dataesr/scientific-paragraphs-categorization huggingface dataset:
Results from dataset (re)processing using MGnify are available in ENA MGnify (https://www. ebi. ac. uk/metagenomics/) using the accession Pipeline Ref. DB ENA Accession MGnify Sample size Raw read count High-quality read count accession Uninfected Infected Uninfected Infected Uninfected Infected CloVR-16S RDP PRJNA188112 MGYS00003431 4 4 179,193 189,399 149,780 157,744 QIIME Greengenes PRJNA244913 MGYS00003191 8 8 106,832 103,428 86,737 83,780 QIIME Greengenes PRJNA255974 MGYS00003192 10 9 77,836 71,752 77,836 71,752 QIIME Greengenes PRJEB6560 MGYS00001732 80 60 3,253,762 2,438,665 3,034,081 2,306,376 QIIME Greengenes PRJEB8312 MGYS00003181 38 93 1,790,824 4,990,294 1,723,425 4,865,341 MR DNA Greengenes PRJNA276586 MGYS00003432 14 48 587,641 2,002,497 500,349 1,657,742 QIIME Greengenes PRJNA349988 MGYS00003433 21 24 4,121,930 6,206,792 3,365,062 4,999,740 QIIME Greengenes PRJNA316208 MGYS00003180 12 12 7,855,514 6,597,567 7,025,186 5,918,376 QIIME Greengenes PRJNA518079 MGYS00004556 5 12 1,213,261 3,302,574 1,196,878 3,263,552 QIIME Greengenes PRJEB21999 MGYS00003147 22 11 8,388,179 4,934,705 7,777,849 4,506,626 QIIME2 Greengenes PRJEB28700 MGYS00003148 11 20 1,946,889 2,578,359 1,873,123 2,487,145 QIIME Greengenes PRJEB29315 MGYS00003460 40 40 1,405,122 1,369,830 1,405,120 1,369,830 Mothur EzBioCloud PRJNA481634 MGYS00003893 7 8 3,335,612 1,405,858 3,194,586 1,351,499 QIIME Greengenes PRJNA486437 MGYS00003894 42 47 5,010,319 5,131,918 4,814,736 4,997,256 Mothur RDP PRJNA487588 MGYS00003908 6 16 88,768 338,701 86,195 328,849 16S rRNA hypervariable region V7-V9 V1-V3 V3-V5 V3-V4 V4 V1-V3 V4 V3-V4 V3-V4 V3-V4 V3-V4 V3-V4 V4 V3-V4 V3-V4 V4 Parasite Type of Type/site of infection sampling Opisthorchis Experimental Colon viverrini Necator Experimental Faeces americanus Nippostrongylus Experimental Small intestine brasiliensis Trichuris muris Experimental Caecum, faeces Multiparasites Natural Stomach, small intestine, caecum, colon Multiparasites Natural Faeces Toxocara cati Natural Faeces N.
EI helminth infections and host gut microbiota composition. MICHELINdb was implemented using the MSSQL Express software (https://www. microsoft. com/enau/sql-server/sql-server-editions-express), accessed via an N-Tier architecture (written in C# and ASP. NET MVC) on which the database (http://www. michelindb. com) resides. Relative abundance (%) Phylum Genus AUC Fold change Uninfected Infected Non-rodents Actinobacteria Collinsella 0. 56 -0. 64 2. 37 3. 69 Actinobacteria Bifidobacterium 0. 54 0. 85 2. 68 2. 26 Bacteroidetes 0. 58 1. 18 18. 83 16. 01 Bacteroides 0. 60 0. 55 6. 97 3. 83 Parabacteroides 0. 58 0. 71 0. 51 0. 37 Alloprevotella 0. 51 0. 69 1. 05 0. 72 Firmicutes 0. 56 -1. 10 48. 94 54. 05 Streptococcus 0. 52 0. 65 2. 58 1. 69 Catenibacterium 0. 53 -0. 41 0. 33 0. 80 Holdemanella 0.
Some mathematical theorems In this section we determine whether the lack of spatial resolution is able to explain the observed discrepancy. First of all we note that if the lack of spatial resolution were able to explain the effect, we would expect the non-zero value observed for the divergence to depend on the pixel size. As far can be seen in the review by  Balthasar (2018) , this is not the case. The review deals with various instruments, and therefore various pixel sizes, but the results are homogeneous, even though obtained using different active regions. In order to investigate this question in a more quantitative manner, we considered the spectropolarimetric data of NOAA 10953 acquired by the SOT/SP experiment on board the HINODE satellite on 1 May 2007 at 10:46 UT. The pixel size was 0.
