dataesr/scientific-paragraphs-categorization huggingface dataset:
S ponges (Porifera phylum) comprise a sister group of "true" animals (Eumetazoa) divided in four major classes and representing a key group to retrace the early evolution of animals. The phylogeny positions of sponges are still unclear, and mitochondrial protein-coding genes may be of help in resolving standing evolutionary issues, as well as in population/ecological studies  (1). Oopsacas minuta is a small white glass sponge (Hexactinellida class, Lyssacinosida order) with a siliceous skeleton. Discovered in the straits of Gibraltar, this sponge is distributed only in the Mediterranean Sea in both deep water and caves  (2). Little information was available until eight mitochondrial DNA (mtDNA) sequences of glass sponges (including a nearly complete mtDNA sequence from Oopsacas minuta) were recently reported but not yet available in GenBank  (3).
Here, we present the complete mtDNA sequence of Oopsacas minuta, the first complete mtDNA sequence of a Lyssacinosida representative released in a database. Recently, we sequenced the draft genome of Oopsacas minuta using Illumina technology with DNA-seq paired-end and Nextera mate pair protocols on a HiSeq2500 sequencer. Adapter sequences were removed and low-quality bases (threshold of 28) of reads were trimmed using Cutadapt (4). After cleaning, 10% of the 395,851,746 paired-end reads were picked randomly and assembled into 50,958 contigs using IDBA-UD  (5). Contigs were scaffolded into 38,533 sequences with the scaffolding tool of the Platanus assembler (6) using the complete data set of clean Illumina reads. The scaffold corresponding to the mtDNA was identified based on the homology search using the partial mtDNA sequence (EF537577.
1) of Sympagella nux, another glass sponge of the order Lyssacinosida. The assembly was checked using read-mapping information of insert sizes and orientation of paired-ends mapped onto mtDNA assembly with Bowtie version 1. 1. 1 (7). The coverage of the mtDNA sequence was estimated at 1,448 based on Bowtie results using SAMtools  (8). The complete mtDNA sequence is 19 kbp long with a GϩC content of 31%. Comparison with mtDNA sequences available in GenBank showed that Sympagella nux (score, 8,587), Iphiteon panicea (score, 5,439), Aphrocallistes vastus (score, 1,477), Lophophysema eversa (score, 1,197), and Bolosoma sp. USNM 1097546 (score, 1,184), all glass sponges, were the closest neighbors of Oopsacas minuta. The structural and functional annotation was performed with the mitochondrial genome annotation (MITOS) server (  9 ) and the ARWEN program  (10).
Annotations of genes were checked using homology searches on GenBank and eventually improved using Artemis  (11). A single DNA strand carried genes with a total of 22 tRNA genes, 2 rRNA genes (one large and one small rRNA subunit), and 14 protein-coding genes. Nonprotein-coding genes and coding sequences represented 20% and 62. 5% of the genome, respectively. This genome has 13 of the respiratory genes common to most animal mtDNA (atp6, atp8, cob, cox1, cox2, cox3, nad1, nad2, nad3, nad4, nad4l, nad5, and nad6) and the atp9 gene found in nearly all sponge mtDNA. No trnaW gene was identified, suggesting a lineage-specific gene loss in the mtDNA sequence of Oopsacas minuta. No occurrence of the ϩ1 frameshifting previously reported in other glass sponge mitochondria was observed. Nucleotide sequence accession numbers.
ACKNOWLEDGMENTS This work has been carried out thanks to the support of the A* MIDEX  project ( ANR-11-IDEX-0001-02 ) funded by the " Investissements d'avenir" French Government program , managed by the  French National Research Agency (ANR). This work was supported by the  Aix-Marseille University  and the Centre national de la recherche scientifique. We thank  ProfileXpert platform  (http://www. profilexpert. fr) for genome sequencing and services of scientific diving and molecular biology of IMBE for sponge sampling and DNA extraction. We thank  Dennis Lavrov  for the communication of mtDNA sequences before releasing in GenBank, and we thank the  OSU Institute  and  Spongex  project partners for their help, especially  Carole Borchiellini ,  Jean Vacelet , Alexander Eres-crossmark Genome Announcements July/August 2015 Volume 3 Issue 4 e00823-15 genomea.
