cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/d1.2010
title: Mineral occurrence maps of Oman Drilling Project Holes GT1A, GT2A, and GT3A

description: This dataset is the supplement for the following paper:
Greenberger, R. N., Harris, M., Ehlmann, B. L., Crotteau, M. A., Kelemen, P. B., Manning, C. E., et al. (2021). Hydrothermal alteration of the ocean crust and patterns in mineralization with depth as measured by micro-imaging infrared spectroscopy. Journal of Geophysical Research: Solid Earth, 126, e2021JB021976. https://doi.org/10.1029/2021JB021976

These datasets are maps of the occurrences of key minerals and mineral groups (clinopyroxene, amphibole, chlorite, epidote, prehnite, zeolite, gypsum, calcite, and kaolinite/montmorillonite) 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 Greenberger et al. (2021). The mineral occurrence maps archived here are part of the supplement of Greenberger et al. (2021) but are too large to be published through the journal. 

Data descriptions are in the supplement of Greenberger et al. (2021), and that paper must be cited with use of these datasets. 

Included files:
1. GT1A_MineralOccurrenceMaps.pdf: Maps of the occurrence of key minerals and mineral groups in Hole GT1A.
2. GT2A_MineralOccurrenceMaps.pdf: Maps of the occurrence of key minerals and mineral groups in Hole GT2A.
3. GT3A_MineralOccurrenceMaps.pdf: Maps of the occurrence of key minerals and mineral groups in Hole GT3A.
description: Related Publication:
Proceedings of the Oman Drilling Project: Scientific Drilling in the Samail Ophiolite, Sultanate of Oman 

Kelemen, P. B.

Matter, J. M.

Teagle, D. A. H.

Coggon, J. A.

Oman Drilling Project Science Team

International Ocean Discovery Program

2020

https://doi.org/10.14379/OmanDP.proc.2020
eng
description: Contact person: Rebecca Greenberger rgreenbe@caltech.edu
DOI: 10.22002/d1.20097
title: CUB-200-2011 Segmentations

description: Segmentation masks for the CUB-200-2011 dataset.
DOI: 10.22002/d1.20096
title: Data for "It's all Relative: Monocular 3D Human Pose Estimation from Weakly Supervised Data" (BMVC 2018)

description: Data for "It's all Relative: Monocular 3D Human Pose Estimation from Weakly Supervised Data" (BMVC 2018).
DOI: 10.22002/d1.20089
title: Caltech Home Objects 2006

description: This dataset contains random objects from home. The objects are taken mostly from kitchen, bathroom and living-room environments. Each directory ("Train" and "Test") contains a subdirectory named 'Gtruth/', containing ground truth .mat files. The .mat files contain a variable 'outline'. For training images, 'outline' contains the corners of a bounding box defining the model in the training image. For test images, 'outline' contains the names of the models present in the image along with a bounding box for each of them. If a same training object is defined by several training images, 'outline' references all these training images, with the same bounding box. You can also find a tar archive of the whole dataset in "HomeObjects06.tar".
DOI: 10.22002/d1.2009
title: Oman Drilling Project Micro-Imaging Spectroscopy Data

description: This record will contain the imaging spectroscopy data of the archive halves of all core recovered by the International Continental Scientific Drilling Program (ICDP) Oman Drilling Project (OmanDP; Kelemen et al., 2020).

The dataset will eventually be available here through the CaltechDATA Large Data Pilot approved in June 2021. At this time, the pilot is not built and ready to accept data. We anticipate having the data here by the end of 2021. 

In the meantime, the shortwave infrared dataset for OmanDP Holes GT1A, GT2A, and GT3A is available through OneDrive. Interested users should contact Rebecca Greenberger (rgreenbe@caltech.edu) to gain access to the OneDrive folder.

Available data include shortwave infrared data cubes as described in Kelemen et al. (2020) processed to reflectance with mineral occurrence maps (Greenberger et al., 2021, JGR Solid Earth). Data paired .img and .hdr files.

