dataesr/scientific-paragraphs-categorization huggingface dataset:
One established criterion to consider the GSMN functional was the production of biomass with balanced growth. Flux Balance Analysis (FBA) is a widely used method to quantitatively model the behavior of the system under given conditions. This optimization problem was based on the principle of mass conservation and considered the steady state assumption (intracellular metabolites at equilibrium). Mathematically, this reaction was modeled by a linear function to be optimized. This point was tested using the quantitative FBA python scripts from the Padmet toolbox, based on the CobraPy package  [47]  and provided in AuReMe. To do this, the same production reactions, transport, and exchange of biomass used in the reconstruction of E. siliculosus GSMN  [24]  were added to our GSMNs (Table  S5  of the Supplementary Materials).
Exploration and Assessment of Carotenoid Biosynthesis Pathways in Brown Algae The manual exploration of the carotenoid biosynthesis pathway (CAROTENOID-PWY) and the first cycle of xanthophylls (PWY-5945) was conducted starting from the pathways encoded in the MetaCyc database (version 22. 6)  [43]  and completed by further literature searches. These 2 pathways encoded the activity of 10 enzymes whose protein sequences were selected, when identified, in E. siliculosus or, if not available, in A. thaliana (sometimes supplemented with other terrestrial plants). These protein sequences are accessible either via the Uniprot database (https://www. uniprot. org) or via the Online Resource for Community Annotation of Eukaryotes (ORCAE) website for E. siliculosus (https://bioinformatics. psb. ugent.
be/orcae/overview/EctsiV2) [49]. Sequences homologous to these enzymes were then searched for in the proteomes of 3 green algae Chlamydomonas reinhardtii, Volvox carteri, Ulva mutabilis, 3 red algae Chondrus crispus, Porphyra umbilicalis, Galdieria sulphuraria and 6 stramenopiles Nannochloropsis gaditana, N. salina, Phaeodactylum tricornutum, C. okamuranus, S. japonica. With the exception of Ulva mutabilis and E. siliculosus, for which homology searches were carried out through the ORCAE portal  [49] , all proteomes are accessible in the Genome database (https://www. ncbi. nlm. nih. gov/genome) of the NCBI. All accession numbers used are available as Table  S6  in Supplementary Materials. Proteome indexing was performed using formatdb (version 2. 2. 16), then homology searches were done with blastp (version 2.
7. 1+). Hits with an e-value of less than 1e-5 were selected for alignment after checking the organization of their protein domains (HmmerWeb  [50]  version 2. 30. 0-https://www. ebi. ac. uk/Tools/hmmer/search/phmmer). The sequence files previously obtained were aligned using the Muscle algorithm implemented in the Seaview software (version 4. 4. 2)  [51]. The associated phylogenetic trees were generated in Seaview using maximum likelihood (PhyML) with the LG (Le et Gascuel) model, the BIONJ algorithm (BIO Neighbor-joining) for the starting tree, and 100 bootstrap replicates. The 5 trees presented in the supplementary data have been edited with Figtree (version 1. 4. 4). The modifications made to the GSMNs are detailed in Appendix A. Some of them are related to the second cycle of xanthophylls (PWY-7949), and fucoxanthin biosynthesis pathway (PWY-7950) encoded in MetaCyc.
The results are shown in Figure  1. Strikingly, there were more reactions, metabolites, and pathways shared exclusively between S. japonica and C. okamuranus (1553 reactions) than exclusively between E. siliculosus and C. okamuranus (22 reactions), although the latter were phylogenetically closer. This was explained by examining the sources of reactions in the GSMNs (Figure  2 ). Of the reactions resulting from the annotations, 52% (S. japonica) and 44% (C. okamuranus) were not supported by the orthology with E. siliculosus. These differences were partly due to recent improvements in databases and annotation methods. The functional annotation of E. siliculosus that we used was done manually 10 years ago by an expert consortium  [52] , whereas we used Trinotate for S. japonica and C. okamuranus GSMNs.
Of the reactions resulting from the annotations, 52% (S. japonica) and 44% (C. okamuranus) were not supported by the orthology with E. siliculosus. These differences were partly due to recent improvements in databases and annotation methods. The functional annotation of E. siliculosus that we used was done manually 10 years ago by an expert consortium  [52] , whereas we used Trinotate for S. japonica and C. okamuranus GSMNs. Therefore, the strong differences between E. siliculosus and the two other algae did not reflect biological differences, but different ways of annotation. One crucial point for the quality check was to build strong pathway-by-pathway expertise by scrutinizing them. AuReMe enabled the curation work to be stored and to reiterated on later versions of the GSMNs. To illustrate these points, intense manual curation centralized on the carotenoid biosynthesis pathway was performed.
