cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7792502
title: ‘Sometimes I like to see what I am doing’: studying outdoor play pedagogical documentation from children’s perspectives

description: This study explores how children respond to and think about their outdoor play pedagogical documentation, and how they engage in outdoor play experiences after they have conversations about their documentation panel. The data source for this study is composed of the author’s observations, and individual interviews with six children. A typological analysis model was used to analyse the collected data [Hatch, J. (2002). <i>Doing qualitative research in education settings</i>. Albany, NY: State University of New York Press]. The findings demonstrate that having conversations about documentation allowed the children to articulate their thoughts about previous outdoor play experiences, and provoke and implement further outdoor play ideas. Finally, a critical discussion on the findings of the study is presented in terms of how children’s perspectives on outdoor play pedagogical documentation can be utilized to promote the quality of pedagogy in outdoor practice.
DOI: 10.6084/m9.figshare.7792502.v1
title: ‘Sometimes I like to see what I am doing’: studying outdoor play pedagogical documentation from children’s perspectives

description: This study explores how children respond to and think about their outdoor play pedagogical documentation, and how they engage in outdoor play experiences after they have conversations about their documentation panel. The data source for this study is composed of the author’s observations, and individual interviews with six children. A typological analysis model was used to analyse the collected data [Hatch, J. (2002). <i>Doing qualitative research in education settings</i>. Albany, NY: State University of New York Press]. The findings demonstrate that having conversations about documentation allowed the children to articulate their thoughts about previous outdoor play experiences, and provoke and implement further outdoor play ideas. Finally, a critical discussion on the findings of the study is presented in terms of how children’s perspectives on outdoor play pedagogical documentation can be utilized to promote the quality of pedagogy in outdoor practice.
DOI: 10.6084/m9.figshare.7792436
title: Handmade tortilla production in the basins of lakes Pátzcuaro and Zirahuén, Mexico

description: The Main Map presented in this paper is the result of intensive fieldwork and mapping of 43 rural communities of the Pátzcuaro and Zirahuén basins in central-western Mexico. It shows the presence of handmade-tortilla workshops and considers the natural resources they demand but also their social, economic and cultural significance in the region. An in-depth survey of 111 Hand Made Tortilla Workshops gave detailed information of tortilla production, type of maize and fuelwood volume demanded in this activity. Traditional tortilla production contributes to the conservation of native maize and indigenous agriculture, and it promotes local and traditional food systems. However, it also represents a challenge given that many of these handmade tortilla workshops use open fire stoves which have negative implications regarding health, environment and pollution in rural livelihoods. This map serves as a platform for local and regional actions within a program involved in eco-technologies and sustainable livelihoods.
DOI: 10.6084/m9.figshare.7792424
title: The Graphical Horseshoe Estimator for Inverse Covariance Matrices

description: <b>We develop a new estimator of the inverse covariance matrix for high-dimensional multivariate normal data using the horseshoe prior. The proposed graphical horseshoe estimator has attractive properties compared to other popular estimators, such as the graphical lasso and the graphical smoothly clipped absolute deviation. The most prominent benefit is that when the true inverse covariance matrix is sparse, the graphical horseshoe provides estimates with small information divergence from the sampling model. The posterior mean under the graphical horseshoe prior can also be almost unbiased under certain conditions. In addition to these theoretical results, we also provide a full Gibbs sampler for implementing our estimator. MATLAB code is available for download from github at</b>http://github.com/liyf1988/GHS<b>. The graphical horseshoe estimator compares favorably to existing techniques in simulations and in a human gene network data analysis. Supplementary materials for this article are available online.</b>
DOI: 10.6084/m9.figshare.7792421
title: Paternal lineages in southern Iberia provide time frames for gene flow from mainland Europe and the Mediterranean world

description: <b>Background:</b> The geography of southern Iberia and an abundant archaeological record of human occupation are ideal conditions for a full understanding of scenarios of genetic history in the area. Recent advances in the phylogeography of Y-chromosome lineages offer the opportunity to set upper bounds for the appearance of different genetic components. <b>Aim:</b> To provide a global knowledge on the Y haplogroups observed in Andalusia with their Y microsatellite variation. Preferential attention is given to the vehement debate about the age, origin and expansion of R1b-M269 clade and sub-lineages. <b>Subject and methods:</b> Four hundred and fourteen male DNA samples from western and eastern autochthonous Andalusians were genotyped for a set of Y-SNPs and Y-STRs. Gene diversity, potential population genetic structures and coalescent times were assessed. <b>Results:</b> Most of the analysed samples belong to the European haplogroup R1b1a1a2-M269, whereas haplogroups E, J, I, G and T show lower frequencies. A phylogenetic dissection of the R1b-M269 was performed and younger time frames than those previously reported in the literature were obtained for its sub-lineages. <b>Conclusion:</b> The particular Andalusian R1b-M269 assemblage confirms the shallow topology of the clade. Moreover, the sharing of lineages with the rest of Europe indicates the impact in Iberia of an amount of pre-existing diversity, with the possible exception of R1b-DF27. Lineages such as J2-M172 and G-M201 highlight the importance of maritime travels of early farmers who reached the Iberian Peninsula.
DOI: 10.6084/m9.figshare.7792436.v2
title: Handmade tortilla production in the basins of lakes Pátzcuaro and Zirahuén, Mexico

