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3,465 results for “mass”
Example imaging mass cytometry raw data
<p>If you are working with these files, please cite them as follows:<br><br>Windhager, J., Zanotelli, V.R.T., Schulz, D. et al. An end-to-end workflow for multiplexed image processing and analysis. Nat Protoc (2023). <a href="https://doi.org/10.1038/s41596-023-00881-0">https://doi.org/10.1038/s41596-023-00881-0</a></p><p>This imaging mass cytometry (IMC) dataset serves as an example to demonstrate raw data processing and downstream analysis tools. The data was generated as part of the <strong>I</strong>ntegrated i<strong>MMU</strong>noprofiling of large adaptive <strong>CAN</strong>cer patient cohorts (IMMUcan) project (<a href="https://immucan.eu">immucan.eu</a>) using the Hyperion imaging system (<a href="https://www.fluidigm.com/products-services/instruments/hyperion">www.fluidigm.com/products-services/instruments/hyperion</a>). To get an overview on the technology and available analysis strategies, please visit <a href="https://bodenmillergroup.github.io/IMCWorkflow/">bodenmillergroup.github.io/IMCWorkflow</a>. The individual data files are described below:</p><ul><li><strong>Patient1.zip, Patient2.zip, Patient3.zip, Patient4.zip</strong>: raw data files of 4 patient samples. Each .zip archive contains a folder in which one .mcd file (IMC raw data) and multiple .txt files (one per acquisition) can be found.</li><li><strong>compensation.zip</strong>: This .zip archive holds a folder which contains one .mcd file and multiple .txt files. Multiple spots of a "spillover slide" were acquired and each .txt file is named based on the spotted metal. This data is used for channel spillover correction. For more information, please refer to the original publication: <a href="https://doi.org/10.1016/j.cels.2018.02.010">Compensation of Signal Spillover in Suspension and Imaging Mass Cytometry</a></li><li><strong>panel.csv</strong>: This file contains metadata for each antibody/channel used in the experiment. The <i>full</i> column indicates which channel should be analysed. The <i>ilastik</i> column specifies which channels were used for ilastik pixel classification and the <i>deepcell</i> column indicates the channels used for deepcell segmentation.</li><li><strong>sample_metadata.csv</strong>: This file links each patient to their cancer type (SCCHN - head and neck cancer; BCC - breast cancer; NSCLC - lung cancer; CRC - colorectal cancer).</li></ul>
Sampled and simulated benthic invertebrate body-mass data from the Porcupine Abyssal Plain Sustained Observatory (4850 m, 48.83° N 16.50 °W, NE Atlantic)
<p>A dataset of sampled and simulated benthic invertebrate body-mass data from the Porcupine Abyssal Plain Sustained Observatory (4850 m, 48.83° N 16.50 °W, NE Atlantic) has been produced. It includes data on macro- and megabenthos derived from a randomly sampled power law distribution, seabed core samples, large-scale seabed photography, and seabed trawls.</p>
Datasets for "Mass-stream trajectories with non-synchronously rotating donors"
<p>Datasets to accompany the publication of the paper "Mass-stream trajectories with non-synchronously rotating donors" by David Hendriks and Rob Izzard (<a href="https://doi.org/10.1093/mnras/stad2077">https://doi.org/10.1093/mnras/stad2077</a>).</p> <p>Below follows an explanation of the contents of this repository:</p> <ul> <li>Hendriks2023_ballistic_stream_datafile.csv: Data file containing the ballistic trajectory data for a ranges of initial stream velocity, donor synchronicity and mass ratio. This file contains a header with extra information.</li> <li>Hendriks2023_ballistic_stream_metadata.json: Settings file containing the configuration for the ballistic stream integration simulations and other meta data.</li> <li>Hendriks2023_binary_populations_exploration_data_Z0.02.csv: Data file containing the binary population data at Z=0.02. This file contains a header with extra information.</li> <li>Hendriks2023_binary_populations_exploration_metadata.json: Settings file containing the configuration for the binary population synthesis simulations, including binary_c-python settings, binary_c information and other meta data.</li> <li>RLOF_Hendriks2023_roche_lobe_interpolation_table.csv: Data file containing Roche-lobe radius data for a range of donor synchronicity and mass ratio (q=M_acc/M_don).</li> <li> readme.md: readme file.</li> </ul>
MESA model files and data for: 'Stellar Neutrino Emission Across The Mass-Metallicity Plane'
