87 Works

Data from: No evidence of foliar disease impact on crop root functional strategies and soil microbial communities: What does this mean for organic coffee?

Stephanie Gagliardi, Jacques Avelino, Roberta Fulthorpe, Elias De Melo Virginio Filho & Marney Isaac
Global climate change is increasing pest and pathogen pressures on plant communities, deteriorating optimal plant functioning. In plant communities, root functional trait expression and microbial communities are important indicators of plant functioning belowground, and, when confronted with pathogens aboveground, can simultaneously reflect plant defence strategies. Yet, while research is continuing to emerge on the response of root functional traits and microbial processes to pathogens aboveground, little work has investigated these interactions in tree-crops, or the...

Global flyway evolution in red knots Calidris canutus and genetic evidence for a Nearctic refugium

Jesse Conklin, Yvonne Verkuil, Phil Battley, Chris Hassell, Job Ten Horn, James Johnson, Pavel Tomkovich, Allan Baker, Theunis Piersma & Michaël Fontaine
Present-day ecology and population structure are the legacies of past climate and habitat perturbations, and this is particularly true for species that are widely distributed at high latitudes. The red knot, Calidris canutus, is an arctic-breeding, long-distance migratory shorebird with six recognized subspecies defined by differences in morphology, migration behavior, and annual-cycle phenology, in a global distribution thought to have arisen just since the Last Glacial Maximum (LGM). We used nextRAD sequencing of 10,881 single-nucleotide...

Accuracy of clinicians’ ability to predict the need for renal replacement therapy: a prospective multicenter study

Alexandre Sitbon, Michael Darmon, Guillaume Geri, Paul Jaubert, Pauline Lamouche-Wilquin, Clément Monet, Lucie Le Fèvre, Marie Baron, Marie-Line Harlay, Côme Bureau, Olivier Joannes-Boyau, Claire Dupuis, Damien Contou, Virginie Lemiale, Marie Simon, Christophe Vinsonneau, Clarisse Blayau, Frederic Jacobs & Lara Zafrani
Abstract Purpose Identifying patients who will receive renal replacement therapy (RRT) during intensive care unit (ICU) stay is a major challenge for intensivists. The objective of this study was to evaluate the performance of physicians in predicting the need for RRT at ICU admission and at acute kidney injury (AKI) diagnosis. Methods Prospective, multicenter study including all adult patients hospitalized in 16 ICUs in October 2020. Physician prediction was estimated at ICU admission and at...

Additional file 1 of European Headache Federation (EHF) consensus on the definition of effective treatment of a migraine attack and of triptan failure

Simona Sacco, Christian Lampl, Faisal Mohammad Amin, Mark Braschinsky, Christina Deligianni, Derya Uludüz, Jan Versijpt, Anne Ducros, Raquel Gil-Gouveia, Zaza Katsarava, Paolo Martelletti, Raffaele Ornello, Bianca Raffaelli, Deirdre M. Boucherie, Patricia Pozo-Rosich, Margarita Sanchez-del-Rio, Alexandra Sinclair, Antoinette Maassen van den Brink & Uwe Reuter
Additional file 1: Figure S1. PRISMA flowchart of systematic review. Table S1. Pain relief at different timepoints. Table S2. Pain relief and pain-free at 2 hours. Table S3. Headache recurrence within 24 hours. Table S4. Rescue medication. Table S5. Response in triptan non-responders. Table S6. Comparisons of different triptan formulations. Table S7. Comparisons between early and late treatment with triptans. Table S8. Agreement on questions submitted in Round 1. Table S9. Conflicts of interest of...

European Headache Federation (EHF) consensus on the definition of effective treatment of a migraine attack and of triptan failure

Simona Sacco, Christian Lampl, Faisal Mohammad Amin, Mark Braschinsky, Christina Deligianni, Derya Uludüz, Jan Versijpt, Anne Ducros, Raquel Gil-Gouveia, Zaza Katsarava, Paolo Martelletti, Raffaele Ornello, Bianca Raffaelli, Deirdre M. Boucherie, Patricia Pozo-Rosich, Margarita Sanchez-del-Rio, Alexandra Sinclair, Antoinette Maassen van den Brink & Uwe Reuter
Abstract Background Triptans are migraine-specific acute treatments. A well-accepted definition of triptan failure is needed in clinical practice and for research. The primary aim of the present Consensus was to provide a definition of triptan failure. To develop this definition, we deemed necessary to develop as first a consensus definition of effective treatment of an acute migraine attack and of triptan-responder. Main body The Consensus process included a preliminary literature review, a Delphi round and...

