dataesr/scientific-paragraphs-categorization huggingface dataset:
Crystal form 4. iE5-tubulin-CPAP 321-397 construct crystals (two complexes per asymmetric unit) were obtained at 293 K in 0. 1 M Mes-K pH 6. 0, 0. 2 M Ca acetate, 20% (V/V) polyethylene glycol 400 and cryoprotected in the crystallization buffer containing 24% (V/V) polyethylene glycol 400. Datasets were collected at 100 K at the SOLEIL Synchrotron (PROXIMA-1 and PROXIMA-2A beamlines). Data for crystal forms 1, 3 and 4 were processed with XDS  (39)  as implemented in the XDSME package  (40). Crystal form 2 data were processed with autoPROC (41) which implements the STARANISO treatment for anisotropy (http://staraniso. globalphasing. org/). Structures were solved by molecular replacement with Phaser (42) using tubulin-iiH5 (pdb id 6GWD) and tubulin-iE5 (pdb id 6GWC) as search models, and refined with BUSTER  (43)  with iterative model building in Coot  (44).
In crystal forms 3 and 4, there was one aRep per complex, in contrast to crystal forms 1 and 2 which comprised an extra aRep (Fig. 1B, D ). Data collection and refinement statistics are reported in Table  S1. Figures of structural models were generated with PyMOL (www. pymol. org). Sequence conservation. The sequence conservation of the CPAP PN2-3 domain (Fig. 1A ) was calculated using the ConSurf program  (45). The analysis was based on 150 sequences retrieved from the UniProt database and having a maximum of 95% sequence identity with human PN2-3 taken as a reference. About 40% of the sequences were from mammals, 55% from birds and 5% from reptiles, and there was one amphibian CPAP. or the ∆loop construct (see also Fig. S1A, B  and Table  1 ). (D) Crystal form 2: structure of tubulin bound to the CPAP ∆loop fragment (magenta).
Acknowledgements We thank  M. Knossow  ( I2BC, Gif-sur-Yvette ) for many useful discussions and for a critical reading of the manuscript. Diffraction data were collected at SOLEIL synchrotron (PROXIMA-1 and PROXIMA-2A beamlines, Saint-Aubin, France). We are most grateful to the machine and beam line groups for making these experiments possible. This work has benefited from the crystallization and protein interaction platforms of I2BC supported by  French Infrastructure for Integrated Structural Biology (FRISBI)   ANR-10-INBS-05. Financial support by  CNRS  and by the  Fondation ARC pour la Recherche sur le Cancer  (Grants  PJA20161204544  and  ARCPJA2021050003651  to B. G. ) is acknowledged.
GWAS reveals major loci for PA We conducted an initial discovery GWAS on a French dataset. We analyzed 562 PA cases (223 women and 339 men) from the Hôpital Européen Georges Pompidou (HEGP) and 950 controls from the Paris Prospective Study III (PPS3) (311 women and 639 men) for ~680,000 genotyped Single Nucleotide Polymorphisms (SNPs) (Supplementary Table  1 ). After a Bonferroni correction for multiple testing, three loci showed a genome-wide significant association (P < 7. 36 × 10 -8 ) (Fig. 1 , Table  1  and Supplementary Data 1). The strongest association was observed on chromosome X around 43. 85 Mb (lead SNP rs5905587: odds ratio (OR) = 1. 596; P = 7. 79  × 10 -12  ). The second genome-wide significant locus was on chromosome 13 around 32. 11 Mb (lead SNP rs1535532: OR = 1. 658; P = 5.
