dataesr/scientific-paragraphs-categorization huggingface dataset:
strain G1 T and other Paenibacillaceae species, we use the Average Genomic Identity of orthologous gene Sequences (AGIOS) program. Briefly, this software combines the Proteinortho software  [53]  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.
83 µm) and a mean length of (C14), a-chymotrypsin, esterase (C4), esterase lipase (C8), naphthyl-AS-BI-phosphohydrolase, phenylalanine arylamidase, leucine arylamidase, cystine arylamidase, valine arylamidase, glycine arylamidase, arginine arylamidase and βglucosidase. Using the API Coryne system, positive reactions are observed for β-glucuronidase, alkaline phosphatase, α-glucosidase, α-galactosidase and N-acetyl-β-glucosaminidase activities. The urease reaction, nitrate reduction and indole production were negative. P. gorillae is susceptible to imipenem, rifampicin, gentamycin, nitrofurantoin and vancomycin, but resistant to metronidazole, trimethoprim/sulfamethoxazole, ceftriaxone, ciprofloxacin and amoxicillin. The G+C content of the genome is 48. 8%. The 16S rRNA and genome sequences are deposited in GenBank under accession numbers JX650054 and CBVJ000000000, respectively.
5 kV; lens, 7 kV). A spectrum was obtained after 675 shots with variable laser power. The time of acquisition was between 30 seconds and 1 minute per spot. The twelve JCD T spectra were imported into the MALDI BioTyper software (version 2. 0, Bruker) and analyzed by standard pattern matching (with default parameter settings) against the main spectra of 3,769 bacteria, including 228 spectra from 96 Clostridium species. The method of identification included the m/z from 3,000 to 15,000 Da. For every spectrum, a maximum of 100 peaks were compared with spectra in database. The resulting score enabled the identification of published species enabled identification at the ification at the genus level, and a score < 1. 7 did not enable any identification. No significant MALDI-TOF score was obtained for strain JCD T against the Bruker database, suggesting that our isolate was not a member of a known species.
We added the spectrum from strain JCD T to our database (Figure  4 ). Finally, the gel view showed the spectral differences with other members of the genus Clostridium (Figure  5 ). Clostridium clariflavum (AB186359) Clostridium cellulolyticum (X71847) Clostridium thermosuccinogenes (Y18180) Clostridium orbiscindens (Y18187) Clostridium methylpentosum (Y18181) Clostridium cellulosi (L09177) Clostridium leptum (AJ305238) Clostridium sporosphaeroides (X66002) Clostridium lentocellum (X71851) Clostridium saccharolyticum (CP002109) Clostridium difficile (AB075770) Clostridium dakarense (KC517358) Clostridium beijerinckii (X68179) Clostridium acetobutylicum (AE001437) Clostridium senegalense (JF824801) Clostridium ramosum (X73440).
Genome project history The organism was selected for sequencing on the basis of its phylogenetic position and 16S rDNA similarity to members of the genus Clostridium, and is part of a study of the human digestive flora aiming at isolating all bacterial species in human feces  [55]. It was the 101 st genome of a Clostridium species and the first genome of C. jeddahense sp. nov. The GenBank accession number is CBYL00000000. The assembly consists of 104 contigs. Table  3  shows the project information and its association with MIGS version 2. 0 compliance  [39].
Genome annotation Open Reading Frames (ORFs) were predicted using Prodigal  [56]  with default parameters. However, the predicted ORFs were excluded if they spanned a sequencing gap region. The predicted bacterial protein sequences were searched against the GenBank  [57]  and Clusters of Orthologous Groups (COG) databases using BLASTP. The tRNAs and rRNAs were predicted using the tRNAScan-SE  [58]  and RNAmmer  [59]  tools, respectively. Signal peptides and numbers of transmembrane helices were predicted using SignalP  [60]  and TMHMM  [61] , respectively. Mobile genetic elements were predicted using PHAST  [62]  and RAST  [63]. 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 work to define ORFans. Artemis  [64]  and DNA Plotter  [65]  were used for data management and visualization of genomic features, respectively. The Mauve alignment tool (version 2. 3. 1) was used for multiple genomic sequence alignment  [66]. To estimate the mean level of nucleotide sequence similarity at the genome level between C. jeddahense and 7 other members of the genus Clostridium, we used the Average Genomic Identity Of gene Sequences (AGIOS) home-made software  [6]. Briefly, this software combines the Proteinortho software  [67]  for detecting orthologous proteins between pairs of genomes, then retrieves the corresponding genes and determines the mean percentage of nucleotide sequence identity among orthologous ORFs using the Needle-man-Wunsch global alignment algorithm.
