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15,702 results for “history”
Single-cell atlases of two lophotrochozoan larvae highlight their complex evolutionary histories
<p>This archive contains all the code and data to reproduce the results of the associated manuscript: Piovani <em>et al</em>, "Single-cell atlases of two lophotrochozoan larvae highlight their complex evolutionary histories". We provide filtered scRNA-seq matrices, protein fasta files for each specie used to run SAMap and GenERA as well as the R-code used to generate the datasets and the jupyter notebook to generate SAMap results. In addition we provide the final Seurat objects and all analysis results which can be consulted without re-running the code.</p>
SeaLiT Ontology - An extension of CIDOC-CRM for the modelling of Maritime History information
<p>The <strong>SeaLiT Ontology</strong> is a formal ontology intended to facilitate the integration, mediation and interchange of heterogeneous information related to <strong>maritime history</strong>. It aims at providing the semantic definitions needed to transform disparate, localised information sources of maritime history into a coherent global resource. It also serves as a common language for domain experts and IT developers to formulate requirements and to agree on system functionalities with respect to the correct handling of historical information.</p> <p>The ontology uses and extends the <strong><a href="https://www.cidoc-crm.org/">CIDOC Conceptual Reference Model</a></strong> (ISO 21127:2014), in particular version 7.2.1, as a general ontology of human activity, things and events happening in space and time.</p> <p>The ontology has been developed following a bottom-up process from primary data collected in the context of the <a href="http://www.sealitproject.eu/"><strong>SeaLiT Project</strong></a> (<em>Seafaring Lives in Transition, Mediterranean Maritime Labour and Shipping, 1850s-1920s</em>). SeaLiT is an international research project, funded by the ERC Starting Grant 2016, which explores the transition from sail to steam navigation and its effects on seafaring populations in the Mediterranean and the Black Sea between the 1850s and the 1920s.</p> <p>More information about the construction of the <strong>SeaLiT Ontology</strong>, the considered data sources, as well as their transformation to a knowledge graph using the SeaLiT Ontology, can be found in the following papers:</p> <blockquote> <p>P. Fafalios, A. Kritsotaki, and M. Doerr, "<em>The SeaLiT Ontology – An Extension of CIDOC-CRM for the Modeling and Integration of Maritime History Information"</em>. ACM Journal on Computing and Cultural Heritage, 2023. <a href="https://doi.org/10.1145/3586080">https://doi.org/10.1145/3586080</a> [<a href="https://arxiv.org/pdf/2301.04493.pdf">pdf</a>, <a href="https://users.ics.forth.gr/~fafalios/files/bibs/fafaliosSeaLiTOntology2023.bib">bib</a>]</p> </blockquote> <blockquote> <p>P. Fafalios, K. Petrakis, G. Samaritakis, K. Doerr, A. Kritsotaki, Y. Tzitzikas, and M. Doerr, "FAST CAT: Collaborative Data Entry and Curation for Semantic Interoperability in Digital Humanities", ACM Journal on Computing and Cultural Heritage, 2021. <a href="https://doi.org/10.1145/3461460">https://doi.org/10.1145/3461460</a> [<a href="http://users.ics.forth.gr/~fafalios/files/pubs/fafaliosJOCCH2021.pdf">pdf</a>, <a href="http://users.ics.forth.gr/~fafalios/files/bibs/fafaliosJOCCH2021.bib">bib</a>]</p> </blockquote> <p>The (resolvable) <strong>namespace </strong>of the ontology is: <a href="http://www.sealitproject.eu/ontology/">http://www.sealitproject.eu/ontology/</a></p> <p>An <strong>OWL implementation</strong> of the ontology is available at: <a href="https://sealitproject.eu/ontology/SeaLiT_Ontology_v1.2.owl">https://sealitproject.eu/ontology/SeaLiT_Ontology_v1.2.owl</a></p> <p><strong>Knowledge graphs </strong>that make use of the SeaLiT Ontology are available at: <a href="https://zenodo.org/record/6460841">https://zenodo.org/record/6460841</a>. These RDF datasets integrate information of 16 different types of archival sources related to maritime history, including crew lists, payrolls, registers of different types, censuses, and employment records.</p>
Code and data: Exploring congruent diversification histories with flexibility and parsimony