Greenberger, R. N., Harris, M., Ehlmann, B. L., Crotteau, M. A., Kelemen, P. B., Manning, C. E., et al. (2021). Hydrothermal alteration of the ocean crust and patterns in mineralization with depth as measured by micro-imaging infrared spectroscopy. Journal of Geophysical Research: Solid Earth, 126, e2021JB021976. https://doi.org/10.1029/2021JB021976
description: Related Publication:
Proceedings of the Oman Drilling Project: Scientific Drilling in the Samail Ophiolite, Sultanate of Oman 

Kelemen, P. B.

Matter, J. M.

Teagle, D. A. H.

Coggon, J. A.

Oman Drilling Project Science Team

International Ocean Discovery Program

2020

https://doi.org/10.14379/OmanDP.proc.2020
eng
description: Contact person: Rebecca Greenberger rgreenbe@caltech.edu
DOI: 10.22002/d1.20088
title: Caltech Motorcycles 2001

description: Motorbikes (Side) dataset. Collected by undergrads at Caltech (Feb '01) from the web. 826 images of motorbikes from the side. JPEG format. ImageData.mat is a MATLAB file containing the variable SubDir_Data which is an 8 x 826 matrix. Each column of this matrix hold the coordinates of the bike within the image, in the form: [x_bot_left y_bot_left x_top_left y_top_left x_top_right y_top_right x_bot_right y_bot_right].
DOI: 10.22002/d1.20085
title: Caltech Cars 2001

description: Car dataset taken by Brad Philip and Paul Updike as part of a Caltech SURF project in summer 2001. 526 images of cars from the rear. 360 x 240 pixels. No scale normalisation. JPEG format. Quite a few repeat images. Taken on the freeways of southern California.
DOI: 10.22002/d1.20061
title: High throughput discovery of enhanced visible photoactivity in Fe-Cr vanadate solar fuels photoanodes

description: .zip file containing the data associated with a publication describing high throughput experimentation of Cr-Fe-V oxide photoanodes.
DOI: 10.22002/d1.20057
title: An amorphous nickel antimonate photoanode for solar fuel generation

description: Source data files of various formats that support the referenced publication. See enclosed readme.txt
DOI: 10.22002/d1.20055
title: Clytia Medusa Cufflinks Transcriptome GTF

description: This is the Marimbe Cufflinks transcriptome for Clytia provided in gtf format
DOI: 10.22002/d1.20048
title: PolymerGasMembraneML

description: Accompanies the work "Machine learning enables interpretable discovery of innovative polymers for gas separation membranes."
DOI: 10.22002/d1.20040
title: Supplemental Materials for the Atlas of Bacterial and Archaeal Cell Structure

description: Supplemental materials (pdb files, images, and narration) for version 2.1 of "The Atlas of Bacterial & Archaeal Cell Structure" by Catherine M. Oikonomou & Grant J. Jensen
DOI: 10.22002/d1.20035
title: Cross-correlation profile along Ridgecrest DAS

description: This data set includes a common-shot gather of noise cross-correlations and the group velocity model used in 'Fault Zone Imaging with Distributed Acoustic Sensing: Surface-to-Surface Wave Scattering'. The number of channels is 1026. The time lag of cross-correlations is 30 sec. The sampling frequency is 50 Hz. The frequencies of the group velocity model are corresponding to 100 points in 1-10 Hz evenly distributed in log space.
DOI: 10.22002/d1.20031
title: bi183 Ex Utero data

description: Matrix and metadata for Aguilera-Castrejon et al. , 2021 ex utero E8.5 embryo data for Caltech Bi183 class
DOI: 10.22002/d1.20030
title: 10 scRNA-seq datasets processed using 3 unspliced counting pipelines

description: This dataset contains ten 10X scRNA-seq datasets (two v2 from Desai et al., DOI: 10.1126/science.abc6506, eight v3 generated by 10X Genomics) that have been processed using pipelines for spliced and unspliced molecule quantification. We used velocyto, kallisto|bustools (kb), and salmon/alevin-fry to process the raw FASTQ files, and output loompy files with spliced and unspliced count matrices. The scripts used for processing, as well as the notebook used for post-processing, visualization, and comparisons are available at https://github.com/pachterlab/gfcp_2022.

