dataesr/scientific-paragraphs-categorization huggingface dataset:
Briefly, after loading cells for 30 min at 37 °C in the dark with 3. 6 M Fluo-4 AM, they were perfused with HEPES-buffered medium, pH 7. 3, containing 10 mM HEPES, 150 mM NaCl, 2. 5 mM KCl, 2 mM CaCl 2 , 1 mM MgCl 2 , 10 mM glucose, 0. 1% BSA, and 3 M nifedipine to block L-type Ca 2ϩ channels. Depolarization was induced by perfusing cells for 10 s with HEPES-buffered medium modified to contain 140 mM KCl and 12. 5 mM NaCl. The increase in fluorescence caused by Ca 2ϩ entry was monitored at 488-nm excitation wavelength through a 40ϫ/NA0. 65 objective, by using a cooled charge-coupled device camera (MicroMax 782 Y; Princeton Instruments) driven by MetaView software (Universal Imaging Corporation). For acute stimulation with agonists, 5 min after the first depolarization, a second depolarization was applied at the end of a 30-s perfusion in the presence of the agonist.
For experiments designed to test the effect of NPFF, NPY, and adrenergic agonists on the response of DAMGO, cells were preincubated for 20 min at room temperature with ligands before recording the effect of acute application of DAMGO, as above. Confocal Microscopy-Cells, seeded on glass coverslips, were incubated for 30 min at room temperature with agonists in HEPES-buffered medium. After fixation for 20 min at 4 °C with 3. 7% formaldehyde, they were mounted in Vectashield medium (AbCys) and observed on an inverted laser scanner confocal microscope (Olympus FV1000) with a 60ϫ/NA1. 4 oil immersion objective at 514-nm excitation wavelength. Images were processed with ImageJ software (National Institutes of Health). FRAP Measurements-Cells were grown on glass coverslips in 6-well plates for 36 h.
7 ). This indicates that the receptors within BiFC heterodimers are still responsive to their ligands. This co-internalization could seem in discordance with the data on Fig. 4 , but in the case of BiFC, co-internalization occurs because of the high stability of the BiFC complex, in contrast to what is observed in Fig. 4  where the heterodimer is likely to be transient  (59 -62). Expression levels of receptors were measured by saturation binding experiments. The specific MOP receptor radioligand [ 3 H]DAMGO labeled 2. 7 Ϯ 0. 2 pmol/mg protein with a K D of 1 Ϯ 0. 2 nM (n ϭ 3), and the specific NPFF 2 receptor radioligand [ 3 H]EYF labeled 1. 5 Ϯ 0. 2 pmol/mg protein with a K D of 2. 5 Ϯ 0. 5 nM (n ϭ 3), thus indicating similar expression levels of both protomers and conserved high affinity.
Therefore, only relatively loose photon identification cuts on the cluster parameters were used in order to maximize the π 0 reconstruction efficiency: the cluster energy for pp collisions was required to be above the minimum ionizing energy E cluster > 0. 3 GeV and the number of cells in a cluster was required to be greater than two to reduce the contribution of hadronic clusters. In the case of the most central Pb-Pb collisions about 80 clusters are reconstructed in PHOS, resulting in an occupancy of up to 1/5 of the 10752 PHOS cells. This leads to a sizable probability of cluster overlap and to a high combinatorial background in the two-cluster invariant mass spectra. A local cluster maximum was defined as a cell with a signal at least π 0 production in pp and Pb-Pb collisions at 2. 76 TeV The histogram and the filled points show the data before and after background subtraction, respectively.
A good agreement in peak position and width between data and simulation is observed in both analyses. The remaining small deviations in the case of PHOS were taken into account as a systematic uncertainty related to the global energy scale. The correction factor ε(p T ) for the PHOS detector response and the acceptance A(p T ) were calculated with GEANT3 Monte Carlo simulations tuned to reproduce the detector response. The factor ε(p T ) takes the loss of neutral pions due to analysis cuts, effects of the finite energy resolution and, in case of Pb-Pb collisions, effects of shower overlaps into account. The shape of the π 0 input spectrum needed for the calculation of ε(p T ) was determined iteratively by using a fit of the corrected spectrum of a given pass as input to the next. In the case of Pb-Pb collisions the embedding technique was used in the PHOS analysis: the PHOS response to single π 0 's was simulated, the simulated π 0 event was added to a real Pb-Pb event on the cell signal level, after which the standard reconstruction procedure was performed.
