cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21637559.v1
title: E$$ENTIAL MEDICINE$ Challenge Database_Pilot_29 Nov 2022

description: This is a pilot of the database that conbined all the data collected from the News Flash, Price Hike$ and Cirlce of LIfe challanges of E$$ENTIAL MEDICINE$. <br> It was designed by students at the University of Sydney.
DOI: 10.5519/qd.2l7sr57e
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (1 records)
DOI: 10.22002/d1.1444
title: Data for 'Imaging cell lineage with a synthetic digital recording system'

description: This deposit contains the data, code, and analysis to recreate the results in the manuscript, 'Imaging cell lineage with a synthetic digital recording system', and the sequence information of relevant constructs. The datasets are organized by figures, and the codes are written for MatLab, R, and Python. Please see the related publication for more details, and contact the corresponding authors for any questions.
description: Related Publication:
Imaging cell lineage with a synthetic digital recording system

https://doi.org/10.1101/2020.02.21.958678
eng
DOI: 10.22002/d1.2195
title: Data for Ph.D. thesis, "Chapter 3: Building serine-integrase based, image-readable recording systems"

description: This deposit contains the data, code, analysis, and sequence files for KeHuan Edmonds's thesis, "Chapter 3: Building serine-integrase based, image-readable recording systems". The datasets are organized by figures, and the codes are written for MatLab and Python.
DOI: 10.22002/d1.1622
title: Supplementary files 2.1 and 2.2

description: Supplementary files for Chapter 2
DOI: 10.22002/d1.1986
title: d13C and d34S of Dissolved Organic Matter (DOM, DOS)

description: Data set of SPE extracted Dissolved Organic Matter samples that accompanies A Phillips' Thesis Chapter 3 on resolving sources of DOM using novel sulfur isotope analysis. Contains relevant metadata as well as measured parameters (d13C, d34S, C/S)
description: Contact person: Sessions, Alex als@gps.caltech.edu
DOI: 10.5281/zenodo.7374621
title: Nanopore sequencing of plasmid cleavage fragments produced with type III CRISPR-associated nucleases NucC, Can1 and Can2

description: Included datasets were generated in the study "<strong>Sequence-specific capture and concentration of viral RNA </strong><strong>by type III CRISPR system enhances diagnostic"</strong> by Nemudraia et al., 2022 For questions contact: Artem Nemudryi (artem.nemudryi@gmail.com) or Blake Wiedenheft (bwiedenheft.com)
description: This work was supported by National Institutes of Health (United States) grant 1K99AI171893-01 (A. Nemudryi). Research in the Wiedenheft lab is supported by the NIH (R35GM134867), the M.J. Murdock Charitable Trust, a young investigator award from Amgen, a generous gift from the Rosolowsky family, and the Montana State University Agricultural Experimental Station (USDA NIFA).
DOI: 10.5281/zenodo.7374620
title: Nanopore sequencing of plasmid cleavage fragments produced with type III CRISPR-associated nucleases NucC, Can1 and Can2

description: Included datasets were generated in the study "<strong>Sequence-specific capture and concentration of viral RNA </strong><strong>by type III CRISPR system enhances diagnostic"</strong> by Nemudraia et al., 2022 For questions contact: Artem Nemudryi (artem.nemudryi@gmail.com) or Blake Wiedenheft (bwiedenheft.com)
description: This work was supported by National Institutes of Health (United States) grant 1K99AI171893-01 (A. Nemudryi). Research in the Wiedenheft lab is supported by the NIH (R35GM134867), the M.J. Murdock Charitable Trust, a young investigator award from Amgen, a generous gift from the Rosolowsky family, and the Montana State University Agricultural Experimental Station (USDA NIFA).
DOI: 10.5281/zenodo.7374289
title: Dataset and R Code for Species-level Avian Influenza Phylogenetic Generalized Least Squares Regression

description: Dataset for Species-level Avian Influenza Phylogenetic Generalized Least Squares (PGLS) Regression:<br> Variables include taxonomic information for each species, # of IAV-positive individuals, # of IAV-tested individuals, the prevalence of IAV, the proportion of diet made up of different food types, the proportion of foraging time spent in different strata (below water, water surface, ground, understory, etc), sampling-related variables (mean latitude, mean date, the proportion of hatch year individuals), migration and territoriality category, climatologic variables, mean clutch size, and mating system. R Code for PGLS and Avian Influenza Prevalence ContMap.
description: This work was supported by the National Center for Advancing Translational Sciences, National Institutes of Health, Award Number TL1TR002546 (Cummings) and a National Science Foundation RAPID, Award Number 2234970 (Hill).
DOI: 10.5281/zenodo.7374288
title: Dataset and R Code for Species-level Avian Influenza Phylogenetic Generalized Least Squares Regression

