cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1332432
title: Defects in calcium homeostasis and mitochondria can be reversed in Pompe disease

description: Mitochondria-induced oxidative stress and flawed autophagy are common features of neurodegenerative and lysosomal storage diseases (LSDs). Although defective autophagy is particularly prominent in Pompe disease, mitochondrial function has escaped examination in this typical LSD. We have found multiple mitochondrial defects in mouse and human models of Pompe disease, a life-threatening cardiac and skeletal muscle myopathy: a profound dysregulation of Ca<sup>2+</sup> homeostasis, mitochondrial Ca<sup>2+</sup> overload, an increase in reactive oxygen species, a decrease in mitochondrial membrane potential, an increase in caspase-independent apoptosis, as well as a decreased oxygen consumption and ATP production of mitochondria. In addition, gene expression studies revealed a striking upregulation of the β 1 subunit of L-type Ca<sup>2+</sup> channel in Pompe muscle cells. This study provides strong evidence that disturbance of Ca<sup>2+</sup> homeostasis and mitochondrial abnormalities in Pompe disease represent early changes in a complex pathogenetic cascade leading from a deficiency of a single lysosomal enzyme to severe and hard-to-treat autophagic myopathy. Remarkably, L-type Ca<sup>2+</sup>channel blockers, commonly used to treat other maladies, reversed these defects, indicating that a similar approach can be beneficial to the plethora of lysosomal and neurodegenerative disorders.
DOI: 10.6084/m9.figshare.1332438.v2
title: Screening of variable importance for optimizing electrodialytic remediation of heavy metals from polluted harbour sediments

description: Using multivariate design and modelling, the optimal conditions for electrodialytic remediation (EDR) of heavy metals were determined for polluted harbour sediments from Hammerfest harbour located in the geographic Arctic region of Norway. The comparative importance of the variables, current density, remediation time, light/no light, the liquid–solid ratio and stirring rate of the sediment suspension, was determined in 15 laboratory-scale EDR experiments by projection to latent structures (PLS). The relation between the X matrix (experimental variables) and the Y matrix (removal efficiencies) was computed and variable importance in the projection was used to assess the influence of the experimental variables. Current density and remediation time proved to have the highest influence on the remediation of the heavy metals Cr, Cu, Ni, Pb and Zn in the studied experimental domain. In addition, it was shown that excluding the acidification time improved the PLS model, indicating the importance of applying a limited experimental domain that covers the removal phases of each heavy metal in the specific sediment. Based on PLS modelling, the optimal conditions for remediating the Hammerfest sediment were determined; operating in the experimental domain of 0.5–0.8 mA/cm<sup>2</sup> and a remediation time after acidification of 450–570 h met acceptable levels according to Norwegian sediment quality guidelines.
DOI: 10.6084/m9.figshare.1332430
title: Examination Students Data

description: Small scale diet survey comparing energy and nutrient intake outside and during exams using within-subject design. Cameras used to aid dietary assessment
DOI: 10.6084/m9.figshare.1332431
title: Differentiation dynamics of mammary epithelial stem cells from Korean holstein dairy cattle under ECM-free conditions

description: The “stem cells” are commonly defined as “cells capable of self-renewal through replication and differentiating into specific lineages”. The mammary gland contains functional stem/progenitor cells. The current study was planned with the objectives to study the differentiation dynamics of Korean Holstein mammary epithelial stem cells (KHMESCs) under the optimum culture conditions. Lineage negative KHMESCs isolated from mammary tissue of lactating cows have shown the typical differentiation dynamics with formation of lobulo–alveolar structures in <i>in vitro</i> culture. This suggests the existence of bipotential mammary epithelial stem cells in the mammary gland. The strong mRNA expression of pluripotency factors indicates stemness, whereas expression of milk protein genes and epithelial cell-specific gene indicate their differentiation capabilities. Further, immunostaining results have shown the differentiation capabilities of KHMESCs into both luminal and basal lineages under the extracellular matrix (ECM, matrigel) free environment. However, under matrigel, the differentiation process was comparatively higher than without matrigel. Immunostaining results also suggested that differentiated cells could secrete milk proteins such as β-casein. To our knowledge, these data represent the first report on the differentiation dynamics and establishment of mammary epithelial stem cells from Korean Holstein with typical stemness properties. It was observed that isolated KHMESCs had normal morphology, growth pattern, differentiation ability, cytogenetic and secretory activity even without ECM. Therefore, it is concluded that established KHMESCs could be used for further studies on Korean Holstein dairy cows related to lactation studies, as non-GMO animal bioreactors and stem cell-based management of bovine mastitis including post-mastitis damage.
DOI: 10.6084/m9.figshare.1332432.v2
title: Defects in calcium homeostasis and mitochondria can be reversed in Pompe disease

