cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14677049
title: Additional file 5 of Samplot: a platform for structural variant visual validation and automated filtering

description: Additional file 5: Supplementary Table 4. Links for VCF file data.
DOI: 10.6084/m9.figshare.14677043.v1
title: Additional file 3 of Samplot: a platform for structural variant visual validation and automated filtering

description: Additional file 3: Supplementary Table 2. Statistics for CHM1/CHM13 allele balance mixture experiment.
DOI: 10.6084/m9.figshare.14677052
title: Additional file 6 of Samplot: a platform for structural variant visual validation and automated filtering

description: Additional file 6: Supplementary Table 5. Software package version numbers.
DOI: 10.6084/m9.figshare.14677040.v1
title: Additional file 2 of Samplot: a platform for structural variant visual validation and automated filtering

description: Additional file 2: Supplementary Table 1. SV calling statistics organized by sample, SV caller, and filtering method.
DOI: 10.6084/m9.figshare.14677052.v1
title: Additional file 6 of Samplot: a platform for structural variant visual validation and automated filtering

description: Additional file 6: Supplementary Table 5. Software package version numbers.
DOI: 10.3886/e141161
title: Childhood Maltreatment and Interpersonal Difficulties in Adulthood: The Mediating Role of Dissociation and Affect Dysregulation

description: Data set used in the publication of Childhood Maltreatment and Interpersonal Difficulties in Adulthood: The Mediating Role of Dissociation and Affect Dysregulation
description: Used prolific academic for participant recruitment and Qualtrics for survey management
DOI: 10.3886/e141161v1
title: Childhood Maltreatment and Interpersonal Difficulties in Adulthood: The Mediating Role of Dissociation and Affect Dysregulation

description: Data set used in the publication of Childhood Maltreatment and Interpersonal Difficulties in Adulthood: The Mediating Role of Dissociation and Affect Dysregulation
description: Used prolific academic for participant recruitment and Qualtrics for survey management
DOI: 10.5281/zenodo.4797997
title: scPNMF: sparse gene encoding of single cells to facilitate gene selection for targeted gene profiling

description: Seven datasets used in the manuscript "scPNMF: sparse gene encoding of single cells to facilitate gene selection for targeted gene profiling". All datasets are saved as SingleCellExperiment objects in R.
DOI: 10.5281/zenodo.4797996
title: scPNMF: sparse gene encoding of single cells to facilitate gene selection for targeted gene profiling

description: Seven datasets used in the manuscript "scPNMF: sparse gene encoding of single cells to facilitate gene selection for targeted gene profiling". All datasets are saved as SingleCellExperiment objects in R.
DOI: 10.25345/c5pv57
title: MassIVE MSV000087516 - Cold-Induced Adaptations to the Proteome of Mouse Subcutaneous White Adipose Tissue (scWAT) Reveal Proteins Relevant for Tissue Remodeling and Plasticity
title: White adipose tissue &#40;WAT&#41; is one of the most dynamic and plastic organs or tissues in the body, capable of expanding its mass in response to positive energy balance &#40;either by proliferation of adipocytes &#45; hyperphasia, or by increasing adipoycyte size &#45; hypertrophy&#41;, developing inducible brown adipocytes through a process termed &#34;browning&#34;, and changing its mitochondrial mass in response to stimuli such as cold exposure. Most notably, cold stimulation and release of norepinephrine from sympathetic nerve terminals is able to drive lipolysis in WAT &#40;and thus smaller lipid droplet size and adipocyte size&#41;, as well as promote sympathetic nerve branching and increased neurite density, as well as development of pockets of browning around these neurite&#45;dense regions of tissue. While several RNA-sequencing &#40;including newer single cell RNAseq studies&#41; have been done in WAT across situations of positive energy balance &#40;such as high fat diet, obesity&#41; or negative energy balance &#40;such as cold stimulation of energy expenditure&#41;, very little work has been done to investigate changes to the adipose proteome while the tissue is actively remodeling. Here, we have carried out proteomics analysis on inguinal subcutaneous &#40;sc&#41;WAT of C57BL&#47;6 mice after 24 or 72hrs of cold stimulation, a period during which UCP1 is actively turned on during the browning process. Through these data, we have found that numerous protein pathways changed by cold stimulation relate to tissue remodeling and plasticity, including changes to mitochondrial dynamics, tissue immune cells, and peripheral nerves.
DOI: 10.6084/m9.figshare.14677167.v1
title: Controls 25 Most Abundant OTUs - Counts and Taxonomy

