dataesr/scientific-paragraphs-categorization huggingface dataset:
Protein modelling For cupredoxins, being well known, several structures have been solved which serve as templates for modelling the globular soluble domain of AcoP. Here we used the Phyre2, Swiss-model and I-TASSER servers 47 obtaining similar results. We note that, given the high homology with the templates, this model is expected to be of reasonable quality along most of the sequence. 48, 49 For Scheme 1, AcoP's TM helix was built manually by threading its sequence as an ideal helix. The model of Cyc2 in Scheme 1 is based on I-TASSER homology modelling guided by coevolution-based restraints as described in ref. 50. For Cyt c 4 of Acidithiobacillus acidophilus (pdb: 1H1O) and Cyt c 4 of Pseudomonas stutzeri, we used available X-ray structures (pdb: 1H1O and 1ETP, respectively). To study protein electrostatics, AcoP models and Cyt c 4 structures were prepared with the PDB2PQR-Propka servers, using the Amber force eld to assign electrostatic charges at the surface of the proteins and the Parse force elds to determine the dipole moments of proteins with PDB2PQR-Propka servers.
Scheme 1 Iron respiratory chain of Acidithiobacillus ferrooxidans. Proteins known to be involved in the iron respiratory chain of A. ferrooxidans are depicted using Pymol Software. The structures of Cyt c 4 (PDB: 1h1o) and Rus (PDB: 1RCY) are known. CcO of Paracoccus denitrificans is depicted (PDB: 3HB3) as an enzyme closely related to CcO of A. ferrooxidans. The structure of AcoP has been predicted using the Phyre 2 server and the transmembrane segment has been added. The structure of Cyc 2 was predicted. 50.
Acknowledgements This work was supported by  ANR  ( ENZYMOR-ANR-16-CE05-0024 ) and  Aix-Marseille University  through  X. Wang 's funding. We acknowledge the national  French EPR network (RENARD, IR3443 ) and the  Aix-Marseille EPR facility. The authors thank  P. Infossi ,  D. Byrne-Kodjabachian  and  Dr C. Gutierrez-Sanchez  ( BIP, IMM, Marseille ) for technical help in enzyme purication and characterization. Marion Taris  is acknowledged for her help in performing ATR-FTIR and PMIRRAS experiments. This work beneted from the facilities of the  Platform of Fermentation of IMM  and expertise from  M. Bauzan , to whom the authors are very grateful. The authors would also like to thank  Dr A. de Poulpiquet  and  Dr B. Gontero  ( BIP, Marseille ) for fruitful discussion.
Scheme 1 1 Scheme 1 Iron respiratory chain of Acidithiobacillus ferrooxidans. Proteins known to be involved in the iron respiratory chain of A. ferrooxidans are depicted using Pymol Software. The structures of Cyt c 4 (PDB: 1h1o) and Rus (PDB: 1RCY) are known. CcO of Paracoccus denitrificans is depicted (PDB: 3HB3) as an enzyme closely related to CcO of A. ferrooxidans. The structure of AcoP has been predicted using the Phyre 2 server and the transmembrane segment has been added. The structure of Cyc 2 was predicted. 50.
75 Numerical Aperture) Mitutoyo objective. Spectra acquired from different random positions on each specimen were averaged to have a reliable picture of the sample bulk. The average spectra were analyzed by using a commercially available software package  [22]  to assess the graphitization degree of samples. X-ray Photoelectron Spectroscopy (XPS) analyses were run on a PHI 5000 Versa Probe II Scanning XPS Microprobe spectrometer (ULVAC-PHI Inc. , Kanagawa, Japan). Measurements were done with a monochromatic Al Kα source (X-ray spot 100 µm) at a power of 24. 8 W. Wide scans and detailed spectra were acquired in Fixed Analyzer Transmission (FAT) mode with a pass energy of 117. 40 eV and 29. 35 eV, respectively. An electron gun was used for charge compensation (1. 0 V 20. 0 µA). Data processing was performed by using the MultiPak software v.
9. 5. 0. 8 (ULVAC-PHI Inc. , Kanagawa, Japan). X-ray Powder Diffraction (XRPD) patterns were collected at room temperature at the ID22 beamline of the ESRF with a wavelength λ = 0. 399946(4) Å up to 2θ = 40 • and a ~0. 5 h/pattern counting time. Data recorded continuously have been then merged using different step sizes spanning from ∆2θ = 0. 005 • to 0. 050 • to highlight different features in the patterns. Patterns merged with the former step size were analyzed via the Rietveld method using the General Structure Analysis System (GSAS) suite of the program  [23]. Scanning Electron Microscopy (SEM) observations were carried out using a Leo 1430 SEM (Zeiss, Oberkochen, Germany). Scanning Transmission Electron Microscopy (STEM) measurements were performed by using a Zeiss Supra 40 Field Emission Scanning Electron Microscope (FE-SEM) (Zeiss, Oberkochen, Germany) working in high vacuum conditions and equipped with the GEMINI column.