description: Mitochondria-induced oxidative stress and flawed autophagy are common features of neurodegenerative and lysosomal storage diseases (LSDs). Although defective autophagy is particularly prominent in Pompe disease, mitochondrial function has escaped examination in this typical LSD. We have found multiple mitochondrial defects in mouse and human models of Pompe disease, a life-threatening cardiac and skeletal muscle myopathy: a profound dysregulation of Ca<sup>2+</sup> homeostasis, mitochondrial Ca<sup>2+</sup> overload, an increase in reactive oxygen species, a decrease in mitochondrial membrane potential, an increase in caspase-independent apoptosis, as well as a decreased oxygen consumption and ATP production of mitochondria. In addition, gene expression studies revealed a striking upregulation of the β 1 subunit of L-type Ca<sup>2+</sup> channel in Pompe muscle cells. This study provides strong evidence that disturbance of Ca<sup>2+</sup> homeostasis and mitochondrial abnormalities in Pompe disease represent early changes in a complex pathogenetic cascade leading from a deficiency of a single lysosomal enzyme to severe and hard-to-treat autophagic myopathy. Remarkably, L-type Ca<sup>2+</sup>channel blockers, commonly used to treat other maladies, reversed these defects, indicating that a similar approach can be beneficial to the plethora of lysosomal and neurodegenerative disorders.
DOI: 10.6084/m9.figshare.1332431.v1
title: Differentiation dynamics of mammary epithelial stem cells from Korean holstein dairy cattle under ECM-free conditions

description: The “stem cells” are commonly defined as “cells capable of self-renewal through replication and differentiating into specific lineages”. The mammary gland contains functional stem/progenitor cells. The current study was planned with the objectives to study the differentiation dynamics of Korean Holstein mammary epithelial stem cells (KHMESCs) under the optimum culture conditions. Lineage negative KHMESCs isolated from mammary tissue of lactating cows have shown the typical differentiation dynamics with formation of lobulo–alveolar structures in <i>in vitro</i> culture. This suggests the existence of bipotential mammary epithelial stem cells in the mammary gland. The strong mRNA expression of pluripotency factors indicates stemness, whereas expression of milk protein genes and epithelial cell-specific gene indicate their differentiation capabilities. Further, immunostaining results have shown the differentiation capabilities of KHMESCs into both luminal and basal lineages under the extracellular matrix (ECM, matrigel) free environment. However, under matrigel, the differentiation process was comparatively higher than without matrigel. Immunostaining results also suggested that differentiated cells could secrete milk proteins such as β-casein. To our knowledge, these data represent the first report on the differentiation dynamics and establishment of mammary epithelial stem cells from Korean Holstein with typical stemness properties. It was observed that isolated KHMESCs had normal morphology, growth pattern, differentiation ability, cytogenetic and secretory activity even without ECM. Therefore, it is concluded that established KHMESCs could be used for further studies on Korean Holstein dairy cows related to lactation studies, as non-GMO animal bioreactors and stem cell-based management of bovine mastitis including post-mastitis damage.
DOI: 10.6084/m9.figshare.1332432.v1
title: Defects in calcium homeostasis and mitochondria can be reversed in Pompe disease