Asaccharolytic. Positive for indole. Cells are susceptible to amoxicillin, amoxicillinclavulanate, imipenem, metronidazole, doxycycline, rifampicin, vancomycin but resistant to ceftriaxone, ciprofloxacin and trimethoprimsulfamethoxazole. The G+C content of the genome is 51. 95%. The 16S rDNA and genome sequences are deposited in GenBank under accession numbers HG726040 and CBYL00000000, respectively. The type strain is JCD T (= CSUR P693 = DSM 27834).
Flight details While the primary focus of the SAMBBA campaign was the study of biomass burning, a number of flights were conducted over areas of unperturbed rainforest to study biogenic processes. The flights occurred after the onset of the transition to the wet season, where the weather within Brazil became more unsettled. Due to wet deposition and a change in synoptic transport, this resulted in generally lower concentrations of anthropogenic emissions compared to the later stages of the dry season, when biomass burning was at its peak. In total, five biogenic flights took place, which are summarised in Fig. 2  and Table  1. The first flight, B735, partly collected high-altitude data between Porto Velho and Manaus. However, periods of flying over the rainforest also took place. The remaining four flights took place out of Porto Velho and followed a similar format to that used during OP3, where one flight took place around midday (local time), with a second flight in the afternoon after refuelling.
, 2010b). Detection limits are around 40 ng m -3 for organics and ammonium and 5 ng m -3 for nitrate and sulfate  (Drewnick et al. , 2009) , with an estimated accuracy (neglecting uncertainty in collection efficiency) of around 10 %. Calibrations were performed using monodis-perse ammonium nitrate and ammonium sulfate to generate ionisation efficiency data for nitrate and relative ionisation efficiencies for ammonium and sulfate. Equivalent volume concentrations incorporating black carbon data (see below) and using the densities recommended by  Cross et al. (2007)  were compared against those from a Scanning Mobility Particle Sizer (SMPS) and the comparison was good (85-90 % of SMPS volume) if a collection efficiency (CE) of 1 was used for most flights during the campaign. Certain flights (in particular B749 and B750) had less favourable volume comparisons (around 50 %), however these took place during higher humidity conditions (see below) and given that the SMPS employed no sheath air drying, its data are seen as an unreliable reflection of the "dry" volume measured by the AMS under these conditions, so a CE of 1 is assumed for all flights for the sake of internal consistency.
The pinhole was cleaned afterwards and subsequent data had more favourable comparisons with the SMPS and other instruments, implying that the blockage was causing a large fraction of the particles to be lost at the inlet. However, the data are still included here because the data on mass ratios should still be representative of the ambient. This is assuming that the losses apply to all chemical constituents equally; while the losses may be size dependent, the composition is likely to be equal for all sizes if it is dominated by secondary material. Measurements of black carbon were made using a Droplet Measurement Technologies (Boulder, CO, USA) Single Particle Soot Photometer (SP2). This is the same instrument that was used in previous FAAM publications  (McMeeking et al. , 2010). It was calibrated using monodisperse AquaDAG (Acheson Industries), with a correction of 0.
The instrument was the same as used during OP3 and full instrumental, operational and calibration details are described in  Murphy et al. (2010). Accuracy for isoprene is estimated at ± 15 % and data were validated against offline gas chromatography analysis of samples taken using the aircraft's Whole Air Sampling (WAS) system, using the methods described by  Hopkins et al. (2011). Measurements of NO were made using a custom-built chemiluminescence instrument (Air Quality Design Inc, Wheat Ridge, CO, USA), with NO 2 measured on a second channel after photolytic conversion to NO. The instrument was the same as used during OP3  (Pike et al. , 2010)  and the use of photolytic (as opposed to catalytic) conversion eliminates possible interference from NO z on the NO 2 channel. Detection limits are of the order of 10 pptv for NO and 15 pptv for NO 2 for 10 s averaged data, with estimated accuracies of 15 % for NO at 0.
