dataesr/scientific-paragraphs-categorization huggingface dataset:
ACKNOWLEDGMENTS. This work was supported in part by a grant from  Agence Nationale de la Recherche  to L. A. (Project  RNAchap ,  ANR-17-CE11-0009-01 ). This work was performed within the framework of the  LABEX ECOFECT  ( ANR-11-LABX-0048 ) of  Université de Lyon , within the program " Investissements d'Avenir"  ( ANR-11-IDEX-0007 ) operated by the  French National Research Agency. We thank  Magali Jaillard  and  Laurent Jacob  for introducing us to the DBGWAS tool and for all subsequent discussions about its use in our project,  Louise Kindingstad  ( Stavanger University Hospital, Norway ) for providing the L. israelensis isolate Vestfold  L18-01051 , and  Olga Soutourina  ( I2BC, France ) for RACE protocols.
Geographical location and charcoal site selection To determine past biomass burned, we compiled a dataset comprising 117 charcoal records from sites 155 located in Central and Eastern Europe (Fig. 1 ; Supplement S1). Of these, 70 records are from peatlands (bogs and fens), whereas 47 records are from lakes. For each record we compiled metadata including geographical coordinates, elevation, depositional environment, and data source (Supplement S1). The overall climate of the study area is temperate with considerable variability across regions due to marine or continental influences: the northern and eastern part have long cold winters and short, warm 160 https://doi. org/10. 5194/bg-2019-260 Preprint. Discussion started: 13 August 2019 c Author(s) 2019. CC BY 4. 0 License. summers, whereas the central and southern parts have relatively warm, wet winters and dry, hot summers.
Charcoal concentrations were transformed into charcoal accumulation rates (CHAR) by multiplying concentrations (charcoal counts [pieces cm -3 ] or charcoal areas [mm 2 cm -3 ]) by 180 sediment-accumulation rates [cm a -1 ] to account for variations in sedimentation among sequences. To allow comparison between and within charcoal records obtained from various depositional environments with different laboratory methods, we have applied the standardisation technique established by  Power et al. (2008)  and modified by  Daniau et al. (2012)  and  Blarquez et al. (2014). The standardisation procedure included a min-max rescaling of CHAR values, followed by a Box-Cox 185 transformation to homogenise within-record variance, and a Z-score transformation using a base period from 12 to 0. 15 ka BP. This period includes the entire dataset, but excludes the effect of recent human impact on fire activity during the post-industrial period.
To reduce the influence of high-resolution https://doi. org/10. 5194/bg-2019-260 Preprint. Discussion started: 13 August 2019 c Author(s) 2019. CC BY 4. 0 License. charcoal records on the composite charcoal record, transformed charcoal records were bootstrapresampled 999 times. Resampled charcoal time series were aggregated by ecoregion and smoothed with 190 a 500-years loess smoother. We then calculated the mean and 90% confidence intervals of the aggregated records to obtain regional biomass-burned trends. For numerical processing of the CHAR series we used the R paleofire package version 4. 0  (Blarquez et al. , 2014).
Pollen-based regional composite of land cover classes We used pollen-based land cover estimates at 200-year time intervals for the period 10. 9 ka BP to 195 present, based on the pseudobiomisation method  (Fyfe et al. , 2015)  to quantify changes in land cover type. The pseudobiomisation approach groups pollen types into land cover classes that are directly comparable to other land cover classifications  (Fyfe et al. , 2015). These land cover estimates are available from the PANGAEA Database for the entire study area, as opposed to other pollen-based quantitative vegetation reconstructions restricted mainly to northwestern Europe  (Fyfe et al. , 2015). We 200 extracted six land cover classes: total forest, closed needleleaf forest, closed broadleaf deciduous forest, heath/scrubland, natural grasslands and open pastures, and arable/disturbed land cover other than heathland.
Simulated-based regional composite of climate conditions Holocene climate conditions were derived from TraCE-21ka (Transient Climate Evolution over the last 21,000 years  (Liu et al. , 2009; He, 2011). This is a transient simulation of the last deglaciation phase (22 225 to 0 ka BP) using the fully coupled NCAR Community Climate System Model version 3 (CCSM3,  Liu et al. , 2009; He, 2011). Atmospheric and land model simulations were performed at the T31 (~3. 75° x 3. 75°) horizontal resolution and approximately 3° in the ocean and sea-ice models. The simulation output data (surface temperature and precipitation) was downloaded at monthly temporal resolution from earthsystemgrid. org. To remove systematic model biases, the climate simulation data was first 230 bias-corrected using monthly climatologies between 1950 and 1980 from the Climate Research Unit (CRU) observational dataset  (Harris et al.
