dataesr/scientific-paragraphs-categorization huggingface dataset:
Wolf ontogeny. Complete ossification of epiphyses is reached in wolves (and dogs) at about one year of age  46. To support the idea that wolf long bones showing fused epiphyses belong to individual that already reached at least the minimum adult body size, we analysed body-size data of extant Italian wolves collected on the field by one of the authors (RF). The sample includes 99 individuals from 2 months-old to adult age (Supplementary Data S2). In the Supplementary Figure  5 , it is shown that 6 to 10 months-old wolves (thus not mature from a skeletal point of view) already reached a body size comparable with that of older individuals. These results give further support to the hypothesis that small long bones from Grotta Paglicci and Grotta Romanelli belong to adult dogs, rather than to young wolves.
X-ray microtomography. A total of 61 specimens, including 45 dog and wolf lower first molars, one dog phalanx and 15 first metacarpals (Supplementary Data S3), were analysed by X-ray microtomography (μCT) at the Multidisciplinary Laboratory of the Abdus Salam International Centre for Theoretical Physics (Trieste, Italy), using a system specifically designed for the study of archaeological and paleontological materials  68. The μCT acquisitions of the specimens were carried out by using a sealed X-ray source (Hamamatsu L8121-03) at variable voltage and current and with a focal spot size of 5 μm (Supplementary Table  9 ). Sets of 1,440 or 2,400 projections of the samples were recorded over a total scan angle of 360° by a flat panel detector (Hamamatsu C7942SK-25). The resulting μCT slices were reconstructed using the commercial software DigiXCT (DIGISENS) in 32-bit format.
We performed generalized Procrustes analyses, principal component analyses (PCA) and between-group principal component analyses (bgPCA) based on the Procrustes shape coordinates  77. The two canid specimens R4 and P6450 were included a posteriori in the bgPCA. Because one of the teeth (P6450) is slightly broken at the cervix on the mesial aspect, we have made three reconstructions for this specimens, aligning the preserved part of the crown with those of an archaeological dog (SC1), a modern wild wolf (377) and a fossil wolf from Grotta Romanelli (P6445). Then, employing the geometric morphometric approach, we performed the contour analysis. The analyses were performed using the package ade4 v. 1. 7-6  78 for R v. 3. 467. Allometry was tested using multiple regressions  79  in which the explanatory variable is the centroid size and the dependent variables are the bgPC scores.
Bait production. Two overlapping long-range PCR products encompassing the whole mitochondrial canine genome were produced. Primers (Supplementary Table  11 ) were designed using the Primer3 program (https :// frodo. wi. mit. edu/prime r3/input. htm). DNA was extracted from the saliva of a special dog of Akita Inu breed and used as template. The PCR purification and subsequent analytical steps to create the baits were carried out following Maricic et al. protocol  50. Raw reads processing and mapping. The EAGER pipeline  82  was used for initial sequencing quality control, adapter trimming and paired-end read merging. Only reads with a minimum overlap of 10 bp and with a minimum total length of 30 bp were kept. Filtered reads were mapped to the reference dog mtDNA (U96639)  83  using BWA-0.
Phylogenetic analysis. The assembled mitochondrial genome was used to reconstruct the canine phylogeny together with previously published sequences from 126 modern and 53 ancient dogs and wolves  88  , 4 coyotes and 3 dholes (Cuon alpinus) (Supplementary Data S4). Alignment of the mitochondrial genomes was performed by Mega7  89  with the Muscle algorithm  90  following criteria proposed in Thalmann et al. 4. BEAST v2. 6. 2  91  was used to determine a phylogenetic tree with Hasegawa-Kishino-Yano and gamma distributed rates (HKY + G) as substitution model, estimated as the best model according to Mega 7  89. Strict clock model and constant population size were used as priors as suggested in Thalmann et al. 4  and Skoglund et al. 3. Tip dates for ancient samples were set according to their radiocarbon calibrated bp ages and used for calibrating and estimating the substitution rate.
