dataesr/scientific-paragraphs-categorization huggingface dataset:
Real-time PCR amplification was performed using a mix of the forward primers, and the resulting reactions were analyzed by capillary electrophoresis on the GenomeLabGeXP using the GeXP Start kit reagents. Relative RNA expression levels were calculated relative to a pooled RNA standard using the GeXP Quant Tool software and were normalized to the GAPDH, β -actin, and HPRT expression levels. Statistical analysis. SPSS 17 (SPSS Science Inc. , Chicago, Illinois) was used for data analysis. Quantitative data were expressed as the mean ± S. E. M. , and were evaluated with an independent samples t-test. Repeated measures were used to analyze bodyweight and bodyweight gain rate. The number of samples were n = 8 for body weight and serum phenotypes, and n = 5 for cartilage indexes. Statistical significance was defined as P < 0.
1 protocol (Applied Biosystems, Courtaboeuf, France). The reaction products were purified by gel filtration using Sephadex G-50 (Amersham, Courtaboeuf, France), run on an ABI PRISM 3130 Genetic Analyser and analysed with the SEQSCAPE v2. 6 software (Applied Biosystems, Courtaboeuf, France). The obtained sequences were subjected to pairwise alignments against curated fungal reference databases available at the on-line MycoBank database (http:// www. mycobank. org/). In addition, a BLAST search against known sequences in NCBI Genbank was performed. Sequence identities with a cut off ≥ 97% over 450 nucleotides in length were considered significant. The best BLAST hits were those showing the highest percentage similarity for a query coverage of more than 90%. Sequences were aligned with the CLUSTALX (version 1.
87 1 Aspergillus Probable maura fumigatus 21 17 M/37 AML 9/24/2009 8/4/2010 Ascomycota Sordariales Cephalothecaceae Cephalotheca 566/566 AB278171 4 No Probable 3 foveolata 22 17 M/37 AML 9/24/2009 9/10/2010 Ascomycota Pleosporales Incertae sedis Genus 470/501 CBS 117477 1 Aspergillus Probable Ascochyta 6 fumigatus 23 18 M/58 AML No 8/16/2010 Not identifiable Candida No NSM glabrata 24 19 M/75 AML No 6/17/2010 Not identifiable Candida No NSM tropicalis HSCT, haematopoietic stem cell transplantation; ALL, acute Lymphoid Leukaemia; AML, acute myeloid leukaemia; CLL, chronic lymphoid leukaemia; NHL, non-Hodgkin lymphoma. 1Collection strain from FUNCBS database (http://www. cbs. knaw. nl/collections/). 2 Collection strain from INDOOR database (http://www. cbs. knaw. nl/indoor/). 3 Aspergillus fumigatus isolation on another respiratory sample.
It is made available under The copyright holder for this preprint (which was not this version posted January 11, 2015. ; https://doi. org/10. 1101/013656 doi: bioRxiv preprint severe, as well as hypotonia and seizures. Magnetic resonance imaging of the brain in four of the affected individuals was reported as normal in two persons and abnormal in two. Of the latter, one person was reported to have cerebral and cerebellar atrophy and another to have cerebral atrophy and a "small pituitary. " Severe gastroesophageal reflux was observed in all three individuals for whom data were available, and four of five individuals had inguinal hernias. Three of the five affected individuals died in infancy or early childhood. One person died of complications of hemophagocytosis in the newborn period while the exact cause of death was unclear in the other two individuals.
One microgram of barcoded shotgun library was hybridized to capture probes targeting ~36. 5 Mb of coding exons (Roche Nimblegen SeqCap EZ Human Exome Library v2. 0) Library quality was determined by examining molecular weight distribution and sample. CC-BY-NC 4. 0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under concentration (Agilent Bioanalyzer). Pooled, barcoded libraries were sequenced via paired-end 50 bp reads with an 8 bp barcode read on Illumina HiSeq sequencers. Demultiplexed BAM files were aligned to a human reference (hg19) using the Burrows-Wheeler Aligner (BWA) 0. 6. 2. Read data from a flow-cell lane were treated independently for alignment and QC purposes in instances where the merging of data from multiple lanes was required.
