dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgment The authors would like to thank  A. Calabrese ,  M. Borghi ,  A. Trenti ,  G. Abbiati ,  J. Lebreuilly , and  M. Flaim  for their helpful comments and discussions, and  E. Moser  for his technical support. Author contribution:  Both S. Biasi  and  F. Ramiro-Manzano  conceived and have made a substantial and equal contribution to all the stages of the study, including writing the paper. F. Turri  has participated in the experiment. Mher Ghulinyan has designed and fabricated the samples. Pierre-Élie Larr é has contributed in the theoretical phase extrapolation. I. Carusotto was the theoretical supervisor and  L. Pavesi  was in charge of the general supervision of the work and contributed to the text.
Overall description of the M. abscessus intracellular transcriptomes RNAseq data from M. abscessus planktonic or intracellular cultures (3 to 4 replicates per condition) were analyzed and compared to identify M. abscessus genes that were up-or down-regulated after Ac and Mϕ co-cultures. Differentially expressed genes (DEG) are thus defined as genes for which expression changes between intracellular and planktonic growth. Transcriptomes of M. abscessus in Ac 4 and 16 hours post-infection (hpi), in Mϕ 16 hpi and transcriptomes of M. chelonae in Ac 16 hpi were obtained and invariant genes were excluded from the analyses. Normalization and hierarchical clustering of normalized raw data confirmed the technical quality of transcriptomes (S1 Fig). DEGs were identified using the DESeq2 package  [30]  (S1 Table ) and the fold change (FC) values were recorded.
NGS sequencing and data analyses Sequencing and statistical analyses were performed in the Transcriptome and Epigenome platform (PF2) of the Pasteur Institute, Paris, France. The cDNA libraries for strains M. abscessus subsp. massiliense 43S and M. chelonae CCUG 47445 were prepared and sequenced on an Illumina HiSeq 2500 system by performing an SRM run (SR: Single Read, PE: Paired-end Reads, M: multiplexed samples) of 51 cycles with 7 index bases read. The quality of the sequencing was assessed with the external FastQC program (https://www. bioinformatics. babraham. ac. uk/projects/fastqc/). After the trimming of adapter sequences and low-quality reads with cutadapt version 1. 11, reads were aligned with RefSeq assemblies (M. abscessus subsp. massiliense strain GO06 assembly (GCF_000277775.
2); M. chelonae CCUG 47445 assembly (GCF_001632805. 1), using the Bowtie software version 0. 12. 7 (http://bowtie-bio. sourceforge. net/index. shtml) with defaults parameters. Genes were counted using feature-Counts 1. 4. 6-p3 from Subreads package (parameters: -g gene -t ID -s 1). Differential analysis of gene expression was performed using the R software (version 3. 3. 1) and the Bioconductor packages DESeq2 (version 1. 12. 3) [30]  using the default parameters and statistical tests for differential expression were performed applying the independent filtering algorithm. A generalized linear model was set in order to test for the differential expression between the biological conditions. For each pairwise comparison, raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg (BH) procedure  [70]  and genes with an adjusted pvalue lower than 0.
05 were considered differentially expressed. Gene orthologs of M. massiliense and M. chelonae genes in the genome of the M. abscessus subsp. abscessus CIP 104536T reference strain were determined by Bi-directionnal Best Hit (BBH) searches using the Opscan software (http://wwwabi. snv. jussieu. fr/public/opscan/). Differentially expressed genes assignment to COGs was performed using the COG automatic Classification from the MicroScope database  [71]. The percentage assignments were compared by performing Fisher's exact tests. GO enrichment analyses were performed with the R software topGO package (Bioconductor)  [72]. Protein signatures were addressed using InterProScan tool (https://www. ebi. ac. uk/ interpro/search/sequence-search).
V. D. was supported by  French Cystic Fibrosis Patients Association Vaincre la Mucoviscidose (VLM)  grant  RF20150501377. Work in the laboratory of R. B. was supported by the  Agence National de Recherche  ( ANR-10-LABX-62-IBEID ,  ANR-16-CE15-0003 , and  ANR-16-CE35 -.
