dataesr/scientific-paragraphs-categorization huggingface dataset:
Study Patients Clinical data and biological samples for this study were prospectively obtained from patients enrolled in a multicenter observational study of ultrasound assessment of lung aeration loss during a weaning trial and its role as a predictor of postextubation distress  [5]. Consecutive patients receiving mechanical ventilation for more than 48 hours were included in the primary study when the underlying disease that had required intubation was considered by the attending physician as reversed, rendering the patient eligible to a first one-hour SBT  [11]. Patients were included in the present study based on the availability of their plasma samples, in order to evaluate plasma sRAGE levels in the setting of weaning from the ventilator.
This study has some limitations. Firstly, plasma sRAGE was not measured in all participants in the original trial, but only in subjects for whom plasma samples were available. Therefore it remains possible that systematic factors contributed in some way to plasma availability. More importantly, our study is not powered enough to avoid a type II error. In order to obtain a power of 80% with a bilateral type I error of 5% in our study, 542 patients would have been needed (n1 = 356; n2 = 186), but differences in sRAGE levels seem relatively low from a clinical perspective and based on available data in such a clinical setting  (9, 10, 14, 15, 22) , suggesting they may not be clinically significant. Therefore we think our clinical justification is more important in this kind of observational, short time courses, exploratory-type designed, study.
Although we were not able to control for these chronic diseases, measured plasma sRAGE levels were consistent with previously reported levels in ICU patients  [10]. Thirdly, measurements of sRAGE in the bronchoalveolar lavage (BAL) of our weaning patients were not feasible in our study, and the expression of sRAGE in the fluid of alveolar space remains unknown in this setting. However, previously published data support the hypothesis that the major source of plasma sRAGE is its release from alveolar type I epithelial cell  [9, 29] ; it seems therefore unlikely that sRAGE levels in the BAL would be different between patients who failed SBT or developed postextubation distress and those who did not in our cohort. Also, the observation time was relatively short, and may not have been sufficient to detect changes in the expression of sRAGE, as measured by ELISA at the protein level.
Today, many of the most common allergenic molecules have been cloned or purified, have had their threedimensional structures elucidated, and can be consistently produced  [6]. Because of the growing number of allergens identified, a systematic allergen nomenclature, approved by the World Health Organization and International Union of Immunological Species (WHO/IUIS) Allergen Nomenclature Subcommittee, has been established. The subcommittee is in charge of developing and maintaining the systematic nomenclature developed for allergenic molecules, as well as a comprehensive database of known allergenic proteins that can be accessed at www. allergen. org. Allergenic molecules are named using their Latin family name (genus and species). For example, allergens that begin with Phl p are from Phleum pratense (timothy grass).
Fluorescence is measured with a laser scanner and results are evaluated using a Microarray Image Analysis (MIA) software, which provides an automatic readout of the results. In addition, addon software is available (ISAC Xplain) that delivers evidence-based allergen information relevant for the individual patient. Using a standard calibration curve, results are reported within a range of 0. 3 to 100 ISAC Standardized Units (ISU-E), giving a semi-quantitative indication of IgE antibody levels. This differs from the units used to report ImmunoCAP results (kU/L), and as such, these measurements are not interchangeable, although they correlate well  [97]. Furthermore, it must be born in mind that the ImmunoCAP technology measures IgE binding under conditions of excess of immobilized allergen whereas ISAC uses low amounts of immobilized allergen allowing for competition with allergen-specific isotypes other than IgE.
Flow cytometry results were acquired on a Gallios flow cytometer (Beckman Coulter) and data analyzed with the Kaluza software package (Beckman Coulter). The anti-mouse mAbs were purchased from Pharmingen for FITC-labeled 2G9 anti I-A d /I-E d clone, or eBioscience for the followings clones: e450-conjugated N418 anti-CD11c (p150/90), APC-conjugated M1/70 anti-CD11b/CR3 a-chain, PE-conjugated 16-10A1 anti-CD80/B7-1, APC-conjugated BM8 anti-F4/80, and PE-conjugated AFS98 anti-CD115. Sampling and preparation of DsRed 2 L. amazonensis amastigotes L. amazonensis strain LV79 (MPRO/BR/1972/M1841) was genetically modified by chromosomal integration of the fluorescent DsRed2 molecule  [26]  and propagated in Swiss nu/nu mice by subcutaneous injection of 10 6 amastigotes into hind footpad. Six to eight weeks after amastigote inoculation lesions were excised and amastigotes purified by a modified version of the method originally described by M.
