dataesr/scientific-paragraphs-categorization huggingface dataset:
g. every 10 min from 10 to 60 min) and analyzing the rate of migration of the water front from the internal part to the periphery for a selection of cassava genotypes with contrasting cooking quality. In this study, the potential of hyperspectral imaging for the visualization of DMC and WAB in fresh and cooked slices of cassava was evaluated. A high-quality model was developed for the prediction of DMC distribution in fresh slices of cassava using the CovSel_MLR model; however, a model for prediction of WAB and texture by HSI may necessitate collecting a larger dataset. In the meantime, PCA coupled with HSI was used for the visualization of WAB variation in cooked slices of boiled cassava, with the potential to investigate the rate of absorption of water during boiling, from the central part towards the periphery of the slices.
No correlation was found between cooking quality and DMC of fresh roots, as observed previously. 9 Moreover, HSI revealed that the heterogeneity of DMC distribution within fresh cassava roots had no effect on cooking quality either. Contrary to cassava, in other roots, tubers, and bananas (RTBs), such as yam, dry matter is a key factor determining cooking quality and consumers' preferences. 54 ence, applying HSI to other RTBs may result in more effective predictions of cooking quality than was found for cassava in the present study. The model to predict and visualize the distribution of DMC and the PCA approach to visualize the distribution of water content after boiling can contribute to a better understanding of cooking behavior of boiled cassava and selection of desirable genotypes. The weak performance of the PLSR models to predict physical parameters (WAB and texture) may be due to the lack of direct correlation between NIR-HSI and physical constituents, and/or the low number of samples in the dataset.
CONCLUSION The current work demonstrated the potential of HSI as a highthroughput tool, since it can detect differences between genotypes. In particular, the heterogeneity of distribution of DMC between the center and the periphery and between the proximal and distal ends of cassava roots is very useful. This could help in understanding, for example, the variation in concentration of relevant nutritive constituents, such as carotenoids. 55 uture research on HSI applied to prediction of cooking quality of cassava can investigate several points, including to increase the dataset of HSI, DMC, WAB, and texture to more than 200 samples, in order to confirm the lack of correlation between the heterogeneity index of DMC distribution and cooking quality, and to improve the model of prediction of WAB and/or texture; to develop a dataset of HSI and various components of cassava roots (starch, amylose, pectins, etc.
ACKNOWLEDGEMENTS We are grateful to  CGIAR Research Program on Roots, Tubers and Bananas (RTB)  and the grant opportunity  INV-008567  (formerly OPP1178942):  Breeding RTB Products for End User Preferences (RTBfoods)  from the  Bill & Melinda Gates Foundation (BMGF) , coordinated by the  French Agricultural Research Centre for International Development (CIRAD , Montpellier, France): https:// rtbfoods. cirad. fr. Previous versions of this paper and the ideas in it benefited greatly from suggestions and comments by  Dr Xiaofei Zhang. We particularly thank  Dr Hernan Ceballos  for his expert feedback on the paper's content and  Clair Hershey  for the English editing. Particular thanks also go to the substantial work of the field team of  CIAT 's  Cassava Program  for growing and harvesting the cassava genotypes, and to the excellent logistical organization of the  Postharvest Quality laboratory team  to prepare all the samples and carry out the multiple analyses with accuracy and timeliness.
Quality criteria for the initial assessment A consultation prior to the initiation of PN by the dietician was carried out in 24% (n = 21/86) of cases. All the pre-therapeutic clinical data (weight at the time of the prescription and one month and six months before, height, Body Mass Index) was reported in 45% (n = 39/86) of cases (table  IX ). The biological evaluation was incomplete: blood ionogram including phosphoremia and magnesemia was carried out in 49% of cases (n = 42/86). Triglyceridemia was measured 3% of cases (n = 3/86).
On the day after injection, the vaginas were inspected to detect any plug that would indicate that copulation took place. Females with no plug and all males were saved for another round of experimentation. Females with a plug were isolated until term delivery, approximately 3 weeks later. At the time of delivery, the number of newborns was recorded. Table  1a  summarizes the results. Table  1. Litter size. Each of the 3 panels reports the number of newborns obtained in one of the 3 experiments. Panel (a) gathered the data obtained by intravaginal injection of 40 µL of Lyral. Panel (b) groups those obtained with Hexanal and panel (c) reports the results obtained with Lyral when the latter was deposited on the back of the "test" mice and not in the vagina; For the 3 panels, columns 1 and 3 correspond to the identity of the "test" and "control" mice respectively, columns 2 and 4 give the size of the litters.
