dataesr/scientific-paragraphs-categorization huggingface dataset:
''S. K. is supported by the  Fondation pour la Recherche M edicale  (grant no. ING20130526624 ), la  Ligue Contre le Cancer (Comit e de Paris) , and  Centre de R ef erence D eficits Immunitaires H er editaires (CEREDIH). S. O. B. is supported by the  Higher Education Funding Council for England. B. V. is supported by the  UK Biotechnology and Biological Sciences Research Council  [ BB/I007806/1 ],  Cancer Research UK  [ C23338/A15965 ), and the  NIHR University College London Hospitals Biomedical Research Centre. B. V. is consultant to  Karus Therapeutics (Oxford, United Kingdom ). S. N. is a  Wellcome Trust Senior Research Fellow in Basic Biomedical Science  ( 095198/Z/10/Z ). S. N. is also supported by the  European Research Council Starting  grant  260477 , the  EU   FP7 collaborative  grant  261441  ( PEVNET  project), and the  NIHR Cambridge Biomedical Research Centre, UK.
The dSTORM images were reconstructed with a pixel size of 10 nm. The ZEN software outputs a text file containing a list of the x and y coordinates and the precision of all detected molecules in the time-series. We used this file to further visualize and treat the data with home-made Matlab program. Image Analysis. The reconstructed super-resolution image is filtered using a hysteresis threshold. The center of mass for each individual nuclear pore central channels is detected from the regional maxima of the H-maxima transform. NPC density is computed from the number of centers of mass weighted by area occupied by the nuclear envelope on the image. The NPC central channel diameter is measured from the reconstructed image by interpolation of the full width at half maximum of the radial autocorrelation.
Acknowledgements The authors want to thank  Jean-Marc Di-Meglio ,  Guillaume Fabre ,  France Lam ,  Jean Antoine Lepesant ,  Valérie Doye ,  Catherine Dargemont ,  Caroline Perrin ,  Reiner Veitia  for their help and discussions on this project, and  Ludovic Maingault  and  Daniel Quintas  for their care of the amphibians. The mouse monoclonal antibodies against Xenopus gp210 were kindly provided by  Pr. Dr. George Krohne  from  Wuerzburg University. This project was supported by the  Université Sorbonne Paris Cité  (" NanoBioSTED " project grant), the  Agence Nationale de la Recherche  ( ANR-14-CE08-0011-01 , " Golden Gates " project grant) and the  DIM Nano K ("RNA flow" project grant ). This project was also supported by the  French National Research Agency  ( ANR-10-INBS-04 , FranceBioimaging, ≪ Investments of the future ≫).
The mean width of the river in the studied area was 150. 2 m; maximum width did not exceed 300 m. Additionally, the receivers were checked once every week to ensure their correct position and location, and were cleaned to prevent dragging by biofouling. Data were collected once per week on 4 gates  (1, 5, 9, 13)  to orientate the active tracking (Fig. 1 ). Active tracking was done from a boat twice a week with a hand-operated receiver in the river sections where fish were detected by the nearby gates. For each fish detected, its depth and the mid-column water flow were recorded. Each passive receiver and each fish localized in active tracking were geo-localized using a differential GPS (Magellan MobileMapper CX). Fish tracking lasted 21 d due to tag battery life duration.
To analyze movement data, a database was constructed including both passive (99. 8%) and active (0. 2%) tracking data. Our acoustic data, obtained with the JSATS technology (frequency = 416 KHz), contained a considerable amount of false detections. Thus, these data required post-treatment using a receiver interface application (WHS Host, Lotek ® ) and R statistical software (R Core Team 2013). The WHS Host application filtered the detections by known fish identification codes and, using R software, we se lected consecutive detections spaced at 5, 10, 15 or 20 s which were considered 'true detections' according to the preliminary tests. The database then consisted of detections associated with a location (the geographical coordinates of either the passive hydro phones or the active trackers), date and time for each fish.
The hydrographical distances between 2 consecutive locations and their orientation (up stream, downstream, lateral, no movement) were estimated using ArcGIS v. 10. 2 (ESRI 2013) and Anaqualand v. 2. 0 (Le  Pichon et al. 2006 ) software as in  Acolas et al. (2012). We considered 'no movement' as corresponding to 2 consecutive locations of the same individual within the detection range of one receiver. Also, fish trajectories were smoothed using an estimation of fish ground swimming speed (maximum set at 0. 8 m s -1 ) between 2 consecutive locations as an approach to discern overestimated data, which mainly occurred in the case of 'lateral movements'. This in volved individuals detected by 2 hydro phones at the same gate, at the same time or within seconds of each other, for which the hydrographical calculations estimated distances as if the fish had moved from one hydrophone location to the other.
