dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgments The authors acknowledge support for LEMTA and IJL by the ''  IMPACT  ULHyS,  Universite de Lorraine Hydrogene Science et Technologie'' project of the ''Lorraine Universite d'Excellence'' (Investissements d'avenir e ANR ). This work was supported partly by the french  PIA  project  « Lorraine Universite d'Excellence » , reference  ANR-15-IDEX-04-LUE. The authors would like to thank  L. Aranda  for his help for TGA experiment. We would like to thank the  imaging core facility called ''Microscopies, Microprobes and Metallography (3M)'' (Institut Jean Lamour, IJL, Nancy, France)  and  J. Ghanbaja  and  Christine Gendarme  for their valuable help. We thank  Stephanie Michel  for the elemental analysis of the prepared samples. We would like to thank the  platform ''Optics and laser'' (Institut Jean Lamour, IJL, Nancy, France).
e. 6 and 5 nm, respectively. The onset potentials (i. e. potentials corresponding to 5 % of the diffusion limiting current) were found equal to 0. 74 V and 0. 71 V (vs RHE) for calix-AgNPs and citrate-AgNPs respectively, while half-wave potentials were determined as 0. 50 V and 0. 47 V (vs RHE) respectively. Such values are in line with those reported for silver-based catalysts under similar conditions (0. 1 M KOH) (see Table  S1 , ESI). Data processing was performed on RRDE experiments to follow the yield of HO 2 -and the number of electrons n exchanged during the ORR process. The number of electrons exchanged can be quantified using the disk and ring currents according to: ( where I D is the modulus of the disk current, I R is the ring current corresponding to the oxidation of HO 2 -and N is the collection efficiency (N=0.
Spectroscopic characterization of the (A3A3')Y26C-4 biohybrid Circular dichroism (CD) spectra were recorded from 185 nm to 260 nm with a data pitch of 0. 2 nm, a scan speed of 50 nm min -1 , a response time of 0. 5 s and a bandwidth of 2 nm using quartz cells with a 1 mm path length, on a Jasco J810 dichrograph. Each spectrum was recorded five times and averaged. The CD signal was corrected with buffer subtraction resulting in the ellipticity (q) in mdeg. Data were acquired from a 2. 2 µM sample of biohybrid previously desalted on a Zeba spin desalting column (Thermo) equilibrated with 20 mM sodium phosphate buffer, pH 7. 5.
Flexibility to certain residues was given by allowing free rotation of side chains. MD simulations were prepared using xleap  [42] , using as the force field FF19SB for proteins, TIP3P for water and GAFF for non-standard residues. MCPB. py was used to parametrize cofactor 4 using the Seminario method [43] for force constants and parameters and RESP for charge and RESP method for charges  [44]. Optimization, frequency and RESP calculations were performed at the same level of theory specified before. The system was solvated using a cubic water box and Na + as counter ions were added to neutralize. MD simulations were performed using AMBER20 software  [32]. Three different energy minimizations were performed to relax the system followed by a heating step in which the system equilibrated from 0 K to 300 K.
Acknowledgements The authors wish to thank the following persons for stimulating discussions:  Olivier Bernard ,  Filipa Lopes ,  Emmanuel Beaudoin ,  Sylvain David ,  Sandra Bouneau ,  Eric Raspaud ,  Fatma Briki ,  Mohend Chaouche ,  Claire Goldmann ,  Denis Ullmo ,  Guillaume Blanc ,  Guillaume Roux ,  Cécile Appert-Rolland ,  Doru Constantin ,  Anne-Soisig Steunou , and  Jacques Treiner. They are also grateful to  Emmanuel Beaudoin  and  Eric Raspaud  for careful reading of the paper and useful suggestions. Finally, they wish to acknowledge financial support from  Centre National de la Recherche Scientifique and Paris-Saclay University.
Assessment of coffee stain degradation for self-cleaning activity Since coffee stains are the leading stains that occur in real life, the fabrics are stained with coffee. The coffee stains were photocatalytically degraded to evaluate the self-cleaning activity of cotton fabrics (coffee bag, 2 g/200 mL brewed at 80 • C distilled water for 2 min). Uncoated (control) and TiO 2 -coated white fabric samples were disintegrated into small pieces (5 cm × 5 cm). The samples were immersed in the hot coffee until the coffee was fully absorbed throughout the fabric. Afterward, the samples were rinsed with clean water and then exposed to light in the SUNTEST solar simulator. The color of coated and uncoated fabric samples was then measured using the color-measuring device (Data Color 600 Dual-Beam Spectrophotometer), and the color differences between uncoated and coated samples were calculated.
