dataesr/scientific-paragraphs-categorization huggingface dataset:
Irvine ICU Cohort UCI is a 422-bed tertiary-care level-1 trauma centre. There are 68 intensive care unit beds across the medical, surgical, neurosurgical, and burn units. All ICU visits between January 1, 2015 and January 27, 2017 were included. This date range was chosen as it coincided with the implementation date of an electronic medical record system at Erasme and concluded with the date of the data pull, so identical time periods could be pulled from both institutions. Only adult patients were included in the study. MAP data of any de-identified patients under norepinephrine infusions were extracted from our electronic medical records at a rate of 1 sample per minute. Standard clinical protocol at UCI for titration of vasopressor infusions in both the surgical and medical ICUs was to maintain MAP between 60 and 80 mmHg.
Erasme OR Cohort Erasme hospital is an 858-bed facility with 28 operating rooms. Members of the research team at Erasme retrospectively extracted a de-identified data set from the electronic medical records (Innovian®, Draeger, Inc, Telford, UK). This data set included surgical patients who received norepinephrine or phenylephrine infusions at any point during the procedure between January 1, 2015 and January 27, 2017. MAP data (at a rate of 1 sample per 20 seconds), vasopressor infusions, surgery type were included in the data set.
The data were analysed using Python (Python Software Foundation, python. org) and NumPy scientific computing package, and R statistics (www. r-project. org). Comparisons between groups were made with Student's t-test for scalar data and chi-square test for categorical data. Confidence intervals are reported at the 95% level. No correction for multiple comparisons was made preferring to risk type II error (false positives) in looking for any possible difference between groups.
80±16, p=0. 996, 95% CI -6 to 6). Some limitations could be advanced. First, the data were retrospectively collected from electronic medical records and is subject to the common limitations of retrospective analysis. However, when data are checked as in the present study, retrospective studies are not submitted to the Osborn effect and could reflect the real life. Second, the reported data only reflect the MAP tendencies in two different centres in USA and Europa. However, no major difference was reported suggesting that the present findings could be extrapolated to numerous other centres, in ORs and ICUs. Thirdly, because we did not have access to post-operative complications (both institutions would have required a hand chart review to properly encode them) we could not assess the influence of the variation of MAP (low and/or high) on patient outcome.
None of the applied EDTA solutions allowed abolishment of stickiness. Additionally, colonies growing on yeast-peptone-dextrose (YPD) agar exhibited a wrinkled morphology, most probably linked to the toxicity of EDTA  (23). Finally, we tried adding Tween 20 (0. 05%) to PBS. Tween 20 eradicated the problems of stickiness and poor disruption and improved the recovery of cells from the biofilms (Fig. 1 ). The effect on cell viability was tested using a planktonic culture of SC5314 that was washed and plated on YPD agar using PBS and PBS-Tween 20 solutions. No impact on viability was observed (data not shown). Thus, in the experiments described below, biofilms were resuspended in a 0. 05% Tween 20-1ϫ PBS solution. However, even after this modification, the ratios of cells that survived AMB treatment were still inconsistent between repeats.
ACKNOWLEDGMENTS Iryna Denega  is part of the  Pasteur-Paris University (PPU) International Ph. D. program and of Ecole Doctorale BioSPC. This project has received funding from the  European Union 's  Horizon 2020 research and innovation program  under the  Marie Sklodowska-Curie  grant agreement  665807 , and from the  Institut Carnot Pasteur Microbes & Santé. This work has been supported by grants from the  French Government 's  Investissement d'Avenir Program (Laboratoire d ' Excellence Integrative Biology of Emerging Infectious Diseases , grant  ANR-10-LABX-62-IBEID ) to C. D.
Flow Cytometry Cell viability was assessed by incubation of cells with Fixable Viability Dye eFluor® 780 (eBioscience, San Diego, CA, USA) following the manufacturer's protocol. Samples were incubated with antibodies for 15 minutes at 4°C. Intracellular staining was performed, for Ki-67 using True Nuclear™ Transcription Factor Fix (BioLegend, San Diego, CA, USA) following the manufacturer's recommendations. The cells were washed twice in PBE (PBS, 0. 5% Bovine Serum Albumin, 2mM EDTA) and analyzed on a Gallios flow cytometer (Beckman Coulter, Villepinte, France). For the analysis of protein expression, level of the geometric mean fluorescence intensity (MFI) was used. Fluorescence Minus One (FMO) controls were performed. Data analysis was performed using Kaluza software (Beckman Coulter) with "logicle" compensation  [21].
