dataesr/scientific-paragraphs-categorization huggingface dataset:
Comparative Analysis of the Proteome Versus Transcriptome In order to evaluate the relationship between previous transcriptomic data reported on the Pt3 morphotypes and the current proteomic data, we analyzed and compared the proteome of the O cells to the transcriptomes reporting in  Ovide et al. (2018)  that compared O vs. F (OF) and O vs. T (OT). Among the 648 intracellular proteins that were specifically identified in the O proteomic data, 35. 65% were also differentially expressed in the transcriptome data comparing OT and OF. A similar comparison was made for the 163 secreted proteins that have been identified in the secretome of the O cells and above 32. 7% were also differentially expressed in the transcriptome dataset (Supplementary Data 6).
, 2007; Stanley and Callow, 2007; Willis et al. , 2013). Therefore, the difference in lifestyle exposed the morphotypes to light variation with the fusiform cells benefiting from a higher exposure. Moreover, it is to note that most of these proteins are involved in the carotenoid biosynthesis pathway (Pds, Psy, Zep, Zds)  (Bertrand, 2010; Scarsini et al. , 2020)  and in photosynthesis (Gsat;  Schoefs and Bertrand, 2005). When comparing previous transcriptomic data  (Ovide et al. , 2018)  and the proteomic datasets described here, some discrepancies and only 1/3 of positive correlation were observed. Such differences could be related to a fine-tuning gene expression that can be due to allele-specific expression (ASE). Such phenomena have been recently described in P. tricornutum  (Hoguin et al.
ACKNOWLEDGMENTS The authors are thankful to  Pr. Patrice Lerouge ,  University of Rouen Normandie  for critical reading of the manuscript and to  Chris Bowler ,  Institut de Biologie de l'Ecole Normale Supérieure (IBENS) ,  CNRS UMR8197 ,  Inserm   U1024  for sharing its P. tricornutum Pt3 strain in 2010.
Acknowledgements The authors acknowledge the many organizations that directly or indirectly supported the completion of this article. We acknowledge the  European Commission  for the ARV (grant number  101036723 ), Syn. ikia (grant number  869918 ),  Hestia  (grant number  957823 ) projects; the  Danish Energy Agency  for supporting the Danish delegates participating IEA EBC Annex 82 through  EUDP  (grant number  64020-2131 );  Innovation Fund Denmark  in relation to SEM4Cities ( IFD 0143-0004 ) and  Flexible Energy Denmark  ( IFD 8090-00069B ); the  Building Technologies Office, Office of Energy Efficiency and Renewable Energy , at the  US Department of Energy , under  Lawrence Berkeley National Laboratory  (contract number  DE-AC02-05CH11231 ); the  Center of Technology and Systems (CTS UNINOVA)  and the  Portuguese Foundation for Science and Technology (FCT)  through the  Strategic Program   UIDB/00066/ 2020 ;  Research Council of Norway in relation to Research Centre on Zero Emission Neighborhoods in Smart Cities -FME-ZEN  (No.
Proton Nuclear Magnetic Resonance Spectroscopy ( 1 H NMR) To prepare samples for 1H NMR analyses, Na alginates were dissolved in D 2 O and dried several times prior to NMR spectrum acquisition. The 1H spectra were achieved at 9. 4T (Proton Larmor frequency of 400. 33 MHz) on the spectrometer AV II 400 MHz (Bruker Corporation, Billerica, MA, USA) using a 5 mm Triple Resonance Broadband Inverse probe, and with temperature regulated at 343 K. Each spectrum consisted of 16 K size of Free Induction Decay recorded with a sweep width of 4800 Hz. Presaturation was applied during the relaxation delay and mixing time. The raw data were apodized by 0. 5 Hz of exponential line broadening prior to Fourier transformation. A total of 32 scans were acquired.
This research was funded by the project  VPMA3 /DESRS-ANPMA-CNRST 'Exploitation de la diversité spécifique et génétique pour une bioraffinerie innovante des algues marines de la côte atlantique marocaine ' and also supported by the  FCT Portugal-CNRST   Morocco bilateral cooperation  project 'Variation of marine-forests traits in range-edge vs. core NE Atlantic upwelling refugia in a context of climatic change'. Not applicable.
