dataesr/scientific-paragraphs-categorization huggingface dataset:
To further quantify the accuracy of the proposed approach against standard FEM, the absorption coefficient  of the porous system is estimated. We evaluate this coefficient numerically in the models by calculating the local average pressure and its gradient at the interface for each frequency. Here, an ideal normal incidence (planar interface perpendicular to the incident direction) is considered. The absorption coefficient with respect to the frequency is plotted in fig. 14  for the considered sound absorption system. The solution calculated by a semi-analytical package "pymls" (based on work of  43  ) serves as a reference. This absorption exhibits multiple resonances from 1 Hz to 5000 Hz. Seventeen points are mostly chosen at the resonance frequencies, to estimate coefficient  for the full FE model and the proposed approach.
Empirical detection of adaptive admixture We analysed the genomes of 15 admixed populations to find signals of adaptive admixture. The datasets and references for all admixed and source populations can be found in S2  ). Admixture proportions were obtained by running ADMIXTURE v1. 23  [96] , considering the K value producing the lowest cross-validation error and a set of "independent" SNPs obtained by running the '--indep-pairwise' command with plink 2. 0, with the following parameters: 50-SNP window, 5-SNP step, and r² threshold of 0. 5. We also verified that the chosen value for K matched the number of source populations for the studied admixed population. Local ancestry was obtained with RFMix v. 1. 5. 4  [39] , after excluding 2 Mb at telomeres and centromeres of each chromosome, as well as monomorphic sites and singletons, and using default parameter values except for the generation time '-G', which was given an estimated value for each population based on literature (S2 Table ).
Acknowledgements We thank all volunteers participating in this research;  Sophie Créno  and the  HPC Core Facility of Institut Pasteur (Paris)  for the management of computational resources;  Omar Alva Sanchez ,  Denis Pierron ,  Thierry Letellier ,  Mario Vicente ,  Carina Schlebusch ,  Andres Moreno-Estrada ,  Andres Ruiz-Linares  and the  Health Aging and Body Composition (Health ABC) Study  for kindly providing access to their data. We also thank  Javier Bougeard ,  Lara Rubio Arauna ,  Jérémy Choin ,  Maxime Rotival ,  Paul Verdu  and  Olivier Tenaillon  for helpful discussions. S. C. -E. is supported by  Sorbonne Université Doctoral College , the  Inception program  ( Investissement d'Avenir  grant  ANR-16-CONV-0005 ) and the  Institut Pasteur. The laboratory of Human Evolutionary Genetics  is supported by the  Institut Pasteur , the  Collège de France , the  CNRS , the  Fondation Allianz-Institut de France , the  French Government 's  Investissement d'Avenir programme, Laboratoires d'Excellence 'Integrative Biology of Emerging Infectious Diseases'  ( ANR-10-LABX-62-IBEID ) and ' Milieu Intérieur ' ( ANR-10-LABX-69-01 ), the  Fondation de France  ( n°00106080 ), and the  Fondation pour la Recherche Médicale  (Equipe FRM  DEQ20180339214 ) and the  French National Research Agency  ( ANR-19-CE35-0005 ).
Table, as well as the final SNP count after merging admixed and source population datasets. For each merged dataset, we: (i) excluded sites with a proportion of missing genotypes > 5%, using plink 2. 0 [93]; (ii) excluded A/T and C/G variant sites; (iii) excluded first and second degree-related individuals (kinship coefficient > 0. 08 computed with KING v2. 2. 2 [94]) and (iv) performed phasing using SHAPEIT v4. 2. 1, using default parameter values. Additionally, we verified the validity of an admixture model for each set of source/admixed populations by computing admixture f3 statistics with admixr package version 0. 7. 1[95] (S2 Table.
Autoradiograms in control and AD group were analyzed using ImageJ software. 1  [ 18 F]florbetapir binding was quantified by delineating regions of interest (ROIs) on four brain sections per animal in four animals of the control and the AD group. Mean gray value for each ROI normalized by area was obtained and statistically compared. The autoradiography method was validated in TgF344 rat, used as a positive control for brain accumulation of amyloid.