The following files are included. raw_loom_sm.tar.gz: all salmon outputs. raw_loom_10x_kb.tar.gz: kb outputs for 10X data. raw_loom_10x_vc.tar.gz: velocyto outputs for 10X data. raw_loom_desai_kb.tar.gz: kb outputs for Desai data. raw_loom_desai_vc.tar.gz: velocyto outputs for Desai data.
description: Related Publication:
RNA velocity unraveled

Gennady Gorin Caltech

Meichen Fang Caltech

Tara Chari Caltech

Lior Pachter Caltech

bioRxiv
eng
DOI: 10.22002/d1.20023
title: Martian landscapes carved from ancient sedimentary basin fill - Data and Model

description: This dataset includes all data and models used in the associated publication.
description: Related Publication:
Carving martian landscapes from ancient sedimentary basins
eng
DOI: 10.22002/d1.2000
title: Cao 2017 C. elegans L2 larvae scRNAseq dataset wrangled into WormBase standard anndata

description: This is part of a curated collection of all C. elegans single cell RNA sequencing 
high throughput data wrangled into the anndata format in .h5ad files 
with standard fields, plus any number of optional fields that vary depending 
on the metadata the authors provide.

For the convention used to wrangle the h5ad files see 
https://github.com/WormBase/anndata-wrangling

Data description: 35,987 L2 larvae profiled with sci-RNA-seq

Original study:
Comprehensive single-cell transcriptional profiling of a multicellular organism

Cao J, Packer JS, Ramani V, Cusanovich DA, Huynh C, Daza R, Qiu X, Lee C, Furlan SN, Steemers FJ, Adey A, Waterston RH, Trapnell C, Shendure J.

Science. 2017 Aug 18;357(6352):661-667. 
https://doi.org/10.1126/science.aam8940.
DOI: 10.22002/d1.1999
title: Ben-David 2021 wormcells-viz data

description: Processed data for the WormBase wormcells-viz app
https://github.com/WormBase/wormcells-viz


Data from https://data.caltech.edu/records/1972 

=== Original study ===

Whole-organism eQTL mapping at cellular resolution with single-cell sequencing

Eyal Ben-David, James Boocock, Longhua Guo, Stefan Zdraljevic, Joshua S Bloom, Leonid Kruglyak

eLife 2021;10:e65857, DOI: https://doi.org/10.7554/eLife.65857
DOI: 10.22002/d1.1995
title: Dataset: dyakCAF1_Tsc1-PA.gff

description: GFF file for the Tsc1 gene in D. yakuba. DyakCAF1_Tsc1.GFF
description: Related Publication:
Drosophila yakuba – Tsc1

Bailey Lose The University of Alabama, Tuscaloosa, AL

Abigail Myers The University of Alabama, Tuscaloosa, AL

Savanah Fondse California State University Stanislaus, Turlock, CA

Ian Alberts University of Evansville, Evansville, IN

Joyce Stamm University of Evansville, Evansville, IN

Jim Youngblom California State University Stanislaus, Turlock, CA

Chinmay P Rele The University of Alabama, Tuscaloosa, AL

Laura Reed The University of Alabama, Tuscaloosa, AL

microPublication Biology

https://doi.org/10.17912/micropub.biology.000474
eng
DOI: 10.22002/d1.1998
title: Size distribution measurement datasets of the "Spider DMA" and "LDMA" particle sizers, collected in Pasadena, CA between 16 May - 11 June 2020.

description: Raw and processed data of ambient aerosol size distributions measured by Spider DMA and Long DMA, at the Caltech campus in Pasadena, CA between 16 May–11 June 2020. Measurements were part of a study of the impacts of the COVID-19 pandemic shutdown on air quality.
description: Related Publication:
Efficacy of a portable, moderate-resolution, fast-scanning DMA for ambient aerosol size distribution measurements

Amanatidis, Stavros     Caltech, Aerosol Dynamics Inc.

