dataesr/scientific-paragraphs-categorization huggingface dataset:
Methods Fourier transform infrared attenuated total reflection. The beetle scales infrared (FTIR ATR) data were collected using a Thermo Scientific Nicolet iS10 Fourier transform infrared (FTIR) instrument equipped with a diamond attenuated total reflection (ATR). A background was collected; the sample was then placed in contact with the diamond ATR surface. A resolution of 2 cm -1 was used and a total of 128 acquisitions. Scanning electron microscopy. SEM Beetle scales and the synthetic cellulose acetate samples were mounted using conductive carbon discs AGG3357N (Agar Ltd) on conductive metal stubs (Agar Ltd). These were sputtered with ~10 nm of gold (Agar Ltd) and imaged on a JEOL JSM-6010LA using the InTouchScope data acquisition software. Transmission electron microscopy. Scales from both the L.
According to the sample geometry and dimensions, we mounted the samples in the vertical direction (Supplementary Figs. 11  and 12 ) in order to have the cross section fully in the horizontal field of view, and then performed multiple overlapping scans in the vertical direction. The Cyphochilus and the L. stigma scales were ~250 and 350 μm, respectively, in length, which corresponded to six scans and eight scans in the vertical with 10 µm overlap between the scans. For each acquisition, 2998 projections were acquired over 360°with a counting time of 150 ms per projection. To avoid artefacts on the reconstructed images and keep the highest 3D resolution, the sample was mounted to give an unobstructed 360°field of view. Beam damage was not observed. The reconstructed scans were then assembled and thresholded to separate the chitin and air pixels and produce the final 3D data sets (Supplementary Movies 3 and 4).
Finite-difference time-domain optical modelling. The FDTD simulations were performed using the commercial software, Lumerical (Lumerical Inc. Canada), which is a 2D-and 3D-solver for Maxwell's equations. For each simulation a 3D matrix containing a structure of interest represented as a binary matrix, where 1 was material and 0 was air. The material in every instance was taken to be chitin, which has a refractive index of 1. 54. Each matrix contained a slab of material that had a real-space size of 5 µm × 20 µm × 25 µm. To study how light propagated along each principle axis, the slabs were divided into 20 cubes, each 5 µm × 5 µm × 5 µm, and a polarised Gaussian source of width 1 μm was directed into different faces of the cubes individually. Monitors collected the light, which exited the cubes, and the results were averaged across all of the cubes for a given slab.
The substrate was a large diameter (50. 8 mm) circular silicon wafer (Prolog Semicor, Ukraine). The NR data were measured at the ISIS pulsed Neutron and Muon Source (Oxfordshire, UK) using the instrument OFFSPEC with neutron wavelengths 2-12 Å. Three incident angles were collected (0. 5°, 1. 5°and 2. 5°) to cover the momentum transfer range 0. 008-0. 238 Å -1 , using a resolution of 2. 5%. The data were reduced using Mantid  49  and Offspec specific routines to stitch the three angles and subsequently rebin the data into one dataset. The data were then modelled using routines based on the scheme of Névot and Croce 50 (Supplementary Fig. 14 ). From modelling a thin film of cellulose acetate has a measured scattering length density value of 1. 64 × 10 -6 Å -2. Spectroscopic ellipsometry. Spectroscopic ellipsometry (M2000V, J.
42 and passed to an imaging spectrograph (Andor Shamrock SR193i). The data capture was performed using the Andor Solis software. A background without the lamp impinging on the spectrometer was collected to account for the electrical dark current. The optical transmission (T) through the glass substrate was collected for each sample measurement followed by the beetle scale/synthetic cellulose acetate region of interest. The field of view for each image entirely filled by a region of the beetle scale; a number of measurements were collected for Cyphochilus and L. stigma, as well as the cellulose acetate films. Reflectance was calculated as 1-T, which can be considered appropriate due to the negligible absorption of chitin  52  and cellulose acetate (Supplementary Fig. 13 ) in the visible range and the excitation NA (~0.
08) being much smaller than collection NA (0. 42). Spin-echo small-angle neutron scattering. The beetle scale samples were prepared using a scalpel blade to remove elytra from Cyphochilus beetles. Individual elytra were stacked together and wrapped in Aluminium foil, which is transparent to thermal neutrons. The SESANS data for the Cyphochilus scales on the elytra were collected the dedicated SESANS instrument at TU Delft in Holland. The number of wings required was determined through trial and error by increasing the number of wings in the beam until sufficient depolarisation of the beam was observed. The final number of elytra used was 28. By estimating the number of scales inside a known area of the wing, an approximate scale density was calculated to be ~9. 7 × 10 -5 scales/μm 2 , making a grand total of ~3.
