dataesr/scientific-paragraphs-categorization huggingface dataset:
Chromosome reconstruction Chromosome reconstruction was based on marker segregation within the biparental population A (74F x Kabusa), consisting of 110 progenies. Linkage analysis was conducted on a per-parent basis, leading to separate reconstruction of a female and a male chromosome. First, from the filtered genotyping matrices obtained through GBS and vcf filtering, as previously described, 20 linkage groups were defined using JoinMap 4. 1 software  [47] , while setting the grouping LOD threshold at 7/8 for both parents. SNPs belonging to linkage group 6 (LG6 corresponding to chromosome 6) were identified and their position on the unordered scaffolds of the D. alata genome v1 (Water Yam Genome Projectftp://yambase. org) was assessed using the Basic Local Alignment Search Tool (BLAST) according to the procedure described in  [44].
Then D. alata scaffolds were ordered and oriented (when possible) based on pairwise recombination frequencies between the SNPs they contained. This was done using the Southgreen Galaxy "Chromosome reconstruction" pipeline based on the Scaffrehunter package  [48] ; available at http://galaxy. southgreen. fr/galaxy/u/ d r o c / p / s c a f f h u n t e r % 2 D % 2 D c h r o m o s o m ereconstruction). Homology between the male and the female reconstructed D. alata chromosome 6 was then visualized using a Circos approach via the circlize R package  [49].
Detection of differentiation and structural variation Male and female differentiation was studied using a Fst approach based on SNPs detected among the four DNA pools on the reconstructed male chromosome 6, as described for the GBS procedure, using the following parameters: minimum depth 20, minor allele frequencies per site > 15% and no missing data. Fst variation along the chromosome was assessed using a sliding window of 500 SNPs (step = 100 SNPs). The significance threshold was calculated at a probability of 0. 01 of a gamma law fitted on the resulting Fst distribution. Structural variation was detected using the scaffremodler package  [48]  available at https://github. com/ SouthGreenPlatform/scaffremodler. First, male and female resequencing datasets were generated by combining raw reads by sex.
These male and female datasets were separately used on the reconstructed male chromosome 6 with the following parameters: minimum read insert size = 150, maximum read insert size = 450 and the very sensitive end-to-end mapping process of bow-tie2  [50]. Then male-specific clusters of discordant reads (probably related to structural variations) were manually identified by comparing the two results files. From the paired-end read mapping performed during the detection of clusters of discordant reads, the coverage difference between male and female pools was calculated as the mean difference between male and female sequencing depths in a sliding window of 200,000 bp (step = 50,000 bp). The significance threshold was calculated at a probability of 0. 01 of a normal law fitted on the resulting difference in distribution coverage.
Additional File 6: Fig. S6. Physical versus genetic distance along the two reconstructed sex-chromosome 6. Up, male chromosome; down, female chromosome. Genetic distance were calculated using JoinMap 4. 1 software (Van Ooijen, 2012; option: recombination frequencies below 0. 45, LODs over 1. 0, ripple value 1, regression mapping and Kosambi mapping function). Additional File 7: Fig. S7. Details on significance thresholds used in male and female resequencing comparative studies. A) Distribution of Fst between male and female and definition of significance threshold. A sliding window of 500 SNPs was used (step = 100 SNPs) to compute Fst. The significance threshold was then assessed at 0. 158. B) Difference in male and female read coverage. A sliding window of 200,000 bp was used (step = 50,000 bp).
Thresholds were assessed at 6. 67 and 2. 59 for significance of over-coverage and under-coverage for males and females, respectively. For both analyses, a gamma distribution was fitted on the empirical distribution using the fitdist function of the fitdistrplus R cran library (red curves). The significance thresholds (vertical red lines) were then assessed using a risk of 0. 01. Additional File 8: Fig. S8. Circos visualization of male-specific discordant read clusters. Discordant read clusters (putative structural variations) were detected using the scaffremodler package  (Martin et al. , 2017)  available at https://github. com/SouthGreenPlatform/scaffremodler. Male and female resequencing datasets were separately used on the reconstructed male chromosome 6. Default options were used with an expected forward-reverse read orientation and a minimal and maximal insert size set at 150 and 450 bp, respectively.
