cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12818717.v6
title: Collaborative Cross and Diversity Outbred liver proteomics manuscript

description: This repository contains:1. Starting peptide data, R scripts to process them, and the resulting quantitative protein data2. R scripts to process the genetic data for the Collaborative Cross and Diversity Outbred mice for further analysis (e.g., QTL, mediation, heritability)3. R scripts to run all analyses reported in manuscript4. Results data5. R scripts to reproduce all figures in manuscript
DOI: 10.21981/2h26-re86
title: etest2

description: etest2
DOI: 10.24431/rw1k586
title: Dissolved inorganic nutrient data from stations sampled on NGA-LTER seasonal cruises, 2018-2020

description: This dataset contains seasonal inorganic macronutrient data from stations sampled on NGA LTER seasonal cruises along cross-shelf lines and in Prince William Sound. Samples were collected during spring, summer and fall cruises from the regular CTD rosette bottles triggered at set depths, from the surface to a maximum depth of 1000 or 1500 meters, depending on the ship used. Specific nutrients measured include nitrate plus nitrite, silicic acid (silicate), and phosphate, with concentrations reported in micromoles per liter (micromolar). The data file format is csv. These data are part of the Northern Gulf of Alaska Long Term Ecological Research (NGA LTER) program. The LTER program is a National Science Foundation–funded network of 28 sites nationwide that focus on the influence of long-term and large-scale phenomenon on ecosystems. Additional funding for sampling is provided by the North Pacific Research Board (NPRB), the Alaska Ocean Observing System (AOOS), and the Exxon Valdez Oil Spill Trustee Council (EVOS) via the Gulf Watch Alaska program.
DOI: 10.17632/dzvgscbd3d.1
title: Data for: Plant functional traits and viewer characteristics co-regulate cultural services provisioning by stormwater bioretention

description: Plant trait data for 15 native Southern California plants recommended for use in stormwater bioretention
DOI: 10.17632/4pv64znhk9.1
title: Data for: Geochemical characteristics comparison between gas from fluid inclusions and wells and its significance for carbon isotope reversal in the Yan'an gas field of the southern Ordos Basin, China

description: Components and carbon isotopic values of natural gas.
DOI: 10.17632/6btrk84ssh.1
title: Data for: Electrospun meshes of poly (n-butyl cyanoacrylate) and their potential applications for drug delivery and tissue engineering

description: This document describes the steps followed to perform the kinetic study of the release of the cytostatic 5-fluorouracil (5FU) from the poly(n-butyl cyanoacrylate) (PBCA) electrospun mesh with the corresponding raw and processed data.
DOI: 10.5281/zenodo.4816215
title: Monthly total freeboard and snow depth over Arctic sea ice from AMSR-E&2 and AVHRR measurements (2003-2020)

description: <strong>[Data description]</strong> Monthly total freeboard (Ft) and snow depth (hs) over Arctic sea ice data for January-February-March months of the 2003-2020 period produced by Lee and Shi et al. (2021, manuscript in preparation) are provided. Both variables are derived from satellite passive infrared and microwave measurements: Total freeboard was obtained from AMSR-E&2 measurements and snow depth was estimated from the AMSR and AVHRR measurements. The uploaded file titled "monthly averaged total freeboard and snow depth (JFM 2003-2020).zip" contains two directories: one for total freeboard and the other for snow depth. Naming convention is "variable_yyyymm.bin" and data format is 32-bit floating point array in shape of 304 x 448 (25 km polar stereographic grid). Here we provide an example Python code to read monthly snow depth of January 2003 using numpy.<br> import numpy as np<br> hs = np.fromfile('hs_200301.bin', dtype=np.float32).reshape(448,304) Geocoordinate tools for the 25 km polar stereographic grid are available at NSIDC website (https://nsidc.org/data/polar-stereo/tools_geo_pixel.html)<br> <br> <strong>[Abbreviations]</strong> AMSR: Advanced Microwave Scanning Radiometer<br> AVHRR: Advanced Very High Resolution Radiometer<br> NSIDC: National Snow and Ice Data Center
description: Update for version 2: ice bottom temperature is changed from -1.8 to -1.5 degree Celsius for snow depth calculation.
DOI: 10.6084/m9.figshare.13583528
title: Extreme pre-fire drought decreases shrub regeneration on fertile soils