The approach enabled efficient data generation data from each fruit (and allowed intra-fruit variation to be addressed) and ensured that sampling sites were of a sufficient distance apart that the measurements could be considered completely independent of one another. As a point of reference, the level of ellagic acid in the peel was determined aer RI. The entire peel of the fruit was desiccated, weighed, and sonicated as described previously. Liquid chromatography-mass spectrometric (LC-MS) analysis. Sample analyses were performed using an Agilent QTOF 6545 with Jetstream ESI spray source coupled to an Agilent 1260 Innity II Quaternary Pump UHPLC (Agilent Technologies, Santa Clara, USA) with 1260 autosampler, column oven compartment and variable wavelength detector. The MS was operated in all-ions mode with scan range 50-1700 m/z, 20 000 : 1 resolution and was calibrated using a reference introduced from the independent ESI reference sprayer.
Samples from the in vitro experiments were injected in negative ionisation mode onto a reverse-phase InnityLab Poroshell 120 EC-C18 (3. 0 × 50 mm, 2. 7 mm) column (Agilent Technologies, Santa Clara, USA) using 0. 1% (v/v) formic acid in water (mobile phase A) and in methanol (mobile phase B). Accurate mass measurements are reported to four decimal places. For improved retention of amino acids, samples from the experiments in fructo were subjected to further LC-MS analyses using a HILIC column (Agilent InnityLab Poroshell 120 HILIC-Z; dimensions, 2. 1 × 100 mm, 2. 7 mm). Details of the gradient schedules are given in ESI Table  S1. † LC-MS operational conditions are in ESI Table  S2. † Identication of phytochemicals. Agilent Qualitative Analysis 10. 0 soware enabled compound searching of sample spectral results against a METLIN database of >80 000 compound entries.
Aer the in vitro RI screening experiment, data generated from the injection of one anodal and one cathodal sample were interrogated using the 'Find by Formula' mining algorithm which returned molecular ions within 5 ppm of the reference library matches. The mass spectra of these 'hits' were exported to a personal compound database and library (PCDL). Where the hit target scores were >99, but were not found in the METLIN database, mass spectra were imported from other sources to nd matches. The PCDL was used as a much smaller database for 'qualifying' hits for the rest of the samples. Qualication of molecular ions was performed using the accurate mass measurement of at least two fragment ions present in the MS/MS library spectra with a coelution score of >75. Relative quantication using the integrated areas of the extracted-ion chromatograms (EIC) was performed in Agilent Quantitative Analysis 10.
The IS was diluted to 10 mg mL -1 in acetonitrile, and 20 mL aliquots were added directly to 0. 5 mL of sample before injection (20 ng mL -1 to 1. 9 mg mL -1 linear calibration range; r 2 $ 0. 99). Data analysis and statistics. Unless otherwise stated, the results are reported as arithmetic means (±standard deviation (SD)). Anodal, cathodal, and passive quantities of extracted ellagic acid were determined directly or, for uncalibrated extracted phytochemicals, relatively from the EIC response measured. From these results, extraction uxes at each sampling interval could then be deduced (units: in mg h -1 or EIC response per h, respectively). Statistical analyses were performed using GraphPad Prism Version 9. 0 soware (San Diego, CA, USA) and the level of statistical signicance was set at a # 0.
Model calibration The parameters for additional bone remodeling and placental diffusion were estimated by Bayesian inference using, respectively, maternal BLLs over pregnancy and paired concentration data in the mothers and newborns at delivery. Rothenberg's study  (Rothenberg et al. , 1994)  was used to estimate additional bone remodeling (parameters CABR and STBR). In their study, Pb in maternal blood was measured in 105 women living in the valley of Mexico between March 1987 and June 1992. Samples were taken from week 12 to week 36 of pregnancy. Among these women, the mean gestational age was 39. 9 weeks, and the mean maternal age was 27. 5 years. Data from a separate study  (Nashashibi et al. , 1999)  was included to calibrate the diffusion constant of Pb in the placenta (KD pl ). This study reported Pb levels in the mother's blood and cord blood at delivery in 47 mother-newborn pairs  (Nashashibi et al.
