dataesr/scientific-paragraphs-categorization huggingface dataset:
Statistical analyses Statistical analysis was performed in the R environment for statistical computing (inclusive of releases between 2021 and 2023). Increasing and decreasing seasonal trends in functional roles were assessed with linear regression. Pairwise comparisons of functional roles (the cumulative sum of all associated ORFs) between the early (May -June) and late (July -Sep) seasons were performed with the two-sided Kruskal-Wallis test based on the chi-squared distribution by ranks, with early and late seasons were delineated by plant phenology (flowering/ senescence in late season). The distribution and dynamics of MAGs' transcripts were compared with Ward's method for hierarchical clustering using euclidian distances of the estimated metatranscriptome abundances using pvclust (version 2.
Predicting the functional potential of focal MAGs We used gapseq  109  to predict completed metabolic pathways in our focal MAGs. We used the 'find -p all -b 200' option to search for pathways against the MetaCyc database. We filtered out incomplete pathways, and the remaining pathways were grouped into broader categories using MetaCyc classification and manually curated to focus on understanding the pathways relevant either for the plant environment or for microbial interactions with plants. These categories were defined as potential involvement in: i) plant (using plant metabolites/cell components), ii) phytohormone (known/potential involvement in phytohormone homeostasis), iii) stress (e. g. , drought, reactive oxygen species), and iv) general (pathways that utilize potential plant-derived products).
Furthermore, we also manually searched for genes/ pathways that were missed by gapseq but are known to be related to adaptation to plant-associated lifestyle, including secretion systems  110, 111  , oxidation of trace gases (H 2 and C. O. )  112, 113  , oxalate degradation, and phytohormone production/degradation. Similar to our biosynthetic gene analysis, the activity of predicted pathways was estimated based on mapped transcripts to identified genes. Contigs of focal MAGS were aligned (BLAST v2. 7. 1 + ) against nine isoprenoid precursor biosynthesis genes previously reported  40. The top hit of each query was considered and accepted as aligned if E-value was less than 1e-5.
Acknowledgements Support for this research was provided by the  Great Lakes Bioenergy Research Center, U. S. Department of Energy, Office of Science, Office of Biological and Environmental Research  (Awards  DE-SC0018409  and  DE-FC02-07ER64494 ), by the  National Science Foundation Long-term Ecological Research Program  ( DEB 1637653  and  1832042 ) at the  Kellogg Biological Station, Michigan State University AgBioResearch , and by the  DOE Center for Advanced Bioenergy and Bioproducts Innovation (U. S. Department of Energy, Office of Science, Office of Biological and Environmental Research  under award number  DE-SC0018420 ). This work was also supported in part by  Michigan State University  through computational resources provided by the  Institute for Cyber-Enabled Research  and in part by the  University of Wisconsin-Madison Wisconsin Energy Institute  as supported by  GLBRC Information Services.
Data availability The raw and processed metagenome and metatranscriptome data generated in this study have been deposited in the Joint Genome Institute Genome Portal database under proposal ID 503249 [https:// genome. jgi. doe. gov/portal/Seadynanfunction/Seadynanfunction. info. html]. The MAGs data generated in this study have been depositied in NCBI under bioproject PRJNA800073. The metadata, including metadata standards for metagenomes, metatranscriptomes, and metagenome-assembled genomes, for this study are provided in the Supplementary Data 1-7. Source data are provided with this paper.
It is a drawing of a man expressing different emotional states through the expression of his face or the variation of his body shape or the addition of abstract symbols (see Fig. 1 ). Although gender and age biases have sometimes been highlighted  [9, 10] , SAM is regularly used in cross-cultural or crossgenerational studies  [11, 10]  as a reference tool. For example, after a review of the literature, Morris et al. state that emotional responses to a ''standardized global advertisement" collected through the SAM, are very close between different cultures (e. g. USA and Taiwan). More generally, the SAM is often used as a reference when adapting to different cultural contexts stimulus databases for psychology studies (audio -IADS  [12] , verbal -ANEW or pictorial -IAPS  [13] ). The Affective Norms for English Words (ANEW) database is a set of normative emotional ratings for a large number of words.
