dataesr/scientific-paragraphs-categorization huggingface dataset:
We reconstruct this second composite cross-section by projecting on a NE-SW transect (B-B') the suite of aggradational successions and their top surfaces identified based on stratigraphic and geochronological data  [14, 18, 19, 24]. Chronometric dating and marine isotope correlations 40 Argon / 39 Argon dating. Full analytical details for individual crystals from each level are given in the supplementary dataset (S2 File). In  Fig 8 results  are presented for each level as probability diagrams  [32]. For reworked volcanic material, the youngest crystal population corresponds to the age of the last volcanic eruption recorded in the deposit or to the last source of reworked material. A homogeneous population is considered relevant when the weighted mean of these crystals has the following statistical characteristics: MSWD < 1.
As we regard it unlikely that the dental tissues remained an open system for more than 200 ka, we only discuss the closed system age results. In contrast to bones, it is not possible to apply DA or DAD calculations to the U-series data sets because the diffusion directions cannot be established. Variations in the analytical results from spot to spot are most likely due to U-micro diffusion processes  [36]. To account for this, we calculated integrated ages for the various dental tissues (lower rows in the individual data tables). To gain further insights into U-migration and the meaning of the calculated U-series age estimates, the results obtained on the various skeletal tissues are compared with the best independent age estimates for layer d (240 to 270 ka) and m (around 350 ka). Level d.
In addition, we also calculated early uptake age estimates (these provide a minimum age estimates). The data are shown in S3 File, Table  C. All samples from level d did not yield US-ESR age estimates, because the U-series results were older than the ESR estimates. For level m, sample 3449 yielded 374 +46/-36 ka and sample 3450 402 +30/-22 ka. The ESR data are peculiar. The dose values of most samples from level d, except 3451, are around 1000 Gy, while the samples from level m yield dose values around 1700 Gy, as could be expected if both sample sets had similar total dose rate values. However, the younger samples have significantly higher U-concentration in the enamel than the older samples. This results in high internal dose rates, which do not allow any solutions for the US-ESR model. When calculating closed system U-series ages, this model yields the oldest possible age for a given U-series/ESR data set, only sample 3451 yields a sensible result while the other yield nonsensical results, some even negative ages.
The small tools of Castel di Guido Sorting and sampling. We have excluded from analysis flake fragments, chunks, natural pieces and the very few unretouched flakes (n = 15). After checking a database by Giovanni Boschian and the monograph catalog  [71]  we also excluded from our database a fairly large number of pieces (88 pieces) for one or more of the following reasons: pieces too rolled, too altered or too damaged for correct identification, various pieces from the site of Malagrotta that had been mixed with Castel di Guido by visiting researchers and pieces without catalog number. Taphonomy. The small tools of Castel di Guido (n = 94) are all of flint or other form of microcrystalline silica, namely what many archaeologist would call "chert" distinguishing flint as characterized by a fine, homogeneous, glossy texture with smooth fracture surfaces and chert as being coarser-textured and opaque.
Acknowledgments Research at Torre in Pietra and on the Castel di Guido lithics was funded by  National Science Foundation  Grant  BCS 1118143  to PV and SS and by a travel grant from  CNRS ,  UMR 7041 ,  ArSca/AnTET , Nanterre to SS. We thank the  Pigorini Museum , the  Italian Institute of Human Paleontology  and the  Dipartimento di Biologia of the University of Pisa  for access to the  Torre in Pietra and Castel di Guido collections  and facilities during analysis. We are grateful to  Anna Maria Moretti ,  Alfonsina Russo  and  Flavia Trucco  of the  Soprintendenza of Lazio  and  Etruria Meridionale  for access to the Torre in Pietra archeological site, allowing us to clean the two preserved sections and take sediment samples for dating. Salvatore Milli  and  Maria Rita Palombo  have provided us with very valuable information on the Torre in Pietra stratigraphy.
Bile acids were silylated with 50 μL of dry toluene, 98 μL of BSTFA and 2 μL of 1-(trimethylsilyl)imidazole (TSIM) at 80°C for 1 h. Then, 50 μL of 400 ppm 5α-cholestane (in dry toluene, providing 100 ppm concentration) was added as an internal standard. All fractions were analysed by gas chromatography mass spectrometry according to  Birk et al. (2012). Individual compounds were identified by the use of mass spectral library databases (NIST) and comparison of mass spectrometric patterns with published mass spectra and authentic standards (see Fig. 1 ).
