dataesr/scientific-paragraphs-categorization huggingface dataset:
We also compiled the dates of all craniofacial procedures: fronto-facial monobloc advancement (FFMBA), fronto-orbital advancement (FOA), posterior expansion, Le Fort III (LIII) and Le Fort I (LI) facial advancements, foramen magnum decompression (FM decompression), and ventriculoperitoneal shunt (VP). Finally, we collected data from sleep studies (polysomnography results with apnea/hypopnea index (AHI)), the use of nocturnal continuous positive airway pressure (CPAP), and the presence of tracheostomy. The 2018 French standard growth and weight curves were used as controls  (Heude et al. , 2019). Three hierarchical linear models were used to account for the repetition of the data over time and thus its non-independence. A random effect was introduced for each individual. The coefficients of the model were compared to 0 using Student t-tests.
Results A total of 294 patients were included and 70 patients could be contacted for data collection (Table  1 ). The mean patient age at data collection was 18. 1 (2. 8-56) years of age. We collected a total of 846 measurements for height and 863 for weight. The mean number of measurements per patient was 12 (1-35) for height and 12 (1-43) for weight. Mean birth length was 51. 3 cm (47-57) and 48. 9 cm (47-53) for boys and girls respectively. Mean birth weight was 3. 5 kg (1. 9-4. 2) and 3. 3 kg (2. 2-4. 4) for boys and girls respectively. In the general population, the average birth measurements for boys were 49. 9 ± 1. 9 cm and 3. 4 ± 0. 49 kg, and the average birth measurements for girls were 49. 2 ± 1. 9 cm and 3. 2 ± 0. 46 kg  (De Onis et al. , 2009). All patients mean birth measurements were within normal values.
The French Constitutional Council also stated on November 15th, 2007, the prohibition of processing personal data that directly or indirectly reveals the racial or ethnic origins of persons, the introduction of variables of race or religion in administrative files and the a priori definition of an "ethno-racial reference system". Therefore, ethnicity could not be considered in our study. All patients included in this study had benefited from numerous craniofacial surgical procedures including, in most cases, fronto-facial monobloc advancement (FFMBA) and Le Fort III facial advancement (LF3). During FFMBA and LF3, several steps such as temporal muscle disinsertion or pterygo-palatal disjunction could have an impact on the patient post-operative amplitude of mouth opening. Furthermore, prolonged management in intensive care could have interfered with normal growth.
The curves were created as a tool for professionals to detect obesity. The PNNS BMI curves are divided into percentiles to establish thresholds (underweight, normal body weight zone, overweight). This study was a case series, with many inherent methodological biases, such as a selection bias since the data we used were provided by patients and families who volunteered to respond by email. It is possible that many of them belonged to a higher socio-professional category, more health-conscious and more inclined to take part into such studies. The average follow-up was 17 years, with a mean patient age of 18. 1 years at the time of the survey. It would be interesting to continue collecting growth charts until the end of adolescence for all patients to definitively assess the adult average height and weight in FCS.
4 ). Heinrich and collaborator proposed a similar explanation for the prolonged G2/M arrest, a key FA hallmark, of FA cells treated with low doses of DNA cross-linking agents  [200]. On the basis of their experimental approach, they suggested that aberrant G2/M arrest does not reflect an abnormal cell cycle response but represents a normal cellular response to "excessive" genotoxic stress induced in FA cells as a consequence of the additive DNA lesions caused by exposure to DNA-damaging agents  [200]. Regardless of the cause(s), increased ROS levels in FA appear to be a potential and promising therapeutic targets  [201]. Based on the rescue effect of antioxidant treatment in vitro and in animal models  [202] [203] [204] [205] , a clinical trial of quercetin, a flavonoid polyphenol with antioxidant properties, is ongoing (clinicaltrials.
gov NCT01720147) to address its effects on hematopoiesis  [206]. Contributing to the argument that accumulating ROS and/or a proinflammatory status can be a key contributor to BMF, these hallmarks characterize other major iBMFSs. In DBA, an FA-like inflammatory signature indicated by TNFα, IL6 and IL1β overexpression was observed in patients and in a zebrafish model, and it was associated, similar to FA  [100, 194, [207] [208] [209] [210] [211] [212] , with p38 activation  [130, 213]. Importantly, in DBA, proinflammatory cytokine inhibition partially attenuates oxidative DNA damage levels and restores hematopoiesis  [130, 213]. SDS is also characterized with impaired energetic metabolism (i. e. , altered mitochondrial homeostasis) and increased intracellular ROS levels  [214] [215] [216] [217].