1 ppbv and 20 % for NO 2 at 0. 1 ppbv. Navigational data were provided by an Applanix (Richmond Hill, ON, Canada) POS AV 510 GPS-aided inertial navigational unit and altitudes are quoted as above mean sea level. Temperature and pressure were provided by flight instrumentation and humidity was measured (as a dew point accurate to ± 0. 2 • C) using two chilled mirror hygrometers; a General Eastern 1011B (GE Measurement & Control) and a Buck Research Instruments (Boulder, CO, USA) model CR2. The data presented here are derived from the General Eastern instrument, although the two instruments were in good agreement.
Acknowledgements. This work was supported by the  UK Natural Environment Research Council (NERC)  through the  SAMBBA  project (grant ref:  NE/J010073/1 ) and a PhD studentship (Eoghan Darbyshire). Airborne data were obtained using the  BAe-146-301 Atmospheric Research Aircraft (ARA)  flown by  Directflight Ltd  and managed by the  Facility for Airborne Atmospheric Measurements (FAAM) , which is a joint entity of  NERC  and the  Met Office. We thank  Ben Johnson  ( Met Office ) and  Karla M. Longo  ( National Institute for Space Research -INPE, Brazil ) for their roles in coordinating the campaign. Isoprene data from WAS sample analysis were provided by  James R. Hopkins  ( National Centre for Atmospheric Science and University of York ). Additional thanks are given to  David O. Topping  ( National Centre for Atmospheric Science and University of Manchester ) for helpful discussions and assistance in the use of the UManSysProp tools.
For propidium iodide (Molecular Probes) DNA staining, embryos were fixed then incubated overnight at room temperature in PBS+RNAse A (15 mg/mL, Sigma), in rotating tubes overnight. PI incubation itself was done after the secondary antibody wash (1. 0 mg/mL solution) by simply shaking the eppendorf for 10 seconds in PBS followed by a 5 minute wash. 30 second centrifugations at 4000 rpm in between steps are enough to pellet all embryos. They were then mounted into Vectashield (Vector Laboratories, Burlingame, CA). Confocal microscope images were captured on an inverted photoscope (DMIRB; Leica Microsystems, Wetzlar, Germany) equipped with a laser confocal imaging system (TCS SP2; Leica) using an HCX PL APO 1. 4 NA 63 oil objective (Leica) at room temperature. 3-D movies were generated using the Volocity 3D Image analysis software (PerkinElmer).
We hypothesized that if bacterial infection regulates the expression of specific tick SG genes, then these genes are likely to be implicated in the transmission of said bacteria. To address this proposition, we compared SG transcriptomes from infected and non-infected ticks. Sequences of differentially expressed genes were analyzed and compared to genes known to be implicated in tick-borne pathogen transmission in other models. Among up-regulated transcripts, we showed that silencing IrSPI, encoding a serine protease inhibitor, correlates with decreased B. henselae SG infection, and also alters tick feeding. These data suggest that IrSPI has a potential as an effective vaccine candidate to control tick burden and tick-borne disease, and that this candidate deserves a deeper interest in the future to estimate such potentialities.
High throughput sequencing of B. henselae-infected and non-infected I. ricinus salivary gland transcripts To generate an I. ricinus SG reference transcriptome, total RNA from BIr and NIr SGs were pooled at equimolar concentrations and cDNA libraries were constructed and normalized prior to sequencing on the GS FLX Titanium platform (454 pyrosequencing, Roche, CT, USA) by GATC Biotech AG (Konstanz, Germany). After trimming sequencing primers and adapter, de novo assembly of all reads was performed with GS De Novo Assembler Software version V2. 5. 3 (454 Life Science Corp, Author Summary I. ricinus is the most common tick species in Europe and the vector for several pathogens, including bacteria from the Bartonella genus. The mechanisms by which ticks modulate their gene expression in response to pathogen infection are poorly understood.
Transcript annotation All isotigs were imported into the BLAST2GO version 2. 5. 0 (www. blast2go. org) program for searches based on sequence identity and Gene Ontology (GO) annotation. In the identity searches, isotigs were compared against the NCBI nr protein database using BlastX with an E-value cutoff of 1. 0E-10. The BLAST results were used to map the consensus sequences with GO terms and to summarize the distribution of the sequences into three main categories: Biological Processes (BP), Cellular Components (CC) and Molecular Functions (MF). The KEGG (Kyoto Encyclopedia of Genes and Genomes) automatic annotation server was used for gene ortholog assignment and pathway mapping for all isotigs. Depending on the similarity of hits against the KEGG database using BlastX, the isotigs were then assigned unique enzyme commission (EC) numbers.
