dataesr/scientific-paragraphs-categorization huggingface dataset:
, 2007). We investigated the proportion of genetic variability explained by a constraining covariance matrix consisting of phenology, latitude, longitude, and altitude for each individual. We tested the global significance of the model using 1,000 permutations. We ran marginal effects permutations to address the significance of each variable. Then, we focused on the effect of phenology alone, using partial RDA to take into account the effect of latitude, longitude, and altitude. Significance was tested running 1,000 permutations. For the PCA, the admixture analysis and the RDA, we selected from the FilteredDataset the SNPs with more than 95% genotyping rate, MAF >0. 05, retaining one SNP per locus and we remove SNP in linkage disequilibrium using the Plink command "indep 50 5 2. " Genome-wide differentiation between each sampling location was measured with Weir and Cockerham's F ST estimator  (Weir & Cockerham, 1984)  implemented in StAMPP  (Pembleton, Cogan, & Forster, 2013).
| Genomic diversity Genome-wide genetic diversity was inferred for each sampling location in the dataset by measuring observed heterozygosity (Ho), proportion of polymorphic loci, and MAF spectrums. For each population and chromosome, and subsequently on average for the entire genome, linkage disequilibrium (LD) decay was measured with Plink and smoothed in R. To contrast with long-term Ne estimates from coalescent simulation in our ABC modeling (see "Analysis of demographic history"), we also inferred recent Ne for each population using SNeP V1. 1  (Barbato, Orozco-terWengel, Tapio, & Bruford, 2015) , which uses LD data, with a MAF ≥0. 05 filter per population. We investigated the nature of SNP variation, that is, synonymous or nonsynonymous, blasting all RAD sequences on the reference genome and the transcriptome of the great tit (ftp://ftp.
| Identification of genomic footprints of selection We used three methods to search for outlier SNPs potentially under divergent selection between blue tit populations. First, we used Bayescan V2. 1  (Foll & Gaggiotti, 2008)   We filtered each of the five datasets for a minimum MAF of 0. 05. We used default parameters except for prior odds that were set at 10,000 in order to limit false positives. We investigated the paral-   2018 ) to list loci with outlier loading scores on the first RDA axes. We compared the loci found using these different methods. We reported in which genes these outliers were found (the list of genes can be found together with the genome published by Laine et al. , 2016 on NCBI).
| Variation of genomic differentiation with recombination rate We investigated variation of F ST with local recombination rate and whether SNP outliers were more often found in regions of low recombination than elsewhere in the genome. We estimated local recombination rates using a coalescent method implemented in Ldhat (McVean, 2004) using linkage disequilibrium signal. Following these authors' recommendation, the dataset was split in blocks of 2,000 SNPs with 500 overlapping SNPs. A MAF of 0. 05 and a maximum of 5% of missing data were allowed. The local recombination rate, ρ = 4Ne r, was then estimated in each block independently with the Bayesian reversible jump MCMC scheme implemented in interval. We used a block penalty of 5, with 30 million MCMC iterations sampled every 5,000 iterations.
The first 250,000 iterations were discarded. To speed up computations, we used the precomputed two locus likelihood table for n = 190 and assuming theta = 0. 001. We estimated ρ in a composite dataset with individuals from every population, habitats, and sex. We tested for correlations between SNP F ST and recombination rate using linear models, for Corsicamainland and for deciduous-evergreen differentiation, independently, and we represented the correlation using a LOESS fit. We tested whether outliers found using Bayescan and the RDA method for both Corsica-mainland and deciduous-evergreen differentiation were more often found in regions of low recombination than elsewhere in the genome using chi-square (χ 2 ) tests, and we represented the pattern using histograms.
We looked for potential salient variations in read depth in and around the putative inversion. We also tested whether the detected inversion was at Hardy-Weinberg equilibrium (using a common χ 2 test) and whether the frequency of the inversion varied geographically and between evergreen and deciduous habitats. To study the history of the putative inversion identified, we aimed at measuring intra-and interspecific genetic distance and absolute divergence, at the inversion and for the entire genome, for several blue tits and great tits. To do that, we first generated a new SNP dataset by running stacks with the same pipeline and parameters as explained earlier, with two mainland great tits, two insular great tits, four mainland blue tits homozygous for the inversion, four mainland blue tits not carrying the inversion, and four Corsican blue tits not carrying the inversion (the inversion was not found in Corsica).