Effect of Aeration and Agitation on Biomass and Biofilm Production Through the use of the Design Expert software, the influence of air inflow and agitation on the growth rate and biofilm production was determined, and the response surfaces are displayed in Figure  3. For biofilm production, increasing the air inflow at low agitation speed resulted in a positive response, while under stronger agitation, an increased aeration led to a negative response (Figure  3a ). On the other hand, the agitation speed did not remarkably affect extracellular biofilm production at high aeration, but it resulted in a strong increase at low air inflows. The highest biofilm production was achieved under 200 rpm and 1 L min -1 of air inflow. As shown by the Pareto chart of standardized effects (Figure  4a ), the agitation speed exerted the strongest effect for biofilm production.
Effect of Aeration and Agitation on Biomass and Biofilm Production Through the use of the Design Expert software, the influence of air inflow and agitation on the growth rate and biofilm production was determined, and the response surfaces are displayed in Figure  3. For biofilm production, increasing the air inflow at low agitation speed resulted in a positive response, while under stronger agitation, an increased aeration led to a negative response (Figure  3a ). On the other hand, the agitation speed did not remarkably affect extracellular biofilm production at high aeration, but it resulted in a strong increase at low air inflows. The highest biofilm production was achieved under   4a ), the agitation speed exerted the strongest effect for biofilm production.
This study aims to investigate the effects of an optimized sowing calendar for wheat over a surface irrigation scheme in the semi-arid region of Haouz (Morocco) on irrigation water requirements, crop growth and development and on yield. For that, a scenario-based simulation approach based on the covariance matrix adaptation-evolution strategy (CMA-ES) was proposed to optimize both the spatiotemporal distribution of sowing dates and the irrigation schedules, and then evaluate wheat crop using the 2011-2012 growing season dataset. Six sowing scenarios were simulated and compared to identify the most optimal spatiotemporal sowing calendar. The obtained results showed that with reference to the existing sowing patterns, early sowing of wheat leads to higher yields compared to late sowing (from 7.
Dataset 2. 3. 1. Meteorological Data To implement and evaluate the proposed approach, we used the meteorological and irrigation data for estimating water requirements, calculating the Ks coefficient, and for estimating the NDVI profile for each spatiotemporal sowing. We also used the Landsat-TM5 image to calculate the observed NDVI profile of each plot. The required data was collected during the 2011-2012 agricultural season in the study area. The reference evapotranspiration (ET 0 ) is an indicator of the evaporative demand of the atmosphere and it is calculated using the FAO Penman-Monteith equation  [61]. The climatic variables (air temperature and humidity, solar radiation and wind speed) needed to estimate ET 0 and rainfall were measured by an automatic weather station that was installed within the R3 district.
Wheat Fields Identification Land cover mapping was established using a classification method based on NDVI time series obtained from satellite images and was validated by field surveys and data provided by the ORMVAH. In our case, among 18 Landsat images collected during the 2011-2012 wheat season, only 2 images were affected by clouds and were not used in this study. We used 16 Landsat-TM5 images well distributed throughout the agricultural season 2011-2012. Thus, the daily values of the NDVI are easily obtained by linear interpolation  [65]. Radiometric calibration and atmospheric corrections were performed on these images based on the reflectance of invariant objects (bare soil, fallows and houses) to provide NDVI time series over the irrigation scheme according to the reported method by  [66].
Funding: This research was conducted within the framework of the  Joint International Laboratory, TREMA (Télédétection et Ressources en Eau en Méditerranée semi-Aride  (http://trema. ucam. ac. ma/), the  Center for Remote Sensing Applications ,  CRSA  (https://crsa. um6p. ma/home)and the  Lab-SIV Laboratory of the Faculty of Science of Agadir. It was supported by the projects:  ERANETMED3-062   CHAAMS "global Change: Assessment and Adaptation to Mediterranean Region Water Scarcity ",  ACCWA-823965/H2020-MSCA-RISE-2018  " Accounting for Climate Change in Water and Agriculture Management " and  PRIMA-S2-ALTOS-2018  "Managing water resources within Mediterranean agrosystems by Accounting for spatiaL sTructures and cOnnectivitieS". Other funding was provided by  PRIMA-IDEWA  projects and  OCP S.
An ERANOS 3D neutron transport solver, VARIANT, is used for this step. The second step performs fuel depletion and reloading to achieve the equilibrium, using the reloading scheme shown on Fig. 3. The third step is for reactivity feedback calculations with a diffusion solver in 3D geometry, except for sodium void worth and sodium expansion effect, calculated with a transport code in 2D RZ geometry. Finally, one should establish a complete set of data for UCRW calculations with the 3D neutron transport code, including the reactivity effects and power shape swings induced by removal of individual rods. MAT5DYN includes a multichannel description, a simplified pin thermal evaluation, and a point-kinetics model for transient simulations. It uses a single-phase description of the coolant, and an extrapolation of the coolant temperature after reaching the boiling temperature.