description: Data used in the manuscript "Extreme pre-fire drought decreases shrub regeneration on fertile soils." <br>Includes six files with key cleaned data: shrub mortality, shrub resprouting size, shrub seedling density, species presence/absence in transects, species cover. <br>Four code files: 'McLaughlin Fire Analyses.Rmd' with all code used for main analyses, figures, and tables, 'Weather Data.R' which generates the figure showing precipitation and drought over the study period, '2016_data_restructuring.R' which is used to clean and compile the raw data, and 'Functions.R' which are functions used by that data restructuring file. <br>All the raw data needed to run the structuring and analyses from scratch are included in the compressed raw_data.zip file. <br>Please contact me cwerner@ucdavis.edu for questions or use.
DOI: 10.6084/m9.figshare.13583528.v2
title: Extreme pre-fire drought decreases shrub regeneration on fertile soils

description: Data used in the manuscript "Extreme pre-fire drought decreases shrub regeneration on fertile soils." <br>Includes six files with key cleaned data: shrub mortality, shrub resprouting size, shrub seedling density, species presence/absence in transects, species cover. <br>Four code files: 'McLaughlin Fire Analyses.Rmd' with all code used for main analyses, figures, and tables, 'Weather Data.R' which generates the figure showing precipitation and drought over the study period, '2016_data_restructuring.R' which is used to clean and compile the raw data, and 'Functions.R' which are functions used by that data restructuring file. <br>All the raw data needed to run the structuring and analyses from scratch are included in the compressed raw_data.zip file. <br>Please contact me cwerner@ucdavis.edu for questions or use.
DOI: 10.6084/m9.figshare.13583528.v1
title: Extreme pre-fire drought decreases shrub regeneration on fertile soils

description: Data used in the manuscript "Extreme pre-fire drought decreases shrub regeneration on fertile soils." Includes six files: shrub mortality, shrub resprouting size, shrub seedling density, species presence/absence in transects, species cover, and R markdown code file used for analyses. Please contact me cwerner@ucdavis.edu for questions or use.
DOI: 10.5519/qd.jlzb7jhg
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (1 records)
DOI: 10.5519/qd.r357aff7
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (1 records)
DOI: 10.5281/zenodo.4747779
title: TEX86L derived bottom water records from the southern Yellow Sea (core site A03-B) over the last 8.8 kyr

description: This is the original data used in the manuscript titled "Gradually cooling of the Yellow Sea Warm Current driven by tropical Pacific subsurface water temperature changes over the past 5 kyr" which has been accepted by Geophysical Research Letters. The data is from a gravity core A03-B recovered from the southern Yellow Sea (123°38′E, 35°28′N; core length: 301 cm; water depth 77.6 m; time span: ~8.8 kyr). This excel includes depth, calendar age, TEX86L, BIT and other proxy record that used to evaluate GDGT derived temperature signal. full Article at: https://doi.org/10.1029/2021GL093534
DOI: 10.5281/zenodo.4747778
title: TEX86L derived bottom water records from the southern Yellow Sea (core site A03-B) over the last 8.8 kyr

description: This is the original data used in the manuscript titled "Gradually cooling of the Yellow Sea Warm Current driven by tropical Pacific subsurface water temperature changes over the past 5 kyr" which has been accepted by Geophysical Research Letters. The data is from a gravity core A03-B recovered from the southern Yellow Sea (123°38′E, 35°28′N; core length: 301 cm; water depth 77.6 m; time span: ~8.8 kyr). This excel includes depth, calendar age, TEX86L, BIT and other proxy record that used to evaluate GDGT derived temperature signal. full Article at: https://doi.org/10.1029/2021GL093534
DOI: 10.3886/e141241
title: Education and Equity in the New South: Educators’ Orientation Toward Newcomers

description: This qualitative study draws on interview data to explore how educators’ social identities shaped their identification with and orientation toward addressing the needs of immigrant-origin English learners in one new-destination high school. Detailed information about research methods can be found in the Penn (2021) AERA Open paper: Beyond Receptivity: Exploring the Role of Identity in Educators’ Orientation Toward Newcomers in a New Immigrant Destination.
DOI: 10.3886/e141241v2
title: Education and Equity in the New South: Educators’ Orientation Toward Newcomers