When it comes to adapting this database to other languages, the SAM is often used as a common language or reference tool (e. g. , in Italian, Spanish, or Portuguese  [14] [15] [16] ). In a study led by Huang et al. , the SAM is even used to highlight cultural differences in image-related affect between Chinese and American young adults. This reflects the team's confidence that the interpretation of the tool is not biased by the culture of the participants  [13]. For soundscape assessment, this tool has already been investigated in some studies reported by Stevens et al. [17] [18] [19]. These authors state that the SAM is an appropriate method for the assessment of soundscapes, more intuitive and less time-consuming than the use of verbal scales. They also show significant relationships between the SAM and soundscape categorization or heartbeat measurement, as would be expected with verbal scales.
The Table  1  shows the verbal attributes presented in Spanish and French and their aimed translation to English. The 24 facial emojis have been selected from the open source image database (see Section 2. 3) and are shown in Fig. 2. 99 Chilean (63 males, 36 females, Mage = 39 years, SDage = 15 years) and 46 French (34 males, 12 females, Mage = 36 years, SDage = 12 years) have participated to the study. Fig. 3  shows principal component analyses of both data sets. The principal component analyses are computed only on the verbal scales, the facial emojis are added as supplementary variables. In view of these results, some initial conclusions can be drawn: It is possible to explore the circle of affects in a similar way, whether with verbal attributes or with facial emojis. The position of facial emojis in relation to verbal attributes in the French and Chilean groups is similar.
7 years, SDage = 3 years). The participants all signed a contract agreeing to share their results in this research, and as a thank you for their participation, the participants received a €20 gift voucher. The verbal scales presented in Table  2  are the French attributes that were selected for the experiment. The SATP Stage 2 protocol (see Section 2. 2) was followed from the calibration phase (open-circuit voltage calibration technique) to the data production. The results of the study carried out in France were added to the international database according to the protocol defined in the SATP.
SATP stage 2 protocol In Stage 2 of the SATP protocol, standardized listening experiments are conducted by each research partner with a sample of approximately 30 participants (aged 18-30, balanced in terms of gender) who are native speakers of the local language. These participants assess the soundscapes based on the data collection instrument translated into the local language. The participants had to listen to the stimuli with calibrated headphones. All research groups use the same set of auditory stimuli, which have been provided by University College London. This set consists of 27 binaural recordings (30 s) recorded in London during the summer and autumn 2019. Following a pilot listening experiment conducted at University College London, 27 desired audio stimuli from a pool of 50 + excerpts have been selected based on having a wellbalanced sound sources types' composition and the potential to elicit a broad range of responses for the attributes in use  [31].
Facial emojis The facial emojis have been selected from Twitter's open-source image database  [33]. Twitter is a very popular social network and many people have already encountered these emojis. Twitter also has the advantage of offering an open-source image database which, moreover, has been used in a preliminary study on the use of facial emojis for the description of affects. [23]. Among the Unicode emoji characters and sequences, 107 represent human faces and about 90 represent facial expressions related to emotions  [34]. From this database, to keep the experimentation time reasonable, 12 smileys were pre-selected. The emojis were selected with the aim of maximizing variance on the circumplex circle of affect. This selection was partly based on the pre-study presented in Section 2. 1.
They must also declare if they have known hearing problems. After an explanation of the test procedure, the participant is asked to listen to the 27 sound recordings of the SATP protocol on headphones, one after the other. The SATP dataset consists of 27 30-s binaural audio recordings made in urban public spaces in London and one 60-s stereo calibration signal. For each of the sound recordings, the participant must answer the following question: ''To what extent would you say that these emoticons represent the sound environment that you hear?" (in french: ''Dans quelle mesure diriez-vous que ces émoticônes représentent l'environnement sonore que vous entendez?"). To do this, the participant must move a slider initially set at the center (50/100), to the left if the facial emoji presented does not match the sound recording (towards 0/100) or inversely to the right (towards 100/100).
Descriptive analysis All the presented results in the descriptive analysis are aggregated by sound recordings using the median value of the attributes before computing the proposed analysis. The aggregated dataset contains 27 sound objects characterized by 12 variables. Fig. 5  shows that the first two dimensions of analyze express 93. 4% of the total dataset inertia (63. 2% for the first dimension and 30. 2% for the second). The two first dimensions are particularly salient for the description of the variance of the data set. Fig. 6  shows the projection of the variables "facial emojis" on the two main planes following the principal component analysis. The observation of emojis suggests that the first dimension corresponds to valence (e. g. , , ) and the second dimension to arousal/eventfulness (e.