description: File showing the normalized abundance and taxonomy classifications of the 25 most abundant OTUs in control samples from T0 and final samples.
DOI: 10.6084/m9.figshare.14677167
title: Controls 25 Most Abundant OTUs - Counts and Taxonomy

description: File showing the normalized abundance and taxonomy classifications of the 25 most abundant OTUs in control samples from T0 and final samples.
DOI: 10.5281/zenodo.4797001
title: Compressing regulatory networks to vectors for interpreting gene expression and genetic variants

description: Reproducing the results of GEEK.
DOI: 10.5281/zenodo.4797000
title: Compressing regulatory networks to vectors for interpreting gene expression and genetic variants

description: Reproducing the results of GEEK.
DOI: 10.5281/zenodo.4798192
title: Effects of cascade dams on phosphorus bioavailability in surface sediments:A comparative study between the Nu River and the Upper Mekong River

description: The dataset include sediments phosphorus concentrations in the Nu River and the Lancang River for January 2018. Seven different phosphorus fractions in sediment samples were extracted, including total inorganic phosphorus (TIP), exchangeable phosphorus (Ex-P), aluminum-bound phosphorus (Al-P), iron-bound phosphorus (Fe-P), Calcium-bound phosphorus (Ca-P), residual phosphorus (Res-P) and organic phosphorus (Org-P) (sheet 1). Sediments particle size, mineral composition and environmental factors (ORP, DO, TOC, TP, Temp, pH, etc.) also were measured at the sampling sites (sheet 2,3,4).
DOI: 10.5281/zenodo.4798191
title: Effects of cascade dams on phosphorus bioavailability in surface sediments:A comparative study between the Nu River and the Upper Mekong River

description: The dataset include sediments phosphorus concentrations in the Nu River and the Lancang River for January 2018. Seven different phosphorus fractions in sediment samples were extracted, including total inorganic phosphorus (TIP), exchangeable phosphorus (Ex-P), aluminum-bound phosphorus (Al-P), iron-bound phosphorus (Fe-P), Calcium-bound phosphorus (Ca-P), residual phosphorus (Res-P) and organic phosphorus (Org-P) (sheet 1). Sediments particle size, mineral composition and environmental factors (ORP, DO, TOC, TP, Temp, pH, etc.) also were measured at the sampling sites (sheet 2,3,4).
DOI: 10.6084/m9.figshare.12848748.v1
title: Intentional design and implementation of a “flipped” upper division geology course: Improving student learning outcomes, persistence, and attitudes

description: Flipped instruction is not new and the literature is extensive with examples of flipped courses. However, there is a lack of studies with a structured, methodical approach to flipped design, implementation, and evaluation of its effectiveness. An upper division geology course was flipped to allow focus on higher-level concepts, especially problem-solving skills, by moving lower-level Bloom taxonomy tasks to out-of-class preparatory work. Intentional design and implementation of this flipped course was based in the literature, and included extensive communication with students. Evaluation of student learning outcomes, persistence, and attitudes between traditional and flipped classrooms were based on quantitative and qualitative evidence collected from a variety of sources, and included formative and summative assessments. Overall, preliminary results showed significant improvement across various metrics of measurement including quizzes, homework, exams, course grades, course evaluations, surveys, and interviews, and suggest the flipped classroom increased students’ learning, persistence, and attitudes toward the course. For example, the percent of students who withdrew or made a D or F in the course decreased from 44% in the traditional to 22% in the flipped course. Despite limitations, including a small sample size, the effectiveness of following specific design principles for flipping an upper division course is demonstrated by multiple lines of evidence, and indicates those considering changing to the flipped classroom need to carefully design and implement their course. This includes a well-designed course structure based on learning outcomes, regular communication with students about course design and expectations, and opportunities for students to provide anonymous feedback.
DOI: 10.6084/m9.figshare.12848751
title: A community framework for geoscience education research: Summary and recommendations for future research priorities

