160 Works

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: Bayesian analysis of hybridization and introgression between the endangered european mink (Mustela lutreola) and the polecat (Mustela putorius)

Maria Teresa Cabria, Johan R Michaux, Benjamín J Gómez-Moliner, Dimitry Skumatov, Tiit Maran, Pascal Fournier, Javier López De Luzuriaga & Rafael Zardoya
Human-mediated global change will probably increase the rates of natural hybridization and genetic introgression between closely related species, and this will have major implications for conservation of the taxa involved. In this study, we analyse both mitochondrial and nuclear data to characterize ongoing hybridization and genetic introgression between two sympatric sister species of mustelids, the endangered European mink (Mustela lutreola) and the more abundant polecat (M. putorius). A total of 317 European mink, 114 polecats...

Data from: Genome-wide single nucleotide polymorphism (SNP) identification and characterization in a non-model organism, the African buffalo (Syncerus caffer), using next generation sequencing

Nathalie Smitz, Pim Van Hooft, Rasmus Heller, Daniel Cornélis, Philippe Chardonnet, Robert Kraus, Ben J. Greyling, Richard Crooijmans, Martien Groenen, Johan Michaux & Ben Greyling
This study aimed to develop a set of SNP markers with high resolution and accuracy within the African buffalo. Such a set can be used, among others, to depict subtle population genetic structure for a better understanding of buffalo population dynamics. In total, 18.5 million DNA sequences of 76 bp were generated by next generation sequencing on an Illumina Genome Analyzer II from a reduced representation library using DNA from a panel of 13 African...

Data from: Phenotype classification of zebrafish embryos by supervised learning

Nathalie Jeanray, Raphaël Marée, Benoist Pruvot, Olivier Stern, Pierre Geurts, Louis Wehenkel & Marc Muller
Zebrafish is increasingly used to assess biological properties of chemical substances and thus is becoming a specific tool for toxicological and pharmacological studies. The effects of chemical substances on embryo survival and development are generally evaluated manually through microscopic observation by an expert and documented by several typical photographs. Here, we present a methodology to automatically classify brightfield images of wildtype zebrafish embryos according to their defects by using an image analysis approach based on...

Data from: Divergent evolutionary morphology of the axial skeleton as a potential key innovation in modern cetaceans

Amandine Gillet, Bruno Frederich & Eric Parmentier
Cetaceans represent the most diverse clade of extant marine tetrapods. Although restructuring of oceans could have contributed to their diversity, other factors might also be involved. Similar to ichthyosaurs and sharks, variation of morphological traits could have promoted the colonization of new ecological niches and supported their diversification. By combining morphological data describing the axial skeleton of 73 cetacean species with phylogenetic comparative methods, we demonstrate that the vertebral morphology of cetaceans is associated to...

Data from: Phylotranscriptomic consolidation of the jawed vertebrate timetree

Iker Irisarri, Denis Baurain, Henner Brinkmann, Frédéric Delsuc, Jean-Yves Sire, Alexander Kupfer, Jörn Petersen, Michael Jarek, Axel Meyer, Miguel Vences & Hervé Philippe
Phylogenomics is extremely powerful but introduces new challenges as no agreement exists on “standards” for data selection, curation and tree inference. We use jawed vertebrates (Gnathostomata) as model to address these issues. Despite considerable efforts in resolving their evolutionary history and macroevolution, few studies have included a full phylogenetic diversity of gnathostomes and some relationships remain controversial. We tested a novel bioinformatic pipeline to assemble large and accurate phylogenomic datasets from RNA sequencing and find...

Data from: Body shape convergence driven by small size optimum in marine angelfishes

Bruno Frédérich, Francesco Santini, Nicolai Konow, Joseph Schnitzler, David Lecchini & Michael E. Alfaro
Convergent evolution of small body size occurs across many vertebrate clades and may reflect an evolutionary response to shared selective pressures. However it remains unclear if other aspects of phenotype undergo convergent evolution in miniaturized lineages. Here we present a comparative analysis of body size and shape evolution in marine angelfishes (Pomacanthidae), a reef fish family characterized by repeated transitions to small body size. We ask if lineages that evolve small sizes show convergent evolution...

The use of psychedelics in the treatment of disorders of consciousness. An interview with Olivia Gosseries by Charlotte Martial.

Olivia Gosseries & Charlotte Martial
In this interview, we discuss the use of psychedelic drugs as a promising treatment in disorders of consciousness. Psilocybin, a classic psychedelic, is currently undergoing substantial clinical investigations in healthy volunteers, but also in clinical populations. Recently, experts in the field of psychedelics have addressed the attractive possibility to use such psychedelics on patients suffering from disorders of consciousness. Building on her empirical and theoretical research on disorders of consciousness, Olivia Gosseries gives us her...

Mechanistic insight on the inhibition of D, D-carboxypeptidase from Mycobacterium tuberculosis by β-lactam antibiotics: an ONIOM acylation study

Thandokuhle Ntombela, Anya Seupersad, Sibusiso Maseko, Collins U. Ibeji, Gideon Tolufashe, Siyabonga Innocent Maphumulo, Tricia Naicker, Sooraj Baijnath, Glenn E. M. Maguire, Thavendran Govender, Gyanu Lamichhane, Bahareh Honarparvar & Hendrik G. Kruger
Mycobacterium tuberculosis cell wall is intricate and impermeable to many agents. A D, D-carboxypeptidase (DacB1) is one of the enzymes involved in the biosynthesis of cell wall peptidoglycan and catalyzes the terminal D-alanine cleavage from pentapeptide precursors. Catalytic activity and mechanism by which DacB1 functions is poorly understood. Herein, we investigated the acylation mechanism of DacB1 by β-lactams using a 6-membered ring transition state model that involves a catalytic water molecule in the reaction pathway....

