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See detailOn the necessity and biological significance of threshold-free regulon prediction outputs
Rigali, Sébastien ULg; Nivelle, Renaud; Tocquin, Pierre ULg

in Molecular Biosystems (2015), 11

The in silico prediction of cis-acting elements in a genome is an efficient way to quickly obtain an overview of the biological processes controlled by a trans-acting factor, and connections between ... [more ▼]

The in silico prediction of cis-acting elements in a genome is an efficient way to quickly obtain an overview of the biological processes controlled by a trans-acting factor, and connections between regulatory networks. Several regulon prediction web tools are available, designed to identify DNA motifs predicted to be bound by transcription factors using position weight matrix-based algorithms. In this paper we expose and discuss the conflicting objectives of software creators (bioinformaticians) and software users (biologists), who aim for reliable and exhaustive prediction outputs, respectively. Software makers, concerned with providing tools that minimise the number of false positive hits, often impose a stringent threshold score for a sequence to be included in the list of the putative cis-acting sites. This rigidity eventually results in the identification of strongly reliable but largely straightforward sites, i.e. those associated with genes already anticipated to be targeted by the studied transcription factor. Importantly, this biased identification of strongly bound sequences contrasts with the biological reality where, in many circumstances, a weak DNA-protein interaction is required for the appropriate gene's expression. We show here a series of transcriptionally controlled systems involving weakly bound cis-acting elements that could never have been discovered because of the policy of preventing software users from modifying the screening parameters. Proposing only trustworthy prediction outputs thus prevents biologists from fully utilising their knowledge background and deciding to analyse statistically irrelevant hits that could nonetheless be potentially involved in subtle, unexpected, though essential cis-trans relationships. [less ▲]

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See detailLe regard (peu optimiste) du soignant sur la personne âgée
Schroyen, Sarah ULg; Missotten, Pierre ULg; Marquet, Manon ULg et al

in Medi-Sphere (2015)

L’âgisme (c’est-à-dire l’ensemble de nos stéréotypes liés à l’avancée en âge) a de nombreuses conséquences négatives tant pour le patient lui-même qu’au sein de la relation entre le patient et le ... [more ▼]

L’âgisme (c’est-à-dire l’ensemble de nos stéréotypes liés à l’avancée en âge) a de nombreuses conséquences négatives tant pour le patient lui-même qu’au sein de la relation entre le patient et le personnel soignant. Au cours de cet article, nous illustrerons les représentations du vieillissement prévalentes chez les soignants et aborderons brièvement les conséquences de l’âgisme sur leurs attitudes de soins. [less ▲]

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See detailEuropean Case-law on Asylum Matters: Interrelation and Interdependence of the European Court of Human Rights and the Court of Justice of the European Union
Mazur Kumric, Nives ULg; Župan, Mirela

in Sander, Gerald G.; Rodin, Siniša; Bodiroga-Vukobrat, Nada (Eds.) New Europe - Old Values?: Reform and Perseverance (Europeanization and Globalization) (2015)

The Council of Europe and the European Union (hereinafter: the EU) are major players and partners in the domain of policy shaping strategies on the European continent, with significant and evergrowing ... [more ▼]

