dataesr/scientific-paragraphs-categorization huggingface dataset:
5%) for which Spec cPL concentration was above 400 μg/L. For these dogs, misdiagnosis could not be excluded, as up to 23% of dogs with acute abdominal disease not related to AP might present Spec cPL results consistent with AP. 48 condly, the retrospective design of the study explains the lack of data for several dogs. Therefore, variables associated with death were possibly falsely excluded because of insufficient statistical power (eg, metabolic acidosis). Also, some risk factors were not tested and could have proven useful in the score determination. For example, cardiovascular injury was not assessed because relevant data necessary to determine this variable were lacking in many cases. Likewise, concomitant diseases such as hyperadrenocorticism or hypothyroidism have not been investigated as a potential risk factor for death because this information was not always available at the time of admission or investigated during AP management.
s -1 during the pulse at 220 mm from the electron output window. DQing was adjusted so as to obtain the same in-depth profile as at CONV dose-rate. The following experiments were performed by varying the pulse width, the number of pulses (repeat frequency 100 Hz) or the distance to the electron output window. (vi) The formation of the MV •+ radical was followed by online optical detection and compared to the signal integral measured at the primary collimator. The beam-on time was below 500 ms, in such a way that no correction for the secondary decay of the MV •+ radical (see § 3. 2) was necessary. (vii) The experiment was repeated by substituting EBT3 films for the methyl viologen cuvette using a PMMA stack providing the same water-equivalent depth (3. 75 mm). Data were blinded. 24-h after irradiation the films were digitized using either an Epson Expression 11000XL, 48-bit color depth flatbed scanner (Suwa, Japan) and FilmQA Pro software following the OneScan protocol (Ashland Advanced Materials), and/or by recording the optical absorption spectrum of the films using a Hitachi (Tokyo, Japan) U-2000 spectrophotometer.
4 mm glass fiber and 70 µm copper layers. The scintillating screen (0. 5 mm thickness gadolinium-based plastic material) converts the energy lost by the radiation into photons which are reflected by a mirror and collected by the photodetectors of a CCD camera (a 540 nm wavelength filtration is obtained limiting the spectral analysis). A variable aperture collimator system (iris) allows modifying the amount of light reaching the CCD camera. The detector signal from the CCD camera is digitalized with 10-bit depth. Dedicated software Lynx 2D ™ is used for image acquisition, raw data correction for image geometrical distortion and background noise. Single frame images with adjusted exposure time can be collected to obtain 2-D dose distributions from the scintillation screen.
-Data analysis Data were analyzed using Kaleidagraph software (Synergy software, Reading, Pennsylvania) to fit time-dependent processes to linear or non-linear mathematical equations according to the Gauss-Levenberg-Marquardt algorithm  [11] ; unless otherwise stated, the results were expressed as mean ± standard deviation. The goodness of fit relative to the functions y = ax or y = ax + b, was appreciated using a Spearman's test with StatEL software (AD Software, Paris).
-Monitoring beam profiles using the Lynx ™ scintillation detector The transverse dose distribution of the electron beam, as well as its characteristics in terms of linearity with the pulse width and dependence on the grid voltage were measured with the Lynx ™ mounted at various positions in front of the emission window, perpendicularly to the beam axis. The "in-pulse" (peak) dose-rates were set at 0. 4-3. 5 10 6 Gy. s -1 throughout. Data analysis was performed in MATLAB ™ Version R2012a. The results (Figure  12 ) show that the response in dose was linear in the range explored. The FWHM value measured at 600 mm from the electron output window was 135 mm. The symmetry of the beam was assessed as the FWHM variation at each angle on a transverse beam profile and was within 1% for all tested conditions (high and low dose-rate).
FUNDING This work was supported by the  Agence Nationale de la Recherche  ( ANR-14-CE36-0008 program ), the  Comprehensive Cancer Center  " SIRIC" program  ( INCa   2011-189 ) of  Institut Curie  and the  Nanotherad IDEX (Paris-Saclay University). Generous financial aid from  Mrs. Marie Mahler  ( Gisikon, Switzerland ), is also acknowledged.
REFERENCE GENOME: ANNOTATION AND CHROMOSOME MAPPING We used an existing reference genome from a male swamp sparrow  (Deane-Coe et al. 2018). To obtain more accurate information on chromosome position, scaffolds were assigned to chromosomes using the Chromosemble command in Satsuma  (Grabherr et al. 2010 ) based on assigned chromosomes in the zebra finch (Taeniopygia guttata) reference genome. We annotated the swamp sparrow assembly with the MAKER pipeline version 2. 31. 8  (Cantarel et al. 2007 ). Gene models were created using the zebra finch. Ensemble protein and cDNA databases (downloaded July 7, 2017 from fhttp://useast. ensembl. org/Taeniopygia_guttata/Info/ Index?redirect=no). Genes were predicted using SNAP using an iterative process to train the program. This produced a total of 13,733 gene models, which represented 71% of the genes annotated in the zebra finch genome.
