dataesr/scientific-paragraphs-categorization huggingface dataset:
Molecular analysis of the ftsI gene Sequences of a 621-bp fragment of ftsI gene (encoding the PBP3), corresponding to nucleotides 977-1597 relative to the ftsI start codon, were used to assign alleles for the corresponding isolates through the PubMLST database and analysed through the tools available on the BIGSdb platform. Sequences were aligned using Multiple Sequence Alignment by CLUSTALW and sequences differing by at least one nucleotide were assigned a unique ftsI allele sequence number. Phylogenetic networks were generated using SplitsTree (version 4. 14. 6) (www. splitstree. org) with default parameters  (19).
Genomic analysis of the invasive isolates We next focused on the genetic typing of the isolates. Whole genome sequences (Illumina) were obtained for 130 of the 136 invasive cultured isolates (96%) and complete MLST schemes were retrieved for (126/130 isolates; 97% of all isolates with WGS data), while partial MLST profiles were obtained for the 4 other isolates. There were 73 different STs identified among the 126 invasive isolates with ST-124 the most frequent (n=10) followed by ST-6 (n=8) and ST-388 (n=5). MLST data were also obtained for 34 of the 100 non-invasive isolates and these belonged to 27 different STs. GrapeTree analysis using MLST allelic profiles is depicted in Fig. 2. The ST were divers and were represented by no more than three isolates (for ST-107), which was distinct to the non-invasive isolates, with only 14 STs shared with the invasive isolates (STs 1, 3, 12, 57, 124, 155, 159, 160, 266, 388, 396, 513, 836 and 1877) (Fig.
Acknowledgements This publication made use of the Haemophilus influenzae Multi Locus Sequence Typing website (https://pubmlst. org/)developed by  Keith Jolley  and sited at the  University of Oxford  ( 18 ). The development of this site has been funded by the  Wellcome Trust. We also acknowledge the  PIBNET-P2M  platform at the  Institut Pasteur. This work was funded by The  Institut Pasteur and Santé Publique France.
Protein Sequences Analyses To test for the presence of potential PEST motifs, amino-acid sequences of eIF4GI, eIF4GII and DAP5 from different animal species (described in Table  1 ) were up-loaded into the ePESTfind software at EMBOSS explorer 1. After running out the ePESTfind software, only the potential PEST motifs displaying a score >5. 0 were taken into account in this study. The alignment showing conservations between eIF4GI and eIF4GII sequences was performed using the LALIGN program 2.
Review Process and Theoretical Foundations A deeper analysis of each study was performed to compile a database in Excel. Statistical analysis of the topics of interest was carried on. The topics are related to the operationalization of social-ecological resilience, such as the conceptual elements, the characteristics of the system and the disturbances of interest, and to the measurement of resilience by a models or by indicators (Figure  2 ). First, the conceptual elements that the studies measured or assessed were identified, such as absorption of disturbance, system identity, reorganization, adaptability, and transformability. Second, principles for enhancing social-ecological resilience were identified as proposed by  Biggs et al. (2012)   [1] , based on their ability to improve the resilience of critical ecosystem services for human well-being in the face of a disturbance  [8].
Models Dynamic models try to capture system complexity, the state and control variables, the thresholds, and the feedbacks between the ecological and the social subsystems. These variables can be measured with a dynamic time series that calculates the equilibrium and the size of the region of interest  [13]  given the configuration of the system  [50]. Models measure how the system responds to a change in relation to a threshold and the relative state of the system to that threshold  [51]. In other words, they try to predict the loss of resilience, given specific thresholds. The results show that 18% of the articles revised present dynamic models and that the majority of these models are conceptual models. Bueno and Basurto (2009)   [52]  measured the resilience of a fishing system through system dynamics using VENSIM software, in which the loss of resilience occurs when a state variable of the system crosses a critical quantitative threshold.
