dataesr/scientific-paragraphs-categorization huggingface dataset:
synonymous sites (dN/dS). We performed a test to determine the expected dN/dS of mapping reads against an incorrect reference genome by using three species of Fusoboacterium, which were formerly considered subspecies of F. nucleatum: F. nucleatum, F. polymorphum, and F. vincentii. These genomes were run through prokka to generate gff files for polymut. The ANI of each genome compared to the other two was determined with MASH  33  as part of the program dRep  34  and found to be below the species-cutoff of 95% identity (Supplemental Figure  S12A ). Nine simulated short-read datasets were generated from each of the three genomes with three read lengths and three different levels of deamination: long read length (100bp), medium read length (75bp), and short read length (50bp), and no deamination, low deamination, and high deamination.
These 9 short-read datasets were each mapped against all three reference genomes using bwa aln and the flags -n 0. 01 -l 1024, and the script polymut. py was used to determine the number of synonymous SNPs, the number of non-synonymous SNPs, and the total number of sites compared, for each mapped bam file (Supplemental figure  S121B-G ). We found that the deamination level did not affect the dN/dS values for any of the species mapped to any of the others. Because the Pacific dataset reads have a short read length, we focused on the results of the short read length dataset, and calculated the average dN/dS for short reads across all deamination levels, which is 1. 94. We took this to be the expected dN/dS value when mapping a species against a closelyrelated but incorrect reference genome. For our samples, collapsed reads were mapped against the Tannerella forsythia genome (NC_016610.
Eukaryotic DNA Identifying eukaryotic taxa within metagenomic datasets is challenging and requires multiple validation steps  35. Additionally, it should be noted that some of the potential dietary items, such as kava (Piper methysticum) and the giant swamp taro (Cyrtosperma merkusii), from the Pacific may not be present in reference databases as they do not have sequenced nuclear or organelle genomes. Within the well-preserved dental calculus samples, we identified DNA from five nonhuman eukaryotic species of interest: cattle (Bos taurus), dog (Canis lupus familiaris), broad fish tapeworm (Dibothriocephalus latus), bamboo (Fargesia denudata), and wheat (Triticum aestivum) (Table  S1 ). Other eukaryotic DNA present in the dataset belonged to commonly recognized contaminants, were assigned to genomes with known contaminating sequences  35  , or represented highly unlikely taxa; these assignments were excluded from subsequent analysis.
Fiji. There were quite a few phytoliths found in the Fiji samples, most of which are probably from grass leaves (blocky, elongate, bilobate and rondel types), along with a couple of samples that contained palm phytoliths (Supplemental Figure  S17A-J ). These are all quite commonly found within the Pacific. There was one phytolith that could be species-specific that did not match anything in our reference database (Supplemental Figure  17B ); further reference samples would be needed to positively identify it, but it resembles phytoliths from the bark of species with medicinal properties in West Africa  42. There are also two phytoliths that look like double-peaked glume rice phytoliths (Supplemental Figure  17A, C ), but they are very degraded so the resemblance may be an artifact. Several of the phytoliths appeared black or burnt (Supplemental Figure  17G, H, I ), which may be an indication of fire use.
Fund (grant nos. UOO0407  and  09-UOO-106 ) and a  University of Otago   Research Grant  awarded to H. B. The support of the leaseholder  M. R. Monvoisin  and family is acknowledged, as is the support and assistance of the traditional landowners and population of Eratap Village. Detailed acknowledgement by the authors of the Vanuatu studies (SB, HB, JF, RS, MS, EW, and FV) are given in the published site reports for each location, and were supported by the  Australian Research Council   DP160103578. We thank  Alexander Hübner  for discussions on strain analyses. This work was supported by the  Werner Siemens Stiftung  ("Paleobiotechnology" to C. W. ), the  Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)  under Germany's  Excellence Strategy EXC 2051 , Project -ID 390713860  (C.