Rabinovitch and colleagues  [27]. Briefly, lesions were minced in PBS supplemented with streptomycin (100 mg/ mL) and penicillin (100 IU/mL), and disrupted by hand in a glass homogenizer. Tissue debris were removed by 2 rounds of centrifugation at 30 g for 10 mn at 4uC. Amastigotes present in the supernatant were washed 2 times by centrifugation at 1500 g for 10 mn at 4uC before distribution in macrophage cultures. A high number of live amastigotes expressing homogenous levels of DsRed2 were recovered as determined by FACS analysis (data not shown).
At this time, compounds (Tables  S2, S3 ) were added to macrophages (1 ml/well) resulting in a final concentration of 1% DMSO in each well. The cultures were then maintained 3 days at 34uC until processing for image acquisition. One hour before image acquisition, the cells were incubated with vital cell-permeant dyes Hoechst 33342 (12 mM) and LysoTracker DND-26 (1 mM) (life technologies). Optimization of operating parameters included an automated dispensing of biological material (macrophages and amastigotes) and chemicals (vehicle, compounds) using the Te-MO 96-channel pipetting head of a TECAN Freedom EVOware platform located under laminar flow in a BSL2 facility. The homogeneity and the reproducibility of all pipetting procedures were assessed by quantitative image analysis during assay development (data not shown).
Image acquisition and analysis After 60 minutes of contact with fluorescent reporters, three channel images were acquired in a fully automated and unbiased manner using a spinning disk confocal microscope (OPERA QEHS, PerkinElmer Technologies) and a 106 air objective (NA = 0. 4) using the following sequential acquisition settings: (i) 561 nm laser line excitation, filter 600/40 for DsRed2 detection, (ii) 488 nm laser line excitation, filter 540/75 for Lysotracker DND-26 detection and (iii) 405 nm laser line excitation, filter 450/ 50 for Hoechst 33342 detection. Fifteen images per channel, covering the entire surface of each well, were collected for reliable statistical analysis taking into account potential cell-distribution and spatial compound effect biases. The images were transferred to the Columbus Conductor TM Database (Perkin Elmer Technologies) for storage and further analysis.
The image analysis was performed by batches in Columbus using custom designed image analysis scripts developed beforehand with the Acapella Image analysis software (version 2. 5 -Perkin Elmer Technologies). The script was subdivided in three object segmentation subroutines detecting successively and independently the nuclei, the PV and the Am with their respective associated features (number, size, and intensity); the living macrophage population characterisation is based on a combination of host cell nucleus size and intensity features which are key characteristics of the relative fitness of the macrophage population. Finally, all the quantitative data generated were exported in readable file format to be subsequently analyzed in the data analysis workflow described below.
All dispensing procedures in the 384-well plates were performed using an automated liquid handling robot without any washing step. (B) Boxplots with whiskers from minimum to maximum of Percent Of negative Control (POC) for the amastigote (Am), parasitophorous vacuoles (PV) and Viability Index (VI) after the following treatments: no compound added (Media), 1% DMSO, 180 mM cycloheximide, 2 mM Leu-oMe and 1 mM Amphothericin B (AmpB) leishmanicidal drug. Sets of 96 data points for each are issued from a representative validation 384-well plate. (C) AmphoB dose-response curves were expressed as POC for (VI) (black circle), (PV) (black square) and (Am) (black triangle). Each concentration has been tested in quadruplicates; error bars represent the data range. IC50 curve fitting and the Spearman correlation coefficient (r, for n = 5) between the IC50 dose curves for the PV and Am outputs were calculated using GraphPad Prism 6 software (GraphPad Software Inc.
In order to avoid biases due to potential heterogeneity of the macrophage monolayer that could arise over time, and to increase the size of the population analyzed, image acquisitions were performed at low magnification using a dry 106 objective for the entire surface of the wells, resulting in acquisition and analysis of all cells for each sample. The images were thereafter segmented using Acapella scripts and the outputs normalized and expressed as percentages of media control (Figure  2B ). The presence of 1% DMSO (C-) did not induce toxic effect on macrophages as demonstrated by the similar values obtained for the VI (Figure  2B  bottom panel and Figure  S3 ). On the contrary, the presence of a toxic compound for the macrophage, like cycloheximide, was easily evidenced by the dramatic decrease of the VI compared to untreated or DMSOtreated samples (Figure  2B , bottom panel).
