dataesr/scientific-paragraphs-categorization huggingface dataset:
Ethics statement Human samples were obtained at the Tropical Medicine Unit of Poniente Hospital (El Ejido, Almeria, Spain) for diagnostic purposes as part of the standard protocol care for sub-Saharan patients attended at such a unit. Anonymised data were collected retrospectively. This study was approved by the Ethics Committee of the Coordinating Site (protocol Schis-01-UMT-2018). At the end of the study, all participants were informed about their parasitological results and free treatment was offered when found positive for schistosomiasis (single 40 mg/kg dose of Praziquantel). Animal samples were obtained at the laboratory of the IHPE (Hôtes-Pathogènes-Environnements), CNRS, Université de Perpignan (Perpignan, France) which has permission A66040 from «Ministère de l'Enseignement supérieur de la Recherche et de l'Innovation (France)» for animal experimentation.
Sequences were edited and assembled using Sequencher v. 5. 4. 6 (Gene Codes Co. ) and aligned with MEGA version 7  (Kumar et al. , 2016) , using default settings. A careful inspection of all nucleotide positions in the raw sequence chromatograms allowing the detection of sequence polymorphisms between S. haematobium and S. bovis, was checked to identify possible heterogeneity, as previously described  (Angora et al. , 2020; Savassi et al. , 2020; Webster et al. , 2013). Homologies were performed using the BLASTN program from the National centre for Biotechnology Information website (http://www. ncbi. nlm. nih. gov/BLAST).
Schistosome egg digitalization and measurements Schistosome egg measurements were performed on 174 samples [84 eggs from human urine (Sh), 47 from a hamster liver (Sb), and 43 from a mouse liver (Sm)] (Table  1 ). The measurements were taken by means of a Computer Image Analysis System (CIAS), including a computer connected to a digital camera linked to a microscope. Each egg was individualised in a 0. 9% NaCl drop on a slide and photographed using a microscope (Leica DMR 72-89663) with 400 magnifications and the high-resolution camera Leica DFC450C controlled by the LAS software. Representative images of the photographed eggs and their spines are shown in Fig. 1. All pictures were taken without coverslip for the establishment of a correct standardisation of the measurements. During the workup of the standardisation, the influence of the coverslip on egg shape and size was assessed.
The same egg was photographed before (Fig. 1D ) and after (Fig. 1E ) a cover slip was gently lowered on the saline solution drop where it was placed. No pressure was applied. In addition, the lack of coverslip allowed the recovery of individual eggs, and preservation in EtOH 70 • , for posterior molecular characterisation. For morphometric characterisation, the software Image Pro-Plus v5. 1 (Media Cybernetics, USA) was used. A total of twenty-five measurements were designed to phenotypically characterise the different schistosome eggs. Twenty-five measurements were designed. In order to identify the ones that give some valuable information about the egg morphology and therefore, were suitable for the principal component analysis, an iterative process of measurement combinations was performed.
Statistical data and analyses Statistical analysis was performed using SPSS Statistics 26. Comparison of the average egg measurements from the different populations was carried out using one-way ANOVA and the Bonferroni test. Values were considered statistically significant when P<0. 05. The software Ene 3. 0 (Servei d'Estadistica Aplicada, Universidad Autonoma de Barcelona, Cerdanyola del Valles, Spain, distributed by GlaxoSmithKline) was used to establish the minimum number of eggs needed to obtain statistically significant results (P: 0. 05, power: 80%). Current statistical techniques in morphometrics make it possible to test the null hypothesis of conspecific populations being simply the allometric extension of each other, provided a common allometric trend is identifiable  (Rohlf and Marcus, 1993).
Biometric data was examined using multivariate analysis. Morphological differences were quantified by geometrical morphometrics, which includes validated methods for analysing variation in organismal shape  (Klingenberg, 2016). These procedures focus on the retention of geometric information throughout a study and provide efficient, statistically powerful analyses that can readily relate abstract, multivariate results to the physical structure of the original specimens  (Slice, 2007). Principal component analysis (PCA) is an estimator of certain parametric structure characteristics of the population. It may also be used as a dimension-reduction technique that identifies orthogonal linear combinations of the original variables that most efficiently reproduce sample variability. The latter use is particularly important in morphometric research as the number of shape variables to be analysed can be very large and often exceeds reasonable sample sizes  (Slice, 2007).
