dataesr/scientific-paragraphs-categorization huggingface dataset:
However, it proved impossible to obtain an unambiguous fit if all the off-diagonal terms were included. According to common practice for tetragonal or near-tetragonal systems  5, 6, 57  , the problem was overcome through the exclusion of the sixth order off-diagonal operators (i. e. , those associated with the B 6 ±4 parameters), allowing the B 4 +4 Ô 4 +4 term (which appears in the main text as B 4  4  Ô 4  4  for convenience) to be the only one describing the lowsymmetry components of the CF. Luminescence spectroscopy. Luminescence data were obtained on powdered specimens of 1Dy and 2Dy using a HORIBA Jobin Yvon Fluorolog fluorimeter equipped an Oxford Instruments helium flow cryostat, a photomultiplier, and an InGaAs NIR detector. Inelastic neutron scattering. INS data were acquired using the direct geometry multi-chopper cold neutron time-of-flight spectrometer TOFTOF  58, 59  at Forschungsneutronenquelle Heinz Maier-Leibnitz FRM II, Garching, Germany and the direct geometry high-flux thermal neutron time-of-flight spectrometer IN4C  60  at Institut Laue-Langevin (ILL), Grenoble, France.
For the measurements on TOFTOF, an aluminum foil bag containing between 1. 3 and 1. 6 g of polycrystalline sample was rolled into a cylinder and inserted into a hollow, cylindrical aluminum can. For the measurements on IN4C the Al foil bag was inserted in a rectangular cadmium frame, and mounted at an angle of 135°to the incoming neutron beam. At IN4C, a standard ILL Orange cryostat was used for temperature control, while at TOFTOF, a standard top-loading cryostat was used for this purpose. All data were analyzed using the LAMP program package  61. The data were corrected for detector efficiency using data from a vanadium sample, and the data taken on TOFTOF were corrected for the background associated with the sample holder by performing an empty can measurement. Model INS spectra were simulated using the "ins" program described elsewhere  62.
Heat capacity. The temperature dependence of the heat capacity C(T), between 1. 8 K and 300 K under zero applied field, was measured on pressed pellets of 1Y and 2Y fixed with Apiezon N grease using a Quantum Design Physical Properties Measurement System (PPMS). SQUID magnetometry. The magnetization and dc magnetic susceptibility data for 1Dy and 2Dy were reported elsewhere  33. The ac magnetic susceptibility measurements were conducted using a Quantum Design MPMS-XL SQUID magnetometer equipped with a 5 T dc magnet. Data were collected at selected frequencies between 1 and 1488 Hz with an oscillating magnetic field of 0. 3 mT with or without an applied dc field up to 500 mT. For all measurements, between 20 and 30 mg of sample was ground into a powder and loaded into a polycarbonate capsule, gently compressed and covered in hexadecane.
Fitting of the frequency dependent ac magnetic susceptibility was carried out using the CC-fit program developed by Nicholas F. Chilton  63. mK ac susceptometry. The ac susceptometer was mounted in an Oxford Instruments Kelvinox400 dilution fridge. For each sample, between 20 and 30 mg was ground into a powder and embedded in Stycast in order to cast a cylinder fitting within the susceptometer. The samples were thermalized by 4 copper wires, each 200 µm in diameter. One end of the wires was encapsulated along with the sample in the Stycast and the other end was attached to the weak link of the dilution fridge. The raw frequency dependent data suffered from a frequency dependent background, and the imaginary component had to be corrected for this prior to Cole-Cole fitting of the data. As it was not feasible to carry out a measurement of a blank, the background was instead determined in the following way.
Acknowledgements M. A. S. , U. B. H. , K. L. , and  J. Be. acknowledge financial support from the  Danish Research Councils for Independent Research  ( 12-125226 ). M. A. S. , U. B. H. , M. R, and  K. L. acknowledge DANSCATT  for financial support for the neutron scattering experiments. For the experiments conducted at FRM II, this project has received funding from the  European Union 's  7th Framework Programme  for research, technological development and demonstration under the NMI3-II Grant number 283883. M. A. S. thanks the  Oticon Foundation  ( 16-2669 ), and the  Augustinus Foundation  ( 16-2917 ) for financial support in relation to a research stay at  Institut für Physikalische Chemie, Universität Stuttgart, Germany. M. P. and J. v. S. thank the  DFG  for funding ( SL104/5-1 ). K. S.
