dataesr/scientific-paragraphs-categorization huggingface dataset:
15. 2), PECF594-conjugated anti-CD11c (HL3), Brilliant Violet 570-conjugated anti-Ly6G (1A8), Allophycocyaninconjugated anti-CD64 (X54-5/7. 1), PE Cy7-conjugated anti-CD24 (M1/69), Brilliant violet 650-conjugated anti-CD45. 2 (104) and Brilliant violet 711-conjugated anti-CD45. 1 (A20) were all from Biolegend. PE-conjugated anti-CCR2 (475301) was from R&D systems. The data were analyzed using the FlowJo software (Tree Star). Cytokine measurement. Cytokine levels were determined by ELISA kits, according to protocols provided by R&D Systems. Microarray and gene-ontology analysis. Caecum specimens from non-infected and infected wild-type and Nlrp12 -/-animals were dissected out and stored at -80 °C in RNAlater® (Ambion, Applied Biosystems, Foster City, CA), until extraction of total RNA accordingly to manufacturer's instructions (Qiagen).
The quality of the extracted RNA was confirmed by Agilent 2100 Bioanalyzer using RNA Nano 6000 (Agilent Technologies). The 4x44K Whole Mouse Genome Oligo Microarrays (Agilent Technologies) was used to determine the gene expression profile of two biological replicates. For each labeling, 2 µg of total RNA per sample were engaged in the synthesis of a fluorescent probe labeled with Cy5 or Cy3 fluorophores. A 2 × 2 factorial experimental design and a dye-swap strategy were used (GEO accession number GSE59940). After a within array loess normalization, raw data were analyzed with the LIMMA package and sets of differentially expressed genes were filtered for a p-value <0. 01 and a limit log fold change >1 by using moderated t-statistic with empirical Bayes shrinkage of the standard errors. Statistics were corrected for multiple testing using False Discovery Rate approach.
A gene-ontology analysis using Panther was next performed on up-and downregulated genes that are referred in Unigene (http://www. pantherdb. org/). Gene expression analysis. Isolated RNA was reverse-transcribed with the High-Capacity cDNA Archive kit (Applied Biosystems), according to the manufacturer's instructions. The resulting cDNA (equivalent to 5 ng of total RNA) was amplified using the SYBR Green real-time PCR kit and detected on a Stratagene Mx3005P (Agilent Technologies). RT-PCR was performed with the forward and reverse primers (sequences available upon request) that were designed using Primer express software, version 1. 0 (Applied Biosystems, Foster City, CA). On completion of the PCR amplification, a DNA melting curve analysis was carried out in order to confirm the presence of a single and specific amplicon.
These regions overlapped 64 mm, so that afterwards the images could be stitched (Figure  3 ), thus increasing the overall field of view. The videos were then converted into still images at pre-established instants and the images were processed to attain one full image of the flume. To process the images and to extract quantitative information, a code in Matlab was made. This code had two main parts. The first one was the stitching operation, where consecutive images were stitched together as shown in Figures  2  and 3. In this operation a correction for the lens distortion was also applied. The second part of the code was the filtering and boundary extracting. A gaussian filter was first applied to smooth the irregularities of the image, followed by a median filter to remove the noise. The bed is then highlighted by imposing a convenient threshold and the Sobel edge-detector algorithm is then used to dete is depicted in Figure  4.
The authors thank  Mr. João Rui Oliveira , technician of the  Hydraulics Laboratory of the University of Minho , for his help with the experiments. This work was financially supported by: Project  PTDC/ECM-HID/6387/2014 -POCI-01-0145-FEDER-016825  -funded by  FEDER  funds through  COMPETE2020 -Programa Operacional Competitividade e Internacionalização (POCI)  and by national funds through  FCT -Fundação para a Ciência e a Tecnologia, I. P.
LUME-Colon 1 followed the guiding principles of the Declaration of Helsinki and was conducted in accordance with good clinical practice as well as local laws and regulations. All patients provided written informed consent. The database cut-off date for these analyses was 14 June 2016. Patients were randomized 1 : 1 to receive oral nintedanib 200 mg twice daily plus BSC or matching placebo twice daily plus BSC in 21-day courses until disease progression, undue toxicity, or withdrawal of consent. Randomization was stratified by previous treatment with regorafenib (yes versus no), time from the onset of metastatic disease until randomization in the trial (<24 versus !24 months), and geographical region (Western Europe, North America and Australia; Asia; and rest of the world). Predefined dose reductions were permitted to manage AEs (supplementary appendix, available at Annals of Oncology online).
