dataesr/scientific-paragraphs-categorization huggingface dataset:
Conflict of interest statement: There are no conflicts of interest to report. Authorship statement: C. R. , C. C. , and S. B. conceived and designed the study, analyzed the data, and drafted the manuscript. G. T. ran the statistical analysis. N. K. collected the data from the EBMT registry and from the centers. A. X. , S. C. , A. T. S. , H. C. S. , M. Y. , V. R. , M. S. , N. K. , M. P. L. , J. D. , A. T. , S. G. , E. C. , T. Z. , A. H. G. , L. R. , S. A. , M. G. V. , A. K. , J. D. S. , P. T. , and M. M. provided data. R. C. , S. C. , and J. S. organized the study. All authors participated in critically reviewing the manuscript and approved the final version.
Data analysis Multiple physiological parameters were collected at baseline, during CPR and after achieving ROSC. Intrathoracic pressure, AoP, RAP, rSO2, and ETCO2 were measured continuously. Measurements were made at baseline, prior to inducing VF, at the end of the untreated VF period, and then multiple times during CPR and after ROSC. Values were averaged over a one-minute period of time,  reflecting a single value for each time point. The CorPP (mmHg) was determined by the difference between the decompression phase AoP and RAP. The physiological effects of epinephrine administration were assessed for each animal over a 60-second period beginning 10 seconds after drug administration, up to the time of the first defibrillation shock in both groups. The average CorPP value for each 10-second epoch for all animals combined was calculated.
, 2023). After isolation, the 8 viruses were thus amplified by one passage on IGROV-1 cells. The sequences of the variants after amplification were identical to those obtained from the primary samples (GISAID accession numbers are indicated in Table  S3 ), indicating that no mutations occurred during this short culture period. The spike mutations in these 8 variants, compared to BA. 2, are depicted in Fig. 1b. We also compared the spike mutations of a larger panel of variants to the Wuhan ancestral strain in Fig. S1b.
Cohorts Serum from bivalent Wuhan/BA. 5 Pfizer vaccine recipients or from infected individuals (Orléans, France). The Neutralizing Power of Anti-SARS-CoV-2 Serum Antibodies (PNAS) cohort is an ongoing prospective, monocentric, longitudinal, observational cohort clinical study aiming to describe the kinetics of neutralizing antibodies after SARS-CoV-2 infection or vaccination (ClinicalTrials. gov identifier: NCT05315583). The cohort takes place in Orléans, France and was previously described  (Bruel et al. , 2022b). This study was approved by the Est II (Besancon) ethical committee. At enrollment, written informed consent was collected, and participants completed a questionnaire that covered sociodemographic characteristics, clinical information and data related to anti-SARS-CoV-2 vaccination.
Serum from bivalent Wuhan/BA. 5 Pfizer vaccinated individuals from Lyon, France. A prospective, multicentric, longitudinal, interventional cohort clinical study (COVID-SER) is conducted at Hospices Civils de Lyon with the objective to evaluate the effectiveness of commercially developed serological test kits currently in development, which will be used for the diagnosis of patients with suspected SARS-CoV-2 infection. The COVID-SER-VAC ancillary study where blood samples was collected at the time of the injection(s) as per the recommended vaccination schedule was conducted (ClinicalTrials. gov identifier: NCT04341142)  (Trouillet-Assant et al. , 2020). A sub-study aimed to build a collection of biological samples and transfer of residual blood products to external partners for the advancement of scientific knowledge on SARS-CoV-2.
In brief, RNA was extracted using the QIAamp Viral RNA extraction kit (Qiagen) with the provided poly-A RNA carrier. Prior to library construction, carrier RNA and host rRNA were depleted using oligo(dT) and custom probes, respectively. The resulting RNA from selective depletion was utilized for random-primed cDNA synthesis with SuperScript IV RT (Invitrogen). Secondstrand cDNA was generated using Escherichia coli DNA ligase, RNase H, and DNA polymerase (New England Biolabs), and then purified with Agencourt AMPure XP beads (Beckman Coulter). Libraries were prepared using the Nextera XT kit and sequenced on an Illumina NextSeq500 platform (2 × 75 cycles). Reads were assembled using Megahit v1. 2. 9. The sequences have been deposited on the GISAID EpiCoV database (Table  S3 ).
