dataesr/scientific-paragraphs-categorization huggingface dataset:
Indeed, these rules are composed of conjunctions of conditions on attributes that conclude on some olfactory qualities. In contrast to black-box models, these rules, assessed by intuitive and mathematically well-funded measures are easy to assimilate for a domain expert. This, in turn, makes development of new hypotheses possible. In sum, our data-mining method should be regarded as an approach that can extract knowledge from a dataset characterized by its complexity, size and heterogeneity. Our approach is therefore situated at the upstream of any hypotheticaldeductive approaches. The generation of descriptive rules allows researchers to start such a hypothetical-deductive approach, and to formulate new scientific assumptions, to establish an experimental methodology and finally to develop and test the validity of predictive models.
Our descriptive model could bring new information for most of these qualities, thus enabling the testing of innovative hypothesis in the field. Importantly, we revealed the existence of descriptive rules for qualities that have not, to the best of our knowledge, been investigated before. These qualities include hay, tarry and smoky. The generated rules will help scientists to better understand the chemical composition of the stimuli that evoke these odors and bring new insights about the way these molecules can interact with the olfactory system at the receptor level. Last but not least, our approach showed also that it was difficult to generate reliable rules for some qualities, particularly the most represented in the database (e. g. , fruity, floral and woody). Although the recall associated with these rules was not high, they were characterized by a low rate of error, and validation was achieved for some of them including the well-known fruity and woody qualities.
Finally, it is noticeable that a series of interesting qualities were described by rules with a good level of confidence but may be not precise enough to warrant detailed interpretation at this stage. These qualities are those that belong to the second quartile (Fig  4 ) and include, for instance, camphor for which validation with novel odorants was performed using two different external datasets. A methodological issue that may be raised from our study relates to the choice of Arctander's book in our methodology. Before answering this question, one must detail why such linguistic sources are used in olfactory research. In general terms, whereas emotional reactions are very prominent in olfaction  [41] , lexical and linguistic processes are relatively limited: spontaneous odor identification performances are around 50% (see  [42] ).
Such an absence has led scientists and those in the industry to develop different sources (atlases, books, websites) listing the olfactory qualities of a series of odorant molecules (Arctander book  [24] , the Dravnieks Atlas  [26] , the Boelens Atlas  [27] , and the Flavornet website (http:// www. flavornet. org)). A comparison of these sources led us to consider the Arctander's book since it contained the highest number of odorant molecules and a reasonable number of qualities per odorant. The book, in being developed by a single scientist, gave the advantage of allowing us to integrate more homogeneous data with less variable response profiles than those collected in other atlases. However, this same feature also opens up the possibility that certain odorants that evoke a given quality could be missed.
One should therefore not discard the possibility that certain molecules that evoke, for instance, the quality "fruity" were not considered by our model in the validation phase because they were just below the perceptual threshold set by Arctander for that particular quality. Given the variability of olfactory perception between individuals, it is conceivable that the same quality of "fruity" could have been the perceptual threshold of another rater. As a consequence of these factors, we face a double challenge: on one hand, there is a clear need to implement some flexibility in olfactory databases, whereby a given molecule can be described by one or several qualities with an associated level of confidence instead of a binary response. On the other hand, in order to account for interindividual variability in olfactory perception, olfactory databases need to consist of data from a large number of individuals.
(n = 5), Earthy (n = 5), 2/ for the Boelens & Haring study: Woody (n = 10), Fruity (n = 9), Green (n = 8) and Balsamic (n = 5), 3/ for the Keller et al. study: Fruity (n = 15), and Sulfuraceous (n = 16; which was compared to a semantically proximal perceptual quality present in the Keller database, namely « Decayed »), and 4/ for the Licon et al. study: Camphor (n = 5). Results are presented in Fig 5. Within each set, an analysis of variance (ANOVA) comparing perceptual values for a given quality for odorants that fulfill the physicochemical rules (Rule (1), black bars) vs. those that did not fulfill the rules (Rule (0), grey bars) was performed. For the Dravnieks dataset, the statistical analysis revealed that odorants that fulfill the rules for woody, earthy and camphor, were respectively perceived as significantly more woody (F(1,43) = 14.
