dataesr/scientific-paragraphs-categorization huggingface dataset:
Nanoparticles Functionalization and Use A boronic acid-based coupling strategy was used for precise orientation of anti-TNFa antibodies (Antibody TNF5, Mabtech) on the surface of 300 nm magnetic nanoparticles (Ademtech, cat. no 2131). 3-aminophenylboronic acid molecules (Sigma) were grafted on the surface of carboxylated beads to act as an affinity head-group for covalent and site-specific IgG attachment. Functionalized nanoparticles were validated and calibrated in microfluidics conditions. Briefly, dose response experiments were performed using recombinant TNF a protein (BioLegend). Resulting calibration data were used to convert nanoparticle fluorescence signal into a number of detected TNFa molecules. The encapsulation of 170 nanoparticles per droplet resulted in the formation of a single homogenous bead-line (in the left part of the droplet) after application of a permanent magnetic field (strength B= 0.
Automated Image Analysis and Processing Time-lapse imaging was performed using a thermalized motorized Nikon inverted microscope and x10 magnification. For each experiment, images were acquired in three fluorescence channels (excitation/emission: 482/520 nm, 531/593 nm, 628/ 692 nm) every 30 min over 3 hours at the temperature of 37°C, and then analyzed by R software using an automated Matlab script for extracting time-lapse fluorescence levels.
Image Processing A Matlab-based software detects and tracks droplets in timelapse image sequences and monitor the status of their content throughout the kinetics. For each field, the analysis procedure can be summarized in three steps: (i) detect contours of the droplets and intra-droplets beadline and cells at t0, (ii) sort the droplets according to the number of cells they contain and initial cell status (alive or dead), and (iii) track the droplets of interest (i. e. strictly containing a single live cell) for monitoring beadline fluorescence and cell status evolution at all time. The software implements the Matlab Image processing toolbox as well as the VLFeat open source library. Software output is a spreadsheet containing localization, morphological and intensity parameters for different intra-droplet objects over time.
CONCLUSION Our results add a new layer of complexity in sepsis-induced immune alterations by highlighting the functional heterogeneity of monocytes. The impact on clinical outcomes and how pharmacological interventions to reverse monocyte deactivation may target the different functional subsets are unanswered questions that deserve further investigations using high-resolution microfluidic assay. microbiology technological institute BIOASTER. The funders were not involved in the study design, collection, analysis, interpretation of data, the writing of this article or the decision to submit it for publication. This research project has received funding from the French Government through the "Investissement d'Avenir" program (grant n°ANR-10-AIRT-03).
Study sample Our study focused on data from 529 health facilities (525 public and 4 private not-for-profit health facilities) providing HIV treatment and care services and using the national Electronic Patient Monitoring System (ePMS). The ePMS is an electronic-last system for capturing patient-level demographic, clinical, and laboratory information at enrolment and for followup review visits among PLHIV registered in HIV care. The system is in use at 529 high volume health facilities (with �500 PLHIV on ART by December 2012) out of 1,620 health facilities providing ART services in Zimbabwe. Despite the ePMS coming into use from 2012 onwards, historical patient-visit data were entered for patients who were alive in ART care and had been enrolled into care dating back to 2004 when ART was first offered in the public sector.
Data management The primary source document for data variables included in this study was the individual ART care booklet which is entered in the ePMS. Data variables abstracted from the EPMS for purposes of this study include sex, date of birth, date of ART initiation, WHO clinical staging, CD4 cell count, current pregnancy status, anemia status at enrolment, dates of VL sample collection and VL test results and date of switching to 2 nd -line ART. Current pregnancy status referred to the last visit when data was collected from 30 June 2017 onwards among the women living with HIV (WLHIV) who were included in this study. This definition was chosen since women are eligible for VL testing during pregnancy in order to assess whether they are at high risk or low risk of mother-to-child transmission of HIV.
Anemia was defined as having hemoglobin levels <13. 5g/dL among men or <12g/dL among women. The ePMS is an offline system with a MySQL database format (Oracle International Corporation, Redwood City, CA, USA) with a Microsoft Access front-end. Upon receipt of routine quarterly submissions of health facility-level data back-up files for the October-December 4 2018 period, selected variables were imported using Stata version 15 (StataCorp, College Station, Texas USA) through the "OBDC data source" command into separate datasets for demographics, clinical data, laboratory tests and patient follow-up visit data. These were separate datasets which were merged into health facility-specific datasets and then appended into one large dataset. The ART number (which is a unique identifier assigned to a patient upon enrolment into life-long HIV care) was used to de-duplicate data for patients who transferred from one health facility to another with the ePMS installed and also to account for their current ART outcomes, especially for patients who were self-transfers and might have been misclassified as lost-to-follow up.
