dataesr/scientific-paragraphs-categorization huggingface dataset:
785907  ( Human Brain  Project  SGA2 ). This study was supported by funding to the  Blue Brain Project , a research center of the E ´cole polytechnique federale de Lausanne (EPFL), from the  Swiss government's ETH Board of the Swiss Federal Institutes of Technology. SD-B was funded by  NIH  grants  U24EB028998 ,  U01EB017695  and  2R01DC012947-06A1 , and  New York State  grant  DOH01-C32250GG-3450000. PG was supported by the  Wellcome Trust  ( 212941 ,  101445 ). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Neurofeedback group The Mensia Koala™ medical device is composed of a software for personalized brain rehabilitation at home Training ("ADHD@Home NFT v1. 1") connected to an EEG amplifier and to an EEG cap. A baseline assessment starts every NF session; the data acquired on the tablet is automatically synchronized with a cloud server in order to make the personalized brain rehabilitation data retrievable on a secured web portal ("ADHD@Home Follow-Up v1. 1") (see Fig. 2 ). The software is used to record data from 8 AgCl scalp electrodes located at standard 10-20 locations (Fpz, Fz, F3, F4, Cz, C3, C4, and Pz) referenced and grounded to the left and right earlobes, respectively. The signals are amplified and digitalized over 24 bits 512 times per seconds. Pre-amplification analogue filters are designed to prevent aliasing so that frequency response of the acquisition is mostly flat between 0.
The SQI is calibrated with data acquired in the clinic under expert supervision thereby setting the level of quality desired for sessions recorded in the home. The definition of typical EEG frequency bands is personalized to account for the discrepancies in the subjects' brain maturation within our paediatric population. The individualized alpha peak frequency (iAPF) is defined as the maximum power value between 7 and 13 Hz at electrode Pz and used to define theta (iAPF-5 to iAPF-1 Hz), beta (iAPF+ 3 to iAPF-5 Hz), and SMR (iAPF+ 2 to iAPF+ 5 Hz). A qEEG assessment is first completed for all patients in order to calibrate the SQI, the iAPF, and determine the subject's EEG profile. A theta/beta ratio (TBR) exceeding 4. 5 is considered significant  [37]  (NCT02251743). During the initiation visit, the clinician presents the system and the neurofeedback application to the patient and his parents and supervises the first "discovery" neurofeedback training session.
ADHD@Home NF integrates algorithms for the identification of artefacts -non-EEG signals such as head movements, muscular contractions, blinks -in order to guarantee that personalized brain rehabilitation is performed based on clean brain signals. Artefacts interrupt the real time feedback of the software if they cannot be corrected sufficiently by the implemented artefact correction algorithms; this is displayed on the game by a cloud masking the sun or a changing background colour.
Analyses of the NF subgroups: In the NFT subgroup from the PP population, comparisons will be performed on the efficacy and safety data as following: - These groups are defined using the longitudinal EEG data collected by the NEWROFEED RCT data and a listing of patients in each group will be provided by Mensia Technologies. The necessary details to replicate the identification of the exact same sub-populations can be obtained from the promoter. Another comparison will be performed between Improvers versus non-improvers: an improver is a patient showing a reduction of the total clinician ADHD RS score of ≥25% from baseline.
3) The adequate protocol is selected based on the computed neuromarker. First, iAPF bands are prefered because it has been reported that the correlation between the theta activity and the core symptoms of ADHD (ADHD-RS) was stronger when the frequency band definitions was corrected for iAPF  [47]. This is particularly relevant for an ADHD pediatric population right within the age range affected by a pathophysiological brain maturation  [48, 49]. Second, the NF protocol (SMR or TBR) is personalized in each child based on his EEG profile. The EEG phenotype is represented with the TBR because it was found to relate to clinical scales of ADHD as well as performance on executive function tests  [50]. Despite failing at being used as a diagnostic neuromarker for ADHD  [16, 51] , it is a promising prognosis marker and has already reportedly being used as such (NCT02251743;  [37] ).