RESULTS AND DISCUSSION We collected XRS carbon K-edge intensities using mapping (or raster scanning) by sequentially moving objects across the photon beam at a given incident energy while measuring the scattered intensity. Several of these maps are acquired at different energy losses through the carbon K-edge to produce a hyperspectral data cube. Illuminating a sample with an incident energy E and setting a fixed analyzer energy E f , the energy loss E = E -E f can create electronic excitations. If E is tuned to a transition involving a bound electron, then the resulting spectroscopy is called XRS spectroscopy. Beside a q-dependent background that is dominated by Compton scattering and collective valence electron excitations such as plasmons at high and low momentum transfers (q), respectively, the XRS spectrum generally contains nondispersive features that are generated when a fraction of incident photon energy is transferred to the sample inner shell electrons, promoting them into unoccupied states  (21).
e. , direct tomography  (19, 26) ]. We performed 3D XRI of a block of Eocene amber containing a morphologically well preserved ant worker, without wings [Oise, France (ca. 53 Ma old); Fig. 3B ]. Experimental conditions were selected to yield a voxel size of 50 × 50 × 50 m 3 , each voxel being associated to its own XRS-based XANES spectrum. The image of the total signal intensity leads to direct observation of most of the morphology of the fossil (Figs. 3C  and 4A ). The three tagmata are visible (head, mesosoma, and metasoma including the petiole without showing segment details-the mandibles, maxillary palps, and remnants of three legs), confirming that the hyperspectral dataset contains enough information to contrast different parts of the fossils. A mean spectrum from 150 pixels in the bulk amber (Fig.
Paleontological samples Two paleontological samples were examined as follows: (i) a fragment of Lepidodendron trunk collected by one of us (P. G. ) on an Upper Carboniferous (ca. 305 Ma ago) coal slag heap in Noyelles-lez-Lens, France, on 15 April 2012; (ii) an insect (inv. no. PA-3822, Hymenoptera: Formicidae) entrapped in amber, an Ic-type resin typical of angiosperms and derived from a Fabaceae. The amber deposit of Oise, found in 1996 at the Quesnoy locality in the Oise River area of Paris Basin in France, has been dated back from the earliest Eocene (approximately 53 million years ago)  (38). The specimen belongs to the paleontological collections of the Muséum National d'Histoire Naturelle (Paris). For comparison, we collected data on purified powder of chitin from shrimp shells (C9752, CAS: 1398-61-4, Sigma-Aldrich, St.
The overall energy resolution was 1. 2 eV. XRI was performed on the specimens without any prior sampling. 4D volumes were taken at ID20 by scanning horizontally the x-ray beam across the sample, and parametrically varying the sample in the vertical position and the x-ray beam energy to create energy losses in the vicinity of the carbon K-edge (280 to 310 eV). The used step sizes were 50 μm in the horizontal and vertical directions. The energy step was 1 eV over the pre-edge region (276. 4 to 282. 4 eV), 0. 5 eV over the carbon K-edge region (282. 4 to 296. 4 eV), and 2 up to 302. 4 eV. This is an early-stage development of the technique, and we have tested several configurations at the beamlines including a survey on radiation damage that can occur. The Lepidodendron XRS data were collected by continuously scanning the sample in the beam at fixed energy, thus reducing the exposure time.
Study design This study was approved by the National Data Protection Authority (Commission Nationale de l'Informatique et des Libertes, CNIL n˚1755849). French regulations stipulate that this study is exempt from Institutional Review Board (IRB) review because it is an observational study using anonymized data from medical records. The study's exempt status was confirmed by the IRB Ile-de-France. During the study period, women were routinely informed that their records could be used for evaluation of medical practices and that they had the right to opt-out of these studies. This was a retrospective analysis of a series of severe-stage DIE patients without a prior history of surgery for endometriosis and who had a monofetal pregnancy followed in a tertiary care center. Women with a diagnosis of DIE based on MRI criteria  [5, 33]  obtained before pregnancy were retained for the study.
Data analysis For each patient, their personal history data and pregnancy-related information were collected including the maternal age, weight, size, assisted reproductive technology (ART), gestity, parity, gestational hypertension, mode of delivery, gestational age at delivery, preterm birth < 37 weeks of gestation, birth weight, small for gestational age offspring, the time interval between the MRI before pregnancy and delivery, and the time interval between delivery and the MRI after pregnancy. For each patient, the distribution of DIE lesions and the presence of OMA were recorded.
