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See detailExtracellular peptidase hunting for improvement of protein production in plant cells and roots
Lallemand, Jérôme ULg; Bouché, Frédéric ULg; Desiron, Carole et al

in Frontiers in Plant Science (2015), 6(37),

Plant-based recombinant protein production systems have gained an extensive interest over the past few years, because of their reduced cost and relative safety. Although the first products are now ... [more ▼]

Plant-based recombinant protein production systems have gained an extensive interest over the past few years, because of their reduced cost and relative safety. Although the first products are now reaching the market, progress are still needed to improve plant hosts and strategies for biopharming. Targeting recombinant proteins toward the extracellular space offers several advantages in terms of protein folding and purification, but degradation events are observed, due to endogenous peptidases. This paper focuses on the analysis of extracellular proteolytic activities in two production systems: cell cultures and root-secretion (rhizosecretion), in Arabidopsis thaliana and Nicotiana tabacum. Proteolytic activities of extracellular proteomes (secretomes) were evaluated in vitro against two substrate proteins: bovine serum albumin (BSA) and human serum immunoglobulins G (hIgGs). Both targets were found to be degraded by the secretomes, BSA being more prone to proteolysis than hIgGs. The analysis of the proteolysis pH-dependence showed that target degradation was mainly dependent upon the production system: rhizosecretomes contained more peptidase activity than extracellular medium of cell suspensions, whereas variations due to plant species were smaller. Using class-specific peptidase inhibitors, serine and metallopeptidases were found to be responsible for degradation of both substrates. An in-depth in silico analysis of genomic and transcriptomic data from Arabidopsis was then performed and led to the identification of a limited number of serine and metallo-peptidases that are consistently expressed in both production systems. These peptidases should be prime candidates for further improvement of plant hosts by targeted silencing. [less ▲]

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See detailQuantitative temperature monitoring of a heat tracing experiment using cross-borehole ERT
Hermans, Thomas ULg; Wildemeersch, Samuel ULg; Jamin, Pierre ULg et al

in Geothermics (2015), 53

The growing demand for renewable energy leads to an increase in the development of geothermal energy projects and heat has become a common tracer in hydrology and hydrogeology. Designing geothermal ... [more ▼]

The growing demand for renewable energy leads to an increase in the development of geothermal energy projects and heat has become a common tracer in hydrology and hydrogeology. Designing geothermal systems requires a multidisciplinary approach including geological and hydrogeological aspects. In this context, electrical resistivity tomography (ERT) can bring relevant, qualitative and quantitative information on the temperature distribution in operating shallow geothermal systems or during heat tracing experiments. We followed a heat tracing experiment in an alluvial aquifer using cross-borehole time-lapse ERT. Heated water was injected in a well while water of the aquifer was extracted at another well. An ERT section was set up across the main flow direction. The results of ERT were transformed into temperature using calibrated petrophysical relationships. These ERT-derived temperatures were then compared to direct temperature measurements in control piezometers collected with distributed temperature sensing (DTS) and groundwater temperature loggers. Spatially, it enabled to map the horizontal and vertical extent of the heated water plume, as well as the zones where maximum temperatures occurred. Quantitatively, the temperatures and breakthrough curves estimated from ERT were in good agreement with the ones observed directly during the rise and maximum of the curve. An overestimation, likely related to 3D effects, was observed for the tail of the heat breakthrough curve. The error made on temperature can be estimated to be between 10 to 20 %, which is a fair value for indirect measurements. From our data, we estimated a quantification threshold for temperature variation of 1.2°C. These results suggest that ERT should be considered when designing heat tracing experiments or geothermal systems. It could help also to assess the geometrical complexity of the concerned reservoirs. It also appears that ERT could be a useful tool to monitor and control geothermal systems once they are in operation. [less ▲]

