dataesr/scientific-paragraphs-categorization huggingface dataset:
A condition resulted in a hexagonal crystal form diffracting X-rays to 1. 80 Å resolution and displaying two molecules in the asymmetric unit. Unexpectedly, although both CcmK3 and CcmK4 were present in the crystallization solution, the corresponding refined structure unambiguously showed the sole presence of K4 subunits in the asymmetric unit, which organize as canonical homo-hexamers as the result of space group symmetry (structure deposited with PDB code 6SCR, statistics presented in the S3 Table ). The monomer structures were basically identical to previously solved structures, with only 0. 25 and 0. 23 Å RMSD for 408 backbone atoms, when compared to structures deposited in the RCSB databank with PDB codes 2A18 and 2A10, respectively. The only novel feature was the observation of a 2D arrangement with similarly-oriented K4 hexamers (Fig 5D ), which therefore differs from the stripped organization described before for the same protein  [13] , and provides an additional proof of the high structural plasticity of BMC-H proteins.
7 μM monomer concentration) that had been pre-incubated overnight, at pH ranging between 5 and 9, in the absence (top lane) or presence of 14% PEG 3350 (bottom). The first lane corresponds to a sample at pH 7 that was maintained at 4˚C throughout the overnight incubation. The bottom panel presents FLAG signals detected for indicated homo-and hetero-hexamers combining His 4 -and FLAG-tagged subunits (2 μM final monomer concentration, indicated by black or violet letters, respectively) that were incubated overnight at room temperature and pH 8 in the absence or in the presence of untagged K4 or K1 homo-hexamers (6 μM monomer). B, Thermal denaturation monitored by DSF (top) and DLS (bottom). Left panels present data collected for CcmK1 (triangles) and CcmK2 (circles) homo-hexamers, as well as for CcmK1/K2 hetero-hexamers (squares).
Right panels show data for CcmK4 (squares) and CcmK3/K4 (circles). In DSF experiments, the proteins were incubated with the Sypro dye and the fluorescence of the probe was monitored as temperature was increased. For DLS assays, changes of the intensity of scattered light of hexamer solutions with temperature were recorded. DSF and DLS data were normalized before analysis. The mean of multiple measurement (see S4 Table ) is shown with black symbols as well as the adjusted sigmoids (red lines). For each trace, only one every two recorded data points are displayed to facilitate figure interpretation. https://doi. org/10. 1371/journal. pone. 0223877. g006.
Also noticeable, purified K4 bands were broad in the Coomassie gels, suggestive of potential degradation of the protein, somehow resembling observations on Syn6803 K4. The presence of K3/K4 hetero-hexamers was confirmed on WB. The intensity of FLAG bands in purified fractions was lower for samples containing K3-FLAG than in combinations resulting in K4 homo-hexamers (Fig  7 ). Taking into consideration that FLAG signals were Western blot analysis of fractions remaining soluble after cellular lysis and centrifugation (top lane) and material purified on TALON resins (bottom). Left panel correspond to samples prepared from cellular cultures that were induced in IPTG (200 μM), whereas data on the right correspond to samples produced under autoinduction conditions. Detection on PVDC membranes was performed with a mouse antiFLAG primary antibody followed by a secondary IgG antimouse-alkaline phosphatase fusion.
We hypothesize that such regulatory mechanisms would serve to control the intrinsic structural promiscuity of BMC shell components, both at the monomer and hexamer levels. This study demonstrate the structural compatibility between Syn6803 K1/K2 and K3/K4 hetero-hexamers. Data were more consistent for the Syn6803 K1/K2 combination, results being unaffected by the choice of tagging configuration (Fig  1 ). WB signal intensities were comparable to those measured for FLAG-labeled homo-hexamers, suggesting that K1/K2 might compete efficiently with homo-hexamer formation in vivo. Moreover, analysis of purified samples by native MS/MS, which confirmed the association of subunits within the same hexamer, permitted to detect almost all possible stoichiometries, supporting the good structural miscibility between the two paralogs.
B, Thermal denaturation monitored by DSF (top) and DLS (bottom). Left panels present data collected for CcmK1 (triangles) and CcmK2 (circles) homo-hexamers, as well as for CcmK1/K2 hetero-hexamers (squares). Right panels show data for CcmK4 (squares) and CcmK3/K4 (circles). In DSF experiments, the proteins were incubated with the Sypro dye and the fluorescence of the probe was monitored as temperature was increased. For DLS assays, changes of the intensity of scattered light of hexamer solutions with temperature were recorded. DSF and DLS data were normalized before analysis. The mean of multiple measurement (see S4 Table)is shown with black symbols as well as the adjusted sigmoids (red lines). For each trace, only one every two recorded data points are displayed to facilitate figure interpretation.
