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See detailOn the Relevance of Sophisticated Structural Annotations for Disulfide Connectivity Pattern Prediction
Becker, Julien ULg; Maes, Francis; Wehenkel, Louis ULg

in PLoS ONE (2013), 8(2), 56621

Disulfide bridges strongly constrain the native structure of many proteins and predicting their formation is therefore a key sub-problem of protein structure and function inference. Most recently proposed ... [more ▼]

Disulfide bridges strongly constrain the native structure of many proteins and predicting their formation is therefore a key sub-problem of protein structure and function inference. Most recently proposed approaches for this prediction problem adopt the following pipeline: first they enrich the primary sequence with structural annotations, second they apply a binary classifier to each candidate pair of cysteines to predict disulfide bonding probabilities and finally, they use a maximum weight graph matching algorithm to derive the predicted disulfide connectivity pattern of a protein. In this paper, we adopt this three step pipeline and propose an extensive study of the relevance of various structural annotations and feature encodings. In particular, we consider five kinds of structural annotations, among which three are novel in the context of disulfide bridge prediction. So as to be usable by machine learning algorithms, these annotations must be encoded into features. For this purpose, we propose four different feature encodings based on local windows and on different kinds of histograms. The combination of structural annotations with these possible encodings leads to a large number of possible feature functions. In order to identify a minimal subset of relevant feature functions among those, we propose an efficient and interpretable feature function selection scheme, designed so as to avoid any form of overfitting. We apply this scheme on top of three supervised learning algorithms: k-nearest neighbors, support vector machines and extremely randomized trees. Our results indicate that the use of only the PSSM (position-specific scoring matrix) together with the CSP (cysteine separation profile) are sufficient to construct a high performance disulfide pattern predictor and that extremely randomized trees reach a disulfide pattern prediction accuracy of on the benchmark dataset SPX+, which corresponds to +3.2% improvement over the state of the art. A web-application is available at http://m24.giga.ulg.ac.be:81/x3CysBridge​s. [less ▲]

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See detailOn the Reliability of Error Localization Indicators
Pascual, Rodrigo; Golinval, Jean-Claude ULg; Razeto, Mario

Conference given outside the academic context (1998)

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See detailOn the representation of real numbers using regular languages
Lecomte, Pierre ULg; Rigo, Michel ULg

in Theory of Computing Systems (2002), 35(1, JAN-FEB), 13-38

Using a lexicographically ordered regular language, we show how to represent an interval of R. We determine exactly the possible representations of any element in this interval and study the function ... [more ▼]

Using a lexicographically ordered regular language, we show how to represent an interval of R. We determine exactly the possible representations of any element in this interval and study the function which maps a representation onto its numerical value. We make explicit the relationship between the convergence of finite words to an infinite word and the convergence of the corresponding approximations to a real number. [less ▲]

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See detailOn the representational systems underlying prospection: Evidence from the event-cueing paradigm.
D'Argembeau, Arnaud ULg; Demblon, Julie ULg

in Cognition (2012), 125(2), 160-167

The ability to think about the future-prospection-is central to many aspects of human cognition and behavior, from planning and decision making, to self-control and the construction of a sense of identity ... [more ▼]

The ability to think about the future-prospection-is central to many aspects of human cognition and behavior, from planning and decision making, to self-control and the construction of a sense of identity. Yet, the exact nature of the representational systems underlying prospection is not fully understood. Recent findings point to the critical role of episodic memory in imagining specific future events, but it is unlikely that prospection depends solely on this system. Using an event-cueing paradigm in two studies, we here show that specific events that people imagine might happen in their personal future are commonly embedded in broader event sequences-termed event clusters-that link a set of envisioned events according to causal and thematic relations. These findings provide novel evidence that prospection relies on multiple representational systems, with general autobiographical knowledge structures providing a frame that organizes imagined events in overarching event sequences. The results further suggest that knowledge about personal goals plays an important role in structuring these event sequences, especially for the distant future. [less ▲]

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See detailOn the residual advection of passive constituents
Delhez, Eric ULg

in Journal of Marine Systems (1996), 8(3-4), 147-169

In this paper, the different approaches used to simulate the long-term advection of passive constituents on tidal shelves are discussed in the framework of large scale hydrodynamic modelling. The direct ... [more ▼]

In this paper, the different approaches used to simulate the long-term advection of passive constituents on tidal shelves are discussed in the framework of large scale hydrodynamic modelling. The direct approach in which the unsteady mesoscale (tides and storm surges) and macroscale (monthly or seasonal mean processes) currents are used is very demanding in computer resources (CPU and memory). On the other hand, the use of residual velocities gives a larger understanding of the long-term transport processes and simplifies numerical treatments. However, the definition of such appropriate velocities is still an open question. In the context of large scale models, Lagrangian residuals are not applicable. Eulerian residual transport velocities fail to represent long-term motions when tidal non-linearities are important. The first order Lagrangian residual velocity introduced by Feng et al. (1986a) and generalized here is shown to be a very good solution. The North-Western European Continental Shelf (NWECS) is used as an example to compare the numerical solutions obtained with the different approaches. [less ▲]