description: Mitochondria-induced oxidative stress and flawed autophagy are common features of neurodegenerative and lysosomal storage diseases (LSDs). Although defective autophagy is particularly prominent in Pompe disease, mitochondrial function has escaped examination in this typical LSD. We have found multiple mitochondrial defects in mouse and human models of Pompe disease, a life-threatening cardiac and skeletal muscle myopathy: a profound dysregulation of Ca<sup>2+</sup> homeostasis, mitochondrial Ca<sup>2+</sup> overload, an increase in reactive oxygen species, a decrease in mitochondrial membrane potential, an increase in caspase-independent apoptosis, as well as a decreased oxygen consumption and ATP production of mitochondria. In addition, gene expression studies revealed a striking upregulation of the beta 1 subunit of L-type Ca<sup>2+</sup> channel in Pompe muscle cells. This study provides strong evidence that disturbance of Ca<sup>2+</sup> homeostasis and mitochondrial abnormalities in Pompe disease represent early changes in a complex pathogenetic cascade leading from a deficiency of a single lysosomal enzyme to severe and hard-to-treat autophagic myopathy. Remarkably, L-type Ca<sup>2+</sup>channel blockers, commonly used to treat other maladies, reversed these defects, indicating that a similar approach can be beneficial to the plethora of lysosomal and neurodegenerative disorders.
DOI: 10.6084/m9.figshare.1332408
title: Materials for Mapping your Data course (British Library Digital Scholarship Training Programme)

description: Materials created by James Baker in June 2014 for the 108 Mapping Data course of the British Library Digital Scholarship Training Programme.
DOI: 10.6084/m9.figshare.1332420
title: Data for "Representing number in real-time processing: Self-paced reading evidence from Arabic"

description: This collection contains the raw and processed data and analysis script for our paper "Representing number in the real-time processing of agreement: Self-paced reading evidence from Arabic" for the Frontiers in Psychology special topic on "Encoding and Navigating Linguistic Representations in Memory" edited by Colin Phillips, Matthew Wagers, and Claudia Felser. This collection contains everything a researcher should need to reproduce the results reported in the paper, as well as to explore alternative hypothesis. Matt Tucker is the corresponding author, and questions about code, data, and the like should be addressed to him.
DOI: 10.6084/m9.figshare.1332408.v3
title: Materials for Mapping your Data course (British Library Digital Scholarship Training Programme)

description: Materials created by James Baker in June 2014 for the 108 Mapping Data course of the British Library Digital Scholarship Training Programme.
DOI: 10.6084/m9.figshare.1332430.v1
title: Examination Students Data

description: Small scale diet survey comparing energy and nutrient intake outside and during exams using within-subject design. Cameras used to aid dietary assessment
DOI: 10.6084/m9.figshare.1332408.v2
title: Materials for Mapping your Data course (British Library Digital Scholarship Training Programme)

description: Materials created by James Baker in June 2014 for the 108 Mapping Data course of the British Library Digital Scholarship Training Programme.
DOI: 10.6084/m9.figshare.1330481
title: Purdue FTE-Database

description: Purdue-FTE database - is a collection of enrollment decisions from four datasets collected in the International Center for Biometric Research. For more information about the dataset, please see "Computational Methods in Biometric Authentication: Statistical Methods for Performance Evaluation", and more information is available from ICBR website, and data collected from Eric Kukula's dissertation.
DOI: 10.6084/m9.figshare.1330481.v1
title: Purdue FTE-Database

description: Purdue-FTE database - is a collection of enrollment decisions from four datasets collected in the International Center for Biometric Research. For more information about the dataset, please see "Computational Methods in Biometric Authentication: Statistical Methods for Performance Evaluation", and more information is available from ICBR website, and data collected from Eric Kukula's dissertation.
DOI: 10.6084/m9.figshare.1330268
title: Fast-Trips 2012 Input-Output

description: Test input and output data for fast-trips
DOI: 10.6084/m9.figshare.1330402
title: Dynamic Responses of Selective Brain White Matter Fiber Tracts to Binge Alcohol and Recovery in the Rat

description: To determine the dynamics of white matter vulnerability to excessive alcohol consumption, diffusion tensor imaging (DTI) was used in an animal model of alcohol exposure. Quantitative, in vivo fiber tracking results are presented from rats with DTI conducted at 3 time points: baseline; after 4 days of intragastric alcohol to blood alcohol levels of ~250mg/dL; and after one week of recovery. Binge alcohol followed by a week of sobriety resulted in rapidly reversible decreases in fractional anisotropy (FA), a measure of the coherence of fiber tracts, in callosal genu and fimbria-fornix but not splenium; and increases in mean diffusivity (MD), an index of freely diffusing water in tissue, selective to the fimbria-fornix. These effects were confirmed with tract-based spatial statistics (TBSS). The directionality of changes in DTI metrics reproduce those observed in human alcoholism. That a single exposure to binge alcohol can cause substantial transient changes detectable in DTI metrics demonstrates the potential for rapid neuroplasticity.
DOI: 10.6084/m9.figshare.1330268.v1
title: Fast-Trips 2012 Input-Output

