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22,922 results for “collections as data”
Ecological data from: Combining botanical collections and ecological data to better describe plant community diversity
<p>In this age of rapid biodiversity loss, we must continue to refine our approaches to describing variation in life on Earth. Combining knowledge and research tools from multiple disciplines is one way to better describe complex natural systems. Understanding plant community diversity requires documenting both pattern and process. We must first know which species exist, and where (i.e., taxonomic and biogeographic patterns), before we can determine why they exist there (i.e., ecological and evolutionary processes). Floristic botanists often use collections-based approaches to elucidate biodiversity patterns, while plant ecologists use hypothesis-driven statistical approaches to describe underlying processes. Because of these different disciplinary histories and research goals, floristic botanists and plant ecologists often remain siloed in their work. Here, using a case study from an urban greenway in Colorado, USA, we illustrate that the collections-based, opportunistic sampling of floristic botanists is highly complementary to the transect- or plot-based sampling of plant ecologists. We found that floristic sampling captured a community species pool four times larger than that captured using ecological transects, with rarefaction and non-parametric species estimation indicating that it would be prohibitive to capture the "true" community species pool if constrained to sampling within transects. We further illustrate that the discrepancy in species pool size between approaches led to a different interpretation of the greenway's ecological condition in some cases (e.g., transects missed uncommon cultivated species escaping from nearby gardens) but not others (e.g., plant species distributions among functional groups were similar between species pools). Finally, we show that while using transects to estimate plant relative abundances necessarily trades off with a fuller assessment of the species pool, it is an indispensable indicator of ecosystem health, as evidenced by three non-native grasses contributing to 50% of plant cover along the highly modified urban greenway. We suggest that actively fostering collaborations between floristic botanists and ecologists can create new insights into the maintenance of species diversity at the community scale.</p>
Outline data for Aterian tanged tools from North African collections
<p>Thresholded photographs of Aterian tanged tools from various collections, each accompanied by its extracted outline in text format.</p>
Data from: Quantifying the dark data in museum fossil collections as palaeontology undergoes a second digital revolution
Large-scale analysis of the fossil record requires aggregation of palaeontological data from individual fossil localities. Prior to computers these synoptic datasets were compiled by hand, a laborious undertaking that took years of effort and forced palaeontologists to make difficult choices about what types of data to tabulate. The advent of desktop computers ushered in palaeontology's first digital revolution – online literature-based databases, such as the Paleobiology Database (PBDB). However, the published literature represents only a small proportion of the palaeontological data housed in museum collections. Although this issue has long been appreciated, the magnitude, and thus potential significance, of these so-called "dark data" has been difficult to determine. Here, in the early phases of a second digital revolution in palaeontology the digitization of museum collections – we provide an estimate of the magnitude of palaeontology's dark data. Digitization of our nine institutions' holdings of Cenozoic marine invertebrate collections from California, Oregon, and Washington in the United States reveals that they represent 23 times the number of unique localities than are currently available in the Paleobiology Database. These data, and the vast quantity of similarly untapped dark data in other museum collections, will when digitally mobilized enhance palaeontologists' ability to make inferences about the patterns and processes of past evolutionary and ecological changes.