Huang, Yuanlong  Caltech

Pushpawela, Buddhi Caltech

Schulze, Benjamin C. Caltech

Kenseth, Christopher M. Caltech

Ward, Ryan X. Caltech

Seinfeld, John H. Caltech

Hering, Susanne V. Aerosol Dynamics Inc.

Flagan, Richard C. Caltech

Atmospheric Measurement Techniques

https://doi.org/10.5194/amt-2021-59
eng
DOI: 10.22002/d1.1994
title: Dataset: dyakCAF1_Tsc1-PA.pep

description: Peptide sequence file for the Tsc1 gene in D. yakuba. DyakCAF1_Tsc1.FAA.
description: Related Publication:
Drosophila yakuba – Tsc1

Bailey Lose The University of Alabama, Tuscaloosa, AL

Abigail Myers The University of Alabama, Tuscaloosa, AL

Savanah Fondse California State University Stanislaus, Turlock, CA

Ian Alberts University of Evansville, Evansville, IN

Joyce Stamm University of Evansville, Evansville, IN

Jim Youngblom California State University Stanislaus, Turlock, CA

Chinmay P Rele The University of Alabama, Tuscaloosa, AL

Laura Reed The University of Alabama, Tuscaloosa, AL

microPublication Biology

https://doi.org/10.17912/micropub.biology.000474
eng
DOI: 10.22002/d1.1993
title: Dataset:DyakCAF1_Tsc1.FNA

description: Fasta sequence file for the Tsc1 gene in D. yakuba. DyakCAF1_Tsc1.FNA
description: Related Publication:
Drosophila yakuba – Tsc1

Bailey Lose The University of Alabama, Tuscaloosa, AL

Abigail Myers The University of Alabama, Tuscaloosa, AL

Savanah Fondse California State University Stanislaus, Turlock, CA

Ian Alberts University of Evansville, Evansville, IN

Joyce Stamm University of Evansville, Evansville, IN

Jim Youngblom California State University Stanislaus, Turlock, CA

Chinmay P Rele The University of Alabama, Tuscaloosa, AL

Laura Reed The University of Alabama, Tuscaloosa, AL

microPublication Biology

https://doi.org/10.17912/micropub.biology.000474
eng
DOI: 10.22002/d1.1983
title: X-ray diffraction and photoelectrochemistry analysis for Materials Structure-Property Factorization

description: #### Package requirements (tested version):
- pandas (1.1.5)
- numpy (1.19.5)
- tensorflow (2.5.0)

#### Ternary plot requirements:
- ternary (1.0.8)
- matplotlib (3.4.2)

Development occurred in an Anaconda environment running Python 3.8.10


### code & data description
##### `NMF_illdiff.ipynb`
    code for data munging, factorization, and visualization of results.

#### source data
##### `base_plates&samples.pck`
    pandas dataframe containing DRNets phase mapping solution and nested dataframes with photoelectrochemical measurement data

##### `EweInterCV3_cathodic.pck`
    pandas dataframe containing potentials from the cathodic sweep of CV measurements
##### `IilldiffCV3_cathodic.pck`
    pandas dataframe containing photocurrents from the cathodic sweep of CV measurements
##### `select_phases_info.csv`
    pandas dataframe containing phase information for DRNets phase mapping solution

#### results
##### `illdiff_basis_info.csv`
    table containing phase information for the 11 factored basis patterns
##### `illdiff_compositions.npy`
    array of [Bi, Cu, V] atomic fractions for 335 samples; shape (335, 3)
##### `illdiff_factored_basis.npy`
    array of factored basis patterns; shape (11, 15)
##### `illdiff_phase_concentrations.npy`
    array of phase concentrations for 335 samples; shape (335, 11)
##### `illdiff_predictions.npy`
    array of predicted photocurrents for 335 samples; shape (335, 15)
DOI: 10.22002/d1.1977
title: CeNGEN scRNAseq dataset wrangled into standard WormBase anndata - 100k C. elegans cells FACS sorted for neurons in  L4 larvae

description: CeNGEN (Taylor et al 2021) scRNAseq dataset wrangled into standard WormBase anndata
100k C. elegans cells FACS sorted to enrich for neurons - 70k cells are neurons, 30k are other types