Additional file 2 of Genomic characterization of peste des petits ruminants vaccine seed “45G37/35-k”, Russia

Olivier Kwiatek, Geneviève Libeau, Samia Guendouz, Chloé Corbanini, Andrey Gogin, Andrey Lunitsin, Irina Sindryakova, Denis Koblasov & Arnaud Bataille
Additional file 2. Distribution of nucleotide and amino acid differences separating the PPR vaccine strains Nigeria/75/1 (Nig75/1) and 45G37/35-k (FRCVM).

Genomic characterization of peste des petits ruminants vaccine seed “45G37/35-k”, Russia

Olivier Kwiatek, Geneviève Libeau, Samia Guendouz, Chloé Corbanini, Andrey Gogin, Andrey Lunitsin, Irina Sindryakova, Denis Koblasov & Arnaud Bataille
Abstract Production of peste des petits ruminants (PPR) vaccines in Russia is based on two attenuated virus strains (“45G37/35-k” and “ARRIAH”) of common origin. Here, the identity of the strain PPRV/45G37/35-k was investigated using a full genome, Illumina deep sequencing approach. Phylogenomic analysis showed that PPRV/45G37/35-k belongs to the same lineage as the widely used PPRV vaccine strain Nigeria/75/1 (lineage II). However, 248 nucleotide differences separate the genomes of these vaccine strains, indicating that the...

A beneficiary-centred strategy to assess the performance of the cascade of PMTCT_Burkina Faso_Appendix.pdf

Léticia Sakana, Anaïs Mennecier, paulin fao, Souleymane Tassembedo, Jean-Pierre Molès, Dramane Kania, Ajani Ousmane Taofiki, Frank Edgar Kadeba, Ibrahima Diallo, Sabrina Eymard-Duvernay, Morgana D’Ottavi, Nicolas Meda, Beatriz Mosqueira, Philippe Van de Perre & Nicolas Nagot
Cross sectional study questionnaire

A beneficiary-centred strategy to assess the performance of the cascade of PMTCT_Burkina Faso_Appendix.pdf

Léticia Sakana, Anaïs Mennecier, paulin fao, Souleymane Tassembedo, Jean-Pierre Molès, Dramane Kania, Ajani Ousmane Taofiki, Frank Edgar Kadeba, Ibrahima Diallo, Sabrina Eymard-Duvernay, Morgana D’Ottavi, Nicolas Meda, Beatriz Mosqueira, Philippe Van de Perre & Nicolas Nagot
Cross sectional study questionnaire

Hospitalizations for infections in primary Sjögren’s syndrome patients: a nationwide incidence study

Radjiv Goulabchand, Alain Makinson, Jacques Morel, Philine Witkowski-Durand-Viel, Nicolas Nagot, Paul Loubet, Camille Roubille, Danièle Noel, David Morquin, Kim Henry, Thibault Mura & Philippe Guilpain
Primary Sjögren’s syndrome (pSS) is an autoimmune disease with increased risk of infections. Here, we assessed whether pSS patients were at higher risk of hospitalization for community and opportunistic infections. We selected newly hospitalized pSS patients between 2011 and 2018, through a nationwide population-based retrospective study using the French Health insurance database. We compared the incidence of hospitalization for several types of infections (according to International Classification for Disease codes, ICD-10) between pSS patients and...

Cellules souches somatiques et hématopoïèse chez le mollusque

Patricia Cavelier, Julien Cau, Jean Marc Strub, Mohamed Jemaa, Nathalie Morin & Claude Delsert
L’origine du renouvellement des tissus fait débat chez le mollusque car aucune évidence de cellules souches n’a été montrée à ce jour au sein de ce vaste phylum. Cette question est d’autant plus fondamentale que la croissance se fait tout au long de la vie du mollusque et que ce groupe renferme les animaux vivants les plus vieux connus, tels ces spécimens du bivalve Arctica islandica âgés de plus de 500 ans. Par ailleurs, l’origine...

Additional file 1 of Joint modeling strategy for using electronic medical records data to build machine learning models: an example of intracerebral hemorrhage

Jianxiang Tang, Xiaoyu Wang, Hongli Wan, Chunying Lin, Zilun Shao, Yang Chang, Hexuan Wang, Yi Wu, Tao Zhang & Yu Du
Additional file 1. Additional file showed the performance with 95% CI of all 84 combinations of joint modeling strategy.

Host-plant adaptation as a driver of incipient speciation in the fall armyworm (Spodoptera frugiperda)

Estelle Fiteni, Karine Durand, Sylvie Gimenez, Robert L. Meagher, Fabrice Legeai, Gael J. Kergoat, Nicolas Nègre, Emmanuelle d’Alençon & Kiwoong Nam
Abstract Background Divergent selection on host-plants is one of the main evolutionary forces driving ecological speciation in phytophagous insects. The ecological speciation might be challenging in the presence of gene flow and assortative mating because the direction of divergence is not necessarily the same between ecological selection (through host-plant adaptation) and assortative mating. The fall armyworm (FAW), a major lepidopteran pest species, is composed of two sympatric strains, corn and rice strains, named after two...

