dataesr/scientific-paragraphs-categorization huggingface dataset:
Crystal data, data collection and structure refinement details are summarized in Tab 1. All non-hydrogen atoms are refined anisotropically. All H atoms were located in difference Fourier electron-density maps and were treated as riding on their parent atoms, with C-H = 0. 950 Å, and Uiso(H) = 1. 2x Uiso(C) for bond length distances and riding restraints, respectively. All calculations were carried out using the WinGX software package  [27]. The cif-files of the studied compounds are available from the Cambridge Structural database under the numbers: CCDC 1995397-1995400. Copies of the available material can be obtained, free of charge, on application to the Director, CCDC, 12 Union Road, Cambridge CB2 1EZ, UK, fax: +44 (0)1223 336033 or Email: deposit@ccdc. cam. ac. uk.
Acknowledgements This work was supported by the  National Science Foundation China (NSFC , Project  51672181 ), the  Czech Republic from ERDF "Institute of Environmental Technology -Excellent Research"  (No. CZ. 02. 1. 01/0. 0/0. 0/16_019/0000853 ). M. H. R thanks the  Sino-German Research Institute  for the support (Project:  GZ 1400 ). S. V. R acknowledges  NSF  ( ECCS-1509786 ). H. Q. T is grateful for the financial support of an  Alexander von Humboldt Foundation  Fellowship. The authors are grateful to  Young Hee Lee  for useful discussions. Open access funding enabled and organized by Projekt DEAL.
This review is focused on studies using C. elegans to investigate its interaction with lactic acid bacteria having evidenced probiotic capacities. The pertinence and the advantages of using C. elegans as a model organism to identify new potentially probiotic strains are analyzed. The new way to use the worm, with the aim to screen microorganisms' collections for specific probiotic characters, is also detailed in the manuscript. This manuscript was written from an exhaustive review of the scientific literature related to the C. elegans model and the in vivo characterization of microbial strain with probiotic potential. All recent articles have been considered without distinction and studied objectively to avoid bias. The compilation of bibliographic data, from the PubMed database, was carried out in three stages.
The first, relating to the comparison of experimental models, was done using the keywords experimental models, in vivo, comparison, mice, rat, zebrafish, C. elegans, Drosophila melanogaster, and Galleria mellonella. The second, in connection with the use of the C. elegans model as the study of probiotics, required the following key words C. elegans, probiotic, live biotherapeutic microorganism, mechanisms, immunity, and pathway. Finally, for the third step, the keywords C. elegans, high-throughput, translational, and prospects were used. In all three steps, the logical operator "AND" was used. Fifty-two publications focused on C. elegans and probiotics are referenced in PubMed database, 19 out of 48 have been published from 2018, 11 of whom in 2019 and already 11 in 2020, confirming the emergence of this model in this research domain.
elegans RNAi Collection, The Wellcome CRC Institute, University of Cambridge, UK, https://www. sourcebioscience. com/life-science-research/clones/rnai-resources/c-elegans-rnaicollection-ahringer/). For example, in an infectious context, the use of transgenic GFP nematodes makes it possible to study the response in vivo by fluorescence analysis  (77, 78). Also, several online and freely accessible tools allow any type of researcher (beginner, confirmed, or expert) to access a large amount of data on the model, covering as well the fields of fundamental biology as applied (WormBase, https://wormbase. org/; WormWiring, https://www. wormwiring. org/; WormAtlas, https://www. wormatlas. org/; WormBook, http://wormbook. org/; OpenWorm, http://openworm. org/). C. elegans model allows transcriptomic, proteomic and networks analysis, offering promising mechanistically insights opportunities  (79) (80) (81).
Results We investigated the composition and the existence of speci c species in three compartments, namely, Sargassum at tide sites, in the surrounding seawater, and in inland seaweed storage sites. Metabarcoding data revealed shifts between compartments in both prokaryotic and eukaryotic communities, and large differences for eukaryotes especially bryozoans, nematodes and ciliates. Among the most abundant nematodes, we identi ed various bacterivores in all compartments, suggesting trophic interactions in Sargassum tides. We also found a number of species of interest, including methanogenic archaea, sulfate-and nitrate-reducing bacteria as well as putative pathogens.