description: The geoscience education research (GER) community has produced a collaborative research framework that summarizes guiding questions for future research to inform and improve undergraduate geoscience teaching and learning. The GER Framework (St. John [Ed.], 2018a) was developed through an iterative process involving multiple stages of community input. In total, approximately 200 geoscience educators and researchers contributed to this project in one or more of the following capacities: as authors, reviewers, survey respondents, workshop participants, webinar participants, town hall participants, and/or focus group participants. Review of survey data, reports, publications, and discussions resulted in a set of guiding questions and research strategies for ten research areas where individual researchers can make important contributions. While presented as distinct research areas, the ten themes have numerous cross-theme opportunities that integrate content areas, skills, and types of students. Cross-theme recommendations regarding strategies for future research are described here, along with suggested synergies with other national efforts in geoscience and STEM education.
DOI: 10.6084/m9.figshare.12848751.v1
title: A community framework for geoscience education research: Summary and recommendations for future research priorities

description: The geoscience education research (GER) community has produced a collaborative research framework that summarizes guiding questions for future research to inform and improve undergraduate geoscience teaching and learning. The GER Framework (St. John [Ed.], 2018a) was developed through an iterative process involving multiple stages of community input. In total, approximately 200 geoscience educators and researchers contributed to this project in one or more of the following capacities: as authors, reviewers, survey respondents, workshop participants, webinar participants, town hall participants, and/or focus group participants. Review of survey data, reports, publications, and discussions resulted in a set of guiding questions and research strategies for ten research areas where individual researchers can make important contributions. While presented as distinct research areas, the ten themes have numerous cross-theme opportunities that integrate content areas, skills, and types of students. Cross-theme recommendations regarding strategies for future research are described here, along with suggested synergies with other national efforts in geoscience and STEM education.
DOI: 10.6084/m9.figshare.12844408
title: Comparing desired workforce skills and reported teaching practices to model students’ experiences in undergraduate geoscience programs

description: A goal of undergraduate geoscience programs is to prepare students for the geoscience workforce. In order to understand the extent to which programs succeed at this goal, we identified desired workforce skills, compiled undergraduate geoscience program requirements, and mapped workforce skills onto faculty responses to the 2016 National Geoscience Faculty Survey categorized by respondent-provided course names for majors-level courses (n = 1037). We used a Bayesian statistical model to determine the posterior probability of students practicing desired workforce skills in undergraduate geoscience programs, using program profiles as the model prior, conditioned by the likelihood of a student practicing workforce skills in each course category based upon survey responses. Probabilistic Monte Carlo simulations of students in each example program were used to calculate the likely number of courses in which a student practiced each skill. Activities to help students develop skills related to geologic reasoning, working as part of a team, quantitative skills (algebra), applying skills in new scenarios, evaluation of scientific literature, temporal thinking, spatial thinking, written communication, and managing uncertainty are frequently encountered by students; on average, students encounter these activities at least seven times during an undergraduate program. In contrast, students encounter activities to help them develop an understanding of societal relevance and systems thinking, on average, fewer than three times during an undergraduate program. Our results provide a snapshot, via instructors’ reporting, of the state of workforce skill development across undergraduate degree programs, and both the approach and data set can be built upon for future studies.
DOI: 10.6084/m9.figshare.12844408.v1
title: Comparing desired workforce skills and reported teaching practices to model students’ experiences in undergraduate geoscience programs

