dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgements. Research for this paper was made possible by grants from the  French National Cancer Institute  ( INCa   2014-123 ) and the  Canadian Institutes of Health Research  ( MOP-133687 ). We would like to thank all the clinicians and scientists who gave us access to their teleconferences and who agreed to be interviewed, in some cases repeatedly. In particular, we would like to express our gratitude to Unicancer, the French hospital federation specialized in cancer care, without whose help we could not have completed this paper. Clinical researchers from the  SAFIR 02 clinical trial (supported by 'Fondation ARC ') also deserve special mention: their activities provided us with much of the material used in this paper. For reasons of confidentiality, we cannot mention the name of the several other practitioners and clinical trials we investigated as part of our project.
on-farm data collection Data related to the general characteristics of the farms, type of feeding, housing, ages when pigs were moved to the different production stages, vaccination and antibiotic treatments were collected during the longitudinal follow-up (table  1 ). antibody response to Salmonella Serum samples (n=2463) were analysed to detect the presence of antibodies against Salmonella with the IDEXX Swine Salmonella Ab Test (IDEXX, Montpellier, France), which has a sensitivity of 99. 1 per cent and a specificity of 99. 4 per cent  10  when used as recommended by the manufacturer. The presence or absence of antibodies to Salmonella in the sample was determined by calculating the sample to positive control (S/P) ratio corresponding to the absorbance value at 650 nm of the sample (S) over the mean absorbance value of the positive control (P).
Survival analysis Survival analysis was used to identify the explanatory variables (collected by the questionnaire and related to PRRSV infection) which were associated with age at Salmonella seroconversion (table  1 ). The first step involved testing the difference in survival distributions between levels of each explanatory variable using the log-rank test (PROC LIFETEST, SAS V. 9. 1, SAS Institute, Cary, USA; P<0. 25). Given that the assumption of linearity in the continuous variables did not hold, all the independent variables were grouped into categories for further analysis. A Cox model (TPHREG procedure, SAS V. 9. 1) was then used to relate each variable where P<0. 25 (univariable log-rank test) to the age at seroconversion. The proportional hazards assumption for the Cox proportional hazards model was checked by examining the log-negative-log plot of the Kaplan-Meier survival function estimates and the Schoenfeld residuals versus log of time and time, respectively.
20 All the selected explanatory variables were checked for multicollinearity (chi-squared test, P<0. 05), and those most strongly associated with the outcome variable and having biological relevance were retained. The last step involved the multivariable Cox proportional hazards model, which included all the factors that had passed the first screening step (TPHREG procedure, SAS V. 9. 1). Since pigs from the same litter could not be considered as independent, a sow cluster effect was used (generalised estimating equations for population-averaged model) and the farm/herd effect was taken as fixed effect. A backward elimination procedure was used by progressively removing variables that were not significant (P>0. 05) by the likelihood ratio chi-squared test. Variables considered to be potential confounders were retained in the final model if they changed the estimates of the hazard ratios by greater than 30 per cent.
Image analysis was performed by two observers in consensus (A. N. and M. L. , with 3 and 10 years of experience in cardiac imaging, respectively) using PACS software, version 4. 7 (Telemis SA, Louvain-la-Neuve, Belgium). The ostial diameters and spatial orientation of the RIPV were assessed on multiplanar reconstructed slices, as described previously  [15]. Briefly, the maximal and minimal RIPV ostial diameters were measured on multiplanar reconstructed slices perpendicular to the RIPV centre line. The angle of the RIPV to the left-to-right axis was measured on axial transverse slices.
Statistical analysis Normally distributed variables are expressed as means ± standard deviations, and were compared using Student's t test. Non-normally distributed variables are expressed as medians (interquartile ranges), and were compared using the Mann-Whitney U test. Categorical variables are expressed as counts and percentages, and were compared using the χ 2 test (or Fisher's exact test, when needed). A P value < 0. 05 was considered statistically significant. The analyses were performed with the SPSS statistical package, version 11. 0 (SPSS Inc. , Chicago, IL, USA).
