dataesr/scientific-paragraphs-categorization huggingface dataset:
The second set of measurements is performed at 2. 5 GHz. Three realistic measurement configurations are considered with different positions of the person-under-test : (i) the subject sits at 60 cm in front of the radar (TEST 1), (ii) same as (i) with body movement (TEST 2), (iii) the antenna is directed towards the back of the subject under test (TEST 3). From the measured signals, the cyclic means are computed and presented in Figure  14. Table  8  summarizes the data for the measurements taken with the radar placed in front of the person under test without movement, and with movement and on the subject's back. The amplitude of breathing is higher for measurements in front of the subject, which could be linked to the physiology and the anatomical position of the lungs in the thoracic cage.
Pixel count method At the end of the growing period (3 weeks) and before the harvesting of shoots, high resolution images of all rhizotrons were taken with a Canon 5D MkII (24megapixel full-frame) camera with 50 mm prime lens. The images were then processed with the imaging software Image-J and converted to binary, where only black ("0")andwhite("255") pixels were displayed (Fig. 2 ). The colours of the pictures were then inverted in order to obtain black roots on a white background. In the binary images, "0" (black/roots) and "255" (white/bulksoil) pixels werecountedineachhalfof the rhizotrons with the Image-J program function "pixel count". Root density in the two areas of the rhizotrons was than measured as the percentage (%) of black pixels (roots) in each half calculated from the total black pixels on the full surface.
Statistical analyses Differences in shoot biomass as well as in root density in the Ni-spiked zones among all N. caerulescens and S. media treatments were assessed through one-way ANOVA and Tukey's HSD post-hoc tests. Welch ANOVA and the Games-Howell post-hoc tests were considered when homogeneity of variance was not met. Differences in root density % between control and Ni-spiked soil zones within each treatment were assessed through Student's T test for independent samples. Correlations among Ni concentrations in the shoots and root density (pixel counts) in the Ni enriched soil were assessed through the Pearson's coefficient r. All statistical tests were performed with the program IBM SPSS statistics 24 considering a significance level of p < 0. 05.
Shoot biomass Values of shoot dry weight are shown in Fig. 3. The Plombieres (Zn) accession of N. caerulescens resulted in a higher average biomass per plant (131 mg in the Nicarbonate treatment; 129 mg in the garnierite treatment) Fig. 2  Rhizotron rooted surface at the end of the experiment: a original picture and b converted to "bits" ("o" and "255" pixels) with the program Image J in order to count black and white pixels compared to the Bergenbach (Ni) accession (47. 7 mg in the Ni-carbonate treatment; 49. 1 mg in the garnierite treatment), even if higher biomass values in the Plombieres accessions was statistical significant (p< 0. 05) only for the Ni-carbonate replicates. The two accessions of S. media had comparable biomass (Fig. 3 ). For both plant species, no significant differences in growth rates were recorded among the two different Ni treatments (Ni-carbonate and garnierite).
Acknowledgments We would like to acknowledge the  Sustain able Mineral Institute of The University of Queensland , where the experiment was conducted, for hosting  Alice Tognacchini  as vis iting PhD student and the  AMS Arbeitsmarktservice of Austria  for supporting her stay abroad during the research. We would also like to thank  Guillaume Echevarria  for providing seeds of Noccaea caerulescens. Funding Information Open access funding provided by  Uni versity of Natural Resources and Life Sciences Vienna (BOKU).
Methods All cases included in the study were histologically confirmed BCCs, SCCs or BSCs consecutively admitted and surgically excised at the seven sites in Poland: Gdansk, Gliwice, Lodz (2 sites), Rzeszow, Warsaw and Wroclaw, during a 21-year period (1999-2019). All patients were Caucasians with skin phototype between I and III, diagnosed and treated either in a public hospital or in a private practice. Information recorded was the patient's age, gender, anatomical localization of the cancer and histological diagnosis. Excision margins, the presence of lymphovascular or perineural invasion, AJCC pT stage, and the status of reexcision specimens were also documented when data was available. Study approved by Human Research Ethics Committee of the Medical University of Lodz, Poland (RNN/209/18/KE) and informed consent was obtained from all organizations the subjects' data is being sourced from.
