dataesr/scientific-paragraphs-categorization huggingface dataset:
Furthermore the Gateway may even potentially host all monitoring services of data operation as well as some remote control or monitoring applications for instruments and devices when applicable. The continuous and cooperative software development within the CTAC requires some consortium shared services such as a software repository, development tools, version track services and software validation test benches. Most are currently implemented and already in use in CTA, and will evolve in the future into a single web-oriented global platform of services. Access to the development services, Gateway, and other CTA web resources will be based on each user's profile and category (e. g. basic, advanced users, managers, collaboration users, etc). For such a purpose an Authentication and Authorization infrastructure is under development and will be applied to extend the use of the CTA Gateway to any user tuned according to their own role and/or access rights.
Data Model In the context of the development of a global Data Model for CTA, some prototyping work has been conducted around the application of Compressed FITs format (CFITS) as a file format for Low Level Data, resulting in a viable and cost-effective solution. For higher level camera data a flexible format is looked for. Three formats are under consideration and prototyped: one based on the Google Protocol Buffers specification, a specific eventio format developed for the HESS experiment, and a stream data format based on satellite missions: packetLib. Packetlib, is a software library that manages complex data layouts described with XML files, providing introspection, having a strong memory management and performing a non linear decoding: this, coupled with the Consultative Committee for Space Data Systems (CCSDS) space packets standard enables a fast and on-the-fly data identification, access and routing.
Pipelines Pipelines refers to all software components necessary to process real and simulated raw data and produce the final end products needed for science analysis, along with any associated quality monitoring and technical data. A pipeline is defined as a sequence of data processing steps that are applied to data to achieve a high-level goal. The logical design of data reconstruction and analysis pipelines is well understood, it relies on the software in use in current experiments such as HESS, MAGIC and VERITAS, complemented by recent explorative developments from precursors such as FACT and ASTRI. Main prototyping activities were around the evaluation of software frameworks based on C/C++ languages, Python, Hadoop using modern MapReduce computing method. Further comparative studies concerned: adapting FITS data format to Hadoop files management methods, combining Python and C++ for inter-process communication in the context of the real-time data streaming  [2]  with FPGA and GPU hardware accelerators.
Information and Computing infrastructures The majority of the computing resources for the CTA massive MC simulation production and analysis are linked to each other with the Grid e-infrastructures and they have allowed DATA to evaluate the Grid approach through a dedicated pathfinder initiative: CTACG. Among the different prototyping activities within CTACG, the DIRAC (Distributed Infrastructure with Remote Agent Control) WMS prototype was intensively tested and evaluated as a solution to handle the MC production. DIRAC was identified as useful and appropriate for the following purposes: (i) Production job handling: e. g. for pipelines (Monte-Carlo Production, Data reduction pipeline, Onsite Reconstruction and Analysis); (ii) User analysis job handling and data management  [4]. Some prototyping activities were conducted in order to build up an SAS through the web-base Science Gateway for CTA.
Organization The organization of the activities within DATA is structured around the evolution of the overall CTA project, the complementary of the CTAC and CTAO roles and their respective internal managements, and the proposed computing and functional models. In Figure  2  an overview of the logical implementation of the DATA baseline design is represented. At the same time some growing operational activities are managed by DATA: e. g. the software development services centrally managed at the computing centre CCIN2P3 and supported by a dedicated international "CTA support group"; the DCI-Grid resources technical coordination for massive MC production (e. g. CTACG), including more than twenty computing centres distributed in several countries (France, Germany, Poland, Italy, Spain and others).
During the construction phase, the DATA project organization will evolve to take into account the requirements settled on by the test and pre-production operation phases of an increasing number of DATA products. The CTAC will organize itself in "competence centres" such as specific and continuous software development groups or technical and auxiliary devices monitoring groups (see Figure  2 ). In the construction phase the same competence groups will be in charge of bringing in operation and support their products. During the operation phase some key experts within the CTAO will have the commitment to guarantee the operation and maintenance of any piece of software and DATA services, while the competence centres will be the CTAC instances, which will guarantee the software and services upgrading according to the contingent needs.
