cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3102970.v1
title: Epigenetic alteration of imprinted genes during neural differentiation of germline-derived pluripotent stem cells

description: Spermatogonial stem cells (SSCs), which are unipotent stem cells in the testes that give rise to sperm, can be converted into germline-derived pluripotent stem (gPS) by self-induction. The androgenetic imprinting pattern of SSCs is maintained even after their reprogramming into gPS cells. In this study, we used an <i>in vitro</i> neural differentiation model to investigate whether the imprinting patterns are maintained or altered during differentiation. The androgenetic patterns of <i>H19, Snrpn</i>, and <i>Mest</i> were maintained even after differentiation of gPS cells into NSCs (gPS-NSCs), whereas the fully unmethylated status of <i>Ndn</i> in SSCs was altered to somatic patterns in gPS cells and gPS-NSCs. Thus, our study demonstrates epigenetic alteration of genomic imprinting during the induction of pluripotency in SSCs and neural differentiation, suggesting that gPS-NSCs can be a useful model to study the roles of imprinted genes in brain development and human neurodevelopmental disorders.
DOI: 10.6084/m9.figshare.3102967.v1
title: Insulin-degrading enzyme secretion from astrocytes is mediated by an autophagy-based unconventional secretory pathway in Alzheimer disease

description: The secretion of proteins that lack a signal sequence to the extracellular milieu is regulated by their transition through the unconventional secretory pathway. IDE (insulin-degrading enzyme) is one of the major proteases of amyloid beta peptide (Aβ), a presumed causative molecule in Alzheimer disease (AD) pathogenesis. IDE acts in the extracellular space despite having no signal sequence, but the underlying mechanism of IDE secretion extracellularly is still unknown. In this study, we found that IDE levels were reduced in the cerebrospinal fluid (CSF) of patients with AD and in pathology-bearing AD-model mice. Since astrocytes are the main cell types for IDE secretion, astrocytes were treated with Aβ. Aβ increased the IDE levels in a time- and concentration-dependent manner. Moreover, IDE secretion was associated with an autophagy-based unconventional secretory pathway, and depended on the activity of RAB8A and GORASP (Golgi reassembly stacking protein). Finally, mice with global haploinsufficiency of an essential autophagy gene, showed decreased IDE levels in the CSF in response to an intracerebroventricular (i.c.v.) injection of Aβ. These results indicate that IDE is secreted from astrocytes through an autophagy-based unconventional secretory pathway in AD conditions, and that the regulation of autophagy is a potential therapeutic target in addressing Aβ pathology.
DOI: 10.6084/m9.figshare.3102859
title: Exploring Ulysses S. Grant’s views and experience with slavery using the C3 Inquiry Framework and Primary Sources

description: This is a conference presentation that later evolved into the manuscripts:Anthony, K. & Morgan, M. K. (2015). Ulysses S. Grant Manumits William Jones: An Example of America’s Entanglement with Slavery. <i>Middle Level Learning, 54</i>, pp. 2-5. Morgan, M.K. & Anthony, K. (2015). Ulysses S. Grant Manumits William Jones: America’s Entanglement with Slavery, A Lesson for Grades 6-8. <i>Middle Level Learning, 54</i>, pp. 6-16.
DOI: 10.6084/m9.figshare.3102730
title: Scene integration without awareness: No conclusive evidence for processing scene congruency during continuous flash suppression

description: This fileset contains the data reported in and materials used in: <br>Moors, P., Boelens, D., van Overwalle, J., Wagemans, J. (2016). Scene integration without awareness: No conclusive evidence for processing scene congruency during continuous flash suppression. Psychological Science. <br>Please note that the stimulus set is not included, because I did not create these stimuli myself. <br><br>
DOI: 10.6084/m9.figshare.3102781
title: Snodgrass & Vanderwart 'Like' Objects

