156 Works

Data from: Performance of glomerular filtration rate estimation equations in Congolese healthy adults: inopportunity of ethnic correction

Justine B. Bukabau, Ernest K. Sumaili, Etienne Cavalier, Hans Pottel, Bejos Kifakiou, Aliocha Nkodila, Jean-Robert R Makulo, Vieux M. Mokoli, Chantal V. Zinga, Augustin L. Longo, Yannick M. Engole, Yannick M. Nlandu, François B. Lepira, Nazaire M. Nseka, Jean-Marie Krzesinski, Pierre Delanaye, Jean Robert R. Makulo & Jean Marie Krzesinski
Context and objective: In the estimation of glomerular filtration rate (GFR), ethnicity is an important determinant. However, all existing equations have been built solely from Caucasian and Afro-American populations and they are potentially inaccurate for estimating GFR in African populations. We therefore evaluated the performance of different estimated GFR (eGFR) equations in predicting measured GFR (mGFR). Methods: In a cross-sectional study, 93 healthy adults were randomly selected in the general population of Kinshasa, Democratic Republic...

Data from: Maternal obesity increases insulin resistance, low-grade inflammation and osteochondrosis lesions in foals and yearlings until 18 months of age

Morgane Robles, Emilie Nouveau, Camille Gautier, Luis Mendoza, Cédric Dubois, Michèle Dahirel, Bénédicte Lagofun, Marie-Christine Aubrière, Jean-Philippe Lejeune, Isabelle Caudron, Isabelle Guenon, Catherine Viguié, Laurence Wimel, Hélène Bouraima-Lelong, Didier Serteyn, Anne Couturier-Tarrade, Pascale Chavatte-Palmer, M-C Aubrière & J-P Lejeune
Obesity is a growing concern in horses. The effects of maternal obesity on maternal metabolism and low-grade inflammation during pregnancy, as well as offspring growth, metabolism, low-grade inflammation, testicular maturation and osteochondrotic lesions until 18 months of age were investigated. Twenty-four mares were used and separated into two groups at insemination according to body condition score (BCS): Normal (N, n=10, BCS ≤4) and Obese (O, n=14, BCS ≥4.25). BCS and plasma glucose, insulin, triglyceride, urea,...

Data from: Architectural differences associated to functional traits among 45 coexisting tree species in central Africa

Grace Jopaul Loubota Panzou, Gauthier Ligot, Sylvie Gourlet-Fleury, Jean-Louis Doucet, Eric Forni, Jean-Joël Loumeto & Adeline Fayolle
1. Architectural traits that determine the light captured in a given environment are an important aspect of the life-history strategies of tropical tree species. In this study, we examined how interspecific variation in architectural traits is related to the functional traits of 45 coexisting tree species in central Africa. 2. At the tree level, we measured tree diameter, total height and crown dimensions for an average of 30 trees per species (range 14–72, total 968...

Data from: A genome-wide data assessment of the African lion (Panthera leo) population genetic structure and diversity in Tanzania

Nathalie Smitz, Olivia Jouvenet, Fredrick Ambwene Ligate, William-George Crosmary, Dennis Ikanda, Philippe Chardonnet, Alessandro Fusari, Kenny Meganck, François Gillet, Mario Melletti & Johan R. Michaux
The African lion (Panthera leo), listed as a vulnerable species on the IUCN Red List of Threatened Species (Appendix II of CITES), is mainly impacted by indiscriminate killing and prey base depletion. Additionally, habitat loss by land degradation and conversion has led to the isolation of some subpopulations, potentially decreasing gene flow and increasing inbreeding depression risks. Genetic drift resulting from weakened connectivity between strongholds can affect the genetic health of the species. In the...

Data from: Resolution of the ordinal phylogeny of mosses using targeted exons from organellar and nuclear genomes

Yang Liu, Matthew G. Johnson, Cymon J. Cox, Rafael Medina, Nicolas Devos, Alain Vanderpoorten, Lars Hedenäs, Neil E. Bell, James R. Shevock, Blanka Aguero, Dietmar Quandt, Norman J. Wickett, A. Jonathan Shaw & Bernard Goffinet
Mosses are a highly diverse lineage of land plants, whose diversification, spanning at least 400 million years, remains phylogenetically ambiguous due to the lack of fossils, massive early extinctions, late radiations, limited morphological variation, and conflicting signal among previously used markers. Here, we present phylogenetic reconstructions based on complete organellar exomes and a comparable set of nuclear genes for this major lineage of land plants. Our analysis of 142 species representing 29 of the 30...