description: Test input and output data for fast-trips
DOI: 10.6084/m9.figshare.1330223
title: Visual attention to dynamic spatial relations in infants and adults

description: Data analysis and one example of a 5-month-old, 12-month-old and an adult gaze behavior during dynamic observation of motion.
DOI: 10.6084/m9.figshare.1330402.v1
title: Dynamic Responses of Selective Brain White Matter Fiber Tracts to Binge Alcohol and Recovery in the Rat

description: To determine the dynamics of white matter vulnerability to excessive alcohol consumption, diffusion tensor imaging (DTI) was used in an animal model of alcohol exposure. Quantitative, in vivo fiber tracking results are presented from rats with DTI conducted at 3 time points: baseline; after 4 days of intragastric alcohol to blood alcohol levels of ~250mg/dL; and after one week of recovery. Binge alcohol followed by a week of sobriety resulted in rapidly reversible decreases in fractional anisotropy (FA), a measure of the coherence of fiber tracts, in callosal genu and fimbria-fornix but not splenium; and increases in mean diffusivity (MD), an index of freely diffusing water in tissue, selective to the fimbria-fornix. These effects were confirmed with tract-based spatial statistics (TBSS). The directionality of changes in DTI metrics reproduce those observed in human alcoholism. That a single exposure to binge alcohol can cause substantial transient changes detectable in DTI metrics demonstrates the potential for rapid neuroplasticity.
DOI: 10.6084/m9.figshare.1330222
title: Irish Surnames and Slave ownership

description: McLysaght's "Irish Families" cross referenced with the U.S. Slave Schedules (1850) and the Slave Compensation Records (1834). I believe that my data, while cursory, is suggestive of the level of slave-ownership among those of Irish descent. Hopefully this ‘first pass’ review will lead to more in-depth research that will tease out the complexities of these family histories.
DOI: 10.6084/m9.figshare.1330223.v1
title: Visual attention to dynamic spatial relations in infants and adults

description: Data analysis and one example of a 5-month-old, 12-month-old and an adult gaze behavior during dynamic observation of motion.
DOI: 10.6084/m9.figshare.1330402.v2
title: Dynamic Responses of Selective Brain White Matter Fiber Tracts to Binge Alcohol and Recovery in the Rat

description: To determine the dynamics of white matter vulnerability to excessive alcohol consumption, diffusion tensor imaging (DTI) was used in an animal model of alcohol exposure. Quantitative, in vivo fiber tracking results are presented from rats with DTI conducted at 3 time points: baseline; after 4 days of intragastric alcohol to blood alcohol levels of ~250mg/dL; and after one week of recovery. Binge alcohol followed by a week of sobriety resulted in rapidly reversible decreases in fractional anisotropy (FA), a measure of the coherence of fiber tracts, in callosal genu and fimbria-fornix but not splenium; and increases in mean diffusivity (MD), an index of freely diffusing water in tissue, selective to the fimbria-fornix. These effects were confirmed with tract-based spatial statistics (TBSS). The directionality of changes in DTI metrics reproduce those observed in human alcoholism. That a single exposure to binge alcohol can cause substantial transient changes detectable in DTI metrics demonstrates the potential for rapid neuroplasticity.
DOI: 10.6084/m9.figshare.1330402.v3
title: Dynamic Responses of Selective Brain White Matter Fiber Tracts to Binge Alcohol and Recovery in the Rat

