98 Works

Additional file 1 of No association between habitat, autogeny and genetics in Moroccan Culex pipiens populations

Soukaina Arich, Yuki Haba, Najlaa Assaid, Megan L. Fritz, Carolyn S. McBride, Mylène Weill, Hassan Taki, M’hammed Sarih & Pierrick Labbé
Additional file 1: Table S1. CQ11 genotype data from previously published studies in Morocco. CQ11 genotype data for C. pipiens s.s. in Morocco retrieved from the literature are indicated with, for each sample, the locality of sampling, the date (year), the type of breeding site (when reported in the publication, “-” when not), the number of individuals of each CQ11 genotypes (homozygotes for the pipiens allele, for the molestus allele, and heterozygotes) and the reference....

Geographic Analysis of the Safety and Efficacy of Filgotinib in Rheumatoid Arthritis

Adis journals on behalf of:, Bernard Combe, Robin Besuyen, Antonio Gómez-Centeno, Tsukasa Matsubara, Juan José Sancho Jimenez, Zhaoyu Yin & Maya H. Buch
The above graphical abstract represents the opinions of the authors. For a full list of declarations, including funding and author disclosure statements, and copyright information, please see the full text online. (see “read the peer-reviewed publication” opposite).

Additional file 1 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 1. Position and frequency of the 248 nucleotide differences separating the PPR vaccine strains Nigeria/75/1 (Nig75/1) and 45G37/35-k (FRCVM). Nucleotide positions corresponding to mutations associated to the attenuation of Nigeria/75/1 are in bold [14].

Additional file 4 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 4. Review History.

Dataset: What makes a teddy bear comforting?

Anne-Sophie Tribot, Nathalie Blanc, Thierry Brassac, François Guilhaumon, Nicolas Casajus & Nicolas Mouquet
This dataset relates to a study intended to identify whether particular physical and sensory characteristics contribute to making a bear more comforting. These data were collected as part of a participatory experiment during the European Researchers' Night, on September 27, 2019, in 13 French cities simultaneously (395 participants). The file "data_teddybears" corresponds to the raw data, whose meaning and coding of each variable is detailed in the file "data_teddybears_metadata". The file "data_teddybears_finals" corresponds to sorted...

Additional file 1 of 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
Additional file 1. Modified MARAIS Score (modified from Marais et al. [27]).

Additional file 1 of 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
Additional file 1: Figure S1. Physician prediction: Visual Likert Scale. Figure S2. PresagEER study timeline. Table S1. Delays between ICU admission, AKI diagnosis and RRT initiation. Table S2. RRT characteristics. Table S3. Characteristics and outcomes of AKI patients (n (%) or median (IQR)). Table S4. Multivariate analysis including variables associated with the risk of requiring RRT (without physician prediction).

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...

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
Abstract Background Outliers and class imbalance in medical data could affect the accuracy of machine learning models. For physicians who want to apply predictive models, how to use the data at hand to build a model and what model to choose are very thorny problems. Therefore, it is necessary to consider outliers, imbalanced data, model selection, and parameter tuning when modeling. Methods This study used a joint modeling strategy consisting of: outlier detection and removal,...

No association between habitat, autogeny and genetics in Moroccan Culex pipiens populations

Soukaina Arich, Yuki Haba, Najlaa Assaid, Megan L. Fritz, Carolyn S. McBride, Mylène Weill, Hassan Taki, M’hammed Sarih & Pierrick Labbé
Abstract Background Mosquitoes of the Culex pipiens complex are found across the globe and are the focus of many research studies. Among the temperate species C. pipiens sensu stricto (s.s.), two forms are usually described: molestus and pipiens. These two forms are indistinguishable in terms of morphology but show behavioral and physiological differences that may have consequences for their associated epidemiology. The two forms are well defined in the northern part of the species distribution,...

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....

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...

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 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 1. Position and frequency of the 248 nucleotide differences separating the PPR vaccine strains Nigeria/75/1 (Nig75/1) and 45G37/35-k (FRCVM). Nucleotide positions corresponding to mutations associated to the attenuation of Nigeria/75/1 are in bold [14].

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...

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.

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...

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...

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...

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...

Medication adherence in women with IBD of childbearing age likely associated with disease knowledge

Robyn Laube, Christian Selinger & Rupert W. Leong
Background:Medication adherence in inflammatory bowel disease (IBD) is crucial, particularly during pregnancy. Unplanned pregnancies are common; therefore, efforts to maximise adherence should not be restricted to pregnant women.Objectives:We aimed to assess medication adherence in women with IBD of childbearing age, regardless of their reproduction plans.Design:We performed a multi-centre pilot questionnaire study of women with IBD age 18–45 years.Methods:Survey questions included patient demographics, disease history, and validated assessments of IBD and pregnancy knowledge, medication adherence and...

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