dataesr/scientific-paragraphs-categorization huggingface dataset:
Functional assay As there were no correlations at the clinical level, we tested the effect of different mutations at the functional level by assaying whether Rab GTPase prenylation is affected differently    depending on the type of CHM mutation. To this end, we measured the levels of unprenylated Rabs in the fibroblasts of 6 patients carrying different classes of CHM mutations (deletion of the whole gene, nonsense mutations or deletion of a single exon). There was no REP-1 protein detectable in any of the patients' fibroblasts (data not shown). Consistently, all of the patients' fibroblasts presented significantly increased levels of unprenylated Rabs compared to control cells (ranging from 4-to 10-fold higher, p<0. 05). There were also significant differences in levels between the patients however this was not related to the genotype as the highest levels were present in one of the patients carrying a whole deletion of the gene and in a patient carrying a UAA nonsense mutation in exon 6 (Fig  3 ).
The research leading to these results has received funding from the following research grants:  Fondo de Investigación Sanitaria -FIS  ( PI:13/00226 ), the  Centre for Biomedical Network Research on Rare Diseases -CIBERER  ( 06/07/0036 ), the  Biobank of University Hospital Fundacion Jimenez Diaz Hospital  ( PT13/0010/0012 ),  ONCE ,  Swiss National Science Foundation  (Grant Number  31003A_156260 ), the  European Union Seventh Framework Programme  [ FP7-People-2012-ITN]  under grant agreement  317472  (EyeTN), the patient associations  France Choroideremia ,  Retina France  and the  Association Française contre les Myopathies. RSA is supported by  Sara Borrell   CD12/00676 , MC by Miguel Servet  CP13/03256  and  RPC by Fundación Conchita Rábago (FCR).
Ser39* Direct sequencing Spain Described 3 c. 141G>A p. Trp47* Direct sequencing Spain Described 6 c. 256C>T p. Gln76* Direct sequencing Spain Described 3 c. 339T>G p. Tyr103* Direct sequencing Spain Described 3 c. 745C>T p. Arg239* Direct sequencing Spain Described 3 c. 877C>T p. Arg293* Direct sequencing 1 Portugal; 1 Poland;2 Described 12 Spain c. 1048C>A p. Ser340* Direct sequencing Spain Described in our cohort 3 [10] c. 1272_1273invTC p. Gln425* Direct sequencing Spain This study 3 c. 1471G>T p. Glu491* Direct sequencing Spain Described 3 c. 1703T>A p. Leu568* Direct sequencing Spain This study 3 Missense c. 49G>T p. Gly17Cys Direct sequencing Belgium This study 3 b Translocation 46,X,t (X;4)(q21:p16) de novo translocation X;4 [t X;4] a Present on Human Gene Mutation Database (HGMD) or Locus specific database (LSDB).
Membranes were then washed with a TBS-0. 1 % Tween-20 solution (140 mM NaCl, 25 mM Tris/HCl pH 7. 5, and 0. 1 % Tween-20), blocked overnight with 5 % bovine serum albumin (BSA) in TBS-Tween-20 0. 1 %, and incubated with primary and secondary antibodies HRP conjugated. Finally, WBs were developed with an ECL chemo-luminescent reagent (Amersham Pharmacia Biotech, Piscataway, NJ, USA). Densitometric analysis of the immunoreactive bands was performed with the Gel Pro Analyzer 4. 0 software Media Cybernetics, Inc. For flow cytometry, 1 9 10 5 cells were used, which were recovered from culture dishes with a solution of 25 mM EDTA (ethylenediaminetetraacetic acid). The cells were washed twice with PBS and later incubated for 30 min with PBS-BSA 2 %, in order to block nonspecific binding sites. The cell were then washed with PBS and incubated for 1 h with the primary antibody (Abcam, ab85362) diluted in PBS-BSA 2 %, then washed twice with PBS, and incubated for 30 min with the secondary antibody.
Afterward, cells were again washed twice with PBS, and fixated in 2 % para-formaldehyde diluted in PBS. Samples were acquired on a FACSort (Becton-Dickinson) flow cytometer and analyzed using the WinMD program, version 2. 9. Analyses were performed on at least 10,000 events from the total population, and the percentage of cells expressing the target protein within this population was determined. All the data were corrected with autofluorescence controls and nonspecific antibody binding.