Acknowledgments The authors would like to thank the  Scientific and Technological Research Council of Turkey (TUBITAK)  for the research grant of  108M211. The authors also would like to thank the  EU and TUBITAK  for funding, in the frame of the collaborative international  Consortium ECOSAFEFARMING  ( TUBITAK 117Y194 ) financed under the  ERA-NET WaterWorks2015 Cofunded Call. This ERA-NET is an integral part of the 2016 Joint Activities developed by the  Water Challenges  for a  Changing World Joint Programme Initiative (Water JPI ).
A degradation indicator is proposed based on the fuel cell polarization model, which is extracted using a non-linear regression process regardless of the operation conditions. Following that, a multi-step window-sliding ESN prognostics method is applied to predict the future evolution of the degradation indicator which is identified online. The parameterization of the ESN is optimized by a genetic algorithm that ensures improved prediction performance. The proposed degradation identification and prognostics methods are verified with a long-term operation experimental dataset of PEM fuel cell. As the measurements are obtained non-intrusively and the proposed method directly uses the output voltage signal, the prognostics can thus be performed in real time. The main contributions of this paper can be summarized as follows: 1.
A real-time degradation indicator of PEM fuel cells is proposed that can be extracted in both static and dynamic/random operation conditions; 2. An enhanced multi-step ESN-based prognostics strategy is adapted for the prediction purpose; The rest of the paper is organized as follows: Section 2 describes the long-term fuel cell degradation experiment and the dataset used to validate the proposed method. Section 3 explains the degradation identification method and Section 4 presents the enhanced multi-step window-sliding ESN prognostics strategy. Finally, Section 5 concludes the paper.
Data description A long-term fuel cell degradation experiment was carried out in FCLAB Research Federation, 1  France, and supported by the PRODIG project, which received funding from region Aquitaine, France. The test bench consists of a hydrogen tank, a pressure reducer, purge valves and hydrogen inlet valves, DC electric loads, DC power modules, two fuel cell stack modules, a compact data acquisition system and a computer for control and data logging. The structure of the two-fuel-cell-stackmodule is shown in Fig. 1. One of the stack modules is used for the dynamic load test, which is supposed to be applied in electric bicycles and is, therefore, tested using a dynamic load profile acquired in real operating conditions. The fuel cell stack is designed with an open cathode and dead-end anode structure and a 24 Vdc air fan is integrated with the stack for air supply and temperature regulation.
ESN-based prognostics method A data-driven prognostics method based on neural network modelling is proposed in this section. The idea is to use the available dataset to build the system behaviour model and to project the current system state to the future. Data-driven prognostics methods have the model-free advantage that can be applied regardless of the physical characteristics of the system. In this section, a typical recurrent neural network (RNN), i. e. , the ESN, is adapted for the prognostics purpose.
is the leaking rate with a range of (0, 1]. The ℎ function is generally adopted as the activation function  (•) of the reservoir, and (•) of the output layer could be defined with a simple linear function such as (•) = 1. and   are initialized randomly and they are constant so that there is no need to train them. Only   is going to be trained by linear regression. When the training dataset is provided, denoted as 𝐗 𝑡 = [𝐱(1), … , 𝐱(𝑁 𝑡 )] and 𝐘 𝑡 = [𝐲(1), … , 𝐲(𝑁 𝑡 )], where   is the number of sequences in the input and the output, the corresponding reservoir states,   = [(1), … , (  )] can be calculated according to (  5 ) and (  6 ). The output weight matrix is calculated as: 𝐰 𝑜𝑢𝑡 = (𝛹 𝑇 𝑡 𝛹 𝑡 + 𝜆𝐈) -1 𝛹 𝑇 𝑡 𝐘 𝑡 ( 8 ) where  is   order unit matrix,  is the regulation parameter and 𝛹 = [1; 𝐗 𝑡 ; 𝐔 𝑡 ] = ⎡ ⎢ ⎢ ⎢ ⎣ 1 1 … 1 𝐱(1) 𝐱(2) … 𝐱(𝑁 𝑡 ) 𝐮(1) 𝐮(2) … 𝐮(𝑁 𝑡 ) ⎤ ⎥ ⎥ ⎥ ⎦ (9) The general working procedure is as following: 1.
