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Survey of Pacific Northwest public land managers science and values project, 2023
This dataset records survey data about public land managers who work in Oregon and Washington (Forest Service, Bureau of Land Management, Fish and Wildlife Service, National Park Service, Oregon Department of Forestry, Washington Department of Natural Resources). Data was collected in 2023 via the online survey platform Qualtrics. Data collection is complete. The dataset includes measures of managers beliefs about 1) variable density thinning of mature growth forests, 2) salvage logging of burned areas, 3) translocation of plant species from hotter and drier seed zones to adapt to climate change. It includes how managers evaluate the usefulness of scientific evidence and the soundness of action prescriptions for each of the three management issues Respondents were randomly assigned to either receive long-term or short-term studies, and positive or negative results. The dataset includes measures of sense of belonging (how much managers believe they belong at their workplace) and measures of public support/public threat (how much they believe the public understands and supports the actions they take on the landscape). The dataset includes respondent agency.
WSC 2007 - 2012 Yahara Watershed surface water quality policies and practices created and implemented by public agencies
This dataset was created June 2012 - August 2013 to contribute to research under the Water Sustainability and Climate project. Interventions collected are those land-based policies and practices written and implemented by public agencies. Policies were implemented in Wisconsin's Yahara Watershed the period 2007-2012. They aim to improve surface water quality through nutrient (phosphorus and nitrogen) and sediment reduction. Interventions included in the mapping must have spatially-explicit, publicly available data through personal communication or website.
CARMEN immunopeptidomics publication associated dataset
<h1>CARMEN: CAnceR imMunopeptidogENomics</h1> <blockquote> <div>An immunopeptidomic dataset accompanying the publication "<a href="http://dx.doi.org/10.1101/2025.05.08.651510" target="_blank" rel="noopener">Expanding the definition of MHC Class I peptide binding promiscuity to support vaccine discovery across cancers with CARMEN</a>" containing peptides determined by mass-spectrometry associated with MHC Class I bindings from 72 publications (2323 samples).</div> </blockquote> <div> </div> <div> <p><strong>Authors:</strong> <a href="mailto:aleksander.palkowski@gmail.com" target="_blank" rel="noopener">Aleksander Palkowski</a>*, <a href="mailto:mwaleron@gmail.com" target="_blank" rel="noopener">Michal Waleron</a>*, <a href="mailto:emilia.daghir@gmail.com" target="_blank" rel="noopener">Emilia Daghir-Wojtkowiak</a>*, <a href="mailto:ashwinkallor@gmail.com" target="_blank" rel="noopener">Ashwin Adrian Kallor</a>*, <a href="mailto:javier.alfaro@proteogenomics.ca" target="_blank" rel="noopener">Javier Antonio Alfaro</a></p> <p>* <em>These authors contributed equally to this work</em></p> </div> <div> </div> <div>The entire dataset consist of four table files in the <a href="https://parquet.apache.org" target="_blank" rel="noopener">Apache Parquet</a> data file format:</div> <ul> <li>main</li> <li>mapped-protein-annotations-pogo</li> <li>mapped-protein-annotations-msfragger</li> <li>hla-sequences</li> </ul> <div> </div> <div><strong>Please refer to the README.md file for details.</strong></div> <div> </div>
City of Seattle, Seattle Public Utilities, Amphibian Egg Mass Counts 2002 - Current, Cedar River Municipal Watershed, King County, WA
This data package contains survey data beginning in 2002 for amphibian egg masses in five small kettle lakes (known as "14 Lakes") in the Cedar River Municipal Watershed, located in King County, Washington, USA. These surveys are conducted annually and are intended to be continued. The lakes range in size from 0.8 to 4.3 acres, have no perennial inlet or outlet, and were formed through glacial outwash deposits. The lakes are located at an elevation of 800 feet and are well suited for pond breeding amphibians because the lakes have no fish. Surveys were conducted annually, typically during the last week of March or first week of April, to coincide with amphibian breeding seasons. Surveyors walked, waded, or paddled the perimeter of each of the lakes during a survey, and tallied the number and type of egg masses that were encountered. Red legged frogs (Rana aurora) were of specific interest for the surveys, though egg masses of other species were noted during some survey years. The lakes represent the largest known breeding concentration of red legged frogs in the municipal watershed. The water depth of the lakes fluctuates year-to-year, which affected the feasibility of surveys. Lower water levels correspond to easier survey conditions: steep slopes and thick vegetation make surveying challenging when the water is high. Surveys were periodically cancelled during years where high water made surveying difficult or during staffing shortages. Counts of red legged frog egg masses across all lakes ranged between 24 and 1778 in a given year.
