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See detailImpact of dependency on the distribution of p-value
Ernst, Marie ULiege; Swan, Yvik ULiege

Conference (2017, August 01)

We study the impact of dependence assumptions on the distribution of p-values and quantiles for repeated testing on dependent data. This leads us to considering the general problem of the quality of a ... [more ▼]

We study the impact of dependence assumptions on the distribution of p-values and quantiles for repeated testing on dependent data. This leads us to considering the general problem of the quality of a binomial approximation to the distribution of a sum of dependent indicator variables. Whenever possible we use classical and adhoc versions of Stein’s method to provide tight bounds on classical probability distances. In many cases, however, the relevant expressions are intractable and we resort to empirical analysis by extensive simulations. We apply our findings to a realistic real-life scenario. [less ▲]

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See detailMolecular Tools for the Detection and Quantification of Toxigenic Cyanobacteria
Kurmayer, Rainer; Sivonen, Kaarina; Wilmotte, Annick ULiege et al

Book published by John Wiley and sons LTD - This edition first published 2017 (2017)

A guide to state-of-the-art molecular tools for monitoring and managing the toxigenicity of cyanobacteria Runaway climate change has made the monitoring and management of toxigenic organisms in the ... [more ▼]

A guide to state-of-the-art molecular tools for monitoring and managing the toxigenicity of cyanobacteria Runaway climate change has made the monitoring and management of toxigenic organisms in the world’s bodies of water more urgent than ever. In order to influence public policy regarding the detection and quantification of those organisms, it is incumbent upon scientists to clearly demonstrate to policy makers the increase of toxigenic cyanobacteria and the threats they pose. As molecular methods can handle many samples in short time, they are the most reliable, cost-effective tools currently available for tracking cyanotoxicity worldwide. This volume arms scientists with the tools they need to track toxigenicity in surface waters and food supplies and, hopefully, to develop new techniques for managing the spread of toxic cyanobacteria. This book offers the first comprehensive treatment of molecular tools for monitoring cyanotoxicity. Growing out of the findings of the landmark European Cooperation in Science and Technology Cyanobacteria project (CYANOCOST), it provides detailed, practical coverage of the full array of available molecular tools and protocols, from water sampling, nucleic acid extraction, and downstream analysis—including PCR and qPCR based methods—to genotyping (DGGE), diagnostic microarrays, and community characterization using next-gen sequencing techniques. [less ▲]

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See detailBioinformatic Processing of Amplicon Sequencing Datasets
Sweetlove, Maxime; Obbels, Dagmar; Verleyen, Elie et al

in Kurmayer, Rainer; Sivonen, Kaarina; Wilmotte, Annick (Eds.) et al Molecular Tools for the Detection and Quantification of Toxigenic Cyanobacteria (2017)

Amplicon sequencing can be a very powerful approach for detecting toxic cyanobacteria or any other kind of microorganism during monitoring programs. However, owing to the huge size of next-generation ... [more ▼]

Amplicon sequencing can be a very powerful approach for detecting toxic cyanobacteria or any other kind of microorganism during monitoring programs. However, owing to the huge size of next-generation sequencing (NGS) datasets (up to several Gb), there is an obvious need for semi-automatic data processing and statistical analysis, as well as visualization of the patterns found. Importantly, raw NGS data contain errors, some of which are easily detected (e.g. too short or low-quality reads), while others remain hidden even after the most stringent quality controls (e.g. chimeras, contaminations, reads with large insertions or deletions, referred to as “indels”). As a consequence, NGS data need to be interpreted with caution, and bioinformatics analysis implementing poor error identification can easily lead to erroneous conclusions. Hence, a crucial step in the analysis of NGS data is the detection and removal of as many erroneous reads as possible. Moreover, bioinformatics involve additional preprocessing steps, including demultiplexing (i.e. grouping reads to samples according to the barcode sequence), deleting non-biological tags together with the adaptors and primer sequences, and removing chimeric sequences. In addition, the bioinformatics pipelines enable the quality-filtered sequences to be clustered into biologically relevant operational taxonomic units (OTUs), which form the basis of the statistical analysis, including the calculation of alpha- and beta-diversity. [less ▲]