09 NC NC (3. 06E-04) MYCMA_RS13910 Acyltransferase MAB_2035 NC NC NC MYCMA_RS13905 Membrane protein (MmpS) MAB_2036 -1. 16 NC -1. 06 (1. 36E-02) (6. 55E-03) MYCMA_RS13900 Hypothetical protein (MmpL) MAB_2037 -0. 68 -0. 86 -0. 72 (8. 24E-03) (8. 24E-03) (6. 97E-07) MYCMA_RS13895 Transporter MAB_2038 NC NC NC MYCMA_RS13890 Lipase (LipH) MAB_2039 NC 0. 86 0. 64 (1. 61E-02) (7. 73E-03) a Mma gene: Mycobacterium massiliense gene (accession number NC_018150. 2). b Mabs gene: Mycobacterium abscessus gene (accession number NC_010397. 1). c NC: no change in gene expression P-values are indicted in brackets. https://doi. org/10. 1371/journal. ppat. 1008069. t001.
During testing, the system was supplied with humidified hydrogen (SHE, anode) and nitrogen (cathode) at a flow rate of 200 mL min -1. The amplitude sinusoidal signal was 10 mV, and the frequency was in the range between 100 kHz and 10 Hz. A DC bias potential of 0. 45 V was used to record the spectra. The conductivity values were calculated according to Eq. (  3 ). Each sample was measured at least five times after it reached a constant value to ensure good data reproducibility.
The thermal decomposition of the sulfonic groups (T OD and T FD values are higher than 240 ˚C and 260 ˚C, respectively (Table  4 )) are in accordance with published data on SPSU, PSU and fluorinated PES copolymers  [27, 20, 21]. This behaviour is similar to that reported for other PEMs based on PES block copolymers. Thus, multiblock copoly(arylene ether sulfone)s show T d5% values above 310 ˚C under similar experimental conditions  [42]. In addition, TGA under isothermal conditions are performed at 100 ˚C, and after 12 h, a loss between 1. 3-2. 8% (Table  4 ) is observed, very close to the weight loss in the first step on the kinetic curve (Figure  3 ). The thermal transitions of the sulfonated copolymers are analysed by DSC. SPES membranes show only one glass transition temperature (T g ) ranging from 184 to 187 ˚C as a function of IEC values (Table  4 ).
Acknowledgements This work was supported by mobility grant of IAAB from  Universidad Carlos III de Madrid  and the Projects from the  regional government [Comunidad de Madrid  through  MATERYENER3CM S2013/MIT-2753  and  S2013/MAE-2975  PILCONAER along with  European Social Fund (ESF) ]. In addition, funds from the  Spanish Government, MINECO  [ MAT2016-78362-C4-3R  and  ENE2017-86711-C3-1-R ] are gratefully acknowledged.
Detailed results for the preprocessing are reported in the Appendix. Computational environment. All the experiments, including the runs of the branch-and-price algorithm from  [12] , are performed on a computer with an i7-6900K processor clocked at 3. 20 GHz and 64 GB RAM under GNU/Linux Ubuntu 16. 04. We use CPLEX 12. 7. 1 and the Concert Technology framework to implement our branch-and-cut algorithms. The Compact Formulation is solved with the CPLEX MIP solver. CPLEX is run in single-threaded mode and all CPLEX parameters are set to their default values. A time limit of one hour is set for each tested instance. Table  2  Instance features (Intersection graphs).
Acknowledgements The authors are indebted to two anonymous referees and one technical editor for their constructive and useful comments. Enrico Malaguti  is supported by the  Air Force Office of Scientific Research  under Award Number  FA9550-17-1-0025. This is a pre-print of an article published in Mathematical Programming Computation. The final authenticated version is available online at: https://doi. org/10. 1007/s12532-019-00167-1.
Statistical analyses Statistical analyses were performed using R 3. 1. 0 (R Development Core Team) opensource software. Linear models created from the nlme package  (Pinheiro et al. , 2018)  were used to study growth parameters with ANOVA, including the effects of water deficit, O3 and genotype. The growth chamber was also tested and excluded from the models because the effect was not significant for all the parameters tested throughout the whole experimental period. Model parameters, G, g0, λ, τ, SLmax were explored in the same way. The lme4 package  (Bates et al. , 2015)  was used to fit a linear mixed-effect model on gas exchange and chlorophyll content data with fixed variables (water deficit and O3 data) whereas biological replicas were random variables. Residual plots of the model were used to assumed heteroscedasticity and variance homogeneity.
Acknowledgements Nicolas Dusart was supported by a PhD grant from the  Ministère de l'Enseignement Supérieur et de la Recherche. The team was supported by the  French National Research Agency through the Laboratory of Excellence ARBRE  ( ANR-12-LABXARBRE-01 ). We thank  S. Martin  for taking care of the O3 facilities and the  nursery of Guéméné-Penfao  for providing the cuttings. This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.