The figure is based on our results and the following references  [5, 53, [55] [56] [57] [58] [59] [60] [61] [62]. Among the terrestrial plants, red, green, and brown algae, lycopene was the first point of connection in the synthesis of carotenoids, since it offered two possible routes: The one of α-carotene and the one of β-carotene. These pathways started respectively, with the action of lycopene ε-cyclase (LYCE) for α-carotene and lycopene β-cyclase (LYCB) for β-carotene  [63]. β-carotene is a carotene present in the majority of photosynthetic organisms, while α-carotene seems to be absent in stramenopiles and red microalgae  [56]. These results were confirmed manually by our homology search. This search also allowed us to identify a single sequence containing one lycopene cyclase domain (PF05834) within the proteomes of brown algae: The lycopene β-cyclase  [55, 56, 64]  (Figure  S4  of the Supplementary Materials).
For the most part, they correspond to metabolites historically qualified as primary (amino acids, essential sugars, ATP, ADP) but also ubiquitous secondary metabolites such as lycopene. The preliminary steps to the IPP synthesis are highlighted by the orthology component of the reconstruction, suggesting and confirming their ancestral origin. In general, all the reactions present within the GSMNs that are supported by orthology with A. thaliana illustrate this phenomenon. However, the list proposed based on this criterion is not exhaustive since, on the one hand, the A. thaliana GSMN preferentially targets "primary metabolites" and, on the other hand, some reactions may have been lost during the mapping steps between the various databases. This point is illustrated by the reactions allowing the synthesis of lycopene from geranylgeranyl diphosphate (triangle in Figure  2 ).
They belong to the core reaction set (similar enzymes in plants and various algal lineages) but are not supported by the A. thaliana component. In contrast, reactions supported only by annotation may indicate a specificity of the species or lineage. A contrario, the presence of gaps, and a fortiori dead ends within GSMNs has a high predictive power by informing either on the computational limit and/or biological specificity related to one species. From a purely bioinformatic point of view, the presence of gaps is directly related to the quality and quantity of data present in the databases. Apart from encoding issues of some metabolites, there is currently little Phaeophyceae referenced data. As such, a gap in the GSMNs may be a direct reflection of the biological specificities of the studied lineages and open up to new questions and biological investigations (i.
To summarize, the non-producibility of these targets can also come from the encoding choice of the referenced metabolites, and in this case, the GSMNs already reflect the biochemical reality of fatty acid metabolism. An additional category of metabolites is those that could even not be incorporated as targets for gap filling because they are not yet connected to biochemical reaction models and thus not incorporated in the Metacyc database. For such molecules, specific tools have been developed to infer new reaction models using detailed comparisons of already known reactions and molecules substructures or to infer the precise structures of the unknown intermediates leading to known metabolites  [25]. The curation of the carotenoid pathway has pointed out one of the limits of automatic GSMN reconstructions with the proposal of genes and reactions leading to the synthesis of α-carotene and its derivatives.
Supplementary Materials: The following are available online at http://www. mdpi. com/2076-3921/8/11/564/s1. Table  S1 : Data from the annotation of algal protein-coding genes, Figure  S1 : Source of the S. japonica (a) and C. okamuranus (b) annotations, Table  S2 : Targets for S. japonica from metabolic data in the literature  [19, [87] [88] [89] [90] [91] [92] [93] [94] [95] , Table  S3 : Targets for C. okamuranus from metabolic data in the literature  [2, [96] [97] [98] [99] , Table  S4 : List of cofactors (seeds) added to the S. japonica and C. okamuranus GSMNs, Table  S5 : List of biomass reactions added to the S. japonica and C. okamuranus GSMNs  [24] , Table  S6 : Accession numbers of enzymes and protein sequences used, Figure  S2 : Pathways of methylerythritol phosphate (MEP) within the S.
japonica and C. okamuranus GSMNs  [43, 54] , Table  S7 : List of reactions and genes associated with the MEP pathways  [43, 54] , Figure  S3 : Pathways of mevalonate (MVA) within the S. japonica and C. okamuranus GSMNs  [43, 54] , Table  S8 : List of reactions and genes associated with the MVA pathways  [43, 54] , This point, therefore, led us to remove from the GSMNs reactions associated with the synthesis of δ-carotene (RXN1F-147), α-carotene (RXN1F-148), ε-carotene (RXN-8028), zeinoxanthin (RXN-5961), α-cryptoxanthin (RXN-12226-only for C. okamuranus GSMNs) and lutein (RXN-8962). The addition of a hydroxyl group at each end of the β-carotene forms zeaxanthin. Within the reconstructed S. japonica and C. okamuranus GSMNs, no reaction allows this modification. However, there are two reactions (RXN-8025 and RXN-8026) within the MetaCyc database that ensure this transformation using an intermediate, β-cryptoxanthin.
