dataesr/scientific-paragraphs-categorization huggingface dataset:
Data collection The Mbacké healthcare centre (14 • 47 ′ 56 ′′ N, 15 • 54 ′ 36 ′′ W, 10 km from Touba) was selected because of its large number of patients, (1,115 patients during the 2015 GMT, unpublished data). It operated 24 h a day during the five-day period of free medical coverage of the GMT (26-28 October 2018, three-day pilot study, 15-19 October 2019, 4-8 October 2020, and 24-28 September 2021). The consultations were provided by medical doctors and nurses. The centre consists of an emergency room and a hospitalisation ward with a capacity of 28 beds. The inclusion criteria were to present with a cough, diarrhoea or febrile systemic illness as the main complaint. The medical team completed a demographic and clinical questionnaire and patients were offered appropriate sampling according to their symptoms.
Bone mineral density measurements and pQCT acquisitions Bone mineral density (BMD; mg of hydroxyapatite/cm 3 ) of ulna and radius was assessed using peripheral quantitative computed tomography (pQCT, XCT 540 Stratec SA+, Norland Stratec, Germany) within 3 days before (native, n = 3 each) decellularization and within 5 days after decellularization end (n = 3 each). In each bone, 30 slices spaced 0. 1 mm apart were acquired, and 10 BMD measures were carried out in distal, central, and proximal locations from the vascular pedicle respectively. The values of the 30 slices were averaged for each bone, before and after decellularization. Data were expressed as mean BMD ±SD.
Acknowledgments Guillaume Rougier  is a fellow of the " Fondation des Gueules Cassées ". This work was also supported by an  F. R. S. -FNRS  ( Fonds National de la Recherche Scientifique, Belgium ) Aspirant Fund granted by  Dr. Louis Maistriaux  (Aspirant Fund: ID 40000380),  Dr. Julie Manon  (Aspirant Fund: ID 40004991), and  Dr. Robin Evrard  (Aspirant Fund: ID 40010491). We gratefully thank the  School of Surgery in Paris of the "Fer à Moulin"  for the loan of microsurgery equipment and global support of this study. The authors additionally thank  Dr. Jérôme Duisit  for providing initial support for this project,  Christine de Ville de Goyet ,  Pascale Segers ,  Gwen Baurin ,  Martial Vergauwen ,  Michelle Cougnon , and  Walter Hudders  for their devoted technical assistance.
Literature Review A literature review was performed between July 5 and July 30, 2021 using the PubMed and Google Scholar databases to identify any literature investigating patient or physician opinions on remote clinical trials, home-and remotebased medical tests, as well as the most commonly used home-and remote-based clinical trial procedures. Search terms included ''hospital-at-home'', ''home care'', ''patient centred care'', ''decentralised'', ''decentralised clinical trial'', ''clinical trial'', and ''home based medical testing''. Papers were limited to those published from 2011 onwards. The literature was filtered by Simon Balanza and Catalina Pen ˜a, from the Instituto Experiencia Paciente, and relevant studies were selected.
In-Depth Interviews Interview 1: Healthcare Professionals Based on the gaps in knowledge identified in the literature review, a semi-structured script for an interview was created to collect first-hand and up-to-date information on the opinions and experience of HCPs with H/RMT in Spain and Brazil (see Supplementary Materials S1 in the Electronic Supplementary Materials for the English translation of the script used). The duration of the interviews was approximately 45-60 min, and the interviews were conducted using the GoogleMeet Ò or Zoom Ò videoconference platforms. These in-depth semi-structured interviews explored the level of knowledge and experience about how H/RMT could be performed, the conditions under which H/RMT could be carried out, the perceived advantages and disadvantages of H/RMT in clinical trials, the HCPs perception of patient experiences with H/RMT, and how this differs from conventional clinical trials.
Literature Review Overall, 47 articles were identified during the literature search. After filtering, 30 were assessed and 16 considered relevant  [1-4, 6-8, 15-17, 19-24]. The literature review identified some articles discussing decentralised clinical trials  [2, 3] , where H/RMT was used for data collection  [24] ; however, limited literature allowed for understanding the value of H/RMT for patients. The scientific literature identified that focuses on H/RMT does so from the perspective of HCPs. Furthermore, there were limited data on patient barriers to H/RMT. The main advantages of H/RMT were related to patient comfort and working with older patients. However, how this concept of comfort is constructed and what it implies in the context of clinical trials was not explored in detail in the literature identified.