The Council of Europe and the European Union (hereinafter: the EU) are major players and partners in the domain of policy shaping strategies on the European continent, with significant and evergrowing impact on international community as a whole. Although the ratio and ideas behind their establishment were not the same (economic versus humanistic), they have, over the time, acquired a similar attitude towards a number of legal issues, including protection of human rights and fundamental freedoms. Unlike the Council of Europe which perceived human rights as a cornerstone of its founding pillars, the EU took a longer way to incorporate them in its priority areas. The latter shift was, however, rapid and these days, one is witnessing a large-scale cooperation instituted between respective regional organisations with the aim of creating a human rights friendly environment. The purpose of this paper is to shed light on one particular segment of their cooperation in the field of human rights protection – asylum law. For the fact that Europe attracts a large contingency of people looking for better life and new beginnings, asylum matters have moved to the forefront of the Council of Europe and EU standard setting policies. The chapter following the introductory remarks gives an overview of the most crucial moments in the chronology of cooperation between the Council of Europe and the EU, observed from the angle of the Convention for the Protection of Human Rights and Fundamental Freedoms (hereinafter: the European Convention) and the related case-law of the two core European judicial organs: the European Court of Human Rights (hereinafter: the ECHR) and the Court of Justice of the European Union (hereinafter: the CJEU). A special emphasis is put on recent developments of historical significance related to the accession of the EU to the European Convention and peculiar legal consequences thereof. Chapter 3 focuses on the so-called Dublin system, a set of norms and mechanisms introduced to regulate a vast area of the asylum policy within the EU. The analysis keeps track with the steps taken in the creation of a common European asylum system, i.e. the three codification stages and their outcomes. Despite being of EU provenance, the respective system serves as a solid legal basis in asylum matters adjudicated by both European courts. Finally, the chapter preceding the conclusion highlights some of the leading asylum cases which demonstrate a close interrelation and interdependance of the European courts and their case-law in the area of European asylum policies. The sub-chapter on the ECHR case-law summarises the most notable facts, elements and standards derived from the judgments in the cases of M. S. S. v. Belgium and Greece, T. I. v. the United Kingdom and K. R. S. v. the United Kingdom, as well as Mohammed Hussein and Others v. the Netherlands and Italy, and Mohammed v. Austria. In the same vein, the CJEU case-law is elaborated in another sub-chapter; namely, the authors draw attention to the cases of N. S. v. Secretary of State for the Home Department and M. E. and others v. Refugee Applications Commissioner, Minister for Justice, Equality and Law Reform; Meki Elgafaji, Noor Elgafaji v. Staatssecretaris van Justitie; and Shamso Abdullahi v. Bundesasylamt. The purpose of this case-law overview and analysis is to sum up major rules, theories and standards originating from the judgements, as well as to find the points of convergence and differentiation between the ECHR and the CJEU in asylum matters. [less ▲]

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See detailCharles Travis, La vision est-elle intentionnelle ?
Ambroise, Bruno; Gauvry, Charlotte ULg

in Dewalque, Arnaud; Gauvry, Charlotte (Eds.) Conscience et représentation. Controverses récentes en philosophie de l'esprit (2015)

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See detailCharles Travis, Déverrouiller le monde extérieur
Gauvry, Charlotte ULg

in Gauvry, Charlotte; Brisart, Robert (Eds.) Concept et perception. Le conceptualisme en question (2015)

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See detailHeidegger : « Être et temps », « Introduction à la métaphysique », « Qu’appelle-t-on penser ? », « Acheminement vers la parole »
Gauvry, Charlotte ULg

in Suratteau, Jean-François (Ed.) Dictionnaire des œuvres philosophiques (2015)

Articles de dictionnaire

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See detailIntroduction
Gauvry, Charlotte ULg

in Dewalque, Arnaud; Gauvry, Charlotte (Eds.) Conscience et représentation. Controverses récentes en philosophie de l'esprit (2015)

Introduction au volume

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See detailGadamer, Vérité et méthode
Gauvry, Charlotte ULg

in Suratteau, Jean-François (Ed.) Dictionnaire des œuvres philosophiques (2015)

article de dictionnaire

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See detailIntroduction
Gauvry, Charlotte ULg

in Brisart, Robert; Gauvry, Charlotte (Eds.) Concept et perception. Le conceptualisme en question (2015)

Introduction au volume

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See detailAcoustic monitoring of O2 production of a seagrass meadow
Felisberto, Paulo; Jesus, Sérgio M.; Zabel, Friedrich et al

in Journal of Experimental Marine Biology and Ecology (2015), 464(0), 75-87

Acoustic data were acquired in October 2011 over a Posidonia oceanica meadow in the Bay of la Revellata, Calvi, Corsica. The purpose was to develop an acoustic system for monitoring the oxygen (O2 ... [more ▼]