The fact that Mensia Koala can be used at home is also believed to contribute to its effectiveness mostly because the sessions occur in a more ecological environment, which could enhance the transfer of learned skills to real life situations. To maintain treatment quality in this context, data recorded at home is sent to a secured web portal offering remote monitoring of sessions compliance, quality, and performance (scores and neuromarkers). Several information are accessible through the interface in order to follow the patient progression during the treatment: alerts and errors logged by the application during the NF sessions at-home, a library with all sessions' report generated during the study accessible for consultation or download, a statistics section with the evolution of neuromarkers and scores across sessions.
| Study design This was an analysis of data pooled from AbbVie-sponsored, prospective, observational studies conducted at 289 sites in 13 countries: Austria (NCT02582658), Belgium (NCT02581163), Canada (NCT02581189), Colombia (NCT02851069), France (NCT02618928), Germany (NCT02615145), Greece (NCT02725866), Hungary (NCT02636608), Ireland (NCT02582671), Israel (NCT02803138), Kuwait (NCT02798315), Poland (NCT02640547) and Romania (NCT02807402). In some countries, the studies are still ongoing. All eligible patients were followed from treatment initiation until 12 weeks after the end of treatment (EOT) (or until premature discontinuation, or in accordance with local clinical practice). Data were recorded in English by each participating centre via a centralized electronic data capture system using web-based case report forms (eCRF).
Comedication use during the DAA-treatment period and changes in comedication management were summarized descriptively for the safety population. Multiple treatments were possible per patient. Patients reporting the use of more than 1 comedication for a given drug class or treatment management profile were counted only once for that combination. All statistical analyses were conducted by Prometris GmbH (Mannheim, Germany) using the SAS ® software package (version 9. 4; SAS Institute Inc. , Cary, NC, USA).
| RE SULTS This pooled analysis included patient-level data from 289 sites. Of these, 98% were based in urban locations and most sites were either academic or university hospitals (39%), or private practices or hospitals (33%) (Figure  S1A ). Most principal investigators at each site were either hepatologists (69%) and/or gastroenterologists (53%) (Figure  S1B ). In terms of patient visits per month, 19% of sites saw <25 HCV-infected patients and 37% saw between 25 and 50 HCVinfected patients. The date of the first patient visit was 6 October 2015. As of 19 February 2018, 4088 patients were enrolled in this study; 238 patients were excluded, and 3850 met the criteria for inclusion in the safety population. One GT4-infected patient from the safety population who had unconfirmed chronic HCV infection was excluded from the core and CPSFU populations.
Patients screening was also completed with hospital informatics database. Patients were enrolled by their specialist in charge. Inclusion criteria were an age ≥ 18 years, being affiliated to national health insurance (therefore having vaccines for free) and having an autoimmune/inflammatory disease with an ongoing biological therapy between April and September 2015. These dates were chosen accordingly to the flu epidemic period and related vaccination campaign in La Reunion and South hemisphere. An exclusion criterion was the refusal of the patient to participate.
Data collection and intervention The following data were collected between December 2015 and August 2016 in medical files from hospital and from patients' general practitioner records: demographics, medical history, type of autoimmune/inflammatory disease and related treatments including immunosuppressive therapy and past/current biological therapies, vaccination status for influenza during 2015 epidemic season and pneumococcal vaccine uptake in the 5 previous years. Other risk factors for seasonal influenza vaccine uptake were listed, which at the time of the study were defined as follow by the 2014 French Health authority recommendations: age ≥65, chronic lung disease, chronic cardiac failure, chronic kidney failure, chronic liver disease, immune deficiency, morbid obesity, diabetes, pregnancy  [10].
Statistical analysis Qualitative variables were expressed as percentages, quantitative variables as means and standard deviation (SD). Normality of the data was assessed using the Shapiro-Wilk test and homoscedasticity using the Levene's test. Comparisons of percentages were performed with the Chi2 test or the Fisher's exact test, as appropriate. Comparison analyses of continuous variables were performed with Student t-test or Mann-Whitney's test. Flu and pneumococcal vaccine uptake determinants were studied separately, by bivariate analysis. To assess independent determinants of vaccine uptake, multivariate analyses by logistic regression were performed. Variables with a p-value <0. 2 at the bivariate analysis were included in the models, and selected by backward stepwise selection procedure (removal criteria: p>0.
Generation of Stable Breast Cancer Cell Lines Expressing mNeptune-TK Fusion Protein under the Control of ALDH1A1 Promoter Based on results from Aldefluor assay and transcriptomic analysis, we designed a modular assembling construct using ALDH1A1 promoter to drive the expression of the mNeptunethymidine kinase fused protein (Figure  2D ). We first tested the efficiency of different sizes of ALDH1A1 promoter around 500, 900, and 1300 bp (data not shown). The size of 1300 bp was chosen to reflect more properly ALDH1A1 expression. Cells were transfected and selected for G418 resistance. mNeptune high cells were then sorted by FACS and plated in FBS containing culture media. Interestingly, mNeptune high cells gave rise to a heterogeneous population with basal level mNeptune high cells and mNeptune neg cells.