, 1999). The gestational age and the mother's age were not reported: for our simulations, we assumed a mean age of women of 29 and a gestational age of 39 weeks at delivery. From these two datasets, the parameters CABR and STBR were estimated as population parameters; KD pl and the interindividual variability of KD pl were estimated in a hierarchical model which produced an estimate of KD pl for each woman. Because the exposure of the women was not known, the daily intake (DI) of each woman was also estimated independently for each woman assuming a constant exposure per unit body weight of the women since the birth. The p-PBPK model was calibrated using a Bayesian approach with Markov Chain Monte Carlo (MCMC) simulations using the Metropolis-Hastings algorithm. A noninformative uniform prior distribution between 0 and 30 was assigned to the magnitude of additional bone remodeling, CABR.
Comparison with literature data The p-PBPK model for Pb was evaluated using observed ratios between Pb levels in the umbilical cord and maternal blood in five studies  (Gulson et al. , 2016a; Ong et al. , 1985; Yazbeck et al. , 2007; Ladele et al. , 2019; Alemam et al. , 2022). Their characteristics are reported in Table  1. Blood samples were collected at delivery or within hours. Mean gestational age was reported in one study  (Ladele et al. , 2019) , otherwise, it was set to 39 weeks.
Software The p-PBPK model (DOI: https://doi. org/10. 5281/zenodo. 8032483) was developed in GNU MCSim  (Bois, 2009; Maszle and Bois, 1997)  version v6. 2. 0. Graphical representations were made using R version 4. 2. 2 (R Core Team, 2022). Data of bone turnover markers and some BLLs were extracted from plots in the original publications with Plot Digitizer free software, version 2. 6. 9-9 October 2020  (Huwaldt, 2014).
Model fit to the calibration data The estimated maternal BLLs and the 95% credibility interval (CI) during pregnancy are presented in Fig. 3  with the data used for model calibration  (Rothenberg et al. , 1994). All mean observations but one are encompassed in the 95% CI. Estimated variability is slightly lower than measured variability represented as the standard error of the mean (SEM). This can be explained by the fact that the model was calibrated with the mean data only, meaning that no variability between women was accounted for. For instance, the same exposure was estimated for all women. The median predicted maternal BLL decreased by 32% between the beginning of pregnancy and the start of additional bone remodeling (21 weeks of fetal age), mainly due to the hemodilution and the increase of the maternal volume of distribution.
, 2017; Abduljalil et al. , 2021; ICRP, 2002; Abduljalil et al. , 2012). Further research and data collection could help in refining other parameters that highly influence the blood levels and the Pb concentrations in target tissues. Adult values were assigned for several of these parameters, as binding parameters in blood (BIND and KBIND), accumulation in bones (LEAD) or tissue's affinity. For that latter, a way to refine their values could be to dose Pb and environmental contaminants in aborted fetuses  (Cao et al. , 2012; Mamsen et al. , 2019). Some uncertainties remain in the placental transfer rates during the early stages of pregnancy because of a lack of knowledge. To calibrate those rates, the only data available are usually the cord blood concentrations at delivery (as in our study).
Predicted maternal exposures were compared with potential exposure levels, using literature data or exposure models, to derive AOP-based margins of exposures. Coupling of the p-PBPK/AOP model enabled to determine whether maternal exposure levels to chemicals were likely to induce effects such as those observed in vitro, considering the critical developmental stages linked to fetal vasculargenesis and angiogenesis. An extension of our work could be to couple the p-PBPK model to dose-effect relationships (as quantitative AOP) to develop a predictive model of the Pb effects on the child neurodevelopmental system during early life. There are several qualitative AOPs related to brain development, including AOP 13 from AOP Wiki, which describes the chronic binding of an antagonist to NMDA receptors during synapse formation (Bal-Price and Meek, 2017).
8. The abundance of 21 OTUs was significantly decreased (blue dots) and that of 4 OTUs (red dots) was significantly increased in the fecal microbiota of L. helveticus-supplemented mice compared to that of control mice (Fig. 8  and Supplementary Fig. 3 ). For each OTU identity, the seed sequence was selected and compared to the 16S ribosomal database of NCBI with BLASTN and default parameters (Table  1 ). Among the 25 OTUs whose abundance were modified by the L. helveticus supplementation, 21 belonged to the Firmicutes phylum, 2 belonged to the Actinobacteria phylum, 1 belonged to the Verrucomicrobia phylum and 1 was not classified (Table  1 ). Twenty-three of the OTU sequences presented percentage identities of less than 98. 5% when they were compared with the sequences of the NCBI database.