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See detailTaxonomic Identification of Cyanobacteria by a Polyphasic Approach
Wilmotte, Annick ULiege; Laughinghouse, Dail Haywood IV; Capelli, Camilla et al

in Kurmayer, Rainer; Sivonen, Kaarina; Wilmotte, Annick (Eds.) et al Molecular Tools for the Detection and Quantification of Toxigenic Cyanobacteria (2017)

In this chapter, we shall discuss the criteria and methods to be adopted for the taxonomic identification and classification of cyanobacteria. This includes a brief introduction of the two Codes of ... [more ▼]

In this chapter, we shall discuss the criteria and methods to be adopted for the taxonomic identification and classification of cyanobacteria. This includes a brief introduction of the two Codes of Nomenclature ruling in parallel on the valid naming of these organisms. We shall then present the major steps important for cyanobacterial taxa identification and their nomenclature. These include: 1) determination of morphology by light microscopy; 2) genetic characterization by single and/or multilocus sequence typing; 3) the assignment of the organism to a taxonomic entity (genus, species, eco- and/or genotype within a species) by reference to, and phylogenetic analysis of, cyanobacterial nucleotide sequences available in public repositories. Ideally, these methods should be accompanied by the determination of other relevant properties (ultrastructural, physiological, biochemical, and ecological characteristics) that may help to define/redefine and circumscribe the cyanobacterial taxon under study. [less ▲]

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See detailIsolation, Purification, and Cultivation of Toxigenic Cyanobacteria
Haande, Sigrid; Jasser, Iwona; Gugger, Muriel et al

in Kurmayer, Rainer; Sivonen, Kaarina; Wilmotte, Annick (Eds.) et al Molecular Tools for the Detection and Quantification of Toxigenic Cyanobacteria (2017)

This chapter summarizes the most commonly used methods for the isolation, purification, and cultivation of toxic cyanobacteria. The aim is to give general advice on how to isolate and maintain clonal ... [more ▼]

This chapter summarizes the most commonly used methods for the isolation, purification, and cultivation of toxic cyanobacteria. The aim is to give general advice on how to isolate and maintain clonal cyanobacterial cultures in order to use them in genetic studies. The traditional methods for the isolation of cyanobacteria into culture are well established and described and there are several excellent reviews with detailed information on culturing techniques [less ▲]

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See detailTesting revealed preference: An algorithmic outlook
Smeulders, Bart ULiege; Crama, Yves ULiege; Spieksma, Frits C.R.

E-print/Working paper (2017)

Revealed preference theory is a domain within economics that studies rationalizability of behavior by (certain types of) utility functions. Given observed behavior in the form of choice data, testing ... [more ▼]

Revealed preference theory is a domain within economics that studies rationalizability of behavior by (certain types of) utility functions. Given observed behavior in the form of choice data, testing whether certain conditions are satisfied gives rise to a variety of computational problems that can be analyzed using operations research techniques. In this survey, we provide an overview of these problems, their theoretical complexity, and available algorithms for tackling them. We focus on consumer choice settings, in particular individual choice, collective choice and stochastic choice settings. [less ▲]

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See detailDNA (Diagnostic) and cDNA Microarray
Rantala-Yilinen, Anne; Sivonen, Kaarina; Wilmotte, Annick ULiege

in Kurmayer, Rainer; Sivonen, Kaarina; Wilmotte, Annick (Eds.) et al Molecular Tools for the Detection and Quantification of Toxigenic Cyanobacteria (2017)

Diagnostic microarrays have been used to study cyanobacterial diversity in environmental samples. They usually include sequences (probes) for only one or a few genes allowing a number of genera/species to ... [more ▼]

