dataesr/scientific-paragraphs-categorization huggingface dataset:
2012 and DeCesar et al. 2013  for recent summaries). Due to the mentioned exponential cutoff of the spectrum, data from instruments such as the CGRO-OSSE and -BATSE mainly show the exponential roll over above 20 keV. As a result, the combined CGRO-OSSE and -BATSE spectrum (20-150 keV) during the discovery outburst of GRO J1008-57 in 1993 was initially described by a bremsstrahlung continuum  (Shrader et al. 1999). As discussed by  Shrader et al. (1999)  for the joint 1993 CGRO/ASCA-GIS (0. 7-10 keV) spectrum and also by  Coe et al. (2007)  for INTEGRAL data from the 2004 June outburst, the soft X-ray spectrum cannot be described by a bremsstrahlung continuum. Instead, a power law spectrum with an exponential cutoff of the form CUTOFFPL(E) ∝ E -Γ e -E/E fold (3) was found to be a good description of the spectrum.
12 (1845 dof). line. This additional Kβ line is included in all spectral fits in this paper. The χ 2 can be further decreased to χ 2 red = 1. 11 (1888 dof) by ignoring the GSO spectrum. The reason are residuals above 75 keV, which might be caused by the putative cyclotron line at 88 keV  (Shrader et al. 1999). The signal quality does not, however, allow to constrain the cyclotron line parameters properly. See Sect. 4. 3 for further discussion of that feature. Adding the simultaneous RXTE spectrum (93032-03-03-01) to the Suzaku data, and taking the Galactic ridge emission into account, does not appreciably change the best fit parameters. Table  3  2 lists the final best fit parameters. Applying the same model to the quasisimultaneous Swift-XRT, RXTE-PCA and RXTE-HEXTE data (RXTE obsid 93032-03-02-00) from the same 2007 outburst also gives a good description of the spectrum (see Fig.
To illustrate the range of parameter variability, Fig. 9  shows contour maps between several continuum parameters calculated from RXTE data during maximum luminosity in 2007 (93032-03-02-00) and at the end of the 2007 outburst (93032-03-03-04). The contour map on the left demonstrates that the black body flux F BB changes significantly over the outburst, while its temperature kT BB can be described by the same values. Keeping this value fixed during both observations at a consistent value improves the uncertainty on the remaining parameters significantly. In particular, a contour map of Γ and E fold reveals a strong correlation. Similar to the black body temperature and the break energy, the folding energy seems to be consistent with a constant value during the outburst, while the photon index changes.
Inspection of the confidence maps reveals that the only spectral parameters for which significant changes are seen in individual spectral fits appear to be the power law flux, F PL , the photon index Γ, and the black body flux F BB. To constrain these parameters well and to reveal the evolution of the remaining parameters, all datasets available during the 2007 outburst (see Table  1 ) including the simultaneous Swift and Suzaku are fit simultaneously with the spectral continuum of Eq. (4) (and the Galactic ridge). In these fits the continuum parameters N H , E fold , and kT , and the flux calibration constant C HEXTE are not allowed to vary between the different observations. The free parameters of the simultaneous fit are the fluxes of the spectral components, F PL and F BB , the photon index, Γ, the iron line equivalent width W, and the PCA background scaling factor b PCA.
Since the initial fit showed that the equivalent width of the iron line W does not change significantly with source flux, in a final fit this parameter is also assumed to be the same for all observations. The resulting model describes all 31 spectra of the 2007 outburst with an χ 2 red = 1. 12 for 2623 dof. Adding all RXTEdata of the 2005 and 2011 April outbursts to check for possible hysteresis effects and refitting shows that the simplified model still gives a good description of all data if the equivalent width of the iron line is allowed to change between different outbursts (but remaining constant during each outburst). With N H = 1. 6 × 10 22 cm -2 , the soft X-ray absorption is too low to be constrained by PCA-data only. For this reason, changes of N H between the outbursts cannot be detected in the PCA data and the column density is held fixed for all outbursts.
