dataesr/scientific-paragraphs-categorization huggingface dataset:
It consists of: 1) Complete and optimal coverage when FD struts presented a normal arterial wall consisting of a continuous layer of endothelial cells that cover an extracellular matrix and smooth muscle cells. 2) Incomplete or non-optimal coverage when struts were in direct contact with the lumen or were covered by an extracellular matrix with poor quality tissue without endothelialization. In addition, we measured the area of neointimal tissue formed over the struts. Each strut was examined in the H&E or Masson's trichrome-stained sections. Using the ImageJ version 1. 60 software (National Institutes of Health, Bethesda, MD, USA) several semiautomatic measurements were carried out: -A1: Total area of the vascular wall (mm 2 ) -A2: Neointima area (mm 2 ) -R1: Ratio A2/A1.
Acknowledgments The authors wish to thank  Dr Heiko Richter  and his team for their assistance with the histopathology analyses. We would also like to thank  Florence Bosselut  ( EMIS research platform, Limoges University Hospital , www. emis-research. com) for her assistance with this experiment at the animal laboratory. We are grateful to  Yann Launay  for the ESEM analysis (CarMaLim platform, Limoges). Multiphoton microscopy was performed on the PLATINOM platform (www. uni lim. fr\platinom), supported by the  European Regional Development Fund  and the  Nouvelle Aquitaine Region  ( FEDER-PILIM 2015-2020 Nouvelle   Aquitaine ).
AKNOWLEDGEMENTS We thank  Delphine Delacour ,  Fabien Alpy ,  Simon de Beco  and the past and current members of  Membrane Dynamics and Intracellular Trafficking team at Institut Jacques Monod  for helpful discussions. We acknowledge the  ImagoSeine core facility  of the IJM, member of the  France BioImaging infrastructure  ( ANR-10-INBS-04 ) and  GIS-IBiSA , with support from  La ligue contre le Cancer  ( R03/75-79 ), the  Region Île-de-France (Sesame) ,  Université Paris Cité (Labex Who Am I) ,  Inserm (Plan Cancer) ,  Région Ile de France (SESAME)  and  Fondation Bettencourt Schueller, France. This work was supported by grants from  Gefluc groupement Les Entreprises Contre le Cancer ,  Cancéropôle Ile de France  and  INCa  ( 2021-1-EMERG-51 ),  La Ligue  contre le cancer ( RS21/75-85 ), the  Agence Nationale de la Recherche  ( ANR-20-CE13-0021 ) and the  Fondation pour la Recherche Médicale  (DEQ.
Replication and explained variance Independent replication of identified signals was performed in data from the Danish Blood Donors study  16  (DBDS). The DBDS includes questionnaire recalled AAM data on 35,472 European women ("Age when menstruation started?"). Mean age at recall was 38. 4 years (SD=12. 9 years) and mean AAM was 13. 1 years (SD=1. 4 years). Indirect confirmation of AAM signals was sought by association with age at voice breaking (AVB) in men in UK Biobank 17 (N=191,235 European men -data field 2385) and the 23andMe study 18 (N=55,781 European men). For signals with missing data for either AVB dataset, we identified proxies using the UK Biobank White European dataset (within 1Mb of the reported signal and R 2 >0. 6), choosing the variant with the highest R 2 value. Given the smaller sample sizes of these cohorts, we performed a Binomial sign test for global replication.
Primary and secondary AAM signals were further checked for pairwise LD within 10 Mb windows using plink (v1. 90b6. 18) 79 and only independent signals (R 2 <0. 05) were retained, prioritising distance-based signals in the case of linkage. Signal selection was performed first using the European-ancestry GWAS meta-analysis, and then supplemented by any signals identified by the All-ancestry GWAS meta-analysis that were uncorrelated (R 2 <0. 05) with any European-ancestry signal. Independent GWAS AAM signals were examined for proximal genes, defined as those within 500kb up-or downstream of the genes start or end sites, using the NCBI RefSeq gene map for GRCh37 (via http://hgdownload. soe. ucsc. edu/goldenPath/hg19/database/).