In addition, neutron diffraction data contain information about the magnetic structure of the sample. Notably, a more accurate and robust description of the atomic structure can be obtained by conducting a joint structural modelling of multiple diffraction patterns from different radiation sources. The present study is based on a compilation of data from three of our earlier studies on CoFe 2 O 4 nanoparticles  (Granados-Miralles et al. , 2018; Ahlburg et al. , 2020; Stingaciu et al. , 2017) , as well as previously unpublished data. The X-ray and neutron diffraction patterns stem from several different CoFe 2 O 4 samples and have been collected using both Co and Cu in-house X-ray diffractometers, as well as various NPD instruments. Here, the data have been re-analysed, yielding a detailed study of the CoFe 2 O 4 nanoparticle structures and the effect of different modelling parameters on the structural analysis.
The study is divided into the following four parts: Part 1, reliable extraction of Fe/Co occupancies in CoFe 2 O 4. This work is based on a study by  Granados-Miralles et al. (2018). Two major points are investigated in this refinement study. (a) Pattern weighting influence: investigation of the effect of using an equal weighting (Ew) for each pattern in the joint refinement compared with a weighting based on information available, i. e. the number of peaks available for each individual pattern (Iw), and with an arbitrary weighting scheme (Aw). (b) Combining different patterns: comparison of the influence of carrying out the joint structural modelling of different combinations of available data from three diffraction sources, i. e. Cu K 1,2 and Co K 1,2 PXRD data and NPD data from the DMC instrument at SINQ (Switzerland).
Both the crystal and magnetic structures are analysed and compared, with emphasis on determining which combination gives the most reliable and accurate description. Part 2, reproducibility of synthesis and refinements. This part investigates the reproducibility of the synthesis using data from samples prepared under identical conditions from a study by  Ahlburg et al. (2020). Diffraction data have been measured multiple times on each individual sample as well as equivalently prepared samples using identical conditions at Comparison between the resonant scattering terms of 8 O, 26 Fe and 27 Co for Cu K 1,2 and Co K 1,2 radiation sources, as well as their neutron scattering lengths, b j. The Fe/Co contrast at Q = 0 was calculated for resonant scattering terms and for the neutron scattering length, ignoring the imaginary term.
Structural characterization Several different X-ray and neutron powder diffraction instruments were used for the structural characterization. An overview of the employed instruments is given in Table  3  and they are described below. Room-temperature PXRD patterns were collected on two in-house Rigaku SmartLab powder X-ray diffractometers (Rigaku, Japan), one equipped with a Cu source (Cu K 1,2 ; 1 = 1. 54059 A ˚; 2 = 1. 54441 A ˚) and the other equipped with a Co source (Co K 1,2 ; 1 = 1. 78892 A ˚; 2 = 1. 79278 A ˚), both in Bragg-Brentano geometry. The powder diffraction patterns were collected using a Dtex/Ultra detector in fluorescence suppression mode and a diffracted beam monochromator was placed in front of the detector on the Cu-source instrument. The data collection is summarized in Table  3.
The NPD patterns were measured at room temperature at two different neutron sources: at the Swiss spallation neutron source (SINQ)  (Blau et al. , 2009; Allenspach, 2000) , Paul Scherrer Institute (PSI), in Switzerland, and at the Institute for Energy Technology (IFE), Kjeller, Norway, using different instrumentation. At SINQ two diffractometers were used: DMC, the cold neutron powder diffractometer (https:// www. psi. ch/en/sinq/dmc), and HRPT, the high-resolution powder diffractometer for thermal neutrons (https:// www. psi. ch/en/sinq/hrpt) (Fischer et al. , 2000). At IFE the PUS diffractometer was used  (Hauback et al. , 2000). The instrumental contributions to the peak broadening of the collected patterns were determined from data collected on standard reference materials at equivalent instrumental configurations.
Vibrating sample magnetometry The magnetic properties of the samples were characterized using a Physical Property Measurement System (PPMS), from Quantum Design, equipped with a vibrating sample magnetometer (VSM). The measurements were performed on coldpressed cylindrical pellets with a diameter of 3 mm, gently compacted using a hand-held press. The field-dependent magnetization curves (expressed in A m 2 kg À1 ) of the pellets were measured by scanning the externally applied field, H app , between AE3 T at 27 C. The saturation magnetization M VSM sat was obtained by applying the law of approach to saturation to the data  (Zhang et al. , 2010).