Statistical analysis The continuous data are presented as means with the standard deviation and as medians and the interquartile range (IQR) 25-75%. Paired analyses were used when comparing pre-and post-pregnancy lesion volumes (mm 3 ) by MRI, and comparisons were performed according to the DIE location. In case of multiple DIE lesions, paired comparisons of lesion volumes before and after pregnancy were also performed according to the largest lesion of each patient. Paired OMA sizes (mm) were compared before and after pregnancy. The quantitative data were compared using the Wilcoxon matched-pairs test. A p-value < 0. 05 was considered statistically significant. The data were analyzed using STATA software for Macintosh (Stata/IC 11. 0 for Mac, StataCorp College Station, TX, USA).
Differentiation among breeds and genetic distances. The level of population differentiation can be quantified using the fixation indexes. The fixation Index (F ST ) for each breed (Table  1 ), estimated as the average of breed pairwise comparisons per SNP and then averaged by breed, shows the highest value for Mora Romagnola (0. 161) and the lowest value for Sarda (0. 092). The overall F ST value from all the SNP markers was 0. 115 (±0. 020), indicating that most of the genetic variation occurred within populations rather than between breeds, as previously reported for pig populations  28, 29. The value obtained is concordant with previous works  28  , where the averaged F ST value calculated between European breeds was 0. 134, ranging from 0. 021 to 0. 209. The overall F ST value obtained in the present work (analyzing data of 70K SNP chip) is considerably lower than the one observed in our previous study (0.
Data analyses. A total of 51,219 SNPs mapped on the 18 autosomes on Sus Scrofa 11. 1 were used to compute, for the 20 studied breeds, the following indicators of genetic diversity: observed (H O ) and expected heterozygosity (H E ), inbreeding coefficient of an individual (I) relative to the subpopulation (S) (F IS ), fixation index (F ST ) and inbreeding coefficient of an individual (I) relative to the total (T) population (F IT ), heterozygosity index based on observed heterozygosity in individuals within breeds (H I ) based on expected heterozygosity in subpopulation (H S ) and based on expected heterozygosity for overall breeds (H T ). Calculations were made with VCFtools software  73. Nei's genetic distances  12  were calculated in R  74  environment. Pairwise distances were used to build a NJ tree with the nj function belonging to the ape 75 library in R.
Study Population Our study employed 1309 eligible mother-newborn pairs with only singleton newborns participating in the ENVIRONAGE birth cohort, situated in the province of Limburg, Belgium  (Janssen et al. , 2017). Recruitment took place between 2010 and 2016 at arrival in the delivery ward of the East-Limburg Hospital in Genk, Belgium. Maternal body mass index (BMI) was determined by dividing weight in kilograms by height in meters squared, based on data obtained during the first antenatal consultation. The conception date was assessed by combining data on the first day of the last menstrual period and the first ultrasonographic examination. After delivery, the mothers filled out a questionnaire regarding information about the in-house environment, education, occupation, health status, smoking, and lifestyle habits.
The coding of maternal educational levels was carried out according to the following criteria: "low", in the absence of any diploma; "middle", in the presence of a highschool diploma; "high" in the presence of a college or university diploma. Maternal smoking status was categorized as "smoking during pregnancy" if the mother had smoked at any time point during pregnancy. Further, a distinction was made between mothers who had their first newborn or their second or more newborn. Newborns' ethnicity was classified as either European, when two or more grandparents were of European origin, or as non-European when three or more grandparents were of non-European origin. Perinatal parameters such as newborns' sex and birth date were collected by the hospital personnel after birth. Due to the availability of OMICs, mtDNA content and insulin measurements, the datasets for every research question were studied in a designated set, resulting in different numbers of participants.
Owing to the availability of mtDNA content and insulin measurements and missing data (as reported in detail in Supplementary Table  S1 ), the analysis of associations between cord blood insulin and mtDNA content employed 882 participants. Epigenome-wide methylation status of the CpG sites was retrieved from cord blood samples in a subset of 197 newborns, enrolled between 2014 and 2015 in the framework of the EXPOsOMICS project (FP7;  Vineis et al. , 2017). The mother-newborn pairs recruited for this study were selected for their complete data on cord blood-insulin, mtDNA content and the applied covariates resulting in a final study sample size of 179 for the association with cord blood insulin and 176 for the association with cord blood mtDNA. Exclusion criteria and numbers due to missing data are reported in Supplementary Table  S1.