Diagnostic microarrays have been used to study cyanobacterial diversity in environmental samples. They usually include sequences (probes) for only one or a few genes allowing a number of genera/species to be detected. In contrast, cDNA microarrays are used for screening genome-wide changes in gene expression and include probes for all or most genes in one strain . The purpose of this sub-chapter is to introduce the principle of a diagnostic microarray (= DNA chip) that uses a ligation detection reaction (LDR) and universal microarray to simultaneously detect and identify all potential microcystin and nodularin producers present in a sample. This is especially useful when monitoring environmental samples that can contain many cyanobacterial genera, including toxin-producing strains. [less ▲]

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See detailMéditations expérimenées sur la TSUM (Transition Secondaire-Université en Mathématiques)
Bair, Jacques ULiege

E-print/Working paper (2017)

L’objectif de ce travail est de mettre par écrit quelques idées personnelles à propos de l’enseignement des mathématiques dans une première année de l’enseignement supérieur et ainsi de réfléchir à propos ... [more ▼]

L’objectif de ce travail est de mettre par écrit quelques idées personnelles à propos de l’enseignement des mathématiques dans une première année de l’enseignement supérieur et ainsi de réfléchir à propos de la transition entre le secondaire et l’Université (TSU, en abrégé) pour un cours de mathématiques. A cet effet, on compare les enseignements secondaire et universitaire, on précise une certaine conception des mathématiques et de leur enseignement au niveau de la TSU. Dans une première annexe se trouve également une étude plus théorique et technique sur la métacognition. Une particularité de ce travail est probablement de relier des idées issues de la littérature spécialisée relative à trois thèmes qui sont souvent développés indépendamment les uns des autres, à savoir l’épistémologie des mathématiques, la pédagogie universitaire et la didactique des mathématiques, le tout étant agencé d’après des convictions personnelles et des expériences professionnelles. [less ▲]

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See detailCorrigendum: Temporality of Features in Near-Death Experience Narratives
Martial, Charlotte ULiege; Cassol, Helena ULiege; Antonopoulos, Georgios ULiege et al

in Frontiers in Human Neuroscience (2017)

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See detailAssessing quality of life using structural equation modeling
Dardenne, Nadia ULiege; Pétré, Benoît ULiege; Husson, Eddy ULiege et al

Poster (2017, August)

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See detailla qualité des sols, un capital
Carnol, Monique ULiege; Krüger, Inken ULiege; Malchair, Sandrine ULiege et al

in Le grand livre de la Forêt 2017 (2017)

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See detailJoints in building structures subjected to exceptional events
Demonceau, Jean-François ULiege; Jaspart, Jean-Pierre ULiege

in Stahlbau, holzbau und Verbundbau - Festschrift zum 60. Geburtstag von Uni.-Prof. Dr.-Ing. Ulrike Kuhlmann (2017)

In this paper, recent developments aiming at characterising the behaviour of joints met in building structures subjected to exceptional events will be summarised. Section 2 gives an overview of the ... [more ▼]

In this paper, recent developments aiming at characterising the behaviour of joints met in building structures subjected to exceptional events will be summarised. Section 2 gives an overview of the investigations conducted on joints subjected to combined bending moments and axial loads. The behaviour of joints subjected to elevated temperatures associated to some specific exceptional events is then addressed in Section 3. Finally, the development of strain rate effects in joint components when subjected to dynamic actions is considered in Section 4. [less ▲]

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See detailSimilarity of the Jovian satellite footprints: spots multiplicity and dynamics
Bonfond, Bertrand ULiege; Grodent, Denis ULiege; Badman, S. V. et al

in Icarus (2017), 292(2017), 208217

In the magnetospheres of Jupiter and Saturn, the intense interaction of the satellites Io, Europa, Ganymede and Enceladus with their surrounding plasma environment leaves a signature in the aurora of the ... [more ▼]

