dataesr/scientific-paragraphs-categorization huggingface dataset:
e. compass bearing) from the release point were recorded. The visually determined vanishing direction was also confirmed as the direction providing the strongest signal from the tag attached to the released hornet. The tracking team, made up of a Sika receiver operator and data recorder, would quickly relocate along the vanishing direction, checking for the direction of strongest signal reception. The tracking team was restricted to using public roads or paths, municipal recreational areas, or land where prior permission to enter had been sought. Consequently, the tracking team could not follow the hornets' flight paths directly but had to triangulate from accessible locations. Variation in the detected signal's strength or direction from a location would indicate whether a tagged hornet was likely stationary or in flight.
Such searching continued until either observed or daylight faded. When a nest was found, its location was recorded and the local hosts (INRA in France; and Department of Environment in Jersey) informed to enable them to activate the locally appropriate management plan and limit the impact of V. velutina. Analysis. Each captured hornet was weighed and all behavioural information recorded after tagging, through to the location of nests. For a range of tag weights and hornet weights, the tag:hornet weight ratio was calculated to determine the threshold relating to good flight performance (Fig. 2 ). Distances between release point and nest location were calculated from the latitude and longitude of the two points (Fig. 3 ). All data are included in the Supplementary Tables. Statistical analysis.
Acknowledgements We thank  Olivier Bonnard  for discussions, sourcing materials, and advice on locating foraging V. velutina workers at  INRA Bordeaux-Aquitaine. We also thank members of  Jersey Beekeeping Association  for their assistance in catching V. velutina workers in Jersey. The work was funded by a  Defra  research project grant ( PH0532 ), with additional support by the  States of Jersey Department of Environment  and generous philanthropic donations by the  South West Beekeeping Associations' Forum (SWBKF) ,  Somerset Beekeeping Association, Dorset Beekeeping Association, Cornwall Beekeeping Association, West Cornwall Beekeeping Association, Devon Beekeeping Association, Bournemouth & South Dorset Beekeeping Association , and  B. J. Sherriff. We are grateful to  INRA Bordeaux-Aquitaine, States of Jersey Department of Environment, and Durrell Wildlife Park  for their welcome and permission to use facilities at their institutions.
The BLLIP parser is a statistical natural language parser which creates several candidate syntax parses of a given sentence and ranks n-best among them. Another advantage of using the BLLIP parser is that it supports NLTK module  [23] , so one can easily manipulate syntactic trees created by the BLLIP parser. Thus, in our research, the BLLIP parser and NLTK modules are mainly used tools for simplification task. Lastly, our system is written in Python 3. 5 and operates on Linux. Coarse simplification system. Our goal at the coarse simplification level is basically to split subordinate phrases from a matrix phrase so that information extraction algorithm treats shorter phrases and yields more accurate results. More specifically, our coarse system splits subordinate phrases that begin with a subordinate conjunction such as if, until, so that, because or relative adverbs such as, when, where, why, but it doesn't split relative clauses, which begin with a relative pronoun such as who, that, which.
Recall and precision score of PatExtractor V 2. 0 for partial solution and problem is as shown in the Table  3. To evaluate the system, we randomly chose 250 patent documents with different topics and extracted information from them. During our experiment, however, we did not observe a significant improvement on precision score after the integration of the coarse simplification system. The precision remained roughly the same (its improvement rate was less than 0. 1%) and recall was not measured because given the structure of the entire system, our simplification does not affect the recall of the algorithm. Nevertheless, more interesting observation could have been possible if more test data, especially annotated data were available. Given the fact that only a small number of phrases are selected to classify and simplify from one patent text, the phrases that were finally used for evaluation (from 250 corpora) were not large in number.
Statistical Analyses Data are expressed as the mean ± standard error of the mean (SEM), as specified in the individual tables and figures. The differences between two groups were assessed using an unpaired, two-tailed Student's t-test. Data sets involving more than two groups were assessed by one-way ANOVA followed by a Tukey's post-hoc test. The differences were considered statistically significant for p < 0. 05, and different superscript letters indicate significant differences between groups. The data were analysed using Software GraphPad Prism 6. 01 (La Jolla, CA, USA). providing the sheep cheese (sheep-1-ENCH) and Aker Biomarine (Oslo, Norway) for providing the fish pills used in the first and second studies, respectively; Actalia (Surgeres, France, P. Gaborit and A. Lauret) for manufacturing the goat cheese (goat ENCH) and J.