More generally, microorganisms are likely to contribute to algae raft formation and maintenance, algae sinking and biodegradation upon beaching  [23] , and could provide important applications in the isolation of valuable compounds  [24]. At molecular level, the bacterial diversity associated with genus Sargassum has been investigated in only a few locations  [25] [26] [27] [28] , but neither the bacterial communities at tide sites nor the eukaryotic ones have ever been explored. Our study aims to investigate the microbial community associated with Sargassum reaching or lying on the beaches along the coastline of two islands from the lesser Antilles, Guadeloupe and Martinique. We used a metabarcoding approach to describe both prokaryotic and eukaryotic diversity. Comparing sequence data from the seaweed-associated fractions to the contiguous waters, we attempted to identify speci c OTUs associated with Sargassum.
The resulting libraries were quanti ed by qPCR and sequenced using a HiSeq 2500 2 × 300 paired-end run by Fasteris SA (Plan-les-Ouates, Switzerland). Sequence processing. Amplicons of the 16S and 18S rRNA gene sequences were analyzed independently with the mothur software version 1. 41. 3  [30] , following a standard operating procedure for Illumina MiSeq data  [31]. First, contigs were assembled between the read pairs. Then the barcode, primer sequences and low-quality sequences were removed (minimum length of 350 bp and maximum length of 420 bp, removing any sequences with ambiguous bases and any sequences with homopolymers longer than 8 bp). The sequences were then aligned to the SILVA reference database release 132  [32]  and preclustered (pre. cluster, diffs = 1). Singletons were excluded, and chimeras were removed with vsearch (Rognes et al.
, 2016) implemented in mothur. The sequences were then classi ed using the k-nearest neighbor (knn) algorithm implemented in mothur and the BLASTN search method (cut-off of 80%) with the SILVA reference database release 132 and the PR2 database v4. 11. 1  [33]  for the 16S and 18S rRNA gene amplicons, respectively. After classi cation, nonbacterial, chloroplast, mitochondria (for the 16S rRNA gene dataset), noneukaryotic, Sargassum (for the 18S rRNA gene dataset) and unknown (for both 16S and 18S rRNA amplicons) sequences were excluded. To account for differences in sampling efforts, 28,491 and 53,263 sequences from the 16S and 18S rRNA gene datasets respectively, were then randomly subsampled from each sample. Finally, operational taxonomic units (OTUs) were generated using the vsearch distance-based greedy clustering algorithm, with an OTU being de ned at the 97% and 99% sequence similarity level for the 16S and 18S rRNA gene reads, respectively.
Diversity and statistical analyses. All the statistical analyses were computed using R software version 3. 6. 3. Principal coordinates analyses (PCoA) and constrained analysis of principal coordinates (CAP) were computed based on Bray-Curtis distances with the phyloseq package  [34]. The effect of compartments on prokaryotic and eukaryotic community composition was tested by non-parametric permutational multivariate analysis of variance (PERMANOVA), as implemented in the vegan function adonis (permutations = 9999), after checking for homogeneity of group dispersions with the vegan function betadisper  [35]. We also used permutation tests for CAP, as implemented in the vegan function anova. cca (permutations = 9999). To test the relationship between the bacterial and eukaryotic community matrices and between microbial community matrices and geographical location, partial Mantel tests were performed using the ecodist package [36], with Pearson correlation coe cient and 10 6 random permutations.
For each clade, we rst collected nearly full length 18S rRNA gene sequences from recent studies  [39] [40] [41]  as reference sequences. These sequences were aligned on the Silva SSU database using SINA v1. 2. 11  [42]  and the subsequent alignments were ltered using trimAl v1. 2rev59 with the gappyout method  [43]. OTU sequences were added to the reference alignments using the --addfragments option of MAFFT v7. 310  [44]. Alignments were trimmed and Smart Model Selection  [45]  was used to determine the best t evolutionary model based on Akaike Information criterion. Subsequently, maximum-likelihood phylogenetic trees were built with PhyML 3. 0  [46]. Branch supports were calculated using a Chi2-based parametric approximate likelihood-ratio test (aLRT)  [47]. Finally, each tree was visualized and edited with iTOL  [48].
