dataesr/scientific-paragraphs-categorization huggingface dataset:
Thus, the interpolation of along-track data collected by just one or two satellites provides only marginal resolution of the mesoscale and smallerscale features of ocean circulation  (Chelton and Schlax, 2003; Le Traon and Dibarboure, 2002; Leeuwenburgh and Stammer, 2002) , which are dominant in the coastal regions. It is probably due to the above-mentioned difficulties that satellite SLA has not been used before to study the sea level Contents lists available at ScienceDirect journal homepage: www. elsevier. com/locate/csr variability in the continental shelf of southeast South America. However,  Ruiz-Etcheverry et al. (2014)  show that at seasonal and longer time-scales gridded SLA satellite altimetry data compares very well to tide gauges (root mean square differences lower than 2. 1 cm) in the region.
g. Fiore et al. , 2009; Framiñan et al. , 1999). Several oceanographic cruises have gathered in-situ observations in part of the shelf influenced by the RdP and PL plumes (e. g. Möller et al. , 2008; Campos et al. , 2013). However, in-situ data alone are unable to provide a comprehensive spatio-temporal description of the dynamics of this extensive and dynamical area. In this area satellite observations provide a unique data set to explore the variability of the region. Indeed, much of the results discussed above derived from the analysis of color and SST remote sensed images (e. g. Romero et al. , 2006; Piola et al. , 2005; Simionato et al. , 2010). The aim of this paper is, taking advantage of the almost 20 years of radar SLA satellite observations, to provide a description of the SLA variability at seasonal and interannual time scales and evaluate the involved processes.
Satellite altimetry data Satellite altimetry data used in this paper were constructed by SSALTO/DUACS. We downloaded from the AVISO web site (ftp:// ftp. cls. fr) the reference version of the gridded sea level anomaly (SLA) data. The processing of along-track data from altimetric missions into gridded fields of SLA is described in Le  Traon et al. (2003). Data are mapped on a 1/31 Mercator projection grid. We extracted the SLA for the region of interest from the global SLA fields for the period 1993-2010 (18 years). The reference version of the altimetry data has the advantage of being constructed using always two simultaneous altimeter missions, one in a 10-day exact repeat orbit (TOPEX/Poseidon, followed by Jason 1 and presently by Jason-2) and the other in a 35-day exact repeat orbit (ERS-1 followed by ERS-2 and then by Envisat).
A 7-year  (1993) (1994) (1995) (1996) (1997) (1998) (1999)  mean SLA is subtracted from the time-series to eliminate the unknown geoid. Data are produced at 7-day and daily intervals. In this work we used both products and, after corroborating that results are not significantly different, the latter are used to allow for a better comparison with other data sets and variables. As discussed by  Chelton et al. (2011) , this dataset has half-power filter cutoff wavelengths at about 21 in latitude and 21 in longitude. For features with Gaussian shape, this corresponds approximately to an e-folding radius of about 0. 41  (Chelton et al. , 2011) , or 37 km for the mean latitude of the region considered here. As a consequence of the time and space sampling of the satellites described above, gridded altimetry data are limited to solve structures larger than 37 km and with periods longer than 20 days.
Data are available at approximately 11 km resolution for the global oceans. The mapping uses simple arithmetic means to produce composite images of 5-day duration. We downloaded the available blended pentads of the SST product that span the period from 12 November 2006 to 6 December 2011. This SST dataset has been successfully used to analyze the variability of the RdP plume from seasonal to sub-annual scales and to detect upwelling events  (Simionato et al. , 2010). Here we use it to study the seasonal variability of the contribution of the thermosteric effect (i. e. due to the solar-radiative forcing only) to the sea-level change.
Wind stress The satellite scatterometer QuikSCAT provided complete coverage of the surface of the ocean from July 20th, 1999 to November 23rd, 2009. We downloaded from the Ifremer web site (www. ifremer. fr/cersat/) a gridded version of the QuikSCAT wind stress at daily temporal resolution and 0. 51 Â 0. 51 spatial resolution. Gridded wind fields were computed by Ifremer from level 2B QuikSCAT scatterometer individual observations provided by JPL/ PO. DAAC. Despite of the fact that QuikSCAT database is shorter than the satellite altimetry database, it allows capture small-scale features that are dynamically important to both the ocean and the atmosphere. However, those features are not resolved in other observationally based wind atlases or in NCEP-NCAR reanalysis fields  (Risien and Chelton, 2008)  that are available for a longer time period.