Acknowledgments: This work was funded by the  EU  Project  QLK1-2002-02362  and  INNOVA. RE-WP 2. 3-P. O. R. -F. E. S. R. 2007/2013. This work was also supported by  Science Foundation Ireland (SFI)  under Grant Number  SFI/12/RC/2273. The authors would like to thank  Argiolas Formaggi s. r. l (Dolianova, Italy)  for kindly.
The AhR and IFN Signalling are the Most Significant Canonical Pathways Regulated by B[α]P in Human T Lymphocytes In order to investigate global signaling pathways affected by B[α]P exposure, the 97 up-regulated and the 61 down-regulated transcripts were next submitted to the IPA software. This analysis revealed that "AhR signaling", "Protein Kinase A signaling", "Estrogen-mediated S-phase entry" and "Cell cycle: G1/S checkpoint regulation" pathways were the four most significant pathways in the gene set up-regulated by B[α]P exposure. Regarding the down-regulated genes, the "IFN signaling", the "granulocyte adhesion and diapedesis", the "role of pattern recognition receptors in recognition of bacteria and viruses", and the "activation of IFN regulatory transcription factor (IRF) by cytosolic pattern recognition receptors' pathways were the most significant pathways regulated by B[α]P exposure (Table  2 ).
a p-values were calculated using the IPA software. b The list of genes whose expression was altered by B[α]P treatment was given for each pathway by the IPA software. Among genes belonging to "AhR signaling", we recently reported the regulation of CYP1A1, CYP1B1 and the cyclin-dependent kinase inhibitor 1A (CDKN1A) in human T lymphocytes upon exposure to B[α]P  [16]. The AhR repressor (AhRR), the cyclin E2 (CCNE2) and the NAD(P)H dehydrogenase (NQO1) have already been reported to be robust targets of B[α]P but, in different cell types, but not in primary T lymphocytes  [19, 20]. We then validated by RT-qPCR assays these changes in AhRR, CCNE2, CDKN1A, CYP1A1, CYP1B1, and NQO1 gene expression changes using the 16 individual RNA samples isolated from CTR and B[α]P-treated T lymphocyte cultures (Figure  3A ).
Interestingly, "IFN signaling" and "activation of IRF by cytosolic pattern recognition receptors" pathways were found to be closely associated with genes exhibiting a significant down-regulation in human T lymphocytes treated with B[α]P (Table  2 ). RT-qPCR analysis further validated the gene expression down-regulations of IFIT3, MX1, OAS1 expressions (all related to "IFN signaling") and of the RNA helicase (DDX58), the IFN-induced protein with helicase C domain (IFIH1) and IFIT2 (all belonging to "activation of IRF by cytosolic pattern recognition receptors") (Figure  3B ), using the same 16 RNA samples as for AhR signaling-related genes (Figure  3B ). Such an analysis identifies these IFN-related proteins as novel target genes for B[α]P. With the aim of better understanding the biological relevance of the changes in the expression of 158 genes upon B[α]P exposure, IPA software was used to analyze the most significant diseases and disordered biological functions regulated in T lymphocytes after B[α]P exposure.
IPA Functional Analysis Revealed the Prominence of Categories Related to Cellular Movement for B[α]P-Regulated Genes in Human T Lymphocytes With the aim of better understanding the biological relevance of the changes in the expression of 158 genes upon B[α]P exposure, IPA software was used to analyze the most significant diseases and disordered biological functions regulated in T lymphocytes after B[α]P exposure. As shown in Table  3 , the five most significant diseases and disorders revealed by such an analysis were cancer, haematological disease, immunological disease, organismal injury and abnormalities, and antimicrobial response. Cellular movement, cell death and survival, cellular function and maintenance, cell-to-cell signaling and interaction and cellular growth and proliferation were the top five significant molecular and cellular functional categories found to be altered in human T lymphocytes after a 48 h treatment with B[α]P (Table  3 ).