Acknowledgements This paper is supported by the project  HAEOLUS , funded by the  Fuel Cells and Hydrogen 2 Joint Undertaking  under the European Union's  Horizon 2020 research and innovation program  under grant agreement No  779469. Any contents herein reflect solely the authors' view. The  FCH 2 JU  and the  European Commission  are not responsible for any use that may be made of the information herein contained. This work is also supported by the  EIPHI Graduate School  (contract  ANR-17-EURE-0002 ) and the project  PRODIG  ( 1494C0045 ) funded by  French Environment and Energy Management Agency.
Material and methods For a biophysical perspective on the French economy, the study by  (Magalhães et al. , 2019 ) is highly relevant. The authors applied economy-wide material flow accounting (ew-MFA) to investigate long term changes in the scale and composition of the French metabolism (European Commission. Statistical Office of the European Union, 2018). This study provided us with detailed data on the extraction and trade with all materials (biomass, fossil energy carriers, ores and metals, non-metallic minerals) from 1830 to 2015. Trade data for petroleum (products) was supplemented by more detailed information on origin and sales areas from the "Direction générale des Douanes". Statistics on refineries' production come from the "Comité Professionnel du Pétrole". These data were used to calculate domestic energy and material consumption from 1920 to 2010 and to quantify the bilateral trade with crude oil and petroleum products.
To quantify energy flows, the data from the material flow database were converted to Joules by applying gross calorific values sourced from  Schandl et al. (2002). To investigate sectoral changes data on agricultural machinery and fuel consumption from a publication on the agricultural transition in France from 1882 to 2013 were integrated  (Harchaoui and Chatzimpiros, 2019). Data on the production and stock of motor vehicles was sourced from  Mitchell (2003). To shed light on the role of the ERP, the OEEC and the French administration, archival research in the National Archives/College Park, MD was conducted, collecting information on refineries, counterpart investments, and their geostrategic relevance. Records from the Economic Cooperation Administration (ECA), the Mutual Security Agency (MSA), and the OEEC were analyzed.
The Technical Oil Committee (TOC) was of overriding importance. It negotiated ERP petro-aid with the ECA. By doing so, the first OEEC-wide official crude oil and petroleum product database was put together that allowed to debate present and envisioned future manifestations of an integrated Western European oil-based energy system  (Morgan, 2012). This paved the way for governance modes aiming at the entanglement of discrete sociotechnical systems. When raw materials became scarce during the Korean War in the early 1950s, the TOC and the Technical Committees for Machinery and Steel devised and coordinated a program which fostered the transition from coal to petroleum in the steel and machinery industry while increasing the output of steel products to facilitate refinery expansion  (Hutton, 1974: 235).
In 1956, the Suez crisis led to shortages of crude oil supplies to Western Europe. In response, the TOC interlinked several Technical Committees to elaborate on fuel diversification in terms of crude oil origin as well as the implementation of new burner technologies for underutilized petroleum-based products  (OEEC, 1958: 28). In both cases, the entanglement of diverse sociotechnical systems created co-benefits that translated into growing economic output and energy consumption  (Graf, 2014: 55). In 1961, the OECD deepened precautionary planning in the oil sector. In 1974, in the wake of the first oil crises, energy agendas were delegated to the newly founded International Energy Agency, a subsidiary of OECD, which built on the oil committees' expertise, personnel, and databases  (Ibid: 62; Schmelzer, 2015: 297).
The test light intensities were provided every 10 s. Finally, the effective PSII quantum yields (F v '/F m ') were obtained. Relative photosynthetic electron transport rates (ETRs) were calculated by multiplying the effective PSII-quantum yields by the incident actinic light intensities. These data were plotted against the incident actinic light intensities and fitted using the Jassby and Platt equation  (Jassby and Platt, 1976)  to estimate the maximum ETRs (ETRmax), the light saturation points of photosynthesis (E k ), and the initial slopes of the ETR vs. irradiance curves (α ETR ).
RT-qPCR reactions Primers were designed using the PearlPrimer  (Marshall, 2004). Sequence data corresponding to the specific targets were retrieved from the database (http://www. nannochloropsis. org/). Primers were designed to flank and overlap the intron-exon boundary to make them specific to the transcripts and avoid binding to genomic DNA. The qPCR reactions were performed by mixing 5 μL of FastStart Universal SYBR Green Master mix (Rox) (Roche Molecular Systems, Inc. , CA, USA) with 1 μL of primer mix (consisting of forward and the reverse primers) at a concentration of 300 nM and 4 μL of the cDNA. The conditions of thermocycling were: 95 • C for 600 s (preincubation), followed by 40 cycles of denaturation at 95 • C for 10 s, annealing/extension at 60 • C for 30 s (LightCycler 96, Roche Molecular Systems, Inc.