Acknowledgments We would like to thank the  Ainu Association of Hokkaido  and team members of the  Baikal-Hokkaido Archaeology Project  for collaborating on the excavation of the Hamanaka-2 site. We thank  T. Fukumine  of the  University of the Ryukyus  for technical assistance. This study was supported in part by  Grants-in-aid for Scientific Research  from the  Japan Society for the Promotion of Science  (Nos. 18370099 ,  22370087 ,  24242030 ,  16H01954 ),  JSPS Core to Core Program (Advanced Research Networks) 'Advanced Core Research Center for the History of Human Ecology in the North,' and a Major Collaborative Research Initiative Award for 'Holocene Hunter-Gatherers of Northeast Asia ,' from the  Social Sciences and Humanities Research Council of Canada  (No. 412-2011-1001 ).
Results and Discussion As the non-target types of sentences were used to assess the understanding of the task, the proportions of yes and no responses were converted into correct and incorrect responses. The accuracy rate for the various control sentences was 94%, showing that the task was correctly understood. The data from 3 participants who provided incorrect answers to 4 or more of the control stimuli were discarded. We were interested in the acceptance (semantic responses) or rejection (pragmatic responses) of the underinformative some target sentences. The responses were coded for pragmatic correctness, that is, an answer of no to the underinformative sentences. Figure  2  illustrates the percentage of pragmatic answers for each of the four versions of the experiment. The statistical analysis revealed a significant effect of the question: an upper-bounding question triggered significantly more pragmatic answers than a lower-bounding question both when the cardinality of the DQ was explicitly stated (Median upper-bounding = 4, Median lower-bounding = 2, Wilcoxon signed-ranks, Z = 3.
g. [33, 34] ), providing a high resolution (cm-scale), quick and non-destructive data measurement of sediment reflectance. Using the Q7/4 diagram  [32] , we assessed the sedimentological potential of spectrophotometric measurements to characterize sedimentary facies and reconstruct sedimentological dynamics. For this study, spectrophotometry data were obtained with a Minolta CM 2600d. The illuminant was D65, which corresponds to average day light, and the wavelengths belong to the extended visible domain from 360 to 740 nm. The measurement aperture was set to 8 mm and the step of measurement to one centimeter. By taking the optical lightness L Ã (White/ Black) vs 700/400 ratio (main slop of the raw spectrum), it is possible to distinguish the different sedimentary end members that constitute the sediment.
A minimum count of 350 Lycopodium spores per sample was required for the assessment of fungal spore concentration  [61]. The zonation of the pollen diagram was performed with the aid of the module CONISS included in Tilia, based on the square roots transformation of stratigraphically constrained TLP counts. Temporal changes in vegetation composition were summarized by performing principal component analysis (PCA) on the terrestrial pollen percentage dataset. The calculation was done by eigenvalue decomposition of the correlation matrix using the Stats package in R (R Core Team, 2015). Principal components one and two explain 75% and 14% of the total In order to explore past biodiversity patterns, we estimated temporal trends in palynological richness (  Fig 8). Palynological richness, defined as the number of taxa per sample at constant pollen sum  [62] , is a frequently used indicator of biodiversity in paleoecology.
Charcoal analysis indicates that fire activity has been mainly connected to pastoralism throughout the record, especially during the first 500 years when fire episode occurrences are associated with the rise of grazing indicators (Fig  8 ). During the Roman period, both dung fungal spores and charcoal data indicate intense human activity, and the likely access of animals to the wetland. During the transition from the Hellenistic to the Roman Imperial period, historical data such as treaties and poetry attest to 1) the importance of milk and derived products of milk in the diet and 2) specialized pastoralism and transhumance in the Cretan mountains  [70]. Fire events were not recorded during a few decades around 100 AD and dung indicators suggest lower grazing pressure in the surroundings of the bog, while evergreen oak forest cover reached its maximum density/ extension.
