dataesr/scientific-paragraphs-categorization huggingface dataset:
Aims. We report the discovery of a massive and dense transiting planet CoRoT-27b on a 3. 58-day orbit around a 4. 2 Gyr-old G2 star. The planet candidate was identified from the CoRoT photometry, and was confirmed as a planet with ground-based spectroscopy. Methods. The confirmation of the planet candidate is based on radial velocity observations combined with imaging to rule out blends. The characterisation of the planet and its host star was carried out using a Bayesian approach where all the data (CoRoT photometry, radial velocities, and spectroscopic characterisation of the star) are used jointly. The Bayesian analysis included a study whether the assumption of white normally distributed noise holds for the CoRoT photometry and whether the use of a non-normal noise distribution offers advantages in parameter estimation and model selection.
4. 4). We find one contaminating star within the CoRoT aperture mask (see Fig. 1 ) and estimate that it contributes 2. 42% ± 0. 95% of the measured flux using a code developed by Bordé and Pasternacki  (Pasternacki et al. 2012). We did not remove the  contamination from the light curve before the combined light curve and RV analysis, but instead included contamination to the model with a normal prior based on the given estimate. The final light curve used in the analysis is shown in Fig. 2. The light curve consists of 6132 c l and 108471 c s points (89% and 95% of all the data), features one large jump near the end of the c l data and several smaller jumps. The light curve contains 12 c l and 11 c s transits. We did not attempt to carry out a global detrending to correct for the jumps and other systematics, but decided to use a local approach to estimate the systematic trends around each individual transit.
Photometric follow-up Ground-based photometric follow-up of CoRoT candidates is verifying whether a transit that is detected in CoRoT's large apertures is on a target star instead of being caused by some nearby binary system  (Deeg et al. 2009 ). An 18-min-long time series was acquired with the 1. 2 m Euler Telescope during a transit on 29 September 2011 with excellent 0. 5 seeing. The seeing was poor, however, when the corresponding off-transit data were taken a day later. This strong difference in seeing meant that the 1% deep transit signal could not observed. However, none of the nearby fainter stars showed any relevant brightness variation. The good on-transit images also did not show any very close contaminating stars with a brightness that is sufficient (R < 20. 5) to cause the transit signal.
3 ± 0. 5 km s -1 , in agreement with the spectroscopic analysis. A simultaneous observation of the sky background allowed monitoring its evolution and impact on the stellar cross-correlation function, but all the observations performed on this faint star were unaffected by the sky background. The HARPS data show a highly dispersed RV sequence, with a standard deviation of 1 km s -1 and peak-to-peak variation of 2. 77 km s -1. The mean error on individual measurements is 140 m/s due to the faintness of the star. The bisector spans, displayed in Fig. 4 , show a standard deviation of 230 m/s without correlation with the RV. This is a good indication that the detected RV signal is due neither to photospheric activity nor to the blending effect of a background star.
Spectral analysis As is now standard practice in the analysis of CoRoT stars, we used the co-added HARPS spectrum to derive the fundamental photospheric quantities of the planet hosting star CoRoT-27, employing two different methods. The derived parameters include the effective temperature (T eff ), surface gravity (log g), metallicity ([M/H]), micro-and macro-turbulence velocities (v micro and v macro , respectively), and sky-projected stellar rotation velocity (v sin i ). A first method relies on the spectral analysis package Spectroscopy Made Easy (SME, version 305), which calculates synthetic spectra of stars and fits them to observed highresolution spectrum  (Valenti & Piskunov 1996). It uses a nonlinear least squares algorithm to solve the model atmosphere parameters (T eff , log g, [M/H]), as well as the v sin i , v micro and v macro velocities.
A set of LTE plane-parallel stellar model atmosphere grids  (Kurucz 1993; Hauschildt et al. 1999; Gustafsson et al. 2008 ) are included with the SME distribution. We also used a customised IDL software suite to derive the fundamental photospheric parameters. We compared the coadded HARPS spectrum with a grid of theoretical model spectra from  Castelli & Kurucz (2004) ,  Coelho et al. (2005) , and  Gustafsson et al. (2008) , using spectral features that are sensitive to the different photospheric parameters. Briefly, we used the wings of the Hα line to estimate the effective temperature of the star, and the Mg  5167, 5173, 5184 Å lines, from the Ca  6162 and 6439 Å lines, and from the Na  D lines to determine its surface gravity. The metal abundance and v micro were derived applying the method described in  Blackwell & Shallis (1979).