005 in the ESP6500 or 1000 Genomes or >0. 05 in an internal exome database of ~700 individuals were excluded prior to analysis. Additionally, variants that were flagged as low quality or potential false positives (quality score ≤ 30, long homopolymer run > 5, low quality by depth < 5, within a cluster of SNPs) were also excluded from analysis. Variants that were only flagged by the strand bias filter flag (strand bias > -0. 10) were included in further analyses as the strand bias flag has previously been found to be applied to valid variants. CNV calls were also generated from exome data with CoNIFER 6. Variants were annotated with the SeattleSeq137 Annotation Server, and variants for which the only functional prediction label was "intergenic," "coding-synonymous," "utr," "near-gene," or "intron" were excluded.
e. , the minimum Genomic Evolutionary Rate Profile score was 4. 73) in NALCN (Table  1  and Figure  2 ). Each variant was confirmed by Sanger sequencing to have arisen de novo and none of the six variants were found in over 71,000 control exomes comprised of the ESP6500, 1000 Genomes phase 1 (Nov 2010 release), internal databases (>1,400 chromosomes), or ExAC (October 20, 2014 release). Because the phenotype of the individuals with mutations in NALCN was variable and overlapped with other DA syndromes, we used molecular inversion probes with 5-bp molecular tags  7  (smMIPs; designed with MIPGEN 8 v. 0. 9. 7) to conduct targeted next-generation sequencing of NALCN in 202 additional samples from persons with DA in which no pathogenic mutation had been found. The 43 coding exons (5,214 bp total) of Ensembl transcript ENST00000251127 and 10 bp flanking each exon (860 bp total) were targeted using smMIPs, for an overall target size of 6,074 bp.
Pooled and phosphorylated smMIPs were added to the capture reactions with 100 ng of genomic DNA from each individual to produce a NALCN library for each individual. The libraries were amplified during 21 cycles of PCR, during which an 8 bp sample barcode was introduced. The barcoded libraries were then pooled and purified using magnetic beads. After Picogreen quantification to determine the appropriate dilution, 10 picomoles of the pool was sequenced on an Illumina MiSeq. MIP collapsing and arm trimming (MIPGEN v1. 0), alignment (BWA 0. 7. 8), and multi-sample genotype calling (GATK Unified Genotyper 3. 2-2-gec30cee) were performed and variants were annotated with SeattleSeq138. We used the same filtering strategy employed in our analysis of the exome sequences to select variants for further confirmation by Sanger sequencing.
Acknowledgements We thank the families for their participation and support;  Christa Poel ,  Karynne Patterson , and  Ian Glass  for technical assistance; and  J. David Spafford  for helpful comments. Our work was supported in part by grants from the  National Institutes of Health / National Human Genome Research Institute  ( 1U54HG006493  to M. B. , D. N. , and J. S. ;  1RC2HG005608  to M. B. , D. N. , and J. S. ;  5R000HG004316  to H. K. T. ),  National Institute of Child Health and Human Development  ( 1R01HD048895  to M. J. B. and  5K23HD057331  to A. E. B), the  Life Sciences Discovery Fund  ( 2065508  and  0905001 ), and the  Washington Research Foundation.
Population We collected data from women, alive or not, with locally advanced HER2-positive (HER2þ) BC or mBC, whose treatment included 1st-line trastuzumab, who were progression-free for at least 3 years after treatment initiation, and still treated or not with trastuzumab. Data were collected during consultations performed as part of routine monitoring, retrospectively to the inclusion, and prospectively for patients still alive at the time of inclusion in the study. The physician collected data available in the patient's medical record, and results of parameters systematically evaluated for the management of the patient's disease. Patients alive at the time of inclusion gave their written informed consent for the automatic processing of their personal data, and its consultation by a duly authorized third party.
Design and objectives This was an epidemiological multicentre study. A total of 160 patients were included and followed-up (for patients alive at inclusion) from March 28, 2011 to November 16, 2012. Among them, 154 had at least one infusion of trastuzumab and were included in the Safety Set, and 128 were included in the Analysed Set. Among the 154 patients of the Safety Set, 134 were alive at inclusion, 130 were alive and followed at 6 months post-inclusion and 121 were alive and followed at 12 months post-inclusion. Among the 128 patients of the Analysed Set, 114 were alive at inclusion, 110 were alive and followed at 6 months post-inclusion, and 102 were alive and followed at 12 months post-inclusion (Fig. 1 ). Data were entered by the investigators in electronic Case Report Forms and transferred to the centralized database.
Physical methods Infrared spectra were recorded on a Perkin-Elmer Spectrum One FT-IR spectrophotometer. ESI (electrospray ionization)-mass spectra were carried out with a Bruker micrOTOF-Q II spectrometer, employing ~10 -5 M solution of the complex, in acetonitrile or methanol. Optical spectra were recorded on a Jasco V-550 UV-visible (UV-vis) spectrophotometer with thermostated cell compartments. Melting point was taken on a Fisher-Johns (Ionomex) apparatus. EPR data were recorded using an Elexsys E 500 Bruker spectrometer, operating at a microwave frequency of approximately 9. 5 GHz. Spectra were recorded using a microwave power of 0. 5 mW (under nonsaturating conditions) with a modulation amplitude of 0. 5 mT. Conductivity measurements were performed using a Horiba F-54 BW conductivity meter on 1.
