dataesr/scientific-paragraphs-categorization huggingface dataset:
Data collection Data were collected in an anonymized database. The collected data were: -Preoperative: age, body mass index (BMI), gender, medical history, surgical indication, American Society of Anesthesia (ASA) score, treatments, emergency procedure. -Intraoperative: surgical access, surgical procedure, compliance with enhanced recovery program. -Postoperative: postoperative complications according to the Dindo Clavien scale  [12] , time between operative day and first flatus, time between operative day and first stool and time between operative day and gastrointestinal (GI) motility recovery. GI motility recovery was defined the GI-2 recovery (presence of stool and the tolerance to oral solid food)  [13]. Information on recovery of stool, flatus or GI function was collected twice a day, in the morning and the evening.
Results One hundred and one (101) patients were included in this prospective database study. Fifty-one (51) patients were male, the median age was 66 years (interquartile range: 55-74) and the median BMI was 23  (20) (21) (22) (23) (24) (25) (26) (27). Forty-nine (49) patients underwent surgery for cancer, 36 for diverticulosis, 13 for nonresectable benign polyps and 3 for inflammatory chronic bowel disease. Sixteen  (16)  patients were ASA 1, 50 were ASA 2, 32 were ASA 3 and 3 were ASA 4. While all patients were managed in accordance with our ERP, only 74 patients showed ≥70% compliance. Emergency surgery was performed on 20 patients and a complication occurred in 35 patients. Baseline description of the population is given in Table  1.
Methods: We will conduct a multi-centre international randomised, controlled, allocation concealed, open, pragmatic clinical trial to compare mechanical ventilation in ARDS patients following application of the Beacon Caresystem to that of standard routine care to investigate whether use of the system results in a reduction in driving pressure across all severities and phases of ARDS. Discussion. Despite 20 years of clinical trial data showing significant improvements in ARDS mortality through mitigation of ventilator induced lung injury, there remains a gap in its personalised application at the bedside. Importantly, the protective effects of higher positive end-expiratory pressure (PEEP) were noted only when there were associated decreases in driving pressure. Hence, the pressures set on the ventilator should be determined by the diseased lungs' pressure-volume relationship which is often unknown or difficult to determine.
Hence, given the emergent nature of the study situation the Beacon Caresystem (with the advice turned off) will be attached to the patient and samples collected. Given the urgent nature of COVID-19 and the process of ECMO, at the discretion of the clinical team, prior to consent/advice below a similar sample of blood may be taken prior to starting ECMO (T0) and hence, often prior to discussion with a personal nominee. If they are not enrolled into the study then this sample will be discarded. No analysis of data or samples will occur until consent/advice as below is obtained. This has been discussed with our Patient and Public Involvement (PPI) representative who is fully supportive of this process. Personal legal representative advice. Due to the acute care trial setting and the vulnerability of the patients' population, a patient information sheet will be provided and advice sought from a third party acting as a consultee; in most cases this person will be a personal consultee, who is someone who knows the person lacking capacity and is able to advise the researcher about that person's wishes and feelings in relation to the project and whether they should participate in the research.
Additional consent provisions for collection and use of participant data and biological specimens Biological samples including blood, urine, broncho-alveolar lavage/brushings will be stored in a biobank for future analysis. All analyses undertaken will relate to furthering the understanding of ARDS. These samples will be identified only by a numerical identifier and results from these tests including genetic information will not be stored in the case notes or given to the subject, their family or doctors involved with their care. The samples will be stored in an approved secure facility. Only approved researchers will be able to access the samples. The sample labels will contain no subject identifiable information. The movement and storage of samples will be carried out in accordance with the Human Tissue Act and respective national regulations.
Interventions Explanation for the choice of comparators In the comparator group, mechanical ventilation is managed according to standard care at the local centre. In this group Beacon advice will be disabled, with the system being used solely for data collection including changes in ventilation. Physiological variables captured in this arm of the study will mirror the intervention arm. The Beacon will remain on the patient for as long as the patient stays in the study centre, is successfully extubated (i. e. not requiring invasive ventilation or nasal high flow oxygenation for >24 hours), attains trachemask for >24 hours, or passes away. In addition, ALPE measurements will be perfomed as per intervention arm. This strategy will allow for comparison of physiological status between control and intervention arms, but will not risk modifying care in the control arm.
