dataesr/scientific-paragraphs-categorization huggingface dataset:
To summarize, an original methodology for deriving urban surface albedo images from remote sensing data without a need of in situ measurements was implemented, although ground measurements could improve the final results. Both calibrations are computationally operational, but the results for the iterative method are considered as preliminary, due to the limited implementation of only a single iteration. Iterative method is expected to be more accurate than for the simpler direct one. Nevertheless, the direct calibration might prove to be easier to use and more robust in case of inaccurate urban datasets, which depends on spatial resolution and geometric co-registration of DART and satellite imagery. Finally, both methods rely on the fact that DART is a reliable RT model simulating both satellite images and the radiative budget of cities with an acceptable accuracy.
Figures5 and 6show comparisons of DART and MODTRAN simulations in the visible and near-infrared and the thermal infrared wavelengths, respectively. Both results demonstrate that the DART update and the introduction of new atmospheric database, combined with an improved radiative transfer modeling approach, brings DART simulations of atmosphere very close to MODTRAN 5. 1 simulations, which is very encouraging especially for simulating accurately the in situ sensors.
Figures 5 5 Figures5 and 6show comparisons of DART and MODTRAN simulations in the visible and near-infrared and the thermal infrared wavelengths, respectively. Both results demonstrate that the DART update and the introduction of new atmospheric database, combined with an improved radiative transfer modeling approach, brings DART simulations of atmosphere very close to MODTRAN 5. 1 simulations, which is very encouraging especially for simulating accurately the in situ sensors.
Computing and mathematics Archiving platform: "Publication archiving platforms such as HAL or ArXiv thus respond in part to this problem and should be supported, along with metadata platforms (MathSciNet, Zentralblatt, etc. ). " 30 Data deposited. The CNRS survey revealed that of the communities that deposit data in HAL: 63% deposit bibliographic records (PAP 2-27); 56% deposit the full text (PAP 2-28). In total, 69% of the communities that do not deposit data in HAL do not use other archives either. Rights on uses to be created from scratch Hearing at the University of Strasbourg: Paul-Antoine Hervieux, 10 July 2015 "In academic communities there is an almost across-the-board lack of awareness of copyright and its implementation measures, regardless of the type of document or data. " In the framework of the CNRS survey, two questions were used to assess the researchers' level of knowledge about their rights.
Text and data mining with regard to copyright Copyright includes a monopoly on reproduction, including the adaptation of works. The publisher owning the property rights for the scientific literature it publishes can therefore prohibit third parties, as well as authors, from making any full or partial reproduction as well as any translation, adaptation or transformation, arrangement or reproduction by any technique or process (Article L. 122-4 of the Intellectual Property Code). TDM does not have its own legal status and this lack is a source of legal insecurity. Indeed, data-exploration services reflect multiple technical operations, including: operations to analyse or process knowledge alone: these are acts undertaken freely; technical operations involving the full-text reproduction of data that can be protected by copyright, and their modification in forms such as sections, extracts, mergers, compilations, etc.
Chlamydomonas has one putative plastidial lysophosphatidic acid acyltransferase, CrLPAAT1 To identify an ortholog of Chlamydomonas plastid-targeted LPAAT, the Chlamydomonas genome database at Phytozome V10. 3 was searched for homologs of Arabidopsis ATS2 (AtLPAAT1: At4 g30580) that encode plastidial LPAAT  (Yu et al. , 2004). The protein encoded by the locus Cre09. g398289 showed the highest level of amino acid sequence identity (i. e. 40%) to AtATS2 (Figure  1a ). Expressed sequence tags (ESTs) for Cre09. g398289 were found in Phytozome V10. 3, suggesting that this locus is expressed in Chlamydomonas cells. We designated this protein CrLPAAT1. CrLPAAT1 contains canonical motifs attributed to LPAAT proteins  (Kim et al. , 2005) , such as NHX4D (motif I), GVIFIDR (motif II), EGTR (motif III) and IVPIVM (motif IV) (highlighted in Figure  1a ).
CrLPAAT1 also contains the hypothetical membrane-spanning domains, as predicted by transmembrane helix prediction (TMHMM,  Krogh et al. , 2001)  (yellow boxes in Figure  1a ). CrLPAAT1 has a putative plastid transit peptide (~51 amino acids; enclosed in a red box in Figure  1a ) as predicted by PredAlgo  (Tardif et al. , 2012) , suggesting that CrLPAAT1 could be targeted to the plastid in C. reinhardtii. In addition to CrLPAAT1, six proteins have been annotated in the Phytozome C. reinhardtii database as phospholipid/glycerol acyltransferases 1-6 (PGA1-PGA6) (Table  1 ; Figure  1b )  (Merchant et al. , 2007). PGA1 and PGA6 belong to the Tafazzin (TAZ) protein family, and are likely involved in cardiolipin transacylation in the mitochondrial phospholipid biosynthesis pathway, and are therefore important for the remodelling of acyl groups in cardiolipin  (Xu et al.
