Web archive derivatives of the collection Geologic Field Trip Guidebooks Web Archive from the Ivy Plus Libraries Confederation. The derivatives were created with the Archives Unleashed Toolkit and Archives Unleashed Cloud. The ivy-12576-parquet.tar.gz derivatives are in the Apache Parquet format, which is a columnar storage format. These derivatives are generally small enough to work with on your local machine, and can be easily converted to Pandas DataFrames. See this notebook for examples. Domains .webpages().groupBy(ExtractDomainDF($"url").alias("url")).count().sort($"count".desc) Produces a DataFrame with the following columns: domain count Web Pages .webpages().select($"crawl_date", $"url", $"mime_type_web_server", $"mime_type_tika", RemoveHTMLDF(RemoveHTTPHeaderDF(($"content"))).alias("content")) Produces a DataFrame with the following columns: crawl_date url mime_type_web_server mime_type_tika content Web Graph .webgraph() Produces a DataFrame with the following columns: crawl_date src dest anchor Image Links .imageLinks() Produces a DataFrame with the following columns: src image_url Binary Analysis Audio Images PDFs Presentation program files Spreadsheets Text files Word processor files The ivy-12576-auk.tar.gz derivatives are the standard set of web archive derivatives produced by the Archives Unleashed Cloud. Gephi file, which can be loaded into Gephi. It will have basic characteristics already computed and a basic layout. Raw Network file, which can also be loaded into Gephi. You will have to use that network program to lay it out yourself. Full text file. In it, each website within the web archive collection will have its full text presented on one line, along with information around when it was crawled, the name of the domain, and the full URL of the content. Domains count file. A text file containing the frequency count of domains captured within your web archive.
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This compilation contains data reported in the manuscript Cardenas, Lamb, Jobe, Mohrig, and Swartz, Morphodynamic preservation of fluvial channel belts. As of Nov 2022, this manuscript is submitted to SEPM (Society for Sedimentary Geology) journal The Sedimentary Record. Compilation contains: (1) Table showing the edge coordinates of each channel belt in the associated manuscript. (2) Table showing centerline point coordinates. (3) Table showing all width measurements for each channel belt. (4) A compilation table showing representative geometric measurements for each belt. (5) A python script to generate paleoflow directions from centerline coordinates. (6) A script to generate various geometric measurements from belt edge coordinates. (7) A script to plot histograms of geometric measurements.
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doi: 10.5061/dryad.4pd33
Heterogeneous data collection in the marine environment has led to large gaps in our knowledge of marine species distributions. To fill these gaps, models calibrated on existing data may be used to predict species distributions in unsampled areas, given that available data are sufficiently representative. Our objective was to evaluate the feasibility of mapping cetacean densities across the entire Mediterranean Sea using models calibrated on available survey data and various environmental covariates. We aggregated 302,481 km of line transect survey effort conducted in the Mediterranean Sea within the past 20 years by many organisations. Survey coverage was highly heterogeneous geographically and seasonally: large data gaps were present in the eastern and southern Mediterranean and in non-summer months. We mapped the extent of interpolation versus extrapolation and the proportion of data nearby in environmental space when models calibrated on existing survey data were used for prediction across the entire Mediterranean Sea. Using model predictions to map cetacean densities in the eastern and southern Mediterranean, characterised by warmer, less productive waters, and more intense eddy activity, would lead to potentially unreliable extrapolations. We stress the need for systematic surveys of cetaceans in these environmentally unique Mediterranean waters, particularly in non-summer months. Mediterranean gap analysis in environmental spaceThis .zip folder contains the data and an R script to reproduce the gap analysis documented in Mannocci et al. 2018.Data_Scientific_Reports.zip
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The archive Muller_etal_2022_SE_1Ga_Opt_PlateMotionModel.zip contains the files for the plate model in an optimised mantle reference frame. GPlates or pyGPlates software (www.gplates.org) is needed to read these files. The archive Muller_etal_2022_SE_mantle-ref-frame-oceanic-crustal-agegrids.zip contains the oceanic crustal age grids in netCDF-4 format for the optimised mantle reference frame plate model, while the archive Muller_etal_2022_SE_PMAG_oceanic-crustal-agegrids.zip contains the oceanic crustal age grids in netCDF-4 format for the paleomagnetic reference frame plate model from Merdith et al. (2021). The agegrids associated with this model can be accessed at: https://repo.gplates.org/webdav/PlateModel_Age_SR_Grids/Muller_etal_2022_SE/