Then, we measure the performances of these selected designs with the ERANOS/MAT5DYN/GERMINAL scheme, to eliminate the prediction error of the surrogate models. The design with the lowest void effect and a near-zero BG was obtained and denoted as A in Table  5 , but the selected design (B) was chosen after filtering the data basis to respect some constraints of the project. Design B is the core that presents the almost lowest void effect, with a low fertile plate, a unique fuel enrichment, no inner/outer height offset, and a pooling of the axial elevations of the inner and outer fuel SAs to simplify the axial structure. Compared to the preliminary configuration, a reduction of 80% of the total void effect has been performed, while achieving a near-zero BG and slightly reducing the assembly pitch.
The Uatumã event is a silicic large igneous province (SLIP) covering an area of 1. 500. 000 km 2 of the Amazonia craton at ca. 1890 -1850 Ma. New paleomagnetic data and U-Pb apatite ages for coeval microgranitic, andesitic, and basaltic dykes in the Carajás Province (southeastern Amazonia craton) are presented. Two primary characteristic remanent magnetizations (ChRMs) were isolated for the Carajás dykes which were combined with published results for coeval rocks in the São Felix do Xingu area, producing two grand mean poles: (1) "CA1", dated at 1880 Ma on zircon and apatite, whose mean site directions cluster around the mean Dm= 132. 8°, Im= 76° (N=26, α95=5°, k= 32. 7), yielding the paleomagnetic pole at 328. 7°E, 23. 3°S, (A95= 8. 7° K=11. 7), and (2) "CA2" from well-dated microgranitic dykes of the Velho Guilherme Suite (1855 Ma U-Pb on zircon and apatite).
, 2016). Final suturing for Baltica resulted from the collision between Fennoscandia and the Volgo-Sarmatia block at ca. 1750 Ma, along the Svecofennian orogeny, which implies these cratonic blocks were separated at ca. 1880 Ma  (Bogdanova et al. , 2013; Bogdanova et al. , 2016; Lubnina et al. , 2016). The present study addresses the reconstruction of the Amazonia craton during the Paleoproterozoic, one of the major pieces of the Columbia jigsaw. The Amazonia craton is considered to have been linked to West Africa at ca. 1960 Ma after the ~2000 Ma Trans-Amazonian/Eburnean Orogeny (Bispo-  Santos et al. , 2014a; D'Agrella-Filho et al. , 2016; Nomade et al. , 2003; Onstott and Hargraves, 1981; Onstott et al. , 1984b; Théveniaut et al. , 2006). A geological link with Baltica was supported by paleomagnetic data including the Amazonia craton in the core of Columbia connection at latest Paleoproterozoic, at ca.
, 2005) ) and McClure (523. 51 ± 2. 09 Ma;  (Schoene and Bowring, 2006 )) apatite standards were analyzed in the same conditions to control the precision and accuracy of the analyses. Data reduction was carried out with the Iolite software  (Paton et al. , 2011)  and the data reduction scheme VizualAge_UcomPbine  (Chew et al. , 2014). During the analyses, the McClure and Durango apatite standards yielded 207 Pb corrected ages of 526. 0 ± 6. 6 Ma (MSWD = 1. 06; probability = 0. 39) and 32. 3 ± 0. 56 Ma (MSWD = 0. 38; probability = 0. 997) respectively, see Supplementary data 2. In two samples (PY44-46 and PY73), some zircons were handpicked. These samples were selected for U-Pb geochronology on zircon. These analyses were carried out by LA-SF-ICP-MS at the Isotopic Geology Laboratory of the Geosciences Institute -UNICAMP  (Brazil).
Isotope data were acquired using a Thermo Element-XR mass spectrometer coupled to an Excite 193 laser ablation system (Photon Machines). The acquisition protocol includes a spot size of 25 µm with a 10 Hz laser frequency and a 40s ablation time according the procedures of  Navarro et al. (2015). The reference material 91500 zircon was used as primary standard  (Wiedenbeck et al. , 1995) , and data reduction was performed using Iolite software  (Paton et al. , 2011). During the course of analyses, the Peixe zircon (age ID-TIMS of 564 ± 4 Ma;  (Dickinson and Gehrels, 2003) ) was used as a secondary reference mineral and gives an age of 568. 6 ± 3. 6 Ma (MSWD= 1. 4) during our analyses (see supplementary data 3).