<p>This repository contains the code and data for the article "Exploring congruent diversification histories with flexibility and parsimony" (abstract bellow).</p> <p>Data :</p> <ul> <li><strong>4705sp_mammal-time.tree</strong>: Species-level calibrated mammalian phylogeny from <em>Alvarez-Carretero et al. </em>(<a href="https://doi.org/10.6084/m9.figshare.14885691">https://doi.org/10.6084/m9.figshare.14885691</a>)</li> <li><strong>mammals_samplingfraction.csv</strong> : Clade-specific sampling fractions from <em>Quintero et al.</em>(<a href="https://www.biorxiv.org/content/10.1101/2022.08.09.503355v1.full">https://www.biorxiv.org/content/10.1101/2022.08.09.503355v1.full</a>).</li> </ul> <p>Code :</p> <ul> <li><strong>CRABS-v1.1.0.9004.zip</strong>: Archived version of the CRABS package with our extension.</li> <li><strong>Mammalian_rates_EBD_HSMRF.rev</strong>: <em>Rev</em> script for the mammalian diversification analysis in RevBayes with regularized priors on diversification rates.</li> <li><strong>Mammalian_rates_EBD_independent.rev</strong>: <em>Rev</em> script for the mammalian diversification analysis in RevBayes with independent diversification rates at each interval.</li> <li><strong>Mammals_proccess_RevBayes_outputs.Rmd</strong>: R notebook for processing the outputs from the RevBayes mammalian diversification analysis, plotting the rates through time, and saving the median trajectories used for further analyses.</li> <li><strong>Exploring_congruent_diversification_histories_with_flexibility_and_parsimony.Rmd</strong>: R notebook for comparing the initial CRABS features and our new extensions. It enables replicating the figures in the article.</li> </ul> <p>Outputs :</p> <ul> <li><strong>output_inferredIntervals_fixedRhp_HSMRF.zip</strong> & <strong>output_inferredIntervals_fixedRhp_independent.zip</strong>: The raw traces from the RevBayes analysis, and the resulting median rate trajectories that are used to construct the congruence class illustrated in the article.</li> </ul> <p><br> Abstract</p> <ol> <li>Using phylogenies of present-day species to estimate diversification rate trajectories -- speciation and extinction rates over time -- is a challenging task due to non-identifiability issues. Given a phylogeny, there exists an infinite set of trajectories that result in the same likelihood; this set has been coined a congruence class. Previous work has developed approaches for sampling trajectories within a given congruence class, with the aim to assess the extent to which congruent scenarios can vary from one another. Based on this sampling approach, it has been suggested that rapid changes in speciation or extinction rates are conserved across the class. Reaching such conclusions requires to sample the broadest possible set of distinct trajectories.</li> <li>We introduce a new method for exploring congruence classes, that we implement in the R package CRABS. Whereas existing methods constrain either the speciation rate or the extinction rate trajectory, ours provides more flexibility by sampling congruent speciation and extinction rate trajectories simultaneously. This allows covering a more representative set of distinct diversification rate trajectories. We also implement a filtering step that allows selecting the most parsimonious trajectories within a class.</li> <li>We demonstrate the utility of our new sampling strategy using a simulated scenario. Next, we apply our approach to the study of mammalian diversification history. We show that rapid changes in speciation and extinction rates need not be conserved across a congruence class, but that selecting the most parsimonious trajectories shrinks the class to concordant scenarios.</li> <li>Our approach opens new avenues both to truly explore the myriad of potential diversification histories consistent with a given phylogeny, embracing the uncertainty inherent to phylogenetic diversification models, and to select among these different histories. This should help refining our inference of diversification trajectories from extant data.</li> </ol>
Individual capture history affects site use and defensive behavior of foraging eastern copperheads at a recreational site in eastern Kentucky, 2022
This package contains behavioral, demographic, and environmental data from a study investigating the role individual capture history plays in shaping foraging and defensive behaviors of eastern copperheads (Agkistrodon contortrix) at a ~0.1 hectare recreational site in the Daniel Boone National Forest, Wolfe county, Kentucky. Behavioral data was collected using a four-stage trial simulating in-situ encounters between humans and vipers, where each stage is scored on a 0-3 scale according to the most extreme behavior exhibited. Each individual's total score was the sum of scores in Stages 1-4. Snakes were located via nightly visual surveys of the site during copperheads' active season. Each copperhead was caught after the conclusion of its' behavioral trial, and demographic information including sex, mass, snout-vent length, and total length were recorded. For snakes that had been detected and tagged at this site previous, PIT tag ID and number of years the individual was previously recaptured were also recorded. Air temperature, relative humidity, and soil temperature at a depth of 3 cm were recorded. Within our study system, result suggest that copperheads' defensive response to human approach is best explained by individual capture history, as opposed to temperature or body size.
