dataesr/scientific-paragraphs-categorization huggingface dataset:
Figure9. Use of the ''batch-mode'' available on MULTILAYER for processing several datasets at once (A) MULTILAYER main interface allowing the selection of a folder containing all datasets to process. (B) Once all datasets are processed (in this case a set of twelve prostate sections), MULTILAYER provides a similar interface than that used for the ''explore mode'', giving access to all different analytical panels when one dataset is selected. In addition, a ''Comparison datasets'' button is displayed. (C) This ''Comparison datasets'' module, allows us to select the samples of interest for processing. Furthermore, it allows us to define the parameters for the spatial community's detection. (D) For selected datasets, users can also define the minimal number of gexels for patterns detection. (E) Panel illustrating the classification of all spatial communities detected per analyzed datasets.
ACKNOWLEDGMENTS This work was supported by the institutional bodies  CEA ,  CNRS, and Universited'Evry-Val d'Essonne. J. M. was supported by  Genopole Thematic Incentive Actions funding  ( ATIGE-2017 ); A. K. by the '' Fondation pour la Recherche Medicale'' (FRM ; funding ALZ 201912009904); and F. S. by the funding  2OI9-L22  from the  Institut National du Cancer (INCa).
Prostate_cancer raw matrices (ST) Berglund et al. , 2018 https://github. com/SysFate/MULTILAYER/tree/ master/Data/Prostate_cancer Software and algorithms MULTILAYER Moehlin et al. , 2021 https://github. com/SysFate/MULTILAYER MULTILAYER compressor Moehlin et al. , 2021 https://github. com/SysFate/MULTILAYER Visium Converter This article https://github. com/SysFate/MULTILAYER.
Study Design and Participants For the present study, we used data from Erasme Hospital of Brussels (Belgium) using the International Severe Acute Respiratory and Emerging Infections Consortium (ISARIC) COVID-19 database. Data were collected and managed using REDCap (Research Electronic Data Capture), a secure, web-based software platform that allows data collection for research studies. For the present study, the database includes individuals for whom data collection commenced on or before 1 September 2020.
Seventy-two patients died during hospitalization and 278 were alive. Demographic data regarding symptoms, comorbidities, laboratory findings on admission and outcomes were retrieved from the ISARIC COVID-19 database of Erasme Hospital and retrospectively reviewed and analyzed. The Strengthening the Reporting of Cohort Studies in Epidemiology statement guidelines were followed in the conduct and reporting of the study (see online Supplemental File, Table  S1 ). Two physicians (G. D. and G. L. ) were responsible for data collection. The characteristics of the sample are given in Table  1. Particular attention was given to the prescription of FIASMAs at admission. Patients with a long-term prescription of FIASMAs at admission were noted as FIASMAs positive (F+). Chronicity was defined as duration equal to or higher than seven half-life for each FIASMA (half-life range: 35-50 min (melatonin) to 20-100 days (amiodarone)).
Statistical Analysis Univariate and multivariate logistic regression models were used to evaluate risk factors of mortality among COVID-19 patients using Statistica (version 7. 1) software  [27]. The dependent variable was the status (alive or deceased) and the independent variables were sex, age, comorbidity, smoking and FIASMAs status. From univariate analyses, each independent variable with significant association with mortality (p < 0. 05) was included in the multivariate analysis except for the FIASMA status, which is a forced variable.
Supplementary Materials: The following are available online at https://www. mdpi. com/1424-824 7/14/3/226/s1, Figure  S1 : Population flow chart for FIASMAs study in COVID-19 patients, Table  S1 : STROBE for FIASMAs study in COVID-19 patients. Author Contributions: G. L. and P. L. C. conceived the idea and designed the study. G. L. had full access to all the data in the study and took responsibility for the integrity of the data and the accuracy of the data analysis. G. D. collected data and took responsibility for its integrity. O. L. M. collected initial data to explore the feasibility of prevalence of FIASMAs in COVID-19 patients. All authors have read and agreed to the published version of the manuscript. Funding: There was no funding for the study. Institutional Review Board Statement: The present study was conducted according to the guidelines of the Declaration of Helsinki, and approved by the Ethics Committee of the Erasme Hospital (Protocol P2020/358 approved the 16 July 2020).
