dataesr/scientific-paragraphs-categorization huggingface dataset:
Study design and population We analysed data from the COVID-19 GRA Vaccine Survey to investigate symptom duration among people with SARDs who reported test-confirmed COVID-19. Briefly, the survey was iteratively developed in collaboration with rheumatologists, investigators, stakeholders and patient partners and disseminated online broadly via social media, email lists of the GRA and patient/physician organisations. The survey was launched globally in English on 2 April 2021, and subsequently translated into 11 other languages (Italian, Hebrew, French, Punjabi, Russian, Spanish, Arabic, Traditional Chinese (Mandarin), Simplified Chinese, Turkish and Hindi). We analysed data up to 15 October 2021, but nearly all responded prior to 1 July 2021. Participants provided consent at the initiation of the survey and confirmed SARD status and age of 18 years or older.
Characteristics The survey collected data on demographics, rheumatic medications and comorbidities. Demographics included age, sex and race/ethnicity (Asian, black, Hispanic/ Latinx/Latin American, Middle Eastern or North African, American Indian/Alaska Native/Aboriginal/Indigenous/First Nations, white or other), WHO geographic region of residence (Americas, European, African, South-East Asian, Western Pacific or Eastern Mediterranean) and education (high school or less, some college, graduated college or graduate/professional degree).
Infections Infections Infections Other studies have also investigated prolonged COVID-19 symptom duration among people with SARDs. A recent study performed in Boston, Massachusetts, USA surveyed 174 people with SARDs who survived confirmed COVID-19 (82% as outpatient) and reported a median symptom duration of 25 days. 10 That study found that a higher proportion of patients (45%) met the CDC definition for prolonged symptom duration than our current study (26. 0%). Unlike the present study, they had data on specific post-COVID-19 symptoms; fatigue, pain, dyspnoea, dysgeusia and anosmia were common. 10 That study also found a high proportion of DMARD disruption and SARD flares after COVID-19, emphasising that COVID-19 may also impact the underlying SARD activity. Another study found that SARD status was not associated with risk for 'long-haul' COVID-19 (defined in that study as 3 months or longer) compared with people without SARDs seen in a New York City academic rheumatology practice.
Strengths of our study include the relatively large sample size of contemporaneous survey data from people with SARDs and test-confirmed COVID-19 as well as the international nature of the study with multiple languages. However, there are also limitations to consider. First, the primary aim of the survey was to gather information about COVID-19 vaccine experience and perceptions. It is possible this may have selected for healthier people. However, survey dissemination did not select for people still experiencing COVID-19 symptoms, which may be a relative strength, as it may be more representative of people with SARDs who had COVID-19. Second, the results relied on self-report that may be inaccurate or subject to recall bias, particularly in those whose infection occurred remotely relative to survey response and in those with high SARD activity, features of which may overlap with COVID-19 symptoms.
] [37]  In conclusion, our study suggests that the majority of people with SARDs and COVID-19 may have symptom resolution by 15 days of onset. However, a subset may experience prolonged symptom duration and experience lengthy duration of symptoms. We found that the severity of acute COVID-19, older age and comorbidities may be associated with prolonged symptom duration. Conversely, those experiencing COVID-19 more recently appeared less likely to experience prolonged COVID-19 duration. Prospective studies are needed to investigate symptom duration after breakthrough infection, among those on specific immunosuppressive therapies and in contemporaneous settings, related to treatment and viral variants. Retrospective studies are also needed to investigate other health-related outcomes, such as clinical events, after acute COVID-19 among people with SARDs that could be performed using population-based and administrative datasets.
Acknowledgements We wish to thank all patients who participated in the  COVID-19 Global Rheumatology Alliance Vaccine Survey. Contributors MD, KK, JL, MSP, ES, SES, JH, JSi and JSp contributed to data collection, data quality control, data analysis and interpretation. They drafted and revised the manuscript critically for important intellectual content and gave final approval of the version published. TTM, CH, MLa, MLe, GF, L-AT and LGR contributed to planning and data collection, reviewed the manuscript and provided important intellectual content. SB, WC, RG, PMM, PCR, PS, ZW and JY contributed to the acquisition, analysis and interpretation of the data. They drafted and revised the manuscript critically for important intellectual content and gave final approval of the version published. JSp,  JSi  and JH directed the work, designed the data collection methods and contributed to the analysis and interpretation of the data.
