dataesr/scientific-paragraphs-categorization huggingface dataset:
In other words, the more closely related the symbionts, the more likely they are to share genome content. Core Metabolic Pathways Shared by All Symbiont Species. The Ca. Thiodiazotropha symbionts rely on multiple pathways to oxidize reduced sulfur compounds to sulfate through a polysulfur or elemental sulfur intermediate and there were no major variations in sulfur oxidation capabilities across all the MAGs (Table  1  and SI Appendix, Table  S2  and Dataset S3 ). The energy generated from sulfur oxidation is used to power inorganic carbon fixation through the CBB cycle (Table  1 ). The MAGs of Ca. T. taylori, T. weberae, T. lotti, T. sp. "RUGA," and T. endolucinida each contained a gene encoding Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) form I (Table  1 ). Ca. T. endolucinida was the only species that possessed two distinct types of RuBisCO, forms I and II.
All five species also encoded the capacity for heterotrophic growth (Table  1 ). The genus name Thiodiazotropha was proposed following the recent discovery that lucinid symbionts are capable of fixing inorganic nitrogen from the atmosphere  (14, 15). Indeed, all five symbionts encoded large gene clusters involved in nitrogen fixation, including the widely used functional marker for nitrogen fixation, dinitrogenase reductase subunit (nifH), the structural genes (nifD and nifK), ferredoxins, and regulatory factors (Dataset S3). All species had a complete denitrification pathway for reducing nitrate and nitrite to nitrogen gas, and thus all had the potential to use nitrate and nitrite as alternative electron acceptors (Table  1 ). Fig. 1. Geographic distribution and host specificity of lucinid symbiont species.
The average nucleotide diversity outside the recombining gene sequences was 3. 6, 2. 4, 1. 9, and 0. 6 single-nucleotide variants per kbp for Ca. T. taylori, Ca. T. lotti, Ca. T. weberae, and Ca. T. endolucinida, respectively (Dataset S6). Although MAGs consist of consensus sequences of the most abundant representatives of an entire bacterial population, the low strain estimates from DESMAN (two or fewer strains) across all MAGs in this study provide confidence that these results are not confounded by strain differences within the gill metagenomes (SI Appendix, Table  S1 ).
Discussion A Single Cosmopolitan Symbiont Species Associates with Multiple Diverse Lucinid Host Species at Locations around the World. We investigated the diversity and the predicted functional variability of the symbionts associated with lucinids on a global scale. Fresh samples were complemented with specimens from museum collections to   S2  and Dataset S3. *This cluster of genes is putatively annotated with the function of methylotrophy. Note that a recent study implicated similar genes in tetrathionate oxidation  (92). expand the scope of the study beyond the most intensively studied lucinid habitats in the Caribbean and Mediterranean Seas  (15, 20, 24). We identified two lucinid symbiont species, Ca. T. taylori and Ca. T. "RUGA. " Ca. T. taylori is found in a remarkable eight different lucinid species from three different subfamilies (Figs.
taylori as a single cosmopolitan species-level group. With an ANI of about 94. 5%, the Ca. T. taylori and Ca. T. "RUGA" MAGs represent distinct, albeit closely related, genetic units (Fig. 1  and Dataset S1). Given that HR rates drop exponentially with decreasing sequence similarity, declining steeply between 90 to 95% ANI  (32) , we speculate that this seemingly small amount of nucleotide divergence likely prevents recombination between Ca. T. "RUGA" and Ca. T. taylori. Indeed, an ANI of 95% is widely used as a threshold for delineating bacterial species, as this is thought to correspond to a level of divergence that prevents genetic exchange by HR  (33) (34) (35). One could speculate that Ca. T. RUGA and Ca. T. taylori previously belonged to a single species-level group but were relatively recently separated and that if the local geographic Ca.
These observations are inconsistent with Ca. T. endolucinida's requiring these metabolic adaptations while they are housed in the buffered environment of the lucinid bacteriocytes. Moreover, our analysis of the C. orbicularis metatranscriptome indicates that the genes encoding RuBisCO form II and respiratory nitrate reductase are expressed at a much lower level compared to RuBisCo form I and the assimilatory nitrate reductases, respectively (Dataset S7). These data are further supported by the much lower abundance of RuBisCo form II proteins compared to form I in the C. orbicularis proteome  (14). Based on these observations, we hypothesize that Ca. T. endolucinida relies on these metabolic functions primarily during its free-living phase and we speculate that Ca. T. endolucinida could occupy an external environmental niche-one characterized by low oxygen availability-distinct from that of Ca.