). A melting curve analysis was performed for each sample to check the specificity of the primers. Target gene data were normalized using the normalization factor calculated based on the expression of the 2 most stable reference genes (housekeeping genes) phosphatidic acid phosphatase (PAP1) and cyclophilin (CYP). Fig. S3  shows the relative gene expression of all the reference genes used in this study under the control (CL) and flashing light (FL) conditions. All calculations were performed using geNorm  (Vandesompele et al. , 2002). The list of primers and the accession numbers are shown in the Supplemental Table  S2. The fold change was calculated dividing the normalized relative expression of the sample (FL) between the normalized relative expression of the control (CL). Therefore, the fold change value of the control (CL) is always 1 for each gene.
05 was applied to each set of normalized values in order to determine statistical differences in abundance levels. RT-PCR data is available in GEO NCBI GSE210188 (https://www. ncbi. nlm. nih. gov/geo/query/acc. cgi?acc=GSE210188). Photosynthetic physiology data, calculations and figure generation scripts are provided and linked to R markdown files deposited in GitHub project: spe238/nanno_gene_expr (https://github. com/spe238/nanno_ gene_expr).
3-hydroxyacyl-ACP, dehydrated by HAD to 3-trans-enoyl-ACP, and again reduced by ENR to acyl-ACP to finally yield a 6-carbon-ACP molecule (Fig. 4 ; [37]). Among these genes, only HAD showed increased differential mRNA abundance level in FL5 as compared to CL (2-times higher, p < 0. 0001, Fig. 3b ) and to the other treatments (p < 0. 05). Despite differential abundance of this gene and the low lipid content observed under FL5, transcript abundances of the other genes involved in FAS remained constant regardless of the FL regime. The expression levels of genes involved in fatty acid trafficking and desaturation are shown in Fig. 3c. Two genes of the long-chain acyl-CoA synthetase protein were found in the N. gaditana genome database (LCS1 and LCS2). Of them, only LCS2 had higher differential mRNA abundance level in FL5 compared to CL (Fig.
Proteomic Data Analysis Label-free and iTRAQ R analyses were performed to identify and quantify the differential expression levels of intracellular proteins. Label-free approach analysis was performed to identify the secretomes. For intracellular proteins, datasets were normalized, counted prior to identification using Mascot 1 and Progenesis software as compared to the P. tricornutum Uniprot database 2. For the quantification and the identification of the differentially regulated intracellular proteins of each morphotype, Progenesis liquid chromatography-mass spectrometry (LC-MS) software (Nonlinear Dynamics, version 4. 1 3  ) was used for labelfree peptide approach as previously described  (Fréret et al. , 2013). Automatic alignment was set to perform two by two comparisons between samples in order to align the LC-MS runs to account for retention time drifts.
A positive match was considered when it was ranked among the first positions and presented a score with a significant threshold of p < 0. 05 and with a false discovery rate (FRD) below 1. Mascot search results were imported back into Progenesis for differential expression and only proteins with an ANOVA p-value ≤ 0. 05 and identified by ≥2 peptides were retained. The quality of the data was checked by principal component analysis (PCA) (Supplementary Figure  1 ). For protein identification in SP and iTRAQ R labeling IP samples, peak lists were extracted (merge MS n scans with the same precursor at ±30 s retention time window and ±50 ppm mass tolerance) and compared with specific databases by using the PEAKS studio 7. 5 proteomics workbench  (Bioinformatics Solutions Inc. , Waterloo, Canada, build 20150615).
The searches were performed with the following specific parameters: enzyme specificity, trypsin; three missed cleavages permitted; fixed modification, carbamidomethylation (C); variable modifications, oxidation (M), pyro-glu from E and Q; monoisotopic; mass tolerance for precursor ions, 5 ppm; mass tolerance for fragment ions, 0. 02 Da; MS scan mode FT-ICR/Orbitrap; MS/MS scan mode, Linear ion Trap; Fragmentation mode, high energy CID; databases, P. tricornutum databases (UniProt Phaeodactylum + AND + tricornutum + AND + %22%28strain + CCAP + 1055%2F1%29%22 and Ensembl release 41 ASM15095v2. pep. 03092018 [see test footnote 2]). Database search results were used for quantitative analysis with PEAKS Q and iTRAQ-4plex as selected methods. Only significant hits with a false discovery rate (FDR ≤ 1) for peptide and protein cut off (-logP ≥ 20 and unique peptides ≥ 2) and fold change > 1.