Conclusions A technical design of the complete data life cycle and management for the CTA observatory has been finalized. A set of solutions and a series of prototypes have been proposed to organize the Science Data Center of the CTA observatory. In the next years, entering in the CTA construction phase, an intense implementation activity is expected within the DATA project. Some major technical choices will be required and the computing model could also evolve in consideration of the CTA sites final location, new requirements and the potential evolution of computing architectures.
Our work demonstrated that RNA purified from EBC can be used for qRT-PCR-based isoform-specific expression analysis of GATA6 and NKX2-1, despite the relatively high fragmentation of the isolated RNA (Appendix Supplementary Results). Similarly, qRT-PCR-based expression of genes has been successfully   (Li et al, 2000)  whereas the GATA6 isoforms were detected in other tissues  (Brewer et al, 1999). Analysis of RNA-sequencing data deposited at The Cancer Genome Atlas (TCGA; http://cancergenome. nih. gov/) confirmed the increased expression of the Em isoform of GATA6 in LC samples when compared with control samples (Fig  EV5 ). However,    EV1. EMBO Molecular Medicine Vol 8 | No 12 | 2016 ª 2016 The Authors discrimination between both NKX2-1 isoforms was not possible due to the data format available at the TCGA.
we performed a Tukey's HSD after multivariate analysis of variance (MANOVA; Table  EV3 ). In the EV Figs, the data are represented as mean AE standard error (mean AE s. e. m. ). One-way ANOVA was used to determine the levels of difference between the groups. P-values ˂ 0. 05 were considered as statistically significant. Two files are provided for reproducing the results presented in the main figures and in the tables: an R Markdown file (GATA6_NK-X2_1_EBC. Rmd) together with a file containing the raw data (Raw_data. csv) as Dataset EV1. (i) Both files have to be located into the folder, in which the output of the R Markdown should be saved. (ii) To run the R Markdown file, R version ≥ 2. 15. 0 and R Studio are required. (iii) After opening the R Markdown file with R Studio, the Knitr option should be selected.
GER, samples collected in Germany; MEX, samples collected in Mexico. D Box plots of Em/Ad of GATA6 (left) or NKX2-1 (right) in FFPE lung tissue sections from controls or LC patients. Samples were staged according to the TNM classification (Sobin et al, 2009). Data information: Each point represents one sample. The five-number summary and the statistical test values from each plot are shown in TablesEV1 and EV2.
Acknowledgements We thank  R. Bender  for technical support;  K. Müller  for support in sample collection;  M. Besssler. J. Kwon  for reagents; and  M. Wheeler  for helpful discussions. G. Barreto  is funded by the " LOEWE-Initiative der Landesförderung " (III  L4-18/15. 0042009 ) and the  DFG  grant  BA 4036/1-2. A. J. Romero-Olmedo  received a doctoral fellowship from  CONACyT-COCyT  ( CVU 510283 ). This work was done within the  Russian Government Program of Competitive Growth  of the  Kazan Federal University.
6 G 0. 4 N reduce it even further. Figures  2(c-h ) are elemental maps of the distribution of the three elements nitrogen, indium and gallium calculated using two different methods for fitting the data, using either a pixel-wise automated edge detection routine  [27]  with inverse power-law or exponential background fit and subtraction in the pre-edge regions, net integration over certain ranges and quantification using tabulated Hartree-Slater cross-sections or a recursive multiple linear-least squares fitting to Hartree-Slater models of edges tabulated in Gatan Digital Micrograph GMS3 software  [28]. The speckle contrast in these maps is a superposition of shot noise (which should depend only on the acquired data and therefore be the same in left and right columns) but also to some degree due to the different background subtraction and fit procedures (where the two algorithms used differ).
The zero loss peak was subtracted prior to the fits and thus not included. The differences are subtle, with a slightly reduced plasmon peak width and a slight undulation of the Ga core loss signal at the lower acceleration voltage which we tentatively attribute to the individual onsets of M 5 , M 4 and M 3 partial edges that become visible when the acceleration voltage is reduced, the energy resolution improved and the collection angle increased. In other words, the plasmon has not really become narrower at lower acceleration voltage but the fitting routine transferred some of the broadening of the core losses at 197kV due to the higher aberrations of the older spectrometer to the plasmon loss region. This directly meant that the database of InGaN reference spectra previously acquired for 197kV in the JEOL microscope (see figure  4a ) had to be compiled afresh, now for monochromated measurements at 60kV.
