cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/d1.234
title: Visualizing endogenous fluorescence throughout a cleared mouse femur

description: The movie shows a MIP image of an entire mouse femur at different angles and zoomed in view of the greater trochanter area. Digital sections with 30 µm thickness are shown at different bone depths at the greater trochanter. Sox9+ cells are labeled with red fluorescent protein (tdTomato), while tissue autofluorescence in green provides structural cues.
description: Related Publication:
Bone CLARITY: clearing, imaging, and computational analysis of osteoprogenitors within intact bone marrow

Chan, Ken Caltech

Greenbaum, Alon Caltech

Gradinaru, Viviana Caltech

Science Translational Medicine

2017-04-26

https://doi.org/10.1126/scitranslmed.aah6518
eng
DOI: 10.22002/d1.2318
title: Vegetation typology classification and data set in Ucayali, Peru

description: This data set is the result of a land cover mapping activity involving a collaborative partnership between researchers and local experts working in and around the Ucayali region of Peru. The objective of this activity was to co-develop a categorization system and geospatial data set for the vegetation in the region that leverages local knowledge while reconciling this knowledge with the strengths and limitations of remote sensing capabilities. The vegetation classes described here will form a technically meaningful basis for active remote sensing data libraries to be subsequently developed using satellite-based Light Detection and Ranging (LiDAR) data.
DOI: 10.22002/d1.2315
title: bi183 BICCN data

description: BICCN 10x data with data incurred batch effects and metadata
DOI: 10.22002/d1.222
title: Identifying and Quantifying Mineral Abundance through VSWIR Microimaging Spectroscopy: A Comparison to XRD and SEM

description: Visible-shortwave infrared microimaging reflectance spectroscopy is a new technique to identify minerals, quantify abundances, and assess textural relationships at sub-millimetre scale without destructive sample preparation. Here we used a prototype instrument to image serpentinized igneous rocks and carbonate-rich travertine deposits to evaluate performance, relative to traditional techniques: XRD (mineralogical analysis of bulk powders with no texture preservation) and SEM/EDS (analysis of phases and textures using chemical data from polished thin sections). VSWIR microimaging spectroscopy is ideal for identifying spatially coherent rare phases, below XRD detection limits. The progress of alteration can also be inferred from spectral parameters and may correspond to phases that are amorphous in XRD. However, VSWIR microimaging spectroscopy can sometimes be challenging with analyses of very dark materials (reflectance <0.05) and mineral mixtures occurring at a spatial scales multiple factors below the pixel size. Abundances derived from linear unmixing typically agree with those from XRD and EDS within ~10%.
description: Sample: A rock was collected from an travertine conglomerate, containing ophiolite clasts. The rock was collected in Oman near the Samail ophiolite (collected Jan 2012; B. Ehlmann; analyzed in Leask & Ehlmann, 2016). Data included are: 1) UCIS (Ultra-Compact Imaging Spectrometer; B. Van Gorp et al) data cube. Data near ends of sensor may be suspect [e.g. under 500 nm, over 2500 nm]. {OM12L_001_UCIS_cube_masked} 2) EDS-SEM mosaic image cube (4x downsampled to despeckle, using a nearest neighbour algorithm). Acquired Caltech October 2015. Chemical data are in atomic %. {om12L_001_SEM_4x_masked} 3) EDS-SEM data warped to UCIS cube [degree 4 convolution, using built-in ENVI warping algorithm and hand-picked ground-control points]. Three UCIS images were mosaicked together to build the base image. Note whole image difficult to match 100% perfectly; easier to line up a smaller subset. {OM12L_001_warp_SEM_to_UCIS} 4) XRD data (quantitative analysis done Aug 2015 by Actlabs). Note that the subsamples of the rock crushed for XRD analysis are not the same subsample imaged, although all come from the same rock. 5) Photographs of rock sample for context (taken by C.Sanders, 2014). {Macro_OM12L_001.JPG; OM12L_001_smoothface_2.jpg}
description: Related Publication:
Identifying and Quantifying Mineral Abundance through VSWIR Microimaging Spectroscopy: A Comparison to XRD and SEM