Immune cell trafficking, hematological system development and function, tissue morphology, digestive system development and function and lymphoid tissue structure and development were the five most significant categories in physiological development and system function associated with B[α]P-modulated genes in T lymphocytes (Table  3 ). a p-values were calculated using the IPA software. b The number of genes whose expression was altered by B[α]P treatment was given for each diseases and functions by the IPA software. Interestingly, these IPA functional data revealed the prominence of categories related to lymphocyte movement for B[α]P-regulated genes. Based on that, we then decided to focus on gene sets linked to this function. Consistent with our transcriptomic data, and using RT-qPCR on the same pools of RNA as those used in microarray experiments, mRNA expressions of the surface receptors CD226, CXCR5, GPR15, and S1PR1, the interleukin IL-22, the plasma-membrane-associated class I myosin MYO1G, NQO1, and the membrane-bound guanine nucleotide binding protein SOS1 were found to be significantly up-regulated after exposure to B[α]P (Figure  4A ).
As shown in Figure  5B , CXCL12 clearly increased the percentage of migrated T lymphocytes, confirming the response of T lymphocytes to this cytokine, and B[α]P significantly 10 of 18 inhibited this CXCL12-induced chemotaxis. We next developed another transwell assay to evaluate T lymphocyte migration through the blood vessel wall. Therefore, we compared the ability of CTR and B[α]P-treated T lymphocytes to migrate across Tumor Necrosis Factor-α-stimulated HMEC-1 in response or not to CXCL12, which also plays an important role in the transendothelial migration of T cells in response to immune processes  [23]. Interestingly, B[α]P decreased T lymphocyte migration across membrane coated with activated endothelial cells, with a significant inhibition in response to CXCL12 (Figure  5C ). Altogether, these data indicate that B[α]P cause a significant inhibition of the CXCL12-induced chemotaxis and transendothelial migration of T lymphocytes, therefore identifying a novel immunotoxic effect of this contaminant.
Int. J. Mol. Sci. 2018, 19, x FOR PEER REVIEW 9 of 16 inhibited this CXCL12-induced chemotaxis. We next developed another transwell assay to evaluate T lymphocyte migration through the blood vessel wall. Therefore, we compared the ability of CTR and B[α]P-treated T lymphocytes to migrate across Tumor Necrosis Factor-α-stimulated HMEC-1 in response or not to CXCL12, which also plays an important role in the transendothelial migration of T cells in response to immune processes  [23]. Interestingly, B[α]P decreased T lymphocyte migration across membrane coated with activated endothelial cells, with a significant inhibition in response to CXCL12 (Figure  5C ). Altogether, these data indicate that B[α]P cause a significant inhibition of the CXCL12-induced chemotaxis and transendothelial migration of T lymphocytes, therefore identifying a novel immunotoxic effect of this contaminant.
Data Normalization The resulting CEL files were processed using the oligo package available performed in R/Bioconductor  [47]. Data were then normalized and background corrected using the SCAN. UPC package  [48]  with the Brainarray custom CDF file for directly mapping Affymetrix probe to Entrez gene identifiers (hta20_Hs_ENTREZG version 21. 0. 0) [49]. Data were uploaded to the NCBI Gene Expression Omnibus (GEO) repository under the accession number GSE117527  [50]. Lists of genes significantly induced or repressed after B[α]P exposure were also uploaded to the TOXsIgN repository under the accession TSP758  [51].
RT-qPCR Assays Total RNA was isolated from the same independent T lymphocyte cultures isolated from 16 blood donors as used for microarray experiments using the TRIzol method (Thermofischer Scientific) and then reverse-transcribed into cDNA using the RT Applied Biosystems kit (Foster City, CA, USA). qPCR assays were performed using gene-specific primers from Eurogentec (Seraing, Belgium). The amplification curves of the PCR products were analyzed with the ABI Prism SDS software using the comparative cycle threshold method. Relative quantification of the steady-state target mRNA levels was calculated after normalization of the total amount of cDNA tested to a 18S mRNA endogenous reference as previously described  [16].
Statistical Analysis Data are expressed as means ± SEM. Statistical significance of the differences was assessed using GraphPad Instat (GraphPad software, INC. , La Jolla, CA, USA) by paired Student's t test or one-way analysis of variance followed by Student-Newman-Keuls post hoc tests. The criterion of significance was p ≤ 0. 05. Supplementary Materials: Supplementary materials can be found at http://www. mdpi. com/1422-0067/19/11/ 3626/s1. Table  S1 : Genes differentially regulated after treatment of human T lymphocytes with 2 µM B[α]P for 48 h. Figure  S1 : Selection criteria for microarray data.