In this case, the 'lateral movement' identified was considered as 'no movement'. The ground swimming speed threshold (0. 8 m s -1 ) was calculated using double the maximum speed that a 3 mo old sturgeon (average fish length of 14. 2 cm in this study) can sustain according to a preliminary current speed test (2 body lengths s -1 ; P. Jatteau pers. comm. ) and the average current velocity estimated during the study (0. 09 m s -1 ). Day, night and twilight time were determined weekly using a sunlight phase web application (SunCalc; Agafonkin 2009) based on this study's date and location. Sunrise and sunset together were considered as twilight (i. e. 06:22 to 08:02 h and 19:40 to 21:21 h, respectively). Movement data were analyzed according to 2 time scales: during the whole study (n = 21 d) and during the first 3 d and remaining days separately.
Movement characterization Whole study During the whole study period, total distance covered by the fish did not differ between treatments (Scheirer-Ray-Hare method, p = 0. 87; family, p = 0. 58; method × family, p = 0. 17; distance covered = 7. 5 ± 7. 0 km). Within each diel cycle, no differences in total distance covered between treatments were found in diurnal (Scheirer-Ray-Hare method, p = 0. 06; family, p = 0. 25; method × family, p = 0. 67) or nocturnal movements (method, F 1, 26 = 0. 44, p = 0. 51; family, F 1, 26 = 0. 16 p = 0. 70; method × family, F 1, 26 = 0. 94, p = 0. 34). As very few fish were detected during twilight (enriched, n = 11; traditional, n = 8), data were only compared by rearing method and no differences were found (MW U = 38, p = 0. 66). However, for all fish the distance covered was significantly different between night and day (MW U = 282, p < 0.
Acknowledgements: This study was funded in 2014 within the French national action plan in favor of European sturgeon restoration by the water agency  Adour Garonne , Aquitaine region,  General Council Gironde  and the regional direction of the environment Ministry. A PhD grant was allocated to E. C. G. by the  National Office of Water and Aquatic Environment (ONEMA)  and the  National Research Institute of Science and Technology for Environment and Agriculture (Irstea). We thank the personnel of  Irstea Saint Seurin experimentation station  for their contribution in the fish rearing,  Philippe Vignac , a professional fisherman, for his help with field work and  Maud Pierre  ( Irstea ) for her advice on data processing. This study was carried out in an approved experimental hatchery facility by the  French Department of Agriculture  (authorization  A33-478-001 ) and followed the standards of the  National Ethic Committee of Animal Use for Scientific Purposes  (authorization  01738.
Strain identification by MALDI-TOF MS and 16S rRNA sequencing In order to explore as exhaustively as possible the bacterial diversity of the faecal sample, the culturomics concept was used to culture this sample using 18 culture conditions  [8]. The purified colonies obtained were identified using MALDI-TOF MS as described previously  [13, 14]. Colonies were deposited on a MTP 96 MALDI-TOF MS target plate (Bruker Daltonics, Leipzig, Germany), which was analysed with a Microflex spectrometer (Bruker Daltonics). The spectra obtained were matched against the references of the 7567 bacteria contained in the database by standard pattern matching (with default parameter settings) with MALDI BioTyper database software 2. 0 (Bruker Daltonics). An identification score over 1. 9 with a validated species allowed the identification at the species level, and a score under 1.
7 did not enable any identification. The 16S rRNA gene was amplified and sequenced as previously described  [15]. The obtained 16S rRNA sequence was compared to those in GenBank (http://blast. ncbi. nlm. nih. gov. gate1. inist. fr/Blast. cgi) to determine the percentage of sequence similarity with the closest bacteria. A new species or genus was defined by a similarity level of the 16S rRNA sequence under 98. 65% or 95% respectively  [16].
All data were collected and processed using Turbomass 6. 1 (Perkin Elmer). FAMEs were identified by a spectral database search using MS Search 2. 0 operated with the Standard Reference Database 1A (National Institute of Standards and Technology (NIST), Gaithersburg, MD, USA) and the FAMEs mass spectral database (Wiley, Chichester, UK). Retention time correlations with estimated nonpolar retention indexes from the NIST database were obtained using a 37-component FAME mix (Supelco; Sigma-Aldrich, Saint-Quentin Fallavier, France); FAME identifications were confirmed using this index. Antibiotic susceptibility testing was performed using a disk diffusion method according to European Committee on Antimicrobial Susceptibility Testing (EUCAST) 2015 recommendations  [17]. Inhibition diameters were measured using the Scan1200 scanner (Interscience, Saint-Nom-La Bretêche, France).