7 × 10 5 scales for 28 elytra. The SESANS data for the CA films were taken on Larmor at the ISIS Spallation Neutron and Muon Source. A total of 30 films were sufficient for depolarisation of the beam. The films were measured in three different orientations with the films mounted vertically, horizontally and at an angle of ~36°. The films were measured with neutrons with a wavelength range of 2-10 Å, a radio frequency of 1 MHz and a beam size of about 5 mm × 5 mm. The data were collected with a count time of 30 min for magnetic field angles of 20, 50 and 75°giving a spin echo range out to 7 μm.
Acknowledgements This project was co-funded by  Innovate UK  (Grant Number  33692-239251 ) in partnership with  AkzoNobel  and the  University of Sheffield. We are grateful to  Dr Andrew Burgess ,  Dr Gareth Crapper ,  Dr David Elliott  and  Dr Phil Taylor  all from  AkzoNobel  for initiation of the project and their continued support throughout this work. We also acknowledge the  Science and Technologies Facilities Council  for access to facilities at the  ESRF  via experiments SC 4363 and  SC 4386  and at the  ISIS Spallation Neutron Source  under experiment RB  810719  (data available at https://doi. org/10. 5286/ISIS. E. 92924017 ) and  RB 1769002  ( NWO Dutch Access)  via  TU Delft.
A Surface-Enhanced Raman Scattering (SERS) spectrum of 4-cyanopyridine (4CNPy) was recorded on silver plasmonic nanoparticles and analyzed by using Density Functional Theory (DFT) calculations. Two simple molecular models of the metal-4CNPy surface complex with a single silver cation or with a neutral dimer (Ag + -4CNPy, Ag 2 -4CNPy), linked through the two possible interacting sites of 4CNPy (aromatic nitrogen, N, and nitrile group, CN), were considered. The calculated vibrational wavenumbers and intensities of the adsorbate and the isolated species are compared with the experimental Raman and SERS results. The analysis of the DFT predictions and the experimental data indicates that 4CNPy adsorbs preferentially on neutral/charged active sites of the silver nanoparticles through the nitrogen atom of the aromatic ring with a perpendicular orientation.
Geometry optimizations were constrained to a planar structure under C 2v symmetry and all the calculated wavenumbers of the discussed complexes are real, indicating that the optimized geometries correspond to equilibrium structures. All the calculations were carried out using the GAUSSIAN 09 package  [39]. The Raman intensities were calculated with the following Equation  [40] : I k = dσ dΩ = π 2 ε 2 0 ( ν1 -νk ) 4 h 8π 2 c νk (S k /45) 1 1 -exp(hc νk /k B T) , (1) Where the intensity of k-th mode is given by the differential cross section (cm 2 /sr), S k is the scattering factor (Å 4 /amu) calculated with the polarizability gradient method by GAUSSIAN 09: S k = 45 dα dQ k 2 + 7 dγ dQ k 2 , ( 2 ) ε 0 is the permittivity of vacuum, c is the speed of light, h is the Planck constant, k b is the Boltzmann constant, T is the temperature, ν1 is the wavenumber of the incident light, νk is the wavenumber of the respective k-th vibrational mode.
Acknowledgments: The authors give thanks to the  Supercomputing and Bioinnovation Center (University of Málaga ) for computational resources and  Rafael Larrosa  for technical support. F. M. M. acknowledges the help of  Prof. Alfonso Pedone  (UniMoRE) and gratefully thanks him for the use of the HPC infrastructure and the useful discussions. The authors also acknowledge MDPI editorial´s invitation to contribute to the special issue dedicated to " Computational and Spectroscopic Studies on Metal Nanoparticles ".
XPS The XPS data were recorded at the ALOISA beamline at Elettra. The molecular coverage was controlled via a quartz microbalance where the deposition parameters were known from other tetrapyrrole experiments performed at this beamline. 43, 44 The N 1s spectra were recorded at a photon energy of 500 eV. The energy scale was calibrated against the Ag 3d 5/2 line at 386. 3 eV. Spectra of the Ag 3d region were measured each time directly aer the acquisition of N 1s spectra. 45 Shirley background was subtracted from all raw data. Fitting of the N 1s region was done using Gaussian curves to avoid the introduction of additional free parameters in Voigt curves. Quantitative analysis from such tting is complicated since even for the unreacted 2H-Pc molecules on a perfectly subtracted background, the spectrum should be tted with at least four peaks, (a) the pyrrolic (NH) species (green), (b) the iminic (central N) species (blue), (c) the aza (outer N) species (blue), and (d) the shake-up peak.