, 2017  culture protocols. Fixation followed by Phalloidin (actin) and Hoechst (nuclei) staining was performed on the four species as described for Clytia hemisphaerica in  Sinigaglia et al. , 2020. Samples were mounted in 50% Citifluor AF1 antifade mountant and imaged using Leica SP8 confocal and Zeiss Axio-Observer microscopes. Extant priapulid worms (Priapulus caudatus) (see Figure  4 -figure supplement 1) were collected (JV) from near the Kristineberg Marine Station (Sweden), fixed with glutaraldehyde and dried (Critical Point) for SEM observations (Univ. Lyon). state funds are managed by the ANR within the Investments of the Future program under reference ANR-10-INBS-02.
Acknowledgements We thank the  China Postdoctoral Science Foundation  (No. 2020M672013 ), the  Natural Science Foundation of China  (Nos. 41902012 ,  41720104002 ,  41876180 ,  41772021 ,  41911530236 ), the  Strategic Priority Research Program  of the  Chinese Academy of Sciences  (No. XDB26000000 ),  111 Project  of the  Ministry of Education of China  (Nos. D17013 ,  D163107 ), the  Most Special Fund  from the  State Key Laboratory of Continental Dynamics ,  Northwest University, China  ( BJ11060 ). This work was also supported by  Agence Nationale de la Recherche (ANR) :  Lucas Leclère   ANR-19-CE13-0003 , the  Région Auvergne-Rhône-Alpes  and the  Univ. of Lyon  ( PAI grant  to JV), for financial support. We thank  J Sun  and  J Luo  for the preparation of microfossils and SEM technical assistance, and the  CTµ (University of Lyon ) for access to electron microscopy.
Cryo-EM single particle analysis of the different compaction states of the mimivirus genomic fiber In order to shed light on the mimivirus genome packaging strategy and to determine the structure of the purified genomic fibers, we performed cryo-EM single-particle analysis. The different conformations of the genomic fiber initially observed by negative staining (Fig. 1 ) and cryo-EM resulted in a highly heterogeneous dataset for single-particle analysis. In order to separate different conformations, in silico sorting through 2D classification (using Relion  (28, 29) ) was performed. Next, we carried out cluster analysis relying on the widths of the helical segments and correlations (real and reciprocal spaces) between the experimental 2D class patterns (Fig. 1 -figures supplement 5 & 6). Three independent clusters (Cl) could be distinguished, corresponding to the compact (Cl1), intermediate (Cl2) and relaxed (Cl3) fiber conformations (Fig.
Models of the three helical assemblies and asymmetric unit were further refined using the real-space refinement program in PHENIX 1. 18. 2  (33). In the 3. 3 Å resolution map of the asymmetric unit, most side chains and notably the FAD co-factor are accommodated by density suggesting that the oxidoreductase enzyme could be active (Fig. 3D ). Density that can be attributed to the FAD cofactor is also present in the Cl2 and Cl3a maps. The atomic models of Cl1a and Cl3a dimers are superimposable with a core RMSD of 0. 68 Å based on Cα atoms. In the Cl1a and Cl2 helices, the monomers in each dimer are interacting with two different dsDNA strands. As a result, the DNA strands are interspersed between two dimers, each also corresponding to a different strand of the protein shell helix (Fig. 3 ).
Data acquisition Tilt series were acquired using SerialEM (57) on a Titan Krios (Thermo Scientific) microscope operated at 300 keV and equipped with a K3 direct electron detector and a GIF BioQuantum energy filter (Gatan). We used the dose-symmetric tilt-scheme (58) starting at 0° with a 3° increment to +/-60° at a nominal magnification of 64,000x, a pixel size of 1. 4 Å and a total fluence of 150 e-/Å² over the 41 tilts (i. e. ~3. 7 e-/Å²/tilt for an exposure time of 0. 8 s fractionated into 0. 2 s frames (supplementary file 4).
Data acquisition Grids were imaged using a Titan Krios (Thermo Scientific) microscope operated at 300 keV and equipped with a K2 direct electron detector and a GIF BioQuantum energy filter (Gatan). 7,656 movie frames were collected using the EPU software (Thermo Scientific) at a nominal magnification of 130,000x with a pixel size of 1. 09 Å and a defocus range of -1 to -3 μm. Micrographs were acquired using EPU (Thermo Scientific) with 8 s exposure time, fractionated into 40 frames and 7. 5 e -/pixel/s (total fluence of 50. 5 e -/Å²) (supplementary file 4).
