dataesr/scientific-paragraphs-categorization huggingface dataset:
Analysis of muscle growth-related gene expression Primers for myogenic determining factor (MyoD), myogenin (MyoG), myocyte-specific enhancer binding factor 2 A (MEF2A), and myostatin (MSTN) (Table  4 ) were designed using the Primer 5. 0 software. Real-time reverse-transcription polymerase chain reaction (RT-PCR)  was performed using the SYBR Green detection kit (TaKaRa, Japan), containing MgCl 2 , dNTP, and HotStar Taq Polymerase. An aliquot (2 μl) of a cDNA template (equal to 25 ng of total RNA) solution was added to a total volume of 10 μl containing 5 μl SYBR Green mix, 0. 2 μl ROX Reference Dye (50 X), and 0. 2 μl each of forward and reverse primers. After a pre-denaturation program (10 s at 95°C), 40 cycles of amplification were performed (95°C for 10 s, 60°C for 20 s), followed by a melting curve program (60-99°C with a heating rate of 0.
The images were detected on chemiluminescence (Applygen Technologies Inc. , Beijing, China). Multiple exposures of each Western blot were performed to ensure linearity of chemiluminescence signals. Western blots were quantified by measuring the intensity of bands with correct molecular weight using AlphaImager 2200 software (Alpha Innotech Corporation, CA, USA). The ratio of intensities of a target protein band and housekeeping protein band was calculated for each filter and the ratios from the different Western blot filters were used for analyzing the relative abundances of target proteins.
On this basis, we studied the prognostic value of SERPINE1 expression, analyzing a retrospective (n = 80) and a prospective (n = 190) cohorts of HNSCC patients. We analyzed SERPINE1 expression in a third patient cohort obtained from The Cancer Genome Atlas database (n = 507). We also analyzed the effect of SERPINE1 expression on proliferation, migration and apoptosis induction in HNSCC cell lines.
78, 95%CI 0. 98-3. 23, p = 0. 057), however the differences observed among groups, did not reach statistical significance in the multivariate analysis. Multivariate Cox analysis, excluding patients treated with surgery, showed that SERPINE1 expression (HR 1. 92, 95%CI 1. 03-3. 59, p = 0. 043) and tumor size (HR 2. 39, 95%CI 1. 29-4. 39, p = 0. 005) were independent risk factors for progression-free survival in patients receiving radiotherapy and chemo-radiotherapy as the main treatment option (Table  3 ). HPV status was analyzed in patients with oropharyngeal cancer treated at Hospital de la Santa Creu i Sant Pau (HSCSP). Thirty-five tumors were HPV negative, 9 HPV positive and HPV status was not available in 20 patients. SERPINE1 maintained its value as a marker of progression-free survival, when we analyzed the mRNA data from the prospective RT-PCR patient cohort, after excluding patients with oropharyngeal HPV positive tumors or oropharyngeal tumors which HPV status was unknown (Supplementary files, Figure  S2 ).
SERPINE1 expression was associated with poor survival in a third cohort of HNSCC patients included in The Cancer Genome Atlas database We analyzed SERPINE1 expression in an independent cohort of HNSCC patients having RNA sequencing results from 520 primary tumors and 44 mucosa samples recorded in The Cancer Genome Atlas (TCGA) database. SERPINE1 expression was significantly higher in tumor than in mucosa samples (p < 0. 001) (Figure  3A ). Kaplan -Meier curves showed that patients with high SERPINE1 tumor expression had shorter survival than patients with low SERPINE1 tumor expression (p < 0. 001) (Figure  3B ). Univariate Cox model analysis showed that overall survival was significantly lower in patients whose tumors expressed high level of SERPINE1 than in patients with low SERPINE1 expression (HR:2.
DISCUSSION We identified SERPINE1 expression as a poor prognostic marker in head and neck squamous cell carcinoma. A high expression of SERPINE1 increased the risk of metastasis and was associated with a poor clinical outcome. We obtained these results analyzing two independent patient cohorts with head and neck cancer (n = 80, n = 190). We used a third patient cohort of HNSCC (n = 507) included in TCGA database to support the association between SERPINE1 expression and patient survival. Despite using different methods to detect SERPINE1 expression in pre-treatment tumor biopsies, we observed a positive association between high SERPINE1 expression and poor clinical outcome in three independent patient cohorts. Taken together, our results show that SERPINE1 expression has a strong prognostic value in patients with head and neck carcinoma.