Acknowledgements K. D. acknowledges support from the  EPFL   Fellows program  cofunded by  Marie Curie ,  FP7  grant agreement no. 291771. C. W. , J. D. and A. S. gratefully acknowledge funding by the  Swiss National Science Foundation  (Grants  PZ00P2_142474  and  200020_157081 ). Beamtimes at Elettra (beamline: ALOISA), the  Swiss Light Source  (beamline:  X-Treme ), and the  European Synchrotron Radiation Facility  (beamline:  ID32 ) are gratefully acknowledged. R. H. received funding from the  Institute of Advances Studies of TU Munich. We thank  Andrea Fondacaro  (ID: 32 ,  European Synchrotron Radiation Facility)  for technical support.
Results and discussion Pressure dependence of the Mo K-edge XANES in Fig. 2 (a) indicates the presence of three phases with transition points above 9. 9 GPa and 26. 3 GPa. After the pressure is released, the system returns back to the α-phase. A phase fraction was evaluated from XANES in the energy range from 19985 to 20075 eV at each pressure using a linear combination analysis (LCA). The experimental XANES spectra at P =0. 2, 18. 5 and 32. 4 GPa were selected as a reference spectra corresponding to pure α-MoO 3 , MoO 3 -II, MoO 3 -III phases, respectively. The obtained results are plotted in Fig. 2 (b) and are in good agreement with X-ray diffraction data  [3]. In the pressure range between ∼10 and 15 GPa, the two phases, α-MoO 3 and MoO 3 -II, coexist in a close ratio, whereas MoO 3 -III phase appears above ∼26 GPa, leading to a change of the XANES.
ACKNOWLEDGMENTS Results discussed in this perspective article have been obtained within the  Simons Collaboration "Cracking the Glass Problem ", in a large collaborative research effort involving several PIs other than the authors ( J. Kurchan ,  A. Liu ,  S. Nagel ,  G. Parisi , and  M. Wyart ) as well as many affiliates, postdocs and PhD students ( A. Altieri ,  C. Brito ,  E. DeGiuli ,  D. Hexner ,  S. Hwang ,  H. Ikeda ,  J. Kundu ,  E. Lerner ,  Q. Liao ,  M. Müller ,  M. Ozawa ,  T. Rizzo ,  C. Scalliet ,  B. Seoane ,  J. P. Sethna ,  S. Spigler ,  G. Tsekenis ,  P. Urbani ,  S. Yaida , and  H. Yoshino ). We thank all of them as well as all the other colleagues with whom we have had the pleasure to carry significant parts of the work described above, in particular M. C. Angelini ,  K.
Daniels ,  O. Dauchot ,  Y. Jin ,  F. Ladieu , and  C. Rainone. We further acknowledge funding from the  Simons Foundation  (Grant #  454933  LB; #454935 GB # 454937 PC; # 454939 EC; #  454941  SF; #  454955  FZ), and from the  European Research Council (ERC)  under the European Union's  Horizon 2020 research and innovation programme  (grant agreement n. 723955 -GlassUniversality). The writing of this publication was supported in part by the  National Science Foundation  under Grant No. NSF   PHY-1748958.
From the measured X-ray diffraction data, reconstructed precession images were generated for several regions of reciprocal space of interest, and we focus here on the (3, k, l ) slice of reciprocal space as a function of temperature as it contains the (3, -2, l ) and (3, 2, l ) lines that were the focus of the discussion in our previous paper  [4]. The X-ray diffraction data recorded at 300 K, 163 K and 161 K were indexed as hexagonal, indicating that the crystal is in phase I at these temperatures. The (3, k, l ) slice of reciprocal space at 161 K is shown in figure  1  (here the indices are specified relative to the orthohexagonal description of the hexagonal phase I in order to facilitate comparison to the results for phase II discussed below). We emphasize that, in figure  1 , no diffraction maxima are observed for even values of k (corresponding to h + k odd) due to the C-centring of the hexagonal phase I when indexed using the orthohexagonal setting.
To see whether there are any structural changes between Ag and ODAg, grazing incidence X-ray diffraction (GIXRD) patterns were measured and compared. To be more sensitive to the surface of the catalyst and to be able to measure all reections (not just the reections parallel to the surface as for the standard Bragg-Brentano XRD conguration), GIXRD was chosen as the most suitable XRD technique. A change in the ratio between (111) and (220) can be observed in the GIXRD data measured at a grazing incidence angle of 4 q of oxide-derived silver compared to the pure silver foil (Fig. 2e ). For the ODAg lms, the ratio (220) over (111) is higher compared to that of untreated Ag. The presence of the (220) peak is an indirect proof of the presence of (110) which is not visible in the XRD pattern since it is a forbidden reection for a fcc lattice.
