dataesr/scientific-paragraphs-categorization huggingface dataset:
CNE display CNEs located in the intron of genes or in intergenic space, and computed from the 46-way UCSC multiple alignment, have been a regular feature of past Genomicus releases. Now, CNEs have been individually named using a simple nomenclature starting with the prefix 'Reg' followed by a three-letter species identifier (e. g. Hsa for human) and a seven-digit number. The names are permanent, will be carried over in successive releases and can be used to directly query the database, as for genes. Alternatively, to view all human CNEs of a given locus at once, the PhyloView display has a 'CNE track' option on the top right menu. By convention, because CNEs are always plotted in the schematic scale display, intronic CNEs are displayed on the lower half of the right-hand intergenic space of the gene in which they are included.
GENOMICUS SOFTWARE IMPLEMENTATION Genomicus is composed of Perl (version 5. 8) scripts and modules, executed with mod perl on an Apache2 (version 2. 2) server and querying a MariaDB (version 5. 5) database. The pages embed inline-SVG drawings in XHTML, while the JavaScript usage is limited to an information panel retrieved with AJAX calls. The interface is optimized for Firefox and Chrome navigators, but it also runs on Safari and Internet Explorer. The source codes of Genomicus and the MariaDB schema can be requested by email.
FUNDING Centre National de la Recherche Scientifique (CNRS) ; the  Agence Nationale de la Recherche  [ Ancestrome  Project  ANR-10-BINF-01-03 ,  ANR Blanc-PAGE   ANR-2011-BSV6-00801 ];  Wellcome Trust  [ WT095908 ];  Euro-pean Molecular Biology Laboratory  [to M. M. ]. Funding for open access charge:  Centre National de la Recherche Scientifique.
075 mm ϫ 150 mm) reversed-phase column (LC Packings). Mass spectra were acquired using a top-10 collisioninduced dissociation (CID) data-dependent acquisition (DDA) method. The LTQ-Orbitrap was programmed to perform a Fourier transform (FT) full scan (60,000 resolution) on 400 -1400 Th mass range with the top ten ions from each scan selected for LTQ-MS/MS with multistage activation on the neutral loss of 24. 49, 32. 66, and 48. 99 Th. FT spectra were internally calibrated using a single lock mass (445. 1200 Th). Target ion numbers were 500,000 for FT full scan on the Orbitrap and 10,000 MSn on the LTQ. The raw MS data were analyzed using the MaxQuant/Andromeda software (v. 1. 2. 2. 5) (  16 ) with a false discovery rate of less than 0. 01 for peptides and phosphosites and a minimum peptide length of six amino acids.
The mass accuracy of the precursor ions was improved by retention time-dependent mass recalibration. Andromeda was used to search the top eight per 100 Da peak lists against the human complete proteome set database (http://www. uniprot. org/uniprot/ ?query ϭ organism:9606ϩkeyword:1185) downloaded on February 22, 2012 (65,835 protein entries), combined with 248 frequently observed contaminants as well as reversed versions of all sequences. This version of the database contains both reviewed sequences from UniProtKB/Swiss-Prot and unreviewed sequences from UniProtKB/ TrEMBL. Enzyme specificity was set to trypsin, additionally allowing cleavage N-terminal to proline and up to two missed cleavages. The search included cysteine carbamidomethylation as a fixed modification, protein N-terminal acetylation, oxidation of methionine and phosphorylation of Ser, Thr, and Tyr as variable modifications.
Peptide identification was based on a search with a mass deviation of the precursor ion up to 7 ppm after recalibration, and the allowed fragment mass deviation was set to 0. 5 Da. Identifications across different replicates and adjacent fractions was performed using the "match between runs" MaxQuant option with a 3 min time window. Quantification of SILAC triplex signals was performed by MaxQuant with standard settings. The phosphoSTY. txt file generated by MaxQuant was uploaded onto Perseus software (v. 1. 2. 0. 17) to calculate B significance of phosphopeptide ratios in each of the three biological replicates  (16). The new table was then uploaded onto the R environment in order to plot log H/M ratios against log M/L ratios and color-display the B significance count (p Ͻ 0. 05) for each quantified phosphopeptide.