Acknowledgments: This work was supported by  The French National Research Program for Environmental and Occupational Health of ANSES  with the support of the  Cancer TMOI of the French National Alliance for Life and Health Sciences (AVIESAN)  [ 2014/1/052 ]. Marie Liamin  is a recipient of  ANSES. We would like to thank  Dr Lagadic-Gossmann  for thorough reading of our manuscript.
1  and 2  were generated using the Illumina platform, which was designed for sequencing short reads and has a practical limit of readout at ∼600 bp. In view of this limitation, we also generated data using the single-molecule, real-time technology from Pacific Biosciences, which could generate sequencing data for molecules kilobases in length  (24, 25). Using the platform from Pacific Biosciences, we further sequenced two plasma DNA libraries from each of the groups. We observed that plasma DNA molecules of 600 bp to 2,000 bp in size accounted for less than 4. 8% of the circulating DNA molecules. SI Appendix, Fig. S6  shows data from the Pacific Biosciences platform and indicates that the proportion of long plasma DNA fragments in mice with Dnase1l3 deletion is higher than that of the WT mice or mice with Dnase1 deletion.
Frequency Distribution of Plasma DNA End Motifs and Dnase1l3 Deletion. We next investigated if there might be DNA sequence motifs that would be preferentially cleaved by DNASE1L3. We reasoned that if DNASE1L3 contributed to the generation of plasma DNA fragments, then the preferred DNA sequence motifs would be present at high frequencies in the plasma of WT mice and reduced in the plasma of Dnase1l3 -/-mice. Hence, we ranked the end motifs of plasma DNA in WT mice in descending order of frequencies (Dataset S1, tab "Wildtype"). Then, we removed from this ranked order any end motif that did not show significant reduction in the Dnase1l3 -/-mice (Dataset S1, tab "Dnase1l3 del"). The top 25 end motifs that were found by such a procedure were all within the top 42 motifs defined in WT mice (Dataset S1), and are listed in Table  1.
e. , Mu104, Mu105, and Mu106) were estimated using reads aligned to the Y chromosome. occasionally at close to 2,000 bp. However, such long molecules were present at very low frequencies with the average percentage of DNA molecules from 600 bp to 2,000 bp in size for WT and Dnase1l3 -/-mice being present at 0. 5% and 2. 1%, respectively (SI Appendix, Fig. S6 ). Most significantly, the relative size distributions of plasma DNA fragments for mice with WT or knockout genotypes as observed using the Pacific Biosciences platform were consistent with those observed using the Illumina platform (Fig. 1 ). Since the long plasma DNA molecules above 600 bp in size only represented less than 5% in the sequences obtained by the Pacific Biosciences platform, these results suggest that sequencing data generated using the Illumina platform had already captured the size profile of most of the plasma DNA molecules in our experimental system.
Hence, for subsequent analyses, we focused only on the Illumina platform. From our data, there was no statistically significant difference in both short (<120 bp) and long (>250 bp) DNA between pregnant Dnase1l3 -/-mice carrying Dnase1l3 +/-fetuses and nonpregnant Dnase1l3 -/-mice (long, P = 0. 33; short, P = 0. 85; Wilcoxon rank-sum test; SI Appendix, Fig. S11 ). We concluded that pregnant Dnase1l3 -/-mice carrying Dnase1l3 +/-fetuses had an overall size distribution of plasma DNA that was similar to nonpregnant Dnase1l3 -/-mice. In particular, such pregnancies maintained the relative size shortening of fetal DNA molecules in maternal plasma, compared with their maternal counterparts. However, using the plasma DNA end motif preference data (Table  1 ), one could further obtain insights into the site of action of DNASE1L3.
1. 0 and Real Time Analysis Software v2. 4. 11 (Illumina). After base calling, adapter sequences and low quality bases (i. e. , quality score < 5) on the 3′ ends of the reads were removed. For the analysis of sequencing data, the sequenced reads were aligned to the non-repeat-masked mouse reference genome (NCBI build 37/UCSC mm9) using the Short Oligonucleotide Alignment Program 2 as previously described  (37, 38). Only paired-end reads which were aligned to the same chromosome in a correct orientation with an insert size less than 5,000 bp were used for downstream analysis. For paired-end reads sharing the same start and end aligned genomic coordinates only one would be kept for further analysis, while the rest were deemed to be PCR duplicates and were discarded. SI Appendix, Table  S1  summarizes the number of sequenced fragments of each sample detected by using the Illumina platform.
