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Effects of Acorn Production on White-Footed Mouse Populations at Harvard Forest 1997-1999
Recently several authors have documented fluctuations in the abundance of white-footed mice (Peromyscus leucopus noveboracensis) with fluctuations in acorn production (Elkinton et al. 1996, Ostfeld et al. 1996, Wolff 1996, Jones et al. 1998). Acorns are the major food source of white-footed mice during winter and are extensively cached. They are also food for many other species as well; over 100 species of birds and mammals feed on acorns (Van Dersal 1940). A large mast crop in fall usually correlates with a large mouse population the following summer, whereas a poor crop correlates with low population numbers. One experimental study supplementing acorns on forest plots demonstrated a concomitant increase in white-footed mice populations (Jones et al. 1998). It has been hypothesized that a large mast crop increases overwinter survival and may allow continued reproduction during the winter months, which results in a larger population the following year. We have four objectives in monitoring acorn abundance at Harvard Forest: 1) test for correlation of estimates of acorn production with estimates of overwinter survival probabilities and abundance of white-footed mice using mark-recapture statistical models (HF054), 2) document annual variation in acorn abundance and quality, which compliments a program at Harvard Forest documenting changes in woody plant phenology with climatic variation (HF003), 3) test hypotheses concerning the correlation of acorn production with environmental factors such as temperature, rainfall, and weevil infestation, and 4) provide data for inter-site comparisons, such as to test for synchrony in production at various scales across the landscape. We estimate acorn production with timed visual surveys following methods adapted from Koenig et al. (1994). Individual tagged trees on two small mammal trapping plots are surveyed each year by two observers. Detailed methods are described in the metadata.
White Pine Needle Decline in Walden Woods and Weston MA 2017-2018
White Pine Needle Decline (WPND) is a suite of four fungal pathogens that attack third, second and in extreme cases first year needles of eastern white pine (Pinus strobus). Premature needle shedding reduces photosynthetic activity and in turn reduces growth rates and overall health of the eastern white pine, an ecologically and economically valuable species in the Northeast United States. Our long-term forest dynamics plots in Weston and Walden Woods are ideal for monitoring these pathogens’ effects on overstory and understory pine. The unique aspect of our study sites is the dense population of understory pine. Many of our plots are typical old-field white pine stands and are densely stocked from lack of cutting. Densely stocked stands have been shown to be more affected by WPND than more open stands (McIntire, 2017).
Density Anomalies in White Pine at Harvard Forest 2019
The density of wood is a primary determinant of the amount of carbon sequestered in forests. For boreal and Mediterranean ecosystems, anomalies from the typical intra-annual density increase in radial growth of conifers are predominantly related to drought. We took 41 wood samples at breast height, ten additional samples near branches, and seven samples from the top of 41 white pines to determine the spatial distribution of density anomalies throughout the stem. We measured the ring width, density anomaly presence, position within a ring, and arc of density anomalies at multiple heights. Even in a mesic forest density anomalies in white pine are predominantly occurring during drier growing seasons. Moreover, we examined the spatial extent of density anomalies within the stems of white pines and discovered density anomalies are more likely to occur near branches, at the top of the tree, and in wider rings. Furthermore, the position of the density anomalies within the rings was remarkably consistent with the anomalies occurring roughly 80% into the fully formed ring at all heights for high-frequency years only as well as all years Density anomalies seem to be triggered by exogenous factors but their distribution within the stem varies along endogenous gradients, thus better understanding these systematic anomalies can help us to understand how wood formation has reacted and will respond to the environment and changes therein.