19, p<0. 001, η 2 = 0. 248; Fig 5a. i), earthy (F(1,43) = 6. 128, p = 0. 017, η 2 = 0. 125; Fig 5a. ii) and camphoreous (F(1,43) = 28. 63, p<0. 001, η 2 = 0. 400; Fig 5a. iii). In the same line, a significant increase in camphor quality was observed for odorants that fulfill the rules for this quality in the Licon et al. dataset (F(1,17) = 6. 804, p = 0. 018, η 2 = 0. 286; Fig 5b). Validation was also observed within the Boelens & Haring dataset, but the results were more mixed. Whereas a significant increase was observed for woody (F(1,54) = 88. 47, p<0. 001, η 2 = 0. 621; Fig 5c. i) and balsamic (F(1,54) = 15. 86, p<0. 001, η 2 = 0. 227; Fig 5c. iv) in odorants that fulfill the physicochemical rules for these respective qualities, this was not the case for the green quality (F(1,54) = 0.
227, p = 0. 636, η 2 = 0. 004; Fig 5c. ii). On a descriptive level, Fig 5c. iii shows that odorants that fulfill the physicochemical criteria for the quality fruity seem to be perceived as more fruity, but this was not significant (F(1,54) = 1. 989, p = 0. 164, η 2 = 0. 036). However, when considering the Keller et al. dataset, validation was reached for fruity: odorants that fulfill criteria for the fruity quality were perceived as more fruity (for both low (F(1,116) = 9. 219, p = 0. 003, η 2 = 0. 074; Fig 5d. i) and with high levels of concentrations (F(1,116) = 11. 76, p<0. 001, η 2 = 0. 092; Fig 5d. ii)), than odorants that did not fulfill the rules. The statistical analysis of this dataset shows also that odorants that fulfill the physicochemical criteria for the quality sulfuraceous were perceived as more decayed at both low (F(1,116) = 10.
Funding: This work was supported by a joint  French/German research program  from both the  French National Agency of Research  (http://www. agence-nationale-recherche. fr) and the  German Research Foundation  (https://www. dfg. de)( ANR/ DFG SHS FRAL program ;  MEROD  Project,  ANR-15-FRAL-0002 ) to MB, and a grant from the  Institut rhonalpin des systemes complexes (IXXI).
Alignment of the sequenced fragments to the reference genome Sequence reads were aligned with BWA-MEM  [21]  to the Coturnix japonica 2. 0 quail reference genome (NCBI assembly accession GCA_001577835. 1; BioProject accession PRJNA314147), which consists of 32 chromosomes or linkage groups and 1095 un-localised scaffolds  [22]. We used the Integrative Genome Viewer (IGV) software http://softw are. broad insti tute. org/softw are/igv/ to visualize the alignment on the reference genome and to check for compatibility of distance and orientation between read-pairs with the size selection that was set for the construction of the libraries. IGV was also used to evaluate read depth. Close examination of such alignments in IGV can be very informative to characterise deletions or duplications, for details (see Additional file 2).
To better understand the rearrangement, the three regions (3′ and 5′ BKPT-Yel, and JUNCT-Yel) were amplified from two yellow heterozygous individuals. For the 3′ and 5′ BKPT-Yel, amplified fragments had the expected size, but for JUNCT-Yel the amplified fragment was longer than expected and, thus, was sequenced (GenBank MK135881). BLAST alignment on the quail reference genome revealed that the JUNCT-Yel sequence comprised three fragments: the 5′ end mapped upstream to the 5′BKPT-Yel and the 3′ end mapped downstream of the 3′BKPT-Yel, which was consistent with a 141,162-bp deletion (Fig. 2a ) (NC-029535 [1,463,709-1,604,872]), while the third fragment aligned with an unexpected internal fragment of 241 bp (Fig. 2a ). BLAST and BWA-MEM were not able to propose a unique position for this 241-bp fragment on the quail reference genome, but showed that it was present within the 141,162-bp deletion.
Acknowledgements The authors greatly appreciate the excellent technical assistance from  Florence Plisson-Petit  and  Damien Trussardi  ( INRA GenPhySE ). We thank the team running the genomic platform of the  Génopole Toulouse Midi-Pyrénées (GeT-PlaGe , https ://get. genotoul. fr/la-plate forme /get-plage /) and especially  Diane Esquerre  for her contribution to the results. We are grateful to the genotoul.