The total systematic uncertainties of the PCM and the PHOS results were calculated by adding the individual contributions in quadrature. The comparisons of the fully corrected π 0 spectra measured by PHOS and PCM in pp and Pb-Pb collisions are presented in Figs. 3  and 4 , respectively. For a better comparison the PCM and PHOS data points were divided by a function which was fitted to the combined spectrum. In all cases, agreement between the two measurements is found. The PHOS and PCM spectra were combined by calculating the average  The horizontal position of the data points within a bin was determined by the procedure described in  [59]. For the pp spectrum a fit with a power law function 1/p n T for p T > 3 GeV/c and a Tsallis function (also used in  [48] ) are shown. The extrapolation of the pp spectrum provided by the Tsallis fit is used in the R AA calculation for p T 8 GeV/c.
By combining soft particle production from a hydrodynamically evolving medium with a model for hadron suppression these models are capable of making predictions for the entire p T range. An important task on the theoretical side will be to establish whether the observed deviations from the data simply indicate a suboptimal adjustment of parameters or hint at important physical phenomena missing in the models. Future analyses based on runs with higher integrated luminosities, e. g. the 2011 LHC Pb-Pb run, will also include the ALICE lead-scintillator electromagnetic calorimeter (EMCal) and will allow us to extend the neutral pion measurement to higher transverse momenta. The role of initial-state effects on the particle production in Pb-Pb collisions will be investigated by measurements of particle production in p-Pb collisions.
The intensity and/or extent of the northeastern Pacific Oxygen Minimum Zone (OMZ) varied in-phase with the Northern Hemisphere high latitude climate on millennial timescales during the last glacial period, indicating the occurrence of atmospheric and oceanic connections under glacial conditions. While millennial variability was reported for both the Greenland and the northern Atlantic Ocean during the last interglacial period, the climatic connections with the northeastern Pacific OMZ has not yet been observed under warm interglacial conditions. Here we present a new geochemical dataset, spanning the past 120 ka, for major components (terrigenous fraction, marine organic matter, biogenic opal, and carbonates) generated by X-ray fluorescence scanning alongside with biological productivity and redox sensitive trace element content (Mo, Ni, Cd) of sediment core MD02-2508 at 23 • N, retrieved from the northern limit of the modern OMZ.
While several studies displayed millennial and/or glacial/interglacial changes of the opal production at low latitude in the eastern Pacific  (Ganeshram and Pedersen, 1998; Kienast et al. , 2006; Dubois et al. , 2010; Pichevin et al. , 2010; Arellano-Torres et al. , 2011; Dubois et al. , 2011; Romero et al. , 2011a; Cartapanis et al. , 2012) , high temporal resolution opal records in northeastern Pacific are still limited. Here we present a new geochemical dataset spanning the last 120 ka from the northern edge of the modern North Pacific OMZ. High-resolution X-ray fluorescence (XRF) measurements for major sediment components (marine organic carbon, opal, carbonates and terrigenous fraction), were performed on MD02-2508 core (MD08, northeastern coastal Pacific), in order to monitor the past productivity variations.
, 2011). High productivity may have led to reduced bottom water oxygenation at site MD08 during interstadials. Changes in the wind patterns were proposed as mechanisms for changes in the strength, duration, and frequency of upwelling events, leading to higher productivity during interstadials events of MIS3. Higher bottom water oxygenation during Heinrich events was suggested to be produced by changes in oxygen advection by NPIW, formed in the northern Pacific. In light of the new datasets on MD08 core, that now cover the past 120 ka, we will focus our discussion on the oceanic and climatic millennial scale variability of the last interglacial period (MIS5).
Conclusions We studied core MD02-2508, retrieved off the Baja California margin, at present northern limit of the northeastern Pacific Oxygen Minimum Zone (OMZ), using high resolution XRF measurements (Si / Ti as a biogenic opal indicator, Ca as a biogenic carbonate indicator, Br as a marine organic carbon indicator, and Ti as a terrigenous fraction indicator) and ICP-MS trace elements measurements (Mo, Ni, Cd), for the last interglacial period (MIS5). The data allowed us to better constrain the millennial scale variability of past biological productivity and oxygenation at the core site over the studied period. Opal, Ni / Al, and Cd / Al increased during the DO interstadial events identified in Greenland ice cores over the MIS5, strongly suggesting an increase in biological productivity. A high Mo / Al ratio within interstadials events indicates that the OMZ strengthened during these intervals.