, 2022a; Planas et al. , 2023). Neutralizing activity and ED50 were measured as described in the "S-Fuse neutralization assay" section. Delta, BA. 1, BA. 4/5, BQ1. 1, XBB. 1. 5/9, XBB. 1. 16, EG. 5. 1, BA. 2. 86 isolated)  were human codon-optimized and produced in silico (GeneArt, Thermo Fisher Scientific) as described  (Bolland et al. , 2023; Buchrieser et al. , 2020). Spike sequences were cloned into a phCMV backbone (GenBank: AJ318514) using Gateway cloning (Thermo Fisher Scientific) or restriction enzyme digestion followed by ligation with T4 DNA ligase (New England Biolabs). The pQCXIP-Empty plasmid was used as a negative control  (Bolland et al. , 2023; Buchrieser et al. , 2020). All plasmids were sequenced by the Eurofins Genomics TubeSeq service. His-tagged recombinant ACE2 ectodomain (amino acids 19-615) was cloned into pcDNA3.
Phylogenetic tree inference and lineage monitoring SARS-CoV-2 contextual sequence names were retrieved from the Nextstrain build of Sept. 18 2023  (Hadfield et al. , 2018). All available SARS-CoV-2 sequences from human infections were downloaded from the GISAID Epicov database (https://gisaid. org/) on October 23, 2023, and only sequences longer than 29000 nucleotides and with less than 1% ambiguities (Ns) were kept. Sequences were reannotated using pangolin (v4. 3. 1, with option --usher), and aligned against the Wuhan-Hu1 reference sequence (GenBank MN908947) using nextalign v2. 14. 0. In addition to this global context, BA. 2. 86 sequences were added to the dataset, using gofasta v1. 2. 1  (Jackson, 2022). The alignment used for phylogenetic reconstruction was made of 2909 sequences (global context sequences with the addition of BA.
2. 86 sequences and their closest relatives). Specific positions of the alignment were masked using goalign v0. 3. 5 (goalign mask command) to decrease phylogenetic noise. Bootstrap alignments were generated using goalign v0. 3. 5 (goalign build seqboot command) and reference and bootstrap trees were inferred using iqtree v2. 2. 0 (iqtree -m GTR -ninit 2 -n 2 -me 0. 05 -nt AUTO -ninit 10 -n 4). Bootstrap supports were computed using gotree v0. 4. 4 (gotree compute support fbp). Mutations that are common and specific to lineages of interest were computed using the outbreak. info R package (https://outbreak-info. github. io/R-outbreak-info) on Oct. 23 rd 2023. Values for some insertions or deletions were manually computed. Hierarchical relationships between lineages were retrieved from the pangolin GitHub repository (https://github.
Statistical analysis Flow cytometry data were analysed using FlowJo v. 10 (TriStar). Calculations were performed using Excel 365 (Microsoft). Figures were generated using Prism 9 (GraphPad Software). Statistical analysis was conducted using GraphPad Prism 9. Statistical significance between different groups was calculated using the tests indicated in each figure legend. provided in the Source Data file. The sequencing data generated in this study have been deposited in the GISAID EpiCoV database (EPI_SET ID: EPI_SET_231113yq). Figure Legends. Figure 3.
Acknowledgements The authors thank the patients who participated to this study, members of the  Virus and Immunity Unit  and other teams for discussion and help,  Julien Puech  from  Hôpital Europeen Georges Pompidou  for organizing the collect and analysis of nasopharyngeal swabs,  Hugo Mouquet  and  Cyril Planchais  for the kind gift of reagents,  Nathalie Aulner  and the staff at the  UtechS Photonic BioImaging (UPBI) core facility (Institut Pasteur) , a member of the  France BioImaging network , for image acquisition and analysis, ,  Fabienne Peira ,  Vanessa Legros ,  Aurelie Theillay ,  Sandra Pallay  and  Daniela Pires Roteia  ( CHU Orléans ) for their help with the cohorts. The authors thank "the  Centre de Ressources biologiques" from Hospices Civils de Lyon  (BRIF number:  BB-0033-00046 ), the members of the  National Reference Center  for viruses of respiratory infections hosted at  Institut Pasteur , and the  Mutualized platform for Microbiology  (P2M).