3 (Qiagen) and the second generation of the modular transcriptional framework developed by Chaussabel and Baldwin  [27]. Considering transcripts with a sum of normalized read count across all samples >150, a 2-fold change cut-off with an adjusted p-value<0. 01 was set to identify differentially expressed genes. Variant calling was performed according to The GATK Best Practices workflow for variant calling on RNA-seq data  [28]. Duplicate reads were marked using MarkDuplicates from Picard Quality by Depth (< 2) values were also performed. Variants were annotated using GATK, SnpSift  [29]  and SnpEff  [30]. ClinVar database (https://www. ncbi. nlm. nih. gov/clinvar/) was used to assess if variants involved in monogenic forms of SLE, primary immunodeficiencies with SLE-like features or interferonopathies were found (clinical significance value: "pathogenic" or "risk factor", 28 genes checked).
Statistical analysis Data were analyzed using GraphPad Prism version 7 (GraphPad software Inc, San Diego, CA, USA). Statistical significances were calculated with two-tailed unpaired Mann-Whitney U-test or two-tailed Spearman rank correlation test. All values are mean ±SEM. P values lower than 0. 05 were considered statistically significant, or lower than 0. 01 for RNA-seq. 1A )  [17, 31, 32]. Immature T1 is the predominant subset in the BM while T2 is predominant in the peripheral blood  [32]. We carried out detailed phenotypic analysis of these populations in the blood of 20 low treated or untreated SLE patients. All except one patient were Caucasian and their main clinical characteristics are presented in Supplementary Table  1. Most patients were female with at least 4 ACR criteria (see methods) but with different clinical and biological presentations of SLE.
This approach identified interferon stimulated genes (ISGs) as the most overexpressed genes in SLE patients compared to controls, i. e. 14 and 25 ISGs in sorted transitional B cells from quiescent and active SLE patients compared to HDs, respectively (Fig. 3A-B ). Results were analyzed using Ingenuity Pathway Analysis, and the modular transcriptional repertoire developed by Chaussabel et al. [27] , which describes 260 modules of genes sets in blood in various immunological conditions. The three IFN-related modules (M 1. 2, M 3. 4, and M 5. 12) driven by type I IFN but also type II IFN (for M 3. 4 and M 5. 12), appeared up-regulated in SLE transitional B cells (Fig. 3C ). IFN signature was already present in quiescent patients and higher in active patients. The analysis of RNA sequences did not highlight deleterious mutations in genes (SNPs and indels called as described in Materials and Methods section) related to monogenic interferonopathies or to IFN pathway (32 genes, including TREX1, TMEM173, RIG-1, CECR1, RNASEH2A, RNASEH2B, RNASEH2C)  [22, 33].
ACKNOWLEDGMENTS We thank  C. Herouard-Molina  ( IGBMC, Illkirch, France ) for expert technical assistance for the whole transcriptome sequencing. Sequencing was performed by the GenomEast platform, a member of the " France Génomique "  consortium  ( ANR-10-INBS-0009 ). We thank  Dr L. Chiche  ( Department of Internal Medicine, Hôpital Européen, Marseille, France ) and  Dr R. Carapito  ( Genomax Plateform ,  INSERM 1109 ,  Université de Strasbourg, Strasbourg, France)  for assistance with the RNA-Seq analysis. A. K. B. has been supported by a  National Institutes of Health Clinical and Translational Science Award  ( 5UL1TR000042-10 )  Trainee Pilot  and a  Center for Musculoskeletal Research Training Grant  ( 2 T32AR053459 ). J. L. B. has been supported by a  Rheumatology Research Foundation (RRF) Scientist Development Award.
The researcher made it clear that it was up to each child whether or not they wanted to participate in the study. This instruction seemed to be well understood as six children said they did not wish to participate, even though their parents had given their written consent. Each child was individually invited to the classroom that the school had set aside for the study and asked to sit in front of a 22-inch screen under which a binocular eye-tracking system (SMI RED 250) had been installed that recorded eye position every four milliseconds. This is a non-intrusive system (no equipment is placed on the participants) which gives participants relatively large freedom of movement. The eye-tracking software (iView X) enabled precise monitoring of the children's eye movements on the screen following a calibration procedure.