The degree of similarity between egg populations was assessed through pairwise Mahalanobis distances  (García-Sanchez et al. , 2020). PCA was carried out using the natural logarithm of measurements applying the BAC software. PVA and Mahalanobis distances were calculated using PAD software and tested by non-parametric permutation tests with 1000 iterations each. Values were considered statistically significant when P<0. 05  (Dujardin, 2002; García-Sanchez et al. , 2019´ ). Nevertheless, to avoid matrix singularities, some measures were discarded because of their partial overlap with other measures. The following 17 non-redundant measurement (i. e. one is not included in another one) were considered: EA, EP, Rmax, Rmin, EL, EW, BE20, BE35, BE50, SE20, SE35, SE40, ER, SL, SBW, SMW and SEW. Linear regression was calculated for the ERatio values and PC1 and PC2 (SPSS Statistics 26).
ITS rDNA sequence analysis ITS rDNA profiles showed that S. haematobium were present in all the six human samples selected for this study. No hybrid profiles were detected in the chromatograms. amongst the 25 sequences obtained for the nuclear Internal Transcribed Spacers (ITSs), two profiles of ITSs were retrieved; one of them (Sh-1A) showed sequence identity (100%) with S. haematobium (consensus sequence retrieved from GenBank = Acc. Nos. GU257398, JQ397400-JQ397414, FJ588861, MT884914 and MT158873) and was obtained in 17 of 25 sequences (68%), and in patients from both, Mauritania and Senegal. The second profile (Sh-2A) presented a heterozygotic signal (C/T) in position 533 of the ITSs alignment and did not correspond to any discriminative position amongst other Schistosoma species with terminal-spined eggs.
Data acquisition A testing machine Bose© ElectroForce 3200 Series (Bose Corporation, Framingham, Massachusetts, US) was used to perform tensile tests (Fig. 1 ). The loads data were acquired with a 22 N load cell (reliability manufacturer error of 0. 11% and a repeatability error of 0. 19%) at a sampling rate of 100 Hz. Dimensions (length and width) as well as the displacements of the samples. Complementary displacement and strain fields were measured by 2D digital image correlation (DIC) (ARAMIS 5 M, GOM mbH, Germany) at 15 frames per second.
Hyperelasticity A isotropic hyperelastic one-degree Ogden model was fitted on each experimental curve depicted on Fig. 4. The uniaxial stress-stretch Ogden function is expressed as: σ = 2μ b ⎛ ⎝ λ b-1 + λ -b 2 -1 ⎞ ⎠ (4) Where μ is the shear modulus and b is a material constant and the stretch ratio defined as λ = ε + 1. The curve fitting was performed with the nonlinear least squares method using the fit function in Matlab R2018b (MatWorks, Natick, MA, USA) and evaluated by a R 2 and RMSE (Root Mean Square Error).
Then the 32nd and the 68th probabilistic value of elastic modulus were calculated from the 32nd and the 68th probabilistic value of the CSA. The Monte-Carlo GUM methodology is described in appendix A. All data were statistically analyzed as follows. The normality of each distribution was verified using Shapiro-Wilk normality tests. Due to the heterogeneity of normal distribution and the unequal distribution size, Wilcoxon rank sum test was performed to quantify the significant difference of all variables (force, stress, displacement, strain, elastic modulus) with respect to the spinal levels, the orientation of loading for the DAC as well as the conservation methods. The significance level was set to p<0. 05. Data analysis was performed using Matlab software  (R2018a version, Matlab®MathWorks, 1984).
The μ Ogden coefficients of the typical curves were found superior to those provided for spinal bovine dura mater at 0. 01 s-1 (5. 0 MPa against almost null in the longitudinal direction and 2. 4 MPa against 2. 2 MPa in the circumferential direction respectively). The b Ogden coefficients were found inferior to those provided in the same study (11. 9 against almost 24. 0 in the longitudinal direction and 10. 5 against 18. 0 in the circumferential direction respectively)  (Persson et al. , 2010). No equivalent data was found to compare the Ogden coefficients of PM. Trends reported in inter-segmental spinal level variation (cervical, thoracic and lumbar) of elastic properties in DAC and PM need to be confirmed due to high standard error induced by within-subject and between-subject variability.