City of Seattle, Seattle Public Utilities, Riparian Permanent Sample Plots 2003-current, Cedar River Municipal Watershed, King County, WA
The City of Seattle’s Cedar River Municipal Watershed is managed to support and supply clean drinking water to the greater Seattle area. The watershed covers 91,000 acres, hosts a rich diversity of plants, animals, and habitats, and is owned by the City of Seattle. From 2003 to 2005, Seattle Public Utilities established 61 permanent sample plots (PSP) in riparian habitats of the Cedar River Municipal Watershed. 31 of these plots (plot #s 1-31) were established in 2003 upstream of Chester Morse Lake, the drinking water reservoir for the City of Seattle. 30 additional plots (plot #s 32-61) were established in 2005 downstream of Chester Morse Lake. In 2012, 6 of the 61 total plots (plot #s 4, 11, 12, 27, 28, 29) were resampled and the sampling methods were simplified. Each sampling year had different surveyors. The riparian permanent sample plots were limited to low gradient, moderately to unconfined reaches along the Cedar River and its tributaries because they typically show the most variability in riparian condition, stream-riparian interactions are greatest, and fish use is highest. Sites were randomly selected along these reaches, with two plots located at each site, one on each side of the stream. Sites were stratified into four stand types: deciduous dominated, mixed deciduous/conifer, conifer dominated in stem exclusion phase with little understory, and conifer dominated differentiated with well-developed understory, with at least five plots in each type. Each plot was measured for tree species and diameter, snag diameter and height, shrub species and cover, herb species and cover, sapling species and cover, percent canopy cover, and other species found in the plots but not previously recorded in the tree, shrub, and herb sampling. Selection of riparian plots for resampling in 2012 was designed to include plots in second and old growth forests and with medium and large stream sizes. Future resampling is expected to occur at an approximately ten-year interval. T
City of Seattle, Seattle Public Utilities, Marbled Murrelet Baseline Surveys 2005-2007, Cedar River Municipal Watershed, King County, WA
From 2005 to 2007, Seattle Public Utilities (SPU) hired consultants to use ornithological radar and protocol audio-visual (AV) surveys to establish baseline information on the distribution and abundance of Marbled Murrelets (Brachyramphus marmoratus) in the Cedar River Municipal Watershed (CRMW), Washington. Across the three years, radar surveys were conducted on 100 mornings at 18 sites, and AV surveys on 92 mornings at 12 sites. The study recorded murrelet targets via radar in all years, with 65 detections in 2005, 89 in 2006, and 25 in 2007. Mean daily landward radar counts ranged between 0 and 4 per morning, and did not differ significantly across years. Although overall radar counts were low, high day-to-day variability was observed (coefficients of variation from 130% to 173%). Monte Carlo simulations showed that with repeated surveys using the same methods, the monitoring program could detect an annual increase of 2–3% in Marbled Murrelet abundance over approximately 25–50 years. AV surveys confirmed murrelet occupancy at two sites: the Rex River in 2005 and the South Fork Cedar River in 2006. No murrelets were detected by AV in 2007, though radar data suggested low-level murrelet presence at several additional sub-basins. The findings indicate that Marbled Murrelets occur at low densities in the CRMW, likely limited by both high inland distance and relatively sparse old-growth forest structure suitable for nesting. The four radar stations established and resampled during the study provide an opportunity for long-term monitoring, offering sufficient power to detect changes in murrelet activity as ongoing forest restoration efforts in the CRMW progress.
