dataesr/scientific-paragraphs-categorization huggingface dataset:
16S rRNA Gene Amplicon Sequencing From this section onward, samples collected from sows that were sampled once and those from sows sampled twice were analyzed together to get the highest statistical power possible. Forty-seven samples were sequenced and 45 were retained after data analysis, containing a total of 4,770,924 sequences. Most of the sequences were bacterial sequences with 4,711,793 sequences (98. 8%) followed by archaeal sequences with 59,129 sequences (1. 3%) and 2 unclassifiable sequences (0. 00004%). A total of 3,377 OTUs were detected, with an average of 106,020 sequences per sample. The lowest values observed for a sample were 18,037 sequences and 490 OTUs and the highest were 560,410 sequences and 1,333 OTUs. Rarefaction was conducted and showed that after subsampling each sample at 18,037 a good coverage was obtained for all the samples (Supplementary Figure  S1 ).
For the Alpha diversity, a significant although small difference in coverage was measured when comparing samples based on their Salmonella shedding status while no differences where The means were based on 1000 subsampling of 18,037 sequences. On the same row a is significantly different from b. Significant p values of 0. 05. found when comparing the animals based on their time of gestation. When the sows were classified both on their Salmonella shedding status and time of gestation, no significant variation in alpha diversity was measured. (Table  3 ) Finally, no relationship was measured between the parity number and the different alpha diversity indices (data not shown). Bacterial beta-diversity was compared between groups. The similarity of the composition of communities at the OTU level was compared using the Jaccard and Bray-Curtis indexes and these distance matrices were plotted using NMDS on 2 axes when relevant (Figures  1A-C ).
ACKNOWLEDGMENTS This work was supported by the  Natural Sciences and Engineering Research Council of Canada  ( NSERC , No:  412247-2010 ), financial partners in the Industrial Research Chair in Meat Safety and the bourse de la Cité de la biotechnologie agroalimentaire, vétérinaire et agroenvironnementale. The authors would also like to thank  F. Ménard Inc. and more particularly  Benoît Laplante  for their collaboration and their participation. Computations were made on the supercomputer Briarée from  Université de Montréal , managed by  Calcul Québec and Compute Canada. The operation of this supercomputer is funded by the  Canada Foundation for Innovation (CFI) , the  Ministère de l'Économie, de la Science et de l'Innovation du Québec (MESI)  and the  Fonds de recherche du Québec -Nature et Technologies (FRQ-NT).
A cross-model validation was applied to the PLS-DA to check for significant discrimination (function "MVA. cmv" and "MVA. test", package "RVaidememoire")  [60]. The percentages of constrained and residual variances were obtained by a redundancy analysis (RDA) on the transformed values. A second RDA analysis considered gut compartments, snail phenotype, and site as explanatory variables to answer whether each of these variables was significant in the model. All statistical analyses were made using R software V. 3. 3. 1 (Vienna, Austria)  [61].
Acknowledgments:  Aurélie Bernard  and  Solenn Ferron  are acknowledged for their technical assistance. The Subantarctic field trip was funded by l' Institut Polaire Paul-Émile Victor, Plouzané, France (IPEV , programme  136 ). Aude Boutet  and  Julien Tommasino  assisted in the field collection of snails and lichens. The authors are also indebted to  Damien Ertz  for lichen identification. The two anonymous referees are acknowledged for their useful comments and discussion on this manuscript.
3, that is why we chose this ADL, a short example is given in  [14]. Reconfigurations operations are implemented using XSLT 11 : the input and output are TACOS+/XML files. When we model that the software is running, only one component model is in use, so that may be viewed as the identity function applied to a component model. In the programs given below, we compute each component model belonging to a reconfiguration path. For each component model, we may verify topological properties, e. g. , checking that a component or binding is present. As in  [14] , these topological properties are computed by means of XQuery programs  [27]. There is no difficulty about the implementation of reconfiguration operations and property checks, so the descriptions put hereafter concern the part implemented by means of automata.
Types Used Now we describe our checking functions at a high level. First we make precise the types used, in order to ease the reading of our functions. The formalism we use is close to type definitions in strong typed functional programming languages like Standard ML  [23]  or Haskell  [22]. Of course, we assume that some types used hereafter-e. g. , 'bool', 'int'-are predefined. We use the same names than in  [14]  for identical notions, and new functions introduced are suffixed by '*' or '**'. As mentioned above, an evolution operation is either the identity function, which expresses that the software is running, or a reconfiguration operation, which is implemented by applying an XSLT stylesheet to an XML document and getting the result as another XML document. At a higher-level, such an evolution operation may be viewed as a function which applies to a component model and returns a component model.
