dataesr/scientific-paragraphs-categorization huggingface dataset:
Although HTS workflows have been developed for yam detection  [36, 57, 58] , they have not yet been incorporated into yam sanitation programs or seed systems, likely because the high cost associated with HTS remains a major limitation. Multiplexing more than one sample on the same run could make HTS more cost-effective, but additional work is required to assess to what extent this would affect sensitivity and suitability for testing in vitro plantlets, especially for viruses with low titer. Another limitation of HTS is that the bioinformatics analysis of HTS datasets requires expertise and computer and data storage resources that may not be readily available  [93]. Additional work is needed to develop bioinformatic pipelines suitable for operators with limited bioinformatic expertise that can be used to analyze HTS data.
Adeniji et al. [104]  designed a more suitable, although small-scale, experimental system in Nigeria, in which they manually inoculated YMV on D. rotundata plants and assessed the impact of infection on a range of physiological traits and yield. For this, they performed virus indexing targeting YMV, YMMV, DaBV (BDALV), and CMV using TAS-ELISA, whose sensitivity and specificity is not optimal, as discussed above. Symptoms and impact of YMV infection on plant growth and yield losses were registered and compared between infected and mock-inoculated plants. However, the presence and impacts of other viruses (such as YVY, YaV1, or DMaV) that have since been identified and shown to be widespread in West Africa  [5, 17, 23, 24] , were not monitored and may well have impacted results obtained in the experiments of Adeniji et al.
Washburn, 2000; Devers & Frankel, 2000). Most of the interviews took place on site and lasted from two to five hours to promote observation and narration. The first part of the interview aimed to grasp the reflexive engagement of the interviewee in the narration of his or her trajectory and activity, organisational choices and sectoral and territorial insertion. During this first part, only precise questions were asked, while the second part included thematic questions. The interviews were transcribed and coded using ATLAS. ti (software used for the qualitative analysis of large volumes of text) to capture the organisational representations and routines of the various stakeholders as accurately as possible.
FUNDING JJ and EM are supported by the  National Research Agency (BLinK   ANR-18-CE92-0015 , Alpalga  ANR-20-CE02-0020 , GlycoAlps  ANR-15-IDEX-02 ,  GRAL  Labex  ANR-10-LABEX-04 , and  EUR CBS ANR-17-EURE-0003 ) and Institut Carnot  3BCAR. EM was supported by the  Kilian Jornet Foundation. MS and KA are supported by the  Japan Society for the Promotion of Science (JSPS) KAKENHI  ( JP18H03941 ). MS was supported by  JSPS KAKENHI  ( 21K05325 ). KA was supported by  JSPS KAKENHI  ( 20K06683 ).
Morphological Identification Isolated fungi were cultured, purified on PDA plates, and incubated at 25 °C, then criteria, such as color and appearance of colonies, were recorded after 10 days  [30]. To force the isolates' sporulation, colonized plug agar of each one was cultured first on malt extract agar medium (MEA; Sigma-Aldrich, St. Louis, MO, USA), then the isolates that did not sporulate directly on MA were transferred into PDA medium supplemented with three to four pine needles already double-autoclaved. Plates were then incubated at 25 °C exposed to 12 h/12 h of light/darkness cycle. The diameters of conidia for each isolate (at least 100 conidia) were noted using the microscope (Olympus EX41) linked with the camera and ImageFocus Plus V2 Software.
PCR program consisted of an initial denaturation step for 3 min at 94 °C, then 35 cycles of 94 °C for 1 min, 55 °C for 1 min, 72 °C for 1 min, and the final extension step took about 10 min at 72 °C. PCR products were visualized by 1. 5% agarose gel electrophoresis, then purified and sequenced by STAB Vida, Lda. (Portugal). Both sequences, forward and reverse, were assembled and aligned using Molecular Evolutionary Genetics Analysis (MEGA) and the Basic Local Alignment Search Tool (BLAST) was used to compare the assembled ITS and cmdA sequences with all the sequenced isolates already deposed in the GeneBank. The phylogenetic tree was created using the maximum likelihood method with 1000 bootstrap values Reference isolates used are reported in Table  1.