Experimental protocol The timeline is presented in Figure  1. After baseline data collection (H0), myocardial infarction was induced by inflation of an angioplasty balloon in the proximal left anterior descending artery (LAD). An angiogram was performed after inflation of the balloon in order to verify the complete occlusion of LAD. Four animals died from refractory ventricular tachycardia within 15 min after LAD occlusion and were therefore excluded from further analyses. After 45 min, animals were randomized to receive LR12 (LR12 group, n = 7) or the vehicle (phosphate-buffered saline) alone (control group, n = 8). LR12 consists of a 12 amino acid part of the extracellular domain of TLT-1 (LQEEDAGEYGCM) and was chemically synthesized TREM-1 during myocardial infarction (Pepscan Presto BV, Lelystad, The Netherlands) as COOH terminally amidated peptide.
Measurements Hemodynamic parameters were continuously monitored throughout the study period and recorded at baseline, every 15 min from H0 to H1. 5 and every 2 h from H2 to H18. The recorded parameters included MAP, mean pulmonary artery pressure, cardiac output, cardiac index, and SvO 2. Systemic oxygen delivery (DO 2 ) and systemic oxygen uptake (VO 2 ), and pulmonary and systemic vascular resistance index were calculated by the Swan-Ganz monitor (Edwards Lifesciences, Irvine, CA, USA). Cardiac Power Index (W/m 2 ) was calculated as MAP*cardiac index/451. 25 ressure-volume (PV) catheter was calibrated before data recordings. The arbitrary relative volume unit number was converted to true volume using pre-warmed Rho calibration cuvette device (reference 910-1060, Millar Inc, Houston, Texas, USA) to determine resistivity of body-temperature heparinized blood.
Ethic statement This study was approved by the "Comité de protection des personnes Ile-de-France II" (registration number 06-09-08), authorized by the "Direction Générale de la Santé" (authorization number 2006-AOO142-49), and registered as an observational study at www. clinicaltrials. gov under identifier NCT01055873. All patients, and their legal guardians for those under 18 years of age, received written information and signed an informed consent form.
Virological assays Env and RT gene sequences were determined from HIV DNA in the blood, as described elsewhere (http://www. hivfrenchresistance. org/). Phylogenetic analyses were carried out on the sequences of the Env and RT genes, to determine virus subtype. The phylogenetic relationships between the RT sequences were evaluated by comparison with sequences from previously reported representatives of group M, including reference sequences for subtypes and all the CRF sequences available from the HIV database or GenBank (http://www. hiv-web. lanl. gov). Clustal X was used for sequence alignment. Phylogenetic trees were constructed by the neighbor-joining method, and the reliability of the branching order was evaluated with Clustal X, by a bootstrapping approach (1000). Bootstrap values 70% were considered to provide significant support for membership of a subtype or a CRF.
Before carrying out multivariate analyses, we checked that there were no interactions between ethnicity and Gag-specific T-cell proliferation for variables with a P value <0. 20 (data not shown) in univariate analyses: we carried out an ANOVA for continuous variables and we assessed the variation of the OR across the strata for categorical variables. These analyses were exploratory and were not, therefore, corrected for multiple comparisons. For multivariate analyses, sex, ethnicity and HIV subtype were included as exposure factors of interest, regardless of their P value. Other variables were included if associated with Gag-specific T-cell proliferation, with a P value <0. 20 in univariate analysis. Collinear variables not included in the models are listed in the table's footnote. Analyses were conducted with SAS software (version 9.
Black patients had lower CD4 T-cell counts and percentages at the time of the study and had spent more time with severe immunosuppression than patients from other ethnic groups (data not shown). As lower levels of CD4 T-cells would be expected to be associated with lower levels of Gag-specific T-cell proliferation, the observed association between Gag-specific T-cell proliferation and black ethnicity would have been strengthened by a CD4 T-cell related bias, if such a bias existed. Ethnicity is related to socioeconomic parameters that may be associated with differences in access to care, even when such care is provided free of charge. Among the youths included in our study, ethnicity was not associated with successful viral suppression or treatment interruption. Among the aviremic patients, the duration of viral suppression was shorter in CD8Rs than in CD8NRs, and such differences were similar in both ethnic groups (i.
Acknowledgments Peptides were provided by the  NIH AIDS Research and Reference Reagent Program. We thank all the patients who agreed to participate in this study. We would also like to thank the nurses and staff members from the various clinical sites. We thank  Sandrine Leveillé  ( Hôpital Robert Debré ),  Geneviève Vaudre  ( Hôpital Trousseau ),  Sylvie Tassi  ( Hôpital Jean Verdier ),  Nora Boudjoudi  ( Hôpital Port Royal ),  Marie-Christine Mourey  ( Hôpital Necker ),  Thierry Wack.