The circularized DNA was mechanically sheared to small fragments with an optimal at 569 bp on the Covaris S2 device in microtubes (Covaris, Woburn, MA, USA). The library profile was visualized on a High Sensitivity Bioanalyzer LabChip (Agilent Technologies), and the final library concentration was measured at 24. 4 nmol/L. The libraries were normalized at 2 nM and pooled. After a denaturation step and dilution at 15 pM, the pool of libraries was loaded onto the reagent cartridge and then onto the instrument along with the flow cell. Automated cluster generation and sequencing run were performed in a single 39-hour run at 2 × 251 bp. Total information of 10. 1 Gb was obtained from a 1189K/mm 2 cluster density with a cluster passing quality control filters of 99. 1% (22 579 000 clusters). The reads obtained were trimmed; assembly was performed by CLC genomicsWB4 software.
Genome annotation and comparison Open reading frames (ORFs) were predicted using Prodigal  [18]  with default parameters, but the predicted ORFs were excluded if they spanned a sequencing gap region. The predicted bacterial protein sequences were searched against the GenBank  [19]  and the Clusters of Orthologous Groups (COGs) databases using BLASTP (E value 1e-03, coverage 0. 7 and identity percentage 30%). If no hit was found, it was searched against the NR database using BLASTP with an E value of 1e-03, a coverage of 0. 7 and an identity percentage of 30%, and if the sequence length was smaller than 80 aa, we used an E value of 1e-05. The tRNAScanSE tool  [20]  was used to find tRNA genes, while ribosomal RNAs were found using RNAmmer  [21]. Lipoprotein signal peptides and the number of transmembrane helices were predicted using Phobius  [22].
Mobile genetic elements were predicted using PHAST  [23]  and RAST  [24]. ORFans were identified if all the BLASTP performed did not give positive results (E value smaller than 1e-03 for ORFs with sequence size larger than 80 aa or E value smaller than 1e-05 for ORFs with sequence length smaller than 80 aa). Such parameter thresholds have already been used in previous studies to define ORFans. Artemis  [25]  and DNA Plotter  [26]  were used for data management and the visualization of genomic features respectively. The Mauve alignment tool (version 2. 3. 1) was used for multiple genomic sequence alignment  [27]. Comparator species for genomic comparison were identified in the 16S RNA tree using Phylopattern software  [28]. The genome of strain mt6 T was compared to those of Alkaliphilus metalliredigens strain QYMF, Clostridium aceticum strain DSM 1496, Alkaliphilus transvaalensis strain SAGM1 and Alkaliphilus oremlandii strain OhILAs.
For each selected genome, the complete genome sequence, proteome genome sequence and Orfeome genome sequence were retrieved from the FTP of NCBI. An annotation of the entire proteome was performed to define the distribution of functional classes of predicted genes according to the clusters of orthologous groups of proteins (using the same method as for the genome annotation). Annotation and comparison processes were performed in the multiagent software system DAGOBAH  [29] , which includes Figenix  [30]  libraries that provide pipeline analysis. To evaluate the genomic similarity between studied genomes, we determined two parameters, digital DNA-DNA hybridization (DH), which exhibits a high correlation with DDH  [31, 32]  and average genomic identity of orthologous gene sequences (AGIOS)  [33] , which was designed to be independent from DDH  [33].
Phenotypic description The growth of the mt6 stains occurred between 25 and 56°C on 5% sheep's blood-enriched Colombia agar. Optimal growth was achieved at 37°C after 48 hours of incubation in both anaerobic and microaerophilic conditions. The cell growth was weaker in aerobic conditions. Strain mt6 was able to grow at pH values ranging from 6 to 8. 5 and 0. 5 to 5% NaCl concentrations. Cells were spore forming and motile, and they formed translucent colonies with a mean diameter of 0. 5 mm on bloodenriched Colombia agar. Microscopic observations showed Gram-stain-negative, rod-shaped cells (Fig. 2 ), and electron microscopy showed rods with a mean diameter of 1 μm and a mean length of 6. 8 μm (Fig. 3 ). Our MALDI-TOF MS database was incremented with the reference spectrum obtained for strain mt6 T (Fig.