DNA database searches and protein sequence analyses The C. reinhardtii genome was searched using the BlastP program implemented in Phytozome v10. 3 (http://phytozome. jgi. doe. gov/ pz/portal. html) (Merchant et al. , 2007)  for proteins that show homology to plant, yeast and bacterial LPAATs. Protein sequence alignments were constructed using Clustal Omega  (Sievers et al. , 2011). Phylogenetic trees were inferred using MEGA6 and the maximum-likelihood method with 1000 bootstrap replications  (Tamura et al. , 2013). The subcellular localization of each LPAAT candidate was predicted using the PredAlgo program (https://giavap-genomes. ibpc. fr/ cgi-bin/predalgodb. perl?page=main)  (Tardif et al. , 2012).
reinhardtii plastids (Kazusa Codon Usage Database at: http://www. kazusa. or. jp/codon/) was synthesized by GenArts (Invitrogen). The synthetic gene (designated CrLPAAT1crc) was then amplified using the primers InFLPAAT-F (5 0 -AAATCCATGGAGATCTTAATGGCTCG-TAAATCATCATTAG-3 0 )/InFLPAAT-R (5 0 -ACGTTTAAACAGATCTT-TATGATGAAGCAGCATAATC-3 0 ), and the resultant fragment was subcloned into the plastid expression vector pLM21 as described  (Michelet et al. , 2011). To enable screening for transformants by immunoblot, CrLPAAT1crc was expressed as a C-terminal fusion to the triple influenza hemagglutinin epitope (3xHA) (the construct was named pLM21-CrLPAAT1crc-HA). The HA epitope has been successfully used to determine the subcellular localization of several proteins in C. reinhardtii, including the plastid-located x-3 fatty acid desaturase 7  (Nguyen et al.
Acknowledgements This work was supported by the  Advanced Biomass R&D Center (ABC)  of  Global Frontier  Project funded by the  Ministry of Science, ICT and Future Planning  ( ABC-2015M3A6A2065746 ) ª 2016 The Authors. Plant Biotechnology Journal published by  Society for Experimental Biology  and  The Association of Applied Biologists  and  John Wiley & Sons Ltd. , 14, 2158-2167 Overexpression of LPAAT1 in Chlamydomonas boosts oil content 2165 awarded to  Y. Lee , grants from  MUsCA  ( ANR-13-JSV5-0005 ) awarded to  Y. Li-Beisson  and a  Grant-in-Aid for Scientific Research  ( 21570034 ) from the  Ministry of Education, Culture, Sports, Science and Technology of Japan  awarded to  I. Nishida. S. Kamisuki  is a visiting student to  POSTECH  under the support of  SEKAI KANRU PROGRAM of Saitama University.
We were able to work around this problem using 40× and 60× lenses and by zooming on the object. CLSM represents an accurate, non-destructive methodology for collecting 3D morphological data on thin sections of chert. We acquired confocal images with a Nikon A1-Si laser-scanning confocal microscope. Images were recorded with pixel dimensions of 0. 31 μm. Autofluorescence of the samples was excited with the following laser lines: 405-nm line of 100 mW cube laser (Coherent Inc. , USA, http://www. coherent. com), 488-nm line of 50 mW sapphire laser (Coherent Inc. , USA), 561-nm line of 50 mW sapphire laser (Coherent Inc. , USA) and 640-nm line of 40 mW cube laser (Coherent Inc. , USA). The quantum efficiency (QE) of the detectors was 20-25%. Autofluorescence signal was collected with 4 photomultiplier-type detectors at the following wavelength emission windows: 425-475 nm for the 405 nm laser, 500-550 nm for the 488 nm laser, 570-620 nm for the 561 nm laser and 675-725 nm for the 640 nm laser.
Samples were visualised with a 29. 9 μm (1. 2 airy units) confocal pinhole and typically 100-400 z-stacks with optical thickness between 200-300 nm each. The fluorescence signal from each z-stack was projected onto a maximum projection image and used to generate a 3D model of the sample with Nikon NIS-Elements software (www. nis-elements. com). Nomenclature. The electronic version of this article in Portable Document Format (PDF) in a work with an ISSN or ISBN will represent a published work according to the International Code of Nomenclature for algae, fungi, and plants, and hence the new names contained in the electronic publication of a PLOS ONE article are effectively published under that Code from the electronic edition alone, so there is no longer any need to provide printed copies. In addition, new names contained in this work have been submitted to MycoBank from where they will be made available to the Global Names Index.
