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See detailmstR: An R package to generate multistage testing designs
Magis, David ULiege; Yan, Duanli; von Davier, Alina

Conference (2017, July 18)

Multistage testing (MST; Yan, von Davier & Lewis, 2014) has become an important framework of tailored testing. Similarly to computerized adaptive testing (CAT) it proposes an optimal routing of the ... [more ▼]

Multistage testing (MST; Yan, von Davier & Lewis, 2014) has become an important framework of tailored testing. Similarly to computerized adaptive testing (CAT) it proposes an optimal routing of the administered items according to the previous test taker’s responses. However, items are not selected and administered as single units but as modules (subsets). The main goal of MST consists in selecting the optimal path of modules across the successive stages of the test. Unfortunately, if various operational testing programs are nowadays considering MST for practical administrations, there is still very limited access to accurate software that can either treat or generate MST scenarios for research purposes. In this talk we succinctly present a new package from the R software, called mstR (Magis, Yan & von Davier, 2017). Built in the same spirit of the package catR for CAT designs, it permits to generate repeated response patterns under a predefined MST scenario by providing the set of modules and related item parameters, the number of stages and the connections between modules from successive stages. Several rules for optimal module selection and ability estimation (under IRT framework or based on test scores) are also available. This talk will mostly focus on the (non-technical) description of package mstR and its main features. An example will also be described as an illustration of this framework. [less ▲]

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See detailFluencyBank: studying typical and disordered speech fluency across languages and contexts
MacWhinney, Brian; Leclercq, Anne-Lise ULiege; Zwitserlood, Rob et al

Conference (2017, July 18)

Mastering the skill to produce fluent speech is a complex task that is still poorly understood. Similarly, the threshold at which typical fluency breakdown begins to attract clinical concern is also a ... [more ▼]

Mastering the skill to produce fluent speech is a complex task that is still poorly understood. Similarly, the threshold at which typical fluency breakdown begins to attract clinical concern is also a matter of frequent disagreement. The goal of the recently funded FluencyBank project, an arm of TalkBank, is to facilitate collection and analysis of expressive speech samples across the lifespan, languages, and clinical diagnoses. Speakers will illustrate the challenges and opportunities available to the study of expressive language development skill. The first speaker (Leclercq) will examine the need for reference data across languages in order to distinguish typical developmental disfluency from stuttering, using data from French. The second speaker (Zwitserlood) will confirm and elaborate on the profile of elevated disfluency profiles in children with SLI, using Dutch data. The third speaker (Byrd) will describe the theoretical and practical challenges of discriminating typical fluency profiles from clinical stuttering in bilinguals, with emphasis on Spanish-English child speakers. The fourth speaker (Ratner) will update information linking language proficiency to stuttering onset and persistence/recovery, showing the complex interactions between speech and language formulation. Each speaker will emphasize the many intertwining skills that underlie the development of spoken language fluency and the benefits of specialized cooperative initiatives such as FluencyBank to collect data for exploration of otherwise impossible to answer hypotheses. Moderator Brian MacWhinney, Co-Investigator of FluencyBank will discuss its development, planned research projects and computational tool development, and illustrate potential applications for use by child language researchers. [less ▲]

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See detailDesigning artificial (β/α)8-barrel proteins from scratch: the Octarellin model
Martina, Cristina Elisa ULiege

Speech/Talk (2017)

De novo protein design is a growing field in protein chemistry, where artificial proteins are first designed in silico and then validated experimentally. Our group has a long tradition in the design of ... [more ▼]

