dataesr/scientific-paragraphs-categorization huggingface dataset:
■ RESULTS AND DISCUSSION Crystal Structure Analysis and Room Temperature Magnetic Susceptibility. The crystal structures of TTF-CA (black form) at RT and 20 K, were determined from their synchrotron XRPD patterns. Figure  1  shows the crystal structure at RT, and the Rietveld graph is shown in the SI file (Figure  S7 ). As previously determined from the analysis of infrared measurements,  13  this material is composed of TTF dimers easily discerned along [001]. The TTF units in the dimers are planar and in an eclipsed configuration, with an interplanar TTF-TTF distance of 3. 27(1) Å, in agreement with values found in the Cambridge Structural Database  36  for TTF compounds that contain (TTF +• ) 2 radical cation dimers. The TTF +• radical cation is generated when one of the dithiolylidene rings in TTF becomes aromatic by losing one electron.
Moreover, in the black polymorph of TTF-CA the columnar arrays of TTF and CA units are linked by multiple weak (nonclassical) hydrogen bonds between H atoms of TTF, O and Cl atoms of CA, and these are shown in Figure  1b. In agreement with the crystal structure and the chemical bonding in the (TTF +• ) 2 and (CA -• ) 2 dimers, the black form of TTF-CA was experimentally found to be diamagnetic with RT mass magnetic susceptibility of -(0. 24 ± 0. 03) × 10 -6 cm 3 /g. We have also noted that the crystal structure of TTF-CA above resembles the one depicted for another ionic and diamagnetic charge transfer salt, TTF-DDQ (DDQ = 2,3dichloro-5,6-dicyano-p-benzoquinone),  39  although its coordinates were not found in the Cambridge Structural Database. 36 he DDQ molecules were reported to be disordered with partial exchange of -CN and -Cl substituents.
In situ interaction experiments over periods of 2, 6, and 10 years between Toarcian argillite and carbon steel discs were carried out in the Tournemire Underground Research Laboratory (URL), yielding a dataset of the materials' geochemical evolution under conditions representative of the future geological disposal of high-level long-lived radioactive wastes. The carbon steel discs were exposed to corrosion due to trapped oxygen. The corrosion rates indicate that the oxidizing transient lasted between 2 and 6 years. A systematic dissolution of calcium phases (Casmectite sheets in I/S and calcite) was observed in the iron diffusion halos. The iron release induced mineralogical dissolution and precipitation reactions, which partly clogged the argillite porosity.
Efficient DNA repair is critical for cell survival and the maintenance of genome integrity. The homologous recombination pathway is responsible for the repair of DNA double-strand breaks within cells. Initiation of this pathway in bacteria can be carried out by either the RecBCD or the RecFOR proteins. An important regulatory player within the RecFOR pathway is the RecOR complex that facilitates RecA loading onto DNA. Here we report new data regarding the assembly of Deinococcus radiodurans RecOR and its interaction with DNA, providing novel mechanistic insight into the mode of action of RecOR in homologous recombination. We present a higher resolution crystal structure of RecOR in an 'open' conformation in which the tetrameric RecR ring flanked by two RecO molecules is accessible for DNA binding.
In this study, tteRecOR was also shown to bind specifically to ssDNA and not to dsDNA and the authors propose a model for ssDNA binding to the heterotrimeric RecOR complex. However, so far there is no structural data available describing the precise mechanisms by which the RecOR complex interacts with DNA substrates. Here we report a combined low-and high-resolution study, involving complementary structural biology approaches, of the drRecOR complex in the presence and absence of DNA. We show that drRecR is dimeric in solution and propose that binding of RecO triggers its tetramerization. A new crystal structure of the drRecOR complex was determined at higher resolution (3. 3 A ˚) in a conformation where the inside of the RecR ring is partially accessible for ssDNA to bind. We demonstrate using small-angle neutron scattering (SANS) that the RecOR complex binds DNA substrates within this accessible cavity but with different binding modes for ssDNA and dsDNA.