16. We then prepared artificially degraded resolution data by averaging the Stokes parameters on 2 2 , 4 2 , and 8 2 pixels. We then submitted these artificially degraded resolution data together with the original data to our inversion code UNNOFIT  (Bommier et al. 2007 ). We did not detect any significant variation in the difference between vertical and horizontal magnetic field gradients as a function of the pixel size. It can then be objected that the typical variation length for the magnetic field may be very small with respect to these pixel sizes (or typical pixel sizes or current instrument pixel sizes). In this case no variation with the pixel size could be observed because of the scale difference between the pixel size and the magnetic field typical variation length. However, such a case can be treated by the theorems we introduce below.
Acknowledgements. I am deeply indebted to  Jacques Dubau ,  Pascal Démoulin ,  Wan-Ü Lydia Tchang-Brillet ,  Nicole Meyer-Vernet  for very fruitful discussions, for their suggestions, comments, analyses and provided references, also  Silvano Bonazzola ,  Nicole Feautrier  and  Sylvie Sahal-Bréchot. I am particularly indebted to  Jean-Louis Leroy  who pointed me the results of his observations cited in Sect. 7, able to confirm the present analysis, and for fruitful discussions also. I am also deeply indebted to  Pr Damien Gignoux , from  Institut Néel ,  Emeritus Professor  at  Université Joseph Fourier, Grenoble (France) , for introduction to magnetized material physics, helpful suggestions and a critical reading of the manuscript. Gérard Belmont  is also greatly thanked for previous discussions.
a manometer with an unidirectional valve. MEP diagnostic accuracy to predict ICU-AW (ICU acquired weakness), weaning success and sursvival within 30 days were assessed using expiratory muscle strength as absolute values (cmH 2 O), as %predicted values and as %lower limit of normal. Results: Due to the paucity of data reporting threshold value for expiratory muscle weakness, we considered our median value (47 cmH 2 O (IQR 44)) as the threshold value for expiratory muscle weakness group (MEP ≤ 47 cmH 2 O) and normal expiratory muscle group (MEP > 47 cmH 2 O). Patients with low MEP received more catecholamines (p = 0. 04) and a higher duration of mechanical ventilation (p = 0. 001). Inversely, higher body mass index was associated with higher MEP. Patients with low MEP presented more ICU-AW compared to normal MEP patients (64% vs.
Patients and methods: The study was approved by the appropriate Ethics Committee and registered with clinicaltrials. gov (NCT03098888). In 16 ICUs, from April 2017 to October 2018, we prospectively collected adverse events (AE) during or within 24 h after BAL and assessed the BAL input for decision-making in consecutive adult patients. AEs were categorized in 5 grades of increasing severity. The occurrence of a clinical AE at least of grade 3, i. e. sufficiently severe to need therapeutic action (s), including modification (s) in respiratory support, defined poor BAL tolerance. The BAL input for decision-making was declared satisfactory if it allowed to interrupt or initiate one or several treatments. Sixty-seven (13. 9%) patients reached the grade 3 of AE or higher. The main predictor of poor BAL tolerance identified by logistic regression was the association of a BAL performed by a non-experienced physician (non-pulmonologist, or intensivist with less than 10 years in the specialty or less than 50 BAL performed) in non-intubated patients (OR: 31.
Conclusion: It demonstrates that shortening the antibiotic prophylaxis treatment time to 24 h does not affect or increase the rate of infections after a pediatric sternotomy surgery compared to 48-h protocole. Prophylaxis in pediatric cardiac surgery should be short-lived. A multicenter prospective study would allow a consensus and confirm this decision. Compliance with ethics regulations: Yes. Rationale: The use of "big data" is getting increasingly popular in the medical field, especially in intensive care where large amounts of data are continuously generated. However, big data can be misleading when essential clinical data are missing. The adequate adjustment for potential confounding factors (e. g. , severity of respiratory distress) should be the key procedure in the big data analyses; however, it is challenging to capture the clinical severity within large electronic databases.
Patients and methods: This retrospective study included all infants < 2 years old with a clinical diagnosis of bronchiolitis, ventilated with non-invasive neurally adjusted ventilatory assist, in a Canadian PICU, between October 2016 and June 2018. We developed an algorithm, using Python 3. 7, which was directly connected to the electronic medical record. The components of the score were collected using structured query language (SQL) queries and processed to derive the A-mWCAS. For validation, the A-mWCAS score was compared to the mWCAS manually computed by a clinical expert (M-mWCAS). Results: Sixty-four infants were included in the study, for which 256 of A-mWCAS and M-mWCAS were generated respectively. The Cohen's Kappa coefficient was applied to estimate the agreement between the two scores which was 0.
