160 Works

Semi-artificial datasets as a resource for validation of bioinformatics pipelines for plant virus detection

Lucie Tamisier, Annelies Haegeman, Yoika Foucart, Nicolas Fouillien, Maher Al Rwahnih, Nihal Buzkan, Thierry Candresse, Michela Chiumenti, Kris De Jonghe, Marie Lefebvre, Paolo Margaria, Jean Sébastien Reynard, Kristian Stevens, Denis Kutnjak & Sébastien Massart
In the last decade, High-Throughput Sequencing (HTS) has revolutionized biology and medicine. This technology allows the sequencing of huge amount of DNA and RNA fragments at a very low price. In medicine, HTS tests for disease diagnostics are already brought into routine practice. However, the adoption in plant health diagnostics is still limited. One of the main bottlenecks is the lack of expertise and consensus on the standardization of the data analysis. The Plant Health...

A Collection of Greek Ritual Norms

Jan-Mathieu Carbon, Saskia Peels & Vinciane Pirenne-Delforge

Indian philosophy and the value of transformative experiences. An interview with Monima Chadha by Edvard Avilés and Matthieu Koroma

Monima Chadha, Edvard Avilés & Matthieu Koroma
In this interview, we engage in a cross-cultural discussion about the diversity of consciousness. Indian philosophy can seem quite cryptic and difficult to follow because it is a primary oral tradition. However, Monima Chadha has developed a series of work aiming at introducing the rich insights of Indian philosophy of mind into Western literature. Indeed, the translation of concepts and practices from the Indian to the Western context requires a solid knowledge of the Indian...

PoPuPS, une pépinière de revues, entre multi-disciplinarité et qualité

Data from: Cultural flies: conformist social learning in fruit flies predicts long-lasting mate-choice traditions

Etienne Danchin, Sabine Nöbel, Arnaud Pocheville, Anne-Cecile Dagaeff, Léa Demay, Mathilde Alphand, Sarah Ranty-Roby, Lara Van Renssen, Magdalena Monier, Eva Gazagne, Mélanie Allain & Guillaume Isabel
Despite theoretical justification for the evolution of animal culture, there is still scant empirical evidence for it beyond mammals and birds, and we still know little about the process of cultural inheritance. Here, we propose a mechanism-driven definition of animal culture and test it in the fruit fly. We found that fruit flies have five cognitive capacities that enable them to transmit mating preferences culturally across generations, potentially fostering persistent traditions (the main marker of...

Dataset of the retrieved oxygen green and red lines from TGO/NOMAD/UVIS dayside limb observations, presented in Soret et al., 2022

Lauriane Soret & Ann Carine Vandaele

Data associated with: Global ecomorphological restructuring of dominant marine reptiles prior to the K/Pg mass extinction

Jamie MacLaren, Rebecca Bennion, Nathalie Bardet & Valentin Fischer
Mosasaurid squamates were the dominant amniote predators in marine ecosystems during most of the Late Cretaceous. Here, we use a suite of biomechanically rooted, functionally descriptive ratios in a framework adapted from population ecology to investigate how the morphofunctional disparity of mosasaurids evolved prior to the Cretaceous-Paleogene (K/Pg) mass extinction. Our results suggest that taxonomic turnover in mosasaurid community composition from Campanian to Maastrichtian is reflected by a notable global increase in morphofunctional disparity, especially...

Data from: Convergence and constraint in the cranial evolution of mosasaurid reptiles and early cetaceans

Rebecca Bennion, Jamie MacLaren, Ellen Coombs, Felix Marx, Olivier Lambert & Valentin Fischer
The repeated return of tetrapods to aquatic life provides some of the best-known examples of convergent evolution. One comparison which has received relatively little focus is that of mosasaurids (a group of Late Cretaceous squamates) and archaic cetaceans (the ancestors of modern whales and dolphins), both of which show high levels of craniodental disparity, similar initial trends in locomotory evolution, and global distributions. Here we investigate convergence in skull ecomorphology during the initial aquatic radiations...

Observation on the effect of platelet-rich plasma combined with drugs in the treatment of herpes zoster neuralgia

Zenghua Zhou, Xin Hu, Fangran Yan, Yanhua Zhou, Ruilin He, Xiaolong Ye & Zongbin Jiang
To observe the effect of ultrasound-guided platelet-rich plasma (PRP) injection in the treatment of herpes zoster neuralgia (HZN). Eighty patients with HZN were randomly divided into observation group and control group, with 40 cases in each group. The observation group was treated with ultrasound-guided PRP injection of target nerves combined with drugs. The control group was treated with drugs alone. The pain scores of before treatment (T0), and 1 week (T1), 1 month (T2), 3...