description: <b>NOTE THAT THE LICENSE IS</b> <i>Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License</i><br>This is a set of 260 colored objects created by Rossion & Pourtois (2004), which is loosely based on the original dataset by Snodgrass & Vanderwart (1980) and provided by Tarr Lab (see the link below).<br>The version provided here converted images from PCT to PNG. Moreover, a description of each image is provided in the definitions.csv file, including WordNet synset, definition, and synonyms (obtained from Snodgrass & Vanderwart, 1980, plus several new ones, namely, baby carriage: stroller, pram; doorknob: doorhandle; rabbit: bunny, hare; refrigerator: fridge).<br>Please cite the following paper when using the dataset:<br><i>Rossion, B., & Pourtois, G. (2004). Revisiting Snodgrass and Vanderwart's object set: The role of surface detail in basic-level object recognition. Perception, 33, 217-236.</i><br>Also, please include the following statement in the paper:<br><i>Stimulus images courtesy of Michael J. Tarr, Center for the Neural Basis of Cognition and Department of Psychology, Carnegie Mellon University, http://www.tarrlab.org/</i>
DOI: 10.6084/m9.figshare.3102766
title: MiR31 in DMD raw data.xls

description: Dataset used for figures in Hildyard et al "Investigating synthetic oligonucleotide targeting of miR31 in Duchenne muscular dystrophy"
DOI: 10.21227/rpkx-6p91
title: CHU Surveillance Violence Detection Dataset

description: The CHU Surveillance Violence Dataset (CSVD) is a collection of CCTV footage of violent and non-violent actions aiming to characterize the composition of violent actions into more specific actions. We produced several simple action classes for violent and non-violent actions do add variety and better distribution among simple and complex action classes for RGB and Action Silhouette Videos (enhanced Optical Flow Images) with their localized actions. The dataset consists of 12 simple action classes: idle, run, walk, high-five, wave, pose, shove, grapple, punch, kick, and clobbering, which are further classified as violent or non-violent actions.
DOI: 10.6084/m9.figshare.3102730.v1
title: Scene integration without awareness: No conclusive evidence for processing scene congruency during continuous flash suppression

description: This fileset contains the data reported in and materials used in: <br>Moors, P., Boelens, D., van Overwalle, J., Wagemans, J. (2016). Scene integration without awareness: No conclusive evidence for processing scene congruency during continuous flash suppression. Psychological Science. <br>Please note that the stimulus set is not included, because I did not create these stimuli myself. <br><br>
DOI: 10.6084/m9.figshare.3102766.v1
title: MiR31 in DMD raw data.xls

description: Dataset used for figures in Hildyard et al "Investigating synthetic oligonucleotide targeting of miR31 in Duchenne muscular dystrophy"
DOI: 10.6084/m9.figshare.3102700
title: Susan B. Anthony’s trial, social justice, and Common Core connections

description: The adoption of Common Core State Standards presents the social studies with an opportunity and a challenge. Common Core State Standards focus on college and career readiness. The focus on college and career readiness is a challenge because the civic education goal of social studies may be lost or overlooked. The opportunity is that social studies is one of those other areas that must be used to help develop literacy. The goal of this paper is to discuss how to use social studies texts, specifically primary sources related to Susan B. Anthony’s trial, to meet literacy and social studies goals.<br>I have provided a link to the published paper below and I have provided the materials I presented at the National Council for Social Studies Conference in 2013. <br>Anthony, K. & Morgan, M.K. (2014). Susan B. Anthony’s trial, social justice, and Common Core connections. <i>The</i> <i>Georgia Social Studies Journal, 4</i>(1), pp. 10-19. http://www.coe.uga.edu/assets/docs/hubs/gssj/Anthony-and-Morgan-2014.pdf<br><br>
DOI: 10.6084/m9.figshare.3102709
title: BEAST_XML.zip

description: BEAST input files for GLM analysis of foot-and-mouth-disease topotypes O SEA and O ME-SA
DOI: 10.6084/m9.figshare.3102709.v1
title: BEAST_XML.zip

description: BEAST input files for GLM analysis of foot-and-mouth-disease topotypes O SEA and O ME-SA
DOI: 10.6084/m9.figshare.3102616
title: S2 Table - Records of Paramuricea clavata

description: This table accompanies an article in Scientific Reports journal. It presents georeferenced records of the red gorgonian Paramuricea clavata across its full geographic and bathymetric distribution. This includes record points from the Eastern Mediterranean Sea to the Atlantic Ocean and from the shallow infralittoral zone to the continental shelf limit (around 200 m). These points were compiled from online databases, published scientific articles, grey literature, local expert knowledge (contacted by the authors) and field surveys where information was lacking in the Portuguese coastline.The table includes the coordinates, depth when available and source reference.
DOI: 10.6084/m9.figshare.3102700.v2
title: Susan B. Anthony’s trial, social justice, and Common Core connections