Acknowledgments C. S. -D. thanks  Isabel van Waveren  ( Naturalis Leiden, Netherlands ),  Raymond van der Ham  ( Naturalis Leiden, Netherlands ) and  Andrew Ross  ( National Museum of Scotland, UK ) for their hospitality and assistance in visiting the collections. She also thanks  Peta Hayes  ( NHM, London ) for her assistance in the collections at the  NHM. Mark Spencer  ( NHM, London ) and  Gordon Beakes  ( Newcastle University, UK ) are thanked for helpful discussion about the fungus. Christopher Rogers  ( Kansas University, USA ) is acknowledged for providing the modern resting eggs.
Regarding biofilm morphology, Hha overexpression leads to amorphous biofilms with a higher percentage of dead cells (Live/Dead cells ratio of 5. 6 ± 1. 4, quantitative analysis by COMSTAT 21 software). Instead, when YmoB was co-expressed, the Live/Dead cell ratio significantly increased to 35. 4 ± 8. 5 and the biofilm was composed by microcolonies uniformly spread on the entire surface (Fig. 2d ). Thus, YmoB or [C117S]YmoB can functionally replace TomB as the Hha antitoxin in E. coli. [C117S]YmoB enhances Hha oxidation in vitro. Hha has a single cysteine residue (C18) highly conserved in the Hha-family of proteins. We hypothesized that the oxygen-dependent antitoxin activity of TomB and [C117S]YmoB towards Hha could be related to the oxidation of this conserved cysteine residue. In addition to their capacity to form disulfide-bonds, cysteine thiol groups can be oxidized to sulfenic (-SOH), sulfinic (-SO 2 H) and sulfonic (-SO 3 H) acids  22.
1 software  [27] [28] [29]  and final refinement in the presence of explicit water with CNS 1. 2. 1 software  30, 31. Refinement statistics are summarized in Table  1. The NMR assignment and the structural models have been deposited in the RCSB PDB with accession numbers RCSB104115 and 2MN2. Details of the process, experiments and NMR calculation are presented in the Supplementary Tables  2  and 3. Figure  5a  shows the superposition of the 20 lowest energy models, which have a root mean square deviation considering all backbone heavy atoms of 1. 89 ± 0. 45 Å, and 0. 87±0. 14 Å if only the residues in the a-helices are compared. [C117S]YmoB forms a compact antiparallel four-helix bundle connected by flexible loops. A one-turn helix H5, containing the C117 in the wild-type form, is located at the C-terminus.
A buried site in the interior of the four-helix bundle where the conserved C18 residue of YmoB is located is a candidate to be the protein 'active site' responsible for the enhanced reaction of Hha with molecular oxygen. The YmoB C18 residue is located close to the Hha binding site. However, its buried location raises the question of how oxygen can reach the cysteine site. Analysis of the structure of [C117S]YmoB using the DoGSi-teScorer software  33  identified a shallow pocket on the surface of [C117S]YmoB formed by K15, E19, F108, F111, S112, G113, I116, S117 and M120 (Fig. 5c ). In some of the NMR structures K15, E19, F108 and F111 side chains define a narrow channel that connects the protein surface with the location of C18. The width of this channel is comparable to that of an oxygen molecule, and we hypothesized that it could facilitate its access to the interior of the four-helix bundle.
The flow cell was incubated with SYTO9 in the dark for 20 min at room temperature. Eight images in random positions were taken with an Olympus FV100 confocal microscope using a long working distance Â 40 Olympus LWDCDPLAN 40LP lens. 3D images of each spot were obtained using IMARIS software, and quantitative analysis of biofilm was performed using COMSTAT software. For the SYTO9 stain preparation, the LIVE/DEAD BacLight Bacterial Viability Kit L7007 was used. Three millilitre of dye was prepared in a 30 ml glass beaker mixing; 7. 5 ml of component A (SYTO 9 dye, 1. 67 mM / propidium iodide, 1. 67 mM), 7. 5 ml of component B (SYTO 9 dye, 1. 67 mM / propidium iodide, 18. 3 mM) and 3 ml of TMM. YmoB mutagenesis. Mutations in YmoB (cysteine to serine, phenylalanine to leucine, phenylalanine to tyrosine) were introduced using the QuickChange site directed mutagenesis Kit (Stratagene) with the appropriate complementary mutagenic primers.