Discussion The present work is the first attempt to identify various pathogens, causing symptoms of dieback and wood canker on the almond tree in the Fez region, Morocco. These included C. hawaiiensis, F. ambrosium, L. theobromae, and C. purpureum. The identification of isolated pathogens was first confirmed by means of cultural and conidial morphology, then DNA sequence data and pathogenicity tests. Molecular detection was used to validate the identity of isolated fungi using the internal transcribed region (ITS) and calmodulin (cmdA). Based on previous reports, the L. theobromae species of the Botryosphaeriaceae is well known as a serious parasite of wood worldwide, infecting an extensive variety of woody trees, and causing diverse disease symptoms, namely dieback, gummosis, and canker  [40].
ACKNOWLEDGEMENTS We thank  St ephane Verger  and  Anne-Lise Routier-Kierzkowska  for helpful comments on the manuscript. This work was funded by an  International Postdoc grant from Vetenskapsra ˚det  ( 2020-06442 ) to K. J. and by grants from the  Knut and Alice Wallenberg Foundation  ( 2014-0032 ),  Kempe Foundation and Vetenskapsra ˚det  ( 2016-00504 ) to R. P. B.
The mean degree of polymerization (mDP) was calculated as the ratio between the summed molar concentrations of all released constitutive units and the summed molar concentrations of lower constitutive units. For analysis of lower molecular weight phenolic compounds, wine was injected directly (0. 5 µL) after centrifugation (15,000 rpm, 15 min) in triplicate. Identifications were performed by comparison of retention times, UV-visible and MS data with those of standards. The concentrations of gallic acid and flavanol monomers, dimers and trimers were calculated from peak areas at 280 nm and those of hydroxycinnamic acids from peak areas at 320 nm, using calibration curves established with commercial standards.
, 2009)  balancing order and position effects. The protocol of the sensory evaluation of one sample is represented in Fig. 1. Briefly, the sensory evaluation consisted in evaluating three consecutive repetitions of the same sample. Thus, for each sample, three glasses containing one sip of 10 mL were presented to the subjects. The consumption of the three glasses had to respect a strict protocol, which has been programmed using TimeSens 1. 0. software (INRAE, Dijon, France). TimeSens controlled the sequence of events. For each event, instructions and timing were displayed on a screen in front of the subject. The protocol of consumption consisted in waiting 30 s before putting the first sample in the mouth, allowing to record the blank of the composition of the air from the nasal cavity by the PTR-ToF-MS.
In-vitro experiments Volatile compounds of the wine samples were analysed by direct injection -HS analysis. All the measurements were performed using a commercial PTR-ToF-MS instrument (PTR-ToF 8000, Ionicon Analytik GmbH, Innsbruck, Austria) with [H 2 O + H] + as reagent ion (O 2 + signal intensity was ca. 0. 5% of the [H 2 O + H] + one). Succeeding several preliminary tests, parameters of the PTR-MS instrument were chosen and set up as following: drift pressure of 231 Pa, drift temperature of 80 • C, transfer line temperature 110 • C and drift voltage of 390 V, resulting in electric field strength to number density ratio (E/N ratio) of 90 Townsend (Td, 1Td = 10 -17 V. cm 2 ). Data were collected using the TofDAQ software provided by the manufacturer of the PTR-ToF-MS. Data acquisition was performed at 1 mass spectrum ranging from m/z 0 to 226 per 0.
Statistical analyses For each studied ion, its 0-50 s area under the curve was analysed with a repeated mixed model of ANOVA using the procedure MIXED from the SAS software. The model featured wines (6 levels) and sips (3 levels) as fixed effects, while panellist and its interaction with wine and sip were random effects with an instructed covariance matrix between them. The sip factor was declared as repeated within panellist by wine and replication with an unstructured covariance matrix. Estimation of the model was done by restricted maximum likelihood (REML). Sip effect was significant for most ions denoting evolutions over time. However, sip by wine interactions were never significant denoting that these evolutions were the same across wine for every ion. Therefore, sip effects will not be reported here, but contributed to a better estimation of the model.