Data from: A new digital method of data collection for spatial point pattern analysis in grassland communities
<p>A major objective of plant ecology research is to determine the underlying processes responsible for the observed spatial distribution patterns of plant species. Plants can be approximated as points in space for this purpose, and thus, spatial point pattern analysis has become increasingly popular in ecological research. The basic piece of data for point pattern analysis is a point location of an ecological object in some study region. Therefore, point pattern analysis can only be performed if data can be collected. However, due to the lack of a convenient sampling method, a few previous studies have used point pattern analysis to examine the spatial patterns of grassland species. This is unfortunate because being able to explore point patterns in grassland systems has widespread implications for population dynamics, community-level patterns and ecological processes. In this study, we develop a new method to measure individual coordinates of species in grassland communities. This method records plant growing positions via digital picture samples that have been sub-blocked within a geographical information system (GIS). Here, we tested out the new method by measuring the individual coordinates of <i>Stipa</i><i> grandis</i> in grazed and ungrazed <i>S. grandis</i> communities in a temperate steppe ecosystem in China. Furthermore, we analyzed the pattern of <i>S. grandis</i> by using the pair correlation function <i>g</i>(<i>r</i>) with both a homogeneous Poisson process and a heterogeneous Poisson process. Our results showed that individuals of <i>S. grandis</i> were overdispersed according to the homogeneous Poisson process at 0-0.16 m in the ungrazed community, while they were clustered at 0.19 m according to the homogeneous and heterogeneous Poisson processes in the grazed community. These results suggest that competitive interactions dominated the ungrazed community, while facilitative interactions dominated the grazed community. In sum, we successfully executed a new sampling method, using digital photography and a Geographical Information System, to collect experimental data on the spatial point patterns for the populations in this grassland community.</p>
Data from: Climate-mediated hybrid zone movement revealed with genomics, museum collection and simulation modeling
Climate-mediated changes in hybridization will dramatically alter the genetic diversity, adaptive capacity and evolutionary trajectory of interbreeding species. Our ability to predict the consequences of such changes will be key to future conservation and management decisions. Here we tested through simulations how recent warming (over a 32-year period) is affecting the geographic extent of a climate-mediated developmental threshold implicated in maintaining a butterfly hybrid zone (Papilio glaucus and Papilio canadensis; Lepidoptera: Papilionidae). These simulations predict a 68 km shift of this hybrid zone. To empirically test this prediction, we assessed genetic and phenotypic changes using contemporary and museum collections and document a 40 km northward shift of this hybrid zone. Interactions between the two species appear relatively unchanged during hybrid zone movement. We found no change in the frequency of hybridization and regions of the genome that experience little to no introgression moved largely in concert with the shifting hybrid zone. Model predictions based on climate scenarios predict this hybrid zone will continue to move northward, but with substantial spatial heterogeneity in the velocity (55-144 km/1°C), shape, and contiguity of movement. Our findings suggest that the presence of non-climatic barriers (e.g., genetic incompatibilities) and/or non-linear responses to climatic gradients may preserve species boundaries as the species shift. Further, we show that variation in the "geography" of hybrid zone movement could result in evolutionary responses that differ for geographically distinct populations spanning hybrid zones and thus have implications for the conservation and management of genetic diversity.
Summary raw wind data from the Southern Ocean collected on board the Antarctic Circumnavigation Expedition (ACE) during the austral summer of 2016/2017.
<p><strong>Dataset abstract</strong></p> <p>A Vaisala MAWS240 meteorological station was installed on the R/V Akademik Tryoshnikov during a circumnavigation of Antarctica in the austral summer season of 2016/2017. This dataset contains the raw wind parameter data that have been extracted from the original raw text data files. Data coverage is from 17th November 2016 until 11th April 2017, with gaps where the ship was in port.</p> <p>True and relative wind speed and direction parameters were recorded with a resolution of three seconds.</p> <p>Datetime should be combined with TIMEDIFF to convert it to UTC.</p> <p>Data from this dataset have been corrected and quality-checked in another published dataset. We recommend these data for further use (Landwehr et al., 2019; DOI 10.5281/zenodo.3379590).</p> <p><strong>Dataset contents</strong></p> <ul> <li>metdata_wind_YYYYMMDD_YYYYMMDD.csv, data file, comma-separated values</li> <li>data_file_header, metadata, text format</li> <li>README.txt, metadata, text format</li> <li>ace_meteorology_raw_wind_summary_change_log.txt</li> </ul> <p>Data files contain data for each leg of the Antarctic Circumnavigation Expedition (ACE). Dates included in the file name are the start and end dates of the legs and therefore the data within the files as well.</p> <p><strong>Change log</strong></p> <p><strong>v1.2</strong> - Added missing data from 2017-02-05 - 2017-02-08 inclusive. Updated this change log file.</p> <p><strong>v1.1</strong> - Added additional data coverage from 2016-11-17 - 2016-11-22 inclusive, into the first data file. Updated README.txt with information about data coverage. Added this change_log file.</p> <p><strong>v1.0</strong> - Initial release of raw summary meteorological data.</p> <p><strong>Dataset license</strong></p> <p>This raw meteorological dataset is made available under the Creative Commons Attribution 4.0 International License (CC BY 4.0) whose full text can be found at https://creativecommons.org/licenses/by/4.0/</p>
L Cysteine Data collected 05/03/2016 at Diamond Light Source I19-1
<p>Data collected 05/03/2016 at Diamond Light Source I19-1 publicly available for users to test data reduction routines. Data are known to produce good merging statistics and final refinements. Three datasets collected on the same crystal with varying data collection times to explore beamline operational efficiency.</p> <p>l-cyst - collected with default set of runs that i19 used in the initial phase (i.e. 0.1 degree images, 0.1s per image)</p> <p>l-cyst_fast - collected with 0.1 degree images, 0.05s per image.</p> <p>l-cyst_very_fast - collected with 0.2 degree images, 0.05s per image.</p>
GERBIL evaluation data of Robust and Collective Entity Disambiguation through Semantic Embeddings
<p>A table containing the SIGIR 2016 experiments performed with GERBIL in context of the SIGIR 2016 work "Robust and Collective Entity Disambiguation through Semantic Embeddings" by Stefan Zwicklbauer, Christin Seifert and Michael Granitzer</p> <p>It also contains the original URL to the GERBIL website</p> <p>Corresponding GitHub Repository:</p> <p>https://github.com/quhfus/</p> <p> </p>
Figure 5. from Collecting and Preserving Marine and Freshwater Isopoda (Crustacea: Peracarida) - Biodiversity Data Journal 3: e4912 (12 May 2015) https://doi.org/10.3897/BDJ.3.e4912
Figure 5. - Kathy Omura holding whirl top bag containing sample which is ready to be filled with ethanol.