M. D. , E. C. and G. V. M. ; data curation, D. N. , A. P. L. , C. L. , S. M. D. , E. C. , and G. V. M. ; formal analysis, D. N. , C. F. , X. L. , and A. P. L. ; funding acquisition, C. L. , A. S. , S. M. D. , and E. C. ; investigation, D. N. ; methodology, A. S. ; resources, L. B. -G. , P. B. , O. G. ; software, M. A. , A. B. , C. F. , and A. S. ; supervision, E. C. and G. V. M. ; writing-original draft, D. N. , E. C. , and G. V. M. ; Writing-review and editing, D. N. , C. F. , A. P. L. , C. L. , A. S. , S. M. D. , E. C. , and G. V. M. All authors approved the submitted version and agreed to be personally accountable for the authors' own contributions. Funding: This research received funding from the French Government via the National Research Agency investment expenditure program IDEALG (ANR-10-BTBR-04) and from Région Bretagne via the grant « SAD 2016 -METALG (9673) ».
Author Contributions: Conceptualization, S. M. D. , E. C. and G. V. M. ; data curation, D. N. , A. P. L. , C. L. , S. M. D. , E. C. , and G. V. M. ; formal analysis, D. N. , C. F. , X. L. , and A. P. L. ; funding acquisition, C. L. , A. S. , S. M. D. , and E. C. ; investigation, D. N. ; methodology, A. S. ; resources, L. B. -G. , P. B. , O. G. ; software, M. A. , A. B. , C. F. , and A. S. ; supervision, E. C. and G. V. M. ; writing-original draft, D. N. , E. C. , and G. V. M. ; Writing-review and editing, D. N. , C. F. , A. P. L. , C. L. , A. S. , S. M. D. , E. C. , and G. V. M. All authors approved the submitted version and agreed to be personally accountable for the authors' own contributions. Funding: This research received funding from the French Government via the National Research Agency investment expenditure program IDEALG (ANR-10-BTBR-04) and from Région Bretagne via the grant « SAD 2016 -METALG (9673) ».
The vehicle was water for injections. Six known mutagens were used as positive controls to check the test system sensitivity: sodium azide, 9-aminoacridine, 2-nitrofluorene, 2-anthramine, and benzo(a)pyrene (dissolved in dimethylsulfoxide), and mitomycin C (dissolved in water). After 48-72 h of incubation at 37 C, revertant colonies (numbers of revertants per plate) were scored using an automatic counter (Sorcerer Automatic Colony Counter software for acquisition of data and Ames Study Manager software for data management; Perceptive Instruments Ltd, UK). Toxicity was evaluated by observation of a decrease in the number of revertant colonies and/or thinning of the bacterial lawn. The criteria for a positive result were a reproducible 2-fold increase (for TA98, TA100, and TA102 strains) or 3-fold increase (for TA1535 and TA1537 strains) in the mean number of revertant colonies when compared with the vehicle control and/or by evidence of a dose relationship.
The estrus cycle stage was determined for 14 consecutive days (from a fresh vaginal lavage stained with methylene blue) over the last 2 weeks of the treatment (study weeks 12 and 13) and treatment-free (study weeks 16 and 17) periods. Histology/pathology. A full macroscopic post-mortem examination was performed. Designated organs were weighed and tissues were preserved. A microscopic histopathology examination was performed on selected tissues (and on any macroscopic lesions) from control and high-dose animals euthanized at the end of the treatment period. As there were no test item-related findings, these examinations were not performed at the end of the treatment-free period. Statistical analysis. Statistical analysis was performed on body weight, food consumption, seminology parameters, hematology, blood biochemistry, thyroid hormones, and urinalysis data (Citox software, version D.
Materials and Methods The methodology adopted in this study is divided into three stages (Figure  1 ). The first stage deals with the evaluation of the energy demand, energy resource, as well as the technical and cost details of the components. These details serve as the major inputs into HOMER, a software capable of performing modelling, simulation and sensitivity analysis of energy system (renewable and conventional). The second stage involves the use of HOMER to simulate and optimize the HRES alternatives. The selection and ranking of HRES at this stage is based on the total net present cost (TNPC). The last stage uses multi-criteria decision-making (MCDM) approach to rank the HRES alternatives based on multiple criteria (social, technical, economic, environmental, and policy).