Before carrying out the search on all the databases, a first search was performed on PubMed to ensure that the combination of the three search categories yielded relevant results, but also to identify different off-topic terms. Indeed, due to the fact that terms related to the adaptability of human functions and behavior are used in a lot of different research areas (e. g. , economy, climate, urbanization, and management), a list of terms to be excluded was constituted and grouped with MeSH.
Finally, the multidisciplinary nature of our team is an asset for relevance, capacity for criticism and reflection as well as ensuring sound scientific judgments, which will be at the core of this review Peer review New results are tested by presenting them to external reviewer in a formative way, and this feedback feeds into further reflection and analysis  [29]. We will ask several scientists, specialized in complex systems, chronic diseases and health, outside of our research team, to analyze our synthesis phase in order to check if we yielded the differences and complementarities between the various research traditions while respecting the principles of historicity, pluralism and contestation. Finally, we will present our recommendation phase to an external evaluator to ensure that it is consistent with the data extracted from the articles and the synthesis phase.
The objective will be to nourish our reflection in the light of the evaluators' feedback to ensure a coherent and structured narrative account of the collected information Terms if possible. Once we refined the three search families and list of terms to exclude, we proceeded to search for articles in the following databases: PubMed, Web of Science, and Science Direct. The electronic search strategy included a combination of Boolean operators and MeSH terms formulated according to the characteristics of each database. Qualitative, quantitative, and mixed methods studies up to January 2021 were eligible, articles such as personal narratives, conferences, editorials, or books (see Additional file 2) were excluded. A complementary search phase will consist in making a reference follow-up within the selected articles, in order to yield unidentified complementary articles.
Finally, the articles that team members were aware of but that were not captured by the search processes were added later, and also submitted to the screening process detailed below. All selected articles were imported and managed using the Zotero citation manager. The second step of the searching phase is screening the articles collected during the first phase based on exclusion criteria, to select only the most relevant to our analysis. Before starting the screening process, all duplicates were removed. In order to determine the exclusion criteria, a sample of articles was selected from those retrieved from the databases, and each team member had to determine why certain articles should be excluded. After several meetings, we were able to determine the main exclusion criteria that allowed us to easily exclude offtopic articles (e.
g. , a lower level of complexity of heart rate variability, in individuals with pathologies compared to healthy subjects, suggests a loss of adaptive capacity. This 6-dimensional matrix was tested on a sample of articles to check for relevance and utility. Several corrections were necessary, further underlining the non-linear aspect of the meta-narrative review methodology. LH will perform the encoding of articles, and monitoring phases at 25, 50, 75, and 100% of the total number of encoded articles will be carried out by the other members of the team, AV, KT, and NH, to ensure encoding consistency. Nevertheless, monitoring in this mapping phase will not be accompanied by a consistency threshold as in the screening phase. Upon the final release of the meta-narrative review, the data extraction spreadsheet will be provided.
Synthesis phase The synthesis phase corresponds to the phase of aggregation and analysis of the information extracted from the articles, in order to answer the questions of the meta-narrative review and to develop a coherent and representative narrative of the adaptability of human functions and behavior assessed through the complex systems approaches. It will be based on several analysis techniques in accordance with the meta-narrative review methodology: paradigm bridging (identifying commonalities), paradigm bracketing (exploring differences), interplay (examining and explaining tensions or contradictions in the data), and meta-theorizing (exploring patterns that cut across different understandings), and takes place in 3 steps. First, data collected during the mapping phase are aggregated during an analysis phase, to help provide a representation of different research traditions.
This procedure ensures the most transparent approach and constitutes an opportunity for data sharing to promote future meta-narrative reviews. Thus, within this discussion, we address the main challenges already encountered and those that we anticipate during the course of the review. The main challenge encountered so far concerns the search and selection of articles. Indeed, within the framework of a meta-narrative review, the objective is to explore different research traditions and therefore yield from the database search all main relevant articles. For our review, the terms adaptability or resilience, for example, are widely cited in numerous scientific specialties, increasing the occurrence of off-topic articles in the early selection stages. As a result, we proceeded to multiply the analyses of sample articles retrieved from the databases, to determine the main relevant terms to be excluded, while retaining relevant articles.