History of Acid Precipitation on the Shawangunk Ridge: Mohonk Preserve Precipitation Depths and pH, 1976 to Present
We, the staff, volunteers and associates of the Mohonk Preserve, have been collecting precipitation data at Mohonk Lake since January 1976. The Level1_MohonkPrecipData includes precipitation depths recorded either during or at the conclusion of every precipitation event. This dataset additionally includes pH measurements for most precipitation collections.The Level2_MohonkPrecipData summarizes data collections into precipitation events where the precipitation depth is cumulative and the pH is averaged for all data collections in that event. We measured precipitation via a National Weather Service Rain Gauge and the pH was measured at a Cooperative Weather Service Station at Mohonk Lake.
Burn history and patch attributes
We present the recorded fire occurrences from 1967 to 2017 for 92 independent Florida Rosemary Scrub patches at Archbold Biological Station, Lake Placid, Florida. In addition, we include a series of habitat attributes, including patch area, patch isolation (described by the Hanski's index), and relative elevation, associated with those patches, as well as presence/absence data for Hypericum cumulicola, a Florida endemic plant.
Dendrochronology study of fire history, Andrews Experimental Forest and central western Cascades, Oregon, 1482-1952
Fire history is documented for an 11,000 hectare (27,110 acre) area in the western Oregon Cascades , including H. J. Andrews Experimental Forest. Fire scar and tree origin data were collected mainly from stumps at 359 sites. Thirty-five fire events are mapped from 1482 to 1952. Mean fire return intervals are derived from data at individual sites, about 5 hectares in size, rather than from the corrected master fire chronology.
Fire history database of the western United States, 1994
To create a database of existing published and unpublished tree-ring reconstructions of fire regimes in forested areas, before circa 1900, west of 100 W longitude in the continental United States, exclusive of Alaska. The studies included in the database are restricted to tree-ring reconstructions of fire history and the information extracted includes citations to the data sources, site information, estimated fire regimes, and information on individual fire events (when readily available). Fire regimes vary greatly across short distances in the western United States, so that a reconstruction of fire history over a small area may not represent the history of a larger area. Therefore, we extracted information on the size of the study area and the amount of fire evidence (number of trees scarred and/or number of tree origin dates) used in computing the fire regimes to allow the user to gauge the applicability of each reconstruction to larger areas.
Road construction history (1952 - 1990), Andrews Experimental Forest
Andrews road construction history is mapped. This data includes the year and 1/2 decade of construction for the road network around the HJ Andrews Experimental Forest. Note that the underlying road network has been revised and updated based on the 2007 LiDAR flight. This road network can be found at GI007: Transportation network locations.
Fire history reconstruction (1482 - 1952), Andrews Experimental Forest and vicinity
Fire History - H J Andrews and Vicinity (1482 - 1952) individual fires and fire frequency. Fire history studies by Peter Teensma provide the base information for this layer. Individual fire episodes were manuscripted onto HJA base maps and digitized. Fire episodes were maintained in thirty one separate polygon coverages, until Arc/Info Version 7 provided the region feature class to accomodate overlapping polygons. REGIONPOLY was used to create regions for each fire episode and then the 31 episode regions were combined using UNION. The field "AGE" = 0 means that a fire occured in the polygon. AGE = 1 means that fire was absent
Fire history dendrochronology study, super old growth data, central western Cascades, Oregon, 2002 (Giglia thesis)
The primary objectives of this study were to assay where super old-growth (SOG) persists on the landscape, what factors enabled it to survive for more than 550 years, and to develop a predictive model for the occurrence of SOG. To meet these objectives, data were synthesized from prior fire history work done in the central western Cascades of Oregon (Morrison and Swanson unpublished; Teensma 1987; Morrison and Swanson 1990; Weisberg 1998). The study involved the following steps: (1) the collection of primary data and maps from each study, (2) the creation of a master database, and (3) analysis of the synthesized data.