-Glucose Positron Emission Tomography Data Analysis Static PET images were reconstructed by the 2D OSEM/FORE algorithm and corrected for attenuation, random coincidences and scatter. The voxel size was 0. 2 mm × 0. 2 mm × 0. 2 mm. Brain PET images were corrected for radioactive decay, injected dose and body weight and was expressed as standardized uptake values (SUV), with SUV = tissue activity (kBq/cc)/[injected dose (kBq)/body weight (g)]. SUV-normalized PET images were spatially co-registered to a standard mouse [ 18 F]FDG PET template  (Schiffer et al. , 2007)  using Pmod software (version 3. 8, PMOD Technologies Ltd. , Zurich, Switzerland). Quantitative SUV values were determined through a volume-of-interest (VOI) analysis in selected brain regions which size is relevant to the spatial resolution of the microPET scanner (∼1.
05) (Figures  1B, C ). We first hypothesized that the absence of detectable amyloid plaques in the mouse model of i. c. v injection of Aβ 25-35 peptide may be due to insufficient sensitivity of the autoradiographic method. Sensitivity of our [ 18 F]florbetapir autoradiographic condition was tested on brain slices from TgF344 rats, known to form amyloid plaques and serving as positive control. Autoradiography data confirmed the presence of amyloid plaques after their incubation with [ 18 F]florbetapir and high radiotracer binding was detected in cortical and hippocampus regions in AD rats but not in wild-type rats (Supplementary Figure  1 ).
Singh et al. 11  reported a dose-related reduction in the risk of dementia among people older than 65 years treated with ULT. These studies remain scarce and controversial. Some of their limitations were the lack of evaluation criteria of cognitive decline  [12] [13] [14] [15]  and short-term follow-ups. Furthermore, analyses were based on general data of the health administrative database. In addition, participants investigated in these studies were not at higher risk of cognitive decline or AD, thus limiting the possibility of studying the link between cognitive decline and ULT. The aim of the present study was to investigate the association between long-term ULT and cognitive decline in a sample of community-dwelling older adults with subjective memory complaints over a five-year follow-up.
Study population. To evaluate a potential association between ULT and cognitive decline, we used data from the Multidomain Alzheimer Preventive Trial (MAPT) Study. The design of MAPT has been previously described in details elsewhere  16. Briefly, the MAPT study is a randomized clinical trial performed in 13 centers in France and Monaco assessing cognitive outcomes in patients at risk of cognitive decline, including subjects older than 70 years with the following criteria: spontaneous memory complaint, limitations in one Instrumental Activity of Daily Living (IADL) or slow gait speed (≤ 0. 8 m/s). Participants were assigned to different interventions for 3 years, and then followed for additional 2 years. Interventions comprised supplementation with omega 3 polyunsaturated fatty acids, multidomain intervention (covering cognitive training, physical activity and nutrition counselling), or both.
These three groups were compared to a placebo group. Follow-up visits were scheduled at 6 and 12 months and then every year to assess outcomes, diseases and corresponding treatments. Participants were invited to come with all their treatment orders. In summary, no statistically significant difference has been noted in the evolution of the main primary outcome (a composite cognitive score) between the four groups at 3 years, after controlling for multiple comparisons  17. From the total of 1,679 participants originally analyzed in the MAPT Study, those with information on ULT were included in the present study (n = 1673). ULT data collection. The use of ULT (Anatomic Therapeutic Chemical code: M04AA01 for allopurinol or M04AA03 for febuxostat) were recorded at each visit. Following the 2016 EULAR recommendations for the management of gout  18  , allopurinol, a xanthine-oxidase (XO) inhibitor  19  , is the first line therapy for chronic gout and febuxostat (which is also a XO-inhibitor) should be used in second intention.
This model was performed without adjustment with the following fixed effects: time, ULT groups and time × group interaction. An adjusted model was then performed by adding the above-mentioned confounding variables as fixed effects. The statistically significant difference at baseline in the composite cognitive score according to the treatment group was also considered in the mixed model. Time was treated as a continuous variable, with a cubic trajectory since the terms time 2 and time 3 were significant. All analyses were performed using SAS software version 9. 4 (SAS Institute Inc. , Cary, NC), and results were considered significant if p < 0. 05. Ethical approval and consent to participate. All participants were recruited by the investigating physicians, after obtaining their written informed consent.
Funding:  A. Ceesay  is a PhD candidate supported by an  Islamic development Bank (IsDB)  postgraduate scholarship (No:  600036461 ). G. Ndow is funded by a  Wellcome Trust   through international Training fellowship  (grant number  224366/Z/21/Z ). M Lemoine  is a recipient of  MRC UK and ANRS MIE funding. BT, IC , and ML received funding from  ANRS|MIE  (grant  12 , 430 ). This work was supported by a public grant overseen by the  French National Research Agency (ANR)  as part of the second " Investissements d'Avenir" program  (reference:  ANR-17-RHUS-0003 ). Institutional Review Board Statement:  Not Applicable.