In addition, the label incorporation into acetate and malate was measured using 1 H 1D-NMR. The carbon flux distribution in strain Sy504 was calculated from these data and is depicted in Fig. 2. In qualitative agreement to the shake flask experiments we found that malate and fumarate were co-secreted into the supernatant and that acetate was the major metabolic by-product in addition to the two C4 compounds. Unexpectedly, we calculated a direct flux from oxaloacetate towards malate of ~ 8 mol%. This result is hard to explain considering that (i) under aerobic conditions this flux normally occurs in the opposite direction, and (ii) malate dehydrogenase was deleted in the analysed strain. A possible explanation for this putative flux is that carbon flux actually passed from oxaloacetate to fumarate and further to malate through aspartate transaminase, aspartase, and fumarase, respectively.
Acknowledgements The authors are grateful to  Amélie Vax ,  Hélène Serrano-Bataille ,  Florence Calvayrac , and  Julie Fredonnet  for their technical assistance. We also acknowledge support from  MetaToul (Metabolomics & Fluxomics facilities, Toulouse, France , http://www. metatoul. fr), which is part of the national infrastructure MetaboHUB- ANR-11-INBS-0010  (The  French National Infrastructure for Metabolomics and Fluxomics , http://www. metabohub. fr).
Equipment and characterization details Infrared spectra are obtained at room temperature (in KBr matrix) on a Perkin Elmer Spectrum GX spectrophotometer. X-ray diffraction data are collected at room temperature with a Bruker D8 Advance diffractometer working in the Bragg-Brentano configuration (q-q) using Ni filtered CuK a radiation (0. 15418 nm) and fitted with a SuperSpeed Vantec Detector. For electron microscopy, the samples are sonicated, dispersed in acetonitrile, and placed onto a holey carbon-copper support grid. Low-magnification TEM experiments are performed on a JEOL Model JEM 1011 operating at 100 kV. HRTEM images are recorded with an FEI Tecnai F20 HRTEM operating at 200 kV. The IeV curves of an individual NP aggregate are acquired on an AFM Smarts SPM 1000 (AIST-NT) in conductivity mode using Pt-coated cantilever tips (HQ:NSC15/Pt fromMicroMash).
Acknowledgements B. Cormary thanks the  Centre National de la Recherche Scientifique (CNRS)  for a post-doctoral fellowship. The authors thank  S. Ladeira  for XRD characterization and  M. Tass  e for AFM and IeV curves. The authors also thank the  GDRI HC3A  (Heteroelements and Coordination Chemistry: from Concepts to Applications). The ICN2 is funded by the  CERCA programme/Generalitat de Catalunya. The ICN2 is supported by the  Severo Ochoa programme of the Spanish Ministry of Economy, Industry and Competitiveness (MINECO , grant no. SEV-2013-0295 ).
In a similar manner, all distances are given in units of r p. The molecular-dynamics simulations are performed in the canonical NVT ensemble by employing Nosé-Hoover dynamics  [86, 87]. The equations of motion are integrated using the velocity-Verlet integrator using a time step of t * = 0. 001  [88]. All simulations are carried out using the LAMMPS molecular-dynamics package  [89]. To study the translational and orientational ordering of the confined system, the system is divided into N bins bins along the z direction and statistics of the number of particles in each bin are collected. The packing fraction profile η(z j ) is determined from η(z j ) = N s σ 3 π 6 N(z j ) L x L y δz , ( 1 ) where z j is the position of bin j, N(z j ) is the number of ring particles in bin j and δz is the width of the bin which is kept at δz ∼ σ in all cases.
During our searches of 3D databanks we came across cases which either seemed to be more distantly related to one of these families (Supplementary Figure  S2a , right hand part and S2a ), to result from convergent evolution or to represent entirely different folds (Supplementary Figures  S2d-f ). We aren't familiar with these enzymes which are at the border of the field of bioenergetics but have nevertheless included these additional cases in the Supplementary Figure  S2  and listed their electrochemical properties in Supplementary Table  S1. The NDH-2-(Figure  5A ) and the FNR-type (Figure  5B ) motifs fall into distinct structural domains with the flavin sandwiched in between these domains. In Figures  5A, B , the N-terminal domains are at the bottom of the depicted structures followed by domains colored in a lighter shade and represented in the upper part of the individual structures.