A MCMC run with 40,000,000 generations, sampling every 2,000 was performed. Effective sampling size (ESS) values and chain convergence were evaluated using Tracer v1. 7. 1  92. ESS values were higher than 200 for all the parameters. The first 10% of iterations were discarded as burn-in and TreeAnnotator v2. 6. 2  91  was used to produce a Maximum Clade Credibility tree, then visualized by FigTree (https ://tree. bio. ed. ac. uk/softw are/figtr ee/). 14 C dates. Dates shown in Fig. 6  were calibrated with the software OxCal v. 4. 3. 2  93  using the IntCal13 curve  94. Date of Palaeolithic dogs (or relative contexts) from France, Germany and Switzerland are from Street et al. 95. The radiocarbon date of Grotta Romanelli is from Calcagnile et al. 41  ; among dates of Grotta Paglicci, four (GrN-14874, F-65, F-66, F-68) are from Berto et al.
NIST Oxalic Acid II (SRM 4990C) was used as primary standard, while IAEA C7 was used as secondary standard to check measurement accuracy. Measured radiocarbon ages were calibrated using OxCal software  93  and IntCal13 calibration curve  94. Four samples were selected from Grotta Paglicci to be dated: • #2269, humerus attributed to a wolf, collected in layer 5C (Final Epigravettian) [98]; • R4, mandible attributed to a canid (see discussion in the text), collected in an Epigravettian reworked layer, whose chronological context was not knowable a priori; • #2992, radius, attributed to Cervus elaphus, collected in layer 4C (Final Epigravettian); • #5090, second phalanx, attributed to Equus ferus, collected in layer 7B (Final Epigravettian). Bones were treated to extract collagen, the carbonaceous fraction useful for dating.
Acknowledgements The authors thanks the  Soprintendenza Archeologia, Belle Arti e Paesaggio delle province di Barletta -Andria -Trani e Foggia  for supporting research at  Grotta Paglicci ,  Prof. A. Palma di Cesnola  for his studies at the site and the  Bioarchaeology Section of Museo delle Civiltà, Museo Nazionale Preistorico Etnografico "Luigi Pigorini " for giving the possibility to re-analyse materials from  Grotta Romanelli.
F esg ts midguts expressing GFP alone (control), or expressing EcR-DN, and EcR-DN + pri. Samples were stained for GFP (green). The graph shows quantification of the number of GFP-positive cells in the different genotypes. G Posterior midguts containing control and Ubr3 null MARCM clones (GFP, green). H esg ts midguts expressing GFP alone (control), or expressing Ubr3-RNAi, and Ubr3-RNAi+ OvoB. Samples were stained for GFP (green). (H 0 ) quantification of GFP-positive cells from H. Data information: Boxes extend from the 25 th to 75 th percentiles, whiskers from min to max, the horizontal line in each box is plotted at the median; data were collected from three independent replicates. P values from Mann-Whitney tests (D) and one-way ANOVA (E,F,H 0 ) are: ns:> 0. Payre  , 2004). Since these pathways are key regulators of normal and cancer stem cells  (Li & Jasper, 2016; Perochon et al, 2018) , we investigated their putative relationship with Svb in intestinal stem cells.
The y-axis is plotted as log(10). B esg ts midguts expressing GFP alone (control), or expressing Arm S10 , Arm S10 + svb-RNAi, Arm S10 + OvoB, TCF-DN, and TCF-DN+ OvoB. Samples were stained for GFP (green). The graph shows quantification of the number of GFP-positive cells in esg ts midguts expressing GFP alone (ctrl), or expressing TCF-DN, TCF-DN+ OvoB, and TCF-DN+ svb-RNAi. The y-axis is plotted as log(10). C The drawing at left schematizes the svb locus, with position of the E3N enhancer. Close-up shows E3N sequence that correspond to binding sites for Pnt (red) and TCF (green). Right subpanels are pictures of posterior midguts showing expression of wild-type E3N-lacZ (E3Nwt), or E3N-Pnt-mt, and E3N-TCF-mt, as seen from X-Gal staining (cyan blue). Data information: Boxes extend from the 25 th to 75 th percentiles, whiskers from min to max, the line in each box is plotted at the median; data were collected from three independent replicates.