Our objective was to identify factors associated with 1-year survival in acute stroke patients requiring mechanical ventilation. Patients and methods: Retrospective analysis of a prospective multicenter database between 1997 and 2016. ICU stroke patients entered in the database and requiring mechanical ventilation within 24 h were included. Were excluded patients with stroke of traumatic origin, subdural hematoma or venous cerebral thrombosis. Factors associated with 1-year survival were identified using a Cox model stratified on inclusion center, adjusted on WFLST occurring during the first 48 h. Data are presented as median [Q1-Q3] or percentages. Cox model results are presented as hazard ratios (HR) and 95% confidence intervals (CI). Results: We identified 419 patients from 14 ICUs, aged 68 [58-76] years and 60% males.
CO-67 Association between targeted temperature management and long-term neurological prognosis: insights from two large datasets from France and north-America Jean-Baptiste Lascarrou Rationale: International guidelines recommend targeted temperature management (TTM) between 32° and 36 °C for out-of-hospital cardiac arrest (CA) patients. However, it is unknown if this treatment is effective whatever the severity of the insult. We aimed to examine the association between TTM and long-term neurological outcome according to the risk evaluated at time of admission in intensive care unit (ICU) using a dedicated and validated score.
Patients and methods: We used data prospectively collected in the Sudden Death Expert Center (SDEC) registry (Great Paris area, France) between May 2011 and December 2017 and in the Resuscitation Outcome Consortium-Continuous Chest Compression (ROC-CCC) between June 2011 and May 2015. We used a modified version of the Cardiac Arrest Hospital Prognosis (mCAHP) score to assess the risk of poor outcome at ICU admission in each of 2 datasets. We finally studied the association between TTM use and long-term neurological prognosis according to mCAHP score at ICU admission divided into tertiles of severity in each of the 2 datasets. Results: There were 2723 patients analyzed in the French dataset and 4202 in the North-American dataset. The mCAHP identified 3 categories: low risk (score < 80 points, 40% of unfavourable outcome), medium risk (80 ≤ score < 105, 80% of unfavourable outcome) and high-risk group (score > 105, 95% of unfavourable outcome).
F-002 Heart rate variability as an indicator of outcome in the ICU? A prospective cohort Laetitia Bodenes, Victoire Pateau, Julien Dolou, Quang-Thang N'guyen, Erwan L'her Service de Medecine Intensive et Réanimation, CHRU de Brest, Brest, France Correspondence: Laetitia Bodenes (Laetitia. bodenes@chu-brest. fr) Ann. Intensive Care 2020, 10 (Suppl 1):F-002 Rationale: The autonomic nervous system is highly adaptable and allows the organism to maintain its balance when experiencing stress. Heart rate variability (HRV) is a mean to evaluate cardiac effects of autonomic nervous system activity and a relation between HRV and outcome has been proposed in various types of patients. We attempted to evaluate the best determinants of such variation in survival prediction using a physiological data-warehousing program (ReaSTOC ClinicalTrials identifier NCT 02893462).
Patients and methods: Physiological tracings were recorded at 125 Hz from the standard monitoring system (Intelliview Philips MP70) using the Synapse Software (LTSI INSERM UMR 1099), for a 2 h period, during the 24 h following ICU admission. All measurements were recorded while patients were laying in bed, with the head at 30° and without any medical intervention. Physiological data were associated with metadata collection by a dedicated research assistant. HRV was derived using Kubios HRV, in either temporal ( (SDNN), (RMSSD) and triangular index (TI)), frequency ( (LF), (HF)), non-linear domains (Poincaré plotting) and entropy. Results: 540 consecutive patients were recorded between May 2014 and April 2019. A lower LF/HF (< 0. 9) and SD2/SD1 (< 1. 3) ratios on admission were associated with a higher ICU mortality.
Patients and methods: We retrospectively studied pediatric patients having an external ventricular drain between July 2018 and July 2019, in a single pediatric intensive care unit. The ICP signals were extracted from a high-frequency database (128 Hz) and pre-processed adequately. To train the algorithms, an annotated database was manually created with two classes: reliable ICP vs. non-reliable ICP (drain system opened to allow cerebrospinal fluid removal). Eleven signal characteristics were compared between the two classes (Mann-Whitney test), and significantly differing variables were tested in the algorithms. We compared the performance of two machine-learning algorithms: the K-Nearest Neighbors (KNN) and the Support Vector Machine (SVM). Using 10-fold cross-validation method, 75% of the data was used to train the algorithms and 25% was used for testing.