Theoretical Method Our present calculations were performed using DFT within the generalized gradient approximation in the form proposed by Perdew and Wang (PW91)  [9, 10]  and the interpolation formula of Vosko, Wilk, and Nusair (VWN)  [11]  as implemented in the Vienna Ab-initio Simulation Package (VASP)  [12]. We utilized the projected augmented wave (PAW)  [13, 14]  method and the wave function was expanded in plane waves using a 400 eV energy cut-off. To take into account electron correlation effects, we have included Hubbardlike Coulomb correction terms in the d shell of the TM-TCNB and TM-Pc materials in the form of the SGGA+U method proposed by Liechtenstein et al. [15]. We did choose the same values of U = 5 eV and J = 0. 90 eV for all materials  [6] [7] [8]. The variation of U term in the region of ± 2 eV does not change the results of this paper.
Acknowledgments This project is funded by the  Région Normandie  and the  European Union. Europe invests in Normandy with the  European Regional Developement Fund (ERDF)  - MAGMA  project. The authors acknowledge the  Centre Régional Informatique et d'Applications Numériques de Normandie (CRIANN ) where simulations were performed as Project No. 2010006. We also thank  Ahmed Albaalbaky  for critical reading of the manuscript. 24-06-2019.
SEM images were analysed with ImageJ software  35. The crystalline structure of fabricated heterostructures was studied using X-ray diffraction spectroscopy (powder diffractometer X'PERT MRD with Cu Kα radiation source). Bi 2 Se 3 nanoribbons grown on AAO substrates were mechanically transferred to a n-type silicon substrate covered with 300 nm of SiO 2. Optical imaging was used to select individual nanoribbons on the Si/SiO 2 chip. Nanoribbon devices for magnetotransport measurements were fabricated by electron beam lithography. To achieve ohmic contacts, the Bi 2 Se 3 nanoribbons were etched with Ar + ions shortly before the metallization (Ti/ Au). Magnetotransport measurements were performed in a Quantum Design Physical Property Measurement System (PPMS). All the data were recorded at base temperature of 2 K and in a four-probe configuration.
Acknowledgements This work was supported by  European Regional Development Fund  project No. 1. 1. 1. 1/16 /A/256and European Union's  Horizon 2020 research and innovation programme  (grant agreement No. 766714/HiTIMe ). GK acknowledges  European Regional Development Fund  project application No  1. 1. 1. 2/VIAA/1/16/198.
In such a case, two corrections are often implemented: (1) defining an ad hoc new contribution to fill the gap, (2) scaling the energy sum to the targeted energy. This strategy is very often used with the virial theorem. Indeed, for the exact wavefunction, the molecular energy is equal to minus the electron kinetic energy, or, equivalently, to half the potential energy. Unfortunately, the scaling parameter that is used in practice can be significantly different from one system to another. It can lead to questionable conclusions when comparing molecules of too much different type. [4] Coming back to question 5, it thus appears that some EDAs should not be used to investigate a molecular dataset composed of several different classes. From this point of view, the investigate systems will influence the EDA choice by precluding the use of some of them.
Measurement Techniques The sunlight-induced thiol-yne reaction was carried out in the visible range photoreactor (Dr Honle, UVA Cube 400 sun simulator). A K Alpha machine (Thermo, East Grinstead, UK) fitted with monochromated Al Kα X-ray source (hν = 1486. 6 eV, 400 µm spot size) was employed to analyze the surface chemical composition. Avantage software was used for spectral acquisition and data processing. A flood gun was used to compensate for the charge build up. Spectral calibration was achieved by setting the Au 4f 7/2 peak at 84 eV  [44, 45]. Raman scattering was measured on a portable ProRaman-L spectrometer (Laser power 15 mW) with 785 nm excitation wavelengths. Spectra were measured 30 times, each of them with 3 s accumulation time.