Analysis of differentially expressed transcripts between B. henselae-infected and non-infected I. ricinus salivary glands Burrows-Wheeler Transform Aligner (BWA)  [18]  was used to align polyA trimmed HiSeq2000 reads against the I. ricinus SG reference transcriptome, i. e. the isotig data produced by 454 pyrosequencing. The resulting sequence alignment/map was used to calculate counts (number of reads that mapped to the reference). Counts per isotig were assessed in both BIr-SG and NIr-SG samples. Isotigs with fewer than five counts were eliminated. To calculate the relative expression profiles in infected ticks, relative abundance (RA) values were computed for each isotig per sample by dividing its sequence count by the total sequence count for each sample. Differentially expressed isotigs between infected and noninfected ticks were detected with R [19] and x 2 statistics tests with Bonferroni correction using IDEG6 software (http://telethon.
bio. unipd. it/bioinfo/IDEG6_form/) [20]. An isotig was considered to be significantly differentially expressed in response to B. henselae infection when the RA had a fold change (FC) $2. 0 and both statistical tests yielded significant values at P#0. 0001. The open reading frame (ORF) of differentially expressed isotigs was determined using the ORF finder webserver at www. ncbi. nlm. nih. gov/projects/gorf. Conserved domains of each differentially expressed isotig were found using the conserved domains database (CDD) webserver version v3. 03 at www. ncbi. nlm. nih. gov/ Structure/cdd/cdd. shtml.
Real time quantitative PCR Validation of the expression profiles of selected genes was performed by real time quantitative RT-PCR (qRT-PCR) on SG RNA samples prepared similarly to those used for the differential transcriptome analysis, as biological replicates. First-strand cDNA was synthesized with the SuperScript III First-Strand Synthesis system for RT-PCR kit (Invitrogen) from 400 ng total RNA. Each qPCR reaction was performed in a total volume of 12 mL with 0. 26 LightCycler 480 DNA SYBR Green I Master Mix (Roche), 10 mM of each primer and 2 mL of template. Reactions were run using the Roche LightCycler 480 System under the following conditions: 95uC 5 min; 95uC, 10 s, 60uC 15 s, 72uC 15 s, 45cycles. Each sample was run in triplicate with results analyzed by Roche LightCycler 480 Software V1.
5. 0. Relative quantification of gene expression was calculated using the comparative Ct method  [21]. The results were then normalized using the I. ricinus actin gene, and sequencespecific primers used for qPCR are listed in Table  1. Statistical analysis was performed using two-tailed Student's t tests and values were considered significant at p#0. 0001. Data analysis was performed with Prism 5. 0 (GraphPad Software, Inc. USA), and results were expressed as mean 6 SEM (standard error of the mean). IrSPI silencing by RNA interference siRNAs targeting IrSPI were designed using the E-RNAi Web service (www. dkfz. de/signaling/e-rnai3/idseq. php) (Table  1 ) and were synthesized in vitro using the Stealth RNAi siRNA construction kit (Life technologies, France). Four nL (25 mM) of siRNA (,10 13 molecules) were injected into the tick hemoceole of B.
For each pair of SGs, one gland was used for gene silencing quantification by qRT-PCR and the other gland for B. henselae quantification by DNA qPCR. RNA was extracted as described previously, and DNA was extracted using the Wizard genomic DNA purification kit (Promega, USA) following manufacturer's instructions. B. henselae was quantified using primers targeting the 16S-23S intergenic spacer (ITS)  [23]  (Table  1 ). Quantitative PCR results were assessed by extrapolation from the standard curve and normalized to I. ricinus actin. Statistical analysis of qPCR was performed using two-tailed Student's t tests. A p value,0. 05 was scored as a significant difference. Data analysis was performed with Prism 5. 0 (GraphPad Software, Inc. USA), qPCRs were performed in triplicate and results expressed as mean 6 SEM.