In these cell lines, we could not observe any expression of mNeptune protein. It is possible that ALDH1A1 promoter activity was not strong enough to induce mNeptune expression in these cells. Indeed, no activity of ALDH was measured by Aldefluor in T47-D cells (data not shown, negative control used by Stemcell Technologies) and ALDH1A3 is the major isoform expressed in MDA-MB-468 and the ALDH isoform responsible for Aldefluor activity. [21] These last observations highlight that as any CSC markers, pALDH1A1:mNeptune is not universal. Interestingly, the amount of mNeptune high cells was proportional with Aldefluor-positive cells (SUM159PT 2. 23% ± 0. 97; MDA-MB-231 2. 57% ± 1. 11; 4T1 12. 01% ± 2. 06; MCF-7 2. 93% ± 0. 42) (Figure  S2C , Supporting Information). As described earlier, ALDH1 enzymatic activity implies several isoforms including ALDH1A1.
Moreover, for the first time ever, we also tracked cells under fluorescent microscope over 5 days of culture. This setup allowed us to observe the light up of mNeptune high cells from mNeptune neg cells in live imaging (Video S2, Supporting Information). All together, these data provide evidences that cells with high ALDH1A1 promoter activity play a role in the resistance to anticancer treatment (radiotherapy and chemotherapy), they also highlight the usefulness of our reporter to track, quantify, and study CSC behaviors in vitro as well as in vivo.
Acknowledgements The authors thank the  Flow Cytometry Core facility  of the  Bio Imaging Center of Lille (BICeL) , which is a shared resource of  INSERM/CHRU of Lille , and particularly  Nathalie Jouy  and  Emilie Floquet  for their help with the FACS experiments. J. B. D. was supported by a grant fellowship from the  ARC  and IRCL charities. The authors thank the  UMR 8199 LIGAN-PM Genomics platform (Lille, France) , which belongs to the " Federation de Recherche" 3508 Labex EGID (European Genomics Institute for Diabetes ;  ANR-10-LABX-46 ) and was supported by the  ANR   Equipex 2010 session  ( ANR-10-EQPX-07-01 ; " LIGAN-PM "). The  LIGAN-PM Genomics platform (Lille, France)  is also supported by the  FEDER  and the  Region Hauts de France. This work was supported by the  INCa  ( French Cancer National Institute) , Grant number  ARC_INCa_LNCC_8068 , by  Ligue contre le Cancer-Septentrion comittee , by the  SIRIC ONCOLille , by " Cancer du sein-Parlons-en!" charity "Pink Ruban " award, and by  GEFLUC  charity.
The series of images are post-processed using VIC-3D software package. 29 3D DIC displacement data is converted into strain values with λ 1 the stretching ratio in the tensile direction, λ 2 and λ 3 are the transversal stretching ratios in the directions of the sample width and thickness respectively. More details on the choice of DIC parameters are provided in ref. The transversal and longitudinal strains are homogeneous in the center of the sample and significantly decrease close to the clamping zones (Figure  1c ). The strain fields in both front and side surfaces are obtained from a region of interest (ROI) in the central part of the sample. The true stress is defined as the ratio between the applied force F and the specimen cross section: 𝜎 𝑇 = 𝐹 𝐿 0 𝑒 0 λ 2 λ 3 (1) where L 0 is the initial length and e 0 the initial width.
Arrows indicate deviation between swelling and DIC methods. Corrections to measure Qc orr using equation 12 can only be applied for specimen cyclically stretched, i. e. for which permanent volumetric strain is measured. Hence, such method is not applicable for specimen stretched up to failure (data at highest stretching ratios in figure  8a ). DSC thermoporosimetry is used to provide an analyse of the size of damaged domains independently of previously described swelling experiments. Such method is based on the principle that solvent molecules crystallized in a rubber matrix are constrained to small volumes and form only relatively small crystallites. Owing to a decrease of the chemical potential of solvent molecules in polymer solution  47  , they exhibit melting temperature depression. Crystallized swollen EPDM previously stretched at different λ are heated to access the melting behaviour as shown in Figure  9.