Sample size The original required sample size for the primary outcome is 110 patients. 55 patients per group will allow detection of a difference of 2 cmH 2 O in driving pressure between the groups with 90% power and a two-sided alpha of 0. 05 assuming a control group driving pressure of 15 cmH2O with a standard deviation of 2. 5 cmH2O and including a 40% dropout (33 patients per group for analysis). We have used data from the MIMIC dataset (as published in Serpa Neto et al (  25 )) for the estimation of the driving pressure. In view of the longitudinal analysis, loss to follow up has taken account of an average mortality of 34% and a 6% drop out. A recalculation of sample size was undertaken in January 2021 (in view of the COVID-19 pandemic) to evaluate whether the extent of driving pressure data being collected was sufficient to answer the primary objective.
This was due to a higher proportion of patients being exclusively on ECMO than expected due to the COVID-19 as well as potential differences in physiology between COVID-19 and non-COVID-19 ARDS. Basing the calculation on a repeated-measures basis using estimates of the intraclass correlation coefficient (ICC) of driving pressure values and the estimate of the coefficient of variation (CV) for days data collected (per patient) we calculated the expected patients required to fulfil the primary outcome. Using the data extract collected for the second Data Monitoring and Ethics Committee (DMEC) meeting (December 2020, n=38) we estimated values for ICC and CV of 0. 3 and 0. 8 respectively. Based on these estimates and by providing alternative scenarios we were able to create the following table: From the above, under the 'worst-case' scenario; with a CV of 1.
Plans for assessment and collection of outcomes DeVENT study data are entered directly into the SMART-TRIAL database and respiratory physiological data will be collected through the beacon Caresystem. Figure  3  shows the Data workflow process. The principle means for data collection will be through electronic data capture through the internet on the SMART Trial database by each individual study site. Each participant will be allocated a unique Participant Study Number at trial entry, and this will be used to identify the individual on the CRF for the duration of the trial. Data will be collected from the time of trial entry until hospital discharge. Trial data will be entered onto a CRF and processed electronically as per ICTU Standard Operating Procedures (SOPs) and the study specific Data Management Plan.
Data queries will be raised electronically. Data will be collected in a pseudo anonymous form on the Beacon Caresystem (measurements by the mechanical ventilator and measurements by Beacon sensors of respiration, gas exchange, lung mechanics, metabolism and entered arterial blood gas results). This breath by breath raw data collected on the Beacon Caresystem will be securely transferred, stored and processed at Aalborg university. Both eCRF and the Beacon Caresystem will contain only coded reference to each subject. Data will be collected from the device after each patient by the research team and with the assistance from clinical engineering support to ensure each patient's data is fully saved on a secure cloud database. The volume of data (breath by breath recording) means that it cannot be recorded on any CRF and University of Aalborg will generate an automatic report per patient.
Data will be entered in the CRF in cases of adverse events related and not related to mechanical ventilation. All additional research patient data will be completed in an electronic Case Report Form (eCRF) which will be configured within the ICCA database (electronic patient record) used in each of the intensive care units under standard operating procedures. Data will be managed according to the NHS Act 2006, the Health and Social Care Act 2012, the Data Protection Act 2018, and the Human Rights Act 1998 and the study will be conducted according to UK code of Good Clinical practice (GCP) for research.
Data management Data entry of the eCRF is the responsibility of the study site. Data are provided manually (data entry). Data entry is performed by site-specific users. System queries will automatically be generated by the site team will create database records for every enrolled subject via the SMART-TRIAL system by entering the eCRF data directly into the SMART-TRIAL database. Prior to subject being enrolled on the database, the subject ID and Randomisation number/code for each subject will be allocated manually by the Study Manager. The Data Manager will perform a quality control check of the Master randomisation list to ensure accuracy and completeness of entries. Prior to database lock, the Study Manager/Monitor will confirm that all subject data has been entered and source data verified in accordance with the study Monitoring Plan.
