dataesr/scientific-paragraphs-categorization huggingface dataset:
stimulus evidence e (Fig. 1a , left) and (  2 ) the proportion of repeated responses as a function of the repeating stimulus evidence ê defined for the tth trial as êt ¼ r tÀ1 e t , with r t-1 = {-1,1} representing if the response in the previous trial was left or right, respectively (Fig. 1b ). Thus, positive (negative)-repeating stimulus evidence denotes trials, in which the animals had evidence to repeat (alternate) their previous choice. In other words, a rightward stimulus with evidence e t = 0. 23 after a left response implied a repeating stimulus evidence equal to êt ¼ À0:23. Both psychometric curves were separately fitted to a 2-parameter probit function (using Matlab function nlinfit): P Rightwards ðeÞ ¼ 1 2 1 þ erf βe þ b ffiffi ffi 2 p ð2Þ P Repeat ðêÞ ¼ 1 2 1 þ erf β 0 ê þ B ffiffi ffi 2 p : ð3Þ The sensitivities β and β' quantified the stimulus discrimination ability, while the fixed side bias B captured the animal side preference for the left (B < 0) or right port (B > 0), and the repeating bias b captured the animal's tendency to repeat (b > 0) or alternate (b < 0) their previous choice.
The parameter β captured a fixed side bias. The sets of weights ω S f , ω A k , ω L k;o , and ω T k;o;q were fitted, together with the parameters π R , π L , and β, to the responses of each rat separately using a generalized expectation-maximization algorithm implemented in Matlab 10 (see section 2 in Supplementary Methods for details). Dynamic variable model of behavior. We developed a dynamical model of the rats behavior in which three latent variables z L and z T accumulated and maintained the lateral and transition evidence, respectively. These variables were updated in each trial using standard updating rules that accumulated responses r o t or transitions T o;q t with weights Δ o L and Δ o;q T , respectively, and had leak terms λ o L and λ o T that were outcome dependent (o, q = +, -).
The variable c T was a variable that modulated the impact of z T on choice and was updated on each trial based only on the trial's outcome. The model combined linearly the net stimulus evidence, the lateral bias γ L = z L and the transition bias γ T = c T × z L × r t-1 and passed them through a probit function. The parameters of the model were fitted by maximizing the log posterior of the observed responses of each rat using the function fmincon from the Matlab Optimization Toolbox (see section 3 in Supplementary Methods for details). Reporting summary. Further information on research design is available in the Nature Research Reporting Summary linked to this article.
Acknowledgements We thank  Anke Braun ,  Anne E. Urai ,  Daniel Duque ,  Gabriela Mochol ,  Genís Prat-Ortega ,  Lluís Hernández ,  Manuel Molano ,  Tobias H. Donner , and  Yerko Fuentealba  for excellent discussions and critical reading of the paper, and  Lejla Bektic  for help with training of the animals. This research was supported by the  Spanish Ministry of Economy and Competitiveness  together with the  European Regional Development Fund  ( BES-2011-049131  to A. H. M. and SAF2015-70324-R to J. R. ). This work has received funding from the  European Research Council (ERC)  under the European Union's  Horizon 2020 research and innovation programme  (Grant agreements No. 683209  to J. R. and  615699  to D. R), from the  European Union Seventh Framework Programme  ( Marie Curie  auction  CEMNET  project  629613  to A.
Alternatively, empirical or semiempirical approaches have been used to obtain reliable loading values  [8] [9] [10]. e technical manual from the US Army, UFC-3-340-2  [8] , is mainly used as the state of the art in structural design offices and constitutes the most widely used experimental database for both civilian and military infrastructure design since it offers the most complete open database of blast wave parameters. ose empirical solutions have the benefit of relying on experimental data but have several drawbacks. e first one is the lack of reliable data for scale distance smaller than 0. 5 m•kg -1/3. Indeed, it is more than questionable to use these databases for close-in structures  [11, 12]. is is mainly due to the chemical reactions between the detonation products and the surrounding air.
(ii) A better accuracy with experimental data from the UFC-3-340-2,  [8]  at later stage of the blast wave propagation. (iii) A reduced computational time for engineering applications. First, the numerical model is presented and the ideal gas equation of state for the detonation products is compared with the classical JWL equation of state. In a second part, the influence of the balloon radius is investigated and all models are evaluated with respect to experimental data found in the UFC-3-340-2. All numerical results are compared to the chosen reference (the UFC-3-340-2), an experimental database accepted by authorities for structural design. A mesh sensitivity analysis is performed to validate the results and finally the impact on the energy balance is evaluated.