7 weeks versus 8 weeks with placebo (HR 0. 75). As coprimary end points, it was planned to analyze OS and PFS at the same time once the required number of OS events had been reached. As expected, there were more PFS than OS events, and therefore no formal power calculation for PFS was done and as many PFS events as possible were included in the analysis. At the time of the OS analyses, it was estimated that 595 analyzable PFS events would have occurred, which would yield a power of 95% for the PFS analysis. HRQoL analyses were not adjusted for multiple testing. Safety data were analyzed descriptively in all treated patients.
Acknowledgements The authors would like to thank the patients, their families, and all the investigators who participated in this study. The authors would also like to thank  Claire Laprun  for her contribution to the design and conduct of the study,  Mouna Sassi  for her contribution to statistical design of the study and review of the manuscript, and  Julien Frenehard  for statistical programming support; all from  Boehringer Ingelheim France S. A. S. , Reims, France. Medical writing assistance, supported financially by  Boehringer Ingelheim , was provided by  Suzanne Patel  ( Syneos Health ) during the preparation of this manuscript. Boehringer Disclosure EVC's institution has received research funds from  Amgen ,  Bayer ,  Boehringer Ingelheim ,  Celgene ,  Ipsen ,  Lilly ,  Merck ,  Merck KGaA ,  Novartis ,  Roche ,  Sanofi  and  Servier.
It targets almost complete coverage of HERVs and MaLRs LTR-retrotransposons of the GRCh38 version of the human genome and Dfam 1. 1 database of repetitive DNA element sequence alignments. The chip also targets more than 1500 human genes mainly coding for immunityrelated proteins  [30]. We investigated HERVs and MaLRs expression in PBMCs by modelling monocyte endotoxin tolerance, consisting in low-dose LPS priming of PBMCs and mimicking monocyte anergy observed in sepsis patients  [50] [51] [52]. Symmetrically, PBMCs were stimulated by single high-dose LPS mimicking gram-negative bacterial infection and illustrating an inflammatory context. This article i) provides an overview of the HERV transcriptome in PBMCs associated with functional LTR characterisation; ii) shows the stimulus-dependent comodulation of HERVs/MaLRs and genes, including tolerisable reversible phenotypes; and iii) demonstrates an integrative view of HERVs/MaLRs and genes in canonical immunity pathways, illustrating the multifaceted nature of interactions between LTR retrotransposons and genes.
In brief, the "HERV prototypes" repertoire was retrieved from selected prototype loci. These are sets of loci which maintain the largest open reading frames for gag pol env genes within a proviral structure flanked by two complete LTR sequences. From these elements, a repeatmasker-based alignment procedure retrieved 29,271 loci divided into 42 groups. The "HERV_Dfam" and "MaLR_Dfam" repertoires were retrieved from Dfam, a database of repetitive elements detected by RepBase consensus and based on Hidden Markov Models (HMM)  [53]  ("Proto versus Dfam" tab, Additional file 2: Table  S1 ). Redundancy between repertoires was removed from the HERV/MaLR repertoire. A summary of the absolute counts and the relative abundance of transcriptionally active elements of the HERV/MaLR transcriptome is given in Fig.
Although poorly represented (2%), the same shift is observed for RdT LTRs. Some LTRs are exclusively RdT (20 LTRs) and some shifted from RdT status to a promoter (37 RdT/Pr LTRs) or polyadenylation (51 RdT/pA LTRs) function. A significant proportion of LTRs (13. 1%) were in promoter (402 Pr LTRs) or polyA (311 pA LTRs) status in all samples (candidate loci validation, Additional file 8: Figure  S6d ). Almost no LTR (0. 6%) shifted through at least three different features including both promoter and polyA functions. Consequently this observation confirms that the shift from promoter to polyA function is an extremely rare if significant event. The same analysis was performed using the complete HERV/MaLR dataset (Additional file 3: Figure  S2 ). Although results should be considered with caution due to the imprecise annotation of HERV_Dfam and MaLR_Dfam LTRs (Additional file 2: Table  S1 ), the overall trends were similar to those observed at the "HERV_prototypes" repertoire level.
a HERV structure distribution. The 42 HERV groups corresponding to the "HERV_prototypes" repertoire are voluntarily depicted as 100% of the HERV-V3 chip. Solo LTR, 5' LTR, 3' LTR and proviral genes account for 100% of the HERV chip in the proportion described in Additional file 2: Table  S1b. The transcriptome pie-chart is obtained from results detailed in Additional file 2: Table  S1c. b LTR features. The descriptive table summarises the assignment of features. a,b,c,d Loss of information from HERV database to understandable functions. a Summary of Additional file 2: Table  S1a , b Summary of Additional file 2: Table  S1b , c Enumeration of LTRs whose function is attributable, i. e. defined as LTRs combining U3 and U5 adjacent structures on the genome and existing probesets onto the chip allowing discrimination between U3 and U5 expression signals, d Enumeration of LTRs whose function is attributed using both a 2 4.
