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Percent cover of under- and mid-story vegetation and seedling counts in the Future of Oak Forests project at Black Rock Forest, Cornwall, NY.
Black Rock Forest established a series of 12, 0.56 ha plots in 2005 to assess impacts of the loss of tree in the genus Quercus on the forest ecosystem (entitled the Future of Oak Forests experiment). Three trunk girdling treatments, with control plots were instituted in 2008. Each plot also contained an ~10m by ~15m deer exclosure to assess the impact of herbivory post-disturbance. In 2006 and 2008, before exclosures were erected, pre-treatment surveys were conducted in all unexclosed (n=120) quadrats. Surveys of all 240 understory quadrats were conducted annually in late summer (August to September) from 2009 to 2018 and then again in 2021. At each quadrat, trained observers identified all vascular plants to species and assigned each species a percent cover value. The percent cover of moss was also recorded but moss species were not identified. Counts of tree seedlings and some woody shrubs were also recorded in addition to percent cover values. Seedlings were considered saplings, and therefore not counted, once they reached 1.3 m tall (breast height).
PIE LTER surveys of salt marsh breeding birds using point counts in Rowley and Newbury, Massachusetts (Reformatted to the ecocomDP Design Pattern)
This data package is formatted as an ecocomDP (Ecological Community Data Pattern). For more information on ecocomDP see https://github.com/EDIorg/ecocomDP. This Level 1 data package was derived from the Level 0 data package found here: https://pasta.lternet.edu/package/metadata/eml/knb-lter-pie/175/8. The abstract below was extracted from the Level 0 data package and is included for context: This data set contains the results of point count surveys of breeding birds in the salt marshes of the Plum Island Estuary. Surveys have been carried out each year in June beginning in 2004 and are ongoing. Currently six circles of 100 m radius are being surveyed. Three of the circles are in plots that had been regularly hayed and three in unhayed plots. Currently only one of the plots is regularly hayed. 85 species recorded as of 2020. Most frequently encountered are Agelaius phoeniceus, Ammospiza caudacuta, Tringa semipalmata. The Plum Island Ecosystems (PIE) LTER is developing a predictive understanding of the response of a linked watershed-marsh-estuarine system in northeastern Massachusetts to rapid environmental change. Over the last 30 years, surface sea water temperatures in the adjacent Gulf of Maine have risen at 3 times the global average, rates of sea-level rise have accelerated, and precipitation has increased. Coupled with these changes in climate and sea level are substantial changes within the rapidly urbanizing watersheds that influence water, sediment, and nutrient delivery to the marsh and estuary. In PIE IV our focus is on: Dynamics of coastal ecosystems in a region of rapid climate change, sea-level rise, and human impacts. NSF OCE LTER-Plum Island Ecosystems: Dynamics of coastal ecosystems in a region of rapid climate change, sea-level rise, and human impacts.
Point-count bird censusing: long-term monitoring of bird abundance and diversity along the Salt River in the greater Phoenix metropolitan area, ongoing since 2013
Waterways are often the focus of restoration efforts in urban areas. In arid regions, passive discharge of urban water sources may stimulate the recovery or growth of wetland and riparian features in dewatered or ephemeral aquatic systems. In the greater Phoenix metropolitan area (GPMA), sections of the Salt and Gila Rivers have been the targets of active restoration through seeding, planting, and irrigation. At the same time, revegetation has occurred in some sections of the rivers in response to runoff from urban water sources (e.g., storm drains). This dataset catalogs the results of bird surveys conducted at several locations along the Salt River in and around the GPMA beginning in March 2013. Monitoring locations focus on reaches of the river with different characteristics, including: (1) urbanized with perennial water and actively restored (n=2 reaches), (2) urbanized with perennial water and passively restored (n=2 reaches), (3) urbanized with ephemeral water but not restored (n=2 reaches), and (4) non-urban reference areas with perennial water (n=1 reach). This program expands on bird monitoring that the CAP LTER conducts at other locations in and around the GPMA, and complements herpetological surveys that are performed at these locations along the Salt River where the bird surveys are performed. This is a long-term monitoring effort of the CAP LTER with on-going data collection.