Population and setting We enrolled in the study all VPT babies born between 24 WG and 31 WG + 6 days in two geographically defined cohorts and admitted alive in neonatal intensive care units (NICU). Infants born with severe birth defects were excluded. The Reunionese OGP cohort enrolled VPT infants born in La Réunion Island (850,000 inhabitants and more than 14,000 births per year) between 2008 and 2013. Obstetrical and neonatal data were collected prospectively using standardised questionnaires by perinatal professionals in each of the seven maternity wards and the six neonatal care units of the island. This DOM includes two level-III neonatal care centres. The EPIPAGE-2 cohort enrolled VPT infants born in year 2011 among 21 of the 22 mainland France's regions (774,585 births). The duration of subject inclusion varied with gestational age (8-month recruitment period between 24 and 26 WG and 6-month recruitment period between 27 and 31 WG)  [9].
Explanatory variables Obstetrical characteristics retrieved were maternal age, chronic or gestational arterial hypertension, pre-gestational or gestational maternal diabetes, premature prolonged rupture of membranes (occurring > 12 h before childbirth), antenatal steroid therapy (defined as any injection of corticosteroids before childbirth), multiple birth, and mode of delivery. Neonatal data retrieved were gestational age (defined by a set of chronological, morphological and neurological criteria: last menstrual period, early ultrasound performed between 7 and 12 WG, morphological and neurological examination conducted at birth), birthweight, small for gestational age (SGA) status (defined as a birthweight ≤3rd percentile of the French AUDIPOG sentinel network growth charts), Apgar score < 7 at 5 min of life, outborn status, and surfactant therapy.
Adverse neonatal outcomes In hospital mortality was higher in Reunionese than in mainland infants (15. 4% versus 9. 6%, p < 0. 001). The primary composite outcome of death during hospitalisation or survival at discharge complicated of at least one severe morbidity was also more common in La Réunion (32. 6% versus 26. 6%, p < 0. 001). Overall, severe morbidity was not different between the two databases, despite NEC was more likely among Reunionese VPT infants (Table  2 ). These findings were consistent across all gestational age strata for the primary composite outcome and its component fatal outcome. Conversely, LOS and medically-treated PDA were less likely in the OGP cohort than in the EPIPAGE-2 cohort (Table  3 ). In per strata analysis, BPD, surgically-treated PDA in the 29-31 WG subgroup and severe retinopathy across the more mature subgroups were more common in the OGP cohort.
Of note, the proportion of extremely immature infants in the 24-26 WG group was slightly higher in the EPIPAGE-2  cohort, given that its protocol favoured the recruitment of extremely immature infants  [9]. Given the possibility of repartition bias, this methodological issue suggests caution in comparing the risk levels between the two databases taken overall. However, this was deemed not to be a significant limitation for comparing outcomes within each specific gestational age group. By identifying pre-existing medical conditions, risk factors, and negative health behaviours through a range of medical and educational interventions, prenatal care can improve health outcomes for mothers and their infants. Interestingly, prenatal access to risk-appropriate neonatal care in La Réunion seemed adequate as suggested by higher proportions of inborn infants and antenatal steroid therapy.
Funding The  EPIPAGE-2  project has been funded with support from the following organisations: The  French Institute of Public Health Research/Institute of Public Health  and its partners: the  French Health Ministry , the  National Institute of Health and Medical Research (INSERM) , the  National Institute of Cancer , and the  National Solidarity Fund for Autonomy (CNSA) ; The  National Research Agency  through the  French EQUIPEX program  of investments in the future (reference  ANR-11-EQPX-0038 ); the  PREMUP Foundation ;  Fondation de France  (reference 00050329); and  Fondation pour la Recherche Médicale  (reference  SPF20160936356 ). The  OGP  project has been funded by the  Agence Régionale de Santé-Indian Ocean regional health agency. The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Homogeneous data have been obtained for all of the experiments. There were four irradiation schemes with two different time exposures and two different dose rates: the first irradiation groups were from eggs to L4 stage (during 64 hours) with 7 and 52 mGy. h -1 reaching 0. 5 and 3. 3 Gy, respectively; the second irradiation groups were from eggs to "old" stage (during 19 days) with the same dose rates reaching 3. 3 Gy and 24 Gy, respectively. Due to the limitation of the maximum dose rate (52 mGy. h -1 ) from the 137 Cs gamma irradiation source (Sup data, Fig S1a ), there was no possibility of obtaining a cumulative dose of 24 Gy at the young stage (L4, 64 h of irradiation). After each completed treatment, samples were washed 3 times with M9 and quickly frozen in a grinder tube with the minimal volume.