description: Dataset for Species-level Avian Influenza Phylogenetic Generalized Least Squares (PGLS) Regression:<br> Variables include taxonomic information for each species, # of IAV-positive individuals, # of IAV-tested individuals, the prevalence of IAV, the proportion of diet made up of different food types, the proportion of foraging time spent in different strata (below water, water surface, ground, understory, etc), sampling-related variables (mean latitude, mean date, the proportion of hatch year individuals), migration and territoriality category, climatologic variables, mean clutch size, and mating system. R Code for PGLS and Avian Influenza Prevalence ContMap.
description: This work was supported by the National Center for Advancing Translational Sciences, National Institutes of Health, Award Number TL1TR002546 (Cummings) and a National Science Foundation RAPID, Award Number 2234970 (Hill).
DOI: 10.6084/m9.figshare.21637580
title: ALCOHOL, INJURY, & OUTCOMES IN OLDER ADULT TRAUMA

description: Data set for <em>Alcohol Use, Injury Characteristics, and Outcomes in Older Adult Trauma Patients</em> <br> <strong>NOTE:</strong><strong> </strong>PLEASE DOWNLOAD THE ORIGINAL FILE TO PROPERLY VIEW DATA AND KEY; PROPER FORMATTING IS NOT REFLECTED IN FIGSHARE'S CONTENT PREVIEW. <br> Thank you for your interest in our research! Please refer to the manuscript for context and our full list of authors.
DOI: 10.6084/m9.figshare.21637580.v1
title: ALCOHOL, INJURY, & OUTCOMES IN OLDER ADULT TRAUMA

description: Data set for <em>Alcohol Use, Injury Characteristics, and Outcomes in Older Adult Trauma Patients</em> <br> <strong>NOTE:</strong><strong> </strong>PLEASE DOWNLOAD THE ORIGINAL FILE TO PROPERLY VIEW DATA AND KEY; PROPER FORMATTING IS NOT REFLECTED IN FIGSHARE'S CONTENT PREVIEW. <br> Thank you for your interest in our research! Please refer to the manuscript for context and our full list of authors.
DOI: 10.5519/qd.ezx7vzqj
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (473 records)
DOI: 10.22002/d1.1987
title: Women Doing Science Instagram Engagement and Survey Results

description: Data set that accompanies Alex Phillips' Thesis Chapter 4 on the social media page Women Doing Science. The Instagram page was analyzed fro trends of engagement and cross referenced with a demographic survey of featured scientists.
description: <br>Cite this record as:<br>Phillips, A. (2021). <i>Women Doing Science Instagram Engagement and Survey Results</i> (Version 1.0) [Data set]. CaltechDATA. https://doi.org/10.22002/D1.1987<br> or choose a different citation style.<br>Download Citation<br>
description: <br>Unique Views: 12<br>Unique Downloads: 0<br> between June 04, 2021 and July 12, 2021<br>More info on how stats are collected<br>
DOI: 10.22002/d1.1407
title: Single cell profiling of capillary blood enables out of clinic human immunity studies

description: Instructions for loading this dataset available at https://github.com/thomsonlab/capblood-seq
DOI: 10.22002/d1.2090
title: Deep parallel characterization of AAV tropism and AAV-mediated transcriptional changes via single-cell RNA sequencing

description: Engineered variants of recombinant adeno-associated viruses (rAAVs) are being developed rapidly to meet the need for gene-therapy delivery vehicles with particular cell-type and tissue tropisms. While high-throughput AAV engineering and selection methods have generated numerous variants, subsequent tropism and response characterization have remained low throughput and lack resolution across the many relevant cell and tissue types. To fully leverage the output of these large screening paradigms across multiple targets, we have developed an experimental and computational single-cell RNA sequencing (scRNA-seq) pipeline for in vivo characterization of barcoded rAAV pools at high resolution. Using this platform, we have both corroborated previously reported viral tropisms and discovered unidentified AAV capsid targeting biases. As expected, we observed that the tropism profile of AAV.CAP-B10 in mice was shifted toward neurons and away from astrocytes when compared with AAV-PHP.eB. Transcriptomic analysis revealed that this neuronal bias is due mainly to increased targeting efficiency for glutamatergic neurons, which we confirmed by RNA fluorescence in situ hybridization. We further uncovered cell subtype tropisms of AAV variants in vascular and glial cells, such as low transduction of pericytes and Myoc+ astrocytes. Additionally, we have observed cell-type-specific transitory responses to systemic AAV-PHP.eB administration, such as upregulation of genes involved in p53 signaling in endothelial cells three days post-injection, which return to control levels by day twenty-five. The presented experimental and computational approaches for parallel characterization of AAV tropism with ability to simultaneously measure the transcriptional response of transduction will facilitate the advancement of safe and precise gene delivery vehicles.
description: Related Publication:
Deep parallel characterization of AAV tropism and AAV-mediated transcriptional changes via single-cell RNA sequencing