In silico optimization of RNA–protein interactions for CRISPR-Cas13-based antimicrobials

Ho-min Park, Yunseol Park, Urta Berani, Eunkyu Bang, Joris Vankerschaver, Arnout Van Messem, Wesley De Neve & Hyunjin Shim
Abstract RNA–protein interactions are crucial for diverse biological processes. In prokaryotes, RNA–protein interactions enable adaptive immunity through CRISPR-Cas systems. These defence systems utilize CRISPR RNA (crRNA) templates acquired from past infections to destroy foreign genetic elements through crRNA-mediated nuclease activities of Cas proteins. Thanks to the programmability and specificity of CRISPR-Cas systems, CRISPR-based antimicrobials have the potential to be repurposed as new types of antibiotics. Unlike traditional antibiotics, these CRISPR-based antimicrobials can be designed to...

Additional file 4 of An integrated in silico-in vitro approach for identifying therapeutic targets against osteoarthritis

Raphaëlle Lesage, Mauricio N. Ferrao Blanco, Roberto Narcisi, Tim Welting, Gerjo J. V. M. van Osch & Liesbet Geris
Additional file 4: Data S1. Subset of genes for gene expression profiles and description of GEO datasets with manual binary annotations.

Additional file 5 of An integrated in silico-in vitro approach for identifying therapeutic targets against osteoarthritis

Raphaëlle Lesage, Mauricio N. Ferrao Blanco, Roberto Narcisi, Tim Welting, Gerjo J. V. M. van Osch & Liesbet Geris
Additional file 5: Fig. S1. Individual dataset clustering and heatmap. The microarray sub-datasets, used in the merged dataset, were also investigated individually. They were pre-processed (i.e. processing steps before merging and correcting for batch effect) in the same way as the merged dataset but the unsupervised clustering analysis was done on each sub-dataset separately in order to compare the biological or OA related information content before and after the data merging. The heatmaps show the...

Additional file 1 of Population dynamics and demographic history of Eurasian collared lemmings

Edana Lord, Aurelio Marangoni, Mateusz Baca, Danijela Popović, Anna V. Goropashnaya, John R. Stewart, Monika V. Knul, Pierre Noiret, Mietje Germonpré, Elodie-Laure Jimenez, Natalia I. Abramson, Sergey Vartanyan, Stefan Prost, Nickolay G. Smirnov, Elena A. Kuzmina, Remi-André Olsen, Vadim B. Fedorov & Love Dalén
Additional file 1: Table S1. Modern Nuclear Genome sample information. Table S2. Ancient Mitogenome Sample Information. Table S3. Modern Mitogenome Sample Information. Table S4. Divergence times for each node in the phylogenetic tree estimated using BEAST. Table S5. The priors used to specify tip-date information for each ancient sample in the phylogenetic analysis. Table S6. Demographic Modelling using Approximate Bayesian Computation. Table S7. Marginal Likelihood Estimation for demographic models: constant size, skyline, skyride. Table S8....

Assessing the effects of survey-inherent disturbance on primate detectability: Recommendations for line transect distance sampling. Dataset

Mattia Bessone, Hjalmar Kühl, Ilka Herbinger, Kouame Paul N'Goran, Papy Asanzi, Barros Pedro Da Costa, Violette Dérozier, Dadis Bush Ernest Fotsing, Beka Bernard Ikembelo, Mpongo Dieumerci Iyomi, Iyomi Bernard Iyatshi, Pierre Kafando, Mbangi Augistin Kambere, Dissondet Baudelaire Moundzoho, Kako Loving Musubaho & Barbara Fruth
Habitat destruction and over-hunting are increasingly threatening the arboreal primates of Central Africa. To establish effective conservation strategies, accurate assessments of primate density, abundance and spatial distribution are required. To date, the method of choice for primate density estimation is line transect distance sampling. However, primates fleeing human observers violate methodological assumptions, biasing the accuracy of resulting estimates. In this study, we used line transect distance sampling to study 5 primate species along 378 km...