0 and searched with Mascot 2. 4 against the same human Complete Proteome Set database, with phosphorylation of Ser, Thr, and Tyr as variable modifications, 7 ppm precursor mass tolerance, 0. 5 Da fragment mass tolerance and trypsin/P digestion. MS2 spectra matching phosphorylated peptides with ion score over 15 were inspected using Prophossi software  (17)  for automatic annotation of unique transitions that pinpoint the position of phosphorylation sites. Ion signals corresponding to phosphorylated peptides were quantified from the maximal intensities measured in their ion chromatograms manually extracted using Qual browser v2. 1 (Thermo Fisher Scientific) with a tolerance of 5 ppm for mass deviation, and normalized to signals of their nonphosphorylated counterparts. Ser 280 phosphorylation of immunoprecipitated receptors was also analyzed by Western blotting using the phosphosite specific antibody.
Western Blotting-Proteins, resolved onto 10% polyacrylamide gels, were transferred to Hybond C nitrocellulose membranes (GE Healthcare). Membranes were immunoblotted with primary antibodies (anti phospho-Ser 280 5-HT 2A receptor, 1:300; anti phospho-Thr 202 / Tyr 204 -Erk1,2, 1:1000; anti Erk1,2, 1:1000; anti-HA, 1:1000; Anti-GFP, 1:1000; anti-RSK2, 1:1000) and then with either anti-mouse or antirabbit horseradish peroxidase-conjugated secondary antibodies (1: 3000, GE Healthcare). Immunoreactivity was detected with an enhanced chemiluminescence method (ECL TM plus detection reagent, GE Healthcare) and immunoreactive bands were quantified by densitometry using the ImageJ software. In protein phosphorylation analyses, the amount of each phosphoprotein was normalized to the amount of the corresponding total protein detected in the sample.
Fifty micrometers-thick sections were cut with a vibratome (Leica), permeabilized with 0. 2% Triton X-100 in Tris buffer saline (TBS) for 20 min, saturated for 1 h with 10% goat serum in TBS containing 0. 03% Triton X-100 and incubated for 48 h at 4 °C with primary antibodies (anti phospho-Ser 280 5HT 2A receptor, 1:100 or anti 5-HT 2A receptor, 1:500) in TBS. After four washes, they were incubated for 1 h with an Alexa Fluor ® 488-conjugated anti-rabbit antibody (1:1000, Invitrogen) in TBS. Immunofluorescent staining was observed with a Zeiss Axioimager Z1 microscope equipped with apotome. Images were acquired using the Axiovision 4. 8 software driving an AxioCam MRm CCD camera (Carl Zeiss Microimaging). Inositol Phosphate Production-Inositol phosphate production was analyzed as previously described  (18).
05% Triton X-100) to label internalized receptors. After three washes, coverslips were mounted on glass slides in Mowiol® 4. 88 (Calbiochem). Series of optical sections were collected with a Zeiss Axioimager Z1 microscope equipped with apotome. Images were acquired using the Axiovision 4. 8 software driving an AxioCam MRm CCD camera (Carl Zeiss Microimaging). ELISA-Quantification of receptor cell surface expression was performed by ELISA under nonpermeabilized conditions as previously described  (18).
MS2 spectra matching phosphorylated peptides were inspected using Prophossi software  (17)  for automatic annotation of unique transitions that pinpoint the position of phosphorylation sites (supplemental Fig. S3 ). In addition to a unique monophosphorylated form (phosphorylated at Ser 280 ), various doubly and triply phosphorylated forms corresponding to phosphorylation on Ser 280 and either on Ser 283 or Ser 287 or Ser 288 or Ser 290 or Ser 291 or on two of these residues) were also detected (Table  I ). Moreover, quantitative analysis of the corresponding ion signals from extracted ion chromatograms showed that the monophosphorylated peptide exhibited the highest relative abundance and that it was up-regulated by DOI or LSD exposure but not by lisuride or ergotamine (Table  I , Fig. 1B , and supplemental Fig.
2E ). As expected and further supporting the specificity of our antibody for phospho-Ser 280 5-HT 2A receptor, no immunoreactive signal was detected in prefrontal cortex of DOI-treated 5-HT 2A receptor knockout mice (Fig. 2E ). Phosphorylation of 5-HT 2A Receptors by Hallucinogens is Protein Kinase C-dependent and Gi/o-independent-We next searched for consensus motifs of phosphorylation by kinases in the Ser 280 flanking sequence by using two different algorithms: (1) Scansite, which defines scores for phosphorylation sites according to a matrix based on an oriented peptide library to determine the optimal substrates of protein kinases  (20) , and (2) Group-based Prediction System (GPS, v2. 1), which classifies protein kinases into a hierarchical structure with four levels and trains its algorithm against the Phos-phoELM database  (21) , in order to determine individual false discovery rate for each kinase  (22).