ACKNOWLEDGEMENTS We would like to thank the patients, caregivers and healthcare professionals for the time and quality of exchange they provided, which made possible the completion of this study. Funding. Sponsorship for the interviews and validation workshops, medical writing support, and publication of the article including the journal's  Rapid Service  and  Open Access  fees were funded by  Servier. Medical Writing, Editorial, and  Other Assistance. Editorial assistance in the preparation of this article was provided by  Simone Tait of Springer Healthcare Communications  during the drafting of this manuscript, and by  Kate Palmer  during post-submission revisions. Support for this assistance was funded by  Servier. Authorship. All named authors meet the International Committee of Medical Journal Editors (ICMJE) criteria for authorship for this article, take responsibility for the integrity of the work as a whole, and have given final approval of the version to be published.
STATISTICAL ANALYSIS Statistical analysis was performed with GraphPad Prism v9. 0. 2 (GraphPad Software Inc. , San Diego, CA, USA). All data are presented as median (1 st and 3 rd quartile). Normality of distribution is assessed by Shapiro-Wilk test. ANOVA for repeated measures is used to analyse more than two related groups followed by multiple comparison Tukey's post-hoc test. Statistical significance was set at p < 0. 05.
The use of oxygen-helium mixture despite the shallow depth allowed a manoeuvrable decompression and faster than with nitrogen. The "decompression procedures" considered that speed rate is determined by the oxygen concentration  [21]. However, oxygen may be toxic with acute neurological toxicity and long-term effects on lungs  [22]. This model driven by oxygen appear effective as previously suggested by Kot   [23]  in Nitrox saturation dives or Blatteau et al. [24]  without VGE detection and non-significant spirometric alteration. Procedures were based on the COMEX database which allowed the development of regulatory procedures in professional diving in France and the REPEX oxygen toxicity threshold  [22, 25]. However, the cumulative oxygen limits could be exceeded for deeper or prolonged dives with special consideration for pulmonary toxicity.
In case of DCS, prolonged in-water decompression would have required adequate thermal protection in dry-suits with a heating system which could be brought to the "Capsule". These data are reassuring but could not be transposed into more temperate waters in the absence of a specific protection system for divers and the habitat. Thermal protection would be an important challenge in another environment. Finally, physiological short and long-term evaluations would be necessary to fully assess this new approach of div- ing procedures. The main limitation of our report is the small sample of selected professional and fit divers. The excursions carried out had very conservative and short duration. This could be explained by spontaneous limitation to stay in safe areas of procedures because that was the first saturation experience for divers.
ACKNOWLEDGEMENTS Authors thank all the team of "Capsule" programme, and particularly  Ghislain Bardout  and  Emmanuelle Périé-Bardout , co-founders and director of the Under the Pole Expeditions, who have enabled the development of this innovative programme. We thank  Dr. Julien Hugon , scientific director of Azoth system, for his assistance for US signal analyse. We thank  Dr. Bruce D'Souza  for his assistance and advice in manuscript revision.
Methods We included hospitalized patients with confirmed or suspected SARS-CoV-2 infection from the International Severe Acute Respiratory and emerging Infection Consortium (ISARIC) database. Key exposure was baseline liver enzymes (AST, ALT, bilirubin). Patients were assigned Liver Injury Classification score based on 3 components of enzymes at admission: Normal; Stage I) Liver injury: any component between 1-3x upper limit of normal (ULN); Stage II) Severe liver injury: any component �3x ULN. Outcomes were hospital mortality, utilization of selected resources, complications, and durations of hospital and ICU stay.
ISARIC hosts data for the largest world-wide cohort of hospitalized COVID-19 patients. Using the ISARIC dataset, we evaluated the prevalence and severity of derangements in liver enzymes among patients admitted to hospital with COVID-19 and the association between liver enzymes measured during the first 24 hours and patient-centred hospital outcomes. clinical data on individuals hospitalised with COVID-19. Due to the sensitive nature of these data and the associated privacy concerns, they are available via a governed data access mechanism following review of a data access committee. Data can be requested via the IDDO COVID-19 Data Sharing Platform (http://www. iddo. org/covid-19). The email is: dataaccess@iddo. org. The Data Access Application, Terms of Access and details of the Data Access Committee are available on the website.
