dataesr/scientific-paragraphs-categorization huggingface dataset:
The pipeline was successfully tested on RNA-seq data of a family from Silene latifolia, a dioecious plant with relatively recent but heteromorphic sex chromosomes. Genes have previously been experimentally characterised as autosomal or sex-linked in this species, which made it possible to assess the performances of the method. 83% of known sex-linked genes that were expressed in the sampled tissue could be identified using the SEX-DETector pipeline. Sensitivity and specificity values were used to compare SEX-DETector to other RNA-seq based approaches that used S. latifolia datasets  (Bergero and Charlesworth, 2011; Chibalina and Filatov, 2011; Muyle, Zemp, et al. , 2012). SEX-DETector showed a much higher sensitivity (0. 63 compared to 0. 25-0. 43) while specificity remained close to 1. Thanks to a statistically grounded method, the SEX-DETector pipeline can detect many more genes than previous approaches, while keeping the inferences extremely reliable.
This was done for the 332 inferred X-hemizygous genes in the S. latifolia dataset, and only 5 of them had a significant match with a male-specific contig. This suggests that very few true X/Y gene pairs were wrongly inferred as X-hemizygous due to a too divergent Y. In S. latifolia, X-Y synonymous divergence ranges from 5% to 25%  (Bergero, Forrest, et al. , 2007). This is comparable to regions in human sex chromosomes that stopped recombining last: the mean X-Y synonymous divergence for strata 3, 4 and 5 in humans is respectively 30%, 10% and 5%  (Skaletsky et al. , 2003). SEX-DETector will therefore perform best in species with sex chromosomes of young or intermediate age, but will also work on recent strata of old systems. A complete list of cases where inferences could be difficult is provided in the online SEX-DETector user manual (p 3-4), along with cases where SEX-DETector could be applied to detect dominant loci associated with a phenotype, other than sex chromosomes.
96. C) WUS1 is known to be X-hemizygous, its weighted sex-linked mean probability is 0. 99. D) BAC284N5-CDS13 SlX6a is known to be sex-linked, its weighted sex-linked mean probability is 0. 82. SEX-DETector on the other hand filters for a posterior probability above 0. 8 (horizontal line on graph) and at leat one sex-linked SNP, so that more contigs can inferred as sex-linked, without increasing the false positive rate compared to other empirical methods (Table  2 ). Tables  Table 1:  Results of the SEX-DETector pipeline on the S. latifolia dataset. ORF Types Numbers ORFs in final assembly 46178 ORFs with enough coverage to be studied 43901 ORFs with enough informative SNPs to compute a segregation probability 17189 ORFs with posterior segregation probability over 0. 8 15164 ORFs assigned to an autosomal segregation type 13807 (91%) ORFs assigned to a X/Y segregation type 1025 (7%) ORFs assigned to a X hemizygous segregation type 332 (2%) Sensitivity Specificity SEX-DETector 0.
Acknowledgements We thank  Alex Widmer  for access to the RNA-seq datasets and comments on the manuscript,  Nicolas Galtier  and  Sylvain Glémin  ( ISEM-Montpellier ) for useful discussions about reads2snp,  Vincent Miele  ( LBBE ) for SEX-DETector profiling and advice on code performance,  Khalid Belkhir  ( ISEMmontpellier ) for providing and adapting Galaxy wrappers for analyses used upstream of SEX-DETector (BWA, reads2snp) and  Philippe Veber  ( LBBE ) for help with Galaxy.
Data The unfolding reaction of a series of G-quadruplex structures by addition of their complementary strand was monitored by fluorescence techniques  [1]. Kinetic constant of this G4 opening process was obtained by playing individual fitting models to the fluorescence data. Furthermore, DNA structures considered in this studied (G-quadruplexes and duplex DNA) were characterized spectroscopically. Their thermal stability (Tm) was studied by monitoring the thermal melting process of the DNA motif by UV (at 260 nm and 295 nm for duplex DNA and G4 DNA respectively). In addition, the polarity of the G-quadruplex was also studied by circular dichroism, which confirmed the correct folding of the G4 structures. The data provide in Figs. 1  and 2  shows the raw emission data for the fluorescence intensity of the labeled DNA strands.
3 °C per min and following the variation of UV absorption at 295 nm and 260 nm. Circular dichroism (CD) spectroscopy: CD experiments were performed with a JASCO J-815 spectropolarimeter equipped with a JASCO CDF-426S Peltier temperature controller, using quartz cells of  1 cm path length. The scans were recorded from 210 to 335 nm wavelength with the following parameters: 0. 5 nm data pitch, 2 nm bandwidth, 100 nm min À 1 scanning speed, and are the result of 3 accumulations.
