dataesr/scientific-paragraphs-categorization huggingface dataset:
1 s pred s role Feed Forward Bilinear Feed Forward Multi-head self-attention + FF J Syntactically-informed self-attention + FF PRP VBP:PRED DT NN VBG:PRED. Multi-head self-attention + FF r I saw the sloth climbing (Abadi et al. , 2015) in TensorFlow(Abadi et al. , 2015)is available at : http://github. com/strubell/ LISA p.
In total, 558 F2 progeny were produced, among which 372 were used for QTL detection (genotyping and phenotyping in infectious challenge). The 186 remaining un-phenotyped progeny were added to the genotype dataset in order to construct a more precise linkage map. At about three months post-hatching, the 372 QTL progeny were anaesthetized with 2-phenoxyethanol (0. 2 mL/L), individually tagged (intraperitoneal implantation of a micro chip "Biolog-Tiny ID") and reared under standard conditions (constant 10 °C and a commercial diet) until infectious challenges.
When mortality reached a plateau (49 and 35 days for the immersion and injection challenge, respectively), surviving fish were sacrificed by anaesthetic overdose, weighed and identified. A piece of caudal fin was clipped from all individuals at the time of identification and stored in 100% ethanol for DNA extraction. Two fish from the immersion challenge and three fish from the injection challenge were discarded because tag recording was not possible. For each challenge, the post-challenge dataset included body weight at the time of challenge, survival status of each fish (dead or alive at the end of the challenge) and time to death (in days after infection, for dead fish only).
Single nucleotide polymorphism discovery and genotyping First, sequencing reads were demultiplexed and assigned to a single individual allowing no mismatch in the P1 barcode and one mismatch in the restriction site. Data from seven samples from F2 progeny that had less than one million reads were removed from the analysis. In order to facilitate detection of PSV  [49] , the dataset was supplemented with 20 DH individuals that were used as external controls. These DH individuals were sequenced in previous projects using the same RAD-sequencing methodology and restriction enzyme (unpublished data). For SNP calling, sequence reads were processed through a de novo analysis using the core pipeline of the software Stacks version 1. 19  [53, 54]. PCR duplicates were removed using the Stacks clone-filter program.
Quality control of SNPs and removal of duplicated loci Sequence data from the two F1 individuals were used to identify polymorphic and monomorphic loci. To be consistent with the pedigree of the QTL family (DH progeny of a cross between two DH homozygous grandparents), only bi-allelic loci were considered (17,460 out of 20,305 polymorphic loci identified in the Stacks catalogue). DH control population The two F0 grandparents and the 20 external DH individuals served as controls to detect putative duplicated loci. Since all DH individuals are expected to be homozygous, a heterozygous genotype at a given locus indicates a PSV rather than a true allelic variant. Therefore, all loci that appeared heterozygous in at least two DH control individuals were discarded (list provided in Additional file 2: Table  S1 ).
Construction of the linkage map The 1. 2 version of the CarthaGène software  [58, 59]  was used to build the F2 family linkage map. The DH progeny were described as a backcross in the CarthaGène software. The group command was used, with the thresholds for two-point distance (Haldane/Ray) and logarithm of odds (LOD) set at 0. 3 and 15, respectively. Linkage groups were assigned to trout chromosomes by blasting the sequences of RAD markers on the most recent published reference trout genome, Omyk_1. 0 [60].
QTL detection QTL mapping was performed by chromosome with the QTLMap software  [61]  (version 0. 9. 8). For each chromosome, the hypothesis that one QTL (H1) versus no QTL (H0) affects the trait of interest was tested with the interval mapping method described in  [62] , using an approximate likelihood ratio test (LRT  [63] ) and scanning the chromosome in intervals of 1 cM. To take into account the fact that the F2 individuals are gynogenetic doubled haploids, they were coded as half-sib from a single sire (F1) and an unknown virtual dam that was different for each F2 fish  [41]. The two challenges, injection and immersion, were analysed separately. The effects of body weight at challenge and aquarium on survival were tested with the average-to-average method (ANOVA) model on time to death and the logistic regression on the status as the end of the challenge with the R software, version 3.