description: The adoption of Common Core State Standards presents the social studies with an opportunity and a challenge. Common Core State Standards focus on college and career readiness. The focus on college and career readiness is a challenge because the civic education goal of social studies may be lost or overlooked. The opportunity is that social studies is one of those other areas that must be used to help develop literacy. The goal of this paper is to discuss how to use social studies texts, specifically primary sources related to Susan B. Anthony’s trial, to meet literacy and social studies goals.<br>I have provided a link to the published paper below and I have provided the materials I presented at the National Council for Social Studies Conference in 2013. <br>Anthony, K. & Morgan, M.K. (2014). Susan B. Anthony’s trial, social justice, and Common Core connections. <i>The</i> <i>Georgia Social Studies Journal, 4</i>(1), pp. 10-19. http://www.coe.uga.edu/assets/docs/hubs/gssj/Anthony-and-Morgan-2014.pdf<br><br>
DOI: 10.6084/m9.figshare.3102544
title: Color and Uncertainty: It is not always Black and White

description: To fully comprehend the meaning and impact of visualized data it is crucial that users are able to perceive and comprehend the inherent uncertainty of the data in a correct and intuitive way. Data uncertainty is frequently visualized through color mappings. Previous studies argued that color hue is not suitable for communicating uncertainty because most hue scales lack an intrinsic perceptual order. In this paper we examine the use of hue for communicating data uncertainty in more detail. We investigated the potential of distinct color triples (rather than the entire spectrum of colors, as used in previously studies) to represent different levels of uncertainty.We identified several color triples that reliably map to an intuitive ordering of certainty. Bipolar color scales constructed from these color triples can be used to communicate uncertainty in visualizations, particularly to audiences of nonspecialists. A ‘traffic light’ configuration (with red and green at the endpoints and either yellow or orange in the middle) communicates uncertainty most intuitively.
DOI: 10.6084/m9.figshare.3102544.v1
title: Color and Uncertainty: It is not always Black and White

description: To fully comprehend the meaning and impact of visualized data it is crucial that users are able to perceive and comprehend the inherent uncertainty of the data in a correct and intuitive way. Data uncertainty is frequently visualized through color mappings. Previous studies argued that color hue is not suitable for communicating uncertainty because most hue scales lack an intrinsic perceptual order. In this paper we examine the use of hue for communicating data uncertainty in more detail. We investigated the potential of distinct color triples (rather than the entire spectrum of colors, as used in previously studies) to represent different levels of uncertainty.We identified several color triples that reliably map to an intuitive ordering of certainty. Bipolar color scales constructed from these color triples can be used to communicate uncertainty in visualizations, particularly to audiences of nonspecialists. A ‘traffic light’ configuration (with red and green at the endpoints and either yellow or orange in the middle) communicates uncertainty most intuitively.
DOI: 10.6084/m9.figshare.3102526
title: Thompson et al 2016 Behavioural Brain Research - data for experiments 1-3

description: Data for experiment 1 of Thompson et al. 2016. Behavioural Brain Research are given in the 'expt 1' file as follows: Housing condition is given in column A. The time spent in the black area of the test tank as a proportion of the total time spent in the black and white areas of the tank is given in column B.<br><br>Data for experiment 2 of Thompson et al. 2016. Behavioural Brain Research are given in the 'expt 2' file as follows:Data on all 48 fish are provided in rows 2-49. Home tank colour and handling treatment (box vs net) are given in columns A and B. Data on behaviour during each minute in the open field test (minutes 1-10) and the novel object test (minutes 11-15) are provided for the following variables: time spent in the central zone of the tank (columns C-Q); mean distance from the central point in the tank (columns R-AF); mean speed of the fish (columns AG-AU). The latency for fish to enter the central zone after the novel object was placed in the centre of the tank is provided in column AV.<br>Data for experiment 3 of Thompson et al. 2016. Behavioural Brain Research are given in the 'expt 3' file as follows: Data on all 56 fish are provided in rows 2-57. Handling treatment (box vs net) is given in column A. Data on behaviour during each minute of the diving-scototaxis test (minutes 1-10) is provided for the following variables: time spent in the black side of the tank (columns B-K); time spent in the bottom third of the tank (columns L-U); mean distance from the bottom corner of the black side of the tank (columns V-AE); mean speed of the fish (columns AF-AO).
DOI: 10.6084/m9.figshare.3102505
title: Experimental SAH hormones