<p>Example MESA model files and stellar evolution tracks for download from "Stellar Neutrino Emission Across The Mass-Metallicity Plane".</p>
Pre-training with simulated ultrasound images for breast mass segmentation and classification - dataset
<p>Dataset assosiated with the MICCAI Workshop on Data Engineering in Medical Imaging paper: "Pre-training with Simulated Ultrasound Images for Breast Mass Segmentation and Classification"</p>
Seed Mass of species from Yasuní National Forest, Ecuador, 2000-2014
We provide data on mean dry and wet mass of > 800 species from Yasuní National Forest, Ecuador collected between 2000 and 2014. Species include trees, shrubs, lianas and herbs. We also provide data on number of seeds per fruit for >1100 species compiled in 2016, along with information on fruit type and dispersal mode. Both of these data sets supplement previously published data on flowering and fruiting phenology from this equatorial, ever-wet rainforest in eastern Ecuador (Garwood et al. 2023). Garwood, N.C., S.J. Wright, R. Valencia, and M.R. Metz. 2023. Rainforest phenology: flower, fruit and seed production from biweekly collections of 200 traps in the Yasuní Forest Dynamics Plot, Ecuador, 2000-2018 ver 1. Environmental Data Initiative. https://doi.org/10.6073/pasta/5e6cb3d7ff741fd9d21965c4a904bc1f (Accessed 2024-03-27).
Air mass back-trajectory modeling output along an urban-rural transect in central Ohio, 2021
This data package contains modeled air parcel back-trajectories generated using the Stochastic Time-Inverted Lagrangian Transport model (STILT) via the R interface. The purpose of the study was to characterize the geochemical and isotopic signatures of dust in relation to different land uses, and to connect the geochemistry of deposited dust to air mass trajectories. Back-trajectories are three-dimensional paths of air parcels from a receptor site (the dust collection site) backwards in time and space for the duration of the tracking interval, calculated iteratively using wind fields from high-resolution gridded meteorological data. To calculate a probability of potential pathways, rather than a single back-trajectory, STILT introduces small random perturbations into the wind fields during each time step. For four sites along an urban-rural transect in central Ohio for June-July 2021, we generated weekly footprints of potential sources for the dust deposited at each site. These back-trajectories can be paired with geochemical data to establish a connection between land use and anthropogenic dust composition. This dataset is complete and will not be updated.
Eriophorum vaginatum flowers and mass per tiller in tussock tundra sites along the Dalton Highway, Alaska 2016
These measurements repeat the measurements made by Shaver et al. (1986) along the Dalton Highway at some of the same sites. Shaver, G. R., N. Fetcher, and F. S. Chapin III. 1986. Growth and flowering in Eriophorum vaginatum: Annual and latitudinal variation. Ecology 67:1524-1535.
Consequences of non-random tree species loss on litter mass loss, nutrient dynamics, carbon cycling, and decomposer communities across a terrestrial-aquatic interface at Coweeta Hydrologic Lab, Otto, NC
Although litter decomposition is a fundamental ecological process, most of our understanding comes from studies of single-species decay. Recently, litter-mixing studies have tested whether monoculture data can be applied to mixed-litter systems. These studies have mainly attempted to detect non-additive effects of litter mixing, which address potential consequences of random species loss. The focus is not on which species are lost, but the decline in diversity per se. Under global change, species loss is likely to be non-random, with some species more vulnerable to extinction than others. Under such scenarios, the effects of individual species (additivity) as well as of species interactions (non-additivity) on decomposition rates are of interest. To examine potential impacts of non-random species loss on ecosystems, we studied additive and non-additive effects of litter mixing on decomposition. A full-factorial litterbag experiment was conducted using four deciduous leaf species, from which mass loss and nitrogen content were measured. Data were analysed using a statistical approach that first looks for additive identity effects based on the presence or absence of species and then significant species interactions occurring beyond those. It partitions non-additive effects into those caused by richness and or composition.