C MyoIA ts midguts expressing GFP and Svb ACT (green), and stained for GFP (green) and PH3 (red). The picture is a single focal plane; the arrow shows a large GFPpositive cell, which is also positive for mitotic PH3. D Summary of the role of Svb ACT and Svb REP in the control of intestinal stem cell maintenance, proliferation, and differentiation. Data information: Boxes extend from the 25 th to 75 th percentiles, whiskers from min to max, the horizontal line in each box is plotted at the median; data were collected from three independent replicates. P values from one-way ANOVA are: ** <0. 01, **** <0. 0001. Scale bars are 20 µm.
After washing, embryos were mounted in Glycerol/PBS (80/20%) and imaged using a Nikon Eclipse 90i microscope using NIS-elements software (Nikon). Each experiment (typical 200 embryos per genotype) was performed at least three times and also included UAS-w-RNAi and w embryos as negative controls. Reporter patterns upon RNAi treatment were classified into "no change", "reduced", or "ectopic" expression; the two latter were kept for additional characterization (Table  EV1 ). For rescuing assays, males carrying pRSQsvb constructs were crossed with females of stock w* btd 1 , svb 1 /FM7-kr > GFP, allowing phenotypical identification of svbmutant embryos. First instar larva cuticles were prepared in Hoyer's/ lactic acid 1:1, imaged with phase-contrast microscopy, and trichomes were counted in the ventral region of A6 segments.
Immunofluorescence Stage-15 embryos were processed using standard protocols, using mouse anti-b-galactosidase (1:500, Promega), rabbit anti-Dyl at 1:400  (Fernandes et al, 2010) , rabbit anti-Min 1:200 (Chanut-Delalande et al, 2006) antibodies, Alexa Fluor-488, or Alexa Fluor-555 secondary antibodies at 1:500 (Molecular Probes). Embryos were mounted in Vectashield mounting media (Vector Laboratories) and imaged using X20 and X40 objectives on a Leica Spe confocal laser scanning microscope with Leica Application Suite software, or a Zeiss 710 confocal microscope using the ZEN software (Zeiss). Adult midguts were dissected in PBS and fixed for 1h at room temperature in a fresh 4% paraformaldehyde solution (Electron microscopy Science) prepared in PBS. Following three washes of 15 min each in 0.
Quantification and statistical analysis Images were analyzed by using ImageJ, with macros we developed for quantification of indicated cell types (codes are available upon request). Briefly, images were acquired with same setting and transformed into multilayered TIFF files. To count the number of cells positive for a given marker (e. g. , GFP), the corresponding channel was used to generate a ROI mask in which DAPI-labeled nuclei were automatically segmented and the number, size, and morphometric features of each object were recorded. Similar analyses were performed for ReDDM assays, quantifying the number of nuclei in GFP + /RFP + progenitors versus GFP À /RFP + differentiated cells. Data of at least three independent experiments were combined. Statistical analyses were carried out with Prism 8 (GraphPad), using nonparametric unpaired two-tailed Mann-Whitney tests for comparison of two samples, and one-way ANOVA for three or more samples, using Welch's ANOVA with Dunnet's T3 correction for multiple comparisons between samples showing normal distribution (Shapiro-Wilk tests alpha = 0.
The graph shows quantification of GFP-positive cells for each genotype. The y-axis is drawn using a log(10) scale. E esg ts midguts expressing GFP alone (control), or expressing Notch Intra Cellular Domain (NICD), and NICD+ OvoB. In close-ups (right), DAPI is shown in purple for improved contrast; the arrow highlights a cell with intermediate phenotype. Data information: Boxes extend from the 25 th to 75 th percentiles, whiskers from min to max, the line in each box is plotted at the median; data were collected from three independent replicates. P values from Mann-Whitney tests (A) and one-way ANOVA (B,D) are: * < 0. 05, ** < 0. 01, *** < 0. 001, **** < 0. 0001. Blue is DAPI. Scale bars are 20 µm.
