dataesr/scientific-paragraphs-categorization huggingface dataset:
1% Tween (TBS-T) with 1% milk overnight at 4 ∘ C, and then rinsed 3 × 10 min each with PBS-T. The sample membrane was incubated in alkaline phosphatase-conjugated secondary antibody (diluted 1/1000) and the protein was detected using Bio-Rad immun-Star chemiluminescence kit. Film exposed to the chemiluminescent signal was digitized using a light box and Pixera Pro150ES digital camera connected to a Power Macintosh. The optical density of the images was calibrated using a photographic calibration step tablet (Kodak) so that data is collected in the linear range of the O. D. The relative density of the labeled protein bands was determined using densitometric measurements with ImageJ. In all studies, once data from the antigen of interest had been collected, the membrane was stripped and labeled for total protein with India ink as a loading control.
). To decrease variations in background illumination, images of both the sections and adjacent blank areas of slide were photographed. The background images were subtracted from the section images using MatLab. Because of the large number of sections to analyze in each histochemical experiment, digital images were collected over three consecutive days. To calibrate for any potential differences between images taken in different sessions (e. g. , changes in light levels), the change in average density of a selected section that was imaged all three days was subtracted from the respective day. Using ImageJ, a systematic random set of points was selected to measure optical densities. The density for the molecular layer and granular cell layers was averaged for each brain from measurements of two sections per brain per experiment.
Acknowledgments This work was supported by  NIH  Grant  NS 34309  to  Michael W. Vogel. The authors would like to thank  Dr. Adam Puche  for his assistance with the acquisition and analysis of microscopy data. The authors also thank  Carol Armstrong ,  Michisuke Yuzaki , and  Jun Nishiyama  for their helpful comments in the preparation of the paper. This paper was prepared while MWV was employed at the  University of Maryland School of Medicine. The opinions expressed in this paper are the author's own and do not reflect the view of the  National Institutes of Health , the  Department of Health and Human Services , or the  United States government.
ACKNOWLEDGMENTS Luca Costa  acknowledges  COST Action TD 1002. Mario S. Rodrigues  acknowledges financial support from  Fundação para a Ciência e Tecnologia   SFRH/BPD/69201/2010. This work was performed at the  Surface Science Laboratory  of the  ESRF  and at the  PSB laboratories in the Carl-Ivar Brändén building in Grenoble.
75 μL of each primer (reverse and forward at 0. 5 μM, Table  1 ) and 2 μL of cDNA. The results were normalized with the ribosomal protein L13a, a housekeeping gene already validated in the seabass. 15 he data were expressed as the mean±standard deviation. Differences between control and groups of fish exposed to 4-NP were evaluated by t-test (P≤0. 05). The calculations were performed using Statgraphics Centurion XV software (StatPoint, Inc. , http://www. statgraphics. com/).
Recombinant protein purification and adsorption Recombinant full-length TNX (from Gly 23 to Gly 4,135 residues according to the GenBank reference NM_174703) and its variants, the TNXEF fragment (consisting of FNIII modules only, from Gly 745 to Thr 3,910 residues) and the FBG domain (C-terminal FBG domain, from Gly 3,911 to Gly 4,135 residues), were produced in stably transfected HEK-293 cells using the pSec-Tag2/hygromycin expression vector (Invitrogen) and purified as described previously  (Lethias et al. , 2001 (Lethias et al. , , 2006)). In brief, recombinant proteins were purified from the conditioned medium by means of two chromatographic steps. The first chromatography was performed on heparin-Sepharose (GE Healthcare) for full-length TNX and TNXEF or on a nickel-chelating column (Ni-nitrilotriacetic acid agarose; QIAGEN) for the FBG domain.
Nonspecific interaction sites were saturated with 1% (wt/vol) BSA for 1 h at 37°C. Cells were seeded onto immobilized recombinant TNX fragments after three washes of the substrates with sterile PBS. In this study, the noncoated condition means that the cell culture support was incubated in the presence of vehicle (PBS) instead of recombinant protein. The cDNA encoding the inserted (I) domain of 11 integrin chain (from Gln 160 to Asn 358 residues according to the GenBank reference NM_ 001004439) was generated by PCR using the PrimeSTAR HS DNA Polymerase (Takara Bio Inc. ) and the following forward, 5-CGCG-GATCCCAGACCTACATGGACATCGTC-3, and reverse, 5-CCCAAGCTTT-CAGTTCTTGTTGGTGCCTTC-3, oligonucleotides. Inserts were cloned into a derivative of the pGEX-KT vector (GE Healthcare) between the BamHI and HindIII sites to generate recombinant GST fusion protein of 11-I.