De novo protein design is a growing field in protein chemistry, where artificial proteins are first designed in silico and then validated experimentally. Our group has a long tradition in the design of artificial (β/α)8-barrel proteins, known as Octarellins [1]. This fold, also known as TIM-barrel, is widespread in nature, particularly in enzymes, and represent an interesting target for therapeutic or biological applications. Here we present a novel protocol for the de novo design of TIM-barrels. Both Rosetta and Modeller modeling softwares were used to create the backbone structure of a TIM-barrel fold and to generate more than 10.000 artificial amino acid sequences. Stability was tested for the more interesting models by running molecular dynamics (MD) simulations, using GROMACS. The best models were chosen for protein production and preliminary biophysical characterization. The design of artificial proteins and the improvement of bioinformatics tools for protein modeling, structure prediction and MD simulations seem to be essential for a comprehensive knowledge of protein structure in general, as well as for an optimal use of the massive amount of data resulting from the numerous genome sequencing projects. [less ▲]

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See detailNegative velocity fluctuations and non-equilibrium fluctuation relation for a driven high critical current vortex state
Bag, Biplab; Shaw, Gorky ULiege; Banerjee, S. S. et al

in Scientific Reports (2017), 7(1), 5531

Under the influence of a constant drive the moving vortex state in 2H-NbS2 superconductor exhibits a negative differential resistance (NDR) transition from a steady flow to an immobile state. This state ... [more ▼]

Under the influence of a constant drive the moving vortex state in 2H-NbS2 superconductor exhibits a negative differential resistance (NDR) transition from a steady flow to an immobile state. This state possesses a high depinning current threshold ( $$\boldsymbolI_\boldsymbolc^\boldsymbolh$$ I c h ) with unconventional depinning characteristics. At currents well above $$\boldsymbolI_\boldsymbolc^\boldsymbolh$$ I c h , the moving vortex state exhibits a multimodal velocity distribution which is characteristic of vortex flow instabilities in the NDR regime. However at lower currents which are just above $$\boldsymbolI_\boldsymbolc^\boldsymbolh$$ I c h , the velocity distribution is non-Gaussian with a tail extending to significant negative velocity values. These unusual negative velocity events correspond to vortices drifting opposite to the driving force direction. We show that this distribution obeys the Gallavotti-Cohen Non-Equilibrium Fluctuation Relation (GC-NEFR). Just above $$\boldsymbolI_\boldsymbolc^\boldsymbolh$$ I c h , we also find a high vortex density fluctuating driven state not obeying the conventional GC-NEFR. The GC-NEFR analysis provides a measure of an effective energy scale (E eff ) associated with the driven vortex state. The E eff corresponds to the average energy dissipated by the fluctuating vortex state above $$\boldsymbolI_\boldsymbolc^\boldsymbolh$$ I c h . We propose the high E eff value corresponds to the onset of high energy dynamic instabilities in this driven vortex state just above $$\boldsymbolI_\boldsymbolc^\boldsymbolh$$ I c h . [less ▲]

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See detailProtein-polysaccharide complexes for improved protein delivery within CaCO3 microparticles
Ramalapa, Bathabile ULiege; Crasson, Oscar ULiege; Vandevenne, Marylène ULiege et al

Conference (2017, July 17)

Introduction: The controlled delivery of proteins within calcium carbonate (CaCO3) particles is currently widely investigated due to accessibility, low cost, safety, pH-sensitive properties, high surface ... [more ▼]