Acknowledgments O. M. is the recipient of a post-doctoral fellowship from the fondation  ARC. This work was supported by the  Aquitaine regional council ,  PIA Nanobiotech program  (Vibbnano  ANR-10-NANO-04 ) and  ANR  grants  Quarpdiem  [ ANR-12-BSV8-0008-01 ] and  Oligoswitch  [ ANR-12-IS07-0001 ].
Contagion trials A contagion experiment was carried out to investigate the presence of intra-and inter-species transmission of disease or other noxious substances linked to our injection method. Experimental blocks consisted of 3 large concrete tanks (5. 00 m × 1. 50 m × 0. 64 m; length × breadth × height) with constant filtered seawater inflow containing six COTS and a total of 30 other coral reef organisms. The 30 specimens belonged to phylums Cnidaria, Echinodermata, Mollusca and Chordata (Table  1 ) and had been collected from a healthy, shallow fringing reef located near the marine hatchery. Coral samples were placed in cages in order to prevent direct feeding injuries from COTS. Three temporal contagion trials were performed: after a seven day acclimation period, the six COTS specimens were randomly assigned to either no injection (three individuals) or a single-shot injection of 10 ml of lime juice (three individuals).
Acknowledgments The authors wish to express their warmest thanks to the staff of the  Vanuatu Fisheries Department in Port-Vila  and the coastal communities involved in this project. We wish to thank  Iago Bonnici  for fruitful discussions and help, to  Christine Sidobre  at  CRIOBE  for preparing the solutions for the immunity measures and to the students and teachers of  Lycée Français Le Clézio of Port-Vila. Authors personal contribution. GM (field work, data elaboration and interpretation, statistical analyses, manuscript preparation and editing), SG (research strategy, manuscript preparation), SM (immunological analyses, statistical analyses, data interpretation, manuscript preparation and editing), MA (research strategy and manuscript editing), RB (research strategy and manuscript editing), JH (research startegy and field work), RK (field work), PD (research strategy and supervision, statistical analyses, data elaboration and interpretation, manuscript preparation and editing).
This project was funded by grants from the  Fisheries Department of Vanuatu  (www. fisheries. gov. vu), grant # COT012. This was the main grant for this work, which covered fieldwork (Vanuatu) and functioning costs (hatchery and aquaculture facilities, technical staff, laboratory materials) of the study. Support was also provided by grants from the  Government of New Caledonia  (www. gouv. nc/portal/page/portal/gouv/), grant for project  MANAO_2015 , covered the hosting of  Gregoire Moutardier  at the  Fisheries Department of Vanuatu during his MSc. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Support was also provided by grants from the  LabEx Corail  (www. labex-corail. fr/),grant for project  DYNACANTH-2015 , covered the field trip of  Dr.
Suzanne Mills  in Vanuatu during the project. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Support was also provided by grants from the  Agence Nationale de la Recherche  ( ANR-11-JSV7-012-01  " Live and Let Die ",  Suzanne C. Mills ) and the  Fundação para a Ciência e Tecnologia  ( SFRH/BPD/26901/2006 ,  Ricardo Beldade ) provided additional support. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Acknowledgments This work was supported by  Agence Nationale de la Recherche  ( ANR-12-BSV2-0011  and  ANR-14-CE09-0008-03 ),  Association Française des Myopathies , and  Institut National du Cancer (INCa   AAP PLBIO 2012 ) grants. Stéphanie Torrino  is supported by  ARC foundation postdoctoral fellowship. This work has been done by a team belonging to the labex CelTisPhyBio  11-LBX-0038. We wish to thank  Weiwei Shen  and  Cédric Blouin  for carefully reading the manuscript and  Maria Daniela Garcia Castillo  for help with editing.
59 upper limit of normal range) 6. Thrombocytopenia or leukopenia 7. Pregnant or lactating women and women at risk of pregnancy 8. Patients taking moderate-strong CYP3A4 inhibitors 9. Patients already taking colchicine 10. Those with evidence of active infection or inflammatory conditions that might be associated with markedly elevated CRP levels in the blood (eg, active rheumatoid arthritis) and those taking other anti-inflammatory therapies (eg, corticosteroids) Demographic and clinical data were recorded. The local Ethics Review Committee approved the study protocol and all patients gave written informed consent before participating.