A gene centred view of the "Role of pattern recognition receptors in recognition of bacteria and viruses" (PRR) pathway is depicted in Fig. 5a. It includes 32 HERV/MaLR loci and 7 genes exclusive to the pathway. Ten out of the 32 HERV/MaLR loci belong exclusively to this pathway. Most of the genes are co-expressed with several retroviral elements, 18 for IFIH1, 18 for IRF7, 17 for OAS3, 15 for OAS2, 7 for PTX3 and 3 for C5AR1, widespread on distinct chromosomes. Interestingly, 4 tolerisable HERV/MaLR loci are present on chromosome 12 within a 39 kb region which overlaps with OAS2 and OAS3 tolerisable genes. Moreover, 4 HERV/MaLR loci are on chromosome 1 in a 32 kb region overlapping with IFI44L and IFI44 genes. RT-PCR amplification of IFI44L, IFI44 genes and 011052301-HERV0472uL HERV loci showed a marked decrease for the ET condition (data not shown).
5% versus 47%), probably due to the largely increased number of targeted groups. Altogether, integrating both more precise data derived from the "HERV_prototype" repertoire and results from the complete HERV/MaLR dataset, about one tenth of LTRs exhibit a constitutive promoter or polyA function while roughly one quarter of LTRs may shift between silent and promoter or polyA functions. Only a few thousandths of LTRs can shift between promoter and polyA, as initially described in cancer  [29] , strengthening what we called "operational determinism", i. e. an LTR is predetermined to act as a promoter or a polyA site. Although all "prototype" groups are active in PBMCs, we observed a higher proportion of gamma-retroviruses, including notably the super spreader HERV-H group and the HERV-W group containing Syncytin 1.
This last column includes additional IFN-γ dependant reversibility of tolerance, consisting of a 2 ng/mL LPS priming step overnight, followed by a 100 ng/mL IFN-γ stimulation step overnight, and finally the 100 ng/mL LPS stimulation step for 6 hours. All PCR reactions were performed in duplicate for each condition. Expression of the housekeeping genes PPIB and RPLP0 was monitored for normalisation. The fold change (FC) was determined using the 2 -ΔΔCt method. The final value of the unstimulated condition was arbitrarily set to one and other values scaled-up in order to provide a final relative differential expression (data were represented by a median and using the log2 scale). Statistically significant differences between two conditions are marked (wilkoxon signed rank test. **: p-value < 0.
The co-expression of genes with a large number of HERV/MaLR elements scattered among different chromosomes, e. g. 18 HERV/MaLR loci located on 10 distinct chromosomes linked with IFIH1, 6 HERVs/MaLRs located on 6 distinct chromosomes linked with PTX3, suggested that they are part of gene networks regulated by shared transcription factors, as previously proposed  [33]. However, we did not observe any tissue-specific transcriptional factor binding sites (TFBS), but an enrichment of the AP-1 binding site with promoter LTR was observed as compared to silent LTR (p-value: 1. 14 10 -4 , data not shown). The similar modulation of MALR1126 LTR promoters belonging to LXR/RXR and NF-κB networks and located on chromosome 5 (050017102-MALR1126uL) and 10 (100175702-MALR1126uL) may reflect such shared regulation.
As a general trend, LTRs were screened for particular histone modification signals by overlap with Encode peaks for H3K27ac, H3K27me3, H3K36me3, H3K4me1, H3K4me3 and H3K9me3 in different immune cells; we found enrichment for the H3K9me3 mark for CD14+ monocytes. The LPS stimulations probably modified the local chromatin configuration leading to global modulation of expression, of the gene and HERV/ MaLR  [75]. Intriguingly, it appears that CD14-positive monocytes are at least twice more enriched in H3K9me3 histone mark than CD4-and CD8-positive T cells, B cells and natural killer cells (data not shown). Taken together, the variability of histone marks, the tolerisable/nontolerisable HERV/MaLR phenotypes and vicinity of genes suggest a common control of expression between HERV/MaLR and genes.