The best classifier was further validated by simulating a real-time ICP analysis, using a 15 s sliding-window approach with 50% overlap. The study was approved by the localresearch ethics committee. Results: Sixteen patients were included in the study. The training database created from 14 patients, contained 320 segments (of 15 s duration) per class and per patient. Eight signal variables were identified and kept to define the segments. The KNN algorithm, with k = 3, led to the best performance, with a mean of 98% (mean ± SD: 98% ± 0. 29%). The KNN was then visually validated on ICP signals from the remaining two patients (Figure ). By simulating a real-time ICP extraction, our algorithm was able to efficiently identify the reliable ICP segments, and to display a mean value only for valid segments.
Patients and methods: We prospectively enrolled adult patients with sepsis (qSOFA score ≥ 2) from January 2017 to July 2019 in the ED (NCT02974790). Focused echocardiography were performed by emergency physicians previously trained to ECMU 1 level. Each patient was evaluated according to a standardized protocol based on a limited number of simple binary clinical questions. Investigators interpreted on-line the echocardiographic examination, determined the hemodynamic profile based on simple yet robust criteria (hypovolemia, left ventricular [LV] or right ventricular [RV] failure, vasoplegia with hyperdynamic state, tamponade, severe mitral or aortic regurgitation, or apparently normal profile), and recorded any substantial change in planned therapeutic management (Surviving Sepsis Campaign 2016).
Patients and methods: A retrospective study was conducted on patients with OP poisoning admitted to our nine-bed medical intensive care unit between January 2018 and December 2018. inclusion criteria were: all patients over 16 years of age and the exlusion criteria were: pesticide poisoning other than OP, alcohol poisoning, drug poisoning, scorpionic poisoning and snake bites. statistical analysis was performed with SPSS software. Results: Forty patients were admitted for acute OP poisoning. In Morocco, organophosphores are available over-the-counter in several forms: Rodentocides, Malathion, Cockroach trap, Baygon Insecticide (Fig. 1 ). The average age was 26 years with a female prévalence of 74. 1%. The intoxications were mostly intentional (85%). The symptomatology was determined by the three syndromes: central syndrome in 50%, muscarinic syndrome in 69%, nicotinic syndrome in 10%.
Survey consisting of 20 questions sent to subscribers of the SRLF mailing list via MailChimp software (Atlanta, USA). Frequencies and percentages were determined for categorical variables and median and interquartile range for continuous variables. The ICUs with or without psychologist were compared using nonparametric Fisher exact test. STATA 14 used (Lakeway Drive, TE, USA). Results: 263 responses were obtained from 197 unique ICUs in France (n = 182), Belgium (n = 6), Switzerland (n = 5), Algeria (n = 2), Morocco (n = 1) and Tunisia (n = 1). 164 (82%) ICUs were part of public hospitals, 33 (18%) of private facilities. 187 (94%) ICUs cared for adult patients, 10 (6%) for children. The median number of beds was 20  [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26]. 79 (40%) ICUs were open to visitors 24/7, 46 (23%), to visitors > 8 h/day and 72 (37%) to visitors < 8 h/day.
The prevalence of severe PTSD symptoms was assessed with the Impact of Events Scale-Revised (IES-R) at 6 weeks and 3 months using a cutoff of 33. Associations between PTSD as evaluated by IES-R at 3 months and patients' characteristics, including HADS scores at admission were investigated using unadjusted linear regression, for univariate and multivariate regression analysis. Statistical analyses were carried out using SPSS for Windows (SPSS, Inc. , Chicago, IL, USA).
Piperacillin was quantified by high performance liquid chromatography. Pharmacokinetics were described using the non-linear mixed effect modeling software MONOLIX. In the initial pharmacokinetics model, GFR was estimated according to the Schwartz 1976 formula. In the study, GFR was estimated with 11 additional formulas, developed with plasma creatinine and/or cystatin C. Biases, precisions, Spearman's rank correlation coefficient and normalized prediction distribution error (NPDE) were used to assess the models. Results: We included 20 children with a median (range) postnatal age of 1. 9 (0. 1-19) years, body weight of 12. 5 (3. 5-69) kg and estimated GFR according to the Schwartz 1976 formula of 160. 5 (38-315) mL min-1. 1. 73 m 2. Piperacillin concentrations were best predicted with the model using the creatinine clearance.