NOESY and TOCSY spectra were recorded using gradient sensitivity-enhanced pulse sequences from the BioPack library (Agilent Inc. ). Mixing time in NOESY experiments was set to 100 ms and to 14 ms in TOCSY experiments. The non-uniform sampling (NUS) schedules were prepared by program nussampler from the MDDNMR software package  40. When appropriate, the sampling probability density was biased for aliphatic  13  C-aliphatic evolution according to the single-bond 13 C-  13  C homonuclear coupling constant of 35 Hz. When appropriate, sampling was exponentially weighted according to the maximum evolution time. Data processing and analysis were carried out with MDDNMR, NMRPipe 41 , NMRViewJ 42 and CARA  43. Proton chemical shifts were referenced using 4,4-dimethyl-4-silapentane-1-sulfonic acid as an internal standard, whereas  15   ).
02 SR2). Ion deconvolution to zero charged monoisotopic masses was performed using Xtract algorithm in Xcalibur software. The relative abundance of the oxidized species was estimated from the ratio of the peptide spectrum matches (PSM) corresponding to peptides with oxidized cysteine (sulfenic, sulfinic or sulfonic acids) with respect to the PSM number of all cysteine-containing peptides. The incubation and digestion steps were carried out at least in duplicate and at least two separate samples of each peptide mixture were analysed by mass-spectrometry. In a separate experiment the relative abundance of oxidized peptides was also calculated considering the chromatographic peak areas of the corresponding peptides using Skyline 3. 1 software  49  , obtaining equivalent results (data not shown).
Acknowledgements We thank  Cristina Madrid  and  Antonio Juarez  for helpful discussions and for providing plasmids and  Laura Villarreal  and  Mar Vilanova  for help in MS experiments and  Laareb Irrem Mohamad  for help in DLS experiments. This work was partially supported by funds from the  Spanish MINECO  ( BIO2010-15683  and  BIO2013-45793R  -cofounded with European Structural Funds,  FEDER-) , the  EC FP7   BioNMR  project (contract  261863 ) and the  ARO  ( W911NF-14-1-0279 ). T. K. W. is the Biotechnology Endowed Professor at the  Pennsylvania State University. NMR experiments were performed at the  ICTS NMR LRB and CCITUB (University of Barcelona ) and the  Swedish NMR Centre (Goteborg University ). MS experiments were performed at  IRB Barcelona MS Core Facility  (member of the BMBS  COST Action BM 1403 and Proteored ,  PRB2-ISCIII (IPT13/0001-ISCIII-SGEFI / ERDF ).
A complex system of electric currents flowing in the ionosphere and magnetosphere originates from the interaction of the solar wind and the Interplanetary Magnetic Field (IMF) with the Earth's magnetic field. These electric currents generate magnetic fields contributing themselves to those measured by both ground observatories and satellites. Here, low-resolution (1 Hz) magnetic vector data recorded between 1 March 2014 and 31 May 2015 by the recently launched Swarm constellation are considered. The core and crustal magnetic fields and part of that originating in the magnetosphere are removed from Swarm measurements using CHAOS-5 model. Low-and mid-latitude residuals of the geomagnetic field representing the ionospheric and the unmodelled magnetospheric contributions are investigated, in the Solar Magnetic frame, according to the polarity of IMF B y (azimuthal) and B z (north-south) components and to different geomagnetic activity levels.
More recently,  Kunagu et al. (2013)  applied a continuous wavelet transform to mid-latitude CHAMP magnetic data focusing primarily on the 27-day periodicity they found in X, Y and Z residuals and in IMF B y. This periodicity, present in geomagnetic components, is characterised by an intermittent temporal structure probably due to a LT dependency, and no LT dependency was found in IMF B y. These findings support results found by  Vennerstrom et al. (2007)  and question those by  Lesur et al. (2005). This controversy has brought us to study the features of residuals in the Solar Magnetic (SM) frame when Swarm data are used. These residuals are estimated as the difference between satellite magnetic measurements and modelled data representing both internal and external magnetic fields. Precisely, we use low and mid-latitudes (between 50° S and 50° N SM latitude) data from Swarm satellites and CHAOS-5 model  (Finlay et al.
2015) , one of the most up-to-date magnetic models able to represent both internal (core and lithosphere) and external magnetic fields. We study the behaviour of calculated residuals according to the polarities of IMF B y and B z and Dipole Local Time (DLT) to verify whether one of the hypotheses previously made on the possible relation between IMF B y and Y component residuals can be confirmed with Swarm data. Then, we investigate the structure of residuals of the horizontal component H of the geomagnetic field as a function of Sym-H index and DLT. Data reprocessing is described in detail in the next section together with the method adopted to gain a deeper knowledge on the magnetic field mapped into analysed residuals. The "Results and discussion" part is devoted to the description of what emerges from the proposed analysis, and finally, in "Conclusions" results are interpreted and the main findings summarised.