The crystal used for data collection resulted from the Silver Bullets condition N 8 (containing 0. 25% w/v 1-Pentanesulfonic acid sodium salt monohydrate; 0. 25% w/v 3,5-dinitrosalicylic acid; 0. 25% 3-aminosalicylic acid; 0. 25% w/v salicylamide; 0. 02 M HEPES sodium, pH 6. 8). Data collection, structure determination and refinement X-ray diffraction data were collected on ID14-4 beamline at the European Synchrotron Radiation Facility (ESRF) in Grenoble, France. The crystal used for data collection belonged to the space group P1 and had unit cell dimensions of a = 63. 130 A ˚, b = 93. 110 A ˚, c = 92. 350 A ˚, a = 103. 6 , b = 110. 42 and g = 106. 22. Diffraction was observed to a maximum resolution of 3. 34 A ˚. Data were processed with the program iMosflm (39) and scaled with SCALA from the CCP4 program suite  (40).
The structure of drRecOR was determined by molecular replacement using the program PHASER  (41)  and drRecR (pdb1VDD) and drRecO (pdb1W3S) as search models. The model was built using the program Coot  (42)  and refinement was carried out with Phenix (43) and Refmac5 (  44 ) using TLS refinement. The quality of the model was checked using the Molprobity server  (45). Structural figures were generated with PYMOL (www. pymol. org).
Small-Angle X-ray scattering Small-angle X-ray scattering (SAXS) experiments were conducted at the ESRF ID14-3 beamline in Grenoble (France). All proteins used were purified by size-exclusion chromatography before SAXS measurements. The buffer of the size-exclusion chromatography step was used as reference for background subtraction for the SAXS measurement. For each sample, six different concentrations ranging between 0. 5 and 10 mg/ml were measured. Protein solution (60 ml) for each sample (and buffer) was exposed to X-rays and scattering data were collected. Ten individual frames of 30 s were collected for every exposure using a Pilatus 1M detector (Dectris). Individual frames were processed automatically and independently using the software BsxCUBE, yielding individual radially averaged curves of normalized intensity versus scattering angle q = 4pSINy/.
Small-angle neutron scattering SANS data were collected with the D22 instrument at the Institut Laue-Langevin in Grenoble, France. All drRecOR samples resulted from the same purification, which was divided to perform the different measurements with and without DNA assuring that observed changes are due to ligand binding and not to differences between protein purifications. The concentration of the RecOR complex was at 2 mg/ml. For the measurements in the presence of DNA, 50mer ssDNA and dsDNA (same oligonucleotide sequences as those used for the fluorescence anisotropy experiments) was added in a slight excess at a DNA:protein ratio of 1. 2:1. Data were recorded using two detector distances at 2 and 10 m with a neutron wavelength of 6 A ˚, covering a q range of 0. 007-0. 35 A ˚À1 , where q is the scattering vector (4psiny/).
Data reduction was performed using the GRASansP software. After SANS data collection the binding of DNA to the drRecOR complex was verified by gel electrophoresis. Small-angle scattering data processing SAXS and SANS data were processed and analysis steps were performed using the ATSAS package  (46)  as described in  (47). The final merged scattering data were further evaluated using PRIMUS. At low angle, the isotropic scattering data can be expressed as the Guinier approximation, I(q) = I(0) exp 1/3 R g 2 q 2. The isotropic scattering intensity I(q) was transformed to the distance distribution function P(r) using the program GNOM, which was also used to calculate the particle maximum dimensions D max. The optimum value of D max was found when the R g obtained from the P(r) plot was equal that obtained from the Guinier analysis.
For ab initio modeling of the SAXS data, 20 sets of independent models were calculated using Dammin  (48) , and then averaged and aligned using DAMAVER  (49). Ab initio modeling of the drRecOR-DNA complexes were performed with the multi-phase dummy-atom modeling program MONSA  (48). Theoretical scattering curves for known structures were calculated and compared with experimental data using CRYSOL (50) for X-ray data and CRYSON  (51)  for neutron data.
Molecular assays were built starting from the crystal structure reported in this work (later called RecOR-'open') using the following procedure. The MODELLER package  (62)  was used to infer the position of the amino acids (G41, V42, K43, G44, P45, L46, S47) of the two RecO loop subunits missing in the crystal structure. After adding proper hydrogen atoms, the protein was fully solvated in a water box of 110 Â 100 Â 125 A ˚. An elongated single-strand of DNA composed of 10 thymine nucleotides was then inserted randomly in the central cavity of the complex, while preventing sterical clashes between ssDNA and proteins. The initial simulation box contains $110 000 atoms. Two different systems were considered involving, respectively, the K23A/R27A double-mutant and the wild-type RecOR complex.
