dataesr/scientific-paragraphs-categorization huggingface dataset:
siRNA transfection Specific siRNA directed against human Rac3 was designed using the criteria established by Tuschl  [15]. Candidate sequences were compared with cDNA sequences and their specificity verified in the non-redundant human DNA database using a BLAST algorithm [accession through NCBI]. The Rac3 siRNA selected was: sense 5'-CUGACGUCUUU CUGAUCUG-3' , antisense 5'-CAGAUCAGAAAGACGUC AG-3'. Eurogentech negative control siRNA was used as control. siRNAs (10 nM) were introduced into cells by INTERFERin ™ -mediated transfection (Ozyme).
Wound healing assay (scratch test) Cells were seeded in triplicate into 24-well plates at 10 5 cells/well in medium containing 2% FBS, and transfected with siRNA anti-Rac3 24 h later. After a further 48 h of incubation in presence of the siRNA, when the cells in all treatment groups had reached confluence, the monolayer was subjected to a scratch test to assess directional motility in healing the "wound". Wound closure was observed by microcinematography (Zeiss) during the following 48 h, with photographs taken every 20 min at 50 X mag-nification. Axiovision software was used to quantify the linear advancement of the migration front in closing the scratch; results are presented as % wound closure, calculated from the mean distances between the two migration fronts at 0, 12, 24 and 48 h after wounding.
Blood containing Calcein-AM-labelled platelets (green) and CellTracker ™ -Red-labelled MDA-MB-231 cells (red) was perfused through the chamber for 10 min at a constant flow rate of 3 ml/min, corresponding to a shear rate of 1500 s -1 , according to the chamber characteristics (5 mm wide and 0. 2 mm high). At the end of perfusion, the chamber was washed with PBS for 1 min at the same shear rate. The microscope was coupled to a 1394 (Scion Corporation) numeric high resolution camera directly linked to a computer equipped with the Scion Visiocapture acquisition software, and 20 random fields were recorded over a 1 cm 2 area in the middle of the perfusion chamber. MDA-MB-231 tumour cell adhesion was estimated by measuring the area they covered using image J software.
Capillary-like structure formation by breast cancer cells: vasculogenic mimicry (VM) Cells were cultivated in culture medium complemented with 10% FBS; after 48 h of siRNA treatment, treatment medium was aspirated and set aside, cells were washed once in PBS, detached with trypsin/EDTA solution, and resuspended in their respective treatment medium; then 2 × 10 4 of these breast cancer cells were seeded per well on growth-factor-rich Matrigel in 96-well plates to analyze the formation of capillary-like structures. After 4 h incubation, the wells were photographed at 100X magnification using an inverted light microscope. The extent of capillary-like tube formation was quantified by measuring the cumulative tube lengths and total number of intersections in three randomly chosen fields from each well using Image-Pro Plus software (Microvision Instruments).
Cell cycle To study the proportion of cells in different cell cycle phases, propidium iodide was used and detected by flow cytometry. Briefly, cells were treated with control or Rac3 siRNA. After 96 h of treatment, cells in the supernatant and adherent cells were collected, washed and fixed with cold ethanol. Cells were stored at -20°C until staining was performed. Cells were incubated with 500 μl of PBS containing 50 μg of RNase A (Sigma Aldrich) and 25 μg of propidium iodide (Sigma Aldrich) for 20 min in the dark. Cells were analysed with a BD FACSCalibur (BD Biosciences), and data were analysed using FlowJo W Mac 9. 5. 2. software.
STB persist less during infection than M. tuberculosis To determine whether the genome differences between the STB and MTBC strains impact on host-pathogen interactions, we first measured their growth in in vitro cultures. Most STB grew 2 to 3 times faster than M. tuberculosis both in liquid (Supplementary Fig. 8 ) and on solid media (data not shown) at 30°c and 37°c, in line with previous observations  10, 11. Upon infection of BALB/c mice (Fig. 4 ) and C57BL6 mice (Supplementary Fig. 9 ) by aerosol, the STB strains effectively multiplied in lungs and disseminated to the spleens during the acute infection phase, but consistently persisted less well during the chronic infection phase compared to M. tuberculosis. While the latter was able to persist in the lungs for up to 30 weeks at levels close to those of the acute phase (peaking at 3 weeks with around 10 7.