Likewise, checking a property may be viewed as a function which applies to a component model and returns a boolean value. Assuming that the component-model type has already been defined, we 9 Architecture Definition Language. 10 eXtensible Markup Language. 11 eXtensible Stylesheet Language Transformations, the language of transformations used for XML documents  [26]. Let us note that if another ADL is used within a project, there exist XSLT programs giving equivalent descriptions in TACOS/XML  [13]. In particular, that is the case for Fractal/ADL. function term-check : event → (component-model × component-model → bool) Let state be the type used for a state of our automata, starting from such a state and a configuration  13 is expressed by the following type: type path-check = state × component-model → bool The following function yields all the transitions starting from a state: function t : state → set-of[transition] the data belonging to a set can be accessed by means of a 'for' expression.
The synthetic nature of the benchmark here proposed is based on previous benchmark studies  (Brette et al. , 2007). This benchmark emulates those neural networks which are composed of neurons with a medium to low number of input synapses (up to 1,280 input synapses per neuron). The simulation performance results may change significantly when simulating biologically realistic experiments (e. g. , cortical networks) which require a much larger number of incoming synapses (up to 10,000 synapses per neuron) and firing rates  (van Albada et al. , 2015). The source code is available for readers at URL: www. ugr. es/ñ luque/restringido/Event_and_Time_Driven_Techniques. rar (user: REVIEWER, password: REVIEWER). All the additional material needed for the benchmark analyses (neural network, synaptic weight, input activity and neuron model description files, as well as the scripts to compile the look-up tables) are also located at the same URL.
ACKNOWLEDGMENTS This study was supported by the  European Union  NR (658479-Spike Control), by the  European Commission  ( 653019 -CEREBSENSING ) to JG, by the  Spanish National Grant NEUROPACT  ( TIN2013-47069-P ) and by the  Spanish National Grant PhD scholarship  ( AP2012-0906 ). We gratefully acknowledge the support of  NVIDIA Corporation  with the donation of two  Titan GPUs  for current EDLUT development.
Mass spectrometry and data reduction Tin stable isotope measurements were carried out using a Thermo-Scientific Neptune Plus multi-collector inductivelycoupled-plasma mass-spectrometer (MC-ICPMS) at the Institut de Physique du Globe de Paris, France. Operating conditions and measurement parameters are summarised in Table  3. Sample and standard solutions were prepared for isotope measurements with Sn concentrations of 100 ng mL -1 in 0. 5 M HCl. Solutions were introduced into the mass spectrometer using an ESI Apex-HF desolvator with a 100 lL min -1 PFA nebuliser. The Neptune was run in low resolution mode, with a mass resolution of ∼1860 (Table  3 ). Ion beams at 116 Sn, 117 Sn, 118 Sn, 119 Sn, 120 Sn, 121 Sb, 122 Sn, 123 Sb and 124 Sn were simultaneously collected in a single cycle using Faraday cups, with all Sn channels connected to amplifiers with 10 11 Y resistors.
Faraday collector gains were calibrated prior to the beginning of each analytical session. Baselines were measured on-peak for a duration of 14 min between every analysis, with the last ca. 120 s being used as the actual baseline and subtracted from the subsequent analysis. Analyses of samples had a duration of 412 s, corresponding to a total of ca. 70 ng of Sn consumed per analysis. Isotope results are reported in d 122/118 Sn notation, which reports the per mil ( ) difference in the 122 Sn/ 118 Sn ratio relative to our in-house Sn isotope standard, which is denoted as Sn_IPGP. All data reduction was conducted offline using the freely available doublespike data reduction tool IsoSpike (www. isospike. org; Creech and Paul, 2015).