Statistical analysis The database was anonymised before analysis. Statistical analyses were performed using the Statistical Package for the Social Sciences (SPSS version 24. 0, Inc, Chicago, IL, USA). The data were described as number and percentages for categorical variables and mean ± standard deviation (SD) or median (range) for continuous variables. Independent Student t-test was used to compare continuous variables between groups and chi-square test (or Fisher exact test) for categorical data. Multivariable logistic regression was used to examine the association between each of the variables and the sickle subphenotype with adjustment for age and sex. P values <0•05 were considered statistically signi cant. All acute clinical events correctlyrecorded in the medical les from birth ( or the beginning of follow-up) to the date of the nal evaluation (April 2017) were included in the analyses.
Cancer case ascertainment When incident cancers or deaths were reported on the annual follow-up, a staff member was sent to the home of the patient or the deceased to complete a detailed questionnaire. This process was followed by sending a team to the appropriate medical centers to gather copies of all available and relevant medical reports. All information was then reviewed by 2-3 expert physicians to verify the diagnosis of cancer or cause of death. Further, cancer cases were blindly matched to the Golestan Population-based Cancer Registry database to avoid any possible misclassifications of cancer cases. Forty participants developed primary urothelial carcinoma of the bladder, of whom 38 had provided a urine sample at enrollment. The cases were sub-categorized into muscle-invasive and non-muscleinvasive BCs, based on their documented stage of disease.
UroMuTERT assay and mutation analysis The single-plex Next-Generation Sequencing assay (UroMuTERT) was previously developed in our laboratory for the detection of lowabundance TERT promoter mutations  [17]. Briefly, UroMuTERT utilizes a single amplicon of 147 bp that was designed to cover the genomic region of the TERT promoter that contain the 2 'hotspot' C228T and C250T mutations. The detailed protocol for amplicon-based Ion Torrent Proton sequencing is provided in the Supplementary data. Variant calling was performed using our Needlestack algorithm based on negative binomial regression analysis and specifically designed for the detection of low-abundance mutations (https://github. com/IARC bioinfo/needlestack)  [21]. A p-value for being a variant (outlier from the regression) was calculated for each sample and further transformed into q-values to account for multiple hypotheses testing (Supplementary Figure  1 ).
Validation by ddPCR assay We developed droplet digital PCR (ddPCR) assays for the two most common TERT promoter mutations: C228T and C250T as well as the two other rare ones C228A and CC242-243TT (Supplementary Table  2 , Supplementary data). All samples positive after UroMuTERT analysis were run in duplicates using 10 ng of urinary DNA. Ten wild-type samples chosen at random were included as technical controls. Analysis of the ddPCR data was performed using the QuantaSoft TM Analysis Pro 1. 0. 596 software from Biorad (Supplementary Figure  2 ). The threshold representing the minimum number of positive droplets for calling a mutation was determined from the Poisson distribution of droplets in wild type and mutated cell lines and was set at 6 or 5 (Supplementary data). All laboratory analyses were conducted blindly to the case or control status of the samples.
Funding sources The work reported in this paper was undertaken during the tenure of MIH's postdoctoral fellowship from the  International Agency for Research on Cancer. MS was supported by the  World Cancer Research Fund International  (grant number:  WCRF 2016/1633 ). The research project was funded by the  French Cancer League , and the Golestan cohort study by the  Cancer Research UK  (grant number:  C20/A5860 ),  Tehran University of Medical Sciences  (grant number:  81/15 ), the  International Agency for Research on Cancer , and the  Intramural Research Program of the U. S. National Cancer Institute. The funders had no role in study design, collection, analysis, and interpretation of data, in manuscript writing or in submission process for publication.
Plant Growth The lupin variety used for inoculation was a spring variety, named Feodora (Jouffray-Drillaud, Cissé, France). Seeds were disinfected for one minute in 70% ethanol, then rinsed three times with sterile distilled water before being placed on water-agar media and incubated at 25 • C in darkness for three days until germination. Inoculated plants were grown at 25 • C day and night, with 16 h of light and 8 h of darkness, and 60% humidity. Plants were watered every two days throughout the experiment. Symptoms were evaluated on all inoculated plants by measurement of the lesion length whenever visible. An ANOVA was performed to study the influence of biological repetition on necrosis length, using the RStudio software (version 3. 2. 5). Differences between variables were determined with multiple comparisons tests with the post hoc Tukey HSD method.