description: The Main Map presented in this paper is the result of intensive fieldwork and mapping of 43 rural communities of the Pátzcuaro and Zirahuén basins in central-western Mexico. It shows the presence of handmade-tortilla workshops and considers the natural resources they demand but also their social, economic and cultural significance in the region. An in-depth survey of 111 Hand Made Tortilla Workshops gave detailed information of tortilla production, type of maize and fuelwood volume demanded in this activity. Traditional tortilla production contributes to the conservation of native maize and indigenous agriculture, and it promotes local and traditional food systems. However, it also represents a challenge given that many of these handmade tortilla workshops use open fire stoves which have negative implications regarding health, environment and pollution in rural livelihoods. This map serves as a platform for local and regional actions within a program involved in eco-technologies and sustainable livelihoods.
DOI: 10.6084/m9.figshare.7792421.v1
title: Paternal lineages in southern Iberia provide time frames for gene flow from mainland Europe and the Mediterranean world

description: <b>Background:</b> The geography of southern Iberia and an abundant archaeological record of human occupation are ideal conditions for a full understanding of scenarios of genetic history in the area. Recent advances in the phylogeography of Y-chromosome lineages offer the opportunity to set upper bounds for the appearance of different genetic components. <b>Aim:</b> To provide a global knowledge on the Y haplogroups observed in Andalusia with their Y microsatellite variation. Preferential attention is given to the vehement debate about the age, origin and expansion of R1b-M269 clade and sub-lineages. <b>Subject and methods:</b> Four hundred and fourteen male DNA samples from western and eastern autochthonous Andalusians were genotyped for a set of Y-SNPs and Y-STRs. Gene diversity, potential population genetic structures and coalescent times were assessed. <b>Results:</b> Most of the analysed samples belong to the European haplogroup R1b1a1a2-M269, whereas haplogroups E, J, I, G and T show lower frequencies. A phylogenetic dissection of the R1b-M269 was performed and younger time frames than those previously reported in the literature were obtained for its sub-lineages. <b>Conclusion:</b> The particular Andalusian R1b-M269 assemblage confirms the shallow topology of the clade. Moreover, the sharing of lineages with the rest of Europe indicates the impact in Iberia of an amount of pre-existing diversity, with the possible exception of R1b-DF27. Lineages such as J2-M172 and G-M201 highlight the importance of maritime travels of early farmers who reached the Iberian Peninsula.
DOI: 10.6084/m9.figshare.7792229
title: Down-regulated TMED10 in Alzheimer disease induces autophagy via ATG4B activation

description: Several studies have shown that dysfunction of macroautophagy/autophagy is associated with many human diseases, including neurodegenerative disease and cancer. To explore the molecular mechanisms of autophagy, we performed a cell-based functional screening with SH-SY5Y cells stably expressing GFP-LC3, using an siRNA library and identified TMED10 (transmembrane p24 trafficking protein 10), previously known as the γ-secretase-modulating protein, as a novel regulator of autophagy. Further investigations revealed that depletion of TMED10 induced the activation of autophagy. Interestingly, protein-protein interaction assays showed that TMED10 directly binds to ATG4B (autophagy related gene 4B cysteine peptidase), and the interaction is diminished under autophagy activation conditions such as rapamycin treatment and serum deprivation. In addition, inhibition of TMED10 significantly enhanced the proteolytic activity of ATG4B for LC3 cleavage. Importantly, the expression of TMED10 in AD (Alzheimer disease) patients was considerably decreased, and downregulation of TMED10 increased amyloid-β (Aβ) production. Treatment with Aβ increased ATG4B proteolytic activity as well as dissociation of TMED10 and ATG4B. Taken together, our results suggest that the AD-associated protein TMED10 negatively regulates autophagy by inhibiting ATG4B activity.<b>Abbreviations</b>: Aβ: amyloid-β; AD: Alzheimer disease; ATG: autophagy related; BECN1: beclin 1; BiFC: bimolecular fluorescence complementation; CD: cytosolic domain; GFP: green fluorescent protein; GLUC: <i>Gaussia</i> luciferase; IP: immunoprecipitation; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; LD: luminal domain; PD: Parkinson disease; ROS: reactive oxygen species; siRNA: small interfering RNA; SNP: single-nucleotide polymorphisms; TD: transmembrane domain; TMED10: transmembrane p24 trafficking protein 10; VC: C terminus of Venus fluorescent protein; VN: N terminus of Venus fluorescent protein.
DOI: 10.6084/m9.figshare.7792229.v1
title: Down-regulated TMED10 in Alzheimer disease induces autophagy via ATG4B activation

