dataesr/scientific-paragraphs-categorization huggingface dataset:
7, to generate ASCII files containing m/z values and signal intensities after calibration, smoothing, and deisotoping function. For each m/z value, the peak intensities of the four acquired spectra per sample were averaged prior to further analysis. The processing method was chosen to filter peaks based on the signal-to-noise (S/N) ratio using an S/N ratio threshold of 3. Furthermore, the processing method took into account isotopic distributions to recalculate S/N ratios in order to finally eliminate those under 10. The mass lists and their corresponding peak intensities (raw data) are given in supplemental Table  S1. GlycoWorkBench, version 2. 0 alpha, from EUROcarbDB  (30) , which encloses the GlycomeDB database for carbohydrate structures (35,873 unique carbohydrate sequences)  (31) , was used to establish our own glycan database from mouse samples, to annotate MALDI-MS and MALDI-MS/MS spectra, and to propose putative glycan structures.
Thirty-nine different ions were finally selected as possible glycan species according to the following criteria: good reproducibility of the signal between the four acquired spectra per sample and between samples (absence or few null values), the presence of a probable corresponding structure in the EUROcarbDB database, S/N ratios over 10, and confirmation of the putative structure via MALDI-TOF/TOF tandem mass spectrometry. Annotated MALDI-MS/MS spectra are displayed in supplemental Fig. S1. Each monoisotopic signal was assigned to a monosaccharide composition and further classified in different families: high mannose, complex, hybrids, and N-acetylhexosamine-ended species. Complex-type Nglycans were then subdivided into several subfamilies for evaluation of antennary rate and terminal glycosylation  (21).
The relative proportion (percent intensity) of each structure or family was calculated as (intensity ϫ 100)/(sum of intensities). Supplemental Table  S2  displays all MALDI-TOF-MS signal intensities and percent intensities for each m/z value of our glycan database and for each acquisition. Normality and equal variance were assessed with percentage intensity data prior to the use of one-way ANOVA to compare the four series of data for each structure or family. The one-way ANOVA on ranks (Kruskal-Wallis) test was used in cases when the normality or the equal variance test failed. All pairwise multiple comparison procedures (Tukey's test and Dunn's method) were used, respectively, only when ANOVA or ANOVA on ranks p values were less than 0. 05. All statistical tests were performed with SigmaPlot software, version 11, and are presented in supplemental Tables  S3  and S4.
Quantitative PCR was carried out using the ABI PRISM 7900 sequence detection system, and the results were normalized to the housekeeping genes GAPDH or 18S. Relative mRNA levels were quantified using the ⌬⌬CT method. Data are presented as mean Ϯ S. E. and are expressed relative to the corresponding control (non-irradiated) sample values. Student's t test, or the Mann-Whitney test when the normality or the equal variance test failed, was used to compare values with SigmaPlot software, version 11 (supplemental Table  S6 ). For all analyses, a p value Ͻ 0. 05 was taken as significant. Multiplexed Cytokine Analysis-Cytokine concentrations in the serum were assayed using a mouse magnetic 3-plex cytokine kit (Bio-Rad) (8 mice per dose and per time point post-irradiation). The kit can simultaneously quantify three mouse cytokines and chemokines: IL-1␤, IL-6, and TNF␣.
The assay was performed according to the manufacturer's protocol. After preparation, samples were processed (50 beads per bead set in 50-l sample size) on a Bio-Plex 200 instrument (Bio-Rad). All the samples were run in duplicate. The data were analyzed using Bio-Plex Manager 6. 0 software. For each assay, a standard curve was generated for detection from 3. 14 pg/ml to 51,408 pg/ml (IL-1␤), 1. 34 pg/ml to 21,960 pg/ml (IL-6), and 2. 73 pg/ml to 44,662 pg/ml (TNF␣). Data are presented as mean Ϯ S. E. Student's t test, or the Mann-Whitney test in the case when the normality or the equal variance test failed, was used to compare values with the SigmaPlot software, version 11. For all analyses, a p value Ͻ 0. 05 was taken as significant.