| ATP assessment Measurement of cellular ATP was performed using a bioluminescent assay (Sigma; FLAA) as per manufacturer ' s instructions. 24 hours before measurement, cells were seeded at 2 × 10 3 per well in a 96-well plate. Where shown, oligomycin (2. 5 μM) was added 10 minutes prior to lysis. After removal of media, cells were washed in PBS (pH 7. 4) and lysed in 50 μL of buffer. 100 μL of ATP assay was added to all wells before luminescence was read (BMG PHERAstar). Data were normalized to total protein per well using a BCA assay (ThermoFisher Scientific). 2. 6 | Total cell protein and cell size evaluation 1 × 10 6 trypsinized cells were washed with PBS and lysed in 60 μL of RIPA buffer for 30 minutes. Protein concentration in the cleared supernatant was determined using the BCA protein method (Thermo Fisher Scientific).
| Gene expression data Gene expression profiles of human tumors were available from a previous study, in which 186 fully genotyped PPGL were analyzed. 14, 15 The data are shown for a subset of these samples carrying germline and somatic mutations in RET (n = 19), NF1 (n = 37), VHL (n = 40) or SDHx (n = 23) genes, as well as two samples of normal adrenal medulla. HG-U133 Plus 2. 0 Affymetrix GeneChip data from this previous study are available online as ArrayExpress entry E-MTAB-733 ( http://www. ebi. ac. uk/array expre ss/ ). Gene expression profiles of wild-type and Sdhb -/-MAF and imCC (CL6 and CL8) were assessed in duplicates using the GeneChip® Mouse Gene 1. 0 ST Array. 10  Data are available as ArrayExpress entry E-MTAB-3403. Principal component analysis (PCA) and hierarchical clustering were performed using ClustVis software  16  with default settings using a gene list of 35 PGC1a target genes and metabolic enzymes.
ACKNOWLEDGMENTS We would like to thank  Professor Mark Viant  and  Dr Stefan Schade  for the use and assistance with the CASY cell counter. We thank  Professors Ed Rainger  and  David Hodson  and  Mr Nick Fine  for kindly providing reagents. KK, AT, and JG are supported by the  Paradifference Foundation , LV, CEG, and BK are supported by  Cancer Research UK  ( C42109/ A26982  and  C42109/A24891 ) and GGL holds a  Wellcome Trust Senior Fellowship  ( 104612/Z/14/Z ).
g. , the type, the size, the spacing and the orientation. To the best of our knowledge, this is the first time such results have been presented in the literature. For the realization of the tag-IDs, the letters are first drawn by using the 'text option' in the 3D modeling software such as AutoCAD 2015 or 3DS Max. After that, the letter layout in imported to the CST Microwave Studio (MWS) simulator for further electromagnetic analysis. The imported letters are placed on a 0. 5 mm thick TLX-8 substrate (ε r = 2. 55 and tan δ = 0. 0019) backed by a ground plane whose size is 4 cm × 2 cm. The size of the substrate ground plane is adjusted to obtain the RCS resonance peaks of the backscattered signals from the letters in the frequency range of 6-13 GHz. The RCS analysis approach is preferred for the letter type of tag-IDs since their relative RCS is much smaller than that of the background; and, hence, it provides more sensitivity in actual measurements to accurately detect these tags  [1, 20, 21, 27].
As shown in Figure  1 , a robust recognition of chipless alphabet tag is conceived out by using a 3-bit encoding of the recorded dual-polarized signature EM properties of the letter-tag to detect it accurately. To evaluate the effect of the changes in the geometrical properties of the tags on the robustness of its detection, we have carried out an extensive detailed analysis of the change in resonance troughs of the RCS signals with the changes in the structural properties of the letters fonts, e. g. , the type, the size, the spacing and the orientation. To the best of our knowledge, this is the first time such results have been presented in the literature. For the realization of the tag-IDs, the letters are first drawn by using the 'text option' in the 3D modeling software such as AutoCAD 2015 or 3DS Max.
) creates a signature reflection response in the backscattered RCS signal. It shows that the metallic letter actually behaves as an EM polarizer. The demonstrated diffraction principle of the metallic letters-tag in Figure  4b  is used here to suggest an efficient data encoding algorithm for the chipless-tags. If we place the three different metallic letters (e. g. , a, b and c) on a dielectric substrate, then there would be three different independent signature resonance frequencies for each letter (more details in Section 4. 1). Since the frequency signature of each letter-ID is different, the signature offers a great advantage for its fast and accurate detection by matching the frequency response characteristics to the database comprising of unique signature frequencies of each letter. In the proposed coding scheme, each bit-status would correspond to '1' or '0', respectively, depending on the presence or absence of the specific resonance frequency signature for the exposed letter-tag.