White Pine Girdling and Compression Experiment at Harvard Forest 2017-2019
Wood formation is a crucial process for carbon sequestration on land, yet how variations in phloem-transported carbon affect wood formation, respiration and nonstructural carbon pools remains poorly understood. To better understand the role of carbon supply on allocation to wood formation, we constrained phloem transport using girdling and compression around the stem of 40 mature white pines to monitor the effects of contrasting carbon supply (enriched above and reduced below the manipulations) on local wood formation and respiration, as well as on nonstructural carbon pools in needles, stems, and roots. This data set contains all data measured during the experiment. This includes wood anatomy, xylogenesis, stem respiration, nonstructural carbon measurements in coarse roots, stems and needles, as well as pre-dawn water potential measurements and pressure measurements from underneath the phloem compression collars. Furthermore, we provide allometric measurements for all trees. The code to process these data and reproduce our results is available in hf348-14-density-anomaly-analysis-code.zip. For more details pertaining to the methods see Rademacher et al. (2021).
Impacts of Phloem Chilling and Compression on Mature White Pine at Harvard Forest 2018
Wood formation is a crucial process for carbon sequestration on land, yet how variations in phloem-transported carbon and temperature affect wood formation, respiration and nonstructural carbon pools remains poorly understood. To better understand the role of carbon supply on allocation to wood formation, we constrained phloem transport using compression and chilling around the stem of 15 mature white pines to monitor the effects of contrasting carbon supply (enriched above and reduced below the manipulations) on local wood formation and respiration, as well as on nonstructural carbon pools in stems and roots. This data set contains all data measured during the experiment. This includes wood anatomical, xylogenetic, dendrochronological, stem CO2 efflux, and nonstructural carbon measurements in coarse roots and stems, as well as pre-dawn water potential measurements of needles and branches. Furthermore, we provide basic allometric measurements for all trees. The code to process these data and reproduce our results is available at https://github.com/TTRademacher/Exp2018Analysis. For more details pertaining to the methods see Rademacher et al. (2021) and contact the investigator.
White Pine Blister Rust (WPBR) Plot Data from the Western United States
As one of North America’s most damaging tree diseases, white pine blister rust (WPBR) is expected to continue to affect high-elevation five-needle (High-5) pine species in the near future. In order to better understand and estimate the risk it poses to white pines, data was compiled from independent studies across the Western U.S. from 1983-2025. This WPBR disease occurrence data includes nearly 6700 points, which were classified into two epidemic types: established or invading, based on the disease intensity value and the amount of time the disease had been present in the area.
Northern red oak regeneration in burned and unburned stands in the White Mountain National Forest, New Hampshire, USA, 2023-2024
This project aimed to determine whether prescribed burning of managed forest stands improves the regeneration of Quercus rubra near its northern range limit in New Hampshire. We measured oak seedling density and growth rates in three pairs of managed stands in which one had received a prescribed burn since 2017. We also measured the density of competing seedlings and shrubs, leaf area index above seedling height, soil nutrients, mycorrhizal colonization, foliar carbon/nitrogen ratio, and stable isotopes of nitrogen and carbon. We found greater oak seedling density and faster oak seedling growth rates in burned stands relative to unburned stands. A subset of these measurements were also collected in additional burned and unburned study stands in the region. A companion mesocosm experiment showed faster growth in oak seedlings grown in soil from burned vs. unburned stands. Together these studies show that the benefits of fire to oak regeneration are mediated both via greater light availability as well as effects mediated via soil.
Diurnal Patterns of Cavitation in Red Maple, Paper Birch and White Ash at Harvard Forest 2011-2012
Previous work at Harvard Forest has suggested that woody plants cavitate and re-dissolve embolisms in xylem on a daily basis. Here we investigated the common assumption that severing stems and petioles under water preserves the hydraulic continuity in the xylem conduits opened by the cut when the xylem is under tension. In red maple and white ash, higher PLC in the afternoon occurred when the measurement segment was excised under water at native xylem tensions, but not when xylem tensions were relaxed prior to sample excision. Bench drying vulnerability curves in which measurement samples were excised at native versus relaxed tensions showed a dramatic effect of cutting under tension in red maple, a moderate effect in sugar maple, and no effect in paper birch. These results suggest that sampling methods can generate PLC patterns indicative of repair under tension by inducing a degree of embolism that is itself a function of xylem tensions at the moment of sample excision.