Leask, Ellen K. Division of Geological & Planetary Sciences, California Institute of Technology

Ehlmann, Bethany L. Division of Geological & Planetary Sciences, California Institute of Technology

8th Workshop on Hyperspectral Image and Signal Processing: Evolution in Remote Sensing (WHISPERS 2016)

2016-08-24
eng
DOI: 10.22002/d1.2207
title: Specious Art 10x VMH Counts(Small Version) for bi183

description: Subsetted version of 10x VMH full count matrix
DOI: 10.22002/d1.2204
title: Specious Art Smartseq VMH Metadata (Small Version) for bi183

description: Metadata for cells (observations) with fewer column labels
DOI: 10.22002/d1.2188
title: Specious Art 10x VMH Metadata (Small Version) for bi183

description: Metadata for 10x VMH cells subsetted for bi183 class
DOI: 10.22002/d1.2187
title: hic_matrix_hbrain

description: Predicted single-cell hic interaction matrix
DOI: 10.22002/d1.2186
title: single-cell atac track hbrain

description: cell-type-specific atac signal tracks
DOI: 10.22002/d1.2185
title: single-cell ATAC-seq human brain

description: single-cell ATAC-seq matrices
DOI: 10.22002/d1.2184
title: scATAK_PBMC

description: Processed single-cell ATAC-seq data
DOI: 10.22002/d1.2177
title: Data related to: "A different perspective on the cost of sex"

description: Sexual reproduction in most animals and its coexistence with parthenogenetic lineages remains paradoxical. The typical 'all-else-equal' explanatory model assumes that sexual and parthenogenetic females both invest identical amounts of resources in reproduction. This leads to a twofold net reproduction rate R0, and exponential growth in the parthenogenetic lineage since it does not invest in the production of males. A sexual lineage must compensate for the different growth rate by substantial advantages in resource allocation and/or survival rate, commonly referred to as the 'cost of sex'. While sexual lineages need to produce one female and one male offspring in every generation, a balance between the reproductive modes could be reached if parthenogenetic lineages had a 50% lower reproductive investment, towards their theoretical lower limit of one female offspring. This 'resource-reduction' would lead to similar net reproduction rates for both reproductive modes and enable their coexistence. Here, we demonstrate that such a resource-reduction characterizes communities comprising of sexual and parthenogenetic decomposer microarthropods: oribatid mites.
By counting the numbers of eggs carried by gravid females, we aimed to approximate net reproduction rates of oribatid mites, including data from seasonal samplings and various microhabitats from different regions and forest types in Germany over a period of 14 years. We examined 77,868 individuals (44,671 and 33,197 sexual and parthenogenetic, respectively) from 104 species (84 sexual and 20 parthenogenetic). Gravidity did not differ between reproductive modes – 47% of sexual vs 45% of parthenogenetic females carried eggs – nor did the relative egg size. By contrast, the numbers of eggs differed dramatically: parthenogenetic females carried on average 1.4 eggs, while sexuals had 2.7 eggs. The reproductive investment of parthenogens, as compared to sexuals, was very close to the 50% expected under the 'resource-reduction' hypothesis. In consequence, estimated net reproduction rates did not differ between the reproductive modes and we conclude that the stable coexistence of parthenogenetic and sexual species in equilibrium communities could be explained by harmonized population dynamics.
DOI: 10.22002/d1.2176
title: Data accompanying "Evidence for deposition of chloride on Mars from small-volume surface water events into the Late Hesperian-Early Amazonian"

description: This data accompanies Leask & Ehlmann, AGU Advances, 2021. We provide two Excel files (.xls) of all of the statistics from examination of the Osterloo et al. 2010 chloride deposits relative to MOLA, CTX, CRISM, and HiRISE. We also provide a comma-separated value file (.csv) that maps the chloride deposits to their geologic unit in the Tanaka et al 2014 global geological map.
description: Related Publication:
Evidence for deposition of chloride on Mars from small-volume surface water events into the Late Hesperian-Early Amazonian