Acoustic data were acquired in October 2011 over a Posidonia oceanica meadow in the Bay of la Revellata, Calvi, Corsica. The purpose was to develop an acoustic system for monitoring the oxygen (O2) production of an entire seagrass meadow. In a shallow water area (b38 m), densely covered by P. oceanica, a sound source transmitted signals in 3 different bands (400–800 Hz, 1.5–3.5 kHz and 6.5–8.5 kHz) toward three self-recording hydrophones at a distance of 100 m, over the period of oneweek. The data showa high correlation between the diel cycle of the acoustic signals' energy received by the hydrophones and the temporal changes in water column O2 concentration as measured by optodes. The results thus show that a simple acoustic acquisition system can be used to monitor the O2-based productivity of a seagrass meadow at the ecosystem level with high temporal resolution. The finding of a significant production of O2 as bubbles in seagrass ecosystems suggests that net primary production is underestimated by methods that rely on the mass balance of dissolved O2 measurements. [less ▲]

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See detailAnalytic solution for the relative motion of satellites in near-circular low-Earth orbits
Martinusi, Vladimir ULg; Dell'Elce, Lamberto ULg; Kerschen, Gaëtan ULg

in Proceedings of the AAS/AIAA Space FLight Mechanics Meeting (2015)

The paper presents the solution to the problem of the relative motion between two satellites orbiting Earth under the influence of the oblateness and atmospheric drag perturbations. Starting from the ... [more ▼]

The paper presents the solution to the problem of the relative motion between two satellites orbiting Earth under the influence of the oblateness and atmospheric drag perturbations. Starting from the analytic solution to the problem of the absolute motion, the closed-form equations of motion are obtained. No simplifying assumptions are made on the relative dynamics. [less ▲]

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See detailDes bandes urbaines en Belgiques?
Collin, Jonathan ULg

Conference given outside the academic context (2015)

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See detailNederlands-Frans in contrast. 2000 lexicologische valstrikken in het Frans voor Nederlandstaligen
Theissen, Siegfried ULg; Hiligsmann, Philippe; Rasier, Laurent ULg et al

Book published by Acco (2015)

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See detailDetermination of arsenic (III) at a nano gold modified solid carbon paste electrode
Sakira, Abdoul Karim; Somé, Issa Touridomon; Ziemons, Eric ULg et al

in Electroanalysis (2015), 27

A selective and sensitive electroanalytical method was developed for arsenic determination based on a nanogold (AuNP) modified solid carbon paste work- ing electrode (SCPE) modified in two steps (i ... [more ▼]

A selective and sensitive electroanalytical method was developed for arsenic determination based on a nanogold (AuNP) modified solid carbon paste work- ing electrode (SCPE) modified in two steps (i) physisorp- tion and (ii) additional electrodeposition of nanogold par- ticles in the presence of iodide. Copper(II) interference was solved by covering the gold layer by a self assembled mono layer (SAM) of glutathione. Using DPASV a linear response of the signal was obtained as a function of As(III) in the concentration range 0.05–20mM (4– 1498 ppb) with a limit of detection of 0.01 mM (0.9 ppb). Sample stirring and degassing were not needed. Applica- tion to the determination of arsenic(III) and (V) in un- derground water samples from Burkina Faso was success- fully achieved. [less ▲]

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See detailAdventitious organogenesis induced in sweet orange (Citrus sinensis L.) var. "half-blood" maltese: morphogenetic and histological study
Benmahmoud, Kaouther; Jedidi, Zmna; Najar, Asma et al

in International Journal of Agronomy and Agricultural Research (2015), 6(2), 1-7

Tunisian citrus crops are faced to several abiotic and biotic constraints among which virus and virus-like diseases are incurable. The production of virus-free plants systematically needs the use of in ... [more ▼]