Implementation and experimental results The DSS is implemented on Visual Basic for Application (VBA) as a user interface. The optimisation models, deterministic and stochastic, have been implemented in Xpress, and integrated in the DSS. VBA provides a platform with a high degree of flexibility and control, for constructing the user interface. It also gives the ability to simply import/export data from/to an external database  (Agilent Technologies, 2007). Xpress is used to search the optimal solution(s) based on the input data for a particular offshore wind farm. An execution of the DSS using a sample case is described in this section, which will detail the input data and output results. The sensitivity of the DSS is also tested by changing the failure rates and size of OWF.
System input data collection The essential system input data of the DSS was collected using an online survey, which was completed by different offshore wind stakeholders. Twenty-nine experts in the sector gave responses to the online survey, including O&M managers, O&M consultants, engineering technicians, and port managers. Further details of the online survey and responses are available on the 2OM project WP1: Maintenance Decision Support Tool  (Li et al, 2015a). Following on from the survey, a number of interviews to key experts in the industry (including O&M managers and port managers), were arranged in order to acquire further practical information of O&M and to validate the DSS and receive constructive feedback on how the DSS could be improved. In addition, working groups with specialists from the sector was another efficient way to understand the operational issues in offshore wind maintenance.
All collected data has been filtered and aggregated, and then entered into the DSS as the system inputs. Characteristics of the nine maintenance categories are pre-defined in the system, including preparation time, repair/replacement time, logistics time and number of technicians required for each maintenance category. The categorisation of preventive (scheduled) and corrective (unscheduled) maintenance is described in section 3. For the technical specification of wind turbines, such as rated capacity and rated wind speed, they are available from the 4cOffshore website (http:// 4cOffshore. com). The VBA-based user interface allows users to modify the parameters and save the settings in the system input data. The saved information can be loaded to the memory for running the system. The user-defined settings are transferred to the software to make decisions for the particular wind farm.
Sample case In order to evaluate the proficiency of DSS an implementation with sample data has been carried out. A user input data form has been created with a series of questions to ask the user for the technical, structural and environmental information for an offshore wind farm. The input information is comprised of wind turbines, balance of plant, location and sea state (see Figure  2 ). The data of Rampion offshore wind farm is used for the user inputs as a sample. Rampion wind farm was a case study for the 2OM (Offshore Operations & Maintenance Mutualisation) project, financed by the EU Interreg IVA France (Channel) -England programme, so the proposed models have been tested on estimated data from the Rampion wind farm since the site (in common with other similar round 3 UK sites) has not yet been built.
Rampion offshore wind farm is off the South Coast of the UK, and it is one of the new 'round 3' sites designated by the UK government. 116 wind turbines are currently planned to be installed at the farm, which are specified technically by the rated capacity of 3. 45MW and the rated wind speed of 12. 5m/s. The average distance from onshore to the farm is 16. 9km and the water depth range is between 19 and 39m. Monopile foundations are used to give each wind turbine a total height of 140m. Two 23-km export cables and 140km array cables will be installed. The mean wind speed over the last 10 years is 10m/s. Figure  3 : System input data form of vessels and technicians Maintenance frequency for both preventive and corrective activities, as the critical parameters to identify the workloads, must be supplied at the next stage (see Figure  4 ).
Centrosome imaging, tracking and analysis Embryos of the control TH27 strain, gpr-1/2(RNAi), zyg-9(RNAi) and the fixed embryos were imaged using an AxioVision imager 2e upright microscope (Zeiss, Jena, Germany). All other embryos were imaged with an AxioImager M1. The microscopes were modified for long-term imaging by adding an extra heat filter in the mercury lamp light path, and by using a 12 nm bandpass excitation filter centered on 485 nm (AHF Analysentechnik, Tübingen, Germany). These filters helped to prevent phototoxicity and reduce bleaching. Images were collected using a 512x512 pixel back-illuminated emCCD camera (iXon+ on the AxioVision and an iXon 3 on the AxioImager) from Andor Technologies (Belfast, UK) running Solis software. We confirmed that photodamage was not serious by checking that the rate of subsequent divisions was normal  (19).
