dataesr/scientific-paragraphs-categorization huggingface dataset:
Sect. 2. 3). Default weights have been used for both OSM and BDT: SVF=4, H/W=3, FB=8, FI=0, FP=0, Hr=6, z0 = 0. 5. Those weights are only used in the "closest distance approach" for LCZ built types. Two main characteristics differentiate LCZ types: building compacity (mainly described by FB, SVF and H/W) and building height (mainly described by Hr, H/W and SVF). FP and FI weights are set to zero since they are secondary characteristics and pervious and impervious data often lack of accuracy in urban areas (at least it is the case for our input datasets). FB and Hr indicators are simply defined and are based on very few input variables, thus do not propagate uncertainties. However, building height is less certain than building footprint (especially for OSM data), thus FB has the highest weight.
Acknowledgements. The research of this paper has been performed in the framework of the project HARPOL ( Harmonizing  and advancing  retrieval approaches for present and future polarimetric space-borne atmospheric missions) , funded through the  ESA   program   EO Science for Society. We acknowledge  Christian Retscher  ( ESA ) for his work as Technical officer for HARPOL. We also acknowledge  Daniele Gasbarra  ( ESA ) and  Alexandru Dandocsi  ( ESA ) for important feedback during the course of the HARPOL project.
https://doi. org/10. 5194/amt-2023-203 Preprint. Discussion started: 16 October 2023 c Author(s) 2023. CC BY 4. 0 License. and T-matrix improved geometrical optics database by Dubovik et al. (2006) along with their proposed spheroid aspect ratio distribution for computing optical properties for a mixture of spheroids and spheres. For retrievals over land RemoTAP uses a surface reflection matrix (Litvinov et al. , 2011)  that accounts for the directional and polarization properties of the surface, based on the Ross-Li model (Wanner et al. , 1995)  total reflectance and the model of Maignan et al. (2009)  for polarized reflectance.
To complete this dataset, the transcriptome of six additional species, including the LFA Ulvophyceae Dilabifilum (Paulbroadya) petersii, were sequenced on an Illumina NovaSeq platform yielding an average of 40 million reads (details of sequencing and assembly statistics in SI Appendix, Table  S3 ). Finally, we collected already available genome assemblies for 22 species covering other classes of chlorophyte green algae, and re-annotated six of them (SI Appendix, Table  S1 ). Completion of the predicted proteomes estimated for all species using BUSCO ranged from 18. 3% to 99. 6% (Fig. 1  and SI Appendix, Fig. S1 ). To ensure the reliability of the comparative analyses, a threshold of 65% completeness and less than 30% of missing BUSCO orthologs was set up, leading to a total of 38 green algal species covering the four main classes of the chlorophytes and including 10 LFA species (nine Trebouxiophyceae and one Ulvophyceae).
TZW2008, while 27 were expanded in LFA (SI Appendix, Table  S5 ). These features are shared by most LFA and thus represent functional modules linked with lichenization, not playing a role at the species-specific level, but rather for lichenization in general. Several seemingly unrelated IPR and PFAM terms were identified as expanded in or mostly specific to LFA species. Those include, for instance, functions linked to the adaptation to high light intensity, such as gluthatione S-transferase (PF13417, IPR040079, respectively 1. 53 and 1. 73 times more represented in LFA than nLFA; 20, 21), or rhodopsin (IPR018229  (26) ) that was present in all LFA species investigated and only four of the 28 nLFA algae (SI Appendix, Table  S4 /S5). Similarly, we identified several functions linked to drought tolerance.
This includes members of the TspO/MBR (PF03073/ IPR004307) family which were identified with a two-fold increase in abundance in LFA compared to nLFA, and has been found induced in drought stress condition as well as essential for adaptation to salt stress in the model moss Physcomitrella patens  (27). We also identified the PFAM domain PF13668 corresponding to Ferritin-like domain known to improve drought tolerance and previously found expanded in the T. gelatinosa genome  (28). This functional category is absent from 10 of the 28 nLFA while conserved in all LFA, and is also four times more abundant in LFA than nLFA. The ferritin-like superfamily category was also among the most significantly enriched IPR term (IPR009078) in putatively secreted proteins of LFA species compared to nLFA (Wilcoxon p-value 6.