Tunisian citrus crops are faced to several abiotic and biotic constraints among which virus and virus-like diseases are incurable. The production of virus-free plants systematically needs the use of in vitro techniques. In this context, somatic embryogenesis and further plantlet regeneration of the Tunisian “half-blood” Maltese orange were obtained using explants consisting in style/stigma collected from unopened flowers. Somatic embryos were induced on Murashige and Skoog medium containing 13.3 µM 6-benzylaminopurine and 500 mg.l-1 malt extract, but their germination was obtained on hormone free-medium. Somatic embryogenesis was induced indirectly from intermediate friable callus initiated at the basal part of the style. Somatic embryos exhibited central procambial cells and were surrounded by a protoderm isolating them from the callus. These embryos had bipolar structure confirmed by the presence of shoot and root apices at cotyledonary stage. The use of cotyledon excised from those embryos failed to regenerate somatic embryos, but gave rise to direct organogenesis in two forms, true buds and protuberances both evolved in shoots after transfer in hormone-free medium. According to histological observations, protuberances are induced from epidermal and subepidermal cells of the cotyledon explant and remain closely attached to their mother tissue even at the shoot stage. [less ▲]

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See detailSolar Energy Prediction: An International Contest to Initiate Interdisciplinary Research on Compelling Meteorological Problems
McGovern, Amy; Gagne II, David John; Eustaquio, Lucas et al

in Bulletin of the American Meteorological Society [= BAMS] (2015)

As meteorological observing systems and models grow in complexity and number, the size of the data becomes overwhelming for humans to analyze using traditional techniques. Computer scientists, and ... [more ▼]

As meteorological observing systems and models grow in complexity and number, the size of the data becomes overwhelming for humans to analyze using traditional techniques. Computer scientists, and specifically machine learning and data mining researchers, are developing frameworks for analyzing big data. The AMS Committee on Artificial Intelligence and its Applications to Environmental Science aims to bring AI researchers and environmental scientists together to increase the synergy between the two. The AI committee has sponsored 4 previous contests on a variety of meteorological problems including wind energy, storm classification, winter hydrometeor classification, and air pollution, with the goal of bringing together the two fields of research. Although these were successful, the audience was limited to existing environmental science researchers (usually 10-20 teams of people primarily within the AMS community). For the 2013/14 contest, we expanded to a global audience by focusing on the compelling problem of solar energy prediction and by having the established forum Kaggle host our contest. Using this forum, we had over 160 teams from all around the world participate. Improved solar energy forecasting is a necessary component of making solar energy a viable alternative power source. This paper summarizes our experiences in the 2013/14 contest, discusses the data in detail, and presents the winning prediction methods. The contest data come from the NOAA/ESRL Global Ensemble Forecasting System Reforecast Version 2 and the Oklahoma Mesonet with sponsorship from EarthRisk Technologies. All winning methods utilized gradient boosted regression trees but differed in parameter choices and interpolation methods. [less ▲]

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See detailSolutrean and Magdalenian ferruginous rocks heat-treatment: accidental and/or deliberate action?
Salomon, Hélène ULg; Vignaud, Colette; Lahlil, Sophia et al

in Journal of Archaeological Science (2015), 55

Heating of prehistoric coloring materials can induce radical changes in color indicative of structural matter transformation. For instance, the structure of the yellow iron oxide-rich mineral, goethite ... [more ▼]

Heating of prehistoric coloring materials can induce radical changes in color indicative of structural matter transformation. For instance, the structure of the yellow iron oxide-rich mineral, goethite, changes into the red iron oxide-rich mineral, hematite, when it is heated to around 250-300°C. For a long time, heating has been thought to be the reason for the high frequencies of red rocks used in camp sites and the red pigments in rock art paintings. However, records of heat-treatment of coloring materials are usually not well documented; the contextual information is not clear enough to confirm intentional heating. Two Solutrean camp sites (the flint workshop Les Maîtreaux and the hunting site Combe Saunière I) and one middle Magdalenian cave with rock art (Grotte Blanchard, La Garenne) allow us to study the heating process of ferruginous rocks. All three sites, which have been excavated relatively recently, have well-defined archaeological records and strong associations between the ferruginous rocks and other artifacts. With the use of X-ray diffraction and electron µ-diffraction for identifying structural modification and SEM-FEG and TEM-FEG for detecting dehydration nano-pores, we have strong evidence for intentional heat-treatment of yellow goethite-rich materials in two archaeological contexts and one site for unintentional heating, where rocks were only partially transformed. Intentional heating to obtain red hematite from primary goethite would have required ingenious methods of temperature control in fireplace settings and purpose-built ground ovens. [less ▲]

