dataesr/scientific-paragraphs-categorization huggingface dataset:
Structure-guided enzyme engineering to improve pMT activity In solution and in X-ray structure, pMT1 shows a hexameric assembly whose minimal functional unit is a dimer  13. pMT1 displays a unique active site formed by amino acid residues from two distinct monomeric chains of the hexamer, with the N-terminus of one monomer covering the catalytic cavity of the other monomer (Fig. 2c ). Using the structure of pMT1 in complex with the cofactor S-adenosylhomocysteine (SAH) and the substrate teleocidin A1 (PDB id: 5GM2) as a template, we modelled pMT1 bound to each of the four isomers of α-irone with the aim of identifying amino acid residues that could be critical to increase cis-α-irone or decrease trans-α-irone production (Fig. 2d, e ). Visual inspection of the pMT1: α-irone complexes enabled us to identify 24 amino acid residues lining the substrateand cofactor-binding pocket.
After transformation, all the colonies were combined with 1 ml phosphate buffer saline solution (PBS) and subjected to plasmid extraction. The purified plasmid was then transformed into BL21 cells and plated on agar with ZYM autoinduction media and incubated at 20 °C for 3 days  25. The colonies formed were collected in 1 ml PBS, and OD was measured. 12. 5 × 250 µl*OD cells were taken for subsequent reaction with psiionone to test methyltransferase activity. All the primers used in the study are provided in Supplementary data 3.
Computational studies The three-dimensional (3D) structure of pMT1 in complex with the cofactor SAH with the substrate teleocidin A1 was retrieved from the PDB database (PDB id: 5GM2). One dimeric unit was used as the template for modelling pMT1 in complex with the four α-irone isomers (1R5R and 1S5S for the trans-α-irone and 1S5R and 1R5S for the cis-αirone). The α-irones were first built and gradually relaxed using the Avogadro software version 1. 1. 1  26. They were then manually docked into the pMT1 active site using the bound substrate teleocidin A1 as a template from crystallographic structure. pMT3 and pMT4 were modelled using Modeller 9. 19  27  and 3D models with the lowest DOPE score were kept for further analyses. The corresponding complexes of pMT3 or pMT4 with the four α-irones were built by superposing pMT1 complexes.
Acknowledgements The authors would like to thank  Dr. Nicholas David Lindley  from the  Singapore Institute of Food and Biotechnology Innovation , and  Dr. Magali Remaud-Simeon ,  Dr. Sophie Bozonnet  from the  Toulouse Biotechnology Institute  for their valuable suggestions. We acknowledge  Dr Ee Lui Ang , and  Dr Hazel Khoo , the  Singapore Institute of Food and Biotechnology Innovation  for supporting this project. This research is supported by the  Agency for Science, Technology, and Research (A*STAR)  under  IAFPP3 -H20H6a0028 ,  AME Young Individual Research Grants :  A1984c0040  ( 2018 ) to X. C. and A2084c0064 (2019) to Z. C.
Data availability All data supporting the findings of this study are available in the article, its supplementary information, and supplementary datas, or upon request from the corresponding authors. The source data for all figures reported in the article and its supplementary information are provided in the Source Data file. The protein structure data generated in this article is available in World wide Protein Data Bank under PDB ID 5GM1 (https://www. wwpdb. org/pdb?id=pdb_00005gm1), 5GM2 (https://www. wwpdb. org/pdb?id=pdb_00005gm2), 1KPG (https:// www. wwpdb. org/pdb?id=pdb_00001KPG), 4F86 (https://www. wwpdb. org/pdb?id=pdb_00004F86), 4PNE (https://www. wwpdb. org/ pdb?id=pdb_00004PNE) and Supplementary data 1. The initial and final configurations for molecular dynamics calculations are provided in Supplementary data 2.
Quantitative (q) PCR analysis RNA was isolated from pools of 25-30 retinal organoids, collected from two different differentiations, using the QiaShredder and RNeasy mini kit (Qiagen) according to the manufacturer's instructions. The RNA was treated with RNase-free DNase (Qiagen), and 300 ng was reversed transcribed using the Superscript III Reverse Transcriptase Kit (Thermo Fisher Scientific). qPCR amplification was performed using 1/20 dilution of cDNA per reaction with specific primers listed in Additional file 1: Table  S1. Reactions were performed using the FastStart SYBR Green I Master mix (Roche) on a LightCycler 480 II thermal cycler (Roche). The results were normalised to GAPDH expression levels and were analysed using LightCycler 480 software and the Microsoft Excel program. Experiments were performed in triplicate and repeated three times.