Study design and ethics The ISARIC-WHO Clinical Characterization Protocol for Severe Emerging Infections provided the framework for prospective observational data collection on hospitalised patients with COVID-19. The protocol, CRFs, consent forms, and study information are available online  [14]. These CRFs were developed to standardise clinical data collection on patients admitted with suspected or confirmed COVID-19, with clinical data on more than 900,000 individuals hospitalised with confirmed COVID-19 infection across 64 countries stored in a central database (as of June 2022). The CRFs collect data on demographics, pre-existing comorbidities and risk factors, signs and symptoms during the acute phase, supportive care and treatments received during hospitalisation, and outcomes  [14].
Variables and definitions Serum bilirubin, ALT, and AST measured at or within 24 hours of hospital admission were considered as the liver enzymes for this analysis, based on availability in the ISARIC database. For the purposes of this analysis, upper limits of normal (ULN) for serum bilirubin, ALT and AST were taken as 1 mg/dL, 40 U/L and 40 U/L respectively. In the absence of an established scale for liver injury based in these laboratory tests, we adapted our criteria from previous studies that have used similar approaches  [8, 9, [16] [17] [18]. Each patient was assigned a Liver Injury Classification (LIC) score at baseline based on the 3 components of LFT on admission: stage 0) Normal: all 3 components �ULN; Stage I) Liver injury: any 1 component between 1-3x ULN; Stage II) Severe liver injury: any 1 component �3x ULN.
For the remaining covariates, those with P <0. 20 in univariable analysis were retained for the multivariable analysis, and backwards elimination was used for model selection. To account for potential effect modifications, two-way interactions were evaluated between LIC and age categories, ICU admission, and receipt of remdesivir. Missing data were not imputed, and analyses used complete cases. In a sensitivity analysis (primary outcome), we included only laboratory confirmed patients. We used R4. 1. 2 [R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. https://www. R-project. org/] for statistical analysis. Deviations from original analysis plan. We originally planned to examine the association between receipt of remdesivir and new liver enzyme elevation, as well as at trends of liver enzymes during the hospital stay.
Results From a total of 708,052 patients in the ISARIC database as of 21 st September 2021, we included 17,531 patients after eliminating those with missing baseline information on liver enzyme tests (n = 686,122 patients) and outcomes (4399 patients). Baseline characteristics of included patients are presented by stages of LIC classification in Table  1. The mean age was 56. 5 (SD 20. 3) years, and 60. 0% of the patients were male. Hypertension (33. 9%) and diabetes (31. 3%) were the most common comorbidities. Around 3. 0% of the cohort had chronic liver disease. Cough (60. 0%) and fever (59. 0%) were the most common presenting symptoms of COVID-19. 45. 6% of patients had normal liver enzymes, 46. 2% had stage 1 liver injury, and 8. 2% of the cohort had stage 2 liver injury (Table  1 ). Patients met criteria for liver injury predominantly through elevations in AST or ALT (S2 Table ).
In a larger cohort (n = 5771) of hospitalized patients from Hubei province  [21] , increasing values of AST, ALT, alkaline phosphatase, and bilirubin were associated with mortality, with AST the most deranged liver enzyme at admission for patients with severe COVID-19, and remaining high throughout hospitalization. Results of our analysis are largely consistent with these prior studies and strengthen the evidence base with a much larger dataset. Multiple mechanisms may explain the frequency and severity of liver involvement in COVID-19. The ubiquitous distribution of the viral entry receptor, ACE2, in human tissues might imply a role for direct cytopathic effects  (22). Both microvesicular and macrovesicular steatosis has been demonstrated in autopsies of patients, with SARS-CoV-2 as the only risk factor for liver injury  [22].
Selection bias is possible, since were able to include only a fraction of the patients represented in the ISARIC database due to missing data on liver enzyme tests and outcomes. Liver enzymes are more likely to be measured in patients with signs or history of liver disease, and in patients presenting with more severe illness at presentation, indicating that the frequency of liver failure reported here is an overestimate of the hospitalised population. Also, we were unable to evaluate the association between remdesivir and other antivirals on the development of liver injury due to extensive missing data.
These observations suggest that resistance to PM can be conferred to pregnant women through vaccination by inducing protective antibodies targeting the surface of placental IE 6. The placenta-sequestering P. falciparum-IE surface displays VAR2CSA, a member of the P. falciparum erythrocyte membrane protein 1 (PfEMP1) family and the main parasite ligand mediating IE adhesion to the key placental receptor CSA  [11] [12] [13] [14]. The large size of VAR2CSA stymies efforts to manufacture full-length recombinant protein, and studies of VAR2CSA domains or fragments that bind CSA have informed the design of constructs that induce anti-adhesion antibodies in small animals (mouse, rat and rabbit)  [15] [16] [17] [18] [19] [20] [21] [22] [23]. Among these VAR2CSA constructs, PAMVAC and PRIMVAC, based on partially overlapping N-terminal fragments of VAR2CSA, have recently been tested in phase I clinical trials in Europe and Africa (ClinicalTrials.
