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306 results for “data archive”
Variation in habitat selection by male Strix nebulosa (Great Gray Owls) across the diel cycle, data archive
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Data from: Silent past: Biogeographic gaps in the Cenozoic fossil archive
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Data from: Time is of the essence: using archived samples to develop a GT-seq panel to preserve continuity of ongoing genetic monitoring
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Heterogeneity of locked-pasture snow conditions modulate habitat and movement choices of a facultative migrant, data archive
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Data archive for: Exploring the use of machine learning to improve vertical profiles of temperature and moisture
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Data retrieval from archival renal biopsies using nonlinear microscopy
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Beetle Team Tribolium Data Archive
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Data from: Evaluating genotyping-in-thousands by sequencing as a genetic monitoring tool for a climate sentinel mammal using non-invasive and archival samples
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Sequencing data for: Tracking climate-change induced biological invasions over 4 decades by metabarcoding archived natural eDNA samplers
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A data archive including processed spiking data, raw EMG datasets, and video data during locomotion behavior from six mice
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Archived data for: Balancing selection, genetic drift, and human mediated-introgression interplay to shape MHC (functional) diversity in Mediterranean brown trout
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Data Appendices for "Textual Scholarship and Contemporary Literary Studies: Jennifer Egan's Editorial Processes and the Archival Edition of Emerald City"
<p>This dataset documents the version variants between Jennifer Egan's early short stories, "The Stylist" and "Sacred Heart". It is a supplement to the article "Textual Scholarship and Contemporary Literary Studies: Jennifer Egan’s Editorial Processes and the Archival Edition of <em>Emerald City</em>" in <em>LIT: Literature Interpretation Theory</em>.</p>
Archive data for: Loss of predation risk from apex predators can exacerbate marine tropicalization caused by extreme climatic events
<p>1. Extreme climatic events (ECEs) and predator removal represent some of the most widespread stressors to ecosystems. Though species interactions can alter ecological effects of climate change (and vice versa), it is less understood whether, when, and how predator removal can interact with ECEs to exacerbate their effects. Understanding the circumstances under which such interactions might occur is critical because predator loss is widespread and ECEs can generate rapid phase shifts in ecosystems which can ultimately lead to tropicalization.</p> <p>2. Our goal was to determine whether loss of predation risk may be an important mechanism governing ecosystem responses to extreme events, and whether the effects of such events, such as tropicalization, can occur even when species range shifts do not. Specifically, our goal was to experimentally simulate loss of an apex predator, the tiger shark (<i>Galeocerdo cuvier</i>) effects on a recently damaged seagrass ecosystem of Shark Bay, Australia by applying documented changes to risk sensitive grazing of dugong (<i>Dugong dugon</i>) herbivores. </p> <p>3. Using a 16-month field experiment established in recently disturbed seagrass meadows, we used previous estimates of risk-sensitive dugong foraging behavior to simulate altered risk-sensitive foraging densities and strategies of dugongs consistent with apex predator loss, and tracked seagrass responses to the simulated grazing.</p> <p>4. Grazing treatments targeted and removed tropical seagrasses, which declined. However, like in other mixed-bed habitats where dugongs forage, treatments also incidentally accelerated temperate seagrass losses, revealing that herbivore behavioral changes in response to predator loss can exacerbate ECE effects and promote tropicalization, even without range expansions or introductions of novel species. </p> <p>5. Our results suggest that changes to herbivore behaviors triggered by loss of predation risk can undermine ecological resilience to ECEs, particularly where long lived herbivores are abundant. By implication, ongoing losses of apex predators may combine with increasingly frequent ECEs to amplify climate change impacts across diverse ecosystems and large spatial scales.</p>
Data from: An archive of longitudinal recordings of the vocalizations of adult Gombe chimpanzees
Studies of chimpanzee vocal communication provide valuable insights into the evolution of communication in complex societies, and also comparative data for understanding the evolution of human language. One particularly valuable dataset of recordings from free-living chimpanzees was collected by Frans X. Plooij and the late Hetty van de Rijt-Plooij at Gombe National Park, Tanzania (1971–73). These audio specimens, which have not yet been analysed, total over 10 h on 28 tapes, including 7 tapes focusing on adult individuals with a total of 605 recordings. In 2014 the first part of that collection of audio specimens covering the vocalizations of the immature Gombe chimpanzees was made available. The data package described here covers the vocalizations of the adult chimpanzees. We expect these recordings will prove useful for studies on topics including referential signalling and the emergence of dialects. The digitized sound recordings were stored in the Macaulay Library and the Dryad Repository. In addition, the original notes on the contexts of the calls were translated and transcribed from Dutch into English.