0 mM solutions of the complex in water. Magnetic susceptibility data were collected with a Quantum Design MPMS SQUID susceptometer. Cyclic voltammetry was recorded with an Autolab PGSTAT20 potentiostat. The counter electrode was a Pt wire, the reference electrode was a calomel electrode isolated in a fritted bridge, and the working electrode was a glassy carbon disk (diameter = 3 mm). Studies were carried out under Ar, in dry acetonitrile (ACROS) using 0. 1 M tetrabutylammonium hexafluorophosphate (TBAPF 6 ) as a supporting electrolyte. Temperature was regulated with a Julabo circulation bath. The working electrode was carefully polished before each voltammogram with a 1 μm diamond paste, sonicated in an ethanol bath, washed with ethanol, and dried with compressed air. The 1 H and 13 C NMR spectra were acquired with a Bruker Avance spectrometer (300.
We also show that MRP2 is repressed following activation of JNK, Erk1/2 and NF-κB pathways by ErbB2. Finally, in datasets of human PDAC samples, ErbB2 and MRP2 expression was conversely correlated. Altogether, we propose that ErbB2 mediates several intracellular mechanisms linked to PDAC cell chemoresistance that may represent potential targets in order to ameliorate chemotherapy response and allow stratification of patients eligible for either gemcitabine or FOLFIRINOX treatment.
ErbB2, hCNT1, hCNT3, ABCG2, MRP1 and MRP2 in PDAC datasets Using PDAC datasets of the NCBI Gene Expression Omnibus (GEO, GSE28735) database, ErbB2, hCNT1, hCNT3, ABCG2, MRP1 and MRP2 mRNA expression was measured in 45 tumors (T) and adjacent non tumor tissues (ANT). We observed that ErbB2, MRP1 and MRP2 expression significantly differed (***p < 0. 001) with ErbB2 and MRP1 increased in tumor tissues whereas MRP2 mRNA level was reduced (Figure  6A ). We confirmed these alterations in GSE16515 dataset (not shown). The tumor samples exhibiting the highest (ErbB2 high , n = 10) or the lowest (ErbB2 low , n = 10) mRNA level for ErbB2 were sorted (***p < 0. 001). We found that MRP2 mRNA level was significantly reduced in ErbB2 high tumors (*p = 0. 0239) compared to ErbB2 low tumors (Figure  6B ).
Western-blotting Total cellular extracts and western blotting were performed as previously described  [40, 41]  using antibodies against phospho-Erk1/2 (Thr202/Tyr204) (clone 20G11, 1/500), Erk1/2 (clone I37F5, 1/500), NF-κB Phospho-p65 (Ser536) (clone 93H1, 1/500), NF-κB p65 (clone E498, 1/500), phospho-SAPK/JNK (Thr183/Tyr185) (9251, 1/500), SAPK/JNK (clone 56G8, 1/500), p53 (9282, 1/500), phospho-p53 (Ser15) (9284, 1/500), from Cell Signaling Technology (Ozyme, Saint Quentin Yvelines, France), hCNT1 (clone H-70, 1/200), NF-κB p50 (H-119, 1/500), MRP2 (H-17, sc-5770, 1/500), Bax (N-20, 1/500), BclXL (H-5, 1/500) from Santa Cruz Biotechnology Inc. (Heidelberg, Germany) or hCNT3 (HPA023311; 1/500), β-actin (A5441, 1/5000) from Sigma-Aldrich (St. Quentin Fallavier, France). Antibodies were diluted in 5% (w/v) non-fat dry milk in Tris-Buffered Saline Tween-20 (TBS-T).
Gene Expression Omnibus microarray Public PC microarrays were analysed from the NCBI Gene Expression Omnibus (GEO) database (http:// www. ncbi. nml. nih. gov/geo/). Two sets of gene-expression profiles from GEO containing both normal pancreas and PC tissue were used: 45 tumors and adjacent non-tumor tissues from PDAC cases (GSE28735) and 52 samples (16 had both tumor and normal expression data, and.
Statistical analyses Statistical analyses were performed using the Graphpad Prism 4. 0 software (Graphpad softwares Inc. , La Jolla, USA). Differences in data of two samples were analysed by the student's t test or ANOVA test with selected comparison using tukey post-hoc test and were considered significant for P-values < 0. 05 *, p < 0. 01 ** or p < 0. 001 ***. For paired tumor and adjacent non tumor samples, paired t test was performed.