description: Experimental SAH in pigs with measurements of acute endocrine stress response. <br>The variable time is minutes from induction of SAH.<br>
DOI: 10.6084/m9.figshare.3102541
title: PLOS ONE: Be Happy Not Sad for Your Youth: The Effect of Emotional Expression on Age Perception

description: These files contain raw and processed data for the PLoS ONE paper entitled: "Be Happy Not Sad For Your Youth: The Effect of Emotional Expression on Age Perception" by Norah Hass, Trent Weston, and Seung-Lark Lim<br>DOI: 10.1371/journal.pone.0152093<br><br><br>
DOI: 10.6084/m9.figshare.3102526.v2
title: Thompson et al 2016 Behavioural Brain Research - data for experiments 1-3

description: Data for experiment 1 of Thompson et al. 2016. Behavioural Brain Research are given in the 'expt 1' file as follows: Housing condition is given in column A. The time spent in the black area of the test tank as a proportion of the total time spent in the black and white areas of the tank is given in column B.<br><br>Data for experiment 2 of Thompson et al. 2016. Behavioural Brain Research are given in the 'expt 2' file as follows:Data on all 48 fish are provided in rows 2-49. Home tank colour and handling treatment (box vs net) are given in columns A and B. Data on behaviour during each minute in the open field test (minutes 1-10) and the novel object test (minutes 11-15) are provided for the following variables: time spent in the central zone of the tank (columns C-Q); mean distance from the central point in the tank (columns R-AF); mean speed of the fish (columns AG-AU). The latency for fish to enter the central zone after the novel object was placed in the centre of the tank is provided in column AV.<br>Data for experiment 3 of Thompson et al. 2016. Behavioural Brain Research are given in the 'expt 3' file as follows: Data on all 56 fish are provided in rows 2-57. Handling treatment (box vs net) is given in column A. Data on behaviour during each minute of the diving-scototaxis test (minutes 1-10) is provided for the following variables: time spent in the black side of the tank (columns B-K); time spent in the bottom third of the tank (columns L-U); mean distance from the bottom corner of the black side of the tank (columns V-AE); mean speed of the fish (columns AF-AO).
DOI: 10.6084/m9.figshare.3102505.v1
title: Experimental SAH hormones

description: Experimental SAH in pigs with measurements of acute endocrine stress response. <br>The variable time is minutes from induction of SAH.<br>
DOI: 10.6084/m9.figshare.3102541.v2
title: PLOS ONE: Be Happy Not Sad for Your Youth: The Effect of Emotional Expression on Age Perception

description: These files contain raw and processed data for the PLoS ONE paper entitled: "Be Happy Not Sad For Your Youth: The Effect of Emotional Expression on Age Perception" by Norah Hass, Trent Weston, and Seung-Lark Lim<br>DOI: 10.1371/journal.pone.0152093<br><br><br>
DOI: 10.6084/m9.figshare.3102541.v1
title: PLOS ONE: Be Happy Not Sad for Your Youth: The Effect of Emotional Expression on Age Perception

description: These files contain raw and processed data for the PLoS ONE paper entitled: "Be Happy Not Sad For Your Youth: The Effect of Emotional Expression on Age Perception" by Norah Hass, Trent Weston, and Seung-Lark Lim<br>DOI: 10.1371/journal.pone.0152093<br><br><br>
DOI: 10.6084/m9.figshare.3102451
title: Characterisation of caecum and crop microbiota of Indian indigenous chicken targeting multiple hypervariable regions within 16S rRNA gene