Aggregate mesquite litter mass-loss following soil-mixing and decomposition in a semi-arid grassland at the Jornada Basin LTER, 2010-2012
This package contains litter mass loss data from a litter decomposition experiment at the Jornada Basin LTER. To assess the role of soil-litter mixing (SLM) in aridland litter decomposition, litterbags were deployed in the Chihuahuan Desert and interrelationships between vegetation structure, SLM, and rates of decomposition were quantified. To assess the role of vegetation structure, litterbags were deployed in contrasting vegetation microsites, including grass, shrub, and bare ground microsites. This dataset contains the mass-loss data (including ash-corrections) from the experiment. This study is complete.
RIV05 Leaf mass in streams in wooded riparian areas and areas where canopy had been cut at Konza Prairie
Our project was designed to test if woody removal in a riparian zone allowed the system to rebound to a grassland state. We hypothesized that removal would decrease organic matter input into streams.
Soil phosphorus, litterfall mass, nitrogen and phosphorus in eight Puerto Rico forests affected by hurricanes Hugo, Bertha, Georges, Irma, and Maria.
Tropical cyclones are intensifying and occurring at higher latitudes in recent decades, but the mechanisms underpinning the resistance (ability to withstand disturbance-induced change) and resilience (pace of return to pre-disturbance reference values) of tropical forests to cyclones remains largely unexplored at the pantropical scale. We conducted a meta-analysis to investigate the role of soil resource availability (i.e., total soil phosphorus concentration) in mediating site-level forest canopy resistance and resilience to cyclones pan-tropically. We evaluated cyclone-induced and post-cyclone litterfall mass (g/m2/day), phosphorus (P) and nitrogen (N) fluxes (mg/m2/day), as well as concentrations (mg/g) across 73 case studies in Australia, Guadeloupe, Hawaii, Mexico, Puerto Rico, and Taiwan (Bomfim et al., in review). This dataset includes information related to 42 case studies in eight Puerto Rico forests affected by hurricanes Hugo, Bertha, Georges, Irma, and Maria between 1989 and 2017. This dataset also includes data for the canopy trimming experiment (CTE) in El Verde. - The compiled Litterfall Mass and Nitrogen and Phosphorus Flux and Concentration data from natural forest ecosystems across Puerto Rico prior to and after eight hurricanes are provided in Forest-Soil-Litterfall-Hurricane_Puerto-Rico.csv. This data file also includes site location, geographical characteristics, elevation, soil phosphorus concentration, geology, and several variables related to each hurricane disturbance. Support for this work was provided by grants BSR-8811902, DEB-9411973, DEB-9705814 , DEB-0080538, DEB-0218039 , DEB-0620910 , DEB-1239764, DEB-1546686, and DEB-1831952 from the National Science Foundation to the University of Puerto Rico as part of the Luquillo Long-Term Ecological Research Program. Additional support provided by the University of Puerto Rico and the International Institute of Tropical Forestry, USDA Forest Service.
Summarized glacier mass balance measurements, McMurdo Dry Valleys, Antarctica (1993-2023, ongoing)
As part of the Long Term Ecological Research (LTER) project in the McMurdo Dry Valleys of Antarctica, a systematic sampling program has been undertaken to monitor glacial mass balance and meltwater flow. This data package contains total mass balance changes at each stake measured on six glaciers (Canada, Commonwealth, Hughes, Suess, Howard, and Taylor) in Taylor Valley and one glacier (Adams) in Miers Valley, all of which are located in the McMurdo Dry Valleys region of Antarctica. These values are the result of an analysis of the raw data presented in other data files (glacier stake heights, snow depths, and snow densities). Included here for each stake is the total water equivalent mass change. The standard deviation or the range for each total is given. Most measurements began during the 93-94 field season. Adams measurements were established during the 14-15 field season. Measurements are ongoing except at Hughes and Suess Glaciers where monitoring ceased following the 08-09 field season. Monitoring the changes in these measurements over time provides a record of mass balance, and aids in determining the role of glaciers in the polar hydrologic cycle.