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See detailClimate-controlled palynofacies and miospore biostratigraphy of the Early Devonian Jauf Formation, northern Saudi Arabia
Breuer, Pierre; Leszczynski, S.; Miller, M.A. et al

in Review of Palaeobotany and Palynology (2015), 212

The Jauf Formation miospore succession is synthesized in terms of paleoenvironments and sequence stratigraphy. The data set for this study is obtained from four overlapping, continuously cored, and ... [more ▼]

The Jauf Formation miospore succession is synthesized in terms of paleoenvironments and sequence stratigraphy. The data set for this study is obtained from four overlapping, continuously cored, and extensively sampled, boreholes that for a 940 ft composite section. The Jauf Formation ranges in age from late Pragian to latest Emsian. The palynological assemblages, recognized herein, provide the basis for recognizing depositional environments present in the Early Devonian of northern Saudi Arabia. Transgressive – regressive cycles are indicated, not only by lithology but by marked changes in the marine to terrestrially dominated palynological assemblages. Flooding events are recognized by the replacement of spore dominated assemblages by organic-walled microphytoplankton. The maximum flooding interval for the Jauf is reinterpreted based on a correlative event consisting of diverse acritarchs and abundant chitinozoans. [Add details on the paly and sequence stratigraphy here. No.cycles and order.] The new northern Gondwanan biozonation developed by Breuer and Steemans (2012) and used here allows a high-resolution regional biozonation for the Arabian Plate and more intercontinental [?] correlation of the Jauf Formation with other Gondwanan and Euramerican localities. One new spore genus (Zonohilates) and four spore species (Insculptospora maxima, Camarozonotriletes alruwailii, Devonomonoletes crassus and Zonohilates vulneratus) are newly proposed. [less ▲]

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See detailSpore assemblages from Upper Ordovician and Lowermost Silurian sediments recovered from the Qusaiba-1 shallow core hole, Qasim region, central Saudi Arabia
Wellman, Charles H.; Steemans, Philippe ULg; Miller, M.A.

in Review of Palaeobotany and Palynology (2015), 212

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See detailAnalytical Procedure Validation and the Quality by Design Paradigm
Rozet, Eric ULg; Lebrun, Pierre ULg; Michiels, Jean-François et al

in Journal of Biopharmaceutical Statistics (2015), 25

Since the adoption of the ICH Q8 document concerning the development of pharmaceutical processes following a quality by design (QbD) approach, there have been many discussions on the opportunity for ... [more ▼]

Since the adoption of the ICH Q8 document concerning the development of pharmaceutical processes following a quality by design (QbD) approach, there have been many discussions on the opportunity for analytical procedure developments to follow a similar approach. While development and optimization of analytical procedure following QbD principles have been largely discussed and described, the place of analytical procedure validation in this framework has not been clarified. This article aims at showing that analytical procedure validation is fully integrated into the QbD paradigm and is an essential step in developing analytical procedures that are effectively fit for purpose. Adequate statistical methodologies have also their role to play: such as design of experiments, statistical modelling, and probabilistic statements. The outcome of analytical procedure validation is also an analytical procedure design space, and from it, control strategy can be set. [less ▲]

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See detailA quality by design approach for longitudinal quality attributes
Lebrun, Pierre ULg; Giacoletti, Katherine; Scherder, Tara et al

in Journal of Biopharmaceutical Statistics (2015), 25

The concept of quality by design (QbD) as published in ICH-Q8 is currently one of the most recurrent topics in the pharmaceutical literature. This guideline recommends the use of information and prior ... [more ▼]