* This work was supported by grants from  la Fondation pour la Recherche Medicale  (Contracts Equipe FRM 2005 and 2009),  ANR  (Contract  n°ANR-08-MNPS-0011 ), CNRS, INSERM University Montpellier 1 and University Montpellier 2. Mass spectrometry experiments were carried out using facilities of the  Functional Proteomic Platform of Montpellier Languedoc-Roussillon. □ S This article contains supplemental Figs. S1 to S5 and Table  S1.
Diagnostic kits targeting nosocomial pathogens or influenza virus are available. It remains to be seen, however, whether such highly multiplexed PCRs can be applied to a wide range of pathogens, some of which are highly variable in sequence, without losing the analytical sensitivity of single PCR, one of the major advantages of the technique. Moreover, the design of numerous primers will have to be constantly updated along with increase in the number of sequences in databases and identification of new pathogens, in order to maintain a high range of detection. Indeed, addition of a new primer pair to an already highly multiplexed PCR requires some degree of revalidation, which can become a laborious and never-ending process. An alternative strategy takes advantage of the increasing availability and speed and decreasing cost per base of NGS offered by deep sequencing machines.
It is now possible to use the tools of metagenomics, which is the study of the microbial genetic sequences recovered directly from a given human, animal, or environmental sample. In this setting, the sequence of all the NA species of the sample are determined and compared with those in databases. This technology has first been used to describe the complexity and the dynamics of microbiomes from different origins, including from the gut, other mucosal sites and the skin, as well as from various human-made (e. g. , sewage) and natural (e. g. , sea) environments. It has also been used to discover new infectious agents. De novo assembly of full length genomes of pathogens can sometimes be achieved directly from the samples, and if not large partial sequences can be subsequently completed by using classical molecular biology tools.
, 2013) , or urinary samples from patients with suspected urinary tract infections  (Hasman et al. , 2014). Another advantage of the technique is its capacity to identify co-infections, which is of great help to adapt therapeutics. Developing a WG-NGS diagnostic pipeline critically relies on two partly interdependent criteria: time to results and database exhaustiveness. Indeed, some sequence knowledge is necessary to design primers for PCR, but the whole genome sequence does not need to be known. Indeed this is also the case for WG-NGS, but lack of information regarding the whole genome sequence and organization will have an impact on sensitivity (some useful reads being at risk of not being properly identified). As the growth of databases is very rapid, being fueled by the development of NGS as a standard tool, such limits will not last long.
Also, the requirements are not the same for pathogen discovery, when the range of detection should typically include the unknown, and medical diagnosis. In this latter case, it is more important to screen samples against a curated database of known pathogens that could be of interest for the physicians. Typical blast analysis of hundreds of million of reads after de novo assembly into larger contigs against the whole NCBI databases using relaxed criteria, which is classical in pathogen discovery, is too time-and resource-consuming to be used in diagnostics. By contrast, stringent mapping of non-assembled reads on a comprehensive database of pathogens, together with the progressive increase of read length permitted by the evolution of sequencers, speeds up the overall process down to a few hours.
We minimized bicarbonate flux through the GABA A channels, using an HEPES-buffered extracellular solution (nominally CO 2and bicarbonate-free  43, 44  ), so that E GABA was an estimation of E Cl. Membrane currents, recorded with a patch-clamp amplifier (Axopatch 200B; Molecular Devices, Foster city, CA, USA), were filtered at 2 kHz, digitized (10 kHz) and acquired with Clampex 10 software (Molecular Devices). The stability of the patch was checked by repetitively monitoring the input and series resistance during the experiment, and recordings were discarded when any of these parameters changed by 410%. Zn2+ loading through gramicidin pores. When indicated (Figure  5  and Supplementary Figure  S3 ), intracellular [Zn 2+ ] was artificially increased in neurons through the perforated patch, using a BAPTA-based intracellular solution (in mM: 140 KCl, 2 MgCl 2 , 10 HEPES, 2 MgATP, 5 BAPTA) supplemented with ZnCl 2 (0.