4 ). Comparisons of the aforementioned spectrum to that of other known species of the Bacillaceae family are represented in the gel view (Fig. 5 ). Reference spectra are available in our online database (http://www. mediterranee-infection. com/article. php?laref=256&ti-tre=urms-database). Strain mt6 T was negative for catalase activity and positive for oxidase activity. Using an API ZYM strip, positive reactions were recorded for alkaline phosphatase, esterase (C4), esterase lipase (C8), leucine arylamidase, α-chymotrypsin, acid phosphatase and naphtol-AS-BI-phosphohydrolase. Nitrate reduction was observed; urease, β-glucosidase and protease activities were positive using an API 20 NE strip. All other reactions were negative on both strips. An API 50CH was used to test the carbohydrates metabolization.
COGs, Clusters of Orthologous Groups database. Positive reactions were recorded for alkaline phosphatase, esterase (C4), esterase lipase (C8), leucine arylamidase, α-chymotrypsin, acid phosphatase and naphtol-AS-BIphosphohydrolase. Urease, β-glucosidase, protease activities and nitrate reduction were also positive. Glycerol, D-lactose, D- fucose, D-mannose, D-cellobiose, D-maltose, salicin, N-acetylglucosamine, potassium-5-ketogluconate and D-arabitol were metabolized. Cells were susceptible to amoxicillin, gentamicin, ceftriaxone, ciprofloxacin, penicillin, imipenem, tobramycin and oxacillin but were resistant to metronidazole, trimethoprim/ sulfamethoxazole, rifampicin, doxycycline, vancomycin, nitrofurantoin and erythromycin. The G+C content of the genome is 43. 75%. The 16S rRNA gene sequence and whole-genome shotgun sequence of R.
26 Nucleotide transport and metabolism H 76 2. 77 Coenzyme transport and metabolism I 66 2. 41 Lipid transport and metabolism P 155 5. 66 Inorganic ion transport and metabolism Q 30 1. 09 Secondary metabolites biosynthesis, transport and catabolism R 273 9. 98 General function prediction only S 189 6. 91 Function unknown - 862 31. 51 Not in COGs COGs, Clusters of Orthologous Groups database. aTotal is based on total number of protein-coding genes in annotated genome. NMNI Tidjani Alou et al. Rubeoparvulum massiliense gen. nov. , sp. nov. enriched Colombia agar. The organism is catalase negative and oxidase positive.
More specifically, a classical elastic-plastic model with anisotropic plasticity is coupled with the Lemaitre damage theory, while the GTN model is combined with the  Hill (1948)  anisotropic yield surface to account for plastic anisotropy. The resulting models are implemented into the finite element code ABAQUS/Explicit, through the user-defined subroutine VUMAT, within the framework of large plastic strains and a fully three-dimensional formulation. Each of these models is then used for the FE simulations of the Nakazima deep drawing test with different specimen geometries in order to predict FLDs. The latter are determined using four different criteria for the onset of localized necking. Three of these criteria are based on the FE simulations of the Nakazima deep drawing test, while the fourth one is based on bifurcation theory (see, e.
Numerical implementation of the constitutive equations In this work, both the modified anisotropic GTN model and the Lemaitre damage model are implemented into the commercial finite element code ABAQUS/Explicit via the user-defined material subroutine VUMAT. The same explicit time integration scheme is used for both damage models, which is based on the fourth-order Runge-Kutta method. This algorithm allows updating the stress state and all of the internal state variables at the end of the loading increment starting from a known state at the beginning of the loading increment. This time integration scheme has the advantage of being straightforward and robust, since no iterative procedure is needed, unlike implicit time integration schemes (see, e. g. ,  Aravas, 1987). However, the time increment must be kept small enough to ensure accuracy and stability (see, e.
g. ,  Li and Nemat-Nasser, 1993; Kojic, 2002). It can be shown that the evolution equations for both the GTN damage model and the Lemaitre damage model can be written in the following compact form of general differential equation: ( ) = u u h u ɺ , ( 29 ) where u encompasses all of the internal variables and stress state, while vector ( ) u h u includes all evolution laws for each damage model. The above condensed differential equation is then integrated over each loading increment, using the forward fourth-order Runge-Kutta time integration scheme. The resulting algorithms for both damage models are implemented into the finite element code ABAQUS/Explicit, via VUMAT user-defined material subroutines, within the framework of large strains and a fully three-dimensional formulation.
During the Nakazima drawing simulation, each specimen is clamped all around its circumferential edges so that the material flow is prevented. The Coulomb friction coefficient is taken equal to 0. 03 for the contact between the punch and the specimen, while it is taken equal to 0. 1 for the contact between the die, the holder and the specimen (see  Kami et al. , 2015). In addition, a holding force of 100 kN is applied during the forming process. The forming tools are modeled as discrete rigid bodies, while the blank is modeled with the eight-node three-dimensional continuum finite element with reduced integration (C3D8R), which is available in the ABAQUS/Explicit software. Note that particular attention has been paid to optimizing the mesh of the blank, as illustrated in Figure  5. Indeed, the central part of the blank, which is subjected to large plastic strains, is discretized with a fine mesh, while the rest of the blank is discretized with a coarse mesh.