In Asi Gonia, local olive cultivation is difficult to infer from pollen data alone. Olea pollen, which does not exceed 5%, may have originated from wild olive trees and/or from extra local populations. The current elevation-limit for olive tree cultivation is ca. 600 m elevation. Given that Olea pollen percentages never reached modern values, we infer that olive trees were not likely to have been locally cultivated at higher elevations in the past. The Turkish administration promoted olive-oil production  [26]  but it does not seem to have reached the eastern edge of the White Mountains. The continuous presence of low-pollinizer Juglans from 100 AD to 650 AD suggests walnut was cultivated in this part of Crete during Roman and 1 st Byzantine times, which is consistent with the hypothesis of its Roman introduction in Crete  [24].
Ecological trajectories and tipping points Pollen data suggest that during the last 2000 years, the vegetation history of Asi Gonia was characterized by three main periods: 1) a first one dominated by evergreen oak forest (until ca. 850 AD); 2) followed by heather maquis (ca. 850 to 1870 AD); 3) and finally by very open landscape with dwarf-shrubs such as Sarcopoterium and Olea at a regional scale (ca. 1900 AD to the present; Figs  5  & 8 ). Atherden & Hall (1999)  interpreted the reconstructed evolution of evergreen oak woodland toward the current phrygana as evidence supporting "the progressive model of human impact" (sensu Oldfield, 1983; i. e. non-reversible vegetation changes over time). Although our data also suggest a long-term linear succession of vegetation communities, the process seems to be more complex, scale-dependent and characterized by rapid changes associated with tipping-points in ecosystem dynamics.
Mais il ne peut pas, non plus, reposer sur la seule routine d'usage d'un logiciel professionnel ou d'une base de données économiques et fi nancières. Dès lors, un suivi diachronique de l'évolution des pages d'accueil permettrait de pondérer l'importance et l'infl uence des changements technologiques face à l'épaisseur du social. De même, une approche monographique fondée sur diff érentes méthodes d'enquête (observation participante, étude des documents prescripteurs, entretiens approfondis…) permettrait d'analyser les critères de choix et les mécanismes de décision qui conduisent les entreprises à considérer la page d'accueil de leur site web institutionnel comme digne d'intérêt et de considération.
Thus, when observing someone performing an action, children will simulate an action plan covertly  (Rizzolatti et al. , 2001)  if this plan is already in their action repertoire  (Woodward, 1999). Csibra and Gergely (2007) , in turn, offer an alternative approach to action understanding in which situational constraints are relevant. "Teleological reasoning [. ] requires the recruitment of the relevant background knowledge that the observer accumulated about the physical constraints of the situation and of the actor"  (Csibra and Gergely, 2007, p. 70). This argument is supported by the fact that infants attribute goals not only to conspecifics but also to abstract and artificial agents. Yet another source that might serve as a database for infants to recognize a structure in the relation between an involved agent and her or his goal is the interaction  (Reddy and Uithol, 2015; Nomikou et al.
Ancient DNA processing and analysis Raw reads from the ancient Phoenician were processed to remove sequencing adaptors and merge paired end fragments, which overlapped by at least 11 base-pairs, using Adapter-Removal (v1. 5. 4)  [16]. Reads were also processed to remove stretches of Ns, bases that had a low quality score (<30), and short reads (<25). To reduce the impact of contamination due to laboratory reagents, all read mapping was done onto a composite reference genome consisting of the Cambridge Reference Sequence for humans (Homo sapiens, GenBank NC_012920), in addition to mitochondrial reference genomes from cow (Bos taurus, GenBank NC_006853), pig (Sus scrofa, NC_0012095. 1), and chicken (Gallus gallus, GenBank NC_001323. 1). The contamination ratio was determined by calculating the ratio of all reads with mapping quality > = 20 for each reference, compared with those for the human mitochondrial reference sequence  [17].
Ancient DNA is usually characterised by C!T transitions at the 5' ends of the molecule, and following double stranded library preparation G!A transitions at the 3' ends of the molecules  [18]. Reads were aligned to the composite reference genome using BWA (0. 7. 10)  [19]  with recommended ancient DNA settings  [20] ; specifically, seeding was disabled (-l 1024), the number of gap opens was set to 2 (-o 2), and the maximum edit distance was set to 0. 03 (-n 0. 03). PCR duplicates were removed from the merged reads using a python script originally developed for the Neanderthal genome project  [21]. These PCR duplicates were also removed from the unmerged reads using Picard's MarkDuplicates tool (http://broadinstitute. github. io/ picard/). To confirm the authenticity of our ancient DNA, the program mapDamage (v2.