Cofactors serving as electron transfer partners are mainly found on either side of the isoalloxazine ring and rarely on its Re-or Si-side (i. e. , above or below the plane of the isoalloxazine moiety). These spatial preferences are independent of the electron transfer properties of the flavin as evidenced by the color-coding (purple for substrates and/or electron transfer partners of gating type enzymes and orange for both-together or bifurcating types). Pdb-entry codes for the structures used in this comparison: subunit F of Complex I (pdb: 3IAM, Bos taurus), dihydroorotate dehydrogenase B, FAD domain (pdb: 1EP3, Lactococcus lactis); dihydroorotate dehydrogenase B, FMN domain (pdb: 1EP3, Lactococcus lactis), sulfite-quinone reductase (pdb: 3HYW, Aquifex aeolicus), dihydropyrimidine dehydrogenase, FMN domain (pdb: 1GTE, Sus scorfa), dihydropyrimidine dehydrogenase, FAD domain (pdb: 1GTE, Sus scorfa), adenylsulfate reductase (pdb: 1JNR, Archaeoglobus fulgidus), NADH-dependent Ferredoxin:NADP oxidoreductase, small subunit (5JCA_S, Thermotoga maritima), heterodisulfide reductase (pdb: 5ODC, Methanothermococcus), NADH-dependent glutamate synthase alpha subunit, FMN domain (pdb: 2VDC, Azospirillum brasilense), NADH-dependent glutamate synthase alpha subunit, FAD domain (pdb: 2VDC), fumarate quinol oxidoreductase (1QLB, Wolinella succinogenes), NADH-dehydrogenase 2 (pdb 4NWZ, Saccharomyces cerevisiae), sarcosine oxidase (pdb: 1X31, Corynebacterium sp.
This new mounting scheme limits the number of filaments simultaneously exposed to the XFEL focus  R and Z positions were identified in averaged patterns of bombesin and β-endorphin (Fig. 5 ) s strong, w weak, vw very weak (about eight TMV filaments and less 50 amyloid protofibrils) and with further development may allow data to be collected from single fibrils. High-quality single-shot diffraction patterns were obtained from TMV. In some cases, asymmetry in the single-shot patterns indicates the presence of a limited number of axial rotations of the exposed particles. There are two implications of this observation. First, it suggests the possibility that the graphene may lock the TMV molecules into a specific rotation. Second, if the range of rotations present is small, then the data may represent a single, or a narrow, section through reciprocal space, rather than the cylindrical average.
For data collected from single fibrils, fixed rotations of the fibrils on the graphene is not necessary, as it is for the case of multiple fibrils in the beam described above. In fact, a variety of rotations will aid filling out 3D reciprocal space. A small range of fibril tilts (i. e. , rotations about an axis normal to the fibril axis), which could be obtained by titling the support frame, would also be required to complete coverage of reciprocal space  31. Such an approach will require development of computational techniques for auto-orientating the diffraction patterns (Supplementary Fig. 7 ). Data from single protofibrils should, therefore, allow reconstruction of the full 3D intensity distribution of a protofibril, similar to that recently demonstrated for crystalline fibrils  31. Such 3D datasets potentially allow model-free structure determination as described above.
All work was conducted in a clean-room environment and frames were prepared immediately before the beamtime to allow for the cleanest graphene surface achievable. X-ray data collection. Each window was shot once with a 40 fs XFEL pulse with a calculated focus of 150 nm at FWHM. The sample-detector distance was set to 85 mm, which gave a resolution of 1. 6 Å in the outer corners of the detector with a photon energy of 8 keV. A total of 126,768 frames were recorded on the 2D Cornell-SLAC pixel array detector (CSPAD) in high gain mode  61. Parasitic scattering was reduced using a post-sample tantalum aperture matching the silicon chip dimensions containing a 4. 8 mm hole located immediately after the sample plane. The experiment was performed under proposal number LM27. The data is publicly available on the CXIDB  62 (ID 75).
The estimated diameter of TMV was used to redetermine the recorded specimen area by each pixel (0. 25 nm). Hit finding. Frames containing defined layer lines instead of arcs from the XFEL were manually selected using the Cheetah Software Suite  65. Manual frame selection from these (comparatively) small datasets was used as existing hit-finding methods are not suitable for these kinds of patterns. Merging. Since single frames had a low degree of misorientation, the alignment and averaging was done manually. A custom graphical utility (Supplementary Fig. 7 ) was used in which the in-plane rotation angle φ and the out-of-plane tilt β are determined. The tilt was determined with the aid of horizontal and vertical guides, which were used to manually check that the layer lines are horizontal and that the non-equatorial peaks on opposite sides of the equator had the same radial coordinate.
Four-quadrant averaging improved the signal-to-noise ratio and filled in the panel gaps in the detector. All selected frames were scaled and averaged. The background on the detector was assumed to be circularly symmetric except for the polarization effect. Since the signal was concentrated in layer lines, pixels from between the layer lines were used to calculate this symmetric background, which was then subtracted from the whole frame. The program used is available at https:// github. com/kartikayyer/RZ-Gui.