DISCOVERY Genomic DNA was extracted using the DNeasy blood and tissue kit (Qiagen, CA, USA) and quantified with the Qubit dsDNA BR Assay Kit (Life Technologies). For the 57 song, savannah, and Nelson's sparrows, we prepared individually barcoded libraries using 1 µg of DNA following the TruSeq DNA PCR-free library preparation kit protocol (San Diego, CA, USA), with an insert size of 350 bp. We pooled 24 libraries using concentrations of adapter-ligated DNA determined through digital PCR into one group. The pooled libraries were sequenced on three Illumina NextSeq500 lanes at the Cornell Institute for Biotechnology core facility. The quality of individual libraries was assessed using FastQC version 0. 11. 5 (http://www. bioinformatics. babraham. ac. uk/projects/fastqc). Resequencing data from the 23 swamp sparrows have been previously published and were obtained from  Deane-Coe et al.
2009 ). We realigned around indels and fixed mate-pairs using GATK version 3. 5  (McKenna et al. 2010). SNP variant discovery and genotyping for the 80 resequenced individuals was performed using the unified genotyper module in GATK. We used the following filtering parameters to remove variants: QD < 2, FS > 40. 0, MQ < 20. 0, and HaplotypeScore > 12. 0. Variants that were not biallelic had minor allele frequencies less than 5%, mean coverage less than 2X or more than 50X, and more than 20% missing data across all individuals were additionally filtered from the data set. To maximize the number of variants within species, we called variants for each comparison separately. This resulted in 13,025,553 SNPs for savannah sparrows, 2,680,218 SNPs for Nelson's sparrows, 2,333,568 SNPs for song sparrows, and 12,352,927 SNPs for swamp sparrows.
DEMOGRAPHIC ANALYSES To estimate the demographic history associated with each uplandsalt marsh split, we fit a range of demographic models to the joint SFS of the upland and salt marsh population for each of the four species in ai version 1. 7  (Gutenkunst et al. 2009 ). Each demographic model consisted of a split between the salt marsh and upland population and we modeled a series of demographic scenarios both with continuous and without gene flow between the two populations (see Fig. S14  for all models and parameters). To generate the joint-SFS input for aI, we filtered VCF files output from GATK for each species using the program VCFtools  (Danecek et al. 2011 ) to include SNPs with mean coverage greater than 8X and less than 50X that were present across all individuals and were biallelic.
We did not filter based on minor allele frequency as these rare variants are important for demographic inference. Next, we removed SNPs that mapped to the z-chromosome, as the z-chromosome has a smaller effective population size than the autosomes. Finally, we excluded all SNPs that were mapped to exons or intervals within 100 kb of exons to produce a final, putatively neutral data set to reduce bias due to selection or linked selection, which can significantly bias demographic inference  (Schrider et al. 2016). This filtering resulted in data sets of  59,586, 128,803, 25,267, and 25,597  SNPs for savannah, swamp, Nelson's, and song sparrows, respectively. ai input files were created from VCF files using perl script developed by Kun Wang (https://github. com/wk8910/bio_tools/blob/master/ 01.
DEMOGRAPHIC SIMULATIONS We simulated a SNP data set based on the best-fit demographic model and parameter estimates from ai within the coalescent simulator msprime  (Kelleher et al. 2016)  to account for the potential influence of the inferred demographic history on the genomic distribution of summary statistics used to infer outliers (i. e. , F ST , pi, and Tajima's D). For each species, we simulated 1072, 1 mb regions to approximate the length of the whole genome sequences. For all simulations, we assumed a passerine mutation rate of 3. 3 × 10 -9  (Zhang et al. 2014 ) and a recombination rate of 0. 14 cm/mb (1. 4 × 10 -8 in msprime units) estimated from Estrildidae finches  (Singhal et al. 2015). We calculated F ST for each SNP, and nucleotide diversity (pi) and Tajima's D for 25 kb windows across the simulated data set within the python package scikitallel  (Alistair and Harding 2017).