Data reprocessing In this study we use low-resolution (1 Hz) magnetic vector measurements taken on board the three Swarm satellites Alpha (A), Bravo (B) and Charlie (C). We analyse Level 1b magnetic data 3  that according to ESA nomenclature are called SW_OPER_MAGx_LR_1B (x = A, B, C) with file counter equal to 0405, in particular measurements rotated in the NEC (North-East-Centre) frame. This version of Swarm vector data is corrected for a disturbance likely due to the position of the Sun with respect to Swarm satellites (details can be found in  Lesur et al. 2015). Selected data cover the time period between 1 March 2014 and 31 May 2015. During this period Swarm A and C have flown at an average altitude of ~470 km and Swarm B of ~520 km. The procedure described in the following has been applied on data from Swarm A, B and C, separately.
All the figures included in this paper refer to Swarm A only, and the same figures drawn with data from Swarm B and C are available as additional files. Since the purpose of this work is to investigate the properties of unmodelled external contributions, the modelled magnetic fields originated from the core and from lithospheric and large-scale magnetospheric sources are removed from Swarm measurements. To achieve this, we subtract from each measurement a value obtained using CHAOS-5  (Finlay et al. 2015)  model that takes into account these contributions. This value is estimated at the same location (latitude, longitude and altitude) and at the same time of Swarm measurement. In CHAOS-5, spherical harmonics degrees from 1 to 90 represent the internal field, and those from 1 to 20 the core field temporal variations.
Spherical harmonics expansion is then made in SM coordinates up to degree 2 for the ring current, in Geocentric Solar Magnetospheric (GSM) coordinates up to degree 2 and order 0 for magnetopause and magnetotail currents  (Olsen et al. 2014 ). We use CHAOS-5_v4 based on Swarm Level 1b and ground observatory data as available in June 2015 and able to model the external field until 6 June 2015. Detailed information on CHAOS-5 (documentation and code) is freely available. 4 fter removal of CHAOS-5 values from Swarm measurements, residuals are corrected for spikes (generally due to brief periods of switched off vector magnetometer) and rotated from the NEC frame into the SM frame to have a better point of view of solar wind influence on examined residuals  (Maus and Lühr 2005). SM frame is Earth-centred with z-axis parallel to the magnetic dipole and positive northward, y-axis perpendicular to the Earth-Sun line and positive duskward and x-axis completing the right-handed system  (Kivelson and Russell 1995).
2c  around 19 DLT, is of about -30 nT. Considering that the contribution due to the ring current ranges between a few tens to several hundreds of nanoTeslas (from quiet to disturbed period), the average unmodelled contribution is quite low. Another possible interpretation of the features observed on Swarm dY and dH residuals is given in terms of the magnetic effect at low and mid-latitudes of net field-aligned currents flowing into the ionosphere on the day-side and out of the ionosphere on the night-side as theoretically hypothesised by  Crooker and Siscoe (1981). However, considering the length of available used data (15 months), and the difficulties in magnetic source separation, we have to stress that the identification of the sources of the observed residuals is not univocal. Nevertheless, the results of this study indicate that the simultaneous use of Swarm data and CHAOS-5 model provides the opportunity to improve geomagnetic field models including effects of current systems that, so far, have not been considered.
This study is a very first attempt to characterise unmodelled contributions in satellite-based models using data from the three Swarm satellites and CHAOS-5 on a 15-month time window. A more detailed analysis of the dependence of geomagnetic residuals on IMF and geomagnetic indices could certainly take advantage of data over a longer time interval therefore allowing the investigation of the seasonal dependence, important especially concerning the FAC variability and the possible contribution of interhemispheric fieldaligned currents, and also the semiannual variation in geomagnetic activity through the Russell-McPherron effect  (Russell and McPherron 1973).
Acknowledgements We thank all members of the  ESA Swarm team  for their precious work, which is the basis for our investigations. Magnetic data used here are the Swarm Level 1b MAGA_LR freely accessible at https://earth. esa. int/web/guest/swarm/data-access. We acknowledge use of  NASA/GSFC's Space Physics Data Facility 's CDAWeb service, and OMNI data, geomagnetic indices and OMNI IMF data were obtained at http://cdaweb. gsfc. nasa. gov/. We are also grateful to the authors of CHAOS-5 for making their model available. Figures 1, 2 and 7,  B1 ,  B2 ,  B7 ,  C1 ,  C2  and  C7  are drawn with the Generic Mapping Tool (Wessel et al. 2013).