Image quantification Quantification of the brush border lengths and the lamina widths was performed using ImageJ software (https:// imagej. nih. gov/ ij/). Five random regions per individual retinal organoid were measured, and 29-79 organoids were analysed depending on the condition. Quantification of immunofluorescence images was performed using the Imaris Software (Bitplane). The area of fluorescence of each marker was analysed and normalised to the area of Hoechst fluorescence of the presumptive outer nuclear layer (ONL). Up to 6 regions were analysed per organoid, and 3 organoids were analysed per condition. Results were further analysed using Microsoft Excel and Graph-Pad Prism 8. 2. 1.
Statistical analyses All data are represented as mean ± standard error of the mean (SEM). Statistical analyses were performed using GraphPad Prism software and significance was determined as p < 0. 05, p < 0. 01 or p < 0. 0001. A one-way ANOVA was used to compare more than 2 groups of data, and if significant, post hoc analysis was performed using an unpaired Student's t-test. In the case of small sample sizes, analyses were performed using a Mann and Whitney test and significance was determined as p < 0. 05. The number of samples per experiment and condition are indicated in the corresponding text and figure legends.
Funding This work was funded by the  ANR  (Grant Number  ANR-20-CE18-0029-02 ), the  LabEx EpiGenMed "Investment  for the future" programme (Grant Number  ANR-10-LABX-12-01 ) and by the patient associations  Aviesan-Unadev ,  Vaincre Usher 2 ,  Fondation de France ,  Retina France and France Choroideremia.
Acknowledgements The authors acknowledge the  European Synchrotron Radiation Facility (ESRF)  for the provision of beamtime at the ID11 beamline and the using laser-heating setup of ID18 beamline. Computations were performed at the  Leibniz Supercomputing Center of the Bavarian Academy of Sciences  and the  Humanities , and the research center for scientific computing at the  University of Bayreuth. DL thanks the  Alexander von Humboldt Foundation , the  Deutsche Forschungsgemeinschaft (DFG , project  LA-4916/ 1-1 ) and the  UKRI   Future Leaders Fellowship  ( MR/ V025724/1 ) for financial support. ND and LD thank the  Federal Ministry of Education and Research, Germany (BMBF , grant no. 05K19WC1 ) and the  Deutsche Forschungsgemeinschaft (DFG  projects  DU 954-11/1 ,  DU 393-9/2 ,  DU 393-13/1 ) for financial support.
In spite of the WJ harvest, the resulting viscous nonlinear elastic response obtained is fully in tune with the literature confirming the database quality. A side of the knowledge improvement on WJ mechanical response, this paper provides accurate data that will enhance predictive simulation work such as finite element analysis. The mechanical step-through brought by the analytical nonlinear characterization over cyclic and ultimate loads is to predict WJ behavior. Actually, principal component analysis highlighted its quality while pointing out indicators, such as failure or hydration criteria, as well as models' limitations.
e. 10 N even though this latter limit has not been reached). As the length increased during sample hydration and was measured a posteriori, the imposed strains defined above were in fact over estimated. For the step 4, the imposed strain average value was 7. 66±0. 50% instead of 10%. All loads were performed at 0. 01 mm s -1 to fulfill the quasi static condition. After mechanical testing, the biggest remaining piece of each sample has been harvested and dried for 48 h at 37 • C to measure the solid matrix mass. Then, they were re-hydrated being immersed in physiological solution for 20 h. Finally, their hydrated masses  ℎ were weighed giving the porosity :  (Gervaso et al. , 2014 ) 𝜑 = 𝑚 ℎ -𝑚 𝑑 𝑚 ℎ (1) The nominal stress , the Green Lagrange strain  and the stretch  were computed from the measured data such as: 𝜎 = 𝐹 𝑆 0 , 𝐸 = 1 2 ( 𝜆 2 -1 ) 𝑎𝑛𝑑 𝜆 = 𝐿 𝐿 0 (2) where  is the measured force for the sample length  while  0 and  0 are respectively the hydrated sample initial length and cross section.
3 + 0. 16  ∕ by  Dorfmann and Ogden (2004). Besides,  1 and ν2 are defined as: 𝜈 1 = 𝑞. 𝜇 [ 1 - 1 3. 5 tanh ( 𝜆 𝑚 -1 0. 1 )] 𝑎𝑛𝑑 ν2 = 𝑞. 𝜇 (7) where  is a fitting parameter and   is the maximal tensile stretch imposed. Adding three parameters (,  and ), in total nine ( ×2+3 = 9) were required to describe a full 10% strain load cycle taking into account the hysteresis (i. e. viscous behavior). Therefore, data were post-processed thanks to a Python script to obtain: the stress strain curves, the elastic moduli for toe and linear regions, the hyperelastic fitting (Appendix A gives the procedure quality compared to  Dorfmann and Ogden (2004)  work) as well as the statistical analysis. Constrained optimization by linear approximation (COBYLA from Scipy) has been used to ensure consistent parameters' values.
