cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12145410
title: The design and evaluation of electromyography and inertial biofeedback in hand motor therapy gaming

description: This article details the design of a co-created, evidence-based biofeedback therapy game addressing the research question: is the biofeedback implementation efficient, effective, and engaging for promoting quality movement during a therapy game focused on hand gestures? First, we engaged nine young people with Cerebral Palsy (CP) as design partners to co-create the biofeedback implementation. A commercially available, tap-controlled game was converted into a gesture-controlled game with added biofeedback. The game is controlled by forearm electromyography and inertial sensors. Changes required to integrate biofeedback are described in detail and highlight the importance of closely linking movement quality to short- and long-term game rewards. After development, 19 participants (8–17 years old) with CP played the game at home for 4 weeks. Participants played 17 ± 9 min/day, 4 ± 1 day/week. The biofeedback implementation proved efficient (i.e. participants reduced compensatory arm movements by 10.2 ± 4.0%), effective (i.e. participants made higher quality gestures over time), and engaging (i.e. participants consistently chose to review biofeedback). Participants found the game usable and enjoyable. Biofeedback design in therapy games should consider principles of motor learning, best practices in video game design, and user perspectives. Design recommendations for integrating biofeedback into therapy games are compiled in an infographic to support interdisciplinary knowledge sharing.
DOI: 10.6084/m9.figshare.12145410.v1
title: The design and evaluation of electromyography and inertial biofeedback in hand motor therapy gaming

description: This article details the design of a co-created, evidence-based biofeedback therapy game addressing the research question: is the biofeedback implementation efficient, effective, and engaging for promoting quality movement during a therapy game focused on hand gestures? First, we engaged nine young people with Cerebral Palsy (CP) as design partners to co-create the biofeedback implementation. A commercially available, tap-controlled game was converted into a gesture-controlled game with added biofeedback. The game is controlled by forearm electromyography and inertial sensors. Changes required to integrate biofeedback are described in detail and highlight the importance of closely linking movement quality to short- and long-term game rewards. After development, 19 participants (8–17 years old) with CP played the game at home for 4 weeks. Participants played 17 ± 9 min/day, 4 ± 1 day/week. The biofeedback implementation proved efficient (i.e. participants reduced compensatory arm movements by 10.2 ± 4.0%), effective (i.e. participants made higher quality gestures over time), and engaging (i.e. participants consistently chose to review biofeedback). Participants found the game usable and enjoyable. Biofeedback design in therapy games should consider principles of motor learning, best practices in video game design, and user perspectives. Design recommendations for integrating biofeedback into therapy games are compiled in an infographic to support interdisciplinary knowledge sharing.
DOI: 10.25497/d7qp4c
title: Managing the Ecological Impacts of Environmental Education on the Dangermond Preserve, The Bren School, University of California Santa Barbara, 2019-2020

description: This dataset is from a master's group thesis project at The Bren School of Environmental Science & Management at the University of California, Santa Barbara, and contains the data files from the analyses (see below for the associated dataset containing the full final written report, which will provide more information on methods and results). The graduate student researchers who completed this project include: Tess Hooper, Daphne Virlar-Knight, Priscilla Hare, Robert Heim, and Jessica Gomez.This project, titled "Managing the Impacts of Environmental Education on Nature Preserves", focused on analyzing the potential ecological impacts that environmental education programming may have on sensitive plant and wildlife species on the Dangermond Preserve. Through mapping areas with sensitive plant and wildlife habitat, the group ranked environmental education trails on the preserve based on ecological impact. They also created a management tool that The Nature Conservancy can use to select trails that provide educational opportunities while reducing impacts to native biodiversity. Notably, the data indicates that all 12 education trails on the preserve pass through areas of low and high ecological impact, and that the best trail depends on each school group’s needs and The Nature Conservancy’s conservation goals. This project intends to help The Nature Conservancy manage its education programs on the Dangermond Preserve, and offers an approach that other land managers can use to inform decisions about balancing the trade-offs of environmental education in biologically diverse areas.The raw data used in the spatial analyses came from The Nature Conservancy and the following open source databases:1. California Wildlife Habitat Relationship Systems2. State Soil Geographic (STATSGO2) Data Base for California3. 2014 California Basin Characteristic Model Downscaled Climate and Hydrology (30-year summaries)4. Consortium of California HerbariaThe project began in April 2019 and ended in June 2020. To access the final written report associated with this project, visit the dataset titled "Managing the Ecological Impacts of Environmental Education on the Dangermond Preserve (Final Report Only), The Bren School, University of California Santa Barbara, 2019-2020".
DOI: 10.25497/d7g59x
title: Integrating Historical Change and Future Projections to Guide Conservation (Final Report Only), The Bren School, University of California Santa Barbara, 2018-2019