Interannual variability To favor the analysis of the variability in interannual time scales we computed the PCs of the interannual component of the gridded SLA dataset presented in Section 2. Only the first mode accounts for a large percentage (51%) of the total variance and seems to have a physical meaning. The map of the factor loadings of this leading mode (Fig. 5a ) depicts a clear change at about 371S. North of this latitude, the correlation between the time series of the factor scores associated to this mode (blue line in Fig. 5b ) and the interannual component of the SLA are larger than 0. 6, whereas southward of 371S they decay up to 0. 3. Largest correlations occur in the regions of influence of the RdP and PL plumes, reaching values close to one at some locations. Therefore, the factor loadings suggest that the leading mode represents interannual variability associated with the impact of fresh waters of continental origin on the shelf.
7 ). Fig. 8c  also reveals that the maximum annual SLA occurs progressively later along the year to the north. This happens in late summer (mid-March) in the southern coast of the RdP, but can occur even in late fall (mid-June) along the Brazilian coast northern 301S. This seems to be indeed the kinematical meaning of the patterns extracted by the PC modes (Fig. 7 ). For the SST, instead, the behavior is pretty different. The maximum of the annual harmonic occurs during the first days of February in the shallow waters of the RdP and PL, whereas in the rest of the study area it takes place at least 15 days later. To verify the phase lag of the SLA annual cycle observed in derived from in-situ data gathered by five TGs located along the coast. TGs amplitudes and phases displayed in Table  1  were estimated by fitting an annual wave to the climatologies shown in Fig.
The reader is referred to  Ruiz-Etcheverry et al. (2014)  for a discussion about differences and similarities between the SLA annual signal as retrieved by satellite altimetry and the TGs. Here we note that the phase lag pattern observed in the previous paragraph, i. e. that the SLA annual cycle peaks before in the southern coast of the RdP than in the Brazilian or Uruguay coasts, is consistently retrieved by both TGs and satellite datasets. Thus, it is evident that the annual cycle of the SLA observed in Figs. 8 and 9 cannot be explained by the radiative solar cycle alone, but there must be another mechanism forcing waters up and down in the proximity of the Uruguayan and Brazilian coasts. As mentioned above, wind stress in the study area displays a marked seasonal cycle: whereas south-westerlies are dominant during autumn-winter, north-easterlies prevail in spring-summer.
Acknowledgments Two anonymous Reviewers and  Professor P. T. Strub  provided useful comments to improve the article. For SST: NOAA  Coastwatch Program , NOAA NESDIS Office of Satellite Data Processing and Distribution, and  NASA Goddard Space Flight Center and Ocean Color Web. This study is a contribution to the  ANPCyT (National Agency for Scientific and Technological Research of Argentina )  PICT 2012 0467 ,  PICT 2010-1831 , the  CONICET (National Council for Scientific and Technological Research of Argentina)   PIP 112 201101 00176 ,  PIP 133 20130100242 CO  and the UBACyT 2011-2014 20020100100840 Projects. LRE is supported by grant  SGP 2076  from the  Inter-American Institute for Global Change Research  which is supported by the  US National Science Foundation  (Grant  GEO-0452325 ).
Microarrays RNA isolation and quality control were performed as previously described  [2, 22]  from cells treated with siRNA T6-1. Applied Biosystems HGS V2 arrays  [23]  were hybridized, washed, and exposed according to the protocols of the technology provider. Raw data were quality controlled  [24] , and normalized using NeONORM (k-parameter = 0. 2)  [25]. Longitudinal analysis was performed using a Kohonen-maps based classifier as described in  [26] , using the CDS statistical test  [27]. The data are freely accessible through the MACE database at http://mace. ihes. fr under accession no. (maceid): 2732656872.