Methods The properties of OH defects were theoretically investigated within the density functional theory (DFT) framework using the PWscf code of the Quantum Espresso package  (Giannozzi et al. , 2009 ; http://www. quantum-espresso. org, last access: 27 May 2020). The modeling scheme used the generalized gradient approximation (GGA) to the exchangecorrelation functional as proposed by  Perdew, Burke and Ernzerhof (PBE functional; Perdew et al. , 1996)  and periodic boundary conditions. The ionic cores were described using optimized norm-conserving Vanderbilt (ONCV) pseudopotentials  (Hamann, 2013; Schlipf and Gygi, 2015). Cutoffs of 80 and 480 Ry on the electronic wave functions and charge density, respectively, were used as in  Balan et al. (2019). Structural properties of α-quartz (SG P3 2 21) were determined using its primitive cell (9 atoms), whereas 2 × 2 × 2 supercells (72 atoms) containing up to four hydrogen atoms were used to model the OH defects.
Code and data availability. Structure drawings have been produced with the Vesta software (Momma and Izumi 2011). PWscf and PHonon codes (Giannozzi et al. , 2009) are available at http://www. quantum-espresso. org/ (last access: 27 May 2020). Defect structures can be obtained on request by contacting Etienne Balan (etienne. balan@sorbonne-universite. fr).
Supervised 2D-Latent Space In order to visually analyze the latent space obtained by the encoder-classifier, we set the dimension of this space to 2 (K z = 2). The interest of such a space is to be able to make a projection of the initial input data space to a space visually accessible to the human brain. We can thus visually analyze the quality of the encoder. Figure  7  shows the 2D latent space obtained for the four databases. We can then see the distribution of data in the latent space as well as the interaction between the different classes. We can thus analyze the overlaps between the classes. One can then choose the area of this latent space in order to generate artificial data. Figure  8  shows examples of images generated from the latent space for Mnist and Fashion Mnist, respectively.
Image Reconstruction and Generation Figure  9  gives all the results obtained for the four databases with different values of β and γ for each of the two latent spaces (K z = 2 and K z = 100). For every database, we randomly generated 40 images as inputs of the VAE. The resulting output image is given according to the experimental parameters. A. Impact of the latent space: The first observation that can be extracted from these tests concerns the influence of the latent space size on the quality of the reconstructed image. We can see that for the two databases Mnist and Fashion-MNIST, the results achieved on the two-dimensional latent space are almost as good as for K z = 100. Nevertheless the quality of the reconstruction alone, obtained by setting the adversary parameter β = 0, is better for K z = 100: the images are less blurred and close to the input image than on the 2D latent space.
On the other hand, the image reconstruction performance obtained on the 2D space is less convincing for the Caltech database. Indeed, we can see that the reconstructed images are very blurred but for the most part close to the original image. Note that the reconstruction was completely impossible for the Omniglot database in 2D space. The only result in this space was obtained by forcing the weight of the adversary loss β to 0. 5, which allowed to generate new world alphabets.
B. Impact of the parameter β: In order to measure the effect of adversarial loss term L adv on the feature reconstruction loss term L rec , we varied the adversarial β parameter during each test sequence in a progressive way. This test allows to evaluate how the data generation effect can affect the reconstruction effect. Generally speaking, we obtain three steps, which are described as follows: • β < ε 1 =⇒ dominant reconstruction effect with blurred images. • ε 1 ≤ β ≤ ε 2 =⇒ reconstruction effect with clearer and more realistic images. • β > ε 2 =⇒ generative effect is dominant. with ε 1 and ε 2 are two thresholds to define. This is clearly illustrated by the MNIST database. Let us take the case of K z = 2: • Up to β = 0. 003, the reconstruction effect is dominant with blurred images.
Optimization results All optimizations are performed using a deterministic algorithm with multistart from 200 initial points. The Matlab function "fmincon" with multi-start option is used to perform the optimizations. Monte Carlo simulations with 10 3 points generated using common random number generation (CRN) technique  [46]  are used to propagate uncertainties. The optimization of the aggregation and the quantile function formulations are performed in the 8 cases shown in Table  3 , however the Pareto front for the bi-objective formulations is constructed for the first case of Table  3  only. In order to compare the results, the deterministic MSE, the mean, the standard deviation and the 90% and 95% quantile functions are evaluated at all deterministic and RBRDO optimum points. Three main kinds of comparison are made: 1.