01-100 μM). The corresponding free Zn 2+ concentrations were calculated using the MaxChelator software: http://www. stanford. edu/ ~cpatton/maxc. html, and are reported in Supplementary Table  S3. Zn +2 imaging. Fluorescence images were acquired at room temperature (24-25 °C) using a customized digital imaging microscope. Excitation of fluorophores at various wavelengths was achieved using a 1-nm-bandwidth polychromatic light selector (Till Polychrome V), equipped with a 150 W xenon lamp (Till Photonics, Hillsboro, OR, USA). Fluorescence was visualized using an upright microscope (Axioskope) equipped with a 40x water-immersion objective (Achroplan CarlZeiss, Oberkochen, Germany) and a digital 12 bit CCD camera system (SensiCam, PCO AG, Kelheim, Germany). All the peripheral hardware control, image acquisition and image processing were achieved using customized software Till Vision v.
Antagonists were usually acutely applied through a parallel tubes of the same perfusion system. DIOA, K252A and PP2 were pre-incubated for 1 h (37 °C) and then continuously applied during the experiments. Sulfasalazine, APV/NBQX, BAPTA-AM and tetrodotoxin citrate were applied during co-culture in the co-culture medium and not superfused during recordings (24 h). The values of EGABA and RMP of control neurons, following different drug treatments are reported in Supplementary Table  S2  and Supplementary Table  S4. Data analysis. Data, analyzed offline, are presented as mean ± S. E. M. ; we used the QuantityOne (Bio-Rad Laboratories S. r. l. ) program for the densitometric analysis of all immunoblots. Origin 7 (Origin software; Microcal Software, Northampton, MA, USA) and Sigmaplot 11 (Systat Software Inc, London, UK) software were used for statistical analysis.
Acknowledgements. This study is dedicated to the memory of  Professor Fabrizio Eusebi , who initiated and inspired this direction of research. The work was supported by grants from  PRIN 2009  (to DR, CL and SDA) and  AIRC  to CL. EM was supported by  PhD programme in Neurophysiology, Sapienza University, Rome. Authors wish to thank  Dr. Stefano Sensi  for critical reading of the manuscript and precious suggestions.
Primer sequences are shown in Table  S1  in File S1. Hybridization on Agilent chips was performed on the TGML platform (TAGC UMR_S 1090, Marseille, France) and raw expression values were quantile normalized under R (version 2. 13. 0) and Bioconductor. Bioinformatics analysis is described in supporting information. Raw data are accessible at GEO site (GSE38968). In all figures, error bars represent SEM. Statistical analysis was mostly performed using unpaired t-test or ANOVA when appropriate (GraphPad Prism software) unless indicated otherwise.
We compared WT versus SHIVA expression data to all public genesets available from MSigDB (Broad Institute) using the GSEA algorithm. Briefly, the GSEA method allows to statistically test whether a set of genes of interest (referred to as a geneset) is distributed randomly in the list of genes that were pre-ranked according to their differential expression ratio between WT and SHIVA. We also re-analyzed public expression data (GSE8290) from fasted WT vs PPARadeficient mouse livers in order to extract the genes that were found either up-or down-regulated and added them to the list of public genesets. As shown in Figure  2A  (complete list in Table  S2  in File S1), a significant fraction of genes found poorly induced in PPARa-deficient versus control fasted B6 mice were also found, as a group, significantly poorly expressed in fasted SHIVA mice (FDR q-value = 1.
This work was supported by funds from the  Centre National de la Recherche Scientifique, Institut National de la Santeet de la Recherche Medicale ,  INCA , European Communities MUGEN projects. S. R. and T. G. were supported by funds from the  Ministry of Research and Fondation pour la Recherche Medicale. T. -P. V. M. was supported by the  Agence Nationale de la Recherche (ANR)  ( PhyloGenDC ,  ANR-09-BLAN-0073-02 ). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Their study is the fi rst longitudinal examination of the HIV care cascade. The investigators assessed the numbers and proportions of individuals in eight distinct stages of the cascade: HIV infected, diagnosed, linked to HIV care, retained in care, antiretroviral treatment indicated, receiving antiretroviral treatment, adherent to antiretroviral treatment, and virologically suppressed. The study's strengths derive from the extensive use of comprehensive linked databases from national and provincial health programmes, and population-based registries from the BC Centre of Excellence in HIV/AIDS (Vancouver, BC, Canada)-the sole provincial agency providing HIV diagnostic testing and distribution of all antiretroviral drugs. Additional information was derived from provincial hospital, pharmacy, and vital statistics databases.