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doi: 10.5061/dryad.3353b
Figure S1: Victoria West cores with overshot preferential removals (a, b, c) and small sized removal (d). Note that although the size of specimen a is also small, the preferential removal is still large when compared with the overall size of the core. The yellow arrows show the preparation of the two surfaces, the red arrows show the preferential flake removal directions, and the blue arrows show scars overlapping the preferential removal. a, b , c and d correspond to the specimens CK2919, CK8091, CK4916 and CK4597 respectively (see Table S1 for raw data).figure S1.jpgFigure S2: Victoria West cores with small removals (a, b, c) and non-ideal blow direction (d). The yellow arrows show the preparation of the two surfaces, and the red arrows show the preferential flake removal directions. a, b , c and d correspond to the specimens CK3708, CK8702, CK5837 and CK3936 respectively (see Table S1 for raw data).figure S2.jpgFigure S3: Victoria West cores from the top of the layer containing the Victoria West core assemblage. The yellow arrows show the preparation of the two surfaces, the red arrows show the preferential flake removal directions, and the blue arrows show scars overlapping the preferential removal. a, b , c and d correspond to the specimens CK3142, CK3004, CK2225 and CK2208 respectively (see Table S1 for raw data).Figure S3.jpgTable S1.Raw data for the Victoria West cores excavated from the Canteen Kopje site.Table S1.xls Prepared core technology illustrates in-depth planning and the presence of a mental template during the core reduction process. This technology is, therefore, a significant indicator in studying the evolution of abstract thought and the cognitive abilities of hominids. Here, we report on Victoria West cores excavated from the Canteen Kopje site in central South Africa, with a preliminary age estimate of approximately 1 Ma (million years ago) for these cores. Technological analysis shows that the Victoria West cores bear similarities to the ‘Volumetric Concept’ as defined for the Levallois, a popular and widely distributed prepared core technology from at least 200 ka (thousand years ago). Although these similarities are present, several notable differences also occur that make the Victoria West a unique and distinctive prepared core technology; these are: elongated and convergent core shapes, consistent blow directions for flake removal, a predominance of large side-struck flakes, and the use of these flakes to make Acheulean large cutting tools. This innovative core reduction strategy at Canteen Kopje extends the roots of prepared core technology to the latter part of the Early Acheulean and clearly demonstrates an increase in the cognitive abilities and complexities of hominids in this time period.
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doi: 10.5061/dryad.5cb57
The Middle to Late Eocene sediments of Texas have yielded a wealth of fossil material that offers a rare window on a diverse and highly endemic mammalian fauna from that time in the southern part of North America. These faunal data are particularly significant because the narrative of mammalian evolution in the Paleogene of North America has traditionally been dominated by taxa that are known from higher latitudes, primarily in the Rocky Mountain and northern Great Plains regions. Here we report on the affinities of two peculiar carnivoraforms from the Chambers Tuff of Trans-Pecos, Texas, that were first described 30 years ago as Miacis cognitus and M. australis. Re-examination of previously described specimens and their inclusion in a cladistic analysis revealed the two taxa to be diminutive basal amphicyonids; as such, they are assigned to new genera Gustafsonia and Angelarctocyon, respectively. These two taxa fill in some of the morphological gaps between the earliest-known amphicyonid genus, Daphoenus, and other Middle-Eocene carnivoraforms, and lend additional support for a basal caniform position of the beardogs outside the Canoidea. The amphicyonid lineage had evidently given rise to at least five rather distinct forms by the end of the Middle Eocene. Their precise geographical origin remains uncertain, but it is plausible that southern North America served as an important stage for a very early phase of amphicyonid radiation. Electronic Supplementary Material 1Nexus file containing character matrix and resulting trees (27 MPTs + strict consensus). Characters 1-99 (with prefix "WHF") are described in Wesley-Hunt & Flynn (2005). See Materials and Methods and Appendix II for additional details.TOMIYA_TSENG_ESM1.nexElectronic Supplementary Material 2Nexus file containing character matrix with alternative coding of Character 31 ("WHF31") and resulting trees (27 MPTs + strict consensus). In this matrix, States 1 and 2 of the original matrix (Electronic Supplementary Material 1) were combined into a single state (new State 1). Note the topology of strict consensus tree is identical to that in Electronic Supplementary Material 1.TOMIYA_TSENG_ESM2.nex