System Modelling The simulation and optimization of the proposed HRES is carried out using Hybrid Optimization of Multiple Electric Renewables (HOMER). HOMER software was used for the modeling, simulation, optimization and sensitivity analysis of grid connected and off-grid energy systems for diverse applications. In order to simulate an energy system, HOMER performs an annual energy balance calculation with a simulation time step of one hour (8760 h). On an hourly basis, it compares the energy demand (thermal and electric) to the hourly energy generated by the system. In order to obtain the energy balance, it performs calculations of energy exchange among the system components. This calculation is carried out for different energy system alternatives. For energy systems with fuel-fired power generator(s) and battery storage system, HOMER also specifies for every hour of the year, the operational strategies behind the use of the generator(s) as well as the scheme for the charging and discharging of the battery bank.
Conclusions Traditionally, the choice of HRES is usually based on a single criterion-total net present cost. However, a single criterion may not be sufficient to ensure sustainability and a well informed choice. In order to address this issue, this paper presented a viability analysis of HRES adoption for a typical low-income household based on multiple criteria. It also explored the effects of energy efficiency techniques on the features of the optimal system that will serve the proposed low-income household. This study explored the use of gasoline, wind as well as solar resource under various configurations for meeting the energy needs of a low income household. This study adopted standard off-grid power system methodologies offered by HOMER software, relevant standards, a MCDM tool (TOPSIS) and relevant literature for the simulation, optimal sizing, and selection of the most suitable HRES for the low-income household.
Most of the ORP proteins are predicted to be metal binding proteins. Hence, Orp3 and Orp4 share 41% similarity to each other and each protein contains two conserved [4Fe-4S] ferredoxin binding motifs (IPR017900), Orp8 is homologous to proteins harboring a non-covalently metal sulfide [S 2 MoS 2 CuS 2 MoS 2 ] cluster  21, 22  and Orp5 is homologous to a protein that binds [2Fe-2S] clusters  23. The actors involved in the maturation of the ORP complex metallo-proteins are yet unknown. In this work, we show that Orp9 from DvH and its homolog Dde3202 from Desulfovibrio alaskensis G20 (DdG20) contain a Mrp/NBP35 domain and we report the biophysical and biochemical characterization of both proteins. We demonstrate that these two proteins possess two domains, each able to bind a Fe-S cluster. We also evidence that only the Mrp/Nbp35 domain can efficiently transfer its Fe-S cluster to apo-targets, such as aconitase and Orp proteins.
Results The Mrp ORP proteins are two-domain proteins. Querying the INTERPRO portail indicated that Mrp ORP belongs to the Mrp/NBP35 ATP-binding proteins (IPR019591), a very large protein family ubiquitous in the domains of Life (Supplementary Table  S1 ). This protein family encompasses the prokaryotic Mrp and ApbC, and the eukaryotic Nbp35 and Cfd1 proteins involved in Fe-S cluster biogenesis  12, 16, 24. Most of the 17,511 members of the Mrp/NBP35 ATP-binding protein family contained a single conserved functional domain, the P-loop containing nucleoside triphosphate hydrolase domain (P-loop NTPase, IPR027417). However, in a few cases this domain is found associated with other domains (Supplementary Table  S2 ). In Mrp ORP , the P-loop NTPase domain is associated with a dinitrogenase iron-molybdenum cofactor biosynthesis domain (Di-Nase, IPR003731), which is usualy found in proteins involved in the biosynthesis of the iron-molybdenum cofactor (FeMo-co), such as NifB and NafY  25.
5, 1 mM MnCl 2 , 25 mM citrate, 0. 25 mM NADP + , 1. 7 U of isocitrate dehydrogenase were added to proteins in 1 mL final volume in a quartz cuvette closed with a rubber cap. AcnB activity was assayed by following the formation of NADPH in the coupled assay as an increase in absorbance at 340 nm  29. Phylogenetic Analysis. According to the INTERPRO database (v62, 17 March 2017), the Mrp ORP (DVU2109) is composed of two domains: a P-loop containing nucleoside triphosphate hydrolase domain (IPR027417) and a dinitrogenase iron-molybdenum cofactor biosynthesis domain (IPR003731). DVU2109 belongs, together with DVU1847 and DVU2330, to the Mrp/NBP35 ATP-binding protein family (IPR019591), which contained 17300 sequences from known cellular organisms and 211 unclassified sequences. The 17300 sequences associated to cellular organisms were retrieved and aligned with MAFFT v7.