Functional Annotation The steps implemented to perform functional annotation are summarized in Figure  1. They lead to a functional Gene Ontology (GO) analysis: GO annotation and GO enrichment were performed using Blast2GO software version 3. 3. 536 4 ). Protein sequences in FASTA were obtained with dataset P. tricornutum ASM15095v2 (Ensembl protist genes 47 5  ). Homology searches have been launched against NCBI nr Database (QBlast). Then, default parameters were used to map, annotate, and run InterPro scan 6. Pie charts were done using the Multi-Level option in Blast2GO considering the biological process  (Ovide et al. , 2018). Intersection analysis was performed using the Venny version 2. 1  (Oliveros, 2007). Pairwise comparison of the morphotype's intracellular proteomes was handled by considering that the fusiform morphotype was the reference as it is described to represent the most common morphotype  (De Martino et al.
Prediction of Signal Peptide and N-Glycosylation Sites on Secreted Proteins The prediction of a potential signal peptide on the secreted proteins has been analyzed by the SignalP version 5 8   (Almagro Armenteros et al. , 2019). The probability was considered correct when the score was greater than 0. 5. The online tool NetNGlyc 9  has been used to predict potential N-glycosylation sites of the secreted proteins. This dataset was then compared to the ones reported in the studies of  Rastogi et al. (2018)  and  Dorrell et al. (2021).
These results suggest that there is not much difference in the intracellular protein profile of TF. Identification of these differential proteins was performed using Blast2GO. This software allows the characterization and classification of proteins into biological processes, molecular and cellular functions according to GO annotation. At this stage, nonsignificantly differentially produced proteins (p-value > 0. 05) identified from the proteomic label-free analysis were removed (11 proteins). Thus, the Blast2GO analysis was run on 680 proteins resulting from the OF pairwise comparison and 48 proteins for the TF pairwise comparison (p-value ≤ 0. 05). From this analysis, about 84% of the intracellular proteins from the OF and 94% of intracellular proteins from the TF pairwise comparison have been annotated with GO terms thus corresponding to a total of 569 and 45 proteins respectively.
Ten proteins from this subset do not display either description or biological function (Table  2 ). Similarly, among the 38 down-regulated proteins, 23 of them exhibited a biological function in relation to cellular adhesion, transport, and catalytic activity (Table  3 ), whereas the functions of 15 proteins were not elucidated yet as they could not be related to any known biological function. When comparing the pie chart representing the TF biological process pairwise comparison (Figure  4 ), we have shown that Only proteins with a log-fold changed lower than 2 are presented. NA, no biological process was associated with the Blast2GO software. the oxidation-reduction biological process represents 27%, the glycolytic process 13%, the proteolysis 11%, the protein folding 10%, thus covering above 61% of the differentially produced proteins.
Differences in Extracellular Secreted Protein Productions Exist Between the Three Pt3 Phaeodactylum tricornutum Morphotypes Proteins that are secreted in the culture media by the diatom cells constitute the secretome. Such proteins may play important roles in cell migration, cell signaling, defense, and communication. These proteins can also be degraded into amino acids and serve as a source of nitrogen and/or carbon. In order to further characterize the P. tricornutum morphotypes, we decided to identify the secretome of the previous enriched cultures. Overall, 949 secreted proteins were identified in the culture media of the three morphotypes with the label-free analysis. As previously described, Blast2GO software was used to attribute GO annotation and determine the biological functions in which these proteins are involved.
Analysis of the Putative Evolutive Origin of the Secreted Proteins In order to determine the origin of the secreted proteins that are secreted by the different morphotypes of P. tricornutum Pt3 strain, we compared the dataset from this study to the one reported in  Dorrell et al. , 2021  (Supplementary Data 5, excel sheets 2-5). The comparison allows us to determine that among the 274 secreted proteins that were identified in the F morphotype, only 22 were also present in the  Dorrell et al. (2021)  dataset. Such subset is enriched mainly in proteins originating from bacteria (8) representing 36. 4%, alveolates (6) representing 27. 2%, and dinoflagellates (4) accounting for 18. 2% (Supplementary Data 5, excel sheets 2, 5). A similar trend was observed for 23 out of 230 proteins identified in the T morphotype.