, 2014). The bias correction was calculated with respect to the last 30 years of the TraCE-21ka simulation (representing pre-industrial conditions) as ratios of the surface temperature (precipitation) from CRU. These ratios were then multiplied to all climate simulation fields of the interval 12 to 0 ka BP. 235 We focus here on the boreal summer (June, July, August, hereafter "JJA") surface temperature (JJA T) and precipitation minus potential evapotranspiration (JJA P-PET), as these parameters are most representative for fuel moisture during the major fire season  (Thonicke et al. , 2001). JJA P-PET was calculated using the Thornthwaite model  (Thornthwaite, 1948) , which requires the surface temperature and average day length of each month as input variables. Surface temperature was taken directly from 240 the bias-corrected TraCE-21ka data and the average day length for each month going back to 12 ka BP was calculated using the Earth's orbital parameter scheme in CCSM3.
Generalized Additive Models We developed generalized additive models (GAMs) to explore the response of biomass burned to changes in percent land cover, dominant functional forest type, and JJA climate. GAMs are models with 250 a linear predictor (here the composite pollen-derived regional land cover class abundance and simulated climate conditions) involving a sum of smooth functions of covariates  (Hastie and Tibshirani, 1990). We used a Gaussian error distribution to fit models with the mgcv package  (Hastie and Tibshirani, 1990). GAMs were estimated with thin plate regression splines using restricted maximum likelihood to automatically determine the optimal level of smoothing for each term in the model and automatic term 255 selection. We calculated Akaike Information Criterion (AIC) weights to identify the models that were best able to predict the observed changes in biomass burned.
AIC weights are a normalized indicator of support for each model given the evidence within each data set while penalising more complex models  (Hastie and Tibshirani, 1990). We obtained AIC scores using the AIC function in R and calculated AIC weights relative to the model with the lowest AIC score using the qpcR package  (Wood, 2017). AIC 260 values can only be compared across a common data set; we therefore fitted the GAMs and calculated AIC weights separately for each ecoregion (including land cover classes, JJA T and JJA P-PET). Visual inspection of plots produced by the gam. precheck R function showed that all selected models were well-fit (Supplement S2). We restricted the GAMs analysis including all predictors to the last 8 ka BP as the proportion of open land cover classes (arable and grassland cover) during this period should 265 predominantly reflect the influence of human impact (see Pollen-based regional composite of land cover).
Warmer 330 summers and/or drier conditions were generally associated with higher biomass burned over large areas in Europe, although a stronger effect of land cover was detected at mid to low latitudes  (Vannière et al. , 2016; Dietze et al. , 2018; Molinari et al. , 2018). Proxy-based climate reconstructions are fragmentary and mostly qualitative, which hampers their inclusion in the generalized additive models. However, proxy climate datasets were used to check whether the model simulations depict general trends in 335 climate conditions. Simulated and proxy-based climate reconstructions are in general good agreement in indicating warm and dry climate conditions for the early Holocene and increased moisture availability during the mid-Holocene in all ecoregions, and cooler summer temperature in the CON ecoregion  (Davis and Brewer, 2009; Heiri et al.
Acknowledgements: TraCE-21ka was made possible by the  DOE INCITE computing program , and supported by  NCAR , the  NSF   P2C2 program , and the  DOE Abrupt Change  and EaSM programs. M. We thank  Metzger  for providing the environmental stratification of Europe, and  O Blarquez  for guidance with the paleofire package. 580 Financial support. This work was supported by the  German Research Foundation  [ FE-1096/4-1 ]. This study is based on the PAGES Global Charcoal Database (www. paleofire. org)initiative developed by https://doi. org/10. 5194/bg-2019-260Preprint. Discussion started: 13 August 2019 c Author(s) 2019. CC BY 4. 0 License. 590  Science Centre in Poland  ( 2015/17/B/ST10/01656  and  2015/17/B/ST10/03430 ), V. A. C and P. K. from  Czech Science Foundation  ( 16-06915S ), S. V, A.