description: A comparative analysis of caecum and crop microbiota of chick, grower and adult stages of Indian indigenous chickens was conducted to investigate the role of the microbiota of the gastrointestinal tract, which play an important role in host performance, health and immunity.High-throughput Illumina sequencing was performed for V3, V4 and V4-V6 hypervariable regions of the 16S rRNA gene. M5RNA and M5NR databases under MG-RAST were used for metagenomic datasets annotation.In the crop, <i>Firmicutes</i> (~78%) and <i>Proteobacteria</i> (~16%) were the predominant phyla whereas in the caecum, <i>Firmicutes</i> (~50%), <i>Bacteroidetes</i> (~29%) and <i>Actinobacteria</i> (~10%) were predominant. The Shannon-Wiener diversity index suggested that sample richness and diversity increased as the chicken aged.For the first time, the presence of <i>Lactobacillus</i> species such as <i>L. frumenti, L. antri, L. mucosae</i> in the chicken crop along with <i>Kineococcus radiotolerans, Desulfohalobium retbaense</i> and <i>L. jensenii</i> in the caecum are reported. Many of these bacterial species have been found to be involved in immune response modulation and disease prevention in pigs and humans. The gut microbiome of the indigenous chicken was enriched with microbes having probiotic potential which might be essential for their adaptability. A comparative analysis of caecum and crop microbiota of chick, grower and adult stages of Indian indigenous chickens was conducted to investigate the role of the microbiota of the gastrointestinal tract, which play an important role in host performance, health and immunity. High-throughput Illumina sequencing was performed for V3, V4 and V4-V6 hypervariable regions of the 16S rRNA gene. M5RNA and M5NR databases under MG-RAST were used for metagenomic datasets annotation. In the crop, <i>Firmicutes</i> (~78%) and <i>Proteobacteria</i> (~16%) were the predominant phyla whereas in the caecum, <i>Firmicutes</i> (~50%), <i>Bacteroidetes</i> (~29%) and <i>Actinobacteria</i> (~10%) were predominant. The Shannon-Wiener diversity index suggested that sample richness and diversity increased as the chicken aged. For the first time, the presence of <i>Lactobacillus</i> species such as <i>L. frumenti, L. antri, L. mucosae</i> in the chicken crop along with <i>Kineococcus radiotolerans, Desulfohalobium retbaense</i> and <i>L. jensenii</i> in the caecum are reported. Many of these bacterial species have been found to be involved in immune response modulation and disease prevention in pigs and humans. The gut microbiome of the indigenous chicken was enriched with microbes having probiotic potential which might be essential for their adaptability.
DOI: 10.6084/m9.figshare.3102400
title: Processes governing the stable isotope composition of water in the St. Lawrence river system, Canada<sup>†</sup>

description: Linkages between δ<sup>18</sup>O–δ<sup>2</sup>H and hydrological processes have been investigated from isotopic time series recorded in the St. Lawrence River basin. Three stations were monitored from 1997 to 2008. They include the Ottawa River, the St. Lawrence River main channel at Montreal and the fluvial estuary. All sites depict seasonal isotopic cycles characterized by heavy isotope depletions during the snowmelt period and heavy isotope enrichments throughout the ice-free period. The data define δ<sup>2</sup>H–δ<sup>18</sup>O regression lines falling below the meteoric water line. In the Ottawa River, calculations suggest that approximately 8 % of the total inflow to the basin is lost through evaporation. In the St. Lawrence River main channel, seasonal isotopic fluctuations most likely reflect hydrological processes occurring within the Great Lakes and mixing with tributaries located downstream. In the St. Lawrence River fluvial estuary, isotopic data allow partitioning streamflow components and suggest that the recorded seasonal variations mainly respond to mixing processes.
DOI: 10.6084/m9.figshare.3102400.v2
title: Processes governing the stable isotope composition of water in the St. Lawrence river system, Canada<sup>†</sup>

description: Linkages between δ<sup>18</sup>O–δ<sup>2</sup>H and hydrological processes have been investigated from isotopic time series recorded in the St. Lawrence River basin. Three stations were monitored from 1997 to 2008. They include the Ottawa River, the St. Lawrence River main channel at Montreal and the fluvial estuary. All sites depict seasonal isotopic cycles characterized by heavy isotope depletions during the snowmelt period and heavy isotope enrichments throughout the ice-free period. The data define δ<sup>2</sup>H–δ<sup>18</sup>O regression lines falling below the meteoric water line. In the Ottawa River, calculations suggest that approximately 8 % of the total inflow to the basin is lost through evaporation. In the St. Lawrence River main channel, seasonal isotopic fluctuations most likely reflect hydrological processes occurring within the Great Lakes and mixing with tributaries located downstream. In the St. Lawrence River fluvial estuary, isotopic data allow partitioning streamflow components and suggest that the recorded seasonal variations mainly respond to mixing processes.