description: Several studies have shown that dysfunction of macroautophagy/autophagy is associated with many human diseases, including neurodegenerative disease and cancer. To explore the molecular mechanisms of autophagy, we performed a cell-based functional screening with SH-SY5Y cells stably expressing GFP-LC3, using an siRNA library and identified TMED10 (transmembrane p24 trafficking protein 10), previously known as the γ-secretase-modulating protein, as a novel regulator of autophagy. Further investigations revealed that depletion of TMED10 induced the activation of autophagy. Interestingly, protein-protein interaction assays showed that TMED10 directly binds to ATG4B (autophagy related gene 4B cysteine peptidase), and the interaction is diminished under autophagy activation conditions such as rapamycin treatment and serum deprivation. In addition, inhibition of TMED10 significantly enhanced the proteolytic activity of ATG4B for LC3 cleavage. Importantly, the expression of TMED10 in AD (Alzheimer disease) patients was considerably decreased, and downregulation of TMED10 increased amyloid-β (Aβ) production. Treatment with Aβ increased ATG4B proteolytic activity as well as dissociation of TMED10 and ATG4B. Taken together, our results suggest that the AD-associated protein TMED10 negatively regulates autophagy by inhibiting ATG4B activity.<b>Abbreviations</b>: Aβ: amyloid-β; AD: Alzheimer disease; ATG: autophagy related; BECN1: beclin 1; BiFC: bimolecular fluorescence complementation; CD: cytosolic domain; GFP: green fluorescent protein; GLUC: <i>Gaussia</i> luciferase; IP: immunoprecipitation; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; LD: luminal domain; PD: Parkinson disease; ROS: reactive oxygen species; siRNA: small interfering RNA; SNP: single-nucleotide polymorphisms; TD: transmembrane domain; TMED10: transmembrane p24 trafficking protein 10; VC: C terminus of Venus fluorescent protein; VN: N terminus of Venus fluorescent protein.
DOI: 10.6084/m9.figshare.7792175
title: Goji berries superfood – contributions for the characterisation of proteome and IgE-binding proteins

description: Goji berries’ bioactive compounds, which allowed classifying them as superfruits, led to an enormous increase of its consumption in western countries. However, the potential risk of allergy is a concern. In this study, we aimed to characterise the proteome of goji berries (<i>Lycium barbarum</i>) and identify proteins with putative role in the allergic reaction (IgE-binding proteins). We firstly used two-dimensional (2D) gel electrophoresis followed by mass spectrometry (MS) to characterise goji berries’ proteome, and then Immunoblot reactivity with plasma from tomato and potato (same botanical family, <i>Solanaceae</i>) allergic individuals was assessed to characterise goji berries IgE-binding proteins. An inhibition assay was further performed to evaluate cross-reactivity among potato, tomato and goji berries. We significantly identified 93 out of the 180 MS analysed spots, corresponding to 29 protein functions. From these, 11 could be identified as goji berries IgE-binding proteins. We further demonstrated cross-reactivity between goji berries, tomato and potato.
DOI: 10.6084/m9.figshare.7792175.v2
title: Goji berries superfood – contributions for the characterisation of proteome and IgE-binding proteins

description: Goji berries’ bioactive compounds, which allowed classifying them as superfruits, led to an enormous increase of its consumption in western countries. However, the potential risk of allergy is a concern. In this study, we aimed to characterise the proteome of goji berries (<i>Lycium barbarum</i>) and identify proteins with putative role in the allergic reaction (IgE-binding proteins). We firstly used two-dimensional (2D) gel electrophoresis followed by mass spectrometry (MS) to characterise goji berries’ proteome, and then Immunoblot reactivity with plasma from tomato and potato (same botanical family, <i>Solanaceae</i>) allergic individuals was assessed to characterise goji berries IgE-binding proteins. An inhibition assay was further performed to evaluate cross-reactivity among potato, tomato and goji berries. We significantly identified 93 out of the 180 MS analysed spots, corresponding to 29 protein functions. From these, 11 could be identified as goji berries IgE-binding proteins. We further demonstrated cross-reactivity between goji berries, tomato and potato.
DOI: 10.6084/m9.figshare.7792160
title: Clustering analysis to identify key genes associated with motor neuron excitability following spinal cord injury