Specific mRNA abundances were determined by realtime quantitative PCR, performed in a LightCycler Real-Time PCR Systems (Roche Diagnostics, Monza, Italy). The reactions, performed in duplicate were carried out in a 10-μL volume containing about 100 ng of cDNA, 0. 5 μmol/L of each primer, and 5 μL of SYBR Premix Ex Taq II (Perfect Real Time, Takara Bio, Japan). Reactions consisted in an initial denaturation step at 95 °C for 30 s and 40 cycles of 95 °C for 5 s and the annealing/ extension temperature for 20 s. The primer sequences and annealing/extension temperatures are indicated in Supplementary Table  1. Threshold cycles were converted to mRNA molecules/μL using standard curves. Each amplification specificity was checked by melting curve analysis at the end of the reaction. The expression data were normalized by geometric mean of the expression of the two housekeeping genes hydroxymethylbilane synthase and ribosomal protein L4.
Immunostaining of the EECs was performed using the indirect immunofluorescence technique. The sections were incubated at 4 °C overnight in a solution containing chromogranin A primary antibody. After washing in PBS, the sections were incubated for 1 h with goat antimouse Alexa Fluor 594 conjugated (Supplementary Table  2 ). For each pig, the parietal cells and the EECs were counted in 20 randomly selected glands well oriented perpendicularly to the surface of the mucosa. Cell counting was performed with a 40× objective lens using Nikon Eclipse Ni microscope and the images were recorded with a Nikon DS-Fi2 (for immunohistochemistry) and Nikon DS-Qi1Nc (for immunofluorescence) digital camera and NIS Elements software BR 4. 20. 01 (Nikon Instruments Europe BV, Amsterdam, the Netherlands). Slight adjustments to contrast and brightness were made using Corel Photo Paint, whereas the figure panels were prepared using Corel Draw (Corel Photo Paint and Corel Draw, Ottawa, ON, Canada).
Statistical analysis Data were analyzed using MIXED models System (SAS Institute Inc. , Cary, NC, USA). The effects of treatment (against an error calculated between litters) and time of slaughter (error within litters) for the STE experiment, and the effects of treatment (between litters) and diet (within litters) for the LTE experiment, were tested respectively. The models also included the interaction term between early treatment and age of slaughter (STE) or late diet (LTE). Results are presented as least-squares means and SEM. For time effects, the following three orthogonal contrasts were tested: (1) linear and (2) quadratic effect among the three ages during suckling (14, 21 and 28 d); (3) "Weaned vs. Suckled", between the post-weaning age (day 42) and the three ages during suckling.
Animals The animals used in these studies were Fischer F344 rats obtained from Harlan UK Ltd. (Oxon, UK). Rats were 6-9 weeks of age and weighed 140-221 g (males) and 85-154 g (females) at the start of dosing in a dose range finding study and the main comet assay. Fischer F344 rats were selected for this study because most of the database for HQ was obtained in this strain and this strain of rats has a greater susceptibility to HQ-related effects on renal tubules  [17, 18]. In addition, a small number of Sprague Dawley rats were treated as concurrent vehicle and positive controls due to the lack of laboratory historical control data in Fischer F344 rats. Animals were housed in wire topped, solid bottomed cages, with a maximum of three animals of the same sex per cage. For periods of time not exceeding 24 h, rats scheduled for urinalysis were housed individually in urine collection cages.
The kidneys from these animals were also assessed for histopathology and increased the number of animals available for histopathology to 12. Final dose administration and sample times were determined by consideration of available toxicokinetic data for HQ and the general recommendations of OECD 489. Duodenum, kidney, and liver were sampled from males and females 30 min after the final dose administration. The sampling time for the somatic tissues was selected based on peak plasma time (T max ) reported in previous toxicokinetic studies  [19, 20] , and is consistent with recent IWGT recommendations  [21]  and OECD 489 (2016). The somatic tissues of the positive control-treated animals were sampled three hours after a single administration, following the sample time used for the laboratory's historical control data.
Male testes were included in this comet assay to examine the possible interaction of HQ with germ cells  [22]. Selection of HQ doses was determined from data obtained in a doserange finding study. Small groups of male and female F344 rats (n = 2 or 3/sex) were dosed with HQ at 300, 420, 600 or 1000 mg/kg body weight/day using the same route, dose volume (except 600 and 1000 mg/kg body weight/day doses, which were dosed at 20 mL/kg due to solubility limitations) and dose administration times as described above for the comet assay. No clinical signs of toxicity were observed at 300 mg/kg/day. At 420 mg/kg/day, only mild, transient signs were observed (piloerection solely in male animals approximately 1-2 h after the second administration). More severe signs (including tremors, decreased activity and hunched posture) were observed at the higher doses with animals reported to be moribund or mortality observed.