3e-05, SI Appendix, Table  S4. ). Lastly, we detected a significant enrichment of the Phospholipase D (IPR015679) in LFA (9/10 species) compared to nLFA (10/28 species), a function previously linked to the stabilization of membrane during desiccation in the LFA Asterochloris erici  (29). High light radiations and drought are two of the main challenges faced by organisms transitioning from an aquatic to a terrestrial environment  (3). The identification of expansion of gene families and biological functions linked to the terrestrial lifestyle as one of the hallmarks of the LFA genomes suggests that the ability to live in terrestrial habitats could be a major prerequisite for the evolution of the ability to form lichens. To determine the evolutionary origin of the terrestrial lifestyle-related features, we conducted targeted phylogenetic analyses of these five genes (SI Appendix, Table  S7 ).
Gene family expansions and horizontal gene transfer shaped the carbohydrate metabolism and catabolism in LFA species. Manual inspection of the lists of LFA-enriched IPRs and PFAMs identified six main functional categories related to carbohydrate metabolism as significantly expanded (3/6) or present  (3/6)  in LFA compared to nLFA (SI Appendix, Table  S4 /S5). Among them, we identified a short-chain dehydrogenase (IPR002347/PF00106, in average 1. 5-1. 6 times more present in LFA) corresponding to a family containing enzymes involved in ribitol biosynthesis. Ribitol is a linear pentose alcohol previously identified as the major sugar produced in diverse lichens such as in Peltigera aphtosa (Coccomyxa photobiont), Xanthoria aureola or Fulgensia bracteata (Trebouxia spp. photobionts)  (30, 31).
The addition of exogenous ribitol to culture of lichen-forming fungi is known to stimulate fungal growth and developmental transitions and has been suggested as a signal for lichen initiation  (31, 32). The enrichment in this functional category across LFA thus indicates that the expanded ability to produce ribitol is not a species-specific feature but is rather linked with the ability to lichenize itself. Following a similar pattern was the IPR003663 (1. 8 times more present in LFA than in nLFA), associated with Sugar/inositol transporter. It is tempting to speculate that such transporters could play a role in the export of ribitol to the fungal partner. Three Glycosyl Hydrolase gene families were found either expanded in LFA (GH31 IPR002659, 1. 6 more times more present in LFA compared to nLFA) or almost specific to LFA (GH8 IPR002037/ PF01270, 8/10 LFA and 3/28 nLFA, Wilcoxon and Fisher p-values: 6.
4. 10-5 and 0. 00013 respectively; GH26 IPR022790, 7/10 LFA and 4/28 nLFA, Wilcoxon and Fisher p-values: 0. 0015 and 0. 0022 respectively). Glycosyl Hydrolases from these families are known to hydrolase large diversities of polysaccharides including those forming the plant and fungal cell walls  (33). In particular, the GH8 enzymes are known to degrade the fungal polysaccharide chitosan and even lichenin, a carbohydrate found in lichens  (34). Cell wall remodeling occurs in all the symbioses between plants and microorganisms, facilitating the progression of the microbial partner in the plant tissues in the case of endosymbiosis  (35, 36) , and observed at the contact sites between symbionts in the case of lichens  (37). The occurrence of an expanded and specific repertoire of Glycosyl Hydrolases in LFA echoes the peculiar patterns of retention and losses of cell wall degrading enzymes linked to symbiotic abilities in fungi  (14, 17, 38, 39).
Finally, a carbohydrate esterase 2 (CE2) N-terminal domain was restricted to LFA (IPR040794/PF17996; 7/10 LFA and 3/28 nLFA, Wilcoxon and Fisher p-values: 0. 00027 and 0. 00087 respectively) and is known, in bacteria, to be involved in deacetylation of plant polysaccharides  (40). Together with the absence of specificities in the Glycosyl Hydrolases repertoire from lichen-forming fungi  (41) , this indicates that LFA may directly contribute to the remodeling of the partners' cell wall during lichenization. Phylogenetic analyses of carbohydrate-related IPRs revealed two evolutionary patterns. First, the increased abundance of GH31 and GH26 is linked to gene-family expansions in the Trebouxiophyceae and/or core Trebouxiophycean clade (Figure  3A  and B ). Such expansion was not observed in the LFA Ulvophyceae Dilabifilum (Paulbroadya) petersii indicative of clade-specific innovations in the Trebouxiophyceae.
S3C ,  (34, 42). In addition to the Trebouxiophyceae, our phylogenetic analysis supports another HGT event of the bacterial GH8 which has also been transferred to fungi. However, no link has been identified between fungal species possessing the GH8-like gene and species forming lichen associations (SI Appendix, Table  S8 ). Unrooteed maximum likelihood tree of GH8 family. Branches are colored as follow: outgroup sequences without the GH8 domains are in grey, while bacteria, fungi and algae GH8 are colored in pink, orange and blue respectively. The red dots indicate the presence of the GH8 functional domain (PF01270). Sequence names have been hidden for readability reasons and can be found in the Supplementary Table  S8. D. Position of GH8-like coding-genes of algae on chromosome. For readability reasons, chromosomes longer than 5Mb are displayed separately.
