cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7302/qq3g-p906
title: CT Data of UMMP VP 81822, Cantius trigonodus right proximal metatarsal 1

description: Reconstructed CT slices for a right proximal metatarsal 1 of the Cantius trigonodus (University of Michigan Museum of Paleontology catalog number UMMP VP 81822), as a series of TIFF images. Raw projections are not included in this dataset.
description: Specimen UMMP VP 81822 was scanned with a Nikon XT H 225ST μCT system housed in the Department of Earth and Environmental Sciences at the University of Michigan. Scans were collected with the following settings: energy settings, 110 kV, 80 µA
description: source to object distance, 43.083057 mm
description: scanned with 3141 projections
description: voxel size, x = y = z = 0.015596 mm
description: slice dimension (in pixels),  x = 538, y = 465
description: number of slices, 931 16-bit TIFF images. Additional metadata can be found in the xtek and vgi files.
DOI: 10.7302/z2m906tq
title: Gelada foraging ecology in the Simien Mountains, Ethiopia

description: This includes data used for analysis for the publication: "Graminivory and fallback foods: Annual diet profile of geladas (Theropithecus gelada) living in the Simien Mountains National Park, Ethiopia".

A revised version of the "foraging.scans.xlsx" file was uploaded as a csv file on Dec 13, 2017 to include the addition of the "crop" as category in the "Diet.Item" column. Previously "crop" was included in the "other" category. An updated version of the "readme_foraging.scans.txt" was uploaded on Dec 13, 2017 to account for this change, provide additional information on variables in the "season" column and to include contact information for the creator of the data set. Revised versions of two other files "readme_rainfall.txt" and "readme_underground.samples.txt" were also uploaded on Dec 13, 2017. Both revisions include additional information to account for missing variables and contact information for the creator of the data set.

The original files are retained in this data set and are marked as being the originals in the file name. Note: A citation to the related article was added to the metadata on March 12, 2018.
description: This dataset contains four files: foraging.scans.csv, transects.csv, underground.samples.csv, and rainfall.csv. Foraging data were collected using instantaneous scan samples from adult geladas, collected at 10-minute intervals. Transect data were collected using the point-intercept method. Underground samples were collected using a soil core. Rainfall data were collected with a rain gauge. Further details of the methods used in each data set are described in the associated meta data.
DOI: 10.7302/9zwy-zs82
title: Data set: Shock Inclination Effects in Preliminary Impulse Propagation Observed by Ground-Based Magnetometers and the Heliophysics System Observatory.

description: This database contains spacecraft and ground-based magnetic field observations made to study the propagation of the preliminary impulse triggered by interplanetary shocks with different inclinations in the XZ plane.
description: The data and figures presented in this data set are classified by "event''. Events consist in solar winds conditions that meet certain conditions: (1) a sudden increase in the solar wind dynamic pressure, and (2) the solar wind dynamic pressure increase occurs during northward interplanetary magnetic field conditions. In order to detect such events, we developed an algorithm that search for the following conditions: (1) the increase of the SYM-H index must be larger than 6 nT
description: (2) the rise time must be in less than 10 minutes
description: (3) the SYM-H increase must occur after at least 15 minutes of northward interplanetary magnetic field and stay for at least 5 minutes. (4) shock information available in the Interplanetary Shock Database of the Center for Astrophysics (CfA), and (5) the preliminary impulse must be recognizable in the ground-based station data from at least 3 stations between a 2-hour local time window. Details about the methodology used for the detection of the events are described in the paper
DOI: 10.7302/pz7e-r328
title: Supplementary Particle Optical Property Data for "Aerosol radiative forcing from the 2010 Eyjafjallajökull volcanic eruptions"

description: This dataset includes spectrally-resolved optical properties for volcanic ash particles from the 2010 Eyjafjallajökull volcanic eruptions.  These properties were used in the climate simulations described by Flanner et al. (2014, doi:10.1002/2014JD021977) to quantify ash radiative forcing from the eruptions.