Fall 2015 crab population monitoring: mid-marsh and creek bank abundance based on crab hole counts at GCE marsh, monitoring sites 1-10
This data set is the Fall 2015 estimate of crab densities at the GCE-LTER marsh sites used for population monitoring. Crab abundance was determined by counting the number of crab holes within a 625 cm^2 quadrat and converting the counts to number per square meter. Counts were made in the mid-marsh and creek bank zones (n = 4 per zone) at GCE sites 1 through 10. Note that this census method does not differentiate which species made a particular hole and therefore only estimates total burrowing crab abundance, potentially including species Uca pugnax, Uca minax, Uca pugilator, Armases cinereum, Eurytium limosum and Sesarma reticulatum. Crab holes that are not actively maintained are quickly covered by tidal activity and other sediment disturbances, therefore plugged holes were assumed to be unoccupied and excluded from the counts.
Fall 2016 crab population monitoring: mid-marsh and creek bank abundance based on crab hole counts at GCE marsh, monitoring sites 1-10
This data set is the Fall 2016 estimate of crab densities at the GCE-LTER marsh sites used for population monitoring. Crab abundance was determined by counting the number of crab holes within a 625 cm^2 quadrat and converting the counts to number per square meter. Counts were made in the mid-marsh and creek bank zones (n = 4 per zone) at GCE sites 1 through 10. Note that this census method does not differentiate which species made a particular hole and therefore only estimates total burrowing crab abundance, potentially including species Uca pugnax, Uca minax, Uca pugilator, Armases cinereum, Eurytium limosum and Sesarma reticulatum. Crab holes that are not actively maintained are quickly covered by tidal activity and other sediment disturbances, therefore plugged holes were assumed to be unoccupied and excluded from the counts.
Fall 2017 crab population monitoring: mid-marsh and creek bank abundance based on crab hole counts at GCE marsh, monitoring sites 1-10
This data set is the Fall 2017 estimate of crab densities at the GCE-LTER marsh sites used for population monitoring. Crab abundance was determined by counting the number of crab holes within a 625 cm^2 quadrat and converting the counts to number per square meter. Counts were made in the mid-marsh and creek bank zones (n = 4 per zone) at GCE sites 1 through 10. Note that this census method does not differentiate which species made a particular hole and therefore only estimates total burrowing crab abundance, potentially including species Uca pugnax, Uca minax, Uca pugilator, Armases cinereum, Eurytium limosum and Sesarma reticulatum. Crab holes that are not actively maintained are quickly covered by tidal activity and other sediment disturbances, therefore plugged holes were assumed to be unoccupied and excluded from the counts.
Fall 2018 crab population monitoring: mid-marsh and creek bank abundance based on crab hole counts at GCE marsh, monitoring sites 1-10
This data set is the Fall 2018 estimate of crab densities at the GCE-LTER marsh sites used for population monitoring. Crab abundance was determined by counting the number of crab holes within a 625 cm^2 quadrat and converting the counts to number per square meter. Counts were made in the mid-marsh and creek bank zones (n = 4 per zone) at GCE sites 1 through 10. Note that this census method does not differentiate which species made a particular hole and therefore only estimates total burrowing crab abundance, potentially including species Uca pugnax, Uca minax, Uca pugilator, Armases cinereum, Eurytium limosum and Sesarma reticulatum. Crab holes that are not actively maintained are quickly covered by tidal activity and other sediment disturbances, therefore plugged holes were assumed to be unoccupied and excluded from the counts.
Grasshopper counts and feeding damage at the GCE-LTER Seawater Addition Long-Term Experiment (SALTEx) in 2016
Grasshopper abundance and feeding damage were investigated at the Georgia Coastal Ecosystems (GCE) LTER Seawater Addition Long-Term Experiment (SALTEx) study area approximately monthly in 2016. We conducted visual surveys in each replicate plot and counted 3 species of grasshopper (Romalea, Leptysma, Orchelimum) and scored grasshopper feeding damage on 2 species of plants (Zizaniopsis, Pontederia).