Characterization methods Thermogravimetric analysis curves (TG/DTG) were recorded using Perkin Elmer TGA7 equipment from 30 °C to 900 °C with a heating rate of 20 °C min -1 under air flow. Nitrogen adsorption-desorption isotherms were acquired at -196 °C with a Micromeritics ASAP 2420 sorptometer. Prior to analysis, the samples were degassed at 200 °C for 16 h. Total surface areas were calculated by the BET method. The pore size distribution, micropore volume, and mesopore surface area and volume were determined from the adsorption data using the methods of non-local density functional theory (NLDFT) with the kernel function for oxide materials with cylindrical pores. 29, 30 hemical analysis of the bare ALPS support and CoRu catalysts was performed by ICP-OES using a Varian 715-ES spectrometer.
Prior to the analyses, the samples (ca. 20 mg) were dissolved in a mixed acid solution of HNO 3 : HF : HCl with a 1 : 1 : 3 volume ratio. Scanning electron microscopy (SEM) has been performed using a Hitachi S-4100 field-emission (FE) gun microscope equipped with a BSE-AUTRATA detector using gold-coated powder specimens. The morphology of the calcined supports and catalyst particles was studied by transmission electron microscopy (TEM) in a Tecnai G2 field emission gun device with EDAX microanalysis working at 200 kV. Samples for TEM studies were prepared by ultrasonic dispersion in ethanol for 1 min. After that, the suspensions were dropped onto a carbon coated copper grid. The TEM-derived Co 3 O 4 particle size distributions for the calcined CRLPS and CRALPS samples were determined by counting about 200 particles in several images taken at different positions on the grid, using the ImageJ software.
32-34)). Data analysis was performed using CasaXPS software (v2. 3. 16). Deconvolution of experimental peaks into components was done using a non-linear, least squares fitting algorithm after Shirley baseline subtraction. XPS peaks were fitted using a 70% Gaussian-30% Lorentzian mixed function. Surface atomic ratios were calculated from the peak area ratios normalized by the corresponding relative sensitivity factors provided by CasaXPS software.
Acknowledgements A. M. acknowledges the  MINECO of Spain  for financial support through the  Severo Ochoa  ( SEV2016-0683 ) and  RTI2018-102161  projects. C. M. -A. and J. P. -P. also acknowledge funding of the  Spanish Ministry of Science Innovation and Universities  (project  PID2019-107968RB-I00 ,  AEI, Spain). S. M. acknowledges the organization of student affairs (Iran) for a sabbatical leave grant. The authors are thankful to the  Microscopy Service of the Universitat Politècnica de València  for its assistance in microscopy characterization. We acknowledge support of the publication fee by the  CSIC Open Access Publication Support Initiative  through its  Unit of Information Resources for Research (URICI).
METHODS All consecutive patients with isolated DMR operated on by the surgical team in 2 separate institutions (Royal Brompton and Harefield NHS Foundation Trust, United Kingdom; Cardio Thoracic Centre of Monaco) between January 2005 and December 2015 (2005-2009, United Kingdom; 2010-2015, Monaco) were included. Exclusion criteria were the absence of research authorization per European law, presence of pacemakerdefibrillator, organic TR, moderate or greater aortic valve disease, mitral stenosis, rheumatic or functional mitral regurgitation (MR) (per guidelines),  16, 17  any previous valve surgery, any other myocardial/pericardial/ congenital heart disease including triple-vessel coronary disease, and the absence of tricuspid annulus measurement on transthoracic echocardiography. The study was approved by the Ethic committee of the Royal Brompton and Harefield NHS Foundation Trust, London, United Kingdom, in March 2017 following a retrospective analysis of anonymous data from patients operated in between January 2005 and December 2009, as well as from the Cardiothoracic Center of Monaco in March 2017 for patients in between January 2010 until December 2015.