description: A detailed description of the methodology used to create these ash particle optical properties can be found in the accompanying journal article (Flanner et al., 2014, doi:10.1002/2014JD021977). Briefly, these properties were generated with Mie solutions and refractive indices described in the journal article.  Calculations were done for 100 particle sizes within each size bin, and sub-bin weighting was achieved with a lognormal size distribution of effective radius 2.24um and geometric standard deviation of 2.8, representing global-mean properties of the ash fields that we applied.  Properties are listed for 14 shortwave bands and 16 longwave bands, with spectral boundaries corresponding to those used in the Rapid Radiative Transfer Model (RRTMG) embedded in the Community Atmosphere Model.  Properties were calculated at 100 wavelengths within each spectral band. Sub-band spectral weighting was achieved with top-of-atmosphere spectral irradiance data for shortwave properties, and with a 250 K Planck function for longwave properties.  An ash density of 2600 kg m^-3 was assumed for translating Mie properties into mass-normalized optical properties.  Note that imaginary refractive indices do not change monotonically with scenario in all parts of the longwave spectrum and generally exhibit smaller relative differences than the shortwave scenarios of refractive index (Figure 1).  This leads to mass absorption cross-sections that are not always monotonic with scenario (e.g., for some wavelength bands and particle sizes the longwave mass absorption in the low scenario exceeds that in the high scenario).  Integrated over all particle sizes and wavelengths, however, these scenarios lead to their respective ordering of global-mean longwave radiative forcing by ash.
DOI: 10.7302/vvqp-ma61
title: Pharmacometabolomics of L-carnitine-Kaplan-Meier survival data: numbers at risk

description: These data were produced from the survival analysis of the pre-treatment metabolomics data generated from the Phase II clinical trial of L-carnitine treatment for septic shock (the RACE trial - see https://clinicaltrials.gov/ct2/show/NCT01665092). The results based on respective acetylcarnitine or valine concentration are presented (pdf). The csv files contain the at risk numbers from the Kaplan-Meier survival analysis. These findings described in our manuscript: Pharmacometabolomics Identifies Candidate Predictor Metabolites of an L-carnitine Treatment Mortality Benefit in Septic Shock.;All of the metabolomics data are available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org which is supported by NIH grant U2C-DK119886 and where it has been assigned Project ID (accession number ST001319).  The data can be accessed directly via its Project DOIs: (DOI: http://dx.doi.org/10.21228/M8VX0Z).
description: Survival analysis was performed on a sub-group of septic shock patients from the RACE trial (https://clinicaltrials.gov/ct2/show/NCT01665092) that received either L-carnitine (18g) or placebo based on pre-treatment serum acetylcarnitine or valine concentration. Acylcarnitines (including acetylcarnitine) were measured using LC-MS and valine, a branched chain amino acid, was measured by nuclear magnetic resonance (NMR)-spectroscopy.
DOI: 10.7302/tbqm-bj52
title: Atlantic Fulfulde-speaking (Mali) village photos

description: Images of villages in Mali in which Atlantic Fulfulde is the primary language. Each file name contains important information about the photos, and are structured thus: LanguageFamily_Language_IdentificationNumber_GeographicCoordinate_Description_Date_InitialsOfThePhotographer
description: Photography
DOI: 10.7302/6fv8-bv53
title: Transcriptomic Profiles of Sepsis in the Human Brain

description: This study was conducted  to detect and analyze modules, or clusters of genes, associated with sepsis, using RNAseq data obtained from 12 participants who died of sepsis and 12 participants who died of non-infectious critical illness while hospitalized.
This deposit contains the input data and parameters needed to reproduce the weighted gene co-expression network analysis (WGCNA) and gene enrichment analysis performed on this data. This analysis requires the R packages "WGCNA" version 1.68 and  "DESeq2" version 1.22.2 available for download from bioconductor (http://bioconductor.org). The external bioinformatics tool DAVID version 6.8 (https://david.ncifcrf.gov/) was used as an additional gene enrichment analysis. Please see the supplemental methods document within this deposit and published research letter for more detailed information. 
description: RNA was isolated from human post-mortem parietal cortex tissue samples. RNAseq was performed by the University of Michigan Advanced Genomics core, data was QC'd and initially analysed by the University of Michigan Bioinformatics core using standardized methods. The secondary analyses was performed using R.
DOI: 10.7302/3m31-yb44
title: Core photos for MV0811-14JC

