dataesr/scientific-paragraphs-categorization huggingface dataset:
9975 ± 0. 04, which represents ~1 ppm) for the time period spanning September 8, 2014 through April 30, 2016. The time-dependence of the difference between 200 the OCO-2 target-mode data and the coincident TCCON data (∆X CO2 ), after the constant bias is removed, is plotted in Fig. 6. The algorithm, calibration and instrument cause no apparent timedependent drift in ∆X CO2 nor their errors. Thus, the bias correction is successful at reducing both the parameter-dependent and constant global biases. However, the target mode measurements are sensitive enough to point to some residual biases that 205 are currently under investigation by the OCO-2 algorithm, calibration and validation teams. These residual biases are more geographically localized in nature, and as such might not be expected to be captured by the standard bias correction, which is designed to minimize globally-relevant biases.
On some, but not all targets over Edwards, the X CO2 appears dependent on surface brightness (Fig. 9 ). All mean target-mode measurements of 235 X CO2 at Edwards are biased lower than the TCCON measurements. Conversely, the Wollongong station, which is situated near the East coast of Australia, is a very dark surface in the visible, and lies between the Tasman Sea to the East and the Illawarra Escarpment to the West (Fig. 10 ). The OCO-2 retrievals of X CO2 are systematically higher than the TCCON measurements for all targetmode measurements, and are particularly high (up to 5 ppm) in July and August (Fig. 11 ), due to 240 the problem discussed above in §3. 1. OCO-2 data over Białystok, located in a dark, forested region, also has a persistent high bias (on the order of 1. 3 ppm) compared with TCCON.
Nadir and Glint Mode Comparisons to TCCON In this section, we evaluate the bias-corrected OCO-2 glint and nadir modes against ground-based TCCON data to reveal mode-dependent biases that were not eliminated using the standard version 7 bias correction. We use the version 7B retrospective OCO-2 "lite" files here, which have had the 255 footprint-dependent, parameter-dependent, and constant scaling biases removed, and we limit ourselves to data for which the "warn level" is less than or equal to 11  (Mandrake et al. , 2013 (Mandrake et al. , , 2015)) , and the "outcome_flag" is zero. These data are available from the CO 2 Virtual Science Data Environment (JPL-Caltech, 2016, http://co2. jpl. nasa. gov) and from GES-DISC (2016). For these comparisons, we choose the following coincidence criteria: a box centred around the TCCON station that 260 spans 5°in latitude and 10°in longitude on the same day as a TCCON measurement, with the exceptions mentioned below.
Data Availability Unfiltered, uncorrected OCO-2 data are available from the Goddard Data Center (GES-DISC, 2016). The filtered and bias-corrected data are contained in "lite" files, which are available from JPL's CO 2 310 portal (JPL-  Caltech, 2016). TCCON data are available from the TCCON data archive, hosted by CDIAC: http://tccon. ornl. gov. Each TCCON dataset used in this paper is cited independently in Table  1  or in the captions of Fig. A1.
Part of this work was performed at the  Jet Propulsion Laboratory, California Institute of Technology , under contract with  NASA. Operation of the Ascension Island site was funded by the  Max Planck Society. The  Bremen, Białystok , and Orléans TCCON sites are funded by the  EU projects InGOS and ICOS-INWIRE , and by the  Senate of Bremen. The Darwin and Wollongong TCCON sites are funded 330 by  NASA  grants  NAG512247  and  NNG05GD07G , and  Australian Research Council  grants  DP140101552 ,  DP110103118 ,  DP0879468 ,  LE0668470 , and  LP0562346. We are grateful to the  DOE ARM program  for technical support at the Darwin TCCON site. ND was supported by an  Australian Research Council  fellowship,  DE140100178. The TCCON site at Île de la Réunion is operated by the  Royal Belgian Institute for Space Aeronomy  with financial support in 2014, 2015 and  2016  under the  EU  project  ICOS-Inwire  and the min-335 isterial decree for ICOS ( FR/35/IC2 ) and local activities supported by  LACy/UMR8105 -Université de La Réunion.
Crystallographic data-collection procedure for high-resolution crystals Data to 1. 20 A ˚resolution were measured using a MAR CCD detector on beamline PXII at the Swiss Light Source (SLS), Villigen, Switzerland at a wavelength of 0. 8349 A ˚  (Pohl et al. , 2006). The sample-to-detector distance was set to 100 mm. All data collections were performed at cryo-temperatures using a 70 K nitrogen stream. Individual data sets were reduced with the d*TREK software  (Pflugrath, 1999).
