dataesr/scientific-paragraphs-categorization huggingface dataset:
org/0000-0002-7899-7192Tytus D. Mak -Mass Spectrometry Data Center,  National Institute of Standards and Technology, Gaithersburg ,  Maryland 20899 , United States; orcid. org/ 0000-0001-9501-5640Shin   Kawano -Database Center for Life Science, Joint Support Center for Data Science Research, Research Organization of Information and Systems , Chiba  277-0871 , Japan; Faculty of  Contemporary Society, Toyama University of International Studies , Toyama 930-1292, Japan; School of Frontier Engineering,  Kitasato University , Sagamihara 252-0373, Japan; orcid. org/ 0000-0002-7969-2972Luis   Mendoza -Institute for Systems Biology, Seattle ,  Washington 98109 , United States; orcid. org/ 0000-0003-0128-8643Tim   Van Den Bossche -VIB-UGent Center for Medical Biotechnology ,  VIB, 9052 Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9052 Ghent, Belgium Ralf Gabriels -VIB-UGent Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9052 Ghent, Belgium ; orcid.
X-Ray Crystallography X-Ray intensity data for 3 Pt and 5 Pt were collected at 146 K or 293 K, respectively, on an XtaLAB Synergy diffractometer with a HyPix detector using monochromatic Cu-K α radiation (λ = 1. 54184 Å). The data were processed by the CrysAlis Pro program  [30]  used for unit cell determination and data reduction. The structures were solved by the program SXELXT  [31]  and refined according to the least-squares procedure (F 2 on all data) by the program SHELXL. [32] Basic experimental data are given in Table  S1  of the Supporting Information. For 3 Pt , all non-hydrogen atoms were found from the first solution obtained from the SHELXT program,  [31]  while for 5 Pt , Pt 2 + cation, two types of Cl À anions (coordinated and uncoordinated) and majority of atoms of the ligand were recognized from the first SHELXT solution.
Cytotoxicity. Cells were seeded at a 4,000 cells/well density in 96-well plates (100 μL/well) and were incubated at 37 °C, 5 % CO 2 for 24 h. The medium was replaced by test compound dilutions in fresh medium (100 μL/well), and cells were incubated at 37 °C, 5 % CO 2 for 48 h. The medium was then replaced with 100 μL of fresh medium containing resazurin (0. 2 mg/ mL). After 4 h of incubation at 37 °C, 5 % CO 2 , plates were read using a SpectraMaxM2 Microplate Reader (λ exc = 540 nm; λ read = 590 nm). Fluorescence data were normalized, data were fitted using GraphPad Prism Software, and IC 50 was calculated by non-linear regression.
Acknowledgements L. G. -G. thanks the  ENS-PSL  for a Ph. D. fellowship. This work was also financially supported by an  ERC   Consolidator Grant PhotoMedMet  to  G. G. ( GA 681679 ), has received support under the  program 'Investissements d'Avenir ' launched by the  French Helv. Chim. Acta 2023, 106, e202300078 www. helv. wiley. com(10 of 12) e202300078 © 2023 The Authors. Helvetica Chimica Acta published by  Wiley-VHCA AG Government  and implemented by the  ANR  with the reference  ANR-10-IDEX-0001 -02 PSL  (G. G. ). The authors acknowledge the  Croatian-French bilateral grant program , COGITO. M. B. acknowledges the  Croatian Science Foundation  for a doctoral scholarship ( DOK-2021-02-7366 ). This work was partially supported by  CAT Pharma  ( KK. 01. 1. 1. 04. 0013 ), a project co-financed by the  Croatian Government  and the  European Union  through the  European Regional Development Fund -the Competitiveness and Cohesion Operational Program.
Computa�on of chemical equilibrium diagram A poten�al-pH diagram for Fe was generated using the HYDRO Medusa Chemical Equilibrium So�ware to elucidate the observed Fe dissolu�on behavior. 38  The so�ware-provided poten�al versus standard hydrogen electrode (SHE) was recalibrated, considering that the poten�al of a 3. 4 M Ag/AgCl solu�on is -0. 2 V rela�ve to SHE. 46  The soluble Fe species considered in the study were Fe 2+ , Fe(OH)2 + , Fe(OH)3, Fe(OH)4 -, Fe2(OH)2 4+ , Fe3(OH)4 5+ , FeO4 2-, FeOH 2+ , Fe(OH)2, Fe(OH)3 -, Fe(OH)4 2-, and FeOH +. In addi�on, the solid Fe species taken into account were Fe(OH)3(s), Fe2O3(s), FeOOH(s), Fe(OH)2(s), Fe3(OH)8(s), and Fe3O4(s). The temperature was set to 25 ⁰C and the total concentra�on of Fe species was maintained at 0. 1 M. All equilibrium constants for the given species were used as reported in the so�ware database,  38, 47  except for Fe2O3 (hema�te).