Acknowledgments The authors gratefully acknowledge two anonymous reviewers for their detailed and constructive comments that improved this manuscript. We also thank  Klaus Mezger  for helpful comments and efficient editorial handling of this manuscript. F. M. acknowledges funding from the  European Research Council [ERC Starting  grant agreement 637503-Pristine] to as well as the financial support of the  UnivEarthS Labex program at Sorbonne Paris Cité  [ ANR-10-LABX-0023  and  ANR-11-IDEX-0005-02 ] and a chaire d' excellence  ANR-Idex Sorbonne Paris Cité. Parts of this work were supported by  IPGP  multidisciplinary  PARI program , and by  Region Île-de-France SESAME  grant no. 12015908.
Data Collection Sociodemographic, Lifestyle and Anthropometric Data Self-administered questionnaires were annually proposed to participants during follow-ups to collect and update data on sociodemographic, lifestyle and behavioural characteristics, including sex, age, geographical region of residence, marital status, number of children, educational level, smoking status, anthropometry and leisure-time physical activity. The latter was estimated using the validated international physical activity questionnaire  [10]. All baseline questionnaires were pilot-tested and then compared against traditional assessment methods  [11, 12].
Dietary Data At baseline, and every 6 months, participants were invited to complete three non-consecutive validated web-based 24-h dietary records, randomly distributed between week and weekend days to take into account intra-individual variability. Twenty-four-hour dietary records used in this cohort were tested against a traditional interview by a dietitian  [13]  and validated; they showed good validity when compared with biomarkers of intake  [14, 15]. Completion was made via a secured user-friendly interface and was designed for self-administration on the Internet. Participants were asked to report all foods and beverages (type and quantity) consumed at each eating occasion. Nutritional values for energy, macronutrients and main micronutrients came from a published nutrient database  [16].
Portion sizes were assessed via a validated picture booklet  [17]  or according to standard measurements. For each participant, daily nutrient intakes were calculated using the ad hoc NutriNet-Santé food composition table  [16]. Polyphenol intakes were assessed by matching this database with the polyphenol content of each reported food from the Phenol-Explorer database  [18]. The 15-point PNNS-GS (Tables  S1  and S2 ) is a validated a priori score reflecting the adherence to the official French nutritional recommendations which has been extensively described elsewhere  [19]. Details on computation of this score are available in Table  1. Briefly, scoring and cut-off values (Table  S1 ) were decided using information provided by national recommendations, themselves based on epidemiologic and clinical evidence.
For this purpose, the generalized linear mixed-effect model was used to take into account the effect of the randomization, with logit link function for binary outcomes and normal link function for continuous outcomes. The GLIMMIX procedure in SAS software version 9. 3 (SAS Institute, Inc. , Cary, NC, USA) was used to obtain adjusted means and proportions for lifestyle and nutritional behaviours, making it possible to use non-normal data. Because the large sample size increases the likelihood of significant statistical tests for very small differences with low biological/clinical relevance, results were interpreted as significant only when p-value was <0. 01 to avoid the error of multiple testing. We discussed the results only when the relative difference in dietary intakes or adherence to recommendations between cases and controls was >5%.
Indeed, quantitative dietary data was accurately assessed via repeated three non-consecutive 24-h dietary records, repeated every six months, accounting for intra-individual day to day and seasonal variability. Some limitations should be acknowledged. First, subjects included in the NutriNet-Santé cohort were volunteers involved in a long-term study on nutrition and health. Therefore, as it is often the case in health-related cohorts, they were probably more health conscious, and therefore may have had healthier diets and practices compared to other patients in the general population. Secondly, CMDs in this study were self-reported, although they were validated. Third, the cross-sectional design of our study did not take into account the duration following diagnosis of the CMD. Lastly, no information was available regarding whether individuals with a CMD had received a nutritional counselling or particular recommendations by medical staff or other stakeholders following their diagnosis.
Acknowledgments: The authors thank all who helped carry out the NutriNet-Santé study and all the dedicated and conscientious volunteers. The authors especially thank  Roland Andrianasolo ,  Cédric Agaesse ,  Nathalie Arnault ,  Stephen Besseau ,  Laurent Bourhis ,  Claudia Chahine Fatoumata Diallo ,  Younes Esseddik ,  Paul Flanzy ,  Veronique Gourlet ,  Anouar Nechba ,  Charlie Ménard ,  Jagatjit Mohinder ,  Fabien Szabo ,  Than Duong Van  and  Charlotte Voetglin  and for their technical contribution to the  NutriNet-Santé study. The authors are very grateful to  Charmion Thompson  for his thorough re-reading of this article.