Statistical analysis Graphs were generated and statistical analysis was carried out using Graphpad Prism 6 software. The tests applied are indicated in the figure legends: two-tailed t tests were used for comparisons between two groups; oneway ANOVA was used to compare multiple groups with one experimental parameter; and two-way ANOVA was used to compare multiple groups with two experimental parameters. When multiples tumor nodules were presented for each mouse, the statistical analyses were performed with the mean value from each mouse. Additional experimental procedures can be found in the Supplemental section.
ACKNOWLEDGMENTS This research was funded by government funding to SIgN,  A*STAR, Singapore. We thank the following people from SIgN:  Benjamin Toh  and  Lu-En Wai  for helpful discussions and assistance with necropsies;  Anis Larbi 's team ( Flow Cytometry platform ) for cell sorting; and  Irfan Khalis Bin Rosdi  ( Mouse Core ) for maintaining the RETAAD mice. We also thank  Lucy Robinson  of  Insight Editing London  for critical review and manuscript editing.
Immunofluorescence and confocal microscopy Aorta sections were stained with the rabbit polyclonal anti 4-HNE-Michael adduct (Calbiochem) and mouse monoclonal antihuman elastin antibodies, alexa-Fluor 488 (green)-and Alexa-Fluor 546 (red)-conjugated secondary antibody were from Molecular Probes (Invitrogen, Cergy-Pontoise, France). The slides were visualized using a Zeiss LSM 510 fluorescence confocal microscope (Le Pecq, France). Picture analysis was done using ImageJ 1. 49j software.
Statistical analyses Estimates of statistical significance were performed by t-test or analysis of variance followed by multiple comparison procedure (using the SigmaStat 3. 5, Systat software). Tests for normality and equal variance were performed by the Kolmogorov-Smirnov test. Differences between means values were evaluated by unpaired t test, to compare two groups, or by one-way ANOVA to compare group I vs the other groups, by the Holm-Sidak test. Values of p o 0. 05 were considered significant.
8) could be identified in these regulatory regions (Supplementary Fig. 3a ). Consistent with these findings, DLPC treatment increased Alox15, Cyp1a1 and Cyp1b1 gene expression in Lrh-1 M þ / þ macrophages, but not in Lrh-1 M À / À macrophages (Fig. 3i ). These data confirm the importance of LRH-1 in the regulation of Alox15, Cyp1a1 and Cyp1b1. Finally, to assess whether these effects on gene expression also translate into changes in endogenous ligand availability, 15-HETE production was assessed. Interestingly, while IL-13 exposure robustly enhanced 15-HETE levels in Lrh-1 M þ / þ macrophages, this effect was completely lost in Lrh-1 M À / À macrophages (Fig. 3j ). These findings indicate that LRH-1 is critically required for IL-13-induced 15-HETE production in macrophages. Importantly, IL-13-induced mobilization of AA was similar in Lrh-1 M þ / þ and Lrh-1 M À / À macrophages (Fig.
To confirm that 15-HETE production through the LRH-1/ CYP1 axis induces PPARg activation, we evaluated PPARg activation in macrophages silenced for Cyp1a1 and Cyp1b1. Interestingly, PPARg activity as determined by the induction of a PPRE luciferase reporter (Fig. 5c ) and the induction of PPARg target genes (Fig. 5d ) by IL-13 were totally inhibited in macrophages deficient for Cyp1a1 and Cyp1b1. Moreover, the induction of a PPRE luciferase reporter (Fig. 5c ) and of PPARg target genes (Fig. 5d ) was still significantly enhanced by IL-13 in Alox15 À / À macrophages, showing that the 12/15 lipoxygenase is not required for PPARg activation mediated by LRH-1. These data are in support of a critical role of CYP1A1 and CYP1B1 in LRH-1-mediated PPARg activation through 15-HETE synthesis. IL-13 activation of macrophages requires STAT6/LRH-1/PPARc.
RT-qPCR was performed on a LightCycler 480 system using LightCycler SYBR Green I Master (Roche Diagnostics). The primers (Eurogentec) were designed with the software Primer 3. Actb (Actin) mRNA was used as the invariant control. Serially diluted samples of pooled cDNA were used as external standards in each run for the quantification. Primer sequences are listed in Supplementary Table  1. In situ hybridization. In situ hybridization was performed with digoxigeninlabelled RNA probe (Plasmid pBSSK Lrh-1) as previously described  44. Briefly, this manual nonradioactive method allows to detect specific complementary mRNA sequences at the cellular level using digoxigenin-labelled probes in a five-step procedure: hybridization of the probe to pretreated tissue at 65 °C; post-hybridization stringent washes; blocking steps to prepare for the immunodetection; primary antibody anti-DIG-AP incubation; and colorimetric enzymatic detection.