Using the variable STATUS, it was also possible to refine the model to search for additional QTL that might have been masked by effects of the main QTL and/ or by epistatic interactions between QTL. A new model ( M2 ) was applied, in which aquarium and the QTL detected for STATUS with model M1 were considered as fixed effects, along with interactions between the QTL used as co-factor and the newly detected QTL. To control the false discovery rate due to multiple-testing, the P values associated with interactions were corrected with the Benjamini-Hochberg method (BH)  [67]  implemented in the R software, version 3. 4. 2 [64]  (stat package version 3. 6. 0, option p. adjust). Finally, ENDURANCE, which was defined as the time until death for fish that died during the experimental period  [68] , was investigated as a complementary description of possible host-pathogen interaction during infection.
Because the test was available only for the unitrait model for the time to death, fish that survived were given a time of death at d + 1, with d the day of death of the last fish that died, but it never reached the chromosome-wide significance level. The percentage of phenotypic variance explained by a QTL in the DH progeny was calculated with the R software  [64] , using ANOVA for ENDURANCE and logistic regression for STATUS.
Genotypes calls and linkage map The catalogue of polymorphic loci, established with 511 individuals (507 unique F2's, 2 F1's and 2 F0's), contained 17,460 bi-allelic loci of which 2867 were discarded from further analysis since they were putative duplicated loci (i. e. they were heterozygous in at least two DH controls, see list in Additional file 2: Table  S1 ). After removing fish with a genotype call rate lower than 20% (n = 444) and markers with more than 70% missing genotypes (n = 11,570), 24 additional individuals that exhibited a rate of heterozygous loci higher than 1% were removed before the last filtering step based on MAF (> 0. 30) and marker call rate (> 90%). The final dataset was composed of 9715 polymorphic loci and 427 F2 progeny (including 310 QTL progeny that were challenged with F.
psychrophilum and 117 individuals with no phenotypic record). Of the 9715 markers, 9654 were mapped to 30 linkage groups (see Additional file 2: Table  S3 ). The total length of the linkage map was 2645. 2 cM. Linkage groups were successfully assigned to chromosomes using the genome assembly Omyk_1. 0 [60]. As previously described  [71, 72] , chromosome 25 (Omy25) is separated into two chromosomes in the INRA SY population. In this paper, Omy25a corresponds to the short arm of Omy25 and Omy25b to its long arm. The 9654 markers accounted for 2130 distinct positions on the genetic map (see Additional file 2: Table  S4 ). At each position, only the marker with the best call rate was kept for further QTL detection (see Additional file 2: Table  S3 ). The final dataset for QTL detection included 310 F2 progeny, one F1 and the two F0 individuals, and 2130 markers.
Funding This project is part of the  RE-SIST  project " Improvement of disease resistance of farmed fish by selective breeding " selected at the 15th " Fonds Unique Interministériel ". This project was labelled by the competitiveness clusters  AQUIMER, Agrimip Innovation ,  Mer Méditerranée  and  Mer Bretagne , and funded by the  French Government BPI France , by the  Bretagne ,  Languedoc-Roussillon  and Aquitaine regional authorities, and by the  Landes and Pyrénées Atlantiques regional councils. The research leading to these results has received funding from the  European Community 's  Seventh Framework Programme  ( FP7/2007-2013 ) under Grant agreement No. 262336  (AQUAEXCEL). This work was performed in collaboration with the  GeT core facility, Toulouse, France  (http://get. genotoul.
Acknowledgements Authors are thankful to the staff of PEIMA and IERP INRA fish facilities for their help in fish production, rearing and management of infectious challenges, to M. Boussaha (INRA) for his help with the CarthaGène software, to P. Le Roy (INRA) for her helpful advice in using the QTLMap software, to T. Callet and D. Lallias (INRA) for their help with the candidate gene detection. Authors are also thankful to P. Haffray and S. Brard-Fudulea (SYSAAF) for their welcome at SYSAAF and for helpful discussions, and to P. Daniel (Laboratoires des Pyrénées et des Landes, Mont-de-Marsan, France) for kindly providing the Flavobacterium psychrophilum strain used in this study. We are grateful to the Genotoul bioinformatics platform Toulouse Midi-Pyrenees for providing help, computing and storage resources.
Statistical analysis Data were expressed as mean values±standard error. Repeated measures ANOVA was used to compare heart rate, wave amplitude and duration, and duration of P-R, Q-T and R-R intervals among different periods and McNemar's test was implemented for comparison of wave configurations. Statistical analysis was performed using SPSS 17 (SPSS for Windows, version 12, SPSS Inc, Chicago, Illinois). Differences were considered statistically significant when the calculated P value was less than 0. 05. Different small superscripts (a, b, c and d) show significant difference (P<0. 05).