0 V 20. 0 μA). Data processing was performed by using the MultiPak software v. 9. 5. 0. 8 (ULVAC-PHI Inc. , Kanagawa, Japan). X-ray Powder Diffraction (XRPD) patterns were collected at room temperature at the ID22 beamline of the ESRF with a wavelength  = 0. 399946(4) Å up to 2θ = 40 and a ~0. 5 h/pattern counting time. Data recorded continuously have been then merged using different step sizes spanning from Δ2θ = 0. 005° to 0. 050° to highlight different features in the patterns. Patterns merged with the former step size were analyzed via the Rietveld method using the General Structure Analysis System (GSAS) suite of the program  [23]. Scanning Electron Microscopy (SEM) observations were carried out using a Leo 1430 SEM (Zeiss, Oberkochen, Germany). Scanning Transmission Electron Microscopy (STEM) measurements were performed by using a Zeiss Supra 40 Field Emission Scanning Electron Microscope (FE-SEM) (Zeiss, Oberkochen, Germany) working in high vacuum conditions and equipped with the GEMINI column.
Funding This work was supported by Grants from the  National Natural Science Foundation of China  ( 31100072 ,  41776175  and  31600286 ) and the  Agricultural Science and Technology Innovation Project of Chinese Academy of Agricultural Sciences  ( CAAS-ASTIP-2013-OCRI ). JJ, FR, and EM were supported by  Agence Nationale de la Recherche  ( ANR-10-LABEX-04   GRAL Labex, Grenoble Alliance for Integrated Structural Cell Biology ;  ANR-11-BTBR-0008  Océanomics; IDEX  UGA CDP Glyco@Alps ;  Institut Carnot   3BCAR ).
Biochemical properties of E. coli Fe-S cluster carriers acteristic UV-visible spectrum in agreement with published data (40) (Fig. 4A ). The degradation of the Fe-S cluster was monitored by the absorbance variation at 420 nm as a function of time when diluted into oxygenated buffer containing a controlled amount of O 2. Under these conditions, the half-life of the NfuA Fe-S cluster was 100 Ϯ 10 min (Fig. 4A ). Holo-ErpA exhibited a 2Fe-2S cluster-characteristic UV-visible spectrum (Fig. 4B ). Upon controlled O 2 exposure, half-life of its cluster was 54 Ϯ 4 min (Fig. 4B ). We also tested the stability of the Fe-S cluster of two other ATC, IscA and SufA, under the same experimental conditions and found half-lives of 45 Ϯ 3 and 55 Ϯ 7 min, respectively (Fig. 4C ). All together, these results showed that Fe-S clusters bound to diverse carriers exhibit different capacities to resist oxidative damage with the following decreasing stability order: NfuA Ͼ ErpA ϭ SufA Ͼ IscA.
Biochemical properties of E. coli Fe-S cluster carriers or with ErpA. The sensorgrams showed binding of IspG to both NfuA and ErpA (Fig. 6 ). Global evaluation using the 1:1 Langmuir binding model yielded K d values of 22. 5 Ϯ 0. 5 M for the IspG/ ErpA interaction and of 30 Ϯ 2 M for the IspG/NfuA interaction. For the experiments performed with IspH, serially diluted NfuA or ErpA was injected into IspH-coated sensor chips. Although sensorgrams showed binding of NfuA and ErpA to IspH, the maximum response, was unattainable, preventing determination of a K d value (data not shown). We also used a bacterial two-hybrid approach to detect interactions between NfuA, ErpA, and IspH. We showed that the BTH101 cells synthesizing T18-IspH and T25-NfuA hybrid proteins exhibited ␤-gal activity, indicating an IspH/NfuA interaction (Fig.
When grown in glucose, the Sdh activity of the LL401 strain was found to be drastically reduced (85%) (Fig. 8 ). In the nfuA mutant, the Sdh activity was decreased by 35% (Fig. 9 ). Collectively, all of these data indicate that maturation of the respiratory complexes I and II is with the assistance of both ErpA and NfuA under aerobic conditions and that maturation of AcnB requires ErpA under aerobic conditions and NfuA under oxidative stress conditions.