In the magnetospheres of Jupiter and Saturn, the intense interaction of the satellites Io, Europa, Ganymede and Enceladus with their surrounding plasma environment leaves a signature in the aurora of the planet. Called satellite footprints, these auroral features appear either as a single spot (Europa and Enceladus) or as multiple spots (Io and Ganymede). Moreover, they can be followed by extended trailing tails in the case of Io and Europa, while no tail has been reported for Ganymede and Enceladus, yet. Here we show that all Jovian footprints can be made of several spots. Furthermore, the footprints all experience brightness variations on timescale of 2-3 minutes. We also demonstrate that the satellite location relative to the plasma sheet is not the only driver for the footprint brightness, but that the plasma environment and the magnetic field strength also play a role. These new findings demonstrate that the Europa and Ganymede footprints are very similar to the Io footprint. As a consequence, the processes expected to take place at Io, such as the bi-directional electron acceleration by Alfvén waves or the partial reflection of these waves on plasma density gradients, can most likely be extended to the other footprints, suggesting that they are indeed universal processes. [less ▲]

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See detailInfluence of urban patterns on flooding
Bruwier, Martin ULiege; Mustafa, Ahmed; Aliaga, Daniel et al

in E-proceedings of the 37th IAHR World Congress (2017, August)

The goal of this paper is to identify the respective influence of different characteristics of urban patterns on urban flooding. A set of 2,290 alternate urban patterns was generated randomly using an ... [more ▼]

The goal of this paper is to identify the respective influence of different characteristics of urban patterns on urban flooding. A set of 2,290 alternate urban patterns was generated randomly using an urban generator tool providing the geometry of buildings and their relative location to the ground, over a square area of 1 km². Steady 2-D hydraulic computations were performed for these 2,290 different urban patterns with identical hydraulic boundary conditions. The computational time was reduced by using an anisotropic porosity model. This model uses relatively coarse computational cells; but preserves information from the detailed topographic data through the use of porosity parameters. Based on the computed maps of waterdepths for the 2,290 urban patterns, a sensitivity analysis based on a multiple linear regression was performed to outline the most influential urban characteristics. [less ▲]

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See detailVoice use among music theory teachers
Schiller, Isabel ULiege; Morsomme, Dominique ULiege; Sfez, Lou et al

Conference (2017, August)

In Belgium, there is a particular group of music teachers referred to as music theory teachers. Working at music schools, they convey theoretical knowledge and practical musical skills to groups of ... [more ▼]

In Belgium, there is a particular group of music teachers referred to as music theory teachers. Working at music schools, they convey theoretical knowledge and practical musical skills to groups of individuals who learn music during their free-time. Even though music theory teachers use both speaking and singing voice intensively at work, little is known about their voice use profiles. This study investigated the vocal loading among French-speaking music theory teachers. Objectives were (1) to describe their professional and extra-professional vocal loading, (2) to determine the relationship between vocal loading and background noise level and (3) to investigate whether objectively measured vocal loading is reflected in music theory teachers’ auto-evaluation of their voice. Using voice dosimetry, 13 music theory teachers were monitored for one workweek. Parameters analysed were F0, voice sound pressure level (SPL), phonation time, vocal loading index (VLI) and background noise SPL. At the end of each monitoring day, subjects self-assessed their voice use by means of visual analogue scales. Results revealed (1) significantly higher vocal loading in the professional context than in the extra-professional context, (2) significant positive correlations between background noise level and the parameters F0, voice SPL and phonation time and (3) significant correlations between the VLI and auto-evaluation data (e.g. voice quality and vocal fatigue). These results highlight that teaching music theory is a profession with high vocal demands. At work, music theory teachers are exposed to high background noise, which seems to influence their voice use and may potentially contribute to the development of voice problems among this population. Visual analogue scales provide a promising tool to subjectively investigate vocal loading among music theory teachers. [less ▲]