This latter table gathered all material parameters, i. e. based  on the experimental data and not related to a model, while Table  2  is dedicated to the models' ones. The linear and bilinear characterizations have been performed on both steps of interest, respectively 4 and 5, leading to plots presented in Fig. 4  and parameters values recorded in Table  2. For better appreciation of characterization procedure, a representative sample (160206_4) has been presented on Figs. 3, 4a and c, while the average results have been plotted overall database on Fig. 4b  and d. The monotone strain loading from 0 to 8% induced an almost linear behavior ( 10%  =  10%  =  10% ) which is appreciated on Fig. 4a  and b  by the olive green straight line. This statement is confirmed by the step 5 curves (cf. bilinear transition point in Fig.
4d ) where the average transition point, in between ''toe'' and ''linear'' regions, is obtained at   = 17. 22% strain related to   = 56. 67 kPa. Fig. 4c  and d  plots show a clear transition in between the regions with a 5. 7 factor from   to   confirming the expected non linear behavior of the WJ samples. Using the three terms model of  Ogden (1972)  as well as the extension developed by  Dorfmann and Ogden (2004) , both last loading steps (4 and 5) have been reproduced as shown on Fig. 4  subplots. The optimization over the whole database led to obtain the average parameters values gathered in Table  2. All data was used to plot correlation matrices and perform principal component analysis (PCA). The global matrix is provided in Fig. B. 6 and Fig. 5  presents a reduced matrix with strong absolute correlations (i.
For this latter model, self correlations are numerous but fitting parameters  10% 2 and  are respectively linked to material parameters  (93% absolute) and  (80% absolute). For accurate analysis, a correlation circle on material and  Dorfmann and Ogden (2004)  parameters has been plotted in Fig. 5b. Being 61. 11% representative, while 60. 41% for  Ogden (1972)  one given in Fig. B. 6, it confirms the previous results. Most of the  Dorfmann and Ogden (2004)  parameter being farther from the circle center attests the identification quality over database. In addition, it exhibits an interesting 2D balanced plane where material parameters, including the identified shear modulus  10% , contribute to the first axis (33. 06%) and model parameters to the second axis (28. 04%) with the anti-correlation between the fitting parameter  and the relative length variation  linking them.
In spite of the WJ harvest, the resulting viscous nonlinear elastic behavior obtained is fully in tune with the literature  (Pennati, 2001; Gervaso et al. , 2014). Even though microscopic material heterogeneities observed and mentioned in the literature, the current results obtained, for random donors, locations and orientations, are presenting a good reproducibility overall database. The maximum relative uncertainty (∕ ||)) on material parameters is below 45% and related to the bilinear stress transition. Besides relieving this macroscopic analysis from microstructural noticeable influences, it points out database quality. Withstanding strain loading up to   = 45. 03% on average, WJ exhibited   = 446. 76 kPa yield stress. These values are respectively higher and lower than the ones presented by  Pennati (2001)  (even considering engineering strain as Pennati (2001) the loading strain is higher with a value of 37.
Although, it remains an important result for clinical applications where interfaces might appear while fixing biomedical devices with membrane shape. For an accurate characterization of the yield point, finite Step 5 corresponds to a load up to sample yield given by the red square point. (c) is dedicated to the representative sample (160206_4) highlighting the bilinear characterization with toe and linear region respectively red and green lines with the red dot transition point. The nonlinear response has been fitted with the Ogden model represented by the orange line. Finally, (d) is the averaging extension over the whole database on which average results of step 4 characterization have been added in dashed blue line with the uncertainty corridor. element simulation could be used to reproduce the experiment and more precisely the boundary conditions at the fixation point.
Quasi-Elastic Neutron Spectroscopy (QENS) measurements were taken on the IRIS spectrometer at the ISIS Neutron and Muon Source 30. The IRIS instrument is capable of reaching Q values of approximately 1. 8 Å -1. In both cases helium closed-cycle refrigerators were used to control the temperature. The raw data were reduced using Mantid and LAMP for the IRIS and IN13 data respectively. Proton experimental NMR data were collected using a Bruker Avance III HD spectrometer operating at 400 MHz and a 5 mm diameter horizontal coil probe. Spin-lattice relaxation times (T 1 ) were recorded using a saturation-recovery method. Spin-lattice relaxation in the rotating frame times (T 1ρ ) were obtained from a 90 • pulse followed by a variable duration spin-lock pulse applied at a field equivalent to 50 kHz.