Regarding the "medium effect", corresponding to Sargassum collected on the seashore compared to Sargassum from inland storage sites, we identi ed 146 prokaryotic and 32 eukaryotic OTUs with differential abundance (Figure  5C-D ). Sargassum samples from the beach showed signi cant enrichment of 93 OTUs prokaryotic OTUs. They contained Saprospiraceae, Flavobacteriaceae, Cyanobacteria, Alphaproteobacteria and Gammaproteobacteria, including the most abundant OTU in our dataset which was assigned to the genus Vibrio, and Planctomycetes (Figure  5C , brown bars). The prokaryotes found to be enriched in terrestrial samples represented 53 OTUs distributed over 9 phyla (Figure  5C , green bars). For the eukaryotes, the marine Sargassum showed signi cant enrichment in 24 OTUs, Dynophyceae, with some members probably from the genus Amphidinium, Bryozoans, Hydrozoans, Bacillariophyceae, a ciliate from the Stichotrichia subclass, and a Pelagophyceae likely to be the Sargassococcus simulans species (Figure  5D , brown bars).
Functional inference of prokaryotic diversity In order to investigate the microbial functions associated with the Sargassum-associated samples, we used FAPROTAX to predict the metabolic functions of the prokaryotic taxa and identi ed 2,831 prokaryotic OTUs (12. 7 % of the global dataset) that could be functionally assigned to a minimum set of 22 functional groups (Figure  6 ). The ve most abundant groups corresponded to chemoheterotrophy (1,260 OTUs; 23. 19% of the abundance), fermentation (314 OTUs; 13. 04% of the abundance), nitrate reduction (71 OTUs; 9. 32% of the abundance), phototrophy (388 OTUs; 6. 98% of the abundance), and respiration of sulfur compounds (404 OTUs; 3. 91% of the abundance) (Figure  6 ). Intracellular parasites, predators or exoparasites, and animal parasites or symbionts, corresponded to a relatively large number of organisms with 491, 263 and 189 OTUs, respectively.
Commonality and differences in eukaryotic diversity Several taxonomic investigations devoted to speci c classes or to the global eukaryotic communities have revealed the micro-and meiofauna associated with Sargassum spp. [19, 49, [64] [65] [66] [67]. The present study reports the largest molecular inventory of eukaryotic species associated with Sargassum. The largest group found corresponded to the opisthokonts, representing 24. 9% of the total diversity and about half (48. 9%) of the abundance. With a total of ~3,600 OTUs, our data highlight the signi cant diversity of metazoans, with considerable differences depending on the Sargassum samples (Additional le 4). With ~2,200 OTUs, the surrounding water was dominated, in decreasing order, by Arthropoda, Bryozoa and Annelida (Additional le 3).
A contrasting result was found for the M. Sarg samples that were dominated by Bryozoan, Arthropoda, Platyhelminthes, Cnidarian and Nematodes (Additional le 3). Bryozoa, a large group of often calci ed aquatic invertebrates  [68] , which is known to contain abundant epibionts on Sargassum species  [15, 66] , were largely present on the surface of the collected Sargassum (Additional le 5). Phylogenetic analyses revealed that among the 490 OTUs assigned to Bryozoan, 438 of them were clustering with Membranipora membranacea (accession: JN680943. 1) (not shown), including the most abundant OTU that largely dominates our dataset with 19. 6% of the total abundance. Other previously described eukaryotes associated with Sargassum sp. were found such as Fungi (~410 OTUs; with putative endophythes of the genus Corollospora or Arthrinium) and Choano agellates (~190 OTUs)  [64, 69].
Nematodes, which represented the most diverse group of Metazoans (21. 4% of their total diversity), showed striking differences depending on the substrate type. They were largely dominant in terrestrial samples, with ~92% of the metazoan's abundance. The association between nematodes and oating Sargassum from the Atlantic region was already noted a century ago  [70]. While colonization of such usually benthic meiofauna could be the result of accidental encounter, benthic nematode species were found attached to the surface of pelagic or benthic Sargassum spp  [71] [72] [73] [74]. In our dataset, we found that the most abundant OTUs could be present in the three different compartments, although with potentially speci c patterns (Figure  4 ). Marine Sargassum-associated nematodes belong to the Enoplia and Monhysterida clades that have previously been described in marine habitats and present bacteriovore and algivore-omnivore-predator trophic behaviors  [39, 75].