Then a PERL program was applied for rigorous dereplication (i. e. clustering of strictly identical sequences). The dereplicated reads were globally aligned using the Infernal tool  82  , and clustered into operational taxonomic units (OTUs) using a similarity threshold of 97%. A filtering step was carried out to remove chimeras based on the quality of their taxonomic assignments. Finally, the retained reads were homogenized by random selection (28,663 reads for 16S rRNA gene sequences) to compare the datasets efficiently and avoid biased community comparisons. The retained high-quality reads were used to determine alpha-diversity metrics after clustering refining with ReClustOR to improve OTUs definition  83  , and taxonomy-based analysis was performed using USEARCH against the SILVA 16S rRNA reference database (r132).
Lipid class distributions Total lipids were extracted from plasma, livers and retinas following the Folch's procedure  84. The distribution of lipids into different classes [phospholipids (PL), triglycerides (TG), diglycerides (DG), free fatty acids (FFA), free cholesterol (Chol), and/or cholesteryl esters (CE)] was determined using a combination of thin-layer chromatography on silica gel-coated quartz rods and flame ionization detection (Iatroscan® system, Iatron, Tokyo, Japan), according to Ackman's technique  85. The values obtained for each compound were corrected according to their response factor using specific calibration curves. Data were reported as a percentage relative to total lipids in the sample (considered as 100%).
Ultra-high-performance liquid chomatography (UHPLC) separation was achieved using an ULTIMATE 3000 LC pump and an ULTIMATE 3000 Autosampler (Thermo Scientific, San Jose, CA, USA). The mobile phase consisted of (A) CH3CN/H2O (96/4, v/v) containing 10mM ammonium acetate and (B) CH3CN/H2O (50/50, v/v) containing 10mM ammonium acetate. The chosen solvent-gradient system of the analytical pump was as follows : 0 min 100% A, 12 min 80% A, 18 min 50% A, 18. 1-30 min 100% A. The flow rate was 500 μL/min, the injection volume was 10 µL and the column was maintained at 50°C. The liquid chromatography system was controlled by Standard Instrument Integration (SII) software based on Dionex Chromeleon TN 7. The process of identification and quantification of phospholipid species was performed on an orbitrap FusionTM Tribrid Mass Spectrometer equipped with an EASY-MAX NG Ion Source (Heated Electrospray Ionization H-ESI) (Thermo Scientific, San Jose, CA, USA).
Phospholipid species were detected by high-resolution mass spectrometry (HRMS) analysis. H-ESI source parameters were optimized and set as follows: ion transfer tube temperature of 285°C, vaporizer temperature of 370°C, sheath gas flow rate of 35 au, sweep gas of 1 au, auxiliary gas flow rate of 25 au. Positive and negative ions were monitored alternatively by switching the polarity approach with a static spray voltage at 3500V and 2800V in positive and negative mode respectively. Mass spectra in full scan mode were obtained using the Orbitrap mass analyzer with the normal mass range and a target resolution of 240,000 (FWHM at m/z 200), in a mass-to-charge ratio m/z ranging from 200 to 1600 using a Quadrupole isolation in a normal mass range. All MS data were recorded using a maximum injection time of 100 ms, automatic gain control (AGC) target (%) at 112.
5, RF lens (%) at 50, and one microscan. An intensity threshold filter of 1. 103 counts was applied. For tandem mass spectrometry (MS/MS) analyses, the data-dependent mode was used for the characterization of phospholipid species. Precursor isolation was performed in the Quadrupole analyzer with an isolation width of m/z 1. 6. Higher-energy collisional dissociation was employed for the fragmentation of phospholipid species with an optimized stepped collision energy of 27%. The linear ion trap was used to acquire spectra for fragment ions in data-dependent mode. The AGC target was set to 2. 104 with a maximum injection time of 50 ms. All MS and MS/MS data were acquired in the profile mode. The Orbitrap Fusion was controlled by XcaliburTM 4. 1 software (Thermo Scientific, San Jose, CA, USA).