Data from: Resurrecting an extinct salmon evolutionarily significant unit: archived scales, historical DNA, and implications for restoration
Archival scales from 603 sockeye salmon (Oncorhynchus nerka), sampled from May to July 1924 in the lower Columbia River, were analyzed for genetic variability at 12 microsatellite loci, and compared to 17 present-day O. nerka populations—exhibiting either anadromous (sockeye salmon) or non-anadromous (kokanee) life histories—from throughout the Columbia River Basin, including areas upstream of impassable dams built subsequent to 1924. Statistical analyses identified four major genetic assemblages of sockeye salmon in the 1924 samples. Two of these putative historical groupings were found to be genetically similar to extant evolutionarily significant units (ESUs) in the Okanogan and Wenatchee rivers (pairwise FST = 0.004 and 0.002, respectively) and assignment tests were able to allocate 77% of the fish in these two historical groupings to the contemporary Okanogan River and Lake Wenatchee ESUs. A third historical genetic grouping was most closely aligned with contemporary sockeye salmon in Redfish Lake, Idaho, although the association was less robust (pairwise FST = 0.060). However, a fourth genetic grouping did not appear to be related to any contemporary sockeye salmon or kokanee population, assigned poorly to the O. nerka baseline, and had distinctive early return migration-timing suggesting that this group represented a putative historical ESU originating in headwater lakes in British Columbia that was likely extirpated sometime after 1924. The lack of a contemporary O. nerka population possessing the genetic legacy of this extinct ESU indicates that efforts to reestablish early-migrating sockeye salmon to the headwater lakes region of the Columbia River will be difficult.
Data from: Extracting DNA from 'jaws': high yield and quality from archived tiger shark (Galeocerdo cuvier) skeletal material
Archived specimens are highly valuable sources of DNA for retrospective genetic/genomic analysis. However, often limited effort has been made to evaluate and optimize extraction methods, which may be crucial for downstream applications. Here, we assessed and optimized the usefulness of abundant archived skeletal material from sharks as a source of DNA for temporal genomic studies. Six different methods for DNA extraction, encompassing two different commercial kits and three different protocols, were applied to material, so-called bio-swarf, from contemporary and archived jaws and vertebrae of tiger sharks (Galeocerdo cuvier). Protocols were compared for DNA yield and quality using a qPCR approach. For jaw swarf, all methods provided relatively high DNA yield and quality, while large differences in yield between protocols were observed for vertebrae. Similar results were obtained from samples of white shark (Carcharodon carcharias). Application of the optimized methods to 38 museum and private angler trophy specimens dating back to 1912 yielded sufficient DNA for downstream genomic analysis for 68% of the samples. No clear relationships between age of samples, DNA quality and quantity were observed, likely reflecting different preparation and storage methods for the trophies. Trial sequencing of DNA capture genomic libraries using 20 000 baits revealed that a significant proportion of captured sequences were derived from tiger sharks. This study demonstrates that archived shark jaws and vertebrae are potential high-yield sources of DNA for genomic-scale analysis. It also highlights that even for similar tissue types, a careful evaluation of extraction protocols can vastly improve DNA yield.
Data from: Return of a giant: DNA from archival museum samples helps to identify a unique cutthroat trout lineage formerly thought to be extinct
Currently one small, native population of the culturally and ecologically important Lahontan cutthroat trout (Oncorhynchus clarkii henshawi, LCT, Federally listed) remains in the Truckee River watershed of northwestern Nevada and northeastern California. The majority of populations in this watershed were extirpated in the 1940's due to invasive species, overharvest, anthropogenic water consumption and changing precipitation regimes. In 1977, a population of cutthroat trout discovered in the Pilot Peak Mountains in the Bonneville basin of Utah, was putatively identified as the extirpated LCT lacustrine lineage native to Pyramid Lake in the Truckee River basin based upon morphological and meristic characters. Our phylogenetic and Bayesian genotype clustering analyses of museum specimens collected from the large lakes (1872-1913) and contemporary samples collected from populations throughout the extant range provide evidence in support of a genetically distinct Truckee River basin origin for this population. Analysis of museum samples alone identified three distinct genotype clusters and historical connectivity among water bodies within the Truckee River basin. Baseline data from museum collections indicate that the extant Pilot Peak strain represents a remnant of the extirpated lacustrine lineage. Given the limitations on high quality data when working with a sparse number of preserved museum samples, we acknowledge that, in the end, this may be a more complicated story. However, the paucity of remnant populations in the Truckee River watershed in combination with data on the distribution of morphological, meristic and genetic data for Lahontan cutthroat trout, suggest that recovery strategies, particularly in the large lacustrine habitats should consider this lineage as an important part of the genetic legacy of this species.