The third isoform was related to an unknown variant of LEDGF-p52 due to the presence of an unusual exon 11 (Figure  S1C ). Using the Human Splicing Finder (www. umd. be/HSF3/) and Sroogle (http://sroogle. tau. ac. il) software, one splice acceptor site and several branch points were predicted upstream this atypical LEDGF exon 11 (Figure  S2 ). The potential impact of the detection in the blood and bone marrow samples from our patient of three NUP98-LEDGF fusion transcripts differing due to an alternative LEDGF exon 11, including one that was unknown, remains to be determined. Moreover, the two shorter versions of NUP98-LEDGF protein lack the IBD domain which would connect these fusion proteins to MLL biology (Figure  S3 ). Overall, we report a novel N9/L10 NUP98-LEDGF molecular rearrangement distinct from N8/ L3, 12 N9/L5, 16 N9/L7,  11, 14  N11/L8,  15  and N12/L8  15  junctions previously reported in the literature (Table  S1  and Figure  S3 ).
Procedure All first-year students at the University of Cape Town in 2017 and Stellenbosch University in 2015 and 2017 (N = 14,575), were invited via email to participate in an anonymous online self-report survey. A total of 1407 students completed the survey (participation rate = 9. 7%). To be included in the study students had to be 18 years or older, and enrolled for the first time at University. Students who did not identify as either male or female (n = 4) and who did not disclose their disability status (n = 1) were excluded from data analysis because there were too few cases to enable a meaningful analysis of these subgroups.
Funding This research was funded by the  MRC Unit on Risk & Resilience in Mental Disorders  and a grant from the  South African Medical Research Council  (awarded to  Jason Bantjes ). The research was also supported by postdoctoral funding made available by  University of Stellenbosch  to  Wylene Saal  and a grant from the  Ithemba Foundation  (awarded to  Janine Roos ). The funders played no role in the design of this research project, collection of data, analysis of data, interpretation of data, or the preparation of this manuscript.
| Image acquisition and quantitative analysis Images were acquired using an Olympus FV-1200 Upright Confocal Microscope or a Zeiss Axio-Imager-Apotome. Z-series of optical sections were performed at 0. 3 μm increment, and blue, green, red, and far-red fluorescence were acquired sequentially. Maximum orthogonal projection of images and plot profiles of immunofluorescence intensity were carried out using Fiji software (NIH, Bethesda, Maryland). At least 50 GABAergic neurons per coverslip, identified by GAD67 + immunostaining, were counted, and the percentage of GAD67 + neurons with Na v /AnkG clusters was determined for at least two coverslips per condition. Results were expressed as mean ± SEM of at least three independent experiments. p-value between the tested condition and control condition were calculated using the Mann-Whitney test, unless otherwise specified.
1% formic acid loaded at 30 μL/min for 8 min; peptides were then separated on a PepMap Acclaim analytical column (0. 075 × 500 mm 2 , 3 μm C18 particles; Thermo Fisher Scientific) at 300 nL/min on a linear gradient of 5-50% acetonitrile in 0. 1% formic acid over 100 min. The 10 most intense precursor ions (m/z 300-2000 and charge state or 2+ or 3+) were isolated at a width of 1. 5 Da, and selected for MS/MS using collision-induced dissociation with a normalized collision energy of 38%. Dynamic exclusion option was enabled with a repeat count of one and exclusion duration of 30 s. Raw data were proceeded using Proteome Discoverer v1. 4 (Thermo Fisher Scientific) with Mascot v2. 4 (Matrix Science, London, UK) against Uniprot (UP Human without isoform, 14. 3 release version), following LC-MS/MS analysis.
(a) Representative diagram of partially overlapping proteomic content of an active (13, green) and an inactive (15, blue) fraction, with 61 proteins present in both fractions, 76 proteins only in the active fraction and 118 only in the inactive fraction. (b) Short list of candidates retained for further testing. Indicated parameters are the percent coverage of the total protein sequence by the identified peptides (Σ coverage), the number of identified peptides that are unique to this protein (no overlap with other proteins in the database) (Σ# unique peptides) and the peptide spectral match (Σ# PSMs), that is, indicating how many times the mass spectra match that of the peptide sequence. Values corresponding to the active fraction (  13 ) are in green and to the inactive fraction (15) are in blue.
