dataesr/scientific-paragraphs-categorization huggingface dataset:
Signals were detected and results analyzed using ABI-Prism 7000 sequence detection software (Applied Biosystems). The expression level of the genes of interest was computed relative to the mRNA expression level of the internal standard r18S as follows: relative mRNA = 1/2 (Ctgene of interest-Ctr 18S). PA-SMC growth assays. PA-SMCs from controls were seeded at a density of 5?10 4 cells/per well in Dulbecco's modified Eagle's medium supplemented with 10% FCS and allowed to adhere. The cells were subjected to 48 h of growth arrest in medium containing 0% FCS then treated with 1 mL of the various conditioned media collected from control PECs. PEC serum-free medium was obtained as follows: at the time of initiating PA-SMC growth arrest, PECs were seeded in 24-well plates at a density of 5?10 4 cells per well and were allowed to adhere and to grow in supplemented MCDB 131 as described above, for 24 h.
Nevertheless, IL-6 and MCP-1, two cytokines previously implicated in PAH  [22] , were expressed at higher levels, both in normoxic and in hypoxic Eng +/2 mice. The higher expression levels of these cytokines were in accordance with the degree of macrophage infiltration, which was more marked in lungs from Eng +/2 mice. We investigated the mechanism by which Eng +/2 mice were partially protected against hypoxic PH and we measured growth factors involved in the development of human and experimental PAH. In keeping with previous data on PAH  [23] , chronic hypoxia was associated with increased preproET-1 expression in both genotypes but the increase was significantly smaller in Eng +/2 mice than in wild-type mice. Because PA-SMC hyperplasia is among the main pathological changes in patients with PAH, we focused on the consequence of ENG deficiency in growth factor production in our experimental PAH model.
This study was supported by grants from the  INSERM , and the  Agence National de la Recherche  ( ANR-08-GENOPAT-004  to S. E. , A. L-V and M. H. ). This article reflects only the authors' views and under no circumstances is the European Community liable for any use that may be made of the information it contains. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Based on our experiments and numerical calculations, we propose in both cases a possible RS mechanism. We studied perpendicular Au (50 nm)/TiO 2 (100 nm)/Cu (70 nm) junctions with electrode area of 20 lm Â 20 lm in a crossbar pattern (see inset of Fig. 1 ). Amorphous TiO 2 films were deposited by reactive sputtering with a pressure of 2. 7 Pa, and a power of 150 W at room temperature. Bottom and top electrodes (BE and TE) were deposited by the thermal evaporation method and a lift-off process. 13 evices from the same crossbar pattern were initialized with either positive or negative voltage ramps. The electrical characterization was performed using a source-measurement unit Keithley 2612A, a personal computer with general purpose interface bus connections and Labview based software. Voltage pulses of variable amplitude and 1 ms time width were injected through the TE (with a delay of 100 ms FIG.
Population and samples For the current cross-sectional analysis, we used the baseline data of two French cohorts of elderly people aged 65 years and over: The AMI (Approche Multidisciplinaire Integree) cohort and Three-City (3C) Study. Between 1999-2000, 9,294 elderly community-dwellers were included in the 3C cohort study, chosen from the electoral rolls of 3 large French cities and their suburbs: Bordeaux (n = 2,104), Dijon (n = 4,931) and Montpellier (n = 2,259). The aim of 3C is to study the vascular risk factors of dementia; its methodology was described previously  [11]. In 2007, AMI included 1,002 subjects living in rural areas in Gironde, an administrative area in southwest France, randomly recruited from the reimbursement database of the unique French Farmer Health Insurance System.
At baseline, 961 of these individuals were living at home. All had worked in the field of agriculture for at least 20 years. The aim of AMI is to study health and aging in elderly farmers living in rural areas. Details on this cohort have been published previously  [12]. For 3C, the protocol was approved by the Consultative Committee for the Protection of Persons participating in Biomedical Research of the Kremlin-Bicetre University Hospital (Paris). AMI was approved by the Ethics Committee of the University Hospital of Bordeaux according to the principles of the Declaration of Helsinki. All participants signed a written consent. In both cohorts, data on socio-demographics, lifestyle, neuropsychological testing, physical examination, blood sampling, symptoms and complaints, medical history and food intake were collected at baseline.