Acknowledgements. We thank  Luc Beaufort  (chief scientist),  Yvon Balut  (IPEV), and the team of the IMAGESVIII-MONA cruise (MD126 North American Margin) on board of  Marion Dufresne. We also thank  Marta Garcia  for technical assistance with ICP-MS measurements,  Frauke Rostek  for additional TOC measurements,  Genevieve Elsworth  for English polishing,  Eric Galbraith  for discussion and support, and  A. Schmittner  and  L. Pichevin  for constructive comments during the review of the manuscript. We are grateful to MESR, the  Collège de France  and  McGill University  for providing salary support to  O. Cartapanis. Paleoclimate  work at CEREGE is supported by grants from the  Collège de France , the  Comer Science and Education Foundation , the  CNRS  ( LEFE-EVE MISLOLA ), and the  European Community  (Project  Past4Future ).
, 2011; Thomas et al. , 2009; Thompson et al. , 2011; Yushkevich et al. , 2010). Therefore we adopted the symmetric approach of registering all time-points to unbiased within-subject average images  (Reuter et al. , 2012; Rohrer et al. , 2013). SPM8, Freesurfer 5. 1 (http://surfer. nmr. mgh. harvard. edu/) and FSL 4. 1. 9 (FMRIB's software library, www. fmrib. ox. ac. uk/fsl) were used for image analysis. The Longitudinal VBM analysis performed in this study consists of the following main steps (Fig. 1 ): 1. Lesion mask creation and lesion filling: T2 lesions were contoured in Dispimage (Department of Medical Physics and Bioengineering, UCL, London) and a binary lesion mask was obtained. T2-weighted images, along with lesion masks, were co-registered to T1-weighted images using rigid registration (SPM8) by maximizing the mutual information of the joint intensity histogram of the images.
Acknowledgments This study was funded by the  Multiple Sclerosis Society of Great Britain and Northern Ireland  and the  NIHR UCLH BRC. Dr Ridgway  is supported by the  Medical research Council  [grant number  MR/ J014257/1 ]. The  Wellcome Trust Centre for Neuroimaging  is supported by core funding from the  Wellcome Trust , grant number  091593/Z/10/ Z. This work has been done as part of the  Du Pré fellowship  from  Multiple Sclerosis International Federation  (MSIF, www. msif. org)granted to  Dr Eshaghi.
On the other hand, the gapless score threshold (d) is surprisingly important: insertions and deletions are frequent enough that there is often no high-scoring gapless alignment. An intriguing idea is to use multiple codesigned sparse seeds. For example, we might use two seed patterns at odd-numbered genome positions, and another two at even-numbered positions. This would use the same memory as two nonsparse seeds, but it might improve alignment. (It cannot be any worse because it includes two nonsparse seeds as a special case. ) However, some preliminary Iedera results (not shown) suggest that (in the case of spaced seeds) the sensitivity gain obtained is small for this computationally intensive design problem. Memory can still be a problem (because not everyone has terabyte memories yet, and we may wish to search huge DNA databases), so low-memory indexes (e.
Sequence assembly Analyses of reads produced by either Illumina (siRNA sequencing) or 454 GS FLX Titanium (Amplified-VANA sequencing) were performed using CLC Genomics Workbench 5. 15. De novo assemblies of contigs were performed with a minimal contig size set at 100 bp and 200 bp for Illumina and 454 GS FLX Titanium reads, respectively. A posteriori mapping of reads against the complete genomes of SWSV (once the full genome had been cloned and sequenced) or SSEV or against parts of these genomes were also performed using CLC Genomics Workbench 5. 15. Primary sequence outputs have been deposited in the sequence read archive of GenBank (accession numbers: VANA_USDA dataset: SRR1207274; VANA_VARX dataset: SRR1207275; siRNA_VARX dataset: SRR1207277).
Sequence analyses Six complete genomes of the novel mastrevirus were recovered from plants VARX, USDA, A0037, B0069, D0005 and E0144 (Table  S1 ) and were aligned with the genomes of representative mastreviruses using MUSCLE (with default settings)  [28]. Similarly, the predicted replication associated protein (Rep) and capsid protein (CP) amino acid sequences encoded by the viruses within the full-genome dataset were also aligned using MUSCLE. Maximum likelihood phylogenetic trees were inferred for the full genomes (TN93+G+I nucleotide substitution model chosen as the best-fit using jModelTest  [29] ), Rep (WAG+G+F amino acid substitution model chosen as the best-fit using ProtTest  [30] ) and CP (rtREV+G+F amino acid substitution model chosen as the best-fit using ProtTest) datasets with PHYML  [31].