Figure 1. from Collecting and Preserving Marine and Freshwater Isopoda (Crustacea: Peracarida) - Biodiversity Data Journal 3: e4912 (12 May 2015) https://doi.org/10.3897/BDJ.3.e4912
Figure 1. - Storage and shipping box also holds dive gear on small boats, large and small photographic trays, 10-12 liter [3 gallon] bucket with modified screw top lid and stainless steel carabiner, mesh dive sack, aquarium fish net, brass-framed mermaid's bra net (240 µm mesh or 63 µm for meiofauna), geology hammer, paint scraper, stainless steel spoon, dive sausage and reel. Photo credit: N. D. Pentcheff.
Figure 4. from Collecting and Preserving Marine and Freshwater Isopoda (Crustacea: Peracarida) - Biodiversity Data Journal 3: e4912 (12 May 2015) https://doi.org/10.3897/BDJ.3.e4912
Figure 4. - N. Dean Pentcheff and Niel Bruce straining seawater containing isopods into mermaid's bra (netting). The bucket is swirled to suspend animals and quickly strained over the netting to retain them.
Supplementary file pwt: Collection sites for black flies from Turkish Thrace, 2002–2006. from Black flies (Diptera: Simuliidae) of Turkish Thrace, with a new record for Turkey - Biodiversity Data Journal 3: e4834 (22 April 2015) https://doi.org/10.3897/BDJ.3.e4834
Collection sites for black flies from Turkish Thrace, 2002–2006.
Figure 2. from Collecting and Preserving Marine and Freshwater Isopoda (Crustacea: Peracarida) - Biodiversity Data Journal 3: e4912 (12 May 2015) https://doi.org/10.3897/BDJ.3.e4912
Figure 2. - Plankton net (240 µm mesh), 25 x 25 cm [10 x 10 inches] 240 µm mesh plankton netting to use with funnel, numbered mesh draw-string collecting bags (28 x 46 cm [11 x 18 inches], 200 or 300 µm mesh, seams reinforced with sew-on edge binding), draw-string cotton sack 41 x 76 cm [16 x 30 inches] for larger bulkier samples, assorted screw-top vials and plastic eye dropper, stainless steel forceps (10 and 25 cm [6 and 10 inches] long), insect collecting forceps for picking up fast moving or fragile animals, leather garden gloves, Optivisor optical glass binocular magnifier (2 diopter, 1.5x), dive light, whirl top bags (2 sizes = 13 x 30 cm [5 x 12 inches] and 12 x 23 cm [4.5 x 9 inches]), fanny pack, and GPS. Photo credit: N. D. Pentcheff.