Finally, in light of the multiple research traditions based on complex systems approaches covering various research topics, we carried out a pre-screening phase and created a specific search methodology on the different databases (see Additional file 2) in order to include only those articles related to the adaptability of human functions and behavior. The third challenge relates to the principle of contestation, with the exposure and understanding of the contradictory data within and between research traditions. However, this principle can be difficult to respect if research traditions do not contradict one another. For example, even when using different models and methods, studies may present their results or theoretical concepts regarding the adaptability of human functions and behavior on a common -notably systemic -interpretative level.
In addition, a significant number of weed seeds were documented. The 15,365 recovered faunal remains stand out as undoubtedly one of the most quantitatively important in this geographical area for this chronology. Of these Schwartz  28  identified a total of 3212 remains. The assemblage is mainly composed of caprine remains (91. 4%), with the sheep/goat ratio not being given. Among the other domestic species recovered, remains of cattle, pigs and dogs are also recorded, but in small numbers. Hunting of wild resources is a minor component (included birds and molluscs). These data have led to propose that the economic model of the site was a lowland mixed farming economy  26. Crno Vrilo is located on the right side of the Miljašić Jaruga River, about 12 km from the modern town of Zadar. It was excavated between 2001 and 2005 by members of the University of Zadar  25.
Methods Mortality profiles. The estimation of the age at death was based on the study of dental remains, mainly from the analysis of tooth eruption and wear patterns. Data on tooth eruption and wear were recorded following Payne  63, 86  , also using his age classes. In addition, these data were supplemented with metric data from the method of Helmer 87 based on the decrease of the crown height (H/DT) with age. Mortality profiles were then constructed following the method of Gerbault et al. 88  which uses the Dirichlet distribution to construct histograms with Bayesian credible intervals that allow us to increase our ability to differentiate between age class representations within an archaeological assemblage. The 'rdirichlet' function of the R package LaplacesDemon (v. 4. 1. 3) was used for this purpose.
1% TFA and UHQ water) and conditioning (0. 1% TFA in 50:50 acetonitrile and UHQ water) solutions. 1 µL of the sample was spotted in triplicate on a MALDI 384 plate with 1 μL of α-cyano-4-hydroxycinnamic acid matrix solution and air dried. MALDI analysis was carried out using a Bruker Ultraflex III MALDI-TOF mass spectrometer at the University of York. Replicates were averaged using the open-source software mMass (www. mmass. org;  81  ) and compared to a database of known m/z markers  [18] [19] [20]. Oxygen isotopes. For the study of reproduction, stable oxygen isotope analysis (δ 18 O) was performed on tooth enamel bioapatite. Following the procedure described in Balasse et al. 89  , sequential sampling was performed on the buccal side of the molar, in the middle lobe of M3. The enamel surface was cleaned by abrasion using a tungsten drill.
Acknowledgements This work has been carried out under the funding of the project Impressa sheep: husbandry practices of the first farming societies in the Eastern Adriatic by the  Fyssen Foundation. In addition, we would like to thank  Natalija Čondić  ( Archaeological Museum of Zadar ) and  Dario Vujević  ( University of Zadar ) for their support in Croatia. We would also like to thank  Maria Saña  ( Autonomous University of Barcelona ),  Alfonso Abecia  ( University of Zaragoza ) and  Stašo Forenbaher  ( Institute for Anthropological Research, Zagreb, retired ) for interesting discussions on different parts of the paper. Finally, we would like to thank  Krista McGrath  for the loan of the  ICTA-UAB laboratories  and for the laboratory support provided. Stable isotope analyses were performed at the  SSMIM (MNHN, Paris ).