For this, we adjusted the equilibrium constant (K) to account for a devia�on in the reported values of its Gibbs free energy of forma�on,  39, 47, 48  thereby ensuring a beter correla�on with the results reported in our study. We set the logK of the reac�on 2Fe 3+ + 3H2O ↔ 6H + + Fe2O3(s) (2) to -1. 5, in accordance with the nota�on used in the Hydro Meduza Database entries. 38.
This experiment was repeated four �mes in total (with the whole dataset available in the Zenodo repository), yielding iden�cal trends that we analyzed in detail based on a typical example discussed below. First, we examine the global electrical current and averaged op�cal signal, expressed as the evolu�on of averaged normalized intensity (Fig. 1c ). Both curves reveal three dis�nct periods. Period 1 ini�ates immediately upon poten�al imposi�on and lasts approximately 2-3 seconds. This period is characterized by a sudden current density increase up to 0. 04 mA/cm 2 , coupled with an abrupt decrease in surface reflec�vity, by approximately 30 %. These changes suggest surfacecontrolled oxida�on with the forma�on of surface films. Upon analyzing raw op�cal images captured on a scale of 10s of µm, as demonstrated in Fig.
It is important to note that the ini�al image at 0 s (not displayed here but available in the Zenodo repository) exhibits a completely white appearance. This corresponds to 100% of 1+∆𝑅𝑅 10 𝑅𝑅 ⁄ , indica�ng that there were no observable changes prior to the applica�on of chronoamperometry, which commenced at the 0-second mark. The areas outside of the electrode are filled with an epoxy resin where no changes occur, hence the normalized reflec�vity remains at 100%, as indicated by the white color in the chosen color scheme of Fig. 3a. The surface darkening towards the electrode center is not discernible on the 10 µm scale from the image insets in Fig. 2c  and is only no�ceable due to the observa�on of the en�re ac�ve area at the scale of hundreds of µm. This observa�on suggests that the kine�cs of localized oxida�on are significantly influenced by the electrode's border at the mm scale, apart from the influence of the Fe interface's crystallographic structure at the µm scale.
Acknowledgements This work was par�ally financially supported by the  Agence Na�onale de la Recherche 10 (ANR)   Jeunes chercheuses ,  jeunes chercheurs ,  ANR JCJC, program  ( OCTAWA  project,  ANR-11 22-CE29-0010-01 ). https://doi. org/10. 26434/chemrxiv-2023-stbm1 ORCID: https://orcid. org/0000-0003-4289-9678 Content not peer-reviewed by ChemRxiv. License:  CC BY-NC-ND 4. 0.
The adsorption mass, film thickness, shear elastic modulus, and shear viscosity were calculated using both the Voigt and power-law modelling with the Dfind software with at least five overtones with a good signal/noise ratio (Biolin Scientific, Q-Sense, Gothenburg, Sweden). The validity of a model was chosen according to the fit quality, χ 2 , and if all general trends were physically reasonable compared to each experimental conditions used and reliable with our previous studies. The adsorbed film was assumed to have both a uniform thickness and density. The film density was assumed to be the inverse of the partial specific volume v s • , ρ = 1 vs • (see data in Table  S1 ) [35,36], i. e. , 1. 703 cm 3 •g -1 for A. senegal and 1. 734 cm 3 •g -1 for A. seyal, respectively. All experiments were conducted at least three times with both new and reused quartz, and all calculated data presented in this study corresponded to the mean ± standard deviation.
Surface Properties Static contact angle measurements were performed with a Tracker TM automatic drop tensiometer (Teclis Scientific, Civrieux d'Azergues, France) in the method of sessile down. Images were analyzed with the WDROP software (Teclis Scientific, Civrieux d'Azergues, France). A drop of 5 µL of a solution containing 10 mM acetate and 50 mM NaCl at the desired pH was deposited on the cleaned sensor surface at room temperature. Images were recorded for 60 s and the measurements obtained at a stable state (i. e. , 30 s) are presented in this study. At least five measurements on different surfaces were averaged to obtain reliable results. Roughness images of bare surfaces were measured by atomic force microscopy (AFM) in the air using INNOVA (Bruker, Palaiseau, France). The images were recorded with low scan rates between 0.