Statistical Analysis Continuous variables are reported as meanAE SD or SEM and categorical variables as number (percentage). Normal distribution was tested by the Shapiro-Wilk test. Differences in continuous variables (eg, IL-1b concentration) were tested via the use of an independent-samples t test or nonparametric test for non-normally distributed data (Mann-Whitney U test), while proportional differences in categorical variables (eg, patient did or did not have hypertension) were tested via the use of Fisher's Exact Test. Multiple, nonpaired samples were tested with 1-way ANOVA or Kruskal-Wallis test and multiple paired samples with Friedman test. All tests were 2-tailed with the acceptable type 1 error set at P<0. 05. Statistical analysis was performed with SPSS 21 software (IBM, Armonk, NY) and figures were created with GraphPad Prism 6.
It also tested for relationships between the feeding guild and the levels of N 2 O production, the abundance of marker genes for ammonia oxidation (amoA and amoB) and denitrification (nirK, nirS and nosZ) processes, and mineral N concentration in termite guts. So far as we are aware, this is the first study to use a single dataset to compare N 2 O production rates by termite species belonging to different feeding guilds and to report the presence of ammonia-oxidation and denitrification marker genes in termite guts.
At Last! All Major Classes of Small Non-Coding RNAs Gathered in a Unique Database Highlight by Claire Francastel and Florent Hubé Small non-coding RNAs (sncRNAs) emerged a few years ago as functionally important molecules involved in nearly all physiological and pathological processes of the cell. Numerous classes of sncRNAs have been reported that include transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs) of course, but also many others like microRNAs (miRNAs) and small nucleolar (snoRNAs), the best known among them. For each class, many databases were built, some of which are now recognized references databases; this is the case for miRBase. org, which is the reference searchable database for annotated miRNAs. However, these databases are not complete since, for example, a few miRNAs annotated in UCSC were still not deposited in miRBase.
Moreover, as many databases of classes of sncRNA of interest have to be assembled and curated for a given study. This drawback has now been fixed with the DASHR database from Leung et al. [2]. Their database accounts for about 48,000 human sncRNA genes and mature sncRNA products, and contains all major classes, including miRNAs, Piwi-interacting (piRNAs), small nuclear, nucleolar, cytoplasmic (sn-, sno-, scRNAs, respectively), tRNAs and tRNAderived fragments, and rRNAs. Version 2. 0 of the database is expected soon, but, already, seeking information in the small RNA world has never been so handy.
Phosphoproteomic analysis of the early purinoceptor signaling response in dystrophic myoblasts Putative P2RX7-evoked signaling cascades in dystrophic muscle cells were investigated using an iTraq-based mass spectrometry approach. Phosphoproteins extracted from wildtype and dystrophic myoblasts treated with 3 mM ATP for 10 min were analyzed using Spectrum Mill (Agilent) and inference values determined via the iQuantitator algorithm. 40 ne thousand two hundred and seventy two unique phosphoproteins were identified, of which 263 showed significant differences in their phosphorylation status evoked by eATP. Pathway analysis was performed using MetaCore and IPA softwares. This approach identified significantly higher phosphorylation status in HSPA2, HSPA8 (heat shock protein 8), 3 HSP90 isoforms and in CDC37 (cell division cycle 37) members of the family of chaperone heat shock proteins in dystrophic myoblasts.
Cysteine residues were blocked in 55 mM iodoacetamide Sigma, I1149) at RT for 30 min. Samples were trypsin digested in 1 mg trypsin (Promega, V5111) per 1 mg protein at 30 C for 15 min. Samples were then iTraq labeled from 114-117 (Sciex, 4374321) dissolved in EtOH for 1 h at RT, then subjected to isoelectric focusing in 24 well, 12. 5% w/v polyacrylamide gel strips (Agilent Technologies, 5188-6424) using an OFFGEL fractionating system (Agilent 3100 Fractionator, Agilent Technologies, Massy, Paris, France) for 48 h. Separated samples were analyzed by ESI-LC-MS (Agilent 6200 TOF, Agilent Technologies, Massy, Paris, France) and phosphopeptide fragments identified by interrogating the Mascot database (Matrix Science) using Spectrum Mill software (Agilent Technologies). Fold changes and significance levels were determined using the iQuantitator  40  algorithm and pathway analysis carried using pathway designer functions of Metacore (Thomson Reuters) and IPA (Ingenuity, Qiagen) software.