DNA Sequencing Using the Pacific Biosciences Sequencing Platform. Sequencing templates were constructed using SMRTbell Template Prep Kit 1. 0 -SPv3 (Pacific Biosciences) according to the manufacturer's instructions, except that the amplicon templates were purified with AMPure PB beads (Pacific Biosciences). Sequencing primer annealing and polymerase binding conditions were calculated with SMRT Link v5. 1. 0 software (Pacific Biosciences). Briefly, sequencing primer v3 was annealed to sequencing template, then polymerase was bound to templates using Sequel Binding and Internal Control Kit 2. 1 (Pacific Biosciences). Sequencing was performed on a Sequel SMRT Cell 1M v2 for each template. Each sequencing movie was collected on the Sequel system for 10 h with Sequel sequencing kit 2. 1 (Pacific Biosciences).
Quantification of Anti-dsDNA IgG Antibodies. Plasma was obtained from mice using the same protocol as described above. Anti-dsDNA IgG titers were determined by ELISA using plates precoated with poly-L-lysine (0. 01% wt/vol in PBS) for 1 h at room temperature and then coated with 0. 01 mg/mL calf thymus DNA as an antigen. After incubation with plasma, the amount of bound IgG was measured with an alkaline phosphatase-conjugated goat anti-mouse IgG antibody (1:1,000; Jackson Immunoresearch). Antigenspecific IgG levels were determined using serial dilutions of the plasma from a positive animal as a standard and expressed as units per milliliter. Statistical Analysis. Analysis was performed using custom-built programs written in Perl and R languages. Statistical difference was calculated using the Wilcoxon rank-sum test unless otherwise specified.
ACKNOWLEDGMENTS. This work was supported by the  Research Grants Council of the Hong Kong SAR Government under Theme-Based Research Scheme   T12-403/15 -N; the  Colton Center for Autoimmunity ; the  Lupus Research Alliance ; and  NIH  Grants  AR071703 ,  AR070591 ,  GM007308 , and  AI100853. Y. M. D. L. is supported by an endowed chair from the  Li Ka Shing Foundation.
MS/MS neutral loss scans were applied to detect PE species (neutral loss of 141 amu) and PS species (neutral loss of 87 amu). For the MS analyses, a source temperature of 250 • C and instrument collision energies of 5-45 eV were used; the optimal settings were adjusted for each lipid class. Nitrogen served as the nebulizing agent (20 psi) and as the drying gas (11 µl/min at 250 • C). The spectra, generated by the instrument, were processed by the Mass Hunter Workstation qualitative analysis software (Agilent Technologies, Inc. , Santa Clara, CA, United States), and the individual phospholipid species were quantified using the internal standards and the free software Lipid Mass Spectrum Analysis (LIMSA)  (Haimi et al. , 2006). Using this software, the spectral peak intensities were converted to concentrations expressed as mole percent (mol%) for each lipid species (relative to the total amount in the lipid class).
Acknowledgments: We thank  Nadège Quintin  for the deposition of the strains described in this work in the UBOculture collection (http://www. univ-brest. fr/souchotheque/CollectionLM2E). We are grateful to  Helen McCombie  for helpful improvements to the written English. This work was supported by the  Agence Nationale de la Recherche  ( ANR-10-BLAN-1725 01-Living Deep ). A. T. was supported by a postdoctoral fellowship from the Conseil Général 29 and from Ifremer. T. B. was supported by a Ph. D. fellowship from the  Conseil Régional de Bretagne.
Furthermore, in this clip model, two parameters govern binding to NA: the NA binding pocket constituted by a specific set of amino acids, and the inner stiffness of the clip, arising from the overall helicase structure. We suggest that the total binding energy (E Bi ) governing the clip state is the sum of the interaction energy (E Int ) inside the cavity of the clip, and the mechanical energy (E M ) stored in the spring of the clip when it is stretched. The differences in unbinding rates we recorded between the tested enzymes led us to calculate E Bi differences between the mutants. Using these values, we tested two possible models to see which of the two energies E Int and E M is altered by the mutations. Our data well fit a model in which mutations negatively alter E Int and not E M (see Supplementary Note) suggesting that all UPF1 variants tested in this study have roughly the same spring stiffness conferred by the protein scaffold, but diverge in their binding interactions with NA inside the clip.