Similarly, we compared the 240 BAH cases (74 women and 166 men) to the 950 PPS3 controls and found genome-wide significant associations for two of the three loci significantly associated with all PA cases, namely the locus on chromosome 13 (lead SNP rs1535532: OR = 1. 981; P = 3. 88 × 10 -9 , Table  1 ) and the locus on chromosome X (rs1005002: OR = 1. 648; P = 5. 99 × 10 -8 , Supplementary Data 1). In total, 25 variants that are distributed over six loci were identified with an association at P < 10 -6 in the discovery GWAS, in the analysis of the full discovery dataset and/or in one stratified analysis (men, women, APA or BAH) (Table  1  and Supplementary Data 1). Five of these loci (chromosome 1, lead SNP rs284277; chromosome 1, lead SNP rs6679531; chromosome 11, lead SNP rs2137320; chromosome 13, lead SNP rs1535532; and chromosome X, lead SNP rs5905587) showed a genome-wide significant association in the analysis of the full discovery dataset and/or in one stratified analysis.
61 × 10 -4 ). Heterogeneity was also observed for the two loci associated with PA in women only on chromosomes 1 (lead SNP rs6679531: P = 1. 5 × 10 -4 ) and 13 (lead SNP rs569016: P = 1. 73 × 10 -5 ) (Supplementary Table  2 ). In contrast, heterogeneity analyses did not confirm differences between APA and BAH in the discovery cohort (Supplementary Table  3 ). Among the genotyped and imputed variants identified, 16 were available after genotyping in the German dataset and were tested for association to replicate suggestive loci. We analyzed 399 PA cases (255 men and 144 women) and 1847 KORA controls (916 men and 931 women). Three of the four significant/suggestive loci identified in the discovery cohort with all PA cases (on chromosomes 1, 11, and 13) were confirmed with a significant association in the German dataset, after Bonferroni correction for the 16 variants tested (P < 0.
0031). In contrast, the fourth locus on chromosome X with a significant association in the discovery cohort did not show a significant association in the German dataset (lead SNP rs1005002: OR = 1. 178; P = 0. 0214) (Table  2  and Supplementary Data 3). For men, two of the three significant loci in the discovery cohort were significantly associated with PA: the locus on chromosomes 1 (lead SNP rs284277) and especially the locus on chromosome 13 (lead SNP rs1535532: OR = 2. 05; P = 3. 36 × 10 -9 ), while the association of the locus on chromosome X was not replicated (Supplementary Table  4 ). The significant association on chromosome 1 and the suggestive one on chromosome 13 that were specific to women in the discovery cohort (lead SNPs rs6679531 and rs1535532 respectively) were not replicated among German women.
Moreover, the locus on chromosome 11 identified with a significant association with APA in the discovery cohort showed an association with APA close to the replication significance level in the German dataset (lead SNP rs2137320: OR = 1. 356; P = 0. 00615), while the suggestive association on chromosome X with APA in the discovery cohort was not replicated. Similarly, we compared the 135 German BAH cases (91 men and 44 women) and 1847 KORA controls and replicated the significant association with the locus on chromosome 13 (lead SNP rs1535532), while the other significant association on chromosome X in the discovery cohort was not replicated (Supplementary Table  7 ). Very similar results were obtained by a meta-analysis combining this German replication dataset and two smaller replication datasets (an Italian dataset, with 107 patients (76 APA, 31 BAH) and 300 normotensive population controls and a second French dataset, with 94 patients (64 APA, 30 BAH) and 199 SUVIMAX controls) (Supplementary Tables 4-9 and Supplementary Data 3).
Interestingly, the significant association of the locus on chromosome 11 (lead SNP rs2137320) with APA was replicated in this meta-analysis and a significant replication signal was also observed with PA in men and in women for this locus, while in the German cohort the association was only replicated with the entire dataset. In conclusion, the significant/suggestive associations of three loci (chromosome 1, lead SNP rs284277; chromosome 11, lead SNP rs2137320; and chromosome 13, lead SNP rs1535532) in the analysis of the full discovery dataset and/or in one stratified analysis were replicated in the German dataset and in the meta-analysis performed on the three replication cohorts, while the associations of the locus on chromosome X and of the two women-specific loci in the discovery cohort were not.