Echocardiographic Evaluation Echocardiography performed by experienced in-hospital sonographers with special interest in mitral and tricuspid valve pathology included comprehensive measures and grading using standardized echocardiographic phrases. Those were stored immediately in an image and data repository and retrieve without alteration or reinterpretation for the study. Degenerative mitral valve disease was defined as excess leaflet motion (type II of Carpentier's classification) resulting from chordal elongation or chordal rupture  18  and DMR severity assessed by integrative grading with quantitative assessment as often as possible. 19 FTR was diagnosed by comprehensive tricuspid valve examination excluding structural abnormalities and graded using standardized phrases according to American Society of Echocardiography guidelines as absent, mild, moderate, and severe.
Clinical Evaluation Patients' demographic and clinical data, including New York Heart Association (NYHA) functional classification, were recorded at baseline and during in-hospital stay by patients' personal physicians in charge and electronically retrieved from medical files without alteration. AFib before/at diagnosis relied on ECG or clinical notes for history of proven AFib. Surgical data included bypass time, crossclamping time, coronary artery bypass graft, maze procedure, and size of the semi-rigid ring for patients with TA. Postoperative renal failure (defined as creatinine level !200 mg/dL), use of intra-aortic balloon pump, inotropic support, implantation of pacemaker before discharge, occurrence of thromboembolic event, reoperation, and length of in-hospital stay were recorded during in-hospital stay by the physician in charge and electronically retrieved from medical files without alteration.
20). The cumulative incidence of moderate/severe FTR was estimated by the competing risk model and assessed with respect to TA and other covariates. Postoperative echocardiographic longitudinal data were analyzed by the generalized linear mixed model (GLMM) in which the covariates were time (both linear and quadratic effects), TA, and interaction between TA and time. Results were expressed as regression coefficients with their standard error. All statistical calculations were performed with SAS (version 9. 4) software package.
Limitations Although we retrospectively identified patients, TAd measurements, FTR assessment, and all echocardiographic and surgical data were prospectively collected, stored immediately postmeasurement, and retrieved electronically without modification. This study involved patients from 2 different centers but operated on by the cardiac team with a uniform standard of care. Echocardiographic measurements were not read by a core laboratory but were uniformly interpreted. Even though tricuspid annular diameter measurement was not part of routine assessment, all echocardiographic preoperative assessment of patients referred to the cardiac team for mitral valve surgery had TAd measurement, thus alleviating the bias of excluded patients without TA dilatation, less likely to have TAd measured on a routine.
ROS production and oxidative damage: Firstly, the fluorescence of CM-H 2 DCFDA (1 μM) was kinetically monitored at 37 • C within BEAS-2B cells  (Sotty et al. , 2020). Secondly, the NRF2 DNA binding activity was studied using TransAM® NRF2 from Active Motif. Associated gene expressions of some members of the NRF2 signaling pathway (i. e. , heme oxygenase 1, HMOX, and NAD(P)H quinone dehydrogenase 1, NQO1) were evaluated by RT-qPCR using specific Taqman™ gene expression assays (HMOX: Hs01110250_m1, NQO1: Hs01045993_g1, and RNA18S: Hs99999901_s1), a StepOnePlus™ Real-Time PCR System, and the Expression Suite Software (ThermoFisher scientific)  (Leclercq et al. , 2018; Sotty et al. , 2020). Thirdly, the concentrations of 4-hydroxynonenal (4-HNE), carbonylated protein (CO-protein), 8-hydroxy-2 ′ -deoxyguanosine (8-OHdG), and glutathione were studied respectively thanks to a home-made competitive ELISA, based on MSD technologies (Mesoscale Discovery, Rockville, MD, USA), using 4-HNE-modified BSA and rabbit polyclonal anti-4-HNE antibody (Abcam), Protein carbonyl content assay kits (Abcam), 8-hydroxy-2 ′ -deoxyguanosine ELISA kit (Cell Biolabs, and GSH/GSSG-Glo™ assay (Promega), as published elsewhere  (Anthérieu et al.