The concept of quality by design (QbD) as published in ICH-Q8 is currently one of the most recurrent topics in the pharmaceutical literature. This guideline recommends the use of information and prior knowledge gathered during pharmaceutical development studies to provide a scientific rationale for the manufacturing process of a product and provide guarantee of future quality. This poses several challenges from a statistical standpoint and requires a shift in paradigm from traditional statistical practices. First, to provide “assurance of quality” of future lots implies the need to make predictions regarding the quality given past evidence and data. Second, the quality attributes described in the Q8 guidelines are not always a set of unique, independent measurements. In many cases, these criteria are com- plicated longitudinal data with successive acceptance criteria over a defined period of time. A common example is a dissolution profile for a modified or extended-release solid dosage form that must fall within acceptance limits at several time points. A Bayesian approach for longitudinal data obtained in various conditions of a design of experiment is provided to elegantly address the ICH-Q8 recommendation to provide assurance of quality and derive a scientifically sound design space. [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 detailPaleomagnetic and geochemical record from cores from the Sea of Marmara, Turkey: Age constraints and implications of sapropelic deposition on early diagenesis
Drab, Laureen; Carlut, Julie; Hubert, Aurelia ULg et al

in Marine Geology (2015), 360

We present results of a multi-proxy analysis of two sediment cores from the Marmara Sea. The cores were ana- lyzed using paleomagnetic and geochemical measurements. Two sapropels are documented in the ... [more ▼]

We present results of a multi-proxy analysis of two sediment cores from the Marmara Sea. The cores were ana- lyzed using paleomagnetic and geochemical measurements. Two sapropels are documented in the last 11 kyr and are recorded in several locations across the Marmara Sea. These two sapropels have contrasting magnetic prop- erties. The magnetic record is affected by intense early diagenesis; the most recent upper sapropelic layer has low remanence and susceptibility values. A record of paleomagnetic inclinations could still be isolated above the dia- genesis front and is compared with secular variation models. The lower sapropel is identified in the deep part of the oldest studied core (Klg07) and has distinct magnetic properties characterized by high remanence and sus- ceptibility values. Using the magnetic properties it is possible to constrain bottom water ventilation and recon- nection episodes between the Marmara Sea and the Black Sea following the sea level rise during the last glacial to inter-glacial transition. [less ▲]

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See detailLes difficultés d'apprentissage procédural chez les enfants dysphasiques
Desmottes, Lise ULg; Meulemans, Thierry ULg; Maillart, Christelle ULg

in ANAE : Approche Neuropsychologique des Apprentissages chez l'Enfant (2015)

Through a review of the literature, this paper shows that linguistic and non-linguistic disorders in children with specific language impairment might be linked to difficulties in procedural learning ... [more ▼]

Through a review of the literature, this paper shows that linguistic and non-linguistic disorders in children with specific language impairment might be linked to difficulties in procedural learning, especially regarding sequential abilities. Indeed, children with specific language impairment encounter difficulties to learn visuo-motor and linguistic sequences. These difficulties are not limited to initial learning but extend to the consolidation stage in long-term memory. Finally, recent studies show that it is possible to improve procedural learning abilities, suggesting new avenues for rehabilitation. [less ▲]

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See detailAphid species and associated natural enemies in field crops: what about the invasive ladybird Harmonia axyridis (Coleoptera: Coccinellidae)?
Vandereycken, Axel ULg; Durieux, Delphine ULg; Joie, Emilie ULg et al

in Entomologie Faunistique = Faunistic Entomology (2015), 68

Following the introduction in the 80's of the invasive coccinellid species Harmonia axyridis (Pallas) in Europe, several studies have begun to focus on the interactions with other aphid predator species ... [more ▼]

Following the introduction in the 80's of the invasive coccinellid species Harmonia axyridis (Pallas) in Europe, several studies have begun to focus on the interactions with other aphid predator species. In this study, aphids and associated predators were sampled to determine their relative abundance in four agricultural crops (broad bean, corn, potato, and wheat) in Belgium during 2010 and 2011. The Moericke trap was used to quantify the mean number of aphids and aphid predators from May to September in both years. A total of 28 aphid species and 21 aphidophagous species were observed. In both years, H. axyridis was among the most abundant aphidophagous predators in all four crops, and was the second most abundant coccinellid species after Coccinella septempunctata L. The community of aphidophagous species was similar across all four inventoried crops. However, the highest population densities of this alien species were recorded in broad bean and potato crops, which also hosted the highest aphid population densities. In conclusion, this study demonstrates that the communities of aphid predators are highly diversified in the agroecosystems, despite the high occurrence of H. axyridis, an introduced predator that has become well established in this environment. [less ▲]