PsPM-HRM1-2: SCR and ECG measurements in response to white noise sounds and an auditory oddball task
<p>This dataset includes skin conductance response (SCR) and electrocardiogram (ECG) for each of 61 healthy unmedicated participants (28 males, 32 females, 1 unassigned, aged 25.8 +/- 4.6 years) in response to 20 broadband white noise sounds (HRM1) or 10 oddball tones in a oddball task (HRM2). Some participants did not did not complete HRM1 or HRM2 or were excluded from analysis such that there are 56 recordings for HRM1 and 58 recordings for HRM2. White noise sounds in HRM1 were 1 s long with 10 ms on- and offset ramp and presented at ~85 dB. Oddball and standard sounds in HRM2 were 50 ms long, with 10 ms on- and offset ramp, and presented at ~75 dB. Sound frequency was 440 Hz or 460 Hz, randomly balanced per participant to oddballs and standards. SOA between white noise sounds and oddball tones was selected randomly on each trial from 30 s, 35 s or 40 s. All stimuli were presented in one block. There is a marker for each sound onset (including standard tones) in the windaq files.</p>
Ecosystem metabolism and associated environmental data for a forested, meadow and reforested reach of White Clay Creek, Chester Co., Pennsylvania; 1971-1975 and 1997-2010
Ecosystem metabolism data for a 3rd-order Piedmont stream were collected during two periods: P1- April 1971 – Dec 1975, and P2- May 1997 – January 2010. Measures were made in a meadow and a forested reach during each period and in a reforested (formerly meadow) reach during the latter years of P2. During P1, measures were made by transferring streambed substrata to chambers in water jackets located on the streambank and measuring dissolved oxygen changes over diel periods. During P2, open system measures of dissolved O2 change were made for several days in warm and cold seasons, with reaeration determined from a propane injection experiment. Metabolism estimates were determined from diel curves of dissolved O2 change. Photosynthetically active radiation (PAR) and chlorophyll were measured concurrent with many measurements in P1 and all measures during P2, and temperature with all measures. Water chemistry parameters (NH4-N, NO3-N, PO4-P, SiO2, Cl, SO4, total alkalinity, pH) associated with each run are included in the data set, as are days since storm of various thresholds. Field procedures, analytical methods and data analyses are detailed in Bott, T.L. & J. D. Newbold, 2023. A multi-year analysis of factors affecting ecosystem metabolism in forested and meadow reaches of a Piedmont Stream. Hydrobiologia
USFWS Adult White Sturgeon Monitoring, San Joaquin River, 2012-2025
Overview The Central Valley Project Improvement Act (CVPIA) funds habitat improvement work and associated monitoring in the Central Valley of California to increase salmonid populations in furtherance of meeting CVPIA fish doubling goals. This data package contains three datasets for adult White Sturgeon (Acipenser transmontanus) monitoring in the San Joaquin River (SJR) conducted by the US Fish and Wildlife Service, Lodi Fish and Wildlife Office. The primary purpose for this sampling was to capture White Sturgeon and implant acoustic telemetry tags for a tracking project. Therefore, the data are useful for determining when and where White Sturgeon were captured, but they should not be used to determine actual distribution or abundance. SJR_Adult_WST_Set Data This dataset contains data from a sampling program using various methods to catch adult White Sturgeon in the San Joaquin River. Sets were made at targeted locations primarily from March-May in 2012-2024 (other dates were occasionally sampled). SJR_Adult_WST_Catch Data This dataset contains data for individual fish caught via gillnets, trammel nets, setlines, or angling in the San Joaquin River. Species and fork length were recorded for all fish. For White Sturgeon, girth, maturation, tag, and surgery information are provided. SJR_Fish_Taxonomy Data This dataset contains data for fish codes used in the Catch datafile. For each species that was captured, the Species codes are listed with the corresponding Interagency Ecological Program code, common name, taxonomy (Phylum, Class, Order, Family, Genus, and Species), and whether or not the species is native to the region.