Genome assembly Sequel II samples were demultiplexed using lima (v1. 9. 0, SMRTlink) and the options --same --minscore 26 -peek-guess. De novo assembly was carried out for each PacBio (Sequel/Sequel II) subreads set using the genome assembler Flye (version 2. 7-b1587)  (67)  in CLR mode and default parameters. Each assembly was polished once as part of the Flye workflow and a second time with the PacBio tool GCpp v2. 0. 0 with default parameters (v1. 9. 0, SMRTlink). The polished assemblies were scaffolded using SSPACE-LongRead v1. 1  (68)  with default parameters. The received scaffolds were taxonomically binned via BLASTx against the NCBI nr database using DIAMOND (--more-sensitive) in MEGAN v. 6. 7. 7 (69), using Max Expected set to 1E-10 and the MEGAN-LR algorithm  (Huson et al. 2018 ) and only scaffolds assigned to the Chlorophyta were retained for subsequent analysis.
tar. gz and proteins from six species investigated in this study (last column of SI Appendix, Table  S1 ). For 14 species, available or generated RNA-Seq data were used as hints in BRAKER2 (SI Appendix, Table  S1 ). The raw fastq reads were cleaned from adapters and the low-quality sequences using cutadapt v2. 1, (80) and TrimGalore v0. 6. 5, (https://github. com/FelixKrueger/TrimGalore) with -q 30 --length 20 options. The cleaned reads were mapped against the corresponding genomes using HISAT2 v2. 1. 0 (81)  with --score-min L,-0. 6,-0. 6 --max-intronlen 10000 --dta options. Duplicated reads were removed using SAMtools v1. 10 (82) , markdup command. These final alignments data were used as input in BRAKER2. We also annotated transcriptomes of four species. First, we assembled the transcriptomes from the raw reads RNAseq using DRAP v1.
92 pipeline  (83). runDrap was first used on the unique samples applying the Oases RNAseq assembly software  (84). For Trebouxia gelatinosa, runMeta was used to merge, without redundancy, the 3 transcripts assemblies predicted based on a fpkm of 1. Predictions of protein-coding genes were performed using TransDecoder v5. 5. 0 (https://github. com/TransDecoder/TransDecoder) and hits from BLASTp against the Swissprot database (downloaded on September 2021) and HMMER search against the Pfam v34 database  (85, 86). Completeness of newly sequenced and annotated genomes and transcriptomes was assessed using BUSCO V4. 1. 4 (87)  with default parameters and using the Chlorophyta "odb10" database (1519 core genes) as reference. Finally, functional annotation was performed for all species investigated using the InterProScan suite v5.
Identification of genes differentially expressed genes between the symbiotic state of Trebouxia sp TZW2008 In order to increase our statistical power by crossing deregulated genes in symbiotic context we used the transcriptomic data from Trebouxia sp TZW2008  (19)  with results of our contraction/expansion analysis. To do so, the raw reads were downloaded (SI Appendix, Table  S1 ) and submitted to the nf-core/rnaseq v3. 4  (95)  workflow in nextflow v21. 04 (96) using -profile debug,genotoul --skip_qc --aligner star_salmon options. Nextflow nf-core rnaseq workflow used bedtools v2. 30. 0 (97), cutadapt v3. 4 (80) implemented in TrimGalore! v 0. 6. 7 (https://github. com/FelixKrueger/TrimGalore), picard v2. 25. 7 (https://broadinstitute. github. io/picard), salmon v1. 5. 2 (98), samtools v1.
Phylogenetic analysis of candidate proteins To place expansions, contractions and gene losses in an evolutionary context, candidate proteins were subjected to phylogenetic analysis. First, homologs of sequences from orthogroups were searched against a database containing the 38 investigated species using the BLASTp v2. 10. 1 algorithm  (105)  and an e-value threshold of 1e-30. Then, retained sequences were aligned using MUSCLE v3. 8. 1551  (106)  or Clustal Omega (107) with default parameters and obtained alignments cleaned with trimAl v1. 4. 1 (108) to remove positions with more than 80% of gaps. Finally, alignments were used as matrix for Maximum Likelihood analysis. First, phylogenetic reconstructions have been performed using FastTree v2. 1. 10 (109) with default parameters to obtain a global topology of the tree.