As for all interventional radiology procedures, 22 the parameters, corresponding to the applied irradiation and quantity of contrast agent required, were reported in each group. Thus, the total air kerma (AK) in milliGray (mGy), dose area product (DAP) in centiGray per square centimeters (cGyÁcm 2 ), fluoroscopy time in minutes, total radiation time in minutes, and amount of iodinated contrast agent in milliliters (mL) were reported. The radiation exposure data were measured automatically and uniformly by various systems. The AK corresponds to the kinetic energy deposited per unit mass, in mGy, and the DAP corresponds to the mean dose absorbed in air from the Xray beam cross-section, multiplied by the surface area of this section, in cGyÁcm 2. The number of catheters used was also noted. In addition, the general demographic data of the population, indication for coronary angiography, access site, number of CABGs to be looked for, and type of CABG for each patient were reported to allow comparison between the 2 groups.
All of these segmentations were performed before the coronary angiography procedure by a senior radiologist or a resident cardiologist. The reconstructed 3D images were then initially registered and overlaid over the real-time fluoroscopic images using a dedicated workstation and image fusion software (AW Workstation with Innova HeartVision; GE Healthcare). The first registration step consisted in aligning the sternotomy wires on both images, as well as the trachea and the vertebrae (Figure  1B ; Video S1). Once achieved, the aorta and CABG reconstructions were displayed, and the search for the latter could be initiated (Figure  2 ; Videos S2 through S4 are examples of 3D reconstruction merged with real-time fluoroscopic). 3D data sets could be displayed and manipulated both from the control room and from table side in the procedure room.
Statistical Analysis As a result of the absence of any published data on this topic, it was not possible to compute the number of subjects required for the study. Continuous data are expressed as median and interquartile range [Q1-Q3] or mean values and SD, and the nominal data as numbers (%). Continuous variables were analyzed with the Mann-Whitney test and the nominal variables were analyzed using the chi-square (v 2 ) test or Fisher's exact test. Our initial analysis compared the nominal variables (surgical approach, cardiologist's experience, and so on) and the continuous variables (age, total number of bypass grafts to be found, number of mammary bypasses to be found, and so on) in the 2 groups. The primary and secondary evaluation criteria were then compared between the 2 groups. Finally, the primary evaluation criteria were indexed according to the number of bypass grafts to be located in each of the 2 groups, in order to remain independent of any differences in terms of the number of bypasses to be located in each of the 2 groups.
(a) Structure of the bilobate amino-terminal domain of GluN1 (GluN1 NTD, PDB ID: 3Q41). 50 The GluN1 NTD was used as antigen for immunization assays in mice. (b) Example of an indirect ELISA assay performed with conditioned media harvested from Glunomab (clone 15A4B2), using a His-tagged mock protein as a control or the His-GluN1 NTD as the specific antigen (1-1000 ng/ml of antibody, N = 4 independent experiments; *Po0. 05 compared between one dose and previous dose; Kruskal-Wallis and Mann-Whitney tests). (c) Immunoblotting performed after SDS-PAGE resolution of recombinant His-GluN1 NTD (20 μg loaded per lane) and immunoglobulin Glunomab (clone 15A4B2) as the primary antibody (N = 2 experiments). (d) Immunostaining performed from hippocampal (CA1) and cortical tissue sections (mice and rats) using either Glunomab (clone 15A4B2) (1 : 400, green) or an antibody against the C-terminal GluN1 subunit (Cter-GluN1, 1 : 400, red) or NeuN (1 : 250, blue).
(e) Control immunostainings performed from liver tissue sections (mice) using either Glunomab (clone 15A4B2) (1 : 400, green) or an antibody against the C-terminal GluN1 subunit (Cter-GluN1, 1 : 400, red). (f) Immunoprecipitation (IP) assays from mouse cortices or primary cultures of cortical neurons using Cter-GluN1 subunit antibody followed by immunoblotting (IB) using Glunomab (clone 15A4B2) (representative data of three independent samples). (g) Calcium video imaging was performed on primary cultures of cortical neurons (12-14 DIV, see Materials and Methods section). After two successive control NMDA stimulations, neurons were incubated for 45 min with buffer (control, n = 98 cells), Glunomab alone (10 μg/ml, n = 46 cells), tPA alone (300 nM, n = 139 cells) or with immunoglobulins corresponding to Glunomab (clone 15A4B2) (10 μg/ml, n = 139 cells) or the clone 6C9B6 (10 μg/ml, n = 119 cells).