Following 3 further washes in PBS, cells were permeabilized in 0. 1% Triton X-100 in PBS, blocked with serum specific to the host of the secondary antibody origin (10%; Sera Labs, S-707-HIS) for 30 min at RT, then incubated with anti-LC3 antibody (Sigma, L7543) overnight at 4 C. Cells were then washed 3 times in 1 x PBS prior to secondary antibody (Alexa Fluor) application for 1 h at room temperature. Coverslips were then washed and mounted on slides using mounting medium (Ibidi, 5000), and images acquired using a Zeiss LSM 5. 10 confocal microscope (Zeiss, Cambridge, Cambridgeshire, UK). Images were analyzed using ImageJ software's particle analysis plugin.
Acknowledgments We thank  Drs F Koch-Nolte  ( University Medical Center, Hamburg ) for providing HEK(P2RX7) cells,  A Young  ( CRUK, Cambridge ) for sharing autophagy expertise,  D Coletti  ( Paris 6 ) for permission to use his skull cell graphic and  Y Geng ,  Y Choi  and  W Michowski  ( Dana Farber, Boston ) for critical reading of the manuscript.
This strain exhibited a 97. 5 % 16S rRNA nucleotide sequence similarity with Bacillus niacini, the phylogenetically closest validly published Bacillus species (Fig. 1 ), when it was compared against NCBI database and Ribosomal Database Project. This value was equal to the percentage of 16S rRNA gene sequence threshold recommended by Meier-Kolthoff et al. for Firmicutes to delineate a new species without carrying out DNA-DNA hybridization with maximum error probability of 0. 01 %  [21]. Different growth temperatures  (28, 30, 37, 45 , 56 °C) were tested. Growth occurred for the temperatures (28-45 °C), but the optimal growth was observed at 37 °C. Colonies were 0. 4-0. 5 mm in diameter on Columbia agar, appear smooth and grey in color at 37 °C. Growth of the strain was tested under anaerobic and microaerophilic conditions using GENbag anaer and GENbag microaer systems, respectively (BioMérieux), and in aerobic conditions, with or without 5 % CO 2.
Using API ZYM, positive reactions were observed for esterase (C 4), esterase lipase (C 8), acid phosphatase, naphthol-AS-BI-phosphohydrolase and β-glucosidase. Negative reactions were observed for alkaline phosphatase, lipase (C 14), leucine arylamidase, valine arylamidase, cystine Fig. 1  Phylogenetic tree highlighting the position of Bacillus jeddahensis strain JCE T relative to other type strains within the Bacillus genus. GenBank accession numbers are indicated in parentheses. Sequences were aligned using MUSCLE, and phylogenetic inferences obtained using the maximum-likelihood method and Kimura 2-parameter model within the MEGA 6 software  [50]. Numbers at the nodes are percentages of bootstrap values obtained by repeating the analysis 1,000 times to generate a majority consensus tree.
0, Bruker) and analyzed by standard pattern matching (with default parameter settings) against 6,335 bacterial spectra including 210 spectra from 110 Bacillus species, used as reference data, in the BioTyper database. Interpretation of scores was as follows: a score ≥ 2 enabled the identification at the species level, a score ≥ 1. 7 but < 2 enabled the identification at the genus level; and a score < 1. 7 did not enable any identification (These scores were established by the manufacturer Bruker Daltonics). For strain JCE T , the obtained scores ranged from 1. 4 to 1. 6, thus suggesting that our isolate was not a member of a known species. We incremented our database with the spectrum from strain JCE T (Fig. 4 ). Spectrum differences with other of Bacillus species are shown in Fig. 5.
Genome project history On the basis of phenotypic characteristics of this strain and because of the low16S rRNA similarity to other members of the genus Bacillus, it is likely that the strain represents a new species and thus it was chosen for genome sequencing. It was the 348th genome of a Bacillus species (Genomes Online Database) and the first genome of Bacillus jeddahensis sp. nov. sequenced. A summary of the project information is shown in Table  2. The Genbank accession number is CCAS00000000 (Table  2 ) and consists of 149 contigs. Table  2  shows the project information and its association with MIGS version 2. 0 compliance  [25]. Growth conditions and genomic DNA preparation B. jeddahensis sp. nov. strain JCE T , CSUR P732, DSM 28281, was grown aerobically on 5 % sheep blood-enriched Columbia agar at 37 °C.