Bio-and image-banking procedures: The scope is to cover all human samples and associated data in the study. The Patient Informed Consent also covers many of the details described here. The types of samples acquired in this study are described above, and includes samples of peripheral blood, urine, bronchial lavage, and bronchial brushes. These samples will be processed from fresh into different formats, for storage at different temperatures. All sample management (acquisition, processing, storage, shipment, analysis, disposal) throughout the study will be in accordance with: • EU and relevant national legal and ethical standards, (including, any national research governance requirements and self regulation). The investigators in the project will provide the Management and Ethics Board with a summary of their applicable national or institutional rules regarding Biobank Activities, as well as changes national legal requirements related to Biobank Activities.
He/she will be, accountable for the safe-keeping of the samples and associated data, unless otherwise specified by law. The location of each sample and image will be recorded and tracked throughout its life cycle to maintain a chain-of-custody, in accordance with the SRM. At the end of the storage time any remaining samples and images will be destroyed and their disposal recorded, unless otherwise required to be anonymised by local ethics. As new scientific data become available we will be able to use this resource of stored samples and images to investigate if this new data is relevant pending additional ethical approval. Samples and images will be stored for up to 20 years. No staff at any storage facilities or facilities outside clinical work areas will have information that directly identifies any subject.
Composition of the data monitoring committee, its role and reporting structure The Data Monitoring and ethics Committee (DMEC) will be comprised of at least 2 independent clinicians, one with experience in clinical trials, and an independent statistician. One of the independent clinicians will have experience in the regulatory aspects of clinical trials involving medical devices. The role of the DMEC will include: monitoring the data and making recommendations to the TSC on whether there are any ethical or safety reasons why the trial should not continue; considering the need for any interim analysis; advising the TSC regarding the release of data and/or information; considering data emerging from other related studies. The DMEC will continually assess both safety and efficacy data on a regular basis with additional meetings convened in the event of any safety concerns.
All SAEs will be reviewed by the Chief Investigator or a designated medically qualified representative to confirm expectedness and causality. Reporting of SAEs and review by the CI will be via the trial data collection system (CRF/eCRF). prior to any patient recruitment taking place. The protocol and all agreed substantial protocol amendments, will be documented and submitted for HRA approval prior to implementation. All non-UK sites will have documents converted to the host language through official translators. Before site(s) can enrol patients into the study confirmation of capacity and capability must be issued by the institution hosting the trial. It is the responsibility of the PI at each site to ensure that all subsequent amendments gain the necessary approvals by the participating site.
4, approved on 16 th June 2021. The first patient was recruited on 19 th March 2020. The last patient was recruited on 4 th May 2021 with the data collection continuing with a planned database lock on 30 th Sept 2021. Aside from the primary and secondary trial outcomes, the exploratory outcomes will have a final patient visit on 26 th March 2022. We were unable to submit this protocol earlier due to clinical pressures as a result of the COVID-19 pandemic.