Functional analysis of the differentially regulated gene (DRG) was carried out in silico using Cytoscape v 3. 8. 2. software (https://cytoscape. org/). Epigenetic alterations: The Global DNA Methylation LINE-1 Assay provided a measure of global DNA methylation shifts in BEAS-2B cells (Active Motif). Active motif's Histone Purification Mini Kit was used to purify core histones from BEAS-2B cells and ELISA kits were used to determine specific H3 post-translational modifications (i. e. , H3Lys9ac and H3Lys27ac versus total H3). HAT and HDAC activities of BEAS-2B cells were determined using HAT and HDAC assays from Active motif, according to the manufacturer's recommendations (; )  (Leclercq et al. , 2017b; Sotty et al. , 2019). Moreover, miRNA expression profiles were studied in BEAS-2B cells.
2 (http://www. targetscan. org/vert_72/), miRNA target Prediction Database (miRDB; http://mirdb. org), and et DIANA TOOLS Tarbase V8 (htt p://carolina. imis. athena-innovation. gr/diana_tools/web/index. php? r=tarbasev8%2Findex). Apoptotic events: Activities of both some initiator caspases (caspase 8 and caspase 9) and executioner caspases (i. e. , caspase 3 and caspase 7) were determined with Caspase Glo® 3/7, Caspase Glo® 8, and Caspase Glo® 9 Assays, as recommended by the manufacturer (Promega)  (Leclercq et al. , 2018; Sotty et al. , 2020). Single-channel dead cell apoptosis kit with Annexin V Pacific Blue™ 488 and SYTOX™ AAdvanced dyes for flow cytometry applications were used as recommended by the manufacturer (ThermoFisher scientific), before BEAS-2B cell analysis using an Attune™ NxT Acoustic Focusing Cytometer (Ther-moFisher scientific) to study apoptotic events.
Statistical analysis Results were expressed as mean values and standard deviations. Comparisons were performed between data from exposed BEAS-2B cells (i. e. , WF-derived Q-UFP) and those from negative controls. After having checked for the Normal distribution of the variables under study, the Student's t-test (p < 0. 05) was used to perform statistical analyses (Software: SPSS v27 for windows). For the in vitro comet assay, it has previously been shown that the tail intensity does not follow a Gaussian distribution. Thus, the non-parametric Mann-Whitney U test was used to evaluate the statistical difference between groups (i. e. between each concentration vs. the respective negative control). All statistical analyses were performed with StatView Software (version 5. 0, SAS Institute Inc. , SAS Campus Drive, Cary, North Carolina 27,513, USA).
e. , hsa-miR-551b# and hsa-miR-331-5p, respectively) were reported as common to BEAS-2B cells acutely exposed to the lowest or the highest doses of Q-UFP. Only hsa-miR-210-3p was up-regulated at the same time in BEAS-2B cells acutely exposed to the highest dose of Q-UFP and in BEAS-2B cells repeatedly exposed to the lowest dose of Q-UFP. Thirdly, functional analysis of the up-regulated DRmiR founded in BEAS-2B acutely or repeatedly exposed to Q-UFP was carried out in silico using three complementary miRNA target Prediction Database (i. e. , TargetScanHuman v7. 2, miRDB, and DIANA TOOLS Tarbase V8), and thereafter compared with the DRG previously identified. Fig. 9A-J  showed the results as Venn Diagrams of  hsa-miR-331-5p, hsa-miR-210-3p, hsa-miR-424-5p, hsa-miR-597-5p, hsa-miR-212-3p, hsa-miR-1260a, hsa-miR-1248, hsa-miR-625-5p, hsa-miR-744-3p, and hsa-miR-766-3p, respectively.