Additional file 11 of An integrated in silico-in vitro approach for identifying therapeutic targets against osteoarthritis

Raphaëlle Lesage, Mauricio N. Ferrao Blanco, Roberto Narcisi, Tim Welting, Gerjo J. V. M. van Osch & Liesbet Geris
Additional file 11: Fig. S3. Screenshot of the user-friendly interface for the virtual chondrocytes App. The standalone Matlab-based applications can be launched and used without Matlab license, provided that the compiler Matlab Runtime is installed ( https://nl.mathworks.com/products/compiler/matlab-runtime.html ). The virtual chondrocyte initial state can be set as healthy or hypertrophic, allowing the user to test any scenarios. All the 60 components may be perturbed alone or in any sort of combination by forcing the variables...

sj-docx-1-cre-10.1177_02692155231152567 - Supplemental material for Effect of robot-assisted gait training on quality of life and depression in neurological impairment: A systematic review and meta-analysis

Meike den Brave, Charlotte Beaudart, Benoit Maertens de Noordhout, Vincent Gillot & Jean-Francois Kaux
Supplemental material, sj-docx-1-cre-10.1177_02692155231152567 for Effect of robot-assisted gait training on quality of life and depression in neurological impairment: A systematic review and meta-analysis by Meike den Brave, Charlotte Beaudart, Benoit Maertens de Noordhout, Vincent Gillot and Jean-Francois Kaux in Clinical Rehabilitation

Data from: Iterative ecological radiation and convergence during the evolutionary history of damselfishes (Pomacentridae)

Bruno Frédérich, Laurie Sorenson, Francesco Santini, Graham J. Slater & Michael E. Alfaro
Coral reef fishes represent one of the most spectacularly diverse assemblages of vertebrates on the planet, but our understanding of their mode of diversification remains limited. Here we test whether the diversity of the damselfishes (Pomacentridae), one of the most species-rich families of reef-associated fishes, was produced by a single or multiple adaptive radiation(s) during their evolutionary history. Tests of the tempo of lineage diversification using a time-calibrated phylogeny including 208 species revealed that crown...

Data from: The shepherds' tale: a genome-wide study across 9 dog breeds implicates two loci in the regulation of fructosamine serum concentration in Belgian shepherds

Simon K. G. Forsberg, Marcin Kierczak, Ingrid Ljungvall, Anne-Christine Merveille, Vassiliki Gouni, Maria Wiberg, Jakob Lundgren Willesen, Sofia Hanås, Anne-Sophie Lequarré, Louise Mejer Sørensen, Laurent Tiret, Kathleen McEntee, Eija Seppälä, Jørgen Koch, Géraldine Battaille, Hannes Lohi, Merete Fredholm, Valerie Chetboul, Jens Häggström, Örjan Carlborg, Kerstin Lindblad-Toh & Katja Höglund
Diabetes mellitus is a serious health problem in both dogs and humans. Certain dog breeds show high prevalence of the disease, whereas other breeds are at low risk. Fructosamine and glycated hemoglobin (HbA1c) are two major biomarkers of glycaemia where serum concentrations reflect glucose turnover over the past few weeks to months. In this study, we searched for genetic factors influencing variation in serum fructosamine concentration in healthy dogs using data from nine dog breeds....

Data from: Trait decoupling promotes evolutionary diversification of the trophic and acoustic system of damselfishes

Bruno Frédérich, Damien Olivier, Glenn Litsios, Michael E. Alfaro, Eric Parmentier & B. Frederich
Trait decoupling, wherein evolutionary release of constraints permits specialization of formerly integrated structures, represents a major conceptual framework for interpreting patterns of organismal diversity. However, few empirical tests of this hypothesis exist. A central prediction, that the tempo of morphological evolution and ecological diversification should increase following decoupling events, remains inadequately tested. In damselfishes (Pomacentridae), a ceratomandibular ligament links the hyoid bar and lower jaws, coupling two main morphofunctional units directly involved in both feeding...

Data from: GLO-Roots: an imaging platform enabling multidimensional characterization of soil-grown roots systems

Ruben Rellán-Álvarez, Guillaume Lobet, Heike Lindner, Pierre-Luc Pradier, Jose Sebastian, Muh-Ching Yee, Yu Geng, Charlotte Trontin, Therese LaRue, Amanda Schrager-Lavelle, Cara H. Haney, Rita Nieu, Julin Maloof, John P. Vogel & José R. Dinneny
Root systems develop different root types that individually sense cues from their local environment and integrate this information with systemic signals. This complex multi-dimensional amalgam of inputs enables continuous adjustment of root growth rates, direction and metabolic activity that define a dynamic physical network. Current methods for analyzing root biology balance physiological relevance with imaging capability. To bridge this divide, we developed an integrated imaging system called Growth and Luminescence Observatory for Roots (GLO-Roots) that...