coli F54, an O18:K1 human fecal isolate sharing many virulence genes found in ExPEC from neonatal meningitis  [55]. The genome of QT598 contains five SPATE-encoding sequences (Figure  1 ). Two of the SPATE genes, tsh and a novel SPATE which we have called sha (for serineprotease hemaglutinin autotransporter), are located on a ColV-type plasmid (pEC598). The vat gene was also identified on a genomic island. Finally, a genomic region was identified containing two distinct SPATE-encoding sequences in close proximity to each other, which we have named tagB and tagC (for tandem autotransporter genes B and C). The tsh open reading frame on plasmid pEC598 shares highest identity to tsh from plasmid pACN001-B (accession number KC853435. 1) [56]  and similar sequences in the NCBI database, differing in only 1 nucleotide, a Gly 1177 -Ser 1177 substitution.
Interestingly, the highly conserved SPATE cleavage site of two consecutive asparagines "EVNNLNK", found between the passenger domain and the β-barrel of most SPATEs  [57] , is absent in Sha. Sha is more closely related to Tsh and Vat proteins than to other SPATEs (Figure  2 ). The global alignment of Sha with Tsh QT598 has 43% identity/56% similarity with 237 gaps, whereas the global alignment of Sha with Vat QT598 is 38% identity/52% similarity with 252 gaps. The vat gene from QT598 is present on a genomic island that includes the vatX regulatory gene, and is located between the E. coli conserved genes yagU and proA adjacent to the thrW-tRNA gene (Figure  1 ). This is a conserved insertion site for vat-encoding genomic islands  [58]. Vat QT598 is a predicted 1376 aa precursor with a single substitution (His 534 -Arg 534 ) compared to Vat from UPEC strain CFT073 (accession number AAN78874.
1). At least 41 predicted Vat protein sequences from different E. coli strains share an identical predicted Vat QT598 sequence, indicating it is a common allelic variant of Vat (Supplemental Table  2 ). These entries include sequences from strains isolated from fecal samples and infections of poultry and two human UTIs that are labeled as "Hbp" or "SepA" proteins in the databank. The two new chromosomal-encoded SPATE genes were named tagB and tagC, Tandem autotransporter genes (Tag) because of their tandem co-localization in the genome of QT598 as well as in various other E. coli strains such as: multidrug-resistant CTX-M-15producing ST131 isolate E. coli JJ1886 (Accession number CP006784), porcine E. coli PCN033 (Accession number CP006632), and E. coli CI5 (Accession number CP011018). The tagB and tagC SPATE-encoding genes from QT598 are located on a genomic island between the E.
The analysis involved 17 amino acid sequences. All positions containing gaps and missing data were eliminated. There were a total of 723 positions in the final dataset. Evolutionary analyses were conducted in MEGA6  [85]. Multiple sequence alignment was performed by Clustal W, and the tree was constructed using the Mega6 software with PhyML/bootstrapping. A cluster of cytotoxic SPATEs (class 1) comprise the green branches, while immunomodulator SPATEs (class 2) are in blue branches. DNA regions encoding SPATE protein sequences are available in NCBI database as follows: EspC, GenBank Accession No. AAC44731, TagB and TagC, MH899681; EspP, NP_052685; SigA, AF200692; Pet, SJK83553; Sat, AAG30168; EatA, CAI79539, SepA, Z48219; Pic, ALT57188; Boa, AAW66606; EaaA, AAF63237; Sha, MH899684; Vat, MH899682; TleA, KF494347; Tsh/Hbp, MH899683.
Error bars represent standard errors of the means (* p < 0. 05, **p < 0. 01, ***p < 0. 001 compared to empty vector using one-way ANOVA). b. Giemsa stain of the 5637 bladder cell line infected with a tagB expressing clone after 2 h demonstrates an aggregative adherence pattern to bladder cells (arrow head). A similar pattern was found for tagC and sha expressing clones (not shown here). Bar represents 50 µm. Clones of E. coli fim-negative strain ORN172 expressing SPATE proteins were grown at different temperatures (25°C, 30°C, 37°C, and 42°C) in polystyrene plate wells for 48 h and then stained with crystal violet. Remaining crystal violet after washing with acetone was measured as absorbance at 595 nm. Data are the means of three independent experiments, and error bars represent standard errors of the means.