Approximate likelihood ratio tests (aLRT) were used to infer relative supports for branches (with branches having ,80% support being collapsed). All pairwise identity analysis of the full genome nucleotide sequences, capsid protein (CP) amino acid sequences, replication associated protein (Rep) amino acid sequences and movement protein (MP) amino acid sequences were carried out using the MUSCLE-based pairwise alignment and identity calculation approach implemented in SDT v1. 0  [32]. The full genome sequence alignment of representative mastrevirus genome sequences together with SWSV was used to detect evidence of recombination in SWSV using RDP 4. 24 with default settings  [33]. Sequences are deposited in GenBank under accession numbers (SWSV-A [SD-VARX-2013] -KJ187746; SWSV-A [SD -USDA-2013] -KJ187745; SWSV-B [SD -B0069-2013] - KJ210622; SWSV-B [SD -D0005-2013] -KJ187747; SWSV-B [SD -E0144-2013] -KJ187748 and SWSV-C [SD -A0037-2013] - KJ187749).
454-based sequencing of VANA from the VARX and USDA sugarcane samples This approach was used in an attempt to detect both RNA and DNA viruses that may be present in the two sugarcane plants  [27]. A total of 2612 and 1635 reads were respectively obtained from the VARX and USDA plants following length and quality filtering. One hundred and eight and 18 contigs were produced by de novo assembly from the VARX-and USDA-derived reads, respectively. Two contigs from the VARX plant (2706 nt and 412 nt) and two from the USDA plant (2706 nt and 649 nt), encoded proteins with between 91 and 100% sequence identity with previously described SSEV proteins (Table1). BLASTx analysis revealed that an additional two contigs from the VARX plant (2122 and 127 nt) and three contigs from the USDA plant (1836, 196 and 312 nt) were homologous with known mastreviruses but were nevertheless only distantly related to mastrevirus sequences currently deposited in GenBank (Table1).
Coverage of the non-coding large and small intergenic regions and the presumed C1 ORF intron were even lower at 17. 5X and 6. 8X, respectively. It is also noteworthy that besides differences in coverage depth, these various genomic regions of SWSV also showed differences in the siRNA size classes that they yielded. While there was an enrichment of the 21 and 22 nt siRNA size classes amongst the total siRNA reads mapping to the V1 and V2 ORFs, there was a depletion of the 21 nt siRNA size classes and an enrichment of the 24 nt size class amongst total siRNA reads mapping to the C1 ORF (Figure  2 ). The LIR and, to a lesser extent, the SIR showed a pattern similar to the C1 ORF region (data not shown). The C1 intron, however, had an extreme over-representation of the 24 nt size class with the other size classes being either nearly (22 nt) or totally (21 and 23 nt) absent (Figure  2 ).
A novel sugarcane-infecting mastrevirus originating from the Nile region The complete genome of SWSV, as recovered from the VARX and USDA plants, is most similar to that of Wheat dwarf India virus (WDIV, Accession number NC_017828), with which it shares 61% genome-wide identity. Whereas the Rep and MP amino acid sequences of SWSV are also most similar to those of WDIV (54. 4% and 44. 8% identity, respectively), the CP is most similar to that of Panicum streak virus (PanSV, NC_001647, 51. 4-53. 9%). Based on the 78% species demarcation threshold set by the Geminivirus study group of the ICTV  [32] , it is clear that the novel mastrevirus should be considered a new species within the genus Mastrevirus of the Family Geminiviridae (Figure  S2 ). This is further confirmed by phylogenetic analyses performed on both the full genome (Figure  3 ) and on the amino acid sequences of its encoded proteins (Figure  4 ).
Flow cytometry Staining and flow cytometric analyses of generated DC were carried out using standard procedures. Briefly, cells were stained with different conjugated antibodies as follows: anti-CD11c (B-ly6), anti-MHC-II (G46-6), anti-CD40 (5C3), anti-CD80 (L307. 4), anti-CD86 (2331), and their respective isotypes controls (BD Biosciences, San Diego, CA, USA) on ice for 30 min, washed thoroughly with PBS-1% BSA. Cells were then fixed with 1% paraformaldehyde and subjected to flow cytometry (FACSCalibur, BectonDickinson-BD, USA). Data were analyzed using Cyflogic software.
Zymography Metalloproteinase activity was determined by zymography. Supernatant of culture from DC/TL treated or not with LMW HA was run on a 10% SDS PAGE containing 0. 1% gelatin (Sigma-Aldrich). The gel was stained with Coomassie Brilliant Blue R-250 for 30 min at room temperature. Gelatinase activity was visualized by negative staining; gel images were obtained with a digital camera (Canon EOS 5D), and were subjected to densitometric analysis using Scion Image software (Scion Corporation, Frederick, MD). Relative MMP-2 activity was obtained by normalizing values to untreated samples (DC/TL). HT1080 cell line supernatant was used as positive control of MMP-2 and MMP-9 activity  [30].