0. 2-9)  [22]  which identifies characteristic aDNA damage patterns, was used with the '-rescale' option to lower the quality score of likely damaged sites. The plots of characteristic damage patterns were individually created for merged and unmerged reads. Finally, Ts (thymines) found at the 5' end of a read and Gs (guanines) at the 3' end of the read, within the first two bases, had their quality scores rescaled to zero. The presence of modern human DNA in the sequencing libraries presents a challenge for ancient DNA, as it can introduce major biases into downstream population genetic and phylogenetic  [23, 24]. Modern human mtDNA contamination levels were estimated using the ContamMix package  [25]. Reads that mapped to the human reference genome were extracted from the PMD filtered BAM file and a variant call file (VCFs) was generated using the GATK Haplotype Caller (v3.
3)  [26]  with settings specific for haploid genomes, such as the mitochondrial genome. This file was filtered for mapping quality (<20), and bases supported by fewer than three reads  [27, 28]. This approach was justified under the assumption that the above quality control (QC) procedure preferentially reduces the quality of the damaged positions in the sequencing reads, which would lead to a reduction in the probability that the damaged position would be called downstream. A coverage plot and a fragment length plot were created for the Phoenician samples using the ggplot2 package for the R programming language  [29]. The fragment length plot was created only using the merged reads, this was done because estimation of the fragment length is error prone using unmerged reads. A consensus sequence containing indels (insertions and/or deletions) was created, and has been deposited in GenBank (KT760574).
In addition to the aforementioned QC measures, non-variant sites that were supported by fewer than three reads were changed to 'Ns'. To assign a haplogroup to the Phoenician, we used Haplo-Grep  [30]  (http://haplogrep. uibk. ac. at/) for Phylotree 16  [31]. All Illumina reads generated for the ancient Phoenician have been submitted to the NCBI short read archive as sample MS10148, accession number PRJNA295854.
Modern sequence processing and analysis The raw reads from the modern Lebanese samples were mapped to the human mitochondrial reference genome (Homo sapiens, GenBank NC_012920) using the BWA  [19]  (v 0. 7. 10) maximal exact matches (MEM) command  [32]. This was followed by PCR duplicate removal using Picard's MarkDuplicates command. Haplogroups were assigned by first generating a jointcalled VCF using the GATK HaplotypeCaller, converting the VCF into the HaploGrep input format, and finally assigning a haplogroup to each Lebanese sample with HaploGrep  [30]  (http://haplogrep. uibk. ac. at/). All 47 complete modern Lebanese mitochondrial genome sequences have been submitted to GenBank (accession numbers KT779157-KT779203).
Phylogenetic Analysis To investigate the phylogenetic relationship of the ancient Phoenician (KT760574) to other U5b2c sequences, we obtained the publicly available U5b2c sequences from GenBank and the supplementary information of a recent publication investigating present day mitochondrial diversity in Portugal  [33]. A maximum likelihood (ML) tree was generated with MEGA using the HKY + I model. Preliminary analyses revealed that the sequence EF758625 and KU587510 had many missing positions reducing the phylogenetic resolution, thus these samples were removed from the final analysis.
Sequence authenticity For human ancient DNA studies two potential sources of contamination exist, these are the reagents  [34]  and modern human DNA  [35]. To reduce the impact and to estimate the effect of reagent contamination, we performed all read mapping to a composite mitochondrial reference genome that included the major reagent contaminators cow, chicken, and pig  [34]. Only 4 reads mapped confidently to these genomes. To assess the totality of modern human DNA contamination we used the program ContamMix with a set of 311 representative modern human mtDNA sequences. This estimated that the ancient Phoenician had been contaminated with 1. 1% (95% C. I. 0. 004%-2. 34%) of modern human DNA. The deamination patterns and fragment lengths (Figs  2  and 3 ) were consistent with those expected from ancient DNA  [36].