ACKNOWLEDGMENTS We thank  Elior Peles  and  Jérome Devaux  for the kind gift of plasmids or antibodies. We thank  Marc Davenne  for discussion and critical reading of the manuscript. We thank  Plateforme d'Imagerie Cellulaire de la Pitié-Salpêtrière  for support with image acquisition. This work was supported by  INSERM , the  French MS research foundation ARSEP, Bouvet-Labruyère prize  to N. SF. The authors declare no competing financial interests.
The tests were performed on a computer controlled Instron 8800 Servo-Hydraulic machine at a constant nominal strain rate of 7. 4x10 -4 s -1. Five samples were deformed for each orientation to ensure data reliability. For the compression tests, Teflon strips were used to reduce the friction between the sample surface and the compression platens. The tension tests were carried out on flat specimens along the extrusion direction with dimensions: 5 mm gage length, 20 mm total length and 0. 5 mm thickness. The mechanical responses were acquired in terms of engineering stress-strain curves. Further, the obtained data were numerically computed to obtain the true stress-strain curve. The CD∥ED samples were deformed to true compression strains of 0. 04, 0. 08, 0. 12 and 0. 18, whereas the CD⊥ED samples were deformed to strains of 0.
Finally, the residual stress surface layer was removed by electrolytic polishing in a solution of ethanol and ortho-phosphoric acid (volume fraction -3:5) at ~0ºC, using a stainless-steel cathode at 3 V for 30 s and 1. 5 V for 2 min  (Biswas et al. , 2010). The orientation mappings were performed using the HKL Channel 5 software. To ensure significant statistics, large areas containing well over 2500 grains were scanned. The acquired data were post-processed using the TSL and ATEX software  (Beausir and Fundenberger, 2017).
j@chu-toulouse. fr Accepted Oct 18, 2019; Epub ahead of print Oct 21, 2019 The novel homozygous missense mutation c. 704G>A (p. Gly235Glu, rs756591404) in P1 was already referenced in some databases, but showed a very low frequency in the Exome Aggregation Consortium (ExAC) with no homozygous individuals for the alternate allele. It affected a highly conserved position and the substitution Gly235Glu was predicted to be deleterious for the protein (in silico protein prediction tools SIFT, Polyphen-2). P2 was compound heterozygous for c. 551A>G (p. Asp184Gly) and c. 563G>A (p. Arg188His). The mutation c. 551A>G had already been reported in 2 families and may affect the function of the protein  (3, 4). The mutation c. 563G>A was unreported. It was predicted as disease-causing by disturbing normal splicing.
Interestingly, a similar pathogenic mechanism was predicted for the previously reported c. 562C>T (p. Arg188Cys) mutation, which affected the same codon (3). P3 was compound heterozygous for c. 309A>G (p. Trp103Ter) and c. 826C>T (p. Arg276Cys). The nonsense variant c. 309A>G was unreported and not referenced in databases. It can be predicted to result in either mRNA decay or in the synthesis of a truncated protein. The previously unreported mutation c. 826C>T showed a very low frequency with no homozygous individuals for the alternate allele and was predicted to be deleterious for the protein (in silico protein prediction tools SIFT, Polyphen-2).
Numerical Results In this section we initially focus on the convergence and the validation of the proposed methodology, before examining different models and measurements for metal characterization at THz and photonic frequencies. Finally, the characteristics of ring resonator filtering structures are studied. Both the geometry design and the mesh initialization are performed using the free open-source software SALOME,  [55]. Concerning the proposed FEM technique, an in house code is developed and incorporated in the open-source platform FEniCS,  [56].
2012; Lanéelle et al. 2013) ; depending on the strains shorter homologues, i. e. C16:0 to C30:0, can be also present. FT-IR measurements have been performed by using a Bruker Alpha II spectrometer allowing an advanced stabilization of source and detector against environmental changes. Measurements have been carried out in ATR mode combining a Platinum ATR module equipped with a diamond crystal, at a resolution value of 3 cm -1 and covering a frequency range between 400 cm -1 and 3500 cm -1. A number of 96 scans has been acquired for each of the two samples investigated for each system. The data collection and the spectra standard reduction (baseline and atmospheric corrections) have been carried out by using the OPUS software. Due to the overlapping of the peaks, the analysis of the complex bands has followed a two-step procedure: in order to identify the component bands, the second derivative has been evaluated as a pre-analysis providing the frequency values and limiting the arbitrary choice of the parameters for the band deconvolution (by using three different software: OPUS 7.
