dataesr/scientific-paragraphs-categorization huggingface dataset:
The research leading to these results received funding from the  French Institutes INRA-INRIA (ARC-VitelBio) , the  French national agency ANR (DIMIMOS) , le  Conseil Général d'Auvergne  ( CPER 2007 ( CPER -2013)  ) and the  European Community 's 6th and 7th  Framework Programmes  ( FP6  and  FP7)  under grant agreement no. 017841  ( Nitro-Europe ) and no. 226701  ( CARBO-Extreme ). All authors have refused to apply for the research bonus scheme set up by the French government in 2010 and have consequently no competing financial interest in this work. This work is dedicated to  Waniya Shahzad  and  Gabin Maire.
Tween 80 was added to SYM medium, because it was found that it stimulated photosynthetic pigment production in cultures of C. halotolerans. The increase in growth yield (determined as dry weight) was 57% in L. syltensis and 21% in P. rubra. Mixotrophic growth of P. rubra was also tested in SYPHC medium containing pyruvate instead of malate in combination with yeast extract as substrate. However, in this medium no light-dependent increase of biomass formation was found (data not shown). Noteworthy, the growth yield of P. rubra in complex medium is much lower compared to L. syltensis and C. halotolerans, which could indicate that in P. rubra mainly pyruvate or malate were utilized for growth, but only a limited amount of the other carbon compounds that are present in yeast extract. The growth response of the tested strains in defined media containing DL-malate as single substrate are shown in Figure  2B , D and F.
For L. syltensis and P. rubra also growth curves with pyruvate were determined, because in both strains this substrate was more efficiently metabolized than malate (data not shown). However, no significant light-dependent increase in growth yield was found for L. syltensis and P. rubra upon incubation with pyruvate as sole carbon source, albeit photosynthetic pigments in amounts comparable to mixotrophically growing strains were produced, so that it can be assumed that during utilization of pyruvate no energy could be gained from the harvested light. Obviously, the metabolized substrate has a large impact on the efficiency of mixotrophic growth in members of the OM60/NOR5 clade, whereas the abundance of photosynthetic pigments does not correlate directly with the energy yield of photophosphorylation.
, 1997; Zhang et al. , 2012). The [Fe 4 S 4 ] cluster in FNR can be regenerated from a cysteine persulfide-coordinated [Fe 2 S 2 ] cluster in the presence of a reductant and ferrous iron. This observation provided some clues about a possible mechanism devoted to the repair of biological [Fe 4 S 4 ] clusters, which represent the vast majority of the cellular Fe-S clusters and are usually [Fe 4 S 4 ] ligated by four cysteines but with one thiolate ligand serving also for siroheme as in Nicotiana tabacum nitrite reductase. PDB codes used for drawing these clusters using Pymol are 3AB5, 3S2Q, 1RFS, 1OFD, 2PU9, and 3B0G, respectively. more sensitive to oxygen compared to [Fe 2 S 2 ] clusters  (Zhang et al. , 2012). Altogether, cluster interconversion may represent an efficient way for the maturation or repair of different types of Fe-S proteins or for the regulation of cellular processes in response either to some changes in the intracellular conditions or to extracellular stimuli.
It is so far unknown if the coordination of their action is mediated through transcriptional control, as in prokaryotes. As an example, it was shown that human ISCU1/2 are repressed during hypoxia by the microRNA-210, as a way to control mitochondrial metabolism under this condition  (Chan et al. , 2009). In plants, although public databases for gene expression can be questioned, almost no report has been published concerning the regulation of the expression of the ISC, SUF or CIA components. None of the above reported transcriptional regulators are encoded in plant or algal genomes. Some studies on isolated genes have been performed showing for example that in A. thaliana, SUFB gene expression is repressed upon iron starvation but the regulatory mechanisms are not known  (Xu et al. , 2005).