3D Ecoli nucleoid stained with SYBR-Gold

Simona Streckaite, Dmitrij Frolov, Jevgenij Chmeliov, Andrius Gelzinis, Cristian Ilioaia, Sylvie Rimsky, Rienk van Grondelle, Leonas Valkunas, Andrew Gall & Bruno Robert
Movie S1 shows volumetric 3D reconstruction of the E. coli bacterial chromatin stained with SYBR® Gold—a rotation around y axis. The sample was scanned with 40 nm x & y steps, and 200 nm z steps, λexc = 488 nm, emission collected at 505–545 nm window. 3D reconstruction was obtained from 12 planes.

Plant community impact on productivity: trait diversity or key(stone) species effects?

Philipp Brun, Cyrille Violle, David Mouillot, Nicolas Mouquet, Brian Enquist, François Munoz, Tamara Munkemuller, Annette Ostling, Niklaus Zimmermann & Wilfried Thuiller
Outside controlled experimental plots, the impact of community attributes on primary productivity has rarely been compared to that of individual species. Here, we identified plant species of high importance for productivity (key species) in >29,000 diverse grassland communities in the European Alps, and compared their effects with those of community-level measures of functional composition (weighted means, variances, skewness, and kurtosis). After accounting for the environment, the five most important key species jointly explained more deviance...

Taxonomy based on limited genomic markers may underestimates species diversity of rockhopper penguins and threaten their conservation

María José Frugone, Theresa Cole, María Eugenia López, Gemma Clucas, Pável Matos-Maraví, Nicolás Lois, Pierre Pistorius, Francesco Bonadonna, Phil Trathan, Andrea Polanowski, Barbara Wienecke, Andrea Raya-Rey, Klemens Pütz, Antje Steinfurth, Ke Bi, Cynthia Wang-Claypool, Rauri C. K. Bowie, Jonathan Waters, Elie Poulin & Juliana Vianna
Delimiting recently diverged species is challenging. During speciation, genetic differentiation may be distributed unevenly across the genome, as different genomic regions can be subject to different selective pressures and evolutionary histories. Reliance on limited numbers of genetic markers that may be underpowered can make species delimitation even more challenging, potentially resulting in taxonomic inconsistencies. Rockhopper penguins of the genus Eudyptes comprise three broadly recognized taxa: northern (E. moseleyi), southern (E. chrysocome), and eastern rockhopper (E....

Does colour impact responses to images in geckos?

Ylenia Chiari, Nathan Katlein, Miranda Ray, Anna Wilkinson, Julien Claude, Maria Kiskowski, Bin Wang & Scott Glaberman
Animals are exposed to different visual stimuli that influence how they perceive and interact with their environment. Visual information such as shape and colour can help the animal detect, discriminate and make appropriate behavioural decisions for mate selection, communication, camouflage, and foraging. In all major vertebrate groups, it has been shown that certain species can discriminate and prefer certain colours and that colours may increase the response to a stimulus. However, since colour is often...

Joint analysis of microsatellites and flanking sequences enlightens complex demographic history of interspecific gene flow and vicariance in rear-edge oak populations

Olivier Lepais, Abdeldjalil Aissi, Errol Véla & Yassine Beghami
Inference of recent population divergence requires fast evolving markers and necessitates to differentiate shared genetic variation caused by ancestral polymorphism and gene flow. Theoretical research shows that the use of compound marker systems integrating linked polymorphisms with different mutational dynamics, such as a microsatellite and its flanking sequences, can improve estimation of population structure and inference of demographic history, especially in the case of complex population dynamics. However, empirical application in natural populations has so...

Additional file 1 of A low-cost genomics workflow enables isolate screening and strain-level analyses within microbiomes

Jon G. Sanders, Weiwei Yan, Deus Mjungu, Elizabeth V. Lonsdorf, John A. Hart, Crickette M. Sanz, David B. Morgan, Martine Peeters, Beatrice H. Hahn & Andrew H. Moeller
Additional file 1: Figure S1. Alluvial plot of protocol efficiency. Figure S2. Relationship between assembly quality and library concentration. Figure S3. Intraspecific nucleotide diversity. Figure S4. Genomic dissimilarity within 16S haplotypes.

Additional file 2 of A low-cost genomics workflow enables isolate screening and strain-level analyses within microbiomes

Jon G. Sanders, Weiwei Yan, Deus Mjungu, Elizabeth V. Lonsdorf, John A. Hart, Crickette M. Sanz, David B. Morgan, Martine Peeters, Beatrice H. Hahn & Andrew H. Moeller
Additional file 2: Table S1. Equipment sourcing and alternatives. Table S2. Sample information. Table S3. Culturing information. Table S4. Cost estimates.