Results Of the 961 subjects included in the AMI cohort and living at home, the standard MNA was available for 851 individuals. Excluded subjects had lower incomes, were more often demented (18% vs. 9%) and dependent for ADLs (11. 0% vs. 5. 0%). Among these 851 subjects, the proxy MNA was available for 692 individuals (81. 3%). The 159 subjects with missing data in the proxy MNA were older, more often widowed, had a lower level of education, a lower income and were in poorer health. The mean age of the 692 included subjects was 75. 5 years (standard deviation (SD) 6. 2). Participants were mainly males (62. 0%), married (71. 0%), had a low level of education (49. 4% primary or less, 32. 2% short secondary school) and half earned between 750 and 1,500 Euros per month (Table  2 ). Of the 9,294 subjects included in the 3C cohort, 603 were excluded due to missing data in the proxy MNA.
First, participants in this analysis were selected since only subjects with no missing data were included. Indeed, in the AMI sample, the standard MNA was available on 851 subjects for whom the frequency of poor nutritional status was estimated to 9%. When considering only subjects with no missing data to reconstruct the proxy MNA, 692 subjects were included, leading to a frequency of poor nutritional status measured with the standard MNA of 7. 4%. Secondly, the proxy MNA lacks sensitivity as it was estimated to be 76. 4%, leading to an underestimation of the frequency of poor nutritional status, although the frequency was corrected using the Rogan-Gladen estimator. The lack of sensitivity is mainly due to border effects since subjects considered as having a poor nutritional status according to the standard MNA were close to the threshold when using the proxy MNA.
committee. When the proposal is accepted, the database access is granted for 6 months. The procedure to get agreement on the transmission of data and materials is described in the website: http://www. three-city-study. com/ancillary-studies. php Funding: The 3C Study is conducted under a partnership agreement between the  Institut National de la Santeet de la Recherche Medicale (INSERM) , the  Victor Segalen -Bordeaux II University  and the  Sanofi-Synthelabo Company. The Fondation pour la  Recherche Me  ´dicale funded the preparation and initiation of the study. The 3C Study is also supported by the  Caisse Nationale Maladie des Travailleurs Salaries ,  Direction Generale de la Sante, Conseils Regionaux of Aquitaine, Languedoc-Roussillon and Bourgogne, Fondation de France, Ministry of Research-INSERM Programme 'Cohortes et collections de donnees biologiques', Mutuelle Generale de l'Education Nationale, Institut de la longevite, Conseil General de la Cote  d'or.
Data for gray/white matter probabilistic template To create the gray/white matter probabilistic template, 15 other subjects were used (mean age: 27 ± 5 y. o. , 9 men and 6 women) as part of an already-published study  (Taso et al. , 2014b). Data were acquired on a 3T MRI system (Verio, Siemens Healthcare, Erlangen, Germany) at the CEMEREM, La Timone Hospital (Marseille, France). The local ethics committee approved all experimental procedures and written informed consent was obtained from each participant. The body coil was used for excitation and signal reception was achieved using a combination of 12-channel head-coil, 4-channel neck coil, 24-channel spine matrix array and flexible 6-channel body coil for thoracic and lumbar levels. The imaging protocol included a multi-echo gradient echo sequence with the following parameters: axial orientation (each slab perpendicular to the spinal cord), five echoes, effective TE = 27 ms, flip angle = 28°, FOV = 180×135 mm 2 , in-plane resolution 0.
Data for validation Validation was assessed from additional 16 healthy subjects (mean age: 25 ± 6 y. o. , 6 men and 10 women). These subjects were different from the subjects used to produce the T 2 template and the gray/white matter template. In order to remove biases associated with scanning at the same institution (e. g. , patient handling, sequence parameters, scanner), these subjects were scanned at another institution (Functional Neuroimaging Unit, CRIUGM, Université de Montréal, Montreal, Canada). Data were acquired on a 3T MRI system (TIM Trio, Siemens Healthcare, Erlangen, Germany) using the commercial 12channel head-coil, 4-channel neck coil and a 24-channel spine matrix array. Sequence used for registration to the template was a T 2 -weighted 3D FSE, sagittal orientation, 52 slices, FOV = 384 mm, voxel size = 1×1×1 mm 3 , TR = 1500 ms, TE = 119 ms, flip angle = 140°, bandwidth = 723 Hz/pixel, parallel acquisition with R=3 (GRAPPA reconstruction).
Fusion between the MNI-Poly and the AMU templates After resampling the AMU template into the voxel grid of the MNI-Poly T 2 template, it is still necessary to register the two datasets so that anatomical features are aligned. Coregistration between MNI-Poly and AMU templates first involved two scaling factors in the x and y directions (i. e. , no z-translation nor rotations were considered given the R-L symmetric nature of the MNI-Poly T 2 and AMU templates). The transformation was estimated slice-wise using regularization constraints along z (smoothing of scaling factors along z). A second step consisted in non-linear co-registration using ANTs  (Avants et al. , 2008). Parameters were: SyN transformation (symmetric image normalization method for estimating diffeomorphic functions), 0. 2 mm gradient step (characterizes the gradient descent optimization), mutual information metric, constrained in the x-y plane, 100x100 iterations (i.