PCR conditions were: 90 seconds at 94uC and then 40 cycles of 30 seconds at 94uC, 30 seconds at 60uC and 30 seconds at 72uC. Values were normalized to levels of glyceraldehyde-3-phosphate dehydrogenase (GAPDH; used as housekeeping) transcript (forward 59-CATCTCTGCCCCCTCTGCTG-39 and reverse 59-GCCTGCTTCACCACCTTCTTG-39). cDNA was quantified using the OligoGreen Single Stranded Quantification kit (Invitrogen) according to the manufacturer's instructions. Data were processed by the DDCt method. The relative amount of the PCR product amplified from untreated cells was set as 1. A nontemplate control (NTC) was run in every assay, and all determinations were performed as triplicates in three separated experiments.
Red blood cells were removed using a lysis solution (0. 15 M NH 4 Cl, 1 mM KHCO 3 , 0. 1 Na 2 -EDTA). The remnant cells were subsequently fixed in 1% paraformaldehyde and subjected to flow cytometric analysis (FACSCalibur, Becton-Dickinson, BD). Data were processed using Cyflogic software.
Acknowledgments We would like to thank  Soledad Arregui  and  Guillermo Gasto  ´n for expert technical assistance;  Silvina Montal ,  Carina Chwat  and  Franco Nievas  for help us to obtain tumor tissue. This work was supported by grants from  Austral University  (to MR: # I01-12 ;  FP I02-12 ;  MG T13-12 ) and from  Agencia Nacional de Promocion Cientı ´fica y Tecnologica (ANPCyT)  grants. To LA:  PICT-2007/00082 ; MG:  PICTO 2008/00115 ; MG and GM: PICT 2010/2818; GM and LA:  PICT 2012/1407. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Experimental A homemade, low-cost (<$10k) multispectral camera system, consisting of interference filters and a lownoise Si-CCD, operating from 400 to 950 nm in 12 spectral bands (full-width at half-maximum (FWHM) of 40 nm), is used to obtain both the reflectance and luminescence images  (Ricciardi et al. , 2009 , Delaney et al. , 2010). For reflectance, the manuscript is illuminated at 160 lux using two 50 W Solux lamps (Solux, Rochester, NY, USA) at ±45°angles from normal. The luminescence image is captured with the same setup described elsewhere  (Delaney et al. , 2010) , with spectral radiance of 40 mW/sr*m 2. The luminescence image is median filtered (1 pixel) and sharpened, and the optical distortion is removed in Adobe® Photoshop® CS5. XRF spectra are collected with an ArtTAX Pro XRF Spectrometer (Bruker AXS Inc.
The paradigm consists of three major steps: 1. The determination of the spectral diversity of the image cube or the number of principal image components, carried out using the minimum noise fraction algorithm, which is a type of principal components analysis. The objective of this algorithm is to determine the level of diversity in the spectral dataset. It yields 'Eigen images' which are orthogonal projections of the pixels in the image cube. The maximum number of Eigen images is the number of spectral bands in the cube. While these images often highlight areas having similar properties they cannot be taken as meaning that these areas were painted with the same materials. In the case presented here, all 12 possible Eigen images showed meaningful information and were retained for the second processing step.
To assist in the clustering of the endmembers, the ENVI Nd-visualizer is used to manually select the well-separated clusters (Fig. 1C ). In the end, 18 clusters were found by this method, giving 18 spectral endmembers that define the image cube (Fig. 1D ). The spectral endmembers can then be compared with spectral databases to identify the pigments present, or used to make 'spectral maps' to guide further studies using other, 'site-specific' methods (such as FORS, XRF, or Raman spectroscopy). The spectral maps are also useful to ensure that the spectral endmembers adequately describe the miniature's surface, i. e. that no endmembers were 'left out' of the analysis. The maps are produced using a spectral angle-mapping (SAM) algorithm. The SAM algorithm identifies pixels in the image cube whose reflectance spectra match those of the endmembers within a specified angle tolerance.
Pigment assignments Pigments are identified using XRF and FORS data collected at sites defined by the endmember maps (Figs. 1 2 3 4 , Table  1 ). These methods are complementary, XRF providing elemental composition, and FORS providing molecular or structural information. The XRF spectra are examined using traditional methods, i. e. peaks in the XRF spectra are assigned to the presence of specific chemical elements, and possible pigments inferred by comparison with databases while taking into account possible effects of paint layering and shielding by heavy elements. The FORS spectra are compared with various in-house and public databases  (Clark et al. , 2007; CNR-IFAC, 2011) , which contain minerals as well as pure and mixed pigments painted out on various supports including parchment. Typically FORS spectra are acquired from several sites within each defined regions.