3 ). In this case, we observed that some spot trains-for instance, the one presented in Figs. 3B-3E , which was identified as contrapsin (serpina 3K) via mass spectrometry fingerprinting in our previous study  (16) -were made up of four dominant colors: red, pink (a mixture of blue and red), white (a mixture of blue, red, and green), and green, from acidic pH to basic pH. This result confirmed the changes we observed between two samples (control and irradiated individuals, Fig. 2 ). Mean relative quantities of the different spots of the contrapsin spot train were evaluated using Progenesis SameSpots software, demonstrating that the more acidic spot increased with the dose of irradiation, whereas the more basic spot decreased (Figs. 3F  and 3G ). Interestingly, the treatment of serum samples with PNGase F markedly changed two-dimensional gel electrophoresis protein profiles whatever the dose of irradiation and allowed the complete disappearance of the contrapsin spot train presented in Fig.
Two-dimensional DIGE Analysis of Glycosylated and Deglycosylated Mouse Serum Proteins-In order to evaluate the contribution of glycan moieties to the discrimination of samples from control and irradiated mice, profiles of high-abundance-protein-depleted serum treated (or not) with PNGase F were compared using a two-dimensional DIGE approach. A total of 733 protein spots were detected in the reference gel, which was constituted by a merged image of all sham-irradiated, irradiated, non-treated, and PNGase F-treated samples. The contribution of glycans branched on protein cores was analyzed using PCA, which gave a simplified view of gel data in a two-parameter map. Firstly, PCA was performed using only proteins exhibiting a p value under 5% given by ANOVA of all groups of serum proteins not treated with PNGase F (Fig.
4A ). This allowed good clustering of animals in two main groups, as the first principal component (PC1) explained about 66% of data variability: controls and animals irradiated at 20 Gy, and animals irradiated at 40 Gy and 80 Gy. Analysis of profiles of serum proteins deglycosylated with PNGase F allowed the selection of 74 proteins assumed to be N-glycosylated because their spot volumes turned null after the treatment. Once again, PCA for these 74 proteins allowed good clustering of two main groups, as PC1 explained 68% of the observed variability: controls and animals irradiated at 20 Gy, and animals irradiated at 40 and 80 Gy (Fig. 4B ). In order to evaluate the contribution of proteins that were not affected by the PNGase F digestion in terms of electrophoretic mobility (i. e. thought to be non-N-glycosylated), we then performed PCA using only protein spots whose volumes did not change after the PNGase F treatment.
We used a comparative glycomic approach that allowed quantitative distinction between the glycan structures derived from whole (non-depleted) sera of control animals and animals irradiated at 20, 40, and 80 Gy (n ϭ 7 or 8 per group). Profiles of permethylated glycans derived from 25 l of raw serum were recorded for the m/z range of 1500 -5000 Da using MALDI-MS (seven or eight biological replicates, two technical replicates per biological replicate, and two spectrum acquisitions per technical replicate) (supplemental Tables  S1  and S2 ). Thirty-nine different ions were finally selected as possible glycan species according to the following criteria: good reproducibility of the signal between the four acquired spectra per sample and between samples (absence or few null values), the presence of a probable corresponding structure in the EUROcarbDB database, S/N ratios over 10, and confirmation of the putative structure via MALDI-TOF/TOF tandem mass spectrometry that allowed composition assignment of the different glycans and classification in different families (supplemental Fig.
S1 ). For instance, some ions were actually not considered in the study because they were unlikely to be N-glycan structures, or because their intensities were too variable between the four acquired spectra per sample. The 39 structures are listed in Table  I , which also displays putative schematic structures determined after MS/MS analysis by MALDI-TOF-TOF and using GlycoWork-Bench software. The presented putative structures were determined on the basis of composition, biosynthetic pathway knowledge, and MS/MS fragmentations. However, MALDI-MS/MS was not able to differentiate isomers. For convenience, only one branching pattern for triantennary structures and one branching pattern for hybrid structures are shown. N-acetyl and N-glycolylneuraminic acids were observed in serum samples from mice.
Profiles of control samples generally appeared as different from those of 80-Gy samples, whereas profiles from 20-Gy and 40-Gy samples were mostly transient between the two conditions. No structure was found to be unique and specific to a particular dose of irradiation. Among these structures, 20 species contained an N-glycolylneuraminic acid residue, 2 species contained an N-acetylneuraminic acid residue, and only 1 species contained both structures. PCA of Measured MALDI-TOF Spectra-PCA was used as a descriptive approach in order to describe the glycomic dataset with exploratory statistics in response to irradiation (Fig. 6 ). It gave a simplified view of spectrum data in a twocomponent map for the control and irradiated samples. The data were analyzed either as a set of individual glycan structures (Fig.