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See detailChemical abundances of fast-rotating OB stars
Cazorla, Constantin ULg; Morel, Thierry ULg; Nazé, Yaël ULg et al

in Proceedings of the International Astronomical Union - New windows on massive stars: asteroseismology, interferometry, and spectropolarimetry (2015)

Fast rotation in massive stars is predicted to induce mixing in their interior, but a population of fast-rotating stars with normal nitrogen abundances at their surface has recently been revealed (Hunter ... [more ▼]

Fast rotation in massive stars is predicted to induce mixing in their interior, but a population of fast-rotating stars with normal nitrogen abundances at their surface has recently been revealed (Hunter et al. 2009; Brott et al. 2011, but see Maeder et al. 2014). However, as the binary fraction of these stars is unknown, no definitive statements about the ability of single-star evolutionary models including rotation to reproduce these observations can be made. Our work combines for the first time a detailed surface abundance analysis with a radial-velocity monitoring for a sample of bright, fast-rotating Galactic OB stars to put strong constraints on stellar evolutionary and interior models. [less ▲]

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See detailLe Transport de marchandises et de personnes sur le Nil en 823 A.H./1420 È.C.
Bauden, Frédéric ULg

in Schubert, Alexander T.; Sijpesteijn, Petra M. (Eds.) Documents and the History of the Early Islamic World (2015)

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See detailDroit constitutionnel belge - Plan général du cours (année 2014-2015)
Behrendt, Christian ULg

Learning material (2014)

Le document constitue le Plan général de l'enseignement de Droit constitutionnel dispensé à l'Université de Liège en 2e année de bachelier en droit et en 2e année de bachelier en science politique.

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See detailThe seed dispersal of the afro- tropical tree species Staudtia kamerunensis (Myristicaceae)
Hambuckers, Alain ULg

Scientific conference (2014, December 27)

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See detailBacterial Community Composition in Three Freshwater Reservoirs of Different Alkalinity and Trophic Status
Llirós, Marc; Inceoğlu, Özgul; García-Armisen, Tamara et al

in PLoS ONE (2014)

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See detailETAT DE LIEU DE LA FILIERE APICOLE EN REPUBLIQUE DEMOCRATIQUE DU CONGO ET EVALUATION DES CAPACITES POLLINISATRICES DES ABEILLES DOMESTIQUES (Apis mellifera adansonii, L.) SUR LA CULTURE DE MELON AFRICAIN (Cucumeropsis mannii Naudin) A KISANGANI.
Posho Ndola, Boniface ULg

Doctoral thesis (2014)

La présente étude s’inscrit dans le cadre de la recherche d’une meilleure compréhension de la filière apicole en RDC, de l’influence de l’environnement sur la qualité de pains d'abeille et de miel pour la ... [more ▼]