Experimental design for following biomolecular levels during radiation and aging Although the study was focused on the young and old stage of worms during radiation and aging, the interest was also to follow their biomolecule levels in between the young and old stage. The biomolecules of interest were: carbonyls, proteins, lipids and nucleic acids. Various effects were monitored every second or third day, when also HOBO data were undertaken. On those days plates were washed 3 times with M9 as mentioned above. After washing the worms, they were transferred onto fresh 6-cm NGM plates with 10 times concentrated bacteria to avoid starvation. The samples for biomolecular labelling were collected from all replicates; i. e. , 10 worms from 10 replicates were taken and quickly frozen in 100 µl of M9.
Statistical analyses Statistical analysis significance was calculated in GraphPad Prism. Before each analysis, the normality (Shapiro-Wilk test) and homogeneity of data variance (Levene's test) were tested. When these assumptions were met, then parametric tests were used; i. e. , one-way ANOVA with post-hoc Tukey test. Otherwise, nonparametric tests were used; i. e. , Kruskal-Wallis with Dunn's multiple comparison test. The lifespan statistical analyses were done with XLSTAT software (Addinsoft, New York, NY, USA). Survival data by the Kaplan-Meier method and differences between survivals were calculated using the Log-Rank test with 99% confidence. Three statistical parameters are presented: Log-rank, Wilcoxon and Tarone-Ware.
Acknowledgments The authors thank the IRSN, MedILS and ERASMUS for their financial support. The authors sincerely thank  Dr Yonghua Li-Beisson  and  Stéphane Cuiné  from  CEA Cadarache / Biam / Lb3m  for the extraction and TLC measurement of lipids in order to confirm the relevance of the staining used in this work. Finally, the authors also thank  Hélène Javot  ( CEA Cadarache ) for her technical support and advice.
Loss on drying: according to Ph. Eur. Microbiological quality: microbiological quality is controlled according to Ph. Eur. 2. 6. 12 for total aerobic microbial count (TAMC) and total combined yeasts and molds count (TYMC) as well as Ph. Eur 2. 6. 13. for specified micro-organisms. Nuclear magnetic resonance: all experiments were conducted on a Bruker AVANCE III spectrometer (BioSpin Bruker, Wissembourg, France) operating at a proton frequency of 500 MHz with a 5 mm gradient indirect detection probe, at a probe temperature of 300 K. The samples were exchanged twice with 99. 8% D 2 O with intermediate freeze drying and dissolved in 0. 6 mL of 99. 96% D 2 O. 1-d proton spectra were acquired with 16 scans and 32 K data points with a spectral width of 5000 Hz. Typical 1 H 9. 5 µs-pulse length and relaxation delay of 1 s were used.
Organs and tissues were processed from all animals and evaluated microscopically after staining with hematoxylin and eosin at the Test Site Charles River Laboratories. Test item formulation: the 20 µg/mL solution was prepared by adding 2 mL of water for injection to each vial containing 40 µg of fucoidan extract, batch PF. 797. IS, before administration. The stability of the reconstituted formulation was 1 week at room temperature. The concentration of the solution was checked and confirmed by Algaia, the actual concentration being about 10% higher than the nominal one. Data analysis: qualitative analysis of mortality, clinical signs, urinalysis, and gross lesions was performed for all animals. Statistical analysis was performed on all the other recorded parameters, divided per sex, to compare all groups versus control group, and all groups each other's, at two different sacrifice time points, using SPSS 24.
Mean PAP, SAP, and HR data were evaluated by the ADI LabChart software. Plasma Thromboxane B2 (TXB2-the stable metabolite of plasma TXA2) levels were measured with an ELISA kit (Cayman Chemicals). Fucoidan was given in several experiments in a dose ranging from 1 to 100 µg/kg, single or repeated. Here one typical experiment's data is shown only. To induce CARPA, zymosan (a glucan from yeast cell walls) was used for direct complement activation.
Supplementary Materials: The following are available online at http://www. mdpi. com/1660-3397/17/12/699/s1, Figure  S1 : Time course of cardiovascular (PAP, SAP and HR) changes following fucoidan and zymosan i. v. injections in pigs. Figure  S2 : Refractive Index (blue line) and Light Scattering (red line) chromatograms of purified fucoidan eluted in 0. 1 M LiNO3 at 0. 5 mL/min with Shodex SB-802. 5 and SB-803 columns  [22]. Figure  S3 : Scheme of extemporaneous preparation of radiolabeled GMP-grade LMW fucoidan (Investigational Medicinal Product). Funding: This work was supported by the EU ("NanoAthero" project FP7-NMP-2012-LARGE-6-309820), and received the financial support from ANR-13-LAB1-0005-01 "FucoChem" and ANR-13-RPIB-0006 "FucoThrombo".