(2013). The Bayesian approach facilitates the use of non-normal noise models in the analysis, and we investigate how the assumptions about the noise properties affect the outcomes of the parameter estimation and secondary eclipse search. The analysis code is written in Python and Fortran and uses the common scientific Python libraries: NumPy, SciPy, Matplotlib  (Hunter 2007) , and PyFITS. We model the transit shape using a version of the Giménez transit model  (Giménez 2006)  optimised for efficient computation of large light curves 1. The MCMC sampling of the posterior density is carried out using emcee (Foreman-Mackey et al. 2012), a Python implementation of the affine invariant Markov chain sampler  (Goodman & Weare 2010). The sampler was chosen for its ability to efficiently sample correlated parameter spaces and for its selfadaptive nature, which reduces the need to tweak the MCMC proposal distribution parameters by hand.
The light curve analysis is carried out for a subset of the data. We include a time span of 15. 3 h centred on each individ-1 The code is freely available from https://github. com/hpparvi/ PyTransit ual transit into the analysis. Instead of detrending the light curve using a static polynomial fit to the out-of-transit data (as often done) or using the light curve filtered with running median or Savitzky-Golay filter, we model the background continuum using a separate Legendre series expansion for each transit. The Legendre polynomials are chosen for their orthogonality over the interval [-1, 1], and the times around each transit are mapped to this interval. The coefficients of the Legendre series are free parameters in the MCMC analysis, which allows us to propagate the uncertainties in the background estimation to the physical parameter estimates.
27, σ = 0. 06) on the quadratic (v) coefficient (see  Csizmadia et al. 2013  for a detailed overview of the effects of limb darkening on parameter estimates from transit light curves). The prior constrains the values of v, but is wide enough to account for the uncertainties in the stellar characterisation and theoretical stellar atmosphere modelling. We let the eccentricity vary freely even when the RV data does not implicitly support significantly non-zero eccentricity. This is done in order to obtain robust estimates of the maximum eccentricity and the physical parameters derived from the analysis. Both the stellar density and semi-major axis estimates have been shown to be sensitive to the orbital eccentricity  (Kipping 2010) , and fixing the eccentricity to zero would lead to underestimated uncertainties for these parameters.
Acknowledgements. First and foremost we would like to thank the anonymous referee for her/his prompt review. H. P. has received support from RoPACS during this research, a  Marie Curie Initial Training Network  funded by the  European Commission's Seventh Framework Programme. H. P. has received funding from the  Väisälä Foundation  through the  Finnish Academy of Science  and Letters during this research. The team at the IAC acknowledges funding by grant  AYA2012-39346-C02  of the  Spanish Ministry of Economy and Competitiveness (MINECO). This research was supported by an appointment to the  NASA   Postdoctoral Program  at the  Ames Research Center , administered by  Oak Ridge Associated Universities  through a contract with  NASA. A. S. acknowledges support from the  European Research Council/European Community  under the  FP7 through Starting Grant  agreement number  239953.
A meeting to set up the EBB was held in Paris in 2001 with 16 founding partners (   The aims of the EBB network were to identify and locate repositories of biological material (DNA, tissues, and cell cultures) pertaining to RDs, to harmonise and disseminate quality banking practices, to distribute quality material and associated data to scientific users, and to disseminate biobank-pertinent knowledge and knowhow to the scientific community through specialised training courses, conferences, articles, and a website. Expected achievements included reorganization of existing biocollections; improvement of medical and scientific collaboration in the field of RDs; and encouragement of research with concomitant development of new diagnostic tools and therapies for RDs. The project was organized into work packages (Table  2 ).