Second, we selected the SNPs from the region of the inversion. Third, Da was measured between the five aforementioned groups of individuals using PopGenome  (Pfeifer, Wittelsbürger, Ramos-Onsins, & Lercher, 2014). Using this measure of Da, we estimated approximately the inversion apparition time using T = Da/2µ  Hudson, Kreitma, Aguadé, 1987) , assuming a standard mutation rate of 1e-8 and with the simplifying assumption of no gene flow and no introgression. Lastly, we represented the divergence between these individuals using an UPGMA tree of bitwise distance using the R package poppr 1. 1. 1 (Kamvar, Tabima, & Grünwald, 2014). (.
| Gene ontology We used the R package topGO  (Alexa & Rahnenführer, 2009)  to investigate the potential gene ontologies (GO) that were statistically enriched for the sets of genes identified among outliers and the inversion, compared to the entire list of genes in which all the SNPs from the entire dataset were found. For the outlier tests, we used GO analyses for each gene list obtained using the different outlier identification methods but also for aggregated lists of all of the gene identified for deciduous-evergreen tests or for Corsica-mainland tests. We used the GO referenced for the zebra finch, T. Guttata (tguttata_gene_ensembl). We report a Fisher enrichment test pvalue and a p-value after applying a Benjamini and Hochberg correction for multiple testing to control for false discovery rate.
In the entire dataset, 2,599 SNPs were identified as nonsynonymous while 6,751 SNPs were identified as synonymous. We Table  S7 ). The Z chromosome harbored a proportion of nonsynonymous mutations 1. 83 times higher than the average for the autosomes. We also observed significant differences in the count of ROH among populations from the mainland versus those from the island but not among populations within the mainland or the island (ANOVA p < 2e-16; Table  S8  for Tukey HSD test).
g. ,  Santure et al. , 2013). However, some statistical issues may limit the interpretation of this result. First, currently available genome scan methods to detect alleles of small effect are statistically limited, especially when applied to relatively small datasets  (Hoban et al. , 2016; Rockman, 2012). Second, a potential lack of power in detecting outliers could arise from the combination of the use of RAD sequencing and a rapid LD decay along the genome, that may result in too low resolution especially in regions with larger recombination rates  (Lowry et al. , 2017). Further Charly. analyses of the potential outliers found here, as well as a new analysis with higher marker density and more individuals, are needed to better document and discuss the potential genes and biological processes implicated.
Jacques Blondel, Marta Szulkin, Monica Arias, Patricia Sourouille, Annick Lucas & Boris Delahaie. We thank the associate editor, two reviewers, and the production team for their constructive comments and edits on previous versions of this manuscript. This project was funded by the European Research Council (starting grant ERC-2013-StG-337365-SHE to AC) and the OSU-OREME. study, conducted fieldwork, laboratory analyses, bioinformatics and statistical analyses, interpreted the results and wrote the manuscript. QR conducted bioinformatics and statistical analyses, interpreted the results and edited the manuscript. AC obtained the ERC grant, conceived the study, performed fieldwork, interpreted the results and edited the manuscript. DATA AVA I L A B I L I T Y S TAT E M E N T Individual sequences with metadata are available on NCBI with the SRA accession PRJNA630135.
Franceschi, Jacques Blondel, Marta Szulkin, Monica Arias, Patricia Sourouille, Annick Lucas & Boris Delahaie. We thank the associate editor, two reviewers, and the production team for their constructive comments and edits on previous versions of this manuscript. This project was funded by the European Research Council (starting grant ERC-2013-StG-337365-SHE to AC) and the OSU-OREME. study, conducted fieldwork, laboratory analyses, bioinformatics and statistical analyses, interpreted the results and wrote the manuscript. QR conducted bioinformatics and statistical analyses, interpreted the results and edited the manuscript. AC obtained the ERC grant, conceived the study, performed fieldwork, interpreted the results and edited the manuscript. DATA AVA I L A B I L I T Y S TAT E M E N T Individual sequences with metadata are available on NCBI with the SRA accession PRJNA630135.