La présente étude s’inscrit dans le cadre de la recherche d’une meilleure compréhension de la filière apicole en RDC, de l’influence de l’environnement sur la qualité de pains d'abeille et de miel pour la survie d’Apis mellifera adansonii, L. 1758 en RDC et de l’impact de la pollinisation des abeilles introduites (A. mellifera adansonii, L. 1758) sur la production de Cucumeropsis mannii (Naudin) à Kisangani. Trois approches ont été adoptées pour faire l’état de lieu de la filière apicole en RDC, dont (1) la distribution des questionnaires structurés aux apiculteurs, (2) des visites de ruchers et (3) des recherches documentaires. Dans le cadre de l’évaluation de la qualité de miels et pains d’abeilles, les échantillons de miels et de pollens ont été collectés dans trois sites écologiquement différents de la RDC. Les échantillons de miels ont été évalués suivant les critères et les protocoles établis par Codex Alimentarius; tandis que les pollens ont été évalués suivant les critères de teneur en protéines et en acides aminés essentiels. Les teneurs en protéines et en acides aminés essentiels de pains d’abeilles collectés ont été déterminées respectivement par la méthode Kjeldahl et par les hydrolyses acides et basiques. Les essais comparatifs de la pollinisation des abeilles domestiques ont été également conduits dans deux sites expérimentaux à Kisangani. Sur chaque site, deux champs d'un hectare séparés de 3 kilomètres ont été installés. Deux colonies d'abeilles ont été installées au milieu du champ expérimental de chaque site pendant la floraison (quand 10 % des plantes ont fleuri). Le second champ expérimental, sans colonies d’abeilles, a été considéré comme témoin. Les résultats obtenus après l’étude exploratoire sur l’apiculture en RDC montrent que l’apiculture congolaise reste encore semi traditionnelle; 54 % des apiculteurs congolais travaillent en coopérative; 100 % du cheptel apicole congolais est constitué d’A. mellifera adansonii, L. ; 96 % des apiculteurs utilisent les ruches Kenyanes; le nombre de ruches utilisé par un apiculteur congolais varie entre 2 et 120; la production d’une colonie par récolte oscille entre 1 et 25 litres de miel; la production annuelle par apiculteur est évaluée entre 10 et 900 litres de miel, le nombre de récoltes de miel effectué par an varie de 1 à 2. Cette étude a révélé que la teneur moyenne en protéines de pollens recueillies en RDC était 14,11 ± 5,27 %. Cette teneur en protéines était faible comparativement aux besoins alimentaires des abeilles en Europe. Tous les échantillons de pollen étaient constitués de dix acides aminés essentiels et leurs concentrations étaient dans la fourchette optimale des exigences alimentaires des abeilles en Europe. Les analyses des échantillons de miels ont révélé que la teneur en sucres réducteurs des échantillons de miel recueillies variait de 63,40 à 73,80 %, la teneur en saccharose était comprise entre 0,30 et 1,90 %, la teneur en eau oscillait entre 16,80 et 22,00 %, le pH des échantillons de miel analysés variait de 4,22 à 4,53, la moyenne de la conductivité électrique de miels récoltés a été ( 47,74 ± 13,93 ) S/cm et la concentration de HMF varié de 1,75 à 31,38 mg / kg de HMF miel. Les miels et les pollens collectés dans la forêt tropicale de Kisangani étaient moyennement plus nutritifs pour les abeilles que ceux de la savane de Kavwaya. Après les observations des essais comparatifs de pollinisation, il a révélé que la pollinisation des abeilles introduites a amélioré significativement le nombre de graines par fruit de 83,78 %, tandis que le nombre de fruits par plante et le poids de graines par fruit ont été améliorés respectivement de 422,89 % et 185,61 % par rapport au témoin. La taille de graine a été positivement influencée par la présence de colonie d’abeille dans le champ de C. mannii (Naudin). Dans cette étude, la distance par rapport aux ruches et l’orientation de vol des ouvrières n'ont pas influencé significativement le rendement et la taille des graines de C. mannii (Naudin) [less ▲]

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See detailTowards generic image classification: an extensive empirical study
Marée, Raphaël ULg; Geurts, Pierre ULg; Wehenkel, Louis ULg

E-print/Working paper (2014)

This paper considers the general problem of image classification without using any prior knowledge about image classes. We study variants of a method based on supervised learning whose common steps are ... [more ▼]

This paper considers the general problem of image classification without using any prior knowledge about image classes. We study variants of a method based on supervised learning whose common steps are the extraction of random subwindows described by raw pixel intensity values and the use of ensemble of extremely randomized trees to directly classify images or to learn image features. The influence of method parameters and variants is thoroughly evaluated so as to provide baselines and guidelines for future studies. Detailed results are provided on 80 publicly available datasets that depict very diverse types of images (more than 3800 image classes and over 1.5 million images). [less ▲]

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