5 and 1 Hz, using FESPA-V2 tips (Bruker) with 2. 8 N m -1 spring constants in the tapping mode. The root-mean-square roughness (RMS) and the roughness factor r were extracted from three separate images obtained in different regions on each cleaned surface with the Gwyddion software (freeware available at http://gwyddion. net/, accessed on 9 February 2021). r is the ratio between the real 3D surface area (A) of the topography determined by AFM to the projected 2D flat surface area (A g ) of the topography, defined as  [37, 38] : r = roughness f actor = A A g (3).
Acute immobilization test Tests were performed according to guideline OECD 202 (Daphnia sp. acute immobilization test). 18 Test media were prepared according to DIN EN ISO 6341:2013-01 (ref. 19) but sodium (Na) was added as sodium chloride (NaCl) instead of sodium bicarbonate (NaHCO 3 ) in order to limit Ln-carbonate precipitation, pH was maintained at 7. 00 ± 0. 2, oxygen concentration was higher than 3 mg L -1 , and salinity did not exceed 0. 585 ppt (ESI data S1 †). Neonates of less than 24 h of age were exposed in 6 well plastic plates (VWR International, Radnor, US). For each conditions (La exposure, Gd exposure and controls), 15 organisms were distributed in three wells and 10 mL of medium were added per well. For determination of the EC 50 of La and Gd, immobilization was studied aer 48 h of exposure at different nominal concentrations from 5 to 30 mg Ln L -1 added as pure standard solution for ICP-MS of Gd(III) and La(III), (N9300127 and N9300118 for La and Gd respectively, PerkinElmer, Waltham, US).
Chemical analysis and speciation modelling The dissolved Ln concentration in the test media was measured aer the bioassays. Samples were ltered through 0. 2 mm cellulose nitrate lter (Whatman, Maidstone, UK), acidied with HNO 3 (Roth, Karlsruhe, Germany) to a nal acid concentration of 2% and measured by total reection X-ray uorescence spectrometry (TRXF) with a Picofox S2 (Bruker AXS Microanalysis GmbH, Billerica, US). The limit of detection La and Gd in liquid samples was 0. 1 mg L -1 when measured for 1000 s with 10 mg L -1 of Ga as internal standard. This is in line with the limit of detection measured by Telgmann et al. 20  for Gd in blood urine (LOD: 0. 1 mg L -1 ). Speciation modelling was performed with Visual MINTEQ version 3. 1 in order to predict the dissolved and solid forms of La and Gd aer equilibrium (ESI data S2 †).
Paper Environmental Science: Processes & Impacts the horizontal plane of the beam in backscattering geometry. Full XRF spectra were collected in each pixel and processed by an in-house Matlab code, available at NANOSCOPIUM, to provide a high resolution distribution of multiple elements such as Ca, zinc (Zn), La, and Gd as well as the Compton (inelastic) scattering which permitted to give further organism's detailed internal morphology. 25 hree organisms per Ln were glued on the pin of a toothpick and were continuously scanned using the FlyScan continuous acquisition mode 26 with 20 to 100 ms of dwell time per pixel with a pixel size of 400 × 400 nm to 1 × 1 mm, depending on the eld of view. The correlative RGB maps were analysed using FIJI. 27 The uorescence intensity of each pixel of La and Gd maps was normalized by the incident intensity of the beam at the respective time of the measurement.
The distribution provided visualisation of the main respiratory organs (the limbs) which were not visible mapping at higher energy, i. e. 17. 02 keV. Controls were also mapped at 7. 25 keV to ensure the absence of Ln in the specimens that were not in contact with Ln during the exposure time. The accumulation of Ln in the different organisms was studied by calculating the ratio between Ln and Ca intensity in the entire specimens mapped on LUCIA (Fig. 5 ). As was observed at NANOSCOPIUM, La and Gd accumulated differently in the organisms. La was found in the intestinal tract while Gd was more diffused in the tissues (ESI data S7 †). The comparison of the Ln/Ca ratio between the different samples permitted to show that the degree of accumulation in the exposed organisms (3 to 4 order of magnitude of difference to the control).
Acknowledgements This work was fund by the  European Union 's  Horizon 2020 research and innovation program  under the  Marie Sklodowska-Curie Grant  Agreement No. 857989. The synchrotron nano and micro-XRF beam time was granted by the SOLEIL synchrotron facilities under the project no. 99210292 at LUCIA beamline and project no. 20210472 at NANOSCOPIUM beamline.