The latter was constructed by mutating residues A23 and A27 observed in the crystal structure of the four RecR subunits to K23 and R27. Proper positioning of the side chains of these lysine and arginine residues was made using the crystal structure of the wild type as a template (later called RecOR-'closed', PDB code 2V1C). All setups and analyses were made with VMD  (63). After 2000 steps of energy minimization, the two molecular assays were thermalized for 100 ns using the following protocol. During the first 5 ns, all the atoms of the system but water and counter-ions were kept fixed. For the next 40 ns, side chains and ssDNA were allowed to move while relaxing gently the position of the backbone atoms with stepwise-diminishing harmonic restraints. The overall system was then equilibrated further during 55 ns.
Finally, data production and analysis was carried out all along the next 150 ns. In a last step, starting from the wild-type and mutant equilibrated RecOR/ssDNA complexes, two apo-RecOR assays were built and subjected to the molecular-dynamics protocol described above. In a nutshell, four different assays were considered in this work, namely apo-and ssDNA complex of the wild-type and double-mutant RecOR complex. For each of them a trajectory of 250 ns was generated representing an overall effort of 1 ms. For the wild-type apo complex, a control simulation of 100 ns was produced starting from the 'open' crystal structure thermalized as described above.
This is possible because DNA has a different scattering length density than proteins. We measured the scattering of the RecOR complex bound to ssDNA and dsDNA in 0%, 65% (matching point of DNA) and 100% deuterium (Figure  5 ). The R g values derived from the data recorded for the RecOR complex bound to ssDNA are similar to these values obtained for the RecOR complex alone, indicating that the solution structure of the complex remains the same in the presence of ssDNA (Figure  5A  and B ). Ab initio modeling of the different phases using the program MONSA resulted in structural models where the DNA substrate is always bound in the center of the RecOR complex and located in the center of the RecR tetrameric ring (Figure  5C ). In contrast, the measurements of drRecOR bound to dsDNA resulted in larger R g values approaching $47 A ˚(Figure  5A ), indicating that the complex undergoes larger conformational changes to bind dsDNA.
4 A ˚(K23A/ R27A) and 72. 8 A ˚(wild-type), in line with the corresponding distance, 71. 6 A ˚, observed in the 'open' crystal structure (Figure  7B ). For the apo systems, the latter distance is markedly shorter, with the mean values of 65. 4 A ˚(K23A/ R27A) and 69. 1 A ˚(wild-type) and navigates continuously between values measured in RecOR-'closed' (61. 4 A ˚) and RecOR-'open' (71. 6 A ˚) assemblies, respectively (Figure  7A  and Supplementary Figure  S5 ). The tilt angle between the normal to RecR tetrameric ring and the axis connecting the center of mass of the two RecO subunits follows a similar trend (Supplementary Figure  S6 ), its mean value switches from $38 in the presence of ssDNA to $29 for the wild type apo system. The CRYSON program was used to fit the experimental SANS data acquired for RecOR with and without ssDNA against structures sampled all along the MD trajectories.
All RecR dimers described so far consist of N-N dimers in which the HhH domain of RecR forms the principal interaction interface  (29) (30) (31) (32) 64). In the available tetrameric structures of RecR  (23, 32) , interactions between the C-terminal regions of two RecR monomers are also observed and the interaction surfaces involved in either N-N or C-C dimer interfaces are similar ($2000 A ˚2). In the case of drRecR, our SAXS data clearly indicate that the stable dimer observed in solution is also the N-N dimer indicating that C-C dimers of drRecR do not form alone in solution. Formation of RecR tetramers, consisting of two N-N dimers interacting via their C-terminal regions, is most likely induced by the interaction of RecR with one of its cellular partners (RecO and/or RecF) and/or with DNA.
The assembly of this hetero-hexameric complex may form in the cell before interaction with its SSB-coated ssDNA substrate (model A) or may alternatively assemble directly on SSB-coated ssDNA (model B). At present our data and the available literature do not allow us to discriminate between these two models. In both cases, RecO is believed to be involved in binding and perhaps also removal of SSB from the DNA. In model A, the threading of ssDNA through the RecOR complex would result in removal of the bound SSB and facilitate the assembly of RecA. In model B, RecO alone may bind to DNA and remove SSB before assembly of the RecOR complex. While our data clearly indicate that RecO triggers the tetramerization of RecR and the subsequent formation of the stable heterohexameric RecOR assembly and that ssDNA can bind inside such a complex, further studies will be needed to distinguish between these two models.