Remaining gaps estimated not to exceed 2 kb correspond to GC-rich and repetitive regions coding for PE_PGRS proteins, and/or the pks5 region (STB-J). For STB-A, a fully finished, contiguous sequence of 4,482,059 bp was obtained by using ~ 80,000 shotgun Sanger reads, Illumina-generated reads and finishing  12, 28. WGS data from STB strains E, G, H, and I were generated using Illumina HiSseq technology and single lanes. Resulting reads that covered the genomes of these STB up to 900x were assembled using the Velvet software  51  and contigs were ordered using M. canettii CIPT 140010059 (STB-A) and M. tuberculosis H37Rv as reference genomes.
Annotation and comparative genomics Annotation and genome comparisons were performed with the Microscope platform  52  , Artemis and Artemis comparison tool (ACT)  53. When applicable, annotations were transferred from those of M. tuberculosis orthologs in the TubercuList/Mycobrowser database, using BLAST matches of > 90% protein sequence identity, an alignable region of > 80% of the shortest protein length in pairwise comparisons and visual inspection of the gene synteny. Pairwise average nucleotide identities were calculated using JSpecies  54. The core/accessory genomes of STB and M. tuberculosis were determined as described  16.
SNP and indel analysis SNiPer pipeline (Genoscope) based on the SSAHA2 package  55  was used to map Illumina reads and detect SNPs and indels of STB strains against a corrected version 56 of the M. tuberculosis H37Rv reference sequence (NC_000962)  12. After exclusion of ambiguous maps on repeat regions, an average of 4. 7 million split paired-end reads of 36 bp (STB-A, -D, -L, -J) or trimmed at 50 bp (STB-K) were mapped at a resulting genome coverage > 40x. SNPs with base coverage < 10, base quality < 25, or heterozygosity > 0. 2 were removed. ACT  53  comparison files were created by using MUMmer and NUCmer softwares  57  to visualize the SNP distribution in local genome regions.
Bacterial growth assays. For histopathological evaluation, whole lungs were harvested from 3 BALB/c mice per group 128 days post-infection, fixed in 4% formalin, and embedded in paraffin. Four mm-thick sections were stained with hematoxylin-eosin. Virulence and cell-analysis-based immunological assays using C57BL/6 and/or SCID mice were performed as described  66, 67. Adaptive immune cells from infected mice were prepared, incubated with conjugated mAbs (Beckton-Dickinson), fixed, and analyzed using a CyAn system and Summit (Beckman Coulter) and FlowJo (Treestar) softwares. b Lower value obtained after exclusion of epitopes of three antigens considered as outliers.
(b) Schematic representation of a 55 kb spanning genomic region that encodes a putative prophage in STB strain I. STB-I genomic positions are marked on horizontal scales in bp. Brackets indicate a portion homologous to a prophage region in the M. marinum genome. Predicted coding sequences are shown above or below scales, corresponding to rightward and leftward transcription, respectively. Colorcoding define features of predicted encoded products as follows. Gray, phage protein without database match or homologous to non-mycobacteriophage proteins of unknown function; blue, phage protein homologous to other mycobacteriophage proteins of unknown function (names of homologs are written in blue text, except for the portion homologous to the M. marinum prophage region); black, STB-I coding sequences and tRNA genes (conserved in other STB strains and M.
Acknowledgments We are grateful to  Stewart Cole  for help in initiating the M. canettii CIPT 140010059 genome sequencing project and advice, to  Thierry Garnier  and  Adamandia Kapopoulou  for help in data management and to  Zoe Rouy  for help with sequence deposal. The work was supported in part by the  Institut Pasteur  ( PTR 314 ,  PTR 383 ), the  European Community 's  FP7 program  Grant no. 260872 , the  Wellcome  trust grant  098051 , and a Genoscope collaborative grant no. 114.
0 Arrays. The fluorescent intensity emitted by the labeled target was measure in Affymetrix GeneChip Scanner 3000 (Affymetrix). Raw data processing was performed using the Affymetrix AGCC software. Genes with significant expression difference between 2 knock-out mice and 2 wt were selected, based on the average knock-out versus wild-type value greater than 1. 3 fold change with a p-value cutoff of 0. 05 (using Student's t-test) or differential expression of selected genes which were confirmed by quantitative RT-PCR. The full data set is available in Gene Expression Omnibus data repository, accession number: GSE47898.