After three hours of culture, the transfected cells were stimulated for 24 hours and RNA was extracted. The RNA quality was verified using a Bioanalyser 2100 (Agilent, Santa Clara, California, USA). Fluorochrome labeling and hybridisation on Mouse Gene 1. 0 ST Array were performed by the Pasteur Institute platform according to the manufacturers' instructions (Affymetrix, Santa Clara, California, USA). The microarray data have been deposited to the ArrayExpress database under the accession number E-MTAB-1957.
Quantitative Reverse Transcription PCR(Q-RT-PCR) Five million CD4 + T cells were purified using the untouched isolation kit (Miltenyi Biotech) from spleens of 6 to 8 week-old 6. VIIIa and 6. VIIIc female mice and used for total RNA isolation (RNeasy Mini Kit, Qiagen). For circadian analyses spleen samples were collected and purified every four hours during a 24-hour period. 200 ng to 10 µg of the total RNA were used for quantitative RT-PCR as previously described  (12). The amplification quantification in arbitrary units was performed by the deltaCt method using three replicates and Arpo as an endogenous control to normalize mRNA levels. The values were presented as mean values +/-standard deviation (SD). Combined data were presented as mean values of the experiments +/-standard error (SE).
Louis, MO, USA) and ionomycin (10 µg/ml, Sigma-Aldrich) in the presence of Brefeldin A (10 µg/ml, BD Biosciences). The cells were washed with phosphate-buffered saline (PBS) 0. 5% BSA and then incubated in the eBioscience fixation/permeabilization buffers according to the manufacturer's protocol, and stained with fluorescent antibodies. FACS was performed on a Cyan flowcytometer (Beckman coulter, Villepinte, France) and analysed using Flowjo software. Statistical analyses were performed using the Mann-Whitney method. Chromatin immunoprecipitation (ChIP) analyses 3 x 10 7 splenocytes or 4 x 10 6 CD4 + T cells of female mice at 6-8 weeks of age were used for ChIP using the protocol described in  (16)  with the following modifications for chromatin digestion: 150 U of MNase (Thermo Scientific, Villebon sur Yvette, France) were added for 10 min at 37°C and the reaction stopped with 4 µl of 500 mM EDTA and protease inhibitors.
Incubation was continued with 50 µl magnetic beads for two hours at 4°C on the rotating wheel. Beads were then washed and eluted as described in  (16). All quantifications were performed by realtime PCR in the presence of SYBR Green (Roche, Boulogne-Billancourt, France) on three replicates using 50 ng of DNA. The results were calculated and normalised as (Ct of IP/ Ct of input)/ (Ct of control-IP/ Ct of input). Data were presented as means of experiments +/-SE, in case of single experiments as means of three technical replicates +/-SD. We have verified that the anti-ARNTL2 antibodies were equally efficient for both the NOD and the C3H allelic version of ARNTL2 in immunoprecipitation experiments followed by Western blotting using an anti-ARNTL2 antibody (Abcam ab86530). For screening of Il21 by ChIP we designed primers from 2500bp 5' of the start codon to 2000bp 3' of the stop codon.
Whilst in the first experiment about half of the genes were either up or downregulated in strain 6. VIIIc compared to strain 6. VIIIa, the Arntl2 overexpression resulted in upregulation of over 80 % of the genes. Using medium stringency in the DAVID (Database for Annotation Visualization and Integrated Discovery) functional annotation we identified 36 clusters amongst the 223 genes that were mostly associated with general cellular function, in particular with ribosome complexes. This may reflect the increased protein production after overexpression. The 44 differential genes identified in the two strains clustered into only four clusters, including ribosomal proteins (enrichment score 2. 12), cytokine activity (score 1. 37), membrane proteins (score 0. 02) and ion binding (score 0. 01). Within the cytokine cluster we identified for example Interferon gamma, Interleukin 3, Interleukin 21, Interleukin 22 and the High mobility group box protein 1.
Acknowledgements Author contributions are as follows: B. L. researched data and wrote the manuscript, C. H. researched data and reviewed the manuscript, U. C. R. researched data and wrote the manuscript. U. C. Rogner  is the guarantor of this study. There are no conflicts of interest. We thank  Philip Avner  and  Christian Boitard  for continuous support during this project,  Agnès Lehuen  and  Yannick Simoni  for helpful discussions,  Guillaume Soubigou  for microarray processing,  Chantal Becourt ,  Corinne Veron  and  Pierre Alcan  for technical assistance. This work was supported by grants from the  ANR , the  ARD , and the  EFSD/JDRF / Novo Nordisk Programme , CORDDIM and by recurrent funding from the  CNRS, INSERM and Institut Pasteur.