Dataset and analyses for publication entitled: “Acclimation of the nitrogen cycle to changes in precipitation”
This dataset contains data and analysis code for the paper entitled “Acclimation of the nitrogen cycle to changes in precipitation" by Currier et al. As the frequency of precipitation extremes are expected to increase, especially in arid regions, we asked how prolonged shifts in water availability facilitate acclimation of the N cycle in a semiarid grassland. Using natural abundances of stable nitrogen isotopes for dominant plants and soils and rainfall manipulation experiments, we tested the hypothesis that N cycling will interact with water availability further amplifying the openness of the N cycle through time. For the dominant plant species, we found the relationship for N availability vs. ambient annual precipitation to be significantly positive, contrary to global spatial models. We also considered the temporal dynamics of our experiments, which imposed directional rainfall manipulations in duration ranging from 5 to 14 years. The slopes of these relationships decreased (became less positive) with more time since the onset of the directional precipitation extremes. These data and metadata supplement long-term foliar and soil isotope data from the Jornada LTER (Dataset ID: knb-lter-jrn.210586001) with a large spatial dataset from NEON data package DP1.10026.001 and Craine et al. 2018 (https://doi.org/10.5061/dryad.v2k2607).
Incentive mechanisms and the provision of public goods: Field experiment data for testing alternative economic frameworks to supply ecosystem restoration on Virginia's Eastern Shore: 2008 data.
This dataset consists of participant responses in one of two economic experiments conducted on Virginia's Eastern Shore during 2008 and 2009 by Elizabeth C. Smith used to gauge resident preferences and willingness-to-pay for ecosystem restoration activities. This dataset was designed to be used to examine a practical method to implement an individualized pricing approach to public good provision, grounded in Lindahl's marginal benefit theory. The study's focus was on ecosystem valuation and market approaches that have potential to provide public goods, examining the potential to generate revenues for public goods from consumers. While willingness-to-pay measurement techniques have been used to assess preferences for many environmental goods, this research goes a step further to explore real money auctions that generate revenues sufficient to pay for restoration activities. The data from the field experiments conducted in coastal Virginia were used, along with laboratory experiment data, to evaluate the performance of auction mechanisms in generating revenues relative to potential (Hicksian) willingness to pay for marginal increments in public goods. The field execution of this experiment involved residents of Virginia's Eastern Shore and local public goods. This application involved half-acre increments of ecosystem restoration for sea grass habitat in coastal lagoons, plantings for migratory bird habitat, and, in some auctions, clam-based increments of water quality services, defined as delaying the harvest of clams for six months beyond normal harvest by an existing aquaculture firm. To perform these tasks, participants were provided a budget, between $90 and $150. The auctioneer described for participants the ecosystem services that may result from additional ecosystem restoration associated with each activity. The actual levels of ecosystem restoration provided were based on aggregate offers reaching a pre-determined (but unknown to the participants) provision p
Incentive mechanisms and the provision of public goods: Field experiment data for testing alternative economic frameworks to supply ecosystem restoration on Virginia's Eastern Shore: 2009 data.
This dataset consists of participant responses in one of two economic experiments conducted on Virginia's Eastern Shore during 2008 and 2009 by Elizabeth C. Smith used to gauge resident preferences and willingness-to-pay for ecosystem restoration activities. This dataset was designed to be used to examine a practical method to implement an individualized pricing approach to public good provision, grounded in Lindahl's marginal benefit theory. The study's focus was on ecosystem valuation and market approaches that have potential to provide public goods, examining the potential to generate revenues for public goods from consumers. While willingness-to-pay measurement techniques have been used to assess preferences for many environmental goods, this research goes a step further to explore real