For more information about the data see the CeNGEN project website:
https://cengen.org

Preprint describing data and analysises:
https://doi.org/10.1101/2020.12.15.422897

Molecular topography of an entire nervous system - bioRxiv 2020

Seth R Taylor, Gabriel Santpere, Alexis Weinreb, Alec Barrett, Molly B. Reilly, Chuan Xu, Erdem Varol, Panos Oikonomou, Lori Glenwinkel, Rebecca McWhirter, Abigail Poff, Manasa Basavaraju, Ibnul Rafi, Eviatar Yemini, Steven J Cook, Alexander Abrams, Berta Vidal, Cyril Cros, Saeed Tavazoie, Nenad Sestan, Marc Hammarlund,  View ORCID ProfileOliver Hobert, David M. Miller III


The file `cengen_author_provided_matrices.zip` contains the original mtx files provided by the authors as outputted by CellRanger, both filtered and unfiltered.

The file `taylor2020.h5ad` contains those matrices and the metadata from the 2020 cengen data release wrangled into the WormBase standard format, which is described at:
https://github.com/WormBase/anndata-wrangling/
DOI: 10.6073/pasta/bd50d016c8c2b1ffddeb8895532f3377
title: North Temperate Lakes LTER: High Frequency Meteorological - Trout Lake Buoy2 - ADCP 2005 - 2006

description: This instrumented buoy on Trout Lake is equipped with a thermistor chain and meteorological sensors that provide fundamental information on lake thermal structure, weather conditions, and lake metabolism. An acoustic Doppler current profiler (ADCP) is associated with this buoy. Data are usually collected every 10 minutes with occasional periods of 2 minute data for short periods to answer specific questions. The thermistors are placed every 0.5-1m from the surface through 13m, and meteorological sensors measure relative humidity, air temperature and wind parameters. In the fall of 2005, the buoy also included 4 Greenspan dissolved oxygen sensors placed at depths from the lake surface to 10m. After correcting for flux to or from the atmosphere and vertical mixing within the water column, high frequency measurements of dissolved gases such as carbon dioxide and oxygen can be used to estimate gross primary productivity, respiration, and net ecosystem productivity, the basic components of whole lake metabolism. Sampling Frequency: varies for instantaneous sample. averaged to hourly and daily values from one minute samples Number of sites: 1
DOI: 10.22002/d1.1972
title: Ben-David et al 2021 scRNAseq dataset wrangled into standard WormBase anndata- 55k cells profiled with 10xv2 at L2 larval stage

description: This is part of a curated collection of all C. elegans single cell RNA sequencing 
high throughput data wrangled into the anndata format in .h5ad files 
with standard fields, plus any number of optional fields that vary depending 
on the metadata the authors provide.

As possible, we attempt to keep the field names lower case, short, descriptive, 
and only using valid Python variable names so they may be accessed via the syntax 
adata.var.field_name

For the convention used to wrangle the h5ad files see 
https://github.com/WormBase/single-cell/blob/main/data_wrangling_convention.md

The notebook used to wrangle the data is available at: 
https://github.com/WormBase/wormcells-notebooks


**Whole-organism eQTL mapping at cellular resolution with single-cell sequencing**

_Eyal Ben-David, James Boocock, Longhua Guo, Stefan Zdraljevic, Joshua S Bloom, Leonid Kruglyak_

eLife 2021;10:e65857, DOI: [https://doi.org/10.7554/eLife.65857](https://doi.org/10.7554/eLife.65857)

### Data description and links

55,508 cells profiled with 10xv2 on L2 larvae

Raw sequencing data is available at https://www.ncbi.nlm.nih.gov/bioproject/658829

The authors kindly provided the original gene count matrix without the soupX modifications, 
which is used to create the .h5ad file in this notebook. The author provided files are:
```
bendavid2021_barcode_metadata_for.csv
bendavid2021_count_matrix_wormsceQTL_unmodified.mm.gz
bendavid2021_gene_metadata.csv
```