Biological samples and quality control Citrated pouches or heparinised tubes blood were obtained from EFS (Etablissement Français du Sang) and used immediately. According to EFS standardised procedures for blood donation and to provisions of the articles R. 1243-49 and following ones of the French Public Health Code, a written non-opposition to the use of his donation for research purposes was obtained from healthy volunteers. The blood donors' personal data were anonymised before blood transfer to our research lab. We obtained the favourable notice of the Local Ethical Committee (Comité de Protection des Personnes Sud-Est II, Bâtiment Pinel, 59 Boulevard Pinel, 69,500 Bron) and the acceptance of the Ministère de la Recherche (declaration DC-2008-64) for handling and conservation of these samples.
Custom Affymetrix HERV-V3 GeneChip microarray HERV-V3 targets 353,994 loci-elements, represented by 4,410,200 probes. The custom HERV GeneChip can discriminate between distinct HERV elements composed of a set of highly informative probesets (located in U3, R, U5 subdomains of solo, 5' and 3' individual LTRs and gag/pol/ env regions), hereinafter referred to as 'HERV prototypes repertoire' , and a set of probesets with lower-quality annotations (located in the first third and last third of the complete LTR, and every 2. 5 kb in the region in between LTRs), hereinafter referred to as 'HERV/ MaLR_Dfam repertoire'. The custom HERV GeneChip also contains probesets targeting LINE1, lncRNA, viruses, and the gene repertoire. The descriptions of the HERVgDB4 database and of the final contents of the HERV-V3 microarray are provided in Additional file 2: Table S1  [30].
A detailed morphometric analysis of the spines was first performed using an in-house macro-program from ImageJ software (Rasband, W. S. , ImageJ, US National Institutes of Health, Bethesda, Maryland, USA, http://imagej. nih. gov/ij/, 1997-2012). Briefly, after maximal projection of the images of each stack and segmentation to produce a binary image, the skeleton of the dendritic tree was analyzed and its length measured. The number of intersections and spines were determined and after binary thinning, the length of the principal axis was measured. These images were subsequently analyzed with NeuronStudio software and spines were classified into "thin, " "mushroom, " and "stubby" according to  Peters and Kaiserman-Abramof (1970)  using the following parameters: the maximum and minimum spine heights were set at 3.
Long-Term Potentiation (LTP) Hippocampal slices were placed under a Nomarski microscope (Zeiss, Germany) equipped with an infrared video camera (Axiocam, Zeiss) in a recording chamber superfused at a flow rate of 1 mL. min -1 with oxygenated PBBS. Pictures were taken using a digital camera (Axiocam, Zeiss) connected to imageacquisition software (Axiovision, Zeiss). Recordings were made at room temperature (20-25 • C) using an Axopatch 200B (Axon Instruments, Foster City, CA, United States) connected via an interface (Digidata 3200) to a computer running pClamp (Axon Instruments). At the beginning of each recording, a tungsten bipolar stimulating electrode was positioned at the stratum radiatum for stimulation of the Schaffer collateral projections to CA1, using a stimulator (STG4002 Multichannel systems) connected to the computer.
Field potentials in the dendritic tree of CA1 neurons were recorded with pipettes (made from borosilicate glass capillary (Hilgenberg, Masfeld, Germany) with resistance of 3-6 M when filled with extracellular solution). The intensity of stimulation was adjusted in each experiment to evoke about 50% of the maximal field potential amplitude without appreciable population spike contamination. Low-frequency stimulation (0. 1 Hz) was applied to the Schaffer collaterals to establish a stable baseline (for 20-30 min) of the excitatory post synaptic potential (EPSP) slope, after which LTP was induced by high-frequency stimulation (HFS; 100 Hz/1 sec), followed by the initial low frequency stimulation. To analyze the time course of the EPSP slope, the recorded fEPSP data were routinely averaged over 1 min (n = 6).
Data Analysis Voltage clamp data were digitized at 0. 5 kHz using a Digidata interface coupled to a microcomputer running p-Clamp 9 (Axon Instruments). Currents were digitally filtered at 1-3 kHz. Average data were expressed as mean ± SEM, n = number of neurons that were recorded. Statistical significance between groups was calculated using the Student t-test, the ANOVA followed by the Fisher test, or the Kruskal-Wallis followed by the Dunn's test and were considered significant at * p < 0. 05, * * p < 0. 01 and * * * p < 0. 001 using a statistical software package (SigmaStat 2. 03, Jandel Sci and Graph Prism software). Cumulative histograms were compared by Kolmogorov-Smirnov analysis using Clampfit (Axon Instruments), with an equal number of events for each group. Significant differences between two groups of data were determined using a Mann-Whitney test for non-parametric data.