Leask, EK Caltech

Ehlmann, BL Caltech

AGU Advances
eng
DOI: 10.22002/d1.2178
title: ACOS GOSAT v9 Super Lite XCO2 data

description: This data set consists of a set of monthly NetCDF files containing the GOSAT quality filtered and bias corrected XCO2 values derived from the version 9 (v9) Atmospheric Carbon Observations from Space (ACOS) Level 2 full physics (L2FP) retrieval algorithm. Only the most essential variables for each satellite observation are preserved in these "superlite" files: latitude and longitude (both at the surface viewing location), the unique sounding identification number (format is: 4 digit year, 2 digit month, 2 digit day, 2 digit hour, 2 digit minute, 2 digit second), and the estimated dry-air mole fraction of total column carbon dioxide in parts per million. The monthly files also contain the set of operational L2FP "lite" files from which the data was extracted, and which can be downloaded from the NASA Goddard Earth Sciences (GES) Data and Information Services Center (DISC) (10.5067/VWSABTO7ZII4). This superlite "teaser" product is a companion to the recently published journal article "An eleven year record of XCO2 estimates derived from GOSAT measurements using the NASA ACOS version 9 retrieval algorithm" in Earth System Science Data by T.E. Taylor, et al. (https://doi.org/10.5194/essd-2021-247) It is meant to provide entry level users with a light weight satellite product for initial exploration. Interested users of the superlite product are encouraged to reach out to Tommy Taylor (tommy.taylor@colostate.edu) and/or Dr. Chris O'Dell (christopher.odell@colostate.edu) with questions on best uses practices for the GOSAT v9 XCO2 data.
description: Related Publication:
An eleven year record of XCO2 estimates derived from GOSAT measurements using the NASA ACOS version 9 retrieval algorithm

Thomas E. Taylor et al Cooperative Institute for Research in the Atmosphere, Colorado State University, Fort Collins, CO, USA

Earth System Science Data

https://doi.org/10.5194/essd-2021-247
eng
description: Contact person: Thomas E. Taylor Tommy.Taylor@colostate.edu
DOI: 10.22002/d1.2175
title: Specious Art Seurat Integrated Tutorial PBMC Dataset

description: All matrices from integration tutorial for Seurat v3, using anchor method
DOI: 10.22002/d1.2174
title: Data for "The Oligocene-Miocene Guadalope-Matarranya Fan, Spain, as an Analog for Long-Lived, Ridge-Bearing Megafans on Mars"

description: This data repository contains three spreadsheets of data referenced in the manuscript:
- Ridge caprock dimensions
- Stratigraphic data
- Dimensions of unexhumed channel belts

Article abstract: Numerous sedimentary fans on Mars have been studied to better understand the early martian hydrological system. Of particular interest is to estimate the duration of fluvial activity from alluvial fan size by dividing deposit volume by bankfull sediment flux. However, such a calculation requires an intermittency factor—a parameter relating sediment flux from channel-filling (bankfull) floods to the long-term mean flux—which is poorly constrained. Here we investigated fluvial fan deposits from the Oligocene–Miocene Caspe Formation, Spain, as an analog to fans on Mars because it has exhumed channel belts that create sinuous ridges in the modern topography, similar to those observed on Mars. We made measurements of the thicknesses of dune and bar sets for exhumed channel belts at nine field sites to reconstruct bankfull channel depth (1.4 m) and bankfull sediment flux (0.48 m3/s). We estimated total bed-material sediment volume of the fan (362 km3) from stratigraphic thickness, previously mapped area containing exhumed channel belts, porosity, and sand fraction. Combined with previous constraints on depositional timespan (~6 Myr), we calculated an intermittency factor of 0.004 (range: 0.0004-0.04). We showed how our approach can be applied to Mars using remote sensing alone through measurements of fluvial ridge morphology. The intermittency factor is among the lowest values used for Mars, implying the possibility of longer depositional timespans exceeding millions of years for martian fans.
description: Related Publication:
The Oligocene-Miocene Guadalope-Matarranya Fan, Spain, as an Analog for Long-Lived, Ridge-Bearing Megafans on Mars