The XANES spectra provide information on the oxidation state, geometry and electronic conguration of the absorber atom while EXAFS data tting allows the ability to reconstruct its local environment to give the concentration of neighbouring atoms (N), the absorber atom's distance to the neighbouring atom (R), and disorder (Debye-Waller factor: s) on a short length scale. X-ray absorption spectra were recorded at the Dutch-Belgian beamline (DUBBLE, 26A) of the European Synchrotron Radiation Facility (ESRF) in Grenoble, France at the silver K-edge (25 515. 59 eV). Fig. 3a  shows the Fourier transforms of reference transmission EXAFS spectra for a 5 mm Ag thin lm and pellets of silver(I) oxide and silver(II) oxide powder dispersed in a cellulose matrix. The EXAFS spectra are extracted and tted according to the EXAFS equation (ESI, eqn (3) †); the data analysis details are reported in the ESI.
† Due to the limited energy (k ¼ 2. 5-10) range achievable in the operando conditions, the data analysis has been mainly focused on the rst two nearest neighbours (coordination shells) of the silver absorber atom: the Ag-O and Ag-Ag coordination shells. The tting results of the reference metal and oxides in Fig. 3a  are reported in Table  1. The reference samples were measured in transmission mode to ensure optimal data quality and to avoid self-absorption processes. 22 However, for samples measured in an electrochemical cell, the total sample + cell thickness would be too large for the X-rays to travel through, therefore all sample measurements were taken in uorescence mode. It is common practice to do this at a conguration where the incident X-rays make a 45 degree angle to the sample.
Acknowledgements This work was nanced by the  Netherlands Organisation for Scientic Research (NWO , project number  FOM-13CO19 ) and  Shell. We thank  DUBBLE  for funding and gratefully acknowledge its staff for assisting in our synchrotron experiments. The authors would like to thank  Bernard Dam  for fruitful discussions,  Joost Middelkoop  for cell design and  Bartek Trześniewski ,  Ming Ma ,  Marco Valenti  and  Kai Liu  for preliminary XAS measurements.
The formation of hetero-hexamers between CcmK3 and CcmK4 from Synechococcus elongatus PCC7942 (Syn7942) could be shown too, thus confirming and complementing results obtained on the same proteins and on paralogs from Halothece PCC 7418 (Hal7418)  [34]. Such observations were reasoned on the basis of sequence identities and compensatory effects for residues implicated in inter-subunit contacts, also by means of dynamic simulations using homology models. The stability of purified hetero-associations was finally investigated by biophysical means and in subunit exchange experiments. Overall, our data together with recent findings strongly suggest that the formation of such hetero-oligomers is likely to occur in cyanobacteria. Although adding to the complexity of BMC shells, this phenomenon might play important roles in modifying the structural robustness and environmental adaptability of BMC shells.
CcmK3 and CcmK3/K4 homology models and molecular dynamics simulations Homology models for CcmK3 Syn6803 homo-hexamers were built using SWISS-MODEL and PHYRE2 algorithms. Templates selected for 3D model reconstruction differed between the two, corresponding to the Syn7942 CcmK1/2 (PDB ID 4OX7, residue identity of 53%) using SWISS-MODEL, or the structure of Syn6803 CcmK4 (2A10, 47% identity) with PHYRE2. Hetero-hexamers were recomposed by replacing one of the monomers of the 2A10 CcmK4 structure by CcmK3 modeled monomers (previously superimposed by minimizing RMSD of monomer main-chain atoms). Few side-chain clashes between monomers in recomposed hexamers were relaxed using steepest descent energy minimization approaches. Molecular dynamics simulations were carried using the AMBER14 forcefield implemented within YASARA software.
05 kJ/mol/200 steps). Simulations were run at 298 K, with integration time steps for intra-molecular and inter-molecular forces of 1 fs and 2 fs, respectively. Two identical 20 ns simulations were run starting from the same structure, but differing by the attribution of random initial atom velocities. Intermediate structures were saved every 250 ps. Dihedral angle analysis and generation of figures was carried out with scripts run within Pymol (https://www. pymol. org/).
AFM imaging Purified protein was diluted 10 to 50-fold with 10 mM NaPi, 300 mM NaCl to pH 6. Typically, 2 μL of the solution was then dispensed onto freshly-cleaved mica and proteins were allowed to adsorb for longer than 10 min. Samples were imaged after dilution with 150 μl of the same buffer. Standard image analysis and treatments were initially performed using NanoScope Analysis software (Bruker). When necessary, AFM images were processed with 0 to 3 th order plane fitting and 0 to 3 rd order flattening to reduce XY tilt. For further details on experimental approach and instrumentation, please refer to  [23].