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The dataset consists of a spreadsheet containing data on GPS surveys, dynamic topography extracted from published models (gplates.org), Shell preservation scoring, Strontium Isotopic Stratigraphy ages, and Global mean Sea Level calculations. Fil: Aguirre, Marina Laura. Universidad Nacional de La Plata. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico La Plata; Argentina. Fil: Richiano, Sebastián Miguel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Geología y Paleontología; Argentina Facultad de Ciencias Naturales y Museo
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Holocene climate variability in the Mediterranean Basin is often cited as a potential driver of societal change, but the mechanisms of this putative influence are generally little explored. In this paper we integrate two tools - agro-ecosystem modeling of potential agricultural yields and spatial analysis of archaeological settlement pattern data - in order to examine the human consequences of past climatic changes. Focusing on a case study in Provence (France), we adapt an agro-ecosystem model to the modeling of potential agricultural productivity during the Holocene. Calibrating this model for past crops and agricultural practices and using a downscaling approach to produce high spatiotemporal resolution paleoclimate data from a Mediterranean Holocene climate reconstruction, we estimate realistic potential agricultural yields under past climatic conditions. These serve as the basis for spatial analysis of archaeological settlement patterns, in which we examine the changing relationship over time between agricultural productivity and settlement location. Using potential agricultural productivity (PAgP) as a measure of the human consequences of climate changes, we focus on the relative magnitudes of 1) climate-driven shifts in PAgP and 2) the potential increases in productivity realizable through agricultural intensification. Together these offer a means of assessing the scale and mechanisms of the vulnerability and resilience of Holocene inhabitants of Provence to climate change. Our results suggest that settlement patterns were closely tied to PAgP throughout most of the Holocene, with the notable exception of the period from the Middle Bronze Age through the Early Iron Age. This pattern does not appear to be linked to any climatically-driven changes in PAgP, and conversely the most salient changes in PAgP during the Holocene cannot be clearly linked to any changes in settlement pattern. We argue that this constitutes evidence that vulnerability and resilience to climate change are strongly dependent on societal variables. LPJmL paleo-agroecological resultsThis dataset includes LPJmL (the Lund-Potsdam-Jena managed land model; see Bondeau et al. 2007 for details) results for high and low assumptions (Par 1 and and Par 2, respectively) about agricultural intensity for two crop types (wheat and peas) over the period 8400 – 1400 BP. Parameterization of LPJmL for past agriculture is based on archaeological, historic, ethnographic, and experimental data about pre-industrial agriculture, detailed in Contreras et al. 2018. These 300m-pixel annual reconstructions of potential agricultural productivity are based on paleoclimate data downscaled (see Contreras et al. 2018b) from Guiot and Kaniewski’s Mediterranean-wide Holocene reconstruction (Guiot and Kaniewski 2015).LPJmL_results.tar.gz
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doi: 10.5061/dryad.279n4
The partial skull of a lion from Natodomeri, northwest Kenya is described. The Natodomeri sites are correlated with Member I of the Kibish Formation, dated to between 195 ka and ∼205 ka. The skull is remarkable for its very great size, equivalent to the largest cave lions (Panthera spelaea) of Pleistocene Eurasia and much larger than any previously known lion from Africa, living or fossil. We hypothesize that this individual represents a previously unknown population or subspecies of lion present in the late Middle and Late Pleistocene of eastern Africa rather than being an indication of climate-driven size increase in lions of that time. This raises questions regarding the extent of our understanding of the pattern and causes of lion evolution in the Late Pleistocene. Natodomeri lion measurements SI_Manthi et alExcel file with measurements used in comparative analyses of this paper