The solvent system consisted of 0. 1% FA in water (solvent A) and 0. 1% FA in ACN (solvent B). Peptides were eluted at 450 nL/min with the following gradient of solvent B: from 1 to 8% over 2 min, from 8 to 35% over 28 min and then 90% for 5 min. The system was operated in positive mode using the following settings: MS1 survey scans (m/z 300 to 1800) were performed at a resolution of 70 000 with an AGC target of 3 × 10 6 and the maximum injection time was set to 50 ms. MS/MS spectra were acquired at a resolution of 17500. The MS2 AGC target was set to 1 × 10 5 and the maximum injection time was set to 100 ms. NanoLC-MS/MS data were searched using a local Mascot server (version 2. 5. 1, MatrixScience, London, UK) in an Arabidopsis thaliana protein sequences database downloaded from the TAIR site (TAIR10 version, Phoenix Bioinformatics, Fremont, CA, USA), to which decoy sequences were added using the in-house developed software tool MSDA  [32].
Bioinformatics Analyses The gene and protein sequences were obtained from the NCBI website (http://www. ncbi. nlm. nih. gov, Rockville Pike, Bethesda MD, USA). ClustalW2 software (http://www. ebi. ac. uk/Tools/msa/ clustalw2/, EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK) was used to perform the multiple sequence alignments. Swiss Model software (http://swissmodel. expasy. org/, Protein Structure Bioinformatics Group, Swiss Institute of Bioinformatics Biozentrum, University of Basel, Switzerland) was used for cICDH modeling by using human cytosolic ICDH sequence structure (PDB ID: 1T0L,  [34] ), and the Geneious 9. 0 software (Biomatters ApS, Aarhus, Denmark) was used for the 3D representation.
Enzyme Activities Are Affected in Mutants In order to study whether cICDH activity is redox sensitive in planta, we measured ICDH activities in leaves from two-weeks old plants of different Arabidopsis mutants. While exhibiting no phenotypic perturbations on the rosette growth, the cytosolic icdh KO mutant shows a marked decrease (-60%) of NADP-ICDH activities (Figure  6A ). This confirmed previous data showing that the cytosolic ICDH contributed to the major pool of the shoot extractible NADP-ICDH activity. Nevertheless, this contribution seems somehow less than reported previously (-90%), possibly due differences in growth conditions or developmental stage of the plants or to the contribution of organellar NADP-ICDH activities  [6]. NADP-dependent ICDH activities were also consistently decreased in the cat2 mutant (Figure  6A ), which is impaired in the major isoform of the peroxisomal H 2 O 2 detoxification enzyme Catalase 2 (Supplemental Figure  S5 ), suggesting that NADP-ICDH activities are affected by oxidizing conditions.
Funding: This research was funded by [ Agence Nationale de la Recherche ] grant number. Acknowledgments: This work was supported by grants from the  Centre National de la Recherche Scientifique  and the  Agence Nationale de la Recherche  ( ANR-Blanc Cynthiol 12-BSV6-0011 ). This work has been supported by  LabEx Agro and LabEx TULIP.
Out of three ANN algorithms, the neuralnet package with two activation functions, "logistic" and "tanh" were implemented. The prediction of the flux was very efficient: RMSE and R 2 were 0. 847, 0. 93 and 0. 804, 0. 94 respectively for logistic and tanh functions using a cross validation procedure. This study showed that a systemic approach such as ANN could be used for accurate prediction of the flux through the metabolic pathway. This could help to save a lot of time and costs, particularly from an industrial perspective.
Experimental details The upper part of glycolysis was reconstructed in vitro (Fig 2 ), with constant concentration of hexokinase andglycerol-3-phosphate dehydrogenase, while the other four enzymes (PGI, PFK, FBA and TPI) concentrations varied. The total enzyme concentration of the four enzymes (PGI, PFK, FBA and TPI) was constant at 101. 9 mg/L. The NADH consumption using the glycerol-3-phosphate dehydrogenase is monitored every 2s with Uvikon 850 spectrometer at 390 nm from 60 to 120s. The linear slope of NADH was calculated as the flux through the pathway. The assays were performed in triplicate by Fievet et al. , 2006, at 25˚C, by adding 1mM ATP at pH 7. 5. Data is given in supplementary information (Table A in S1 File).
Structure of ANN The artificial neural network built with a single layer of hidden units  [68]  using statistical tool R (version 3. 4. 3) (R Core Team (2013). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. http://www. R-project. org/) using three different packages: nnet (version 7. 3-12)  [69] , neuralnet (version 1. 33)  [70]  and RSNNS (version 0. 4-10)  [71]. The network consists of three layers: a) Input (I), b) Hidden layer (H) and c) Output. These layers are connected by edges or neurons. The weighted sum of neuron inputs is submitted to a function which conditions neuron activation. There is no rule for deciding the number of neuron units in a single hidden layer; to choose the best algorithm out of three (i. e. nnet, neuralnet and RSNNS), we first chose the number of hidden units according to Equation 1 and compared the RMSE (Equation  2 ) and coefficient of determination (R 2 ) (Equation  3 ) values between the three methods.