OTU Identification, Taxonomic Assignment, and Statistical Analyses Microbiota profiles were analyzed using QIIME (version 1. 9. 1)  (Caporaso et al. , 2010b). Rectal and vaginal microbiota analyses were performed separately and independently for each animal. OTU picking was performed using the uclust algorithm  (Edgar, 2010)  with identity set at 97%. Representative sets of sequences were aligned with the PyNAST algorithm  (Caporaso et al. , 2010a). Taxonomic assignments were performed using the RDP classifier  (Wang et al. , 2007)  trained on the Greengenes database  (Desantis et al. , 2006). Taxa with abundance <1% in all animals were filtered out and aggregated to provide a complete view of the rectal and vaginal compartments. Alpha diversity was calculated based on the Simpson diversity index.
Graphical and Multidimensional Scaling Representations Graphical representations of relative taxonomy abundance were generated using GraphPad Prism version 7 for Windows (GraphPad Software, La Jolla California USA, www. graphpad. com), Tableau Software (version 10, Seattle Washington USA), and R software (https://www. r-project. org/). The tree representation showing the taxa commonly or specifically found in the rectum and vaginal tissues was constructed as the union of the two taxonomic trees generated by QIIME. Multidimensional scaling (MDS) representations were generated based on the SVD-MDS algorithm  (Becavin et al. , 2011). Distances between microbial profiles were computed as Euclidian distances between their relative abundances of identified taxa. The Kruskal Stress indicated in each MDS representation corresponds to the percentage of information lost in the dimensionality reduction process.
6 to 0. 5%. Non-identified taxa were also present in the vagina of all animals from an abundance of 1. 7-3. 6%. L. apodemi 1 1. 1 L. johnsonii 1 1. 1 L. nagelii 1 1. 1 CB804C had the highest number of identified taxa (34) and was also the only one to have detectable Lactobacillus in its vaginal microbiota (mean abundance of 2. 46%) (Figure  2D , lower pie charts). Lactobacillus was present in all 15 collected vaginal samples but varied in abundance from 0. 06 to 10. 54%. The QIIME analysis was unable to determine the specific species based on the GreenGene database. Further analysis, using RefSeq database  (Pruitt et al. , 2007)  identified the closest Lactobacillus species, in terms of sequence homology to be closely related to Lactobacillus crispatus (52. 13%), Lactobacillus helveticus (23.
Vaginal Cynomolgus Macaque Microbiota Display Similar Composition and Abundance to Woman Vaginal Microbiota Belonging to CST-IV-A We compared the cynomolgus macaque vaginal microbial profiles with those of humans using a previously published dataset of human vaginal samples collected cross-sectionally  (Ravel et al. , 2010). This dataset consists of samples from 376 patients assigned to five community state types (CST) designated CST I, II, III, IV-A, IV-B, and CST V. The MDS analysis clearly showed that the cynomolgus macaque vaginal microbiota is most similar, in terms of taxonomic composition and relative abundance, to a subset of women's vaginal microbiota belonging to CST IV-A (Figure  3C ).
Longitudinal analysis of the vaginal and rectal microbiota in non-human-primate models are necessary for this purpose. Further investigations in macaque models are necessary to understand whether the rectal or vaginal microbiota affect susceptibility to infections and local immune response. Ultimately, access to a well-characterized cynomolgus macaque model in which the vaginal microbiota could be manipulated (local antibiotic treatments and/or local administration of specific bacterial strains) to mimic that of human, will help us to decipher the role of the vaginal microbiota play in the protection against STIs in human. and the Grant ANR-17-E15-0020-03 funding the ACROBAT project. JR was supported by the National Institute for Allergy and Infectious Diseases of the National Institutes of Health under award number U19AI084044.
ACKNOWLEDGMENTS The authors would like to thank  Thierry Pedron  and  Azadeh Saffarian  from the  Institut Pasteur in Paris  for their valuable contributions and advice concerning this study. The authors also would like to thank the  Biomics Pole  of the CITECH structure at the  Institut Pasteur in Paris  for the sequencing services and all members of the  ASW  and  L2I  groups of the IDMIT infrastructure.
FUNDING This work was funded by the  French Agence Nationale de Recherches sur le Sida et les Hépatites Virales (ANRS). This work was supported by the  French government Programme d'Investissements d'Avenir (PIA)  under Grant  ANR-11-INBS-0008  funding the  Infectious Disease Models and Innovative Therapies (IDMIT, Fontenay-aux-Roses, France)  infrastructure.