Eye-tracking data The eye-tracking data were analyzed and extracted using eye-tracking software (BeGaze, SMI). To this end, we first created areas of interest (AOI) corresponding to the area(s) within the stimulus from which we wanted to extract the eye-tracking metrics. Two AOIs were chosen: one corresponding to the entire message (the whole health warning; e. g. , "For your health, avoid snacking between meals. www. mangerbouger. fr") and another corresponding to the central message -the part conveying the health recommendation, e. g. , "avoid snacking between meals" -which is the only part of the four different warnings that varies. The two standard eye-tracking metrics, number of eye fixations and eye fixation duration, were extracted for both AOIs of each commercial. The number of eye fixations corresponds to the total number of eye fixations within an AOI.
Number of participants who looked at the health warnings displayed on the TV ads One participant was excluded from the analysis of this part of the study due to unsatisfactory data recording. This led to a final sample of 49 children. The results reveal a clear lack of attention to health warnings: 42. 9% of children (21 of 49)   did not make any eye fixations on the message (Table  1 ). Moreover, 24. 5% made only one fixation. In other words, more than two thirds of the children made no or one eye fixation. With respect to the central message only, 55. 1% made no fixations on this part of the message, 26. 5% made a single fixation, and 18. 4% made more than one fixation. As it is impossible to read the content of the message by making solely one eye fixation (the mean duration of a fixation on the health warnings is less than 300 milliseconds), we may conclude that at least 81% of the children did not process the health recommendation.
Number of participants who looked at the health warnings on the print ads For this part of the study, all of the data recordings were satisfactory, yielding a final sample of 50 children. The results reveal an enormous lack of attention to health warnings: among the 50 children, 47 made no fixations on the warnings, two made a single fixation, and only one made more than one fixation. Considering only the central part of the message, the results show that 48 children did not make any fixations on the messages, which means that only two children looked at them.
Patients Details of the GRAALL-2003 and -2005 studies are provided in the Online Supplementary Methods. Informed consent was obtained from all patients before inclusion into the trials. Both studies were conducted in accordance with the Declaration of Helsinki and approved by local and multicenter research ethical committees. The complete study protocols are detailed in the Online Data Supplement. Both trials were registered at http:/www. ClinicalTrials. gov (NCT00222027, NCT00327678). The criteria for inclusion in the current project were a diagnosis of T-ALL and the availability of diagnostic material for NGS analysis of DNMT3A genotype. Survival outcomes of the 198 patients (36 from GRAALL-2003 and 162 from GRAALL-2005) who fulfilled these criteria did not differ from those of the remaining 139 T-ALL patients of the study cohorts.
Univariate and bivariate analyses assessing the impact of DNMT3A mutations and age were performed with a Cox model. Variables that were significantly associated with outcome in univariate analysis were considered as covariates in multivariate Cox models. The proportional-hazards assumption was checked before conducting multivariate analyses. Statistical analyses were performed with STATA software (STATA 12. 0 Corporation, College Station, TX, USA). All P values were twosided, with P<0. 05 denoting statistical significance.
Patient characteristics and data related to GHDT, management of hypotension, monitoring of temperature and depth of anaesthesia, lung ventilation, point of care haemoglobin testing were collected. Results: 807 patients were included. Only 2 % of patients [95% CI: 1-3] received GHDT in full accordance with guidelines. Depth of anaesthesia monitoring was largely performed (53%, [95% CI: 50-56]). The multifaceted strategy of lung-protective ventilation combining low tidal volumes (6-8ml/kg), PEEP of 5-8 cm cmH2O, and repeated recruitment manoeuvres, was Introduction Elderly patients constitute an increasingly large proportion of high surgical risk patients. Their management in major surgery is associated with significant postoperative morbidity and mortality. Postoperative deaths in patients over 70 years represent 80 % of the overall postoperative mortality in the UK  [1].