PCC 6803, and (F). [Fe 4 S 4 ] ligated by four cysteines but with one thiolate ligand serving also for siroheme as in Nicotiana tabacum nitrite reductase. PDB codes used for drawing these clusters using Pymol are 3AB5, 3S2Q, 1RFS, 1OFD, 2PU9, and 3B0G, respectively.
Scans stored as 16-bit TIFF (tagged information file format) image files and data analysis were performed with GenePix Pro 7. 2. Low quality spots (spots smaller than 40 m in diameter and/or exhibiting a signal-noise ratio higher than 2) were flagged and filtered out. Median values for each spot were log transformed (log 2 ) and normalized by the Lowess method to account for any difference in total intensity between the scanned images using Acuity microarray analysis software (version 4. 0; Axon Instrument Inc. ). Two independent microarray experiments were performed. A 1. 0-fold difference from the 1:1 hybridization ratio was taken as indicative of differential gene expression. Two-dimensional Gel Electrophoresis-50-ml cultures of strains BW25113 and JW3435 (⌬tusA) were grown aerobically at 37 °C for 8 h.
75 ϫ A 550 ][A 600 ϫ t ϫ V], where t equals the time of reaction and V equals the volume (ml) of cells added to the assay tubes. Expression of the Genes from the ISC Operon, tusA, and iscU-Plasmids pDB1282 (coding for Azotobacter vinelandii IscS, IscU, IscA, HscB, HscA, Fdx, and IscX), pJD34 (coding for TusA), pJD54 (coding for IscU), pET15b, and pEB327 were expressed in the BW25113(DE3) strain. Expression of TusA, IscU, and pET15b was induced by the addition of 20 M IPTG for 8 h. Expression of both the ISC genes and pEB327 was induced by the addition of 0. 1% arabinose. Cells were harvested, and NR and TMAOR activity was measured in the same manner as described above for the mutant strains. Surface Plasmon Resonance (SPR) Measurements-All binding experiments were performed with the SPR-based instrument Biacore TM T200 on CM5 sensor chips at a temperature of 25 °C and a flow rate of 10 l/min using Biacore control T200 software and evaluation T200 software (GE Healthcare) as described previously  (39).
Acknowledgments-We thank  Lothar Lehnhardt  and  Zoya Ignatova of Potsdam)  for their help with the two-dimensional gel electrophoresis experiments and  Johannes Fritsch  and  Oliver Lenz  ( Humboldt University Berlin ) for their support in the detection of hydrogenase activity. Nataliya Lupilova  ( Ruhr-University Bochum ) and  Angelika Lehmann  ( University of Potsdam ) are thanked for their technical assistance. Roel M. Schaaper  ( NIEHS, National Institutes of Health ) is thanked for the suggestion of initial experiments and helpful discussions. Mita Mullick Chowdhury  and  Julia Lücke  ( University of Potsdam ) are thanked for initial experiments. We also thank  Dennis Dean  ( Virginia Polytechnic Institute ) for providing plasmid pDB1282 and  Gottfried Unden  ( University of Mainz ) for providing strain IMW151a.
Pegylated Fe@Au NPs Characterization By taking advantage of the high Au-S affinity, the gold surface of Fe@Au NPs was stained through chemisorption with FITC-PEG 5000 -SH. Surface gold staining with fluorescence was attested by confocal microscopy. Fig- ure  5  shows a 3D-picture constructed with ImageJ recorded from a Z-stack of 28 different views (longitudinal sec-tions on the Z-axis) with the green emission mode (λ em = 520 nm, λ ex = 490 nm). It should be noted that an additional red emission mode (with λ em = 620 nm, λ ex =590 nm) was also tested as negative control (data not shown). This latter, as expected, could not result into any red light emission. Green staining is only located at the surface of nanoparticles and clearly evidences their acicular shape. This experiment shows that Fe@Au NPs have been functionalized with the FITC-PEG-SH.