309 (default parameters)  48. The quality of the resulting alignment was verified with SEAVIEW v4. 6. 1  49. 1,146 partial or poor-quality sequences were discarded. The 16,154 conserved sequences, among which 99 combine IPR027417 and the IPR003731, were realigned with MAFFT (default parameters). The resulting alignment was trimmed with BMGE (BLOSUM30 option)  50  and used to infer the phylogeny of the Mrp/Nbp35 ATP-binding protein family with FASTTREE v2. 1. 9  51. Among the 17,300 protein sequences from known cellular organisms retrieved from INTERPRO, the 110 sequences displaying the highest similarity with Mrp orp were identified with BLASTP (default parameters)  52. The corresponding sequences were aligned with MAFFT using the accurate option L-INS-I option, which allowed accurate multiple alignment construction.
The resulting alignment was trimmed with BMGE (BLOSUM30 option) and used to infer a maximum likelihood tree with IQ-TREE v1. 5. 3  53  using the LG + I + G4 evolutionary model as suggested by the model selection tool implemented in IQ-TREE (BIC criterion). The robustness of the resulting tree was assessed with the non-parametric bootstrap procedure implemented in IQ-TREE (100 replicates of the original dataset)  54. Microscopy Experiments. The 3 fusion GFP strains were grown until the middle of the exponential growth phase (OD 600nm of approximately 0. 4 to 0. 5) in medium C. Cells were concentrated 2 times by centrifugation. The buffer used for this concentration contained 10 mM Tris-HCl (pH 7. 6), 8 mM MgSO 4 , 1 mM KH 2 PO 4. In order to stain DNA, this buffer was supplemented with 5 ng/μL of 4' ,6-diamidino-2-phenylindole (DAPI).
After 20 min of incubation in the dark, the cells were washed three times in TPM buffer. The DNA was stained under anaerobic conditions to limit the exposure of the cells to air. The pictures were acquired after 10 min of air exposure, which was required for oxygen GFP maturation. The cells were placed between a coverslip and an agar pad of 2% agarose. Pictures were acquired with a Nikon TiE-PFS inverted epifluorescence microscope, 100x NA1. 3 oil PhC objective (Nikon), and Hamamatsu Orca-R2 camera. For fluorescent images, a Nikon intenselight C-HGFI fluorescence lamp was used. Specific filters were used for each wavelength (Semrok HQ DAPI/CFP/GFP/YFP/ TxRed). Image processing was controlled by the NIS-Element software (Nikon). EPR Spectroscopy. The EPR spectra of 0. 1 mM Mrp ORP_ CT, in 100 mM Tris-HCl, 500 mM NaCl, 3 mM DTT pH 8.
To measure the cyclic voltammograms a µautolab (ECO Chemie, Utrecht, The Netherlands) was used being the data collect and analyzed on GPES software package (ECO chemie). Cyclic voltammetric measurements were performed on a potential window from +0. 1 to -0. 9 V (vs SHE), and the scan rate dependence investigated between 0. 005 and 0. 1 V s -1. Protein and Metal Quantifications for Mrp ORP _CT. Iron quantification was performed by inductively coupled plasma (ICP) emission analysis in a Jobin-Yvon (Ultima) instrument (at UCIBIO), using the Reagecom 23 ICP multielements as standard solution in a concentration range of 0. 05 to 3 ppm. Total Protein was quantified using the Pierce TM 660 nm Protein Assay (Thermo), with bovine serum albumin (Sigma) as standard protein.
Acknowledgements We gratefully acknowledge the contribution of  Marielle Bauzan  for the bacterial growth ( Fermentation Platform of the Mediterranean Institute of Microbiology (IMM) ) and  Deborah Byrne  for the gel filtation experiment (Protein Production Platform of the  Mediterranean Institute of Microbiology (IMM) ). The  French National Research Agency (ANR)  funded this research project ( ANR-12-ISV8-0003-01 ). This work was supported by  Fundação para a Ciência e Tecnologia (FCT)  (grant to SRP,  FCT-ANR/BBB-MET/0023/2012 , and to CC,  SFRH/ BD/87898/2012 ) and by the  Belgian Federal Science Policy Office (Belspo)  (grant to BD,  IAP7/44 , iPROS project). Unidade de Ciências Biomoleculares Aplicadas-UCIBIO  was financed by national funds from  FCT/MEC  ( UID/ Multi/04378/2013 ) and co-financed by the  ERDF  under the  PT2020 Partnership Agreement  ( POCI-01-0145-FEDER-007728 ).