Tumor progression was considered as an increase in tumor size of 25% or higher, or the appearance of new lesions (local or regional recurrences, and distant metastases). Cancer-specific survival (CSS) was defined as time from diagnosis to death from cancer. HPV status, detected using the short PCRfragment-10 (SPF-10) assay (Lab. Biomedical Products, Rijswik, the Nederland's), was available for oropharyngeal tumors treated at HSCSP. A single patient with a HPV positive tumor was included in the retrospective study. In the prospective study, thirty-five tumors were HPV negative, 9 HPV positive and HPV status was not available in 20 patients. We also analyzed SERPINE1 mRNA levels in 520 primary tumor samples and 44 normal mucosas obtained from HNSCC patients included in The Cancer Genome Atlas (TCGA) database (https://tcga-data.
Immunostained sections were quantified by two independent observers using a Olympus BX51 microscope. The percentage of positive cells (0-100%) and the overall intensity of staining (1, no staining or weak; 2, moderate; and 3, strong) were established analyzing five randomly choosen microscopic fields at 100x magnification for each sample. SERPINE1 expression was only evaluated in tumor cells. There was inter-observer agreement in 95% of the samples; the remaining slides were re-evaluated and consensus decisions were made. Images were acquired using an Olympus DP72 digital camera and processed with CellD Imaging 3. 3 software (Olympus).
Images were captured using the DP73 Olympus digital camera (Olympus Corporation, Japan). The extent of migration was determined by the area fraction occupied by cells in five ×100 fields using CellSens dimension v1. 9 software (Olympus Corporation, Japan). Experiments were performed in triplicate and repeated three times. For cytotoxicity assays, cells seeded in 96 well/ plates (2500 cells/well), were exposed to cisplatin at a concentration ranging from 2. 5 to 80 μM for 48 hours. We determined drug sensitivity measuring cell metabolic capacity using the XTT Cell proliferation kit II, as previously described (Roche Diagnostics, Germany)  [62]. The half maximal inhibitory concentration (IC50) was calculated by linear interpolation as previously described  [62]. To determine cisplatin-induced apoptosis, we treated cells with 15-40 μM cisplatin for 16 hours.
Statistical analysis In the RT-PCR analysis and the TCGA database, the cut off to distinguish patients with high SERPINE1 expression and patients with low SERPINE1 expression was determined using Classification and Regression Tree Analysis (CART)  [64]. CART analysis selected the cutoff with the best sensitivity and specificity to distinguish patients with a high risk of disease relapse from patients with low risk according to PA-1 expression. Mann-Whitney and Kruskal-Wallis tests were used to assess the association between sex, age, tumor site, tumor size, node status, tumor differentiation, tobacco and alcohol consumption, rate of recurrences, with SERPINE1 expression. We distinguished between local (same anatomic site for recurrence and primary tumor) and metastatic (node recurrences or distant metastasis) recurrences.
Kaplan-Meier analysis and Log-Rank test were used to analyze differences in LRFS, PFS and CSS between the subgroups of patients established according to SERPINE1 expression. A multivariate Cox model was used to test the association between sex, tumor size, node involvement, age or SERPINE1 mRNA expression with PFS and CSS. To analyze differences between two or more conditions in "in vitro" assays, we used the non-parametric Mann-Whitney U or Kruskal-Wallis tests. Statistical analyses were performed using the SPSS v. 22 (IBM Corporation, Armonk, NY) software. Differences were considered significant at p-values < 0. 05 in all the applied tests.
Gel image analysis and statistical analysis of proteins' abundance Images were aligned and spots were detected and quantified using the Progenesis SameSpots software (version 3. 3, Nonlinear Dynamics) using the automated algorithm. All detected spots were manually checked and artifact spots were removed. Data were exported as raw values and statistical analyses were conducted in R (R Core Team, 2013) using the prot2D  (Artigaud, Gauthier & Pichereau, 2013)  and limma packages  (Smyth, 2004)  from the Bioconductor suite  (Gentleman et al. , 2004). Data were normalized (quantile normalization) and the samples were paired compared between hypoxia and normoxia conditions using moderated t-test at each temperature with 5 replicates per condition. For comparisons, we used a moderated t-test, which is a modified t-test, for which the standard errors have been moderated across spots, increasing the reliability of the test  (Smyth, 2004; Artigaud, Gauthier & Pichereau, 2013).