The acquisition frame rate was 31. 23 frames/s for the iXon+ 32. 95 frames/s for the iXon3, and with 4096 frames (corresponding to a total time of 131 s and 124. 3 s respectively), the frequency ranges were 7. 6 mHz to 15. 6 Hz and 8. 0 mHz to 16. 5 Hz s respectively. The time interval used for measurements started 30 seconds after nuclear envelope breakdown. All analysis software was written in Matlab (The Mathworks). Statistical significance calculated with a two-tailed Welch t-test.
Power spectra and curve fitting From the time-series of the spindle's transverse position, we computed the one-sided power spectral density function, # , where f is frequency, using MatLab's fast Fourier transform  (21). We refer to this as the power spectrum. It has the property that 2 where # is the maximum frequency, # is the value in the ith frequency increment, # is the frequency increment and # is the variance of the time series. We fit the data to a Lorentzian model and to second-order model. where # and # are the shorter and longer time constants. This reduces to the Lorentzian when #. To estimate the parameter values we performed least-square fitting, minimizing: # 5 where # is averaged power spectrum over the 8 embryos, # is the theoretical spectral density (the Lorentzian or the second-order model) and i indexes the different frequencies.
The stability of spindle positioning To assess the stability of the spindle centering machinery, we measured the variance of the fluctuations of spindle position and orientation in individual embryos. We band-pass filtered the time-traces between 0. 1 Hz and 1. 1 Hz using the robust local regression algorithm (rloess)  (21)  to remove mean, residual drift (see below), avoid any contribution from spindle oscillations (0. 04 Hz, (  26 )) and remove high-frequency noise due to the tracking algorithm (see below). The standard deviations of these filtered traces were 35. 8 ± 18. 0 nm (mean in quadrature ± SD, N = 30) along the AP-axis (Sx) and 22. 8 ± 3. 6 nm along the transverse axis (Sy) (Table  1 , top line). These data are displayed in Table  2. The standard deviation of the filtered orientation (Sa) was 0.
Acknowledgements The authors thank  Dr C. Kozlowski & Dr F. Nedelec  for providing their landing assay algorithm,  Drs C. Brangwynne ,  H. Bouvrais ,  L. Chesneau & Y. Le Cunff  for comments on the manuscript and  Drs H. Fantana ,  V. Bormuth ,  G. Greenan & E. Schäffer  for stimulating discussions. J. P. was supported by the  Human Frontier Science Program Organization. The PécréauxLab was funded by the  CNRS/INSERM and "Ligue Nationale Contre le Cancer, LNCC" (ATIP/Avenir)  and by the " Région Bretagne " (grant AniDyn). B. M. was supported by a LNCC PhD fellowship. JH was supported by the  Max Planck Society and Yale University. We thank an anonymous reviewer of an earlier draft of this manuscript for detailed criticisms which led to a substantial improvement in the analysis of the data.
SPECT data analysis Image data analysis of SPECT/CT data was performed using the Inveon™ Research Workspace software package (Siemens Healthcare, Erlangen, Germany). Volumes of interest (VOIs) in equal size and orientation were applied in order to quantify tracer uptake in left and right striatum as well as in the cerebellum. A 50% threshold of the VOI maximum was applied to the VOI for right striatum, and the resulting VOI 50%right was mirrored to the left brain hemisphere in order to quantify the left striatum (VOI 50%left ). [ 123 I]Ioflupane uptake was quantified as mean specific tracer uptake ([mean uptake striatum 50%left/rightmean uptake cerebellum] / mean uptake cerebellum) and the specific uptake ratio left/right was calculated. Representative images show SPECT and magnetic resonance (MR) images that were coregistered using the contour of the mouse skull.