Stranding and decaying stranded Sargassum along the shore could induce alterations in the structure of the intertidal soft-bottom and help nematode fauna to colonize the macroalgae. On the other hand, Halicephalobus (Tylenchina) and Rhabditidae, which are bacterivores  [39] , presented exclusive or speci c patterns associated with terrestrial sites. Regarding the Halicephalobus OTUs, the best blast hit for Otu00067 and Otu00111 was Halicephalobus mephisto (accession number GQ918144), a bacterivore nematode found a the terrestrial deep subsurface that presented hypoxic conditions and a temperature of 37°C  [76]. Similar conditions are expected to occur in T. Sarg samples. After the Opisthokonts, the Alveolata were the second most diverse superphylum in our samples, including 1,932 dinophyceae and 1,557 ciliate OTUs, corresponding to 15.
The M. Sarg samples only showed 4 OTUs that were differentially present in this compartment compared to T. Sarg which had two of the three most abundant OTUs in the whole dataset (a Cyanobiaceae and a Cryomorphaceae). In the terrestrial samples, 11 OTUs were considered as biomarkers, with Saprospiraceae (3 OTUs) and new environmental members of the Rivulariaceae family. Altogether, our data revealed a number of potential new molecular markers associated with Sargassum racks from the Caribbean, with a number of them corresponding to potentially new or poorly described species involved in the trophic food webs at tide sites.
Conclusions Our study demonstrates speci c micro-and meiofauna depending on the Sargassum samples and identi ed speci c prokaryotic (archeae and bacteria) and eukaryotic biomarkers for marine waters at tide sites, near-shore and beach stranded wracks, and inland storage sites. The description of members of the meiofauna (i. e. , ciliates and nematodes) that may play important roles in determining community structures provides a rm grounding for further investigation of algal organic matter decomposition and nutrient transfers between the trophic levels, and emphasizes the need for careful investigation of the entire diversity that contributes to gas production. Based on our results, carefully designed molecular studies with the aim of delivering comparative data analyses can provide effective information on species dispersal via drifting Sargassum, and on biogeographical differences in the Sargassum holobiont.
Acknowledgments This work was supported by the  Labex DRIIHM , the  French "Investissements d'Avenir" program  ( ANR-11-LABX-0010 ), managed by the  ANR  and the  Human-Environment Observatory Littoral Caraïbe. We also acknowledge the essential nancial support of the  Agence de l'Environnement et de la Maîtrise de l'Energie (ADEME).
The dataset was made available to us on April 21 st. Given the time constraints and the crisis context, the hypotheses developed and tested in the present study were not subjected to a specific pre-registration. Details on the overall survey structure and content are presented in Section A of the Supplementary Appendix (SA). All methods were performed in accordance with relevant French and European guidelines and regulations. The study was approved by the Paris School of Economics IRB (Certificate 2020-009). Although PYG is a member of the Paris School of Economics IRB, PYG did not participate in reviewing the proposal. The survey respondents were recruited by Qualtrics and paid 4. 45 € per completed questionnaire. The IRB waived the need for informed consent as (i) respondents' anonymity and RGPD compliance were guaranteed by Qualtrics; (ii) the experimental section of the survey used innocuous priming (iii) respondents were free to opt out of the survey at any moment.
Initially the meta-analysis revealed a significant bilingual advantage, but the effect size was small in magnitude (Hedges' g = 0. 06, p < 0. 05). However, after correcting for publication bias using the PET-PEESE model  (Stanley and Doucouliagos, 2014) , the difference between bilinguals and monolinguals was no longer significant. (Hedges' g = -0. 08, p = 0. 099). Further analyses revealed that task and age were not significant moderators of study level effect sizes. The key finding from this review is that the bilingual advantage may be an artifact of publication bias. Paap (2019) also presented evidence suggesting the bilingual advantage may be attributed to publication bias. This review summarized data from 109 studies. The included studies measured executive functioning using either the Stroop, Simon, Flanker, or Attentional Network Tasks.
Study Design This report included both published and unpublished studies. Published studies were identified by searching the following electronic databases: Psychological Information Database (PsycINFO), Ageline, Medical Literature Analysis and Retrieval System Online (MEDLINE), Cumulative Index to Nursing and Allied Health Literature (CINAHL), Education Resources Information Center (ERIC), and Excerpta Medical Database (EMBASE). The search strategy used to identify relevant studies involved searching titles and abstracts for records containing synonyms for "bilingualism" and "executive functioning. " The complete search syntax used to search each database is available for download via the Open Science Framework (https://osf. io/ ykp5w/?view_only=1d90f8c86146466e8dcfb6c4d23a334f). The first search was executed in January, 2017.