Data analysis Statistical tests were conducted on log-normalized data using SPSS 23 software. The independent Mann-Whitney U test and t-test were applied to compare means of MP concentrations and discriminate significant differences between water and sediment. The homogeneity of variances for the t-test was checked using Levene's statistic test. Kruskal-Wallis test was carried out to reveal significant differences (p < 0. 05) of pH in sediment samples among the four investigated land uses. Furthermore, to compare the means of MP concentrations between different land-uses, a oneway analysis of variance (ANOVA) was used. To check the equality of means and verify significant differences between the means, the robust Welch and Brown-Forsythe tests based on p-values < 0. 05 were employed. The Levene statistic test was used to check the homogeneity of variances and select the most efficient way to carry out one-way ANOVA.
Structural characterization Scanning electron microscopy (Zeiss-Gemini 500 SEM) was used to measure film thickness and inspect morphology, while the atomic composition was determined by energy dispersive Xray spectroscopy (EDX), setting the acceleration voltage of 15 kV and using the EDAX Genesis spectra analysis software. EDX measurements were performed on several areas of the samples with 1 lm thick film thickness without observable signal from the Si substrate. The deviation between multiple SEM-EDX measurements for a specific ZrCu film composition was always below 0. 4 at. %. All EDX data reported in this paper are given in at. %. Atomic force microscope (AFM) measurements were carried out with a Digital Instruments Dimension 3100 AFM, to evaluate the surface topology and the roughness.
Acknowledgements Dr. M. Ghidelli  acknowledges the financial support of  Partenariats Hubert Curien (PHC)   PROCOPE 2021  project '' New-Glasses " (Grant # 46735ZG ) financing the cooperation between  Max-Planck-Institut für Eisenforschung GmbH (MPIE)  and  Laboratoire des Sciences des Procédés et des Matériaux (LSPM). Dr. J. P. Best  acknowledges the German side of this scheme supported through the  Deutsche Akademische Austauschdienst (DAAD) program  " Programme des projektbezogenen Personenaustauschs (PPP) " (Project-ID:  57561649 ) financed by the  Bundesministerium für Bildung und Forschung (BMBF).
We thus tested the impact of these mutations on viral infectivity using lentivector pseudotypes. P5C3-escaping spike proteins were significantly less infectious than the wild-type control in both the ancestral D614G and Delta backgrounds, correlating with a drop in affinity for the viral ACE2 receptor in an in vitro binding assay, whereas the P2G3-escaping K444T substitution had a milder effect in both assays (Fig. 6b, c ). Yet, an examination of the GISAID EpiCoV database revealed that mutations G476D, F486S or N487K/D/S found in P5C3 escapees are only exceptionally encountered in SARS-Cov-2 isolates, together The buried surface area formed by the indicated Fabs are outlined on the RBD surface and coloured correspondingly (Fab-RBD structures AZD1061, PDB-7L7E; REGN10987, PDB-6XDG; S309, PDB-7BEP).
SARS-CoV-2 live virus stocks. All biosafety level 3 procedures were approved by the Swiss Federal Office of Public Health. The SARS-Cov-2 D614G isolate and B. 1. 1. 7 clone have previously been described  21. Beta (EPI_ISL_981782), Gamma (EPI_ISL_981707), Delta B1. 617. 2 (EPI_ISL_1811202) and Omicron B. 1. 1. 529. 1 (EPI_ISL_7605546) early isolates were a kind gift from I. Eckerle, Geneva University Hospitals. Viral stocks were prepared in EPISERF medium on Vero E6 or Calu-3 (for Omicron) cells, aliquoted, frozen and titrated on Vero E6 cells.
Tracheal swabs, nasopharyngeal swabs and bronchoalveolar lavages were performed on all NHPs throughout the study to monitor levels of both genomic and subgenomic RNA for the SARS-CoV-2 virus. Blinding was performed whereby the technician analysing samples for RNA and virus titration was not aware of the treatment groups being evaluated and all animals and data points were included in the analysis. The NHP sample size was selected on the basis of the large, 1-to 2-log reduction in viral RNA anticipated in the tracheal, nasopharyngeal and/or BAL samples, with an effective therapy that can provide statistically significant differences between treated and untreated NHPs. These sample size assumptions were confirmed with the statistical differences observed in viral RNA levels evaluated using the Mann-Whitney two-sided tests to compare control and treatment groups.