In other words, co-reference between P11 and P14 is not explicitly marked through specific mechanisms. Note that Bharatanatyam clearly operates with an iconic semantics; the dance posture that conveys that a man is sitting, [P11], or holding a spear, [P14], resembles that which it describes. [P21] [P22] [P23] [P24] [P25] Figure 2: disjoint reference condition The crucial observation, which Patel-Grosz et al (to appear) replicate in two follow-up studies, is that the dancer marks a new position in the visual space in [P23], which she then assumes in 49 Videos with stick figures, from which these screen shots are taken were generated by the Qualisys Track Manager software (QTM, Qualisys AB, Gothenburg, Sweden). The complete set of videos from this study can be found at https://www. youtube. com/playlist?list=PL0dCnZzwa9N5Q3qPHb9M79II_TUb8A5Ww Figure  1  corresponds to 0:10-0:12 in video "Set1 1A": https://youtu.
This research was supported by funding from the  Faculty of Humanities  career development grant at the  University of Oslo  [PI: Patel-Grosz], and from the  European Research Council (ERC)  under the European Union's  Horizon 2020 research and innovation programme  [grant agreement No  788077 , Orisem, PI: Schlenker]. Research was conducted at  DEC ,  Ecole Normale Supérieure -PSL University. DEC is supported by grant  FrontCog ANR-17-EURE-0017.
The spectra were processed using the ARTAX software. By comparing the spectra with an internal database, the application verifies any correspondence with known metal alloys. The preliminary verification of the calibration of the instrument was carried out with a standard sample of sterling silver. Surface corrosion products were analysed using the hand-held spectrometer Bruker BRAVO (Bruker Raman Verification Optics) equipped with a fibre optic probe to analyse specific areas of the sample and a high quantum efficiency array CCD detector to ensure a good signal-to-noise ratio in the acquired spectra. The spectrometer provides a spectral resolution of 10-12 cm -1 and features a double laser excitation with different wavelengths (Duo LASER ™) and benefits from a patented SSE ™ (Sequentially Shifted Excitation) technology capable of mitigating the phenomena of fluorescence  [56].
The lasers simultaneously affect the sample, resulting in high sensitivity over a wide spectral range from 178 cm -1 to 3200 cm -1. Data acquisition and processing was carried out with the OPUS 7. 0 software. The identification of the spectra was carried out by comparing the RRUFF reference database  [57]  and further references were obtained from the literature data  [58]. Based on morphological and chemical characteristics, 13 representative coins were selected for the FESEM-EDS analyses performed by a Zeiss Merlin VP FESEM (Field Emission Scanning Electron Microscope) microscope, equipped with a large Gemini II working chamber, which allowed the coins to be inserted directly into the sample chamber. It is equipped with an Oxford EDS X-Max spectrometer. The samples were investigated in both SE and BSE modes working on variable pressure and the images were recorded at different acceleration voltages in the range from 3 to 10 kV with 10 seconds for acquisition and at different working distances.
Digital Image Analysis (DIA) was processed with ImageJ software (public Java domain image processing) in order to distinguish different areas on the basis of the chemical composition derived by the SEM/EDS analysis. From the total area captured in BSE, Ag-rich areas were subtracted to estimate their distribution. Segmented and total areas were calculated by software in microns and subsequently converted to percentage values. For the visualisation of the 3D internal microstructure (pores, cracks) of coins X-ray computed microtomography (µ-CT), analyses were conducted at the OV-INGV (Osservatorio Vesuviano-Istituto Nazionale di Geofisica e Vulcanologia) of Naples on a selection of six coins chosen on the basis of the monetary attribution, the different mints and their state of conservation. In this study, microtomographic analyses have been performed using a Carl Zeiss Xradia Versa-410 3D X-ray microscope.