Our analysis identified a large number of SVs of short size (SV insert size ,50 kb) (Table  S2  and Table  S3 ). Since our experiment was designed to focus on large rearrangements, it remains an issue to define the subset of these short SVs that are somatic. Nevertheless, we could determine that these short SVs were mostly deletions (59%) and insertions (30%) and that they fell frequently in intergenic regions (55%) and intronic regions (34%). When comparing these predicted SVs of short size with the Database of Genomic Variants (DGV, hg19, v9)  [21] , it turned out that 45% of all predicted short SVs were annotated as known SVs in DGV.
In the case of the CLB-Re cell line, we selected 19 inter-chromosomal SVs for validation, including 15 between chromosome arms 2p and 3p, and 4 intra-chromosomal SV, i. e. , one deletion predicted at 4q and 3 deletions predicted at 2p. These 23 rearrangements were validated by PCR analysis. Since this cell line has been established at relapse (Table  1 ), we sought to determine whether such rearrangements were already present in the patient's tumor at diagnosis. The analysis of 13 rearrangements indicated that they were present in the tumor DNA at diagnosis and absent in the blood DNA (Figure  S2  and data not shown). In order to characterize breakpoints at the base-pair resolution, conventional Sanger sequencing of the PCR fragments was performed followed by a BLAT search  [22]  on the human reference genome.
Public Database Accession Numbers for Data SRA accession number ERP001414 for mate pair sequencing data. ArrayExpress accession number E-MTAB-1367 for RNAseq data (http://www. ebi. ac. uk/ena/data/view/ERP001988). Figure  S2  Rearrangements detected in the CLB-Re cell line established at relapse were already present at diagnosis. A, A subset of the links identified by the mate-pair analysis between chromosomes 2 and 3 was further confirmed by PCR experiments, both on the genomic DNA of the CLB-Re cell line and also after whole genome amplification (WGA). DNA from the matched tumor at diagnosis as well as from lymphocytes was also investigated. B, Examples of rearrangements detected after WGA on the gDNA of the cell line established at relapse that were also detected after WGA of the DNA at diagnosis, demonstrating that these rearrangements were not relapse-specific and not linked to the cell culture process.
Data Alignment Whole genome. For each sample, reads were aligned to the human NCBI Build 37 reference genome (hg19, downloaded from http://genome. ucsc. edu) using Bowtie  [39]  and BFAST  [40]. Any potential PCR duplicates and singletons (read pairs mapping in inward orientation and with an abnormally short insert size) were excluded (see Methods S1 for the detailed workflow). Finally, we obtained from 906 to 2 155 thousand ''abnormal'' read pairs and from 13 to 30 million ''normal'' read pairs per sample (Table  S1 ). RNA-seq. For each sample, reads were aligned to the human NCBI Build 37 reference genome (hg19) and a library of exon junctions provided by Lifescope using the SOLiD Lifescope v. 2. 5 software. Reads were filtered using mapping quality (threshold 5). Any potential PCR duplicates were excluded (see Methods S1).
Statistical analysis Data of mesocosm triplicates are presented as mean, after Student's t-test was used to verify that no significant difference occurred between replicates, either in dust-amended or control mesocosms (p > 0. 05, 31 < n < 44). Student's ttest and multiple regressions conducted on the entire dataset between the measured Chl a concentration in the two size classes and the Chl a concentration of the specific groups (ChemTax analysis), as well as between cellular abundances (flow cytometry) and Chl a-group specific abundance values (ChemTax analysis), were performed by using the programme Statistica (StatSoft, OK, USA). The integration of the datasets concerning pigments (> 3 µm) and nanophytoplankton cellular abundance (flow cytometry) was performed based on the assumption of a very low microphytoplanktonic biomass (so their negligible contribution to total Chl a) in relation with the severe oligotrophic field conditions, and in agreement with the very low biomass of large-sized Bacillariophyceae (ChemTax analysis; see result section).
Picophytoplankton accounted for ∼ 70 % of total phytoplankton biomass, in both DM and CM, remaining almost stable during the entire experiment, while decreasing to ∼ 60 % after the second dust addition, only in DM (Fig. 1e, f ). Concerning the contribution of phytoplankton groups on the two size classes, we performed multiple regressions on the entire dataset (i. e. , samples taken soon before and after each dust addition) between the measured Chl a concentra-tion of the two size classes and the Chl a concentration of the specific groups (retrieved from ChemTax analysis): ), daily integrated light (mol photons m -2 d -1 ), nitrate (NO - 3 , µM), nitrite (NO - 2 , µM), dissolved inorganic phosphorus (DIP, nmol L -1 ), orthosilicic acid (Si(OH) 4 , µmol L -1 ), dissolved iron (DFe, nmol L -1 ), bacteria abundance (10 5 cells mL -1 ).