Horizontal Gene Transfer demonstration Three different approaches were used to validate the putative horizontal gene transfer of the GH8. First, the GH8-coding gene of algae has been verified to be anchored in large scaffolds and surrounded by other algal genes. Visualization of GH8-like positions on scaffolds was performed unsing the R package chromoMap v0. 3. 1. Secondly, reads from sequencing were mapped on the region containing the algal GH8 to control for chimeric assembly using minimap2 v2. 17-r941  (115)  and default parameters. Finally, a phylogenetic analysis has been conducted to place algal GH8 in an evolutionary context. Using the BLASTp v2. 10. 1+ algorithm  (105)  with an e-value threshold of 1e-30 homologs of algal GH8-like were searched against three different database: the JGI fungal resources (accessed in February 2020, contains more than 1600 fungal genomes), the nonredundant protein database from NCBI (BLAST db v5) and the SymDB database covering Viridiplantae species  (15).
Obtained sequences were subjected to phylogenetic analysis as described above and using Clustal Omega for the alignment step and the fast tree reconstruction option from IQ-TREE. Presence of the GH8 functional domain (PF01270) was determined with hmmsearch function from the HMMER v3. 3 package (116) with default parameters. family. Branches are colored as follow: outgroup sequences without the GH8 domains are in grey, while bacteria, fungi and algae GH8 are colored in pink, orange and blue respectively. The red dots indicate the presence of the GH8 functional domain (PF01270). Sequence names have been hidden for readability reasons and can be found in the Supplementary Table  S8. D. Position of GH8-like coding-genes of algae on chromosome. For readability reasons, chromosomes longer than 5Mb are displayed separately.
Acknowledgments J. K. , C. L. and P-M. D are supported by the project  Engineering Nitrogen Symbiosis for Africa (ENSA)  currently funded through a grant to the  University of Cambridge  by the  Bill & Melinda Gates Foundation  ( OPP1172165 ) and the  UK Foreign, Commonwealth and Development Office as Engineering Nitrogen Symbiosis for Africa  ( OPP1172165 ). This work was supported by the  "Laboratoires d'Excellence (LABEX) "  TULIP  ( ANR-10-LABX-41 )" and by the  "École Universitaire de Recherche (EUR) "  TULIP-GS  ( ANR-18-EURE-0019 ). F. D. G. was supported by the  LOEWE-Centre for Translational Biodiversity Genomics (TBG)  funded by the  Hessen State Ministry of Higher Education, Research and the Arts (HMWK). We thank  Carola Greve  for assistance with PacBio library preparation,  Anjuli Calchera  for bioinformatic support,  Andreas Beck  for assistance with the micromanipulator algal cell isolation,  Nicolas Piganeau  and  Bas Tolhuis  for their helpful advice on PacBio sequencing and technical support.
Wide Angle X-ray Scattering (WAXS) In order to derive information on phase composition and degree of masks crystallinity depending on photodegradation level, WAXS data were collected on a Bruker Kappa Apex II diffractometer equipped with a mirror monochromator and a Cu Kα microsource (λ = 1. 5406 Å). Measurements were recorded in transmission mode on a two-dimensional detector placed at a 0. 065 m distance from the samples. The reader is referred to Appendix A for details on data acquisition, evaluation and analysis of WAXS diffractions curves. Following a procedure available elsewhere  [32, 38, 43, 49] , for each analysed sample we estimated a crystalline index (denoted as CI X ) defined by the ratio between area under the peaks corresponding to all crystalline phases and total area under the entire WAXS curve.
Atomic Force Microscopy (AFM) To address surface topography of mask samples, AFM experiments were performed on a FastScan Dimension Icon equipped with a Nanoscope V controller (Bruker). AFM imaging was carried out using contact mode at ambient temperature in air. The reader is referred to Appendix A for details on samples preparation and adopted AFM probes. Surface roughness of fibres was estimated on XY images using Bruker NanoScope Analysis software (version 1. 9). Roughness calculations were based on the entire images of the upper surface of cylinders laid lengthwise on the support. As fibres featured curved surfaces, flattening procedure was applied before roughness estimation. The entire images we considered for roughness evaluation consisted of 5-micron squares for the inner and outer layers and 2-micron squares for the middle one.