The surgical procedures were selected following analysis of the 2010 French Hospital Discharge database (PMSI) which contains medical procedures for all patients admitted to public and private hospitals in 2010, identified by their code according to medical classification for clinical procedures and discharge diagnoses encoded in the International Classification of Diseases, 10 th revision (ICD-10 codes). These procedures were chosen because they were associated with a 24. 0 % [95% CI: 23. 7-24. 4] incidence of a composite criteria combining 30-day major postoperative complications (acute kidney injury, acute myocardial infarction, heart failure, stroke, severe sepsis, septic shock, acute respiratory failure requiring non-invasive ventilation or intubation, delirium) and mortality in patients aged ≥ 75 years having at least one comorbidity among the following: ischaemic coronary disease, cardiac arrhythmia, congestive heart failure, peripheral vascular disease, dementia, stroke, chronic obstructive pulmonary disease (COPD), chronic respiratory failure, chronic alcohol abuse, active cancer, diabetes, chronic renal failure.
All participants were included from induction of anaesthesia to the end of surgery and received general anaesthesia. The study had an online application for collecting and managing data on patients recruited. The physicians had to fill an electronic case report form (eCRF) with the following patient variables: age (≥75 or ≥ 80 years), ASA score (I, II, III, IV, V), comorbidities (ischemic coronary disease, cardiac arrhythmia, congestive heart failure, peripheral vascular disease, dementia, stroke, chronic obstructive pulmonary disease, chronic respiratory failure, chronic alcohol abuse, active cancer, diabetes), type (femoralneck fracture surgery, intraperitoneal abdominal surgery, vascular surgery) and nature (elective, emergency) of the surgery. Data collected are shown in Table  1. Data were collected as yes or no responses except for temperature at the end of surgery, value of blood pressure defining hypotension, tidal volume and PEEP level where quantitative parameters were required.
For a rate of adhesion to the recommendations expected between 20% and 50%, inclusion of 800 patients allows to evaluate the rate of adhesion (α = 5% 1-β =80%) with a margin of error of 3,5%. Statistical analysis was performed using Stata 13 software (StataCorp LP, College Station, TX, US). The tests were two-sided, with a type I error set at α = 0. 05. Subject's characteristics were presented as median [range] for continuous data (assumption of normality was assessed using the Shapiro-Wilk test) and as the number of patients and associated percentages with 95%CI for categorical parameters. Comparisons between the independent groups were performed using the chi-squared or Fisher's exact tests for categorical variables, and using Student t-test or Mann-Whitney test for quantitative parameters (normality, assumption of homoscedasticity studied using Fisher-Snedecor test).
This is the subject of a current prospective, randomised, controlled study: the PERCEPOLIS Study: PERte Cellulaire Endothéliale après PhacOémuLsification Intra et Supracapsulaire (Endothelial cell loss after intra or supracapsular phacoemulsification, NCT02535819 / IDRCB 2015-A00789-49) where phacoemulsification is performed using the "Garde-a-vous" technique in one group and a standard endocapsular technique in the control group. The aim of this article is to provide a detailed and standardised description of a supracapsular technique called "garde-a-vous" technique. This technique, developed and refined by the authors, is an evolution of the supracapsular technique, but performed with up-to-date technology and in micro-coaxial mode with the aim of achieving a safe procedure as gentle as possible for the zonules and also as fast as possible in terms of total intervention time.
The UST (ultrasound time or average phacoemulsification time APT) represented the number of seconds the foot pedal remained in the third position. The EPT was the equivalent phacoemulsification time at 100% power (EPT = phacoemulsification time x average phacoemulsification power). The US power, UST and EPT values were automatically calculated by the device and displayed on the monitor of the machine. Secondary outcomes assessed included % of topical anesthesia, average power of IOL, pain felt on an analog scale from 0 to 10 and finally the possible complications met. The authors compared the data obtained after the intervention according to the "garde-a-vous" technique or according to the "divide and conquer". The choice of the technique depended in one hand on the operating habits of each surgeon in the service, some preferring the "garde-a-vous" technique and the others the "divide and conquer" technique and in the other hand of the degree of pupillary dilatation at the time of surgery.