Acknowledgements This work was funded by  Janssen Pharmaceuticals  through a  PhD grant  ( J. Leblanc ). The authors are deeply indebted to  Janssen Pharmaceuticals , the  Ministère de l'Enseignement Supérieur et de la Recherche , the  Centre National de la Recherche Scientifique (CNRS)  and  Nantes Université  for their support. The authors greatly acknowledge  J. Hémez ,  Dr. L. Arzel  and  I. Louvet  ( AMaCC platform ,  CEISAM UMR CNRS 6230, Nantes Université ) for their chromatography and mass spectrometry analytical contributions to this work. This work includes NMR experiments carried out on the CEISAM NMR platform. The authors acknowledge  Dr. Virginie Silvestre  for technical assistance in NMR experiments and structural assignments.
g. pure cubic vs pure diamond. But now we can combine pairs and sets of pairs of Stokes vectors in such a way that any non-singular P matrix can be created. This dramatically increases the number of possible measurement schemes that can be compared together. To further illustrate the advantages of the vector method over the matrix method, we analysed the input SNR, output SNR and condition number produced by both the vector and matrix calculation methods on our own data where the outcome of this can be seen in Table  1  and Fig. 4. We hasten to add that both the matrix and vector methods use data drawn from the same complete dataset, the variation between them lies in different subsets of the complete dataset being used. It should be highlighted that due to the extremely large number of possible unique subsets that can be used in the vector methodology, we have limited the investigation of these to a randomly chosen selection of 10,000 per value of N, which denotes the size of the subsets to be drawn from the complete dataset of 36 measurements.
Conclusion This paper compares the efficacy of increasing the SNR of a time-varying, over-determined Mueller matrix by using the vector method of calculation versus the matrix method. The data used was experimentally derived from an investigation into the time-varying signal of an electro-optic BSO crystal undergoing cyclical impact from a helium plasma ionisation wave. To compare the two methods we calculated the SNR of the intensity measurements used for calculation and the SNR of the resulting Mueller matrices, which we denoted input SNR and output SNR respectively. Alongside this, we calculated the condition number of the matrices used to determine the Mueller matrices. The results of these three statistics clearly show that the vector method is consistently better than the matrix method.
Characterization techniques UV-Visible spectra were recorded on a Perkin Elmer Lambda 1050 spectrometer equipped with a three-detectors module to work in the 175 -3300 nm wavelength domain. The spectra were recorded using a quartz Suprasil™ demountable cell with an optical path length of 0. 2 mm. The kinetics of reduction of Ru(III) was followed by this technique for solutions containing (i) 16. 3 mM of Ru(acac)3 and (ii) 8. 15 mM of both Ru(acac)3 and Co(acac)2 in octan-1-ol. For this purpose, aliquots were taken every 10 °C during the heating ramp and at different times of the stage at 190°C. The oxidation state and the local environment of metal species in the precursor solutions of Ru, CoxRu100-x (x=20, 50 and 80) and Co has been followed in situ during the heating ramp from RT to boiling temperature by time-resolved X-ray Absorption Spectroscopy at SOLEIL Synchrotron facility on the Quick-EXAFS ROCK beamline using a specially designed PEEK cell (see Figure  S2 ).
The corresponding powders, obtained following the procedure described in section 2. 2, have also been analyzed. The spectra were normalized using the graphic interface normal_gui 38 written in Python and dedicated to spectra measured on ROCK for a massive and quick normalization allowing the reconstruction of a matrix of experience. Multivariate-Curve Resolution with Alternative-Least Squares (MCR-ALS) methodology 39 using the MCR-ALS gui 2. 0 developed by R. Tauler et al. on the Matlab® platform 40 was used for isolating from the experience matrix the concentration profiles of the species participating to the reaction and their associated XAS spectra. The use of MCR-ALS applied for XAS analysis is extensively described in the literature. [41] [42] [43] [44]  The analysis of the spectra was performed using Demeter (Athena and Artemis programs).
45  For measurements of NPs produced ex situ, pellets were prepared by carefully mixing the asprepared powders with boron nitride (weight ratio of NPs to BN of ca. 1:2 and 1:5 for Ru and Co80Ru20, respectively). Before recording the XAS data, a scan of the sample in x and y orthogonal directions was carried out at a fixed monochromator energy in order to check the pellet homogeneity. The SAXS data were acquired on a homemade laboratory instrument with a Mo X-ray generator. 46  The samples were recorded in a cell with Kapton windows in the q range from 0. 01 to 0. 2 Å -1. Calibration of the q range was performed using dodecanol while absolute intensity was obtained using a Lupolen standard. Analysis of the data was performed using Sasview free software. 47  The evolution of H2 during particle synthesis was measured using a Bronkhorst flowmeter linked to a micro-computer.