Differential expression analysis Extracted read counts were used for the analysis of differential gene expression, that was conducted using the Bioconductor package edgeR version 3. 10. 0 (Robinson et al. , 2010)  in the R environment (version 3. 2. 2). Samples were grouped according to condition, temperature and time. The edgeR "calcNormFactors" normalization function was used to find a set of scaling factors for the library sizes that minimized the log-fold changes between samples. The scale factors were computed using a trimmed mean of M-values (TMM) between samples  (Robinson et al. , 2010). After estimating dispersions, the "glmLRT" test provided in edgeR was used to assess differential expressed genes (DEGs) between experimental conditions, with a threshold for a significant false discovery rate (FDR) set to < 0.
Go term enrichment analysis A functional interpretation of the lists of significant genes was obtained through enrichment analysis using the Database for Annotation, Visualization, and Integrated Discovery (DAVID) software. ''Biological process'' (BP) annotation category (BP_FAT) was used by setting the gene count equal to 3 and the ease value equal to 0. 05. Since DAVID database contains functional annotation data for a limited number of species, it was necessary to link the C. gigas genes with sequence identifiers that could be recognized in DAVID. This process was accomplished using Uniprot/Swiss-prot accession IDs corresponding to each contig. These identifiers were used to define different "gene lists" of DA transcripts (up and down-regulated separately) and a ''background'' (all the expressed genes) in the bioinformatic tool DAVID.
Protein and Citrate synthase activity Total protein extraction was performed as described in  (Guévélou et al. , 2013)  using 600 mg of oyster powder. Total protein concentration of each lysate was determined using the DC protein assay (Bio-Rad, Hercules, California, USA). The resulting lysates were divided in aliquots and stored at -80°C until enzymatic assays. All the assays were performed in triplicate at 21°C. Enzyme activity was measured using Nunc TM 96-well microplates (Thermo Fisher Scientific, Waltham, Massachusetts, USA), a synergy HT microplate reader and the software Gen5, both from Biotek (Winooski, Vermont, USA). Enzymatic activity was measured and related to the total protein concentration of each sample. Enzymatic activity of citrate synthase (CS; EC 2. 3. 3. 1) was measured using 20 μL of total protein lysates as described in  (Epelboin et al.
Acknowledgment The authors warmly thank  Claudie Quéré  and  Valerian le Roy  for biochemical analyses and samples preparation. The authors are grateful to  Benjamin Morga  and  Nicole Faury  from the  Laboratoire de génétique et Pathologie des Mollusques Marins (LGPMM) ,  Ifremer ,  La Tremblade , France for RNA extraction and in libraries preparation, to  Guillaume Mitta  for revising the manuscript and  Joanne Mulvena  for her help with English editing. This study is set within the framework of the  "Laboratoires d'Excellences (LABEX) "  TULIP  ( ANR-10-LABX-41 ). Results presented in this paper are reproduced from the PhD thesis of  Lizenn Delisle  ( University of Western Brittany (Université de Bretagne Occidentale ), France, 2018).
WG4: Data and Research Studies -Big Data Approaches Working group 4 will work to design and implement a concept for a large and comprehensive data registry, identifying appropriate strategies for data collection and management, as well as methods for ensuring high data quality. The data registry, including available datasets in which vascular aging biomarkers were used, will help consolidate existing evidence on the usefulness of vascular aging biomarkers for cardiovascular risk prediction and for tracking efficacy of treatments, and will help to identify novel risk factors for vascular ageing. A focus of this group will be on promoting implementation of big data approaches. Furthermore, the registry will constitute the basis for facilitating future shared initiatives, including the design of a novel generation of interventional trials.