12 for 932 dof). Note, however, that the spectra can also be described by adding a secondary black body component with a temperature of 0. 25 keV. This latter approach results in an even better description of the data (χ 2 red = 1. 07 for 922 dof). The parameters of both possible models are shown in Table  6  and the spectra with the secondary black body model applied are shown in Fig. 12. Data from the outbursts of GRO J1008-57 in 2012 show that there is indeed an additional soft excess instead of a partial covering material (see Sect. 6 and 7 below). Twelve days after the last Swift pointing during the outburst, on MJD 55932, Swift started to observe GRO J1008-57 again. Until MJD 55958 six additional observations were made (see Table  1 ). Even though the Swift-BAT did not detect the source (Fig.
13 ), Swift-XRT images clearly reveal an X-ray source at the position of GRO J1008-57, indicating that the neutron star was still accreting. Although the extracted Swift-XRT spectra have a few hundred photons only, by performing a combined fit of all six spectra and using the same model as described above (without need of a partial coverer model or secondary black body), the data can be well described with an χ 2 red = 1. 05 for 65 dof. The final parameters are listed in Table  7. The hydrogen column density is slightly larger compared to the value during the main outburst in 2011 December. This can be explained by the position of the neutron star on the orbit, which is behind the companion as seen from Earth. Here, the line of sight crosses a much larger region within the system (see Fig.
Predicting the Unpredictable: The 2012 November Type II Outburst of GRO J1008-57 Although GRO J1008-57 seems to be predictable in both, the occurrence of outbursts and the spectral shape, an unexpected and unpredictable behavior occurred right after the outburst in 2012 August, which itself occurred at expected time. Instead of fading into quiescence the outburst decay lasted several weeks, during which several flares were detected (see Fig. 13 ). An epoch folding  (Leahy et al. 1983 ) of the flaring activity in the light curve reveals significant variability on timescales on the order of 10 d and above (see  Fig. 13, inset). Swift observed GRO J1008-57 during the flaring activity on 2012 September 26/27. Due to the low flux (∼1. 14 × 10 -9 erg s -1 cm -2 ), the XRT data were grouped to achieve a a minimum signal-to-noise ratio of 5.
9  shows, however, that the data is consistent with a constant folding energy. In case of GRO J1008-57, the spectrum hardens with increasing luminosity. Recent theoretical work by  Becker et al. (2012)  describes several spectral states depending on the source luminosity, where sources with luminosities below the Eddington limit are expected to show this kind of correlation. Assuming a source distance of 5. 8 kpc  (Riquelme et al. 2012 ) and using the maximum flux values given in Table  3 , the peak luminosity of GRO J1008-57 is around 3 × 10 37 erg s -1. This value is close to the critical luminosity reported by  Becker et al. (2012) , which scales like L crit ∼ 1. 5 × 10 37 B 16/15 12. Thus, GRO J1008-57 is likely to be a subcritical accretor during type I outbursts. The most remarkable result of the analysis of the giant type II outburst of GRO J1008-57 is that the spectral model found for type I outbursts (Eq.
4 keV iron Kα line. For N H 10 23 cm -2 , self-absorption is not important and the iron line equivalent width and the hydrogen column density scale roughly linearly  (Eikmann 2012). The generally low observed equivalent widths indicate that the fluorescence line originates in the absorbing material. In most observations, N H is in agreement with the interstellar value, although some intrinsic absorption cannot be ruled out. During the 2012 August outburst, the best fit Fe Kα equivalent width is much larger (although with large uncertainties). This larger equivalent width could be due to the addition of a line from reflection from, e. g. , an enhanced Be disk. If the X-rays are reflected by material, the equivalent width increases significantly up to a factor of 100. The data analyzed within this paper can not confirm the claimed cyclotron line at 88 keV by  Shrader et al.