description: This dataset contains core photos for the jumbo piston core MV0811-14JC (34.2818°N 120.0360°W, water depth: 582 m) retrieved in 2008.11 on R/V Melville off Southern California. MV0811-14JC contains 10 sections (section 1-10). Sections 1-3 were scanned at the LacCore Facility (National Lacustrine Core Facility) at University of Minnesota, while photos for section 4-10 were taken at Marine Geology Repository at Oregon State University. The study is funded by NSF-OCE 1304327.;Data citation: Hendy, I.L., Wang, Y. (2019). Core photos for MV0811-14JC [Data set]. University of Michigan Deep Blue Data Repository. https://doi.org/10.7302/3m31-yb44
description: The core photos were obtained from high-resolution line scan imaging system.
DOI: 10.7302/679b-dw96
title: CRIMSON open source project - Graphical User Interface (GUI) Source Code and Application Examples for PLOS Computational Biology

description: This repository contains the source code for the CRIMSON GUI, as required in the PLOS Computational Biology publication:

CRIMSON: An Open-Source Software Framework for Cardiovascular Integrated Modelling and Simulation by the same authors.;This is a snapshot of the software; build dependencies can be found at 	
https://doi.org/10.7302/ssj9-n788. Please visit 
https://github.com/carthurs/CRIMSONGUI/releases/tag/PLOS_Comp_Bio & www.crimson.software for more general information and the most up to date version of the software.;Software can be compiled in Windows.
description: This deposit concerns the CRIMSON (CardiovasculaR Integrated Modelling and SimulatiON) software environment. CRIMSON provides a powerful, customizable and user-friendly system for performing three-dimensional and reduced-order computational haemodynamics studies via a pipeline which involves: 1) segmenting vascular structures from medical images
description: 2) constructing analytic arterial and venous geometric models
description: 3) performing finite element mesh generation
description: 4) designing, and 5) applying boundary conditions
description: 6) running incompressible Navier-Stokes simulations of blood flow with fluid-structure interaction capabilities
description: and 7) post-processing and visualizing the results, including velocity, pressure and wall shear stress fields.
description: A key aim of CRIMSON is to create a software environment that makes powerful computational haemodynamics tools accessible to a wide audience, including clinicians and students, both within our research laboratories and throughout the community. The overall philosophy is to leverage best-in-class open source standards for medical image processing, parallel flow computation, geometric solid modelling, data assimilation, and mesh generation. It is actively used by researchers in Europe, North and South America, Asia, and Australia. It has been applied to numerous clinical problems
description: we illustrate applications of CRIMSON to real-world problems using examples ranging from pre-operative surgical planning to medical device design optimization.
description: CRIMSON binaries for Microsoft Windows 10, documentation and example input files are freely available for download from www.crimson.software.
DOI: 10.7302/z24q7s64
title: Data in support of the study "Modeled Response of Greenland Snowmelt to the Presence of Biomass Burning-Based Absorbing Aerosols in the Atmosphere and Snow"

description: Biomass burning produces smoke aerosols that are emitted into the atmosphere. Some smoke constituents, notably black carbon (BC), are highly effective light-absorbing aerosols (LAA). Emitted LAA can be transported to high albedo regions like the Greenland Ice Sheet (GrIS) and affect local snowmelt. In the summer, the effects of LAA in Greenland are uncertain. To explore how LAA affect GrIS snowmelt and surface energy flux in the summer, we conduct idealized global climate model simulations with perturbed aerosol amounts and properties in the GrIS snow and overlying atmosphere. The in-snow and atmospheric aerosol burdens we select range from background values measured on the GrIS to unrealistically high values. This helps us explore the linearity of snowmelt response and to achieve high signal-to-noise ratios. With LAA operating only in the atmosphere, we find no significant change in snowmelt due to the competing effects of surface dimming and tropospheric warming. Regardless of atmospheric LAA presence, in-snow BC-equivalent mixing ratios greater than ~60 ng/g produce statistically significant snowmelt increases over much of the GrIS. We find that net surface energy flux changes correspond well to snowmelt changes for all cases. The dominant component of surface energy flux change is solar energy flux, but sensible and longwave energy fluxes respond to temperature changes. Atmospheric LAA dampen the magnitude of solar radiation absorbed by in-snow LAA when both varieties are simulated. In general, the significant melt and surface energy flux changes we simulate occur with LAA quantities that have never been recorded in Greenland.
description: The data are model output from climate simulations conducted with the Community Earth System Model (CESM) version 1.0.3
DOI: 10.7302/ph8z-rr39
title: Adverse events associated with intra-hospital transport of critically-ill children: a systematic review dataset