description: This qualitative study draws on interview data to explore how educators’ social identities shaped their identification with and orientation toward addressing the needs of immigrant-origin English learners in one new-destination high school. Detailed information about research methods can be found in the Penn (2021) AERA Open paper: Beyond Receptivity: Exploring the Role of Identity in Educators’ Orientation Toward Newcomers in a New Immigrant Destination.
DOI: 10.3886/e141241v1
title: Education and Equity in the South: Educators’ Orientation Toward Newcomers

description: This qualitative study draws on interview data to explore how educators’ social identities shaped their identification with and orientation toward addressing the needs of immigrant-origin English learners in one new-destination high school. Detailed information about research methods can be found in the Penn (2021) AERA Open paper: Beyond Receptivity: Exploring the Role of Identity in Educators’ Orientation Toward Newcomers in a New Immigrant Destination.
DOI: 10.6084/m9.figshare.11734239.v1
title: Statistical assessment of biosimilarity based on the relative distance between follow-on biologics for time-to-event endpoints

description: The two-arm parallel design that is commonly used to assess biosimilarity has the drawback that it does not take into account the inherent variability within the reference products. The three-arm parallel design was proposed in order to solve this problem. The purpose of this article was to extend the previous results to the time-to-event endpoints in the exponential model, the Cox proportional hazard model, and the restricted mean survival time. The relative distance is defined, and the corresponding test procedures are developed based on asymptotic theory. The type I error rates and powers are investigated theoretically and empirically.
DOI: 10.6084/m9.figshare.12933342
title: A Comparative Study of TOST and UMPT Procedures for Evaluating Dispersion Equivalence

description: The two one-sided tests (TOST) procedure is widely applied for assessing bioequivalence between two different drugs in clinical studies. The same notion can be applied to construct TOST method for establishing dispersion equivalence. In addition to the TOST extension, a uniformly most power test (UMPT) for equivalence in variability has been described in the literature. This article presents analytic and numerical comparisons to clarify the limitation and strength of the two procedures. The UMPT approach has comparatively superior control of Type I errors and demands more involved computations than the TOST method. To enhance the utility of the recommended UMPT procedure, a full set of computer algorithms are constructed to implement the described hypothesis testing and power calculation. Optimal sample size determinations are also developed for planning equivalence designs under different allocation and cost concerns. The suggested procedures are demonstrated with the data regarding the dispersion comparability between two measuring devices of breaking strengths in dental medicine.
DOI: 10.6084/m9.figshare.12933342.v2
title: A Comparative Study of TOST and UMPT Procedures for Evaluating Dispersion Equivalence

description: The two one-sided tests (TOST) procedure is widely applied for assessing bioequivalence between two different drugs in clinical studies. The same notion can be applied to construct TOST method for establishing dispersion equivalence. In addition to the TOST extension, a uniformly most power test (UMPT) for equivalence in variability has been described in the literature. This article presents analytic and numerical comparisons to clarify the limitation and strength of the two procedures. The UMPT approach has comparatively superior control of Type I errors and demands more involved computations than the TOST method. To enhance the utility of the recommended UMPT procedure, a full set of computer algorithms are constructed to implement the described hypothesis testing and power calculation. Optimal sample size determinations are also developed for planning equivalence designs under different allocation and cost concerns. The suggested procedures are demonstrated with the data regarding the dispersion comparability between two measuring devices of breaking strengths in dental medicine.
DOI: 10.6084/m9.figshare.12933342.v1
title: A comparative study of TOST and UMPT procedures for evaluating dispersion equivalence