Vegetation history classification for Watersheds 1, 2, and 3, Andrews Experimental Forest, 1959-1990
The objective of this study was to create GIS layers depicting vegetation cover over the history of the small experimental watersheds (WS 1, 2, and 3) based on aerial photography from the 1950s to 1990, for landscape ecology and spatial modeling studies. Aerial photos were interpreted for hydrologically relevant vegetation types (conifer, broadleaf, grasses and bare soil) cover classes, and forest age class was determined for each year (1959, 1962, 1967, 1972, 1979, and 1990). Vegetation data for functional groups (conifer, evergreen broadleaf, deciduous broadleaf) was aggregated from species data available in TP073 for the long term vegetation plots in Watershed 1.
Daily climate summary: Meterologic Measurements at Cedar Creek Natural History Area
Meteorological measurements include air temperature, precipitation, wind speed and direction, soil temperature, and relative humidity. These measurements are taken on an hourly basis.
The effects of agricultural land-use history on non-native plant invasion in Bent Creek Experimental Forest in 2006
The researchers considered the effects of agricultural land-use legacies on the distribution of non-native invasive plants a century after abandonment in a watershed in western North Carolina, USA. The study was conducted at the Bent Creek Experimental Forest (BCEF) 15 km southwest of Asheville, North Carolina, USA, in the Pisgah National Forest. Forest sites that were previously in cultivation and abandoned ca. 1905 were compared with nearby reference sites that were never cultivated. The most common invasive plants were Celastrus orbiculatus Thunb., Microstegium vimineum Trin., and Lonicera japonica Thunb. (Kuhman, Pearson, and Turner 2011). Disentangling the cause–effect relationships between land-use history, the biotic community, and the abiotic template presents a challenge, but understanding the role of land-use legacies may provide important insights regarding the mechanisms underlying the establishment and spread of invasive plants in forest ecosystems (Kuhman, Pearson, and Turner 2011). A total of 86 plots were established at Bent Creek Experimental Forest during the summer of 2006. Specifically, the study was conducted between June and August 2006. Half of these were established in historic agricultural plots and half in reference plots that were not formerly used for agriculture (pasture or rowcrops) based on the 1941 Forest Service Report by William Nesbitt and the appended land-use history map (History of early settlement and land use on the Bent Creek Experimental Forest Buncombe County, NC. 1941). Historic agriculture and reference plots were paired based on similarities in topography and bedrock geology (typically in relatively close proximity to one another). Within sites, two plots were established, one adjacent to the road and one 50 m away from the road (labeled as "A" and "B", respectively, in the "Plot #").
Does land-use history facilitate non-native plant invasion? A field experiment with Celastrus orbiculatus in the Bent Creek Experimental Forest in the southern Appalachians from 2008 to 2009
Although historic land use is often implicated in non-native plant invasion of forests, little is known about how land-use legacies might actually facilitate invasion. The researchers conducted a 2-year field seeding experiment in western North Carolina, USA, to compare germination and first-year seedling survival of Celastrus orbiculatus Thunb. in stands that had been cultivated and abandoned a century earlier and were dominated by tulip poplar (Liriodendron tulipifera L.), and in paired stands that had never been cultivated and were dominated by oaks (Quercus spp.). Experiments were conducted at five sites with paired tulip poplar and oak stands by varying litter mass (none, low, or high) and litter type (tulip poplar or oak).
Throw trap and electrofishing data collected during 1996–2022 from the Everglades, Florida, United States for the publication "Contrasting invasion histories and effects of three non-native fishes observed with long-term monitoring data"
This dataset was used to analyze the effects of three non-native fishes in the Florida Everglades for a publication in the journal Biological Invasions. The dataset incorporates plot-level mean densities (# of individuals per square meter) of common aquatic animals collected during 1996–2022 from 17 sites across three regions of the Everglades: Taylor Slough, Shark River Slough, and Water Conservation Area 3A. Prey species included are nine common small fishes and three common decapod species (two crayfish species and grass shrimp). The dataset includes throw trap data on three predator taxa: African Jewelfish (Hemichromis letourneuxi), Mayan Cichlids (Mayaheros uruphthalmus), and sunfishes (Lepomis spp.). Annual indices of mean wet season electrofishing catch-per-unit-effort of Asian Swamp Eels (Monopterus albus/javanesis), Mayan Cichlids, sunfishes, and the three other large 'top predator' fishes (Amia calva, Lepisosteus platyrhincus, Micropterus salmoides) are included for plots where electrofishing was performed from 1997-2021. Hydrologic measures used in analyses and R code used to conduct analyses are also included.