Molecular modeling NBD1 and NBD2 crystal structures were retrieved from Protein Data Bank (PDB: 2BBO and 3GD7). All the ligands and cofactors were removed; hydrogen atoms were added to the protein structure using Autodock 4. 2  (Morris et al, 2009). The missing part of the structure 2BBO (aa 405-435) was added, even if it does not influence the following in silico procedures. Same can be applied for the amino acid mutations (F409L, F429S, F433L, G550E, R553Q, R555K, H667R). To minimize contacts between hydrogens, the structures were subjected to Amber force field keeping all the heavy atoms fixed. Peptides P31-43 (LGQQQPFPPQQPY) and 4QA (LGQAAPFP-PAAPY) were built using PEP-FOLD3, by generating five clusters sorted using sOPEP energy value  (Morris et al, 2009). Protein-protein docking analysis was performed using two FFTbased docking software packages PIPER  (Shen et al, 2014)  and Zdock  (Kozakov et al, 2006).
All the peptides produced by the combination of different amino acid substitutions were subjected to PEP-FOLD3 protocol and docked against NBD1 through the combined PIPER/Zdock approach. The peptide presenting an Ala substitution in 4 th , 5 th , 10 th , and 11 th positions (4QA) was selected as the best solution as control peptide unable to interact with NBD1 (sampling percentage of only 12% compared to the 75% of P31-43). The same protein-protein docking and molecular dynamics approaches were used to investigate the binding of P31-43 to CFTR structure obtained via electron microscopy (PDB code: 5UAK) and parameterized as described before. In this particular case and during molecular dynamics processes, the transmembrane domains and the R-Domain were kept fixed, the first being immersed in a membrane system, the latter because its position is not completely determined in the structure.
Each sensorgram (time-course of the surface plasmon resonance signal) was corrected for the response obtained in the control flow cell and normalized to baseline. Data were analyzed using the 2. 0. 3 BIAevaluation software (GE Healthcare). At least three independent experiments for each analysis were performed. Peptide-protein interactions were further studied exploiting a different biochemical strategy: recombinant NBD1, both wild type and/or its mutants, was incubated at 4°C for 30 0 in 40 mM Tris pH 7. 5 in the presence of the biotinylated P31-43 peptide unless otherwise indicated and resolved in native conditions by  BN-PAGE (Novex, Invitrogen). The complexes were then blotted onto PVDF membrane in accordance with the manufacturer's instructions, and the interacting partners (biotinylated peptide/binding proteins) were detected with streptavidin-HRP antibody (PerkinElmer).
Short-circuit current [expressed as Isc (lA/cm 2 )] and resistance were acquired or calculated using the VCC-600 transepithelial clamp from Physiologic Instruments and the Acquire &Analyze2Á3 software for data acquisition (Physiologic Instruments), as previously described  (Gondzik & Awayda, 2011; Marchelletta et al, 2013; Tosco et al, 2016; Romani et al, 2017). To evaluate the effect of the direct addition of P31-43 (100 lM each) to the bathing solution, the solution was supplied with 100 lM amiloride after stabilization and then: (i) P31-43 or the control peptide (100 lM each) was directly added to the bathing solution for 3-5 min before adding forskolin (20 lM; for a minimum of 5 min under each condition) or (ii) P31-43 (100 lM) was directly supplied, as before, 3-5 min after forskolin stimulation.
ELISA ELISA was performed on tissue samples using standard ELISA kits (R&D Systems) for IL-1b, TNF-a, Mip2a, IL-15, IL-17A, IFN-c, IL-21, IL-10, and TGF-b. According to the manufacturer's instructions, samples were read in triplicate at 450 nm in a microplate Reader (Bio-Rad, Milan, Italy) using Microplate Manager 5. 2. 1 software. Values were normalized to protein concentration evaluated by Bradford analysis.
Proximity ligation assay The proximity ligation assay was performed using Duolinkâ in situ reagents (Olink Biosciences) following the manufacturer's specifications. The cells were fixed with 4% PFA in PBS for 15 min at room temperature. After blocking with 0. 1% Triton X-100 and 0. 5% BSA dissolved in PBS, the cells were incubated overnight at 4°C with primary antibodies. After incubation with Duolink PLA anti-rabbit Plus and anti-mouse Minus probes (1:5 dilution, Olink Bioscience) at 37°C for 1 h, ligation, rolling circle amplification, and detection were performed using the Duolink In Situ Detection Reagents Red (Olink Bioscience). Nuclei were counterstained with DAPI. PLA signals were documented by means of a Leica SP8 confocal microscope and quantified with CellProfiler software for image analysis  (Festa et al, 2018).