Abiotic Stress Factors Combined with Sm Infection Three abiotic stressors were tested: starvation, larval densification and sieving. Starvation consisted in taking away the feed substrate present in the tray 24 h prior to data collection as shown in Figure  1 : Two larval densities were tested, a high density (0. 8 g/cm 2 of larvae; approximatively 2000 larvae per cup), and a low density (0. 4 g/cm 2 of larvae; approximatively 1000 larvae per cup) with a mean larval weight of 14 mg, about 6 weeks after egg hatching. Sieving was applied to separate the larvae from the feces. High sieving stress was applied for 30 s by the automatic sieve SYSMO from 3R Company, while low sieving stress was applied by separating the larvae by manual sieving using sieves with a diameter of 200 mm and a mesh of 0.
Analyses of variance (ANOVA) were then used to assess the significance of the main effects and the interactions that were identified by the half normal plots. If the ANOVA's indicated a significant effect, Tukey post hoc tests (package emmeans in R) were used to determine if there were differences among the different factors' levels. Similarly, given that group variances where unequal, a group variance structure was fitted using a generalized least-squares regression model in the R-package nlme.
The protocol used is illustrated in Figure  7. Pathogen persistence was measured in the feces, based on the hypothesis that if Sm was still present in the feces, following a period where larvae were provided non-inoculated wheat bran, it should indicate that Sm could remain for a certain time in Tm's digestive tube and therefore inform about its persistence. The results are indicated in Figure  7  as the number of colonies growing on the erythritol plates from a suspension of feces. The data showed that there was a certain level of variation among batches, each containing five larvae. Sm could disappear after two days or to the opposite, survive and sometimes multiply after three days. For instance, in batch 4, Sm appeared in the feces after three days while it was not detected in the 56-72 h period.
Funding: This work was supported by the  French National Research Agency (ANR ConTarKid  grant to C. E. C. ,  ANR-15-CE14-0024 ), the  French National Institute of Health and Medical Research (Inserm)  and the  Sorbonne University. E. R. is a doctoral fellow of the  French Ministry of National Education ("Ecole Doctorale de Physiologie and Physiopathologie ", ED 394). L. B. is a fellow of the SFAR (" Société Française d'Anesthésie et de Réanimation"). Informed Consent Statement: Not applicable.
Embryo, tadpole and eye collection Xenopus laevis embryos were obtained by conventional methods of hormone-induced egg laying and in vitro fertilization  (Sive et al. , 2007) , staged according to Nieuwkoop and Faber's table of development  (Nieuwkoop and Faber, 1994) , and raised at 18-20°C. Before whole eye dissection, tadpoles were anesthetized in 0. 005% benzocaine. Dissected eye area was measured using AxioVision REL 7. 8 software (Zeiss).
Immunodetection was performed using Super Signal West Pico or Femto Chemiluminescence Kit (Pierce). Quantification was done using Fiji software  (Schindelin et al. , 2012) ). Molecular combing and detection by fluorescent antibodies DNA was extracted and combed as described  (Marheineke et al. , 2009). Biotin was detected with AlexaFluor594 conjugated streptavidin followed by anti-avidin biotinylated antibodies. This was repeated twice, then followed by mouse anti-human ssDNA antibody, AlexaFluor488 rabbit anti-mouse, and AlexaFluor488 goat anti-rabbit for enhancement  (Gaggioli et al. , 2013). Images of the combed DNA molecules were acquired and measured as described  (Marheineke et al. , 2009). The fields of view were chosen at random. Several hundred of DNA fibers were analyzed for each experiment.
Measurements on each molecule were made using Fiji software  (Schindelin et al. , 2012)  and compiled using macros in Microsoft Excel. Replication eyes were defined as the incorporation tracks of biotin-dUTP. Replication eyes were considered to be the products of two replication forks, incorporation tracks at the extremities of DNA fibers were considered to be the products of one replication fork. Tracts of biotin-labelled DNA needed to be at least 1 kb to be considered significant and scored as eyes. When the label was discontinuous, the tract of unlabeled DNA needed to be at least 1 kb to be considered a real gap. The replication extent was determined as the sum of eye lengths divided by the total DNA length. Fork density was calculated as the total DNA divided by the total number of forks.