Acknowledgements We are grateful for the guidance from  Gerald Stubbs ,  Vanderbilt University , his enthusiasm on the work and for his advice on the paper. We thank  John Spence ,  ASU  for the support and critical reading of this paper. We appreciate the support by the electron holography group at the  University of Zurich  that provided the experimental equipment to acquire the low energy electron images presented here. We thank  R. J. Dwayne Miller ,  Robert Bueckert ,  Philipp Pelz , and  Guenther Kassier  for TEM access and training. We thank  Roger Wepf  and  Eckhard Mandelkow  for support,  Toshiro Oda  for valuable discussions, and  Julia Maracke  for Solid Edge drawings. We acknowledge support from the  Helmholtz Association  through project-oriented funds to DESY, the  Hamburg Center of Ultrafast Imaging, University of Hamburg , the  Human Frontiers Science Program  ( RGP0010/2017 ), and the  U.
Acknowledgments Authors are grateful to the  National Natural Science Foundation of China  ( 51373131 ), Fundamental R e s e a r c h F u n d s f o r t h e C e n t r a l U n i v e r s i t i e s ( XDJK2016A017  and  XDJK2016C033  ), Project of  Basic Science and Advanced Technology Research, Chongqing Science and Technology Commission  (cstc2016,  jcyjA0796 ), and the  Talent Project of Southwest University  ( SWU115034 ). LGP2 is part of the  LabEx Tec 21 (Investissements d'Avenirgrant  agreement  n°ANR-11-LABX-0030 ) and of the  PolyNat Carnot Institut (Investissements d'Avenir- grant agreement  n°ANR-11-CARN-030-01 ).
The obtained yellow resin-like product was dried and powdered in a mortar. The dry gel was then mixed with the eutectic mixture of NaCl (99%, Alfa Aesar) and KCl (99%, Alfa Aesar) with 1 : 10 molar excess of the salts. Aer annealing of the mixture in an alumina crucible at 750 C for 2 h, nal powder was extracted from the salt by repeated washing with water. Such obtained powder was used for further characterization. X-ray diffraction (XRD) measurements were performed using a Rigaku SmartLab diffractometer using CuKa 1,2 radiation at 30 mA and 40 kV. Diffraction data were recorded in a 2q range from 10 to 90 in 0. 02 step. Transmission electron microscopy (TEM) samples were prepared by evaporating a drop of diluted suspension of nanoparticles in ethanol on a carbon-coated copper grid. The nanoparticles were studied using a TECNAI Spirit G2 apparatus.
Crystallography Crystals suitable for X-ray diffraction were selected under immersion oil in ambient conditions and attached to a MiTeGen microloop. The crystals were mounted in a stream of cold nitrogen at 120(2) K and centered in the X-ray beam using a video camera. Data collections were performed with Mo Ka (l ¼ 0. 71073 Å) radiation on a Bruker Quazar SMART APEX II, operating at 50 kV and 30 mA using graphite monochromated radiation. The data were collected using a routine to survey reciprocal space, and reduction was performed using soware included in Bruker Apex2 suite. 22 The structures were solved using direct methods. 23, 24 Non-hydrogen atoms were rened anisotropically using weighted full-matrix least-squares on F 2 , followed by difference Fourier synthesis. 25, 26 All hydrogen atoms were included in the nal structure factor calculation at idealized positions and were allowed to ride on the neighboring atoms with relative isotropic displacement coefficients.
The Platon SQUEEZE routine  18  was used to account for diffuse electron density arising from interstitial solvent, which could not be modeled atomistically. Powder X-ray diffraction data were recorded using a PANalytical X'Pert PRO MPD diffractometer with Bragg-Brentano geometry, Cu-Ka radiation (l ¼ 1. 54184 Å) and a graphite back scattering monochromator, using glass capillaries. X-ray absorption X-ray absorption experiments at the Co K-edge were carried out at the ID12 beamline of the European Synchrotron Radiation Facility (Grenoble, France), dedicated to polarization dependent X-ray spectroscopy in the 2-15 keV energy range. A high ux of circularly polarized photons was provided by an HELIOS-II undulator. X-rays were monochromatized by a Si h111i double crystal monochromator. Linearly polarized X-rays were obtained using a 0.