Statistical analyses The data are presented as mean ± standard deviation of the mean (SEM), except those including bacterial communities. Statistical analyses were performed using the GraphPad Prism software for all analyses except those including bacterial communities, which were performed with R (version 4. 1. 2). The non-parametric Mann and Whitney or Krus-kal-Wallis tests were used to compare data from the two groups (after Bonferroni correction). The p-values of less than 0. 05 were considered statistically significant (* p < 0. 05, ** p < 0. 01, *** p < 0. 001 and **** p < 0. 0001). OTUs differences between the two groups (mice receiving L. helveticus against those of the control group) were assessed by pairwise comparison of normalized sequence counts using Negative Binomial Wald Tests from the DESeq2 package  89.
More precisely, the DESeq2 package performed three steps: (1) estimation of size factors, which are used to normalize library sizes in a model-based fashion; (2) estimation of dispersions from the negative binomial likelihood for each feature, and subsequent shrinkage of each dispersion estimate towards the local trendline by empirical Bayes; (3) fitting each feature to the specified class groupings with negative binomial generalized linear models and performing hypothesis testing, for which we chose the default Wald test. Then, DeSeq2 helped to decrease the false discovery rate of OTUs, using the Benjamini and Hochberg method by default. The adjusted p-values < 0. 1 were considered as significant for the DeSeq2 analysis. To compare the OTUs modified by the probiotic supplementation with either fatty acid amounts or gene expression levels, Spearman correlation analyses (and related p-values) were performed with the 'cor.
This work was funded by Agence Nationale de la Recherche [ANR-11-LABX-0021-01]; INRAE; French "Investissements d'Avenir" program, project ISITE-BFC (contract ANR-15-IDEX-0003); Conseil Régional de Bourgogne, Franche-Comté [PARI grant]; FEDER (European Regional Development Fund) and Institut Carnot Qualiment [grant INPROBIAUS].
Individual RFP+ neurons were reliably identified over time, based on their morphology and relative position to neighboring cells (Figures  1H, I ). As observed previously, we noted a slight expansion in the size of glomeruli, an increase in distance between labeled neurons in control condition  (Platel et al. , 2019)  but a marked shrinkage under UNO  (Angelova et al. , 2019). We quantified the percentage of cell loss under control and UNO condition and between cell types, GABA versus DA. We performed a 2-way ANOVA on data ranks with ctl/UNO and cell-type as fixed effects. This revealed a significant effect of both "ctl/UNO" (p < 0. 001) and "cell type" (p < 0. 01), showing that "UNO" increased cell death and that cell death is higher in GABAergic neurons. However, the interaction between the two fixed effects was not significant, suggesting that deprivation does not trigger a population-specific cell death response.
We found a significant effect between "ctl/UNO × time" interaction (p < 0,01) and "cell type × time" interaction (p < 0,05). Under control conditions, quantification of RFP cell numbers revealed that overall cell loss at t2 was detected at low levels in all observed animals (GABAergic: 1%, DA: 0. 0%, Figures  2D, F ). Four weeks after reversal of UNO, cell loss was almost non-detectable in both populations (GABAergic: from 13% ± 1. 7 at t1 to 1% ± 0. 8 at t2, p < 0,05, DA: from 4. 5 ± 2. 6 to 0. 4 ± 0. 4%, Figures  2E, F ). Thus, the impact of UNO on neuronal death was abruptly reversed when sensory information was reinstalled. To assess the evolution of TH expression, we calculated the intensity ratio of GFP over RFP in individual DA-neurons. We performed an ANOVA on data ranks with repeated measures (t1-t2-t3) analysis with ctl/UNO as fixed effects and found an interaction "ctl/UNO × time" (p < 0,05).
Chronic in vivo imaging analysis Quantitative analyses were performed on raw image stacks using FIJI software  (Schindelin et al. , 2012). All neurons identified on the first image were assigned a number using ImageJ overlay. Based on morphology and relative position each neuron was individually numbered and tracked during the successive imaging sessions. They were then labeled as TH-GFP positive or not. Detection of lost cells was performed solely on RFP expression. Results were summarized in Microsoft Excel. Occasionally neurons located at the border of an image were placed outside of the imaged field in one of the following sessions. These cells were excluded from further analyses. Animals showing an evident degradation of the imaging window were excluded from further imaging sessions.