are indexed by an arbitrary fixed set $J$. Parameter perturbations on the right-hand side of the inequalities are required to be merely bounded, and thus the natural parameter space is $l_{\infty}(J)$. Our basic strategy consists of linearizing the parameterized convex system via splitting convex inequalities into linear ones by using the Fenchel-Legendre conjugate. This approach yields that arbitrary bounded right-hand side perturbations of the convex system turn on constant-by-blocks perturbations in the linearized system. Based on advanced variational analysis, we derive a precise formula for computing the exact Lipschitzian bound of the feasible solution map of block-perturbed linear systems, which involves only the system's data, and then show that this exact bound agrees with the coderivative norm of the aforementioned mapping. In this way we extend to the convex setting the results of [3] developed for arbitrary perturbations with no block structure in the linear framework under the boundedness assumption on the system's coefficients. The latter boundedness assumption is removed in this paper when the decision space is reflexive. The last section provides the aimed application to the convex case

Altering crystal growth and annealing in ice-templated scaffolds.

The potential applications of ice-templating porous materials are constantly expanding, especially as scaffolds for tissue engineering. Ice-templating, a process utilizing ice nucleation and growth within an aqueous solution, consists of a cooling stage (before ice nucleation) and a freezing stage (during ice formation). While heat release during cooling can change scaffold isotropy, the freezing stage, where ice crystals grow and anneal, determines the final size of scaffold features. To investigate the path of heat flow within collagen slurries during solidification, a series of ice-templating molds were designed with varying the contact area with the heat sink, in the form of the freeze drier shelf. Contact with the heat sink was found to be critical in determining the efficiency of the release of latent heat within the perspex molds. Isotropic collagen scaffolds were produced with pores which ranged from 90 μm up to 180 μm as the contact area decreased. In addition, low-temperature ice annealing was observed within the structures. After 20 h at -30 °C, conditions which mimic storage prior to lyophilization, scaffold architecture was observed to coarsen significantly. In future, ice-templating molds should consider not only heat conduction during the cooling phase of solidification, but the effects of heat flow during ice growth and annealing.The authors gratefully acknowledge the financial support of the Gates Cambridge Trust, the Newton Trust, and ERC Advanced Grant 320598 3D-E. A.H. held a Daphne Jackson Fellowship funded by the University of Cambridge.This is the final version of the article. It first appeared from Springer via http://dx.doi.org/10.1007/s10853-015-9343-

Always on my mind: Cross-brain associations of mental health symptoms during simultaneous parent-child scanning.

How parents manifest symptoms of anxiety or depression may affect how children learn to modulate their own distress, thereby influencing the children's risk for developing an anxiety or mood disorder. Conversely, children's mental health symptoms may impact parents' experiences of negative emotions. Therefore, mental health symptoms can have bidirectional effects in parent-child relationships, particularly during moments of distress or frustration (e.g., when a parent or child makes a costly mistake). The present study used simultaneous functional magnetic resonance imaging (fMRI) of parent-adolescent dyads to examine how brain activity when responding to each other's costly errors (i.e., dyadic error processing) may be associated with symptoms of anxiety and depression. While undergoing simultaneous fMRI scans, healthy dyads completed a task involving feigned errors that indicated their family member made a costly mistake. Inter-brain, random-effects multivariate modeling revealed that parents who exhibited decreased medial prefrontal cortex and posterior cingulate cortex activation when viewing their child's costly error response had children with more symptoms of depression and anxiety. Adolescents with increased anterior insula activation when viewing a costly error made by their parent had more anxious parents. These results reveal cross-brain associations between mental health symptomatology and brain activity during parent-child dyadic error processing