money auctions that generate revenues sufficient to pay for restoration activities. The data from the field experiments conducted in coastal Virginia were used, along with laboratory experiment data, to evaluate the performance of auction mechanisms in generating revenues relative to potential (Hicksian) willingness to pay for marginal increments in public goods. The field execution of this experiment involved residents of Virginia's Eastern Shore and local public goods. This application involved half-acre increments of ecosystem restoration for sea grass habitat in coastal lagoons, plantings for migratory bird habitat, and, in some auctions, clam-based increments of water quality services, defined as delaying the harvest of clams for six months beyond normal harvest by an existing aquaculture firm. To perform these tasks, participants were provided a budget, between $90 and $150. The auctioneer described for participants the ecosystem services that may result from additional ecosystem restoration associated with each activity. The actual levels of ecosystem restoration provided were based on aggregate offers reaching a pre-determined (but unknown to the participants) provision p
Supplementary Data to journal publication on 'The Foundations of the Patagonian Icefields'
<p>Partitioning and comparison of ice discharge estimates from the the Patagonian Icefields comprising associated uncertainties. For further details please refer to the notes in the individual files and/or consult the associated publication entitled 'The Foundations of the Patagonian Icefields' published in Communications Earth & Environment.</p>
Data associated with the following publication: Developing the Playground Play Value and Usability Audit Tool (PVUA): An Evaluation of Content Validity via an Expert Panel
<p>This data set contains the supporting data associated with the following publication:</p> <p>Morgenthaler, T., Loebach, J., Lynch, H., Pentland, D., Kottorp, A., & Schulze, C. (in press). Developing the Playground Play Value and Usability Audit Tool (PVUA): An Evaluation of Content Validity via an Expert Panel. Children, Youth and Environments. [DOI was not yet available when the data set was published]</p> <p>The data set includes the following files:</p> <ul> <li>read me file [contains all relevant information to understand and reuse this data set] </li> <li>13 additional files [for description, see read me file]</li> </ul> <p>For more information, please contact the lead researcher, Thomas Morgenthaler (tom.morgenthaler@gmail.com or 121101888@umail.ucc.ie)</p> <p> </p>
GHG Dataset for the frontiers publication "Soil Nitrous Oxide Emission and Methane Exchange from Diversified Cropping Systems in Pannonian Region"
<p>GHG Dataset used in the Frontiers Publication "Soil Nitrous Oxide Emission and Methane Exchange from Diversified Cropping Systems in Pannonian Region". Additionally including CO2 besides N2O and CH4. Includes 3 cropping seasons.</p> <p>The data is also available online on the GHG flux visualisation and calculation tool "gasflxvis": https://sae-interactive-data.ethz.ch/gasflxvis/</p> <p>Further details on the calulation are provided both on gasflxvis and the Frontiers publication. Calculation procedure according the following PLOS ONE publication: http://dx.doi.org/10.1371/journal.pone.0200876</p>
A Benchmark dataset on Semantic Change in Scholarly Publications on Disability
<p>This is a benchmark dataset for semantic shift detection in disability-related corpora, including collected title and abstract text from PubMed and ArXiv, annotation sets based on domain experts and LLMs, and extracted KGs (Wikidata entity claims). The corpus from PubMed covers the period from the 1900s to 2023, while the corpus from ArXiv covers the period from the 1990s to 2023. The corpus was filtered based on 16 disability-related target words. In the annotation sets, '1' indicates that a semantic shift occurred for a target word, while '0' indicates the opposite. In particular, the LLM-based annotation sets include their generated text, and we used the Llama2 and GPT-4 models. '7b' refers to the parameter size of the Llama2 model. Graph_data.zip contains Wikidata entity claims.</p>
Supplementary dataset to publication: Complete Genome Sequence of Ovine Mycobacterium avium subsp. paratuberculosis Strain JIII-386 (MAP-S/type III) and Its Comparison to MAP-S/type I, MAP-C, and M. avium Complex Genomes.