description: To determine the dynamics of white matter vulnerability to excessive alcohol consumption, diffusion tensor imaging (DTI) was used in an animal model of alcohol exposure. Quantitative, in vivo fiber tracking results are presented from rats with DTI conducted at 3 time points: baseline; after 4 days of intragastric alcohol to blood alcohol levels of ~250mg/dL; and after one week of recovery. Binge alcohol followed by a week of sobriety resulted in rapidly reversible decreases in fractional anisotropy (FA), a measure of the coherence of fiber tracts, in callosal genu and fimbria-fornix but not splenium; and increases in mean diffusivity (MD), an index of freely diffusing water in tissue, selective to the fimbria-fornix. These effects were confirmed with tract-based spatial statistics (TBSS). The directionality of changes in DTI metrics reproduce those observed in human alcoholism. That a single exposure to binge alcohol can cause substantial transient changes detectable in DTI metrics demonstrates the potential for rapid neuroplasticity.
DOI: 10.6084/m9.figshare.1330402.v5
title: Dynamic Responses of Selective Brain White Matter Fiber Tracts to Binge Alcohol and Recovery in the Rat

description: To determine the dynamics of white matter vulnerability to excessive alcohol consumption, diffusion tensor imaging (DTI) was used in an animal model of alcohol exposure. Quantitative, in vivo fiber tracking results are presented from rats with DTI conducted at 3 time points: baseline; after 4 days of intragastric alcohol to blood alcohol levels of ~250mg/dL; and after one week of recovery. Binge alcohol followed by a week of sobriety resulted in rapidly reversible decreases in fractional anisotropy (FA), a measure of the coherence of fiber tracts, in callosal genu and fimbria-fornix but not splenium; and increases in mean diffusivity (MD), an index of freely diffusing water in tissue, selective to the fimbria-fornix. These effects were confirmed with tract-based spatial statistics (TBSS). The directionality of changes in DTI metrics reproduce those observed in human alcoholism. That a single exposure to binge alcohol can cause substantial transient changes detectable in DTI metrics demonstrates the potential for rapid neuroplasticity.
DOI: 10.6084/m9.figshare.1330402.v4
title: Dynamic Responses of Selective Brain White Matter Fiber Tracts to Binge Alcohol and Recovery in the Rat

description: To determine the dynamics of white matter vulnerability to excessive alcohol consumption, diffusion tensor imaging (DTI) was used in an animal model of alcohol exposure. Quantitative, in vivo fiber tracking results are presented from rats with DTI conducted at 3 time points: baseline; after 4 days of intragastric alcohol to blood alcohol levels of ~250mg/dL; and after one week of recovery. Binge alcohol followed by a week of sobriety resulted in rapidly reversible decreases in fractional anisotropy (FA), a measure of the coherence of fiber tracts, in callosal genu and fimbria-fornix but not splenium; and increases in mean diffusivity (MD), an index of freely diffusing water in tissue, selective to the fimbria-fornix. These effects were confirmed with tract-based spatial statistics (TBSS). The directionality of changes in DTI metrics reproduce those observed in human alcoholism. That a single exposure to binge alcohol can cause substantial transient changes detectable in DTI metrics demonstrates the potential for rapid neuroplasticity.
DOI: 10.6084/m9.figshare.1330166
title: Safety Monitoring for Elders

description: experiment video for safy monitoring paper
DOI: 10.6084/m9.figshare.1330166.v1
title: Safety Monitoring for Elders

description: experiment video for safy monitoring paper
DOI: 10.6084/m9.figshare.1330143
title: Nonlinear spike-and-slab sparse coding for interpretable image encoding. PLOS ONE

description: 3) Natural image occlusions This dataset contains an image of underbrush in a forest (taken bridge.jpg, which has been used for denoising bench-marking [33]), which is rich with occluding branches and twigs. From this original noise-free image, we cut a 110 × 110 pixel occlusion-rich section and scaled it up to 256 × 256 pixels to use in our dataset. To compose the dataset, we cut the 256 × 256 image (with pixel values ranging from (0, 255)) into N = 61009 overlapping image patches of D = 9 × 9 pixels, then add independent Gaussian noise with σ = 5. In the corresponding publication, the data is shown in Figure8A-B. [33] Mairal, J., Bach, F., Ponce, J., Sapiro, G., and Zisserman, A. (2009): Non-local sparse models for image<br>restoration. International Conference on Computer Vision 25.
DOI: 10.6084/m9.figshare.1330144
title: Nonlinear spike-and-slab sparse coding for interpretable image encoding 4) Natural image patches. PLOS ONE

description: 4) Natural image patches This file explains the natural image patches data used in the final experiment of the corresponding publication.