dataesr/scientific-paragraphs-categorization huggingface dataset:
Data Analysis For in vitro experiments, data were derived from at least three independent experiments, each being performed with a culture derived from one animal (N 5 3 experiments corresponds to three different mice). Cell numbers were counted on a Leica DMI6000 microscope. Percentages of GFAP, DCX, O4, nestin, or ßIII-tubulin immunoreactive cells were determined from counts in 15 fields of view in each coverslip with a 403 objective, by an observer blind to the assay (more than 250 cells were counted per coverslip). Proliferative symmetric (SOX21/SOX21), asymmetric (SOX21/SOX2-), and differentiative symmetric divisions (SOX2-/SOX2-) were counted with a spectral confocal FV-1000 station installed on an inverted microscope IX-81 (Olympus). Percentages of each type of cell pairs were determined from 20 to 60 cell pair counts in each coverslip with a 603 objective, by an observer blind to the assay.
For in vivo experiments, numbers of Ki67 and percentages of Ki67/SOX2 or BrdU/Ki67 labeled cells within the SVZ were determined for each mouse, on 13 brain sections collected at regular intervals from 1. 42 mm anterior relative to Bregma to 0. 1 mm posterior relative to Bregma (according to Franklin and Paxinos, The mouse brain in stereotaxic coordinates, 3 rd Edition, 2008), with a 603 objective, by an observer blind to the assay. Statistical significance of differences was examined by one-way analysis of variance followed by the post hoc Bonferroni test for multiple comparisons or by non-parametric Mann and Whitney test for comparison by pairs (Statview 5. 00 software). Statistical significance level was set for p values <. 05 and represented on the figures by: * for p <. 05, ** for p <.
SVZ Cells Possess Functional SOC SOC are mainly formed of Orai1 and/or TRPC1 calcium channels of the plasma membrane. STIM1, a sensor of calcium levels in the ER, activates SOC. To investigate if SVZ cells possess the machinery required for SOCE, we cultured SVZ cells derived from adult mice brains as neurospheres and analyzed on these cultures the presence of TRPC1, Orai1, and STIM1. RT-PCR (Fig. 1A ) together with Western blotting (Fig. 1B ) and immunostaining analysis (Fig. 1C-1E ) showed that SVZ cells express TRPC1, Orai1, and STIM1. Possible physiological relevance of these in vitro data was assessed on mice brain sections and established that TRPC1, Orai1, and STIM1 are also found in SVZ cells in vivo (Fig. 1F-1H ). Next we determined whether SOC are functional in SVZ cells by measuring with calcium imaging their ability to support calcium entries in response to the depletion of ER calcium stores.
ACKNOWLEDGMENTS We are indebted to  Anne Cantereau  for her advices with confocal microscopy and  Laetitia Cousin  for technical assistance with brain section immunostaining and ELISA experiments. We thank  Image UP  microscopy core facilities and  PREBIOS  facilities for animal handling. This work was supported by  La Ligue Contre le Cancer Grand Ouest Comit es de la Vienne et des Deux Sevres, R egion Poitou-Charentes, FEDER HABISAN  and  ACI  from  Universities of Tours  and of Poitiers. E. Terri e holds a Ph. D. fellowship from  R egion Nouvelle-Aquitaine.
Silver Nanowires Characterization Short and long polyvinylpyrrolidone (PVP) coated AgNW suspensions (S-AgNW and L-AgNW) were purchased from nanoComposix (San Diego, CA, USA) and were stored in lightproof bottles in an anaerobic chamber. Both solutions of AgNW were imaged by SEM and the length and diameter observed were in agreement with manufacturer specifications and with previous observations  [26]  (Table  S1 ). AgNW were supplied into water at 1 mg/mL suspension. They were diluted into complete keratinocytes culture medium, then agitated gently for 1 min and they were well dispersed without aggregation, as observed throughout this study by light microscopy (data not shown). AgNW settling rates were assessed by measuring a series of optical absorption spectra (Ocean Optics, Largo, FL, USA) of unstirred 4-mL suspensions of 1 µg/mL S-AgNW and L-AgNW in keratinocyte culture media (KSFM; Life Tech.