Ethics approval This study was approved by the Medical Research Council of Zimbabwe (Approval Number: MRCZ/A/2160) and the Joint Research Ethics Committee (JREC) for University of Zimbabwe College of Health Sciences and Parirenyatwa Group Hospitals (Approval Number: JREC/12/ 17). The ethics committee waived the requirement for informed consent by participants as VL testing is part of ministry of health routine standard of care for monitoring HIV treatment response. Data were also fully anonymized as patient names were excluded in the abstraction of data. Instead patient ART numbers (which are unique identifiers assigned to patients upon enrolment in HIV care) were abstracted and later replaced in the electronic database with a sequential number to ensure patients cannot be traced back to the facility.
Study area and data collection A cross-sectional study was carried out in 8 localities, representing 8 bioclimatic zones in Tunisia (Table  1  and Fig 1). Mixed-breed dogs were randomly sampled during rabies vaccination campaigns organized by regional veterinary services between June and August 2016. Informed consent was obtained from each owner. Stray dogs were not included in our study as they were difficult to catch. All dogs were subjected to a rapid physical examination for compatible clinical signs with CanL, including skin lesions, exfoliative dermatitis, erosiveulcerative lesions, lymphadenomegaly, weight loss, and onychogryphosis  [20]. A sample of peripheral blood (5 mL) was taken from each dog's radial vein. Whole blood was collected in tubes with no additives for an indirect fluorescent antibody test (IFAT) and also in tubes with Ethylenediaminetetra-acetic acid (EDTA)-anticoagulant for DNA extraction and PCR analysis.
Quantitative RT-PCR for TSLP The expression of short and long form TSLP was quantified as described  (21, 22). Briefly, total RNA was extracted using Trizol. Five hundred nanograms of RNA was treated with ezDNase Enzyme (Thermo Fisher) to remove genomic DNA and reverse transcribed into cDNA using the kit SuperScript IV VILO Master Mix according to the manufacturer's instructions (Thermo Fisher). Quantitative PCR was performed using reported primers  (21)  and the PowerUp SYBR Green Master Mix according to the manufacturer's instructions (Thermo Fisher). Reactions were performed in triplicates, with glyceraldehyde-3-phosphate dehydrogenase (GAPDH) as the internal control. Amplification, data acquisition, and analysis were carried out using the LightCycler 480 Software (Roche, Mannheim, Germany).
MicroRNA Microarray Analysis Confluent HNECs in 12-well plates were stimulated with medium or P1 (clade B, 125 mM) for 6 h at 37°C. Total RNA was extracted using Trizol. Before analysis, lfTSLP RNA upregulation was confirmed by qPCR as described above and RNA quality was assessed with Agilent 2100 bioanalyzer according to the manufacturer's instructions (Agilent Technologies). Three untreated and treated paired samples from three independent experiments were analyzed by GeneChip miRNA 4. 0 arrays (Affymetrix, Thermo Fisher) containing probes for 2,578 human mature microRNAs and 2,025 premature microRNAs (https://assets. thermofisher. com/TFS-Assets/LSG/brochures/ miRNA_4-0_and_4-1_datasheet. pdf). Potential microRNA targets were analyzed with the Ingenuity Pathway Analysis (IPA) software (Qiagen).
Specific labeling was quantified by flow cytometry with a Guava EasyCyte flow cytometer (Merck-Millipore), and analyzed with the dedicated InCyte software, using the following strategy: CD20+ B cells were first gated and cells double positive for OVA-FITC+ and APC-conjugated anti-IgA or anti-IgG were determined as OVA-IgA or IgG-specific Bcells, respectively.
ACKNOWLEDGMENTS The authors wish to thank  Clotilde Ramandriapita ,  Cochin Institute , for helpful discussion about calcium measurements and  Thomas Guilbert  from  IMAGIC platform at Cochin Institute  for calcium measurement experiments and their analyses. This study was supported by grants from l 'Agence Nationale de Recherches sur le Sida et les Heṕatites Virales (ANRS)  ( AO2015-2-17046 ) and from the  Fondation pour la Recherche Medicale  (Grant : « Equipe FRM ») to MB. LX was supported by the  China Scholarship Council.