9, A-D , where the four end rings are compared with that of the DFT-calculated in vitro structure  (42). Both cycles of the (blue-absorbing) ␤-carotene perpendicular to the membrane plane (Bcr645 in Protein Data Bank structure 3ARC) make a large angle with the conjugated CϭC chain (dihedral angles 59º and 68°; Fig. 9, C  and D ). This is quite different for the (red-absorbing) ␤-carotene parallel to the membrane (Bcr651), where one of the cycles makes a dihedral angle of only 12°with the plane of the CϭC chain, as seen in Fig. 9A. Once again, this twisting back into the plane allows the end ring to lie more or less parallel to an overlapping aromatic residue, this time PHE113 of the PsbD polypeptide (ϳ3. 9 Å away; Fig. 9A ). Note that the second end ring, although lying out of the plane, also makes a smaller angle than those measured for the blue-absorbing Car (48°; Fig.
Control Software Homemade software enabled on-line acquisition, monitoring and regulation of operating parameters (stirring rate, pH, temperature, partial pressure of dissolved oxygen, base and antifoam additions). Oxygen consumption rate and carbon dioxide production rate were calculated from mass balances, taking into account the evolution of the gas volume in the reactor, inlet airflow (measured by a mass flowmeter, Brooks, USA), temperature, humidity and pressure. The residual substrate concentration in the fermentor was evaluated by homemade software based on carbon and redox balances taking into account online acquisition data.
Ferredoxin in Iron-Sulfur Cluster Biogenesis SAXS Methods-Synchrotron radiation x-ray scattering data were collected on the EMBL P12 beamline at the PETRA III storage ring (DESY, Hamburg). Measurements were carried out at 10 °C with 2. 5-5. 0 mg/ml of solutions. The data were recorded using a 2-m PILATUS detector (DECTRIS, Switzerland) at a sample detector distance of 3. 0 m and a wavelength of ϭ 0. 1 nm, covering the range of momentum transfer 0. 12 Ͻ s Ͻ 4. 50 nm Ϫ1 (s ϭ 4 sin/, where 2 is the scattering angle). No measurable radiation damage was detected. Data treatment was carried out by ATSAS package  (29)  according to a protocol already described  (19). The scattering patterns of the IscS dimer (PDB code 1P3W) and IscS⅐Fdx complex were calculated using CRYSOL  (30). In Vivo Validation-The strains used in this work are E.
1D ). CyaY is thus able to displace holo-Fdx from IscS. These results tell us that the IscS interaction is specific for holo-Fdx in agreement with the indications of previous two-hybrid data  (15)  and that the binding site overlaps with CyaY. Holo-Fdx Binds IscS with Micromolar Affinity-To confirm and quantify this observation, we measured the affinity of holo-Fdx for IscS by BLI. We immobilized holo-Fdx and measured the binding affinity by titration of the protein with increasing concentrations of IscS (Fig. 2A ). Holo-Fdx binds to IscS with fast k on and k off rates, which allow evaluation of the K d at the equilibrium. The K d value obtained was 1. 5 Ϯ 0. 4 M, which is comparable with the K d between IscU and IscS (1. 5 Ϯ 0. 3 M)  (19). We then checked holo-Fdx binding to IscS in the presence of IscU or CyaY using BLI.
49). The residues found to interact with IscS are all part of an acidic patch on holo-Fdx. To quantify this hypothesis, holo-Fdx binding to the IscS mutants was measured by BLI. IscS_R39E/W45E, IscS_K101E/ K105E, and IscS_E334S/R340S all had K d values indistinguishable from that of wild-type IscS, whereas no binding was observed with IscS_R220E/R223E/R225E (data not shown). Taken together, these results indicate that IscS residues Arg 220 , Arg 223 , and/or Arg 225 are involved in the interaction with holo-Fdx. Model Building and Experimental Validation of the Holo-Fdx⅐IscS Complex-Initial models of the holo-Fdx⅐IscS complex were generated using HADDOCK  (28, 33). This method makes use of experimental data to guide molecular docking. IscS residues Arg 220 , Arg 223 , and Arg 225 and holo-Fdx residues Gln 68 , Asp 70 , Asp 71 , Asp 74 , Lys 75 , Trp 77 , Leu 79 , Glu 80 , Pro 81 , and Glu 82 were imposed as active AIRs with passive AIRs defined automatically by HADDOCK.