Patients and methods: Prospective, descriptive, mono-centric study, from January 2012 to January 2019. All patients under the age of 15 who have benefited from an implantable chamber catheter, whose insertion procedure is as follows: local anesthesia, surgical asepsis (polyvidone iodine) in an operating room, double disinfection, no antibiotic prophylaxis, routes used: subclavian (89%), internal jugular (11%) by anatomic registration. The main criteria of judgment are: the incidence of local and general infections, their time of onset, responsible microorganisms. Statistical analysis used the Statistical Package for the Social Sciences software. Results: 4480 patients were included, the average incidence density of early infection is 0. 61/1000 day-catheters. The time of onset of infection is essentially between the 2nd and 3rd week post-exposure, of which 20% is general infection.
Rationale: The 5-Fluorouracil (5-FU)-induced hyperammonemic encephalopathy is a rare but serious 5-FU adverse drug reaction, which could require the admission of patients in intensive care unit (ICU). Given the paucity of data regarding this 5-FU adverse drug reaction, we performed a retrospective national survey from the French pharmacovigilance database to better characterize 5-FU-induced hyperammonemic encephalopathy and its management. Patients and methods: Since the inception of the French pharmacovigilance database, we identified all patients that experienced 5-FU-induced encephalopathy. Variables regarding epidemiology, characteristics, management and prognosis of these patients were collected and analyzed. Results: From 1985 to 2018, 30 patients (60[55-66] years-old, 43% of women) were included.
Conclusion: This post hoc analysis showed that local signs were related to CRBSIs in the ICU. Local signs were independently associated with specific patient's and catheter's conditions. In the first 7 days of catheter maintenance, local signs were predictive for CRBSI. Compliance with ethics regulations: Yes. Rationale: Pneumococcal meningitis (PM) is the leading cause of bacterial meningitis in adult patients requiring ICU admission and is associated with a high case fatality rate (CFR), ranging from 15 to more than 33% (1-3). Patients with PM may develop sepsis or septic shock that may impact management and outcomes. We aim to describe the epidemiology and outcomes of PM associated with sepsis in adult patients in France. Patients and methods: We analysed the occurrence of PM with sepsis from 2010 to 2015 in adult patients, using the national French hospital Database PMSI (Programme de Médicalisation des Systèmes d'Information).
Patients and methods: A retrospective analysis of a prospective datawarehousing project (ReaStoc clinicalTrials identifier NCT 02893462) on ICU patients who did not require invasive ventilation. Physiological parameters were collected on admission, within a 24-h delay. NEWS, HRV (in time, frequency, and non-linear domains), and iROX were computed and integrated into the prediction model. Analysis was performed using MedCalc and Matlab machine-learning work-package. Results: One hundred and twelve patients were included. Patients who died in the ICU (n = 8) had highest NEWS as compared with ICU survivors (9. 0 [5. 0-11. 6] vs. 6. 0 [5. 0-7. 0] respectively; p = 0. 03). The iROX was higher  (18. 4 [15. 7-19. 8] vs. 9. 0 [5. 8-20. 9], p = 0. 008) and most HRV parameters also depicted higher values for ICU survivors.
Patients and methods: We performed a retrospective single-center descriptive study including all patients hospitalized in Robert-Debré University Hospital PICU and colonized with SA between the 1st of January 2011 and the 31st of December 2013. Data were collected using the microbiology department's prospective database, hospital records, and biological results reporting software. The results of the descriptive analysis were expressed as numbers and percentages for qualitative variables and as mean and standard deviation for quantitative variables. Two-tailed Fisher's exact test for quantitative variables and Chi-square test for qualitative variable were used. Risk of infection was modeled using a multivariate logistical regression analysis. Results: Among the 2383 patients hospitalized during the studied period, 573 patients were colonized with SA.
Patients and methods: The survey was endorsed by the acute respiratory failure section and the clinicaltrials group of the European Society of Intensive Care Medicine (ESICM). The pool was sent out via an email on June 27 2019 to the ESICM members worldwide. The following closed questions were: country, years in ICU, kind of ICU, kind of hospitals, kind of respirators, ATC use (never, always or in some patients), reasons to or not to use ATC, ventilatory mode in which ATC was used. The database was frozen on August 1 st 2019 after two reminders. We used the Gross National Income per capita (USD) provided by the world bank2016 to transform the respondent's country into a geographical-economical variable with 3 levels: High-Europe, high-nonEurope and middle  (1). ATC use was coded as yes or no.