Hamster challenge model SARS-CoV-2 infection. KU LEUVEN R&D has developed and validated a SARS-CoV-2 Syrian golden hamster infection model that is suitable for the evaluation of potential antiviral activity of novel antibodies  [37] [38] [39]. The SARS-CoV-2 strain used in this study, BetaCov/Belgium/GHB-03021/2020 (EPI ISL 109407976|2020-02-03), was recovered from a nasopharyngeal swab taken from an RT-qPCR-confirmed asymptomatic patient who returned from Wuhan, China in the beginning of February 2020. A close relation with the prototypic Wuhan-Hu-1 2019-nCoV (GenBank accession 11 no. MN908947. 3) strain was confirmed by phylogenetic analysis. Infectious virus was isolated by serial passaging on HuH7 and Vero E6 cells  37  ; passage 6 virus was used for the study described here. The titre of the virus stock was determined by endpoint dilution on Vero E6 cells by the Reed and Muench method.
Cryo-EM. Cryo-EM grids were prepared with a Vitrobot Mark IV (ThermoFisher). Quantifoil R1. 2/1. 3 Au 400 holey carbon grids were glow-discharged for 120 s at 15 mA using a PELCO easiGlow device (Ted Pella). Omicron spike (3. 0 µl, 0. 7 mg ml -1 ) mixed with 0. 16 mg ml -1 each of P5C3 and P2G3 Fab fragments (final ratio of 3. 2 uM Omicron spike:1. 5 uM P5C3:1. 5 uM P2G3) was applied to the glow-discharged grids, blotted for 6 s under blot force 10 at 100% humidity and 4 °C in the sample chamber, and the blotted grid was plunge-frozen in liquid nitrogen-cooled liquid ethane. Grids were screened for particle presence and ice quality on a TFS Glacios microscope (200 kV), and the best grids were transferred to a TFS Titan Krios G4. Cryo-EM data were collected using a TFS Titan Krios G4 transmission electron microscope, equipped with a Cold-FEG on a Falcon IV detector in electron counting mode.
Falcon IV gain references were collected just before data collection. Data were collected using TFS EPU v2. 12. 1 utilizing the aberration-free image shift protocol, recording 4 micrographs per ice hole. Movies were recorded at a magnification of ×165,000, corresponding to the 0. 83 Å pixel size at the specimen level, with defocus values ranging from -0. 8 to -2. 5 µm. Exposures were automatically adjusted to 60 e -Å -2 total dose, resulting in an exposure time of approximately 3 s per movie. In total, 22,758 micrographs in EER format were collected. Cryo-EM image processing. On-the-fly processing was first performed during data acquisition to evaluate data quality during screening by using cryoSPARC live v3. 3. 1  41. The obtained ab-initio structures were used for better particle picking for template creation.
Cryo-electron microscopy model building. A model of a spike trimer (PDB ID 7QO7; https://www. rcsb. org/structure/7QO7) or AlphaFold2 (ColabFold implementation) models of the P5C3 and P2G3 Fabs were fit into the cryo-EM maps with UCSF Chimera. These docked models were extended and rebuilt manually with refinement, using Coot and Phenix  44, 45. Figures were prepared in UCSF Chimera, UCSF ChimeraX and Pymol  43. Numbering of the full-length spike models within the global map is based on Omicron numbering. Numbering of models containing just the RBD within the local maps is based on wild-type numbering. Fab numbering at one from the first constant domains for the heavy (CH1) and light chains (CL), respectively. Buried surface area measurements and centroid measurements were calculated within ChimeraX.
Acknowledgements We thank the  Service of Immunology and Allergy at the Lausanne University Hospital  for analysis of serum samples for levels of anti-spike protein IgG antibodies;  I. Eckerle ,  M. Bekliz  and the  Virology laboratory of Geneva University Hospital  for the Omicron RNA sample and variant isolates collection; the  Geneva Genome Center  for sequencing and  J. Duc  for the development of in-house scripts for analyses;  L. Durrer ,  R. Schier ,  M. François  and  S. Quinche  from the  EPFL Protein Production and Structure Core Facility  for mammalian cell production and purification of proteins;  A. Myasnikov ,  B. Beckert  and  S. Nazarov  from the  Dubochet Center for Imaging  (an  EPFL, UNIGE, UNIL initiative ) for cryo-EM grids preparation and data collection, and  D. Demurtas  for set up of cryo-EM condition for automated acquisition in related studies not included in this manuscript;  D.