After 3 day in vitro (DIV), the original medium was replaced with a serum-free medium. Cultures were maintained at 37 °C in 5% CO 2. To investigate the impact of tPA on NMDAR diffusion, cultures were pre-incubated 45 min with either active tPA (300 nM, 37 °C) or tPAm (nonproteolytic tPA, 300 nM, 37 °C). QD detection and subsequent analysis were performed as previously described. 7 Briefly, hippocampal neurons (11-12 DIV) were incubated for 10 min (37 °C) with polyclonal antibodies against GluN1 NTD subunit (Alomone Labs; 1 : 200). Neurons were then washed and incubated for 10 min (37 °C) with QDs 655 goat F(ab') 2 anti-rabbit (1 : 10 000). Green MitoTracker (1 : 1000) was used as a synaptic marker. For the data illustrated in Figure  7 , neurons were incubated for 10 min (37 °C) with either the control anti-GluN1 NTD subunit (1 : 200) or the Glunomab antibodies (1 : 200).
The same protocol was followed, except that neurons were incubated with QD 655 goat F(ab') 2 anti-rabbit or anti-mouse. Signals were detected using a EM-CCD camera (Quantem, Roper Scientific, Evry, France). QDs were followed on randomly selected dendritic regions for up to 20 min. QD recording sessions were processed with the Metamorph software (Universal Imaging Corporation, Chester, PA, USA). Instantaneous diffusion coefficient distributions of GluN1-QD are represented using median and interquartile range. The top white portion, the line between the white and the black portions and the bottom black portion correspond of the first quartile, the median and the third quartile, respectively. Calcium video imaging and x-link protocol in neurons. Cortical neurons were prepared from E14. 5 Swiss mice as previously described.
% of responsiveness ¼ AUC ð Þa= AUC ð Þb ½ Ã 100 with (AUC)a: sum of area under curve of Fura-2 ratio during both NMDA stimulations after treatment and (AUC)b: sum of area under curve of Fura-2 ratio during NMDA stimulations before treatment. Experiments were performed at room temperature, on the stage of a Leica DMI6000B inverted microscope equipped with a 150 W Xenon high stability lamp and a Leica 40 × , 1. 3 numerical aperture epifluorescence oil immersion objective (Wetzlar, Germany). Fura-2 (excitation: 340, 380 nm, emission: 510 nm) ratio images were acquired with a Digital CMOS camera (Hamamatsu, ORCA-Flash2. 8 C11440-10C, Massy, France) and digitized (2048 ×2048 pixels) using Metafluor 6. 1 software (Universal Imaging Corporation). For x-link procedures, neurons were treated for 15 min with primary anti-GluN1 (1 : 20) and secondary (1 : 30) antibodies (x-link) (Figure  3  and Supplementary Figure  1 ).
Images were captured using a CoolSnap camera and visualized with Metavue 5. 0 software (Molecular Devices, Sunnyvale, CA, USA). Epitope mapping and Alascan. Epitope mapping and Alascan are presented in Supplementary Figure  3. A total of 141 overlapping pentadecapeptides, frame-shifted by three or one residue covering the entire amino-acid sequence of GluN1 NTD (residues 19-371), were prepared using the Spot technique according to the protocol previously described by Laune et al. 49  Briefly, peptides were assembled using Fmoc chemistry on a cellulose membrane containing an aminopolyethyleneglycol moiety. The C-terminal residue of each peptide was coupled to the moiety. After Fmoc deprotection, the other amino acids were sequentially added as in conventional solid-phase peptide synthesis. Finally, the side-chain protecting groups were removed by trifluoroacetic acid treatment in the presence of appropriate scavengers, whereas the linkage of the peptides to the membrane was maintained.
We used the same set up and data analysis as mentioned in the methods section for calcium video imaging in neurons. Concentrations of tPA and Glunomab were also of 300 nM and 10 μg/ml, respectively. NMDA exposures were performed at 100 μM for 30 s and the duration of treatments was of 20 min between the two rounds of NMDA stimulations. Site-directed mutagenesis. Mutagenesis of rat wt-GluN1-1b (GluN1-1b K178V or GluN1-1b K190V) was performed with the QuikChange XL Kit (VWR International France, Fontenay-sous-Bois, France) and the following primers: 5′-GGCAGCGCAGgtGCGCTTGGAG-3′ and 5′-CGTCCCTCGTGGTCGTCG-3′ (to GluN1-1b K178V), 5′-ACGGGAGTCCgtgAGTAAAAAAAGGAACTATG-3′ and 5′-TC CTCCAGCAACGTCTCC-3′ (to GluN1-1b K190V). Mutations were confirmed by sequence analysis. Site-directed mutagenesis strategy in K2 domain of tPA sequencing procedure have been described previously.