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See detailOn the road to inclusion and respect for diversity : challenges for a quality. An experience being led in the French Community of Belgium
Camus, Pascale ULg

Conference (2010, December 08)

The conference has been centred on an approach of conditions that make each and every child really feel welcome in ECEC services. Following the European childcare network activities in the nineties, the ... [more ▼]

The conference has been centred on an approach of conditions that make each and every child really feel welcome in ECEC services. Following the European childcare network activities in the nineties, the French Community Government (Belgium) has decided to issue the Quality and Care Code : every person who takes care of a child aged 0 to 12 has to elaborate and implement an educational project called in French “projet d’accueil”. This project has to follow the objectives defined by the Quality and Care Code. There is an essential challenge, on various levels of course, but more specifically in terms of development of ECEC services quality : services should be accessible to every child and his family. A short stop on what is meant by “quality of ECEC services” has been proposed. [less ▲]

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See detailOn the Road to Killingworth: Boston B.A.E.F. Fellows Get-Together(s)
Reuchamps, Min ULg

in B.A.E.F. Belgian American Educational Foundation (Ed.) Liber Amicorum for 30th years of Prof. Boulpaep Presidency (2007)

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See detailOn the Robustness of Air-Sea Flux Estimates of Carbon Dioxide from Ocean Inversions
Mikaloff Fletcher, S. E.; Gruber, N. P.; Jacobson, A. et al

Conference (2004, December)

Inverse methods analogous to those used for atmospheric inversions have been adapted to estimate regional air-sea fluxes of carbon dioxide using ocean interior observations of dissolved inorganic carbon ... [more ▼]

Inverse methods analogous to those used for atmospheric inversions have been adapted to estimate regional air-sea fluxes of carbon dioxide using ocean interior observations of dissolved inorganic carbon and related tracers and an Ocean General Circulation Model (OGCM). We estimate seperately the preindustrial component and the component due to the anthropogenic perturbation of atmospheric carbon dioxide. Previous sensitivity studies have shown that model circulation is one of the most important sources of error in the ocean inversion. We present estimates of preindustrial and anthropogenic air-sea carbon dioxide exchange using a suite of nine different OGCM's in order to quantify the robustness of our results and explore the role of different representations of ocean circulation in the inversion. Most of the large scale features of the inverse estimates are robust across all models. The preindustrial inverse estimates generally follow the expected pattern of uptake at high latitudes and out gassing in the tropics; however, all of the models call for out gassing in the Southern Ocean between 44S and 58 S. The greatest anthropogenic carbon uptake occurs at mid- to high- latitudes, with a large anthropogenic carbon sink in the Southern Ocean, while the bulk of the anthropogenic carbon storage occurs at mid-latitudes. Preliminary results also suggest interesting, robust differences between these inverse estimates and estimates from forward model simulations. Both the preindustrial and anthropogenic carbon dioxide flux estimates are most robust at mid and high northern latitudes, except for the high latitude North Atlantic. The carbon dioxide flux estimates are most uncertain in the Southern Ocean, where the inverse estimates are strongly dependent on the rates of deep water ventilation in the OGCM. The preindustrial inverse estimates for the Indian Ocean are also sensitive to the choice of OGCM, and the anthropogenic estimates have significant uncertainties in the tropical Pacific. Over large spatial scales, inverse estimates based on different OGCM's are in better agreement than estimates based on forward simulations of the same models, but this is not necessarily true for smaller model regions. [less ▲]

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See detailOn the Role of Out-of-Equilibrium Microstructures in Ti-6Al-4V and in Stainless Steel 316L Processed by Selective Laser Melting in Determining their Mechanical Properties
Mertens, Anne ULg; Reginster, Sylvie ULg; Paydas, Hakan ULg et al

Conference (2013, September 12)

Additive manufacturing processes such as Selective Laser Melting (SLM) appear very promising in view of the economic production of near-net-shape, complex and (almost) fully dense parts from metallic ... [more ▼]