Average fragment size was determined using a LabChip GX (PerkinElmer, Waltham, MA, USA) instrument. The libraries were normalized and pooled before being denatured in 0. 05N NaOH and neutralized using HT1 buffer. ExAMP was added to the mix following the manufacturer's instructions. The pool was loaded at 200 pM on an Illumina cBot, and the flowcell was run on a HiSeq 4000 for 2 × 100 cycles (paired-end mode). A phiX library was used as a control and mixed with libraries at 1% level. The Illumina control software was HCS HD 3. 4. 0. 38, the real-time analysis program was RTA v. 2. 7. 7. The bcl2fastq2 v2. 20 program was then used to demultiplex samples and generate fastq reads. These data have been submitted to the ENA (European Nucleotide Archive) with the bioproject accession number PRJEB40331.
Read quality check and cleaning were performed on ABiMS Galaxy platform (galaxy. sb-roscoff. fr). Low quality reads were cleaned using Trimmomatic with the default parameters  [36]. Paired reads were pseudo-aligned and quantified onto the sequenced and annotated C. lupini RB221 genome using Salmon package (Version 0. 8. 2) of Galaxy platform  [37]. Genes which had a minimum of 100 counts per million (cpm) values in at least three repetitions were kept for further analysis. In planta, gene expression for each time post-inoculation was first compared to the liquid culture condition to identify differentially-expressed genes (DEGs) during host interaction, using DESeq2. Then, a pairwise comparison between two close time points (i. e. , 84 hpi vs. 72 hpi, 72 hpi vs. 60 hpi, 60 hpi vs. 48 hpi and 48 hpi vs.
5 m/z, normalized collision energy 27. Step 2 was repeated for the eight most intense ions detected in step 1 with the following criteria: intensity threshold superior as 8. 3 × 103, precursor charge step of 2 and 3, dynamic exclusion of 50 s, peptide match on and exclusion of isotopes. Raw data were transformed to mzXML format using msconvert (proteowizard 3. 0. 7069, [39] ). Data were searched with X!Tandem (version 2015. 04. 01. 1,  [40] ) against the RB221 strain C. lupini genome, Lupinus angustifolius cv. Tanjil genome (AOCW00000000. 1) and a homemade database containing standard contaminants. Trypsin digestion was set in strict mode with one authorized missed cleavage. Cysteine carbamidomethylation was set as a fixed modification. Methionine oxidation, protein Nter acetylation with or without excision of methionine, Nter glutamine deamidation, Nter carbamidomethyl cysteine deamidation, and Nter glutamic acid dehydration were set as potential modifications.
To identify additional peptides for proteins identified after this first pass, all samples were submitted to a second pass (refine mode of X!Tandem), in which the excision of Nter peptide signal, tryptophane oxidation, glutamine and asparagine deamidation were added as potential modifications. Additional missed cleavages were authorized at this step. Protein inference was performed by using X!TandemPipeline (cpp) v0. 2. 18  [41]  with the following parameters: peptide e-value less than 0. 01, protein e-value less than 10 -5 , two identified peptide by protein. Inference was performed using all samples together. Using a reverse version of the Colletotrichum lupini and Lupinus angustifolius database as a decoy, the FDR was estimated by X!Tandem to 0. 05% and 0. 01% for peptide-spectrum match and protein identification, respectively.
biocomp. unibo. it/gpipe/pred. htm, [48]  and GPIsom, http://gpi. unibe. ch/, [49] ). Candidate effectors were predicted from the set of secreted peptides showing less than 300 amino acid residues, using EffectorP 1. 0 and 2. 0 (http://effectorp. csiro. au/, [49] ). The CAZymes were predicted using dbCAN meta server  [50]  with HMMER program to annotate CAZymes domain boundaries using dbCAN HMM (Hidden Markov Model) database with a cut off e-value of 1. 0 × 10 -15 and a coverage upper than 0. 35. Predicted proteases were identified by the blast of protein sequences in PHMMER and MEROPS databases using a cut-off e-value of 1. 0 × 10 -5. Nonpeptidase homologue proteins were excluded. Transmembrane transporters were predicted from nonsecreted proteins with TransporterTP server (http://bioinfo3.
noble. org/transporter/) [51] using a cut-off e-value of 1. 0 × 10 -3. Genes associated with the synthesis of secondary metabolites were identified using Smurf (http://smurf. jcvi. org/index. php) [52, 53]  with default parameters. The prediction of other protein sequences was performed using Blast2GO, which attributed Gene Ontology (GO) term, Interpro number and PFAM number to genes that showed conserved domains. Different families of transcription factors were identified based on conserved domains. In addition, Necrosis and Ethylene-inducing Proteins (NEPs) were predicted using conserved domains specific to NEP-like proteins (IPR008701/PF05630)  [54]. Cytochrome P450 were identified via the family conserved domain (PF00067)  [55]. Nudix proteins were identified by a family conserved domain (PF00293; IPR015797)  [56].