The R object as processed by the authors with soupX is also available on GitHub together with all the code to make the figures and calculate the numbers reported in the paper:

[https://github.com/eyalbenda/worm_sceQTL/](https://github.com/eyalbenda/worm_sceQTL/)
DOI: 10.22002/d1.1960
title: Binned genomes from varnish metagenomes

description: Binned metagenome assembled genomes accompanying the manuscript "An ecophysiological explanation for manganese enrichment in rock varnish" by Lingappa et al.
DOI: 10.22002/d1.1956
title: Data set for manuscript "Tonga Slab Morphology and Stress Variations..."

description: Data associated with this manuscript, including raster files for generating Figures 3 and 4 in paper, as well as one tomography file.
description: Related Publication:
Tonga slab morphology and stress variations controlled by a relic slab: Implications for deep earthquakes in the Tonga-Fiji region

Liu, H., Gurnis, M., Leng, W., Jia, Z., & Zhan, Z. Caltech and USTC

Geophysical Research Letters

2021-03-22

https://doi.org/10.1029/2020GL091331
eng
DOI: 10.22002/d1.1946
title: Resolving simulated sequences of earthquakes and fault interactions: implications for physics-based seismic hazard assessment

description: Included is simulated data pertaining to the article "Resolving simulated sequences of earthquakes and fault interactions: implications of physics-based seismic hazard assessment" submitted to the Journal of Geophysical Research: Solid Earth.
DOI: 10.22002/d1.1948
title: CLARS-FTS XCH4 and XCO2 retrievals (June 2013 - May 2014) from GFIT3 algorithm

description: Remote sensing of greenhouse gases (GHGs) in cities, where high GHG emissions are typically associated with heavy aerosol loading, is challenging due to retrieval uncertainties caused by imperfect characterization of scattering by aerosols. We investigate this problem by developing GFIT3, a full physics algorithm to retrieve GHGs (CO2 and CH4) by accounting for aerosol scattering effects in polluted urban atmospheres. In particular, the algorithm includes coarse (including sea salt and dust) and fine (including organic carbon, black carbon, and sulfate) mode aerosols in the radiative transfer model. The performance of GFIT3 is assessed using high spectral resolution observations over the Los Angeles (LA) megacity made by the California Laboratory for Atmospheric Remote Sensing–Fourier Transform Spectrometer (CLARS–FTS). CLARS–FTS is located on Mt. Wilson, California, at 1.67 km a.s.l. overlooking the LA basin, and makes observations of reflected sunlight in the near-infrared spectral range. The first set of evaluations are performed by conducting retrieval experiments using synthetic spectra. We find that errors in the retrievals of column-averaged dry air mole fractions of CO2 (XCO2) and CH4 (XCH4) due to uncertainties in the aerosol optical properties and atmospheric a priori profiles are less than 1 % on average. This indicates that atmospheric scattering does not induce a large bias in the retrievals when the aerosols are properly characterised. The methodology is then further evaluated by comparing GHG retrievals using GFIT3 with those obtained from the CLARS-GFIT algorithm (used for currently operational CLARS retrievals) that does not account for aerosol scattering. We find a significant correlation between retrieval bias and aerosol optical depth (AOD). Comparison of GFIT3 AOD retrievals with collocated ground-based observations from AERONET shows that the developed algorithm produces very accurate results, with biases in AOD estimates of about 0.02. Finally, we assess the uncertainty in the widely used tracer-tracer ratio method to obtain CH4 emissions based on CO2 emissions, and find that using the CH4 / CO2 ratio effectively cancels out biases due to aerosol scattering. Overall, this study of applying GFIT3 to CLARS-FTS observations improves our understanding of the impact of aerosol scattering on the remote sensing of GHGs in polluted urban atmospheric environments. GHG retrievals from CLARS-FTS are potentially complementary to existing ground-based and space-borne observations to monitor anthropogenic GHG fluxes in megacities.
description: Related Publication:
GFIT3: A full physics retrieval algorithm for remote sensing of greenhouse gases in the presence of aerosols

https://doi.org/10.5194/amt-2021-84
eng