Recrystallization and data collection of solubilized protein Lili-Mip crystals obtained in vivo were solubilized in 50 mM sodium acetate pH 5. 0. Size-exclusion chromatography was carried out on the solubilized protein using a Superdex 200 prep-grade column. The protein eluted as a homogenous and monodisperse fraction at 95. 5 ml and was used for crystallization. Based on the  Bio-Rad Gel Filtration Standard (Bio-Rad catalogue No. 151-1901) , the Lili-Mip protein was calculated to elute as a monomer with a molecular weight of about 24 kDa. Purified Lili-Mip was crystallized in 25% PEG 10 000 at a concentration of 2 mg ml À1 and a temperature of 293 K. The high PEG concentration in the crystallization condition served as the cryoprotectant and hence additional PEG or glycerol were not added.
The sizes of the recrystallized and the in vivo grown crystals were similar. The size of the crystal used for data collection was about 15 Â 20 mm. X-ray diffraction data for these crystals was collected on the PROXIMA-1 beamline at the SOLEIL synchrotron, France, at a wavelength of 0. 97857 A ˚. The sample-to-detector distance was set to 270. 6 mm. All data collections were performed at cryotemperature using a 100 K nitrogen stream.
Structure determination by S-SAD Ab initio structure determination was performed by measuring the anomalous scattering signal of S atoms at a wavelength of 2. 7 A ˚(4. 6 keV). Data from seven crystals were merged to further enhance the anomalous signal. Reflections were collected with a Dectris PILATUS 2M-F detector on BL-1A at Photon Factory (PF), Tsukuba, Japan. The sampleto-detector distance was set to 60 mm. 720 of data were collected from each crystal, with an exposure time of 0. 2 s per image and an oscillation angle of 0. 2. The sulfur substructure was determined using the SHELXC, SHELXD and SHELXE pipeline  (Sheldrick, 1990). Three sites of anomalous scatterers, corresponding to two disulfide bridges and one Met S atom, were initially obtained. The correct hand was selected using the map correlation coefficient as the indicator.
Structure refinements The three structures of Lili-Mip at 1. 2, 1. 75 and 2. 5 A resolution were refined through iterative cycles of restrained refinement using the PHENIX suite  (Adams et al. , 2010)  coupled with manual model building of electron densities generated with Coot  (Emsley & Cowtan, 2004)  until convergence (Table  1 ). Atomic coordinates and structure factors for the reported crystal structures have been deposited in the Protein Data Bank with accession codes 4nyr (Lili-Mip from S-SAD phasing), 4nyq (Lili-Mip at 1. 2 A ˚resolution) and 5epq (in vitro-crystallized Lili-Mip). The difference maps showing the electron densities for the heterogeneous residues were prepared using BUSTER v. 2. 10. 2  (Smart et al. , 2012). Alternate conformations of these heterogeneous residues were modelled with multiple occupancies using Coot.
Samples containing 0. 5 mg of the digested peptides were loaded onto a Zorbax 300SB-C18, 5 mm, 5 Â 0. 3 mm column using solvent A (100% acetonitrile with 0. 1% formic acid) at a flow rate of 30 ml min À1 for 5 min. Following trapping and desalting, the peptides were transferred to an analytical column (Eksigent HALO C18 2. 7 um, 90 A ˚, 100 Â 0. 5 mm) with a flow rate of 15 ml per min and resolved with a 40 min LC-MS run for Asp-N digested deglycosylated peptides and a 30 min LC-MS run for glycosylated peptides digested with trypsin or Asp-N. LC was carried out using a Eksigent nanoLC 425 and MS was performed using a AB Sciex TripleTOF 5600 +. The raw data were acquired using the Analyst software v. 1. 6. The MS analysis was performed in IDA mode with ten MSMS experiments. Data processing was performed with the ProteinPilot software.
5 ps. All bonds were constrained using the Linear Constraint Solver (LINCS) algorithm. The topologies of oleic acid and linoleic acid were generated using the PRODRG server (Schu ¨ttelkopf & van Aalten, 2004). The system was simulated under periodic boundary conditions with cutoffs of 10 A ˚for van der Waals terms. Long-range interactions were calculated using the particle mesh Ewald (PME) method. Principal component analysis (PCA) was also carried out using tools within the GROMACS package. The porcupine plots were generated using the mode-vectors script of PyMOL (DeLano, 2002).