Bioinformatic analysis Presence of AT sequences in silico was determined in E. coli genomes available from the NCBI database by Blast analyses using the tagB, tagC and sha sequences from the QT598 genome. Phylogenetic analyses of the predicted full-length passenger domain sequence of each SPATE were performed by Clustal W, and the phylogenetic tree was constructed using PhyML/bootstrapping in MEGA6  [85]. The Conserved Domain Database (CDD) and SignalP were used to predict the three domains of the AT proteins  [86, 87]. The I-TASSER server and chimera were used for three-dimensional (3D) structure  [65, 66]  visualization of the predicted Sha AT protein, and the Protein Data Bank (PDB) server was used to obtain the predicted 3-D structure of the Sha protein for comparison to Hbp  [88]. Amino acid sequence comparisons were performed using Clone Manager Suite 7 (SciED, Denver, CO, USA) and online BLAST programs available from the National Center for Biotechnology Information (NCBI).
Construction of plasmids AT-encoding genes were amplified by PCR using specific primers (listed in Supplemental Table  2 ). The tagB, tagC, sha, vat, and tsh genes were amplified from QT598. The espC gene was amplified from EPEC strain E2348/69 (Accession number AF297061)  [60]. To clone tagB, tagC, espC, sha, tsh, and vat, PCR products contained 15 bp extensions homologous to the pBCsk+ multi-cloning site. Linearized pBCsk+ digested with XhoI and BamHI was used to clone inserts by fusion reaction with the Quick-fusion cloning kit (Biotool, Houston, TX, USA). All the recombinant plasmids (pIJ548, pIJ549, pIJ550, pIJ551, pIJ552, pIJ553) were first transformed into E. coli DH5α then the plasmids were extracted using a Miniprep kit according to the manufacturer's recommendations (Bio Basic) and transformed into E.
Acknowledgments We thank  E. Bonneil , manager at the proteomics platform of  Université de Montréal  for assistance with mass spectrometry and peptide analysis and  Y. Lopez de Los Santos  for assistance for 3-D model prediction comparison of autotransporters. Funding for this work was supported by  NSERC   Canada Discovery Grants   2014-06622  and  2019-06642  (C. M. D. ) and a collaborative ACIP grant from the  Institut Pasteur International Network  (to A. T. , S. G. -R. , and C. M. D).
This effect will also likely vary within the urban area as a function of land use (LU), which refers to the function to which a land parcel is dedicated. For example, the effect may be more pronounced in fine-grained, highly heterogeneous residential areas than in coarse-grained, more homogeneous commercial ones  (Herold et al. , 2002; Zhao and Sander, 2018). Advanced technology allows the production of urban LC maps with a very fine (i. e. , ≤1 m) resolution (e. g. ,  Zhou and Troy, 2008). Yet, such fine resolution LC maps are not readily available for all locations  (Gong et al. , 2019) , and the resources needed to produce them may not be affordable for every ES mapping project, especially in low-income countries and outside academic institutions. When available, detailed maps often need to be aggregated to coarser resolution, due, amongst several reasons, to computational limitations or constraints on integrating them with other datasets  (Raj et al.
Data Analysis Analyses of landcover (LC) and ecosystem services (ES) maps were performed for each landscape (urban districts as well as residential and commercial zones) at each resolution. LC structure was quantified with three class-level landscape metrics, using FRAGSTATS 4. 2 (McGarigal et al. , 2012) : proportion of landscape, mean patch size and clumpiness index. Patches were delineated using the 8 cells neighbor rule. As it is based on cell adjacency, calculating the clumpiness index is sensitive to cell size: for identical LC maps (in term of structure), the clumpiness index value decreases as cell size increases, because the ratio of interior to border cells decreases  (McGarigal, 2015). To isolate the real changes in LC structure from this calculation bias, each of the coarser resolution LC maps was resampled (cell-center method) to a spatial resolution of 1 m before computing the clumpiness index.
This resampling clipped larger cells into several smaller cells, but had no effect on LC structure per se. For the ES maps, the mean ES component quantity/m 2 of the landscape (ES quantity) was computed for carbon storage, and for cooling and pollination potential supply, demand and flow. Results obtained at 1 m resolution were considered to be the reference against which results from the coarser resolution maps were compared. The effect of data resolution on LC and ES metrics was calculated as the percentage of variation in the value of the metric at a coarser resolution compared to 1 m resolution, following Equation (1): Metric variation = (V ir -V io )/V io * 100 (1) where V ir = value of metric i at resolution r, and V io = value of metric i at the original resolution of 1 m. In addition to the three landscape metrics described above, the total percentage of cells that changed LC class with aggregation (cell-by-cell analysis) was calculated in ArcMap.