<p>This is the modified supplemented material to the publication “Complete genome sequence of ovine Mycobacterium avium subsp. paratuberculosis strain JIII-386 (MAP-S/type III) and its comparison to MAP-S/type I, MAP-C, and M. avium complex genomes”.</p> <p>The complete circular genome of Mycobacterium avium subsp. paratuberculosis (MAP) strain JIII-386 from Germany, closed by Nanopore technology in this study, was presented and compared with the draft genome of JIII-386, previously published in [doi:10.1093/gbe/ew154], the closed genome of the MAP-S/type I strain Telford, the MAP-S/type III draft genome of strain S397, twelve closed MAP-C (type II) strains and eight closed Mycobacterium avium (M. a.) strains of subsp. hominissuis (MAH) and subsp. avium (MAA). Structural comparisons clearly revealed the mosaic nature of MAP genomes, the differences between MAP subtypes I, II and III, and the higher diversity of MAP-S compared to MAP-C genomes. </p> <p>The material provides a wealth of detailed results from these analyses and comparisons. These include a list of identified ncRNA and Riboswitches, as well as additional genes in finished JIII-386, the gene content of identified prophage regions, copy number of identified transposable elements and a list of selected virulence-associated genes in the different MAP-type (I - III) strains. The genomic islands identified and included genes along with their predicted functions were presented for six MAP genomes (belonging to MAP-S/type I and III, and MAP-C), one MAH genome and one MAA genome. One table shows the corresponding genomic islands in the genomes of JIII-386, Telford and three MAP-C genomes. Furthermore, homologous genes of known MAP-S specific Large Sequence Polymorphisms regions (LSP<sup>S</sup> = LSP-S) were recorded in different MAP-S type strains, one MAH and one MAA strain, as well as genes of deletions #1 (LSP<sup>A</sup>-20), #2, and s-delta-1, previously described as MAP-S-specific deletions, their presence or absence in 3 MAP-S, 12 MAP-C, 4 MAH, and 4 MAA strains were listed. Different presence or absence of genes, but also identified frameshifts or disruptions of various virulence-associated genes could lead to the different MAP-type specific phenotypic characteristics. Comprehensive core and pan genome analyses (results listed in six tables) revealed unique genes and genes likely to have been acquired by horizontal gene transfer in different MAP types and subtypes, but also emphasized the highly conserved and close relationship, and the complex evolution of M. a. strains.</p> <p> </p>
Code and data set for data analysis published as manuscript "Bacttle: a microbiology educational board game for lay public and schools"
<p>Code that processed raw data and plots the figures of the manuscript "Bacttle: a microbiology educational board game for lay public and schools"</p> <p>Below is a table with the original survey questions. The ID corresponds to the column displayed on the data set. When letters are followed by a number (1 or 2), it means that the question was answered before playing the game (1) and after playing the game (2).</p> <table> <tbody> <tr> <td> <p><em>ID<sup>1</sup></em></p> </td> <td> <p><em>Question text</em></p> </td> <td> <p><em>Possible answers<sup>2</sup></em></p> </td> </tr> <tr> <td> <p><em>A</em></p> </td> <td> <p>How old are you?</p> </td> <td> <p> </p> </td> </tr> <tr> <td> <p><em>B</em></p> </td> <td> <p>Do you know what a bacterium is?</p> </td> <td> <p>y/n</p> </td> </tr> <tr> <td> <p><em>C</em></p> </td> <td> <p>Do you know what a bacterial capsule is?</p> </td> <td> <p>y/n</p> </td> </tr> <tr> <td> <p><em>D</em></p> </td> <td> <p>Do bacteria have tools to harm each other?</p> </td> <td> <p>y/n/idk</p> </td> </tr> <tr> <td> <p><em>E</em></p> </td> <td> <p>Do bacteria reproduce at the same pace?</p> </td> <td> <p>y/n/idk</p> </td> </tr> <tr> <td> <p><em>F</em></p> </td> <td> <p>What is sporulation?</p> </td> <td> <p>A resistant state that some bacteria can achieve under unfavorable conditions.</p> </td> </tr> <tr> <td> <p>The release of toxins by bacteria.</p> </td> </tr> <tr> <td> <p>idk</p> </td> </tr> <tr> <td> <p><em>G</em></p> </td> <td> <p>What are flagella used for?</p> </td> <td> <p>Sticking to surfaces.</p> </td> </tr> <tr> <td> <p>Motility in liquid environments.</p> </td> </tr> <tr> <td> <p>idk</p> </td> </tr> <tr> <td> <p><em>H</em></p> </td> <td> <p>What does it mean to be lithotrophic?</p> </td> <td> <p>A bacterium can get energy from minerals.</p> </td> </tr> <tr> <td> <p>A bacterium can get energy from the sunlight.</p> </td> </tr> <tr> <td> <p>idk</p> </td> </tr> <tr> <td> <p><em>I</em></p> </td> <td> <p>Can bacteria be infected by viruses?</p> </td> <td> <p>y/n/idk</p> </td> </tr> <tr> <td> <p><em>J</em></p> </td> <td> <p>Are all bacteria harmful for humans?