This similarity metric was based on a 2D image cross-correlation scheme, invariant to image shifts, and mirroring  (67). The number of sub-clusters was manually chosen by visual inspection. For the most populated 2D classes corresponding to the most compact conformations, the number of sub-clusters was small: n=2 sub-clusters, Cl1a and Cl1b, and n=1 sub-cluster for the intermediate class, Cl2. However, the number of sub-clusters was higher (n=5) for the relaxed conformation (Cl3 from green to purple in Fig. 1 -figure supplement 6), highlighting the overall heterogeneity of our dataset with compact, intermediate, relaxed states and even loss of one protein strands (Cl3b) and unwound ribbons.
Focused refinement of a single oxidoreductase dimer The Cl1a 3D map was used to make a mask corresponding to a single dimer of oxidoreductases through the segmentation module (71) of the program Chimera (72) (this mask was deposited as part of the EMDB D_1292117739). With Relion and this mask we performed partial signal subtraction  (73)  to remove the information of the other dimers from the experimental images generating a new stack of subtracted images. This was followed by focused refinement with an initial model created (command "relion_reconstruct") from the subtracted dataset and the corresponding orientation/centering parameters from the partial signal subtraction. CTF parameters refinement was performed followed by a last 3D refinement step and post-processing (B-factor applied -45).
DNA focused refinement The 3D EM maps of Cl1a and Cl2 were used to make masks for each DNA strand separately with ChimeraX  (74). Each strand was used in a partial signal subtraction removing information from all proteins keeping only information near the presumed DNA regions on the corresponding experimental images. The subtracted (DNA only) datasets were merged and subjected to 2D classification to allow visual assessment of the quality of the subtracted images (Fig. 3 -figure supplement 1). 3D refinement was performed followed by 3D classification and final refinement of the best 3D classes (Fig. 3E , Fig. 3 -figure  supplement  2). For the Cl3a compaction state (where some barely visible densities could correspond to remaining DNA) a cylinder with a diameter corresponding to the lumen of the relaxed structure (140 Å) was used as mask for partial signal subtraction in an attempt to enhance the information from the presumed DNA regions.
Automatic picking of the three different conformations (Cl1a, Cl2, Cl3a) Projections from the different helical maps were used as new input for automatic picking of each Cl1a, Cl2 and Cl3a clusters to get more homogeneous datasets for each conformation  (75). For each dataset a final round of extraction (box size Cl1a: 380 pixels, 121,429 segments; Cl2: 400 pixels, 8479 segments; Cl3a: 400 pixels, 11,958 segments) and 3D refinement with solvent flattening (Central z length 30%) was performed using the appropriate helical parameters and additional symmetries (none for Cl1a, C3 for Cl2 and D5 for Cl3a). This led to the improved maps presented in Figs. 2 3 , Fig. 2 -figures supplement 1-3 (Cl1a: 3. 7 Å; Cl2: 4. 0 Å; Cl3a: 3. 7 Å; FSC threshold 0. 5, masked). Post-processing was performed with B-factor -80 (supplementary file 1, Fig.
Structures refinement The resolution of the EM map enabled to fit the R135 dimeric structure (30) (PDB 4Z24) into the maps using UCSF Chimera 1. 13. 1  (72). The qu_143 and qu_946 models were obtained using SWISS-MODEL (76) (closest PDB homologue: 4Z24). It is only at that stage that the best fitted qu_946 model was manually inspected and additional N-terminal residues built using the extra density available in the cryo-EM map of the 5-start compact reconstruction (Fig. 3 ). The entire protein shell built using the corresponding helical parameters were finally fitted into the Cl1a and Cl3a maps and were further refined against the map using the realspace refinement program in PHENIX 1. 18. 2 (33) (Fig. 2 -figures supplement 1-2). The qu_143 and qu_946 models were also used to build the entire shell using the Cl2 helical parameters and symmetry and were further refined using the real-space refinement program in.