(TIF) Figure  S2  FACS-based phenotype analysis of primary mouse macrophages before plating in 384-well plate. Kinetics analysis of CD115 (A) and F4/80 (B) macrophage specific markers on adherent cells harvested at different time points during the culture of bone marrow cell in the presence of mrCSF-1. On day 6, the best yield of viable macrophage expressing high levels of CD115 and F4/80 was obtained (Thick solid line and data not shown). (C, D) Live macrophages recovered after 6 days were analyzed for the following markers: CD115, F4/80, CD11c, CD80 and CD11b, all of which are displayed at the plasma membrane of steady state mouse macrophages. The presence of MHC Class II Parasites cultured in medium alone (C2, 0% growth inhibition) or in the presence of 1 mM Amphotericin B (C+, 100% growth inhibition) were used as negative and positive controls, respectively.
After 64 h incubation with compounds, resazurin (2. 5 mg/ml) was added to each well and parasites were incubated for an additional 8 h before measuring resofurin fluorescence (lex = 550 nm, bandwidth = 9 nm; lem = 590 nm, bandwidth = 20 nm). Each compound concentration was tested in quadruplicates and the average 6 standard deviation is displayed. EC50 values were calculated using SigmaPlot (SPSS, SSI, San Jose,CA, USA) 4-parameter logistic nonlinear regression analysis (values in parenthesis in the upper right panel). doi:10. 1371/journal. pntd. 0002154. g004 molecules allows evaluating the percentage of non-steady state macrophages. The percentage of macrophages positive for these markers (C) and the Mean Fluorescence Intensity ratios (markerspecific over isotype control staining) (D) are shown.
Box and whisker plots show the distribution of the data from 10 experiments: bottom line, 25th percentile; middle line, median; top line, 75th percentile; whiskers, fifth and 95th percentiles. (TIF) Figure  S3  1% DMSO does not induce toxicity to the macrophage population. Boxplots with whiskers from minimum to maximum of number of viable cells for no treatment (''media'') versus 1% DMSO treated wells. Data were gathered from n = 15 and n = 64 wells for ''media'' and DMSO respectively on 4 independent 384-well plates. A 2-way ANNOVA test performed on each plate did not reveal significant differences between the two conditions. (TIF) Figure  S4  Fingerprint of hit classes after data classification for quadruplicate samples in plates P1 to P4. All compounds are listed for every replicates (R1 to R4) in each plate (P1 to P4).
One hour before image acquisition on the confocal plate reader, the fluorescent reporters Hoechst 33342 and LysoTracker DND-26 were added to the macrophage cultures (diamond). All dispensing procedures in the 384-well plates were performed using an automated liquid handling robot without any washing step. (B) Boxplots with whiskers from minimum to maximum of Percent Of negative Control (POC) for the amastigote (Am), parasitophorous vacuoles (PV) and Viability Index (VI) after the following treatments: no compound added (Media), 1% DMSO, 180 mM cycloheximide, 2 mM Leu-oMe and 1 mM Amphothericin B (AmpB) leishmanicidal drug. Sets of 96 data points for each are issued from a representative validation 384-well plate. (C) AmphoB dose-response curves were expressed as POC for (VI) (black circle), (PV) (black square) and (Am) (black triangle).
Acknowledgments The authors would like to thank all the members of the  FP7 LEISHDRUG consortium, Pr. Conrad Ku ¨nick  for the gift of the Paullone derivatives and fruitful and engaging result discussions and  Dr Thierry Lang  and  Sophie Goyard  for the gift of transgenic L. amazonensis parasites expressing the DsRed2 fluorescent reporter. We are thankful to our colleagues from the Imagopole, specifically  Emmanuelle Perret  for her enthusiasm and great professionalism and the '' Immunophysiologie et Parasitisme '' team members for the continuous support throughout this study and more particularly to  Drs. Joseph Dragavon  and  Florian Ru  ¨ckel for critical reading and proof reading of the manuscript.
4. 30 minutes to 2 hours of recovery were allowed before intracellular recordings. Sharp micropipettes were filled with 1. 2-2 M potassium acetate and 4 mM KCl and had resistances of 80-110 Mohm after bevelling. Patch electrodes (tip resistance: 2-3 Mohm) were filled with a solution containing (in mM): 135 Kgluconate, 0. 1 CaCl 2 , 5 MgCl 2 , 1 EGTA, 10 HEPES, and 4 Na-ATP, 15 phosphocreatine and 50 units/ml creatine phosphokinase (pH adjusted to 7. 3 with KOH, osmolarity 290 mOsm). The liquid junction potential (+10 mV) was systematically corrected at the beginning of the recording. Patch recordings were performed at 32uC. Access and series resistances were constantly monitored and data from neurons with more that 20% of changes from initial value were discarded. The dynamic-clamp technique  [26] [27] [28]  was used to inject computer-generated conductances in real neurons.