Mean remanence directions and paleomagnetic poles were calculated using  Fisher (1953)  statistics. Paleomagnetic data processing and calculations was carried out using PALEOMAC package  (Cogné, 2003). GPlates were used for paleogeographic reconstructions  (Boyden et al. , 2011). In addition, magnetic mineralogy of each site was investigated to determine the carriers of magnetic remanence. Hysteresis loops, isothermal remanent magnetization (IRM) and first order reverse curves (FORC) for selected samples were performed to determine magnetic carriers and domain states, using a MicroMag-VSM, Model 3900 (Princeton Measurements Corporation). Thermomagnetic experiments (susceptibility versus temperature) were conducted in an argon atmosphere in low-and high-temperature conditions using a CS-4 apparatus coupled to the KLY-4S Kappabridge instrument (AGICO, Brno, Czech.
, 2017). The SF1 and CD1 components exhibited both polarities. In view of the similarity in the directions of both SF1 and CD1 components (Figure  7 -B), we can use this dataset to calculate a grand mean pole for the Uatumã SLIP, i. e. , a mean pole calculated from multiple distinct but broadly coeval cooling units of a large igneous province (e. g. , the Umkondo LIP;  (Swanson-Hysell et al. , 2015) ). The grand mean direction (named CA1 -Carajás component) was calculated for the Carajás magmatic event: Dm= 132. 8°, Im= 76° (N=26, α95=5°, k= 32. 7). The respective CA1 paleomagnetic pole is located at 328. 7°E, 23. 3°S (A95= 8. 7° K=11. 7) (Table  4 ; Figure  7-B ). Nine among the twenty-six sites of the CA1 pole were precisely dated by U-Pb method (zircon and baddeleyite)  (Antonio et al. , 2017; Oliveira, 2006; Pinho et al.
, 2017). CA1 component is carried by stable hematite in the rhyolitic rocks of São Felix do Xingu area and PSD magnetite in basaltic dykes of Tucumã and Rio Maria areas. The CA1 pole (328. 7°E, 23. 3°S, A95= 8. 7°) satisfies 6 (Q=6) out of the 6 quality criteria proposed by  Van der Voo (1990) , if we discard his seventh criterion as suggested in the Paleomagia database for Precambrian rocks  (Pivarunas et al. , 2018; Veikkolainen et al. , 2017b) : (  1 ) the four U-Pb dating on apatite and one U-Pb age on zircon from andesitic and basaltic dykes (this study) yielded consistent ages around 1880 Ma, and paleomagnetic analysis on the same dykes revealed similar ChRM directions. These ages are concordant with two U-Pb baddeleyite ages (1880±2 Ma, 1885±2 Ma) determined on two other basaltic dykes in the Rio Maria area  (Teixeira et al.
, 2017). (  5 ) The fact that the same paleomagnetic results were disclosed for volcanic rocks of the São Felix do Xingu area and the Carajás dyke swarm in Tucumã and Rio Maria areas, some 300 km apart implies that no tilting affected these rocks after their emplacement, at least between the studied areas. Moreover, these two areas must belong to the same geological province and a separation into different geological domains as proposed by  Vasquez et al. (2008)  is no longer sustainable. (6) The CA1 component pass a reversal test, which implies the secular variation was averaged out. (7) Even if we discard this criterion, the CA1 pole is different from poles calculated for younger units in the Amazonia craton according to the compiled Precambrian Paleomagnetic database for Amazonia by D'Agrella-  Filho et al.
000 km 2 , the Uatumã SLIP and its thermal footprint have the potential to induce a regional remagnetization. (6) Two polarities were observed, which implies that secular variation was average out. (7) Although the seventh criterion of Van der Voo (1990) may be disregarded for Precambrian rocks (see above), it is obeyed by this component, since it doesn't have any similarity with younger paleomagnetic data available for the Amazonia craton. So, the CA2 grand mean pole can be considered as key (Q= 6) with an age of ~1855 Ma.
Two younger paleomagnetic poles (CD3 and CD4) were also obtained: a ca. 200 Ma pole (CD3 pole) for Jurassic dykes from Carajás is located at 82. 3°S, 325. 6°E (A95= 9. 5°); the CD4 pole (63. 4°S, 113. 7°E, A95= 10. 8°) was obtained for some of the dykes and basement rocks whose age is yet undefined. A revision of the Paleoproterozoic APW paths for Amazonia and West Africa supports a new geological configuration between these two cratons  (Chardon et al. , 2020)  which allows to restore the Sassandra shear zone in West Africa with the North Guiana Through and other shear zones in Guiana Shield. The discrepancy in the ~1890-1850 Ma Paleomagnetic poles observed in several cratons in the world could be better explained by a true polar wander event. However, new good-quality paleomagnetic data is necessary to resolve this issue.