1). Since the frequency signature of each letter-ID is different, the signature offers a great advantage for its fast and accurate detection by matching the frequency response characteristics to the database comprising of unique signature frequencies of each letter. In the proposed coding scheme, each bit-status would correspond to '1' or '0', respectively, depending on the presence or absence of the specific resonance frequency signature for the exposed letter-tag. The resonance response of the pre-determined system, without the metallic letter layer, can be measured for effective and accurate detection of the tag.
Background: Influenza generates a significant societal impact on morbidity, mortality, and associated costs. The study objective was to identify factors associated with influenza-like-illness (ILI) episodes during seasonal influenza epidemics among the general population. Methods: A prospective study was conducted with the GrippeNet. fr crowdsourced cohort between 2012/13 and 2017/18. After having completed a yearly profile survey detailing socio-demographic, lifestyle and health characteristics, participants reported weekly data on symptoms. Factors associated with at least one ILI episode per influenza epidemic, using the European Centre for Disease Prevention and Control case definition, were analyzed through a conditional logistic regression model. Results: From 2012/13 to 2017/18, 6992 individuals participated at least once, and 61% of them were women (n = 4258).
GrippeNet. fr data collection GN is a crowdsourced surveillance system operating each year from November to April in mainland France since 2012. It is part of a broader European platform Influenzanet, where ten countries are involved  [15]. Individuals from the GN cohort report their influenzarelated symptoms through a dedicated website (https:// www. grippenet. fr). Consent is informed and implied through registration and voluntarily completing a profile survey. This profile survey can be updated throughout the season, and covers socio-demographic (gender, age, household composition, occupation, place of residency); lifestyle (having pets, daily contacts, daily transportation means, smoking habit); and health-related characteristics (height and weight to estimate the body mass index (BMI), chronic treatments for at least one comorbidity including asthma, diabetes, immunosuppression, heart, kidney or pulmonary diseases, influenza vaccination status for the current and past seasons, respiratory allergies)  [17, 18].
Conclusion The identification of risk factors from the general population performed in this study confirms and further completes the list of factors observed through traditional surveillance systems. These findings can help target specific communication and influenza prevention campaigns at the population level aimed at reducing the spread of the disease. Some ILI risk factors, as gender, public transport use and having pets are still debated, they should be further investigated. The ILI case definition used here is the ILI ECDC definition c Participants receiving a chronic treatment for at least one of the following diseases: asthma, diabetes, immunosuppression, heart, kidney, and pulmonary diseases. Inclusion of the gathered variable "At least one comorbidity" only in the analyses. The datasets used and/or analysed during the current study are available from the authors on reasonable request.
The same unit also controls raster scanning by moving XY piezo actuator that carries the cell sample in a Petri dish. The ion current that flows between the probing and the reference electrodes located inside the SICM pipette and in the bath, respectively (Fig. 1B ), is constantly measured by the control electronics. When the pipette vertical position (Fig. 1C , top trace) approaches the sample surface to a distance equal to ;1 radius of pipette opening, the ion current (I pip ) drops (Fig. 1C , bottom trace). This drop is used by the control DNM2 MUTATION-INDUCED CHANGES IN MORPHOLOGY AND KINETICS OF CCPS software to stop the approach and record the vertical position of Z piezo actuator as the sample height at a given imaging point. Then, the pipette is withdrawn, and the sample is moved to the next location or pixel.
Simultaneous fluorescence confocal imaging is performed by focusing a laser beam at the pipette tip  (42, 43). This provides colocalized fluorescence excitation, which is then recorded by a photomultiplier. Confocal autofocusing is achieved by vertical movement of the objective-focusing piezo actuator that is synchronized with the SICM height measurement by Z piezo actuator. This eliminates the need for numerous confocal slicing and subsequent 3-dimensional (3D) reconstruction and allows the fluorescence data to be acquired precisely from the apical membrane in a single scan (red dashed line, Fig. 1B ). SICM topographical 3D images can be shown either in 2-dimensional view with the height color coded so that the lower areas appear darker and higher areas lighter or as 3D projections. Figure  1D  shows the example of a 3D topography scan of a cell cytoplasmic membrane where the CCP can be seen as dark invagination (left panel) as well as corresponding fluorescence of clathrin light chain (CLC) a-green fluorescent protein (GFP) (right panel).