(1999, see Sect. 4. 3) , who argued that this feature is rather the second harmonic. Although there are slight deviations from the continuum visible in both, RXTE-HEXTE and Suzaku-GSO data, the signal does not allow to constrain any parameters. During the "giant" 2012 November outburst of GRO J1008-57, the signal quality of the Suzaku-PIN and -GSO data could be used to further investigate this claimed high energy cyclotron line. These data were not used here since no background data were available at the time of writing. However,  Yamamoto et al. (2013)  were able to fit the spectra with preliminary background corrections. These authors claimed a cyclotron feature between 74 and 78 keV, close to the feature at 88 keV reported by  Shrader et al. (1999). In conclusion, the fact that the spectrum of several outbursts of GRO J1008-57 can be modelled with the single simple model of Eqs.
Acknowledgements. We thank the RXTE-, Swift-and Suzaku-teams for their role in scheduling all observations used within this paper and for accepting our proposals. We especially thank  Evan Smith  for his help in scheduling the RXTE observations in 2011 April. Many thanks to  Hans Krimm  for providing the BAT-spectrum during the 2012 giant outburst. We acknowledge funding by the  Bundesministerium für Wirtschaft und Technologie  under  Deutsches Zentrum für Luft-und Raumfahrt  grants  50OR0808 ,  50OR0905 ,  50OR1113 , and the  Deutscher Akademischer Austauschdienst. This work has been partially supported by the  Spanish Ministerio de Ciencia e Innovación  through projects  AYA2010-15431  and  AIB2010DE-00054. All figures shown in this paper were produced using the SLXfig module, developed by  John E.
Data Concurrent with sampling for other biogeochemical and biological variables, seawater samples for determining the carbon dioxide system were taken daily from the integrated water sampler. Samples for total alkalinity (A T ) and total dissolved inorganic carbon (C T ) were drawn into 500ml borosilicate bottles. No filtering of samples prior to analysis was done due to the lack of significant calcifying plankton  (Schulz et al. , 2013; Brussaard et al. , 2013; Niehoff et al. , 2013). A T was measured using Gran potentiometric titration  (Gran, 1952 ) on a VINDTA system  (Mintrop et al. , 2000)  with a precision of 2 µmol kg -1. C T was determined using coulometric titration  (Johnson et al. , 1987)  with a precision of ≤ 2 µmol kg -1. Measurements for both C T and A T were calibrated against certified reference material and values adjusted according to the offsets for each measurement series (CRM; Batch No.
CO 2 system calculations The measured C T and A T , with associated temperatures, salinity and dissolved nutrient data, were applied to the CO2SYS program for Matlab  (van Heuven et al. , 2011)  to calculate additional carbon dioxide system variables. To be consistent with  Bellerby et al. (2008) , we used the dissociation constants for carbonic acid of  Dickson and Millero (1987) , boric acid from  Dickson (1990a) , sulphuric acid following  Dickson (1990b)  and the CO 2 solubility coefficients from  Weiss (1974). Values are reported as in situ concentrations. Seawater pH is reported on the total hydrogen scale (pH T ) and pCO 2 in µatm. To estimate NCP and the stoichiometric rates of carbon to nutrient uptake, we used measurements of total inorganic carbon concentration (C T ), total alkalinity (A T ), inorganic nutrient concentrations (phosphate -PO 3- 4 , nitrate -NO - 3 , nitrite -NO - 2 , and ammonium -NH + 4 )  (Schulz et al.
A. Silyakova et al. : Pelagic community production and carbon-nutrient stoichiometry Table  1. Mean values of pCO 2 and pH T (total scale) levels in mesocosms for every phase, post-nutrients period t 14 -t 27 and the overall period t 8 -t 27. pCO 2 and pH T are calculated from total carbon and total alkalinity using CO2SYS for Matlab  (van Heuven et al. , 2011). The dissociation constant for carbonic acid was adopted from  Dickson and Millero (1987) , for boric acid from  Dickson (1990a) , for sulfuric acid from  Dickson (1990b) ; CO 2 solubility coefficient was adopted from  Weiss (1974).