An additional search was undertaken in March, 2018 and then again in December, 2019 to ensure that any records published since the initial search were also included in the meta-analysis. Unpublished studies were found by searching the reference lists from three recent reviews  (Lehtonen et al. , 2018; Donnelly et al. , 2019; Paap, 2019). This method was chosen to identify unpublished literature as there is no consensus about which databases used to search for gray literature. In this review we also wanted to ensure that the analyses of unpublished literature would include the same studies used in past meta-analysis, which was achieved using this method.
Study Inclusion and Exclusion Criteria Studies were included in this review if they met the following criteria. First, participants in each study needed to be healthy adults or children. Studies undertaken with clinical samples (e. g. , ADHD or ASD) were excluded. In cases where a study presented data from both clinical and healthy samples (e. g. ,  Mor et al. , 2015) , only data from healthy participants were extracted. Second, the study needed to compare a group comprising bilingual participants to a group comprising monolingual participants on an executive functioning task. Studies presenting data from only bidialectal  (Antoniou et al. , 2016; Wu et al. , 2016; Scaltritti et al. , 2017)  or trilingual groups were excluded. Where a study included both bilingual and trilingual/bidialectal samples, only data from bilingual participants were extracted.
Effect Size Calculations and Data Extraction Procedures Data was extracted from each study so that Hedges' g (Hedges and Olkin, 1985) could be computed. Hedges' g measures differences between groups in standard deviation units, adjusted for sample size. For each study, data were extracted in order to compute effect sizes for the Stroop Task, Simon Task, Attentional Network Task, Flanker Task, Trail Making Test, Task-Switching Paradigms, and Card Sort Tasks. It was common for studies to quantify performance using accuracy, reaction time, and/or a measure of an interference effect. Effect sizes were computed separately for each of these variables. For each task, data were extracted so that separate effect sizes could be obtained for incongruent and congruent trials, as well as for an interference effect.
This variable measures the increased cognitive demands required to resolve incongruent, relative to congruent, trials. On this variable, smaller values indicate that task is placing fewer demands on executive functioning processes. This variable is referred to as the interference effect in this report. Since the focus of this report was to examine the effects of bilingualism on executive functioning, effect sizes from incongruent trials and interference scores were primarily of interest. However, for completeness, data were also extracted to compute effect sizes summarizing performance on congruent trials as well. For congruent trials, incongruent trials, and the interference effect, positive Hedges' g values indicate superior performance by the bilingual group. Effect sizes for these variables were computed separately for accuracy and reaction time data.
For accuracy data, effect sizes ranged from -0. 170 to 0. 178. On the Attentional Network Task, the average effect size was positive and significant, although small in magnitude. This result indicates that for congruent trials on this task, bilinguals are more accurate than monolinguals. There were no other significant results from this set of analyses. Mixed-effects subgroup analyses comparing differences in these task-level average effect sizes were not significant (p = 0. 727). Thus, for accuracy data obtained from congruent trials, the type of task used was not influencing effect sizes. Effect sizes for reaction time data collected from congruent trials ranged from -0. 198 to 0. 278. The average effect sizes from the Trail Making Test, Attentional Network Task, and Simon Task were all positive and significant, though small.
Specimens Specimens included in molecular analyses. DNA extraction numbers unique to each individual are indicated in phylogenetic trees as well as in lists of material examined and in figure captions (numbers are between brackets). Our molecular data set includes 190 Peronia individuals, only eleven of which correspond to COI sequences obtained from GenBank or BOLD (Table  2 ). Anatomical descriptions are based on those 179 Peronia individuals for which sequences were generated for the present study as well as the available type material for existing names (see below). All DNA sequences for the eleven outgroups are from our previous studies  (Dayrat et al. 2016 (Dayrat et al. , 2017 (Dayrat et al. , 2018 (Dayrat et al. , 2019a, b, c, d;, b, c, d; Dayrat and Goulding 2017; Goulding et al. 2018a, b, c) , with the exception of the nuclear sequences for Laspionchis boucheti, which are new (Table  2 ).