Snow, ice, and total glacier mass balance measurements, McMurdo Dry Valleys, Antarctica (1993-2023, ongoing)
As part of the Long Term Ecological Research (LTER) project in the McMurdo Dry Valleys of Antarctica, a systematic sampling program has been undertaken to monitor glacial mass balance and meltwater flow. This data package includes mass balance changes at each stake on six glaciers (Canada, Commonwealth, Hughes, Suess, Howard, and Taylor) in Taylor Valley and one glacier (Adams) in Miers Valley, all of which are located in the McMurdo Dry Valleys region of Antarctica. The values are the result of an analysis of the raw data presented in other data files (glacier stake heights, snow depths, and glacier snow densities). Included here for each stake are the change in ice and snow water equivalent (mass) values, and the total mass change. The standard deviation or the range for each total is also given. Most measurements began during the 93-94 field season. Adams measurements were established during the 14-15 field season. Measurements are ongoing except at Hughes and Suess Glaciers where monitoring ceased following the 08-09 field season. Monitoring the changes in these measurements over time provides a record of mass balance, and aids in determining the role of glaciers in the polar hydrologic cycle.
Ash-free dry mass data from drift net experiments in glacial-melt streams of Fryxell Basin, McMurdo Dry Valleys, Antarctica, during the 2022-2023 austral summer
During the 2022-2023 austral summer, 12 drift net experiments were conducted in four glacial-melt streams—Aiken Creek, Green Creek, Lost Seal Stream, and Von Guerard Stream—to quantify particulate organic matter (POM) flux from streams to downstream lakes. Streams are located in Fryxell Basin, within Taylor Valley in the McMurdo Dry Valleys of Antarctica. Drift nets were deployed near the mouth of each stream and sampled every 4 to 12 hours to collect POM. Collected as part of the McMurdo Dry Valleys LTER project, these data provide insight into the temporal variability of organic material transport in polar desert ecosystems.
Butterfly heavy metal content, wing size, egg count, and brain mass in the Minneapolis-St. Paul (MSP) Metropolitan Area
We collected 26 common species of butterflies across a gradient of lead pollution in the Twin Cities metropolitan area (Minneapolis and St. Paul, MN, USA). We measured their thorax lead concentrations and their body condition including wing area, number of eggs, and brain mass. We also quantified lead in the soil, host plant leaves, and air (through lichen bio-monitors) at sites where the butterflies were collected.
In silico Database for Identification of Microorganisms by Liquid Chromatography-Mass Spectrometry (LC-MS1)
<p>Modern methods of mass spectrometry have emerged recently allowing reliable, fast and cost-effective identification of pathogenic microorganisms. For example, matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) has revolutionized the way pathogenic microorganisms are identified in today’s routine clinical microbiology. Furthermore, recent years have witnessed also substantial progress in the development of liquid chromatography-mass spectrometry (LC-MS) based proteomics for microbiological applications.</p> <p>In this context, we introduce a new concept for microbial identification by mass spectrometry. The proposed approach involves efficient extraction of proteins from cultivated microbial cells, digestion by trypsin and LC-MS measurements. MS1 data are then extracted and systematically tested against <em>in silico</em> libraries of peptide mass data. The first version of such a database has been computed from UniProt Knowledgebase [Swiss-Prot and TrEMBL] and contains more than 12,000 strain-specific synthetic mass profiles. The database is stored in the pkf data format which is interpretable by the MicrobeMS software package (requires MicrobeMS version 0.82, or later).</p> <p><em>For details see the following preprint: Lasch, P. Schneider, A. Blumenscheit, C. and Doellinger, J. “Identification of Microorganisms by Liquid Chromatography-Mass Spectrometry (LC-MS1) and in silico Peptide Mass Data”. bioRxiv preprint, http://dx.doi.org/10.1101/870089.</em></p>
Catalog of Coronal Mass Ejections Observed in Conjunction between Radially Aligned Spacecraft in the Inner Heliosphere