Colocalization with expression or protein QTL data Tissue enrichment for GWAS associations was performed using LD score regression applied to tissue-specific expression (LDSC-SEG)  80  and tissue-specific annotations from GTEx, accessed via https://github. com/bulik/ldsc/wiki/Cell-type-specificanalyses. Significantly enriched tissues (P<0. 05) were then included in colocalization analyses with the tissue-specific and cross-tissue meta-analysed GTEx eQTL data (V7 60 , available via https://gtexportal. org and using the fixed-effects summary statistics for the latter), in addition to data from the eQTLGen 81 and Brain-eMeta 59 studies. Including genomic variants with at least suggestive association with AAM (GWAS P<5x10 -5 ), we applied Summary data-based Mendelian Randomization and Heterogeneity in Independent Instruments (SMR-HEIDI, version 0.
High-confidence AAM genes Independent GWAS signals from the All-and the European-ancestry meta-analyses were annotated with their top G2G scoring gene, using corresponding GWAS data (i. e. , European analysis signals were annotated with genes from the European G2G, etc. ). Genes implicated by at least two concordant sources were considered to be high-confidence AAM genes. High-confidence AAM genes were functionally annotated using STRING  87. Links to rare monogenic disorders were annotated from the Online Mendelian Inheritance in Man (OMIM) database (via Online Mendelian Inheritance in Man, OMIM®. McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University (Baltimore, MD), accesed November 2022. World Wide Web URL: https://omim. org/). Finally, we used GTEx, a publicly available resource of tissue-specific gene expression, to lookup the tissue expression of 1080 AAM genes highlighted by G2G  60.
ZNF483 genome-wide binding analysis We used fGWAS (v. 0. 3. 6  32  ), a hierarchical model for joint analysis of GWAS and genomic annotations, to test for enrichment of GWAS AAM signals among ZNF483 transcription factor binding sites. fGWAS models a maximum likelihood parameter estimate for enrichment of a transcription factor (in this case ZNF483). To perform this, we annotated the European-ancestry GWAS AAM summary statistics with the ZNF483 binding sites from the ENCODE ChIP-seq data derived from human HepG2 cell line (ENCSR436PIH). We also used Signed LD Profile regression (SLDP, https://github. com/yakirr/sldp, Reshef et al. 33  ) to explore the directional effect of ZNF483 function on AAM. We tested whether alleles that are predicted to increase the binding of ZNF483 have a combined tendency to increase or decrease AAM.
Data availability Cohorts should be contacted individually for access to their raw data. UK Biobank data are available on application (https://www. ukbiobank. ac. uk/enable-yourresearch/register). Summary statistics from the meta-analysis excluding 23andMe will be made available upon publication. Access to the full summary statistics including 23andMe results, can be obtained from 23andMe after completion of a Data Transfer Agreement (https://research. 23andme. com/dataset-access/).
Comparison of the proteomes of corresponding M-flies We further hypothesize that the proteome changes in M2-flies (as compared to M1-flies) overlap with those of M0-flies because both dietary manipulations decreased the rhabdomere size. Lastly, we also expect an overlap between the proteome changes in M2-and M3-flies due to a general metabolic response to a lipid-rich diet. Hence, we took advantage of these four (M0-, M1-, M2-and M3-flies) proteomic datasets to perform a pairwise comparison and successive subtraction of similarly regulated proteins in multiple datasets to identify those, whose abundance specifically responds to membrane lipid unsaturation.
The M3-diet containing three short chain saturated TAGs also decreased the phototransduction protein levels but did not cause any obvious rhabdomere damage. This suggests that rhabdomere defects are not the cause for the decreased phototransduction protein expression, which is also consistent with our previous finding that crumbs mutants have severe rhabdomere defects, but do not exhibit significant changes in the levels of phototransduction proteins or Rh1  14. The molecular mechanisms that underlie the impacts of these three different dietary manipulations on the expression levels of phototransduction proteins remain to be elucidated. In conclusion, we anticipate that these insights into the molecular responses of the Drosophila eye proteome to specific lipid manipulations and the datasets that we generated will be useful resources for the genetic dissection of the mechanisms that maintain visual function when the eye is exposed to dietary challenges.