X-ray structure determination The first Lili-Mip X-ray crystal structure was solved at 2. 5 A resolution by the single-wavelength anomalous dispersion (SAD) method using the anomalous scattering from S atoms in cysteines and methionines  (Dauter et al. , 1999)  of the protein. The sulfur SAD (S-SAD) structure was determined using data collected from multiple extracted crystals (Supplementary Movie S1). A complete native data set was collected from a single crystal that diffracted to 1. 2 A ˚resolution. Additionally, several crystals were solubilized and recrystallized in vitro. A third data set was collected from an in vitro-grown Lili-Mip crystal. The starting model for refinement of these two data sets was the refined structure obtained from the S-SAD data. Crystallographic details are presented in Table  1.
51. The expected Bijvoet ratio for four free cysteines and one methionine at 4. 59 keV was calculated to be 1. 62%, which is higher than the reported Wang limit of 0. 6%  (Wang, 1985). High-redundancy data were collected from 11 isomorphous crystals. The phasing power of each independent data set was too weak for successful phase determination. As a consequence, various combinations of these data sets were initiated and compared in terms of phase determination and anomalous correlation (cutoff set at 30%). Seven data sets were retained, with an average redundancy, R sym and mean I/(I) of 23. 0, 0. 067 and 38. 1, respectively (Table  1 ). From these combined data, structure determination and automatic density modification resulted in maps that could be used to build the initial structure. The final refined structure has a total of 139 out of 151 residues built, with R work and R free values of 15.
Despite several attempts, the difference density could not be accounted for by modelling alternate conformations for these residues. Visualization of the OMIT maps obtained after deletion of these residues revealed features corresponding to the presence of multiple sequences. It is rare that crystals of heterogeneous proteins diffract to atomic resolution, owing to their intrinsic disorder. Amino-acid sequence heterogeneity was observed in the structures determined from all three data sets. Two of the data sets were completely collected from a single crystal, while one data set (used for S-SAD) was collected from multiple crystals. We therefore exclude the possibility that this heterogeneity results solely owing to the merging of data sets from multiple crystals for the S-SAD structure determination.
Acknowledgements We thank the beamline crews at APS IMCA and GMCA and  Kevin P. Battaile ,  BNL X12 ,  ALS 4. 2. 2  and  Jay Nix ,  SLS PXII  and  Ehmke Pohl ,  Photon Factory BL-1A  and  SOLEIL PROXIMA-1. We thank  Jim Pflugrath  for contributing to the fulfilment of this project. We thank infrastructure support from  R. Sowdhamini ,  NCBS  towards carrying out molecular dynamics simulations. SB would like to thank the  Department of Biotechnology, Government of India  for a fellowship. SR would like to acknowledge grant  BT/PR5801/INF/22/156/2012  from the  Department of Biotechnology, Government of India.
The Instrumentation Unit The Instrumentation Unit is composed of one Instrumentation Base container (IB) laid on the seabed and of an inductive Instrumentation Line (IL), maintained vertical by a buoy, and supporting various autonomous instruments powered on internal batteries. The IU is recoverable in order to allow the change of batteries and the periodical recalibration required by some of the instruments. The design is directly derived from the ALBATROSS project (Autonomous Line with a Broad Acoustic Transmission for Research in Oceanography and Sea Sciences) which was recently deployed close to the KM3NeT-Fr site. It is totally autonomous and will communicate its data through an acoustic modem to an Instrumented Interface Module (IIM) to be connected to the KM3NeT-Fr node, as part of the European Multidisciplinary Seafloor and water-column Observatory network.
The Instrumentation Base The instrumentation Base consists of a Titanium cylindrical container attached to a dead weight, that will contain -an Inductive Modem (IM) foreseen IM to be the Seabird IMM, with a RS232 data interface -the power system for the IMM (either provided by the CB or by an internal battery) -the communication interface with the CB. Based on the experience of the ALBATROSS project, the possibility to use an acoustic modem instead of an Ethernet cable is currently under study, with the potential advantage of reducing the number of wet mateable connectors and hence the risk of failure at (de)connection.
Nitrate isotope mass balance The availability of a large database of trace chemical species measurements at Dome C during a portion of the OPALE field campaign (December 2011) offers a unique opportu- 3 ) values in the atmosphere to ones calculated from concurrent observations. As discussed at length in recent studies (for example, by  Morin et al. , 2011, and Vicars et al. , 2013) , the 17 O-excess transfer functions associated with the various nitrate production pathways (i. e. , 17 O(NO - 3 ) i values) can be estimated as a function of the 17 O of nitrate precursor gases (i. e. , NO x , O 3 , OH, etc. ) using mass balance calculations that trace the origin of oxygen atoms transferred during the chemical transformation of NO x in the atmosphere. All atmospheric nitrate production channels involve either NO 2 or a NO x reservoir species derived from NO 2 (e.