https://doi.org/10.1101/2021.06.25.449955
eng
DOI: 10.22002/d1.20181
title: Ligand-receptor promiscuity enables complex computations

description: This folder provides all data and code needed to reproduce the analysis and figures of Chapter 2 ("Ligand-Receptor Promiscuity Enables Complex Computations") in the associated thesis, "Principles of Addressing Specificity in Promiscuous Ligand-Receptor Systems." All code is written in Python, with analysis provided in a Jupyter notebook.
DOI: 10.22002/d1.1692
title: Ligand-receptor promiscuity enables cellular addressing

description: In multicellular organisms, secreted ligands selectively activate, or "address," specific target cell populations to control cell fate decision-making and other processes. Key cell-cell communication pathways use multiple promiscuously interacting ligands and receptors, provoking the question of how addressing specificity can emerge from molecular promiscuity. To investigate this issue, we developed a general mathematical modeling framework based on the bone morphogenetic protein (BMP) pathway architecture. We find that promiscuously interacting ligand-receptor systems allow a small number of ligands, acting in combinations, to address a larger number of individual cell types, defined by their receptor expression profiles. Promiscuous systems outperform seemingly more specific one-to-one signaling architectures in addressing capability. Combinatorial addressing extends to groups of cell types, is robust to receptor expression noise, grows more powerful with increasing numbers of receptor variants, and is maximized by specific biochemical parameter relationships. Together, these results identify design principles governing cellular addressing by ligand combinations.
description: This dataset contains the data, code, and scripts to reproduce the results in the manuscript, "Ligand-receptor promiscuity enables cellular addressing." Within this resource, data and scripts are organized by figure. All code is written in Python, with analysis scripts provided as Jupyter notebooks.
DOI: 10.22002/d1.2091
title: Supplementary Table S1 presents motile cell counts and mean swimming speeds for wild type and ΔhpnH Bradyrhizobium diazoefficiens.

description: This dataset presents motile cell counts and mean swimming speeds for wild type and ΔhpnH Bradyrhizobium diazoefficiens.
description: Related Publication:
Extended Hopanoid Loss Reduces Bacterial Motility and Surface Attachment and Leads to Heterogeneity in Root Nodule Growth Kinetics in a Bradyrhizobium-Aeschynomene Symbiosis

Brittany J. Belin Division of Biology and Biological Engineering, California Institute of Technology

Elise M. Tookmanian Division of Chemistry and Chemical Engineering, California Institute of Technology

Jaime de Anda Department of Bioengineering, Department of Chemistry and Biochemistry, and California NanoSystems Institute, University of California Los Angeles

Gerard C. Wong Department of Bioengineering, Department of Chemistry and Biochemistry, and California NanoSystems Institute, University of California Los Angeles

Dianne K. Newman Division of Biology and Biological Engineering & Division of Geological and Planetary Sciences, California Institute of Technology

Molecular Plant-Microbe Interactions

2019-09-27

https://doi.org/10.1094/MPMI-04-19-0111-R
eng
DOI: 10.22002/d1.1597
title: Hyperspectral reflectance at Niwot Ridge, Colorado 2017-2018

description: 2 individual datasets are provided to accompany the following article: Rui Cheng, Troy S. Magney, Debsunder Dutta, David R. Bowling, Barry A. Logan, SeanP. Burns, Peter D. Blanken, Katja Grossmann, Sophia Lopez, Andrew D. Richardson,Jochen Stutz, and Christian Frankenberg. Accepted online Aug 2 2020. Decomposing reflectance spectra to track gross primary productionin a subalpine evergreen forest. Biogeosciences. doi: 10.5194/bg-2020-41. This dataset will provide researchers with daily-averaged and canopy-averaged reflectance spectra for the evergreen needleleaf forest presented in the main figures presented in the paper. More information on the methods can be found in the paper and supplementary information doi: 10.5194/bg-2020-41. Please contact Rui Cheng, rui.cheng@caltech.edu, if you plan to use the data or have any questions.
description: Related Publication:
Decomposing reflectance spectra to track gross primary production in a subalpine evergreen forest