As the temperature increases 1/τ l begins to increase from 200 K, as it is coming into the time-window of the measurement. The corresponding Arrhenius plot can be seen in Figure  5F , although the activation energy could only be estimated for 1/τ l , as this showed a linear region. The data for 1/τ s shows a step at 250 K and this could be real, however as mentioned previously, this could simply be modelling a fast component, the origin of which is unclear. One option may be that it is due to a change slight change in the type of motion. The fitted Arrhenius parameters for 1/τ l are E a /k B = 788 (68) K and f 0 = 640(150) GHz. One of the limitations of the IRIS data is that we have had to sum over all of Q, and although we have been able to extract information on the frequency of two different processes, we have lost all spatial information.
6  The temperature dependence of the parameters extracted from the NMR experiments for TEA(TCNQ) 2 , where A: is the PWRA for the T 1 data with a Larmor frequency of 400 MHz, B: is the PWRA for the T 1ρ data, where the data shows maxima when the molecular motion is about 50 kHz. The solid blue line is the dielectric loss at 50 kHz, with data shown between 150 and 220 K, showing remarkable agreement between the two data sets. C: is the full width at half maximum associated with the NMR peak. The red solid lines are fits to the data using equations using equations 6, 7 and 8. its square root, would be proportional to the FWHM). The measurements within this paper were performed on a sample where the TCNQ moeity was deuterated, therefore the one expected difference is that we should not see a flattening out of the FWHM at high temperatures.
The FWHM, in our case, will tend to zero as there are no static protons within the structure. It is difficult to interpret the FWHM quantitatively, however, one can see from the flattening of the curve in Figure  6C  at 220 K, that the overall fluctuation rate is exceeding 15 kHz. This is consistent with the FWHM being sensitive to the same motional process as observed in the T 1ρ experiment. Moreover, the FWHM data shows that this motion must involve relatively large re-orientations of the TEA cations, since a small-amplitude libration-type motion would not result in significant changes to 1 H linewidths. The merit of these measurements on the deuterated sample is that they reveal a continuous decrease of the linewidth associated with the cation as the temperature increases. This is consistent with a gradual evolution from a restricted flip-type motion to a more isotropic reorientation of the cations as the TCNQ host structure expands.
Acknowledgements We thank the  ISIS neutron and Muon Source, STFC  for beam time on IRIS and RIKEN for access to the  RIKEN-RAL Muon Facility. Our thanks also go to  Stephen Cottrell  for valuable advice and  Ian Silverwood  for help with performing the experiment on IRIS. We also thank the  ILL  for beam time on IN13 as well as  Dr Francesca Natali  for advice on data analysis.
Electron paramagnetic resonance (EPR) spectroscopy EPR measurements were carried out on a BRUKER ELEXSYS 500 X-band CW-ESR spectrometer, equipped with a BVT 3000 digital temperature controller. The spectra were recorded at 120 K in frozen DMSO solutions otherwise noticed. Typical acquisition parameters were as follows: microwave power 10-20 mW, modulation frequency 100 kHz, modulation gain 3 G. Simulations were performed using the EasySpin toolbox developed for MATLAB  (Stoll and Schweiger, 2006).
1% Triton X-100). Nuclei and cell membrane were counterstained with 4',6-diamidino-2-phenylindole (DAPI) (1:500, 5 min) and Alexa-633 conjugate of wheat germ agglutinin (WGA) (2 μg/ml, 10 min, Thermo Scientific) respectively. The slides were mounted and prepared for fluorescence and confocal microscopy. Images were captured using a Leica TCS SP5 laser scanning confocal microscope with a PL APO 63×/1. 4-0. 6 Oil objective and processed using Imaris software.
Acknowledgments The  Servei d'Anàlisi Química (UAB)  and  Spectropole facilities (AMU)  are kindly acknowledged for allocating instrument time. Alejandro Garcia Torrado  is acknowledged for his contributions to the synthesis and characterization of the H 2 L2 ligand and the C2 complex. Some of the figures were partly designed using BioRender ® software. QP and SR-C acknowledge the  Ministerio de Educación, Cultura y Deporte  the financial support of an  FPU grant. The authors from the  UAB are members of the "Grup de Recerca de la Generalitat de Catalunya " ref. 2017SGR-864  and  2017SGR-1584.