Additive manufacturing processes such as Selective Laser Melting (SLM) appear very promising in view of the economic production of near-net-shape, complex and (almost) fully dense parts from metallic materials such as Ti alloys and stainless steels. Practically, in SLM, a metallic powder is deposited layer-by-layer in a powder bed and then molten locally according to the desired shape. An important feature of this process is that the structure undergoes an ultra-fast cooling once the beam leaves the working zone, thus giving rise to strongly out-of-equilibrium microstructures. In the case of Ti alloy Ti-6Al-4V, in particular, the microstructural anisotropy resulting from the epitaxial growth of the newly deposited layer on the material previously solidified has been shown to exert a very strong influence on the mechanical properties [1]. In the present work, the microstructures and mechanical properties of Ti-6Al-4V and of stainless steel 316L processed by SLM have been characterised in details. Since these two materials exhibit quite different physical behaviours, their careful comparison might shed more light into the role of phenomena such as epitaxial growth, out-of-equilibrium phase transformation and/or internal stresses in determining the mechanical properties of metallic parts processed by SLM. [less ▲]

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See detailOn the role of pressure in elasto-inertial turbulence
Terrapon, Vincent ULg; Dubief, Yves; Soria, Julio

in Journal of Turbulence (2014), 16(1), 26-43

The dynamics of elasto-inertial turbulence is investigated numerically from the perspective of the coupling between polymer dynamics and flow structures. In particular, direct numerical simulations of ... [more ▼]

The dynamics of elasto-inertial turbulence is investigated numerically from the perspective of the coupling between polymer dynamics and flow structures. In particular, direct numerical simulations of channel flow with Reynolds numbers ranging from 1000 to 6000 are used to study the formation and dynamics of elastic instabilities and their effects on the flow. Based on the splitting of the pressure into inertial and polymeric contributions, it is shown that the polymeric pressure is a non-negligible component of the total pressure fluctuations, although the rapid inertial part dominates. Unlike Newtonian flows, the slow inertial part is almost negligible in elasto-inertial turbulence. Statistics on the different terms of the Reynolds stress transport equation also illustrate the energy transfers between polymers and turbulence and the redistributive role of pressure. Finally, the trains of cylindrical structures around sheets of high polymer extension that are characteristics of elasto-inertial turbulence are shown to be correlated with the polymeric pressure fluctuations. [less ▲]

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See detailOn the Role of the Deterministic and Circumferential Stresses in Throughflow Calculations
Simon, Jean-Francois; Léonard, Olivier ULg

in Proceedings of the ASME Turbo Expo 2008 (2008, June)

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See detailOn the Role of the Deterministic and Circumferential Stresses in Throughflow Calculations
Simon, Jean-Francois; Thomas, Jean-Philippe ULg; Léonard, Olivier ULg

in Journal of Turbomachinery (2009), 131(3),

This paper presents a throughflow analysis tool developed in the context of the average-passage flow model elaborated by Adamczyk. The Adamczyk's flow model describes the 3D time-averaged flow field ... [more ▼]

This paper presents a throughflow analysis tool developed in the context of the average-passage flow model elaborated by Adamczyk. The Adamczyk's flow model describes the 3D time-averaged flow field within a blade row passage. The set of equations that governs this flow field is obtained by performing a Reynolds averaging, a time averaging, and a passage-to-passage averaging on the Navier–Stokes equations. The throughflow level of approximation is obtained by performing an additional circumferential averaging on the 3D average-passage flow. The resulting set of equations is similar to the 2D axisymmetric Navier–Stokes equations, but additional terms resulting from the averages show up: blade forces, blade blockage factor, Reynolds stresses, deterministic stresses, passage-to-passage stresses, and circumferential stresses. This set of equations represents the ultimate throughflow model provided that all stresses and blade forces can be modeled. The relative importance of these additional terms is studied in the present contribution. The stresses and the blade forces are determined from 3D steady and unsteady databases (a low-speed compressor stage and a transonic turbine stage) and incorporated in a throughflow model based on the axisymmetric Navier–Stokes equations. A good agreement between the throughflow solution and the averaged 3D results is obtained. These results are also compared to those obtained with a more “classical” throughflow approach based on a Navier–Stokes formulation for the endwall losses, correlations for profile losses, and a simple radial mixing model assuming turbulent diffusion. [less ▲]

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See detailOn the Role of the Running Coupling Constant in a Quark Model Analysis of T-odd TMDs
Courtoy, Aurore ULg

in International Journal of Modern Physics Conference Series (2011), 04

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See detailOn the role of the ventromedial prefrontal cortex in self-processing: the valuation hypothesis
D'Argembeau, Arnaud ULg

in Frontiers in Human Neuroscience (2013), 7

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See detailOn the scalar meson exchange in the baryon spectra
Stassart, Pierre ULg; Stancu, Floarea ULg; Richard, J. M. et al

in Journal of Physics : G Nuclear & Particle Physics (2000), G26

We explore the role of a scalar meson exchange interaction between quarks in a semirelativistic constituent quark model where the quarks are also subject to a linear confinement. We study how the spectrum ... [more ▼]