Cell viability was expressed relatively of absorbance of negative control (non-treated cells). Data analyses were performed with Excel 2013 for Windows. In order to ensure that there was no interference between the MTT and AgNW, the same experiment was performed without cells and the NW were pelleted by centrifugation (15 min at 800 g) before the addition of MTT. The absorbance measured was similar to the background (data not shown). In order to determine if Ag + ions released from the AgNW had any contribution to the observed loss of viability, we performed an ion-release experiment. After 24-h incubation with cells, cell supernatants were harvested, centrifuged (15 min at 800 g), and the supernatants were transferred onto other cells for another 24 h prior to a second MTT assay that was performed as described previously.
Cytoviva Microscopy HPK were grown on glass coverslips and exposed for 72 h to 1. 56 µg/mL of AgNW. After incubation, the cells were rinsed with PBS, fixed in 4% paraformaldehyde and stained with Hoechst 33342. Dark-field micrographs and hyperspectral images were acquired with a CytoViva hyperspectral microscopy system (CEA, NanoSafety Platform, Grenoble, France). The hyperspectral data were converted to text files using ENVI software and analysed in the IgorPro software using the GG Macros routines developed for spectromicroscopy. The lineshapes of all visible-to-near-infrared (V-NIR) spectra dominated the output of the lamp and the precise alignment of the condenser, making quantitative spectroscopy very difficult. However, by subtracting a spectrum from a nearby bright Ag-free biological structure, V-NIR spectra of AgNW and AgNR could be obtained.
AgNW Characterization The two sizes of commercial PVP-coated AgNW used in this study came from the same supplier as prior studies and as described in the methods section. They possessed similar dimensions and minor nanorods (AgNR) contamination as described previously  [9, 26]. The average dimensions were approximately 2 µm × 40 nm (length × diameter) for the short samples (S-AgNW) and 20 µm × 50 nm for the long sample (L-AgNW) (Table  S1 ). AgNW diluted into complete keratinocytes culture medium were well dispersed without aggregation, as observed throughout this study by light microscopy (data not shown). We followed AgNW settling in culture medium by measuring the decrease of absorbance at 380 nm (Figure  1A ). L-AgNW settled faster than S-AgNW. Although the spectrophotometric data cannot easily be converted to settling rates, it is likely that the L-AgNW settled completely within 24 h in the well-plates used for toxicity assays.
Acute Cytotoxicity The acute cytotoxicity of AgNW and Ag + to human primary keratinocytes (HPK) was assessed using the MTT assay. Both types of AgNW induced moderate toxicity (Figure  2A ) with a shallow dose response curve showing 35% and 50% viability after 24 h at the highest concentration tested (50 µg/mL) for the S-and L-AgNW, respectively. Much higher cytotoxicity was observed for Ag + with a sharper dose response, zero cell viability at 12. 5 µg/mL and a calculated LD50 of 4 µg/mL. Similar cytotoxicity was observed with the neutral red uptake assay (data not shown). In order to investigate the possible contribution of Ag + release in the cell medium to the toxicity of AgNW, we harvested the cell supernatant after 24 h of exposure, centrifuged it, and added it to a fresh cell sample to perform an MTT assay after the 24-h incubation.
Acknowledgments: The authors wish to thank the members of the Prométhée proteomic platform,  M. J. Stasia  and members of her team ( IBP, CHU, Grenoble, France ),  K. Pernet Gallay  ( GIN, Grenoble, France ),  F. Roussel-Dherbey  ( CMTC, Grenoble, France ),  B. Faure  and  F. Saint Antonin  ( CEA, Grenoble, France ). The NanoSetasizer and Ultramicrotome used in this study was part of  Nano-ID  platform which was funded by the  EQUIPEX  project  ANR-10-EQPX-39-01. The project leading to this publication received funding from  Excellence Initiative of Aix-Marseille University -A*MIDEX, a  French "Investissements d'Avenir" program , through its associated  Labex   SERENADE  project". This work was also supported from the  Université Grenoble Alpes  ( UGA-PEPS AGIR ) and the  Labex OSUG@2020  ( ANR10 LABX56 ).
b Nicolas et al. [116]  European Journal of Human Genetics 2016. c Wallon et al. [181]  Journal of Alzheimer's Disease 2012 affected genomic positions where the same change had been reported as pathogenic in sporadic cases or families. Although no parental data was available for those cases, it still does indicate that these positions are affected by recurrent DNMs. In addition, two FUS DNMs are also present in the gnomAD database consisting of genetic variations identified in controls free of severe pediatric disease, with a maximum allele count of 5 (out of ~ 138,000 individuals)  [95]. One of these was the recurrent nonsense DNM. This suggests that, although cases with a DNM in FUS were all young, the mutations may not be fully penetrant in other genomic contexts. Of the six reported PRNP DNMs, including one possibly post-zygotic mutation  [8] , all were reported in additional independent cases or families  [34, 41, 63, 81, 154].