Epigenome-Wide Methylation DNA was extracted and processed at the Epigenetics Group, IARC. Specifically, DNA was bisulfite-converted using the Zymo EZ DNA methylation TM kit (Zymo, Irvine, CA, United States). DNA was then hybridized to Illumina Infinium Human Methylation 450K BeadChip arrays (66) and scanned using the Illumina HiScanSQ system. After background subtraction using Illumina GenomeStudio raw intensity data were submitted to pre-processing, including normalization, using in-house software within the R statistical computing environment. Furthermore, quality control of samples was carried out and failed samples were excluded on the basis of Illumina's detection p-value greater than 0. 01 and bead count lower than 3. For probes using the Infinium II design additional background subtraction and dye bias correction were performed.
Methylation levels at each CpG locus were expressed by Beta-values, as defined by the ratio of signal intensity originating from methylated CpGs over the sum of methylated and unmethylated CpGs. Finally, data were trimmed for outliers with values larger than 3 interquartile ranges below the first quartile or above the fourth quartile. CpG sites were annotated using the Bioconductor package IlluminaHumanMethylation450kanno. ilmn12. hg19 in R for the annotation of Illumina's 450K methylation arrays.
Relationship Between Cord Blood Insulin Levels and mtDNA Content To investigate the association between cord blood insulin levels and mtDNA content a multiple linear regression model was applied. The values for mtDNA content and cord blood insulin were log 10 transformed to ensure normality of the data. Adjustment for platelet count and possible batch effects on the qPCR reaction was performed by calculating the residuals of the log 10 transformed mtDNA content. In a second model, an additional adjustment was performed for newborns' sex and gestational age, ethnicity, and birth weight as well as maternal smoking status, maternal age, early-pregnancy BMI and education, parity and season of conception. Additionally, the regression coefficients for both models were calculated, for the adjusted model expressed as partial Pearson correlation, using the ppcor package in R  (Kim, 2015).
05/(20 × 29,164) = 8. 6e-8 were considered significant. The corresponding EntrezGeneID numbers of the genes allocated to the significant transcript-probe IDs formed the final input for the two over-representation analyses (ORA). They were uploaded into the R Package RDAVIDWebService (version 1. 20)  (Fresno and Fernández, 2013)  which retrieves data from the online pathway analysis tool, DAVID 6. 8  (Huang et al. , 2007) , 1  using an application programming interface (API). Furthermore, a second approach was followed by employing functionalities of the R package ReactomePA  (Yu and He, 2016) , developed for the analysis and visualization of the REACTOME pathway database. In both cases, the identification of enriched pathways was performed against the default background of all genes expressed in Homo sapiens.
To ensure comparability between the outcomes the first steps of the pre-processing, before the actual implementation of the specifying algorithm, were applied in parallel for both methods. Missing methylation Beta-values were imputed with values of the k nearest neighbors using a Euclidean metric provided by the Bioconductor package "impute". Consequently, the retrieved values were logit transformed to the M-value scale for better compliance with the modeling assumptions  (Du et al. , 2010). Probes already identified as being crossreactive, mapped to the sex chromosomes or within two nucleotides or closer to single nucleotide polymorphisms were filtered out as previously proposed  (Chen et al. , 2013). Batch effects due to the use of different chips were corrected using the "correctBatchEffect" function of the Bioconductor package BEclear  (Akulenko et al.
Gene Expression and Pathway Analyses Within the matrix of 20 × 29,164 = 583,280 CpG-transcript pairs we identified 233 significant pairs (p < 8. 6e-8, Bonferroni), corresponding to 201 unique genes, associated with cord blood insulin, and 585 significant pairs (p < 8. 6e-8, Bonferroni), corresponding to 281 unique genes, for the association with mtDNA content. The associations of the corresponding CpGtranscript pairs, and therefore the genes, with cord blood insulin and mtDNA content were in both directions, meaning, that hyper-, as well as hypomethylation, and equally transcriptional up-, as well as downregulation, were present. We found 27 enriched pathways/gene-disease-associations for cord blood insulin and 21 for mtDNA content with an overlap of 19 common pathways/gene-disease-associations in the ORA, using RDAVIDWebService (Table  2 ).