In 2008, Telethon had unified all its biobanks, creating the Telethon Network of Genetic Biobanks (TNGB) biobanknetwork. telethon. it, the first of this kind in Italy, with a virtual catalogue of biospecimens and associated data that presently lists more than 750 rare defects. 2  In 2012, the natural progression has been to join the two Networks, EBB and TNGB. Of note, all neuromuscular biobanks of TNGB were already EBB members. A total of 10 additional partners have joined the EBB network since 2007 making to date a total of 21 biobanks plus 4 non-biobank members (Table  1 ). Of note, biobanks from three additional countries (UK, Canada, and Israel) have been accepted. From 2007, on the network only pays for joint services such as the website, the catalogue updating and annual meetings; while all the EBB partners had to cover their own costs regarding the operation of the biobanks either with institutional funding or with specific grants (such as Telethon grants supporting TNGB).
Membership The entry of new, European and non-European biobanks into the EBB network is encouraged. To this end, an evaluation procedure and specific assessment criteria have been established. Such criteria ensure adherence to minimum entry conditions that include the following: presence of collections of RD biological samples and their availability to the scientific community, a quality-control (QC) system in place for the management of the biobank, with standard operating procedures (SOPs) regulating sample and data acquisition, and sample processing, storage, and distribution. The candidate biobanks should also adhere to Ethical, Legal and Social Implication (ELSI) principles and comply with the recommandations issued by the Oviedo Convention and the OECD Task Force on Biological Resource Centers,  1, 8  and with the national and European laws and regulations.
ACHIEVEMENTS AND RECOGNITION In addition to complying with workpackage tasks (Table  2 ), the EEB has prepared 29 SOPs pertaining to sample and data acquisition, sample processing and storage, and sample distribution; has published (2005) a book on ethical and legal issues concerning international biobanking; 9 has been awarded the Newropeans Grand Prix 2004 for Research and Technology; has been cited as a 'European model of coordination and of integration of Biological Resource Centres for the optimisation and improvement of the use of human biomaterial at European level', in 2006, by the Institute for Prospective Technological Studies/European Science and Technology Observatory network. An immediate outcome of the effort to establish the EBB network was the improved functioning of each EBB biobank member.
Each biobank was forced to better organize the data to be included into the catalogue and to harmonize SOPs. This was facilitated by personnel training provided by the EBB organization, and by exchange of solutions within the network, including sharing rules for sample distribution and network acknowledgement in publications making use of EBB-supplied samples. Being part of the network, with specific agreed rights and duties under the network's governance model, also contributed to improvement for the individual biobanks, for example, systematically recording biobanking activities, adhering to SOPs, and complying with ELSI principles. The catalogue A great deal of work was devoted to drawing the EBB catalogue, in particular to define: catalogue content, vocabulary lists used for the minimum data set (normalized terms), how to update the catalogue, and how to search in the catalogue.
The partners agreed on the following minimum data set: (i) type of sample, (ii) classification of the disease based on ICD-10 identifier and name, MIM number and name, (iii) number of families, (iv) number of patients, (v) anatomic origin, and (vi) biobank contact. As 2011 the catalogue was further implemented by the addition of an optional field for the ORPHA code, specially developed by Orphanet (www. orpha. net), as commonly used coding systems, like ICD or SNOMED CT codes, do not cover most of the RD names. The web-based EBB catalogue (http://www. eurobiobank. org/en/ services/CatalogueHome. html) makes it possible to search for biological samples by type of biological material and disease. Of more than 500 000 samples stored in the EBB biobanks, 130 000 were available on the catalogue at the end of 2013; 188 400 new samples were collected from 2003 to 2013 and 73 400 samples were distributed over the same period.
QUALITY-MANAGEMENT SYSTEM The setting up of common SOP's for sample collection, processing and storage, the standardization of samples access policies, the adoption of a common minimum data set and controlled terminologies necessary to build the EBB catalogue were the first approach towards a QC system. A further step was taken by the EBB network in 2009 through the development of a satisfaction questionnaire to be sent to the users, for checking the quality of the services provided by the EBB biobanks. During years 2009-2010, each partner sent the questionnaire to the users who, once had the document filled in, sent their feedback anonymously to EURORDIS. The evaluation of the questionnaires received revealed that the users were overall either 'very satisfied' or 'satisfied' with the service, and that EBB was seen as an essential service for scientists involved in research on RD who would otherwise have no access to these samples.