We then inferred the mean, SD, and 95th and 99th percentiles for the distribution of these summary statistics to compare with observed data from each species pair. We compared the cutoff used to identify outliers with the simulated distribution for each summary statistic to ensure that cutoffs were conservative and neutral demography did not bias our inferences of outlier loci. Second, we ran a series of simulations to account for the high uncertainty associated with some parameters. For each species pair, we simulated a SNP data set and calculated the F ST distribution as above 1000 times while randomly drawing parameter values for the demographic model from a uniform distribution bounded by the upper and lower 95% CIs of each parameter. We inferred the 95th and 99th percentile for each simulated F ST distribution and then compared the 99th percentile of the distribution of these percentiles from all 1000 simulations to the empirical cutoff (mean F ST + 5 × SD).
POPULATION GENOMICS AND PATTERNS OF DIVERGENCE For each of the four species' upland-saltmarsh comparisons, PCA was performed on all SNPs using the SNPRELATE package in R  (Team 2016). We calculated nucleotide diversity (pi), individual heterozygosity, and Tajima's D using 25 kb windows in VCFtools. We characterized genome-wide patterns of divergence by calculating F ST values using VCFtools. We calculated F ST for both 25 kb windows and for individual SNPs. Divergent peaks were visualized using Manhattan plots, which were constructed using the R package qqman. Within each species comparison, we classified windows as divergent if mean F ST was more than 5 standard deviations above the genome-wide mean. We report results based on a 5 standard deviation cutoff after simulations based on demographic data confirm that this is a conservative approach to identifying outliers.
To identify potential selective sweeps in elevated regions of differentiation, we compared values of Tajima's D and pi inside and outside of outlier windows (i. e. , assessing whether regions of elevated differentiation had corresponding dips in Tajima's D and pi). To do this in a way that accounted for differences in sample size between neutral and elevated windows, we used a permutation test to compare the Tajima's D and pi estimates from the outlier windows to the same number of randomly chosen neutral windows. Finally, differentiated peaks were inspected in Geneious version 9. 1. 5  (Kearse et al. 2012 ) and compiled a list of gene models within 50 kb of each region and obtained information on these annotations from the UniProt database (http://www. uniprot. org/). To characterize putative candidate genes, we used ontology information from the Zebra Finch Ensemble database.
ACKNOWLEDGMENTS This material is based upon work supported by the  National Science Foundation Postdoctoral Research Fellowship in Biology  under grant No. DBI 1523719 ,  NSF   DEB-1555754 , and the  Cornell University Center for Vertebrate Genomics. We thank  M. Correll ,  K. Ruskin ,  M. Emond , and  R Zembal  for help in the field. We thank  L. Campagna ,  D. Toews ,  N. Hofmeister ,  D. Hooper ,  E. Miller ,  T. Nguyen ,  S. Billerman ,  J. Berv ,  S. Aguillon , and three anonymous reviewers for valuable feedback and comments on an earlier draft of this manuscript. The authors declare no conflict of interest.
When < → ∞, the classical time-independent plasticity expression is recovered. Therefore, the evolution laws can be expressed as follows: x 9w = £ x 9w ¤ =NŸ =NŸ and -x = £ x 9w ¤ =NŸ =NŸ = x 9w (17) where £ x 9w = > " x 9w 4 N x 9w is the Lagrange viscoplastic multiplier homogenous to a strain rate. Using a backward Euler method, the previous constitutive laws have been time-discretized, and the resulting incremental laws have been implemented into the finite element code Cast3m®  [20].
I. 4 Objectives of the work The Gθ-integral can be computed by means of the procedure G_THETA implemented in the finite element code Cast3m®. This procedure can deal with elastic, elasto-plastic and viscoplastic problems based on 2D, 3D or axisymmetric geometries, and can account for the behavior of homogenous, non-homogeneous or composite materials. It can also be used to separate the mixed modes for homogenous and isotropic materials. However, this procedure is complicated and it's very difficult to adapt it to external constitutive laws. In addition, by analyzing the analytical form of Gθ-integral, one can notice that it is expressed in term of displacement, strain and stress mechanical fields. In this context, the idea was to apply directly the Gθ integral form based on the CH_THETA procedure implemented into the finite element code Cast3m® in order to create a * field.