The samples for LOM were immersed for 1 min in a 5 ml HF þ 10 g H 2 C 2 O 4 þ 50 ml H 2 O reagent solution at RT to reveal the microstructural constituents. LOM was carried out with a Zeiss Axioplan optical microscope using polarised light illumination, while SEM and EDX using a FEI Quanta 200 field emission gun scanning electron microscope (FEG-SEM) operated in backscattered electron mode (BSE) at 20 kV. Quantification of the grain size of parent b grains was determined by LOM using the ASTM standard E 1382-91 as implemented in the software Axio Vision 4. 8. 2. Thin-foil specimens were prepared for transmission electron microscopy (TEM) by dimpling followed by ion milling using a Gatan precision ion polishing system (PIPS) device employed at 4 kV. The samples were examined with a Tecnai F20 microscope operated at 200 kV.
The evolution of phase volume fractions and lattice parameters was determined during continuous heating at 20 and 100 K/min using the Rietveld method as implemented in the software Maud  [19]. For that, the phases identified during transformations summarized in Table  3  were considered. plates observed by LOM (Fig. 1b ) extends down to the nm-scale. This image presents an overview of units of fine acicular martensite of ~20e200 nm in thickness. Also, impingement between primary and secondary aʺ plates can be identified extensively within the microstructure. A local example of this effect is presented in detail in the bright field TEM image of Fig. 1e ). This is a consequence of the growth of thin secondary aʺ plates at nucleation sites generated by the previously formed primary aʺ variants during the initial stage of the b / aʺ transformation.
Acknowledgements  P. Barriobero-Vila  acknowledges the  K-Project  " Non-destructive testing and tomography Plus " supported by the  COMET-Program  of the  Austrian Research Promotion Agency (FFG)  and the provinces of  Upper Austria  (O € O) and  Styria (St). The  European Synchrotron Radiation Facility (ESRF)  is acknowledged for the provision of synchrotron radiation facilities in the framework of the MA-2909 proposal. The  University Service Centre for Transmission Electron Microscopy (USTEM) of the Vienna University of Technology (TU Wien)  is acknowledged for the provision of TEM and FEG-SEM microscopes.
Statistical analyses Each experiment was repeated independently a minimum of three times (unless otherwise indicated); error bars represent the standard error of the mean of replicate experiments (unless otherwise indicated). Data were analysed using appropriate statistical tests as indicated in figure legends using the GraphPad Prism software. P values are represented in the figures by the following symbols: ns for P ≥ 0. 05, * for P between 0. 01 and 0. 05, ** for P between 0. 001 and 0. 01, *** for P ≤ 0. 001.
Secreted TEPs promote Toll pathway activation Besides phagocytosis, hallmarks of systemic immunity in Drosophila are melanisation, clotting and production of antimicrobial peptides by the fat body. Thus, we assessed the contribution of TEPs to these three processes. There was no striking difference in melanin deposition at the wound site in adults when comparing TEPq Δ and wildtype animals (Additional file 1: Figure  S1D ), indicating that TEPs are dispensable for this process. Similarly, formation of clot fibres in the haemolymph, as assessed by the hanging drop method  [45] , was comparable to that of wild-type larvae (data not shown). We next investigated the role of TEPs in the regulation of the Toll and Imd pathways, using antimicrobial peptide genes as read-outs  [1]. We measured expression of the Imd target gene Diptericin (Dpt) in response to infection with the Gram-negative bacterium E.
Acknowledgements We thank  Mélanie Appertet ,  Tess Baticle ,  Fanny Schüpfer  and  Tiffany Thebault  for technical help, and  Loïc Tauzin  of the  Flow Cytometry Core Facility at EPFL  for assistance with flow cytometry experiments. We are grateful to  Claudine Neyen  for comments on the manuscript,  Dominique Ferrandon  for fly stocks and  Erjun Ling  for Metarhizium anisopliae 2575-RFP stock.
While there is an extensive literature on the tendency to mimic emotional expressions in adults, it is unclear how this skill emerges and develops over time. Specifically, it is unclear whether infants mimic discrete emotion-related facial actions, whether their facial displays are moderated by contextual cues and whether infants' emotional mimicry is constrained by developmental changes in the ability to discriminate emotions. We therefore investigate these questions using, Baby-FACS to code infants' facial displays and eye-movement tracking to examine infants' looking times at facial expressions. Three-, 7-, and 12-month-old participants were exposed to dynamic facial expressions (joy, anger, fear, disgust, sadness) of a virtual model which either looked at the infant or had an averted gaze.