In the present study, a proteomic analysis utilizing twodimensional DIGE of the serum of a man irradiated by accident who was developing CRS at the time of blood collection  (7)  gave us the opportunity to observe similar shifts in the pI of human serum proteins during CRS. Observed in both humans and mice, these alterations might be of importance in the response to ionizing radiation. Because the first dimension of the procedure (isoelectric focusing) is exquisitely sensitive to molecular charge variations in sialic acid content  (28) , we investigated post-translational modification changes such as glycosylation in mouse after irradiation at 20, 40, and 80 Gy in the course of the development of CRS 14 days post-irradiation. Using exploratory statistics (PCA), comparisons of native and PNGase F-digested serum proteins via two-dimensional DIGE suggested that the large variations observed in the proteomic dataset between control and irradiated animals were mostly explained by glycosylated proteins.
Acknowledgments-We thank  Dr. Anne-Sophie Vercoutter-Edouart  ( UGSF, Lille ) and  Dr. David Marsh  for correcting the manuscript. We are also grateful to  Dr. Anne Harduin-Lepers  ( UGSF, Lille ) for her expertise and advice on glycosyltransferase genes and to  Dr. Yann Guerardel  ( UGSF, Lille ) for his help in MS/MS spectra interpretations. * The research leading to these results has received funding from  Electricitede France  ( Groupe Gestion Projet -Radioprotection ) and from the  European Union 's  Seventh Framework Programme  ( FP7/ 2007-2013 ) under Grant Agreement No. 241536.
Experimental protocol During the first visit, participants' stature and body mass were recorded followed by a submaximal fitness test based on the Åstrand-Rhyming method  (ACSM, 2006). The test comprised of four progressive exercise stages on a treadmill (h/p/cosmos mercury 4. 0 h/p/cosmos sports and medical gmbh, Nussdorf, Traunstein, Germany) each lasting 5 minutes. Heart rate (Polar Electro Oy, Kemple, Finland) was recorded during the last minute of each stage. Estimation of VO 2max was based upon the linear relationship between heart rate and work rate based upon treadmill speed and angle  (Epstein et al. 1987)  and data extrapolated to their age predicted heart rate max. For the main tests, pre and post-test nude mass were recorded. Participants self-inserted a rectal thermistor (Grant Instrument Ltd, Cambridge, UK) 10 cm beyond the anal sphincter.
Data analysis Statistical analysis was conducted using Statistical Package (SPSS) version 18. 0. Analysis of the main effect of condition, location and time were analysed using three-way repeated measures ANOVA. Post hoc comparisons using Bonferroni correction were performed to analyse individual differences. In some instances, differences between conditions were analysed using Paired samples ttest and corrected for multiple comparisons. Pearson's correlation analysis was performed to assess the relationship between local thermal comfort and each physiological parameter (w local, ΔGSC, T sk and T c ). Where data were observed to have non-linear relations (scatterplots), they were first transformed using appropriate transformations to produce an approximate linear relationship and subsequently they were analysed with the standard linear Pearson correlation to assess the relationship.
Optically selected sample Galaxies belonging to the Coma supercluster, which lies at a mean distance of 100 Mpc, have apparent radii small enough that their SDSS images are only little affected by the "shredding" of large galaxies into multiple pieces, which leads to wrong magnitude determinations 2   (Blanton et al. 2005a,b,c). Hence a reliable optically selected sample can be extracted from the SDSS spectroscopic database following the criteria described in  Gavazzi et al. (2010 Gavazzi et al. ( , 2011) )  which we only briefly summarize here. We searched the SDSS DR7 spectroscopic database  (Abazajian et al. 2009)  in regions 1 and 2 (see Figure  1 ) for all galaxies with   (Haynes et al. 2011). In both regions only galaxies in the interval 3900 < cz < 9500 km s -1 are considered. Sample 1 includes 5026 galaxies of all morphological types optically selected from SDSS (small black dots) in the union of regions 1+2.