Library construction, sequencing and data processing Extracted DNA samples (4 replicates) were sent to Microsynth AG (Balgach, Switzerland) for sequencing. This company provides sample quality control and Nextera two-step PCR amplification using primer set 515f/806r targeting the V4 region of 16S rDNA  [41] , PCR product purification, quantification and equimolar pooling. Then, PCR libraries were sequenced on an Illumina MiSeq platform using a v2 500 cycles kit. Downstream processing including demultiplexing, merging, primer removal, quality filtering, trimming of Illumina adaptor residuals, chimera removal, operational taxonomic unit (OTU) clustering and OTU assignments were performed by Microsynth. Raw sequence files are available on the NCBI Short Read Archive (SRA) database under Bio-Project ID: PRJNA997609 and accession numbers: SAMN36684029 to 36684040.
Statistical analysis Time-to-event data analysis was used to investigate the direct or indirect (i. e. mask as a support of food resource) effects of mask and its ageing on G. roeselii survival. This approach allowed to (i) consider events occurring during the whole study period (not only at the final time point) and (ii) account for right-censored values, i. e. organisms whose death was not observed within the study period. Kaplan-Meier curves were used for time-to-event data representation. Log-rank tests were performed to compare survival curves between pairwise treatments. Bonferroni correction was applied for multiple comparisons (n = 3 ad hoc planned pairwise comparisons). To test differences between treatments, one-way ANOVAs were performed when assumptions concerning normality of data distribution (Shapiro-Wilk test) and homoscedasticity (Bartlett test) were met, followed by post-hoc Tukey tests.
In addition, for 28 days-degraded IL, ML and OL specimen, the curves feature a shallow bump in the 1400-1000 cm -1 range, which we attribute to C-O-X species  [45]. Using FTIR data, the helical content HC IR was calculated as detailed in Materials and Method section. Values are reported in Table  1  and vary between 0. 84 and 0. 95, without clear dependence on the duration of degradation. A stronger impact of UV exposure on HC IR might have been expected after inspection of data by Aslanzadeh and Haghighat Kish  [9]  who reported helical content value as high as 0. 95 for melt-spun PP fibres after 200 h ageing at 25 • C under UV-C radiation exposure. On the other hand, using attenuated total reflection (ATR) technique, Blais and co-workers  [13]  evidenced a restructuration of the surface layer of PP samples with a continuous increase of the helical content from 0.
Last, the nature of the adopted degradation treatment seems to be of outmost importance in defining the electrostatic features of the surfaces, including sign of the charge. Indeed, whereas Slepička et al. [83]  reported an increase in μ towards positive values for PP surfaces subjected to argon-plasma irradiation, our results display an opposite trend for PP materials exposed to UV for 3 and 28 days (Fig. 3A ). Moreover, results provided in Fig. 3B  versus pH do not show significant change in debris charge with increasing UV-exposure duration, which agrees with the similar slopes μ versus log(c KNO3 ) at c KNO3 > 100 mM in Fig. 3A. Granulometry. Granulometry results are given in Fig. 3C  for samples exposed to UV for 28 days. Data acquired on 3 days UV-exposed samples were not considered for such measurements, as they were not reproducible.
Characterization of river-biofilm formed on masks After 4 weeks incubation in Moselle River, pristine and 1 or 3 days UV-exposed mask samples were collected and brought back to the laboratory. DNA quantities obtained on 1-cm diameter discs are given in Fig. 6A. With increasing the level of UV-mediated alteration, the data reveal a well-marked decrease of the mean total DNA concentration extracted from the masks and therewith a reduction of the overall biomass in the biofilms. However, this conclusion is tempered by ANOVA test that suggests a non-statistical significance of the observed trend (p = 0. 113). In addition, for the same amount of extracted DNA analysed, the number of 16S rRNA gene copies seems to be lower on photodegraded masks, thus indicating a reduction in the number of bacteria within the biofilms (Fig.
Acknowledgement This work was financially supported by the  Observatoire Terre et Environnement de Lorraine (OTELo)  from  Nancy, France (Interdisciplinary Project BAlesMAsques). This work was performed with ressources from the  Pôle de Compétences en Physico-Chimie de l'Environnement ,  Pôle de Compétences en Chimie Analytique Environnementale , and  Pôle de Compétences en Biologie Environnementale ,  ANATELo ,  LIEC laboratory ,  UMR 7360   CNRS -Université de Lorraine. The  LERMAB laboratory  ( EA 4370-Université de Lorraine ) is thanked for providing the accelerated ageing chamber. The scanning electron micrographs were acquired on a microscope of the  SCMEM-GEORESSOURCES  ( UMR 7360 CNRS-Université de Lorraine ) with assistance of  Andreï Lecomte. Christophe Cloquet  from the  SARM  ( CRPG, CNRS-Université de Lorraine ) is thanked for his contribution to elemental chemical analysis.