(i. e. , Fold-Change: FC > 1. 5 or < 0. 66, p < 0. 05). Fig. 9. Venn diagrams representing the target genes of differentially regulated microRNA (i. e. , has-miR-331-5p, Fig. 9A ; has-miR-210-3p, Fig. 9B ; has-miR-424-5p, Fig. 9C ; has-miR-597-5p, Fig. 9D ; has-miR-212-3p, Fig. 9E ; has-miR-1260a, Fig. 9F ; has-miR-1248, Fig. 9G ; has-miR-625-5p, Fig. 9H ; has-miR-744-3p, Fig. 9I ; and has-miR-755-3p, Fig. 9J ), as assessed using TargetScanHuman v7. 2 (http://www. targetscan. org/vert_72/), miRNA target Prediction Database (miRDB; http://mirdb. org), and DIANA TOOLS Tarbase V8 (http://carolina. imis. athena-innovation. gr/diana_tools/web/index. php?r=tarbasev8%2Findex), and crossed with differentially deregulated genes by quasi-ultrafine particle (Q-UFP) fraction of welding fumes emitted by gas metal arc welding-stainless steel.
(2019) , studying and comparing the expression of miR-210-3p in different non-small cell lung cancer cell (NSCLC) lines and BEAS-2B cell line, indicated that it can regulate the proliferation and apoptosis by targeting Transcription Regulator Family Member A. However, as highlighted by  Jardim (2011)  and  Vrijens et al. (2015) , although miRNA changes may be sensitive indicators of the effects of acute and chronic environmental exposure such as WF-derived Q-UFP, further studies should be conducted to elucidate the role of the mediation effect of miRNA between the exposure and the effect to provide a more accurate evaluation of the consequences of these miRNA changes. The functional analysis of the up-regulated DRmiR founded in BEAS-2B acutely or repeatedly exposed to Q-UFP, carried out in silico using three complementary miRNA target Prediction Database (i.
Galanin Receptor 2 (GALR2) was the target gene only predicted by miRDB, also reported within the DRG reported in BEAS-2B cells acutely and/or repeatedly exposed to Q-UFP. Moreover, 10 target genes, only predicted by DIANA TOOLS Tarbase V8, were among the DRG of BEAS-2B cells acutely and/or repeatedly exposed to Q-UFP: SMAD Family Member 4: SMAD4, Peroxisome Proliferator Activated Receptor Gamma: PPARG, NKD Inhibitor Of WNT Signaling Pathway 1: NKD1, Apoptosis Regulator: BCL2, Cyclin-dependent kinase 4: CDK4, Toll Like Receptor 6 T LR6, Lymphoid Enhancer Binding Factor 1: LEF1, Lysophosphatidic Acid Receptor 2: LPAR2, Adenosine A1 Receptor: ADORA1, and Calcitonin Receptor Like Receptor: CALCRL. Some target genes also founded among the DRG of BEAS-2B cells acutely and/or repeatedly exposed to Q-UFP were predicted by two of the three miRNA target Prediction Databases: Transcription Factor 7: TCF7, Proenkephalin: PENK, Apoptosis Regulator: BCL2, Lymphoid Enhancer Binding Factor 1: LEF1, Wnt Family Member 5B: WNT5B by TargetScanHuman v7.
2 and miRDB, on the one hand, and Inhibitor Of Nuclear Factor Kappa B Kinase Regulatory Subunit Gamma: IKBKG and Kinase Suppressor Of Ras: KSR1 by TargetScanHuman v7. 2 and DIANA TOOLS Tarbase V8, on the other hand. At least, only three target genes also founded within the DRG of BEAS-2B cells acutely and/or repeatedly exposed to Q-UFP were predicted by all the three miRNA target Prediction Databases: Neural Cell Adhesion Molecule 1: NCAM1, RAS P21 Protein Activator 1: RASA1, Adenosine A1 Receptor: ADORA1.