Protein-protein interaction and recurrence of variants in large cohorts of Parkinson disease patients One WES study was performed on 21 trios of early-onset PD (onset before 40 years)  [84]  (Table  3 ). Twenty DNMs (19 non-synonymous) were identified for which in silico functional gene annotation and protein-protein interaction analyses were performed using the STRING bioinformatics tool. Three genes showed significant interactions with the known PD genes: PTEN, VABP, and ASNA1. Additional rare variants were identified from exome data of more than 1200 cases from the International Parkinson's Disease Genomics Consortium (IPDGC). Although functional pathways link PTEN to PD pathophysiology, the putative role of the DNMs found in patients with PD remains to be elucidated. In particular, the DNM identified in the replication sample is predicted to result in a loss of function and hence supposed to cause Cowden syndrome.
In addition, while this variant occurred de novo, the proband's father was also affected with PD, showing non-co-segregation. VAPB missense mutations have been previously shown to cause autosomal-dominant ALS. The patient identified in the PD trio study presented an unknown in-frame deletion of one residue and two additional cases from the IPDGC dataset presented rare coding mutations in the same domain as the one reported to carry ALS-causative mutations. Whether or not these mutations have a functional effect and are related to PD pathophysiology remains to be determined. Very recently, a trio-based WES study reported 39 earlyonset PD patients of Han Chinese origin  [58]. After prioritization of DNMs based on protein-protein interactions and expression profiles in the brain, 12 genes were selected for case-control sequencing analyses.
Network enrich- ment analysis Abeta network): significant enrich- ment in DNM in the network com- pared to the rest of the exome Protein net- work analysis (STRING). Follow-up analy- sis of the most significant genes by searching for a recurrence among > 1200 exomes of PD patients Selection of 12 candidate genes among the DNM, replication in two case-control datasets (rare non-synonymous variants) Functional assess- ment in drosophila Average non-syn- onymous DNM per proband 1. 00 0. 90 0. 89 No. of trios Sequencing technol- ogy 14 a WES (Agilent Sure- Select Human All Exon, Illumina) 21 WES (Nextera Rapid Capture, Illumina) 39 b WES (NimbleGen capture, Illumna) Age at onset (mean, range) 50 years (44-58) NA 30. 79 years Inclusion criteria Diagnosis supported by biomarkers or post-mortem examination, no family history of dementia in first and second degree relatives, parents alive with normal cognitive score Age at onset < 40 years, typical presentation of PD with negative family history, absence of patho- genic mutations in any of the known PD genes Age at onset < 36 years, typical presentation of PD with negative family history, no genetic cause or environmental risk factor, no consan- guinity References Disease Rovelet-Lecrux Early-onset Alzhei- et al.
FUNDING LD was supported by the  foundation Fédération pour la Recherche sur le Cerveau , the  Fondation Thierry Latran (SpastALS) , the  Association pour la Recherche sur la Sclérose Latérale Amyotrophique (ARSLA) ,  Amyotrophic Lateral Sclerosis Association  ( Investigator Initiated Award ),  Fondation Frick , AFM (# 18280 ),  Virtual Helmholtz Institute  ( VI-510 ),  Motor Neuron Disease Association and Agence Nationale de la Recherche  ( ANR, EpiFUS, TOFU ). DV and DB were supported by grants from  France Alzheimer/Fondation de France  ( InsTauBrain  project),  FHU VasCog research network (Lille, France) and programs d'investissements d'avenir LabEx (excellence laboratory) DISTALZ (Development of Innovative Strategies  for a Transdisciplinary approach to Alzheimer's disease). Research in ÅP laboratory was supported by grants from the  Swedish Research Council , The  Region of Scania grants (ALF)  and the  Swedish Brain Foundation.