Quantification and statistical analyses For quantifications of labeled EdU + cells by manual cell counting in the CMZ, 16 to 11 retinas per conditions with a minimum of 2 sections per retina were analyzed. Dissected eye areas and the number of cells per embryo were measured using Adobe Photoshop CS4 software. All experiments were performed at least in duplicate. Shown in figures are results from one representative experiment unless specified. Statistical analyses (GraphPad Prism software, version 8. 3. 0) were performed using a Mann-Whitney test or Wilcoxon signed ranked test as mentioned in the figure legends.
partner repository with the dataset identifiers PXD029345 and 10. 6019/PXD029345. and AP-1 at enhancers drives oncogenic growth. Nat Cell Biol 17:1218-1227. doi:10. 1038/ncb3216 Zhao B, Li L, Lei Q, Guan KL. 2010. The Hippo-YAP pathway in organ size control and tumorigenesis: An updated version. Genes Dev. doi:10. 1101/gad. 1909210 Zhao B, Ye X, Yu Jindan, Li L, Li W, Li S, Yu Jianjun, Lin JD, Wang CY, Chinnaiyan AM, Lai ZC, Guan KL. 2008. TEAD mediates YAP-dependent gene induction and growth control. Genes Dev 22:1962-1971. doi:10. 1101/gad. 1664408.
Soft agar assay for colony formation Soft agar assay was performed in six-well plate using a 2 ml basal layer of 0. 63% bacto-agar (Becton Dickinson) in complemented DMEM. Cells were trypsinized, counted and plated at 6000 cells per well in 0. 42% bacto-agar in complemented DMEM medium. Depending on the cell lines, after 3 to 4 weeks, the colonies were stained with 0. 4% crystal violet overnight at 37 • C and counted. Images were captured using Argimed software (Microvision instruments, France) and quantified using NHI ImageJ software. Only particles ranging from 30 to 1000 000 pixels were counted. Each experiment was repeated at least twice with two replicates each. Average numbers of colonies from each experiment were plotted.
Reactions in triplicate were carried out in the MiniOpticon real-time PCR machine (Biorad, France) under the following conditions: initial denaturation at 95 • C for 3 min and then 45 cycles of denaturation at 95 • C for 10 s, annealing/extension at 60 • C for 30 s. Melting curves were obtained to examine the purity of amplified products. Absolute quantitative data and Cq values were obtained by analysis with BioRad MFX Software 2. 0 by second derivative method. Normalization of data was done with RPLP0 as reference gene and HeLa cells as calibrator. We used the following equation: [copy numbers of target gene in a sample/copy numbers of RPLPO in a sample)]/[copy numbers of target gene in HeLa cells/copy numbers of RPLPO in HeLa cells]. To reveal a correlation between PRNP and APP mRNA expression (Fig.
Flow cytometry analysis Living cells were recovered and stained with the antibodies against CD24 (clone ML5), CD44 (clone C26), and CD230 (PrP, clone 4D5) from eBioscience. Isotypic controls were from BD Biosciences (San Jose, CA, USA). Cell immunolabelling was performed in PBS 1% BSA according to manufacturer's recommendations. Cells were analyzed on a SORP LSR-II analyzer (Configuration: 488 nm, 561 nm, 405 nm, 355 nm, and 635 nm). For each experiment, 10,000 to 20,000 cells were analyzed. Gating strategy was performed following exclusion of debris and cellular aggregates and live/dead discrimination. The positive populations were identified using an isotypic control to determine the negative populations. Data were treated with FlowJo v7. 6. 1 software (Tree Star). ΔΔMFI (median fluorescence intensity) and percentage expression as compared to control were calculated.
Statistical analysis ICC stainings and Western blots were quantified using ImageJ v1. 49o (NIH, USAStatistical analysis was carried out with GraphPad Prism v5 (GraphPad Software, La Jolla, CA, USA). ). The same software was used to design graphs. Values were subjected to a Shapiro-Wilk normality test. When data did not show a normal distribution, they were compared by a Kruskal-Wallis test with a Dunns (compare all pairs of columns) post test. Differences were considered statistically significant for p values < 0. 05.
Acknowledgements Denis Biard  dedicates this work to his wife, daughter, son and son-inlaw, as well as to all health professionals in hospitals during the COVID-19 pandemic. D. Biard  thanks  Prof. A. Sarasin  for its evaluation of our manuscript. D. Biard  is indebted to  Caroline Jan  ( CEA, MIRCEN ) for access to the MIRCEN's microscopy facility. D. Biard  is also grateful for  Dr R. Chammas  ( Sao Paulo University, Brazil ),  Dr P. May  ( CNRS Villejuif, France ),  Dr C Gazin  ( CNRS-CEA, Evry, France ),  Dr M. F. Poupon  ( CNRS, Paris, France ),  Dr B. Bugler  ( CNRS, Toulouse, France ), Theranexus and  Drs L. Gauthier  and  I. Délic  ( CEA, Fontenay aux Roses, France ) for providing validated cell lines. All experiments have been carried out in accordance with the quality management program developed by the  CEA  and otherwise described in details in an  UPEC teaching program  ( Master STA2E parcours Biologie Intégrative ).