</p> </td> <td> <p>y/n/idk</p> </td> </tr> <tr> <td> <p><em>K</em></p> </td> <td> <p>How many bacteria are in a coffee spoon of yoghurt?</p> </td> <td> <p>Millions</p> </td> </tr> <tr> <td> <p>Hundreds</p> </td> </tr> <tr> <td> <p>idk</p> </td> </tr> <tr> <td> <p><em>L</em></p> </td> <td> <p>How easy did you find the gameplay?</p> </td> <td> <p>VE/E/A/D/VD</p> </td> </tr> <tr> <td> <p><em>M</em></p> </td> <td> <p>Did you find the card content easy to understand?</p> </td> <td> <p>VE/E/A/D/VD</p> </td> </tr> <tr> <td> <p><em>N</em></p> </td> <td> <p>Did you like the setup of the game?</p> </td> <td> <p>y/n/idk</p> </td> </tr> <tr> <td> <p><em>O</em></p> </td> <td> <p>Would you like to play this game again?</p> </td> <td> <p>y/n/idk</p> </td> </tr> <tr> <td> <p><em>P</em></p> </td> <td> <p>What can we improve?</p> </td> <td> <p> </p> </td> </tr> </tbody> </table> <p>1) Question A categorizes the player’s age; B and C assess the initial level of knowledge in microbiology (none -both questions are answered negatively-, basic -player knows what a bacterium is but not a bacterial capsule-, or advanced -both answers are positive-); questions D-I score knowledge acquisition; J and K are control questions; L-O evaluate the appreciation of the game; and P is an optional free text-entry answer for additional feedback. <br>2) y= yes, n=no, idk=I don’t know, VE=very easy, E=easy, A=adequate, D=difficult, VD=very difficult.</p>
Four lipidomics datasets (mouse liver, mouse pancreatic islets, mouse soleus muscle and mouse visceral adipose tissue), generated for the publication Mehl et al., "A multiorgan map of metabolic, signalling, and inflammatory pathways that coordinately control fasting glycemia in mice"
<p>Mehl, Thorens et al present a multiomics study aimiing to<span> identify the pathways that are coordinately regulated in pancreatic </span><span>b</span><span>-cells, muscle, liver, and fat to control fasting glycemia we fed C57Bl/6, DBA/2 and Balb/c mice a regular chow or a high fat diet for 3, 10 and 30 days. We measured fasted glycemia, insulinemia and whole-body insulin resistance. Transcriptomic and lipidomic analysis were used in a data fusion approach to identify organ-specific pathways related to the glycemic levels across all conditions investigated. In pancreatic islets, constant insulinemia despite higher glycemic levels were associated with reduced expression of mRNAs encoding hormone and neurotransmitter receptors as well as OXPHOS, cadherins, integrins and gap junction proteins. Higher glycemia and whole-body insulin resistance were associated, in muscle, with reduced expression of mRNAs encoding insulin signaling proteins and enzymes of the glycolysis, Krebs’ cycle and OXPHOS pathways, as well as endocytosis and exocytosis proteins; in hepatocytes, with lower expression of mRNAs of the insulin signaling pathway, of branched chain amino acid catabolism and of OXPHOS; in adipose tissue, with increased expression of mRNAs of innate immunity and lipid catabolism. These data provide a map of the pathways that are coordinately recruited in the investigated tissues to control fasting glycemia and a resource for further studies of interorgan communication in glucose homeostasis. </span></p>
City of Seattle, Seattle Public Utilities, Knotweed Control 2010-current, Cedar River Municipal Watershed, King County, WA
The City of Seattle’s Cedar River Municipal Watershed is managed to support and supply clean drinking water to the greater Seattle area. The watershed covers 91,000 acres, hosts a rich diversity of plants, animals, and habitats, and is owned by the City of Seattle. In 1999, the noxious weed knotweed was detected in the watershed and control was limited to manual and mechanical methods due to an herbicide moratorium intended to prevent broadcast spraying of roadside vegetation. These manual control methods were largely unsuccessful and impractical for controlling acres of knotweed growing in remote locations of the watershed. In 2010, Seattle Public Utilities passed the first ordinance through Seattle City Council to approve the limited use of imazapyr to control knotweed in the watershed for three years. Successive knotweed ordinances have been passed, allowing for herbicide control of knotweed in the watershed from 2010-current. The reports included in this package are provided to Seattle City Council annually as a requirement of the ordinance. The data table provides the control history since the passage of the first ordinance and includes information about patch size and amount of imazapyr used. This data package will be updated annually with ongoing control efforts.