However, as aroma persistence (i. e. , 50-80 s) was not evaluated by TDS sensory analysis, further trials to confirm this interesting outcome are necessary. is a wine ester contributing to wine aroma. Its organoleptic profile can be described as fruity, apple, grape  (Waterhouse et al. , 2016). Together with ethyl hexanoate and ethyl octanoate, ethyl decanoate is considered as being a highly positive aroma compound of young wine "bouquet", introducing fruity flavour notes  (Waterhouse et al. , 2016). Thus, the decrease of the fruity attribute in OW compared to BW in TDS experiment could be linked to the decrease of ethyl decanoate during the process of wine oxidation. During the parallel in-vitro experiment (no saliva) conducted by Headspace -Solid Phase Microextraction -Gas Chromatography -Mass Spectrometry (HS-SPME -GC-MS) analyses (data not shown), a similar result has been obtained, confirming a significant lower concentration of ethyl decanoate, together with other important wine esters (e.
1a ). In addition, it seems that DISC trials conducted in the Mediterranean Sea are characterized by lower R Δθ compared to DISC trials from the Red Sea and the Great Barrier Reef. This might be related to differences in cue availability, that is affected by environmental conditions such as water turbidity and overcast sky conditions  19. The fact that both the original and subsampled DISC datasets exhibited quantile distribution significantly higher than what is expected under CRW further supports the indication for directed movement by fish larvae. Previous studies demonstrated that increase in sampling length (or reduction in sampling frequency) leads to an obstruction of the short-term persistence, making it appear more BRW, and leading to a decrease in the animal's apparent speed  49, 50.
g. , CRW composite, in which there is more than a single CRW pattern per a given sequence, and zig zag patterns, in which consecutive turning angles are drawn from von mises distributions centered around positive and negative values, respectively (Supplementary note 4). We apply our methods to a database of 835 in situ orientation trials gathered on larvae of 21 species from eight families of perciform fishes at various tropical and warm-water locations in East Asia  14, 15  , Australia  [16] [17] [18]  , Mediterranean  52  and Red Sea  19  , synthesized from eight previously published studies (Table  1 ). These studies examined the orientation behavior of settlement-stage  17  and pre-settlement-stage 18 larvae 15 of reef-14 , non-reef  20  , and pelagic 15 fish species. In addition, some of these studies examine whether larval fish use directional information from the sun for oriented movement  19, 52  , as well as the difference in orientation patterns between individuals versus groups of larvae  16.
The number of observations per DISC deployment (N obs = 90, 180 or 300; see Table  1 ) varies with the recording frequency of larval positions, ranging from 2 to 10 seconds (Table  1 ). Some of the DISC trials had missing data due to the fact that the position of the larva is not always identified during the manual digitization of the DISC trials, due to the small size of the larva and due to unfavorable visibility conditions  54. Trials that had N obs smaller than the required number were not used for the analyses. For the DISC trials, N obs that had to be larger than 90% of the maximal N obs designated per group (i. e. , N obs > 81, 162, 270). Trials with N obs higher than the maximal N obs were trimmed to contain the maximal N obs per species , retaining the later-in-time data. For the scuba-following trials, the number of observations had to be N obs > 20 due to the sensitivity of the analysis to a low number of observations.
Acknowledgements We would like to thank everyone who have contributed to these valuable datasets over the years. We thank the three anonymous reviewers whose comments and suggestions helped improve and clarify this manuscript. I. B. was funded by the  National Academy of Science, Engineering and Medicine -Gulf research Program NASEM-GRP  award number  2000007703  to  Steven Murawski  and C. B. P; R. F. and J. O. I were funded by the  Paris Lab of the Rosenstiel School of Marine and Atmospheric Sciences  and a grant from the  Partner University Fund  (PUF); M. K. was funded by the  Binational Science Foundation BSF  Grant number 2008144; J. M. L. and U. S. were funded by the  Australia Research Council (ARC)   Discovery Grant   DP110100695. The Study was made possible through a  National Science Foundation  Award  NSF-OCE 1459156  to C.
(1995). Then, binary thresholding (B&W) was performed using Otsu's method  (Otsu, 1979; Gée et al. , 2021). Finally, the distribution of leaf area vs. relative plant height was determined. All the imageprocessing algorithms were implemented in Matlab (Version 2016b, The Mathworks, Natick, MA, United States). Then, plant height and width, leaf area and biomass as well as total above-ground biomass were measured. For the latter two, leaves (including petioles), stems, and reproductive parts were discriminated. At each sampling stage and for each variety, these measurements were used to determine eight parameters (Figures  1A-H ) characterizing potential plant morphology by fitting key state variables (e. g. , plant height or width) against above-ground biomass using the plants grown in unshaded conditions.