Fall 2019 crab population monitoring: mid-marsh and creek bank abundance based on crab hole counts at GCE marsh, monitoring sites 1-10
This data set is the Fall 2019 estimate of crab densities at the GCE-LTER marsh sites used for population monitoring. Crab abundance was determined by counting the number of crab holes within a 625 cm^2 quadrat and converting the counts to number per square meter. Counts were made in the mid-marsh and creek bank zones (n = 4 per zone) at GCE sites 1 through 10. Note that this census method does not differentiate which species made a particular hole and therefore only estimates total burrowing crab abundance, potentially including species Uca pugnax, Uca minax, Uca pugilator, Armases cinereum, Eurytium limosum and Sesarma reticulatum. Crab holes that are not actively maintained are quickly covered by tidal activity and other sediment disturbances, therefore plugged holes were assumed to be unoccupied and excluded from the counts.
Rabbit feces counts on 1m x 1m plots from the long-term Small Mammal Exclosure Study (SMES) at Jornada Basin LTER, 1995-2020
This data package contains rabbit feces count data from plots with various levels of herbivore exclusion on Jornada Experimental Range (JER) and Chihuahuan Desert Rangeland Research Center (CDRRC) lands. Study sites were established in 1995; one in black grama grassland and the other in creosotebush shrubland to compare the impact of herbivores on ecosystem processes between these vegetation types. Parallel studies were established at the Sevilleta LTER site (New Mexico, USA) and Mapimi Biosphere Reserve (Durango, Mexico). Each study site is 1 km by 0.5 km in area. Four replicate experimental blocks were randomly located at the grassland study site to measure vegetation responses using exclusion treatments including a) all mammalian herbivores, including cattle, lagomorphs, and rodents, b) lagomorphs and cattle only, c) cattle only, and d) control accessible to all herbivores. Because grazing cattle are excluded from the entire creosote site, only three replicate experimental blocks were randomly located there including a) all mammalian herbivores, including lagomorphs, and rodents, b) lagomorphs only, and c) control accessible to all herbivores. Thirty-six sampling points were positioned at 5.8-meter intervals on a systematically located 6 by 6 point grid within each plot. A permanent one-meter by one-meter vegetation measurement quadrat is located at each of the 36 points. Each year in spring and fall from 1995-2005, the total number of rabbit feces were counted within each quadrat. After 2005, sampling frequency channged to every 5 years and data collected record only presence or absence of feces. This study is ongoing.
Flower counts in the black sand extended growing season experiment, 2023.
As a result of climate change, the Rocky Mountain Front Range is experiencing warmer summers and earlier snowmelt. Due to the importance of snow for regulating soil temperature, growing season length, and available moisture in alpine ecosystems, even small shifts in the snow-free period could have large impacts. The focus of the Black Sand Extended Growing Season Length Experiment is to examine how terrain-related differences in climate exposure influence the way alpine habitats respond to climate change via earlier snowmelt. To simulate how climate exposure may affect plant communities, NWT LTER researchers established 5 experimental sites each containing a pair 10 x 40m rectangular plots. These sites include north and south facing aspects, subalpine and alpine tundra meadows in a range of hydrological conditions (e.g. dry meadows, moist meadows, wet meadows). We accelerated snowmelt in one plot of each block by adding chemically inert black sand, while keeping the second plot as an unmanipulated control; black sand was added to these plots after snow had naturally melted. This dataset includes ~biweekly flower counts from late June – late August 2023, which can be used to estimate onset, peak, and end of flowering and how these might change under a longer growing season due to black sand application.
Nekton species counts and density from flume net collections along Rowley River tidal creeks associated with long term fertilization experiments, Rowley, MA.