Once ensured that the load cell has been properly seated on the top cap, the values for the LVDT and the load cell in the program for the data acqusition were set to zero. Consequently, in the test control appartus, the velocity was set as 0. 5mm/min for all the tests. The compression test was stopped once the force reached the load cell limiting value (10kN). The oedometer cell was then removed, the height with the top cap was measured and then the top cap was removed and the sand-rubber sample was allowed to relax. A final measurement of height was also done after the relaxation.
The number of attached cells after each time was analyzed using ImageJ. After each time, the samples containing attached cells were fixed using 4% paraformaldehyde/2. 5% glutaraldehyde in PBS for 10 minutes. After that, the samples were fixed using graded ethanol solution (50%, 70%, 90% and 100%, 10 minutes each). Next, the samples were fixed using ethanol:hexamethyldisilazane solution (1:1) for 30 minutes. Finally, the samples were fixed in hexamethyldisilazane for 30 minutes (room temperature). Before SEM analysis, the samples with fixed cells were sputter-coated with a thin gold film. Cell area monolayer percentage covering the sample surface was quantified with the ImageJ software from SEM images at 1,000× magnification.
Acknowledgments AOL and FRM would like to thank the  National Council for Scientific and Technological Development (CNPq  grant numbers:  AOL -303752/2017-3  and  FRM -304133/2017-5 ). EP and RZV acknowledge financial support from  Saint Petersburg State University ,  Event 3 project (id 26130576 ). DPO would like to thank  FAPESP  for financial support ( 2013/06258-0 ).
Data availability. This whole-genome shotgun project was deposited at DDBJ/ENA/ GenBank under the accession numbers RQUX00000000 to RQVN00000000 as listed in Table  1  (BioProject number PRJNA506647; BioSample numbers SAMN10465589 to SAMN10465605). The versions described in this paper are versions RQUX01000000 to RQVN01000000. The Sequence Read Archive accession numbers are SRX5189907 to SRX5189923.
SAMN10465589 SAMN10465590 SAMN10465591 SAMN10465592 SAMN10465593 SAMN10465594 SAMN10465595 SAMN10465596 SAMN10465597 SAMN10465598 SAMN10465599 SAMN10465600 SAMN10465601 SAMN10465602 SAMN10465603 SAMN10465604 SAMN10465605 Accession no. RQUX00000000 RQUY00000000 RQUZ00000000 RQVA00000000 RQVB00000000 RQVC00000000 RQVD00000000 RQVE00000000 RQVF00000000 RQVG00000000 RQVH00000000 RQVI00000000 RQVJ00000000 RQVK00000000 RQVL00000000 RQVM00000000 RQVN00000000 Species Strain V. ratti ATCC 17746 T V. caviae DSM 20738 T V. seminalis ADV 4313. 2 T ϭ CIP 107810T Veillonella sp. CHU110 ϭ 14/09/02᎑B᎑6149 Veillonella sp. Va140 ϭ CHU594 ϭ 03/11/05᎑B᎑4237 Veillonella sp. Va138 ϭ CHU732 ϭ 06/09/06᎑B᎑3252 Veillonella sp. Va143 ϭ CHU740 ϭ 09/10/06᎑B᎑1508 Veillonella sp. 3891 ϭ 12/03/14᎑B᎑3204 Veillonella sp. 3913 ϭ 09/03/14᎑B᎑7013 Veillonella sp.
3627 ϭ CHU4040 ϭ 99141203627 Veillonella sp. CHU3735 ϭ CNR 79/14 ϭ 14/01/14᎑B᎑2378 Veillonella sp. 3960 ϭ CHU4076 ϭ 99141423960 Veillonella sp. 3310 ϭ CHU5981 ϭ 99162773310 Veillonella sp. Va137 ϭ 19/07/06᎑3404 Veillonella sp. Va139 ϭ 10/01/06᎑3360 Veillonella sp. Va141 ϭ 20/06/06᎑2457 Veillonella sp. Va142 ϭ 08/06/05᎑3381 a BioProject number, PRJNA506647. Volume 8 Issue 12 e01743-18 mra. asm. org 2.
On May 8, 2017, the foundation formally handed the proposal for the hotel to the mayors of Alblasserdam, Hendrik-Ido-Ambacht, and Papendrecht. The recent financial crisis delayed the project, and it waits for a project developer. Recently, the community of Alblasserdam has selected a work of art by artist Rosalinde van Ingen-Schenau to symbolize the region and serve as a meeting point for tourists (Municipality Alblasserdam 2017). Financed by the municipality and also the province of Zuid-Holland, Anamorphosis was placed in the harbor area at the end of 2017. These works of art are a sort of cultural heritage (Fig. 7 ). Similarly, the Oude Werf shipyard is only remembered in pictures and books, and on the Internet  (Homoet 2018a ). The redevelopment of the site started in March 1952 with filling up the mill pond and dismantling the saw mill (Molen Database 2018).