<p>This catalog lists 47 CME events observed in a longitudinal conjunction between MESSENGER, Venus Express, STEREO, and Wind/ACE. We list the onset date and time of the probable CME candidate. If the CME was observed by LASCO onboard the SOHO<br> spacecraft, we report the average CME onset time as calculated in the CDAW catalog (average between first-order-constant speed and second-order-constant acceleration onset times). Otherwise, we report the time of the first STEREO/COR image containing the<br> CME. We then list the arrival times of the shock/discontinuity, magnetic ejecta leading edge and trailing edge at spacecraft 1 and 2. Arrival times at MESSENGER are listed from Winslow et al. (2015, 2017), Venus Express from Good and Forsyth (2016), STEREO from Jian, Russell, Luhmann, and Galvin (2018), and L1 from Richardson and Cane (2010). We also list the heliocentric distances of the spacecraft at the CME onset time, the longitudinal separation between the spacecraft when the discontinuity/ejecta arrives<br> at spacecraft 1, and the maximum magnetic field strength observed in the CME (including both the sheath and the ejecta) at each spacecraft. The maximum magnetic field strength measured in the CME at MESSENGER are listed from Winslow et al. (2015, 2017), the maximum magnetic field strength measured in the ejecta at Venus Express are listed from Good and Forsyth (2016). The longitudinal separations are in Heliographic Inertial (HGI) coordinates. We also list the initial CME speed. For the speed, we select the coronagraph which observed the CME closest to a limb event. Limb views signicantly minimize projection effects as compared to halo views and provide a better estimate of CME speeds. When LASCO observed the CME as a limb event, we report the second-order CME speed at 20 Rs (solar radius) listed in the CDAW catalog. For STEREO observations, we report the maximum<br> speed as listed in the CACTus catalog. We also list the average impact speeds at spacecraft 1 from the DBM (Vrsnak et al., 2013) and either the average impact speeds (when spacecraft 2 is Venus Express) or the maximum CME speed (when spacecraft 2 is<br> STEREO/Wind/ACE) measured at spacecraft 2. The maximum CME speeds measured at STEREO are listed from Jian et al. (2018) and at L1 listed from Richardson and Cane. (2010). We list the average transit speeds as well between the Sun and spacecraft 1,<br> spacecraft 1 and spacecraft 2, and the Sun and spacecraft 2.</p>
Laser Desorption Low-Temperature Plasma Mass Spectrometry Imaging (LD-LTP MSI) of tobacco seedlings
<p>Mass spectrometry imaging (MSI) data set in imzML format, of complete tobacco (<em>Nicotiana tabacum</em>) seedling using Laser Desorption Low-Temperature Plasma ionization. Mapping the ion that corresponds to nicotine shows accumulation in the roots and at the borders of leaves.</p> <p>The experiment is described in:</p> <p>Elucidating the Distribution of Plant Metabolites from Native Tissues with Laser Desorption Low-Temperature Plasma Mass Spectrometry Imaging, Abigail Moreno-Pedraza, Ignacio Rosas-Román, Nancy Shyrley Garcia-Rojas, Héctor Guillén-Alonso, Cesaré Ovando-Vázquez, David Díaz-Ramírez, Jessica Cuevas-Contreras, Fredd Vergara, Nayelli Marsch-Martínez, Jorge Molina-Torres, and Robert Winkler, Analytical Chemistry <strong>2019</strong> <em>91</em> (4), 2734-2743</p>
Laser Desorption Low-Temperature Plasma Mass Spectrometry Imaging (LD-LTP MSI) of San Pedro cactus
<p>Mass spectrometry imaging (MSI) data set in imzML format, obtained from San Pedro cactus (<em>Echinopsis pachanoi</em>) cross-section using Laser Desorption Low-Temperature Plasma ionization. Mapping the ion that corresponds to mescaline shows a star-like distribution of this interesting alkaloid.</p> <p>The experiment is described in:</p> <p>Elucidating the Distribution of Plant Metabolites from Native Tissues with Laser Desorption Low-Temperature Plasma Mass Spectrometry Imaging, Abigail Moreno-Pedraza, Ignacio Rosas-Román, Nancy Shyrley Garcia-Rojas, Héctor Guillén-Alonso, Cesaré Ovando-Vázquez, David Díaz-Ramírez, Jessica Cuevas-Contreras, Fredd Vergara, Nayelli Marsch-Martínez, Jorge Molina-Torres, and Robert Winkler, Analytical Chemistry <strong>2019</strong> <em>91</em> (4), 2734-2743</p> <p>DOI: 10.1021/acs.analchem.8b04406</p> <p> </p>
ScienceDex guides
Understand access before you commit
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.