Fifteen minutes after the excitotoxic lesion, a 200 μl intravenous bolus injection of tPA (10 mg/kg) or saline with or without Glunomab (160 μg) was given via a catheter previously inserted into the tail vein. Solutions were injected by the use of a micropipette made with hematologic micropipettes. Twenty-four hours later, mice were killed and the brains removed and frozen in isopentane. Cryostat-cut coronal brain sections (20 μm) were stained with thionine and a volumetric analysis of brain lesions was performed with the Image J software (NIH software, National Institute of Health, Bethesda, MD, USA). Region of interest were determined through the use of a stereotoxic atlas for the mouse and an image analysis system (Scion Image Scion Corporation, Frederick, MD, USA) was used to measure lesion corresponding to the nonstained area (n = 7, 8 or 9 per group).
Acknowledgements. We thank  N Colloc 'h for her help and expertize in using the software PYMOL,  S Cobo  for technical assistance. We thank also  F Docagne ,  B Roussel  and  A Young  for their comments and help for editing. This work was supported by grants from the  INSERM (French National Institute for Health and Medical Research) ,  TC2N  ( European Trans Channel Neuroscience Network ),  FP7 ERANET-NEURON network   3-275-006 , Equipe FRM  N°DEQ20140329555 , the  Regional Council of Lower Normandy , the  CNRS (Centre National Recherche Scientifique)  and the  IDEX Bordeaux.
Ortholog sequences downloaded from GenBank were aligned using the expresso extension of T-Coffee to create the initial pMSA. 22 23 The initial alignment was checked by hand in Geneious V. 7. 1. 4 ( http://www. geneious. com) for anomalies that might be attributed to gene model errors rather than actual Routines from the PHYLIP package (V. 3. 69),  24 constrained using the known phylogeny of the species included in our alignments, were used to estimate substitutions per position within each alignment and to calculate the distance matrices required by MAPP. The complete alignments, phylogenetic trees and distances are available upon request. PolyPhen-2 (genetics. bwh. harvard. edu/pph2/)  25 and CADD (cadd. gs. washington. edu/)  17 operate without user-supplied alignments. PolyPhen-2 uses a combination of internally generated pMSAs, functional annotations and structural information to evaluate missense substitutions;  19  we used its output variable 'pph2_prob' as a continuous variable score.
We treated groups outside of the reference as categorical variables for OR calculations. For the threshold analysis, we used the same reference group and adjusted the NPS threshold until the group containing scores above the set threshold had an OR≥2. 5. For the regressions, NPS was treated as the independent variable and the resultant OR of each group as the dependent variable weighted to the number of individuals in each group, excluding subjects in the middle quintile. p Values were found by testing the regression coefficient equal to 0 or 1. To combine the risk estimates from the rMS and NPS, we multiplied the NPS and OR from the rMS. All analyses were performed using multivariable unconditional logistic regression using Stata V. 12. 1 software (StataCorp, College Station, Texas, USA).
17 For variant evaluation, we adjusted our pMSAs to two depths: human through platypus (mammals only), and human through the organism required for 3S/P for each individual gene. Receiver operating characteristic (ROC) curves were generated for each method and depth (if applicable). Area under the curve (AUCs) were similar for all methods (see online supplementary table  S3  and supplementary figure  S1 ). The correlations between the missense analysis programs were highest between Polyphen-2 and CADD (R 2 =0. 56), but the R 2 for any combination of missense analysis programs was never >0. 8, so none of the missense analysis programs were dropped from further analysis (see online supplementary table  S4 ). We then toggled the severity score for each of the four programs to find the lowest score where the OR for key domain rMS above the score reached at least 2.
5 (figure  1A-D ). The thresholds at which each of the four rMS analysis programs reached OR≥2. 5 for key domain rMS were above a score of 11 for MAPP when using pMSAs consisting of organisms from human through 3S/P, C35 for Align-GVGD when using pMSAs consisting of organisms from human through 3S/P, 23 for CADD and 0. 9 for PolyPhen-2 (see online supplementary table  S5 ). It was interesting that neither Align-GVGD nor MAPP was able to achieve an OR≥2. 5 with a pMSA that consisted only of mammals (human through platypus). It appears that these sequences, although generally more complete than those from more distant organisms, do not offer adequate variation to stratify variants. Examining the variants that were placed in the OR≥2. 5 category by multiple missense analysis programs, we found that an overlap of at least two of the missense analysis programs resulted in a classification of variants with an OR≥2.