ACKNOWLEDGMENTS We thank  MH Gevaert  and  R Siminsky  ( Department of Histology, Faculty of Medicine, University of Lille 2 ) for their technical help, the IFR114/IMPRT confocal microscopy platform (M. Tardivel), and animal facility ( D. Taillieu ). Nicolas Skrypek is the recipient of a PhD fellowship from the  Centre Hospitalier Régional et Universitaire (CHRU) de Lille/région Nord-Pas de Calais. Romain Vasseur  is a recipient of a PhD fellowship from the  Université de Lille 2. Audrey Vincent  is the recipient of a postdoctoral fellowship from the  Fondation ARC and Région Nord-Pas de Calais. Isabelle Van Seuningen. is the recipient of a " Contrat Hospitalier de Recherche Translationnelle "/CHRT 2010, AVIESAN. This work is supported by grants from  la Ligue Nationale Contre le Cancer  ( Equipe Labellisée Ligue 2010, IVS ), from  SIRIC ONCOLille ,  Grant INCaDGOS-Inserm 6041 (IVS, NJ)  and from " Contrat de Plan Etat Région " CPER Cancer 2007-2013 (IVS).
Robust optimization in machining Sun et al. [19]  have conducted a robust multi-objective optimization by particle swarm method in the field of metal forming; the objective and constraint functions are obtained by a design of numerical experiments. In addition, they used the six-sigma principle to assess the variations of stress caused by disturbances of the decision variables. Similarly, through the computerassisted manufacturing (CAM), Jeang  [20]  was able to obtain a robust substitution model by linking the machining time and the uncertainties of decision variables using the design of experiences methodology and response surface, implemented under the CATIA TM software. The minimization of the machining time under uncertainty, taking into account the quality of the machined surface, has opened new perspectives.
Strain gauges of 350 Ohm (HBM K-LY41-6/350-3-2M) are connected to a data acquisition system HBM Spider 8. 30 and the data processing is made with Catman Easy software. Digital image correlation system is also performed during tensile tests. Such technique aims at matching two digital images of a surface observed at two different states of load, generally in the reference state (unloaded) and in a deformed state  (Sutton et al. 2000). The markers used for matching the images with the DIC system are done by painting white points on the sample surface (see Fig. 2 ). The processed image with four markers allows then to obtain the strain during the load for each direction (axial and lateral). The DIC uses an Aramis sensor made of two CCD cameras 1392 x 1040 pixels. However for plane structures, only one camera is needed for measuring the 2D strain.
Results Table  1  and Fig. 7  show the elastic constants estimation obtained by means of the three different methods used to characterize the carbon fibre/epoxy composite. Since tensile test with strain gauge measurements is the technique normalized by ISO standards, results are compared to this method. Indeed, we can see a good accuracy between the 0° tensile test with strain gauges and the only data provided by the manufacturer, namely the axial Young modulus. Regarding DIC technique, we can note a very accurate determination of Young moduli (error of 5% on the mean) and (error of 2% on the mean), whereas results are less precise for Poisson ratio (error of 15 % on the mean) and shear modulus (error of 8% on the mean). Latter moduli are determined from lateral strains measurement. For carbon fibre composite subjected to axial tension, these strains exhibit a low amplitude and are then more affected by measurement inaccuracies.
They detect the so-called "slow" nucleons produced in the interaction by nuclear de-excitation processes, or knocked out by wounded nucleons  [26, 27]. The relationship of the energy deposited in the ZDC to the number of collisions requires a detailed model to describe the slow nucleon production. A heuristic approach, based on a parameterization of data from low energy experiments, is discussed in the present paper. We will show that centrality estimators using forward neutron energy and those using central multiplicity give consistent results for N part and N coll , demonstrating their connection to the collision geometry. Based on the considerations outlined above we study two different procedures for centrality estimation. The first procedure is to determine the centrality with charged particle multiplicity.
To relate the ZDC signal to the collision geometry we have developed a heuristic model for slow nucleon emission, based on a parameterization of data from low energy experiments. This heuristic approach however can provide only a model-dependent N coll determination. However, one can study the correlation of two or more observables out of which at least one is expected to scale linearly with N coll. Examples are i) the target-going multiplicity proportional to the number of wounded target nucleons (N target part = N part -1 = N coll ), ii) the multiplicity at mid-rapidity proportional to the number of participants (N part = N coll + 1), iii) the yield of hard probes, like high-p T particles at mid-rapidity proportional to N coll. These scalings can be used as an ansatz when calculating N coll based on an event selection using the ZDC.