4, approved on 16 th June 2021. The first patient was recruited on 19 th March 2020. The last patient was recruited on 4 th May 2021 with the data collection continuing with a planned database lock on 30 th Sept 2021. Aside from the primary and secondary trial outcomes, the exploratory outcomes will have a final patient visit on 26 th March 2022. We were unable to submit this protocol earlier due to clinical pressures as a result of the COVID-19 pandemic. Abbreviations ICU TIDIeR Intensive Care Unit Template for intervention description and replication Abbreviation / IRAS TMF Full Wording Integrated Research Application System Trial Master File Acronym MHRA TMG Medicines and Healthcare products Regulatory Agency Trial Management Group ABG MOCA TSC Arterial Blood Gas The Montreal Cognitive Assessment Trial Steering Committee AE NHS VCO 2 Adverse Event National Health Service Carbon Dioxide production ALPE NIHR VILI Automatic Lung Parameter Estimation National Institute for Health Research Ventilator Induced Lung Injury APACHE II NIV VO 2 Acute Physiology and Chronic Health Evaluation Score II Non Invasive Ventilation Oxygen Consumption APMIC NMBD Vt Anaesthesia, Pain Medicine and Intensive Care Neuromuscular Blocking Drugs Tidal Volume APRV PaCO 2 Airway Pressure Release Ventilation Partial Pressure of Carbon Dioxide in arterial blood ARDS PaO 2 Acute Respiratory Distress Syndrome Partial Pressure of Oxygen in arterial blood BAL PBW Bronchoalveolar lavage Predicted Body Weight CI PEEP Chief Investigator Positive End Expiratory Pressure CO 2 P/F ratio Carbon Dioxide PaO 2 /FiO 2 ratio CONSORT PI Consolidated Standards of Reporting Trials Principal Investigator COVID-19 PIS Novel Coronavirus Disease 2019 Patient Information Sheet CRF/eCRF PPI Case Report Form/Electronic Case Report Form Patient and Public Involvement CTU Pplat Clinical Trials Unit Plateau Pressure DMEC PTSD Data Monitoring and Ethics Committee Post Traumatic Stress Disorder DNAR PTSS 14 Do Not Attempt Resuscitation Post Traumatic Stress Syndrome Questionnaire ECMO RALE Extracorporeal Membrane Oxygenation Radiographic Assessment of Lung Oedema ECCO 2 R REC ExtraCorporeal Carbon Dioxide Removal Research Ethics Committee EQ-5D-5L RR EuroQoL-5 Dimension Questionnaire (5 level version) Respiratory Rate EELV SAE End-Expiratory lung Volume Serious Adverse Event FE'CO 2 SAP End-tidal CO 2 fraction Statistical Analysis Plan FiO 2 SAPS II Fraction of Inspired Oxygen Simplified Acute Physiology Score GCP SBT Good Clinical Practice Spontaneous Breathing Trial HADS SGRQ Hospital Anxiety and Depression Score St George's Respiratory Questionnaire HRA SOFA Health Research Authority Sequential Organ Failure Assessment HRQoL SOPs Health Related Quality of Life Standard Operating Procedures ICF SpO 2 Informed Consent Form Oxygen Saturation ICH SRM International Council on Harmonisation Study Reference Manual ICTU TAPSE Imperial Clinical Trials Unit Tricuspid Annular Plane Systolic Excursion.
In this model, microarray analyses highlighted modulations of the expression of genes regulating specific metabolic pathways, including cholesterol metabolism. Thus, indole appears as a potential therapeutic tool for NAFLD treatment. In accordance with this hypothesis, a recent article reported that the concentration of circulating indole was inversely associated with the BMI and with the degree of liver lipid accumulation in humans, and that a high dose of indole (50 mg/kg) given over 3 wk decreased hepatic CK is a beneficiary of the AgreenSkills+ fellowship program, which has received funding from the EU's Seventh Framework Programme under grant agreement N • FP7-609398 (AgreenSkills+ contract). PDC is a senior research associate at FRS-FNRS (Fonds de la Recherche Scientifique) and recipient of grants from FNRS (WELBIO-CR-2019C-02R, "The Excellence of Science: EOS 30770923") and the Funds Baillet Latour (Grant for Medical Research 2015).
Tissue mRNA analyses Total RNA was isolated from tissues using TriPure Isolation Reagent (Roche Diagnostics). cDNA was prepared by reverse transcription of 1 μg total RNA using the Reverse Transcription System (Promega). Real-time PCR was performed with a QuantStudio 3 Real-Time PCR System (Applied Biosystems) using MasterMix GoTaq (Promega). Data were analyzed according to the 2-CT method. The purity of the amplified products was verified by analyzing the melting curve obtained at the end of the amplification step. The ribosomal protein L19 (Rpl19) gene was used as reference gene. Sequences of primers used are listed in Supplemental Table  2.
Western blots (experiment 1) Western blot analyses on liver samples were performed as previously described  (8)  for the NF-κB and protein kinase B/mechanistic target of rapamycin (AKT/MTOR) signaling pathways [primary antibodies detecting respectively NF-κB p65, phospho-NF-κB p65 (Ser536), NF-κB inhibitor α (IKBA) and phospho-IKBA (Ser32), AKT, phospho-AKT (Ser473), MTOR and phospho-MTOR (Ser2448); Cell Signaling Technology). beta-actin was used as control protein (Abcam). Signals were revealed using the SuperSignal West Pico substrate with Femto Chemiluminescent substrate addition for the NF-κB pathway (Thermo Fisher Scientific), and analyzed with the ImageQuant TL instrument and software v. 8. 1 (GE Healthcare).