Rui Cheng California Institute of Technology

Biogeosciences

https://doi.org/10.5194/bg-2020-41
eng
DOI: 10.3886/e101132v1-130913
title: National Estimates of Police Use of Force

description: This project uses data on police use of force reported in the 2012 LEMAS Survey and, in combination with arrest data from the FBI Uniform Crime Reporting Program, produces a national estimates of the amount of force used by the state, county, and local general purpose law enforcement agencies during in 2012.<br>
description: See documentation in codebook for ICPSR Study 36164<br><br>Base Sampling Weight for Each Stratum<br>Non-Response Adjustment for Stratum<br>Final Weight for Each Stratum<br><br>
description: Response Rates: The 2012 LEMAS survey had an 86% response rate.<br>
description: Local police departments and sheriffs’ offices are chosen for the LEMAS Survey using a stratified sample design based on number of<br>sworn personnel. The original 2013 LEMAS sample included 3,336 state and local law enforcement agencies. It was designed to be<br>representative of all general purpose state and local law enforcement agencies in the United States, with separate samples drawn of<br>local police departments and sheriffs’ offices. All 50 primary state law enforcement agencies (state police and highway patrol) were<br>included. Agencies serving special jurisdictions (such as schools, airports, or parks), or with special enforcement responsibilities (such<br>as conservation laws or alcohol laws), were considered out of scope for the survey.<br><br>See ICPSR Study 36164 Codebook for additional details.<br><br>BJS has not provided a list of agencies sampled but which did not respond to this survey.<br><br>
description: Smallest Geographic Unit: Varied
description: web-based survey;
DOI: 10.5281/zenodo.6537159
title: Mapa bairros de Fortaleza-CE

description: Script, dados e arquivo shape.
DOI: 10.5281/zenodo.6537158
title: Mapa bairros de Fortaleza-CE

description: Script, dados e arquivo shape.
DOI: 10.22002/d1.1437
title: Sequences associated with Anders Knight's thesis research

description: DNA and amino-acid sequences for proteins and oligonucleotide primer sequences used as part of Anders Knight's thesis research. Stored in csv format.
DOI: 10.22002/d1.1398
title: Phenazine survival TnSeq

description: This dataset is supplementary material for Scott Saunders's thesis. Specifically it is associated with the appendix: IDENTIFYING MECHANISMS OF PHENAZINE CYCLING WITH TN-SEQ.

This dataset is the result of a genetic screen for mechanisms of phenazine mediated survival in Pseudomonas aeruginosa. Please see the thesis, "Mechanisms of phenazine-mediated extracellular electron transfer by Pseudomonas aeruginosa" for more detail.
description: Related Publication:
Mechanisms of phenazine-mediated extracellular electron transfer by Pseudomonas aeruginosa

Caltech Thesis

2020-04-01
eng
DOI: 10.34740/kaggle/dsv/4611725
title: BBC News
DOI: 10.5281/zenodo.7374765
title: Spatial analysis of Measles Vaccination Coverage in the State of São Paulo

description: Dataset for the article Spatial Analysis of Measles Vaccination Coverage in the State of São Paulo. The aim of the present study was to evaluate first and second dose of measles vaccine coverage (VC) in the cities of São Paulo and its spatial dynamics between 2015 and 2020. Method: It is a mixed-type ecological study After calculating the VC, the following four categories were created: very low, low, adequate, and high, and the spatial autocorrelation of VC was analyzed using the Global and Local Moran’s statistics. The dataset is divided by year and by vaccine type.
DOI: 10.5281/zenodo.7374764
title: Spatial analysis of Measles Vaccination Coverage in the State of São Paulo

description: Dataset for the article Spatial Analysis of Measles Vaccination Coverage in the State of São Paulo. The aim of the present study was to evaluate first and second dose of measles vaccine coverage (VC) in the cities of São Paulo and its spatial dynamics between 2015 and 2020. Method: It is a mixed-type ecological study After calculating the VC, the following four categories were created: very low, low, adequate, and high, and the spatial autocorrelation of VC was analyzed using the Global and Local Moran’s statistics. The dataset is divided by year and by vaccine type.
DOI: 10.25346/s6/rxic1u
title: Basilica of Santa Maria Maggiore Archive

description: Coming soon.
DOI: 10.25346/s6/f0tc7i
title: Basilica of Santa Maria Maggiore VSim Files

description: Coming soon.
DOI: 10.25346/s6/9bochq
title: The Colosseum (Flavian Amphitheater) Archive