, 2010). In some assays, collagen was denaturated by heating the solution for 30 min at 95°C before being added to the wells. Wells were then saturated with T-PBS-BSA (0. 1% Tween and 1% BSA in PBS) for 2 h and incubated for a further 2 h with purified recombinant GST or GST-11-I (1 µM) diluted in T-PBS-BSA in the presence of 2 mM MgCl 2. Wells were rinsed with T-PBS (0. 1% Tween in PBS), incubated for 1 h with an anti-GST antibody diluted 1:500 in T-PBS-BSA. Bound antibodies were further revealed with anti-rabbit IgG antibody conjugated to peroxidase (Dako) for 30 min. After a final series of washes, bound peroxidase was detected with H 2 O 2 and 2,2'azinobis(3-ethylbenthiazoline-6-sulfonic acid), and the absorbance was read at 405 nm. Each data point represents the mean of triplicate determinations for GST-11-I, corrected for GST alone values, and interaction data are presented as bar plots of mean values ± SD.
BSA was used as a negative control. Quantitative real-time RT-PCR Total RNA was extracted from NMuMG cells with the RNeasy kit (QIA-GEN) and digested with DNase I (RQ1 RNase-free DNase; Promega) to remove any contaminating genomic DNA. Reverse transcription was performed with 1 µg RNA and 12. 5 ng/µl anchored oligo-dT 23 primer (5-dT 23 VVV-3, in which V represents an A, C, or G nucleotide) in the presence of 200 U of a reverse transcriptase kit (SuperScript II; Invitrogen). Quantitative real-time PCR reactions were performed from a dilution (1:10) of cDNA solution in a PCR detection system (iCycler iQ; Bio-Rad Laboratories) and with specific primers designed according to sequences available in databanks or published by other authors (Table  1 ). Gene expression levels protein G-Sepharose (GE Healthcare) at 4°C for 1 h.
, 2006 5-ACGACTTGTTGTGGCCATTTC-3 () Snail1 (Snai1) 5-CCACTGCAACCGTGCTTTT-3 (+) 66 58 40 Thuault et al. , 2008 5-CACATCCGAGTGGGTTTGG-3 () Zeb1 5-ACAAGACACCGCCGTCATTT-3 (+) 120 58 40 Thuault et al. , 2008 5-GCAGGTGAGCAACTGGGAAA-3 () Gapdh 5-TGTGTCCGTCGTGGATCTGA-3 (+) 76 58 40 Valcourt et al. , 2007 5-CCTGCTTCACCACCTTCTTGA-3 () Accession numbers were obtained from GenBank.
In fact, sequence analysis suggested that family A GPCRs share the same arrangement, showing a high sequence similarity of the seven transmembrane helices, confirming the suitability of rhodopsin as a template  (Li et al. , 2010). During the last decade, we have seen a dramatic improvement in crystallization methods. Indeed, after about 7 years from the first solved structure of a mammalian GPCR, several three-dimensional structures have been published. The second crystallized GPCR was β 2 -adrenergic receptor (β 2 AR;  Cherezov et al. , 2007; Rasmussen et al. , 2007)  and then the β 1 AR  (Warne et al. , 2008). Subsequently, an exponential growth of crystallized GPCR structures in the protein data bank was observed. Actually, the three dimensional structures available of class A GPCRs comprise: the adenosine A 2A receptor  (Jaakola et al.
Vilar et al. (2010)  evaluated the applicability of ligand-based and structure-based models to quantitative affinity predictions and virtual screening for ligands of the β 2 AR. The crystal structure of β 2 AR has been used by  Kolb et al. (2009)  to investigate the advantages and limitations of the structure-based approach in ligand discovery. The authors docked about 1,000,000 commercially available compounds against the β 2 AR structure. Twenty five hits have been selected and submitted to biological evaluation. Six compounds were active with binding affinities <4 μM, with the best molecule that showed a Ki of 9 nM. Moreover, five of these molecules have been found as inverse agonists  (Kolb et al. , 2009). Sabio et al. (2008)  and  Topiol and Sabio (2008)  performed a high-throughput docking with proprietary and commercial databases to investigate the usefulness of crystal structure for discovery of novel chemical classes acting as β 2 AR inhibitors.