1B ). Quantification of TAF6a protein levels from three independent experiments using the ImageJ software package (http://rsbweb. nih. gov/ij/) indicated that si1 and si2 typically reduced TAF6a protein levels by 70-80% and 40-60%, respectively. To determine the impact of the loss of total TAF6 protein on cell viability we employed the methylene blue colorimetric assay (see materials and methods). Both siRNAs that depleted TAF6 resulted in a concomitant loss of cell viability (Fig. 1C-D ). We conclude that TAF6 expression is essential for cell viability in human cells, extending previous results demonstrating that TAF6 is essential for viability in distinct organisms including S. cerevisae  [28, 29] , Drosophila  [30]  and zebrafish  [31]. We next used si1, the siRNA that most efficiently reduced total TAF6 expression and resulted in the highest loss of viability, to further determine the impact of knock-down of TAF6 on the transcriptome using microarray analysis.
Acknowledgments BB thanks the  European Union  for support via a  Marie-Curie  Fellowship as well as  Dr. Juan Valca  ´rcel and the members of his team for helpful input at the inception of this work. E. Wilhelm  holds an  Alexandre Graham Bell Canada Graduate Scholarship  from the  National Science and Engineering Council of Canada (NSERC). We gratefully acknowledge  Annie Leclerc  for the preparation of figures. BB is a member of the  Centre de recherche sur la biologie de l'ARN  and the  FRSQ-funded Centre de recherche clinique E ´tienne-Le Bel.
Genome sequencing Single-end multiplex libraries were created with multiplexed protocol according to the manufacturer's specification; the sequencing was performed on the Illumina HiSeq 2000 platform. The read length was 110-bp for both C. difficile CII7 and C. difficile CII7xCD37(A). Then reads were assembled de novo into contigs using Velvet  (Zerbino & Birney, 2008 ) (Options: Kmer : 71 and 75 respectively for CII7 and CII7xCD37(A) ; -short ; -fastq ; -unused_reads ; -read_trkg). Finally contigs (minimum size, 500 bases) were reorganized and oriented based on alignment to the finished genome of C. difficile strain 630 (CD630)  (Sebaihia et al. , 2006). Contigs that did not match CD630 were localized at the end to obtain each genome scaffold. The short reads genomic data have been deposited in the European Nucleotide Archive (ENA) under accession number 'PRJEB1488' and can be accessed online (http://www.
faecalis JH2-2 was observed (Fig. 2 ). The genome of the transconjugant CII7xCD37a was completely sequenced and compared to that of CD37 (GenBank accession number AHJJ01). The transposon was detected within a copy of the 23S rRNA gene, and no other genetic material from strain CII7 was detected in CII7xCD37a. The integration site of the element was also determined in all transconjugants by sspPCR and confirmed by subsequent PCR and Sanger sequencing. In total, seven different insertion sites were detected in the eight C. difficile transconjugants examined, whereas a unique insertion site was identified in the ten E. faecalis transconjugants analysed. All target sites of the element contained a central AG dinucleotide (Table  2 ). Integration within a copy of the 23S rRNA gene was confirmed in CII7xCD37a and the transposon was also found in a copy of this gene in CII7xCD196Rd, although at a different site.
In CII7xCD37d the transposon was located between orthologs of C. difficile 630 CD630_31060 and CD630_31070, like in the donor C. difficile CII7, whereas in CII7xCD196Rc it was detected within the coding sequences of the ortholog of CD630_28310, like in C. difficile 2007855. Finally, the transposon was integrated at the same position within a copy of the tRNA Arg gene in transconjugants CII7xCD37c and CII7xCD196Rb. In all E. faecalis transconjugants, the transposon was always located within a copy of the tRNA Arg gene. Although no genomic data were available about strain JH2-2, it can be hypothesised that, like E. faecalis V583 and OG1RF (Genbank accession number NC_004668 and CP002621, respectively), its genome contains several copies of the tRNA Arg gene. Interestingly, the element always integrated the same locus (Fig.
3152104 and 3152105 in C. difficile 2007855; GenBank accession number FN665654) determines a 207nt-elongation of the CDS coding for a replication initiation factor homologous to orf20 of Tn916. The same insertion is also present in the transposon from the C. difficile M68 strain (GenBank accession number FN668375). The replacement of a guanine by a thymine at position 9691 (positions 3149490 in C. difficile 2007855) causes the substitution of a methionine by an isoleucine within the sequence of a protein with unknown function. The transposon is located between orthologs of C. difficile 630 CD630_31060 and CD630_31070 in C. difficile CII7, while it is integrated within the coding sequences of the ortholog of CD630_28310 and CD630_33170 in strains 2007855 and M68, respectively.