description: A goal of undergraduate geoscience programs is to prepare students for the geoscience workforce. In order to understand the extent to which programs succeed at this goal, we identified desired workforce skills, compiled undergraduate geoscience program requirements, and mapped workforce skills onto faculty responses to the 2016 National Geoscience Faculty Survey categorized by respondent-provided course names for majors-level courses (n = 1037). We used a Bayesian statistical model to determine the posterior probability of students practicing desired workforce skills in undergraduate geoscience programs, using program profiles as the model prior, conditioned by the likelihood of a student practicing workforce skills in each course category based upon survey responses. Probabilistic Monte Carlo simulations of students in each example program were used to calculate the likely number of courses in which a student practiced each skill. Activities to help students develop skills related to geologic reasoning, working as part of a team, quantitative skills (algebra), applying skills in new scenarios, evaluation of scientific literature, temporal thinking, spatial thinking, written communication, and managing uncertainty are frequently encountered by students; on average, students encounter these activities at least seven times during an undergraduate program. In contrast, students encounter activities to help them develop an understanding of societal relevance and systems thinking, on average, fewer than three times during an undergraduate program. Our results provide a snapshot, via instructors’ reporting, of the state of workforce skill development across undergraduate degree programs, and both the approach and data set can be built upon for future studies.
DOI: 10.6084/m9.figshare.12848748
title: Intentional design and implementation of a “flipped” upper division geology course: Improving student learning outcomes, persistence, and attitudes

description: Flipped instruction is not new and the literature is extensive with examples of flipped courses. However, there is a lack of studies with a structured, methodical approach to flipped design, implementation, and evaluation of its effectiveness. An upper division geology course was flipped to allow focus on higher-level concepts, especially problem-solving skills, by moving lower-level Bloom taxonomy tasks to out-of-class preparatory work. Intentional design and implementation of this flipped course was based in the literature, and included extensive communication with students. Evaluation of student learning outcomes, persistence, and attitudes between traditional and flipped classrooms were based on quantitative and qualitative evidence collected from a variety of sources, and included formative and summative assessments. Overall, preliminary results showed significant improvement across various metrics of measurement including quizzes, homework, exams, course grades, course evaluations, surveys, and interviews, and suggest the flipped classroom increased students’ learning, persistence, and attitudes toward the course. For example, the percent of students who withdrew or made a D or F in the course decreased from 44% in the traditional to 22% in the flipped course. Despite limitations, including a small sample size, the effectiveness of following specific design principles for flipping an upper division course is demonstrated by multiple lines of evidence, and indicates those considering changing to the flipped classroom need to carefully design and implement their course. This includes a well-designed course structure based on learning outcomes, regular communication with students about course design and expectations, and opportunities for students to provide anonymous feedback.
DOI: 10.5281/zenodo.4798378
title: Gauged catchment with catchment characteristics and at-site estimated flood quantiles in QLD, NSW and VIC, Australia

description: This repository contains the data (summarized catchment characteristics and flood quantiles) related to the article entitled <em>A Network Approach for Delineating Homogeneous Regions in Regional Flood Frequency Analysis </em>submitted to Water Resources Research. For some selected catchment characteristics, detail description is listed below: tc: time of concentration in hours X =ln(Q) where Q is annual maximum flow in m3/s Mean X = average of X values SD X = standard deviation of X values SKEW X = skewness of X values I62= rainfall intensity (mm/h) for 6 hours duration and 2 years return periods, and so on for I650= rainfall intensity (mm/h) for 6 hours duration and 50 years return periods, MAR = mean annual rainfall (mm) SF = safe factor (no unit) MAE = Mean annual potential evapotranspiration (mm) SDEN = stream density (km/sq km) S1085 = slope of main stream m/km FOREST= fraction forest area in a catchment
DOI: 10.5281/zenodo.3571465
title: Gauged catchment with catchment characteristics and at-site estimated flood quantiles in QLD, NSW and VIC, Australia