Acknowledgements. The research leading to these results received funding from the  European Community 's  Seventh Framework Programme  ( FP7/2007-2013 ) under the grant agreement number  237890. We would like to thank  INSU  for its financial support for lab experiments through its  LEFE program. The  Agence nationale de la recherche (ANR)  is gratefully acknowledged for its financial support through the  OPALE  project (contract  NT09-451281 ). The  Institute Polaire Paul-Emile Victor (IPEV)  supported the research and polar logistics through the program SUNITEDC No. 1011. This work has been partially supported by a grant from  Labex OSUG@2020  (Investissements d'avenir - ANR10 LABX56 ). We would also like to thank all the field team members present during the OPALE campaign. Meteorological data were obtained from " IPEV/PNRA :  Routine Meteorological Observation at Station Concordia".
The Northwest European Shelf is one of the best-studied continental shelf regions in the world with data coverage that is considered sufficient to allow calculation of seasonal air-sea CO 2 fluxes with high confidence  [Thomas et al. , 2004; Chen et al. , 2013; Laruelle et al. , 2014]. The Hebrides Shelf, to the west of Scotland, makes up the north-western extremity of the NW European Shelf and accounts for $7% of the total area of the NW European Shelf. It is, however, a region of significant exchange of water with the open ocean with models and long-term observations suggesting typical onshore wind-driven exchanges and compensating downwelling offshelf fluxes of $1 Sv  [Holt et al. , 2009; Huthnance et al. , 2009; Huthnance, 2010; Wakelin et al. , 2012]. The strong downwelling circulation along the Hebrides Shelf edge, and more widely along the NW European Shelf edge, is considered a vital conduit for the export of carbon to the open ocean but it remains poorly constrained observationally  [Holt et al.
Consequently usable data only exist for part of transect C and along transects D-G. Data from the 150 kHz instrument are used to provide current information along transect A. Inspection of the data after the cruise identified several additional problems with data coverage and beam penetration into the water column so the entire data set was reprocessed using the Python based ''CODAS processing'' routines developed by the University of Hawaii (http://currents. soest. hawaii. edu/docs/adcp_ doc/index. html). The reprocessing of the data resulted in the production of a data set with a 10 m vertical bin resolution and a 15 min averaging period (5 m vertical resolution for the 150 kHz data). The VM-ADCP data were detided to remove barotropic tidal oscillations using Oregon State University's Ocean Topography Experiment/Poseidon Cross Over Global Inverse Solution  [Egbert et al.
, 1994; Egbert and Erofeeva, 2002]  using a 1/30th degree resolution tidal model of the northwest European Shelf  [Egbert et al. , 2010 ; model available at http://volkov. oce. orst. edu/tides/] and a Matlab-based toolbox to access and extract the tidal components (http://polaris. esr. org/ptm_index. html).
Nevertheless, EEL cruises in 1996 (D223), 2005 (CD176), and 2006 (D312) were conducted in October and the VMADCP data from these cruises allows for a comparative study to the observations we report here. In Table  5 , we summarize our main findings. Despite crossing the shelf at similar latitudes (due to fixed station positions), there is considerable variability in the appearance of the Slope Current in the EEL cruise data sets. For example, the apparent width of the current varied almost 4-fold from 19 km at its narrowest  (October 2006)  to 76 km at its widest (October 2005). While latitudinal variability in the Slope Current width was recognized by  Dickson et al. [1986] , there appears to be limited description in the literature of changes in Slope Current width on interannual timescales.
Surface Ekman Fluxes Our surface wind-driven Ekman fluxes appear larger than typical flux estimates reported in the literature, which are often based on annually averaged data (e. g. , 1. 17 m 2 s 21 ; Huthnance, 2010). Significant seasonal variability in the surface Ekman flux term is recognized however and when viewed in this context our average transport of 2. 04 6 0. 12 m 2 s 21 (Table  1 ) is not too dissimilar to the mean winter value of 1. 73 m 2 s 21 reported by  Huthnance et al. [2009]  or the mean annual value of 1. 71 m 2 s 21 derived from the results of  Wakelin et al. [2012]. There is also the possibility that wind speeds and wind directions during October-November 2014 were favorable for onshore transport. The region experiences prevailing westerly winds and during the observation period strong southerly winds were dominant and these may have enhanced the onshore surface flux, particularly as the Hebrides Shelf is broadly orientated north-south.