Circuit modeling The circuits were modeled under the NEURON simulator and are described in the Results. Cortical and thalamic model neurons are based on single-compartment Hodgkin Huxley type models developed in previous modeling studies  [103, 104]. The cortical neuron is based on a pyramidal layer 4 cell and the thalamic cells are based on a thalamocortical relay cell. The model retinal cells consisted in random spike-train generators mimicking the discharge pattern of an ON-center Y cell. Model parameters for cell passive properties, synaptic currents and synaptic bombardment are summarized in Table  1  Cellular models, current kinetics and BICN implementations are described in the sections below. The model files are available on ModelDB website, accession number 150240.
F. Classical cross-correlation analysis between the retinal and cortical spike trains with a bin size of 1 ms. The correlations were calculated using MATLAB (MathWorks) xcorr function and normalized so that the autocorrelations at zero lag are identically 1. White areas indicate that the function could not calculate the correlations and returned ''NaN'' values. (TIF) Text S1 Focused attention: A synaptic bombardment decorrelation hypothesis. Supporting evidences for the implication of synaptic bombardment decorrelation in focused attention. We propose a phenomenological model based on the segregation effect described in Figure  S6. Based upon the findings of the present study, we make the prediction of the existence of dynamic functional maps of correlation and decorrelation in V1 and the thalamus.
SB was supported by the  French DGA (Direction Generale de l'Armement). This work was supported by the  CNRS , the  Agence Nationale de la Recherche  ( ANR-10-BLAN-1402 :  V1-Complex ) and EC contracts (Facets ( FP6-2004-IST-FETPI 15879 ),  Brain-i-nets  ( FP7-2009-ICT-FET 243914 ) and  BrainScales  ( FP7-269921) ). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Microarrays and data processing Experiments were performed at the National Facility for DNA Microarrays (Aveiro, Portugal). Three independent 2D and 3D AGS cell cultures were selected for total RNA extraction using TRI Reagent. RNA quantity and quality were assessed using the Nanodrop ND-1000 (Thermo Scientific) and 2100 Bioanalyzer (Agilent Technologies) systems, and only samples with a RNA integrity number above nine were considered for further study. Preparation and labelling of the RNA was performed using the One-Color Microarray-Based Gene Expression Analysis Quick Amp Labelling kit (Agilent Technologies). Briefly, 600 ng of total RNA from 2D and 3D biological replicas was used as input together with spike-in controls to generate Cyanine 3-labelled cRNA. The amplified cRNA samples were purified with RNeasy Mini kit (Qiagen) and hybridized to Human Gene expression 4 Â 44K v2 Microarray slides (Agilent Technologies) at 65 C for 17 h.
After washing procedures, images of the hybridizations were acquired using a G2505B Microarray Scanner (Agilent Technologies). The Feature Extraction software was used for spot identification, background subtraction and quantification of the fluorescent signal. Raw expression data were processed using BRB-ArrayTools v3. 8. 1 software  (37). After base 2 log transformation and average of probe replicates, normalization was applied using the median intensity over the entire array to minimize systematic variance. Differentially expressed transcripts between the two culture conditions were filtered using the Class Comparison tool, performing an unpaired sample t-test with a P < 0. 01 and considering a minimal 1. 5-fold change. Hierarchical clustering analysis of significantly altered genes was conducted in TIGR MultiExperiment Viewer v4.
8. 1 software (38) using Euclidean correlation and average linkage clustering, and expression values indicated colorimetrically. Functional annotation of differentially expressed genes, identified by extending the unpaired t-test parameter to P < 0. 05 and maintaining the minimal fold change was performed with DAVID program  (39). Microarray data have been submitted to the ArrayExpress database (http://www. ebi. ac. uk/arrayexpress/) and assigned the identifier E-MTAB-1234. The complete list of differentially expressed genes is detailed in Supplementary Table  S2.