Flow Cytometry Immunophenotyping was performed using antibodies detailed in supplemental online Table  1. All incubations were conducted in media composed of 0. 5% BSA, 0. 4% EDTA in PBS (-Ca 2+ , -Mg 2+ ). Before antibody incubation, cells were blocked using incubation media containing 10% donkey serum for 15 minutes at 4°C. Antibodies were conjugated with either FITC or PE, whereas nonlabeled antibodies were detected using an appropriate FITC-or PE-conjugated secondary antibody. All antibody incubations were carried out for 15 minutes at 4°C and then washed with incubation media three times. Appropriate labeled isotype controls were used to define the specific gates. Analysis was performed on FACSCalibur with CellQuest software (BD Biosciences, San Diego, CA, http://www. bdbiosciences. com).
All primers were designed using Primer3 software, and complete sequences are provided in supplemental online Table  3. Briefly, samples were denatured for 5 minutes at 95°C, cycled 40 times at 95°C for 15 seconds, followed by 40 cycles at an annealing temperature of 60°C for 30 seconds and finally 72°C for 30 seconds, using a MyIQ thermocycler (Bio-Rad). qRT-PCR was performed using three independent RNA samples, and triplicate readings were taken for each experimental sample and normalized against the reference gene glyceraldehyde-3-phosphate dehydrogenase (GAPDH) to calculate the expression of each target gene. PCR products were verified using 4% agarose gel electrophoresis with 0. 1% ethidium bromide against a TrackIt 1Kb Plus DNA ladder (Invitrogen).
Adipogenic Potential of Porcine Skeletal Muscle-Derived PICs Murine PICs have been shown previously to differentiate into adipocytes, and their adipogenic potential has been shown to correspond to a subpopulation expressing PDGFRa  [13]. Therefore, we subjected pPICs to adipogenic differentiation to assess their potential. After 7 days of adipogenic differentiation, pPICs were found to have accumulated some intracellular lipid, identified by Oil Red O staining (data not shown); however, cells were never found to have adopted the characteristic adipocyte morphology. Whether this is a real difference between the porcine and the murine PICs, or that to induce the adipocyte lineage in pPICs requires a different cocktail combination, remains to be elucidated. The fact that pPIC clones rapidly acquire a senescent phenotype, whereas the mixed population does not, suggests that it will require determining the multipotency of different clone derivatives to resolve this issue.
Calculating noise level and percentage of long-range contacts We calculated two measures that provide estimates of the noise level and efficiency of the assay. The first is the interchromosomal contact probability (ICP) index  (Kalhor et al. 2011) : ICP = +interchr contact counts +intrachr contact countsð > 1 kbÞ : In the denominator, the intrachromosomal contact counts exclude contacts between pairs of loci #1-kb apart. Smaller ICP values indicate a better signal-to-noise ratio, assuming that the real data (signal) will be enriched for intrachromosomal contacts, whereas noise will be dominated by interchromosomal contacts. The second number is the percent of long-range contacts (PLRC) extracted from the initial set of paired-end reads that remain after filtering the reads that mapped to human genome: PLRC = +interchr contact counts + +intrachr contact counts > 20 kb ð Þ Number of raw reads after human DNA filtering : The bigger this percentage is, the more information the data set provides about nonadjacent chromatin contacts for the amount of sequencing in hand.
Eigenvalue decomposition and chromatin compartments To identify chromatin compartments, for each stage, we carried out eigenvalue decomposition on the matrix of Euclidean distances between locus pairs. For each chromosome we used the intrachromosomal 3D distance matrix at a resolution of 10 kb, where each 10-kb locus is represented by the 3D coordinate of its midpoint. We then calculated the Spearman correlation between each pair of rows of the 3D distance matrix and applied eigenvalue decomposition (using the eig function in MATLAB) to this correlation matrix. The sign of the first eigenvector defined a compartment assignment for each 10-kb locus at each stage. We also aggregated all three stages and calculated a set of aggregate compartments (Supplemental Fig. 3 , fourth row of figures on each page) which divided each chromosome into three main compartments (i.