The final assembly identified 149 large contigs (>1. 5 kb) generating a genome size of 4. 76 Mb which corresponds to a genome coverage of 94. 91x. [29]  and BLASTn against the GenBank database. Signal peptides and numbers of transmembrane helices were predicted using SignalP  [30]  and TMHMM  [31] , respectively. ORFans were identified if their BLASTP E-value was lower than 1e-03 for alignment length greater than 80 amino acids. If alignment lengths were smaller than 80 amino acids, we used an E-value of 1e-05. Such parameter thresholds have already been used in previous works to define ORFans. Artemis  [32]  and DNA Plotter  [33]  were used for data management and visualization of genomic features, respectively. Mauve alignment tool (version 2. 3. 1) was used for multiple genomic sequence alignment  [34].
To estimate the mean level of nucleotide sequence similarity at the genome level between B. jeddahensis sp nov. strain JCE T and nine other members of the genus Bacillus, we use the Average Genomic Identity of orthologous gene Sequences (AGIOS) program. Briefly, this software combines the Proteinortho software  [35]  to detect orthologous proteins between genomes compared on a pair-wise basis, then retrieves the corresponding genes and determines the mean percentage of nucleotide sequence identity among orthologous ORFs using the Needleman-Wunsch global alignment algorithm. Moreover, we used Genome-to-Genome Distance Calculator (GGDC) web server available at (http://ggdc. dsmz. de) to estimate of the overall similarity among the compared genomes and to replace the wet-lab DNA-DNA hybridization (DDH) by a digital DDH (dDDH)  [36, 37].
Cells stain Gram-positive, are   The G + C content of the genome is 39. 42 %. The 16S rRNA and genome sequences are deposited in GenBank under accession numbers HG931339 and CCAS00000000, respectively. The type strain JCE T (= CSUR P732 = DSM 28281) was isolated from the fecal flora of an obese man from Jeddah in Saudi Arabia.
Acknowledgements This work was funded by the  Deanship of Scientific Research (DSR) ,  King Abdulaziz University , under grant No. ( 1-141/1433 HiCi ). The authors, therefore, acknowledge technical and financial support of  KAU. Fadi Bittar  was supported by a  Chair of Excellence IRD  provided by the  Institut de Recherche pour le Développement / Méditerranée-Infection foundation.
We used the fluorophore ATTO-532 due to its weak variation in emission with temperature  32  and the corresponding quencher Black Hole Quencher 1 (BHQ1) placed at positions 47 and 26, respectively (Eurogentec). We confirmed the folding of the linker into a double-helix stem by fluorimetry using an excitation wavelength of 510 nm and a collection window from 530-650 nm (FLSP920 spectrofluorimeter from Edinburgh Instruments, UK). A 100 nM solution of aptadimer in PBS (10 mM PB pH ¼ 7. 4, 145 mM NaCl, 5 mM KCl, 1 mM CaCl 2 , 1 mM MgCl 2 ) was heated from room temperature to 60 C by consecutive steps of 5 C separated by 5 min (dataset in Figure  1(b) ). Fluorescence emission started to build up at $25 C and reached its apex at 50 C, following a sigmoidal profile centered at 39 C (line plot in Fig.
Note the positions of the fluorophore and quencher, which are indicated by a star and a circle, respectively. In the lower panel, the crystal structure of thrombin (red) with the two aptamers HD1 (4DII pdb) and HD22 (4I7Y pdb) shown in the same colors as in the upper panel is represented with PyMol software. The distance between the lagging ends of the aptamers is 7. 3 nm. (b) The dataset shows the fluorescence signal collected from the aptadimer as a function of temperature, and the corresponding fit is obtained with a sigmoidal model centered at 39 C. Note that the system was stabilized during 5 min before each fluorescence intensity measurement. of 2:1 led to an increase in fluorescence of 52%. Note that we obtained a detectable signal with 5 nM of thrombin. This lower concentration is somewhat larger than that reported with dual-reporter assays using optimal FRET couples of $0.
With these calibrations completed, we subsequently focused on thrombin detection in murine plasma diluted 10-and 100-fold in PBS. We observed the same response in PBS or with 1% plasma (yellow curves in Figure  3 ). Hence we spiked the 1% plasma solution with 50 nM thrombin, and observed an onset in fluorescence intensity of 110%, which was larger than the signal collected with thrombin in PBS and rather corresponded to an effective thrombin concentration of 100 nM (blue datasets in Fig. 3 ). Given that this is specific to thrombin, we suggest that this response is mediated by the presence of thrombin as well as intermediate species between prothrombin and thrombin in plasma. 2  In any case, this high fluorescence intensity signal may also account for the large signal enhancement of more than 120% with 10-fold diluted plasma (dashed curve in Fig.