A. =195), with increasing velocity toward the Hercules supercluster (R. A. = 240). r ≤17. 77 mag, which matches the selection criterion of the SDSS spectral catalog  (Strauss et al. 2002) , in the redshift interval 3900 < cz < 9500 km s -1. We obtained 4790 targets. For each, we extracted the coordinates, the u, g, r, i, z Petrosian magnitudes (AB system, not corrected for internal extinction), and the spectroscopic information, including the principal (nuclear) line intensities and the redshift. The morphological classification of all galaxies was performed by individual visual inspection of SDSS color images. To fill in the incompleteness of SDSS for luminous galaxies due to shredding and fiber conflict, we added 133 CGCG  (Zwicky et al. 1961 (Zwicky et al. -1968 ) galaxies with known redshifts from NED that were not included in the SDSS spectral database.
For these objects, we also took the u, g, r, i, z Petrosian magnitudes using the SDSS DR7 navigation tool, which provides accurate magnitudes. Additional galaxies that could not be found in the SDSS spectroscopic catalog were searched for using NED. For these targets, we again evaluated the u, g, r, i, z magnitudes using the SDSS navigator, and of these we selected 76 objects that meet the condition r ≤ 17. 77 mag. We repeated a similar search in the ALFALFA database  (Haynes et al. 2011 ) in region 2, where we found 28 additional HI-selected systems with r ≤ 17. 77 mag, that were not included in the SDSS spectral database. In total, our optical sample consists of 5026 galaxies: 4790 from SDSS and 236 from other sources. Of the 5026, 2146 galaxies lie in region 2. The stellar mass was derived from the i magnitudes and gi color using the transformation log M * M ⊙ = -1.
G. G. acknowledges financial support from the Italian MIUR PRIN contract 200854ECE5. R. G. and M. P. H. are supported by US NSF grants AST-0607007 and AST-1107390 and by a Brinson Foundation grant. Support for M. F. was provided by NASA through Hubble Fellowship grant HF-51305. 01-A awarded by the Space Telescope Science Institute, which is operated by the Association of.
Acknowledgements. The authors would like to acknowledge the work of the entire ALFALFA collaboration team in observing, flagging, and extracting the catalog of galaxies used in this work and thank  Shan Huang  for providing original data. This research has made use of the GOLDmine database (Gavazzi et al. 2003) and of the NASA/IPAC Extragalactic Database (NED) which is operated by the  Jet Propulsion Laboratory, California Institute of Technology , under contract with the  National Aeronautics and Space Administration. We wish to thank the unknown referee whose criticism helped us to improve the manuscript. Funding for the  Sloan Digital Sky Survey (SDSS ) and SDSS-II has been provided by the  Alfred P. Sloan Foundation , the Participating Institutions, the  National Science Foundation , the  U.
Participants Participants were enrolled into an institutional review board-approved project with parents providing informed consent for participation. Over an 18-month period, 32 children and adults (18 males and 14 females) were seen. Referral sources included the Phelan-McDermid Syndrome Foundation, on-going research studies and word-of mouth. Patients ranged in age from 1. 6 to 45. 4 years (mean 8. 8, SD 9. 2). All patients were of Caucasian descent. Phenotypic data were available on all participants with rates of 90% to 100% completion on diagnostic, cognitive and clinical genetics evaluations. Half of the participants received structured neurological examinations by a neurologist, but all patients were assessed for neurologic abnormalities during the clinical genetics evaluation.
The mixture was first hybridized at 60°C for 16 h, followed by a ligation reaction; 5 μl of the ligation reaction product was used for PCR. PCR products were subjected to capillary electrophoresis on an ABI 3130 genetic analyzer (Applied Biosystems, Foster City, CA, USA). Raw traces from the electrophoresis were imported into GeneMarker software (SoftGenetics, State College, PA, USA) for MLPA analysis. After population normalization, data were compared with a synthetic control sample, which represents the median of all normal samples in the experiment. A threshold of dosage change <0. 75 was used to identify deletions, and a threshold >1. 30 was used to identify duplications. Twenty-nine samples were genotyped on Illumina Omni 2. 5-8 v1 array (Illumina, San Diego, CA, USA) containing a total of 2,379,855 markers.