Stream Storm Sample Data from White Clay Creek (WCC) Watershed in 2021
These data were collected to explore Nitrogen update dynamics in the water column of small streams during storm events. Data was collected using a combination of passive sampling and grab sampling of suspended sediments from the stream channel. Analysis of samples include: dissolved and total chemistry, suspended sediment load, biological and microbiological characteristics, and Nitrogen uptake rates.
White Cedar Ring Width Data from Michigan Upper Peninsula, 1869-2022
This project used tree cores to reconstruct growth over time and correlate that with climate variables including maximum monthly temperature, monthly precipitation, and vapor pressure deficit.
Bird Abundances at the Hubbard Brook Experimental Forest (1969-present) and on three replicate plots (1986-2000) in the White Mountain National Forest
Bird abundances have been determined from timed censuses, territory maps and nest locations at the Hubbard Brook Experimental Forest from 1969 to the present. This data set includes counts of the number of adult birds (males and females) per 10 ha at HBEF (1969 - present) and on three additional plots within the White Mountain National Forest (1986 - 2000). These data were gathered as part of the Hubbard Brook Ecosystem Study (HBES). The HBES is a collaborative effort at the Hubbard Brook Experimental Forest, which is operated and maintained by the USDA Forest Service, Northern Research Station.
Carbon exchange responses of rehydrated and incubated biological soil crust samples from White Sands National Park in 2020-2022
This dataset contains photosynthetic light response data from biological soil crusts collected from a gypsum sand sheet at White Sands National Park, NM, USA in three different seasons. This study aims to 1) assess the carbon fixation capacity of biocrust types; 2) assess biocrust carbon fixation response under varying incubation times; 3) and understand variability in carbon fixation response in different seasons. Sample collection occurred in July 2020 (summer), September 2021 (fall), and March 2022 (winter). The biocrust types of interest were light cyanobacterial, dark cyanobacterial, Peltula lichen, Clavascidium lichen, and moss crusts. Samples were collected with the intention of taking carbon fixation measurements after different incubation periods (30 min, 2 hr, 6 hr, 12hr, or 24 hr in 2020, and 30 min, 2 hr, 6 hr, 12hr, 24 hr, or 36 hr in 2021 and 2022). For each condition (biocrust type and incubation time) there were five replicates in 2020 (total n=125) and ten replicates in 2021 and 2022 (total n=300). After collection, the intact samples were re-wetted and subjected to their respective incubation period and measured for photosynthetic response. The resulting light response curves and photosynthetic information was be used for comparing biocrust type, incubation time response differences, and seasonal variation to understand variability of biocrust carbon flux response at a single site. This data set includes the light response curve values and photosynthetic data calculated from these curves and raw LICOR output files compiled into 3 spreadsheet files. The included 2020 data is also associated with the White Sands National Park data from Jornada Study 549. This dataset accompanies the in-press article by Hoellrich et al. (2023) cited below, and the study is now complete. Hoellrich, Mikaela R., Darren K. James, David Bustos, Anthony Darrouzet-Nardi, Louis S. Santiago, and Nicole Pietrasiak. "Biocrust carbon exchange varies with crust type and time on Ch
Multi-faceted analyses of Poland's Bronze and Early Iron Age hoards: Fig.1. Location of hoards mentioned in the text: white dots represent locations of hoards examined in the Biography of Hoards project; black dots represent locations of hoards examined in other multi-faceted projects
<p>The set contains a figure, with data, on the location of the hoards included (described in the related paper).<br><br>The paper and data were prepared as part of a project funded by the National Science Centre, Poland: <em>A Biography of Late Bronze and Early Iron Ages Hoards. A Multi-Faceted Analysis of Metal Objects Related to Monumental Constructions in Poland</em> (UMO-2021/41/B/HS3/00038)</p>