Statistical analysis GraphPad Prism software 6. 01 (GraphPad Software) was used for analysis. Data are expressed as means AE SD. Statistical significance was calculated by ANOVA (Bonferroni's post hoc test) for multiple comparisons and by Student's t-test for single comparisons. We considered all P-values < 0. 05 to be significant. The in vivo groups consisted of 10 mice/group. The data reported are either representative of at least three experiments. Expanded View for this article is available online.
Acknowledgements We thank  B. Scholte  ( Erasmus Medical Center Rotterdam ), who provided Cftrt-m1EUR mice ( F508del mice, European Economic Community European Coordination Action for Research in Cystic Fibrosis program  EU  FP6 SHMCT-2005-018932 ). This project was supported by the  Italian Institute of Health , under the frame of E-Rare-2, the  ERA-Net for Research on Rare Diseases "RescueCFTRpreclinic"  (to LM and GK), by the  Specific Targeted Research Project FunMeta  ( ERC-2011-AdG-293714  to LR). GK is supported by the  Ligue contre le Cancer Comité de Charente-Maritime  (équipe labelisée);  Agence Nationale de la Recherche  ( ANR )-Projets blancs;  ANR  under the frame of E-Rare-2;  Association pour la Recherche sur le Cancer (ARC) ;  Cancéropôle Ile-de-France ;  Chancelerie des universités de Paris  ( Legs Poix ),  Fondation pour la Recherche Médicale (FRM) ; a donation by Elior; the  European Commission (ArtForce) ; the  European Research Council (ERC) ;  Fondation Carrefour; Institut National du Cancer (INCa) ;  Inserm (HTE) ;  Institut Universitaire de France ;  LeDucq Foundation ; the  LabEx Immuno-Oncology ; the  RHU Torino Lumière ; the  Searave Foundation ; the  SIRIC Stratified Oncology Cell DNA Repair and Tumor Immune Elimination (SOCRATE) ; the  SIRIC Cancer Research and Personalized Medicine (CARPEM) ; and the  Paris Alliance of Cancer Research Institutes (PACRI).
5 g peak , 1. 0 g peak , and 2. 0 g peak ) and sweeping frequencies (either sweeping up or sweeping down within the range between 10 Hz and 600 Hz) are applied on the KEH by the vibrator. The sweeping rate is 1 Hz/s. The models chosen for measurement are the ones offering the maximum capacitance variation ratio either in air or in vacuum (i. e. , Models G and R). The prototypes are characterized in both with and without the mini-ball, in air and in vacuum, respectively. The prototype is biased by a DC voltage (varying from 20 V up to 45 V), and loaded with an optimal resistor of 6. 6 MΩ. The voltage on the resistive load is read by the data acquisition card, and the average output power corresponding to each frequency is calculated accordingly and recorded by the LabVIEW program. In AC/DC power conversion experiment, the KEHs are biased with varied DC voltage (from 5 V to 65 V).
Singlefrequency sinusoidal acceleration with constant amplitude (10 Hz, 2 g peak ) is applied to the vibrator. The output signal of the prototype is rectified by half-wave, and the energy is stored with a reservoir capacitor C res = 1 μF. The voltage evolution with time is monitored by the data acquisition card, and recorded by LabVIEW program, and the power is calculated accordingly. During the experiment of data transmission, the KEH is excited either by a vibrator driven by sinusoidal signals or by the hand shaking motions. The energy from the prototype is rectified and stored in a reservoir capacitor C res = 1 μF, and the voltage across it (V res ) is monitored by the data acquisition card. The energy in C res is released to a data transmission module through a manually controlled mechanical switch, as long as the voltage reaches the maximum allowable voltage, and the power supply is suspended when V res drops below the minimum allowable voltage  23.
The data communication module implements an RFID chip EM4324 provided by EM Microelectronic, the working voltage of which is 1. 1 V to 3. 3 V. The RFID chip communicates with a remote reader under the framework of EPC Gen-2 Class-1 standard at the frequency of 868 MHz. The tag reading is performed periodically by an Impinj reader from a distance above the maximum distance of passive reading (2. 5 m). The emission power of the reader is 1 mW, and the time slot between two tag readings is 38 ms. The measurement electronics can be found in the supplementary materials, including the circuits for capacitance measurement, AC power measurement, AC/DC power conversion and data transmission, respectively. The model of the amplifiers (U 1 and U 2 ) is OPA445 from Texas Instruments, while the diodes are low-leakage models PAD5 from Vishay.