Methods A group of clinicians and scientists with a special interest in mycology from Asia, Australia, Brazil, Europe and North America was invited to attend the advisory board. All attendees had published extensively in the field of preclinical and clinical mycology and clinical trials, were members of international and national guidelines groups, or were members of international bodies representing mycology [e. g. International Society for Human and Animal Mycology (ISHAM), ESCMID and ECMM]. One expert, J. P. D. , chaired the meeting and helped design the pre-and post-meeting questionnaires sent to attendees. A pre-meeting questionnaire was sent to the experts to review their practice in the investigation and management of IA, setting the scene for Review JAC the advisory board (Table  S1 , available as Supplementary data at JAC Online).
M. A. S. is supported by a National Health and Medical Research Council Centre of Research Excellence Grant, and has received research grants from, is an advisor to, or received lecture honoraria from F2G Ltd, Gilead Sciences, Merck Sharp & Dohme (MSD) and Pfizer. Y. -C. C. is supported by the Ministry of Science and Technology and Ministry of Health and Warfare, Taiwan, has received a research grant from Gilead Sciences, has been an advisor/consultant to Gilead Sciences, Pfizer, MSD, F2G Ltd, and has received lecture honoraria from Gilead Sciences, Pfizer, MSD and Astellas Pharma. C. C. has been an advisor/consultant to Astellas Pharma, Basilea, Gilead Sciences, Mundipharma, MSD, Pfizer, F2G Ltd and Schering Plough, and has received lecture honoraria from Astellas Pharma, Gilead Sciences, MSD, Pfizer and Schering Plough.
O. A. C. is supported by the German Federal Ministry of Research and Education and the European Commission, and has received research grants from, is an advisor to, or received lecture honoraria from Actelion, Allecra Therapeutics, Amplyx, Astellas, Basilea, Biosys UK Limited, Cidara, Da Volterra, Entasis, F2G Ltd, Gilead Sciences, Grupo Biotoscana, Janssen Pharmaceuticals, Matinas BioPharma, The Medicines Company, MedPace, Melinta Therapeutics, Menarini Ricerche, MSD, Octapharma, Paratek Pharmaceuticals, Pfizer, PSI, Rempex, Scynexis, Seres Therapeutics, Tetraphase and Vical. M. C. -E. has received grants from Astellas Pharma, bioMerieux, Gilead Sciences, MSD, Pfizer, Schering Plough, Soria Melguizo SA, Ferrer International, F2G Ltd, Amplyx, Basilea and Cidara and Syntex, has been an advisor/consultant to the Panamerican Health Organization, Astellas Pharma, Gilead Sciences, MSD, Pfizer, F2G Ltd and Schering Plough, and has received lecture honoraria from Gilead Sciences, MSD, Pfizer, Astellas Pharma and Schering Plough.
Phagocytosis assay Purified neutrophils (5x10 6 cells/mL) were incubated at 37 • C, 5% CO 2 for 6 h in sterile RPMI supplemented with 10% FBS, 25 mM HEPES, and 100 U/mL penicillin + 100 μg/mL streptomycin (Wisent, St-Bruno, QC, Canada) with the indicated concentrations of BPA, BPS, BPA-gluc and BPS-gluc, or DMSO at 10 μM as vehicle control. Cells were next washed, resuspended at 5x10 6 cells/mL in Hank's Balanced Salt Solution (HBSS; Wisent, St-Bruno, QC, Canada) and further incubated with 100 nM fMLP for 2 h at 37 • C, 5% CO 2. Cells were then centrifuged at 300 g for 3 min, resuspended in 120 μL HBSS + 30 μL FITC-labelled E. coli (VWR Life Science, Seradigm, Mississauga, ON, Canada) and incubated 1 h at 37 • C, 5% CO 2. Cells were then washed and resuspended in HBSS, acquired on a FACSCalibur flow cytometer (BD Biosciences, Mississauga, ON, Canada) and analyzed using the FlowJo 10 software (FlowJo, LLC, Ashland, OR, USA).