3 amplification was significantly lower in late-stage Rag2 À/À OTII p53 À/À T cell lymphomas, as compared to early-stage Rag2 À/À OTII p53 À/À T cell lymphomas (p = 0. 007) (Figure  3E ). These results show that T cell development block in Rag2 À/À p53 À/À animals contributes to the onset of early T cell lymphomas carrying clonal 9qA4-5. 3 amplifications. OncoGenomic Analysis of the 9qA4-5. 3 Amplicon in Mice and Humans Mouse 9qA4-5. 3 corresponds to the syntenic 11q23. 3-25 region in humans that contains 142 genes, including 11 genes (ARHGAP32, ARHGEF12, CBL, DDX6, ETS1, FLI1, HINFP, KCNJ5, MLL/KMT2A, PAFAH1B2, and PCSK7) reported within the network of cancer genes database  (An et al. , 2016 ) (Figure  4A ). 11q23 is frequently rearranged or amplified in hematological malignancies due to the presence of the mixed-lineage leukemia gene (MLL, also termed KMT2A for lysine [K]-specific methyltransferase 2A), whose alterations represent one of the most common recurring oncogenic events in leukemia  (Greaves and Wiemels, 2003; Yunis et al.
, 1989; Zeisig et al. , 2012). While MLL aberrations most frequently occur in the form of chromosomal rearrangements leading to the production of chimeric fusions, partial tandem duplications, and internal exonic deletions, studies have revealed amplification of the associated genomic region without characteristic MLL rearrangements in approximately 1% of AML and rare cases of myelodysplastic syndrome, as well as acute lymphoblastic leukemia  (Greaves and Wiemels, 2003; Yip and So, 2013). Because these studies relied primarily on focus cytogenetics, we thought that the frequency of this amplicon in leukemia might have been underestimated. To test this possibility, we looked for amplification of the region 11q23. 3-25 in a series of 187 AML samples for which copy number alteration data were available within The Cancer Genome Atlas (TCGA) database  (Ley et al.
Mouse 9qA4-5. 3 corresponds to the syntenic 11q23. 3-25 region in humans that is frequently rearranged or amplified in acute leukemia and that accounts for more than 70% of infant leukemias  (Greaves and Wiemels, 2003; Yip and So, 2013; Yunis et al. , 1989). This region contains 11 genes, including MLL, reported within the network of cancer genes database  (An et al. , 2016). Interestingly, focal 11q23 amplification without characteristic oncogenic MLL fusions  (Liu et al. , 2009)  is thought to occur in approximately 1% of AML and Myelodysplastic syndrome (MDS) and is associated with adverse outcomes  (Yip and So, 2013). Through mining the genomes of 187 adult de novo AML patients  (Ley et al. , 2013) , we identified 11q23 amplification in 5. 3% of the samples, with 2. 7% of the cases harboring focal 11q23 amplifications, indicating that genetic instability at this locus might account for a higher number of (A) Syntenic map of mouse chr.
The following antibodies were used for cell surface staining: anti-CD4 (RM4-5, 1:200 dilution), anti-CD8 (53-6. 7, 1:200 dilution or YTS156. 7. 7, 1:200 dilution), anti-CD3e (145-2C11, 1:200 dilution), anti-CD44 (IM7, 1:200 dilution), anti-CD25 (PC61, 1:200 dilution), anti-TCRb (H57-597,1:200 dilution) and anti-CD28 (E18, 1:200 dilution). Flow cytometry was performed on a FACS Canto II (BD Bioscience) and data were analyzed using FlowJo (TreeStar).
ACKNOWLEDGMENTS We thank the  Institut Pasteur genomics platform  and the  New York Genome Center team  for help with whole-genome sequencing;  Philippe Bousso  for providing Rag2 À/À OTII animals;  Ana Cumano  for providing the anti-CD28 antibody; and  Erika Brunet  and  Thomas Mercher  for helpful discussions. The  Deriano Lab  is funded by the  Institut Pasteur , the  Institut National Du Cancer  ( PLBIO16-181 ) as well as by the  European Research Council  under the  ERC starting grant  agreement  310917. J. J. B. is a BioSPC/UniversiteParis 5 and  Fondation pour la Recherche Medicale  ( FDT20170739035 ) doctoral fellow.
METHOD DETAILS Flow cytometry analysis of tumor cells Lymphoid tumors were analyzed by flow cytometry with antibodies against surface T cell markers (anti-CD4 (RM4-5, 1:200 dilution), anti-CD8 (53-6. 7, 1:200 dilution or YTS156. 7. 7, 1:200 dilution), anti-CD3e (145-2C11, 1:200 dilution), anti-CD44 (IM7, 1:200 dilution), anti-CD25 (PC61, 1:200 dilution), anti-TCRb (H57-597, 1:200 dilution) and anti-CD28 (E18, 1:200 dilution)) and surface B cell markers (anti-B220 (RA3-6B2, 1:200 dilution), anti-CD43 (S7, 1:150 dilution), anti-CD19 (1D3, 1:200 dilution), anti-IgM (R6-60. 2, 1:150 dilution), anti-IgD (11-26c. 2a, 1:200 dilution), anti-c-Kit (2B8,1:300 dilution)). Flow cytometry was performed on a FACS Canto II (BD Bioscience) and data were analyzed using FlowJo (TreeStar).