JGR: Planets
eng
DOI: 10.22002/d1.2162
title: Microbial shotgun metagenomics from low microbial biomass human samples assisted by effective host depletion

description: Data and figures
DOI: 10.22002/d1.2155
title: Data set for "Intermittent lab earthquakes in dynamically weakening fault gouge"

description: Data sets cover results presented in Rubino, Rosakis, Lapusta, "Intermittent lab earthquakes in dynamically weakening fault gouge", Nature, 2022. Each file corresponds to a different figure, tabs are for different panels in each figure.
description: Related Publication:
Dynamic triggering and rapid weakening in lab earthquakes with rock gouge

Rubino, Vito Caltech

Rosakis, Ares Caltech

Lapusta, Nadia Caltech

Nature
eng
DOI: 10.22002/d1.2151
title: Mouse transcript database for HCR probe design in Gradinaru lab

description: This is the database used for designing HCR probes using the script developed in the Gradinaru lab (https://github.com/GradinaruLab/HCRprobe)
DOI: 10.22002/d1.2150
title: Data set for manuscript "Dynamics of the abrupt change in Pacific Plate motion around 50 Ma"

description: The files contained in this reconstructions present the plate tectonic reconstructions and the predicted velocity field from the geodynamic models presented in this data
description: Related Publication:
Dynamics of the abrupt change in Pacific Plate motion around 50 Ma

Hu, J.  Caltech

Gurnis, M. Caltech

Rudi, J. Argonne National Laboratory

Stadler, G. NYU

Muller, R. D Sydney University, Sydney, NSW, Australia

Nature Geoscience

2021-12-01
eng
DOI: 10.22002/d1.2142
title: Hydration Imaging Spectroscopy Dataset for Oman Drilling Project Holes GT1A, GT2A, and GT3A

description: This dataset contains paired .img and .hdr files of calculated water content used for the following paper: Crotteau, M.A., Greenberger, R. N., Ehlmann, B. L., Rossman, G.R., Harris, M., Kelemen, P. B., Teagle, D. A. H., et al. (2021). Characterizing Hydration of the Ocean Crust Using Shortwave Infrared Microimaging Spectroscopy of ICDP Oman Drilling Project Cores. Journal of Geophysical Research: Solid Earth. This dataset contains the .img and .hdr files with weight percent water values for each pixel for the International Continental Scientific Drilling Program (ICDP) Oman Drilling Project (OmanDP) Holes GT1A, GT2A, and GT3A. The hydration values were derived from imaging spectroscopy measurements of the archive half of the OmanDP cores, with methods for data acquisition described in Kelemen et al. (2020) and data analysis in Crotteau et al. (2021). Data descriptions are in the supplement of Crotteau et al. (2021), and that paper must be cited with use of this dataset. Included files: 1. GT1A_HydrationMaps.zip: Zip file containing paired .img and .hdr files containing calcuated hydration for each core section in Hole GT1A. 2. GT2A_HydrationMaps.zip: Zip file containing paired .img and .hdr files containing calcuated hydration for each core section in Hole GT2A. 3. GT3A_HydrationMaps.zip: Zip file containing paired .img and .hdr files containing calcuated hydration for each core section in Hole GT3A.
DOI: 10.22002/d1.2141
title: Hydration Maps of Oman Drilling Project Holes GT1A, GT2A, and GT3A