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See detailSupervised inference of biological networks with trees : Application to genetic interactions in yeast
Schrynemackers, Marie ULg

Doctoral thesis (2015)

Networks or graphs provide a natural representation of molecular biology knowledge, in particular to model relationships between biological entities such as genes, proteins, drugs, or diseases. Because of ... [more ▼]

Networks or graphs provide a natural representation of molecular biology knowledge, in particular to model relationships between biological entities such as genes, proteins, drugs, or diseases. Because of the effort, the cost, or the lack of the experiments necessary to the elucidation of these networks, computational approaches for network inference have been frequently investigated in the literature. In this thesis, we focus on supervised network inference methods. These methods exploit supervised machine learning algorithms to train a model for identifying new interacting pairs of nodes from a training sample of known interacting and possibly non-interacting pairs and additional measurement data about the network nodes. Our contributions in this area are divided into three parts. First, the thesis examines the problem of the assessment of supervised network inference methods. Indeed, their reliable validation (in silico) poses a number of new challenges with respect to standard classification problems, related to the fact that pairs of objects are to be classified and to the specificities of biological networks. We perform a critical review and assessment of protocols and measures proposed in the literature. Through theoretical considerations and in silico experiments, we analyze in depth how important factors influence the outcome of performance estimation. These factors include the amount of information available for the interacting entities, the sparsity and topology of biological networks, and the lack of experimentally verified non-interacting pairs. From this analysis, we derived specific guidelines so as to how best exploit and evaluate machine learning techniques for network inference. Second, we systematically investigate, theoretically and empirically, the exploitation of tree- based methods for network inference. We consider these methods in the context of the two main generic classification-based approaches for network inference: the local approach, which trains a separate model for each network node, and the global approach, which trains a single model over pairs of nodes. We present and formalize these two approaches, extending the former for the prediction of interactions between two unseen network nodes, and discuss their specializations to tree-based methods, highlighting their interpretability and drawing links with clustering techniques. Extensive experiments are carried out with these methods on various biological networks that clearly highlight that these methods are competitive with existing methods. The interpretability of the resulting method family is illustrated on a drug-protein interaction network. In the last part of the thesis, we built on the experience gained in the two previous parts to try to predict at best the genetic interaction network in yeast S.cerevisiae. For that purpose, we collected a large dataset, assembling 4 millions gene pairs that were experimentally tested in the context of 11 different studies and 23 sets of measurements to use as gene input features for the inference. Through several cross-validation experiments on the resulting dataset, we showed that predicting genetic interactions is indeed possible to some useful extent and that actually in some settings, the accuracy of computational methods is not very far from that of experimental techniques. [less ▲]

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See detailAnalyzing Access, Egress, and Main Transport Mode of Public Transit Journeys: Evidence from the Flemish National Household Travel Survey
Creemers, Lieve; Bellemans, Tom; Janssens, Davy et al

in Proceedings of the 94th Annual Meeting of the Transportation Research Board (2015)

The primary objective of this paper is to explore the influence of socio-demographic and contextual variables on the multimodal character of public transit journeys. Accounting for multimodality in public ... [more ▼]

The primary objective of this paper is to explore the influence of socio-demographic and contextual variables on the multimodal character of public transit journeys. Accounting for multimodality in public transit journeys is important from a demand modeling point of view, especially in the assessment of new projected public transit infrastructure. To meet the objective, data from the national household travel survey of Flanders (Belgium) is analyzed. Based on 2,202 public transit journeys, the main public transit mode choice (bus/tram/metro or train) and access/egress mode choice are simultaneously estimated using a multinomial logit model, and by explicitly making a distinction between unimodal and multimodal transit journeys. The results indicate that various socio-demographical (e.g. age, gender, level of education, household income) and contextual factors (e.g. journey distance, journey motive, urbanization degree, car availability) significantly influence the joint decision process. Total journey distance and car availability are identified as the most important explanatory variables. In terms of model performance, the model appears to yield satisfactory predictions, justifying the integration of the model in more general demand modeling frameworks. [less ▲]

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