Positron emission computed tomography (PET) Radiosynthesis of [ 18 F]DPA-714 (N,N-diethyl-2-(2-(4-(2-[ 18 F]fluoroethoxy)phenyl)-5,7dimethylpyrazolo[1,5-a]pyrimidin-3-yl)acetamide) was conducted as described elsewhere  (Damont et al. , 2008 , James et al. , 2008). Animals were anaesthetised with 1. 5% isoflurane (Abbott Animal Health) in 100% O 2 and the lateral tail vein was cannulated as described above. PET studies were performed on a high resolution small animal scanner (32 module quadHIDAC, Oxford Positron Systems Ltd. , Oxford, U. K. ). Data reconstruction was performed using a one-pass listmode EM algorithm (EMrecon)  (Kösters et al. , 2011). Animals were injected with 10 MBq [ 18 F]DPA-714 i. v. and images were acquired 45-75 min p. i. Following the PET acquisition, the animal bed was transferred to the CT scanner (Inveon, Siemens Healthcare) for acquiring anatomical information.
Magnetic resonance imaging (MRI) Mice were anaesthetised with 1. 5% isoflurane (DeltaSelect; Dreieich, Germany) in O 2 /compressed air, 30/70 1L/min. MRI was performed with a 9. 4 T small animal MR scanner with 20 cm bore size (Bio-Spec 94/20; Bruker BioSpin MRI GmbH, Ettlingen, Germany), operated with the ParaVision 5. 1 software (Bruker BioSpin MRI GmbH). Using a heliumcooled cryoprobe (Bruker BioSpin MRI GmbH), we obtained anatomical 2D T2w RARE brain images in three imaging planes (TR/TE 3000-5000/50, 12-28 slices, slice thickness 0. 5 mm, field of view 2 cm², matrix 256², in plane resolution 78 µm²).
PET data analysis PET and MR image data were analysed using VINCI software  (Vollmar et al. , 2004). Fusion of PET and CT images was performed using the landmark tool of the VINCI software and PET/CT and MR images were co-registered using the contour of the mouse skull. Coregistered images were matched to a mouse brain template generated from the Swanson mouse brain atlas  (Swanson, 2001)  and VOIs for SN and striatum were defined based on the brain atlas. Quantification is based on mean tracer uptake values for the respective VOIs. The VOI for the right unlesioned striatum was used as background VOI.
Bioluminescence imaging (BLI) After virus injection, BLI was performed on a weekly basis using the IVIS Spectrum Imaging System and Living Image 4. 0 software (PerkinElmer, Waltham, MA, USA). The day before measurement, fur on the head was removed using depilatory cream (Pilca) under isoflurane (Abbott Animal Health) anaesthesia. Mice were injected i. p. with 300 mg/kg D-luciferin in phosphate buffered saline (PBS) without calcium and magnesium (PAA Laboratories). 3 min post D-luciferin injection, mice were anaesthetised with 2. 5% isoflurane in 100% oxygen and.
Effect of neurodegeneration and -inflammation on neural stem cell proliferation and migration In order to study the effect of neurodegeneration and neuroinflammation on neural stem cell (NSC) proliferation and migration in the unilateral 6-OHDA PD model, we first established injections of virus particles into the SVZ of FVB mice (the experimental setup is illustrated in supplemental Fig. S3 ). FVB mice were used because pigmented fur and skin of C57Bl6 do not allow for reliable quantification of optical imaging data due to light absorption and scattering. The plasmid used for production of lentiviral particles encodes mCherry and firefly luciferase protein and is driven by a cytomegalovirus (CMV) promoter (supplemental Fig. S1 ). BLI was conducted weekly in order to follow migration of infected neuroblasts, and proliferation and migration of progeny of infected NSCs in the same animal over time.
Degeneration of dopaminergic cell bodies is accompanied by acute neuroinflammation Degeneration of dopaminergic neurons was reported to be accompanied by neuroinflammatory processes in patients  (Imamura et al. , 2003 , McGeer et al. , 1988) , and in animal models of PD  (Akiyama and McGeer, 1989, Czlonkowska et al. , 1996). Our in vivo PET study showed an acute increase in TSPO-ligand accumulation at the direct lesion site in 6-OHDA compared to vehicle injected animals, while tracer accumulation in the striatum was significantly, but very slightly (Mdn 6-OHDA = 1. 03, Mdn vehicle = 0. 95) increased. However, visual inspection of the PET datasets as well as analysis of the corresponding immunohistochemistry for Iba1 and TSPO gave no evidence for significant microglial activation in the striatum.