Carbonates Corrosion Products Another element that contributes to modifying the original composition of the coins is carbon: carbon dioxide, conveyed by humidity, gives rise to compounds that we see as corrosion patinas on the analysed coins. Most of the corroded coins presented a green patina (Figure  7a ). The mamillary or botryoidal texture of this corrosion product was investigated via optical and electron microscopes at various magnifications (Figure  7b ). In EDS analyses, this green area presented carbon in association with oxygen and copper (Figure  7c ). Raman analyses have identi-fied the presence of a copper carbonate with peaks at 265, 350, 430, 525, 1059, 1094 cm -1 attributable to the malachite (Cu 2 CO 3 (OH) 2 ) (Figure  7d ; Table  3 ))  [58]. Carbonate-based patinas: the copper carbonate is presented with the stereomicrograph (a), the SE image (b) and the related EDS microanalysis spectrum (c), finally with the Raman spectrum acquired on the coin # 30 (in black) and malachite reference spectrum (in green) from the RUFF database (d); similarly, lead carbonate is presented with the stereomicrograph (e), the SE image (f) and the related EDS microanalysis spectrum (g); finally with the Raman spectrum acquired on coin #06 (in black) and cerussite reference spectrum (in green) from the RUFF database (h).
Research Design and Participants To ensure the data richness and an overall perspective of these questions, this study combines the view of people with the lived experience of dementia and those with professional expertise in dementia. Focus groups and semi-structured interviews were carried out with various stakeholders from Greater Manchester between February and August 2021. Due to Covid-19 restrictions, data collection was conducted mostly via video call. Only four interviews were conducted face-to-face, as originally intended. Eleven staff members, trustees or volunteers from organisations and charities supporting the social participation and empowerment of people living with dementia (e. g. , NHS, Age UK local entities, peer-support groups, and community activities) took part in one of the three focus groups.
Data Collection and Ethics The three focus groups (n = 11 participants) and the 17 individual interviews (n = 20 participants) were conducted by the first and the last author. Data were recorded by means of video calls using their Manchester Met Microsoft Teams accounts to comply with data requirements for dealing with sensitive research material  [33, 34]. To reduce the risk of fatigue, interviews were conducted as short as possible, lasting, on average, 40 to 60 min and not exceeding 90 min. The raw data recordings were deleted after the verbatim was transcribed and anonymised, usually 3-4 weeks after the recording and no later than three months after the end of the project. This study follows the ethical guidelines outlined in the Declaration of Helsinki and is approved by the Art and Humanities Research Ethics and Governance Committee of the Manchester Metropolitan University (reference number: 26864).
Data Analysis Thematic analysis was undertaken to identify and describe the key features of participating in activities, as reported by the participants. Both inductive and deductive analyses were conducted on participants' verbatim comments, following Guest, MacQueen, and Namey's  [35]  applied approach to thematic analysis. Emerging themes, sub-themes and categories have been discussed by the research group. Based on these, the main researcher and first author developed the data codebook (see Table  3 ). This codebook has been discussed and refined with co-authors in an iterative process. The themes and sub-themes were further defined and clarified with two co-authors until a variance in the coding of within 10% was achieved. The transcripts and coding framework were entered into NVIVO 12 to assist the management of further qualitative data analysis.
Participants and procedure From November 23, 2021, to 19 February 2022, a Google Forms poll was used to gather cross-sectional data. To acquire data from Tunisian students, we employed a snowball sampling strategy among Tunisian student Facebook users. This strategy is increasingly used in social network investigations  [30]. Participants completed an informed consent form using a particular Google Gmail account. Then they asked their friends to do the poll. This process allows to construct a customized ballot box to govern numerous replies. We utilized Google's Cloud Computing infrastructure, which allows each user to submit one and only one survey response. However, this method needs a Google email account and restricts access to users' IP addresses for concerns of privacy and security. The research ful lled the "CHERRIES" Recommended Standards for Online Surveys  [31].
We note that the PSMC curves exhibited larger uctuations for some of these scenarios and were not always perfectly timed with the observed ones. This mismatch however represents a secondary issue given the poorer t of the PSMC curves computed under the other published models (Figure  3A, B ). We performed additional robustness tests to account for the fact that modern datasets can typically use genomic data with dierent sampling strategies, coverage properties and sequencing quality. We ltered the simulated genetic data for the S' and CRF analyses so as to mimic the original analyses performed on the 1000 Genomes Project dataset with low coverage  (Durbin et al. , 2010)  (cf. Notes S1. 3. 2). We found that our results were consistent irrespective of the shifts in allele frequency spectra induced by low coverage (Notes S10.