The MM exp and excluded volume of the holo-Fdx⅐IscS complex are clearly different from those of the isolated IscS and correspond to a stoichiometry of 2:2 for the binary complex. The overall parameters (R g ϭ 31. 0 Å, D max ϭ 112 Å) of holo-Fdx⅐IscS complex are close to those of the CyaY⅐IscS complex (R g ϭ 31. 1 Å, D max ϭ 109 Å) and differ significantly from those of the IscU⅐IscS complex (R g ϭ 35. 0 Å, D max ϭ 121 Å) excluding the possibility that Fdx binds on the periphery of the IscS dimer. Multiple runs of the program DAMMIF  (34) , a fast version of DAMMIN  (35)  were used to produce average ab initio models. The shape envelope of isolated IscS overlaps well with the crystallographic dimeric structure (PDB 1P3W)  (36)  with a good fit     2. to the data (Table  3  and Fig. 7B ). The shape envelope of the holo-Fdx⅐IscS complex is more globular suggesting that the Fdx proteins are located close to the cavity ("pocket") near the interface between the two IscS monomers.
N-and 15 N/ 13 C-labeled proteins were expressed in E. coli BL21(DE3) in M9 minimal medium prepared with [ 15 N](NH 4 ) 2 SO 4 ( 15 N 2 , 99%, CIL) and/or D-[ 13 C]glucose (U-13 C 6 , 99%, CIL). For [ 15 N/ 2 H]Fdx the growth medium was prepared with 99% deuterium oxide (D, 99. 9%, CIL) and D-[ 12 C/ 2 H]glucose (1,2,3,4,5,6,6-D7, 98%, CIL). NMR Titrations-Full spectral assignment was obtained by standard methods and deposited to the BMRB database (entry number 19273). [ 15 N]-or [ 15 N/ 2 H]Fdx or Fdx mutants were titrated with IscS, IscS mutants, IscU and/or CyaY, all in NMR binding buffer (20 mM Tris, 150 mM NaCl, 20 mM tris(2-carboxyethyl)phosphine, pH 8) at 298 K. 15 N-SOFAST HMQC spectra (27) were recorded on Bruker 700 AvanceIII and Bruker 600 MHz AvanceI spectrometers with TCI Cryoprobes.
5 mV. The self-potential data were combined to provide a map, which represents the distribution of the electrical potential with respect to the potential of a reference taken as zero. These data were krigged with Surfer Software and the resulting map is shown in Figure  2 , the zero reference point was chosen at Toro Bravo lake. The self-potential distribution displays a classical dipolar anomaly with a peaked positive lobe (250 mV) around the youngest dome (Ti), and extended negative lobes on the upper part of the flanks and on the older domes D1 -D3. The negative anomalies reach -3400 mV south of the dome. A more variable behavior is observed in the area of the ancient collapse of the old Ticsani dome, on the NW flank of the present volcano. On this side of the volcano, the mean self-potential values are typically 1000 mV higher than on the SW side.
Two fumaroles are located in the summit area and, for altitudes greater than 4800 m asl, the ground temperature data show a systematic thermal anomaly (seen in Figure  3  of the main text and in Figure  S4 ) suggesting the existence of a hydrothermal system at the summit of the edifice of Ticsani. In addition to these data, we also consider ten springs related to the Ticsani volcano  (Cruz, 2006)  and located at less than 15 km from the summit. The temperatures of these springs have been measured up to four times a year since  [2005] [2006]. The springs are located on the W and NW slope of the Ticsani volcano and exhibit temperatures from 10 to 89 • C, i. e. close to the boiling temperature at atmospheric pressure corresponding to 3000 m asl. The temperatures have been recorded with ESPEC RT-12 probe till year 2011 and with TECPEL 318 type K sensor since 2011-2012.