Data processing for protein identification and quantification Mascot v2. 2. 04 (Matrix Science, London, UK) was used for peptide identifications against the custom-made database containing the sequence of the target protein, to which sequences of human keratins and porcine trypsin were added. For eye proteome analysis, the Drosophila reference proteome database from UniProt was used. The database searches were performed with the following mascot settings: precursor mass tolerance of 5 ppm; fragment mass tolerance of 0. 6 Da and 0. 03 Da for the Velos and QE-HF data respectively; fixed modification: carbamidomethyl (C); variable modifications: acetyl (protein N-terminus), oxidation (M); Label: 13C (6) (K), Label: 13C (6) 15N (4) (R), 2 missed cleavages were allowed. More details of mascot search parameters are provided (Table  11 ).
Acknowledgements/funding This publication was supported by the  National Eye Institute of the National Institutes of Health  under Award Number  R01EY029659  to J. R. and internal funding of  MPI CBG, Dresden. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Whole-rock geochemical analyses Samples were crushed at Thin Section Lab (TSL, Toul, France) following a standard protocol to obtain adequate powder fractions using agate mortars. Chemical analyses (Supplementary Table  1 ) were performed by the Service d'Analyse des Roches et des Minéraux (SARM; CRPG-CNRS, Nancy, France) using an ICP-AES (inductively coupled plasmaatomic emission spectroscopy) for major-elements and an ICP-MS (inductively coupled plasma-mass spectrometry) for trace-elements, following the techniques described in  Carignan et al. [2001]. All geochemical classification and tectonic discrimination diagrams used in this study were drawn using the GCDkit software  [Janousek et al. , 2006].
Acknowledgements This study is dedicated to the memory of  Jean-Louis Paquette  who greatly contributed, among other things, to our understanding of the  French Massif Central. Xavier Le Coz (Géosciences Rennes)  is thanked for the making of the thin sections, and  Cindy Maliverney  ( TSL ) for sample preparations. Jean Poujol  is thanked for his hospitality during the two sampling fieldtrips and  Sara Mullin  for correcting the English content. Finally, the authors want to thank  J. Barbarand ,  V. Bosse  and  S. Duchêne  for their insightful comments on the previous version of this manuscript.
The overlap presence of bronchiectasis, bronchial asthma and liver disease was also reported in addition to routinely collected epidemiologic, clinical and functional data. This case-finding program is still ongoing. The data of the present study correspond to the time period from September 2018 to October 2021. Normal serum AAT levels were considered at 0. 9À2 g/L by nephelometry by local laboratory standards. Following genetic results, analysis considers adults as homozygous or compound heterozygous for pathogenic variants. All adult patients included in the study fulfilled the criteria of the European Respiratory Society for the diagnosis and treatment of pulmonary disease in AATD. 3  The AATD genetic analysis was performed at the German AAT Laboratory at the University of Marburg (MV, CFV, TG).
For that analysis dried blood spot (DBS) samples were tested using the Progenika AAT genotyping kit (Progenika Biopharma, S, A, Derio, Spain) which can simultaneously identify and genotype 14 deficiency variants of the SERPINA1 gene based on Luminex xMAP-Technology (Luminex, Austin, TX, USA). For samples in which we suspected the presence of other mutations, due to low serum AAT levels, isoelectric focusing (IEF) was performed. 17, 18 If the results from Luminex technology and IEF tests did not correlate or an indication of a rare mutation existed, gene sequencing (Next Generation Sequencing) was done. For sequencing the DBS samples were shipped to a reference laboratory [Progenika Biopharma, Spain]. We have described the laboratory methods in detail elsewhere. 17 Epidemiological, clinical, laboratory and functional data were collected in a standardized manner.
Death data were recorded until October 2021, except for cases lost to follow-up. Rare and ultra-rare mutations were discussed systematically with experts from the German AAT Laboratory at the University of Marburg (MV, CFV, TG) in collaboration, when necessary, with the expert Center for Diagnosis of Inherited Alpha1-antitrypsin Deficiency at the University of Pavia on web meetings (IF, SO). Selected patients were discussed monthly in a web-based multidisciplinary meeting dedicated to AATD (www. respifil. fr) for consultation (MB, CL, VC, JFM). All patients signed written informed consent and the study was approved by the Medical Ethics Committee of General University Hospital "Attikon", Athens, Greece (EBD 633/24À09À2018).
Statistical analysis Normality of the distributions was checked with Kolmogorov-Smirnov test. Categorical variables are presented as n (%), whereas numerical variables are presented as median (interquartile ranges) since the distribution of data was skewed. Comparisons between AAT levels in the different groups were performed using Kruskal Wallis test. Statistical significance was established at the level of p 0. 05. Data were analyzed using SPSS 17. 0 for Windows (SPSS Inc. , Chicago, IL, USA) and graphs were created using Graph Pad Prism 5 (GraphPad Software, Inc. , La Jolla, CA, USA).