description: The two one-sided tests (TOST) procedure is widely applied for assessing bioequivalence between two different drugs in clinical studies. The same notion can be applied to construct TOST method for establishing dispersion equivalence. In addition to the TOST extension, a uniformly most power test (UMPT) for equivalence in variability has been described in the literature. This article presents analytic and numerical comparisons to clarify the limitation and strength of the two procedures. The UMPT approach has comparatively superior control of Type I errors and demands more involved computations than the TOST method. To enhance the utility of the recommended UMPT procedure, a full set of computer algorithms are constructed to implement the described hypothesis testing and power calculation. Optimal sample size determinations are also developed for planning equivalence designs under different allocation and cost concerns. The suggested procedures are demonstrated with the data regarding the dispersion comparability between two measuring devices of breaking strengths in dental medicine.
DOI: 10.6084/m9.figshare.13194899
title: Bootstrap Cross-Validation Improves Model Selection in Pharmacometrics

description: Cross-validation assesses the predictive ability of a model, allowing one to rank models accordingly. Although the nonparametric bootstrap is almost always used to assess the variability of a parameter, it can be used as the basis for cross-validation if one keeps track of which items were not selected in a given bootstrap iteration. The items which were selected constitute the training data and the omitted items constitute the testing data. This bootstrap cross-validation (BS-CV) allows model selection to be made on the basis of predictive ability by comparing the median values of ensembles of summary statistics of testing data. BS-CV is herein demonstrated using several summary statistics, including a new one termed the simple metric for prediction quality, and using the warfarin data included in the Monolix distribution with 13 pharmacokinetics (PK) models and 12 pharmacodynamics models. Of note the two best PK models by Akaike’s information criterion (AIC) had the worst predictive ability, underscoring the danger of using single realizations of a random variable (such as AIC) as the basis for model selection. Using these data BS-CV was able to discriminate between similar indirect response models (inhibition of input vs. stimulation of output). This could be useful in situations in which the mechanism of action is unknown (unlike warfarin).
DOI: 10.6084/m9.figshare.13194899.v1
title: Bootstrap Cross-Validation Improves Model Selection in Pharmacometrics

description: Cross-validation assesses the predictive ability of a model, allowing one to rank models accordingly. Although the nonparametric bootstrap is almost always used to assess the variability of a parameter, it can be used as the basis for cross-validation if one keeps track of which items were not selected in a given bootstrap iteration. The items which were selected constitute the training data and the omitted items constitute the testing data. This bootstrap cross-validation (BS-CV) allows model selection to be made on the basis of predictive ability by comparing the median values of ensembles of summary statistics of testing data. BS-CV is herein demonstrated using several summary statistics, including a new one termed the simple metric for prediction quality, and using the warfarin data included in the Monolix distribution with 13 pharmacokinetics (PK) models and 12 pharmacodynamics models. Of note the two best PK models by Akaike’s information criterion (AIC) had the worst predictive ability, underscoring the danger of using single realizations of a random variable (such as AIC) as the basis for model selection. Using these data BS-CV was able to discriminate between similar indirect response models (inhibition of input vs. stimulation of output). This could be useful in situations in which the mechanism of action is unknown (unlike warfarin).
DOI: 10.6084/m9.figshare.7334708
title: Assessment of the Severity of Paravalvular Regurgitation and its Role on Survival After Transcatheter Aortic Valve Replacement

description: <b>Background:</b> To evaluate the impact of various measurements of paravalvular regurgitation (PVR) on survival after transcatheter aortic valve replacement (TAVR). PVR can be difficult to grade and both its incidence and impact on survival may be decreasing as TAVR evolves. <b>Methods:</b> This retrospective study included 911 patients undergoing TAVR in two institutions. PVR was graded according to the 3-grade scheme proposed by the guidelines (PVR grade), and subsequently grade 2 and 3, and grade 0 and 1 were lumped together. PVR was also graded as a composite score (PVR score), based on 6 commonly used metrics. PVR grade, PVR score and its six individual components were tested against the risk of both 1-year and longer term mortality after TAVR. <b>Results:</b> Patients with moderate/severe PVR had a higher Society of Thoracic Sugeons (STS) score, higher levels of serum creatinine and larger left atria compared to patients with none/mild PVR. Moderate/severe PVR was more frequent with self-expandable and larger valves. After adjusting for American College of Cardiology (ACC) TAVR risk score, neither PVR grade, PVR score nor its six components were associated with an increased risk of mortality at 1-year (severe PVR adjusted HR: 0.75, 95% Confidence Interval [CI]: 0.19, 3.01, <i>p</i> = 0.50). However, intervention for clinically severe PVR increased the risk of mortality by more than 7-fold (adjusted hazard ratio [HR]: 7.6, 95% CI: 2.4, 23.5, <i>p</i> <b>Conclusions:</b> In the contemporary era, moderate-severe PVR is uncommon. However, re-intervention for PVR portends a poor prognosis. This highlights the crucial importance of clinical judgment over imaging alone.
DOI: 10.6084/m9.figshare.7334708.v2
title: Assessment of the Severity of Paravalvular Regurgitation and its Role on Survival After Transcatheter Aortic Valve Replacement