Introduction: The controlled delivery of proteins within calcium carbonate (CaCO3) particles is currently widely investigated due to accessibility, low cost, safety, pH-sensitive properties, high surface area and high porosity. The success of these carriers has been driven by the ionic interactions between proteins and particles making the encapsulation of proteins highly dependent on the pH of reaction solutions and the isoelectric point of the protein. This poses a great limitation on the successful loading of proteins into microparticles. In this study we explored the use of polysaccharide-protein complexes to enhance the encapsulation of otherwise poorly encapsulated proteins in CaCO3 microparticles. Methods: A chitin binding domain (ChBD) was inserted on the protein β-lactamase to form a chimeric protein. A protein-polysaccharide complex was formed between the protein and hyaluronic acid (HA) owing to the intrinsic affinity of the ChBD to HA. The chimeric protein was then loaded into CaCO3 microparticles using super critical CO2 technology aided by the templating effect of HA on CaCO3. The microparticles were characterised for size, surface charge, polymorphism and protein loading. Bioactivity and stability of the encapsulated β-lactamase was characterised by kinetic reaction with nitrocefin. A thrombin cleavage site was inserted onto the gene sequence of the protein to achieve release of the protein from the microparticles by proteases mediation using thrombin. Results: Vaterite CaCO3 microparticles of sizes ranging between 6 and 8 µm were produced. The presence of the ChBD on the β-lactamase increased the encapsulation of the protein by 6 fold when complexed with HA. Thrombin mediated release increased the release of the protein from the microparticles within 36 hours from <25% to 87%. The protein-polysaccharide complex demonstrated success in encapsulation of the protein while retaining up to 81% activity of the protein and allowing controlled release by proteases. Conclusion: Protein-polysaccharide complexation demonstrates an excellent approach for the delivery of sensitive biomacromolecules which can otherwise be complicated due to electrostatic hindrances. Future prospects include using the methods we have developed for encapsulation of therapeutic proteins and using calcium carbonate as a carrier and scaffold for example in bone regeneration. [less ▲]

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See detailPrevention Library and Resources in four languages (QP Library)
Comité de Bibliografía en Prevención Cuaternaria; WONCA SIG P4 & O; Pizanelli, Miguel et al

Textual, factual or bibliographical database (2017)

Since Quaternary Prevention is very extensive and complex, during the design process for database input, an indexing structure with the use of coding tools and categories was considered. This design will ... [more ▼]

Since Quaternary Prevention is very extensive and complex, during the design process for database input, an indexing structure with the use of coding tools and categories was considered. This design will allow the addition of materials and will provide easy access to them. To add documents, 13 data fields must be populated. To access the input data form, for the purpose of adding documents, use this link: http://j.tinyurl.com/P4-Library To avoid duplication of data entries, it is necessary to review and perform an audit. In the beginning, we will provide this tutorial to a few data entry collaborators. To become a data entry collaborator, please send an e-mail to the following address: quaternaryprevention@gmail.com Charts are available in eight languages to code with Q-Codes: http://3cgp.docpatient.net/tabular/ [less ▲]

Detailed reference viewed: 154 (1 ULiège)
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See detailGlobal regression model for moisture content determination using near-infrared spectroscopy
Clavaud, Matthieu ULiege; Roggo, Yves; Degardin, Klara et al

in European Journal of Pharmaceutics and Biopharmaceutics (2017), 119

Near-infrared (NIR) global quantitative models were evaluated for the moisture content (MC) determination of three different freeze-dried drug products. The quantitative models were based on 3822 spectra ... [more ▼]

Near-infrared (NIR) global quantitative models were evaluated for the moisture content (MC) determination of three different freeze-dried drug products. The quantitative models were based on 3822 spectra measured on two identical spectrometers to include variability. The MC, measured with the reference Karl Fischer (KF) method, were ranged from 0.05% to 4.96%. Linear and non-linear regression models using Partial Least Square (PLS), Decision Tree (DT), Bayesian Ridge Regression (Bayes-RR), K-Nearest Neighbors (KNN), and Support Vector Regression (SVR) algorithms were created and evaluated. Among them, the SVR model was retained for a global application. The Standard Error of Calibration (SEC) and the Standard Error of Prediction (SEP) were respectively 0.12% and 0.15%. This model was then evaluated in terms of total error and risk-based assessment, linearity, and accuracy. It was observed that MC can be fastly and simultaneously determined in freeze-dried pharmaceutical products thanks to a global NIR model created with different medicines. This innovative approach allows to speed up the validation time and the in-lab release analyses. [less ▲]