[37]. Then, the dataset is aggregated by sound recordings using the median value. As before, the aggregated dataset contains 27 sound objects characterized by 12 variables. Transformation to ISOPleasant/ISOEventful was done on the Eq. 1 and 2: ISOPleasant ¼ ðp À aÞ þ cosð p 180 Þ Ã ðca À chÞ þ cosð p 180 Þ Ã ðv À mÞ Ã 1 4 þ ffiffiffiffiffiffi 32 p ð1Þ ISOEventful ¼ ðe À uÞ þ cosð p 180 Þ Ã ðch À caÞ þ cosð p 180 Þ Ã ðv À mÞ Ã 1 4 þ ffiffiffiffiffiffi 32 p ð2Þ The correspondences between the parameters of the equation and verbal attributes and facial emojis are presented in Table  2. Some verbal attributes have one or more easily determined equivalents. But, in other cases, where no equivalent could be easily found, the assumption of a perfect symmetry between the antonymous attributes is then made (e.
Nevertheless, the participants have relatively similar languages (originally Latin) and cultures. It would also be interesting to replicate the experiment presented in this study with a more culturally diverse population or in relation to their language skills. Also, a limitation of the study addresses the fact that in the coming years, the standard representation of emojis may change. However, the use of human faces representing emotions in a similar context probably remains something universal, as the studies presented in the introduction indicate. Only the representations of the Twitter database have been tested. However, the conclusions would probably have been very similar to other databases as the representations are very close. The use of smileys can also pave the way for describing elements of the sound environment using a standardized pictorial language beyond emotions.
For example, the emoji explicitly evokes silence or the emojis , or evoke classically assessed urban sound sourcess. Finally, this unicode database is constantly growing, and if, for example, a facial emoji seems to be missing to describe the chaotic dimension, new ones, not available at the time of the experiment, could be coming up like the unicode  U + 1FAE8 (also called shaking-head) and be appropriate for this attribute. Also, Fig. 7  shows that carries the weight of a third axis of variability in responses. The shape of the emoji may evoke surprise. It can be hypothesized that this emoji carries the dimension of familiarity with the sound environment, the third dimension proposed in Axelsson's study  [39]  and in Viollon's study  [40]. This hypothesis deserves to be explored in more detail.
Data sets Over the past few decades, the French Antarctic supply ship "l'Astrolabe" provided the opportunity to scientists to perform (mainly in the austral summer), sea-surface measurements and sampling from Hobart, Tasmania (43 • S 147 • E) to the French Antarctic base Dumont D'Urville (66 • S, 140 • E). As part of the SURVOSTRAL program (https://www. legos. omp. eu/survostral), continuous underway temperature and salinity "surface" seawater (at around 5 m), were measured since 1993 from R/V "l'Astrolabe" via a thermosalinograph (TSG). The raw data were recorded every minute. These raw data were then corrected for any bias (compared with discrete sample measurements), and by a median filter (over ±12 min) to reduce the noise of the measurements. These raw and corrected data sets are freely available (https://sss.
sedoo. fr;  Alory et al. , 2015). Below, we used the corrected data set. Similarly, as part of the MINERVE program (https://campagnes. flotteoceanogra-phique. fr/series/128/fr/), designed to quantify the interannual variability of the CO 2 properties in the Southern Ocean south of Tasmania, total alkalinity (A T ) and total CO 2 (C T ) were also sampled and measured from R/V "l'Astrolabe". These data are freely available (https://data. ifremer. fr/SISMER). For the purpose of this work, we are focusing only on the transect Hobart -Dumont D'Urville which occurred in February 19-23, 2010. The choice of this transect was randomly picked among the transects where Total alkalinity (A T ) and Total CO 2 (C T ) were measured. The measurement accuracy of sea-surface salinity (SSS), during this 2010 cruise is estimated to be ±0.
Results for underway SST and SSS measurements During the 2010 cruise, the SST and SSS properties were measured and recorded along with the ship's position (latitude and longitude) every minute. Since the ship was mainly sailing southward, and at a more or less constant speed, we will consider that the"X" axis is only the latitude (L). Since the TSG instrument measurement error for the temperature and salinity can be estimated as ±0. 001 • C and ± 0. 005, respectively, we would desire an interpolation maximum error of half that of the measurements. Thus, we define MaxErrT = ± 0. 0005 • C and MaxErrS = ± 0. 0025, for SST and SSS, respectively. Consequently, the overall uncertainty of the interpolated data along the whole cruise track would be less than (0. 001 + 0. 0005) ± 0. 0015 • C for temperature and (0.