1% in water). Peptide solutions were mixed with the α-Cyano-4-hydroxycinnamic acid (HCCA, 10 mg/ml of a ACN/TFA/water (60/4/36:v/v/v) solution), and spotted on a polished steel target using the dried droplet method. Peptides were analyzed by Matrix-Assisted Laser Desorption Ionization Time-Of-Flight tandem mass spectrometry (MALDI TOF-TOF) in positive ion reflector mode, using an Autoflex III (Bruker Daltonics, Billerca, Massachusetts, USA) mass spectrometer. The flexControl software (v3. 0; Bruker Daltonics, Billerca, Massachusetts, USA) was programmed to acquire successively PMF spectra and MS/MS from the dominant peaks. Mass spectra were analyzed with flexAnalysis (v3. 0; Bruker Daltonics, Billerca, Massachusetts, USA) by applying the following conditions: TopHat algorithm for baseline subtraction, Savitzky-Golay analysis for smoothing (0.
2 m/z; number of cycles: 1) and SNAP algorithm for peak detection (signal-to-noise ratio: 6 for MS and 1. 5 for MS/MS). The charge state of the peptides was assumed to be +1. Porcine trypsin fragments were used for internal mass calibration. Proteins were identified with the PEAKS software (v 5. 3; Bioinformatics Solutions, Waterloo, Ontario, Canada), using MS/MS-based identification and de novo peptide sequencing. A custom-made expression sequence tags (EST) database (see below) was used with the following search parameters: carbamidomethylation of cysteine was set as a fixed modification; oxidation of methionine and phosphorylation of serine, threonine or tyrosine were set as variable modifications; one missing cleavage during trypsin digestion was allowed. Protein identification was considered as unambiguous when a minimum of two peptides matched with a minimum score of 20.
False discovery rates were also estimated using a reverse database as decoy. The EST database (available as http://figshare. com/articles/Pecten maximus EST database/1328466) was constructed by combining P. maximus sequences from Illumina RNAseq sequenced from mantle tissues  (Artigaud et al. , 2014a) , and from hemocyte cells  (Pauletto et al. , 2014). Overall, the database included a total of 252 888 P. maximus EST. EST sequences were annotated by homology searches against a non-redundant protein database using the Blast algorithm from NCBI with an e-value cut-off of 1 • e -10 (  Altschul et al. , 1997).
Funding This research was funded by grants from the  Région Bretagne , i. e. , the  Pemadapt  project (ref. 6368) and a doctoral fellowship to  Sébastien Artigaud  ( Protmar  project, ref. 6197). COMANCHE  ( ANR-2010-STRA-010 ) program from the  French National Research Agency (ANR)  also supported our research. This work also fits in the general objectives of the axis 6 of  LabexMER  ( ANR-10-LABX-19 ). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Data Deposition The following information was supplied regarding the deposition of related data: The 2-DE Gels from the experiment are available in FigShare: http://figshare. com/ articles/2 DE Gels of Pecten maximus gills at three different temperatures and two O2 levels normoxia or hypoxia /1328460. The database we used for mass spectrometry is also available in FigShare: http://figshare. com/articles/Pecten maximus EST database/1328466.
Histological and immunohistochemical analyses On day 27, the scar tissue was harvested with a rim of healthy normal tissue. Tissue samples were fixed in 10 % buffered formalin before embedding in paraffin. For histological analysis, tissue sections (3 μm) were deparaffinized, rehydrated and then stained with Masson's trichrome or picro-sirius red. Following staining, slides were dehydrated with graded solutions of ethanol and methylcyclohexane baths and sealed with Permount mounting medium (Thermo Fisher Scientific, Saint Aubin, France). For Masson's trichrome, stained slides were scanned with a Mirax Scanner (Zeiss, Marly le Roi, France) and images were taken using a digital camera (Hitachi HV F22) and Mirax Scan 150 software (v 1. 2, Zeiss). Images were analyzed using Pannoramic viewer software (v 1.
Assessment of skin perfusion For all the experiments, animals were anesthetized with isoflurane and then placed in a heated environment to maintain a stable cutaneous temperature (35. 0 ± 0. 5 °C) throughout the measurements. Mice were placed in the prone position and skin blood flow (SBF) was measured using a laser Doppler imager (PERISCAN PIM3, Perimed, Sweden). SBF was recorded for 1 min and signal analysis was performed off-line by calculating the average perfusion on each surface (43 mm 2 ) of interest (PIMSoft software, Perimed, Järfälla, Sweden).