Acknowledging flood risk allows us to think of ways to reduce the possible consequences of flooding. Again, cultural heritage offers inspiration to this effort. The peninsula of Marken, an island until the closure of the Zuiderzee in 1932, still has some of the seventeenth century wooden pole houses that stood above fluctuating water levels  (Holland 2018). Another example of what the cultural heritage offers is the twenty-five thousand year-old strategy of living on mounds in flood-prone areas. This approach to building lets the flood water spread out on a larger than usual surface. As a result, the water level stays much lower than it does between dikes; the water is also able to move more steadily and slowly than the occasional explosive flood after a dike breach. Floods themselves also leave behind a cultural heritage, in dike breach ponds or the curved shape of a dike, which can remind younger generations of where and how frequently they occurred.
She is Director of insitu World Heritage consulting and Secretary General of the Institute for Research on European Agricultural Landscapes (EUCALAND), a German nonprofit association which is compiling a database of European agricultural landscapes (https://www. fealfuture. org/eatlas/en). Her projects also address UNESCO world heritage and the revitalization of rural areas. Open Access This chapter is licensed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivatives 4. 0 International License (http://creativecommons. org/licenses/bync-nd/4. 0/), which permits any noncommercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license and indicate if you modified the licensed material.
://de. wikipedia. org/wiki/Kujawien[16/06/2017]. Wikipedia entry about the region Kujawien in Poland Alexandra Kruse studied agriculture, landscape development, nature protection and geology in Kiel, Germany. She is the director of insitu World Heritage consulting and secretary general of the Institute for Research on European Agricultural Landscapes e. V. (EUCALAND) (https://eucaland. net), a German nonprofit association which is compiling a database of European agricultural landscapes (https://www. feal-future. org/eatlas/en). Her projects also address UNESCO World Heritage and the revitalization of rural areas. Bernd Paulowitz a historian and political scientist, is World Heritage Coordinator at the Department for Heritage Preservation in Hamburg and World Heritage Manager of the WH-Site "Speicherstadt and Kontorhaus District with Chilehaus".
Acknowledgements Acknowledgements The author is indebted to  Lisa Ackerman  (Interim Chief Executive Officer, Acknowledgements We would like to thank  Deltares , in the Netherlands, and Arquinistas, in Mexico, for their work and support in the development of the project " Parque del Agua Monte Alban ". Our gratitude to the faculty of  Archaeology of Leiden University , for the facilities given to make the archaeological survey in Monte Alban possible, as well as to  Svenja Kerkhof ,  Nienke Verstraaten ,  Philippa Jorissen , and  Tom Lovett  for participating and involving in this project. Thanks to  Instituto Nacional de Antropología e Historia , in particular  Dirección de la Zona Arqueològica de Monte Albàn  and  Coordinación Nacional de Arqueología , for conceding the permits required to conduct survey in Monte Alban.
Acknowledgements The authors are cooperating in the Institute for Research on European Agricultural Landscapes e. V. (www. eucalandnetwork. net/), a network that discussed the subject on a workshop at  Utrecht University  (The Netherlands), from April 24, 2013 to April 26, 2013. The case studies are written by  Hans Renes  (case study 1),  Martina Slámová  (case study 2), and  Sebastian Eiter  and  Oskar Puschmann  (case study 3). The authors thank  Ton Markus  ( Faculty of Geosciences Utrecht University ) for drawing Figs. 3 and4.
Acknowledgements This study was made possible by the material and support of Towada city,  Shibusawa Bunko ,  Aomori Prefecture  office,  Inaoi Tochi Kairyoku ,  Towada Kanko , and  Nitobe Kinenkan. The original research started with funding from the  Toyota Foundation  and later developed through support from the  Ministry of Literature. The project evolved to its current theme thanks to the advices by  Professor Masamitsu Ogiwara  and  Mr. Mamoru Okubo , and to the conference on Water and Heritage for the Future organized by ICOMOS, the  Center for Global Heritage and Development (CGHD) , and  Delft University of Technology. I appreciate the support of  Professor Carola Hein  for inviting me to the conference and helping edit my text. Acknowledgements This work was supported by  JSPS KAKENHI  Grant Number  16H02386.