Limitations and Wider Applications This study presents a detailed observational assessment of the Ekman drain for the Hebrides Shelf and indicates that there is a significant export of organic carbon to the open ocean, as well as significant variability in export fluxes along the shelf break. Nevertheless, the data set we present here is not perfect. Obvious weaknesses include the patchy VMADCP coverage, the horizontal sampling resolution, which was relatively crude compared to the width of the Slope Current, and the westward extent of sampling, which may not have fully resolved the true western boundary of the Slope Current on all transects. Nevertheless, our measurements of the Slope Current itself are comparable with previous observations and with recent modeled fluxes, and our carbon fluxes agree well with prior measurements and shelf-wide synthesis efforts, suggesting that the limitations of the data may not significantly impact the overall conclusions.
Conclusions During October and November 2014, the Hebrides Shelf was a moderate sink for atmospheric CO 2 , with a mean shelf wide air-sea CO 2 flux of 23. 2 mmol C m 22 d 21. This equated to a total regional sink of 20. 0021 Tg C d 21 , comparable to estimates derived from more extensive database analyses. Transport of carbon off shelf via the downwelling circulation that is typical of this shelf region, resulted in a total offshelf carbon flux of 2. 18 Tg C d 21 (4. 21 tonnes C m 21 d 21 ), of which 93. 6% was inorganic and 6. 4% was organic with DOC representing 95% of the organic flux. On a per unit area basis, the export of POC from the Hebrides Shelf of 10. 01 mmol C m 22 d 21 was found to be 5 times larger than the global mean. An equivalent calculation based on global shelf break length indicated the mean offshelf POC flux of 12.
Acknowledgments We thank the following for access to data, ECMWF for the  ERA-Interim  product (http://apps. ecmwf. int/datasets/), the  NOAA-ESRL Physical Sciences Division, Boulder, Colorado , for NCEP-II reanalysis products (http:// www. esrl. noaa. gov/psd/),and global CO 2 records (http://www. esrl. noaa. gov/gmd/ccgg/trends/global. html#global). We also thank the anonymous reviewer, editor, and  John Huthnance  for comments on an earlier version of this paper. L. A. Salt held post-doctoral grants from the  Conseil G en eral du Finister and R egion Bretagne. Cruise DY017 was a  NERC National Capability  funded cruise conducted in support of the  UK NERC/ DEFRA cofunded Shelf Sea Biogeochemistry programme  ( NE/ K001701/1 ). Data are available via the  British Oceanographic Data Centre  (www.
Study Site and Oak Stands Data was obtained from two Quercus robur L. field experiments in the Landes de Gascogne region in south-western France. The experiments were in community-owned forests and an agreement allowing samples to be taken from was signed with INRA. One experiment was located near Biscarosse ("B1 site" at 44°26N-1°04W, 40m a. s. l, S1 Fig) and the other near Pontenx-les-Forges ("P8 site" at 44°17N-1°04W). Oaks were planted in November 1994, after two years in a nursery. Each experiment site consisted of six rows of 17 oaks with 2 m between adjacent trees in each row and 3 m separating the rows. The rows corresponded to three geographic provenances of Q. robur: two rows were planted with seedlings raised from acorns collected in the Vouzeron forest (47°15N-2°13E) located 400 km northeast of the study site, two rows were of local provenance, from the Hermitage forest (44°44N-0°46W), and two rows were of local provenance originating from a forest 75 km further south, at Bias (44°08N-1°13W).
Dendrochronology In April 2013, an increment core was obtained 0. 30 m above ground level, from all the surviving oaks, on the main stem and up to two additional stems; individuals with a bushy appearance, with no main stem and more than three stems were discarded. The cores were planed with a cutter and digitalised on a scanner at a resolution of 1600 dpi. Ring widths were measured to the nearest 0. 01 mm on the image, with dendrochronology software (Windendro TM , Regent Instruments Inc. , Canada). The series were cross-dated with the Gleichläufigkeit index in Windendro software (i. e. , the percentage of cases of agreement in the signs of the firstdifference of two time series). We rejected the few samples with inner tree rings dating from 1998 or later due to apex death followed by re-sprouting, or for which the core missed the pith.