A low-cost genomics workflow enables isolate screening and strain-level analyses within microbiomes

Jon G. Sanders, Weiwei Yan, Deus Mjungu, Elizabeth V. Lonsdorf, John A. Hart, Crickette M. Sanz, David B. Morgan, Martine Peeters, Beatrice H. Hahn & Andrew H. Moeller
Abstract Earth’s environments harbor complex consortia of microbes that affect processes ranging from host health to biogeochemical cycles. Understanding their evolution and function is limited by an inability to isolate genomes in a high-throughput manner. Here, we present a workflow for bacterial whole-genome sequencing using open-source labware and the OpenTrons robotics platform, reducing costs to approximately $10 per genome. We assess genomic diversity within 45 gut bacterial species from wild-living chimpanzees and bonobos. We quantify...

Accuracy of clinicians’ ability to predict the need for renal replacement therapy: a prospective multicenter study

Alexandre Sitbon, Michael Darmon, Guillaume Geri, Paul Jaubert, Pauline Lamouche-Wilquin, Clément Monet, Lucie Le Fèvre, Marie Baron, Marie-Line Harlay, Côme Bureau, Olivier Joannes-Boyau, Claire Dupuis, Damien Contou, Virginie Lemiale, Marie Simon, Christophe Vinsonneau, Clarisse Blayau, Frederic Jacobs & Lara Zafrani
Abstract Purpose Identifying patients who will receive renal replacement therapy (RRT) during intensive care unit (ICU) stay is a major challenge for intensivists. The objective of this study was to evaluate the performance of physicians in predicting the need for RRT at ICU admission and at acute kidney injury (AKI) diagnosis. Methods Prospective, multicenter study including all adult patients hospitalized in 16 ICUs in October 2020. Physician prediction was estimated at ICU admission and at...

Additional file 1 of Host-plant adaptation as a driver of incipient speciation in the fall armyworm (Spodoptera frugiperda)

Estelle Fiteni, Karine Durand, Sylvie Gimenez, Robert L. Meagher, Fabrice Legeai, Gael J. Kergoat, Nicolas Nègre, Emmanuelle d’Alençon & Kiwoong Nam
Additional file 1: Table S1. Summary statistics of genome assemblies showing contiguity and correctness of the assemblies (BUSCO) generated in this study and other published assemblies. Table S2. The information of each sample used in this study. Table S3. Position of targets of selective sweeps specific to the corn or grass group. Table S5. Summary statistics of genome assemblies showing contiguity and correctness of the assemblies generated using SALSA2 and 3D-DNA. Table S6. The list...

Intensified tuberculosis treatment to reduce the mortality of HIV-infected and uninfected patients with tuberculosis meningitis (INTENSE-TBM): study protocol for a phase III randomized controlled trial

Thomas Maitre, Maryline Bonnet, Alexandra Calmy, Mihaja Raberahona, Rivonirina Andry Rakotoarivelo, Niaina Rakotosamimanana, Juan Ambrosioni, José M. Miró, Pierre Debeaudrap, Conrad Muzoora, Angharad Davis, Graeme Meintjes, Sean Wasserman, Robert Wilkinson, Serge Eholié, Frédéric Ello Nogbou, Maria-Camilla Calvo-Cortes, Corine Chazallon, Vanessa Machault, Xavier Anglaret & Fabrice Bonnet
Abstract Background Tuberculous meningitis (TBM) is the most lethal and disabling form of tuberculosis (TB), particularly in sub-Saharan Africa. Current anti-TB treatment is poorly effective since TBM mortality reaches 40% in HIV-negative patients and up to 70% in HIV-co-infected patients. To reduce TBM-induced morbidity and mortality, the INTENSE-TBM trial evaluates two interventions in both HIV-infected and uninfected patients: an anti-TB treatment intensification using oral high-dose rifampicin (35 mg/kg daily) and linezolid (1200 mg daily and...

Hospitalizations for infections in primary Sjögren’s syndrome patients: a nationwide incidence study

Radjiv Goulabchand, Alain Makinson, Jacques Morel, Philine Witkowski-Durand-Viel, Nicolas Nagot, Paul Loubet, Camille Roubille, Danièle Noel, David Morquin, Kim Henry, Thibault Mura & Philippe Guilpain
Primary Sjögren’s syndrome (pSS) is an autoimmune disease with increased risk of infections. Here, we assessed whether pSS patients were at higher risk of hospitalization for community and opportunistic infections. We selected newly hospitalized pSS patients between 2011 and 2018, through a nationwide population-based retrospective study using the French Health insurance database. We compared the incidence of hospitalization for several types of infections (according to International Classification for Disease codes, ICD-10) between pSS patients and...

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  • University of Montpellier
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