Multiple regressions were performed on the complete dataset (i. e. , samples taken soon before and after each dust addition) between cellular abundance and Chl a-group specific concentration values. For the picophytoplankton community, none of the tested multiple regressions was significant, probably suggesting a huge diversity in pigment content of the distinct groups alternating during the experiment. By contrast, for the nanophytoplankton community, the following result was obtained (n = 112, R 2 = 0. 52, p < 0. 001): Nano Cell Abundance = 0. 322 Dinophyceae (5) +0. 349 Haptophyceae + 0. 203 Chlorophyceae +0. 267 Bacillariophyceae The highest pigment contribution to cellular abundance was due to Haptophyceae, followed by Dinophyceae, Bacillariophyceae and lastly Chlorophyceae, a finding that might highlight the distinct Chl a cellular content among these groups, in relation to their different cell size.
Phytoplankton biomass increase vs. nutrient conditions In this section, we aim at relating the increase of Chl a concentration observed after dust additions with the use of nutrient, on a daily basis. We chose three days in which phytoplankton biomass increased just after the dust additions, and assumed that the impact of grazing or cell death was negligible. Daily variations of Chl a concentration and nutrient concentration were calculated on mean data measured at -0. 1 and -5 m depths, being more homogeneous than data collected at -10 m (mainly after the second dust addition). The increase in Chl a concentration per day (µg Chl a L -1 d -1 ) for the two phytoplankton size classes, and the relative decrease in nutrient concentration (µg nutrient L -1 d -1 ), after dust additions, are reported in Table  2.
Effects of the dust additions on the physiological state of the phytoplankton community Concomitant to changes in the composition and structure of the phytoplankton community, the physiological state of the community evolves, as shown by the increase of the pigment content per cell in picophytoplankton, a response that was also previously reported in LNLC region surface layers of the Atlantic Ocean  (Davey et al. , 2008; Moore et al. , 2008). By taking advantage of the absent detection of Prochlorococcus, we combined HPLC-fractionated pigment and flow cytometry data to estimate the zeaxanthin (Zeax) content per Synechococcus cell. Synechococcus Zeax cellular content ranges between 0. 3 and 1. 5 fg Zeax cell -1 , being lower than previously reported in literature  (Kana et al. , 1988; Morel et al.
8 ). Both measurements are not correlated by pooling together all data of control and dust mesocosms, or only using dataset of dust mesocosms (data not shown). By separating the two dust additions, no significant correlation is found during the first dust addition period (Fig. 8a ), whereas rel ETR max and 13 C PP are significantly correlated during the second dust addition period (R 2 = 0. 29, p < 0. 05; Fig. 8b ). It should be noticed that gross and net primary production are significantly correlated in control mesocosms (R 2 = 0. 30, p < 0. 01; Fig. 8c ), as expected for a picophytoplankton-predominant community, ecophysiologically adapted to oligotrophy. When nutrients are added to the system, net primary production increases, and two distinct responses are found, depending on phytoplankton cell size constraints.
The stronger increase in nano-and microphytoplankton biomass after the second than the first dust addition seems instead to explain the significant correlation between rel ETR max and 13 C PP found in the dataset concerning the second dust addition. This result possibly suggests that, in a community in which the abundance of large-sized cells becomes relevant, net and gross primary production increase because of an enhanced PSII ETR, indicating the direct effect of nutrient limitation on cells capacity of light capture and/or PSII excitation energy transfer. We may, therefore, infer that the regulation of photobiological processes is differently influenced by nutrient availability in both phytoplankton size classes, in agreement with previous studies  (Mei et al. , 2009; Chen and Liu, 2010) , recalling the metabolic theory of ecology  (Brown et al.
Acknowledgements. This work was funded by the  ANR-DUNE  under the contract " ANR-07-BLAN-30 0126-01 ". V. Giovagnetti 's PhD was financially supported by the  Stazione Zoologica A. Dohrn. J. M. Dominici  and collaborators of the " Réserve naturelle de Scandola, Parc naturel régional de Corse " are gratefully acknowledged for their help and cooperation in performing the experiments and implementing the field work conducted in the bay of  Elbo. P. Catala  is acknowledged for having performed cytometry analysis. The authors would like to thank all the participants of the DUNE-2 project, which were involved in developing the experimental design and performing the experiments. Comments by two anonymous reviewers have been very helpful to improve the quality of this manuscript. Edited by:  E. Marañón  www.