Les reproductions fidèles d'oeuvres de l'esprit en deux dimensions appartenant au domaine public appartiennent elles aussi au domaine public. La personne qui les réalise ne peut prétendre au bénéfice du droit de propriété décrit au présent article. Pourquoi limiter cette règle aux oeuvres en deux dimensions ? Parce que les photographies d'objets (statues, monuments, etc. ) offrent plus facilement prise à l'originalité, le photographe bénéficiant d'une plus grande lati- tude dans le choix de l'angle de prise de vue. Mais de telles photos doivent néanmoins être originales pour pouvoir bénéficier de la protection du droit d'auteur. 14° Empêcher la neutralisation du domaine public par le droit des bases de données Le droit des bases de données  95  pose un réel problème au domaine public, car il permet de faire renaître une couche de droits sur les oeuvres numérisées figurant sur un site internet, dans une bibliothèque numérique ou dans une base de données.
Réponse de Smith Peter à Calimaq 28 octobre 2012 à 08 h 22 Je vous trouve bien meilleur, tout d'un coup / Vos dernières remarques me font rire, très sérieusement / Un revenu minimum à la création : ce n'est pas un peu ce qu'un sens de certains éléments que j'ai pu lire ? Mais plus encore, tu parles de buz', c'est intéressant / À quoi tient ce texte de bon aloi, sérieusement ? À quoi tes années de travail et de recherche tiennent-elles (que tu nous fais partager -comme d'autres d'ailleurs -et rassure -toi je t'en suis sérieusement reconnaissant) - ? /. Le revenu minimum*, il est versé à qui, sérieusement ? Ceci dit, et, j'en resterais là… Je ne suis pas là pour faire objet de polémique… Et j'en resterais à des commentaires bien précis, des questionnements sur les textes… Il s'agit bien de cela, n'est-ce pas ? Donc, je reprends : bien commun, bien public, domaine public… Attends, je réfléchis, domaine public, et espace protégé, place publique et partage des droits… droits économiques et valeurs de société… Attends, je réfléchis / bien commun et accès aux bases de données… Attends, nous réfléchissons… Qui fait usage de cette question, à ton avis, sérieusement ? Personnellement, je suis plutôt heureux de voir cette question mise sur la place du marché de la ville… surtout lorsqu'on veut être placier.
Information Sources and Search Strategy Studies of interest were identified by searching electronic databases and reference lists of screened studies and review articles. Date restriction was not applied. The final search was updated in July 2018. In addition, previously published review articles on this topic were hand searched for identifying additional references. A Boolean search strategy was designed and applied to the National Library of Medicine's MEDLINE database (PubMed). The search strategy included the following medical subject headings or keywords: "(vasopressin) AND (sepsis OR severe sepsis OR septic shock) AND (hypotension OR vasodilatory OR shock)".
Study Selection and Data Extraction Three authors (LZ, ML, and GD) performed the literature search. In the first step, studies were screened according to their titles and abstracts, and studies that did not meet the eligibility criteria were excluded. Next, full texts of the selected studies were evaluated in detail. One author (GD) extracted the following data from all the selected studies: first author name, publication year, study design, inclusion criteria, trial arms, patient number, and primary outcome parameters.
We explored the use of an early perfusion of terlipressin in association with norepinephrine regarding a SOFA outcome after 72 hours of treatment. 32 Hammond and colleagues found equivalent results using an early perfusion of vasopressin in association of norepinephrine. 33 This trend of early association between vasopressors is supported by physio pathological hypothesis and editorials but needs to be confirmed by randomized clinical trials. 34 To confirm these findings, we initiated a RCT (NCT03336814) to evaluate the effect of terlipressin infusion versus placebo in the early stage of septic shock in patients with no heart failure. Early synergy use of vasopressors in patients with septic shock may increase in the future. This highlight the need of data regarding their weaning order to prevent adverse effect.