Acknowledgements We would like to thank  C. Polesello , all members of the  FP laboratory  and  G. Kolahgar  for invaluable help, as well as  T. Reiff ,  S. Ahmed , and  B. Edgar  for kind sharing of unpublished results. We are also grateful to  M. Bou Sleiman  and  Z. Zhai  for discussions and critical reading of the manuscript. We thank  P. Valenti  for excellent assistance in the early stages of this work,  O. Bohner ,  J. Favier , and  A. Destenabes  for help in transgenic lines,  S. Bosch  and the LITC platform (https://www-litc. biotoul. fr/)for imaging. We thank  A. Bardin ,  H. Bellen ,  D. Bilder ,  J. Chen ,  J. P. Couso ,  A. Debec ,  F. J. D ıaz-Benjumea ,  M. Dominguez ,  B. Edgar ,  N. Frankel ,  D. Stern ,  D. St Johnston , and  N. Tapon  for providing fly stocks and reagents, the  Bloomington Drosophila Stock Center, Kyoto Drosophila Genomics and Genetic Resources, Vienna Drosophila Resource Center, Flybase and Developmental Studies Hybridoma Bank  for key data and materials.
Software ImageJ 1. 52a https://imagej. net/ RRID:SCR_003070 Fiji http://fiji. sc RRID:SCR_002285 Prism 8 GraphPad RRID:SCR_002798 Photoshop CC Adobe RRID:SCR_014199 FlyBase http://flybase. org/ RRID:SCR_006549 Clustal Omega http://www. ebi. ac. uk/Tools/msa/ clustalo/ RRID:SCR_001591 MUSCLE http://www. ebi. ac. uk/Tools/msa/ muscle/ RRID:SCR_011812 JASPAR http://jaspar. genereg. net RRID:SCR_003030 Clone Manager Software http://www. scied. com/pr_cmbas. htm RRID:SCR_014521 ZEN Digital Imaging for Light Microscopy http://www. zeiss. com/microsc opy/en_us/products/microscopesoftware/zen. html RRID:SCR_013672 Leica Application Suite https://www. nikoninstruments. c om/Products/Software RRID:SCR_016555 NIS-Elements https://www. nikoninstruments. c om/Products/Software RRID:SCR_014329.
Samples were stained for GFP (green) and b-catenin (purple). The graph shows quantification of GFP-positive cells for each genotype. The y-axis is drawn using a log(10) scale. E esg ts midguts expressing GFP alone (control), or expressing Notch Intra Cellular Domain (NICD), and NICD+ OvoB. In close-ups (right), DAPI is shown in purple for improved contrast; the arrow highlights a cell with intermediate phenotype. Data information: Boxes extend from the 25 th to 75 th percentiles, whiskers from min to max, the line in each box is plotted at the median; data were collected from three independent replicates. P values from Mann-Whitney tests (A) and one-way ANOVA (B,D) are: * < 0. 05, ** < 0. 01, *** < 0. 001, **** < 0. 0001. Blue is DAPI. Scale bars are 20 µm.
| Phylogenetic analyses For phylogenetic reconstructions, we expanded our dataset with additional mitogenome sequences from GenBank (Tables  1  and S1 ). The Pongo, Gorilla, Pan, Homo). We aligned sequences with Muscle 3. 8. 31 (Edgar, 2010)  in AliView 1. 18  (Larsson, 2014)  and corrected the alignment by eye. We reconstructed phylogenetic trees with the maximumlikelihood (ML) method using IQ-TREE 1. 5. 2  (Nguyen, Schmidt, von Haeseler, & Minh, 2015)  and Bayesian inference (BI) using MrBayes 3. 2. 6  (Ronquist et al. , 2012). For all reconstructions, we treated the mitogenome as a single partition and applied the optimal substitution model (TVM+I+G) as determined with ModelFinder  (Chernomor, von Haeseler, & Minh, 2016; Kalyaanamoorthy, Minh, Wong, von Haeseler, & Jermiin, 2017)  in IQ-TREE under the Bayesian Information Criterion (BIC).