SICM instrumentation All experiments were performed using the SICM setup that is capable of better than 20 nm topographical resolution on live cells as previously reported  (45). The instrument was controlled by inhouse-written software that was also used for data acquisition and analysis. The SICM imaging head controlled by SICM scanner controller (Ionscope, Cambridge, United Kingdom) was built using P-733. 2DD XY Piezo-Nanopositioning Stage (PI, Karlsruhe, Germany) 40 mm travel (xy movement of the sample) and P-753. 21 piezo actuator (PI) 25 mm travel (z movement of pipette). Piezo stages were driven by 200 W peak-power lowvoltage PZT amplifier E-505 (PI) in capacitive sensor-controlled closed-loop using Sensor & Position Servo-Control Module E-509 (PI). The XY piezo scanner was incorporated into a heavy stainless-steel platform, which was placed onto an inverted Nikon TE2000-U microscope (Nikon, Tokyo, Japan) table spring preloaded and equipped with differential micrometers (Opto-Sigma, Santa Ana, CA, USA) for precise positioning.
spring ;7 mm above the taper. Nanopipettes were pulled from borosilicate glass (outer diameter, 1 mm; inner diameter, 0. 5 mm; Intracell, Saint Ives, United Kingdom) using a laser-based puller Model P-2000 (Sutter Instruments, Novato, CA, USA). The pipettes displayed resistances of ;400 MV (range 300-500 MV. ) and had an estimated inner diameter of 30 nm. The pipette inner diameters are estimated from the pipette resistance using a half cone angle of 3°. Pipette current was detected via an Axopatch 200B (Molecular Devices, Sunnyvale, CA, USA) using a gain of 1 mV/pA and a low-pass filter setting of 5 kHz. The internal holding voltage source of the Axopatch 200B was used to supply a DC voltage of +200 mV to the pipette. The outputs of the capacitive sensors from all 3 piezo elements were monitored using Axon Digidata 1322A (Molecular Devices) and Clampex 9.
1% and then exposed to rabbit polyclonal anti-clathrin heavy chain antibody (Abcam, Cambridge, MA, USA), rabbit polyclonal anti-caveolin 1 (Santa Cruz Biotechnology, Dallas, TX, USA), or rabbit polyclonal anti-glyceraldehyde-3-phosphate dehydrogenase antibody (Santa Cruz Biotechnology) in PBS-Tween 20 0. 1% and milk 1% overnight at 4°C. Membranes were rinsed in PBS-Tween 20 0. 1% and incubated 1 h with horseradish peroxidase-conjugated secondary antibody (anti-rabbit from Jackson ImmunoResearch, West Grove, PA, USA) in PBS-Tween 20 0. 1%. Chemiluminescence was detected using ECL Detection Kit (Merck, Darmstadt, Germany) in a G-Box Imaging System (Ozyme, Paris, France), and signal quantification was performed using ImageJ software (National Institutes of Health, Bethesda, MD, USA).
Such diaphragms that form at caveolar openings could physically prevent the SICM nanopipette from entering caveoli. Therefore, the spatial resolution of correlative SICM-FCS requires further improvement in order to make topographical imaging of caveoli possible. In order to enable better comparison of our findings with previously published observations, we also measured the uptake of fluorescently labeled Tfn and CTxB and found that it is reduced in cells with p. R465W and p. R522H. Although uptake data support our findings at individual pit level and indicate that both CME levels are reduced by these mutations, the results have to be treated with caution because a substantial proportion of Tfn is uptaken by clathrin-and dynamin-independent mechanisms. Indeed, cells transfected with GTPase-deficient K44A mutant dynamin or treated with dynamin inhibitor Dynasore, often used as a negative control, on average show only 70% reduction in uptake at best  (11, 22).
ACKNOWLEDGMENTS The authors thank  Dr. P. Novak  ( Queen Mary University of London ) for scanning software development,  Dr. Andy Rogers  ( Royal Brompton and Harefield NHS Trust ) for expertise in TEM, and  Dr. Benedict Reilly-O'Donnell  ( National Heart and Lung Institute, Department of Cardiac Medicine, Imperial College London, London, United Kingdom ) for proofreading of the manuscript. This work was supported by PhD studentship to T. A. from  Muscular Dystrophy UK  (Grant  P49914  to A. S. ),  Biotechnology and Biological Sciences Research Council (BBSRC)  funding to A. S. ( BB/M022080/1 ), the  Agence Nationale de la Recherche  (Grant  ANR-14-CE12-0009  to M. B. and  Young Researcher  Grant  ANR-14-CE12-0001-01  to S. V. ), and  British Heart Foundation (BHF)  funding for J. G. and  I.