Acknowledgements The authors would like to acknowledge the contribution of the following collaborators in patient care:  Aimilia Tsaroucha  ( 2nd Pulmonary Department, Athens Chest Hospital "Sotiria", Athens Greece ),  Ilias C Papanikolaou  ( Department of Pulmonary Medicine, Corfu General Hospital ),  Michael Kitrou  ( Patras, Greece ),  Aggeliki Haritou  ( Ioannina, Greece ),  Zafeirios Sardelis  (7th  Pulmonary Department, Athens Chest Hospital "Sotiria", Athens Greece ),  Nikolaos Koulouris ,  Eleni Stagaki  (1st  Respiratory Medicine Department of the National, Kapodistrian University of Athens, Athens, Greece), Gerasimos Apollonatos (Peristeri, Athens, Greece ),  Maria Tsiamita  ( Department of Respiratory Medicine, General Hospital of Patras, University of Patras ),  Panagiota Loukopoulou  ( Aigio, Greece ),  David Tsoukas  ( Florina, Greece ),  Stamatia Markou  ( Xanthi, Greece ),  Panagiotis Mavroudis  ( Hygeia Hospital, Athens ),  Ioanna Korbila ,  Galateia Verykokou ,  Maria Maniati ,  Konstantinos Kagouridis  ( 2nd Pulmonary Medicine Department, General University Hospital "Attikon", Medical School, National and Kapodistrian University of Athens ),  Konstantinos Douros ,  Smaragdi Fessatou ,  Ino Kanavaki ,  Vassiliki Papaevangelou  ( Third Department of Pediatrics "Attikon" University Hospital, National and Kapodistrian University of Athens School of Medicine Athens ),  Iraklis Tsangaris  ( Second Department of Critical Care Medicine, General University Hospital "Attikon", Medical School, National and Kapodistrian University of Athens ) (all in Greece) and  Julie Traclet  ( Service de pneumologie , centre national coordinateur de r ef erence des maladies pulmonaires rares,  Hôpital Louis Pradel ,  Hospices Civils de Lyon, Universit e de Lyon, Universit e Claude Bernard Lyon 1, UMR754 INRA, IVPC, Lyon, France ).
Nuclear accidents such as Fukushima Daiichi have highlighted the potential of passive safety systems to replace or complement active safety systems as part of the overall prevention and/or mitigation strategies. In addition, passive systems are key features of Small Modular Reactors (SMRs), for which they are becoming almost unavoidable and are part of the basic design of many reactors available in today's nuclear market. Nevertheless, their potential to significantly increase the safety of nuclear power plants still needs to be strengthened, in particular the ability of computer codes to determine their performance and reliability in industrial applications and support the safety demonstration. The PASTELS project (September 2020-February 2024), funded by the European Commission "Euratom H2020" programme, is devoted to the study of passive systems relying on natural circulation.
Motivation of the project The PASTELS project aims to significantly increase the knowledge of passive systems for European nuclear actors. One of the main objectives of the project is to evaluate and improve the ability of several thermalhydraulic system and CFD codes, used in the nuclear community for design and safety demonstration, to accurately model key physical phenomena for passive systems such as natural circulation loops (  [5] ). Given the increasing use of passive systems in non-European nuclear power plants, it is essential, especially with the rise of SMRs, such as NUWARD™, that largely integrate these systems into their design, that the European nuclear community adapts its numerical reference tools to study these promising technologies. This must be undertaken based on relevant and representative experimental data of the passive systems of interest.
PASTELS overall structure The PASTELS project is structured in five different work packages (WP, see Fig. The aim of WP3 is to generate experimental data on the performance of a specific SACO design adapted to PWR under operational and plant accident conditions. WP4 aims to perform a series of tests on natural circulation and heat transfer in a type of low-pressure open loop CWC. In WP2, WP3 and WP4, the experimental data available in the project will be carried out in conjunction with deterministic studies using thermal and hydraulic numerical tools at different scales, including system codes such as CATHARE-3 ([9]), ATHLET ([10],  [11] ), APROS (  [12] ), RELAP-5 (  [13] ) and TRACE (  [14] ), CFD codes such as neptu-ne_cfd (  [15] ) or FLUENT (  [16] ), and severe accident codes, such as ASTEC (  [17] ) and MELCOR (  [18] ).