Structural refinement The structural analyses were carried out using the FullProf Suite software  (Rodrı ´guez-Carvajal, 1993). The crystalline CoFe 2 O 4 phase was in all cases described in the space group Fd3m with the Laue class m3m. As described by  Andersen et al. (2019) , the magnetic structure was implemented as an Table  3  Wavelength (), angular coverage (2), step resolution of the detector (Á2), Q coverage and Q step size (ÁQ) of the two X-ray instruments and the three neutron powder diffractometers. The number in parentheses refers to the relevant part of the study. Both DMC and HRPT used a radial collimator to reduce the background signal from the surroundings. additional magnetic phase with the lowest-symmetry space group of the corresponding centring, i. e. F1. The special positions of Fe 3+ and Co 2+ cations were specified, and the first 24 symmetry operations of the Fd3m space group were provided to generate all atomic magnetic moments.
Source (A ˚) Detector Monochromator 2 range ( ) Á2 ( ) Q coverage (A ˚À1 ) ÁQ (A ˚À1 ) Cu K 1, The peak profile parameters were described using the Thompson-Cox-Hastings (TCH) pseudo-Voigt function  (Thompson et al. , 1987) , while the crystallites were assumed to be strain free. The crystallite size was extracted from the Lorentzian isotropic size parameter, Y, which was constrained between data sets through appropriate consideration of the wavelength. This constraining process is explained in detail in the supporting information. The scale factors for X-ray data sets were refined individually, in contrast to the scale factors for nuclear and magnetic phase for the neutron data, which were kept identical as they belong to the same data set. The backgrounds were described by Chebyshev polynomials, with a maximum of six refinable coefficients (Bck_0, 1, 2, 3, 4 and 5).
The wavelength for the neutron data was refined, allowing a single common unit-cell parameter to be refined for all the diffraction patterns, along with the zero point. The fractional coordinates of oxygen (x, x, x) were also refined. The site occupation fraction (Occ) was refined with a constraint, as were the atomic displacement parameters (ADPs) and the atomic magnetic dipolar moment (R x ). The refinement of these three parameters is described below. For low-Q-coverage neutron data (Q max < 4 A ˚, i. e. DMC), the ADPs were refined as one common isotropic displacement parameter (B ov ) for all atoms. We set the Td and Oh sites to be fully occupied while refining the relative Co and Fe occupancies with the total Co and Fe content constrained to the nominal Co:Fe ratio of 1:2. This means that CoFe 2 O 4 was refined as (Co 2+ 1Àx Fe 3+ x ) Td [Co 2+ x Fe 3+ 2Àx ] Oh O 4 , with x being the inversion degree, where x = 0 is normal spinel and x = 1 is fully inverse.
For the uncertainties, the standard deviation provided by the FullProf Suite software was used except for the crystallite size. Here, the uncertainty was chosen to be equal to the unitcell length, i. e. 0. 8 nm, instead of the very low (0. 001-0. 01 nm) mathematical uncertainties provided by FullProf. Given that the unit cell constitutes the smallest crystal unit, we consider using the cell parameter as the uncertainty for the average crystallite size to be more appropriate from a physical perspective. The uncertainty of the calculated net intrinsic magnetization (M neutron ) is based on the standard deviation of each element constituting the calculation. (a) Pattern weighting influence. When jointly refining multiple diffraction patterns, the weighting between data sets must be carefully considered as this may significantly influence the outcome of the refinement.
As noted by both  Deutsch et al. (2012)  and  Coppens et al. (1981) , the weighting scheme constitutes one of the main issues in joint refinement strategies. Yet, this remains a topic of much debate, with the literature providing no definitive answer, and thus the weighting schemes are generally somewhat subjectively chosen. Two weighting schemes seem to be prevalent: (i) a weighting that minimizes the sum of the goodness of fit (R factors and 2 ) of each pattern  (Deutsch et al. , 2012; Coppens et al. , 1981; Duckworth et al. , 1969; Kibalin et al. , 2017)  and (ii) a weighting scheme that minimizes the sum of the goodness of fit normalized per data number for each pattern, by using log functions  (Deutsch et al. , 2012; Kibalin et al. , 2017; Gillet & Becker, 2004). The scheme adopted by the FullProf Suite software appears to correspond to (i), by considering the residual function defined as 2 ¼ P n i¼1 w i ½y i À y c;i ðÞ 2 , where ½y i À y c;i ðÞ 2 represents the difference between the experimental and the calculated patterns, while the statistical weight w i is defined as the inverse of the squared variance of the observed pattern, i.