To check the validity of this approach, manual segmentations 14/37 were performed on three random subjects from C1 to T3, without any interpolation (about 160 slices per subject). The 3D DICE coefficient was computed between the semi-manual ROI and the manual ROI. Results gave 3D DICE of 0. 994, 0. 985 and 0. 997 for each subject respectively, suggesting that the semi-manual approach is an acceptable ground truth for assessing registration accuracy with the template. The semi-manual segmentations from the validation data (15 subjects) were then used to calculate following metrics describing goodness of the spine cross-section measurement:  Differences between the spinal cord cross-section areas, for each perpendicular slice along the length of the cord from C1 to T3.  3D Dice Kappa overlap coefficient  (Dice, 1945) , comparing the manuallysegmented cord and the template-based segmentation warped to the native space of the subject's anatomical data.
Applications and Perspectives The outputs of the registration pipeline include two warping fields: one to register the template to the subject's anatomical data (forward) and the other to register the subject's anatomical data to the template (backward). Moreover, other useful data associated with the template are provided in the subject's anatomical space, such as spinal cord and CSF binary masks, white and gray matter probabilistic masks and labeling of vertebral level. For example, the CSF mask can be used to estimate a physiological noise regressor in fMRI experiments  (Brooks et al. , 2008) , which otherwise has to be performed manually. The probabilistic white matter template, once registered to the subject's space, represents useful information to automatically quantify multi-parametric data sensitive to white matter microstructure, such as DTI and magnetization transfer.
Conclusion This paper presented an unbiased average anatomical template of the human spinal cord, as well as a quasi-automatic image processing pipeline that registers new subjects to the template. The template can notably be used for measurements of spinal cord crosssectional area, voxel-based morphometry, identification of anatomical features (e. g. , vertebral levels, white and gray matter location) and unbiased extraction of multiparametric data. The MNI-Poly-AMU template and image processing software are freely available for MINC (http://www. bic. mni. mcgill. ca/ServicesAtlases) and for NIFTI file format (http://sourceforge. net/projects/spinalcordtoolbox/).
Acknowledgements The authors thank  Kevin Nigaud  (CENIR),  Carollyn Hurst  and  André Cyr  ( CRIUGM ) for assistance with MRI acquisitions. This study was supported by the  Association Française contre les Myopathies (AFM) , the  Institut pour la Recherche sur la Moelle épinière et l'Encéphale (IRME) , the  SensoriMotor Rehabilitation Research Team of the Canadian Institute of Health Research , the  National MS Society  [ FG1892A1/1 ], the  Fonds de Recherche du Québec-Santé , the  Quebec BioImaging Network  and the  Natural Sciences and Engineering Research Council of Canada  and the  French National Research Agency  (" Investissements d'Avenir" ,  A*MIDEX  project  n°ANR-11-IDEX-0001-02 ).
The kinase reaction was initiated by addition of 5 ml of buffer consisting of 100 mM 3-[n-morpholino] propanesulfonic acid pH 7. 2, 20 mM paranitrophenyl phosphate, 40 mM b-glycerolphosphate, 20 mM MgCl 2 , 10 mM EGTA, 0. 2 mM EDTA, 5 mM cAMP-dependent protein kinase inhibitor, 2 mM benzamidine, 40 mg/ml leupeptin, 40 mg/ml aprotinin, 600 mM ATP, 2 mg H1/ml, 3 mg MBP/ml) and 500 mCi/ml [c-32 P]ATP (GE Healthcare Life Sciences, UK). The reaction was conducted for 30 min at 30uC and terminated by the addition of 10 ml Laemmli sample buffer and boiling for 3 min. After electrophoresis on 15% SDS PAGE gels, it was stained with Coomasie Blue R250, destained overnight, dried and autoradiographed. Phosphorylated histone H1 and MBP signals were visualised by MultiGauge 2. 0 software and related to metaphase I oocytes after 24 h cultivation, where we expected the peak of kinase activity  [34].
To unveil the presumed monogenetic cause of disease, single-nucleotide polymorphism (SNP) array-based homozygosity mapping of P1 and P2 (Fig. 1b  and Supplementary Table  4 ) was combined with exome sequencing (ES) (Fig. 1c ) of P1. Single-nucleotide variants (SNVs) and insertion/deletion variants resulting from ES were filtered for those present inside homozygous candidate intervals shared between both affected patients. Synonymous and non-coding variants were excluded. We identified a single homozygous variant on chromosome 17q21 in MAP3K14 (c. C1694G, p. Pro565Arg) present in both patients (Fig. 1d  and Supplementary Fig. 1 ), which was not detected in dbSNPbuild137, 1000Genomes, ENSEMBL, UCSC, NCBI or EVS (Exome Variant Server) public SNP databases. The Pro565 residue of NIK is located within the kinase domain of the protein (Fig.