description: This dataset is from a master's group thesis project at The Bren School of Environmental Science & Management at the University of California, Santa Barbara, and contains the final written report only (see below for the associated datasets containing the project analyses and data packages). The student researchers who completed this project include: Brad Anderson, Meghan Bowen, Lucy Genua, Kym Howo, and Genelle Ives.California’s coastal habitats face increasing threats from climate change and development. The Dangermond Preserve, located in western Santa Barbara County and manage by The Nature Conservancy, remains largely undeveloped but was managed as a cattle ranch for over a century. This project aims to inform conservation planning at the preserve by studying the property’s history and anticipating its future. This combined approach is important because, given our increasing awareness of climate change, conservation that focuses on recreating past conditions or maintaining current conditions may not be ideal or possible. This project had four objectives: 1) identify changes in area and structure of natural habitats over time, 2) predict plant distribution changes under future climate scenarios, 3) investigate the impact of ranching infrastructure on the threatened California red-legged frog distribution, and 4) prioritize conservation actions. An analysis of historic aerial imagery and vegetation maps showed that grassland area at the preserve has declined since the 1930s, whereas woodland and shrubland areas have increased. Ground surveys of coast live oak indicated, however, that oak recruitment has possibly declined over the same time period. Climate forecasting showed that some northern plant species and locally endemic species might decline at the preserve, while southern species that prefer warmer temperatures could expand. Finally, an analysis of streams and water features indicated that the preserve’s red-legged frog population may be supported by ranching stock ponds. In light of these results, we made recommendations for conservation, monitoring, and future research priorities.This project began in April 2018 and completed in June 2019. To access the data files and analyses associated with this project, visit the dataset titled "Integrating Historical Change and Future Projections to Guide Conservation, The Bren School, University of California Santa Barbara, 2018-2019".
DOI: 10.25497/d7kw2f
title: Managing the Ecological Impacts of Environmental Education on the Dangermond Preserve (Final Report Only), The Bren School, University of California Santa Barbara, 2019-2020

description: This dataset is from a master's group thesis project at The Bren School of Environmental Science & Management at the University of California, Santa Barbara, and contains the final written report only (see below for the associated dataset containing the project analyses and data packages). The graduate student researchers who completed this project include: Tess Hooper, Daphne Virlar-Knight, Priscilla Hare, Robert Heim, and Jessica Gomez.This project, titled "Managing the Impacts of Environmental Education on Nature Preserves", focused on analyzing the potential ecological impacts that environmental education programming may have on sensitive plant and wildlife species on the Dangermond Preserve. Through mapping areas with sensitive plant and wildlife habitat, the group ranked environmental education trails on the preserve based on ecological impact. They also created a management tool that The Nature Conservancy can use to select trails that provide educational opportunities while reducing impacts to native biodiversity. Notably, the data indicates that all 12 education trails on the preserve pass through areas of low and high ecological impact, and that the best trail depends on each school group’s needs and The Nature Conservancy’s conservation goals. This project intends to help The Nature Conservancy manage its education programs on the Dangermond Preserve, and offers an approach that other land managers can use to inform decisions about balancing the trade-offs of environmental education in biologically diverse areas.The raw data used in the spatial analyses came from The Nature Conservancy and the following open source databases:1. California Wildlife Habitat Relationship Systems2. State Soil Geographic (STATSGO2) Data Base for California3. 2014 California Basin Characteristic Model Downscaled Climate and Hydrology (30-year summaries)4. Consortium of California HerbariaAnalyses were conducted using ArcGIS, MaxENT, and RStudio. The project began in April 2019 and ended in June 2020.To access data files associated with this project, visit the dataset titled Managing the Ecological Impacts of Environmental Education on the Dangermond Preserve, The Bren School, University of California Santa Barbara, 2019-2020"
DOI: 10.25497/d7bc70
title: Integrating Historical Change and Future Projections to Guide Conservation, The Bren School, University of California Santa Barbara, 2018-2019.