Design, synthesis, and molecular dynamics simulation studies of quinoline derivatives as protease inhibitors against SARS-CoV-2

Vishal K. Singh, Himani Chaurasia, Priyanka Kumari, Anup Som, Richa Mishra, Ritika Srivastava, Farha Naaz, Anuradha Singh & Ramendra K. Singh
A new series of quinoline derivatives has been designed and synthesized as probable protease inhibitors (PIs) against severe acute respiratory syndrome coronavirus 2. In silico studies using DS v20.1.0.19295 software have shown that these compounds behaved as PIs while interacting at the allosteric site of target Mpro enzyme (6LU7). The designed compounds have shown promising docking results, which revealed that all compounds formed hydrogen bonds with His41, His164, Glu166, Tyr54, Asp187, and showed π-interaction with...

Design, synthesis, and molecular dynamics simulation studies of quinoline derivatives as protease inhibitors against SARS-CoV-2

Vishal K. Singh, Himani Chaurasia, Priyanka Kumari, Anup Som, Richa Mishra, Ritika Srivastava, Farha Naaz, Anuradha Singh & Ramendra K. Singh
A new series of quinoline derivatives has been designed and synthesized as probable protease inhibitors (PIs) against severe acute respiratory syndrome coronavirus 2. In silico studies using DS v20.1.0.19295 software have shown that these compounds behaved as PIs while interacting at the allosteric site of target Mpro enzyme (6LU7). The designed compounds have shown promising docking results, which revealed that all compounds formed hydrogen bonds with His41, His164, Glu166, Tyr54, Asp187, and showed π-interaction with...

Data from: Personality and gonadal development as sources of individual variation in response to GnRH challenge in female great tits

Samuel P. Caro, Charlotte A. Cornil, Kees Van Oers & Marcel E. Visser
Seasonal timing of reproduction is a key life-history trait, but we know little about the mechanisms underlying individual variation in female endocrine profiles associated with reproduction. In birds, 17β-estradiol is a key reproductive hormone that links brain neuroendocrine mechanisms, involved in information processing and decision making, to downstream mechanisms in the liver, where egg-yolk is produced. Here we test, using a simulated induction of the reproductive system through a GnRH-challenge, whether the ovary of pre-breeding...

Supplementary Information for Biogeography a key influence on distal forelimb variation in horses through the Cenozoic

Jamie MacLaren
Locomotion in terrestrial tetrapods is reliant on interactions between distal limb bones (e.g. metapodials and phalanges). The metapodial-phalangeal joint in horse (Equidae) limbs is highly specialised, facilitating vital functions (shock absorption; elastic recoil). While joint shape has changed throughout horse evolution, potential drivers of these modifications have not been quantitatively assessed. Here, I examine the morphology of the forelimb metacarpophalangeal (MCP) joint of horses and their extinct kin (palaeotheres) using geometric morphometrics and disparity analyses,...

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 12 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 12: Table S4. Targets and associated small molecules or growth factors for in vitro validation. The first row indicates the targets to be perturbed, [+] stands for activation while [-] stands for inhibition. The name (resp. cat number) of the small molecule or growth factor employed to achieve that effect is indicated in the row called ‘Molecule name’ (resp. ‘Cat n°’).

Additional file 14 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 14: Fig. S5. Illustration of the algorithm for the asynchronous updating of variables with a simplified (3 nodes) example network. The network represents interactions happening in one of the subnetworks (protein= fast reactions or genetic = slow reactions). Inhibitions are represented in red and activations are in black. The mathematical rules corresponding to the network are displayed. If the rules result in a value lower than 0 (resp. higher than 1), the value...

Additional file 1 of Predictors of nursing home admission in the older population in Belgium: a longitudinal follow-up of health interview survey participants

Finaba Berete, Stefaan Demarest, Rana Charafeddine, Karin De Ridder, Johan Vanoverloop, Herman Van Oyen, Olivier Bruyère & Johan Van der Heyden
Additional file 1.

Predictors of nursing home admission in the older population in Belgium: a longitudinal follow-up of health interview survey participants

Finaba Berete, Stefaan Demarest, Rana Charafeddine, Karin De Ridder, Johan Vanoverloop, Herman Van Oyen, Olivier Bruyère & Johan Van der Heyden
Abstract Background This study examines predictors of nursing home admission (NHA) in Belgium in order to contribute to a better planning of the future demand for nursing home (NH) services and health care resources. Methods Data derived from the Belgian 2013 health interview survey were linked at individual level with health insurance data (2012 tot 2018). Only community dwelling participants, aged ≥65 years at the time of the survey were included in this study (n...

Additional file 2 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 2: Supplementary materials and methods. Information regarding supplemental methods. Figure S1. PSMC plot for Dicrostonyx torquatus using three different mutation rates estimated for mouse (Mus musculus).

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
Abstract Background Ancient DNA studies suggest that Late Pleistocene climatic changes had a significant effect on population dynamics in Arctic species. The Eurasian collared lemming (Dicrostonyx torquatus) is a keystone species in the Arctic ecosystem. Earlier studies have indicated that past climatic fluctuations were important drivers of past population dynamics in this species. Results Here, we analysed 59 ancient and 54 modern mitogenomes from across Eurasia, along with one modern nuclear genome. Our results suggest...