Acknowledgements. This work is a contribution to the " European   Project on Ocean Acidification" (EPOCA)  which received funding from the  European Community 's  Seventh Framework Programme  ( FP7/2007(FP7/ -2013 ) ) under grant agreement No. 211384. This work was partially funded by the project  Marine Ecosystem Response  to a Changing Climate (MERCLIM No. 184860 ) financed by the program NORKLIMA through the  Norwegian Research Council , " Marine Ecosystem Evolution in a Changing Environment " (MEECE No. 212085 ) and " Basin-scale Analysis, Synthesis and Integration" (EURO-BASIN  No. 26493 ). We gratefully acknowledge the logistical support of  Greenpeace International  for its assistance with the transport of the mesocosm facility from Kiel to  Ny-Ålesund  and back to Kiel. We also thank the captains and crews of M/V ESPERANZA of Greenpeace and  R/V Viking Explorer  of the  University Centre in Svalbard (UNIS)  for assistance during mesocosm transport and during deployment and recovery in Kongsfjorden.
cDNA templates for PCR amplification were synthesized from 2 lg of total RNA using a SuperScript II RNAse H reverse transcriptase kit (Gibco/BRL, Cergy Pontoise, France) for 90 min at 42 °C in the presence of random hexamer primers. Amplification. An appropriate volume of the cDNA obtained by RT was used in subsequent PCR amplification of mPRa and L19 ribosomal mRNA (endogenous internal standard). Primers for RT-PCR amplification were designed using Oligo Primer Analysis Software version 6. 54, Molecular Biology Insights Inc. , USA. Primers used for mPRa were 5 0 -GGCCTCCTTCACCTACCTCT-3 0 (sense) and 5 0 -CAGA CCCGGCTTCTGGCTGT-3 0 (antisense); primers for L19 were 5 0 -CTGAAGGTCAAAGGGAATGTG-3 0 (sense) and 5 0 -GG ACAGAGTCTTGATGATCTC-3 0 (antisense). Each PCR contained 100 ng of cDNA template, 1Â Taq DNA polymerase buffer, 200 lM of each dNTP, 1 U of Taq DNA polymerase (ATGC), and 0.
2 lM of specific primers, in a total volume of 50 ll. The conditions of amplification were 2 min at 94 °C, followed by 30 cycles at 94 °C for 1 min, 56 °C for 1 min, and 72 °C for 1 min. The PCRs would be expected to yield a product, at 284 bp for mPRa and 194 bp for L19. Aliquots of the amplified products and 100 bp DNA ladder were separated on a 1. 2% agarose gel and visualized by ethidium bromide staining. The gels were subsequently quantified using the Biorad Image Analysis System and Molecular Analyst for Macintosh software (Marnes-la-Coquette, France). The relative levels of gene expression were measured by determining the ratio between the products generated from the mPRa genes and the endogenous internal standard (L19) in separate reactions. Validation of semi-quantitative RT-PCR was determined and the optimal number of cycles and cDNA concentration for remaining in the log phase of amplification were chosen (see  Labombarda et al.
Blots were then treated with enhanced chemiluminescence (Amersham Pharmacia, Velizy-Villacoublay, France) according to the manufacturer's instructions and exposed to X-ray film. The specificity of the GP47 antiserum was confirmed by (1) substituting the antiserum with pre-immune serum; (2) blocking the diluted anti-mPRa-serum GP47 (1/5000) with the peptide (10 lg/ml), and incubating the mixture at room temperature for 2 h (see  Labombarda et al. , 2010). Signals were acquired directly using Chemidoc Molecular Imager (Bio-Rad, Marnes-la-Coquette, France) and quantified by Quantity-one software (Bio-Rad). Blots were also exposed to X-ray films. Films were scanned and signals quantified using ImageJ software. Data were analyzed by one-way analysis of variance (ANOVA) followed by Bonferroni post hoc tests.