FUTURE DEVELOPMENTS AND CHALLENGES The legal and regulatory frameworks that apply to this area are still fragmented, with variation of practice across the different areas of medical research. 46, 47 Biobanks have to live with these frameworks and practices, which have raised a number of complex issues for society. For example, next-generation sequencing techniques pose important issues in relation to the management of incidental findings. 48, 49 lthough tools aimed at facilitating data and sample sharing are being developed,  48  privacy regulations and requirements vary between countries, rendering sample transfer between countries problematic. In addition, issues of communication between RD patient registries and RD biobanks still need to be addressed. A related problem is that different names are often used for a single disease creating difficulties when searching by disease.
Other issues facing biobanking are the lack of standards, agreed vocabulary, common data elements, and best practices for collecting data and processing samples. An accreditation and evaluation system to recognise biobanks that provide high-quality samples, and reward and acknowledge scientists who establish and maintain biobanks, should be established. In this regard, BRIF, the recently proposed quantitative parameter to assess the use of bioresources by the biomedical community, will represent a starting point for biobank recognition. 44 Another important issue in RD biobanking is sustainability. Clearly, the pharmaceutical industry has little interest in funding small RD biobanks that contain and exchange limited numbers of samples. Specific funding for RD biobanks is therefore essential.
Finally, very few biobanks are concerned solely with RD samples, whereas some collections make material available only for specific types of studies and not others. In particular, biomaterials collected in natural history studies and clinical trials should be deposited in biobanks (with a broad consent allowing secondary use of the samples). Currently, most samples collected in these studies are 'private' to these studies/investigators and cannot be shared (and often get destroyed at the end of the study). In this regard, the promotion of collaborations between biobanks and patient associations, in addition to helping gather more RD samples and associated data and make them available to researchers, could better address ethical and legal challenges because of the solidarity-based nature of the underlying agreements.
50 ecently, an application sent by the EBB scientific coordinator to RD-Connect's executive committee, expressing EBB's interest in becoming a partner of the RD-Connect platform, received formal approval. RD-Connect's objective in biobanking is to provide access to RD biobanks that collect and provide standardised, quality-controlled biomaterials. In this regard, a dynamic, updated, searchable catalogue of biological samples linked to clinical data from patient registries and to patients' 'omics' data will represent RD-Connect's major output. 51 n this context, EBB's main aim is to contribute expertise to promote high professional standards and best practices in RD biobanking and implement the integration with RD patient registries. The RD-Connect project was developed under IRDiRC (International Rare Disease Research Consortium), a European Commission and US National Institute of Health initiative to coordinate research funding on RDs, and RD-Connect activities and policies are interconnected with those of IRDiRC.
ACKNOWLEDGEMENTS EBB thanks  EURORDIS  for administrative support,  Fondazione Telethon  for administrative and financial support, the  EC  for providing funds (grants:  FP5 EuroBioBank , contract N. 02769;  FP6 TREAT-NMD , contract N. 036825; and  FP7 RD-Connect , grant agreement N. 305444), and  AFM  for the vision of the network and for encouraging the network to get together. EBB gratefully acknowledges patients and collaborating clinicians/researchers for contributing samples and data to the network, and biobank staffs for running the EBB biobanks. The MRC support to the biobank in London and Newcastle is also gratefully acknowledged.
We chose to characterize soil water availability along the growing season through the time course of Ψ S values, averaged among the four locations. Therefore, Ψ S values were extrapolated for the missing period (May-early June) based on the relationship observed between SWC and Ψ S measurements at each measuring depth. A feed-forward Neural Network (Matlab R2012a, Mathworks, Natick, MA, USA) was used to interpolate missing values. The correlation between predicted and measured values ranged between 0. 83 and 0. 98 for different soil depths (see  Broeckx et al. 2013 ).