Norovirus Quantification A microfluidic-based digital one-step RT-PCR, that allow quantification without external calibration curves was performed using primers and probes targeting the ORF1-2 region  (Polo et al. 2016 ). Positive and negative controls were included in each series, and quantification was calculated using the Poisson distribution (QuantStudio™ 3D Analysis Suite™ Cloud Software, version 3. 0. 3; ThermoFisher). The final result was expressed as RNA copies/µl.
General De Novo Assembly De novo assembly was performed with quality-controlled reads using SPAdes v. 3. 10. 1  (Bankevich et al. 2012). A variety of assembly conditions were examined but in general assembly with no error correction or read normalization yielded the largest initial contig set. Virus specific contigs were identified using Usearch  (Edgar 2010) , against a set of 1 3 39 virus family or subfamily specific protein databases and virus family specific contigs were further assembled into larger contigs using mapping of the contigs against the closest identified full genome. A penultimate consensus genome was generated from the contigs. A final check of the genome was performed by mapping all quality-controlled reads to the penultimate consensus genome and a final majority nucleotide consensus genome was generated.
Virus Family Specific De Novo Assembly All virus family-specific reads were then harvested by mapping to a comprehensive set of all sequences > 500 nt available for that family in GenBank using Bowtie2  (Langmead et al. 2012). The resulting virus family-specific reads were de novo assembled using SPAdes v. 3. 10. 1  (Bankevich et al. 2012). Contigs shorter than 500nt were removed from subsequent analysis and contigs with coverage below 10 (determined by Bowtie2 mapping) were carefully examined to avoid assembling contigs with varying coverage. Further assembly and genome checking were performed as described above.
2012; Verhoef et al. 2015). Although the SureSelect target enrichment array is designed to capture Caliciviridae sequences, these targeted sequences were still less than 1% of the total reads after capture, suggesting non-specific binding. Since the binding and wash conditions are propriety to the manufacturer and the actual bait concentrations are not provided, specificity improvements are limited. This method also allowed to identify a norovirus GIV. 1 strain. This genogroup is sporadically detected in sewage samples, and may be under-appreciated as a cause of gastroenteritis, presumably because only a small number of sequences are available in GenBank causing difficulties in primer design  (Sima et al. 2011; La Rosa et al. 2012). The two other methods also allowed to characterize some norovirus sequence, all of them being already reported in the NoroNet network  (van Beek et al.
2015; Sano et al. 2016). To access this sequence information, we need to develop reproducible, simple, fast and easy to apply methods. The viral agnostic metagenomics approach is still an expensive approach when considering the library preparation or sequencing runs, but all the steps of the methods described here can easily be performed in environmental laboratory already performing PCR analysis as it just needs a centrifuge and basic equipment. data/view/PRJEB 31600 and to Genbank with the following (temporary) accession number: from MK789654 to MK789656 for NoV GI, from MK907785 to MK907802 for NoV GII, MK726262 for NoV GIV. Open Access This article is distributed under the terms of the Creative Commons Attribution 4. 0 International License (http://creat iveco mmons. org/licen ses/by/4.
Stereochemistry of C-5 and C-6 in CR-591 (1) and CR-777 (2) The ROESY spectrum of compounds 1 and 2 supported by the 3D structures obtained from Chem3D software (ChemBio3D, Perkin Elmer, Waltham, MA, US) allowed us to determine the configuration at C-5 and C6. ROE correlations were observed for both compounds between H-6 and H-4 and between H-6 and H-8. H-9 did not correlate with H-4, H-6, and H-8. According to these data, only the conformation shown in Figure  7  accounts for the observed ROE correlations, corresponding to (4S, 5R, 6S) stereochemistry. NMR data recorded for 2 closely resemble those of compound 1. The main difference between 2 and 1 was the peptide linked to the withanolide core through C-6. According to NRM data (see NMR tables), we linked a glutathione tripeptide moiety to C-6 thanks to the HMBC correlation between the methylidene function of cysteine residue 3.