Then, five shade-response parameters (Figures  1I-M ) were estimated by fitting the main morphology variables (e. g. , specific leaf area SLA) against shading intensity (i. e. , 1 -PAR in shaded/PAR in unshaded conditions) with a non-linear regression using all (shaded and unshaded) plants sampled at the same stage. Finally, for each variety, the parameter values from the five sampling stages were extrapolated to obtain parameter values for 11 BBCH stages ranging from emergence (stage 0) to full maturity (stage 10), using non-parametric regressions. All statistical analyses were carried out, using SAS (PROC REG, NLIN, and LOESS). Further details can be found in section B of the Supplementary Material.
Create Virtual Pea Varieties To determine correlations among pea parameters, Pearson correlations coefficients were calculated among the 220 parameters of the seven parameterized pea varieties, using corr() of Hmisc package of R (R Core Team, 2016). In addition, the minimum and maximum values for each quantitative parameter were determined for pea (section D. 3 of the Supplementary Material). This range of variation was extended to [0. 9 × min, 1. 1 × max] for each parameter, but capped to remain biologically realistic (e. g. , a proportion such as a harvest index needed to be in [0, 1] g/g). Furthermore, ten virtual pea varieties were created by randomly drawing parameter values inside the extended range of variation of the seven actual varieties following a Latin Hypercube Sampling (LHS) plan and using the correlation matrix as constraints.
03-0. 06). The Latin Hypercube Sampling (LHS) plan thus allowed decorrelating management variables. Correlations among rotation variables or between rotation and situation were much higher (0. 12-0. 21), reflecting the rotation rules fixed for each situation. Pea parameters were highly correlated (0. 23-0. 3), reflecting the biological correlations among variety characteristics, which we introduced by constraining the LHS via parameter correlations. The 9 × 400 cropping systems were simulated over 12 consecutive years to assess long-term effects and repeated five times with five weather series consisting of randomly chosen records from the INRAE Dijon weather station (INRAE Climatik database). Each system × repetition was run twice, once starting with weeds and once without, to assess potential crop yield.
Branches are combinations of predictor values that lead to predictions contained in leaf nodes. The trees were computed with the R package mvpart (Glenn  De'ath, 2014). The optimal tree size was internally identified using a 10-fold cross-validation procedure to avoid overfitting. In the following, R 2 refers to the cross-validated R 2 of the resulting tree. Predictors (including surrogate variables that would split the data set exactly as the primary splitting variables) were ranked according to their relative Variable Importance Predictor (VIP, rescaled here by dividing by the total amount of variability explained by the tree, see section D. 4 of the Supplementary Material). The CARTs were built, allowing up to "perfect" 20 surrogates (i. e. , with raw agreement = 1) per split. In addition, the probability that the analyzed response variable increases when the predictor value increases were estimated by summing the relative number of individuals that split the branch toward a higher predictor value, over all tree nodes including the predictor as a primary or surrogate splitting variable.
Only pea crops with herbicides were used here. The highlighted branches show the best and third-best performances (which are also shown in Table  5A ). Boxes show principal and surrogate predictors and thresholds for splitting branches (only for the two highlighted branches). Leaves (at the bottom of the tree) and nodes show indicator values normed to [0 = lowest yield, 1 = highest yield of simulated data set]; leaves are colored from red (lowest yield) through yellow (intermeidate yield) to green (highest yield). Percentages below nodes show the proportion of individuals that fall into that node. The root node at the top of the tree has 100% since the dataset has not been split yet  (Colbach, 2021  ). nearly flowering onset and then continuously decreased until full maturity, regardless of the variety.
As variety performance has been shown to vary among regions and years  (McDonald, 2003; Jacob et al. , 2017) , our study must now be repeated in other pedoclimates to adapt the selection and farming guidelines. These will probably vary, as they do here among cropping systems. agreement N 727217 (ReMIX project), and the Casdar RAID project funded by the French Ministry in charge of Agriculture and Food (Ministère de l'Agriculture et de l'Alimentation, avec la contribution financière du compte d'affectation spéciale 'Développement agricole et rural').