description: This repository contains the data (summarized catchment characteristics and flood quantiles) related to the article entitled <em>A Network Approach for Delineating Homogeneous Regions in Regional Flood Frequency Analysis </em>submitted to Water Resources Research. For some selected catchment characteristics, detail description is listed below: tc: time of concentration in hours X =ln(Q) where Q is annual maximum flow in m3/s Mean X = average of X values SD X = standard deviation of X values SKEW X = skewness of X values I62= rainfall intensity (mm/h) for 6 hours duration and 2 years return periods, and so on for I650= rainfall intensity (mm/h) for 6 hours duration and 50 years return periods, MAR = mean annual rainfall (mm) SF = safe factor (no unit) MAE = Mean annual potential evapotranspiration (mm) SDEN = stream density (km/sq km) S1085 = slope of main stream m/km FOREST= fraction forest area in a catchment
DOI: 10.6084/m9.figshare.14676830
title: Additional file 4 of Transcriptome analysis of potential candidate genes and molecular pathways in colitis-associated colorectal cancer of Mkp-1-deficient mice

description: Additional file 4. The list of DEGs for carcinoma stage in wild type and Mkp-1 knockout mice.
DOI: 10.25345/c5k528
title: MassIVE MSV000087517 - Proteomic analysis of tropomyosin isoforms expressed and purified from Expi293F (human) cells.
title: Proteomic analysis of tropomyosin isoforms expressed and purified from Expi293F (human) cells.
DOI: 10.5281/zenodo.4722605
title: Data accompanying the publication "Quantum tomography of an entangled three-qubit state in silicon"

description: Data accompanying the publication "Quantum tomography of an entangled three-qubit state in silicon".
DOI: 10.5281/zenodo.4722604
title: Data accompanying the publication "Quantum tomography of an entangled three-qubit state in silicon"

description: Data accompanying the publication "Quantum tomography of an entangled three-qubit state in silicon".
DOI: 10.6084/m9.figshare.14677785
title: "Exploring Global Korea Scholarship as a Public Diplomacy Tool" Replication Files - Journal of Asian and African Studies

description: Replication files for the article entitled "Exploring Global Korea Scholarship as a Public Diplomacy Tool" (Journal of Asian and African Studies).
DOI: 10.6084/m9.figshare.14677785.v2
title: "Exploring Global Korea Scholarship as a Public Diplomacy Tool" Replication Files - Journal of Asian and African Studies

description: Replication files for the article entitled "Exploring Global Korea Scholarship as a Public Diplomacy Tool" (Journal of Asian and African Studies).
DOI: 10.6084/m9.figshare.14677785.v1
title: Untitled Item

description: Replication files for the article entitled "Exploring Global Korea Scholarship as a Public Diplomacy Tool" (Journal of Asian and African Studies).
DOI: 10.6084/m9.figshare.13561994
title: A High Spatial Resolution Satellite Remote Sensing Time Series Analysis of Cape Bounty, Melville Island, Nunavut (2004–2018)

description: Changes in vegetation have been observed in areas of the Arctic due to changing climate. This study examines a normalized difference vegetation index (NDVI) time series (2004–2018) of high spatial resolution satellite data (i.e., IKONOS, WorldView-2, WorldView-3) to determine if vegetation abundance has changed over the Cape Bounty Arctic Watershed Observatory, Melville Island, Nunavut. Image data were corrected to top-of-atmosphere reflectance and normalized for time series analysis using the pseudo-invariant feature (PIF) method. Percent vegetation cover measurements and indices derived from local climate data (growing degree days base 5 °C; GDD<sub>5</sub>) were used to contextualize NDVI trends in different vegetation types and within active layer detachments (ALDs). NDVI showed similar patterns within the different vegetation types and across the ALDs. There was no significant change in NDVI nor in GDD<sub>5</sub> over time. However, there were statistically significant (<i>p</i> 5 and NDVI for all vegetation types. Using field measurements with high spatial resolution remote sensing data helps link changes in NDVI with changes to vegetation and earth surface processes. The challenges of integrating high spatial resolution satellite data from different sensors in a time series analysis are also discussed.