description: <b>Background:</b> To evaluate the impact of various measurements of paravalvular regurgitation (PVR) on survival after transcatheter aortic valve replacement (TAVR). PVR can be difficult to grade and both its incidence and impact on survival may be decreasing as TAVR evolves. <b>Methods:</b> This retrospective study included 911 patients undergoing TAVR in two institutions. PVR was graded according to the 3-grade scheme proposed by the guidelines (PVR grade), and subsequently grade 2 and 3, and grade 0 and 1 were lumped together. PVR was also graded as a composite score (PVR score), based on 6 commonly used metrics. PVR grade, PVR score and its six individual components were tested against the risk of both 1-year and longer term mortality after TAVR. <b>Results:</b> Patients with moderate/severe PVR had a higher Society of Thoracic Sugeons (STS) score, higher levels of serum creatinine and larger left atria compared to patients with none/mild PVR. Moderate/severe PVR was more frequent with self-expandable and larger valves. After adjusting for American College of Cardiology (ACC) TAVR risk score, neither PVR grade, PVR score nor its six components were associated with an increased risk of mortality at 1-year (severe PVR adjusted HR: 0.75, 95% Confidence Interval [CI]: 0.19, 3.01, <i>p</i> = 0.50). However, intervention for clinically severe PVR increased the risk of mortality by more than 7-fold (adjusted hazard ratio [HR]: 7.6, 95% CI: 2.4, 23.5, <i>p</i> <b>Conclusions:</b> In the contemporary era, moderate-severe PVR is uncommon. However, re-intervention for PVR portends a poor prognosis. This highlights the crucial importance of clinical judgment over imaging alone.
DOI: 10.6084/m9.figshare.7464383
title: Device Closure of Patent Foramen Ovale—Is it Time to Update the Guidelines?

description: <b>Background:</b> The current American Association of Neurology guidelines do not recommend patent foramen ovale (PFO) closure for prevention of cryptogenic strokes, however recent findings from randomized control trials (RCT) have challenged this recommendation. We performed a comprehensive analysis of RCTs available to date to compare PFO closure to medical therapy in patients with cryptogenic stroke. <b>Methods:</b> Five databases were analyzed including EMBASE, PubMed, Cochrane, Scopus and Web-of-Science from January 2000 to September 2018. We included RCTs comparing device closure of PFO versus medical therapy in patients with cryptogenic stroke. Heterogeneity was determined using Cochrane’s Q statistics. A random effects model was used. <b>Results:</b> Six randomized controlled trials and 3,560 patients were included in the analysis. Mean follow-up was 47 ± 19 months. Device closure was associated with a 42% reduction in recurrent embolic strokes when compared to medical therapy (risk ratio (RR): 0.58, 95% CI: 0.39–0.88, <i>p</i> = 0.009). This occurred despite atrial fibrillation occurring at a higher rate with device closure when compared to medical therapy (RR: 4.75, 95% CI: 2.35–9.60, <i>p</i> <b>Conclusions:</b> PFO device closure in appropriately selected patients with cryptogenic stroke is associated with a significant reduction in the risk of recurrent ischemic stroke. The increased incidence of atrial fibrillation associated with device closure appears to be transient. Long-term monitoring may be essential.
DOI: 10.6084/m9.figshare.7221605
title: Percutaneous Management of Acquired Right Ventricular Outflow Tract Obstruction due to Giant Coronary Vein Graft Aneurysm

description: Percutaneous Management of Acquired Right Ventricular Outflow Tract Obstruction due to Giant Coronary Vein Graft Aneurysm