If the pupillary dilation was greater than or equal to 6 mm, the technique chosen was most often the "subluxation" technique and if the dilation was less than 5 mm, the technique most often used corresponded to the classical technique of "divide and conquer ". The study data were collected daily by the operating room nurse immediately after the operation with respect to the pain measurement scale and the duration of the surgery and by the assistants for other data collected. The pain rating scale was an analog scale evaluated from 0 to 10 (0 corresponding to no pain and 10 to extreme pain). Patients were asked about the pain felt just after the operation. The procedure times were collected using a stopwatch, triggered at the time of the first incision and stopped at the time of the final leak test, the gestures were observed live on the control video.
The operation-specific data was collected by the assistant: the ultrasound rate, UST, and EPT appeared on the Stelaris device screen at the end of the procedure. Complications collected corresponding to the eventual occurrence of a posterior capsular rupture were also collected by the assistant present in the operating room. All patients were informed about the objectives of the study. Patients who did not opposed to the use of their data were included. The study was conducted according to the CNIL (French Data Protection Authority) MR-003 methodology (n° 2061208v0) and has been approved by the Ethics Committee of the French Society of Ophthalmology (IRB 00008855 Société Française d'Ophtalmologie IRB#1).
Implications of all the available evidence These findings make pola one of the most promising novel candidates for further clinical evaluation in combination regimens in treatment-refractory patients and also in a first-line setting in B-cell non-Hodgkin lymphoma. Clinical development is continuing with pola, with studies investigating this ADC in combination with other anti-lymphoma agents in patients with non-Hodgkin lymphoma. Pola is currently being investigated in a randomised phase 3 study as first-line diffuse large B-cell lymphoma treatment in combination with ritximabi, cyclophosphamide, doxorubicin, and prednisone (R-CHP-Pola) and compared with the standard R-CHOP regimen (POLARIX study, NCT03274492). The POLARIX study is one of the first clinical trials where the goal is to replace systemic chemotherapy agents with a novel agent, such as an ADC, with the potential of improving on the efficacy as well as safety and tolerability of treatment regimens for patients with non-Hodgkin lymphoma.
Abstract (250 words) Purpose Antibody-drug conjugates (ADCs), polatuzumab vedotin (pola) and pinatuzumab vedotin (pina), demonstrated clinical activity/tolerability in phase 1 trials. This multicentre, open-label phase 1b/2 study (ROMULUS; NCT01691898) evaluated rituximab (R)-pola/pina in patients with relapsed/refractory diffuse large B-cell lymphoma and follicular lymphoma. Patients and methods Patients were randomised 1:1 using a dynamic hierarchical randomisation scheme to R-pola or R-pina (R, 375 mg/m²; ADCs, 2•4 mg/kg) every 3 weeks until progressive disease/unacceptable toxicity up to 1 year. Primary objectives: safety/tolerability and antitumour response.
Stratification factors were implemented to ensure the balance of the pola and pina arms at randomisation and were not reflected in the analyses. 1] [12]  For relapsed/refractory follicular lymphoma, estimated progression-free survival (PFS) is heterogeneous depending on a number of clinicogenomic factors, however, data from the PI3K delta inhibitor literature shows that median PFS is approximately 11 months. 13, 14 levant institutional review boards and ethics committees of each participating centre approved the trial protocols. All patients provided written informed consent. The protocol is available at clinicaltrials. gov.
Statistical analysis Planned target accrual was 120 patients in two separate cohorts (n=40 relapsed/refractory follicular lymphoma, n=80 relapsed/refractory diffuse large B-cell lymphoma). Target sample sizes were determined to provide sufficient precision in estimating separately the objective response rate (ORR) with R-pina or R-pola. An observed response rate of 40% would result in a 90% confidence interval (CI) of ~22-58% for the follicular lymphoma cohort, and ~27-53% for the diffuse large B-cell lymphoma cohort. For treatment-emergent adverse events, with 40 patients there was an 87% chance of observing ≥1 adverse event, with a true incidence of 5%. ORRs in patients with baseline measurable disease and ≥1 post-treatment tumour assessment were calculated on the basis of best response at the data cutoff date.
PFS, duration of response (DOR), and overall survival were analysed by the Kaplan-Meier method and defined as time from the day of enrolment/randomisation (PFS, overall survival) or response (DOR) to progressive disease or death; if these events were absent, PFS and DOR were censored on the day of the last tumour assessment. Safety analyses were based on the safetyevaluable population, which included all patients who received ≥1 dose of study treatment. The study is registered with ClinicalTrials. gov: NCT01691898.