Acknowledgments We genuinely thank  Alain Poisson  for the initiation of the MINERVE program, as well as  Elodie Kestenare  and  Rosemary Morrow  for the SURVOSTRAL data and helpful comments. We are grateful to  Daniel Davis  for helpful discussions, thoughtful suggestions, and providing language help. We thank the  Terres Austral et Antactique Françaises (TAAF)  and the  Institut Paul Emile Victor (IPEV)  for logistic support during the 2010 cruise.
Azido-PEG3-biotin was then covalently attached to the alkyne group of transferred SiaNAl units and biotin was detected using an HRP-conjugated anti-biotin antibody. As shown in Fig. 2B , significant and reproducible data were obtained on both acceptors showing that the fish ST8Sia IV is active, stable and efficiently transfers SiaNAl from CMP-SiaNAl. Initial velocity was proportional to the enzyme amount up to 20 µL and sialylated product appearance was linear up to 4 h of sialylation (Fig. 2C ). However, the fish ST8Sia II-r1 and ST8Sia II-r2 demonstrated no chemoenzymatic modification of these substrates under these conditions (Supplementary Fig. S1 ). This is in line with a previous study by Kitajima's group reporting very low levels of enzymatic activity of recombinant polysialyltransferases from O.
A previous study reported crystallization of the single chain Fv fragment of mAb735 (scFv735) in complex with an octasialic acid polymer of α2,8-linked Neu5Ac (PDB entry 3WBD)  37. In this complex, two antibody molecules (A and B) facing each other are associated with an octasialic acid. As illustrated in Fig. 6A , one scFv735 molecule (B) interacts with Sia2-Sia4, whereas the other (A) interacts with Sia6 -Sia8. The antigen-binding site is comprised of six complementarity-determining regions (CDR) L1, L2, L3 and H1, H2, and H3 interacting with three consecutive Sias through direct and indirect hydrogen bonds. Six amino acids are involved in direct hydrogen bonds; four of them Tyr37, Arg55, Tyr159 and Asp232 are critical for antigen recognition, whereas Tyr160 and Tyr179 are less important.
3-1-069/18; November 2018) and all the methods were carried out in accordance with relevant Institutional guidelines and regulations and with the ARRIVE guidelines. Brain and kidney tissues from whitefish were snap frozen in liquid nitrogen and kept at -80 °C for RNA isolation. Bioinformatics analyses of polysialyltransferases sequences and molecular docking. Nucleotide sequences of st8Sia2r-1/st8sia2a (NCBI nucleotide accession code: XM_041891035), st8sia2r-2/st8sia2b (XM_041836579) and st8sia4 (XM_041897387) genes from closely related Coregonus clupeaformis were synchronised with the transcriptome of Coregonus maraena (Bioproject ID: 302,355) previously  19  and compared with the orthologous sequences in human ST8SIA2 (NM_006011) and ST8SIA4 (NM_005668). Multiple sequence alignments of the corresponding protein sequences were achieved using ClustalW at PRABI-Gerland (https:// npsa-prabi.
ibcp. fr/ cgi-bin/ npsa_ autom at. pl? page=/ NPSA/ npsa_ clust alw. html). The amino acid sequence analysis was performed using the software of Expert Protein Analysis System (ExPASy; Swiss Institute of Bioinformatics, Switzerland; website (https:// www. expasy. org/, last accessed on: 04 November 2022). Hydropathy analyses and determination of potential N-glycosylation sites were performed using the servers TMHMM-2. 0: Prediction of Transmembrane Regions (https:// servi ces. healt htech. dtu. dk/ servi ce. php? TMHMM-2. 0, last accessed on: 04 November 2022) and the NetNGlyc 1. 0 Internet program (https:// servi ces. healt htech. dtu. dk/ servi ce. php? NetNG lyc-1. 0, last accessed on: 04 November 2022) of ExPASy. Sequences were also submitted to Compute pI/MW (ExPASy) analysis to determine their theoretical molecular weight.