Results and discussion Here, we have considered three weighting schemes and made a simple comparative study of the influence of the pattern weighting on the refinement of atomic and microstructural parameters of cobalt ferrite. In conclusion, we found that the three tested weighting models gave very similar results and/or are within the uncertainty of each other, indicating that the weighting scheme does not hugely affect the refinements of the present data. Therefore, in the following, we have used the standard FullProf weighting model using equivalent weight of all patterns. The study of the three weighting schemes can be found in the supporting information. (b) Combining different patterns. Joint refinements of different combinations of the PXRD (Co and/or Cu) and NPD data are evaluated, with special emphasis on investigating the reliability/consistency of the Co/Fe occupation fractions obtained from the refinements.
Refinements of seven different combinations of the three patterns were tested using equal weighting: (i) DMC/Co/Cu, (ii) DMC/Co, (iii) DMC/Cu, (iv) Co/Cu, (v) DMC, (vi) Co and (vii) Cu. Table  4  gives an overview of the extracted refinement parameters. Each individual pattern is described in the supporting information. The refined powder diffraction patterns from combination (i) (DMC/Co/Cu) can be seen in Fig. 2 , while the six remaining combinations of patterns are reported in Fig. S2  (see the supporting information). The in-depth investigation of the different combinations reveals the models that best describe the crystal and magnetic structure, as well as the Co/Fe occupation fraction. The different models are discussed in the following. Using only the data set (vii) (Cu) is not a good choice for refining the Co/Fe site occupation fractions as unphysical values are obtained.
This is not surprising because the Cu data have almost no scattering contrast between Co and Fe. The neutron data with limited Q range alone  [model (v) ] are also not a good choice, as the refinement yields an unrealistic description of the ADPs due to the limited number of Bragg peaks  (Andersen, Bøjesen et al. , 2018). It is perhaps more surprising that the data set (vi) (Co) actually performs very well compared with the combined X-ray and neutron models. If information on Fe/Co occupation is sought, using data set (vi) (Co) alone saves time with regard to data collection. The refinement of data set (vi) (Co) is close to identical to combinations (i) (DMC/Cu/Co) and (ii) (DMC/Co). This contradicts the common notion that in-house PXRD data alone cannot be used to extract reasonable occupation fractions for neighbouring elements.
The diffraction data were previously published by  Granados-Miralles et al. (2018) , but all refinements were redone for this work. The refinements of data set combinations (iv) (Co/Cu) and (vi) (Co) yield very similar structural descriptions, indicating that, in this case, the inclusion of the Cu pattern does not significantly degrade the accuracy of the results. (i) (ii) (iii) (iv) (v) (vi) (vii In conclusion, four of the examined data combinations can be used to obtain a reliable refinement of Fe/Co occupancies in CoFe 2 O 4 : (i) (DMC/Co/Cu), (ii) (DMC/Co), (iii) (DMC/ Cu) and (vi) (Co). A neutron diffraction pattern with a larger Q range would also be able to produce reliable refinements of Fe/Co occupancies and the magnetic moment. Despite the limited Q range of the DMC instrument, it was shown that only six peaks in NPD data are sufficient to extract reliable magnetic moments.
Combining NPD with PXRD data gives a more robust refinement of the occupation factors as it removes correlations between ADPs and magnetic moments inherent to a single data set. Moreover, the refined formula unit magnetic moment m f. u. value is close to that of the bulk CoFe 2 O 4 , and good agreement was seen between the calculated net intrinsic magnetization and the saturation magnetization obtained by VSM measurement. Even if combinations (ii) (DMC/Co) and (iii) (DMC/Cu) are comparable, we recommend using the model involving the Co source (ii) as it also carries information about the Fe/Co occupancies. Combination (i) (DMC/Co/Cu) constituted our benchmark as it has the largest quantity of data; however, the joint refinement of combination (ii) (DMC/Co) gives close to identical values to combination (i) (DMC/Co/Cu), and therefore combination (ii) is favoured as it involves collecting and treating fewer data to obtain the same result.
Part 2, reproducibility study This second part of the study investigates the reproducibility of the autoclave synthesis method on the basis of data from three CoFe 2 O 4 nanoparticle samples (A, B and C), reported by Ahlburg et al. (2020), synthesized under identical conditions. The reproducibility of the PXRD and NPD measurements, as well as the Rietveld refinements, was investigated. The NPD data were measured three times for the samples A and C, while sample B was measured twice at the DMC instrument. All these multiple measurements were acquired under identical conditions. Table  5  shows the refined structural values obtained for samples A, B, and C, while their diffraction patterns can be found in the supporting information (Figs. S3-S5 ). The unit cell, apparent crystallite size (ACS) and oxygen position are all identical within the uncertainties of each repetition and between all samples.