Phagocytosis is not altered by bisphenols As the phagocytic capacity is an assessment of a critical neutrophil function, we next used FITC-labelled E. coli and evaluated the effects of bisphenols by flow cytometry. We observed that the percentage of phagocytizing neutrophils (FITC + cells) was around 60%, with a mean fluorescence intensity (MFI) of about 400, both of which were not significantly modulated by the presence of bisphenols (Fig. 4A ; representative histogram plot for a set of data using 1 nM of bisphenols). However, even if bisphenols showed a slight tendency to decrease the MFI as compared to control, no significant differences in the percentage of FITC + cells nor MFI were observed for any compound or concentration tested (Fig. 4B-C ). Since phagocytosis depends on ROS production, we also evaluated, using the same culture condition as the phagocytosis assay, the production of superoxide anions by performing a cytochrome c reduction test.
Funding This work was supported by the  Natural Sciences and Engineering Research Council (NSERC)  of  Canada  under Grant number  RGPIN-2015-05413. The acquisition of the extracellular flux analyzer was supported by a  John R. Evans Leaders  equipment and infrastructure grant (# 33805 ) from the  Canada Foundation for Innovation (CFI)  awarded to MP. AK is the recipient of an M. Sc. fellowship from  La Fondation du CHU de Québec. MP is a  Junior 2 scholar  from the  Fonds de recherche du Québec-Santé (FRQS).
Data charting and analysis Based on trends and concepts identified during screening, a list of relevant data categories was developed to guide data extraction. Each of the three main reviewers (GKI, JRB, DL) extracted data from five papers to evaluate the list's comprehensiveness. Additional categories were added after this pre-testing, as well as during the extraction process when new trends were identified. One of the three main reviewers extracted data from each of the studies. Multiple discussions throughout this process were used to ensure consistency. The data from this charting process is available at: https://osf. io/b5cdq/. This data includes charting from both the initial and the updated searches. Extracted data include: study type (qualitative or quantitative), publication source, author affiliation, publication date, country of study population, number of participants, response rate, population selection criteria, product of study, data collection method, qualitative and quantitative models and associated analysis units (willingness-to-pay and Likert scale), specific results about perceptions of antimicrobial use and several binary variables for statistical analysis.
Finally, we had the language capacity to include English only texts. Therefore, some otherwise relevant Canadian and European studies were excluded. Between the title and abstract stage and full text screening stage of this review, we further decided to exclude any texts that did not contain primary data collection (reflected in the amended protocol). As a result, most of the news articles and opinion pieces that were originally included were excluded. This decision was made in an effort to avoid bias given that we could not ensure that all non-academic texts about this topic were captured. However, several news articles with extractable data were included in the final analysis because they cited studies that were not otherwise captured through database and grey literature searches. Although our search strategy was comprehensive in its use of "antimicrobial" and the other associated terms listed above, extracted studies about consumer concern all focused on antibiotic use as opposed to antimicrobial use; and the term "antibiotic" was overwhelmingly used in these studies.
Many animal agriculture products were investigated, with no single type dominating the body of literature (Table  2 ). The most frequently investigated single product categories are pork (15. 3%) and beef (12. 9%), poultry (10. 5%), and dairy (10. 5%). The most frequent product category is the generic category (24. 2%), which includes studies that investigated "food," "organic food," "meats," and/or other similarly broad categories. Multiple product studies were tied for the second most frequent category (15. 3%) and included a range of product combinations from pork and eggs to dairy and apples. Studies often had multiple themes but those tallied in Table  2  were identified by reviewers as the primary focus of each study. We found 18 distinct research themes for which antibiotic perception data could be assessed.
Conclusion This review was prompted by our interest in consumer perceptions about antimicrobial use in animal husbandry. Initial readings about this topic indicated that reasons for consumer concern are wide-ranging and consumers are often confused about the use of antimicrobials in animal agriculture. Despite their confusion, consumer perceptions are an important influence on animal agriculture practices. To understand what consumers see as the risks and benefits of antimicrobial use in animal agriculture, and to gauge which research and methodological gaps exist in this literature, we conducted a scoping review. Through an exhaustive search strategy and systematic screening process, we identified 124 texts that fulfilled our inclusion criteria. We extracted relevant data from these texts for analysis, including the available data on consumer concern.