To investigate to what extent analogous interactions could be found between the antibody and polySia chains made of eight Neu5Gc or Kdn, we took as reference direct and indirect interactions described for mAb735 complexed with polyNeu5Ac in ProteinDataBank (PDB) 3WBD and modified the Neu5Ac to Neu5Gc/Kdn molecules in the PDB 3WBD using the biocomputing software UCSF Chimera. The complex was minimized using the AMBER force field, and charges were computed using ANTECHAMBER  43.
The fluorescence was detected using the inverted Zeiss LSM780 confocal microscope with a 40 × oil immersion and data were collected with the ZEN 2010 software (Zeiss, Oberkochen, Germany). The images were analyzed with ImageJ software. Western blot analyses. WB was used to visualize and quantify tagged recombinant proteins secreted from transiently transfected HEK293 or CHO-K1 cells. For that purpose, 20 μL of culture media of transfected cells were boiled 5 min at 95 °C in 4 × Laemmli buffer (235 mM Tris-HCl pH 6. 8, 8% SDS, 40% glycerol, 10% β-mercaptoethanol, 0. 01% bromophenol blue), and resolved by 8% SDS-PAGE. Proteins were transferred onto Amersham Protran nitrocellulose membrane (GE Healthcare Life Sciences) for 75 min at 200 mA and checked with Ponceau red staining (5% acetic acid, 0.
2%, pH 6. 2) in a final volume of 100 μL. After sialylation, the wells were washed with PBS-T 0. 05%, then the CuAAC labeling reaction was performed by adding 100 μL of a solution containing 300 μM CuSO 4 , 600 μM BTTAA, 2. 5 mM sodium ascorbate and 250 μM azide-PEG3-biotin in PBS  44. After 1 h at 37 °C, the reaction was stopped by washing three times with PBS-T 0. 05%, then 100 μL of an HRP-conjugated anti-biotin antibody (32 ng/mL) were added for 1 h at 37 °C. After washing, 100 μL of TMB were added and incubated for 20 min at RT in the dark. Finally, the absorbance was measured at 620 nm with a spectrophotometer (SpectroStar Nano, BMG Labtech). The data were analyzed with GraphPad using the statistical ANOVA test between samples. Polysialylation assays were also performed at 27 °C for 4 h in 100 mM cacodylate buffer with 100 μM CMP-Sia (i.
Statistical analyses. The statistical analyses were performed with GraphPad Prism software (version 9. 5. 1) using One-way ANOVA and a multiple comparison Tukey test. Following labels are used: p < 0. 05 (*); p < 0. 01 (**); p < 0. 001 (***); p < 0. 0001 (***); ns, not significant (p ≥ 0. 05). Ethics statements. These experiments had been approved by the Landesamt für Landwirtschaft, Lebensmittelsicherheit und Fischerei, Mecklenburg-Vorpommern, according to the German animal welfare law (approval ID: LALLF M-V/TSD/7221. 3-1-069/18; November 2018) and all the methods were carried out in accordance with relevant Institutional guidelines and regulations and with the ARRIVE guidelines.
Acknowledgements We gratefully thank  Martina Mühlenhoff  ( MHH, GER ) for the gift of endoN and mAb735,  Joachim Bentrop  ( KIT, GER ) for the activated-leukocyte cellular adherence molecule (ALCAM) 3×FLAG tagged recombinant plasmid,  Wu Di  for the rainbow trout CSS (rtCSS) and  Lan-Yi Chang  for the PSGP-L and PSGP-H preparation. In addition, the authors thank for the excellent technical help of  Gesine Krüger.
Funding M. D. is a recipient of a doctoral fellowship from the  French Ministry and Region Hauts-de-France. The contribution of the  COST Action   CA18103 -INNOGLY supported by the  European Cooperation in Science and Technology (COST)  is greatly acknowledged. This work was supported by the  CNRS , the  ANR-21-CE44-0032  (project  PsaMar ), the  German Academic Exchange Service (DAAD)  (PN: 57446225 ), a grant of the  Deutsche Forschungsgemeinschaft  ( GA 1755 5-1 ), a  PHC Procope grant  (project  n°42533RC ) and the  University of Lille.
Quantification of immunogold-particle distance to the plasma membrane Immunogold-labeled images (using an MBP antibody) were acquired using a Tecnai12 transmission electron microscope. The distance to the plasma membrane of positive particles in the cytoplasm were measured using ImageJ software, https://imagej. nih. gov/ij/. The frequency distribution of particle distance (in nm) was plotted using R software, https://www. r-project. org/. Between, 35 to 40 cells were analyzed per condition.