Genetic and Phylogenetic Analysis of Pseudomonas ST1 and Pantoea Paga Two genomes, Pseudomonas ST1 and Pantoea paga strains have been sequenced earlier and deposited under the accession numbers VKOF00000000. 1  [37]  and VLTF00000000  [38] , respectively. Genomes of Pseudomonas ST1 and Pantoea paga strains were analyzed on the Mage platform  [39]  to compute clusters of orthologous genes (COGs)  [40]. Using antiSMASH  [41]  genes clusters involved in the biosynthesis of secondary metabolites and virulence factors  [42]  were identified. Using GBDP distances calculated from 16S rDNA gene sequences, phylogenetic trees were created with FastME 2. 1. 6. 1. The branch lengths are scaled in terms of GBDP distance formula d5. The numbers above branches are GBDP pseudo-bootstrap support values > 60% from 100 replications, with an average branch support of 52.
Replicates of five plants per cultivar with ten lateral wounds was used (in total, fifty wounds per treatment condition and cultivar). In control plants no inoculation with bacterial strains was performed. Olive trees were assessed 6 months after inoculation and the percentage of knot formation was calculated for each treatment (number of wounds with symptoms/total number of wounds × 100). Treatments were evaluated based on the incidence of disease. The data for knot formation in different treatments were subjected to an analysis of variance using generalised linear models in SAS software (SAS Institute Inc. , Cary, NC, USA). Differences between groups were determined by the LSD test at p ≤ 0. 05. To confirm the presence of bacteria in lateral wounds, bacteria from the olive knots and plant tissue around the wounds were cultured from the plants that showed symptoms of infection as well as from the plants that did not develop symptoms including control plants.
Funding: This research was funded by the  project Biodiversity and Molecular Plant Breeding, Centre of Excellence for Biodiversity and Molecular Plant Breeding  ( CoE CroP-BioDiv ),  Zagreb ,  Croatia , grant number  KK. 01. 1. 1. 01. 0005 ; by the  Split-Dalmatia County  grant for the project "Agents, transmitters and bio-control of olive knot disease in the olive groves of the Split Dalmatia County". M. R. B. is a Ph. D. fellow supported by a  French government  scholarship in 2019/2020 that was coordinated by the  Ministry of Science and Education of Republic of Croatia, Agency for Mobility and EU Programmes and Embassy of the French Republic  to the  Republic of Croatia. Institutional Review Board Statement: Not applicable. Informed Consent Statement: Not applicable.
The SAP is primarily secreted by hepatocytes and macrophages into the circulation and acts as a soluble pattern recognition receptor of the innate immune system  61. Database searches and functional enrichment analysis demonstrated that SAP associated with HDL might play a role in cholesterol removal from cells  62. Furthermore, there is mounting evidence that in mice treated with SAP, the plasma paraoxonase1 (PON1) activity was increased  63. In this regard, a significantly greater paraoxonase activity level was observed in the EFA + CLA group, albeit limited to day 49  2. At the last timepoint (day 63 PP), concurrent with the shift to a positive EB in the EFA + CLA group, no other pathways were detected or activated apart from common APO pathways (overlapping pathways). This suggests that the beneficial effects of supplemented FA were more relevant during physiological and immunological challenges in the early PP phase.
05). The identified and the quantified peptide ions were then searched against Bos taurus decoy database (Uniprot, download date: 2019/11/07, a total of 37,513 entries) in MASCOT (version 2. 5. 1) interrogation engine, with the following setting: trypsin as an enzyme digest of a protein, tryptic specificity to cleavage C-terminal after lysine or arginine residues, allowing two missed cleavages, variable modification to carbamidomethylation (C) and oxidation (M), mass tolerance to 10 ppm for precursor ions and 0. 02 Da for fragment ions, and FDR < 0. 01. Accordingly, the corresponding proteins with at least two peptides and two unique validated peptides were identified and quantified based on their intensities. Before statistical analysis, logarithmic transformation was applied to protein intensities, and missing intensities (with the frequency of less than 50% of samples) were imputed and replaced by the 1/5 of the minimum positive value of each variable in the original dataset.