Only R x is affected by Table  5  List of refined parameters for samples A, B and C. The magnetic moment dipole was refined anti-parallel on the Td and Oh sites. Net intrinsic magnetization (M neutron ) was calculated on the basis of the R x values obtained from the refinement. The multiple measurements are referred as A1, A2, A3, B1, B2, and C1, C2, C3. The 'Average' column is based on the multiple refined parameters obtained for samples A, B and C. The uncertainties of the average column are based on the standard deviation. The neutron diffraction data are part of an in situ study published by  Ahlburg et al. (2020) , but all refinements were redone for this work. All measurements made using model (ii) (DMC/Co). 2 ) 81 (  2 ) 82 (  2 ) 79 (  2 ) 80 (  2 ) 81 (  2 ) 81 (  2 ) 81 (  2 ) 81 (  1 ) Occ(Co 2+ ) Oh (%) 41 (  1 ) 41 (  1 ) 41 (  1 ) 40 (  1 ) 40 (  1 ) 40 (  1 ) 40 (  1 ) 40 (  1 ) 40 (  1 ) Occ(Fe 3+ ) Oh (%) 59 (  1 ) 59 (  1 ) 59 (  1 ) 60 (  1 ) 60 (  1 ) 60 (  1 ) 60 (  1 ) 60 (  1.
There is no apparent reason for the higher M neutron value in sample C. The other samples have M neutron and M VSM corresponding very well. Average. To determine the reproducibility of the autoclave synthesis, an 'Average' column was added in Table  4. The 'Average' compares the statistical average of the refined values of all samples. As a statistical average is employed, the uncertainty of each parameter was based on the standard deviation method. Generally, the statistical average corroborates the individual parameters of each sample. In summary, the comparison of the refinements of multiple data sets from the same sample shows hardly any variations, which clearly indicates that both the data collection of the DMC instrument and the Rietveld refinements yield strongly reproducible results.
3 (a), and it is identified as hematite, -Fe 2 O 3 (space group R3c, No. 167). The formation of -Fe 2 O 3 cannot be avoided when using a precursor with pH below 12  (Cote et al. , 2003; Zhao et al. , 2007). However, regarding the quantity of OH À ions introduced by the sodium hydroxide solution, the pH is estimated as being equal to 15. 2. Therefore the presence of hematite is unexpected, and the hematite content within sample FR220 is estimated to be <1 wt%. The Cu source was used because the Co source had not yet been installed in the laboratory. The sloping background can be explained by the fluorescence signal decaying at a high angle (Q > 5 A ˚À1 ) and is clearly visible in all of the PXRD patterns in Fig. 3. From the results in part 1(b) and the refinements of model (iii) (DMC/Cu), it was expected that replacing DMC data with data from PUS, which has twice the Q range (Table  2 ), would yield a robust description.
Additionally, for FR220 the model may not correctly describe the system, because the interstitial sites are forced to be fully occupied and vacancies could occur on the octahedral site. The temperature used during the synthesis is included in the name of the sample. The refinement model employed a combination of PXRD data (Cu K) and NPD data from PUS. Due to the high Q range of the NPD data, the Td and Oh site occupancies could be refined independently. The distribution of both Fe 3+ and Co 2+ within Td and Oh sites is detailed as x and y, respectively. m f. u. and M neutron were calculated on the basis of the refined site occupancy and R x. The X-ray and magnetic data were previously published by  Stingaciu et al. (2017) , but the neutron data and all refinements have not been previously published.
Conclusion The present study consists of four distinct parts, each dedicated to examining the robustness, reproducibility and reliability of structural parameters obtained from Rietveld analysis of powder diffraction data (X-ray and neutron). Nanocrys-talline cobalt ferrite, CoFe 2 O 4 , was used as a sample prepared using different synthesis conditions and collected using different instrumentation and radiation sources. The study devotes special attention to the reliability of the site occupancies of Co 2+ and Fe 3+ in CoFe 2 O 4 , as the atomic structure is the key parameter for examining the structure-property relationship in spinel ferrites. In part 1(b) it was demonstrated that combining X-ray powder diffraction from Cu and Co sources with low-Q-range neutron powder diffraction data gives reliable Fe/Co occupancies and magnetic structure for CoFe 2 O 4.