Acknowledgements This work was supported by the  CNRS , the  University of Bordeaux , the  Conseil Régional de la Nouvelle Aquitaine , the  France Canada Research fund  (PhD fellowship for AS), the  European Union 's  Horizon 2020 research and innovation program  under the  Marie Sklodowska-Curie  grant agreement No  706556  CHIMMM (Postdoctoral fellowship for MC), the  Erasmus Mundus European program  (PhD fellowship for VB), the  ANR  project  CHIROTS   ANR-11-JS07-013-01  ( PR, PhD  fellowship for AN), the  European Synchrotron Radiation Facility  (beamtimes  CH-4171 ,  CH-4457  and  CH-5009 ), the GDR MCM-2 and the MOLSPIN COST action CA15128. The authors warmly thank  K. Ollefs ,  F. Guillou ,  A. Hen ,  P. Voisin ,  M. Rouzières ,  L. Etienne  and  D. Denux  for technical assistance and  L.
Microscopic imaging. GUVs were imaged on a confocal microscope (Nikon Eclipse Ti-E inverted microscope equipped with a Nikon A1R confocal laser scanning system, 60x oil immersion objective, NA = 1. 49, 4 laser lines: 405 nm, 488 nm, 561 nm, 640 nm; Nikon Instruments). The software NIS-elements (Nikon) was used for image acquisition and analysis.
Acknowledgements This work has been supported by the  German Federal Ministry of Education and Research (BMBF)  in the framework of the  EU ERASynBio project SynGlycTis , by the  Ministry of Science, Research and the Arts of Baden-Württemberg  (Az:  33-7532. 20 ),by the  Excellence Initiative of the German Research Foundation  [EXC 294] and the  German Research Foundation  grants "IRTG 1642 -Soft  Matter Science: Concepts for the design of functional materials " and " RTG 2202 -Transport across and into membranes ". TS acknowledges support by the  Franco-German University  (PhD-track program " Polymer Sciences" and the program  " Cotutelle de thèse ") and the  Collège Doctoral européen (Programme doctorale international). We are grateful to  Klas-Ola Blixt  and  Nicolai Stuhr-Hansen  ( University of Copenhagen, Denmark ) for providing us with the cholesterol-substituted glycopeptide with a GalNAc-moiety.
Acknowledgements The authors would like to thank  Mikhail Klimov , at the  Materials Characterization Facility (MCF)  at  UCF  for conducting the SIMS measurements and  Michel Lahaye  at  PLACAMAT  ( UMS 3626 ) for the microprobe measurements. Programme IdEx Bordeaux -LAPHIA  ( ANR-10-IDEX-03-02 ); French Aquitaine region (20121101025);  National Science Foundation (NSF)  award # DMR-1308946. AST microlens.
We also examined the dataset of proteins obtained by the quantitative proteomics analysis using two tools, Downstream Effect Analysis and Upstream Regulator Analysis of the Ingenuity Pathways Analysis software. Our analyses confirm the association of the proteome profile observed in BAG3-silenced cells with an increase in cell survival and a decrease in cell proliferation and invasion, and highlight the possible involvement of four tumor suppressor miRNAs and TP53/63 proteins in BAG3 activity.
Quantitative proteomics analysis of BAG3silenced 8505C cells Wild type 8505C cells were grown in heavy media while siBAG3 and siScrambled treated cells were grown in light media. Control cells were respectively pooled in equal amounts with siBAG3-and siScrambled-transfected cells and protein extracts were trypsin digested and analyzed by mass spectrometry as beyond described. For each condition, samples were analyzed in 3 biological replicates (3 independent transfections) and each biological replicate was analyzed in 3 technical replicates (3 independent LC-MSMS analyses). MS analysis allowed performing relative quantification of 1167 proteins (Supplementary Table  1 ). To find proteins that significantly changed expression profiles, data were mined with the software Perseus 1. 5. 2. 6. The protein ratios obtained from the samples control vs siScrambled were compared to the protein ratios obtained by the samples control vs siBAG3 building a "volcano plot" (Figure  1 ).
Apoptosis evaluation BAG3 is well reported to inhibit apoptosis in ATC cells  [7, 8]. The roles of CAV1 and SERPINB2 in regulating apoptosis is unclear to date. To elucidate CAV1 and SERPINB2 effects on apoptosis, we evaluated by flow cytometry the percentage on Annexin-V positive cells upon silencing of BAG3, CAV1 and SERPINB2 in 8505C cells. The percentage of Annexin-V positive cells underwent a marked increase in siBAG3 and siSERPINB2 transfected cells, as compared to control cells. Percentage of late apoptotic cells in siBAG3, siCAV1 and siSERPINB2 treated cells were 14,5%, 9,6% and 14%, respectively (Figure  3 ). BAG3, CAV1 and SERPINB2 silencing efficiency was assessed by RT-qPCR (Supplementary Figure  3 ). Taken together, these data confirm the well-known role of BAG3 as apoptosis inhibitor and suggest a similar role for SERPINB2.