Funding Work in OS lab is funded by  Institut Pasteur ,  Urgence COVID-19 Fundraising Campaign of Institut Pasteur ,  Fondation pour la Recherche Médicale (FRM) , ANRS, the  Vaccine Research Institute  ( ANR-10-LABX-77 ),  Labex IBEID  ( ANR-10-LABX-62-IBEID ),  ANR / FRM Flash Covid PROTEO-SARS -CoV-2 ,  ANR Coronamito ,  HERA european  funding,  Sanofi  and  IDISCOVR. DP is supported by the  Vaccine Research Institute. The E. S. -L. laboratory is funded by  Institut Pasteur , the  INCEPTION program (Investissements d'Avenir  grant  ANR-16-CONV-0005 ), the  Ixcore foundation  for research, the  French Government 's  Investissement d'Avenir programme ,  Laboratoire d'Excellence 'Integrative Biology of Emerging Infectious Diseases'  (grant no. ANR-10-LABX-62-IBEID ), the  HERA Project DURABLE  (grant no  101102733 ) and the  NIH PICREID  (grant no  U01AI151758 ).
Healthy subjects The study was approved by an ethical committee (Ancillary project included in trial N° NCT03233282). Within a single session, 19 healthy subjects (10 females, 23. 2 ± 4. 4 years) had to perform a 14 blocks long calibration, where responses to provide were instructed, followed by 50 very simple open questions for testing. The questions were printed on screen. Fourteen subjects were complete naive users while 5 subjects (n° 1, 2, 16, 17 and 18) had already taken part to one fairly similar auditory BCI experiment about a month before. Only subject n° 2 had to be excluded because it turned out that he did not perform the task as instructed to.
Patients with severe motor impairment Seven patients were recruited at the University Hospitals of Lyon and Saint-Etienne, in rehabilitation wards and reference centers for ALS. We informed the patients and their legal representatives about the protocol. After that, patients gave their agreement with a "yes-no" motor code, and for each of them, as they couldn't write, their legal representative gave a written consent. The study was approved by the ethical committee Sud-Est III (Clinical trial N° NCT02567201). Clinical information for each patient is reported in Table  2. The clinical investigators of the reference centers for ALS assessed the patients with the ALS Functional Rating Scale  [20]. Each patient underwent a single recording session. To limit the cognitive load, we did not use questions but only direct instructions.
Acknowledgements We thank the people with LIS and  ALS  and their relatives for their active participation to this study and for their very valuable feedbacks. We thank  Lesly Fornoni  for her help in writing the ethical committee files. We thank  Pr Jean-Christophe Antoine ,  Dr Emilien Bernard , and  Pr Jean-Philippe Camdessanché  from the university hospitals of  Saint-Etienne and Lyon  for their valuable feedbacks and their help in recruiting the persons with ALS. We thank  Pauline Mandon  for her help in experimenting with patients. PS, JM, EM, PG and JL were funded by two grants from the  Fondation pour la Recherche Médicale  (FRM,  DEA20140629858 & FDM201906008524 ) ; PS and JM were also funded by the  French government  ( ANR-17-CE40-0005 , MindMadeClear). AO, JM, EM and DM were funded by the  Fondation pour la Recherche Médicale  (FRM,  ING20121226307 ).
Methods A cohort study of all type 2 diabetes free of CVRD as of January 1st 2014, was identi ed and followed-up for 5 years within the French SNDS nationwide claims database. The cumulative incidence of the rst occurring CVRD manifestation was estimated using the cumulative incidence function, with death as a competing risk. Cumulative hospitalization costs of each CVRD manifestations were estimated from the perspective of all payers.
A recent population-based cohort study demonstrated that four out of ve persons with type 2 diabetes will suffer from a major cardiovascular or renal disease (CVRD) over their lifetime  [20]. However, the risk of the rst occurring CVRD manifestation is not well known. A large multinational cohort study was designed with a core protocol to estimate this risk for patients initially free of CVRD, as well as the impact of each CVRD manifestation on health care utilization through the cumulative cost of CVRD hospitalization over time, using various databases (primary care, pharmacist, hospital, claims, registry database…) in different countries. First results of the risk were published for six countries, three from a sample of the population using primary and hospital care (England, Germany, Netherlands), one from a sample of the population using only hospital information (Japan) and two from the whole population of a relatively small country using only hospital information (Norway, Sweden)  [17].