ACKNOWLEDGEMENTS We thank the  Prof. W. Teixeira , the careful contribution of  R. Mitchell , and one anonymous reviewer for constructive comments on the manuscript. We thank the  Universidade Federal do Pará (UFPA)  for the field trip logistical support and  FAPESP  (grants  2012/20335-4 ,  2013/22957-5 ,  2016/13689-5 ,  2017/18840-6 ) for financial support. RD acknowledge support from  Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq ;  Proc. 306108/2014-3  and  304648/2019-1 ) and the  Instituto Nacional de Ciência e Tecnologia de Geociências da Amazônia/Geociam (CNPq-FAPESPA-CAPES-PETROBRAS, Proc. 573733/2008-2 ).
Data cleaning and preprocessing A cleaning step was performed to filter out unusable data: metabolites with more than 50 % of values lying outside the quantification detection limits were removed from the datasets. For all potentially withdrawn features, a Chi-squared test was performed between the number of values within bounds and out-of-bounds in pSS and non-pSS Sicca patients, to prevent removal of discriminating features, i. e. features with a significant difference between the 2 groups. Metabolite concentrations were then normalized before further analyses as described  [52]. 2. 6. Statistical workflow (Fig. 1B ).
General statistics Quantitative data were presented with medians, and 25th and 75th quartiles. Qualitative data were presented as absolute values and as percentages. Quantitative data were compared using a Student's t-test or a Mann-Whitney test as appropriate. Qualitative data were compared using a Chi-squared test or a Fisher's test as appropriate. The type I error was 5 %. Image manipulation and formatting were performed using GNU Image Manipulation Program (GIMP) software (version 2. 10). The analyses were carried out using R software (version 4. 0. 1, R-project-org, Vienna, Austria) and SPSS (v23. 0, IBM Corp, NY, USA). R packages are listed hereafter: FactoMineR for principal component analysis (PCA)  [53] ; Rpart for stratified partitioning  [54] ; glmnet for logistic regression with or without regularization  [55]  based on λ with 1 standard error (SE)  [58] ; randomForest  [56] ; and pROC to evaluate the area under curves for receiver operating characteristic curves -area under the curve (ROC-AUC)  [57].
Random telegraph signal occurrence The RTS has been investigated by acquiring the DCR output of each pixel for 600 s, limiting our data taking to this time window. The presence of the RTS has been first investigated in the devices before irradiation. Some DCR discrete fluctuations have been found in the pre-irradiated samples with small switching activity: in the measured time window, we observe just one or two DCR fluctuations. The fraction of SPADs showing such behaviour has been found to be about 5%. After the irradiation, beside the DCR increase, the appearance of a RTS behaviour (Fig. 7 ) has been observed in most of the SPADs. Moreover, it has been found that RTS occurrence is strictly related to the DCR value, as shown in Fig. 8. In fact, there is a higher probability to observe an RTS behaviour for SPADs that exhibit high DCR after irradiation.
Ethics Statement The database is registered with the Commission Nationale de l'Informatique et des Libertés. In accordance with the ethical standards of our hospital's institutional review board and French law, written informed consent was not needed for demographic and hospital-outcome data analyses because this observational study did not modify existing diagnostic or therapeutic strategies; however, patients were informed of their inclusion in the study. This work adheres to the World Medical Association Declaration of Helsinki. The manuscript was prepared in accordance with the STrengthening the Reporting of Observational studies in Epidemiology (STROBE) statement.
The patient had an intravenous line placed by the nurse and was positioned in a Leksell-G stereotactic frame. Tridimensional gadolinium-enhanced and uid-attenuated inversion recovery sequences were performed on a 1. 5 Tesla MR scanner (Signa, General Electric, Boston, MA). Once these images were acquired, the trajectory and depth coordinates were calculated with Framelink (Medtronic, Minneapolis, MN) software. The biopsy path was carefully chosen so as to avoid damaging critical super cial and deep veins and arteries. This route was simultaneously controlled millimeter-by-millimeter in the 3 spatial planes (3D view), and in the perpendicular and parallel oblique views of the needle trajectory. After the MRI, the patient was transported to the operating room. Oxygen goggles, electrodes for electrocardiographic monitoring, pulse oximeter and an automatic blood pressure cuff were placed on the patient.