Notably, production of interferon-g and TNFa were markedly reduced in patient NK cells, in comparison with stimulated healthy donor cells (Fig. 7c ). Although patient NK cells expressed comparable levels of perforin compared with healthy donor cells (Supplementary Fig. 8 ), they degranulated at a significantly lower frequency as measured by the expression of CD107a (LAMP1) on the cell surface after stimulation (Fig. 7c ). To further define the cytolytic potential of these cells, we evaluated key components of cytotoxicity by quantitative confocal microscopy. Patient-derived NK cells failed to accumulate F-actin at the immunological synapse following incubation with susceptible targets (Fig. 7d, e ). In addition, lytic granules failed to polarize to the lytic synapse (Fig. 7e ). In concert with the flow cytometric analyses, these data suggest a marked inability of NIK Pro565Arg NK cells to become activated and exert cytolytic function.
Methods Patient and ethics. This study has been approved by the ethics committee at the Medical University of Vienna, Austria. Biological material was obtained on informed consent in accordance with the Declaration of Helsinki. Clinical data from the patients was provided in anonymized form by the responsible physician(s). The patients were evaluated, followed up and treated at the Department of Immunology at Ankara University in Turkey, covered by the local ethics agreement. Homozygosity mapping. Affymetrix 6. 0 SNP-based homozygosity mapping was performed in both patients and in both parents of P1, to map homozygous intervals common to both patients but not present in the parents. Ten microlitres of 50 ng ml À 1 DNA from the patients were used. The protocol was carried out according to the Affymetrix Genome-Wide Human SNP Nsp/Sty 6.
0 protocol. The results were analysed using the Affymetrix Genotyping Console software and PLINK whole genome data analysis toolset (http://pngu. mgh. harvard. edu/Bpurcell/plink/) as previously described  61. Exome sequencing. A multiplexed 50-bp paired-end read ES was carried out for P1 on Illumina HiSeq2000 Sequencer running on HiSeq Control Software 1. 4. 8, Real Time Analysis Software 1. 12. 4. 2. The sample preparation used 1 mg of genomic DNA fragmented using Illumina TruSeq DNA Sample Preparation Guide and the Illumina TruSeq Exome Enrichment Guide version 3. The DNA fragment clusters generated ran in a multiplexed pool with five other samples distributed on three lanes of the flow cell. The data analysis was carried out as previously described  62  using Burrows-Wheeler Aligner to align the reads to the human genome 19.
Insertion/deletion realignment was performed as well as GATK (Genome Analysis Toolkit) base quality score recalibration. For SNV and insertion/deletion calling, Unified Genotyper and GATK Variant quality score recalibration was performed. SNV and insertion/deletion lists were uploaded to SeattleSeq Annotation database. Known variants (present in 1000Genomes or dbSNP build 137, date of accession: 2 January 2012) were excluded and the lists were filtered for nonsense, missense and splicesite variants present within the homozygous regions detected in both patients and absent in the parents. In addition, ENSEMBL, UCSC, NCBI and EVS public SNP databases (date of accession: 20 February 2012) were interrogated for presence of the variant. The validation and segregation of the variants found in the final hit list from ES were performed using capillary sequencing on genomic DNA from both patients and family members as described below.
Variant validation by capillary sequencing. Primers for the variants detected with whole ES were designed using ExonPrimer software from the Helmholtz Center Munich (http://ihg. gsf. de/ihg/ExonPrimer. html) and PrimerZ  63  , respectively, and ordered from Sigma Aldrich, Austria. PCR amplification of the detected variants was performed using Expand High Fidelity PCR System (Roche, Basel, Switzerland). Capillary sequencing of amplicons was performed on the Applied Biosystems 3130xl Genetic Analyzer capillary sequencer running 3130xl Genetic Analyzer Data Collection Software v3. 0, using Big Dye Terminator v3. 1 Cycle Sequencing Kit (Applied Biosystems, Germany). Sequence Analysis Software Version 5. 2 was used for analysis of the sequences and heterozygous signals with ambiguity code were indicated when 25% of the signal intensity was exceeded.