Cet article présente une application de l'approche de modélisation multi-échelle à base d'agent en s'appuyant sur un modèle spécifique (NMDC) pour décrire et modeliser une classe de problèmes environnementaux. Le modèle NMDC permet à l'expert du domaine de décrire le domaine d'application sous-jacent en termes de concepts environnementaux et ne nécessite pas de compétences techniques spécifiques, ni de détails de mise en oeuvre. Nous montrons comment l'outil TiC (Tool-in-Context) associé développé à partir du modèle NMDC peut aider l'expert du domaine à décrire dans un langage naturel (spécifique) le problème environnemental. Cette description est la base pour l'outil TiC de générer un outil de simulation. A travers cet outil, nous transformons le langage spécifique en code multi-agents NetLogo, facilitant ainsi un premier prototype de l'application pouvant être utilisé par l'expert de domaine.
5. Action 'cut local wood'. 6. Action 'buy wood'. 7. Action 'plant trees'. We summarize the conceptual population of the AiC metamodel as described in the previous section. The relational data representation is derived from the grouping as shown in Figure  9. This is the data representation as used internally in TiC. We will discuss the resulting relations stepwise, and show how the conceptual population is represented in the relational scheme. (See section 5. 1, section 5. 2, section 5. 3 ).
Syntax-driven editor support As can be seen from listing 1, our syntax-driven editor is aware of the keywords of the corresponding AiC language and where to place them. It knows about all the grammatical constructs, and it includes nice tools such as syntax coloring, code completion, and validation. The editor also includes rules that express constraints that could not be expressed from the AiC metamodel. These rules are implemented with XTend Language (see  [24] ). These constraints concern especially the uniqueness of the actors groups identifier( the name of an Actor (ActorID) is unique), the the uniqueness of action name, the governance relations between actor group (an actor or level can not govern itself) and the uniqueness of some general parameters. The editor also provide Outline View facilitating navigation through the program code and Quickfix to correct some errors that may occur when editing the program.
The TiC simulator user interface Listing 2 show the general scheme of the generated NetLogo  [21, 22]  code of Laf model from the AiC model. We observe in this figure an early implementation of the Laf model characterized by processing of parameters, creating different classes of agents, creating the body of all the functions and procedures that define the actions of the agents, the initialization of simulation environment, and a general scheme for the main program. As we see, there remains only to user to complete the code functions and procedure according to the agent's goals. The TiC tool offers the user two big advantages : Data consistency from data collection phase to the code generation is therefore carried out by the domain expert. The data transfer of one competence to another is no more useful.
A questionnaire comprising 15 items sent to 372 units. The analysis of 153 responses was conducted from dynamic crosstabs in Excel and using the R software available online. The survey confirmed that the use of placebos in hospital is frequent, with nearly 2/3 of professionals answering the questionnaire declared to use it. The oral capsule is the most commonly used form. Placebo is mainly administered at night, in case of pain, insomnia or anxiety, to so-called "difficult" patients. Placebo is not always given after medical prescription. In most cases, patients are not informed that they receive a placebo. The majority of professionals believed in the placebo effect but considered to be insufficiently informed and trained in the use of placebo in current practice. Although the placebo effect is now demonstrated, ethical and legal considerations recommend placebo treatment only on medical prescription, with the prior information of the patient.
MATERIALS AND METHODS We analyzed LFP signals and spiking data recorded simultaneously on multiple electrodes in motor cortex of two macaque monkeys during the performance of a visuomotor delayed center-out reaching task. We used previously obtained data, from which other results have been presented  (Kilavik et al. 2010 (Kilavik et al. , 2012 (Kilavik et al. , 2014;; Ponce-Alvarez et al. 2010; Confais et al. 2012). We have already shown that this dataset contains strong LFP oscillations in the beta range, which are systematically modulated in amplitude and peak frequency by the behavioral task  (Kilavik et al. 2012). We have also reported on robust and specific modulations in neuronal spiking activity in relation to the behavioral task  (Confais et al. 2012 ). The experimental data can be shared upon request.