The flume nets were deployed with the purpose of capturing salt marsh nekton. Nekton species were identified to the lowest taxonomic level using species keys. The TIDE project aims to simulate eutrophication on a large scale by the addition of NO3- aiming to reach 70μM concentrations from May to September every year during the growing season. This fertilization of the marsh has been going on at Sweeney Creek since the 2004 growing season through 2016 and at Clubhead Creek in 2005 and from 2009 till 2016. Years 2017-2020 are enrichment recovery years.
Fish Counts and Lengths in South Bay and Hog Island Bay, Virginia 2012-2018
To study how seagrass restoration affects coastal fish communities over time, we sampled fishes at each site once or twice per year with beach seines (7.6 m wide × 1.8 m tall; 1.5 m deep pocket with 6.4 mm mesh) hauled along 25-m transects in the summer (May or June) and autumn (September or October) from 2012 through 2018. Researchers ceased sampling at the 4 initially unvegetated sites in South Bay after 2015, when these sites were colonized by seagrass, although seining occurred once more at these sites during the autumn of 2017. During each sampling event, we counted, measured (total length), and identified fish to the lowest possible taxon in the field prior to release. All seine hauls occurred during the day and within 3 hours of low tide for logistical reasons (n = 204). Due to methodological changes, after 2018 surveys are recorded in a different dataset VCR22364 "Abundance and Size of Seagrass-Associated Fishes in the Virginia Coastal Lagoons, 2019-xxxx" https://doi.org/10.6073/pasta/400c84b859e81e9a1e5212bccb37b759.
Oyster fauna lengths, counts, and biomass from restored and reference reefs in Virginia coastal bays, 2005-2023
Oyster reef fauna counts and lengths were sampled at natural "reference" reefs and restored shell plant reefs located in the Virginia Coast Reserve. Overfishing and disease decimated oyster reefs in the Virginia Coast Reserve in the 1900s. Reference reefs were defined as remnant reefs that naturally recovered in the early 2000s to develop the pronounced vertical structure and multiple oyster size classes that represent the desired endpoint of restoration efforts. Nearly every year since 2003, The Nature Conservancy and Virginia Marine Resource Commission have constructed oyster reefs in intertidal areas in the VCR. To construct the restored reefs, practitioners launched dredged, fossilized oyster shell from barges to intertidal locations chosen for their bottom stability and accessibility (locations lacked oysters prior to construction). Whelk shell supplemented the oyster shell at some of the restored reefs. TNC practitioners monitor select restored and reference reefs annually for adult and spat live oysters, adult and spat box oysters, mud crabs, mud snails, oyster drills, live clams, and mussels.
Atlantic ghost crab (Ocypode quadrata) burrow counts at shorebird nests and randomly available sites on Metompkin Island, Virginia, 2022
Atlantic ghost crabs (Ocypode quadrata) are predators of beach-nesting shorebirds, their nests, and their chicks on the United States' Atlantic and Gulf coasts. Ghost crabs may also disturb birds, altering their foraging, habitat use, or nest and brood attendance patterns. Shorebird conservation strategies often involve predator and disturbance management to improve reproductive success, but efforts rarely target ghost crabs. Despite the threat to shorebird reproductive success, ghost crabs are a poorly understood part of the beach ecosystem and additional knowledge about ghost crab habitat selection is needed to inform shorebird conservation. We monitored ghost crab activity, defined as burrow abundance, throughout the shorebird breeding season on Metompkin Island, Virginia, an important breeding site for piping plovers (Charadrius melodus) and American oystercatchers (Haematopus palliatus). We counted burrows at shorebird nests and random points throughout the shorebird breeding season and tested whether ghost crab activity was greater at shorebird nest sites than random sites. We observed burrows at all nest sites in our study area (n = 63 nests), but found fewer burrows at nest sites than random sites. Ghost crabs may avoid shorebird nest sites due to aggressive defensive behaviors from incubating adults or differences in microhabitat characteristics selected by shorebirds versus ghost crabs. We also tested the effects of date, air temperature, habitat type, and shell cover on the abundance of ghost crab burrows. We found that while burrows were present across the barrier island landscape, there were more burrows in sandy habitats with sparse to little shell cover and in and behind the dunes relative to the beach and beach-front berm. Ghost crab activity increased later in the shorebird breeding season and as air temperature increased. Understanding when and where ghost crabs are most likely to be active in the landscape can aid decision-making to benefit imperi
Improving anxiety research novel approach to reveal trait anxiety through summary measures of multiple states - raw count data set - RNAseq
<p>Raw count data of the RNAseq analysis of a project and manuscript under the title "Improving anxiety research novel approach to reveal trait anxiety through summary measures of multiple states". The header of the table includes the subject identifiers except the first column "genes". The latter column includes all assessed gene identifiers.</p>
Martian crater ages and crater counting - Does the impact flux of small and large asteroids varied through time on Mars, the Earth and the Moon?