Peptides were sampled on a 300 µm x 5 mm PepMap C18 precolumn and separated on a 75 µm x 250 mm C18 column (Reprosil-Pur 120 C18-AQ, 1. 9 μm, Dr. Maisch) using a 60-min gradient for fiber preparations and a 140-min gradient for virion. MS and MS/MS data were acquired using Xcalibur (Thermo Scientific). Peptides and proteins were identified using Mascot (version 2. 7. 0) through concomitant searches against mimivirus reunion, classical contaminant databases (homemade) and the corresponding reversed databases. The Proline software  (78)  was used to filter the results: conservation of rank 1 peptides, peptide score ≥ 25, peptide length ≥ 6, peptide-spectrum-match identification false discovery rate < 1% as calculated on scores by employing the reverse database strategy, and minimum of 1 specific peptide per identified protein group.
68 in the second. Based on our model, a 5-start genomic fiber containing the complete mimivirus genome  (1, 196 ,989 bp) should be composed of ~95,000 GMC-oxidoreductases subunits (~93,000 for a 6-start). This gives a molecular ratio of 12. 5 dsDNA base pairs per GMCoxidoreductase subunit, which would be more than experimentally measured. However, in the cryo-EM dataset, there are at most 50% of genomic fibers containing the DNA genome (mostly Cl1), while some DNA strands can be observed attached to the relaxed genomic fiber Cl3 but the vast majority of released DNA was lost during purification of the genomic fiber. Applying an estimated loss of 50 % to the total DNA compared to the measured values, we obtain a ratio, which is in the same order of magnitude of the ones measured in the purified genomic fiber samples.
The projection views of the different RNA polymerase were produced by converting the PDB model into a volume density through EMAN2's e2pdb2mrc software, and converting the volume into a 2D projection using a dedicated python script, ultimately applying a gaussian blur filter (σ=2. 9Å) in order to roughly simulate the whole imaging transfer function. The projections dataset of all orientations of the vaccinia virus RNA polymerase structure was produced with a 5° rotation step in all angles (PDB: 6RIC, equivalent subunits identified by our MS-based proteomics of purified mimivirus genomic fibers). Preferred projections (Fig. 4C(P)) orientations were manually assessed.
Acknowledgements The cryo-EM work was performed at the multi-user Cryo-EM Facility at CSSB. We thank  Jean-Michel Claverie  for his comments on the manuscript and discussions all along the project. We thank  Irina Gutsche ,  Ambroise Desfosses ,  Eric Durand  and  Juan Reguera  for their helpful support on structural work. We thank  Carolin Seuring  for support and technical help. Processing was performed on the DESY Maxwell cluster, at  IBS  and  IGS. We thank  Wolfgang Lugmayr  for assistance and  Sebastien Santini  and  Guy Schoehn  for support. The preliminary electron microscopy experiments were performed on the  PiCSL-FBI core facility  ( Nicolas Brouilly ,  Fabrice Richard  and  Aïcha Aouane ,  IBDM, AMU-Marseille ), member of the  France-BioImaging national research infrastructure and on the IMM imaging platform (Artemis Kosta ).
Funding: This project has received funding from the  European Research Council (ERC)  under the European Union's  Horizon 2020 research and innovation program  (grant agreement No  832601 ). This work was also partially supported by the  French National Research Agency   ANR-16-CE11-0033-01. Proteomic experiments were partly supported by  ProFI  ( ANR-10-INBS-08-01 ) and GRAL, a program from the  Chemistry Biology Health (CBH) Graduate School of University Grenoble Alpes  ( ANR-17-EURE-0003 ).
Data and materials availability: Mimivirus reunion genome has been deposited under the following accession number: BankIt2382307 Seq1 MW004169. 3D reconstruction maps and the corresponding PDB have been deposited to EMDB (Deposition number Cl1a: 7YX4, EMD-14354; Cl1a focused refined: 7PTV, EMD-13641; Cl3a: 7YX5, EMD-14355; Cl2: 7YX3, EMD-14353). The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD021585 and 10. 6019/PXD021585. The tomograms have been deposited in EMPIAR under the accession number 1131.