We explore the role of a scalar meson exchange interaction between quarks in a semirelativistic constituent quark model where the quarks are also subject to a linear confinement. We study how the spectrum evolves when the strength of the scalar meson exchange increases. Our results are relevant to the long-standing problem of the relative position of the first positive-parity (Roper resonance) and the first orbitally excited states in the baryon spectrum. [less ▲]

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See detailOn the Seismic Modelling of Rotating B-type Pulsators in the Traditional Approximation
Aerts, C.; Dupret, Marc-Antoine ULg

in ASP Conference Proceeding, Vol. 462, 103 (2012, September 01)

The CoRoT and Kepler data revolutionised our view on stellar pulsation. For massive stars, the space data revealed the simultaneous presence of low-amplitude low-order modes and dominant high-order ... [more ▼]

The CoRoT and Kepler data revolutionised our view on stellar pulsation. For massive stars, the space data revealed the simultaneous presence of low-amplitude low-order modes and dominant high-order gravity modes in several B-type pulsators. The interpretation of such a rich set of detected oscillations requires new tools. We present computations of oscillations for B-type pulsators taking into account the effects of the Coriolis force in the so-called traditional approximation. We discuss the limitations of classical frequency matching to tune these stars seismically and show that the predictive power is limited in the case of high-order gravity mode pulsators, except if numerous modes of consecutive radial order can be identified. [less ▲]

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See detailOn the sensitivity of closure phases to faint companions in optical long baseline interferometry
Le Bouquin, Jean-Baptiste; Absil, Olivier ULg

in Astronomy and Astrophysics (2012), 541

We explore the sensitivity and completeness of long baseline interferometric observations for detecting unknown, faint companions around bright unresolved stars. We derive a linear expression for the ... [more ▼]

We explore the sensitivity and completeness of long baseline interferometric observations for detecting unknown, faint companions around bright unresolved stars. We derive a linear expression for the closure phase signature of a faint companion in the high contrast regime (<0.1), and provide a quantitative estimation of the detection efficiency for the currently offered four-telescope configurations at the Very Large Telescope Interferometer. The results are compared to the performances provided by linear and Y-shaped interferometric configurations in order to identify the ideal array. We find that all configurations have a similar efficiency in discovering companions wider than 10mas. Assuming a closure phase accuracy of 0.25deg, that is typical of state-of-the-art instruments, we predict a median dynamic range of up to six magnitudes when stacking observations obtained at five different hour angles. Surveying bright stars to search for faint companions can be considered as an ideal filler programme for modern interferometric facilities because that places few constraints on the choice of the interferometric configuration. [less ▲]

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See detailOn the separation of net ecosystem exchange into assimilation and ecosystem respiration: review and improved algorithm
Reichstein, Markus; Falge, Eva; Baldocchi, Dennis et al

in Global Change Biology (2005), 11(9), 1424-1439

This paper discusses the advantages and disadvantages of the different methods that separate net ecosystem exchange (NEE) into its major components, gross ecosystem carbon uptake (GEP) and ecosystem ... [more ▼]

This paper discusses the advantages and disadvantages of the different methods that separate net ecosystem exchange (NEE) into its major components, gross ecosystem carbon uptake (GEP) and ecosystem respiration (R-eco). In particular, we analyse the effect of the extrapolation of night-time values of ecosystem respiration into the daytime; this is usually done with a temperature response function that is derived from long-term data sets. For this analysis, we used 16 one-year-long data sets of carbon dioxide exchange measurements from European and US-American eddy covariance networks. These sites span from the boreal to Mediterranean climates, and include deciduous and evergreen forest, scrubland and crop ecosystems. We show that the temperature sensitivity of R-eco, derived from long-term (annual) data sets, does not reflect the short-term temperature sensitivity that is effective when extrapolating from night- to daytime. Specifically, in summer active ecosystems the long-term temperature sensitivity exceeds the short-term sensitivity. Thus, in those ecosystems, the application of a long-term temperature sensitivity to the extrapolation of respiration from night to day leads to a systematic overestimation of ecosystem respiration from half-hourly to annual time-scales, which can reach > 25% for an annual budget and which consequently affects estimates of GEP. Conversely, in summer passive (Mediterranean) ecosystems, the long-term temperature sensitivity is lower than the short-term temperature sensitivity resulting in underestimation of annual sums of respiration. We introduce a new generic algorithm that derives a short-term temperature sensitivity of R-eco from eddy covariance data that applies this to the extrapolation from night- to daytime, and that further performs a filling of data gaps that exploits both, the covariance between fluxes and meteorological drivers and the temporal structure of the fluxes. While this algorithm should give less biased estimates of GEP and R-eco, we discuss the remaining biases and recommend that eddy covariance measurements are still backed by ancillary flux measurements that can reduce the uncertainties inherent in the eddy covariance data. [less ▲]

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