Data from: Differentiation in neutral genes and a candidate gene in the pied flycatcher: using biological archives to track global climate change
Global climate change is one of the major driving forces for adaptive shifts in migration and breeding phenology and possibly impacts demographic changes if a species fails to adapt sufficiently. In Western Europe, pied flycatchers (Ficedula hypoleuca) have insufficiently adapted their breeding phenology to the ongoing advance of food peaks within their breeding area and consequently suffered local population declines. We address the question whether this population decline led to a loss of genetic variation, using two neutral marker sets (mitochondrial control region and microsatellites), and one potentially selectively non-neutral marker (avian Clock gene). We report temporal changes in genetic diversity in extant populations and biological archives over more than a century, using samples from sites differing in the extent of climate change. Comparing genetic differentiation over this period revealed that only the recent Dutch population, which underwent population declines, showed slightly lower genetic variation than the historic Dutch population. As that loss of variation was only moderate and not observed in all markers, current gene flow across Western and Central European populations might have compensated local loss of variation over the last decades. A comparison of genetic differentiation in neutral loci versus the Clock gene locus provided evidence for stabilizing selection. Furthermore, in all genetic markers, we found a greater genetic differentiation in space than in time. This pattern suggests that local adaptation or historic processes might have a stronger effect on the population structure and genetic variation in the pied flycatcher than recent global climate changes.
Data from: Changes in Eocene plant diversity and composition of the vegetation: the lacustrine archive of Messel (Germany)
Based on high resolution palynological analysis of 680 samples from a core, short-term changes in plant diversity and floristic composition within the Paleogene greenhouse have been detected in the lacustrine succession of a Lower to Middle Eocene maar lake at Messel (Federal State of Hesse, Germany). The microfloristic data show that taxonomic diversity increased rapidly within some decades during recolonization of a volcanically devastated area around the lake. With the establishment of a climax vegetation at the end of recolonization the maximum in palynological diversity was reached in the crater area. During the following 640 Kyr the composition of the palynospectrum changed only gradually. However, different richness and evenness estimations show that alpha and gamma diversity decreased up to 35% which can be related to the establishment of an equilibrium stage within the climax vegetation that led to the dominance of an assemblage of self-replacing species. Nevertheless, time series analysis of alpha diversity changes within the climax vegetation reveals that orbitally controlled climate change of Milankovitch and Sub-Milanovitch order influenced the diversity of the vegetation resulting in a rise of beta diversity. Based on the composition of the vegetation and comparison to modern analogues our analysis now proves that Eocene paratropical plant diversity increased during periods of slightly higher temperature and precipitation. Therefore, both composition and diversity of the vegetation was highly susceptible to minor-scale short-term changes in climate even during equable greenhouse conditions.
Data of Paper "Turning a Multilingual Historical Archive into an Information System through Post-OCR Correction and Content-Based Indexation"
<p>We evaluated our approach on a collection of 946 historical documents belonging to the Biblioteca Nacional de Catalunya (BNC), spanning from 1914 to 1951. Each document is the issue of a magazine, comprising different articles by different authors. This implies that, despite the thematic nature of magazines and specific issues, there is a certain degree of heterogeneity in each document. Magazines were selected based on their relevance w.r.t. art in general and, more specifically, early 20th century avant-garde movements (e.g., Dadaism, Cubism, etc.). For each document, we have the scanning of the original artifact and the plain raw text extracted through ABBYY FineReader OCR tool. To the best of our knowledge, this is the first Catalan-dominated OCR corpus ever released. </p>
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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.