description: The research adheres to PRISMA-HARM recommendations for systematic reviews. The reproducible search strategies for all databases, the citation export files from all databases, and the eligibility screening decisions are included in the dataset. 
description: Comprehensive literature searches were run in Ovid MEDLINE, Embase.com, CINAHL (EBSCOhost), and the Cochrane Central Register of Controlled Trials. The results of all searches were exported to Endnote X8. All citations were screened for eligibility in two rounds by three authors, using predefined criteria. The first round of screening involved titles and abstracts. The second round consisted of full-text review, with data extraction occurring for all studies that survived the screening process.
DOI: 10.7302/v6r0-2j38
title: WRF-Chem Central US - Hygroscopicity tests

description: WRF-Chem model
description: WRF-Chem model
DOI: 10.7302/7gfh-6436
title: Simplified endoscopic mucosal assessment of Crohn's disease

description: Data comparing the Simplified Endoscopic Mucosal Assessment for Crohn's Disease (SEMA-CD) from video recordings of colonoscopies to SEMA-CD scoring of their corresponding colonoscopy reports from pediatric patients with Crohn's disease.
description: SEMA-CD scoring from colonoscopy reports was recorded from central readers via Qualtrics, cleaned with Stata, and exported into Excel.
description: SEMA-CD scoring from previous colonoscopy videos published at https://doi.org/10.1093/ibd/izaa307
DOI: 10.7302/9nxx-hd15
title: Core photos for core SPR0901-04BC

description: This dataset contains photo of the box core SPR0901-04BC (34.2816°N, 120.0415°W, 588 m water depth) retrieved from 2009.1 on the R/V Sproul. The study is funded by OCE-0752093.;Data citation: Hendy, I.L., Wang, Y. (2019). Core photo for SPR0901-04BC [Data set]. University of Michigan Deep Blue Data Repository. https://doi.org/10.7302/9nxx-hd15
description: The box core SPR0901-04BC only has one section. The core photo was obtained from the high-resolution line scan imaging system of the LacCore Facility (National Lacustrine Core Facility) at University of Minnesota.
DOI: 10.7302/43d3-1867
title: Bounce-Averaged Quasi-Linear Diffusion Model Simulation Input/Output on Mars’ Crustal Magnetic Field

description: This scaled acceleration time series has been used in the graduate class, NA540, as an example of hydrodynamic impact. For a more detailed description of the tests, please see: Troesch, A.W. and Kang, C.-G., "Hydrodynamic Impact Loads on Three Dimensional Bodies," Proceedings of the 16th Symposium on Naval Hydrodynamics, Berkeley, July 1986, National Academy Press, Washington, D.C., 1987, pp. 537-558.
description: Impact time series measured with piezoelectric accelerometer.  Drop test experiments conducted in University of Michigan, Marine Hydrodynamics Laboratory, Department of Naval Architecture and Marine Engineering.
DOI: 10.7302/mhjr-k798
title: Perturbative Sit-to-Stand Experiment Dataset and Stability Basin Code

description: This work was collected to evaluate Stability Basins for characterizing the limits of human stability during Sit-to-Stand. ;MATLAB code was used to process the data into individual trials. Trials are labeled by Sit-to-Stand type (Natural, Momentum-Transfer, or Quasi-Static) and experimental condition. MATLAB code for analyzing the data and computing Stability Basins is provided. A GUI is provided to animate a subject's movement and display projections of the Stability Basins in the horizontal and vertical planes. 
description: Kinematic motion capture data was collected from 11 subjects participating in a perturbative Sit-to-Stand experiment. Motor-driven cables were attached to the subjects' waists, pulling them forwards or backwards as they stood from a chair. MATLAB was used to process the data into individual trials, which are presented here.
DOI: 10.7302/1e6p-dp51
title: Dogon Tiranige Audio Files