Therefore, we aimed to determine the biological mechanisms leading to this false-positivity. Whole-genome sequencing of C. farmerii N2252 (PRJNA837042) and C. amalonaticus CHUV-445 (PRJNA837049) were performed by Illumina sequencing platform, and data analysis identified only a single ß-lactamase gene in each isolate, corresponding to the chromosomal class A ß-lactamase genes bla SED-1 and bla CdiA , respectively. This confirmed the false-positive result obtained with the NG-Test CTX-M MULTI. Recently, OXY-1-type b-lactamases from Klebsiella oxytoca were also shown to cross-react with the monoclonal antibodies contained in the NG-Test CTX-M MULTI assay, giving rise to false-positive results  [18]. Interestingly, OXY-2-type b-lactamases, sharing 89% amino-acid identity with OXY-1-type enzymes, gave negative results with the NG-Test CTX-M MULTI.
Image acquisition: The fluorescent images for the height measurements were acquired using a Leica SP8 X line scanning confocal system equipped with Z galvanometric stage, controlled by LAS X interface and equipped with Oko lab stage top incubator. Using a 63x (1. 4 NA, oil) or 40x (1. 3 NA, oil) objective, a tile scan covering the size of a FN grid was performed with z steps of 0. 5 µm. To get a larger field of view for computing the power spectrum, the phase contrast acquisitions were obtained using one of the microscopes with the corresponding objectives: inverted Olympus CKX41 (4x, 0. 13 NA Phase, Olympus); SANYO MCOK-5M incubator microscope (10x, 0. 25 NA Phase, Olympus). These microscopes are equipped with a CCD camera (Hamamatsu C4742-95 / 4 C8484-03G02; Sentech XGA) and operated by Hamamatsu Wasabi / Micromanager and MTR-4000 softwares respectively.
The interval between acquisitions were either 5 min, 10 min or 20 min and all the imaging was performed at 37 • C for 48 h. To prevent evaporation of media during imaging, either mineral oil (M8410, Sigma Aldrich) was added or the imaging chamber was covered with a glass Petri dish. Image processing: The images were analyzed using FIJI application  [32]  and the power spectra were computed using Matlab software. The schemes were drawn using Inkscape and the plot showing the difference in height were obtained using Graphpad Prism 7. The height variations in the monolayer were obtained using a custom written FIJI plugin. The plugin allows visualization of changes in height as variations in intensities by encoding the height as intensity value to the corresponding pixel. In order to get the power spectrum of the pulsations, the velocity field was obtained by Particle Image Velocimetry (PIV) using the Matlab based PIVlab application  [33].
ACKNOWLEDGMENTS The MDCK-GFP-E-Cadherin cells were a kind gift from  Nelson lab. , Stanford. We are grateful to  Guillaume Salbreux  for discussions and many key insights into the theoretical model. We thank the  Riveline lab. for discussions and comments, and acknowledge the help of  Basile Gurchenkov ,  Yves Lutz  and  Pascal Kessler  from the  IGBMC imaging facility. We thank the late  Marcel Boeglin  for writing the Fiji plugin to perform height measurements. R. T. was an  IGBMC international PhD program  fellow supported by  LabEx INRT  funds. M. M. I acknowledges funding from  Science and Engineering Research Board  ( MTR/2020/000605 ). D. R. acknowledges support from  CNRS.
Both this current system and the associated equatorward electric fields and westward drifts (opposite to corotation) were found to be reasonably consistent with predictions of the corotation-enforcement current model of  Cowley et al. (2005 Cowley et al. ( , 2008 Cowley et al. ( , 2017)). The amount of angular momentum and power extracted from the ionosphere to the magnetodisk by the calculated current systems, as well as the total power dissipated into the thermosphere via Joule heating and electron precipitation, were also estimated. Finally, the E×B drift velocities derived from Juno multi-instrument data by  Wang et al. (2021)  could be compared with horizontal ionospheric E×B plasma drifts derived from Earth-based telescopic observations of the Doppler shift of Jovian H 3 + IR emissions  (Stallard, 2001; Johnson et al.