I. ricinus salivary gland transcriptome analysis To obtain a high coverage of tick SG transcripts, normalized cDNA libraries from BIr-SGs and NIr-SGs were sequenced twice using the GS FLX titanium platform. After trimming and removing superfluous sequences (primers and adapters), all reads were used for transcript assembly, generating 30,853 contigs and 15,756 isogroups composed of 24,539 isotigs (Table  2 ). The description of contig and isotig sizes are shown in Figures  1A  and 1B  respectively. Sequence identity percentages between translated I. ricinus SG isotigs and the nr protein database were identified with BlastX using Blast2GO software. Out of the 24,539 assembled isotig sequences, 14,736 sequences (60. 1%) had significant similarity (Evalue#1E-10) with sequences present in GenBank.
Of these, 10,713 (72. 7%) had closest alignment with Ixodes scapularis sequences, 1,332 (9. 0%) with Amblyomma maculatum sequences, 568 (3. 9%) with I. ricinus, 481 (3. 3%) with Ixodes pacificus sequences, and 63 (0. 4%) with Ixodes persulcatus sequences (Figure  2 ). The database of Blast results was then used to annotate the isotigs with GO terms. Isotigs were classified according to the categories of biological processes (BP) in which they may be implicated, the cellular components (CC) with which they may be linked, or a related molecular function (MF). One or more GO IDs were assigned to 10,859 (44. 3%) isotigs. The number of isotigs that could be annotated as belonging to either BP, CC and MF categories were 5,308, 7,213 and 9,283, respectively. In the BP category, 'oxidation reduction' (12.
Analysis of differently expressed transcripts between B. henselae-infected and non-infected tick salivary glands In order to investigate the differential expression of transcripts between BIr-SGs and NIr-SGs, corresponding 39UTR cDNA libraries were sequenced, which generated 210 and 150 million raw sequences reads, respectively. Isotigs with an RA fold change (FC) of $2 and x 2 #0. 0001 were selected as significantly differentially expressed, resulting in 5. 5% of isotigs (1,346/ 24,539) which varied in their expression following B. henselae infection (Additional file 1). Of these, 829 isotigs were up-regulated in B. henselae-infected ticks and 517 isotigs were down-regulated after bacterial infection. Based on translated sequence identity with protein database sequences, isotigs were classified into three groups: (a) proteins with identity to proteins of known function, (b) proteins with identity to proteins of unknown function and (c) proteins without identity (Additional file 1 and Table  3 ).
Among the first group, proteins were classified into nine protein families, out of which four contained both up-regulated and down-regulated transcripts in response to pathogen infection, while five corresponded to transcripts that were only down-regulated in response to infection (Table  3 ). The expression of five selected transcripts was validated by qRT-PCR on SG RNA samples from a biological replicate (Figure  4 ). Two transcripts corresponding to the BPTI/Kuntiz family of serine protease inhibitors (GenBank accession number: KF531922) and Salp15 superfamily protein (GenBank accession number: KF531924), respectively were overexpressed by B. henselae infection; three transcripts, corresponding to tick salivary peptide group1 protein (GenBank accession number: KF531923), Salp15 superfamily protein (GenBank accession number: KF531925), and arthropod defensins (GenBank accession number: KF531926), respectively, were down-regulated by B.
Silencing the IrSPI gene decreases tick feeding capacity as well as infection of tick SGs by B. henselae The transcript encoding a BPTI/Kunitz type serine protease inhibitor, thereafter named IrSPI (for I. ricinus serine protease inhibitor; GenBank accession number: KF531922), that was overexpressed in response to bacteril infection was selected for functional analysis in ticks. RNAi was used to evaluate the effect of IrSPI silencing on tick feeding as well as tick salivary gland infection by B. henselae. siRNA injection was performed in females arising from infected nymphs and larvae, prior to the provision of an additional uninfected blood meal, to ensure ''total'' SG infection of the adult females (see material and methods section). IrSPI transcript abundance was suppressed by 90% (p = 0.
Discussion Recent NGS advances enabled us to perform an exhaustive analysis of the I. ricinus SG transcriptome following infection with B. henselae, as a relevant model system for studying tick-pathogen interactions. This analysis highlights the existence of major groups of genes which vary in response to infection, including those encoding proteins involved in protein binding, oxidation reduction or proteolysis, or that are integral to membranes, either nuclear or cytoplasmic. These results provide a reference databank for the I. ricinus SG transcriptome, which is particularly relevant in the absence of an I. ricinus genome sequence. Equally importantly this study provides abundant genetic information on the I. ricinus response to pathogen infection. Until now, most studies of tick SG transcriptomes were based on EST analyses  [14].