ACKNOWLEDGEMENTS The  VALOCAL  project was funded by the  CNRS Interdisciplinary Mission (MI-CNRS ) with support from the  Institute of Sciences and Engineering and Systems (INSIS-CNRS ). The authors thank these authorities, which have made possible through this funding to initiate transdisciplinary work on an original issue of energy optimization. Figure 6: Pareto diagram for CO2 emission and heating supply bill reduction This work is supported by the  French National Research Agency  in the framework of the " Investissements d'avenir" program  ( ANR-15-IDEX-02 ).
The present paper aims at investigating the impact of airfoil design on the propulsion system for a Martian rotary wing micro air vehicle (MAV). The main challenge for flying on Mars is the atmosphere's density and speed of sound that are significantly lower than on Earth. It leads to compressible ultra-low Reynolds number (Re c ă 10 4 ) flows for a 30 centimers diameter coaxial rotorcraft. Since those flows are unknown in the biosphere, numerical tools have not been validated yet. Therefore, the test section from a known depressurized experiment is simulated in 3D for solver assessment. XFoil, program for the analysis of subsonic airfoil, is also evaluated in Martian flow conditions for evaluating its ability to be used in a optimization process. Based on XFoil's performance evaluations, both camber line and thickness distribution are optimized in 2D incompressible and compressible flows.
ACKNOWLEDGEMENTS The authors would like to thank the  "Centre National d' Études Spatiales" (CNES)  for its support in the experimental campaign. We would also like to thank the people involved from  ISAE-SUPAERO  ( Rémy Chanton ,  Sylvain Belliot ,  Xavier Foulquier ,  Sébastien Prothin ,  Thierry Jardin ,  Valérie Allain  and  Bernard Rivière ) and from  Propulsion Lab-oratory at ONERA  ( Christophe Corato ,  Jérome Anthoine ,  Jean-Charles Durand  and  Jouke Hijlkema ).
Acknowledgments. The four authors thank the Center for Interdisciplinary Research in Biology ( Collège de France ) for travel funding. ABB and ASJ would like to thank  CIMAT , A. C. and especially  Víctor Rivero  for support and for his comments on this project, which started during Airam's PhD thesis. ABB is supported by  CONACYT  postdoctoral grant  234823 , and  ASJ  by  CONACYT  grant  CB-2014/243068.
As indicated in  [15] , an improper initialization on the parameters value range may damage the overall performance of a PF. Thus, in this paper, a new strategy for parameters initialization is proposed considering failure times data from reliability tests. Before an equipment is put into volume production, reliability tests are performed to verify the reliability of the equipment. During these tests, a number of equipment samples are tested for a predefined period, which may fail or survive the test. Based on the failure times data, the equipment reliability can be derived  [19]. In this paper, a Monte Carlo-based approach is proposed for the parameters initialization, using the failure times data obtained during the reliability tests. The likelihoods of the values of each unknown parameters combination with respect to the collected failure times data are calculated and the prior distribution of these parameters is obtained.
Acknowledgments The first author is partially supported by the  National Science Foundation  under agreement no. DMS-1352216 , by an  Alfred P. Sloan Research Fellowship , by the  Université Paris 13 , and by the  University of Minnesota. The second author is partially supported by the  A. N. R. (Agence Nationale de la Recherche)  under the program  ANR-14-CE25-0002.
AT-3: In a further step, motivated by the comparison to data on early tumor initiation that will be performed below, we will define further specific parameter modifications for transformed cells in a step subsequent to AT-2. This will be motivated in the respective subsection. For cancer cells, the same equation of motion as for normal hepatocytes is used (see Sect. 5). In those simulations where assumption (AT-3) applies, the parameters differ between normal hepatocytes and carcinoma cells. The simulations have been carried out on a cluster of Linux-based workstations using the simulation software CellSys  (Hoehme and Drasdo 2010). CellSys is a modular framework implemented in C++ that utilizes SuperLU  (Li 2005)  for solving systems of equations, OpenMP for parallelization and OpenGL for visualization.
Acknowledgements DD gratefully acknowledges support by the projects  EU-CancerSys ,  EU-PASSPORT ,  EU-NOTOX ,  BMBF-Virtual Liver Network, BMBF-LiSym  and  ANR-IFLOW , FB support by  EU-CancerSys , SH by  EU-CancerSys and BMBF-VLN , WW by project  EU-CancerSys  and  EU NOTOX ,  JGH  by  EU CancerSys, BMBF-VLN, BMBF LiSym. Open Access This article is distributed under the terms of the Creative Commons Attribution 4. 0 International License (http://creativecommons. org/licenses/by/4. 0/),which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.