Primer design Multiple forward and reverse oligonucleotide primers were designed to PCR-amplify specific loci from the cob, nad1 and cox1 mitochondrial genes of E. multilocularis, using the Primer3 software (http://primer3. ut. ee/). Primers previously reported by Nakao et al. [11]  and Trachsel et al. [27]  were also included. We selected four highly polymorphic regions (344 to 409 nucleotide sites) to be able to identify multiple haplotypes of E. multilocularis. The location of primers and target regions are shown in S1 Appendix. Illumina adapters were added to the selected primers, obtaining four forward and four reverse primers per locus with 0-3 N's included between the adapter and the primer-binding region  [24]. The primer design was as follows: 5'-Illumina adapter sequence-0-3N's-Primer binding regions -3'.
PCR products were purified with AMPure XP Magnetic Beads (1X) (Beckman Coulter, Inc. ), following the manufacturer's recommended protocol. Illumina indices and P5/P7 sequencing tags (Oligonucleotide sequences 2016 Illumina, Inc. ) were then added to the PCR amplicons. The P5/P7 tags were combined to make up unique forward/reverse barcode combinations to identify individual samples. The following PCR conditions were used: 5 μL of KAPA HiFi HotStart Fidelity Buffer (5x) (KAPA Biosystems, USA), 1. 25 μL of Forward Primer (S501-S520) (10 μM), 1. 25 μL of Reverse Primer (N701-N726) (10 μM), 0. 75 μL of dNTPs (10 mM), 0. 5 μL KAPA HiFi HotStart Polymerase (0. 5 U), 13. 25 μL of ddH2O, and 3 μL of first-round clean PCR product as template. The thermocycling parameters were: 98˚C for 45s, followed by nine cycles of 98˚C for 20s, 63˚C for 20s, 72˚C for 2 min.
Bioinformatic analysis Sequence data were analyzed using the open-source R package Dada2, pipeline version 1. 8  [28]  and the application Cutadapt 2. 10  [29]. Samples were automatically demultiplexed with the MiSeq, based on the supplied index combinations. Cutadapt was used on the raw pairedend reads to detect and trim off regions matching the primer sequences, discarding unmatched reads. Trimmed reads were analyzed following the Dada2 pipeline workflow, which included filtering, dereplication of identical reads, sample inference, chimera identification, merging of paired-end reads and construction of an amplicon sequence variant (ASV) table. During filtering, a maximum of 2 and 5 expected errors, predicted by the quality scores of sequences, were allowed for the forward and reverse reads, respectively, discarding reads shorter than 200 bp according to the length of the amplicon expected  [28].
Detailed information regarding the analysis pipeline can be found at www. nemabiome. ca. For haplotype assignment, ASVs sequences were aligned in Geneious 10. 0. 9 (Biomatters Ltd, New Zealand) and compared with Echinococcus spp. reference sequences available in the GenBank database, using the Nucleotide BLAST tool (https://blast. ncbi. nlm. nih. gov/Blast. cgi). The proportion of ASVs per sample at each locus was calculated by dividing the number of raw reads per ASV by the total number of reads per sample. ASVs with a proportion of < 0. 05% per sample were considered as trace amplicon contamination  [24]. Results of each locus were concatenated to identify the final haplotype, and their final relative proportion in each sample corresponds to the mean of the proportion at all loci. The identity of the concatenated sequences was confirmed by Sanger-sequencing the full length of cob, cox1, and nad2 genes of individual worms from the same hosts, using primers and PCR conditions reported by Nakao et al.
The Em ECA haplotype was the most frequent in Alberta, with a prevalence of 92. 1% (95% CI 78. 6-98. 3) in coyotes, and 100% (95% CI 83. 2-100) in foxes. In coyotes from British Columbia, the Em BC1 was the most frequent, with a prevalence of 75% (3/4), and in coyotes from Saskatchewan, the most prevalent was Em ESK2 founded in 100% of samples (5/5). The prevalence and relative abundance of each haplotype are summarized in Table  2. New generated sequences have been submitted to GenBank (Accession numbers: MW591188-MW591189, MW602654-MW602657).