Materials and Methods Sample Collection. Live clams were collected from sites throughout the Caribbean and Mediterranean (SI Appendix, SI Methods and Dataset S1). Gills were dissected in the field and preserved in RNAlater (AM7020; Life Technologies) or DNA/RNA Shield (R1100-250; ZymoBiomics) according to manufacturer's instructions and stored at -20 °C. Samples from locations in the Pacific and Indian Oceans came from the collections of the Natural History Museum (NHM) in London and the Florida Natural History Museum (FLMNH), Gainesville, FL (SI Appendix, SI Methods and Dataset S1). Access was permitted and organized by Dr. John Taylor (NHM) and Dr. Gustav Paulay and Dr. Amanda Bemis (FLMNH). SI Appendix, SI Methods and Dataset S1 list all the species used, sampling locations, dates, and sample sizes.
DNA Extraction, Preparation, and Sequencing. DNA was extracted from gill tissues using the Qiagen DNeasy Blood and Tissue kit (69506; Qiagen) or the animal tissue protocol from Analytikjena Innuprep DNA Mini Kit (845-KS-1041250) (SI Appendix, SI Methods). Samples were either treated with RNase or directly quantified before DNA libraries were prepared using Illumina-compatible library prep kits (Dataset S1 and SI Appendix, SI Methods and Table  S5 ). All libraries were sequenced with Illumina technology to generate paired-end reads of 150 bp or 250 bp length (SI Appendix, SI Methods and Dataset S1). Quality Filtering, Assembly, and Bacterial Genome Binning. Read libraries were trimmed, PhiX contamination-filtered, and quality-checked using BBMAP v37. 61's BBDUK feature  (53) ; parameters used are in SI Appendix, SI Methods and the Jupyter notebook.
Individual read libraries were assembled using SPAdes v3. 13. 1  (54, 55) ; parameters used are in SI Appendix, SI Methods. The resulting metagenomic assembly scaffolds were binned using a combination of Anvi'o v6. 1  (56, 57)   (SI Appendix, SI Methods). The bins were checked for completion using Checkm's taxonomy specific workflow and manually refined using "anvi-refine" (SI Appendix, SI Methods). MAGs that were determined to be 90% or more complete and less than 10% contaminated post refinement, referred to as high-quality MAGs, were used for further analyses. Potential strain numbers in individual clams/metagenomes were calculated using DESMAN v2. 1. 1  (61)  and the snakemake workflow (62) on the program (SI Appendix, SI Methods). Phylogenetic Analyses. Only the MAGs taxonomically assigned to Sedimenticolaceae or Chromatiaceae, using GTDB v0.
3. 3 (63)  were used in this study. We also downloaded publically available MAGs of other lucinid symbionts (Ca. Thiodiazotropha spp. and Sedimenticola spp. ), alongside A. vinosum as an outgroup, for this analysis (complete list of accession numbers in Dataset S1). The publicly available MAGs were quality-checked and filtered using the methods described above (and in SI Appendix, SI Methods). The CheckM v1. 1. 3 (64)  lineage workflow was used to identify, align, and concatenate a default set of 43 universal marker genes from all the available MAGs (Dataset S1); concatenated marker gene alignment can be found on Figshare  (19). This concatenated amino acid alignment was then submitted to the W-IQ-TREE server (65) using default settings (SI Appendix, SI Methods) and the resulting maximum likelihood tree was visualized using the Interactive Tree Of Life (iTOL) v5  (66).
Images were captured on a Leica TCS SP8 X confocal laser scanning microscope using a 63× objective (SI Appendix, SI Methods). Functional Annotation and Pangenomic Analysis of Bacterial Genomes. Anvi'o's pangenomic workflow was used for orthologous group clustering and functional comparisons (SI Appendix, SI Methods). We annotated all features containing open reading frames (ORFs) using eggNOG-mapper v2 (70) with eggNOG database v5. 0  (71). All ORFs were also annotated with Pfam domains (72) using HMMER v3. 3 (73) (parameters in SI Appendix, SI Methods). All high-quality MAGs were also used to create pangenome in Anvi'o with an mcl inflation value of 8; pangenomic genomes database and profiles are on Figshare  (74, 75). The MAGs were also annotated on the Rapid Annotation using Subsystem Technology (RAST) web server (https://rast.