Our analysis raises additional questions regarding standard clinical genetic testing practices using panel tests. For the established moderate-risk genes ATM, CHEK2 and NBN, the majority of the pathogenic variants that the test can actually detect are rMS, likely to be reported to patients as VUS, and likely to be normalised during counselling. In this circumstance, how does one answer the clinical validity question, "Are the variants the test is intended to identify associated with disease risk, and are these risks well quantified?"  41  What is the impact on studies intended to explore the penetrance and tumour spectrum of pathogenic variants in these genes if the studies focus on T+SJVs even though these may represent a minority of the pathogenic variants? One path forward lies in a more nuanced use of the IARC 5-class system for variant classification and reporting to incorporate more data from ongoing research on missense substitution evaluation.
This alternative mechanism of tumor spread, distinct from intravascular dissemination, has been termed extravascular migratory metastasis or EVMM  20. Current data have shown that tumor cells manifest angiotropism to both microvessels and larger vessels  18  ; however the involvement of mature and perfused microvessels versus neovessels still requires further investigation. In the present work, we have used a murine brain melanoma model, in which tumor cells are injected directly into the brain as a primary site of tumor development. We have analyzed 3D images obtained during the progressive interaction of green fluorescent tagged melanoma cells with red fluorescent lectin tagged vessels. We have investigated the implication of mature vessels versus neovessels in tumor spreading along vessels.
4 (PBS), and placed in 10 mM sodium citrate buffer, pH 8. 5, for 30 min at 80 °C for antigen retrieval. Following 3 brief washes in PBS, sections were then blocked and permeabilized in 10% normal donkey serum containing 0. 3% Triton X-100 for 30 min and transferred to MOM block (Vector Labs) for 1 hr at room temperature (RT). After 3 additional washes in PBS, primary antibody cocktails were diluted in blocking solution and left overnight at RT. The following antibodies were used: antibodies against Serpin-B2 at 1:200 (PAI-2 Antibody: sc-6649 Santa Cruz Biotechnology) and Glut-1 at 1:500 (400060-50UG, EMD Millipore) according to the manufacturers' instructions. Image processing. Registration and mosaicking of hundreds of individual images to form one large full frame image of the coronal brain sections was performed with the LAS AF software (Leica Microsystems, Wetzlar, Germany).
Acknowledgements Confocal imaging was performed at the  California NanoSystems Institute (CNSI) Advanced Light Microscopy/ Spectroscopy Shared Resource Facility  at  UCLA  with support from a  NIH/National Center for Advancing Translational Science UCLA   CTSI Grant  ( UL1TR000124 ). The authors also thanks  Olivier Brun  from  Leica Microsystems  for providing access to the SP8 X microscope used in Figure 3 and Supplementary Movie S1.
Watson et al. [2008]  make a comprehensive review and pointed out that the CityEngine software is a procedural modeling tool. And setting up random parameters can produce all kinds of stochastic model, which generated a massive model of the city. Whiting et al. [2009]  put forward a procedural modeling method of stable masonry building, which plays an important role in the analysis of the historical architecture. Vanegas et al. [2010]  proposed a passive computer vision method with existing maps and aerial data, which can automatically generate3D building model. By using multiple aerial images, the method can generate single coherent whole building geometric model. Jerry et al. [2011] put forward a procedural modeling algorithm based on syntax, which by optimizing the possible space to generate the corresponding construction.
Texture Mapping Data and Facade Images Data Texture mapping data and facade images data are acquired as pictures, these pictures are taken by the high resolution digital camera from the different direction of each building, and will be used as the texture maps of 3D modeling or the facade images for facade modeling. At the same time, the roof texture maps can also be captured in Google Earth to represent or express it successfully. In order to get high quality pictures, it is better to take by the high resolution digital camera. The better choice will be sunny day either morning or evening, or in cloudy weather without rain. Under these weather conditions, pictures are not influenced by the light to ensure that the clarity of pictures. For the roof texture maps, we acquire them in Google Earth.
Generation of the Geographic Base Map ArcGIS Desktop is a complete set of GIS platform product developed by Esri Company (www. esri. com). It provides the ability of powerful map production, spatial data management, spatial analysis and spatial information integration, as well as publishing and sharing. ArcGIS Desktop includes a set of application: the ArcMap and ArcCatalog, ArcGlobe and ArcScene, ArcToolbox and model builder. Through the use of these applications and interface, you can perform any GIS from simple to advanced tasks. The high resolution spatial image of Shanghai University containing coordinates and elevation information acquired in Google Earth is seen as the geographic base map of procedural modeling. First of all, we should import the image into the software of ArcMap with Spatial Reference Systems of PCS_WGS_1984_UTM_Zone_51N.