Therefore, these results are consistent with the unmerged reads originating from larger DNA fragments being ancient. Arintero site in León in Northwestern Spain  [42]. Our Phoenician differed from the La Braña 1 complete mitochondrial genome at eight sites (positions 3882, 5351, 5773, 6023, 9869, 16069, 16126, and 16192). The mutations at sites 16069 and 16126 appear to be private mutations for La Braña. It appears that the U5b2c1 haplogroup is rare in modern populations, with only a few modern sequences published  [33, 38, 46]  or available in public databases (Family Tree DNA). All of the reported U5b2c1 carriers are of presumably (if not specifically stated) European ancestry, from Spain, Portugal, England, Ireland, Scotland, the United States and Germany. Three of the additional non-defining mutations found in our Phoenician, 5351G, 6023A, and 9869T, are shared with one "European" sample  [46]  and an individual from central Portugal  [33].
Interestingly, Fig  5  shows that our Phoenician sample is most closely related to the modern sample from central Portugal. The unidentified "European" sequence (EF758625) which was deleted A maximum likelihood (ML) tree for the ancient Phoenician (KT760574) and other publicly available U5b2c sequences. All samples other than our Phoenician and the La Braña sample are from modern populations. Each node is annotated with the GenBank accession number or sample identification (e. g. Z2478 from  [33] ), source or author if published, and the origin of the sample if recorded  [33, [38] [39] [40] [41] [42]. doi:10. 1371/journal. pone. 0155046. g005 from the analysis due to missing data, also carries the three mutations which define the branch on which we find the Phoenician and the Portuguese sample.
A separate branch within U5b2c1 contains five samples, from England and Germany or otherwise unidentified as to location of origin, with the La Braña Mesolithic sample (JX186998) on its own branch. Given the limited numbers of published full mitochondrial genomes, it is difficult to identify a likely origin for the mutations defining the Phoenician and Portuguese branch, but it is currently not inconsistent with a Southwest European origin. While the U5b2c2 sequences all originate in Centraland North-Western European or likely derived populations (e. g. US Caucasian), and the U5b2c sequences in GenBank (KC847158 and KU587510, which was excluded from the analysis due to missing data) originate in Germany and England respectively (both samples from Family Tree DNA), it is likely that U5b2c originated in Central/Northwestern Europe.
Genbank accession numbers are provided in the text: A consensus sequence containing indels (insertions and/or deletions) was created, and has been deposited in GenBank (KT760574). All Illumina reads generated for the ancient Phoenician have been submitted to the NCBI short read archive as sample MS10148, accession number PRJNA295854. All 47 complete modern Lebanese mitochondrial genome sequences have been submitted to GenBank (accession numbers KT779157.
ACKNOWLEDGEMENTS This work benefitted from conversations/correspondence with  John Lazenby  ( University of Newcastle ) and  Craig Hanyan  ( Brock University, St Catharines, Ontario, Canada ). The satellite imagery in Figure 1 was provided by  Trent Hare ,  USGS, Flagstaff, Arizona (credit JPL, NASA/USGS ). We gratefully acknowledge assistance from  Sarah  and  Paul Ginty-Ciselar , custodians of the Refuge du Viso, License granting authority of the  Prefét des Hautes Alpes , to conduct excavations on the French side of the  Traversette (Réserve Naturelle Ristolas-Mont Viso) , and staff of the  Pian del Re  and  Giacoletti  refuges in the upper Po River catchment. We also acknowledge funding support from the  QUESTOR centre (PP) , the  Invest Northern Ireland Grant for R&D programme (CCRA) ,  Invest Northern Ireland (AK) , the  Geological Survey of Ireland (INFOMAR)  and the  Irish Research Council  ( RS/2012/499 , BK),  H2020   REMEDIATE Marie Curie ETN, Grant  agreement no.
Measurements were also taken regardless of the side (right or left hand) since this factor is not statistically significant enough to impact or change the results at the scale of the study. Actually, according to a morphometric study led by E. Nowak on a child population, morphometric differences between right and left hands are less important than differences of hand measurements between males and females  17. We have selected the measurements criteria in accordance with the data available in the archaeological sample. Some of them are similar to measurements previously used by Snow  13  , Chazine and Noury  18  , and Sinclair et al. 14  in the framework of other methods and purposes. In this study, 7 measurements were taken with a sliding caliper on each individual (Tab. A2, fig. 3):  -W i = width of the second digit (index) measured at the mid phalanx, just above the proximal inter-phalangeal joint.