Total RNA was extracted using TRIzol (Thermo Fisher Scientific) according to the manufacturer's instructions. rRNA depletion and library construction were carried out at the Vienna Biocenter Core Facilities GmbH as described in Yuen et al. (47). The RNA-sequencing reads were trimmed and processed as previously described by Yuen et al. (47). We used BBMAP (slow = t, ambiguous = best, minid = 0. 99) to align the processed reads to the MAG of Ca. T. endolucinida (GCA_001715975. 1), an endosymbiont of C. orbicularis from Guadeloupe  (53). FeatureCounts was used to quantify gene-level transcript abundances, which were subsequently converted to transcripts per million  (78). Metatranscriptomic results can be found in Dataset S7. Recombination Rates and Nucleotide Diversity of Bacterial Symbionts.
To infer recombination events in bacterial genomes, we used the maximum likelihood implementation of ClonalFrame, ClonalFrameML  (23). High-quality MAGs were aligned using progressiveMauve, in Mauve v2. 0  (79). Nucleotide sequences (i. e. , core genes) shared within the groups of MAGs analyzed were extracted with stripSubsetLCBs, a script previously described in ref. 80. These core genes were realigned with MUSCLE (81) and cleaned with trimAl (82) (parameters in SI Appendix, SI Methods). RAxML v8. 2. 10 (83) was used to build a phylogenetic tree from this new alignment as described in ref. 84. All alignments are available on Figshare  (85) (86) (87). The resulting tree and alignment were fed into ClonalFrameML to calculate the ratio of recombination vs. mutation events with default parameters (See Dataset S1 for MAGs used in this analysis).
Recombination events were computed and visualized in R v6. 3. 2 with the script cfml_results. R (SI Appendix, SI Methods). GUBBINS was used to estimate average nucleotide diversities inside and outside the clonal frame  (88). We also used the clonal frame alignments to reconstruct and visualize the phylogenetic relationships of the Ca. T. taylori MAGs as previously described (SI Appendix, SI Methods). All scripts used can be found in the associated Jupyter Notebook  (89). Data Availability. The data (raw reads, metagenomic assemblies, and MAGs) have been deposited with links to BioProject accession number PRJNA679177 in the NCBI BioProject database (https://www. ncbi. nlm. nih. gov/bioproject/). The BioSample accession numbers for the MAGS are SAMN16825223-SAMN16825285 and SAMN16952162-SAMN16952207 are the corresponding raw read sets.
using CONCOCT v1. 1. 0 (58) and MetaBAT v2. 15 (59) (details and parameters in SI Appendix, SI Methods and Dataset S1). The bins were then compared using dRep v2. 4. 2's dereplicate workflow (60) Osvatic et al. PNAS | 7 of 10 Global biogeography of chemosynthetic symbionts reveals both localized and globally distributed symbiont groups https://doi. org/10. 1073/pnas. 2104378118.
ACKNOWLEDGMENTS. We thank  Gustav Paulay  ( FLMNH, Gainesville, FL ),  Amanda Bemis , and  John Taylor  ( NHM, London ) for providing preserved samples. John Taylor also provided high-resolution images of lucinid clams for Fig. 2. We thank  Liz Hambleton  ( University of Vienna ),  Miriam Weber ,  Christian Lott ,  Boris Unger ,  Dorothée Makarow ,  Natalie Elisabeth  ( University of California, Berkeley ),  Diana Chin ,  Tim Oortwijn , and  Arthur Curry  for providing fresh samples. We also thank  Thalassa  for 300 million y of sheltering lucinids. We are grateful to  Stephanie Markert  for providing access to the proteomics data,  Ipek Yamin Meric  and  Nora Grossschmidt  for helping with DNA extractions,  Marina DeLeón  for help with fieldwork and travels in  Costa Rica ,  Cassandra Ettinger  for early discussions of the study, and  Guillaume Jospin  for support with the bioinformatic analyses.
We thank  Xavier Didelot  for discussions on the recombination analysis. L. G. E. W. was supported by Grant  GMBF5603  from the  Gordon and Betty Moore Foundation  (J. A. E. was Principal Investigator on the same grant). The work was also supported by the  European Research Council   Starting Grant EvoLucin  and a  Vienna Research Grant for Young Investigators  from the  Vienna Science and Technology Fund (WWTF ,  VRG14-021 ) and the  Austrian Academy of Sciences. Sequencing was carried out at the  DNA Technologies and Expression Analysis Cores at the University of California, Davis Genome Center  (supported by  NIH   Shared Instrumentation Grant   1S10OD010786-01 ), the  Biomedical Sequencing Facility at CeMM  (https://www. biomedical-sequencing. org/) in Vienna, Austria, and at the  Joint Microbiome Facility (JMF)  of the  Medical University of Vienna  and the  University of Vienna  (project  ID 1911-1 ).