Finally, in order to combine the results obtained in the discovery and replication datasets, we performed a global meta-analysis, using the four cohorts (Table  2  and Supplementary Tables  10  and 11 ). Among the 26 variants showing an association at P < 10 -6 in our discovery GWAS, 18 variants were available in at least another dataset and thus considered in the global meta-analysis. Almost all the genome-wide significant associations observed in the discovery GWAS (either in the analysis of the full discovery dataset or in one stratified analysis) were confirmed by the global meta-analysis (P < 7. 36 × 10 -8 ), both with the fixed-effect and the random-effect models (Table  2  and Supplementary Tables  10  and 11 ). The two exceptions were the association of the locus on chromosome X, which only reached a suggestive significance level for BAH in the global meta-analysis (lead SNP rs1005002; OR = 1.
A1 risk allele, A2 second allele, Freq risk allele frequency, OR (CI) odds ratio (95% confidence interval). in the discovery cohort and did not even reach suggestive significance in the fixed-effect global meta-analysis model. Four of the five loci with a significant association in the full discovery dataset and/or in one stratified analysis (the three loci whose association was replicated in the replication datasets and the locus on chromosome X) were thus significantly associated in the global metaanalysis as well. The sixth locus located on chromosome 13, which showed suggestive evidence of association in the discovery cohort in the analysis restricted to women, also showed a suggestive association in the random-effect model (lead SNP: rs569016; OR = 1. 356; P = 3. 61 × 10 -7 ). Finally, heterogeneity analysis confirmed that the locus associated with PA in men on chromosome 13 (lead SNP rs1535532) showed a very significantly heterogeneous association between men and women (P = 5.
Identification of potential genes associated with PA Within the four main loci associated with PA at genome-wide significance level in the full discovery dataset and/or in one stratified analysis, a total of 51 protein coding genes are located within a 1 Mb interval around the identified variants (Fig. 2 , and Supplementary Fig. 3 ). The lead SNP rs284277 on chromosome 1, as well as the other SNPs of the locus, cluster within the CASZ1 gene, while the locus on chromosome 13 (top SNP rs1535532) lies upstream of RXFP2 (Fig. 2a, b ). On the X-chromosome, (top SNP rs5905587) SNPs are located within or in proximity to the NDP gene (Supplementary Figure  3a ). On chromosome 11, rs2137320 is located within the LSP1 gene (Supplementary Fig. 3c ). eQTL analysis using the Genotype-Tissue Expression (GTEx) project showed that all SNPs on the locus on chromosome 13 are top eQTLs for RXFP2 in the adrenal gland and most variants on the X chromosome are eQTLs for NDP (Supplementary Table  12 , Supplementary Data 4 and www.
4c ). RXFP2 was expressed similarly in both control adrenals and APA (Supplementary Fig. 4b  and d ). Overall, expression of CASZ1 and RXFP2 was heterogeneous in APA and no differences were observed between APA carrying different somatic mutations (n = 122, RXFP2, p = 0. 9167; CASZ1, p = 0. 2113 Kruskal-Wallis test). To explore the chromatin regulatory landscape in the adrenal gland in the two PA-associated loci located on chromosome 1 and 13, we investigated datasets from the ENCODE project. We profiled regions of open chromatin using ATAC-seq signals  52  and analyzed the distribution of three histone marks associated with regulatory elements: H3K4me3, H3K27ac and H3K4me1  53, 54  (Fig. 2c ). Several regions of accessible chromatin were observed within CASZ1 on chromosome1, with a common pattern between males and females.