46 µmol s -1. Before logging at each step of the A-C i curves, steady state (F s ) and maximum fluorescence (F m ′) were measured during a light-saturating pulse (7 mmol m -2 s -1 ) and the efficiency of Photosystem II (Φ PSII ) was determined as: Φ PSII m s m = - ′ ′ F F F. Photosynthesis and WUE in a poplar short-rotation plantation 703 Tree Physiology Volume 34, 2014 Then, the CO 2 concentration in the chamber was set back to 400 ppm. Once the net assimilation rate had stabilized, the response to varying light intensities was recorded (A-light curve). Leaf photosynthesis was measured at eight PPFD intensities in the following order: 1500, 1000, 800, 600, 400, 200, 100, 0 µmol m -2 s -1. A minimum of 2 min of leaf equilibration was set at each step before data were logged. Dark respiration was defined as the absolute CO 2 exchange rate measured during the last step of the A-light curve.
Statistical analysis Some data were missing at random (MAR) and could be ignored for parameters and genotypes that were measured from the third MC onwards  (Verbeke and Molenberghs 2000). The mixed procedure for repeated measurements was used to analyse the effects of genotype and seasonality on the above-mentioned parameters. Measurements were performed seven times during the growing season (repeated variable 'MC') on the same four replicate trees of each genotype (subject variable 'Tree'). A linear mixed model with fixed effects genotype, MC and their interaction-indicating the genotype-specific behaviour in time-was used. The unstructured repeated covariance structure was chosen and the variance component was estimated using restricted maximum likelihood (REML). When significant genotype or MC effects were found, pairwise comparisons of the means were performed using the Bonferroni adjustment (see Table  S2A  available as Supplementary Data at Tree Physiology Online).
Relationships between photosynthetic, WUE and isotopic parameters were examined using linear and nonlinear regression analyses and coefficients of determination (R 2 ) as well as genotype-specific Spearman's rank correlation coefficients. All statistical tests were considered significant when P < 0. 05. All statistical analyses were performed in SPSS 20. 0 (IBM Corp. , SPSS Statistics for Windows, Armonk, NY, USA).
Parameters df Genotype Df MC df Genotype × MC  Tree Physiology Online at http://www. treephys. oxfordjournals. org Photosynthesis and WUE in a poplar short-rotation plantation 709  Tree Physiology Volume 34, 2014 Leaf photosynthetic parameters recorded in this study were consistent with data previously reported for several poplar species and hybrids  (Roupsard et al. 1996 , Pons and Westbeek 2004 , Ripullone et al. 2004 , Monclus et al. 2006 , Gornall and Guy 2007 , Soolanayakanahally et al. 2009 , Fichot et al. 2010 , 2011). Eddy covariance measurements of net ecosystem CO 2 fluxes performed during the same period confirmed a net ecosystem carbon uptake until the end of September  (Broeckx et al. 2013 , Zona et al. 2013). This indicated a good agreement between the timing of leaf-level and canopy-level photosynthetic processes in the plantation.
Secondly, A sat and g s-sat were measured under saturating conditions after the sampled leaf had acclimated to the chamber conditions, such that the values of WUE i reflected 'maximal' functioning. This optimal functioning is obviously not maintained during the entire leaf lifespan. Thirdly, finite but variable g m can affect WUE i and influence the relationship between WUE i and Δ 13 C bl  (Warren and Adams 2006 , Flexas et al. 2008 , Seibt et al. 2008 , Soolanayakanahally et al. 2009 ). The hyperbolic relationship Photosynthesis and WUE in a poplar short-rotation plantation 711 Tree Physiology Volume 34, 2014 observed between WUE i and g m /g s-sat supports this line of reasoning and is consistent with both theory  (Flexas et al. 2013)  and data reported for different species  (Galmes et al.
Funding This research has received funding from the  European Research Council  under the  European Commission 's  Seventh Framework Programme  (FP7/2007-2013) as  ERC  grant agreement no. 233366  (POPFULL), as well as from the  Flemish Hercules Foundation as Infrastructure  contract  ZW09-06. Further funding was provided by the  Flemish Methusalem Programme  and by the  Research Council of the University of Antwerp. Funding to pay the Open Access publication charges for this article was provided by the  European Commission 's  Seventh Framework Programme  (FP7/2007-2013) as  ERC  grant agreement n°  233366  (POPFULL).