<ul> <li>The SM_mars_crater_dating.xlsx table contains all the information used to date the 49 martian impact craters considered in this study (< 600 Ma). </li> </ul> <ol> <li>CRATER ID </li> <li>CRATER NAME</li> <li>DIAM KM </li> <li>LAT </li> <li>LONG </li> <li>DEPTH RIM KM </li> <li>DEPTH SURF KM </li> <li>DEPTH FLOOR KM </li> <li>NUMBER LAYER</li> <li>MORPHO EJECTA </li> <li>PRESERVATION </li> <li>COUNT AREA KM2: counting area from ejecta banket mapping </li> <li>COUNT AREA ASCI* KM2: counting area after removal of surfaces contaminated by secondary craters </li> <li>THRESHOLD AREA KM2: minimum size of Voronoi polygon area below which all associated detected craters are considered of secondary origin</li> <li>NB SEC: number of secondary craters dentified by ASCI </li> <li>PERCENT SEC</li> <li>NB CRAT 100M: total number of craters > 100 m detected by the CDA** on the CTX global mosaic*** over the counting area</li> <li>NB PRIM 100M: number of craters identified as primaries by ASCI</li> <li>TURNOFF DIAM KM: minimum crater diameter used to fit the crater-size frequency distribution (CSFD) with an isochron</li> <li>NB CRAT FIT: number of craters used to fit the CSFD with an isochron</li> <li>AGE GA: model age based on Hartmann (2005) chronology model**** and Michael et al. (2016) fitting technique*****</li> <li>AGE MAX GA</li> <li>AGE MIN GA</li> <li>N(1): equivalent number of accumulated craters >1km per km2</li> <li>N(1) MAX</li> <li>N(1) MIN</li> </ol> <p>*ASCI: Automatic Secondary Crater Identification: A. Lagain, K. Servis, G. K. Benedix, C. Norman, S. Anderson, P. A. Bland, Model Age Derivation of Large Martian Impact Craters, Using Automatic Crater Counting Methods, Earth and Space Science 8 (2) (2021). doi:10.1029/2020EA001598.</p> <p>**CDA: Crater Detection Algorithm: G. K. Benedix, A. Lagain, K. Chai, S. Meka, S. Anderson, C. Norman, P. A. Bland, J. Paxman, M. C. Towner, T. Tan, Deriving Surface Ages on Mars Using Automated Crater Counting, Earth and Space Science 7 (3) (2020). doi:10.1029/2019EA001005.</p> <p>*** CTX global mosaic: Context Camera global mosaic: J. L. Dickson, L. A. Kerber, C. I. Fassett, B. L. Ehlmann, A Global, Blended CTX Mosaic of Mars with Vectorized Seam Mapping: A New Mosaicking Pipeline Using Principles of Non-Destructive Image Editing, in: Lunar and Planetary Science Conference (2018), p. 2480.</p> <p>**** W. K. Hartmann, Martian cratering 8: Isochron refinement and the chronology of Mars, Icarus 174 (2) (2005) 294–320. doi:10.1016/j.icarus.2004.11.023.</p> <p>***** G. G. Michael, T. Kneissl, A. Neesemann, Planetary surface dating from crater size-frequency distribution measurements: Poisson timing analysis, Icarus 277 (2016) 279–285. doi:10.1016/j.icarus.2016.05.019.</p> <ul> <li>The crater_counting.csv table contains the location and size of impact craters used to derive the ages of the 49 craters younger than 600 Ma old presented in this study. </li> </ul>
Sample dataset: ovitrap sticks pictures and observed egg count
<p>This dataset consists of 300 ovitrap sticks pictures that contain at least one <em>Aedes aegypty</em> egg. The pictures were taken with an iPhone 7 mobile phone and were used to assess the performance of a mosquito egg counter algorithm and application (<a href="https://ovitrap-monitor.netlify.app/">https://ovitrap-monitor.netlify.app/</a>). The ovitraps are part of a weekly surveillance program carried out in the city of Córdoba (Argentina) by the Health Ministry authorities. This dataset is a smaple obtained between December 2021 and March 2022. We also include a text file with the code of the ovitraps and the number of eggs counted by a technician under magnifying glasses (i.e., observed counts).</p>
Forward and backward Raman scattering photon counts in a FTTH topology.