To verify the hypothesis that the absence of ATAC-seq signal within this locus could be due to an insufficient representation in the ENCODE datasets of cells expressing RFXP2, we analyzed the epigenetic landscape of two control genes, CYP11B1 and CYP11B2. CYP11B1 is expressed throughout the zona fasciculata, the largest part of the adrenal cortex, while CYP11B2 is expressed only in the zona glomerulosa, which represents only a few layer of cells underneath the capsule. Using the ENCODE dataset, we were able to detect H3K4me3 at the CYP11B1 promoter, but not at CYP11B2. This observation strongly suggests that the investigated datasets on the whole adrenal gland do not provide sufficient information to detect signals for genes expressed in a restricted subset of cells. The expression of CASZ1 and RXFP2 was thus explored by RNAscope in the adrenal cortex of adrenals with APA.
CASZ1 was mainly expressed in the zona glomerulosa extending into the zona fasciculata, albeit at lower levels; staining was also observed in APA (Fig. 3a  and Supplementary Fig. 5 ). RXFP2 mRNA expression was localized mainly to sub-capsular cells and the outer zona glomerulosa; expression in APA was low. To identify cells expressing CASZ1 and RXFP2, we interrogated single-nucleus RNA-sequencing (snRNAseq) data generated on five adjacent tissues from two adrenal glands from patients with APA. By using Seurat software25 and Uniform Manifold Approximation and Projection (UMAP) clustering we were able to detect a total of 20 different cell clusters (Fig. 3b , left panel). CASZ1 and RXFP2 were projected within the different clusters as well as CYP11B2 to identify aldosterone producing cells (Fig.
Controls The Paris Prospective Study 3 (PPS3) is an observational prospective study evaluating the role of a set of novel biomarkers on cardiovascular disease in a healthy population  77. Briefly, the PPS3 cohort consists of 10,157 volunteers aged 50 to 75 years recruited from a large preventative medical center, the Centre d'Investigations Préventives et Cliniques in Paris (France) between June 2008 and May 2012. All participants have provided written informed consent and the study protocol was approved by the Ethics Committee of the Cochin Hospital (Paris). The study is registered in the international trial registry (URL: http://www. clinicaltrials. gov. Unique identifier: NCT00741728). Genotyping was performed on 4056 index subjects using the Illumina HumanExome-12v1. 1 BeadChip as described in ref.
After quality control, DNAs have been aliquoted in 96-well plates (JANUS liquid handling robot, PerkinElmer) for genotyping; sample tracking was ensured by a systematic barcode scanning for each sample. Two DNA positive controls were systematically inserted in a random fashion into the plates. Genotyping was performed on Illumina OmniExpressExome8v1-2 (discovery cohort) or Illumina Global Screening Array chips (replication cohorts), on a high throughput Illumina automated platform, in accordance with the standard automated protocol of Illumina® Infinium HD Assay (Illumina ®, San Diego, USA). Several quality controls were systematically included during the process and reading of the chips was performed on iScan+ scanners (Illumina®, San Diego, USA). Primary analysis of the results was done using the GenomeStudio software (Illumina®, San Diego, USA).
GWAS analysis For each discovery or replication dataset, we applied a logistic regression (additive) model as implemented in PLINK version 1. 9 (for genotype data) and version 2. 0. 2. 3 (for imputed dosage data) (www. cog-genomics. org/plink)  84 to test the association with PA, including as covariates the sex as well as the first ten components obtained by the multidimensional scaling method applied to the identity-by-state matrix. For SNPs on the X chromosome, we coded male pseudogenotypes 0 or 2, instead of 0 or 1, to model X-inactivation. A genomewide significant p-value threshold at p < 7. 36 × 10 -8 was considered for genotyped data. Association observed at a locus in the discovery cohort was replicated if its association was significant in the German cohort, irrespective of the global meta-analysis results.