Multicopy suppression of the nfuA growth defect by erpA The results above showed that NfuA and ErpA contribute to the maturation of the same set of enzymes. Therefore, we tested whether NfuA and ErpA are functionally redundant in vivo. For this, we made use of a multicopy-based suppression approach. A pBAD derivative plasmid expressing erpA (pBAD-erpA) suppressed paraquat sensitivity of the nfuA mutant (Fig. 11 ). In contrast, increased nfuA gene dosage failed to suppress nonviability caused by erpA mutation under aerobiosis (Fig. 12 ). Last, pBAD-iscA and pBAD-sufA, plasmids expressing iscA and sufA, respectively, failed to suppress ⌬nfuA mutant sensitivity to paraquat (Fig. 11 ). Altogether, these data showed that ErpA overproduction overcomes the need of NfuA for IspG/H maturation but that the converse is not true.
Acknowledgements The authors thank to the  Mexican Council for Science and Technology CONACyT  for financial support through  Fondo Sectorial CONACYT-SENER-Sustentabilidad Energética (Grant-246079 ). J. A. Díaz-Real acknowledges to CONACYT for graduate studies scholarship No. 242857  and the financial support for the research internship at the  University of Poitiers. He also acknowledges to  Prof. Nicolás Alonso-Vante  for the big support and formality of tutoring into the field of photoelectro-.
The 35-mL testing tubes were sealed with rubber septa, continuously stirred and irradiated in a thermostated water bath. Amounts of liberated (1) carbon dioxide in gas phase, (2) hydrogen in gas phase, and (3) acetone in liquid phase (after powder separation) were determined by gas chromatography (GC-TCD (1-2) and GC-FID (3)), details and experimental set-ups shown elsewhere  [96, 101]. Numerical simulations of light field enhancement was carried out by finite-difference time-domain (FDTD) method using the Lumerical software package. To calculate the cross sections of extinction, which is combined absorption and scattering, a standard procedure using totalfield scattered-field light source was implemented. Calculations were carried out for the linearly polarized light using complex refractive index of titania (anatase) available in the database of Lumerical.
Using the load simulation software on the computer, various parameters are set, such as the displacement, drag coefficient, propeller diameter, and loading and unloading control of the propeller. More details can be found in  [23]. It should be noted that the interference to a real operating ship due to waves, weather or changes in displacement is ignored in this paper, which will be considered in our future work. The load power time series with T = 4 working periods of ship simulation are collected. The experiment takes the first three cycles of load power sequence as training samples of MRA-WNN, and the 4th cycle data as test samples. The output results of trained network models are compared. The single operation cycle of the ship is 120 min, and the sampling interval is 1 s. The whole operation period of a ship, like ferry or water buses, includes start-up, acceleration, full speed ahead, deceleration and stop.
This also shows that the improved NSGA-II algorithm proposed in this paper adopts the Pareto non-dominant principle to deal with the relationship between various objectives. It is not necessary to specify the weight coefficient of each target to obtain the real trade-off characteristics of the Pareto solution set. As can be seen from Figure  9 , the changes in the battery group SOC are all within the specified range for both compared strategies. The experimental data show that the battery group SOC of the fuzzy logic rules based strategy fluctuates in the 53. 4-79. 5% range, and the overall fluctuation range is higher than that of the proposed strategy. For the proposed strategy, the SOC interval of battery pack is 57. 9-79. 9%, and the overall change range is smooth. Moreover, at the end of the ship operation, the final SOC values are 77% and 62% for the proposed strategy and fuzzy logic rules based strategy, respectively.
Lastly, different thermal post-treatments were finally evaluated to complete Pt nanoparticles reduction or crystallization:   I. Characterization. -X-ray diffraction (XRD) measurements were performed using an X'Pert pro Philips diffractometer (Cu Kα,λ = 1. 5405 Å). The diffractometer was operated at 45 kV and 30 mA. The data were collected in steps of 0. 05 • from 20 • to 90 • in 2-θ mode with a Pixcel counter. The distribution and dispersion of Pt nanoparticles onto the ATO support were analyzed by HRTEM (high-resolution transmission electron microscopy) or HAADF/STEM (high-angular dark-field scanning TEM) using a spherical aberration probe-corrected FEI-Themis microscope operating at 200 kV and equipped with a Super-X system (4 Silicon Drift Detectors) optimized for high-speed X-ray energydispersive spectrometry (X-EDS) measurements.