Colebrook-White friction factor data
<p>The Colebrook-White equation is a fundamental formula in fluid mechanics, widely used to determine the friction factor in turbulent flow through pipes. It is crucial for calculating head losses in pipelines and for the design and optimization of hydraulic systems. In this dataset, the friction factor (f) is obtained via numerical solution using the Newton-Raphson method, with a truncation accuracy of 1e-6.</p> <p>The first and second columns of the provided dataset pertain to the Reynolds number (Re) and relative roughness (ε/D) variables, respectively. The data were generated across specified ranges [4500-2250000] with constant step of 4500 for Re and [0.00005, 0.0005, 0.005, 0.05, and 0.5] for ε/D. The third column presents of the f values calculated using the Colebrook-White equation, which is given as:</p> <div> </div> <div>1/(\sqrt(f)) = -2*log((\epsilon/D)/3.7 + 2.51/(Re*\sqrt(f)))</div> <div> </div> <div> </div> <div>This dataset has multiple applications: it facilitates evaluating empirical formulas approximating the Colebrook-White equation and provides a valuable foundation for developing machine learning models to accurately predict the friction factor. Beyond aiding hydraulic system design, this dataset is a useful resource for researchers and engineers aiming to optimize pipeline flow, model turbulent pipe flow behavior, and advance computational methods in fluid dynamics.</div>
Data and code for the manuscript "From white to green: Snow cover loss and increased vegetation productivity in the European Alps"
<p>Data and code used for the manuscript "From white to green: Snow cover loss and increased vegetation productivity in the European Alps" by Rumpf et al., submitted December 2021 to Science</p> <p>See file ReadMe.txt for a description of the content and the original publication for further explanations.</p> <p>You are free to use these data and code for scientific purposes but are obliged to cite the above-mentioned publication.<br> For further questions, contact sabine.rumpf@unibas.ch</p>
Neurodevelopmental Patterns of Early Postnatal White Matter Maturation Represent Distinct Underlying Microstructure and Histology
<p>This dataset includes:</p> <ol> <li>T2w Template from the dHCP datasets.</li> <li>4D weekly average maps from the dHCP study: i) average T2w; ii) average T2w/T1w signal ratio; iii) average neurite density index [from NODDI]; iv) average free water map [from NODDI].</li> <li>NMF results - NeWMaPs from the dHCP study across multiple resolutions (ranging from 2-20 NMFs).</li> </ol> <p> </p>
Kodaikanal Solar Observatory (KoSO) White-Light Sunspot Regions Masks (1904-2017)
<p>Regular observations at the Kodaikanal Solar Observatory (KoSO) began in 1904 using a white-light telescope with a 10-cm aperture lens and an f/15 light beam. Between 1912 and 1917, the objective lens was changed several times. In 1918, a 15-cm achromatic lens was installed. This new configuration produced a 20.4 cm size image of the Sun in the image plane. Photographic plates were used to capture the image. The same telescope has been used since 1918 up until 2017 to take regular white-light observations of the Sun. This data set provides the sunspot mask in HDF5 format for all the White Light Observations acquired at KoSO. Each HDF5 file contains the sunspot mask for all the observations for that year. The sunspot masks are provided in two different coordinate systems: (i) Full Disk as observed and (ii) Carrington heliographic coordinate, which is transformed from full disk using near point interpolation. Each data set also contains metadata in the form of HDF5 attributes. The Carrington co-ordinate data if full Sun map, hence the near-side of the Sun is the region where values in the mask in non-zero, where as sunspot regions are filled with value 2. </p> <p>A <strong>Python package (KoSOpy), which can be located on <a href="https://github.com/Kodaikanal-Solar-Observatory/kosopy" target="_blank" rel="noopener">GitHub</a>,</strong> is being developed which can be used to navigate through these data sets.</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.