ATAC-seq and ChIP-seq analysis ENCODE ATAC-seq and ChIP-seq files from adrenal gland were downloaded and visualized using pyGenometracks package (https:// pygenometracks. readthedocs. io). We used the public database GENCODEv38 (https://ftp. ebi. ac. uk/pub/databases/gencode/Gencode_ human/release_39/gencode. v39. annotation. gtf. gz) to retrieve genomic data. UCSC lift-over online tool (https://genome. ucsc. edu/cgi-bin/ hgLiftOver) was used to convert the original assemblies used in the GWAS into GRCh38 using chromosome coordinates. Publicly available ATAC-seq and ChIP-seq datasets used in this study, accessible through the ENCODE portal (https://www. encodeproject. org/), are listed in Supplementary Table  13.
Slides were washed and incubated with an avidin-biotin-peroxydase complex (Vectastain ABC Elite; Vector Laboratories) for 30 min, developed using diaminobenzidin (Vector Laboratories; Burlingame, USA) and counterstained with hematoxilin (Sigma-Aldrich; St Louis, MO USA). For two patients, whose adrenals were analyzed by RNAscope experiments, snRNAseq data on the adjacent cortex were also available; characteristics of their adrenals are presented in Supplementary Figure  11.
Proteins were solubilized for 30 min at 4 °C, under end-over-end rotation, and then centrifuged at 13,000 rpm for 15 min at 4 °C. Protein concentration was determined using Bradford protein assay (Biorad). 15 µg of proteins were submitted to 10% SDS-PAGE and transferred onto nitrocellulose membrane. Membranes were blotted with the following antibodies: mouse anti-aldosterone synthase antibody (1:500, clone CYP11B2-41-13, kindly provided by Dr C Gomez Sanchez  92  and mouse anti-tubulin (T9026, 1:2000, Sigma Aldrich). Signals were developed by Clarity Max™ Western ECL substrate (Biorad, Hercules, CA) and detected by Fujifilm Las-4000 mini Luminescent image analyzer (Fujifilm, Tokyo-Japan) and quantified by Multi gauge software (Fujifilm, Tokyo-Japan). Expression of total proteins was normalized to the expression of the housekeeping protein tubulin.
Statistical analyses Quantitative variables are reported as means ± SEM when Gaussian distribution or medians and interquartile range when no Gaussian distribution. Pairwise comparisons were done with unpaired t test or Mann-Whitney test respectively; global comparison was evaluated using ANOVA or Kruskall Wallis test, followed by Sidak's or Dunn's multiple comparison test. A p value < 0. 05 was considered significant for comparisons between two groups. Analyses were performed using Graphpad Prism 9 (GraphPad software Inc, San Diego, CA) or Med-Calc19 (MedCalc software Ltd). Open Access This article is licensed under a Creative Commons Attribution 4. 0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.
Acknowledgements This work was funded through institutional support from INSERM, by the  Agence Nationale pour la Recherche  ( ANR-13-ISV1-0006-01 ,  ANR-15-CE14-0017-03 ,  ANR-18-CE93-0003-01 ) and the  Fondation pour la Recherche Médicale  ( DEQ20140329556  and  EQU201903007864 ). A. F. was supported by the  Laboratory of Excellence GENMED (Medical Genomics)  grant no. ANR-10-LABX-0013  managed by the  National Research Agency (ANR)  part of the  Investment for the Future program. M. R. is supported by the  Else Kröner-Fresenius  in support of the  German Conns Registry-Else-Kröner Hyperaldosteronism Registry  ( 2013_A182  and  2015_A171  and  2019_A104 ), the  European Research Council (ERC)  under the European Union's  Horizon 2020 research and innovation program  (grant agreement No  694913 ) and the  Deutsche Forschungsgemeinschaft  project number  444776998  to  M.