Hydraulic Constraints on Two Life History Stages of Larrea tridentata in a Chihuahuan Desert Creosote Shrubland at the Sevilleta National Wildlife Refuge, New Mexico (2002-2003)
Maintaining high rates of water loss during times of high resource availability could allow establishing woody desert perennials to grow quickly by allowing them to take advantage of the fleeting but abundant monsoonal moisture typical of warm deserts like the Chihuahuan. However, a plant cannot endlessly increase water loss in order to grow faster --there are hydraulic constraints on rates of water loss. The hydraulic properties of each particular plant xylem and soil microsite, as well as the AR:AL absorbing root area to transpiring leaf area ratio) interact to set limits on rates of water loss. If transpiration rates become too high, cavitation may limit the ability of the xylem to supply water to the leaves. The main objective of this study was to test two hypotheses on a population of Larrea tridentata at the Sevilleta LTER in central New Mexico (1) do small plants grow faster and use water less conservatively than large, and (2) are there differences in the hydraulic constraints on small and large plants. Measurements were made every six weeks in the spring, summer and fall from April 2002 - August 2003. Field measurements of shoot growth, gas exchange and plant and soil water potentials were made to determine growth rates and water use. Measurements of leaf specific conductance determined the ability of the xylem to supply water to the leaves. Excavation findings were used to estimate (AR:AL). Xylem vulnerability curves and soil texture analysis were used to determine the hydraulic properties of the plant xylem and soil. A model determined where the limiting conductance occurred in the plant-soil continuum.
Fig. 29 in Systematics of the enigmatic South American Streblopus Van Lansberge, 1874 dung beetles and their transatlantic origin: a case study on the role of dispersal events in the biogeographical history of the Scarabaeinae (Coleoptera: Scarabaeidae)
Fig. 29. Current distribution of Streblopus van Lansberge, 1874 and the Old World groups with which it is believed to be more closely related plotted on an Upper Cretaceous palaeomap (~ 80 million years ago). Based particularly on the hypothesis in Tarasov & Génier (2015) that Streblopus is part of a clade otherwise composed uniquely of dung beetle lineages either exclusively distributed in Africa (Circellium, Chalconotus and Gyronotus) or with a distribution largely centred on that continent (Scarabaeini), and on the dating of the origin of the Scarabaeini as 71 million years ago (Gunter et al. 2016), we propose that the lineage that would eventually lead to Streblopus branched off from those groups in Africa some time between 95 and 71 million years ago, and that one of its descendent lineages (the only one living today) dispersed from its original continent to South America during the late Upper Cretaceous or the early Cenozoic. Since Africa and South America have not been connected by land since the Lower Cretaceous, the only way the ancestor of Streblopus could have reached South America was through transoceanic dispersal across the early South Atlantic. That dispersal probably happened by rafting on floating pieces of plants or other debris, as probably occurred with a large number of other organisms. Palaeomap modified from Scotese (2016); distribution area based on Balthasar (1963), Scholtz & Howden (1987), Davis et al. (2008) and our own results.
Fig. 14. Profemora. A‒B. Streblopus opatroides van Lansberge, 1874. A in Systematics of the enigmatic South American Streblopus Van Lansberge, 1874 dung beetles and their transatlantic origin: a case study on the role of dispersal events in the biogeographical history of the Scarabaeinae (Coleoptera: Scarabaeidae)
Fig. 14. Profemora. A‒B. Streblopus opatroides van Lansberge, 1874. A. ♂. B. ♀. C‒D. S. punctatus (Balthasar, 1938). C. ♂. D. ♀. Note the differences between the species and sexes in relation to the overall shape of the profemora and the presence of spurs on the anterior edge in males.
Fig. 12. Pronotum. A. Streblopus opatroides van Lansberge, 1874. B. S in Systematics of the enigmatic South American Streblopus Van Lansberge, 1874 dung beetles and their transatlantic origin: a case study on the role of dispersal events in the biogeographical history of the Scarabaeinae (Coleoptera: Scarabaeidae)
Fig. 12. Pronotum. A. Streblopus opatroides van Lansberge, 1874. B. S. punctatus (Balthasar, 1938). Note the differences in the umbilicate punctation and colour between the species.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.