The logistic function with 13 hidden units gives a RMSE of 0. 847, R 2 of 0. 93 and tanh function RMSE of 0. 804, and R 2 of 0. 94 with 6 hidden units. The R-script to build the ANN with leave-one-out cross validation is given in R-Scripts A in S1 File. Experimental flux was compared with the ANN predicted flux by leave-one-outcross-validation procedure, using chosen hidden units with logistic and tanh function (Fig  4 ). The effects of enzyme concentrations on the predicted flux and experimental flux were compared, and found to follow a similar trend (Fig  5 ). During the cross validation of the neural network model, a negative flux value was predicted for one combination of enzymes (Table  1 : Index-3). This is because, during a leave-oneout procedure (LOOcv), one combination of the four enzymes is not included in the model training and has to be predicted.
Laser diffraction analysis Stirred yogurts were diluted 1:10 (w/w) with purified water in a 100 mL pot and the microgels were dispersed by reversing the pot several times. Size distributions were measured by laser diffraction with a MasterSizer 2000 (Malvern Instruments, UK). To achieve a constant level of obscuration, only some drops of 1:10 diluted stirred yogurts were poured in dispersant tank for the measurement (three repetitions), resulting in a total dilution of 1:100. A refractive index of 1. 33 for water and 1. 46 for the microgels (refractive index of milk proteins), and an absorption index of 0. 01 for the microgels were used  (Huc et al. , 2016). Several data were deduced from the PSD (Malvern Instruments Ltd. , 2007): size volume distribution, particle sizes representing less than 10% (d(0.
2D dynamic image analysis Dynamic image analysis was performed using a QICPIC/R modular particle size and shape analyzer and a LIXELL wet dispersing unit (Sympatec GmbH, DE). A precision M4 lens measuring from 1 to 750 µm with a 0. 5 mm cuvette was used. Stirred yogurts were diluted 1:2000 (w/w) with purified water in a 1000 mL beaker to disperse the microgels and the dispersed microgels were then stirred at 100 rpm for 1 min and pumped into the dispersing unit with a peristaltic pump (Masterflex L/S Model 77201-60, Cole-Parmer, FR) at a flow rate of 25 mL/min. For each dilution, two 30-second image acquisitions were performed at 10 Hz. The images were processed using PAQXOS application software (PAQXOS, Version 2. 2. 2, Sympatec GmbH, DE). Size measurement data such as volume distribution, d(0.
Data computation from 3D reconstruction From the 3D reconstructions, Scan IP TM software provided several data on both size and shape, some of which were either recovered or processed in this study. First, the software provided the number of individual microgels identified in the 3D reconstruction and their corresponding volume (µm 3 ). In order to obtain the size distribution of the microgels in equivalent sphere, their volumes were discretized (logarithmic scale). To ensure good quality discretization, at least eight classes were required to plot each distribution (i. e. with volume fractions greater than 0%), with a minimum of two classes per decade. Like with laser diffraction, d(0. 1) (µm), d(0. 5) (median diameter, µm), d(0. 9) (µm), D  [3, 2] , D  [4, 3]  and span were retrieved from the reconstituted size distribution.
Acknowledgements This work was funded by a single interministerial fund (France) through a collaborative  R&D  project certified by Vitagora and Valorial competitiveness clusters as well as by the research programs of the  Fonds de recherche du Québec -Nature et technologies ,  Novalait Inc. , the  Ministère de l'Agriculture, des Pêcheries et de l'Alimentation du Québec (MAPAQ) , and the  Fondation Famille-Choquette. The authors would like to thank  Philippe Violle , sales manager of  Sympatec France , for his help and advice with the dynamic image analysis processing. The authors also thank  Paul Menut  and  Artemio Plana-Fattori  for sharing their experience and contributing to the development and improvement of this paper.
LTbEu(NO3)3•(H2O)2. A mixture of LTb (0,70 g, 1 mmol) and of Eu(NO3)3. 6H2O (0. 47 g, 1. 05 mmol) in methanol (20 mL) was stirred for four hours at room temperature. The resulting light yellow precipitate was filtered off, washed with isopropanol and diethyl oxide. Yield 0. 85 g (79%). Anal. Calcd for  C30H37EuN7O17Tb (1078. 6): C 33. 41, H 3. 46, N 9. 09. Found: C 33. 25, H 3. 19, N 8. 77. MS (FAB + , 3-nitrobenzyl alcohol matrix): m/z (%) 981 (100), [LTbEu(NO3)2] +. Physical measurements. Elemental analyses were carried out by the Service de Microanalyse du Laboratoire de Chimie de Coordination, Toulouse (C, H, N). Magnetic susceptibility data were collected on powdered samples of the different compounds with use of a SQUID-based sample magnetometer on a QUANTUM Design Model MPMS instrument under an applied field of 0.