Focus on WP4: PASI facility adaptation and CWC experiments The PASI facility ([27], [28]) at LUT University (LUT), Lappeenranta, Finland, is a one-loop model of an open passive containment cooling system (Fig. 12 ). The applicable reference system for the PASI test facility is the passive containment heat removal system of the AES-2006 type pressurized water reactor. The design height scale of the PASI facility versus the reference system is 1:2. PASI consists of a steam vessel including a bundle of heat exchanger tubes, a natural circulating water loop connected to a water pool at atmospheric pressure, and measurement and data acquisition systems (Fig. 13 ). A valve was also installed in the downcomer in order to control the overall mass flowrate in the loop. The PASI test program within PASTELS aims to address the different objectives of the project: -Understanding in more detail the physical behaviour of a thermosiphon cooling system in an interaction between the containment as a heat source and the external water tank as a heat sink.
-Characterization of the system performance for a geometry that has been designed in similarity with the actual system design present in an AES-2006 reactor maintaining relative gravitational and frictional pressure losses in the scaling -Development of an extending database with sufficient measurements in order to help the community of researchers and designers to simulate the phenomena with their own codes and standards. -Test 1-4 to characterize the cooling system behaviour and natural circulation in the thermosiphon loop under different heating powers and the effect of the added loop flow resistance -Test 5-6 to explore the influence of the gravity head on the performance of the loop and on initiation of the loop flow oscillations -Test 7-8 to explore the impact of modified geometry of the sparger (closing of the pressure distribution hole in the top part of the riser pipeline) on the system behavior.
Decreasing heating power reduced the oscillation frequency of the loop flow, but the amplitude stayed constant. After each increase in the flow resistance using the valve, the void fraction in the riser increased and the system found at once a new quasi-steady state and the heat was adequately  Pre-test analysis has been carried out in the project with the different system codes AC 2 -ATHLET, CATHARE-3, RELAP5, TRACE (see Deliverable D4. 3 ([30] )) and also with the "lumped parameter code MEL-COR" used for severe accident analysis. A general agreement has been found by all the codes on the qualitative results with development of the oscillations in the thermosiphon loop despite some differences on quantitative parameters such as power extraction, ranges of mass flow rate during oscillations.
By early 2024, the PASTELS project should be completed and will propose some "methodologies and guidelines for validation and use of numerical tools" and a "roadmap for European versions of SACO and CWC". No direct follow-up is planned after the end of the PASTELS project in 2024. Nevertheless, the lessons learn on the physical behaviour and simulation of innovative passive safety systems would be used as input data for the next Euratom Research and Training Programme 2023-2025. In this programme, one innovative action is proposed on Safety of light  water small modular reactors (LW-SMRs). Most of the partners of the PASTELS project are already involved in defining the programme for this new project, which will also be supported by relevant new test facilities designed to address SMR issues.
Acknowledgments The  PASTELS  project has received funding from the  Euratom research  and training programme  2019-2020  under grant agreement No  945275. This text reflects only the author's view and the Commission is not responsible for any use that may be made of the information contained therein. The  PASTELS  project idea has also obtained the  NUGENIA  label on 23/09/2019 (Certificate number:  2019NUG0076 ) prior to the submission of the project to the  European Commission.
Acknowledgments We acknowledge the MM4 ( Margin Modelling Phase 4 ) industry partners (BP,  Conoco Phillips ,  Statoil ,  Petrobras ,  Total ,  Shell ,  BHP-Billiton , and BG) for financial support and discussions. https://doi. org/10. 5194/egusphere-2023-2171 Preprint. Discussion started: 28 September 2023 c Author(s) 2023. CC BY 4. 0  License.
Acknowledgments Some strains were provided by the CGC, which is funded by  NIH Office of Research Infrastructure Programs  ( P40 OD010440 ). We thank  Mark Alkema  and  Alex Byrne  for strains and technical support. We like to thank  Andrés Garelli ,  Guillermo Spitzmaul ,  Gabriela Salvador ,  Mark Alkema ,  Inés Carrera  and  Claire Bénard  for helpful discussions.