Modern procedures in analytical chemistry generate enormous amounts of data, which must be processed and interpreted. The treatment of such high-dimensional datasets often necessitates the prior selection of a reduced number of variables in order to extract knowledge about the system under study and to maximize the predictability of the models built. Therefore, this article describes a variable selection method for multiclass classification problems using two-class ROC analysis and its associated area under the ROC curve as a variable selection criterion. The variable selection method has been successfully applied to two datasets. For comparison purposes, two other variable selection methods, ReliefF and mRMR, were used and double crossvalidation PLS-DA was applied using: (1) all variables and (2) the variables selected using the three methods.
• A variable selection method for multiclass classification problems using two-class ROC analysis • The area under the ROC curve, a direct measure of the separation between two classes, is used as a criterion for variable selection • Multiclass problems are reduced to two-class problems by calculating two similarity vectors between pairs of samples belonging to the same and to different classes • Variables selected maximize the AUC and the separation between the two similarity vectors • Variables selected bring closer together in the multivariate space samples belonging to the same class and separate samples belonging to different classes • The method was successfully applied to two datasets representing 6 different properties Comment citer ce document : De Figueiredo, M. , Cordella, C. , Jouan-Rimbaud Bouveresse, D.
Hence, since multiclass ROC analysis is often sensitive to skewed classes, two-class ROC analysis still remains the preferred approach. As well, while visualization of the curves and surfaces for multiclass ROC analyses may be difficult, this is not the case for two-class ROC analyses. Nevertheless, the performances of classification models assessed with ROC analysis will only be as good as the data they are fed with. Modern procedures in analytical chemistry generate enormous amounts of (correlated) data, which must be processed and interpreted. The exploitation of such high-dimensional datasets often necessitates the prior selection of a reduced number of variables. Therefore, this paper describes a variable selection method for multiclass classification problems using two-class ROC analysis and its associated AUC value as a variable selection criterion.
M A N U S C R I P T A C C E P T E D ACCEPTED MANUSCRIPT ity measurements between samples belonging to the same class and between samples belonging to different classes. In this way, although the method is based on a two-class ROC analysis, it can be applied for the selection of variables in a multiclass context prior to the use of other chemometric tools, such as Partial Least Squares Discriminant Analysis (PLS-DA). The present variable selection method has been successfully applied on two different datasets: mid-infrared spectra of fresh meats and visible/near-infrared spectra of apples. For comparison purposes, the variable selection method presented here was compared with two others, namely ReliefF and minimum-Redundancy-Maximum-Relevance (mRMR). Double cross-validation PLS-DA was applied, on the one hand, to the datasets using all variables and, on the other hand, using the variables selected by the three different methods.
Fresh meat samples The fresh meat dataset consists of spectra in the mid-infrared region between 1005 and 1868 cm -1 corresponding to 448 data points. The dataset, downloaded from the Quadram Institute website (https://asu. quadram. ac. uk/example-datasets-for-download/), contains a total of 120 measurements on minced fresh meat samples from three animal species (chicken, turkey and pork). Experimental details about acquisition are presented in Al-Jowder et al. [12]. The aim of the study was to determine if MIR spectroscopy could be used for meat authentication. The 120 fresh meat spectra were preprocessed using the Savitky-Golay filter to calculate the first derivative with a window size of 11 points  [13]. The spectra were then normalized by Standard Normal Variate (SNV) transformation  [14].
Apple samples The apple dataset consists of apple spectra acquired in the visible/near-infrared region between 380 and 2000 nm using a step of 0. 5 nm to give a total of 3241 data points. Experimental details are presented in Barros and Rutledge  [15]. After reduction of the data dimensionality by box-averaging, a final step of 7. 5 nm was obtained for a total of 217 data points per spectrum. Spectra were then normalized by SNV. The dataset contains a total of 94 measurements on apples of two varieties, Jonagold and Cox Orange Pippin. The apples were stored under controlled conditions to bring them to three different levels of ripeness, namely fresh, medium and mealy. Spectra were measured on two sides of each apple corresponding to faces considered as greener and redder.