9 mg/mL using Vivaspin 0. 5 mL membrane concentrators (10 kDa MWCO). Screening of crystallization conditions was performed using Mosquito drop dispensing automate (TTPLabtech) and crystallization screens (Qiagen). Drops were prepared by mixing 150 nL of protein solution with an equivalent volume of screening solution, at 12 ˚C. Crystals formed in drops prepared from reservoirs containing 22% (w/v) PEG 4000, 0. 2 M ammonium sulfate and 0. 1 M sodium acetate at pH 4. 6. Crystals were briefly immersed in the reservoir solution supplemented with 20% ethylen-glycol before being cooled at 100 K in a cooled gaseous nitrogen flux. Diffraction data were collected on beamline ID30A3 at ESRF (European Synchrotron Radiation Facility, Grenoble, France) and processed using AUTOPROC (Global-Phasing, Cambridge, UK) and XDS.
The structure was solved using the molecular replacement method, as implemented in PHASER  [37]. As the crystal potentially contained both CcmK3 and CcmK4, a model was built from the structure of CcmK4 (PDB entry 2A18), truncating all non-common side chains to alanine. The structure was refined with REFMAC  [38]  and COOT  [39]  from the CCP4 suite of programs  [40] , and deposited in the RCSB databank with PDB code 6SCR.
Protein thermal denaturation studies Differential Scanning Fluorimetry was used to characterize the thermal stability of selected homo-and hetero-heterohexamers. Mixtures of 20-μl of the sample (8-10 μM final, considering hexamers) and SYPRO Orange (× 100; Invitrogen) in Sol C were subjected to a temperature gradient from 20 to 100 ˚C with increments of 0. 3 ˚C every 10 sec. Measurements were performed in triplicate in 96-well plates (Bio-Rad) with a real-time PCR CFX96 System (Bio-Rad). Melting temperatures (T m ) were extracted after adjustment of the full set of data from 2-3 experiments to a sigmoidal function using PRISM software, after normalization of fluorescence intensities. Temperature-induced aggregation was evaluated using Dynamic Light Scattering. Assays were conducted on 10 μL of the protein sample in Sol C, applying a temperature gradient from 20 to 100 ˚C.
Selection of engineered Syn6803 CcmK constructs Prior to studying the compatibility between the different Syn6803 CcmK components, we established the expression and solubility profiles of untagged proteins in E. coli. Collected data proved good expression of all 4 paralogs. Abundant soluble material was present after lysis in all cases, exception made of CcmK3 (abbreviated K3, S1 Fig). The impact of tagging was also examined. Short peptides were selected and placed at either the N-or C-terminus. Overall, C-ter tagging was better tolerated. Thus, CcmK1 (K1) and CcmK2 (K2) were expressed and remained soluble regardless of the peptide tag identity at Cterminus (S2 Fig). Multiple bands observed for CcmK4 (K4) pointed to proteolysis phenomena. At the N-terminus, expression was restricted to His 4 and FLAG constructs, and only K2 and K4 remained soluble.
Hetero-hexamer formation confirmed by native MS BMC-H proteins are prone to assemble into large patches, observed in vitro but also during recombinant expression inside cells. Therefore, data presented in the previous section might Western blot analysis of TALONpurified fractions. After running SDS-PAGE gels, and transferring proteins onto PVDC membranes, detection was performed with a mouse antiFLAG primary antibody followed by a secondary IgG antimouse-alkaline phosphatase fusion. The figure was prepared from two independent western blots that were performed in parallel. White vertical lines are to highlight the resulting image discontinuities. https://doi. org/10. 1371/journal. pone. 0223877. g001 be explained as being the consequence of the purification of mixed assemblies combining different homo-hexamers.
To clarify this possibility, three type of experiments were carried out. First, purified fractions that according to WB data contained hetero-hexamers (i. e. combinations between K1 and K2, or between His 4 -K4 and K3) were analyzed by size-exclusion chromatography (SEC). The His 4 -K4/K3-FLAG sample eluted at volumes characteristic of homohexamers, whereas K1-His 4 /K2-FLAG showed intermediate behavior between hexamers and dodecamers. This elution behavior had been observed before for Syn6803 K2 homo-hexamers, and is assumed to arise from formation of dodecamers consisting of stacked hexamers  [15, 23, 41]. Second, cells expressing separately each homo-hexamer (His 4 -or FLAG-tagged) were mixed up before lysis and purification. Fractions recovered from TALON resins did not reveal bands of FLAG-tagged proteins in WB.