We reconstructed the BI tree using four independent Markov Chain Monte Carlo (MCMC) runs, each with 1 million generations, tree and parameter sampling every 100 generations, and a burnin of 25%. To check for convergence of all parameters and adequacy of the burn-in, we assessed the uncorrected potential-scale reduction factor (PSRF)  (Gelman & Rubin, 1992)  as calculated by MrBayes. We calculated posterior probabilities (PP) and a phylogram with mean branch lengths from the posterior density of trees using MrBayes. To obtain node support for the ML analysis, we performed 10,000 ultrafast bootstrap (BS) replications  (Minh, Nguyen, & von Haeseler, 2013). We visualized all phylogenetic trees in FigTree 1. 4. 2 (http://tree. bio. ed. ac. uk/ software/figtree/). To further visualize relationships among the 21 baboon mitogenomes, we constructed a haplotype network in SplitsTree v.
4. 15. 1  (Huson & Bryant, 2006). We calculated divergence times in BEAST 2. 4. 8  (Bouckaert et al. , 2014)   (i) Papio -Theropithecus. Details about prior settings can be found in Table  S2  and a detailed discussion about selected node constraints is presented in  Roos, Kothe, Alba, Delson, and Zinner (2019). We ran the analysis for 100 million generations with tree and parameter sampling setting in every 5,000 generations. To assess the adequacy of a 10% burn-in and convergence of all parameters, we inspected the trace of the parameters across generations using Tracer 1. 6 (http:// tree. bio. ed. ac. uk/software/tracer/). We combined sampling distributions of four independent replicates with LogCombiner 2. 4. 8 and summarized trees with a 10% burn-in using TreeAnnotator 2. 4. 8 (both programs are part of the BEAST package).
3-38. 7 (detailed information is provided in Table  S1 ). All newly generated mitogenomes consisted of the 22 tRNA genes, 2 rRNA genes, 13 protein-coding genes, and the control region in the order typically observed in mammals. All protein-coding genes were correctly transcribed without any premature stop codons, indicative of the absence of numts (nuclear mitochondrial DNA) in our dataset. F I G U R E 3 Phylogenetic trees as obtained from ML and BI analyses revealed identical branching patterns with mainly strong node support (BS 100%, PP 1. 0; Figures  3  and S2 ). Among baboons, P. cynocephalus from the Udzungwa National Park, carrying mtDNA closely related to that of the sympatric R. kipunji  (Zinner et al. , 2018) , diverged first, 3. 56 million years ago (Ma) (95% highest posterior densities [HPDs]: 2.
final dataset was comprised of 33 sequences, including, besides the 10 newly generated baboon mitogenomes, the 10 baboon mitogenomes published by Zinner et al. (2013) (their geographic origins are depicted in Figures 2 and S1) and the olive baboon mitogenome from Gombe National Park, Tanzania, published by Roos et al. (2018), as well as mitogenomes of various nonbaboon taxa (Theropithecus, Lophocebus, Macaca, Chlorocebus, Colobus, Trachypithecus, Hylobates,.
ACKNOWLEDGMENTS We thank  Christiane Schwarz  for her excellent laboratory work. We are also grateful to two reviewers for their constructive and helpful comments. This study was supported by grants of the  German Research Foundation (DFG)  to  Christian Roos  ( RO3055/2-1 ) and  Sascha Knauf  ( KN1097/3-1 ). Open access funding enabled and organized by Projekt DEAL.