This filtration process removed 32% and 34% of the total amount of reads. Mapping of the cDNA sequences was then done with STAR_2. 4. 0a versus mm10 mouse genome build using RNA-seq Encode recommendations. For molecule counting based on UMI counts, we used the Dropseq Core Computational Protocol version 1. 0. 1 (dropseq. jar) from McCarrol  (Macosko et al. , 2015)  using GTF gene model from Ensembl release GRCm38. 83. The Digital Expression function of dropseq. jar was used with default parameters (edit distance = 1) to produce a matrix of molecule counts that were used in the subsequent statistical analysis.
Statistical Analysis and Biological Theme Analysis Choroid plexus samples were analyzed separately. Quality control of RNAseq data was performed with in-house R scripts. Purity of biological samples was verified by inspection of CD4 expression levels. CD4 samples with non-zero expression levels for CD8a and CD8b were considered of poor quality and excluded. Low abundance genes were filtered out, then sequencing depth normalization and differential expression analysis where carried out using the Bioconductor package DESeq2  (Love et al. , 2014). P-values were adjusted for multiple testing using the Benjamini-Hochberg procedure, which controls the false discovery rate. No gene reached statistical significance at the 0. 05 level after adjustment. For choroid plexus samples, mild differential expression was observed between enriched and standard environments and candidate differentially expressed genes were selected based on a nominal p-value < 0.
05. Heatmaps were generated using the R package pheatmap (Pretty Heatmaps V 1. 0. 8, https://CRAN. R-project. org/package=pheatmap). Canonical pathways and molecular function analyses were carried out using Ingenuity Pathway Analysis (IPA, Qiagen Bioinformatics). Gene Set Enrichment Analysis was performed using GSEA, by comparing the modifications observed in EE vs. SE to modifications observed in the same subcellular population in the immune set of data (C7) or a larger set of data (C2). Pathways with a normalized p value < 0. 05 were considered as enriched.
Data Analysis Two-way ANOVA, followed by a post-hoc Tukey's multiple comparison tests were performed when data followed the normality Shapiro-Wilk test. Otherwise, the non-parametric ANOVA Kruskal-Wallis test was used followed by a post hoc + Dunn's test. Voltage clamp data were digitized at 0. 5 kHz using a Digidata interface coupled to a microcomputer running p-Clamp 9 (Axon Instruments). Currents were digitally filtered at 1-3 kHz. Average data are expressed as mean ± SEM, n = number of neurons that were recorded. Statistical significance between groups was calculated using the Student t-test, the ANOVA followed by the Fisher test, or the Kruskal-Wallis followed by the Mann-Whitney test and were considered significant at * p < 0. 05, * * p < 0. 01 or p < 0. 02 as mentioned, and * * * p < 0.
We thus used GSEA to compare the overall changes induced between EE and SE housing conditions in the CD4 + T cells from choroid plexus, to previous data already published by others from the immunology set (C7, which uses only experiments performed on immune cells). We selected the pathways that corresponded to the variations observed in EE vs. SE with a p < 0. 05 and sorted them according to the normalized enrichment score. We selected only experiments that used the same cell type (i. e. , CD4 + T cells) by filtering according to the name of the experiments (Figures  5C, D ). Overall, the gene expression profile obtained suggests that CD4 + T cells from choroid plexus in EE animals have an activated phenotype as compared to those from SE mice that presented a naïve profile. As a conclusion, EE modifies gene expression in CD4 + T cells from the choroid plexus and their profiles might differ slightly as compared to SE.
FUNDING HZ was financed by a Labex ICST (Ion Channel Science and Therapeutics) fellowship. This work was partly supported by the Fondation de l'Avenir (AP-rm-16-011-Chabry). It was developed in close collaboration with the UCAGenomiX, the functional genomics platform of Nice Sophia Antipolis, a partner of the National Infrastructure France Génomique (ANR-10-INBS-09-03).
ACKNOWLEDGMENTS We wish to thank  Lucien Relmy , and  Alain Barbot  for their assistance in the animal care facility;  Iris Grosjean ,  Sophie Abelanet , and  Frederic Brau  from the imaging platform of IPMC;  Delphine Debayle  and  Anne Sophie Gay  from the proteomic platform of IPMC; and  Emilie Murris ,  Melanie Guyot ,  Sarah Nicolas ,  Carine Gandin ,  Valentine Golzné ,  Elisa Dourneau ,  Maud Maillaut ,  Douglas Daoudlarian ,  Carmelo Luci , and  Cathy Widmann  for helpful discussions. We warmly thank  Barbara Demeinex  and  Cristina Luongo  for their advice on the thyroid system. We thank  Abby Cuttriss  from the  UCA Office of International Scientific Visibility  for comments on the English version of the manuscript. We also warmly thank  Caroline Vieuille  from  ANASTATS  and  Thomas Lorivel  for their help with statistical analyses.