Statistical analysis Statistical analysis was performed using Graphpad Prism 4 software. All the data are expressed as means ± SEM. For the wound healing rate, unpaired t-tests were carried out to evaluate statistical significance. For complete wound closure, the Kruskal-Wallis test was followed by a Dunn's multiple comparison test to estimate the significance of differences for between-group comparisons. For skin perfusion and assessment of endothelium-independent and -dependent response experiments, one-way analysis of variance (ANOVA) was followed by a multiple comparison test to estimate the significance of differences for betweengroup comparisons. Significance was defined at p < 0. 05.
Acknowledgements We would like to thank the  IHU OPeRa  for funding ASC development, the  Hospices Civils de Lyon (HCL)  for giving us permission to carry out this study, and the laboratory of  Pr M. Ovize  ( University of Lyon ) for taking care of the mice. This study was sponsored by the  Revitacare laboratory. We thank the local animal care facility (AnexPeau,  LBTI UMR CNRS 5305 , Lyon) and  Jocelyne Vial  for technical assistance on animal care.
Patient Recruitment The study protocol was approved by the ethics committee of the Affiliated Hospital of Jiangnan University (Wuxi 4th People's Hospital) and registered at ClinicalTrials. gov (NCT02441972). Thirty patients were recruited after their routine 18 F-FDG PET/CT examination, and each patient gave written and informed consent before the 18 F-Alfatide II PET/CT study. The final diagnosis of bone lesions was established based on the comprehensive assessment of all available data and clinical follow up.
8, 50 mAs, 120 kV (peak)) was performed first for each of the 2 scans. Raw CT data were reconstructed into 3. 75 mm-thick sections of transverse images, and reformatted sagittal and coronal CT images were generated. CT-based attenuation-corrected PET images were reconstructed with a standard iterative algorithm (OSEM, 3 iterative steps, 21 subsets) and reviewed using the same Siemens MMWP workstation.
Statistical Analysis Data were expressed as mean ± SD. K statistic was used to determine inter-reader agreement for visual analysis. The McNemar test was used to compare 18 F-FDG and 18 F-Alfatide II PET/CT with respect to sensitivity of the two methods. Diagnostic values for bone lesion detection were calculated on a per-lesion basis. For all statistical analyses, a p value <0. 05 was considered statistically significant.
In brief, after transient transfection of cells for 24 h with 40 nM of antagomir against miR-190b or mimic of miR-190b (synthetized by Qiagen), the cells were growth in normal medium for 48, 72 or 120 h to be then treated with 0. 5 mg/ml of the MTT labeling reagent at 37 °C for 1 to 3 h and lysed in 150 μl of dimethyl sulfoxide at room temperature for 30 min. The cell viability was thus determined by reading the absorbance at 450 to 570 nm of signal generated by MTT reduction which is directly proportional to the cell number. For each cell line, the data were collected from three independent experiments and compared to the control group obtained by transfection of non-targeting siRNA as negative control in miRNA inhibition experiments or miRNA inhibitor as negative control in miRNA mimic experiment.
Retrospective cohort study of sporadic GISTs We retrospectively collected NF1-GISTs and sporadic GISTs from 29 community hospitals and 3 institutions in Japan between 2001 and 2010. We sent survey forms to 32 hospitals and institutes, which identified 23 primary NF1-GIST patients among 1314 patients with a primary GIST who underwent surgery during this period. Clinical and pathological data for these NF1-GISTs were collected with tissue samples for pathological examination when available. Clinicopathologic data for sporadic GISTs other than those in NF1-GIST patients were obtained from 19 hospitals. Detailed clinicopathologic data were obtained from 927 of the 1314 primary sporadic GIST patients. This study was approved by the institutional review board of Osaka University Hospital and Osaka Police Hospital and was conducted according to institutional guidelines.
Statistical analysis Statistical analyses were performed using the Chi squared test, Fisher's exact test, Student's t test, and the Mann-Whitney U test. The recurrence-free survival (RFS) was calculated from the date of surgery to the date of first tumor recurrence or to the date of death, censoring living patients without recurrence at the time of data collection. The overall survival (OS) was calculated from the date of surgery to the date of death, censoring living patients. RFS and OS between the groups were compared using the Kaplan-Meier life-table method with the log-rank test. The p values were two-sided, and p values \0. 05 were considered significant. The data were analyzed using the Statistical Package for Social Sciences, version 17. 0 (SPSS Inc. , Chicago, IL, USA).