Sample and Procedures A convenience sample of Brazilian internet users aged between 18 and 89 years was recruited online via social media platforms and email, between September 2018 and July 2019. Data collection was carried out anonymously through the online research platform Survey Monkey, and the questionnaire could be accessed and answered via smartphone, computer, or tablet. At the end of the questionnaire, participants were offered feedback on their results from the questionnaire on problematic internet use, for which an email address was requested. Those who provided the email address were invited, in August 2019, to answer the PIUQ-SF-9 scale again for the retest validation. The invitation was made in an automated way so that the researchers did not have contact with the participants' email contacts.
The time between the test and the retest was at least 4 weeks. All participants who filled in the sociodemographic data and completed at least 90% of the PIUQ-SF-9 were included. The missings were at random and were excluded from subsequent analyzes. The sample size estimate was 1,000, considered "excellent" for carrying out the confirmatory factor analysis (CFA) and other psychometric testings  (18, 19). This cross-sectional study is part of a multicentric project carried out in 16 countries, whose main objective is to assess cross-cultural aspects of internet and smartphone problematic use. The study was approved by the Research Ethics Committee of the Hospital de Clínicas de Porto Alegre (protocol number 89702318. 2. 0000. 5327), and it was conducted in accordance with the Declaration of Helsinki.
Statistical Analysis The analyses were performed in R environment (version 3. 2. 2) implemented by the lavaan package  (26). In addition, semTools package was used to estimate reliability measures  (27) , and semPlot package was used to produce the MIMIC diagram  (28). For ordered categorical variables, the Diagonal Weighted Least Squares estimation method and polychoric correlation coefficients were used with robust estimation of the means, variances, and standard errors. CFA was performed to verify the structural validity of the instrument. In addition to the analysis of the fitted model suggested by the original study  (12) , other three alternative models were also evaluated as proposed by a recent study that verified the psychometric properties of this questionnaire in nine European countries  (14).
The MIMIC is a variety of Structural Equation Modeling, which describes the effects of covariates on latent variables and the inter-relationships of latent variables, thus providing better insight than traditional correlational analysis  (32, 33). Based on the literature, it was assumed that age would have a negative effect on the PIUQ-SF-9 factors while time spent online, self-perception of problematic internet use, and depression symptoms would have a positive effect on the PIUQ-SF-9 factors. Floor and ceiling effects are considered to be present if more than 15% of respondents achieved the lowest or highest possible score, respectively  (34). The dataset and the analysis script were uploaded can be accessed from the following link: https://github. com/wagnerLM/PIUQ/blob/main/PIUQ-SF-9_script_data.
Demographic Data A total of 1,525 people answered the sociodemographic part, the questions about internet use and the PIUQ-SF-9 (72. 7% were female, mean age was 38. 7 years ± 13. 5). A total of 735 participants informed their email at the end of the questionnaire and were invited to complete the PIUQ-SF-9 retest. Thus, 237 out of the 735 responded to the PIUQ-9 retest (74. 7% were female, mean age was 38. 1 years ± 13. 8), in an average time of 6 months after the original completion. The main sociodemographic data of the test and retest samples are presented in Table  1.
Specifications table Subject Area: Neuroscience More specific subject area: Intracellular calcium dynamics Method name: Simple and quick standard error on the ratiometric calcium estimator Name and reference of original method: Sébastien Joucla, Andreas Pippow, Peter Kloppenburg and Christophe  Pouzat (2010)  Quantitative estimation of calcium dynamics from ratiometric measurements: A direct, non-ratioing, method Journal of Neurophysiology 103: 1130-1144 Resource availability: Python codes, data and all the information required to reproduce the manuscript results can be found on GitLab: https://gitlab. com/c _ pouzat/gettingse-on-ratiometric-ca-estimator.
Despite the ubiquity of ratiometric measurements in neuroscience and cell physiology, we are aware of a single paper-by some of us  [1]  -where the 'standard error question' was directly addressed. The method proposed in  [1]  requires a 3 wavelengths protocol: measurements at 340, 380 and 360 (the isosbestic wavelength) nm; it drops, so to speak, the above advantage of working with a ratiometric estimator since it fits directly the adu 340 and adu 380 data (at the cost of estimating some geometry related parameters) and it requires a model of the autofluorescence dynamics if the latter is not stationnary. It therefore requires a slightly more complicated '3 wavelengths' recording protocol as well as a more involved fitting procedure. The dataset of the companion paper  [3]  exhibits a clear but reversible autofluorescence rundown that cannot be ignored since autofluorescence accounts for half of the signal in the ROI.