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See detailAn active bacterial community linked to high chl-a concentrations in Antarctic winter-pack ice and evidence for the development of an anaerobic sea-ice bacterial community
Eronen-Rasimus, Eeva; Luhtanen, Anne-Mari; Rintala, Janne-Markus et al

in ISME Journal (The) (2017), 1-11

Antarctic sea-ice bacterial community composition and dynamics in various developmental stages were investigated during the austral winter in 2013. Thick snow cover likely insulated the ice, leading to ... [more ▼]

Antarctic sea-ice bacterial community composition and dynamics in various developmental stages were investigated during the austral winter in 2013. Thick snow cover likely insulated the ice, leading to high (o4 μg l–1) chlorophyll-a (chl-a) concentrations and consequent bacterial production. Typical sea-ice bacterial genera, for example, Octadecabacter, Polaribacter and Glaciecola, often abundant in spring and summer during the sea-ice algal bloom, predominated in the communities. The variability in bacterial community composition in the different ice types was mainly explained by the chl-a concentrations, suggesting that as in spring and summer sea ice, the sea-ice bacteria and algae may also be coupled during the Antarctic winter. Coupling between the bacterial community and sea-ice algae was further supported by significant correlations between bacterial abundance and production with chl-a. In addition, sulphate-reducing bacteria (for example, Desulforhopalus) together with odour of H2S were observed in thick, apparently anoxic ice, suggesting that the development of the anaerobic bacterial community may occur in sea ice under suitable conditions. In all, the results show that bacterial community in Antarctic sea ice can stay active throughout the winter period and thus possible future warming of sea ice and consequent increase in bacterial production may lead to changes in bacteria-mediated processes in the Antarctic sea-ice zone. [less ▲]

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See detailEffects of an experimental resource pulse on the macrofaunal assemblage inhabiting seagrass macrophytodetritus
Remy, François ULiege; Gobert, Sylvie ULiege; Lepoint, Gilles ULiege

in Belgian Journal of Zoology (2017), 147(1), 1-15

Physical disturbances and resource pulses are major structuring drivers of terrestrial and aquatic ecosystems. The accumulations of exported dead leaves from the Neptune grass, Posidonia oceanica (L ... [more ▼]

Physical disturbances and resource pulses are major structuring drivers of terrestrial and aquatic ecosystems. The accumulations of exported dead leaves from the Neptune grass, Posidonia oceanica (L.) Delile are ephemeral and highly dynamic detrital habitats offering food sources and shelter for vagile macrofauna community. These habitats are frequently subject to wind and storms which can add “new” detrital material to previous accumulations; these can be defined as resource pulses and could potentially impact the associated macrofauna. This study assesses the impact of an experimental resource pulse on the macrofauna associated with exported P. oceanica litter accumulations. The experimental design consisted of two pulse treatments (the addition of dead leaves with and without the associated fauna), and two controls (one procedural, and one total control), where the added material was left underwater for 14 days. Invertebrates then present in the sampled detritus were all identified and counted. Our data suggest that the responses of these invertebrates to resource pulses present intermediate characteristics between aquatic and terrestrial ecosystems responses. Inputting a moderate amount of dead P. oceanica leaves into experimental mesocosms had a non-negligible impact and rapidly affected the macrofauna community. Specialist detritivores species were boosted while herbivore/detritivore species dramatically decreased. Predators also showed a modest but significant density increase, demonstrating the fast propagation of the pulse response throughout the entire community and through several trophic levels. Strict hypoxia-tolerant species were also only observed in the treated mesocosms, indicating the strong influence of resource pulses on physico-chemical conditions occurring inside litter accumulations. [less ▲]

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See detailCosmological Time, Entropy and Infinity
Hauret, Clémentine ULiege; Magain, Pierre ULiege; Biernaux, Judith ULiege

in Entropy (2017), 19(7),

Time is a parameter playing a central role in our most fundamental modelling of natural laws. Relativity theory shows that the comparison of times measured by different clocks depends on their relative ... [more ▼]