Research data supporting: "Non-trivial stimuli-responsive collective behaviours emerging from microscopic dynamic complexity in supramolecular polymer systems"
<p>Contains the relevant simulation data and input files. See "readme.txt" for information.</p>
Cetacean & environmental data collected on Iveragh during LIVE Project (2020-2022)
<p>The data sets consists of cetacean data (sightings and strandings) collected during the LIVE Project, on the Iveragh peninsula, Co. Kerry, Ireland.</p> <p>These include land-based effort watches (October 2021 - September 2022), boat effort surveys (summer 2022), casual sightings reported through LIVE researcher (2020-2022) and data obtained from the Irish Whale and Dolphin Group website (2020-2022).</p> <p>Tidal data from Dingle Harbour and environmental parameters recorded through Buoy M3 are also available here.</p>
Dataset: A continuous open source data collection platform for architectural technical debt assessment
<p>The dataset and replication package of the study "A continuous open source data collection platform for architectural technical debt assessment".</p> <p> </p> <p>Abstract</p> <p>Architectural decisions are the most important source of technical debt. In recent years, researchers spent an increasing amount of effort investigating this specific category of technical debt, with quantitative methods, and in particular static analysis, being the most common approach to investigate such a topic.</p> <p> </p> <p>However, quantitative studies are susceptible, to varying degrees, to external validity threats, which hinder the generalisation of their findings.</p> <p>In response to this concern, researchers strive to expand the scope of their study by incorporating a larger number of projects into their analyses. This practice is typically executed on a case-by-case basis, necessitating substantial data collection efforts that have to be repeated for each new study.</p> <p> </p> <p>To address this issue, this paper presents our initial attempt at tackling this problem and enabling researchers to study architectural smells at large scale, a well-known indicator of architectural technical debt. Specifically, we introduce a novel approach to data collection pipeline that leverages Apache Airflow to continuously generate up-to-date, large-scale datasets using Arcan, a tool for architectural smells detection (or any other tool).</p> <p>Finally, we present the publicly-available dataset resulting from the first three months of execution of the pipeline, that includes over 30,000 analysed commits and releases from over 10,000 open source GitHub projects written in 5 different programming languages and amounting to over a billion of lines of code analysed.</p>
SCXRD data PX2-0041_pin01_1 from a DatZ crystal collected on PROXIMA 2A 2023-09-06
<p>Single crystal X-ray diffraction data test data (DatZ) collected on PROXIMA 2A 2023-09-06 during start-up of the check list for Run 4 2023. Puck name = PX2-0041. Pin number = 01. Protein crystal DatZ contains zinc. Data file prefix = PX2-0041_pin01_1.</p>
Data from: Determinants of hyena participation in risky collective action
<p>Collective action problems arise when cooperating individuals suffer costs of cooperation, while the benefits of cooperation are received by both cooperators and defectors. We address this problem using data from spotted hyenas fighting with lions. Lions are much larger, and kill many hyenas, so these fights require cooperative mobbing by hyenas for them to succeed. We identify factors that predict: when hyena groups engage in cooperative fights with lions, which individuals choose to participate, and how the benefits of victory are distributed among cooperators and non-cooperators. We find that cooperative mobbing is better predicted by lower costs (no male lions, more hyenas) than higher benefits (need for food). Individual participation is facilitated by social factors, both over the long term (close kin, social bond strength) and the short term (greeting interactions prior to cooperation). Finally, we find some direct benefits of participation: after cooperation, participants were more likely to feed at contested carcasses than non-participants. Overall, these results are consistent with the hypothesis that, when animals face dangerous cooperative dilemmas, selection favors flexible strategies that are sensitive to dynamic factors emerging over multiple time-scales.</p>
Chesley et al., 2023 - Gofar Oceanic Transform Fault CSEM data from fault-perpendicular profiles (collected 2022)
<p>This repository contains processed and edited controlled-source electromagnetic amplitude and phase data from the Gofar oceanic transform fault with corresponding bathymetry files. The files beginning "dataFile.." are the amplitudes and phases and the files beginning "topo..." are the bathymetry information. Each profile in this repository crosses the fault approximately perpendicularly.</p>
Additional morphometrical and ecological data collected during the 2018 expedition of the UMMZ in Nicaragua
<p>Nicaragua is a biodiverse country, but documented herpetological specimens are underrepresented when compared to other neighboring countries. In 2018 we conducted a collaborative expedition between the University of Michigan Museum of Zoology and Nicaraguan biologists. We visited three collection sites in the Pacific lowlands, Caribbean lowlands, and the Central Highlands, representing three major biogeographic regions. We collected specimens of 100 species from a total of 106 encountered. We provide accession numbers, morphological, genetic, and ecological information for these specimens. We recorded 23 new departmental and the first country record of <em>Metlapilcoatlus indomitus</em> (Smith & Ferrari-Castro, 2008), helping filling gaps in the known distribution of the species within Nicaragua and the Central American region. When available, we provide species range maps and comparative genetic tree including conspecific reference sequences from the region.</p>
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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.