2011; Marguet et al. 2006). FT-IR measurements have been performed on bacterial cells in order to provide an identification of different strains by the investigation of five main spectral regions, which has been used for food characterization and for creating bacterial databases  (Davis and Mauer 2010; Naumann et al. 1991; Naumann 2000; Oberreuter et al. 2002; Filipa et al. 2004; Jiang et al. 2004). The qualitative comparison between the existing spectra of bacterial cells and our data on mycolates extracted from the corynebacterial mycomembrane opens the way for different conclusions: i) the five regions that are usually characterized for the bacterial investigations  (Davis and Mauer 2010; Naumann et al. 1991; Naumann 2000; Oberreuter et al. 2002)  show vibrational features which are analogous to those observed in our extracted TMM-TDM spectrum, so allowing to conclude that mycolates and carbohydrates play a key role strongly affecting the whole membrane and bacterial behavior; ii) although a series of isolation and extraction procedures have been applied to obtain the mycolate mixture, the similarity of the bacterial and mycolate mixture spectra and especially the presence of all the significant peaks related to the vibrational modes, whose characterization allows the bacterial identification, represent a validity proof of our approach; iii) the presence of protein traces in our FT-IR mycolate mixture spectrum revealed itself a great advantage, since in the bacterial IR spectra the amide I and amide II contributions often predominate  (Davis and Mauer 2010; Filipa et al.
We develop a comparative analysis of the processes of dynamic necking and fragmentation in elasto-plastic and hyperelastic ductile rings subjected to rapid radial expansion. For that purpose, finite element simulations have been carried out using the commercial code ABAQUS/Explicit. Expanding velocities which range between 25 m/s and 600 m/s have been investigated. The elasto-plastic material and the hyperelastic material are modelled with constitutive equations which provide nearly the same stress-strain response during monotonic uniaxial tensile loading, and fracture is assumed to occur at the same level of deformation energy. The computations have revealed that, while the number of necks nucleated in the elasto-plastic and hyperelastic rings is similar, the mechanisms which control their development are significantly different.
The numerical perturbations introduced by the software are sufficient to perturb the field variables, breaking the symmetry of the problem and thus allowing for flow localization  (Rusinek and Zaera, 2007; Vadillo et al. , 2012). It was discussed in the works of  Rodríguez-Martínez et al. (2013a ,b, 2017)  and Vaz-Romero et al. (2017) that, while the numerical perturbations are not controlled by the user, at high strain rates they do not dictate the average distance between necks but they just allow for the localization to occur. It was shown that the localization pattern obtained in ABAQUS/Explicit calculations, in non-linear elastic and elasto-plastic materials, is controlled, to a large extent, by the constitutive behaviour of the material, inertia effects and stress multiaxiality. Moreover, we have also checked that the numerical perturbations have small influence in the fragmentation results reported in this paper.
Acknowledgements AM and JARM acknowledge the support by the  French State  through the program Investment in the future operated by the  National Research Agency (ANR)  and referenced by  ANR-11-LABX-0008-01  (LabEx DAMAS). AVR acknowledges the financial support obtained from the  University Carlos III of Madrid  through the  programme Ayudas para la movilidad -Convocatoria 2017. The research leading to these results has received funding from the  European Research Council (ERC)  under the European Union's  Horizon 2020 research and innovation programme. Project PURPOSE , grant agreement  758056.
GTEx data preprocessing, filtering and merging We downloaded NHGRI GTEx v6. 0 imputed genotyping data and RNA-seq data (phs000424. v6. p1, 2015-10-05 release) from dbGaP (approved protocol #9112). The RNA-Seq data were preprocessed by using Bioconductor R YARN package  17  and normalised in a tissue-aware manner by using smooth quantile normalisation Bioconductor R qsmooth package. 18 We identified and removed GTEx-11ILO due to potential sex misannotation. We also filtered out sex chromosomes and mitochondrial genes, retaining 29,242 genes. We excluded five sex-specific tissues (prostate, testis, uterus, vagina and ovary) and grouped skin samples from the lower leg (sun exposed) and from the suprapubic region (sun unexposed) based on overall gene expression similarity between these sites. For our analysis, we only considered tissues for which we had both RNA-seq and imputed genotyping data for at least 200 individuals.