The PCA method was used to determine the number of species formed during heating. A set of 3 species has to be considered to account for the observed experimental data (see Figure  S14 ). The spectra of species obtained by MCR-ALS are given in Figure  6a  and their EXAFS signals in Figure  S15. The evolution of each of these species during heating is plotted in Figure  6b. Note that the spectrum at the Co K-edge for the powder obtained for 1h30 at 190°C is also presented as A4 in Figure  6a. In this manner, a complete picture of the different species generated during the course of the reaction can be obtained. The spectrum of the first Co pure species in octan-1ol before heating (at RT), denoted A1, is nearly identical to that of the Co(acac)2 solid precursor. As for pure Ru(acac)3, this shows that there is no reduction of Co(II) at RT (vide supra) and no significant modification of the Co environment.
Acknowledgments This work was done as a part of the  ANR TANOPOL  project ( ANR-15-CE07-0011-01 ). It benefited from a 2018  JSPS  grant for  B. Azeredo. Ning Huang  thanks  CSC  for his PhD grant. SasView application, originally developed under  NSF  award  DMR-0520547  was used. SasView contains.
code developed with funding from the European Union's Horizon 2020 research and innovation program under the SINE2020 project, grant agreement No 654000. XAS measurements were supported by a public grant overseen by the French National Research Agency (ANR) as part of the "Investissements d'Avenir" program (reference: ANR-10-EQPX-45). The analysis of XAS results benefited from the use of Demeter software and MCR-ALS 2. 0 Matlab® toolbox available freely. We acknowledge SOLEIL for provision of synchrotron radiation facilities (ROCK beamline, Proposal number 20181004).
Funding: O. V. S. , S. E. M. , E. I. F. , I. M. N. , O. V. B. and A. A. D. were funded by  RFBR  grant  20-53-12036 , E. I. F. was supported by  RFBR   20-33-90292. C. H. and M. E. B. were supported by  DFG-RBS Russia Cooperation-Project-No 429529433. Institutional Review Board Statement: Not applicable. Informed Consent Statement: Not applicable.
alanbakeri, and W. pinnata were measured using XRF, which has the main benefit that identical samples could be meastred directly after VNIR measurement. The XRF analysis used a Thermo Fisher Scientific Niton XL3t 950 GOLDD+ analyser with the in-built 'Soils Mode' and 'Main filter' configurations for 30 s. The XRF spectra were extracted and processed in GeoPIXE software using a pipeline developed for plant leaves  (Purwadi et al. 2022).
Statistical correlations between spectral variations and Ni concentrations Spectral variations were defined as differences in the reflectance value of one band to the remaining 2150 bands. The differences were calculated for all 2151 bands, thus producing a 2151 × 2151 matrix per sample. The matrixes then were related to samples' Ni concentrations, and the results are shown in Figs. 4, 5, 6, 7 and 8. The one dataset for hydrated leaves, B. coddii, had correlation values as high as R 0. 9 in spectral variations centred around 1000 nm. An elongated pattern indicating correlation values ranging from R 0. 4 to 0. 8 was observed when the subtractors were between 1000 and 1300 nm, and the subtracted bands were > 1300 nm. The correlation maps between the spectral reflectance of B. coddii dehydrated leaves and Ni concentrations revealed different patterns.
One possible explanation is that spectral variations in the long wavelength region are mainly affected by strong water absorption bands, and significant overlapping absorption bands occur in this region  (Grabska et al. 2017). A random forest classification is a simple classification method built upon an ensemble of decision trees. In this study, 100 decision trees were trained to distinguish 'normal' plant leaves from hyperaccumulator plant leaves based on the spectral reflectance of the dehydrated leaves. During the training, each decision tree is asked a true or false question whether the spectrum belongs to a 'normal' or hyperaccumulator plant. During the validation processes, 100 decision trees are tested against validation datasets to answer the same question, and no spectrum was misclassified, thus producing 100% accuracy.
85 nm and spatial resolution < 0. 1 m  (Jaud et al. 2018)  This compares to aircraft hyperspectral data that typically have 10-20 nm spectral resolution between and 2 and 10 m spatial resolution  (Cocks et al. 1998). This short study is clearly preliminary in nature and its findings need substantial validation and investigation to elucidate the nature of the spectral features found in relation to Ni in (hyperaccumulator) leaves. If fully validated, VNIR reflectance spectroscopy could offer many benefits over other methods used to discover hyperaccumulator plants. This includes a reduction in the cost and time of collecting samples from the field by measuring existing herbarium specimens with a VNIR spectrometer for discovery of novel hyperaccumulators. An additional benefit is that reflectance spectroscopy does not require radiation safety permits as is required for the use of XRF instrumentation.