Acknowledgements This research was funded by the  German Academic Exchange Service (DAAD)  from the funds of the  German Federal Ministry of Education and Research, BMBF  ( 57565165 ). E. H. H. is supported by the  Cluster of Excellence "Advanced Imaging of Matter" of the Deutsche Forschungsgemeinschaft (DFG)   EXC 2056-project ID 390715994. This project received financial support from the  CNRS  through the  International Emerging Actions program  ( IEA00669 , SECOWIN). The authors are grateful to the  Central Division of Electron Microscopy (BEEM)  of  TUHH  for providing access to an FEI Talos F200X. The authors thank  Professor Manfred Eich  of the  Institute of Optical and Electronic Materials of TUHH  for providing the photoelectrochemistry setup and  Dr. Fatemeh Ebrahimi  for useful discussions.
Results Cortex wide decoupling of function and structure (Fig. 1 ). We first established the spatial distribution of structure-function coupling in the human brain, using node-level association analyses. Specifically, we mapped how patterns of intrinsic functional connectivity reflect similarity of cortical microstructure across all cortical regions, using the S1200 sample of the Human Connectome Project young adult dataset  50  (see Methods for details on participants and neuroimaging processing). To construct microstructure profile covariance (MPC) matrices, we sampled intracortical T1w/T2w values at 12 different cortical depths  22  , and correlated dept-wise cortical profiles between the parcels (Fig. 1A ). To control for curvature effects, equivolumetric surfaces were used  57. Resting-state functional connectivity (rsFC) matrices were calculated by cross-correlating the neural timeseries between all pairs of 400 cortical nodes  58  (Fig.
It is of note that although the Allen human brain atlas is the most densely sampled transcriptomic dataset of the human brain to date, it comes with various limitations, such as sex and age imbalance  64, 93. Thus, findings from our study relating to gene expression should be interpreted with caution. In particular, although we selected only genes that were relatively consistent across donors, there may still be a bias toward those genes having higher expression rates in males than in females. In the current study, we report genetic uncoupling in transmodal regions in humans using a twin-design and differences between humans and macaques in terms of structure-function associations. We were able to compare humans and macaques directly using previously established cross-species alignment techniques  41  in combination with histologically validated in vivo microstructure profile covariance analysis  22.
In NHPs, this pattern was reduced relative to humans, and functional meta-analyses indicated that this difference was most likely associated with social-cognition and autobiographical memory. These data are consistent with the hypothesis that primate brain organization has evolved to support structure-function decoupling, which may facilitate types of cognition that benefit from learning and social interactions, enabling important features of cultural enrichment that are thought to be a characteristic of our species. To test this hypothesis, future work should expand our approach to include a wider range of species, and explore their association with different functional states in a more detailed manner. These studies will be an important step towards the understanding of how evolution has shaped neural function to support important features of human cognition, a research goal, which is likely to become increasingly feasible with growing availability of open multispecies in vivo datasets  38, 39, 95.
e. , h 2 = σ 2 g /σ 2 p. Phenotypes showing stronger covariances between genetically more similar individuals than between genetically less similar individuals have higher heritability. SOLAR contrasts the detected covariance matrices, here node-wide rsFC/MPC and coupling of rsFC and MPC, with the structure of the covariance matrix predicted by kinship. We studied heritability with simultaneous estimation for the effects of potential covariates. For this study, we included covariates including age, sex, age 2 , and age * sex. To evaluate robustness of our heritability findings of rsFC with respect to intra-individual variation we additionally computed heritability considering possible within-subject variation described in previous work  61, 78. Macaque data. All datasets in this study were from openly available sources.
The macaque data used for our main analyses stemmed from one cohort (University of California, Davis) of the recently established PRIME-DE (https://fcon_1000. projects. nitrc. org/indi/indiPRIME. html)  38. The full dataset consisted of 19 rhesus macaque monkeys (macaca mulatta, all female, age ± SD = 20. 38 ± 0. 93 years, weight = 9. 70 ± 1. 58 kg) scanned on a Siemens Skyra 3T with 4-channel clamshell coil. All the animals were scanned under anesthesia. In brief, the macaques were sedated with injection of ketamine (10 mg/kg), dexmedetomidine (0. 01 mg/kg), and buprenorphine (0. 01 mg/kg). The anesthesia was maintained with isoflurane at 1-2%. The details of the scan and anesthesia protocol can be found at (https:// fcon_1000. projects. nitrc. org/indi/PRIME/ucdavis. html). The neuroimaging experiments and associated procedures were performed at the California National Primate Research Center (CNPRC) under protocols approved by the University of California, Davis Institutional Animal Care and Use Committee  107.