ACKNOWLEDGMENTS The experimental work has been supported by the  European Research Council (ERC) , the  Scottish Funding Council , the  UK EPSRC  and the  Swiss National Science Foundation (SNSF). Theoretical work was supported by the  ERC  grant  ERC-319286-QMAC  and by the  SNSF (NCCR MARVEL ). The Flatiron Institute is a division of the  Simons Foundation. AG and MZ gratefully acknowledge useful discussions with  Gabriel Kotliar ,  Andrew J. Millis  and  Jernej Mravlje.
Basic geometrical considerations yield the dependence of fluorescence intensity I NV on the angle of excitation polarization ϕ e as I NV (ϕ e ) = I 0 for OOP-oriented NVs and I NV (ϕ e ) = I 0 sin 2 (ϕ eϕ NV ) + 1 9 cos 2 (ϕ eϕ NV ) otherwise, where ϕ NV is the azimuthal angle of the NV axis (cf. Fig. 2(c ))  [21, 22]. In our experiment, we used a liquid crystal polarization rotator (Thorlabs) to rotate the linear polarization of the excitation laser, set to a power below NV saturation, while collecting single NV fluorescence without polarization discrimination. Fig. 3(a)  shows data for three representative NVs oriented along the three non-OOP-oriented NV axes, where we observe distinct minima of I(ϕ e ), reaching ∼ 0. 23 I 0 at ϕ e = ϕ NV for each dataset. As expected, ϕ NV is shifted by ±120 • between the three cases.
Holographic X-ray nanoimaging generated 2D projection images (phase contrast maps) and stereographic images with ∼40-nm resolution. Full 3D reconstructions with ∼80-nm resolution were obtained from holotomography. Nanofocus X-ray fluorescence (XRF) of the same specimens provided 2D elemental maps with ∼40-nm resolution. Microfocus XRF of duplicate samples provided 2D elemental maps that could be complemented by Ag L III -edge X-ray absorption spectra to determine silver speciation. Key findings from these data are summarized in Fig. 2. The X-ray images revealed a striking difference in the intracellular fate of AgNWs with different diameters. Intracellular 93-nm AgNWs were slightly bent with respect to nanowires after synthesis and suspension in cell culture media but nevertheless retained the elongate nanowire morphology (Fig.
The present study of AgNWs with the same mean lengths but different mean diameters will allow more quantitative assessment of the hypothesis that membrane forces exerted on internalized fibers can cause deformation (SI Appendix). For 10-μm-long AgNWs, the predicted compression forces due to membrane bending elasticity could reach 100 pN, while the linear-rod buckling force requires ∼200 pN. However, the presence of initial curvature, lattice defects and strain or the action of intracellular degradation processes could weaken the AgNWs. A conceptual model for stiffness dependent AgNW toxicity is given in Fig. 4 , and an accompanying quantitative model for the dose-dependence of the cellular cytotoxicity of AgNWs is described in SI Appendix and plotted in Fig. 1. Following calibration of the model at low AgNW dose, good agreement with the cell viability data at higher doses supports the concept that cell mortality is determined by the fraction of AgNWs that puncture endolysosome membranes and subsequently undergo surface chemical reactions in the cytosol.
Aliquots were transferred into new well plates to quantify formazan production from the absorbance at 560 nm using a microplate reader (FLUOstar OMEGA, BMG Labtech). Initial trials using cell-free controls and a centrifugation step found that the AgNWs were not transferred in the quantitation step and did not interfere with the assay. The dose-response data for AgNO 3 gave excellent agreement with prior studies  (26). Cell viability was expressed as percentage relatively to negative control (nontreated cells) using alternative dose metrics: silver mass concentration in SI Appendix, Fig. S2  and number of particles per volume in Fig. 1  C and D and SI Appendix, Fig. S4. Viability assays for other cell lines are described in SI Appendix and included similar controls. The impact of AgNW exposure to L929 cells on oxidative stress production, mitochondrial membrane potential, intracellular calcium level and membrane integrity was assessed using fluorescent probes as described in SI Appendix.