The remainders were manually classified in putative functional groups according to Hmmscan, BLASTP and based on their predicted function. It is noteworthy that a pathogenicity-related class was created which included genes involved in stress responses and other pathogenicity factors such as genes involved in toxin synthesis. Nudix and NEP were further included in this class while cytochrome P450 genes were included in the oxidoreduction class. Proteins without predicted function, without predicted conserved domain, or with contradictory prediction were characterized as hypothetical proteins. All predicted functions were further validated using Hmmscan program and Pfam database (version 33. 0) with a cut-off e-value of 1. 0 × 10 -3 , and a BLASTP searches to the GenBank nr database (release 233) using an e-valuethreshold of 1.
Transcriptomic and Proteomic Data and Selection Transcriptomic analysis was performed on RNA extracted from a liquid culture of C. lupini RB221, and from lupin hypocotyl inoculated with the same strain at 24, 48, 60, 72 and 84 hpi. For each sample, the total number of reads varied between 50. 6 M and 85. 5 M. Between 94. 83% and 98. 41% of total read pairs were kept after the cleaning step performed with Trimmomatic. Of these, 83. 19% to 93. 14% were paired and kept for further analysis (Table  S1 ). The average mapping rate for the reads from RB221 liquid culture growth was 84. 91%. The average mapping rate from infected plants ranged from 0. 18% at 24 hpi to 3. 54% at 84 hpi (Table  S1 ). With the aim of identifying C. lupini proteins produced during the onset of lupin infection, total proteins were extracted from lupin plants at 36, 60, 72, 84 and 96 hpi with RB221.
Carbohydrate Active Enzymes (CAZymes) CAZymes play an important role in many carbohydrate metabolism processes, some of which are related to host pathogenicity as degrading or binding enzymes to the host plant cell wall. A total of 63 candidate CAZymes were detected from the DEG list, 14 from the QP list and 12 were shared by both analyses (Figure  5A ). These CAZymes belonged to six classes: 13 associated with auxiliary activities, 38 to glycosyl hydrolases including one associated with a starch binding domain (CBM20) and another associated with a polysaccharide deacetylase (CE4), seven to glycosyl transferases, one polysaccharide lyases, five to carbohydrate esterases and one to carbohydrate-binding modules (Table  2 ). The analysis of C. lupini genome led to the identification of 798 CAZyme-encoding genes, indicating that 7.
9% of total CAZyme-encoding genes were differentially expressed compared to control conditions. Among the 65 predicted CAZymes, 28 were secreted proteins (including six from the QP list) and two were small-secreted proteins. The DEGs associated with CAZymes were mostly upregulated in the late stage of the infection, including a set of 23 genes specifically upregulated 84 hpi. Among significantly downregulated genes, downregulation was also more intense after 72 hpi  CAZymes play an important role in many carbohydrate metabolism processes, some of which are related to host pathogenicity as degrading or binding enzymes to the host plant cell wall. A total of 63 candidate CAZymes were detected from the DEG list, 14 from the QP list and 12 were shared by both analyses (Figure  5A ). These CAZymes belonged to six classes: 13 associated with auxiliary activities, 38 to glycosyl hydrolases including one associated with a starch binding domain (CBM20) and another associated with a polysaccharide deacetylase (CE4), seven to glycosyl transferases, one polysaccharide lyases, five to carbohydrate esterases and one to carbohydrate-binding modules (Table  2 ).
One CAZyme was identified as a putative glucose-methanol-choline (GMC) oxidoreductase, described previously in Glomerella cingulata, C. higginsianum and C. graminicola and other phytopathogenic ascomycetes as reductases of plant-produced anti-fungal quinones and phenoxy-radicals  [88, 89]. Early stages of plant penetration are also characterized by the induction of genes encoding effectors. For instance, in C. higginsianum, candidate effectors were mostly upregulated during the biotrophic phase at 40 hpi  [11]. In C. lupini, we found only one DEG encoding a candidate effector (CLUP02_08501) upregulated at 24 hpi versus 11 at 48 hpi and 19 at 60 hpi. Among the genes encoding candidate effectors, some contained conserved domains associated with pathogenicity functions such as a lysin-motif domain (IPR018392/PF01476; CLUP02_16647) described as involved in the sequestration of chitin oligosaccharides to avoid recognition by the host and plant defense induction  [90] , or a fungal hydrophobin domain (PF06766) generally found on the outer surface of conidia and hyphal wall, and involved in mediating contact and communication between the fungus and its environment  [91].