S. workers may be commonly exposed. The parameters included genotoxicity, inflammation, pathology, and extrapulmonary translocation. CNT/F selection was initially based on provided company diameter. Nominal tube diameter was the simplest way to delineate samples for testing and previous studies indicate a changing toxicity profile with increasing diameter (or rigidity)  [16, 39, 45, 50]. The selected materials ranged from 6 to 150 nm in diameter according to company specifications. Determining the materials to test according to diameter, other key physicochemical characteristics also were expected to vary, such as length  (5-200 μm) , thus providing a proper representation of the CNT/F material class. A seventh MWCNT, Mitsui-7/MWCNT-7, was added as a benchmark material given the IARC carcinogenicity classification and the large amount of historical toxicity data available for the four parameters of interest.
Two-dimensional agglomerate sizing Samples of CNT/F were prepared in physiologic dispersion medium and the dispersed samples were prepared for field emission scanning electron microscopy (FE-SEM; Hitachi S-4800, Tokyo, Japan). Measurements were collected using measuring tools of the microscope's provided software (FE-PC SEM Ver. 2. 8, Hitachi High Technologies America). The largest crosswise diameter of 75 agglomerates were measured for each material. Materials were subsequently categorized into distinct groups of agglomeration defined as either spherical agglomerates or bundles of fibers with one dimension greater than three times the other dimension, referred to as bundled agglomerates. Bundled agglomerates had both a diameter and length measurement.
Statistical analysis In vitro assays of cytotoxicity and oxidative stress were analyzed using one-way (particle type) and two-way (particle type by dose) analyses of variance. Post hoc comparisons were evaluated with Fishers LSD test. Some variables were transformed using the natural log prior to analysis to meet the model assumptions of homogeneous variance. Significance was achieved at a p < 0. 05. All analyses were carried out using SAS/STAT version 9. 4 for Windows, and JMP statistical software version 12 (SAS, Cary NC).
Feature selection and principal component analysis To permit selection of the minimal number of features among all characterization and L-W-AR properties that could potentially discriminate between each material investigated, feature selection was performed with a random forest-based approach  [135]  using the "Boruta" algorithm  [136]  in the R statistical environment  [137]. The Boruta algorithm adds randomness to the variables in the dataset by creating shuffled copies of all variables ("shadow features"). "Boruta" iteratively assesses if each variable has a higher Z-score than the maximum Zscore of its shadow features. At each iteration, variables with Z-scores lower than shadow features are deemed unimportant and removed subsequently by the algorithm to capture all the important, interesting features one might have in the dataset with respect to a dependent variable, in this case each material itself.
Material and methods Ant colonies were collected in French Guiana at three locations: Montagne des Singes, Kourou (5. 07225N, 52. 69407W), Campus Agronomique, Kourou (5. 17312N, 52. 65480W), and Sinnamary (5. 28482N, 52. 91403W). Colonies were collected in Brazil at Oiapoque, state of Amapá (3. 84151N, 51. 84112W) (Table  1 ). Sampling permission was given by the Instituto Chico Mendes de Conservação da Biodiversidade (ICMBio) to Luísa Antônia Campos Barros (SISBIO accession number 32459). Specimens were identified by Jacques Hubert Charles Delabie and deposited in the reference collection at the Laboratório de Mirmecologia, Centro de Pesquisas do Cacau (CPDC/ Brazil), as items #5802 and #5803. Metaphases were obtained from the cerebral ganglia of the larvae after meconium elimination, according to  Imai et al.
Myrmicinae: Solenopsidini: Solenopsis Our analysis found 2n = 32 in female Solenopsis geminata and n = 16 in males with most chromosomes (26) being metacentric or submetacentric (Fig. 5c, d ). The genus Solenopsis Westwood, 1840 is difficult to identify at the species level, although these species form obvious natural groups (Pacheco and Mackay 2013). The chromosome number for this species in our analysis is the same as that observed in five previously described fire ant species including S. geminata, (reviewed in Lorite and Palomeque 2010) which belong to the subgenus Solenopsis (Pacheco and Mackay 2013). We compared our data with those from colonies of S. geminata from the USA  (Crozier 1970)  and India  (Imai et al. 1984). The karyotype from French Guiana is similar to that from India, despite certain differences in chromosome classification.
Myrmicinae: Crematogastrini: Crematogaster The ant genus Crematogaster is a global, widespread, and species-rich clade. It currently comprises 498 valid species and is divided into two subgenera, Crematogaster sensu stricto and Crematogaster (Orthocrema) Santschi, 1918  (Blaimer 2012a, b). The subgenus Orthocrema is more complex, and numerous clades exist within this group. Crematogaster longispina, which belongs to the subgenus Orthocrema, has 2n = 24, and all chromosomes are meta/submetacentrics (Fig. 5e ). This is the first New World Crematogaster karyotype ever described, which makes reasonable comparisons difficult. Karyotype data is available for 17 morphospecies of Crematogaster from Malaysia, Indonesia, India, Japan, and Australia (reviewed in Lorite and Palomeque 2010). Within Crematogaster spp.