Funding sources This work benefited from grants or contributions from " Action Santé Travail 59-62 ", " Institut National de Recherche et de Sécurité", "Institut Mines Télécom Lille Douai", University of Lille , and the  CLIMIBIO and CaPPA projects. The  CaPPA  project is funded by the  French National Research Agency (ANR)  through the  PIA (Programme d'Investissement d'Avenir)  under contract " ANR-11-LABX-0005-01 " and by the  Regional Council "Hauts-de-France", and the "European Funds for Regional Economic Development" (FEDER).
Methods: We performed our analysis on VENTILA dataset, an observational, prospective, international, multi-centre study, performed to investigate the effect of baseline characteristics and management changes over time on the allcause mortality rate in mechanically ventilated patients in ICU. Our cohort includes 12,596 adult patients older than 18, associated with 12,755 distinct admissions in ICUs across 37 countries and receiving invasive and non-invasive mechanical ventilation. We carry out four different analysis. Initially we select typical mechanical ventilation parameters and evaluate the machine learning model on both, the overall cohort and a subgroup of patients admitted with respiratory disorders. Furthermore, we carry out sensitivity analysis to evaluate whether inclusion of variables related to the function of other organs, improve the predictive performance of the model for both the overall cohort as well as the subgroup of patients with respiratory disorders.
Results: Predictive performance of RNN-based model was higher with Area Under the Receiver Operating Characteristic (ROC) Curve (AUC) of 0. 72 (± 0. 01) and Average Precision (AP) of 0. 57 (± 0. 01) in comparison to RF and LR for the overall patient dataset. Higher predictive performance was recorded in the subgroup of patients admitted with respiratory disorders with AUC of 0. 75 (± 0. 02) and AP of 0. 65 (± 0. 03). Inclusion of function of other organs further.
Different studies have evaluated the use of ML for the treatment of sepsis, assessing patient prognosis and/ or risk for prolonged clinical courses and several other applications  [6]. Regarding assessment of patients on mechanical ventilation and/ or prognostication of ICUpatients by AI, various studies were conducted that demonstrated that ML can be used as a prognostication tool for ICU-mortality  [7, 8]. Parreco et al. were able to reliably identify patients at risk for tracheostomy and prolonged MV in their study on 20,262 ICU stays out of the MIMIC-III database  [9]. Chen et al. were able to detect ventilator-associated pneumonia in patients on MV by using ML for the analysis of sensor arrays on exhaled breath samples  [10]. Different other studies with promising results have been conducted in this field, which makes a future use of ML in clinical daily routine on the ICU likely.
Setting and data sources VENTILA cohort dataset is a combination of four observational, prospective, international multi-center studies  [14] [15] [16] , performed to investigate the effect of baseline characteristics and management changes over time on the all-cause mortality rate in mechanically ventilated patients in ICU. VENTILA cohort includes adult patients older than 18, admitted to ICU receiving invasive (endotracheal tube or tracheostomy) and non-invasive (bilevel positive airway pressure (BIPAP) or continuous positive airway pressure (CPAP) with nasal or facial mask) mechanical ventilation for at least 12 and 1 h, respectively. Data recorded for all the patients included basic demographics, cause of requiring mechanical ventilation, the occurrence of complications, ICU and hospital discharge outcome and length of stay.
Furthermore, daily collected data, resulting in a single average value, are recorded for variables such as arterial gases, mechanical ventilation parameters and variables related to the function of other organs. All the patients in this cohort study were followed for mortality and length-of-stay outcomes during the period of receiving mechanical ventilation, ICU stay, up to 28 days over one month period in  1998, 2004, 2010, and 2016. Only the investigative group members and research coordinators at each site were aware of the purpose and the precise timing of the study. We evaluate our method on a sub-sample of VEN-TILA dataset containing data associated with 12,755 distinct hospital admissions for 12,596 adult patients (aged 18 years or above) admitted during one-month sample periods (in 2004, 2010 and 2016) from participating ICUs across 37 countries.