Results and Discussion The efficiency of the two deposition protocols was evaluated by considering i) the structure and the morphology of the Pt nanoparticles (XRD, HRTEM and HAADF/STEM), ii) the specific surface area (S Pt ) and iii) the electrocatalytic activity for the oxygen reduction reaction (ORR) measured in RDE configuration. The stability of the most promising Pt/ATO electrocatalysts toward AST was also evaluated. It is noteworthy on Figure  1  that the Pt nanoparticles deposited on the ATO aerogel surface by the EG method are essentially interconnected to form filaments. HRTEM images even suggest that the filaments actually consist of individual crystallites of 2 or 3 nm in diameter. Such an arrangement was not observed after similar deposition on carbon XC72. 30 Considering the morphology described above (filament) it is not relevant to estimate the Pt nanoparticle size from the specific surface area data (the Pt nanoparticles are far from being spherical).
Acknowledgments The authors thank  Pierre Ilbizian  for supercritical drying. This work was funded by the  French National Research Agency PROG-ELEC program , ( ANR-12-PRGE-007  project  SURICAT ) and the  European Union 's  Seventh Framework Program for the Fuel Cells and Hydrogen Joint Technology Initiative  under grant agreement  n325239  ( FCH-JU  project  Nano-CAT ). It was supported by  Capenergies and Tenerrdis. This work was partly (in LEPMI) performed within the framework of the  Centre of Excellence of Multifunctional Architectured Materials "CEMAM " n •  AN-10-LABX-44-01. Marian Chatenet  thanks the  French IUF  for its support. ORCID F. Maillard https://orcid. org/ 0000-0002-6470-8900M. Chatenet https://orcid. org/ 0000-0002-9673-4775  C. Beauger https://orcid. org/ 0000-0002-6164-1587.
Cyanobacteria are a well-known source of bioproducts which renders culturable strains a valuable resource for biotechnology purposes. We describe here the establishment of a cyanobacterial culture collection (CC) and present the first version of the strain catalog and its online database (http://lege. ciimar. up. pt/). The LEGE CC holds 386 strains, mainly collected in coastal (48%), estuarine (11%), and fresh (34%) water bodies, for the most part from Portugal (84%). By following the most recent taxonomic classification, LEGE CC strains were classified into at least 46 genera from six orders (41% belong to the Synechococcales), several of them are unique among the phylogenetic diversity of the cyanobacteria. For all strains, primary data were obtained and secondary data were surveyed and reviewed, which can be reached through the strain sheets either in the catalog or in the online database.
An overview on the notable biodiversity of LEGE CC strains is showcased, including a searchable phylogenetic tree and images for all strains. With this work, 80% of the LEGE CC strains have now their 16S rRNA gene sequences deposited in GenBank. Also, based in primary data, it is demonstrated that several LEGE CC strains are a promising source of extracellular polymeric substances (EPS). Through a review of previously published data, it is exposed that LEGE CC strains have the potential or actual capacity to produce a variety of biotechnologically interesting compounds, including common cyanotoxins or unprecedented bioactive molecules. Phylogenetic diversity of LEGE CC strains does not entirely reflect chemodiversity. Further bioprospecting should, therefore, account for strain specificity of the valuable cyanobacterial holdings of LEGE CC.
In this work, we illustrate (1) the process followed to establish LEGE CC, and give an overview of the collection by presenting (2) the catalog of strains, (3) the online database (http://lege. ciimar. up. pt/), and by revealing (4) their phylogenetic diversity. Cyanobacterial strains in LEGE CC were (re-)identified using an approach combining morphological and phylogenetic data, as recommended by  Komárek (2016) , which confers added value to the collection. Likewise, based on some novel and existing data, we reviewed (5) biotechnologically relevant information from the strains, and make some (6) considerations on the relation between biodiversity and chemodiversity for the discovery of natural compounds from cyanobacterial strains. Altogether, the disclosed data from the strains makes LEGE CC a valuable resource for further bioprospecting, toxicological, and/or taxonomic studies.
Light microscopy and morphological characterization Morphological characteristics of LEGE CC strains were examined and microphotographed using a Leica DMLB light microscope coupled to a Leica ICC50 HD digital camera (Leica Microsystems, Germany). Morphometric measurements were then performed using the image analysis software Leica Application Suite version 4. 2. 0 (Leica Microsystems). Strains were analyzed during the exponential phase of growth (i. e. , 2to 3-week old cultures, depending on the strain; culture conditions for each strain can be found in the catalog (Online Resource 3). Each quantifiable morphological character was measured at least 20 times, along different positions of the slide preparation. These include size of vegetative, specialized, or dormant cells, and of filaments or colonies.