Conclusion Our study increased the number of karyotyped Amazonian ant species from 18 to 34. The karyotype of 16 species were analyzed, six of them for the first time, which permitted comparisons with previously studied species, including population studies of leaf-cutting ants (Atta sexdens and Acromyrmex balzani). Although cytogenetic analysis of more than 800 ant species is available, there are no data for many genera, including many Neotropical ones. This paper includes the first description of the karyotype of a Crematogaster species ever reported for the New World. Conventional cytogenetics constitutes a powerful tool in characterizing cryptic biodiversity  (Cioffi et al. 2018). For example, our study of D. imitator showed substantial differences between chromosome numbers of the previously studied Atlantic forest karyotype and that of our study, strongly suggesting the presence of different species.
Acknowledgments Financial support for this study was provided by " Investissement d'Avenir " grants managed by the  French Agence Nationale de la Recherche  ( DRIIHM ref. ANR-11-LA-BX-0010  and CEBA, ref. ANR-10-LABX-25-01 ), by the  Programa de Auxílio ao Pesquisador   -PAPESQ/UNIFAP/2017 , by the  PO-FEDER   2014-2020 ,  Région Guyane (BiNG , ref. GY0007194), and by the  scholarship grant  from  Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)  to LIS.
) and importance of using guidelines for empirical antibiotic prescriptions (decrease indications of cephalosporins, limit the use of broad-spectrum antibiotics including carbapenems and linezolid, early stop of antibiotics) (Additional file 1). All these measures were continued since 2013 and were intensified after a second outbreak in July 2014. Data regarding isolation of Enterobacter spp. and antimicrobial susceptibility profiles were obtained from the microbiology department. In the studied NICU, screening for bacterial gut colonisation is routinely conducted weekly for all patients by collecting stools from diapers. Enterobacter spp. is identified when it is predominant in the stool (culture on non-selective agar) and/or if it grows on ChromiD BLSE® (bioMérieux, Marcy-l'Etoile, France).
The annual number of patients exposed to antibiotics during the study period was retrieved from ICCA software and from the database of the pharmacy. Data were obtained for carbapenems, cefotaxime and other betalactams (including amoxicillin, amoxicillin-clavulanic acid and penicillin G) from 2012 to 2017. Antibiotics use was represented as number of exposed patients for 1000 patient-day. During the second outbreak in 2014, to evaluate the genetic relationships of Enterobacter cloacae strains from the NICU, whole genome sequencing (WGS) was performed on a subset of six strains including the four strains isolated in blood/CSF in July 2014 and two additional strains isolated from stools of non-infected neonates during the same period. Briefly, after DNA extraction, paired-end libraries of 100 bp read length were sequenced on an Illumina MiSeq platform.
All primary antibodies were probed with a secondary horseradish peroxidase (HRP)-conjugated antibody (Vector, USA). A chemiluminescence assay (ECL, Amersham, USA) was used for detection; the autoradiographic films thus obtained were quantified using ImageJ2 software  [36]. Independent samples t-test was used to analyse the differences between samples. p values < 0. 05 were considered significant.
EVs were purified by centrifugation at 1ʹ000g for 15 min and then at 2ʹ000g for 15 min to eliminate cell debris. Supernatants were further centrifuged at 18ʹ000g for 30 min to obtain the lEV pellet. The resulting supernatant was pelleted by ultracentrifugation at 110ʹ000g for 70 min. The sEV pellet was washed in 3 ml PBS, centrifuged again and resuspended in PBS. EV amount and size was measured by NanoSight tracking analysis (NTA). sEVs and lEVs were loaded into the sample chamber of an LM10 unit (NanoSight, Malvern Instruments Ltd, UK). Three 30 or 60 s videos were recorded for each sample and analysed with NanoSight NTA 3. 1 software. Data were expressed as mean ± SD of the three recordings. Samples containing a large number of particles were diluted before the analysis and the relative sEV and lEV concentration was calculated according to the dilution factor.