NF1-GISTs represent a rare sub-fraction of sporadic GISTs Next, we collected histologically confirmed GISTs, including NF1-GISTs, from patients who underwent surgery between 2001 and 2010 at 32 hospitals in Japan. In total, 1314 primary GISTs were collected, including 23 primary NF1-GISTs (1. 75 %; CI: 1. 17-2. 61 %). Six of the 23 NF1-GISTs were detected by CT screening, and when these 6 NF1-patients were excluded from the analysis, NF1-GISTs accounted for 1. 30 % (CI: 0. 81-2. 07 %) of the sporadic GISTs. A similar investigation was performed using data obtained from the French Netsarc/Rreps networks study. In this registry, 18 NF1-GIST patients (1. 1 %; CI: 0. 75-1. 85 %) were identified among 1528 GIST cases. Thus, NF1-GISTs are estimated at 1. 1-1. 3 % of primary sporadic GISTs. Clinicopathologic features were compared between the non-NF1-GISTs and NF1-GISTs (Table  3 ).
Acknowledgments We would like to thank the staff at each hospital and institution for collecting data for this study. Data collection collaborators included  Drs. Takeshi Omori ,  Osaka Police Hospital ;  Takashi Ishikawa ,  Niigata University Medical and Dental Hospital ;  Masahiro Yamamura ,  Kawasaki Medical School ;  Shinya Tokunaga ,  Osaka City General Hospital; Syunji Endo, Higashiosaka Municipal Hospital ;  Hirofumi Noro ,  Otemae Hospital ;  Hiroshi Imamura ,  Toyonaka Municipal Hospital ;  Atsushi Takeno ,  Kansai Rosai Hospital ;  Kazuo Kinoshita ,  Sumitomo Hospital ; and  Masashi Yamamoto ,  Kobe University Hospital ; and  Jean-Francois Emile, Universitede Versailles Saint-Quentin. The work is supported by the  Japanese Study Group on GIST and The Research Group for Rare Neoplasms of Japan.
Motivation In the last 30 years, data assimilation techniques have become very popular in geophysics. They aim to combine in an optimal way, through priors on the involved errors, different kinds of information in order to provide an accurate estimate of the geophysical state. Because of the complexity to describe accurately the dynamic of the ocean or the atmosphere, mathematical models are in practice idealised and simplified representations of the reality. Observations are then necessary to monitor the evolution of these geophysical states. Observations used in operational systems historically come from synoptic data. Those data are collected by stations, aircrafts, radiosounding, balloons, and drifters. The distribution of such observations is sparse and heterogeneous both in space and time.
Bijective transformations. In this paragraph the whole dataset is used, possibly after a change of variable (Pixels, Fourier, Wavelet, Curvelet). Table  3  presents the RMSE ratio of the zonal component of the velocity with respect to the SNR. The following remarks can be stated: (1) We can first see that the pixel distance combined with a diagonal matrix performs poorly, even with a small noise level, and even more so with a large one. In that case, ignoring the error correlations is severely detrimental to the analysis. (2) On the contrary, using a diagonal error covariance matrix in combination with a change of space reintroduces information about the noise correlation, allowing for much better results and an increased robustness to the noise level, as we can see with the curvelets, Daubechies wavelets, and Fourier.
However, when we compare these to Table  3  we can see that thresholding has a small negative impact on the analysis, particularly for the Daubechies wavelets. This approach may still be useful in case the dataset is too large to be handled efficiently by the data assimilation system. 5. 4. 3. Rate of convergence. Figure  6  shows the behaviour of the cost function (left) during the minimisation and the associated analysis RMS error (right) for three selected experiments (Pix(Scalar, D 8 (Diag and C(Diag). The convergence rate is higher in the pixel space than in a wavelet or curvelet space (left panel). However, the minimum reached at convergence is better in the wavelet or curvelet space (right panel). For those experiments, the RMSE decrease rate is the same in the pixel space and wavelet space.
Skeletal muscle samples were fixed by immersion in 2. 5% glutaraldehyde and 2. 5% paraformaldehyde in cacodylate buffer (0. 1 M, pH 7. 4) and washed in cacodylate buffer for 30 min and kept at 4 °C. Post-fixation was performed with 1% osmium tetraoxide in 0. 1 M cacodylate buffer for 1 h at 4 °C and dehydration through graded alcohol (50, 70, 90 and 100%) and propylene oxide for 30 min each. Samples were oriented longitudinally and embedded in Epon 812. Ultrathin sections were cut at 70 nm and contrasted with uranyl acetate and lead citrate, and examined at 70 kv with a Morgagni 268D electron microscope. Images were captured digitally by a Mega View III camera (Soft Imaging System). Mitochondria density and cross-section area were determined from the electron micrographs using ImageJ software.