Time is a parameter playing a central role in our most fundamental modelling of natural laws. Relativity theory shows that the comparison of times measured by different clocks depends on their relative motion and on the strength of the gravitational field in which they are embedded. In standard cosmology, the time parameter is the one measured by fundamental clocks (i.e., clocks at rest with respect to the expanding space). This proper time is assumed to flow at a constant rate throughout the whole history of the universe. We make the alternative hypothesis that the rate at which the cosmological time flows depends on the dynamical state of the universe. In thermodynamics, the arrow of time is strongly related to the second law, which states that the entropy of an isolated system will always increase with time or, at best, stay constant. Hence, we assume that the time measured by fundamental clocks is proportional to the entropy of the region of the universe that is causally connected to them. Under that simple assumption, we find it possible to build toy cosmological models that present an acceleration of their expansion without any need for dark energy while being spatially closed and finite, avoiding the need to deal with infinite values. [less ▲]

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See detailRegression analysis of potato dormancy integrating genetic and environmental factors.
Visse-Mansiaux, Margot ULiege; Vanderschuren, Hervé ULiege; Soyeurt, Hélène ULiege et al

Conference (2017, July 14)

Potato dormancy is usually described as the period required by potato tubers to initiate sprouting after harvest. The dormancy parameter is key for the potato value chain because it defines the storage ... [more ▼]

Potato dormancy is usually described as the period required by potato tubers to initiate sprouting after harvest. The dormancy parameter is key for the potato value chain because it defines the storage period during which no anti-sprouting treatment is required. Dormancy is known to have a genetic component because the time from harvest to sprouting varies between potato varieties. A better characterization of dormancy helps optimizing storage by reducing the frequency of anti-sprouting applications. Reducing the anti-sprouting treatments not only helps lowering storage costs but it also provides an immediate benefit for human health and for the environment. The main objective of the present study is to develop a model predicting the dormancy length in function of the cultivar and the growing conditions of the considered year. So, 2 sources of informations were used: 1) average dormancy of cultivars provided by breeders (breeders dormancy) 2) average dormancy of cultivars obtained from field experiments (field dormancy). The field experiments were managed in Switzerland during 25 years in four different locations and for 721 varieties of potatoes. Field data were registered during the growing season such as weather data (e.g. temperature, rainfall etc.), soil data and crop management data. One month after harvest, the potatoes were stored at 8°C in wooden crates containing 7 kg of potato tubers. The dormancy was defined as the time between the harvest and the emergence of the first sprouts. The data (n=3’730) were analyzed as follow: (1) calculation of the field dormancy, which is the average dormancy length of the tested cultivars from the field data; (2) merging of field dormancy and breeders dormancy records (3) univariate regressions to study the link between the breeders and field dormancy records; (3) ANOVA to identify the parameters with the highest influence on the dormancy length; (4) creation of a model using these identified parameters in order to predict the sprouting date of potato stocks based on the field data; (5) validation of the model. Our results highlight the heterogeneity of the dormancy data provided by the potato breeders. Our results also stress the importance of climatic and field parameters to estimate the dormancy length of a given potato stock. We discuss the practical consequences for growers and potato storage companies. [less ▲]

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See detailA Novel Accelerometer-Based Method for Stride Length Estimation
Boutaayamou, Mohamed ULiege; Schwartz, Cédric ULiege; Denoël, Vincent ULiege et al

Poster (2017, July 14)

We demonstrate the feasibility of accurately and precisely estimating the left/right average stride length from measured heel/toe accelerations in the gait of healthy, old adults. Our approach relies on ... [more ▼]

We demonstrate the feasibility of accurately and precisely estimating the left/right average stride length from measured heel/toe accelerations in the gait of healthy, old adults. Our approach relies on (1) a novel method that uses only accelerometer data without the need of additional data from, e.g., gyroscopes and/or magnetometers, and on (2) the validation of the results using reference 3D optoelectronic system data. [less ▲]

Detailed reference viewed: 34 (8 ULiège)