2  (a). Furthermore, we used Digital Micrograph™ software to find, the spots of the planes (110), (  012 ) and (102) with interplanar distances of 0. 384, 0. 312 and 0. 309 nm, respectively. These results correspond with the XRD data and confirm the orthorhombic perovskite structure of SmNiO 3 with space group Pbnm. Additionally, the compositional homogeneity within the film was verified by performing EDS mappings. From Fig. 2(c ), the uniform distribution of elements throughout the thickness of the film is corroborated. Only a blue layer which is richer in oxygen is of note and corresponds to a SiO 2 interlayer between the silicon substrate and the SmNiO 3-δ film. The atomic percentages measured were Sm = 18%, Ni = 19% and O 2 = 63%. It is important to note that, although only one area is shown in the present work, the TEM investigation confirmed the presence of many large grains (see Fig.
Acknowledgements A. L. D. and T. -Q. N. acknowledge the support from the  US Department of Energy  under Award no. DE-SC0017659. G. N. M. R. acknowledges financial support from the  University of Lille ,  UCCS  laboratory and IR-RMN-THC FR-3050 CNRS France for conducting solid-state NMR measurements. H. V. acknowledges the support from  IR RENARD  ( FR384 ).
3. 2. X-ray Analysis, MTT Assay, and Binding Capacity. The designed drug carrier possesses the benefit of quick identification through direct external application of a magnetic field. This was made possible by incorporating iron oxide nanoparticles in the drug carrier. Figure  6  confirms that the drug loaded with the carrier reached near the magnet after the mice were administered with the dose. The dose-response data was used to measure the toxicity of the polymer toward healthy cells. Hence, the MTT (3-(4, 5dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide)   assay was performed describing the percentage of living cells. The cell viability of the polymer was measured against noncancerous cell lines (HepG2) and is given in Figure  7. This data showed that by increasing the concentration of polymer (MIDC), the percentage of living cells increased, proving that the polymer is non-toxic to healthy cells.
ACKNOWLEDGEMENTS We thank  Sebastian Buchberger ,  Brendan Edwards ,  Lewis Hart ,  Chris Hooley ,  Federico Mazzola ,  Martin McClaren ,  Philip Murgatroyd ,  Luke Rhode  and  Gesa Siemann  for useful discussions and technical assistance. We gratefully acknowledge support from the  Leverhulme Trust  and the  Royal Society. Via membership of the UK's HEC Materials Chemistry Consortium , which is funded by the  EPSRC  ( EP/L000202 ,  EP/ R029431 ,  EP/T022213 ), this work used the  ARCHER2   UK National Supercomputing Service  (www. archer2. ac. uk) and the  UK Materials and Molecular Modelling (MMM) Hub  ( Thomas -EP/P020194 & Young -EP/T022213 ). W. R. is grateful to  University College London  for awarding a Graduate Research Scholarship and an  Overseas Research Scholarship. O. J. C. and  K.
U. acknowledge PhD  studentship support from the  UK Engineering and Physical Sciences Research Council (EPSRC , Grant Nos. EP/ K503162/1  and  EP/L015110/1 ). I. M. and E. A. -M. acknowledge studentship support from the  International Max-Planck Research School for Chemistry and Physics of Quantum Materials. S. R. K. acknowledges the  EPSRC Centre for Doctoral Training in the Advanced Characterisation of Materials (CDT-ACM ,  EP/S023259/1 ) for funding a PhD studentship. The MBE growth facility was funded through an  EPSRC  strategic equipment grant:  EP/M023958/1. We thank SOLEIL synchrotron for access to the CASSIOPEE beamline (proposal Nos. 20181599 and 20171202). The research leading to this result has been supported by the  project CALIPSOplus  under Grant Agreement 730872 from the  EU   Framework Programme for Research and Innovation HORIZON 2020.
Acknowledgements Financial support from  CNRS  and  Université de Toulouse  is acknowledged. CALMIP is gratefully acknowledged for access to supercomputing facilities. C. B. wishes to thank the "région  Auvergne-Rhône-Alpes"  for financial support. The NMR service of the ICT is gratefully acknowledged, as well as  Mrs. C. Absalon  for LIFDI MS analysis. We thank  T. Personeni  for preparing samples for EPR experiments and  Dr. W. Schipper  from  SWAN-H  for insightful discussions.
Acknowledgments The authors would like to thank the  French Ministry of High Education and Research for PhD  grant funding. The authors wish to thank  C. Boule  from the  Centre Technologique des Microstructures CTµ of the University of Lyon  I for TEM micrographs,  A. Crepet  for  Size Exclusion Chromatography (SEC) experiments ,  Carlos Fernandez de Alba  and  Fernande da Cruz  for NMR experiments, and  Pulsalys-SATT Lyon Saint-Etienne  for its financial support.