There are only a relative small number of directions in the phase-space of the atmospheric system along which the most important processes occur. Maximum growth is measured in terms of total energy. The adjoint of the tangent forward propagator with respect to the total norm is defined, and the singular vectors (the fastest growing perturbations) are computed by solving an eigenvalue problem. Singular vector method is schematically described in Figure  5. In addition to the breeding and singular vector methods there are Ensemble Transform Kalman Filter technique (ETKF;  Bishop et al. , 2001; Wang & Bishop, 2003)  and Ensemble Data Assimilation (EDA;  Houtekamer, 1996; Buizza, 2008). ETKF is similar to the breeding method except that the rescaling factor is replaced by a transformation matrix.
These ensembles can have an assimilation cycle which uses a wide class of meteorological observations, in some cases including radar data trying to represent as much as possible actual precipitation processes. They need lateral boundary conditions typically coming from global ensembles or coarser limited area ensembles. Just to mention two examples of limited area ensembles, we resume below the characteristics of the COSMO-DE ensemble (Deutscher Wetterdienst) and the AEMET-SREPS. Other operational limited area ensembles are: the Norwegian targeted EPS LAMEPS  (Frogner & Iversen, 2002) , the Hungarian LAMEPS based on ALADIN  (Hágel & Horányi, 2007) , the multi-model GLAMEPS (ALADIN and HIRLAM consortium) and the limited area version of MOGREPS (MetOffice). The COSMO-DE Ensemble is based on the convection resolving model COSMO-DE.
The central line SC2350 ("LION") extended upward more than 2 km from the seafloor at 2350 m up to 150 m below sea surface. It included an additional sediment trap and current meter pair at mid-water depth (∼ 1000-m depth). SC2350 and HC2300 lines were equipped with additional CTD sensors (see Sect. 3. 2: Hydrological time series and profiles). The dynamics of the mooring lines were assessed using the Mooring Design and Dynamics software  (Dewey, 1999)  and validated by comparing the modeled deepening of the line to the pressure sensor records of current meters and/or CTD probes. Tilting and deepening of the mooring lines were insignificant during periods of weak current velocity (< 11 cm s -1 ) in spring and summer, and increased during periods of stronger currents (up to 39 cm s -1 ), mostly recorded during winter 2008-2009.
Hydrological time series and profiles Conductivity, temperature and depth time series were recorded at the SC2350 and HC2300 stations with SBE 37SMP instruments (Table  2 ). Four CTD sensors were clamped at 158, 690, 1507, and 2315-m depth on the SC2350 line, and one CTD sensor was clamped at 2287-m depth on the HC2300 line. RBR1000 temperature loggers were also clamped on the upper kilometer of the SC2350 line between SBE 37SMP CTD sensors to increase the vertical resolution (resulting in 8 sensors in the first deployment and up to 21 sensors in the third deployment). CTD data were corrected for offset and drift using pre-and post-deployment calibrations performed by Sea-Bird Electronics. Additional comparisons between instruments were performed with respect to CTD casts carried out prior and after the turnarounds of mooring lines.
Sediment trap time series Settling particles were collected with automated sediment traps. SC2160 and SC2240 lines held Technicap PPS5 coneshaped trap with a 1 m 2 mouth covered with a honeycomb baffle (with cells 10 cm deep and 1 cm in diameter). PPS5 traps were equipped with 24 collecting bottles. The sampling interval was set to 7 days during the first deployment  (28 March 2008 to 29 August 2008)     velocity, the trap shape and aspect ratio (height/diameter), the tilt, and the settling velocity of particles  (Baker et al. , 1988; White, 1990; Buesseler, 1991 and reference therein). Despite hydrodynamic biases associated with intermittent strong currents and tilt, and different trap designs (conical and baffled PPS5 versus unbaffled cylindric PPS3), the similarities of temporal variability of near-bottom fluxes at the different sites suggests that data are robust enough to draw conclusions on the overall seasonal and interannual variability of downward particle fluxes in the study area.
Integrated net heat fluxes Components (sensible, latent and radiative) of atmospheric heat fluxes were collected from ECMWF (European Centre for Medium-Range Weather Forecasts). The model is based on a 0. 25 • × 0. 25 • lat/long grid and 3-h forecast intervals. We chose to extract data from the closest grid point (42 • N, 4. 75 • E) to MF-LION location (Fig. 1 ).