Acknowledgments: This work was supported by  Inserm ,  Université de Paris, University Paris 13, Semmelweis University ,  Academic Medical Center, X. Bichat Hospital ,  UMS034  (FRIM),  Bracco Research Center and Algues & Mer. This work has been performed on a platform member of  France Life Imaging network  (grant  ANR-11-INBS-0006 ). Authors would like to thanks  Eurofin Amatsigroup, Labéo and Algaia  for the production of the GMP batch and its certified characterization.
Acknowledgments The authors would like to thank  Dr. Philippe Contencin  and  Dr. Annahita Ghassemi  for their valuable contribution to the elaboration and revision of the manuscript. This study has been sponsored by  Church & Dwight, Co. , Inc. Poster presentation: Partial presentations of this work have been made as posters at the " VIII Rhinology Breaking Barriers  to  Excellence" Congress at Sao Paulo (Brazil) , and at the "27th Congress of the  European Rhinologic Society" at London  ( United Kingdom ), both in April 2018.
Adequacy of specific MN intake for small populations can also be quantified using composite diet analysis or dietary recall with composition data  13, 17, 19. Household surveys or Food and Agriculture Organisation (FAO) Food Balance Sheets (FBS) are utilised for larger populations to derive consumption data for MNs  42  to better inform public health policies in addressing deficiencies. However, the FBS is dependent on locally-relevant food composition data which may be lacking in low-income countries where there is a lack of infrastructure to support the analyses of all MNs in food groups, some of which are measured at parts-per-billion concentrations (e. g. Se, I) and often requires sophisticated equipment such as ICP-MS  43. Country specific food composition data are often lacking and instead utilise a small number of datasets often from high income countries  44  or from analyses that are decades old  45.
Results All data are reported as median (Q1, Q3) in Supplementary Tables, unless stated otherwise. Crop data are presented as dry weight (DW; n = 1496). Soil (n = 282) and plant samples were collected across simplified soil categories with calcareous and non-calcareous characteristics  27. For ease of description, these regions will be referred to simply as 'Kenya' and 'Tanzania'. 1  with site metadata, uncertainty on measurements and limits of detection for analyses, whilst soil data has been summarised in Table  1. Median Ca concentrations for calcareous soils were 18,117 and 8,269 mg kg -1 , with a median pH of 7. 0 and 7. 1 in Tanzania and Kenya, respectively. In comparison, the median Ca concentration in non-calcareous soils was 7,643 and 2,776 mg kg -1 and pH of 5. 8 and 5. 3 in Tanzania and Kenya, respectively.
4-11, 144-636, 3-24 mg kg -1 for Ca, Cu, Fe and Zn, respectively. It is likely that the lower values in these comparative studies resulted from differing techniques that did not provide a 'true' elemental measurement, such as aqua regia for partial dissolutions, as opposed to the use of HF/HNO 3 / HClO 4 in this study for a 'total' dissolution of trace and major elements. There is no fixed pattern across the soil micronutrients when comparing non-calcareous/calcareous soils, other than Se, I Mo median concentrations are higher in non-calcareous soils for both countries. The influence of soil type on food group micronutrient composition is difficult to discern for this dataset. For example, Table  3  summarises the percentage of variance in crop element concentrations as explained by soil predictor variables for each food group for a combined Tanzania-Kenya dataset, with not all variance explained by key soil parameters (e.
Ca Food supply estimations for food items originating from calcareous/non-calcareous soils and published composition data were 57. 2/45. 1/15. 1 mg capita -1 day -1 and 19. 5/20. 7/14. 1 mg capita -1 day -1 for Tanzania and Kenya, respectively. These values are comparable to Schmidhuber et al. 4  estimates of 13 to 21 mg capita -1 day -1 for Fe from a worldwide database including Kenya and Tanzania, although this study suggests higher intake values in the Kilimanjaro district. Measured supply values are comparable to Mali of 22. 8 mg capita -1 day -1 63. Similarly to Ca, the estimated Fe supply is notably higher than published values for both countries, yet little difference is apparent between soil types as was observed by Siyame et al. 17  in Malawi. The risk of Fe deficiency does not vary particularly between soil types, but for Tanzania differs considerably for males compared to published values, with a 20 and 7% risk of Fe deficiency for each soil, compared to 100% using published values and 100% for all female estimates.