Acknowledgments We thank  Reza Kalhor  for advice on the Hi-C protocol and  Carolina Borsoi Moraes  for advice on the FISH protocol;  Harianto Tjong  for sharing the source code for volume exclusion simulation on the yeast genome;  John Weger ,  Rebecca Sun , and  Glenn Hicks  ( Institute for Integrative Genome Biology, University of California Riverside ) for their assistance in the library preparation and sequencing process; and  Serena Cervantes  for technical assistance in microscopy and image processing. The following reagents were obtained through the  MR4  as part of the  BEI Resources Repository, NIAID, NIH: Plasmodium  falciparum strain  3D7 (MRA-102 ) deposited by  D. J. Carucci. We thank  Stanley Fields  and  Zhi-jun Duan  for feedback on the manuscript. This study was financially supported by a  Computing Research Association CIFellows award (NSF  award  CIF 1136996  to F.
A. ), the  Human Frontier Science Program  (grant  LT000507/2011-L  to E. M. B. ), the  National Institutes of Health  (grants  R01 AI85077-01A1  to K. G. L. R. and  R01 AI106775-01  to W. S. N. and K. G. L. R. ), the  European Research Council  (grant  SMAC-ERC-280032  to J. -P. V. ), the  European Commission  (grant  HEALTH-F5-2012-305626  to J. -P. V. and N. V), and the  French National Research Agency  (grant  ANR-11-BINF-0001  to J. -P. V. and N. V. ). Author contributions: W. S. N. and K. G. L. R. conceived the project. E. M. B. and S. M. B. carried out the Hi-C and FISH experiments. J. P. maintained P. falciparum cultures and assisted in experimental.
Searching for Relevant Studies We used a combination of a protocol-driven method and a "snowballing technique" to search for relevant studies. Details of the electronic search strategy in eight databases are provided in the supplemental online data for this study. The search strategy was designed to include data from both animal and human studies. The languages of publication were restricted to English, French, Spanish, and Portuguese. Reference lists of query studies were inspected to identify any additional relevant published or unpublished data. Details of the literature search in the "gray literature" are also provided in the supplemental online data.
Data Extraction and Subgroup Analyses We extracted data concerning animal model (gender and species), method used to generate periodontal defects, type of periodontal defect, cell source, type of cell carrier, randomization, study duration, and quality of reporting. We planned to determine whether differences in the efficacy or safety of periodontal regeneration between experimental and control groups were influenced by these characteristics. The chi-square test was used to perform subgroup analyses if at least three groups of two or more studies were available.
Statistical Analysis and Data Charting Animal and human studies were analyzed separately. We performed meta-analyses on standardized mean differences using an inverse variance random-effects method. Review Manager 5. 2 (The Cochrane Collaboration, Copenhagen, Denmark, http://www. cochrane. org) was used to plot the data. Only studies with an appropriate control group were considered for quantitative analysis. When a study had several experimental groups, each group was included separately in the quantitative analysis. The funnel plot was visually examined, and an Egger's test was performed using the "metabias" command in Stata 11. 1 (StataCorp, College Station, TX, http://www. stata. com) to determine publication bias. The studies determined to be significantly responsible for publication bias (e.
ACKNOWLEDGMENTS This study was supported by funding from the  Universit é de Toulouse , the  Toulouse Faculty of Dentistry , the  Paul Sabatier University , and the  Toulouse University Hospital  (P. M. , J. -N. V. , C. N. , V. P. B. , L. C. , P. K. ). M. L. S. was supported by a grant from the  U. S. Public Health Service, National Institutes of Health, National Institute of Dental and Craniofacial Research  ( DE13045 ). We thank  Bridget Samuels  ( University of Southern California ) for proofreading the manuscript.
Ethics Statement The human blood was obtained with informed consent from all participants under protocols approved by the IRB of the NIAID and the study was conducted on the registered protocol NCT00001230 (for the United States) and NCT01593722 (in Cameroon). Oral consent was obtained from illiterate participants in the presence of village elders as approved by the ethical review committees. The animal procedures were conducted in accordance with the guidelines with animal care and use committee at the National Institutes of Health and University of Georgia. The use of non-human primates for research was approved by the Committee on the Ethical Use of Animals in Research (CEUAR), Research Foundation for Tropical Diseases and Environment (ReFoTDe), Cameroon. All relevant guidelines of the International Primatological Society (IPS) on the acquisition, care and breeding of non-human primates (Second Ed, 2007) for research were followed.