City of Seattle, Seattle Public Utilities, Goshawk Nesting 1992 - Current, Cedar River Municipal Watershed and South Fork Tolt River Municipal Watershed, King County, WA
This data package contains American goshawk (Astur atricapillus) (formally known as Northern Goshawk [Accipiter gentilis]) survey data and nest location records, beginning in 1992 to present day, from the Cedar River Municipal Watershed and the South Fork Tolt River Municipal Watershed in King County, Washington, USA. Goshawks are classified as a sensitive species and are included in the Habitat Conservation Plan for the Cedar River Municipal Watershed. Surveys have been conducted periodically at historical nesting territories, depending on staff capacity and the potential for disturbances from planned infrastructure projects or forest thinning operations. These surveys were not based on a statistically valid random sampling design and did not always strictly follow established protocols. Survey methods primarily included broadcast surveys using a portable cassette player and megaphone but also involved active searches for nests or signs, as well as opportunistic detections during other forest management activities. At some nest sites, plot-level forest structure and characteristics were also documented. Nest productivity monitoring was generally not conducted, as the primary objective of the surveys was to minimize disturbance and prevent inadvertent destruction of nests.
City of Seattle, Seattle Public Utilities, Restoration Thinning Trial, 2005 - 2017, Cedar River Municipal Watershed, King County, WA
The Restoration Thinning (RT) Program in the Cedar River Municipal Watershed (CRMW) was one of three forest restoration programs (the others being Ecological Thinning and Planting) defined and funded through the Cedar River Watershed Habitat Conservation Plan (HCP) that was signed and initiated in April of 2000. Restoration thinning and ecological thinning projects were combined into the 'Upland Forest Thinning' project and are ongoing today to meet objectives outlined in the Habitat Conservation Plan and Forest Managment Plan. The primary goal of the RT program, which is analogous to pre-commercial thinning, was to actively thin dense young second-growth forest stands (generally less than 30 years old) to facilitate ecological development towards old-growth forest habitat conditions. Objectives of RT include: Reduce competition among trees. Stimulate tree growth. Increase light penetration under the top tree canopy. Increase tree and understory plant species diversity. Accelerate forest development beyond the competitive exclusion stage towards a more biologically diverse stage. Extend the forest development stand initiation stage such that diverse species become established and diverse stand structures develop. Provide multiple development pathways for variable forest stand structures. Reduce long-term fire hazard. Increase resilience to catastrophic windthrow, insect, or disease outbreak. Increase habitat connectivity and structural variability of riparian areas. This data package describes a forest restoration trial in young conifer forests of the western central Cascade Range in Washington State, USA. Young second-growth forests often regenerate as very dense, homogeneous stands following harvesting. These forests have low species diversity and trees often experience strong competition for resources. To increase tree vigor and growth and stimulate development of diverse understory, shrub species stands are thinned with the long-term goal to restore diverse func
City of Seattle, Seattle Public Utilities, Riparian Restoration 2001-current, Cedar River Municipal Watershed, King County, WA
The City of Seattle’s Cedar River Municipal Watershed is managed to support and supply clean drinking water to the greater Seattle area. The watershed covers 91,000 acres, hosts a rich diversity of plants, animals, and habitats, and is owned by the City of Seattle. In 2001 the City of Seattle prepared a multi-species Habitat Conservation Plan (HCP) to comply with the federal Endangered Species Act and to address a variety of related natural resource issues in the Cedar River Watershed. As defined in the HCP, the riparian zone is the area adjacent to surface waters and areas of high groundwater levels where the terrestrial system both influences, and is influenced by, the aquatic system. The City’s strategies for the riparian ecosystem are designed to protect the region’s supply of high-quality drinking water, to preserve and enhance stream and riparian ecosystems within the municipal watershed, and to restore and rehabilitate stream and riparian functions. This package includes as-builts from riparian restoration projects, shapefiles of planting locations, and their associated monitoring data. The data is a result of monitoring that occurred after installation of riparian restoration projects in the Cedar River Municipal Watershed. The monitoring data includes plant survivorship but varies by project in what information was collected. The monitoring data was collected by multiple people over many years. Some projects were monitored for several years after project installation and some projects were monitored only once. Some projects included experimental plantings that were assigned a variety of treatments to test the efficacy of different planting strategies. In this instance, the monitoring data can be used to identify the success of the various strategies. Monitoring tabular data will be updated as more restoration projects are installed, and as previously installed projects receive continued monitoring.
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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.