Protein extraction and western blot analysis Cells were lysed for 30 min on ice in a lysis buffer containing 20 mM Tris-HCl (pH 7. 5), 150 mM NaCl, 2 mM ethylenediaminetetraacetic acid and 1% IGEPAL (Sigma), supplemented with Complete protease inhibitor cocktail (Roche Applied Science), 1 mM PMSF and 1 mM Na 3 VO 4. Lysates were centrifuged at 12 000 rpm for 20 min at 4 C and the supernatant recovered. Protein concentration was determined using the BCA Protein Assay Reagent (Thermo Scientific). Protein extracts (30-50 mg) were run on 10% sodium dodecyl sulphate-polyacrylamide gel electrophoresis, transferred to a nitrocellulose membrane, blotted overnight with appropriate antibodies (Supplementary Table  S1 ), and signals revealed with ECL detection kit (GE Healthcare Life Sciences). Actin levels were used to normalize protein expression, and quantification of western blots was performed using Fiji software  (40).
Flow cytometry Caco-2 cells were harvested 48 h after transfection at confluence and fixed with 1% paraformaldehyde for 20 min at room temperature followed by permeabilization with 0. 1% Triton X-100 (Sigma) for 5 min on ice. Staining was performed with anti-MEX3A antibody and visualized with goat anti-rabbit FITC-conjugated secondary antibody. For DNA content assessment, cells were incubated with a propidium iodide (50 mg/ml) and RNAse A (200 mg/ml) solution (Sigma) for 30 min at room temperature. Samples were read in a FACSCanto II (BD Biosciences) flow cytometer, and analysis was performed using the FlowJo software.
Immunofluorescence and microscopy Cells grown on coverslips were fixed using ice-cold methanol for 10 min. For Caco-2 3D assay, cysts were fixed with a 2% paraformaldehyde and 0. 05% glutaraldehyde solution at room temperature for 20 min, followed by quenching with 0. 1% NaBH 4 and permeabilization with 0. 5% Triton X-100. Paraffin-embedded wild-type murine tissue sections (4 mm) were deparaffinized with clear-rite (Thermo Scientific) and rehydrated. All samples were blocked with non-immune serum diluted in 10% BSA-PBS, followed by incubation with appropriate antibodies (Supplementary Table  S1 ) diluted in 5% BSA-PBS. Nuclei were counterstained with 4 0 ,6-diamidino-2-phenylindole (DAPI, Sigma), and coverslips mounted on microscope slides with Vectashield (Vector). Imaging acquisition was based on optical sectioning and adjusted for brightness and contrast with Fiji software  (40).
ACKNOWLEDGEMENTS The authors are grateful to  Professor Leonor David  for fruitful discussion, valuable experimental advice throughout the project and critical reading of the manuscript. They thank  Dr Catarina Leita˜o  for technical assistance in flow cytometry and  Dr Patrı´cia Castro  for technical assistance in confocal microscopy. The overall study was coordinated by  R. A. with contributions from M. B. ; B. P. , S. S. , R. B. and L. C. performed the experiments; M. P. , JP. R. and JN. F. provided essential reagents; B. P. and R. A. conceived and designed the experiments; B. P. and R. A. wrote the manuscript; all authors contributed to different aspects of data analysis and critical revision of the manuscript.
FUNDING Fundac¸a˜o para a Cieˆncia e a  Tecnologia (FCT)-Programa Operacional Cieˆncia e Inovac¸a˜o 2010 do Quadro Comunita´rio de Apoio III  and  FEDER [PTDC/ SAU-OBD/64490/2006 ]. IPATIMUP is an  Associate Laboratory of the Portuguese Ministry of Science, Technology and Higher Education  and is partially supported by  FCT. B. P. and R. B. acknowledge  FCT  for financial support [ SFRH/BD/43168/2008  and  SFRH/BPD/ 68276/2010 , respectively]. M. B. was supported by a grant from the  Fondation ARC , and N. T. C. was the recipient of a fellowship from the  Fondation pour la Recherche Me´dicale. Funding for open access charge:  FCT [SFRH/ BD/43168/2008 ].
The boundary conditions for MAR are provided by several GCMs included in the IPCC ( Intergovernmental Panel on Climate Change ) fifth assessment report (AR5). This work fits into the ICE2SEA project (http: //www. ice2sea. eu) of the 7th Framework Program (FP7), which aims to improve the projections of future sea level rise due to the contribution of melt from land-based ice. After a brief description of the MAR model in Sect. 2, Sect. 3 compares the MAR output obtained with ERA-Interim reanalysis forcing data over the period 1980-2012 with those obtained from MAR forced by the selected GCMs. In Sect. 4, we analyse future SMB projections. Section 5 describes the sensitivity of the SMB components to a fixed temperature anomaly independently from the forcing GCM and scenario. Finally, in Sect.