description: This dataset is from a master's group thesis project at The Bren School of Environmental Science & Management at the University of California, Santa Barbara, and contains the data files from the analyses (see below for the associated dataset containing the Final Written Report, which will contain more detailed information about methods and results). The student researchers who completed this project include: Brad Anderson, Meghan Bowen, Lucy Genua, Kym Howo, and Genelle Ives.California’s coastal habitats face increasing threats from climate change and development. The Dangermond Preserve, located in western Santa Barbara County and managed by The Nature Conservancy, remains largely undeveloped but was managed as a cattle ranch for over a century. This project aims to inform conservation planning at the preserve by studying the property’s history and anticipating its future. This combined approach is important because, given our increasing awareness of climate change, conservation that focuses on recreating past conditions or maintaining current conditions may not be ideal or possible. This project had four objectives: 1) identify changes in area and structure of natural habitats over time, 2) predict plant distribution changes under future climate scenarios, 3) investigate the impact of ranching infrastructure on the threatened California red-legged frog distribution, and 4) prioritize conservation actions. An analysis of historic aerial imagery and vegetation maps showed that grassland area at the preserve has declined since the 1930s, whereas woodland and shrubland areas have increased. Ground surveys of coast live oak indicated, however, that oak recruitment has possibly declined over the same time period. Climate forecasting showed that some northern plant species and locally endemic species might decline at the preserve, while southern species that prefer warmer temperatures could expand. Finally, an analysis of streams and water features indicated that the preserve’s red-legged frog population may be supported by ranching stock ponds. In light of these results, we made recommendations for conservation, monitoring, and future research priorities.The raw data used in these analyses were obtained from the following organizations and open source databases:1) FrameFinder through UC Santa Barbara's Special Collections Library2) EarthExplorer through the US Geological Survey3) Weislander Vegetation Type Mapping through UC Berkeley4) The Nature Conservancy5) Consortium of California Herbaria6) Basin Characterization Model7) Soil Survey Geographic DatabaseThe project began in April 2018 and ended in June 2019. To access the final written report associated with this project, see the associated data set titled "Integrating Historical Change and Future Projections to Guide Conservation (Final Report Only), The Bren School, University of California Santa Barbara, 2018-2019".
DOI: 10.5281/zenodo.6484869
title: Local chromatin context dictates the genetic determinants of the heterochromatin spreading reaction. Analysis Code and Primary data.

description: Uploaded under this Zenodo DOI is the following: 1. the Analysis Code used for Flow Cytometry analysis in the paper, GO complex analysis (Figure 3) and Hit visualization (Figure 1, 2 S1, S4 Figs). 2. The primary Flow Cytometry data from both the initial screen (ScreenFlowFCS) and validation experiments (ValidationFlowFCS) are included as .zip files. 3. a .zip folder is uploaded that contains all the analysis code for the ChIP-Seq experiments.
DOI: 10.25497/d79g6b
title: Dangermond Preserve Plant List 2019

description: Voucher status, scientific name, common name, family, provenance, and rarity of the plants found on the Dangermond Preserve
DOI: 10.25497/d7f59m
title: Dangermond Preserve Bird List - 2019

description: The scientific, common name, conservation status, and source of bird occurrences at the Dangermond Preserve. List is current as of 2019
DOI: 10.5281/zenodo.6484952
title: NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition

description: These are the plumed input files needed to reproduce the funnel metadynamics results for cellobiose binding to WT 1ECE, Y245G mutant, and W212A mutant.
DOI: 10.5281/zenodo.4624428
title: NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition

description: These are the plumed input files needed to reproduce the funnel metadynamics results for cellobiose binding to WT 1ECE, Y245G mutant, and W212A mutant.
DOI: 10.25497/d75p4d
title: Dangermond Preserve Mammal List 2020

description: List of mammals found at the Dangermond Preserve as of 2020
DOI: 10.5281/zenodo.4559695
title: The Surface Water Chemistry (SWatCh) database

description: This is the dataset presented in the following manuscript: The Surface Water Chemistry (SWatCh) database: A standardized global database of water chemistry to facilitate large-sample hydrological research, which is currently under review at Earth System Science Data. Openly accessible global scale surface water chemistry datasets are urgently needed to detect widespread trends and problems, to help identify their possible solutions, and determine critical spatial data gaps where more monitoring is required. Existing datasets are limited in availability, sample size/sampling frequency, and geographic scope. These limitations inhibit the answering of emerging transboundary water chemistry questions, for example, the detection and understanding of delayed recovery from freshwater acidification. Here, we begin to address these limitations by compiling the global surface water chemistry (SWatCh) database. We collect, clean, standardize, and aggregate open access data provided by six national and international agencies to compile a database containing information on sites, methods, and samples, and a GIS shapefile of site locations. We remove poor quality data (for example, values flagged as “suspect” or “rejected”), standardize variable naming conventions and units, and perform other data cleaning steps required for statistical analysis. The database contains water chemistry data for streams, rivers, canals, ponds, lakes, and reservoirs across seven continents, 24 variables, 33,722 sites, and over 5 million samples collected between 1960 and 2022. Similar to prior research, we identify critical spatial data gaps on the African and Asian continents, highlighting the need for more data collection and sharing initiatives in these areas, especially considering freshwater ecosystems in these environs are predicted to be among the most heavily impacted by climate change. We identify the main challenges associated with compiling global databases – limited data availability, dissimilar sample collection and analysis methodology, and reporting ambiguity – and provide recommended solutions. By addressing these challenges and consolidating data from various sources into one standardized, openly available, high quality, and trans-boundary database, SWatCh allows users to conduct powerful and robust statistical analyses of global surface water chemistry.
description: The code used to generate the SWatCh database is published on Github: https://github.com/LobkeRotteveel/SWatCh
DOI: 10.5281/zenodo.6369360
title: Simulated exome-sequencing data for a family study of lymphoid cancer