Wyatt  and members of the  CARE-IMI  work package 4 team for helpful discussions. G. P. and R. L. received a grant from the  Corona Accelerated R&D in Europe (CARE)  project funded by the  Innovative Medicines Initiative 2 Joint Undertaking (JU)  under grant agreement no. 101005077. The JU received support from the  European Union 's  Horizon 2020 research and innovation programme , the  European Federation of Pharmaceutical Industries Associations (EFPIA) , the  Bill & Melinda Gates Foundation ,  Global Health Drug Discovery Institute  and the  University of Dundee. The content of this publication only reflects the authors' view and the JU is not responsible for any use that may be made of the information it contains. Additional funding was provided.
Data Policy information about availability of data All manuscripts must include a data availability statement. This statement should provide the following information, where applicable: -Accession codes, unique identifiers, or web links for publicly available datasets -A description of any restrictions on data availability -For clinical datasets or third party data, please ensure that the statement adheres to our policy All data supporting the findings of this study are available within the paper and in the Source Data. The reconstructed maps of the global Omicron Spike with Fabs bound are available from the EMDB database, C1 symmetry, EMDB-14141. The atomic model for the full-length Omicron Spike with Fabs bound is available from the PDB database, PDB-7QTI. The local focussed-refinement map of the RBD-up with two Fabs bound is available from the EMDB database, EMDB-14142.
The atomic model for the RBD-up with two Fabs bound in the locally refined map is available from the PDB database, PDB-7QTJ. The local focussed-refinement map of the RBD-down with P2G3 Fab bound is available from the EMDB database, EMDB-14143. The atomic model for the RBD-down with P2G3 Fab bound in the locally refined map is available from the PDB database, PDB-7QTK. Data exclusions No data was excluded from the in vitro studies except in the rare case of technical failure. In hamster challenge studies, no control animals were excluded. In treated groups, animals with undetectable levels of serum antibodies were excluded from the analysis as this indicated a technical failure in the drug administration.
Data availability All data supporting the findings of this study are available within the paper and in the Source Data. The reconstructed maps of the global Omicron spike with Fabs bound are available from the EMDB database, C1 symmetry, EMDB-14141. The atomic model for the full-length Omicron spike with Fabs bound is available from the PDB database, PDB-7QTI. The local focused-refinement map of the RBD-up with two Fabs bound is available from the EMDB database, EMDB-14142. The atomic model for the RBD-up with two Fabs bound in the locally refined map is available from the PDB database, PDB-7QTJ. The local focused-refinement map of the RBD-down with P2G3 Fab bound is available from the EMDB database, EMDB-14143. The atomic model for the RBD-down with P2G3 Fab bound in the locally refined map is available from the PDB database, PDB-7QTK.
M E T HOD Participants and procedure A total of 6272 emerging adults completed the study survey. The mean age of the participants was 21. 54 years (SD = 3. 13, range 18-30 years). See Table  1  for further demographics for the entire sample and for each individual country. Participants were recruited from university research sites and online forums located in each of the collaborating countries: Australia (N = 597), Belgium (N = 618), Canada (N = 768), China (N = 669), Italy (N = 661), Japan (N = 622), Spain (N = 821) and the United States (N = 1516). People participated online using Qualtrics survey software. Informed consent was collected online prior to beginning the survey. In some cases, course credit or a chance to win a nominal financial reward was used to encourage participation (i.
The strongest correlations were found between RNase E and constituents of the RNA degradosome (Figures  3C  and 3D ), with the translation initiation factor InfA (Figure  3E ), with the DNA repair enzyme UvrA (Figure  3F ), and with the stress-response proteins   A  and B ) STRING protein-protein interaction analyses of the whole-cell proteome after rne overexpression (A) and silencing (B). Proteins were grouped according to their functional category using Mycobrowser and color-coded. Symbols represent exclusive, upregulated and downregulated proteins compared to control bacteria. The PANTHER classification system was used for gene ontology analysis, to identify additional clusters. Data are from five independent replicates. See also Table  S1. Obg  (Kumar et al. , 2017) and Lsr2 (Figures 3I and 3J).