Data from: The determinants of tropical forest deciduousness: disentangling the effects of rainfall and geology in central Africa

Dakis-Yaoba Ouédraogo, Adeline Fayolle, Sylvie Gourlet-Fleury, Frédéric Mortier, Vincent Freycon, Nicolas Fauvet, Suzanne Rabaud, Guillaume Cornu, Fabrice Bénédet, Jean-François Gillet, Richard Oslisly, Jean-Louis Doucet, Philippe Lejeune & Charly Favier
Understanding the environmental determinants of forests deciduousness i.e. proportion of deciduous trees in a forest stand, is of great importance when predicting the impact of ongoing global climate change on forests. In this study, we examine (i) how forest deciduousness varies in relation to rainfall and geology, and (ii) whether the influence of geology on deciduousness could be related to differences in soil fertility and water content between geological substrates. The study was conducted in...

Data from: Closing a gap in tropical forest biomass estimation: taking crown mass variation into account in pantropical allometries

Pierre Ploton, Nicholas Barbier, Stéphane Takoudjou Momo, Maxime Réjou-Méchain, Faustin Boyemba Bosela, Georges Chuyong, Gilles Dauby, Vincent Droissart, Adeline Fayolle, Rosa Calisto Goodman, Mathieu Henry, Narcisse Guy Kamdem, John Katembo Mukirania, David Kenfack, Moses Libalah, Alfred Ngomanda, Vivien Rossi, Bonaventure Sonké, Nicolas Texier, Duncan Thomas, Donatien Zebaze, Pierre Couteron, Uta Berger & Raphaël Pélissier
Accurately monitoring tropical forest carbon stocks is an outstanding challenge. Allometric models that consider tree diameter, height and wood density as predictors are currently used in most tropical forest carbon studies. In particular, a pantropical biomass model has been widely used for approximately a decade, and its most recent version will certainly constitute a reference in the coming years. However, this reference model shows a systematic bias for the largest trees. Because large trees are...

Data from: Teruelia diezii gen. et sp. nov.: an early polysporangiophyte from the Lower Devonian of the Iberian Peninsula

Borja Cascales-Miñana & Philippe Gerrienne
A new basal land plant, Teruelia diezii gen. et sp. nov., is described from the shallow-water marine deposits of the Lower Devonian (Lochkovian–Pragian) Nogueras Formation of the Iberian Peninsula (north Gondwana palaeocontinent). Teruelia is preserved as a compression fossil and consists of isotomously branched, robust stems terminated in large, fusiform, twisted sporangia. This morphology suggests that Teruelia is very probably equivalent to Aglaophyton, a permineralized early polysporangiophyte known up to now only from the Lower...

Data from: Maternal nutrition during pregnancy affects testicular and bone development, glucose metabolism and response to overnutrition in weaned horses up to two years

Camille Gautier, Luis Mendoza, Hélène Bouraima-Lelong, Isabelle Guenon, Pauline Peugnet, Cédric Dubois, Sylvaine Camous, Anne Tarrade, Morgane Robles, Didier Serteyn, Isabelle Caudron, Jean-Philippe Lejeune, Laurence Wimel, Michèle Dahirel & Pascale Chavatte-Palmer
Pregnant mares and post-weaning foals are often fed concentrates rich in soluble carbohydrates, together with forage. Recent studies suggest that the use of concentrates is linked to alterations of metabolism and the development of osteochondrosis in foals. The aim of this study was to determine if broodmare diet during gestation affects metabolism, osteoarticular status and growth of yearlings overfed from 20 to 24 months of age and/or sexual maturity in prepubertal colts. Twenty-four saddlebred mares...

Data from: Non-reef environments impact the diversification of extant jacks, remoras and allies (Carangoidei, Percomorpha)

Bruno Frederich, Giuseppe Marramà, Giorgio Carnevale & Francesco Santini
Various factors may impact the processes of diversification of a clade. In the marine realm, it has been shown that coral reef environments have promoted diversification in various fish groups. With the exception of requiem sharks, all the groups showing a higher level of diversity in reefs than in non-reef habitats have diets based predominantly on plankton, algae or benthic invertebrates. Here we explore the pattern of diversification of carangoid fishes, a clade that includes...

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  • University of Liège
  • KU Leuven
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  • Delft University of Technology
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  • Université Libre de Bruxelles
  • Royal Belgian Institute of Natural Sciences
  • South African National Biodiversity Institute
  • University of Aberdeen
  • University of Alaska Fairbanks