In contrast, the expression of most of the DEGs encoding candidate effectors remained stable or decreased significantly from 48 hpi onwards, except for 2 genes which expression was significantly increased from 72 and 84 hpi (CLUP02_01667 and CLUP02_12726). The former was identified as a putative ToxB-encoding gene, a toxin also produced by the rice blast fungus Pyrenophora tritici-repentis  [92]. The latter gene contained two previously-described domains, the IPR015131/PF09044 domain identified as a toxin killer and the IPR029167/PF15474 involved in meiosis mechanism. These domains were already described among the predicted effectors of Fusarium graminearum  [93, 94]. Concerning CAZymes, 38 and 59 genes out of 63 were respectively upregulated at 72 and 84 hpi, mostly represented by glycosyl hydrolases and cellobiose dehydrogenases involved in plant cell degradation.
Funding: This research and the  APC  were supported by the  PROGRAILIVE  project, grant number  RBRE160116CR0530019 , funded by the  regions of Bretagne and Pays de la Loire (France)  and the  European Union (FEADER) ; this research and the  APC  were supported by  AsCoLuP ,  Ascochyta Colletotrichum Lupin Pois  chiche CASDAR n • 19AIP5913.
| Statistical analysis The statistical package SAS (SAS Inst. Inc. ) was used for statistical G n = rotation (within year) effect (n = 1…11); (Y i × P j ) = year × ploidy interaction; (Y i × H l ) = year × heading date interaction; (P j × H l ) = ploidy × heading date interaction; (G n × P j ) = rotation (within year) × year interaction; (G n × H l ) = rotation (within year) × heading date interaction; e ijklmn = residual error term. In addition, differences in pre-grazing sward height were shown to have a significant positive relationship (p <. 001) with PostGSH (r 2 = 0. 68). Comparing.
Statistical methods The data will be reviewed at the end of the study, prior to statistical analysis. The aim will be to review the progress of the study, identify potential problems and classify any minor or major deviations. The variables measured at baseline will be described for all patients in both groups in terms of numbers and percentages for each category for categorical variables and minimum, maximum, average, standard deviation and quartile values for quantitative variables. The primary endpoint is the difference in CMT in the treated eye between D0 and M2. CMT measurements will be converted into logarithmic CMT: logarithmic CMT = log10(CMT/250). The main objective is to demonstrate the noninferiority of the group with subconjunctival triamcinolone injection compared with the group with intravitreal injection of a dexamethasone implant.
Comparisons between the groups will be performed using Chisquared or Fisher tests for intermittent ocular hypertension, cataract, endophthalmitis, glycaemic and blood pressure imbalances in both arms. There will be no imputation for missing data for these secondary end points. For the economic assessment, mean costs and their corresponding 95% CIs will be presented. The ICERs will be estimated along with their corresponding acceptability curves, i. e. the curves indicating the probability that an intervention is cost effective conditional on society's willingness to pay for an additional unit of effectiveness (i. e. an additional QALY gained) and considering the sampling uncertainty around the estimated ICERs. As costs and ICERs are not normally distributed, the 95% CI and the cost-effectiveness acceptability curves will be determined using the nonparametric bootstrap resampling technique.
Sample size This TRIOZ trial aims to demonstrate the noninferiority of subconjunctival triamcinolone injections compared to intravitreal dexamethasone implants. Noninferiority will be evaluated in terms of the difference in macular thickness in the treated eye between D0 and M2. The deadline of M2 was chosen based on the plan for the Huron study on dexamethasone (NCT000333814) and a retrospective study on triamcinolone at CHU Nantes. Preliminary data observed retrospectively in Nantes between 2011 and 2013 in 25 patients who received triamcinolone injections showed a decrease of 0. 12 ± 0. 12 log OCT at M1 (D0, 0. 27 ± 0. 11; M1, 0. 15 ± 0. 08) and of 0. 09 at M3 (0. 18 ± 0. 11). The difference in macular thickness between D0 and M2 is assumed to be the same in the two groups and the common standard deviation is set at 0.