Acknowledgments: We thank  Y. Hirotsu  and  T. Egami  for constructive discussion and  H. Sheng  for providing Zr-Pt embedded atom model potentials and  J. Saida  for Zr 80 Pt 20 ribbons. This work was sponsored by " WPI Research Center Initiative for Atoms, Molecules and Materials," Ministry of Education, Culture, Sports, Science and Technology of Japan ;  Grants-in-Aid for Scientific Research  ( 24360260  and  24656400 ),  Japan Society for the Promotion of Science ; "A mathematical challenge to a new phase of materials science,"  Japan Science and Technology Agency-Core Research for Evolutional Science and Technology ; and the  National Natural Science Foundation of China  (grant  51271113 ).
Data collection, structure determination and refinement Data sets from a single ligand-bound SAP102-3 PDZ domain crystal were collected on the NSLS beamline X6A at Brookhaven National Laboratory (Upton, NY) tuned to a wavelength of 0. 9795 Å and at 100 K with a frame oscillation of 1° using the ADSC Quantum 270 detector. Indexing and integration of the collected images were accomplished using the HKL2000 suite of programs  [8]. Intensities were converted to structure factors using the program Truncate. The ligand domain structure was solved by molecular replacement with the program PHASER  [9]  using coordinates of the S14 third PDZ domain from DLG4/PSD-95 (PDB accession codes: 3JVQ). The unambiguous solution contained two complexes in the asymmetric unit. The fluorogenic ligand was clearly visible from the initial F o -F c difference electron density map.
Fluorescence titration For each titration, the peptide concentration was kept constant (around 2 to 4 μM) and the protein concentration was varied from values lower or close to the anticipated K D to saturation of the fluorescence signal increase. A 130 μL S15 solution in PBS (pH 7. 4) was prepared for each protein concentration. Dissociation constants were evaluated using the following equation  [16]  by nonlinear least-squares analysis using the program GraphPad Prism: 1 where F is the fluorescence reading, [Prot] is the protein concentration in mol. L -1 , Kd is the dissociation constant of the PDZ domain and peptide, F o is the initial fluorescence value (fraction bound = 0), and F max is the fluorescence value at saturation (fraction bound = 1). Each Kd value is the average of at least three independent experiments.
ACKNOWLEDGMENT This research was supported by  NSF   CHE-0414243  (to B. I. ), the  Cell Migration Consortium  ( GM064346 ), the  Marie Curie postdoctoral Fellowship (PICK-CPP , M. S. ) and the  ANR  (ChemTraffic, M. S. , D. C. ). We are grateful to the staff at the  NSLS beamline X6A  for access via the  General User program.
This feature has been tested with an X-ray fluorescence set-up and described elsewhere  (Petitgirard et al. , 2012). Diffraction patterns were collected with a 160 mm-diameter CCD detector from Marresearch, located at $ 200 mm from the sample. Debye rings were integrated with the Fit2D software  (Hammersley et al. , 1996)  and refined with GSAS  (Toby, 2001). For continuous double-sided laser heating, two CW Nd:YAG fiber lasers (IPG photonics) with = 1. 064 mm and providing a maximum total power of 220 W are used to heat each side of the sample in the DAC (Fig. 1 ). The beam spot is in the fundamental transfer mode TEM 00 , or Gaussian profile; the beam has a very high quality with M 2 = 1. 02 and the laser output power has a high stability of AE 0. 5%. UV-grade fused silica lenses with typical focusing distance of 70 mm are used to concentrate the laser power onto an area of typically 30 mm diameter.
, 2003). In a cumulative mode and using the X-ray pulse as the probe and the laser as the pump it should be possible to synchronize XRD with the pulsed laser data An in situ X-ray diffraction stack plot of the mineral MnS 2 during CO 2 laser heating. Temperature measurements were taken every 30 s and the full time lapse of this plot is 5 min. in such a fast regime. Such experiments will surely make the link with future shock experiments that will take place at synchrotron sources and at even higher speeds at facilities such as free-electron lasers. The developments presented in this paper for double-sided pyrometry together with the successful installation of a CO 2 laser offer capabilities to probe samples with wide compositional diversities used by the different communities involved in high-pressure science.