Statistical Analysis Continuous data were expressed as median and interquartile range, and categorical variables were expressed as frequency. Overall survival (OS) was defined from the date of original mbp-RFA to the patient's death, or the last date of follow-up, the last visit. Follow-up was recorded until June 1, 2015. Patients who underwent liver transplantation during follow-up were censored at the date of transplantation. Tumor RFS (including local tumor progression and distant recurrence) was measured from the date of original mbp-RFA to the date of the first tumor progression or death or last date of follow-up without tumor progression. Survival curves were estimated using the Kaplan-Meier method. Univariate and multivariate Univariate Cox proportional hazards regressions were performed to determine the parameters associated with OS and RFS in naive patients.
Medical data concerning childhood cancer (type of cancer, year and age at diagnosis, type of treatment) were obtained from medical records. All other data came from the interviews. The interview guide was structured around the health and social trajectories of individuals. Besides the description of immediate and longterm effects of cancer or other unrelated diseases, participants were asked how they currently dealt with late effects of childhood cancer. In addition, the participants were invited to depict the larger familial and social context in which their health trajectory took form, as well as the extent to which they had incorporated the illness in their identity. To investigate the subjective meaning of childhood cancer for interviewees, and to explore the way cancer had been integrated in their personal history and identity, we asked about the doing of cancer narratives, i.
e. how cancer had been evoked in the family, in particular with parents, and, over the life course, with friends, partners, children, and significant others. Interviews lasted one hour and a quarter, on average. All were tape recorded and transcribed. We used an inductive approach in data analysis  (Strauss and Corbin 1998). We followed the pattern coding approach suggested by  Miles and Huberman (1994). Content analysis was computer-assisted with qualitative data analysis software (Nvivo). The study received approval from the national commission controlling data collection in France (CNIL) and from the Ethics Committee of the French National Institute of Medical Research and Health (INSERM). Informed consent to inclusion in the study was obtained from all participants. Initials and names have been changed for this article.
Mapping the underlying density field, including non-visible dark matter, using weak gravitational lensing measurements is now a standard tool in cosmology. Due to its importance to the science results of current and upcoming surveys, the quality of the convergence reconstruction methods should be well understood. We compare three methods: Kaiser-Squires (KS), Wiener filter, and Glimpse. KS is a direct inversion, not accounting for survey masks or noise. The Wiener filter is well-motivated for Gaussian density fields in a Bayesian framework. Glimpse uses sparsity, aiming to reconstruct non-linearities in the density field. We compare these methods with several tests using public Dark Energy Survey (DES) Science Verification (SV) data and realistic DES simulations. The Wiener filter and Glimpse offer substantial improvements over smoothed KS with a range of metrics.
from measurements of galaxy shapes. Images of distant galaxies are deformed by the inhomogeneous matter distribution along the line of sight. Any matter can contribute to the lensing effect, making it a direct probe of non-visible dark matter. Weak lensing, which takes advantage of the statistical power from many small distortions (that is, gravitational lensing induced "shears"), is now a well established tool in constraining cosmology. The Dark Energy Survey (DES) has used the 2-point correlation function of shear to contribute to excellent constraints on cosmological parameters and models, including the nature of dark energy (DES  Collaboration et al. 2017). Shear 2-point correlation functions have been used to constrain cosmology from many other survey datasets  (van Uitert et al. 2017 , Kilbinger et al.
(2015)  and  Vikram et al. (2015)  in which the original DES SV mass map was created using the  Kaiser & Squires (1993)  method. In this paper we compare three quite different methods: Kaiser-Squires (KS); Wiener filtering  (Wiener 1949) ; and Glimpse  (Leonard et al. 2014 , Lanusse et al. 2016 ), a sparsity-based reconstruction method. The Kaiser-Squires method is a direct inversion from shear to convergence, taking no account of missing data or the effect of noise. The Wiener filter and Glimpse assume different prior knowledge about the underlying convergence to account for the effects of noise and missing data. In Sec. 2 we describe the theoretical foundation for weak lensing mass mapping and the three different methods used for this work. In Sec. 3 we describe the DES SV shear data, the accompanying simulations, and the redMaPPer galaxy cluster catalogue.