Notwithstanding, the estimated change of beta coefficients between cord blood insulin and mtDNA content was of the same order of magnitude as observed in the large sample (0. 09 vs. 0. 12). In addition, the omics related signature might entail a more detailed effect of the metabolic changes we observed in the larger database. Furthermore, we identified several additional mechanisms, not directly involved in mitochondrial functioning or insulin metabolism, including neuronal development, histone modification, CYP-metabolism, and biological aging, and showed associations, which have not yet been described in human neonatal studies. Several findings point in the direction of neuronal development and signaling as an important target of insulin as well as mitochondrial  (dys-) function during prenatal development.
The DMR analyses revealed an association with ZFP57, a zinc-finger transcription factor expressed during early development and essential for the maintenance of DNA and histone methylation at imprinted control regions  (Quenneville et al. , 2011; Boonen et al. , 2013). The output of the genome is controlled by DNA methylation, histone modification, non-coding RNAs, and chromatin remodeling which interact with each other  (Alfano et al. , 2018). Our finding might be interpreted as a mechanism of this cooperation. The DMRs found at CYP2E1 were verified in the analysis with the DMRcate package as well as with Bumphunter. CYP2E1 encodes for a monooxygenase which metabolizes xenobiotics and is induced by ethanol, diabetic conditions, and starvation  (Leung and Nieto, 2013). CYP2E1 expression has been reported to be inhibited by insulin, and to be associated with obesity  (Moncion et al.
FUNDING The ENVIRONAGE birth cohort is supported by grants from the  European Research Council  (Grant No. ERC-2012-StG310898 ), the  Flemish Scientific Fund (FWO , Grant No. 1516112N/G. 0873. 11. N. 10 ), and the  STOP  project (Grant No. 774548-H2020 ). The laboratory analysis of epigenome-wide DNA methylation was carried out within the scope of the  European Commission Seventh Framework program  grant  EXPOsOMICS ZH , and AG). ZH and AG and the  Epigenetics Group at IARC  are supported by grants from the  Institut National du Cancer (INCa, Plan Cancer-EVA-INSERM, France ). BR was financially supported by the  University Research Fund (Bijzonder Onderzoeksfonds Universiteit Hasselt ).
Western Blotting For immunoblot analysis, macrophages were lysed in 1× laemmli buffer and the protein concentration was determined using Bicinchoninic Acid Protein Assay (BCA, Sigma-Aldrich). Equal amounts of protein was separated by electrophoresis on 10% SDS-PAGE gel, transferred to PVDF membrane and subsequently probed with the respective antibodies as per manufacturer recommendations. In the present study, the following primary antibodies were purchased either from Sigma Aldrich, Merck [FKHRL1-D12 (p-FOXO3 Thr32 ), FKHRL-1 (FOXO3), β-actin] or from Cell Signaling Technology, USA (Akt and p-Akt Ser473 ). Western blots were quantified by densitometric analysis using Image J software.
Cells were then transfected using program Raw264. 7 on Lonza 4D-nucleofector device. Cells were rapidly transferred to 37 • C preheated medium and incubated for 24 h at 37 • C, 5% CO 2. Twenty-four hours post-transfection, macrophages were either mock-treated or infected with BCG at an MOI of 1:10. After 6 h, macrophages were assessed for viability using Annexin-V staining and the remaining cells were harvested, lysed and luciferase activity was measured using Thermo Scientific Varioscan Flash Plate reader as per manufacturer's recommendations (Promega, Madison, WI, USA). The promoter activities are shown as relative light unit (RLU) and normalized to 100% GFP positive and viable cells (Figure  S2 ) using the following equation: Promoter activity = RLU x 100 % GFP positive and viable cells (1).
These results suggest that FOXO3-mediated down regulation of IL-10 in BCG-infected macrophages mainly occurs through site 2 on which FOXO3 might bind and block the transcription. To confirm our observation, we performed CHIP followed by a PCR using two primers flanking the -203 position, as indicated in materials and methods section. The result revealed a strong interaction between FOXO3 and the amplified region containing the motifs at -203 in non-infected cells, while BCG infection displaced FOXO3, releasing IL-10 transcription (Figure  4C ). This data correlates with the observed higher basal activity of IL-10 promoter that bears a mutated site 2 (-203) (Figure  4B ). Taken together, we demonstrate that FOXO3 transcription factor binds to IL-10 promoter at position -203 and negatively regulates its expression.