The sequences were then verified using BLAST search of EMBL and GenBank databases to ensure that there was no homology with other mRNAs. The oligonucleotides were labeled with [ 35 S]dATP (1000 mCi/mmol, Perkin Elmer, France) to a specific activity of 2 Â 10 9 cpm/lg using terminal deoxynucleotidyltransferase (Amersham Pharmacia, Velizy-Villacoublay, France). Adjacent brain sections were incubated in the presence of the 35 Slabeled probes according to a previously described protocol  (Guennoun et al. , 1995). Briefly, 0. 25 ng of labeled probe in the hybridization buffer (50% deionized formamide, 10% dextran sulfate, 500 lg/ml denatured salmon sperm DNA, 1% Denhardt's solution, 5% sarcosyl, 250 lg/ml yeast tRNA, 200 mM dithiothreitol, and 20 mM Na 2 PO 4 in 2Â saline-sodium citrate, SSC) was applied on tissue sections and hybridization proceeded overnight at 40 °C.
After washing in PBS, slides were incubated with Alexa Fluor 488-goat anti-mouse secondary antibody (1/200, Molecular Probes, Eugene, OR, USA) for 2 h. The slides were washed in PBS then mounted with fluoromount and observed under the confocal microscopy. Negative controls were also processed using the immune-depleted antibody preparation or normal serum in place of anti-NeuN, or anti-S-100 a/b chain, or anti-CC1, or anti-Ox-42. Double immunofluorescence labeling was visualized using a confocal Zeiss LSM 510 microscope (Carl Zeiss GmbH, Jena, Germany). Images were sequentially acquired with green (488 nm) and red (543 nm) excitations to avoid cross talk between channels. Images were acquired sequentially in a line-scanning mode through an optical section of 1 lm in the z-axis and analysis was performed using Bioscan Optimas II software.
RESULTS mPRa mRNA is expressed in the adult mouse brain at similar levels in males and females The presence of mPRa transcripts in the brain was demonstrated by RT-PCR using total RNA isolated from adult male and female mouse brains. As expected, RT-PCR amplification generated a fragment of 284 bp. Sequencing of the amplified products and analysis by the NCBI BLAST program showed that the nucleotide sequence was homologous (100% identity) to the expected fragment in the sequence of mouse mPRa (GI2195525). Similar levels of mPRa transcripts were observed in the brain of males and females as shown by semi-quantitative RT-PCR (Fig. 1A ).
Patients and data collection We examined 48 cases of HP (from 48 different patients) diagnosed in the pathology department of Rangueil Hospital (Toulouse, France) in 2008. We excluded patients with a history of familial adenomatous polyposis or hyperplastic polyposis and HP which display criteria of sessile serrated adenomas according to Torlakovic  [9, 31]. All polyps measured less than 1 cm with an average diameter of 3 mm. For comparison, we also selected 12 normal colonic tissue specimens from resected non-complicated diverticular disease and 15 adenomas (10 low, and 5 high grade dysplasia adenomas). Clinical data (age, gender, site, size, number of HP at diagnosis, history of colorectal adenoma, or adenocarcinoma and the presence of synchronous adenoma or adenocarcinoma were collected for all 48 patients (Table  1 ).
Statistical analysis Univariate analysis was conducted to compare clinical and immunohistochemistry findings between the different study groups using the Chi 2 test or Fisher exact test (when required) for categorical variables and the nonparametric rank tests (Wilcoxon-Mann-Whitney or Kruskal_-Wallis) or Cuzick nonparametric test for trend across ordered groups for quantitative variables. Spearman nonparametric correlation test was used to assess the correlations between the expression of progastrin and p-ERK or pY-STAT3. All tests were two-sided and statistical significance was set at a p value of 0. 05. ***p < 0. 001; **0. 001 < p < 0. 01; *0. 01 < p < 0. 05. Analyses were performed using the statistical software, STATA v11  [34].