Model geometry We use COMSOL Multiphysics V3. 5 to analyse a 2D finite-element model of coupled transient water and heat transport and a post-processing code resolving Laplace equation for electric potential considering partial saturation, a non-reactive flow, and temperatures not exceeding 200 • C. We believe that these assumptions will not lead to significant errors, because the main question of our study concerns the distribution of the water phase outside the summit region rather then the processes related to the degassing of the magma conduit. We postulate the existence of a magmatic body (used as a heat source) below the youngest dome in agreement with the elevated ground temperatures measured in this area (Figure  3 ). We place the heat source at a depth of 10 km below the surface which corresponds to the inferred depth of the major events in the 2005 seismic swarm  (Holtkamp et al.
Acknowledgments We thank  INGEMMET  for financial and technical support of the field work,  J. P. Metaxian  for his help in the coordination of the work,  F. Jouanne  for fruitful discussions,  S. Hurwitz  and  J. -F. Lenat  for constructive remarks which greatly improved the modeling and the manuscript. We used Latex, JabRef, and InkScape open source software, ASTER GDEM is a product of  METI  and  NASA. A. Revil is supported by  DOE  ( Energy efficiency and Renewable Energy Geothermal Technologies Program ) grants. Award # GO18195  and # DE-EE0005513.
The experimental results were interpreted by a comparison with DFT calculations of the hyperfine parameters with the Wien2k software package  [33]  using the generalized gradient approximation and Perdew-Burke-Ernzerhof exchange-correlation functional  [34]. The studied system of psML-Fe/W(110) was approximated by a slab of seven W(110) atomic layers with the pseudomorphic Fe monolayer on each side. A 3 × 5 × 1 k-point mesh was used. The radii of the muffin-tin spheres were: 1. 16 Å for tungsten, 1. 0 Å for iron and 0. 79 Å-0. 85 Å for oxygen, depending on its distance from the surface. For the calculation of the Fermi energy a tetrahedron method was applied  [35]. The entire system was relaxed, and this process led to an Fe-W interlayer spacing of 1. 93 Å, which is in good agreement with previous data obtained with the VASP code  [2].
The spectra were fitted using the Recoil software  [42]  by a convolution of quadrupole doublets composed of Lorentzian lines with a Gaussian distribution of the quadrupole splittings. Additionally, the isomer shifts and the quadrupole splittings were assumed to be linearly correlated. Within the above simplifications, both assumptions (i) and (ii) gave reasonable results; case (i) is shown as an example by the solid lines in Fig. 6 , and the corresponding QS distributions are shown in the insets in Fig. 6  and are summarized in Table  1. Both fits reveal similar IS and QS values for the corresponding spectral components. One component is similar to the dominant component of the clean monolayer and indicates that the influence of oxygen does not extent much beyond a small electron transfer and does not result in the formation of well-defined ionic states of Fe.
Acknowledgments This work was supported in part by the  National Science Center (NCN) ,  Poland  (Grant No. 2011/02/A/ST3/00150 ), by the  Team Program of the Foundation for Polish Science  cofinanced by the  EU European Regional Development Fund , by the  Polish-Austrian Scientific and Technological Cooperation Program , and by the  Austrian Science Fund FWF  project No. P-20713-N20. This research has received also funding from the  Marian Smoluchowski Krakow Research Consortium -a  Leading National Research Centre KNOW  supported by the  Ministry of Science and Higher Education. The calculations were performed in the ACK Cyfronet AGH, computational Grant No. NiSW/IBM_BC_HS21/ AGH/035/2007.