Experimental Conditions The data were recorded during a dedicated LHC run of 4 weeks in January and February 2013. Data have been taken with two beam configurations, by inverting the direction of the two particle species, referred to as p-Pb and Pb-p, respectively, for the situations where the proton beam is moving towards positive rapidities, or vice versa. The two-in-one-magnet design of the LHC imposes the same magnetic rigidity of the beams in the two rings ,implying that the ratio of beam energies is fixed to be exactly equal to the ratio of the charge/mass ratios of each beam. Protons at 4 TeV energy collided onto fully stripped 208  82 Pb ions at 1. 58 TeV per nucleon energy resulting in collisions at √ s NN = 5. 02 TeV in the nucleon-nucleon centre-of-mass system (cms), which moves with a rapidity of ∆y NN = 0.
The fraction of remaining beam-related background after all requirements is estimated from control triggers on non-colliding or empty bunches, and found to be negligible. The resulting event sample corresponds to a so-called visible cross-section of 2. 09 ± 0. 07 barn measured in a van der Meer scan  [32]. From Monte Carlo simulations we expect that the sample consists mainly of non-single diffractive (NSD) collisions and a negligible contribution of single-diffractive (SD) and electromagnetic interactions. The VZERO-AND trigger is not fully efficient for NSD events. Previous Monte Carlo studies (for details see  [24] ) have shown that the inefficiency is observed mostly for events without reconstructed vertex, i. e. with no particles produced at central rapidities. Given the fraction of such events in data (1.
Acknowledgments: The authors would thank Mythili Prakasam, both Stanislas Peshev and M Eric Lebraud, Michel Lahaye, Laetitia Etienne and Kiyoshi Shimamura for, respectively, dielectric measurements on KNLSTN crystals, XRD analysis on KNLSTN samples, EPMA characterization, ICP-OES chemical measurements on BCTZ and KNLSTN crystals and raw materials provision. The Groupement d'Intérêt Scientifique (GIS) Advanced Materials in Aquitaine (AMA) through the Crystal Growth National Facility (CGNF) and the European Commission through the International Doctor School on Functional Materials (IDS-FUNMAT) international doctoral school for financial support are gratefully acknowledged.
Acknowledgements. We would like to thank  Dr. Stéphane Larouche  for supplying the sets of retrieved permitivities and permeabilities published in [30]. This work was supported by the  Agence Nationale pour la Recherche  (Grant  2011-BS0902101   Metakoustik-Aerospace Valley ) and was performed under the auspices of the  Labex  AMADEUS  ANR-10-LABX-0042-AMADEUS  with the help of the  French state Initiative d'Excellence IdEx   ANR-10-IDEX-003-02.
Model-Based Systems Engineering (MBSE)   with the SysML language allows the designer to include requirement capture and design representation in a single model. This paper proposes a methodology to obtain the best design alternative, from a SysML design, by using multi-objective optimization techniques. A SysML model is extended with stereotypes, objective functions, variability and constraints. Then an integer representation of the problem can be generated and solved as a constraint satisfaction problem (CSP). The paper illustrates our methodology using an Embedded Cognitive Safety System (ECSS) design. From a component repository and redundancy alternatives, the best design alternatives are generated, to minimize the total cost and maximize the estimated system reliability.
INTRODUCTION Embedded system design has become an important development activity, due to the industrial demands for new functions integration and design. These systems are mainly composed of software. However hardware components such as sensors, CPU and embedded networks have to be considered too. The designer must implement an architecture that fulfills the functionalities according to the requirements, but numerous indicators such as cost, weight and reliability have to be optimized too. These indicators typically compete with one another: Improving one of them often leads to degrading another one. In this context, this paper considers that the designer has a twofold objective: to obtain the set of optimal architecture designs and to obtain it using a Model-Based System Engineering approach that seamlessly unifies system modeling in SysML and architecture optimization.
With this approach, the DSE can be done in a stepwise manner, exploring the system model first, and then the software, hardware and allocation alternatives with current DSE approaches. The system structure is also a key point for metric evaluation (i. e. cost, weight and reliability). In this context, the objective for the designer using MBSE and SysML is to obtain the best trade-off system structure, in order to optimize objective functions such as cost and reliability. This multiobjective optimization problem can be described in mathematical term as follows: Above, f is the objective function vector and S the set of constraints. Our approach is to suggest the best configurations to the designer, that is, to find the Pareto-optimal solutions. Pareto-optimal solutions have the lowest (or equivalently low) values for all objective functions.