description: This dataset is the supplement for the following paper: Crotteau, M.A., Greenberger, R. N., Ehlmann, B. L., Rossman, G.R., Harris, M., Kelemen, P. B., Teagle, D. A. H., et al. (2021). Characterizing Hydration of the Ocean Crust Using Shortwave Infrared Microimaging Spectroscopy of ICDP Oman Drilling Project Cores. Journal of Geophysical Research: Solid Earth. These datasets are maps of hydration for the International Continental Scientific Drilling Program (ICDP) Oman Drilling Project (OmanDP) Holes GT1A, GT2A, and GT3A. The maps were derived from imaging spectroscopy measurements of the archive half of the OmanDP cores, with methods for data acquisition described in Kelemen et al. (2020) and data analysis in Crotteau et al. (2021). The hydration maps archived here are part of the supplement of Crotteau et al. (2021) but are too large to be published through the journal. Data descriptions are in the supplement of Crotteau et al. (2021), and that paper must be cited with use of these datasets. Included files: 1. GT1A_HydrationMaps.pdf: Maps of the hydration in Hole GT1A. 2. GT2A_HydrationMaps.pdf: Maps of the hydration in Hole GT2A. 3. GT3A_HydrationMaps.pdf: Maps of the hydration in Hole GT3A.
DOI: 10.22002/d1.2140
title: evSeq: Cost-Effective Amplicon Sequencing of Every Variant in a Protein Library

description: All raw and processed data generated in the study "evSeq: Cost-Effective Amplicon Sequencing of Every Variant in Protein Libraries".
DOI: 10.22002/d1.2136
title: Az Zabirah South Zone chemistry data

description: Tabular data for whole-rock chemistry of bauxite samples from the Az Zabirah South Zone bauxite deposit, Saudi Arabia.
DOI: 10.22002/d1.2135
title: Shear velocity model measured by Ridgecrest DAS

description: This data set includes the data used in producing the figures in 'Sub-kilometer correlation between near-surface structure and ground motion measured with distributed acoustic sensing'. 
1. Earthquake strain rates recorded by DAS, with a sample rate of 250 Hz.
2. Noise cross-correlation along the DAS array, with a sample rate of 50 Hz.
3. Shear velocity model along the DAS array. The channel spacing is 8 m. The grid size in depth is 10 m.
DOI: 10.22002/d1.2133
title: Supplemental Data for Resonances of the InSight Seismometer on Mars

description: The data are in miniseed format. This is a standard exchange format for seismic data
description: Related Publication:
Resonances of the InSight Seismometer on Mars

Kenneth Hurst NASA Jet Propulsion Laboratory, California Institute of Technology

Bulletin of the Seismological Society of America
eng
DOI: 10.22002/d1.2130
title: List of ATFS-1 targets

description: mitochondrial Unfolded Protein  Response ATFS-1 targets
description: Related Publication:
High confidence ATFS-1 target genes for quantifying activation of the mitochondrial unfolded protein response

Van Raamsdonk, Jeremy 1 Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada 2 Metabolic Disorders and Complications Program, and Brain Repair and Integrative Neuroscience Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada 3 Division of Experimental Medicine, Department of Medicine, McGill University, Montreal, Quebec, Canada 4 Department of Genetics, Harvard Medical School, Boston, MA, USA

microPublication Biology

2021-09-27

https://doi.org/10.17912/micropub.biology.000484
eng
description: Contact person: Van Raamsdonk, Jeremy jeremy.vanraamsdonk@mcgill.ca
DOI: 10.22002/d1.2127
title: Continental United States Solar Irradiance