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Web archive derivatives of the collection Geologic Field Trip Guidebooks Web Archive from the Ivy Plus Libraries Confederation. The derivatives were created with the Archives Unleashed Toolkit and Archives Unleashed Cloud. The ivy-12576-parquet.tar.gz derivatives are in the Apache Parquet format, which is a columnar storage format. These derivatives are generally small enough to work with on your local machine, and can be easily converted to Pandas DataFrames. See this notebook for examples. Domains .webpages().groupBy(ExtractDomainDF($"url").alias("url")).count().sort($"count".desc) Produces a DataFrame with the following columns: domain count Web Pages .webpages().select($"crawl_date", $"url", $"mime_type_web_server", $"mime_type_tika", RemoveHTMLDF(RemoveHTTPHeaderDF(($"content"))).alias("content")) Produces a DataFrame with the following columns: crawl_date url mime_type_web_server mime_type_tika content Web Graph .webgraph() Produces a DataFrame with the following columns: crawl_date src dest anchor Image Links .imageLinks() Produces a DataFrame with the following columns: src image_url Binary Analysis Audio Images PDFs Presentation program files Spreadsheets Text files Word processor files The ivy-12576-auk.tar.gz derivatives are the standard set of web archive derivatives produced by the Archives Unleashed Cloud. Gephi file, which can be loaded into Gephi. It will have basic characteristics already computed and a basic layout. Raw Network file, which can also be loaded into Gephi. You will have to use that network program to lay it out yourself. Full text file. In it, each website within the web archive collection will have its full text presented on one line, along with information around when it was crawled, the name of the domain, and the full URL of the content. Domains count file. A text file containing the frequency count of domains captured within your web archive.
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This compilation contains data reported in the manuscript Cardenas, Lamb, Jobe, Mohrig, and Swartz, Morphodynamic preservation of fluvial channel belts. As of Nov 2022, this manuscript is submitted to SEPM (Society for Sedimentary Geology) journal The Sedimentary Record. Compilation contains: (1) Table showing the edge coordinates of each channel belt in the associated manuscript. (2) Table showing centerline point coordinates. (3) Table showing all width measurements for each channel belt. (4) A compilation table showing representative geometric measurements for each belt. (5) A python script to generate paleoflow directions from centerline coordinates. (6) A script to generate various geometric measurements from belt edge coordinates. (7) A script to plot histograms of geometric measurements.
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doi: 10.5061/dryad.4pd33
Heterogeneous data collection in the marine environment has led to large gaps in our knowledge of marine species distributions. To fill these gaps, models calibrated on existing data may be used to predict species distributions in unsampled areas, given that available data are sufficiently representative. Our objective was to evaluate the feasibility of mapping cetacean densities across the entire Mediterranean Sea using models calibrated on available survey data and various environmental covariates. We aggregated 302,481 km of line transect survey effort conducted in the Mediterranean Sea within the past 20 years by many organisations. Survey coverage was highly heterogeneous geographically and seasonally: large data gaps were present in the eastern and southern Mediterranean and in non-summer months. We mapped the extent of interpolation versus extrapolation and the proportion of data nearby in environmental space when models calibrated on existing survey data were used for prediction across the entire Mediterranean Sea. Using model predictions to map cetacean densities in the eastern and southern Mediterranean, characterised by warmer, less productive waters, and more intense eddy activity, would lead to potentially unreliable extrapolations. We stress the need for systematic surveys of cetaceans in these environmentally unique Mediterranean waters, particularly in non-summer months. Mediterranean gap analysis in environmental spaceThis .zip folder contains the data and an R script to reproduce the gap analysis documented in Mannocci et al. 2018.Data_Scientific_Reports.zip
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The archive Muller_etal_2022_SE_1Ga_Opt_PlateMotionModel.zip contains the files for the plate model in an optimised mantle reference frame. GPlates or pyGPlates software (www.gplates.org) is needed to read these files. The archive Muller_etal_2022_SE_mantle-ref-frame-oceanic-crustal-agegrids.zip contains the oceanic crustal age grids in netCDF-4 format for the optimised mantle reference frame plate model, while the archive Muller_etal_2022_SE_PMAG_oceanic-crustal-agegrids.zip contains the oceanic crustal age grids in netCDF-4 format for the paleomagnetic reference frame plate model from Merdith et al. (2021). The agegrids associated with this model can be accessed at: https://repo.gplates.org/webdav/PlateModel_Age_SR_Grids/Muller_etal_2022_SE/
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doi: 10.5061/dryad.3353b