<p>This set comprises a simulation tool in Mathematica for the generated Raman noise in a<br> GPON-based FTTH topology. This set takes into consideration various FTTH parameters,<br> such as the number of Optical Network Terminals (ONTs) and the splitting ratios, as well<br> as the drop and feeder fiber lengths, as it is depicted in Figure 1, providing in the output<br> the expected Raman noise counts calculated in counts per second (cps) detected in a<br> Single Photon Detector (SPD). The user of the code can manipulate various setup<br> parameters, such as the filtering passband and loss, as well as the specific SPAD<br> parameters which can be selected to be operating either in gated or free running mode.<br> The code provides as an output the expected noise count rates (cps) associated with the<br> forward and backward Raman scattering effect.<br> </p>
Project Tycho Level 2 data: Counts of multiple diseases reported in UNITED STATES OF AMERICA, 1888-2014
Project Tycho data include counts of infectious disease cases or deaths per time interval. A count is equivalent to a data point.<p></p><p>Project Tycho level 2 version 1.1.0 data include data counts that have been filtered from the raw data to render standardized data that can be used immediately for analysis. All level 2 data were originally reported in a consistent format and have not been transformed into a standard format by Project Tycho staff, except for smallpox records that included repeated counts for the same location and week, but sometimes with different numbers. These duplicate smallpox records have been averaged into one count for each location and week. Level 2 data include counts for a wide variety of diseases and locations for varying time periods. Because we removed data in an inconsistent format from level 2 data, counts may be missing for certain diseases, locations, or years. For the most complete collection of standardized data, we encourage users to use Project Tycho version 2.0 datasets.</p><p>More detailed methods and additional information about the origin of Projec Tycho level 2 version 1.1.0 data can be found in our original publication in the New England Journal of Medicine: <a href="http://www.nejm.org/doi/full/10.1056/NEJMms1215400">http://www.nejm.org/doi/full/10.1056/NEJMms1215400</a></p><p>Level 2 version 1.1.0 data is represented in a CSV file with 11 columns:</p><ul><li>epi_week: a six digit number that represents the year and epidemiological week for which disease cases or deaths were reported (yyyyww)</li><li>country: a two digit country abbreviation, only including "US" in version 1.1.0</li><li>state: the two digit postal code state abbreviation that represents the state for which a count has been reported</li><li>loc: the name of a state or city for which a count has been reported, capitalized</li><li>loc_type: the type of location (STATE or CITY) for which a count has been reported</li><li>disease: the disease for which a count has been reported, in all capitals</li><li>event: an indicator representing the disease outcome reported, including "CASES" or "DEATHS"</li><li>number: the reported number of cases or deaths</li><li>from_date: the start date of the time interval for which a count was reported, as yyyy-mm-dd</li><li>to_date: the end date of the time interval for which a count was reported, as yyyy-mm-dd</li><li>url: the URL of the source document from which the count was obtained</li></ul><p></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.