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See detailLEARNING CHEMICAL KINETICS AT SECONDARY SCHOOL LEVEL: MISCONCEPTIONS AND ALTERNATIVE APPROACH
Karous, Hamad ULiege; Nihant, Brigitte ULiege; Leyh, Bernard ULiege

Conference (2017, August)

Chemical kinetics occupies a central position in describing and understanding the dynamic behaviour of matter. It is then expected that this topic shares a significant part in the teaching curricula ... [more ▼]

Chemical kinetics occupies a central position in describing and understanding the dynamic behaviour of matter. It is then expected that this topic shares a significant part in the teaching curricula. Nevertheless, the review of the scarce literature on the topic reveals that little is usually invested to adequately include this field in the major programs. Most studies demonstrate that the teaching approaches in chemical kinetics often remain limited to the qualitative macroscopic description and do not identify the necessary relevant links between the macroscopic and the submicroscopic scales. Consequently, low levels of conceptual understanding and many misconceptions can be identified at the students’ level. Based on the constructivist approach in which the learners build their own cognitive structure, a new teaching sequence including qualitative and quantitative aspects of chemical kinetics for secondary school students (15-17 years old) is proposed. This teaching sequence allows the students to develop an ability to use corpuscular models as explanatory tools as well as an adequate conceptual understanding of chemical kinetics. This approach integrates visualization tools along with active learning strategies using, e.g., interactive websites. [less ▲]

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See detailCharacterising Industrial Sites' Flexibility with Reservoir Models
Cuvelier, Thibaut ULiege

Poster (2017, August)

Electro-intensive industrial sites are very dependent on electricity prices to remain competitive. Nevertheless, they can often tune their processes in order to decrease their electricity consumption ... [more ▼]

Electro-intensive industrial sites are very dependent on electricity prices to remain competitive. Nevertheless, they can often tune their processes in order to decrease their electricity consumption during the most critical periods, for example by using decision support systems based on mathematical modelling of their processes. Our goal is to estimate the flexibility potential of a complete site, not to tune each process very precisely. To this end, we propose a generic paradigm to help conceiving such models: reservoirs are the basic building block, which allows for great expressiveness while being close to the physics. More specifically, we do not need very precise models for our purposes, but ones that can be efficiently included in optimisation models. Our first results show that the obtained reservoir models can give sufficiently good approximations for metallurgical and other processes. [less ▲]

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See detailEarly eukaryotes: insights from microanalyses of proterozoic microfossils
Cornet, Yohan ULiege; Beghin, Jérémie ULiege; Kabamba Baludikay, Blaise ULiege et al

in Goldschmidt Abstracts, 2017 (2017, August)

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See detailCombining semi-automated image analysis techniques with machine learning algorithms to accelerate large scale genetic studies
Atkinson, Jonathan; Lobet, Guillaume; Noll, Manuel ULiege et al

in GigaScience (2017)

Background: Genetic analyses of plant root systems require large datasets of extracted architectural traits. To quantify such traits from images of root systems, researchers often have to choose between ... [more ▼]

Background: Genetic analyses of plant root systems require large datasets of extracted architectural traits. To quantify such traits from images of root systems, researchers often have to choose between automated tools (that are prone to error and extract only a limited number of architectural traits) or semi-automated ones (that are highly time consuming). Findings: We trained a Random Forest algorithm to infer architectural traits from automatically extracted image descriptors. The training was performed on a subset of the dataset, then applied to its entirety. This strategy allowed us to (i) decrease the image analysis time by 73% and (ii) extract meaningful architectural traits based on image descriptors. We also show that these traits are sufficient to identify Quantitative Trait Loci that had previously been discovered using a semi-automated method. Conclusions: We have shown that combining semi-automated image analysis with machine learning algorithms has the power to increase the throughput of large scale root studies. We expect that such an approach will enable the quantification of more complex root systems for genetic studies. We also believe that our approach could be extended to other areas of plant phenotyping. [less ▲]

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