Statistical analyses and graphical output In experiment 1, four B6. V-Lep ob/+ JRj mice (1 ob/+ C and 3 ob/+ I mice) presented abnormal hepatic and metabolic profiles with high cellular and hepatic damage at the end of the experiment associated with high urinary bilirubin concentrations before the onset of experimental procedures and were thus excluded from all analyses. All data were analyzed using R 3. 4. 3 software (R Foundation). H&E histology scoring was analyzed using a nonparametric Kruskal-Wallis test with the experimental group as factor. When significant (P < 0. 05), groups were compared pairwise with a Wilcoxon test. For all other variables, to verify homoscedasticity of the data, a Levene test was performed, and data were log transformed when needed. qPCR data being log normally distributed (asymmetrical distribution), the log transformation was applied systematically for these kind of data.
A linear mixed model followed by a 2-way ANOVA was used with indole treatment and genotype (experiment 1) or diet (experiment 2) as fixed effects and the cage as random effect. Pairwise comparisons within each genotype (ob/+ C compared with ob/+ I, and ob/ob C compared with ob/+ I) or diet (LF C compared with LF I, and HF C compared with HF I) were performed using a Tukey post hoc test. In experiment 1, to have an overview of the general trends in the data sets, multivariate partial least squares discriminant analyses (PLS-DAs) were also performed using the mixOmics package  (28, 29)  on parameters related to hepatic damage, inflammation, macrophage activity, and fibrosis. The error rate (max. distance) was used to assess the performances of the analyses using the leave one out method according to the guidelines of the R mixOmics package  (28).
Using both genotypes the error rate was high (59. 7%), and genotype was the main factor separating the individuals hiding treatment effect (Supplemental Figure  2 ), thus analyses were performed and presented separately for each genotype. For all statistical tests P < 0. 05 was considered significant. Graphical outputs were obtained using GraphPad Prism 5 (GraphPad Software; univariate analyses) and R mixOmics package (multivariate analyses).
Acknowledgments We thank  V Allaeys ,  I Blave ,  R Selleslagh , and  B Es Saadi  for their technical support in the project. The authors' responsibilities were as follows-CK, AMN, and NMD: designed the research; CK, AMN, and SL: conducted the research; QL: analyzed the behavioral test data; PB: analyzed and scored H&E staining; CK, AMN, and NMD: wrote the paper. QL, SL, MB, JR, NL, LBB, and PDC: provided intellectual input and contributed to the writing of the report; NMD: planned and supervised all experiments; and all authors: read and approved the final manuscript.
Study population NutriNet-Santé is a web-based cohort focusing on the relationships between nutrition and health along with the determinants of nutrition-related behaviors  [21]. The recruitment of French adults started in 2009 and is still ongoing. The NutriNet-Santé study is conducted in accordance with the Declaration of Helsinki, and all procedures were approved by the Institutional Review Board of the French Institute for Health and Medical Research (IRB INSERM #0000388FWA00005831) and by the National Commission on Informatics and Liberty (CNIL #908,450 and #909,216). All participants provided informed consent and an electronic signature. The study is registered at ClinicalTrials. gov (#NCT03335644).
Data collection NutriNet-Santé participants regularly complete questionnaires through a dedicated and secured online platform. Upon inclusion and then every year, a set of 5 validated questionnaires collect data related to sociodemographic and lifestyle characteristics, health status and medication use, dietary intakes, physical activity (short form of the International Physical Activity Questionnaire [IPAQ]) and anthropometrics. Dietary intakes are assessed every 6 months, each time through 3 non-consecutive, validated 24-hour dietary records, randomly distributed over 2 weeks, including 2 weekdays and 1 weekend day  [22] [23] [24]. Portion sizes are estimated using validated photographs, standard containers, or directly in g/L. The food content in energy, alcohol, and macro-and micro-nutrients are derived from the NutriNet-Santé food composition table which is continuously updated and currently comprise > 3500 items.