Reads were aligned to reference sequences using the Sequencher software, version 4. 10. 1. In silico analyses and modelling of NIK protein structure. The algorithms SIFT  64 , PolyPhen2 (ref. 65)  (website accessed: 27 March 2012) and CUPSAT  66  (website accessed: 9 December 2013) tools were used to predict the effect of the identified mutation on protein function. To obtain a hypothesis about the change in protein structure and dynamics of the NIK variant compared with the wild-type, molecular dynamics (MD) simulations of NIK wild-type and NIK Pro565Arg were performed using the coarsegrained model FREADY  67  implemented in MOIL 68 molecular modelling package. We initiated the MD simulations from the crystal structure of NIK (PDB ID 4G3D, chain A  14  ) and let it run for 50 ns at 300 K.
Cells were then fixed and permeabilized with Cytofix/Cytoperm solution (BD Biosciences). All analyses were performed using FlowJo X (TreeStar Inc. ) and data were graphed with Prism 6. 0 (GraphPad Software). Flow cytometry-based sorting of peripheral B-cell populations stained with anti-CD19-PerCP-Cy5. 5, anti-CD27-BV421, anti-CD3-APC-H7 and anti-IgD-FITC as described above was performed on ultra-high-speed six-way digital cell sorter from Beckmann Coulter at the Medical University Vienna Flow Cytometry Core Facility. Magnetic microbeads based sorting of peripheral B cells was performed using anti-CD20 paramagnetic labelling according to the manufacturer's instructions (130-091-104, Miltenyi Biotec, Bergisch-Gladbach, Germany). Quantitative real-time PCR analysis. Extraction of RNA from sorted B cells was performed using RNeasy kit from Qiagen, first-strand complementary DNA synthesis was done using Expand Reverse Transcriptase from Roche using both oligo-dT and random hexamer primers, and gene expression was analysed by quantitative PCR using Kappa Sybr Fast qPCR MasterMix ABI Bioprism from Kappa Biosystems on 7900HT Fast Real-Time PCR System from Applied Biosciences according to manufacturers' instructions.
9), 20% glycerol, 50 mM KCl, 400 mM NaCl, 1 mM EDTA, 1 mM dithiothreitol, 5 mM b-glycerophosphate, 1 mM phenylmethyl sulphonyl fluoride, 5 mg ml À 1 apronitin, 10 mM NaF, 5 mg ml À 1 leupeptin and 5 mM Na 3 VO 4 , and subsequently subjected to SDS-PAGE and immunoblot analysis. Amplification and sequence analysis of IGH transcripts. IgA and IgG transcripts were amplified from cDNA of thawed PBMCs using subgroup-specific forward primers in the leader sequence of IGHV3 and IGHV4 in combination with a Ca or Cg consensus reverse primer  22, 74. All PCR products were cloned into the pGEM-T easy vector (Promega) and prepared for sequencing on an ABIPRISM 3130xl (Applied Biosystems). Obtained sequences were analysed with the IMGT database (http://www. imgt. org/) for IGHV, IGHD and IGHJ use, and mutation analysis  75.
0. Immunostaining of lymphotoxin-stimulated fibroblasts. Fibroblasts of patient (P2) and healthy donor were stimulated with 100 ng ml À 1 of lymphotoxin a1/b2 (R&D Systems, 678-LY-010) for 4 h. After stimulation, cells were fixed with 4% formaldehyde in PBS for 30 min and then blocked and permeabilized with solution containing 10% FCS plus 0. 1% Triton X-100. Cells were immunostained with DAPI and rabbit antibodies against NFkB2 (p100/p52) (Cell Signaling, 3017) and NF-kB (p105/p50) (Cell Signaling, 3035) at a dilution of 1:100, respectively, and afterwards with anti-rabbit Alexa Fluor 546-conjugated antibody at a dilution of 1:500 (Life Technologies, A10040). Images were acquired on a Leica AF6000 fluorescent microscope using Leica LASAF software for acquisition. Images were taken at Â 64 magnification.
Acknowledgements We thank the patients and their families for participation in the study. The help of all contributing medical, technical and administrative staff is greatly acknowledged. We thank  Nina Serwas ,  Tatjana Hirschmugl  and Ays¸enur O ¨ztu ¨rk for help with experimental procedures and critical scientific discussions. This study was supported by grants from the  European Research Council  ( ERC StG 310857  to K. B. ) and the  Austrian Science Fund (FWF) START  programme  Y595-B13  (to K. B. ), the  Deutsche Forschungsgemeinschaft  ( TRR130 ,  P06 ) and the  German Cancer Research Fund  (both to H. E. and H. S. ). S. K. is supported by  CAPES-PDSE doctoral fellowship  (process number  6911/12-9 ).