Data were normalized for GAPDH promoter binding and expressed relative to IgG. ChIP primer sequences are listed in Supplementary Table  2. Reporter assays and site-directed mutagenesis. Genomic DNA was extracted from mouse kidneys and the corresponding Cyp1a1 and Cyp1b1 promoter fragments were amplified by PCR with primers containing KpnI and XhoI restriction sites. The PCR products were then cloned into pENTR-D/TOPO (Invitrogen/ Lifetechnologies) plasmids, which were digested with KpnI and XhoI and then ligated into pGL4. 12 (Promega) reporter plasmids. Mutagenesis was carried out with the GeneArt mutagenesis kit (Invitrogen/ Lifetechnologies) according to the manufacturer's instructions. The sequences of reporter constructs were analysed and confirmed. Flow cytometry. The analysis was performed on nonadherent macrophages  47  harvested by washing the peritoneal cavity with 5 ml of sterile NaCl 0.
9%. Collected cells were centrifuged at 1,500 r. p. m. for 10 min and the cell pellet was suspended in PBS medium supplemented with 1% fetal calf serum (FCS). Surface expressed Dectin-1 or CD36 was detected, respectively, using fluoroscein isothiocyanate (FITC)-Dectin-1 monoclonal antibody (mAb; Serotec MCA2289F, 1/100) or PE-CD36 mAb (Santa Cruz, sc-13572, 1/100) and was compared with an irrelevant appropriate isotype control. To evaluate the mannose receptor (MR) surface expression, we have used MR-specific ligand conjugated with FITC (Sigma A7790, 1 mg ml À 1 ). All stainings were performed on PBS-1% FCS medium. A population of 10,000 cells was analysed for each data point. All analyses were carried out in a Becton Dickinson FACScalibur using the CellQuestPro software. B and T lymphocytes were isolated from the mouse spleen with a PE-B220 mAb (RD System FAB1217P, 1/10) and a PE-CD3 mAb (eBiosciences MCA500, 1/10) using a Becton Dickinson Influx cell sorter.
Acknowledgements We thank  Philippe Batigne  and  Benedicte Bertrand  from the  UniversitePaul Sabatier  for excellent technical support, and  Alexia Zakaroff-Girard  and  Christiane Pe  ´cher (TRI imaging platform,  IFR150/I2MC ) for flow cytometry technical assistance. This research project has received, through BIOASTER investment, funding from the  French Government  through the  Investissement d'Avenir programme  (grant n°ANR- 10-AIRT-03 ). This research was also supported by a grant from l' Association de la Recherche contre le Cancer (ARC)  awarded to L. L. ( DOC20120605122 ) and  Swiss Cancer Ligue  (to K. S. ).
Results We present here clonotypeR, a software package to identify and analyze antigen receptors from highthroughput sequence libraries. ClonotypeR is designed to process, organize and analyze very large numbers of sequences, in the order of millions, typically produced by Roche 454 or Illumina instruments, and is made of two parts. The first contains shell scripts and reference segment sequences to produce a data file where each line represents a the detection of a clonotype in a sequence read. The second part is a R module available from Bioconductor, to load and filter the data, and prepare clonotype abundance tables ready for analysis with third-party tools for differential representation analysis, sample clustering, etc. To analyze clonotype data at the nucleotide level, we introduce unique clonotype identifiers based on those developed by  Yassai et al.
The somatic recombination is imprecise and therefore the sequence of the CDR3 has to be determined experimentally. Flanking the CDR3, there are two structural motifs that are essential for the receptor's function and therefore strongly conserved: a cysteine at the end of the V segment and a FGxG motif in the J segment  (Sant'Angelo et al. , 1997). Characterizing the receptor clonotype diversity requires the identification of the V and J segments and sequencing the CDR3, as well as suitable and robust statistics  (Boudinot et al. , 2008; Benichou et al. , 2012). ClonotypeR is the combination of support scripts to align and extract CDR3s, and a package for the R language for statistical computing, also available through Bioconductor.