description: This repository contains all the data files for a simulated exome-sequencing study of 150 families ascertained to contain at least four members affected with lymphoid cancer. The simulated data can be found in the files section below. The files are: SLiM_output.txt - contains the SLiM-simulated, exome-wide, SNV data generated under an American-admixture demographic model, for the American-admixed sub-population only. SLiM_output_chr8&9.txt - contains the SLiM-simulated data above for all source populations as well as the American-admixed sub-population, but only for chromosomes 8 and 9. sample_info.txt - contains pedigree information of all the disease-affected individuals and individuals connecting them along a line of descent, for all 150 ascertained pedigrees. Genotypes.zip - a zipfile that contains 22 text files of genotypes for each chromosome. The genotypes are for simulated single-nucleotide variants on the exome and are in gene-dosage format. SNVmaps.zip - a zipfile that contains 22 text files giving the single-nucleotide variant information for each chromosome. familial_cRV.txt - contains the familial causal rare variants for all 150 ascertained pedigrees. study_peds.txt - contains the 150 pedigrees ascertained to contain four or more relatives affected with lymphoid cancer. PLINKfiles.zip - a zipfile that contains PLINK .fam, .bim and .bed files for all 22 of the chromosomes. All the scripts used to generate these data can be found in the GitHub repository archived at https://zenodo.org/record/6347546. We have also uploaded one intermediate .Rdata file, Chromwide.Rdata, to save the user substantial time when running the associated RMarkdown script for the simulation. We recommend loading Chromwide.Rdata into your R work-space rather than generating it from scratch.
description: funding acknowledgement- Natural Sciences and Engineering Research Council of Canada RGPIN-04296-2018
DOI: 10.6084/m9.figshare.19653123
title: Supplementary Fig. S1-S8, Tables S1-S7 and GTF files_Goldfarb et al_Endocrinology (2022)_Interplay between sex-biased GH-regulated mouse liver transcriptome and hepatic zonation revealed by single nucleus RNAseq

description: Supplementary Figs. S1-S8, Tables S1-S7, and GTF files from a study entitled: Interplay between sex-biased GH-regulated mouse liver transcriptome and hepatic zonation revealed by single nucleus RNAseq [Goldfarb et al, Endocrinology (2022)] <br> Abstract: The zonation of liver metabolic processes is well-characterized; however, little is known about the cell type-specificity and zonation of sexually dimorphic gene expression or its GH-dependent transcriptional regulators. We address these issues using single nucleus RNA-sequencing of 32,000 nuclei representing nine major liver cell types. Nuclei were extracted from livers from adult male and female mice, from males infused with GH continuously, mimicking the female plasma GH pattern, and from mice exposed to TCPOBOP, a xenobiotic agonist ligand of the nuclear receptor CAR that perturbs sex-biased gene expression. Analysis of these rich transcriptomic datasets revealed: 1) expression of sex-biased genes and their GH-dependent transcriptional regulators is primarily restricted to hepatocytes and is not a feature of liver non-parenchymal cells; 2) many sex-biased transcripts show sex-dependent zonation within the liver lobule; 3) gene expression is substantially feminized in both periportal and pericentral hepatocytes when male mice are infused with GH continuously; 4) sequencing nuclei increases the sensitivity for detecting thousands of nuclear-enriched lncRNAs and enables determination of their liver cell type-specificity, sex-bias and hepatocyte zonation profiles; 5) the periportal to pericentral hepatocyte cell ratio is significantly higher in male than female liver; and 6) TCPOBOP exposure disrupts both sex-specific gene expression and hepatocyte zonation within the liver lobule. These findings highlight the complex interconnections between hepatic sexual dimorphism and zonation at the single cell level and reveal how endogenous hormones and foreign chemical exposure can alter these interactions across the liver lobule with large effects on both protein-coding genes and lncRNAs.