Mechanistic insight on the inhibition of D, D-carboxypeptidase from Mycobacterium tuberculosis by β-lactam antibiotics: an ONIOM acylation study

Thandokuhle Ntombela, Anya Seupersad, Sibusiso Maseko, Collins U. Ibeji, Gideon Tolufashe, Siyabonga Innocent Maphumulo, Tricia Naicker, Sooraj Baijnath, Glenn E. M. Maguire, Thavendran Govender, Gyanu Lamichhane, Bahareh Honarparvar & Hendrik G. Kruger
Mycobacterium tuberculosis cell wall is intricate and impermeable to many agents. A D, D-carboxypeptidase (DacB1) is one of the enzymes involved in the biosynthesis of cell wall peptidoglycan and catalyzes the terminal D-alanine cleavage from pentapeptide precursors. Catalytic activity and mechanism by which DacB1 functions is poorly understood. Herein, we investigated the acylation mechanism of DacB1 by β-lactams using a 6-membered ring transition state model that involves a catalytic water molecule in the reaction pathway....

Data from: Shale-hosted biota from the Dismal Lakes Group in Arctic Canada supports an early Mesoproterozoic diversification of eukaryotes

Corentin C. Loron, Galen P. Halverson, Robert H. Rainbird, Tom Skulski, Elizabeth C. Turner & Emmanuelle J. Javaux
The Mesoproterozoic is an important era for the development of eukaryotic organisms in oceans. The earliest unambiguous eukaryotic microfossils are reported in late Paleoproterozoic shales from China and Australia. During the Mesoproterozoic, eukaryotes diversified in taxonomy, metabolism and ecology, with the advent of eukaryotic photosynthesis, osmotrophy, multicellularity, and predation. Despite these biological innovations, their fossil record is scarce before the late Mesoproterozoic. Here, we document an assemblage of organic-walled microfossils from the 1590-1270 Ma Dismal...

Perineuronal nets in HVC and plasticity in male canary song

Jacques Balthazart
Songbirds learn their vocalizations during developmental sensitive periods of song memorization and sensorimotor learning. Some seasonal songbirds, called open-ended learners, recapitulate transitions from sensorimotor learning and song crystallization on a seasonal basis during adulthood. In adult male canaries, sensorimotor learning occurs each year in autumn and leads to modifications of the syllable repertoire during successive breeding seasons. We previously showed that perineuronal nets (PNN) expression in song control nuclei decreases during this sensorimotor learning period....

Data from: Seed and pollen dispersal distances in two African legume timber trees and their reproductive potential under selective logging

Olivier J. Hardy, Boris Delaide, Hélène Hainaut, Jean-François Gillet, Pauline Gillet, Esra Kaymak, Nina Vankerckhove, Jérôme Duminil & Jean-Louis Doucet
The natural regeneration of tree species depends on seed and pollen dispersal. To assess if limited dispersal could be critical for the sustainability of selective logging practices, we performed parentage analyses in two Central African legume canopy species displaying contrasted floral and fruit traits: Distemonanthus benthamianus and Erythrophleum suaveolens. We also developed new tools linking forward dispersal kernels with backward migration rates to better characterize long-distance dispersal. Much longer pollen dispersal in D. benthamianus (mean...

Near-death experience in the public debate: Not reflecting the current scientific evidence

Charlotte Martial
On January 6th 2021, Netflix released a new docu-series called "Surviving Death", whose first episode is dedicated to near-death experiences (NDEs). We asked ALIUS member and NDE expert Charlotte Martial (neuropsychologist and post-doctoral researcher at the Coma Science Group) to share her perspective about this episode. She watched it with great interest and shares her enthusiasm that popular media addresses this fascinating and growing area of research, which has not received the scientific and medical...

El miedo a los estereotipos en Qué solos se quedan los muertos, de Mempo Giardinelli

Kristine Vanden Berghe
pp. 70-83. We analyze Qué solos se quedan los muertos, a novel about crimes in the Mexican city of Zacatecas published in 1985 by Mempo Giardinelli, an Argentine writer who was exiled in Mexico. This analysis about how the author represents his host country, Mexican literature and the genre of crime fiction shows that he tries to avoid the use of national (Mexico) and genre (the crime novel) stereotypes. In this way, he aspires to...

Dataset to study the population genomics of introduced Nile tilapia (Oreochromis niloticus (Linnaeus, 1758)) in the Democratic Republic of the Congo: repeated introductions since colonial times with multiple sources

Mare Geraerts, Carl Vangestel, Tom Artois, Jorge Manuel De Oliveira Fernandes, Michiel W. P. Jorissen, Auguste Chocha Manda, Célestin Danadu Mizani, Karen Smeets, Jos Snoeks, Gontran Sonet, Yang Tingbao, Maarten Van Steenberge, Emmanuel Vreven, Soleil Lunkayilakio Wamuini, Maarten P. M. Vanhove & Tine Huyse
During colonial times, Nile tilapia Oreochromis niloticus (Linnaeus, 1758) was introduced in non-native parts of the Congo Basin (Democratic Republic of the Congo, DRC) for the first time. Currently, it is the most farmed cichlid in the DRC, and is present throughout the Congo Basin. Although Nile tilapia has been reported as an invasive species, documentation of historical introductions into this basin and its consequences are scant. Here, we study the genetic consequences of these...

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