, 2010)  in codon color mode. The final reference list combines segments from the α, β, γ and δ loci, therefore clonotypeR can detect accidental contaminations of one sample type with another during the preparation or the sequencing of the libraries, as well as rare Vα-Jδ rearrangements. In the second step, the CDR3 boundaries are confirmed using the vectorstrip program from EMBOSS  (Rice et al. , 2000) , requesting a perfect match with 20 nucleotides before the conserved cysteine. This independent detection of the V-CDR3 junction acts as a second filter for stringency and prevents from accidental frame shifts in case the BWA alignments did not reach the cysteine codon. The boundary of the J segment, downstream the FGxG motif, is then searched with the same strategy. The CDR3 is then translated using BioPerl  (Stajich et al.
The abundance of CDR3s can also be quantified using their nucleotide sequence. As a compact representation of nucleotide-characterized clonotypes, we implemented of the nomenclature of  (Yassai et al. , 2009) , which assigns a unique synthetic identifier to each clonotype. However, tests on large scale data revealed that this nomenclature sometimes produces identifiers that are not unique to a clonotype. For example, aAn. 1A14-1A43L9 represents a clonotype of 9 aminoacids, made by the junction of the TRAV 14-1 and TRAJ 43 segments, where the non-templated part is a GCT codon for alanin, inserted between a templated alanin from the V segment and a templated glutamin from the J segment. We show in Table  1  that this identifier corresponds to more than one clonotype. We propose to solve this problem by using a "long" variant of the identifier, where the full translated sequence is represented.
Discussion ClonotypeR differs from Decombinator  (Thomas et al. , 2013)  by its design taking advantages of long reads. On-line tools like IMGT/HighV-QUEST  (Alamyar et al. , 2012)  are limited in the amount of data they accept. Moreover, local processing gives full control of the software pipeline used, and therefore reproducibility of the results. Local installations in virtual machines are also becoming relevant for cloud computing. ClonotypeR accepts user-provided reference alignments, for instance to analyze human data, take into account genetic polymorphisms, or study B cell receptors (BCRs). However, because of the somatic hypermutations, work on BCRs will need further adjustments. To study colonotype abundance at the nucleotide level, we introduced a modification of the unique identifiers introduced by  Yassai et al.
(2009) , in order to keep a strict one-to-one correspondence between clonotypes and their identifiers. This format is slightly longer, and might be shortened by removing the last part indicating the number of aminoacids, since in our modified version they are all represented. Alternatively, it may be interesting to replace this length information by a measurement of the edit distance between the clonotype and the juxtaposed V and J segments. For our initial release, we focused on T cell receptors sequenced in Roche 454, Illumina, or capillary sequencers. However, ClonotypeR can handle the typical throughputs produced by HiSeq instruments. On a desktop computer running Debian Linux with a quad-core hyperthreaded CPU and 12 Gb of RAM, we could reprocess the 38 million CD8 + TRα (TRA) reads deposited as SRR407172 in NCBI GEO by  (Genolet et al.
, 2012)  in 10 hours. This deep data was obtained from naive mice and therefore broadly covers the 4,142 possible V-J segment combinations. Our results were in good match with the original analysis, with respectively 28 vs. 29 millions aligned reads, (17 vs. 15 millions unambiguous), and 3,653 vs. 3,901 different combinations of V and J segments. ClonotypeR runs on Linux and Mac OS, as well as Windows (Bioconductor only). It fills the gap between the sequencer and the data analysis, without requiring online data submission, and facilitates the application of tools designed for digital gene analysis and diversity analysis to the field of immune repertoire studies.
Funding We thank  Jack Gorsky  for useful comments on the Yassai nomenclature. This work was supported by research grants from  MEXT  and  JSPS  to SH (19059014 and  20689012 ), from  MEXT  to  RIKEN CLST  and  RIKEN OSC , and from a  RIKEN presidential grant. EMF received a  JSPS long-term post-doctoral fellowship  ( P08627 ).
ISGylation machinery is induced by Listeria and ISGylation protects against infection Since ISG15 can mediate its protective effect through conjugation-dependent or conjugationindependent mechanisms, we wanted to determine if conjugation contributed to ISG15's role in defense against Listeria. Therefore, we initially assessed whether Listeria could induce the enzymes required for ISGylation. To this end, we performed RNASeq of Lovo cells infected with Listeria for 24 hr compared to uninfected cells. The RNASeq data has been uploaded to Array Express with the accession E-MTAB-3649  (Radoshevich et al. , 2015b). We found that UBE1L (E1), UBE2L6 (E2), HERC5 and TRIM25 (E3s) mRNA are all significantly upregulated following Listeria infection, as is the deconjugating enzyme USP18 (Figure  3G ).