Aim, design and setting of the study The aim of the study was to estimate the 5-year cumulative incidence of the rst occurred CVRD manifestation and the 5-year cumulative hospitalization cost of each CVRD manifestation for all type 2 diabetes free of CVRD at baseline from the whole population of a large European country, according to primary and hospital care. A 5-year follow-up cohort study was designed within the French SNDS nationwide claims database with 4 years of database history before patient inclusion. The SNDS links the national mandatory public health insurance system claims database to the national hospital-discharge summaries database and the national death registry, using a unique national pseudonymised identi er  [22]   [23]. It currently includes about 99% of the French population, more than 67 million persons from birth (or immigration) to death (or emigration), even if a subject changes occupation or retires, and irrespective of socioeconomic status.
Characteristics of participants All type 2 diabetes adult patients free of CVRD identi ed on January 1st, 2014 (index date) with 4-year database history and 5-years of follow-up (or until death) were included in the cohort after exclusion of those with cancer history, organ transplantation or immunosuppressive treatment for transplantation. The end of the study follow-up (2018) comes before the SGLT2i reimbursement in France and therefore their use in this country. Inclusion and exclusion criteria were de ned using the 4-year database history information and long-term disease registrations before the index date. Type 2 diabetes was de ned as patients with type 2 diabetes hospital discharged or long-term disease registration diagnosis (E11 ICD-10 code), or with ≥ 3 non-insulin antidiabetic drugs dispensing (or ≥ 2 if at least one big packaging)  [9, 24].
Results From about 2 million type 2 diabetes adults with a 4-year database history, no cancer or transplantation, and full study follow-up, around three-quarters (76. 5%) were free of CVRD at baseline (Fig. 1 ). The mean age of the CVRD-free population was 65 years, with a sex-ratio close to one (48. 2% of men), very few having microvascular complications, mostly treated with antidiabetic monotherapy, sulfonylurea being the most used antidiabetic and 10,4% using insulin, while 3 out of 4 having a cardiovascular drug dispensing, for treatment or prevention, within the 3 months before the index date (Table  1 ). The picture is completely different to that of patients with at least one CVRD comorbidity (Table  1 ). The outcome incidence rate for the CVRD-free cohort was 3. 9 per 1,000 person-years (‰PY) for MI, 5.
This may correspond to the well-known north-south cardiovascular risk demonstrated by the Monica project  [33] , with higher incidence in northern European countries such as Norway, Sweden, England, and to a lesser extent Germany and Netherlands, compared to France. This was also due to the information available in the various databases. Indeed, three of the six countries (Norway, Sweden and Japan) only took into account inpatients who were generally more severe than the rest of the population with healthier outpatients. Furthermore, the proportion of patients free of CVRD at baseline in our study could underestimated with patients having CVRD history before the 4-year history taking into account for the patient selection, and without long-term disease registration for the corresponding CVRD history.
9 vs 18. 5‰PY) and about 2. 5‰PY less for HF, stroke and MI (11. 0 vs 13. 4, 5. 1 vs 7. 5, and 3. 9 vs 6. 5 respectively), and slightly higher for PAD (6. 2 vs 5. 0‰PY). However, incidence rates of outcomes present variations according to the country management and the type of database. These variations can be partly explained by the north-south gradient of cardiovascular disease  [33]. This should be the case for Japan, which has one of the lowest cardiovascular risks among industrialized countries  [35] , while it had one of the higher CRD incidence rates in the 6-country study after 2. 5 years of follow-up, probably because only CVRD-free inpatients were taken into account in their study. Conversely, the lowest incidence rates were observed in England with the GP CPRD electronic medical record which probably missed hospitalizations for number of patients.
Our incidence rates were close to those of Germany which use similar claims database as the French SNDS. Nevertheless, the global picture with respective share of cumulative incidences of a rst CVRD manifestation was similar across the 6 countries, as well as in France, with CKD as the rst CVRD manifestation followed by HF, which together accounted for 63% of the rst CVRD event in both studies. A large type 2 diabetes cohort from the national Swedish registry and followed-up for 5. 7 years showed that type 2 diabetes without other risk factors had no or weak increase risk of MI, stroke or mortality compared to the general population, while they had a clear increase of HF risk  [12]. This important HF incidence is particularly worrying in view of the very poor prognosis of this pathology with a reduced life expectancy compared to myocardial infarction and even to most solid cancers (except lung)  [36].
The burden of HF and CKD in patients with type 2 diabetes. as well as the cost associated with it, encourages the consideration of early detection measures as well as preventive therapeutic strategies to limit the impact of these two complications. According to the ENTRED study on annual screening for CKD in France, annual albuminuria testing is performed in less than 30% of patients with diabetes, opening up prospects for major improvements in this screening  [39]. Beyond screening for complications, our data raise the question of the bene t of preventive use of speci c treatments that could reduce the incidence of new cases of HF and CKD. A recent study, performed on a large international database, explored the incidence of new onset HF in patients with diabetes, depending on whether or not they were treated with SGLT2-inhibitors.