Data on both phenoxyethanol and phenoxyacetic acid from ToxCast and the PubChem database were evaluated. This showed that both substances exhibited very little biological activity in the available assays. To identify a PoD to use in the risk assessment, HTTr data were generated in 3 cell lines (HepRG, HepG2 and MCF-7 cells) and a no-observed-transcriptional-effect level (NOTEL) was calculated (see Section 3. 4. 2. ). The exposure values, PoDs and resulting bioactivity exposure ratios are presented in Table  1. A major limitation of the data available at the time of the workshop was the lack of HTTr data on phenoxyacetic acid, or confirmation that this metabolite was generated in the bioactivity assays performed. It was therefore not possible arrive at a conclusion for this case study. The challenges associated with this case study were definition of a BER that would be considered low risk, and characterising the uncertainty, especially concerning the range of biological activities and hence potential toxicities that were covered by the limited set of cell lines (three in total) used in the HTTr experiments.
Red line = Plasma C max free (μM); pink band = uncertainty band in plasma level prediction. 1 = IL1β+TNFα+IFNγ; 2 = IL1β+TNFα+IFNγ+TGFβ. BERs calculated to be between 2500 and 38000. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article. ) case study used any pre-existing animal data (thus emulating the 'animal free' development of a novel molecule) and did not attempt to predict/interpret adverse effects in animals.
The common tools and overall approach used to illustrate the application and integration of NAMs for the evaluation of systemic effects for two cosmetic ingredients across both case studies are described in Fig. 3 ; details for each of the workflow components are further outlined in the sections below. For both case studies, ToxCast data were available. These data were used in the phenoxyethanol case study, but not considered in the coumarin case because the case study authors took the decision to emulate the development of a new cosmetic ingredient, where no ToxCast data would be available. Instead, coumarin was evaluated using in vitro pharmacological profiling was performed (using the SafetyScreen44™ panel  (Bowes et al. , 2012) ) and the BioMap Diversity 8 Panel to characterize effects relevant to safety pharmacology and inflammatory disease  (Houck et al.
One limitation in both systemic case studies was that the topic of the case study (the chemical of interest) was likely to be represented in the dataset used to inform the knowledge-based system that was applied to predict metabolic products (Meteor Nexus version 3. 1. 0 (Lhasa Ltd. ). It will therefore be helpful to conduct further case studies on novel chemistries, to assess the performance as well as the efficiency of the approach used, and to better address aspects of uncertainty. It was also highlighted that beyond more case studies, more in silico efforts are needed towards predicting dermal penetration and metabolism.
These types of limitations can be overcome with adequate access to examples of NGRA and training materials. Understanding and acknowledging the limitations regarding animal models and traditional approaches to risk assessment are also critical so that in the future, NAMs may improve accuracy and increase confidence by providing a more complete understanding of the response to a xenobiotic. Defining acceptable levels of confidence prior to data generation in NGRA approaches is rarely straightforward. These approaches should use existing information and, therefore, directly depend on the quality of the databases used for hazard characterization and on the accuracy of exposure estimates. In addition, when filling data gaps, using an iterative approach also entails using various methodologies bearing their specific intrinsic errors, and a priori confidence determination may not always be exhaustive.
Workshop participants indicated that this framework should be nonprescriptive, guided, and context-driven and should outline the basic components deemed essential to gather the data required for decisionmaking. This new framework would most likely be inspired by the SEURAT-1 ab initio workflow and, to help guide risk assessors, would expand the various steps of this workflow by proposing relevant NAMs at each step of the iterative process, and crucially the decision points that indicate follow up is necessary. Without being prescriptive, the new NGRA framework would nonetheless need to provide an extensive coverage of the tools and approaches helpful for data mining, data generation, traditional and novel dataset integration, as well as propose an intuitive user interface designed specifically to meet the needs of safety assessors.
The stained slides were then unmounted and resin was removed, and then trypsin was deposited on the ROI using a piezo chemical inkjet printer. The digested ROI was then subjected to liquid junction peptide (A) Histopathological data obtained from immunocytochemistry performed with anti-P53 on tissue sections of sentinel nodes (SNs), either healthy (Aa) or cancerous (Ab, Ac, and Ad), from grade I (Ab) with magnification (Ab' and Ab''), grade II (Ac) with magnification (Ac'), and grade III (Ad) with magnification (Ad'). Similarly, results were obtained with their corresponding endometrial tissue, either healthy (Ae) or cancerous (Af, Ag, and Ah), at grade I (Af) with magnification (Af' and Af''), grade II (Ag) with magnification (Ag'), and grade III (Ah) with magnification (Ah'). See also IHC images in the Supplemental information).