These findings were further validated using X-ray structures of β 2 AR/Timolol  (Hanson et al. , 2008) , via in silico high-throughput docking of proprietary and commercial databases. This study resulted in the identification of ligands with relevant affinity for β 2 AR  (Sabio et al. , 2008; Topiol and Sabio, 2008). More recently,  Weiss et al. (2013)  reported a prospective, large library virtual screen of 3. 4 million molecules, yielding four full agonists and two partial agonists. The exploration of features that confer selectivity to the designed compounds has also been investigated by  Xing et al. (2009). The authors developed a selective pharmacophore model based on a series of selective β 2 AR agonists, presenting the first study using a ligand-based computational approach to generate specific three-dimensional pharmacophore hypotheses for the β 2 AR from its selective agonists.
Endothelin receptors In mammals, endothelins (ETs) are potent regulators of vessel functions involved in the pathophysiology of cancer, congestive heart failure, cardiovascular, proteinuria, and glomerulosclerosis. These peptides (ET 1-3 ) exert their biological effects via activation of four ET receptors, ET A , ET B1 , ET B2 , and ET C. Activation of the ET A receptor is associated with pronounced vasoconstriction whereas ET B receptor occupation is linked to vasodilation. In addition, other subtypes of the ET B receptor exist, one mediating vasodilation (ET B1 ) and the other eliciting constriction (ET B2 ). An additional receptor subtype, ET C , has been identified although its physiological significance is uncertain  (Pollock et al. , 1995 ) Funk et al. (2004)  applied a pharmacophore model of endothelin-A (ET A ) selective receptor antagonists for screening a chemical database and identified two structurally novel lead compounds with satisfactory affinity for ET A receptor.
IV. CONCLUSIONS In many experimental situations diffusion constants are determined by a linear fit of an experimentally generated MSD curve. In general Brownian particles are subjected to external forces and this extra drift means that they do not behave as pure Brownian motion. The effect of interaction means that the average MSD only becomes proportional to t at late times. In this region the diffusion constant can be extracted via a fitting procedure, for instance a linear fit (which may not necessarily be the best way to fit such data  [15, 16] ) will yield a slope proportional to 2κ e and also a constant 2C where it intercepts the vertical axis. If the particle is Brownian in an external conservative force field, we have shown that this constant must be positive and in one dimension we have found an analytical expression for it.
A shift in the temperature observed to obtain the same characteristic was explained as a change in heat sinking of the cables rather than a physical change of the device  [9]. Apart from the prototype production and electronic testing of these micro-calorimeters, work performed so far has involved Monte Carlo particle transport simulations and heat transfer simulations. The former is performed using Geant4 to aid the design of the prototypes  [9]  and will play an essential role in deriving microdosimetric spectra from the measured signal distributions. For the heat transfer simulations finite element calculations using Comsol Multiphysics software were executed to characterise the temperature equilibration within the absorber and heat losses to the silicon substrate  [11]. To validate the operation of the micro-calorimeters and, in the future, to investigate the assumption made in ionisation-based microdosimeters that there is a proportionality between ionisation and energy deposition, comparisons will be performed with a silicon-microtelescope  [12, 13]  and a mini-TEPC  [14]  that both have been tested extensively in proton beams  [15, 16].
Results of work package 2 will contribute to this validation by giving information about the microdosimetric spectra of the radiations in coincidence with the ionisation clusters size produced at nanometric scale. The simulation of both, the physical and the chemical stage of the irradiation are needed in the model in order to account for total (direct and indirect) early effects on DNA. Starting from the simulation of the chemical stage available in the Geant4-DNA package, results on the spatial distribution of radiation-induced radicals obtained in work package 3 will be included to improve this model. All the aforementioned data and simulation tools are used in this work package to simulate (at nanometric scale) the microbeam irradiations being performed in work package 4. The initial objective is to identify and determine the parameters in the simulation that are significant for a correlation to the experimental Ȗ-H2AX results.
Acknowledged complications with gavage The issues we have raised here are largely but not completely unacknowledged in the literature and are compounded by other issues also widely recognized. For example, a common complication with gavage involves perforation of the esophagus or stomach  [41]. Additional complications involve the accidental introduction of fluids into the trachea or lungs, asphyxia, inflammation, weight loss, hemorrhage, and reflux  [41, 50]. Other studies report high frequencies of morbidity and mortality due to the use of gavage; several report rates greater than 50%  [38]. Numerous factors can influence the success of gavage, including the level of experience of the technician, size and type of probe used, volume administered, repetitive dosing and vehicle used  [42]. Because of the relatively high frequency of gavage-related complications and the need for highly trained animal care staff, some animal welfare groups propose that alternative dosing methods be used whenever possible  [6].