Reincke  ( RE 752/31-1 ). F. B. and M. R. are supported by the  Deutsche Forschungsgemeinschaft (DFG)  (within the  CRC/Transregio 205/1  " The Adrenal: Central Relay in Health and Disease "). F. B. is supported by the  Clinical Research Priority Program  of the  University of Zurich  for the CRPP HYRENE. The  PPS3 Study  was supported by grants from  The National Research Agency (ANR) , the  Research Foundation for Hypertension (RFHTA) , the  Research Institute in Public Health (IRESP) , the  Region Ile de France  ( Domaine d'Intérêt Majeur ) and a  European Horizon   H2020  grant. The  HYPERGENES project (European Network for Genetic-Epidemiological Studies)  was supported by grant  HEALTH-2007-201550 , funded by the  European Union  within the  FP7. The KORA study was initiated and financed by the  Helmholtz Zentrum München -German Research Center for Environmental Health , which is funded by the  German Federal Ministry of Education and Research (BMBF)  and by the  State of Bavaria.
Data availability Summary statistics that support the findings of this GWAS has been deposited in the GWAS catalog database under accession codes GCST90129615, GCST90129616, GCST90129617, GCST90129618, GCST90129619, GCST90129620, GCST90129621, GCST90129622, GCST90129623, GCST90129624 [https://www. ebi. ac. uk/gwas/]. The individual level genotype data will not be publicly available since they contain information that could compromise research participant privacy and consent. snRNAseq data have been deposited in the NCBI Gene Expression Omnibus (GEO) database [https://www. ncbi. nlm. nih. gov/geo/] under accession code GSE210381. ATAC-seq and ChIP-seq datasets used in this study were retrieved from public databases and a full list of files with accession is available in Supplementary Table  13.
Study design and patients This is a prospective multicenter observational cohort study. Patients admitted between December 7th, 2021 (week 49/21) and May 1st, 2022 (week 17/22) in one of the 20 participating ICUs (17 from the Greater Paris area and 3 from the North-East of France) were eligible for inclusion in the SEVARVIR cohort study (NCT05162508) if they presented the following inclusion criteria: age ≥ 18 years, SARS-CoV-2 infection con rmed by a positive reverse transcriptase-polymerase chain reaction (RT-PCR) in nasopharyngeal swab samples, admission in the ICU for acute respiratory failure (i. e. , peripheral oxygen saturation (SpO 2 ) ≤ 90% and need for supplemental oxygen or any kind of ventilator support), patient or next of keen informed of study inclusion. Patients with SARS-CoV-2 infection but no acute respiratory failure or with a RT-PCR cycle threshold (Ct) value > 32 in nasopharyngeal swabs were not included.
The study was approved by the Comité de Protection des Personnes Sud-Méditerranée I (N° EudraCT/ID-RCB: 2021-A02914-37). Informed consent was obtained from all patients or their relatives. Demographics, clinical and laboratory variables were recorded upon ICU admission and during ICU stay. Patients' frailty was assessed using the Clinical Frailty Scale 6. The severity of the disease upon ICU admission was assessed using the World Health Organization (WHO) 10-point ordinal scale  7  , the sequential organ failure assessment (SOFA 8 ) score, and the simpli ed acute physiology score (SAPS) II score  9. Acute respiratory distress syndrome (ARDS) was de ned according to the Berlin de nition  10. The primary clinical endpoint of the study was day-28 mortality.
SARS-CoV-2 variant determination Full-length SARS-CoV-2 genomes from all included patients were sequenced by means of next-generation sequencing. Brie y, viral RNA was extracted from nasopharyngeal swabs in viral transport medium using NucliSENS® easyMAG kit on EMAG device (bioMérieux, Marcy-l'Étoile, France). Sequencing was performed with the Illumina ® COVIDSeq Test (Illumina, San Diego, California), that uses 98-target multiplex ampli cations along the full SARS-CoV-2 genome. The libraries were sequenced with NextSeq 500/550 High Output Kit v2. 5 (75 Cycles) on a NextSeq 500 device (Illumina). The sequences were demultiplexed and assembled as full-length genomes by means of the DRAGEN COVIDSeq Test Pipeline on a local DRAGEN server (Illumina). Lineages and clades were interpreted using Pangolin and NextClade, before being submitted to the GISAID international database (https://www.