Shotgun proteomics of EC Proteins from the 12 samples (normal and grades I-III) were extracted and subjected to shotgun proteomics analyses. 1,280 proteins showed a significant difference in expression level. After filtering proteins based on a minimum number of values in at least one of the four defined groups (2/3 of valid values), 913 proteins were obtained (Data S3). According to the Venn diagram, 11 proteins were specific to healthy endometrial tissue, 24 to grade I EC, 14 to grade II, and 19 for grade III (Figure  3D ; Table  S3 ). Moreover, principal-component analyses (PCAs) revealed a clear separation between the different grades and healthy endometrial tissue (Figure  3E ). The volcano plot associated with the heatmap confirmed the presence of 2 clusters, i. e. , a cluster representative of normal endometrial tissue and cluster 2 related to EC (Figure  3F ).
Mutations Several studies have evaluated genetic mutation frequencies in individuals with EC of different tumor grades. 31 In this context, we sought to determine whether these mutations can be translated and detected in proteins. For that purpose, we used a human database combined with the XMan v. 2 database. 32 This database contains information about mutated peptides that can be found in some cancers, extracted from the COSMIC database. Sixty-six mutated peptides were identified (Data S4). Among the proteins from which mutated peptides were identified, we retrieved collagen alpha 1, histones, laminin 1, myosin 9, HDGF, CAP-1, fibrinogen beta unit, tenascin, PTBP1, actin, hemoglobin subunits, integrin beta 2, ACTBL, SRP-14, annexin 6, TMP2, HCLS1, and lactotransferrin (Data S4). Laminin subunit alpha-1 mutated peptide (Figure  7A ) is only detected in EC grade II tissue, and HDGF protein is identified in SLN grade I (Data S4).
Ghost proteins 4] [35] [36] [37]  From our proteomics data, 36 alternative proteins were identified, with more than 80% derived from non-coding RNA (ncRNA), and 10% of the mRNA coding for RefProt is derived from the 5 0 UTR, 11% from the 3 0 UTR, and 3% from a shift in the CDS (coding sequence) (Data S5). Eleven are common to all tissues (Data S5). Six are common to all grades of sentinel nodes and grade II of EC tissues (Data S5). Only Alt-RBKS, Alt-LOC100128398, Alt-RP11-193H5. 1, Alt-CTA-212A2. 3, and Alt-HNRNPA1P58 are not expressed in normal endometrial tissue. Alt-CTA-212A2. 3, Alt-HNRNPA1P58, Alt-SLC13A1, and Alt-AP002884. 2 are absent in normal lymph nodes (Data S5). A heatmap of the different ghost proteins demonstrates the presence of 7 alternative proteins in sentinel nodes. Alt-HMGN2P3 and Alt-CACUL1 are overexpressed in grade II and III SLNs.
A randomized number was assigned to everyone. This clinical study (Sentirad-1502, EudraCT: 2015-001732-38): Randomized study comparing sentinel node (SN) policy to current French initial staging protocols in early-stage endometrial carcinomas at intermediate and high risk of recurrence is supported by the French cancer clinical research projects funding program 2014 (National Cancer Institute, INCa). The endometrioid and sentinel nodes biopsies were obtained from patients of the Centre Oscar Lambret (Lille, France). All experiments were approved by the local Ethics Committee (CPP Nord-Ouest I on July 20th, 2015, CPP 03/008/2015) in accordance with the French and European legislation on this topic. The study complies with the MR004 reference methodology adopted by the French Data Protection Authority (Paris, France), and we checked that patients did not object to the use of their data and biological samples for research purposes.
QUANTIFICATION AND STATISTICAL ANALYSIS Data interrogation and analyses All MS data were processed with MaxQuant 51,52 (Version 1. 5. 6. 5) using the Andromeda 55 search engine. The proteins were identified by searching MS and MS/MS data against the Decoy version of the complete proteome for Homo sapiens in the UniProt database (Release March 2017, 70941 entries) combined with 262 commonly detected contaminants. Trypsin specificity was used for digestion mode, with N-terminal acetylation and methionine oxidation selected as a variable modification. We allowed up to two missed cleavages. Initial mass accuracy of 6 ppm was selected for MS spectra, and the MS/MS tolerance was set to 20 ppm for the HCD data. For the identification parameters, FDR at the peptide spectrum matches (PSM) and protein level was set to 1%, and a minimum of 2 peptides per protein in which 1 was unique.