Array-CGH Array-CGH was performed using a 180 K whole-genome platform (design 22060, Agilent Technologies, Santa Clara, USA), with an average spacing of 18 Kb between probes. Scanned images of the arrays were processed and analyzed using Feature Extraction software and Genomic Workbench software (both from Agilent Technologies), together with the statistical algorithm ADM-2, and using a sensitivity threshold of 6. 7. We applied a 'loop design' in our hybridizations as previously described  [19] , resulting in two reverse labeling hybridizations per sample. Alterations had to encompass at least three consecutive probes with aberrant log 2 values to be called by the software, and those not detected in both dye-swap experiments were excluded from the analysis.
Analysis The detected copy number variations were compared to CNVs reported in the Database of Genomic Variants (DGV; http://dgv. tcag. ca/dgv/app/home; freeze December, 2011). We arbitrarily classified CNVs into "rare" and "common" by considering as "rare" those CNVs encompassing coding sequences and present in frequencies < 0. 1% in DGV, that does not exclude that some rare CNVs might contain smaller segments which can vary in copy number in the population. Mann-Whitney and Fisher-exact tests were used to compare patients and controls for frequency, gene density and size distribution of CNVs. Gene annotation was performed using the University of California Santa Cruz Genome Browser (UCSC) and the Catalog of Somatic Mutations (COSMIC; http:// cancer. sanger. ac. uk/cancergenome/projects/cosmic/).
To avoid any experimental bias, we next addressed the question whether SDC-4 construct overexpression could lead to a saturation of heparan sulfate chain biosynthesis enzymes, and therefore to lower sulfated heparan sulfate chains. The degree of sulfatation of syndecan-4 glycosaminoglycan chains is essential for the binding of RANTES/CCL5  (Gandhi and Mancera, 2008). Heparan sulfate chains present at the cell surface were increased by the SDC-4 overexpression as assessed by flow cytometry using specific antiheparan sulfate antibodies (Fig. 1F ). Moreover, the levels of heparan sulfate chains were similar whatever the SDC-4 variant overexpressed (data not shown). As assessed by real-time RT-PCR, the levels of mRNA encoding for EXT1 and EXT2, which are involved in the first step of heparan sulfate chain biosynthesis, were unaffected by SDC-4 overexpression (data not shown).
2 ) cells versus 41164 in SDC4L188QQ-GFP cells stimulated by RANTES/CCL5 or 34969 in unstimulated SDC4A198del-GFP (PDZ 2 ) cells versus 410610 in SDC4A198del-GFP cells stimulated by RANTES/CCL5 (Fig. 2A ). These results were confirmed by a migration wound healing assay and an invasion transwell assay (data not shown). Cell migration involves formation of a leading edge in the direction of migration and adhesion points from which tension is generated to move the cell body forward. Disassembly of adhesion points occurs at the back of the cell, a region known as the trailing edge. In order to analyze the morphology of the SDC-4 transfected-cells, live fluorescent microscopy was carried out. This technique enables the visualization of only one cell per observation field and was repeated six times.
, 2014). Upon Go ¨6976 cell treatment, endothelial cell migration and vascular tube formation induced by RANTES/CCL5 were largely decreased in SDC4WT-transfected cells as compared to SDC4WT-transfected cells in the absence of inhibitor (Fig. 4B, C ). These data were confirmed and even more pronounced after PKCa inhibition by the transfection with a dominant negative PKCa plasmid. Strikingly, in the absence of RANTES/CCL5 stimulation, endothelial cell migration was increased upon Go ¨6976 cell treatment, conversely to HUV-EC-C vascular sprout length. Finally, endothelial cells were co-transfected with SDC4WT-GFP or the SDC4-GFP mutants and with a Ds-red PKCa and their localization was visualized with a confocal microscope. The low red signal associated with PKCa and the high green signal due to the intracellular accumulation of SDC4WT-GFP do not allow the precise quantification of co-localized signals.