Results Local and systemic reactogenicity. Overall, vaccines were well tolerated by the Aotus monkeys. No death occurred during the vaccination period. Fifteen out of 40 monkeys showed some muscle firmness at the injection site after vaccination with no edema, redness or warmth. Hardened areas of the muscle were measured using a caliper to determine the time at which the reaction dissipated from the animals. This muscle induration was observed across all vaccination groups, including the Pfs25 control group, and resolved within 7 days post-vaccination. No sign of systemic reaction or change in behavior was observed. Detailed description of clinical observations post-immunization is presented as Supplementary Data File 1. PMV-induced antibodies in Aotus exhibit strong homologous activity. Forty naive female Aotus monkeys received three immunizations of PAMVAC (n = 9), PRIMVAC (n = 9), ID1-ID2a_ M1010 (n = 9) and Pfs25 (n = 13) at 4-week intervals (Fig.
Two lots of CS2 inoculums with similar parasite binding phenotype (predominantly binding to CD36 receptor) were used in this work (Supplementary Table  1 ). CS2 infections in pregnant monkeys were performed with thawed parasites inoculated in the saphenous vein. Infected animals were observed twice a day and monitored daily with parasitemia data collected from day 3 until animals were cured. P. falciparum infection was confirmed by PCR detection on peripheral blood 3 days after CS2 inoculation (for detailed parasitological data and other clinically relevant information, see Supplementary Data File 2). The infected pregnant monkeys were asymptomatic during this brief CS2 infection, and all animals were cured with mefloquine after end of pregnancy. As full normal gestation is ~19 weeks  54  , infection was initiated at ~17 weeks to allow for 7 days infection, and C-section performed at ~18 weeks to ensure placental sample collection.
Briefly, baculovirus expression clone and high-titer virus stock was produced by Protein Expression Laboratory (NCI-Leidos) using a synthetic codon optimized gene encoding ID1-ID2a_M1010 (GenBank Accession number KU665625). Recombinant ID1-ID2a_M1010 has a non-native amino-terminal alanine. All five putative N-linked glycosylation sites were mutated from NxT/S to NxA at positions T440, S507, S518, T694 and T732 relative to VAR2CSA FCR3. An in-frame His-tag was included on the carboxyl terminal end to facilitate purification. Bench-scale production was done in 10 liters bioreactor glass connected to Biostat BDCU controlling system (Sartorius-Stedim). The cells grew in SFX-insect medium (Hyclone) to a concentration of 2 × 10 6 per milliliter and were infected with 3 multiplicities of infection of the recombinant virus.
Acknowledgements This work was supported by the  Intramural Research Program  of the  National Institute of Allergy and Infectious Diseases, National Institutes of Health ; the  Danish Research Councils , The  Eurostars Programme , the  European Union  in the  Seventh program Framework Programme  ( FP7-HEALTH-2012-INNOVATION ; under grant agreement  304815 ), the  Danish Advanced Technology Foundation  (under grant number  005-2011-1 ), the  Bill and Melinda Gates Foundation  (grant numbers  42387  and  OPP1055855  to S. G. R. ); the  French National Research Agency  ( ANR-16-CE11-0014-01 ), grants from  Laboratory of Excellence   GR-Ex , reference  ANR-11-LABX-0051  and the  French Parasitology consortium ParaFrap  ( ANR-11-LABX0024 ). The labex GR-Ex is funded by the program ' Investissements d'avenir ' of the  French National Research Agency , reference  ANR-11-IDEX-0005-02 ; a grant from the  Bundesministerium für Bildung und Forschung (BMBF) ,  Germany  through  Kreditanstalt für Wiederaufbau (KfW)  (reference no.