Additional file 3 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 3: Table S2. List of variables and mouse genes correspondence. All mathematical variables and the corresponding node in the network have names written in upper cases and do not reflect the official human or mouse nomenclatures. To relate those variables to actual genes more easily, we provide this table of correspondence. A related mouse gene name and NCBI ID is indicated for each variable. Nevertheless, this is not exhaustive since some variables represent...

Additional file 6 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 6: Data S2. GRN inference and validation. (Microsoft Excel Worksheet). The GRN inference with the 3 algorithms and the consensus matrix are reported. We have set stringent rules and only interactions that were inferred by the 3 algorithms were included in the mechanistic model: those interactions are all reported in Fig. 2D. The validity of the inferred interactions was investigated by searching the GeneCard database. The relevant GeneHancer IDs are reported when supportive...

Additional file 8 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 8: Data S3. Attractors complete protein and gene expression profiles. (Microsoft Excel Worksheet). The predicted profiles of the 3 attractors are reported for all variables. The dataset contains the values of the fast sub-variables (i.e. protein subnetwork), slow sub-variables (i.e. gene subnetwork) and the global functional activity.

Data from: Partitioning the relative contribution of one-phase and two-phase seed dispersal when evaluating seed dispersal effectiveness

Laurence Culot, Marie-Claude Huynen & Eckhard W. Heymann
Seed dispersal effectiveness (SDE) is a conceptual framework that aims at quantifying the contribution of seed dispersal vectors to plant fitness. While it is well recognized that diplochorous dispersal systems, characterized by two successive dispersal steps performed by two different vectors (Phase I = primary seed dispersal and Phase II = secondary seed dispersal) are common in temperate and tropical regions, little attention has been given to distinguishing the relative contribution of one-phase and two-phase...

Data from: Postglacial climate changes and rise of three ecotypes of harbor porpoises, Phocoena phocoena, in western Palearctic waters

Michaël C. Fontaine, Kathleen Roland, Isabelle Calves, Frederic Austerlitz, Friso P. Palstra, Krystal A. Tolley, Sean Ryan, Marisa Ferreira, Thierry Jauniaux, Angela Llavona, Bayram Öztürk, Ayaka A. Öztürk, Vincent Ridoux, Emer Rogan, Ursula Siebert, Marina Sequeira, Gísli A. Vikingsson, Asunción Borrell, Johan R. Michaux & Alex Aguilar
Despite no obvious barriers to gene flow in the marine realm, environmental variation and ecological specializations can lead to genetic differentiation in highly mobile predators. Here, we investigated the genetic structure of the harbor porpoise over the entire species distribution range in western Palearctic waters. Combined analyses of ten microsatellite loci and a 5,085 bases-pairs portion of the mitochondrial genome revealed the existence of three ecotypes, equally divergent at the mitochondrial genome, distributed in the...

Data from: The scent of inbreeding: male sex pheromones betray inbred males

Erik Van Bergen, Paul M. Brakefield, Stéphanie Heuskin, Bas J. Zwaan & Caroline M. Nieberding
Inbreeding depression results from mating among genetically related individuals and impairs reproductive success. The decrease in male mating success is usually attributed to an impact on multiple fitness-related traits that reduce the general condition of inbred males. Here we find that the production of the male sex pheromone is reduced significantly by inbreeding in the butterfly Bicyclus anynana. Other traits indicative of the general condition, including flight performance, are also negatively affected in male butterflies...

Data from: How bees deter elephants: beehive trials with forest elephants (Loxodonta africana cyclotis) in Gabon

Steeve Ngama, Lisa Korte, Jérôme Bindelle, Cédric Vermeulen & John R. Poulsen
In Gabon, like elsewhere in Africa, crops are often sources of conflict between humans and wildlife. Wildlife damage to crops can drastically reduce income, amplifying poverty and creating a negative perception of wild animal conservation among rural people. In this context, crop-raiding animals like elephants quickly become “problem animals”. To deter elephants from raiding crops beehives have been successfully employed in East Africa; however, this method has not yet been tested in Central Africa. We...

Genomic footprints of recovery in the European bison

Tom Druet, Kamil Oleński, Laurence Flori, Amandine Bertrand, Wanda Olech, Malgorzata Tokarska, Stanislaw Kaminski & Mathieu Gautier
After extinction in the wild in the beginning of the twentieth century, the European bison has been successfully recovered in two distinct genetic lines from only twelve and seven captive founders. We here aimed at characterizing the levels of realized inbreeding in these two restored lines to provide empirical insights into the genomic footprints left by population recovery from a small number of founders. To that end, we genotyped 183 European bison born over the...

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