Rac1-GTP activity was determined by pull down assay and analyzed using specific Rac1-GTP antibodies by western blot. Scale bars: 10 mm. Rac1 activation depends on the suppression of RhoG by a SDC4synectin-RhoGDI1 complex and activation via PKCa  (Elfenbein et al. , 2009). Syntenin, the first-described syndecan-binding partner, binds also to SDC-4, leading to a regulation of integrin recycling  (Morgan et al. , 2013). The identification and the precise role of PDZ proteins interacting with SDC-4 in RANTES/CCL5 activities are actually unknown. In summary, our data demonstrate that SDC-4 is a typical coreceptor for the chemokine RANTES/CCL5 and that the interaction of both partners leads to activation of PKCa through the intracellular domain of SDC-4. Regarding the multiple role of RANTES/CCL5 in various pathologies, including cancer, viral diseases and inflammation, deciphering the mechanism by which RANTES/CCL5 exerts its biological activities is a preliminary step to develop new therapeutic strategy, for example by targeting the binding of the chemokine to its proteoglycan receptor.
Cell spreading Transfected cells, incubated for 2 hours with or without RANTES/CCL5 were stained with Alexa Fluor 568-phalloidin (1:200, Invitrogen) and observed with a fluorescence microscope (Zeiss, AXIOPHOT, N˚/ MicMac, Le Pecq, France) as previously described  (Charni et al. , 2009). Ten fields of stained cells were photographed and cell areas were evaluated on 40 cells with Scion Imager (Scion Image Software and National Institutes of Health, Release Beta 3b Software).
2D-angiogenesis For 2D angiogenesis assay, 1. 5610 4 transfected cells were seeded on Matrigel-coated 8 wells Labtek for 24 hours with or without RANTES/ CCL5 pre-incubated or not for 2 hours with Go ¨6976, a specific PKC inhibitor  (Suffee et al. , 2012). Cells were fixed, stained with Crystal Violet (Sigma-Aldrich) and photographed under phase contrast microscope (Olympus CK40, Rungis, France). The length of 30 vascular sprouts was evaluated using Scion Imager (Scion Imager Software).
Molecular characterization, performed by the French National Reference Centre for Staphylococci, using DNA microarray (Alere StaphyType DNA microarray; Alere Technologies GmbH, Jena, Germany), highlighted that the strain has an agr allele type 4, and was assigned to clonal complex CC121  [4]  (MLST ST 121). Data confirmed that the strain harboured PVL genes but also genes encoding enterotoxins B, K and Q and the egc cluster. Treatment with fosfomycin and ofloxacin was started at admission (D0) without need for surgery. Apyrexia was obtained within 48 hours and the inflammatory syndrome improved. An echocardiography ruled out endocarditis. The antibiotic therapy lasted six weeks and was changed at D16 for oral rifampicin and ofloxacin. On the same day, control MRI showed a decline of the perirectal infiltration and a disappearance of the collection in the left side of the prostate (Figure  3 ).
Analysis Images were acquired with a laser scanning confocal microscope (Olympus IX 81, Olympus, Tokyo, Japan) equipped with a 20× or 40× objective, or with an epifluorescence microscope (Leica DM5500 B, Leica). Quantifications following in vivo electroporations are based on an average cell count of 254 successfully transfected cells per animal (n ≥5). Each animal represented 1 'n' number. Morphological criteria to define RGCs were bipolar morphology and apical connection to the LV lumen. Morphological criteria to define non-RGCs were absence of apical and basal processes (i. e. , roundish appearance), and absence of contact to the LV lumen  [31, 32]. All data are expressed as mean and standard error of the mean (±SEM). P values were determined using unpaired t-test or two-way ANOVA followed by Dunnett's post hoc test (GraphPad Prism v5 software, San Diego, CA, USA).
Acknowledgements BF, KA, and AHC were supported by a National Research Project grant ( NRP63 ;  406340_128291 ) and by a research grant ( 31003A_127082 ) from the  Swiss National Fund. MF and SR were supported by a grant from the  Swiss National Fund  ( 31003A_127082 ) and by the  NCCR  project  1 , respectively. KA and AHC were also supported by personal grants from the  Forschungskredit  ( K-41211-01-01 ) of the  University of Zurich  or from the  Mexican Government (CONACYT) , respectively.
Data quantitation Cell numbers were counted using confocal ×40 and ×63 photomicrographs. For histologically normal tissues at two months, the percentage of YFP + cells (labeled "Nor" in Figures  2Y-A' , S1G, and "Cont" in Figure  3Q ) represents the ratio of YFP + cells to total basal or luminal cells. For tumor tissues at later ages, the percentage of YFP + cells (labeled "Tum" in Figures  2Y-A' , S1G, and "T+E2" in Figure  3Q ) represents the ratio of clustered YFP + cells in tumor lesions to total epithelial cells within these lesions. Statistical analyses were performed using a two-sample t-test. At least three animals for each experiment or genotype were analyzed.