Figure S1: Victoria West cores with overshot preferential removals (a, b, c) and small sized removal (d). Note that although the size of specimen a is also small, the preferential removal is still large when compared with the overall size of the core. The yellow arrows show the preparation of the two surfaces, the red arrows show the preferential flake removal directions, and the blue arrows show scars overlapping the preferential removal. a, b , c and d correspond to the specimens CK2919, CK8091, CK4916 and CK4597 respectively (see Table S1 for raw data).figure S1.jpgFigure S2: Victoria West cores with small removals (a, b, c) and non-ideal blow direction (d). The yellow arrows show the preparation of the two surfaces, and the red arrows show the preferential flake removal directions. a, b , c and d correspond to the specimens CK3708, CK8702, CK5837 and CK3936 respectively (see Table S1 for raw data).figure S2.jpgFigure S3: Victoria West cores from the top of the layer containing the Victoria West core assemblage. The yellow arrows show the preparation of the two surfaces, the red arrows show the preferential flake removal directions, and the blue arrows show scars overlapping the preferential removal. a, b , c and d correspond to the specimens CK3142, CK3004, CK2225 and CK2208 respectively (see Table S1 for raw data).Figure S3.jpgTable S1.Raw data for the Victoria West cores excavated from the Canteen Kopje site.Table S1.xls Prepared core technology illustrates in-depth planning and the presence of a mental template during the core reduction process. This technology is, therefore, a significant indicator in studying the evolution of abstract thought and the cognitive abilities of hominids. Here, we report on Victoria West cores excavated from the Canteen Kopje site in central South Africa, with a preliminary age estimate of approximately 1 Ma (million years ago) for these cores. Technological analysis shows that the Victoria West cores bear similarities to the ‘Volumetric Concept’ as defined for the Levallois, a popular and widely distributed prepared core technology from at least 200 ka (thousand years ago). Although these similarities are present, several notable differences also occur that make the Victoria West a unique and distinctive prepared core technology; these are: elongated and convergent core shapes, consistent blow directions for flake removal, a predominance of large side-struck flakes, and the use of these flakes to make Acheulean large cutting tools. This innovative core reduction strategy at Canteen Kopje extends the roots of prepared core technology to the latter part of the Early Acheulean and clearly demonstrates an increase in the cognitive abilities and complexities of hominids in this time period.
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doi: 10.5061/dryad.5cb57
The Middle to Late Eocene sediments of Texas have yielded a wealth of fossil material that offers a rare window on a diverse and highly endemic mammalian fauna from that time in the southern part of North America. These faunal data are particularly significant because the narrative of mammalian evolution in the Paleogene of North America has traditionally been dominated by taxa that are known from higher latitudes, primarily in the Rocky Mountain and northern Great Plains regions. Here we report on the affinities of two peculiar carnivoraforms from the Chambers Tuff of Trans-Pecos, Texas, that were first described 30 years ago as Miacis cognitus and M. australis. Re-examination of previously described specimens and their inclusion in a cladistic analysis revealed the two taxa to be diminutive basal amphicyonids; as such, they are assigned to new genera Gustafsonia and Angelarctocyon, respectively. These two taxa fill in some of the morphological gaps between the earliest-known amphicyonid genus, Daphoenus, and other Middle-Eocene carnivoraforms, and lend additional support for a basal caniform position of the beardogs outside the Canoidea. The amphicyonid lineage had evidently given rise to at least five rather distinct forms by the end of the Middle Eocene. Their precise geographical origin remains uncertain, but it is plausible that southern North America served as an important stage for a very early phase of amphicyonid radiation. Electronic Supplementary Material 1Nexus file containing character matrix and resulting trees (27 MPTs + strict consensus). Characters 1-99 (with prefix "WHF") are described in Wesley-Hunt & Flynn (2005). See Materials and Methods and Appendix II for additional details.TOMIYA_TSENG_ESM1.nexElectronic Supplementary Material 2Nexus file containing character matrix with alternative coding of Character 31 ("WHF31") and resulting trees (27 MPTs + strict consensus). In this matrix, States 1 and 2 of the original matrix (Electronic Supplementary Material 1) were combined into a single state (new State 1). Note the topology of strict consensus tree is identical to that in Electronic Supplementary Material 1.TOMIYA_TSENG_ESM2.nex
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