Simulated data We are going to use the first transient of dataset DA_121219_E1 of the companion paper  [3]. The 'static' parameters -that is the parameters not link to the calcium dynamics -used for the simulation are the actual experimental parameters rounded to the third decimal ( Table  1  ). The simulated calcium dynamics is a monoexponential decay mimicking the tail of the transient: Ca (t) = Ca 0 + 0 if t < t 0 δ exp (-(t -t 0 ) /τ ) if t ≥ t 0 and the parameter values ( Table  2  ) are just a rounded version of the fitting procedure output (see companion paper  [3]  ). The simulated data obtained in that way are shown on Fig. 1  (blue traces) together with the actual data (red curves) they are supposed to mimic. At a qualitative level at least, our data generation model is able to produce realistic looking simulations.
Software and simulation details The methodological details of the measurements to which the analysis presented in the present manuscript was applied are described in the companion paper  [3]. The simulations, computations and figures of the present manuscript were done with Python 3 ( https://www. python. org/ ), numpy ( https://numpy. org/ ), scipy and matplotlib ( https://matplotlib. org/ ). The Python codes and the data required to reproduce the simulations and figures presented in this manuscript can be downloaded from GitLab ( https://gitlab. com/c _ pouzat/ getting-se-on-ratiometric-ca-estimator ). The use of scipy was kept to a bare minimum to maximize code lifeduration ( scipy tends to evolve too fast with minimal concern for backward compatibility). The random number generators used were therefore the ones of numpy : the uniform random number generator derives from the Permuted Congruential Generator (64-bit, PCG64) ( https://www.
One last model feature that was tested is its capability of reproducing three-stage drying protocols, which were found to be beneficial for reducing manufacturing costs while keeping optimal electrode properties. The results obtained show that our model is able to capture qualitatively such a behavior, confirming that applying high DR at the beginning and end of drying and low DR in between outputs less heterogeneous electrodes. In terms of perspectives, the computational workflow described in this article should be tested for a wide range of electrode formulations, AM particle size distributions, CBD sizes and DRs to verify its generalizability to different scenarios. In that sense, the code developed during this work will be released freely on the ARTISTIC project Github [69] for any computational researcher possibly interested into it, while it is already implemented in the ARTISTIC computational platform through an user-friendly interface [ 70 ].
Computational section The slurry and dried electrode simulations (155 AM and 5821 CBD particles) were performed through the open source molecular dynamics software LAMMPS and took ∼6 h and ∼6. 5 days by using one and two node(s) (128 GB of RAM) composed of 2 processors (Intel® Xeon® CPU E5-2680 v4 @ 2. 40 GHz, 14 cores) on the MatriCs platform (Université de Picardie Jules Verne), respectively. The initial structure (prior the slurry equilibration) was generated to match the experimental composition and AM particles size distribution by locating randomly the AM and CBD particles in a simulation box big enough (200 × 200 × 500 m, x × y × z ) to avoid significant particle overlap. All the details about the random structure generation can be found in the Supporting Information of Reference  [41].
Acknowledgments The authors acknowledge the European Union's  Horizon 2020 research and innovation programme  for the funding support through the  European Research Council  (grant agreement  772873 , " ARTISTIC  " project). A. A. F. acknowledges  Institut Universitaire de France  for the support. Results obtained using LAMMPS were achieved thanks to the  MatriCS HPC  platform from  Université de Picardie Jules Verne , particularly using the ARTISTIC project-dedicated computational nodes. The authors acknowledge  Dr. Garima Shukla  and  Dr. Emiliano N. Primo  from  LRCS-Amiens (France ) for very useful discussions.
Data and code availability The code developed along this work are available freely on the ARTISTIC project Github [69]  in two versions, one accounting for the atmospheric pressure as described in the model workflow section and the second one accounting for it through an effective gravity. In addition, this procedure is already implemented for free in the ARTISTIC computational platform, using here the effective gravity approach, through an user-friendly interface allowing to select the desired electrode composition (weight ratio between AM and CBD), SC, AM particle size distribution, CBD size, drying and calendering conditions [ 70 ].