CONCLUSIONS In this work, four different necking criteria have been proposed and compared for the prediction of FLDs for the AA6016-T4 aluminum alloy. For the material constitutive modeling, two approaches to ductile damage have also been considered: the Lemaitre continuum damage theory and the GTN damage description, which was extended to the Hill'48 quadratic yield surface to account for the plastic anisotropy of the material. Both damage models have been numerically implemented into the commercial finite element code ABAQUS/Explicit via the user-defined material subroutine VUMAT. The main contributions of the current study and associated conclusions may be summarized as follows: • The Lemaitre damage parameters have been identified using an inverse identification procedure based on FE fitting of an experimental load-displacement response of a standard tensile test; • Based on FE simulations of the Nakazima deep drawing test and four different localized necking criteria, numerical FLDs have been determined for the AA6016-T4 aluminum sheet and compared with the experimental FLD.
Acknowledgements This research was supported by the  Austrian Science Funds (FWF)  and the  Agence Nationale de Recherche (ANR)  in the joint project  IMAGINE  ( FWF  project number  I1115-N19 ,  ANR  project  12-IS04-0006 ) and by the  EGIDE-O ¨AD AMADEUS Austrian-French exchange programme  (no  28948WD  and  FR 11/2013 ). The Avance III 700 MHz NMR spectrometer was co-financed by the  European Union  through the  INTERREG IV ETC-AT-CZ programme  ( EFRE RU2-EU-124/100-2010 , project  M00146  ' RERI-uasb '). Berangere  Dubrulle-Bre  ´on is acknowledged for helpful discussions on fluctuation-dissipation theorem.
2 × SSC) at 37 °C. Hybridized mRNA was detected using sheep antibody anti-digoxigenin conjugated with horseradish peroxidase (Roche, Indianapolis, IN, USA; 1:50 v/v) and peroxidase activity was revealed by 3,3′diaminobenzidine (DAB) reaction. Sections were counterstained with Toluidine blue and mounted with Permount (Thermo Fisher Scientific). Slides were visualized with a Nikon E800 microscope (Nikon, Melville, NY, USA) and images acquired using a CoolSNAP-Pro CCD digital camera and Image-Pro Express Software (Media Cybernetics, Silver Spring, MD, USA).
Myeloperoxidase (MPO) activity MPO activity was measured as an index of granulocyte infiltration, as previously described  [27]. Briefly, cell pellets from knee joint lavages were homogenized in a potassium phosphate-buffered (pH = 6) solution containing 0. 5% hexadecyltrimethylammonium bromide. MPO activity was measured in the presence of o-dianisidine dihydrocholoride (Sigma-Aldrich) by optical density readings at 450 nm in a FlexStation 3 microplate reader (Molecular Devices, Sunnyvale, CA, USA). Sample results were interpolated into a linear regression generated with a standard curve of MPO (0. 05-0. 8 U/mL; Sigma-Aldrich). Data were expressed as units of MPO/mL.
Cytokine and chemokine quantification The concentration of IL-1β, -6, -17A and (C-X-C) ligand (CXCL)1/KC in the supernatant of knee joint washes was determined by using CBA Flex Kits, according to the manufacturer's instructions (BD, Franklin Lakes, NJ, USA). Data were acquired in a FACSCanto II flow cytometer (BD) and analyzed with the program FCAP Array v3. 0 (Soft Flow Inc. , Pecs, Hungary). Detection limits for IL-1β, IL-6, IL-17A and CXCL1/KC were 4. 32, 9. 01, 8. 72 and 10. 48 pg/mL, respectively.
Acknowledgements We acknowledge  Drs. Mireille Sebbag  and  Gilles Dietrich  for their valuable inputs on the manuscript and  Dr. Nicolas Cenac  for the assistance with the histopathological analysis. The authors acknowledge the technical assistance provided by  Daniela Teixeira  from the flow cytometry facility of the  Department of Microbiology, Immunology and Parasitology  and  Jacilene Barbosa  from the  INFAR DNA Sequencing and Molecular Biology facility ,  UNIFESP-EPM ;  Sophie Allart  and  Astrid Canivet  from the  CPTP Imaging facility ;  Florence Capilla  and  Christine Salon  and the animal facility staff of  US006.