description: The data was obtained from the National Renewable Energy Laboratory's (NREL's) National Solar Radiation Database (NSRDB), with a focus on the continental United States. we consider solar irradiance data from the NSRDB in terms of direct normal irradiance (DNI) and diffused horizontal irradiance (DHI) at an approximately 4-km x 1/2-hr spatiotemporal resolution. The solar dataset produced for this work samples data at an hourly temporal resolution from  6 am to 6 pm for the years 2007 to 2013. The test dataset contains datapoints sampled from 2014. A 1D array of data points is provided along with latitude and longitude metadata for each point. We re-arrange this 1D array into a 2D image based on the lat/long metadata. These 2D arrays of DNI and DHI are chipped into 100 x 100 patches. Low resolution imagery is obtained by sampling high resolution data at every fifth data point. All data files are made available as PNGs in their respective LR or HR resolutions.
DOI: 10.22002/d1.2126
title: Continental United States Wind Speeds

description: The data was obtained from the National Renewable Energy Laboratory's (NREL's) Wind Integration National Database (WIND) Toolkit, with a focus on the continental United States. Wind velocity data is comprised of westward (ua) and southward (va) wind components, calculated from wind speeds and directions 100-km from Earth's surface. The WIND Toolkit has a spatial resolution of 2 km x 1 hr spatiotemporal resolution. Our wind dataset contains data sampled at a 4-hourly temporal resolution for the years 2007 to 2013. The sample test dataset contains data sampled at a 4-hourly temporal resolution for 2014.
We transform 2D data arrays of wind speed and direction into  corresponding ua and va wind speed components. These are chipped into 100x100 patches. Low resolution imagery is obtained by sampling high resolution data at every fifth data point as instructed by NREL's guidelines. All data files are made available as PNGs in their respective LR or HR resolutions.
DOI: 10.22002/d1.2122
title: Observations of Volatile Organic Compounds in the Los Angeles Basin during COVID-19

description: VOC mixing ratios measured in Pasadena, CA from 4/16/2020-7/19/2020
DOI: 10.25810/4c3b-b819.55
title: World Newspaper Coverage of Climate Change or Global Warming, 2004-2022 - October 2022

description: The Media and Climate Change Observatory Data monitors 127 sources (across newspapers, radio and TV) in 59 countries in seven different regions around the world. Data is assembled by accessing archives through the Lexis Nexis, Proquest and Factiva databases via the University of Colorado libraries. More information may be found at: http://mecco.colorado.edu.
DOI: 10.22002/d1.2114
title: Extended Data tables

description: Table 1. Putative pre-RC proteins coded by the C. albicans genome
Table 2. Comparison of putative CaORC sequences with ORC sequences of S. cerevisiae and S. pombe. The systematic names, ORF and protein length along with isoelectric pH of the ORC1-6 in S. cerevisiae, S. pombe and C. albicans.
Table 3.Pairwise alignment results of CaORC proteins with other eukaryotes 
Sc – Saccharomyces cerevisiae; Sp – Schizosaccharomyces pombe; Ca – Candida albicans; Dm – Drosophila melanogaster; Xl – Xenopus laevis; Mm – Mus musculus; Hs – Homo sapiens
Table 4. Comparison of  Walker A and Walker B motifs of CaORC proteins with other species
Table 5. Putative signature of Walker motifs in CaORC proteins
Table 6. Domains of C.albicans ORC proteins compared with other eukaryotes
Table 7. Comparison of the Clustal W scores and lengths of the ORC associated proteins in S. cerevisiae and S. pombe with C. albicans.
Sc – Saccharomyces cerevisiae; Sp – Schizosaccharomyces pombe; Ca – Candida albicans
NA-Not applicable
Table 8. Cscore values of CaORC proteins
Table 9. SMART predictions of pre-RC proteins' interactions
description: Related Publication:
Identification and in silico analysis of the origin recognition complex in the human fungal pathogen Candida albicans

Sreedevi Padmanabhan Molecular Biology Laboratory, Veer Bahadur Singh Purvanchal University, Jaunpur- 222003, Uttar Pradesh, India.

microPublication Biology

2021-09-13

https://doi.org/10.17912/micropub.biology.000465
eng
description: Contact person: Sreedevi Padmanabhan sreepbc@gmail.com