description: Coming soon
DOI: 10.6084/m9.figshare.21599544
title: fusion_proteins_to_functions.tsv.gz

description: Dataset detailing assignment of bacterial proteins to functions determined by Fusion. File is tab-separated. Columns in file: fusion_protein_id -&gt; internal identifier ncbi_accession -&gt; accession number of protein as reported in NCBI protein database seguid -&gt; SegUID of protein sequence protein_name -&gt; name of protein as extracted from fasta file (Genbank) sequence_type -&gt; whether protein orginates from bacterial genome (chromosome) or plasmid fusion_function_id -&gt; fusion function identifier (fuctions start with prefix 'P-', singletons start with prefix 'S-') organism_name -&gt; name of bacterial organism ncbi_taxid -&gt; taxid of organism as annoated in NCBI ncbi_species_taxid -&gt; species taxid of organism as annotated by NCBI assembly_accession -&gt; assemby accession id
DOI: 10.6084/m9.figshare.21599544.v2
title: fusion_proteins_to_functions.tsv.gz

description: Dataset detailing assignment of bacterial proteins to functions determined by Fusion. File is tab-separated. Columns in file: fusion_protein_id -&gt; internal identifier ncbi_accession -&gt; accession number of protein as reported in NCBI protein database seguid -&gt; SegUID of protein sequence protein_name -&gt; name of protein as extracted from fasta file (Genbank) sequence_type -&gt; whether protein orginates from bacterial genome (chromosome) or plasmid fusion_function_id -&gt; fusion function identifier (fuctions start with prefix 'P-', singletons start with prefix 'S-') organism_name -&gt; name of bacterial organism ncbi_taxid -&gt; taxid of organism as annoated in NCBI ncbi_species_taxid -&gt; species taxid of organism as annotated by NCBI assembly_accession -&gt; assemby accession id
DOI: 10.6084/m9.figshare.21599544.v1
title: fusion_proteins_to_functions.tsv.gz

description: Dataset detailing assignment of bacterial proteins to functions determined by Fusion. File is tab-separated. Columns in file: fusion_protein_id -&gt; internal identifier ncbi_accession -&gt; accession number of protein as reported in NCBI protein database seguid -&gt; SegUID of protein sequence protein_name -&gt; name of protein as extracted from fasta file (Genbank) sequence_type -&gt; whether protein orginates from bacterial genome (chromosome) or plasmid fusion_function_id -&gt; fusion function identifier (fuctions start with prefix 'P-', singletons start with prefix 'S-') organism_name -&gt; name of bacterial organism ncbi_taxid -&gt; taxid of organism as annoated in NCBI ncbi_species_taxid -&gt; species taxid of organism as annotated by NCBI assembly_accession -&gt; assemby accession id
DOI: 10.25346/s6/mvrdmr
title: The Colosseum (Flavian Amphitheater) VSim Files

description: Coming soon.
DOI: 10.6084/m9.figshare.21637988
title: Fusion based organism similarities (balanced organism set)

description: This dataset contains Fusion function profile based organsim similarities reported in (tbd)
DOI: 10.6084/m9.figshare.21637988.v1
title: Fusion based organism similarities (balanced organism set)

description: This dataset contains Fusion function profile based organsim similarities reported in (tbd)
DOI: 10.6084/m9.figshare.21637754
title: THE INFLUENCE OF VARIOUS PREHEATING AND DIRECTION OF MAGNETIC FIELD ON COMBUSTION CHARACTERISTICS OF PALM OIL DROPLETS FOR BOILER COMBUSTION IN POWER GENERATION SYSTEM

description: The effects of various preheating palm oil and the direction of magnetic field on the behavior of flames in the combustion process. it was found that the higher the preheating, the easier the length of the broken carbon chain will be to diffuse into the surrounding environment, magnetic field attracts the molecules of oxygen and fuel toward the reaction zone, causing the combustion to occur rapidly and the more reactive the combustion speed, the flame is short and more stable.
DOI: 10.3886/e162581
title: Code for: "Monopsony in the U.S. Labor Market"

description: This paper quantifies employer market power in U.S. manufacturing and how it has changed over time. Using administrative data, we estimate plant-level markdowns—the ratio between a plant’s marginal revenue product of labor and its wage. We find most manufacturing plants operate in a monopsonistic environment, with an average markdown of 1.53, implying a worker earning only 65 cents on the marginal dollar generated. To investigate long-term trends for the entire sector, we propose a novel, theoretically grounded measure for the aggregate markdown. We find that it decreased between the late 1970s and the early 2000s, but has been sharply increasing since.