Using deep wide-field photometry three-year data (Y3) from the Dark Energy Survey (DES), we present a panoramic study of the Fornax dwarf spheroidal galaxy. The data presented here -a small subset of the full survey -uniformly covers a region of 25 square degrees centered on the galaxy to a depth of g∼ 23. 5. We use this data to study the structural properties of Fornax, overall stellar population, and its member stars in different evolutionary phases. We also search for possible signs of tidal disturbance. Fornax is found to be significantly more spatially extended than what early studies suggested. No statistically significant distortions or signs of tidal disturbances were found down to a surface brightness limit of ∼ 32. 1 mag/arcsec 2. However, there are hints of shell-like features located ∼ 30 ′ -40 ′ from the center of Fornax that may be stellar debris from past merger events.
We also find that intermediate age and young main-sequence populations show different orientation at the galaxy center and have many substructures. The deep DES Y3 data allows us to characterize the age of those substructures with great accuracy, both those previously known and those newly discovered Wang et al. in this work, on the basis of their color-magnitude diagram morphology. We find that the youngest overdensities are all found on the Eastern side of Fornax, where the Fornax field population itself is slightly younger than in the West. The high quality DES Y3 data reveals that Fornax has many rich structures, and provides insights into its complex formation history.
However, their data was only marginally able to reach the MSTO of Fornax, resulting in only a low number of tracer stars beyond the tidal radius. In contrast, the Fornax system and its environs have been covered recently by the DES survey using deep and homogeneous imaging from the Dark Energy Camera (DECam;  Flaugher et al. 2015)  mounted on the 4m Blanco Telescope at Cerro Tololo Inter-American Observatory in Chile  (Flaugher et al. 2015). The resulting data is deeper than any previous wide-field studies such as  Bate et al. (2015)  and therefore allows for a better se-lection of different stellar tracer features from the CMD to reduce contamination in its low luminosity outskirts. In this article we present an extensive wide-field study of Fornax's stellar population using deep g and r band photometry reaching down to the MSTO stars from DES Y3 data that covers 25 deg 2 of the Fornax dSph.
DATA DES is a deep, wide-area imaging survey in the grizY bands performed with the DECam mounted on the 4-m Blanco Telescope at Cerro Tololo Inter-American Observatory in Chile. Here, we use wide-field imaging data from the first three years of DES operation (DES Y3). DES Y3 is the first DES data set to cover the full DES footprint, which covers ∼ 5000 deg 2 of the southern Galactic cap including the Fornax dSph galaxy area. The details of the DES Y3 data reduction can be found in  Morganson et al. (2018) , and the definition of the stargalaxy classification model can be found in  Shipp et al. (2018). Here we briefly describe some of the procedures. The DES Y3 images were processed by the DES data management pipeline. Individual exposures were remapped to a consistent pixel grid and coadded to increase imaging depth  (Morganson et al.
CONCLUSIONS AND DISCUSSIONS In this work we utilize the DES Y3 data that has homogeneous wide-field coverage of the Fornax dSph galaxy down to a depth of g, r ∼ 23. 5 to study several properties of the galaxy. We have fitted the Fornax structural parameters with several different model including Plummer, Sersic, Exponential, and King profiles, and found that Sersic model gives the best fit to the data while other models seem to fail to capture the complex light profile shape of Fornax. We also found that our data indicates Fornax is more extended than what was shown in previous studies. For example our results show slightly larger half-light radius than the literature values, which were derived either from shallower data or incomplete coverage. Our derived King tidal radius r t , which has the value of 77.
We have studied the young populations in Fornax by focusing on the distribution and morphology of blue stars (gr <0) on the young MS. Stars that occupy this region of the CMD have ages typically below 2 Gyr, and can be used to study the spatial distribution of Fornax in a regime where previous studies have seen hints of interactions or accretion  (Coleman et al. 2004 (Coleman et al. , 2005)). The depth of DES Y3 data allows us to study the stellar population content in young stars with greater accuracy than was previously possible using other wide-field surveys such as VST/ATLAS. The spatial density of young stars (see Figure  6 ) shows a very different morphology than the distribution of old stars in Fornax. While the dominant 4-7 Gyr old stars have a position angle of nearly 45 degrees, the inner young stars are in bimodal distribution that is more aligned along the right ascension direction.