The most recent comparative genomic analysis  (15)  identified 597 proteins that were present in plants and green algae (based on mutual best BLAST hits and similarity criteria) but were not identified in bacteria, archaea, fungi, and mammals. Of these 597 proteins, 311 were not assigned a biological function, although multiple bioinformatic techniques were used to probe their importance in plant-specific processes. Sequence motifs, identified by BLAST analyses, had been associated with 231 of these GreenCut "unknowns. " This information along with assignments of subcellular location, coexpression analysis, and transcript abundance information from both Arabidopsis thaliana and Chlamydomonas reinhardtii (Arabidopsis and Chlamydomonas throughout) have resulted in hypotheses concerning potential functions of some of these proteins  (15) ; testing such hypotheses requires extensive experimentation.
Lipid Extraction and Quantification Total lipids were analyzed as described in The Plant Organelle Database 2  [16]  [Ikuo Nishida, Lipid extraction from Arabidopsis mitochondria, http://podb. nibb. ac. jp/Organellome/ bin/findFunctional?status = confirm&method = 1&Species = & Keywords = &Category = Biochemical assays]. CC-503 cells (approximately 5. 0610 7 ) were grown in TAP medium containing either BFA or DMSO alone (solvent control) and subjected to lipid extraction. Briefly, cells were harvested by centrifugation at 2,000 g for 20 min. The pellets were immersed in 2 mL of boiling isopropanol and heated for 5 min at 80uC to inactivate lipases. After cooling, 2 mL each of methanol and chloroform and 1. 24 mL of water were added to the sample and the mixture was vortexed for 5 min. The extract was centrifuged (10 min, 2,000 g), the resultant supernatant decanted to a new 10-mL screw-capped glass tube, and the pellet re-extracted with 2 mL of methanol, 1 mL of chloroform, and 0.
This research was supported by grants from the  Global Frontier Program  ( 2011-0031345 ) of the Republic of  Korea  awarded to YL and HO, from  Gyeongbuk Sea Grant Program  funded by the  Ministry of Oceans and Fisheries , Korea, from a  Grant-in-Aid for Scientific Research  ( 21570034 ) from the  Ministry of Education, Culture, Sports, Science and Technology of Japan  awarded to IN, and from the  French ANR (DIESALG)  awarded to YL-B. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Particulate absorption and pigment data The spectral absorption data used in this work were measured with a WETLabs AC-S instrument, an in situ spectrophotometer that provides hyperspectral absorption and attenuation data in the range 400-750 nm with ∼4 nm resolution  (Moore et al. , 1997; Rhoades et al. , 2004). The spectral range and measurement wavelengths vary slightly between sensors and for a specific sensor following factory calibration. Several different AC-S instruments were used during the collection of spectral absorption in this study. The instruments were deployed using an in-line system that allows nearly continuous sampling of surface ocean water; details of the flow-through system are provided in  Slade et al. (2010). Total absorption was measured on unfiltered bulk seawater, followed by 0.
, 2013). Five different AC-S sensors from four different labs (serial numbers 007, 043, 057, 082, 091) were used with the flow-through technique during the Tara Oceans expedition, a 2. 5 year-long expedition from fall of 2009 to spring of 2012 along a 57,000 nautical miles oceanic route spanning the Indian, Atlantic and Pacific oceans  (Karsenti et al. , 2011). The particulate absorption data from Tara Oceans have been binned to one-minute temporal resolution. Data points with coincident HPLC data are selected from this one-minute binned dataset (hereafter ''match-up points''); 87 of the 210 match-up points used in this paper are from this Tara Oceans dataset. The Tara Oceans data are further binned to 1 km 2 resolution, resulting in 69,944 data points from across the globe. We apply our method, described below, to this 1 km 2 binned dataset after demonstrating the ability to detect pigments by decomposition of absorption spectra.