Samples were processed according to the manufacturer's protocol and normalization and genotype calling were performed using Illumina Genome Studio software V2011. 1. All samples had an array call rate above 99%, SD for log R ratio values in the autosomes <0. 28 and SD for B allele frequency values <0. 06. Copy number variants (CNVs) were called using PennCNV algorithm  [43]. Fragmented CNVs were merged and the breakpoints were inspected by visual investigation of log R ratio and B allele frequency values within and in the vicinity of the called CNVs. The exact deletion breakpoints in the 22q13 region were confirmed using the moving average of the number of markers with B allele frequency between 0. 45 and 0. 55, in addition to the visual investigation of the PennCNV call. Genomic locations are based on GRCh37 (hg 19).
The ADI-R sample included 30 out of 32 participants. Two of the youngest participants (<25 months) were not administered the ADI-R as it has been shown to have strongest validity in individuals with chronological and mental ages over 18 months. Strict interpretation of the ADI-R indicates that 18 out of 30 participants (60%) met full criteria on the ADI-R. An additional 11 participants met criteria in two of three domains. Eight of these 11 participants had subthreshold scores on the repetitive behaviors domain (that is, 1 to 2 points below). Figure  2  presents the average scores of each domain and subdomain of the ADI-R. The data reflect deficits across No blood was available for participant SH27 or his parents so we present the findings of the clinical report, which used the Affymetrix 6.
Definition of neonatal death Neonatal death was defined as "a disease or injury which initiated the train of morbid events leading directly to death" within the first 28 days of life. The primary causes of neonatal death were broadly grouped under four major headings: (1) birth asphyxia, (2) sepsis (pneumonia, septicemia, and meningitis), (3) prematurity, and (4) other. Data were analyzed using STATA Statistical Software: Release 11 (StataCorp LP College Station, TX, USA). The median and range were used for quantitative variables that were not normally distributed, and mean and 95% confidence intervals (CI) were used for normally distributed variables. Categorical variables were tabulated using frequencies and percentages. The Chi-square test was used for testing the significance of associations between categorical variables.
Acknowledgements The authors thank  L. Lam  ( Department of Physiology, University of Toronto ) for her excellent technical assistance. This work was supported by  Canadian Institutes of Health Research  grant  MOP-69018  ( A. Giacca ). K. Koulajian was supported by scholarships from the  Banting and Best Diabetes Centre (University of Toronto ),  Ontario Graduate Scholarship  and  Ontario Graduate Scholarship for Science and Technology.
Fluorescent Microscopy Studies Cells were observed under MacroFluo Leica Z16 APO with PLANAPO 5. 09/ 0. 50 LWD objective and 9. 2 magnification (Leica, Germany). Exposure time was 10 ms (white light) and 1000 ms (fluorescent light). Cells were excited at 587 nm, fluorescence emission was read at 610 nm. Three images per condition were recorded. Images were analyzed with ImageJ software. The same brightness scale was set for all images in one experiment. Three-dimensional profiles of each single cell were obtained by the use of Interactive 3D Surface Plot Plugin to ImageJ software. Mean gray scale values were computed for each single cell in each fluorescent image separately and they were considered as equivalent of the fluorescent emission intensity of each single cell. Statistical analysis was performed with MAT-LAB 2011b (MathWorks).
Statistical distribution of mean gray values was described with box plots. One box was created for each condition (each value of electric field intensity). In each box, the central mark is median, the edges of the box are the 25 and 75th percentiles, the whiskers extend to the most extreme data points not considered outliers, and outliers are plotted individually (marked with crosses). Flow Cytometry Analysis Each sample was transferred to tube (Starlab, Switzerland) in ice and analyzed by flow cytometry (FACSCalibur, Becton-Dickinson) to determine the efficiency of electropermeabilization (the level of fluorescence associated with electropermeabilization). The samples were excited using the 488 nm line of an argon laser and detection of fluorescence was performed in FL-2 channel (for PI detection) or FL-3 channel (for Photofrin detection).
Acknowledgments JW and MBD would like to thank  Socrates-Erasmus Programme. This research was partially conducted in the framework of  COST Action   TD1104 ,  National Science Centre , Grant  2011/01/D/NZ4/01255 , and grant  219/2012  for BioNanopore Students Association from  Wroclaw University of Technology. The fluorescence measurements in Toulouse were done with the TRI core facility at the  IPBS (Genotoul, Toulouse, France) , which is supported by the  Association Recherche Cancer ,  Region Midi Pyrenees  and Grand Toulouse cluster. Open Access This article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution, and reproduction in any medium, provided the original author(s) and the source are credited.