description: Tiranige is a Dogon language spoken in villages on the high plateau near the western edge of the Dogon (Bandiagara) plateau, and in villages at the base of the cliffs and slopes leading down from the plateau to the sandy plains. As of May 2018 I am still working on a drafted Tiranige grammar which I hope to complete in 2019. The grammar draft currently ends with six short texts transcribed from dictation. The only audio recording is therefore labeled Text 07. The speakers are Amadou Toloba and Boubacar Toloba. Most but not all of it (17.5 minutes out of about 22) has been partially transcribed. The plan is to complete the grammar and to transcribe and translate at least Text 07. 
description: These recordings were made with a Tascam digital microphone.
DOI: 10.7302/vfer-6744
title: Widespread and persistent deposition of iron formations for two billion years: Compilation Dataset

description: This IF compilation was assembled from the existing literature to understand if preservation biases affected the record of iron formations. 
description: We compiled estimates of the initial iron formation (IF) masses, estimated by various authors (cited for each IF) using the observed thicknesses and areal extents of each IF.  Ages of each IF were constrained using relevant geochronological age constraints (cited for each IF). Units of age estimates are in million years ago or mega-annum (Ma) and masses are shown in gigatons (Gt).
DOI: 10.7302/dxhn-0q11
title: Single-molecule microscopy image data and analysis files for “A translational riboswitch coordinates nascent transcription–translation coupling.”

description: These data were generated to study the dynamics of RNAP-ribosome interactions on a nascent mRNA with a preQ1-sensing translational riboswitch in its 5’ untranslated region (UTR). Using single-molecule fluorescence co-localization, we monitored direct transient binding of 30S ribosomal subunit to the individual nascent mRNA molecules in surface-immobilized paused elongation complexes (PECs). Also, using a novel protein-induced fluorescence enhancement assay we monitored the real-time transcription rate of RNA polymerase (RNAP) under different experimental conditions. The DNA template including the preQ1 riboswitch from B. anthracis under the control of the T7A1 promoter was cloned into pUC19 plasmid. Transcription templates for in vitro transcription were generated by PCR. 
description: Single-molecule experiments were performed on a prism-based TIRF microscope (IX 71
description: Olympus) with a 1.2-numerical aperture 60X water-immersion objective (Olympus UplanApo) and an intensified CCD camera (I-Pentamax, Princeton Instruments). Transient binding of Cy5 labeled 30S subunit to individual Cy3 labeled PEC mRNA molecules immobilized to the surface of the custom-built sample cell was monitored for ~16 min. Both Cy3 and Cy5 dyes were directly and simultaneously excited using 532 nm (green) and 638 nm (red) diode lasers, respectively. Emission from Cy3 and Cy5 were recorded at a 100 ms exposure time. For monitoring real-time transcription rates, the transcription was restarted from a surface-immobilized halted complex (HC) at ~10 s of the movie collection by slowly flowing 50 µl imaging solution containing a mixture of all four rNTPs. The end of the transcription was characterized by the occurrence of a protein-induced fluorescence enhancement (PIFE) signal.
Fluorescence intensity versus time traces for individual molecules (‘.traces’ files) were first extracted from raw movie files using custom-written MATLAB scripts (The MathWorks). From the .traces files, genuine single-molecule fluorescence time traces were extracted manually and analyzed using custom scripts written in Matlab and the QuB software suite (State University of New York at Buffalo). Finally, kinetic analyses were performed using hidden-Markov modeling (HMM) with a segmental k-means algorithm as implemented in the program QuB.
DOI: 10.7302/1yqh-yt41
title: Substance use disorder education in medical schools: A scoping review of the literature [Literature Search Files]

description: The dataset includes all citations considered for inclusion in the scoping review. The citations are accessible in Endnote (enlx) and Microsoft Excel (xlsx), as well as the primary citation export files from each database. The literature search strategies are included for reproducibility and transparency purposes. See the published methods for more information.
description: The data in this work originate from the literature searches of several citation databases, including MEDLINE (Ovid), Embase (Elsevier), ERIC (FirstSearch), and Web of Science (Clarivate).