SEURAT software classified RNA expression into clusters numbered 0 to 10 (Fig 3E, first panel) that formed two main groups: clusters 0, 2, 3, 4, and 5 formed part of one pool (Fig. 3E , right pool), whereas clusters 1, 6, 7, 8, 9, and 10 formed another (Fig. 3E , left pool). Of note the SingleR software, trained on the Immunologic Genome Project database of mRNA profiles, identified cells from the right pool as "neutrophils", whereas cells from the left pool were identified as "monocytes/macrophages", probably due to the expression of genes such as Mhc-II and Cd274 (encoding PD-L1). Certain genes, such as Itgam (Fig. 3E ), were similarly expressed in clusters from the two pools, in agreement with the neutrophil signature. However, differential expression of the H2-Eb1 and H2-Ab1 genes from the MHC-II complex or Il1b and Il1r2 inflammatory genes clearly segregated between the two pools (Fig.
Lung cell preparation and flow cytometry Briefly, euthanized mice were perfused with PBS and the left lung lobes digested for 1 h with collagenase D (1. 5 mg/ml, Roche) and DNAse A (40 U/ml, Roche) before filtering cells through a 100 μM nylon cell strainer (BD Falcon). For extracellular staining, cells were incubated 20 min with 2% total mouse serum and labeled in PBS supplemented with 5% FCS and 0. 1% total mouse serum with antibodies against the surface markers, all from BD Biosciences (listed in Supplementary Table  1 ). Intracellular mature IL-1β production was measured using anti IL-1β biotin conjugated antibody (Rockland) after treatment for 2 h at 37°C with 5 μg/ml brefeldin A (Sigma-Aldrich). Cells were washed and fixed with BD cell fix diluted 4X in PBS. Data were acquired on a LSR Fortessa™ X-20 Flow cytometer (Becton Dickinson) and the results analyzed using Kaluza software (Beckman Coulter).
Medium-throughput and single-cell RNA sequencing of neutrophils For medium-throughput analysis of gene expression in neutrophils, total RNA was extracted from FACS-sorted neutrophils from the right accessory lung lobe homogenized using Lysing matrix D tubes from MP Biomedicals and a Precellys® using a NucleoSpin RNA kit with DNase treatment (Macherey Nagel). Total RNA was reverse transcribed using an iScript™ Reverse Transcriptase mix (Biorad) and gene expression assessed using a BioMark HD (Fluidigm) according to the manufacturer's instructions or a LightCycler® 480 Real-Time PCR System (Roche). The annealing temperature was 62°C. All primers are listed in Supplementary Table  2. Data were analyzed using Fluidigm RealTime PCR software or Lc480 software to determine the cycle threshold (Ct) values.
1 Gel Beads and a Master Mix to form a Gel Beads-in-emulsion using the 10X Genomics Chromium technology. Approximately 12,000 cells were used. The Single Cell 3' libraries were then generated as recommended by the manufacturer (10x Genomics). The libraries were equimolarly pooled and sequenced (paired-end sequencing) using one lane of an Illumina NovaSeq6000 device (IntegraGen, France), yielding a total of 640 million reads. Raw sequencing data are available under the following BioProject accession number PRJNA1026083. Fastq files were analyzed the sequences and aligned against those of the Mus musculus genome mm10 (GRCm38-release 98) using the cellrangercount pipeline of CellRanger software (v6. 0. 2). Downstream analyses were performed using R (v4. 3. 0), Rstudio and the following packages: Seurat (v4.
4. 0), SingleR (v2. 2. 0), celldex(v1. 10. 1). Quality controls first included empty droplets and doublets removal. Then, only droplets with at least 100 features and 1000 counts were retained. Normalization was done using the LogNormalize method and the 3000 most variable features. Dimension reduction method was performed by Principal Component Analysis (PCA) retaining the first 9 principal components with a resolution of 0. 8 to identify the clusters with FindClusters. Cell-type inference was performed using SingleR and the Immunologic Genome Project database retrieved through celldex package.
Histology The right cranial lung lobe was fixed in 4% paraformaldehyde for 48 h. Subsequently, the tissue was dehydrated and stored in 70% ethanol before being embedded in paraffin. Five micrometer sections were cut and stained with hematoxylin and eosin (H&E) using a slide stainer (ST5020; Leica Biosystems, Nußloch, Germany). All slides were scanned on a slide scanner (AxioScan Z1; Zeiss, Oberkochen, Germany). Morphological analyses were performed using QuPath software  (65) ; available at https://qupath. github. io/, version 0. 4. Briefly, airway lesions were quantified using a semi-automated macro. The total area of tissue was automatically measured using a threshold and the lesions blindly measured manually for all slides. Data for each mouse consist of the mean of eight sections, cut every 100 µm, to accurately represent the whole lung.