Data and applications For illustrative purposes, we present excess mortality measures by losses/gains in life expectancy at age 60 (e 60 ) in 2020 for 95 départements of Metropolitan France, which correspond to the third level of the Nomenclature of Units for Territorial Statistics (NUTS) used by Eurostat. French Human Mortality Database  [37]  provides annual deaths (D) and population at 1st January by single age at death (with an open age interval 95+), sex, and département for each year between 1970 and 2020. We define exposures (E) as the mean of populations at 1st January for two consecutive years. For comparison, we gather populations and deaths to obtain data for 22 bigger régions (NUTS 2 level). Outcomes for this larger geographical level as well as for both sexes are provided in the Supplementary Materials B.
Search strategy and information sources This systematic review was conducted in accordance with the PRISMA statement  [34]. First, the literature was screened on NPIs in PD pain to define our search terms. To identify the largest number of potentially eligible studies as possible, we determined the population intervention comparison and outcome (PICO) criteria as search terms, as described in the Cochrane handbook  [35]  (Table  1 ). The review was registered on PROSPERO in February 2022 (ID number: 309266). In order to conduct a systematic review, we submitted our search terms in a broad panel of the database to consider the multimodal aspect of pain (biopsychosocial model). Between December 2021 and March 2022, the following databases were independently searched by two authors (M. H. and M.
Study selection process The steps of the selection process were depicted in the PRISMA diagram (Fig. 1 ), all steps were independently scrutinized by two authors (M. H. and M. B. ). The results with identified search terms were collected from the databases described above, the first selection was made with the title of the articles, excluding articles with non-PD patients, articles about pharmacological or surgical interventions and duplicates, for the main screening as well as the non-invasive neuromodulation supplementary search. Then, the abstracts were screened to exclude those that did not correspond to our eligibility criteria. To ensure that all relevant articles on PD pain management by NPI were identified, the bibliography of each article was also screened for the detection of any supplementary related publications.
Description of the flow chart Search terms submitted to the databases led us to 711 records that two independent authors (M. H. and M. B. ) investigated between January 2022 and March 2022. After deleting duplications, these records were firstly selected by their title in accordance to our eligibility criteria described in the method section. From the remaining 76 records, we excluded 57 after reading the abstracts. The selection was made following the PICO criteria and the majority of excluded articles were uncontrolled clinical trials (comparison) and/or without pain assessment (outcome). Then we added 32 titles that we considered relevant based on the references of the screened records, as well as seven articles identified from the supplementary research about neuromodulation. Finally, we read 58 full-text articles leading to the inclusion of 19 RCTs in our review.
Studies characteristics The characteristics of the selected studies are presented in the Table  2. The studies were published between 2004 to 2021. Our review gathered data from 976 subjects, age range 50 to 79 years, and mean Hoehn and Yahr score between 1. 5 and 3. 0. The number of patients by study ranged from 15 to 270 subjects. All clinical trials were randomised and controlled with parallel groups except one that used a crossover design. Study duration was from three weeks to one year including follow-up, which was the case for eleven studies (follow-up from four weeks to thirty weeks after the last intervention). Two studies verified that all the patients had chronic pain either by including pain duration greater than three months as an inclusion criteria  [41]  or by only evaluating patients with musculoskeletal pain.
2. 2  (Simão et al. , 2015) , using the Aves (n=8782) OrthoDB v10 database  (Kriventseva et al. , 2019). We also used TransRate v1. 0. 3  (Smith-Unna et al. , 2016)  to further assess completeness. The Ex90N50 statistic was quantified as a measure of contiguity, where the N50 value is computed based on the top 90% of transcripts based on expression levels  (Haas et al. , 2013). Expression levels were estimated by mapping the trimmed reads used for the assembly back to the assembled transcripts using Salmon v1. 10. 2  (Patro et al. , 2017)  and statistics were calculated using the TrinityStats. pl script  (Haas et al. , 2013). The Trinotate software (github. com/Trinotate/Trinotate/wiki, v4. 0. 1) was used to annotate the transcriptomes and predict coding regions. First, coding regions were predicted within using  TransDecoder (github.