Plasmid DNA was isolated using NZY Miniprep kit (NYZtech, Portugal) and sequenced at GATC Biotech using M13 primers. All nucleotide sequences were manually inspected for quality and assembled for each strain using the Geneious (v8. 1. 8) software package Fig. 1  The workflow followed during the data gathering on the LEGE CC strains, the completed and expected outputs of the process and the planned updates (standard flowchart symbols were used). The LEGE CC website can be accessed at http://lege. ciimar. up. pt  (Biomatters Limited, New Zealand). Two hundred and twenty-four novel sequences associated with this study were deposited in the GenBank database under the accession numbers KU951663-KU951886.
Phylogenetic analyses Molecular-based analyses were conducted using the bioinformatics software package MEGA7  (Kumar et al. 2016). Two phylogenetic analyses based on 16S rRNA gene sequences were performed, one that reflects the overall cyanobacterial diversity present at LEGE CC and a second analysis that highlights the connection between such biodiversity and its associated chemodiversity. In both cases, sequences were aligned using the ClustalW algorithm  (Thompson et al. 1994 ) and phylogenies were inferred by using the Maximum Likelihood (ML) method  (Felsenstein 1981)  based on the General Time Reversible model  (Rodriguez et al. 1990 ), which was the nucleotide substitution model that best fitted the alignments data as evaluated by the corrected Akaike Information Criterion  (Sugiura 1978).
Results and discussion Three hundred and eighty-six cyanobacterial strains are included in the first version of the catalog of LEGE CC (see Fig. 2  for a morphological overview). For each particular strain, primary and secondary data collected in this study (Fig. 1 ), such as species identification, origin, morphometric information, morphological description, and ecophysiological properties of the strain, microphotographs, literature references, synonyms for the strain, accession numbers for sequences, etc. , can be retrieved in the corresponding catalog sheet (Online Resource 3) or be searched in the website database of the culture collection at http://lege. ciimar. up. pt.
2011) , as was already demonstrated for one of our strains, Synechocystis sp. LEGE 00032  (Ribeiro et al. 2008). Also, six strains (Fig. 3 ) have had their genomes sequenced and these will be made publicly available, following curation. One such strain, Cyanobium sp. LEGE 06113, has been included on a submitted patent application for a promising anti-malarial compound. Some strains held in LEGE CC have an earthy odor, something that may indicate the presence of odiferous metabolites such as 2methlyisoborneol or geosmin  (Giglio et al. 2010) , two volatile organic compounds that pose problems in drinking water supply systems. This qualitative data was included in the catalog of strains (Online Resource 3).
Bioactive compounds: 1 portoamides, 2 bartolosides, 3 dehydroabietic acid, 4 abietic acid, 5 hierridin B, and 6 anabaenopeptins A and D. Notice that the production (+) or absence of production (-) of the different compounds were confirmed by analytical techniques such as HPLC, LC-MS, or NMR. Metabolites between parentheses and symbols in gray indicate unpublished data. Symbols indicate the existence of data (either for the detection or non-detection) on: toxicity, bioactivity, or allelopathy assays (▲); screening of metabolites by MALDI-TOF Mass Spectrometry or by LC-MS analysis coupled with molecular networking [13] (■); cyanotoxins (•, first column); other than cyanotoxins nonribosomal peptide synthetases, polyketide synthases, or hybrid NRPS-PKS (•, second column); ribosomally synthesized and posttranslationally modified peptides  (Martins et al.
Conclusions Acting as repositories of strains and of their genetic material, mBRCs facilitate the access to their diversity, their (meta)data and their associated natural compounds, being able to satisfy the needs of academia or the industry. With this in mind, we decided to organize our cyanobacterial strains into a publicly available culture collection. The cyanobacterial diversity that currently makes up the LEGE CC is an increasingly important bioresource, either from the taxonomic point of view (e. g. Ramos et al. 2010 in Komárek et al. 2014; Brito et al. 2017)  or from a biotechnological perspective (e. g. ,  Brito et al. 2015). LEGE CC is now a member of the WFCC (WDCM #1089), also part of EMBRC. PT, the Portuguese node of the research infrastructure European Marine Biological Resource Centre.
Acknowledgements VR gratefully acknowledges financial support from a  Fundação para a Ciência e a Tecnologia (FCT)  fellowship  SFRH/BD/ 80153/2011. The Project NOMORFILM has received funding from the  European Union 's  Horizon 2020 Research and Innovation Programme  under grant agreement No. 634588. Structured Program  of  R&D&I INNOVMAR-Innovation and Sustainability in the Management and Exploitation of Marine Resources  (reference  NORTE-01-0145-FEDER-000035 ,  Research Line NOVELMAR) , funded by the  Northern Regional Operational Program  ( NORTE2020 ) through the  European Regional Development Fund (ERDF). PNL acknowledges funding from  FCT  through contract ( IF/01358/2014 ).