These data were scaled with measurements performed, for T 1. 8 K, using a commercial SQUID magnetometer and a physical measurement platform equipped with ac susceptibility options. The zero field (H = 0) ac susceptibility χ ′ and χ ′′ components of Fe 8 show the typical SMM behavior (Fig. 2 ). Maxima of χ ′′ measured at different frequencies define T b and occur when τ ≃ 1/ω, where τ is the magnetic relaxation time. As Fig. 2  shows, τ approximately follows Arrhenius' law τ ≃ τ 0 exp (U/k B T ), where U is the activation energy and τ 0 is an attempt time. However, a closer inspection reveals that the slope of the Arrhenius plot increases gradually with temperature, from a low-T value U/k B ≃ 22 K to more than 32 K. While the former U value agrees with tunneling taking place via m = ±5 states, the latter is close to the maximum energy (≃ 32.
Microstructure reconstructions resulting from diffraction contrast tomography data of polycrystalline bulk strontium titanate were reinvestigated by means of electron backscatter diffraction (EBSD) characterization. Corresponding twodimensional grain maps from the two characterization methods were aligned and compared, focusing on the spatial resolution at the internal interfaces. The compared grain boundary networks show a remarkably good agreement both morphologically and in crystallographic orientation. Deviations are critically assessed and discussed in the context of diffraction data reconstruction and EBSD data collection techniques.
Diffraction and phase contrast tomography The specimen was subjected to X-ray diffraction contrast tomography measurements using the setup and technical details described elsewhere  (Johnson et al. , 2008; Ludwig et al. , 2009; Reischig et al. , 2013). The X-ray DCT experiments were performed at the Materials Science Beamline ID11 of the European Synchrotron Radiation Facility (ESRF). Data acquisition was performed during full 360 scans with an angular stepping of 0. 05 , taking in total 7200 images. This rendered the exploitation of Friedel pairs during microstructure reconstruction possible. In the course of the data analysis procedure, diffraction spots are segmented from the raw images and pairs of diffraction spots that are 180 separated are identified  (Ludwig et al. , 2009; Johnson et al.
, 2008; Reischig et al. , 2013). Groups of these Friedel pairs belonging to the same grain are then collected and individual grains are reconstructed using an algebraic tomographic reconstruction algorithm  (Batenburg et al. , 2010; Batenburg & Sijbers, 2011). After assembly of the grain volumes into the common sample volume, the resulting grain map will contain small regions close to grain boundaries and triple junctions which remain unassigned  (Ludwig et al. , 2009). In order to ensure the assembly of these reconstructed individual grains to fill the entire volume, a uniform dilation procedure based on the dilate function of the MATLAB (The MathWorks Inc. , Natick, MA, USA) image processing toolbox is applied. In the voxelated reconstruction of the microstructure, voxels belonging to a given grain have a unique gray value (label), and for each of the grains the crystallographic orientation is stored in an accompanying data structure.
In parallel to the collection of diffraction signals used for grain reconstruction, conventional absorption images are used to reconstruct the attenuation coefficient in the sample volume. Attenuation contrast does not allow for detection of porosities below a certain size -in our case about 3-5 mm. Therefore, the infor-mation was complemented by PCT  (Cloetens et al. , 1997). A separate PCT data set was acquired using the same experimental setup but a larger sample-detector distance. The freespace propagation leads to edge enhancement (Fresnel diffraction) which increases the visibility of small pores. The resulting three-dimensional reconstruction of porosities inside the specimen is superimposed with the DCT reconstruction, so that the pores are recovered after the dilation step of the DCT reconstruction which has generated a dense volume.
01 s. This leads to a rate of mapping of about 70 patterns per second. The actual lateral resolution of the EBSD technique is higher than the chosen step size. It depends on the energy of the primary electrons, the defect density of the material and the orientation of the sample  (Isabell & Dravid, 1997; Zaefferer, 2007). The cubic perovskite structure with a lattice constant of 0. 3905 nm and space group 221 was used for indexing the diffraction patterns. Grains were identified if they had a size of at least three pixels and a misorientation inside the grain of less than 3. Grain boundary networks were generated using the OIM software package (EDAX Inc. , Mahwah, NJ, USA). Post-processing involved scaling of the total image and unidirectional stretching to correct for tilt. Prior to pore detection, which was done on color images of the orientation maps, image noise was reduced using the 5 Â 5 median filter implemented in MATLAB.