Secondary antibodies were peroxidase-conjugated anti-mouse IgG and anti-rabbit IgG (Jackson ImmunoResearch Laboratories). Peroxidase activity was detected by enhanced chemiluminescence (Amersham Biosciences). For quantitative analysis of the results, the films were scanned (LAS 3000, Fujifilm) and the density of each band was estimated with the MultiGaugeH software (Fujifilm). The density of each band was divided by the density of the GAPDH or actin band, and the obtained value was normalized with respect to that obtained under control conditions.
Reverse-transcription Quantitative Real-time PCR (RT-qPCR) RNAs were isolated with the NucleospinH kit (Macherey-Nagel). Reverse transcription was carried out for 1 h at 55uC with 1 mg total RNA, oligo dT primers, dNTPs and Superscript II reverse transcriptase (Invitrogen; 200 units). Primers for PCR (see Table  S1 ) were designed with the NCBI-Primer-BLAST software (http://blast. ncbi. nlm. nih. gov/). The PCR protocol was as recommended for the Mx3005P Real-time PCR SystemH (Stratagene). Accumulation of PCR products was measured by SYBR greenH fluorescence (SYBR GreenH master mix; Applied Biosystems). Raw data analysis was performed with the MxProH software (Agilent). For each sample, Ct(gene) -Ct(gapdh) was calculated, and this value was used to calculate the ratio of test gene mRNA to gapdh internal control mRNA.
16), an Apochromat (20x, NA:0. 8), or a Plan Neofluar (40x, NA: 1. 3) objective. Images (12 bits, 1388/1040 pixels, no binning) were recorded with an Axiocam HRc camera (Zeiss) (3200uK) and AxioVisionH Software was used for microscope image analysis (Zeiss). Images to be combined in a panel shared the same initial properties and gamma, and were exported as 8-bit TIFF files. They were subjected to the same software brightness and contrast adjustments in PowerPointH.
Actin was used as loading control. Data are representative of two independent experiments C. Concentrated conditioned medium from a culture of young (YF-CM) or senescent fibroblasts (SF-CM) was resolved by electrophoresis in a silverstained preparative gel. A band corresponding to the molecular weight of TIMP-1 was almost absent in SF-CM. The band corresponding to the molecular weight of albumin was not significantly affected. D. Identification of the presumed TIMP-1 by mass spectrometry. The bands believed to contain TIMP-1 were manually excised, washed with ultrapure water until totally destained, and then dried after adding 100 mL ACN and incubating for 10 min. After the supernatant was discarded, the tubes were left open for 10 min to allow complete solvent evaporation. Spots were rehydrated with a solution containing Trypsin Enhancer (Promega) in 50 mM ammonium bicarbonate and a solution containing 3 mL of 40 mg/mL Trypsin Gaged (Promega) in 50 mM acetic acid and then trypsin-digested.
C. Analysis by in-gel zymography of the proteinolytic activity of MMP-1 and MMP-2 secreted by young and senescent NHDFs and present in the conditioned media (respectively YF-CM and SF-CM). FGM was used as a control for basal MMP activities present in serum. The analysis was done by SDS-PAGE with a gel containing 0. 1% gelatin. Either 5 ml (upper part) or 20 ml conditioned medium was loaded. White bands denote the presence of proteins with gelatinolytic activity. L and A indicate, respectively, the latent and active forms of the MMPs. Data are representative of 6 independent experiments performed with cells from donors 2F1966 and 1619. doi:10. 1371/journal. pone. 0063607. g002.
Acknowledgments The authors acknowledge the contributions of H. Drobecq in mass spectrometry and  Dr. E. Werkmeister  and  A. Bongiovanni  in microscopy. Microscopy was performed at the  Microscopy-Imaging Facility of the Bio Imaging Center Lille Nord-de-France. We thank  Dr. N. Delhem  and  O. Morales  for the gift of interleukin primers, and  Dr. JE. Mejı ´a  for critical reading of the manuscript.