Facial stimuli We created silent movie clips of two 3D virtual models' face, one male and one female, displaying five dynamic expressions, namely anger, disgust, fear, joy, sadness and one static neutral face, with either a static direct or a static averted gaze. These facial expressions were generated with the Poser 9 software by manipulating polygon groups comparable to the action units (AUs) described in the FACS  (Ekman & Friesen, 1978). A certified FACS coder manipulated AUs corresponding to prototypical expressions by using the following codes  (Ekman & Friesen, 1978) : AUs 6 (cheek raiser) +12 (lip corner puller) +25 (lips part) for joy, AUs 4 (brow lowerer) +24 (lip pressor) for anger, AU 9 (nose wrinkle) for disgust, AUs 1+2 (brow raiser) +4+5 (upper lid raiser) +20 (lip stretcher) for fear, and AUs 1 (inner brow raiser) +4+15 (lip corner depressor) for sadness.
Testing Each infant completed 12 trials corresponding to either a male or a female virtual model displaying 5 expressions (anger, disgust, fear, joy, sadness) or remaining neutral, with the gaze either direct or averted, using the ExperimentCenter software. During each trial, the same 2-s animated sequence was repeated 3 times. The 6-s trials were randomly presented with a 3-s inter-trial interval during which a blue screen was displayed to signal the end of trial. The model's gender was counterbalanced with half of participants seeing the female and half the male model. For each infant, the orientation of the model's averted gaze was counterbalanced between trials with 6 of 12 trials testing direct gaze, 3 testing averted gaze to the right and 3 testing averted gaze to the left.
Behavior Recording Eye movements of infants were followed for each eye with a sampling rate set at 250 Hz by using the SMI eye-movement tracking system during the trials displaying the facial stimuli. Eye-movement data were extracted off line for both eyes using the BeGaze Software. Infants' facial responses to facial stimuli were recorded with a video camera. These recordings were analyzed offline, using Baby FACS, to score infants' facial responses contingent to the models'emotional expressions. Negative expressions were defined using the following AUs  (Camras et al. , 2007; Rosenstein & Oster, 1988; Soussignan & Schaal, 1996) : 4 (brows lowered), 1+4 (inner portions of brows raised and pulled together), 3+4 (brows knotted and knitted), 1+2+4 (entire brows raised), 9 (nose wrinkled), 10 (upper lip raised), 11 (nasolabial furrow deepened), 14 (lip corners tightened), 15 (lip corners pulled down), 17 (chin raised), 20 (lip stretched), and 23/24 (lip pressed/tightened).
At 1. 5 mpf, however, induction appeared less efficient in the medial domain of Dl (Figure  S3G , red asterisk). Together, this strategy allowed us to pulse-label RGs with H2a-mCherry at all stages, and perform fate tracking at the population level. A birthdating method implies that the tracer highlights cells generated within a restricted number of cell divisions following induction. Therefore, a non-dividing RG should retain its initial mCherry staining, whereas daughter cells of a dividing RG should inherit half its mCherry content, progressively diluting out the label. Low amounts of 9TB and short chase times were used to validate these dilution properties on polyclones induced at 1 dpf and analyzed at 5 dpf (Figure  1B ). The amount of mCherry per nucleus was inferred from summing mCherry fluorescence staining intensity over the whole nucleus volume, measured using Imaris software.
ACKNOWLEDGMENTS We thank members of the  L. B. -C. laboratory  for their critical input,  W. Supatto  for advice on image analysis, and  M. O'Connell  for critical proofreading. Work in the L. B. -C. laboratory was funded by the  Agence Nationale de la Recherche  (grant  ANR-2012-BSV4-0004-01 ),  Ecole des Neurosciences de Paris (ENP) ,  European Research Council  ( AdG 322936 ), and  Labex Revive. E. B. 's contribution was supported by  Agence Nationale de la Recherche  (contracts  ANR-10-INBS-04   France BioImaging  and  ANR-11-EQPX-0029 Morphoscope2 ). G. F. was recipient of a fellowship from the  Erasmus Programme. C. H. was supported by the  Medical Research Council  ( G0901525 ) and  European Union ZF-Health Programme.