Variant calling was verified with the find variations/SNPs tool in Geneious with standard settings (maximum variant p-value 10 -6 , minimum strand bias p-value 10 -5 when exceeding 65% bias). Raw sequence reads have been deposited in NCBI's Sequence Read Archive (SRA; BioProject PRJNA665979) and mitogenome sequences are available in GenBank (accession num- bers: MT279060-MT279069). Additional information is provided in Table S1. We measured library concentrations and size distributions with a Qubit fluorometer and Bioanalyzer, respectively, and quantified molarity via qPCR using the NEBNext Library Quant Kit (New England Biolabs). Sequencing was conducted on an Illumina HiSeq 4000 (.
EDX was performed with an INCA X-Stream-2 detector (Oxford Instruments) attached to the TM4000 SEM and AztecOne software (Oxford instruments) at 10mm working distance. Blind chemical mapping (all elements considered) on random regions of the valves were performed in the first round of observations, and selected elements (carbon, nitrogen, oxygen, calcium and phosphorus) were mapped in the second time on selected regions (bright versus non-bright regions). Weight and atomic percentages were retained for quantitative study.
Acknowledgments: This work was supported by the  Institut Hospitalo-Universitaire (IHU) Méditerranée-Infection, Marseille, France. We sincerely thank  Takashi Irie ,  Kyoko Imai ,  Shigeki Matsubara ,  Yusuke Ominami ,  Akiko Hisada , and all the  Hitashi team of Japan  for the collaborative study between HHT and IHU, and for the installation and services of the TM4000 and SU5000 microscopes in our facility. The authors would like to thank the  Algerian Ministry of Higher Education and Scientific Research  for supporting N. H. during his thesis at the  IHU Méditérranée-Infection.
g. biosynthesis of secondary metabolites, carotenoids, etc. ). Thus, even though an initial step of automatic annotation is mandatory, functional annotation of predicted coding sequences (CDS) still requires extensive expert human curation to be reliable, especially for non-model organisms. With the exponential increase of newly sequenced genomes, manually curating individual genomes is however a highly time-consuming and inefficient approach. A smart alternative is to curate several phylogenetically related genomes at a time, after gathering sequences into Clusters of Likely Orthologous Genes (CLOGs), i. e. genes that exhibit reciprocal best hits to one another and are hypothesized to have the same function in the different members of the dataset  (5, 6). This strategy, notably used in the NCBI's 'prokaryotic genome annotation pipeline'  (7)  for annotating new genomes or re-annotating older genomes before inclusion in the RefSeq database, allows propagating rich, functional annotations made at CLOG level to all proteins composing the CLOG and makes it possible to unify and standardize these annotations across all sequenced strains.
Here we present Cyanorak v2. 1, an information system based on CLOGs that is dedicated to the annotation, comparison and visualization of picocyanobacterial genomes. Initially created in the mid 2000's by A. Dufresne and co-authors to compare the first 14 genomes of marine and brackish picocyanobacteria  (8) , the Cyanorak database has significantly increased since then and relies on a completely redesigned and tremendously enriched information system (v2. 1) which, contrary to Cyanorak v1, is scalable, i. e. conceived to allow addition of more genomes. The current database encompasses 95 genomes and two metagenome-assembled genomes (MAGs), including 31 newly released Synechococcus and Cyanobium genomes  (9) , which have been closed using a customdesigned assembly and scaffolding pipeline  (10).
All strains whose genomes have been included in the Cyanorak v2. 1 database belong to Cyanobacteria Subsection I, Cluster 5 sensu Herdman  (11) , a short-rod shaped group that forms a deep monophyletic branch within this ancient phylum  (12). The common ancestor of all Cluster 5 members is thought to have diverged from other cyanobacteria about 1 Gy ago, during the Mesoproterozoic period  (13). Members of Cluster 5 are also called 'α-cyanobacteria', based on the occurrence in their cytoplasm of specific α-type carboxysomes, phylogenetically and structurally closer to that of thiobacilles than to the β-type carboxysomes found in all other cyanobacteria, so-called 'β-cyanobacteria'  (14). Cluster 5 itself is split into four major groups, including the monophyletic, strictly marine Prochlorococcus lineage and three deeply branching groups, called sub-clusters (SC) 5.