Description of the data set We first present an overview of the auroras imaged by Juno's UVS instrument during the first 30 perijoves. The Jovian UV aurora appears very dynamic in UVS images. These UVS images reveal also a strong North/South contrast and temporal variability. For each perijove, the main oval is clearly visible (see auroral imaging in figures 3 and 4), but with different morphologies. In both hemispheres, for some perijoves, the main oval displays a regular and smooth longitudinal and latitudinal distribution, while for others it shows strong spatial inhomogeneities at the local scale corresponding to small sectors of large brightness being adjacent to regions of much lower brightness, in a disordered manner. This complex and highly variable morphology of Jupiter's aurora have been described and classified by  Grodent et al.
Data Availability Statement All Juno data used in this study are available at the Planetary Data System of NASA and can also be accessed through the AMDA (http://amda. cdpp. eu/, Génot et al. , 2021)      tool developed by CDPP (http://cdpp. eu) and the CLweb tool developed by Emmanuel Penou at IRAP (http://clweb. irap. omp. eu). For cross-comparisons purposes, the authors made use of the APIS service (https://apis. obspm. fr, Lamy et al. , 2015). The scripts used to perform the study are available on GitHub and archived in Zenodo (Al Saati et al. ,     2022a). For practical purposes, all the data needed to run the codes are archived in Zenodo  (Al Saati et al. , 2022b).
2 ± 0. 6 g as opposed to 30. 4 ± 13. 6 g). The root system was less developed and was made of longer, thinner, and more tapered roots. Even after dehydration with alcohol or acetone, the soil-grown (SG) plants displayed larger root diameters (up to 1500 µ m as opposed to 250-500 µ m). The biomass could be stimulated via the addition of growth regulators. The use of brassinosteroid analogs on a hydroponic vetiver culture was reported  [24] , but it did not affect the dry matter of the vetiver roots. A GC/MS-based analysis of the HS-SPME-sampled root VOCs of SG plants revealed a complex profile of 43 peaks (Figure  2 ). The substances making up most of the major peaks could be identified based on a comparison of their mass spectrum and retention index with reference substances that were previously entered in databases (Table  1 ).
More surprisingly, the only other abundant VOC found in the HPA-grown vetiver roots was isodaucene  (19) , a substance that was not seen in our SG plant root extracts and that has not yet been reported in vetiver. Similar analyses carried out on independent four-monthold HPA-grown plants in May and November 2015 generated analogous GC/MS profiles. This daucane-type sesquiterpene is present in a dozen plant families (Apiaceae  [25, 26] , The biomass could be stimulated via the addition of growth regulators. The use of brassinosteroid analogs on a hydroponic vetiver culture was reported  [24] , but it did not affect the dry matter of the vetiver roots. A GC/MS-based analysis of the HS-SPME-sampled root VOCs of SG plants revealed a complex profile of 43 peaks (Figure  2 ). The substances making up most of the major peaks could be identified based on a comparison of their mass spectrum and retention index with reference substances that were previously entered in databases (Table  1 ).
25 mm) coated with a 0. 25 µm film of 5% phenylarylene and 95% dimethylpolysiloxane (ZB-5ms, Phenomenex, Le Pecq, France) and a quadrupole analyzer. A split injection with a ratio of 5 was used for all samples. The column oven temperature was initially maintained at 70 • C for 3 min, linearly increased to 260 • C at 3 • C min -1 , and maintained at 260 • C for 10 min. The injection port and ion source temperatures were set at 250 • C and 200 • C, respectively. Helium was used as the carrier gas at a flow rate of 1 mL min -1. Electronic impact ionization was performed at 70 eV, and the quadrupole functioned under scan mode, with a scan range of 35-350 m/z and an acquisition time of 0. 20 s. Compounds were identified by their mass spectral and retention index similarities with reference compounds in standard reference databases  [38, 54].
Table. S2 ). When we could not find studies reporting transcriptomic regulation of gene in one targeted process, we selected studies showing the implication of genes using mutant approaches. If available, we selected already designed PCR primers based on our bibliography analysis. However if no primers were already published for the gene targeted, we designed our own primers. The design of primers followed a set of stringent criteria, as generally suggested in qRT-PCR protocols (e. g. PrimerExpress Software v2. 0 Application Manual, Applied Biosystems). To minimize the risk of amplifying contaminating genomic DNA, primers spanning at least one exon-exon junction, or annealing to different exons, were designed when possible. The specificity of each primer was confirmed by comparing its sequence with all predicted rice coding sequences (CDS) using the Primer3Plus software to ensure that at least one primer of each pair targets a unique site within the set of predicted rice CDS.