Animal preparation and data recording Two adult male Rhesus monkeys (T and M, both 9kg) participated in this study. Care and treatment of the animals during all stages of the experiments conformed to the European and French Government Regulations applicable at the time the experiments were performed (86/609/EEC). After learning an arm-reaching task (see below) the monkeys were prepared for multielectrode recordings in the right hemisphere of the motor cortex, contra-lateral to the trained arm. The recording chamber locations above primary motor and dorsal pre-motor cortex were verified with T1-weighted MRI scans in both monkeys, and also with intracortical micro-stimulation in monkey M (see details in  Kilavik et al. 2010). Across all included recording locations, the sampled regions spanned about 4 and 13mm diameter on the All rights reserved.
Offline spike sorting on the raw signals was additionally performed in Matlab (The MathWorks Inc. , USA) by using Principal Component Analysis in the toolbox MClust (http://www. stat. washington. edu/mclust/) when the online spike sorting was considered as non-optimal. In parallel, the amplified raw signal was hardware low-pass filtered online at 250Hz to obtain the low-frequency LFP signal, which was stored with a temporal resolution of 1 kHz. Behavioral data were transmitted online to AlphaMap (AlphaOmega) from the CORTEX software (NIMH, http://dally. nimh. nih. gov), which was used to control the task.
D2 entailed visuomotor integration and movement preparation while waiting for the GO signal. The reaction and movement times were computed online to reward the monkey after target hold, with a maximum allowance of 500ms for each. For data analysis, the reaction times were redefined offline using the arm trajectories. Trajectories were measured in x and y vectors at 1ms resolution. The mean of each x and y vector during the 500ms before GO in each trial was used as the movement's starting position. The moment when reaching a 2mm deviation, minus a fixed latency of 35ms (average movement duration from the starting position to the threshold), was determined as movement onset. From each of the two vectors (x and y), the shortest time was defined as RT. These values were controlled by visual inspection of single trial trajectories (see  Kilavik et al.
Data selection and analysis While the monkeys performed the reaching task we recorded neuronal activity from motor cortex. We recorded 90 sessions in 37 days in monkey T and 151 sessions in 73 days in monkey M. Consecutive sessions in the same day were made after lowering further the All rights reserved. No reuse allowed without permission. (which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint. http://dx. doi. org/10. 1101/586727 doi: bioRxiv preprint first posted online  Mar. 24, 2019;  electrodes to sample new neurons. This provided a total of 287 and 759 individual recording sites in monkeys T and M, respectively. A site is here defined as the conjunction of a specific chamber coordinate of the electrode entry and the cortical depth.
After site elimination due to lack of sufficiently recorded trials, or large recording artifacts affecting either the lower (LFP) or higher (spiking activity) frequencies, 127 and 358 sites remained for further analysis, from 66 and 135 individual sessions, for monkeys T and M, respectively. These essentially constitute the conjunction between the LFP datasets studied in  Kilavik et al. (2012)  and the single neuron datasets studied in  Confais et al. (2012). All analyses were conducted offline by using Matlab (The MathWorks, Inc. ). We studied a low beta band that was strong in both animals. In addition, in monkey M who also had a marked beta band at higher frequency (see  Kilavik et al. 2012  and example in Fig. 1E ), the analysis was repeated for this band. We first band-pass filtered the LFP around the average peak beta frequency for each band with a zero-phase 4 th order Butterworth filter.
2010 ). Thus, average reaction and movement times were both shorter than their maximally allowed durations of 500ms each, so that the analysis typically also includes most of the required 300ms target-hold time. The beta-neuron correlations were calculated separately for the preferred and nonpreferred (opposite) movement direction for the neuron in each pair, where preferred direction was taken as the one with maximal trial-averaged spike rate any time after the presentation of SC up to trial end. This was done to evaluate whether the task-related correlation with LFP beta amplitude depended on the involvement of the neuron in coding for the cued movement. The single trial data in these two directions was cut in 300ms non-overlapping consecutive windows. The window duration of 300ms was in part chosen based on the typical duration of beta bursts in our dataset (200-500ms), see example in Figure  2B ; see also  Murthy and Fetz 1992).