description: <b>Purpose:</b> As a neurodegenerative disease, spinal cord injury can lead to the loss of autonomic function, muscle function, or sensation. This study is designed to identify the key genes implicated in the excitability of motor neurons following spinal cord injury. <b>Materials and methods:</b> The GSE19701 dataset was obtained from Gene Expression Omnibus. It includes a total of 31 motor neurons after spinal cord injury (samples at day 0, 2, 7, 21 and 60 following injury). After the data were preprocessed by the Robust Multi-array Average method, soft clustering analysis was conducted by the Fuzzy C-Means method in the Mfuzz package to identify the differentially expressed genes. Afterward, the differentially expressed genes were analyzed with enrichment analysis using the DAVID online tool. Based on Cytoscape software, a protein-protein interaction network was constructed and then module analysis was carried out. Furthermore, miRNA-differentially expressed gene pairs were downloaded from the miRWalk2.0 database and the miRNA regulatory network was visualized by Cytoscape software. <b>Results:</b> We found 218 upregulated genes and 526 downregulated genes. In the protein-protein interaction network, Uba3, Sumo1, and Pik3ca had higher scores, and Uba3 interacted with Sumo1. Among the eight modules identified from the protein–protein interaction network, module 1 and 8 were significantly enriched in pathways related to degenerative diseases of the nervous system. Additionally, <i>Pdcd4</i> was targeted by <i>miR-21</i> in the miRNA regulatory network. <b>Conclusion:</b><i>Uba3</i>, <i>Sumo1</i>, <i>Pik3ca</i> and <i>miR-21</i> targeting <i>Pdcd4</i> might be responsible for the excitability of motor neurons after spinal cord injury.
DOI: 10.6084/m9.figshare.7792160.v1
title: Clustering analysis to identify key genes associated with motor neuron excitability following spinal cord injury

description: <b>Purpose:</b> As a neurodegenerative disease, spinal cord injury can lead to the loss of autonomic function, muscle function, or sensation. This study is designed to identify the key genes implicated in the excitability of motor neurons following spinal cord injury. <b>Materials and methods:</b> The GSE19701 dataset was obtained from Gene Expression Omnibus. It includes a total of 31 motor neurons after spinal cord injury (samples at day 0, 2, 7, 21 and 60 following injury). After the data were preprocessed by the Robust Multi-array Average method, soft clustering analysis was conducted by the Fuzzy C-Means method in the Mfuzz package to identify the differentially expressed genes. Afterward, the differentially expressed genes were analyzed with enrichment analysis using the DAVID online tool. Based on Cytoscape software, a protein-protein interaction network was constructed and then module analysis was carried out. Furthermore, miRNA-differentially expressed gene pairs were downloaded from the miRWalk2.0 database and the miRNA regulatory network was visualized by Cytoscape software. <b>Results:</b> We found 218 upregulated genes and 526 downregulated genes. In the protein-protein interaction network, Uba3, Sumo1, and Pik3ca had higher scores, and Uba3 interacted with Sumo1. Among the eight modules identified from the protein–protein interaction network, module 1 and 8 were significantly enriched in pathways related to degenerative diseases of the nervous system. Additionally, <i>Pdcd4</i> was targeted by <i>miR-21</i> in the miRNA regulatory network. <b>Conclusion:</b><i>Uba3</i>, <i>Sumo1</i>, <i>Pik3ca</i> and <i>miR-21</i> targeting <i>Pdcd4</i> might be responsible for the excitability of motor neurons after spinal cord injury.
DOI: 10.6084/m9.figshare.7792175.v1
title: Goji berries superfood – contributions for the characterisation of proteome and IgE-binding proteins

description: Goji berries’ bioactive compounds, which allowed classifying them as superfruits, led to an enormous increase of its consumption in western countries. However, the potential risk of allergy is a concern. In this study, we aimed to characterise the proteome of goji berries (<i>Lycium barbarum</i>) and identify proteins with putative role in the allergic reaction (IgE-binding proteins). We firstly used two-dimensional (2D) gel electrophoresis followed by mass spectrometry (MS) to characterise goji berries’ proteome, and then Immunoblot reactivity with plasma from tomato and potato (same botanical family, <i>Solanaceae</i>) allergic individuals was assessed to characterise goji berries IgE-binding proteins. An inhibition assay was further performed to evaluate cross-reactivity among potato, tomato and goji berries. We significantly identified 93 out of the 180 MS analysed spots, corresponding to 29 protein functions. From these, 11 could be identified as goji berries IgE-binding proteins. We further demonstrated cross-reactivity between goji berries, tomato and potato.
DOI: 10.6084/m9.figshare.7792115
title: Multivariate Outliers and the O3 Plot

description: <b>Identifying and dealing with outliers is an important part of data analysis. A new visualization, the O3 plot, is introduced to aid in the display and understanding of patterns of multivariate outliers. It uses the results of identifying outliers for every possible combination of dataset variables to provide insight into why particular cases are outliers. The O3 plot can be used to compare the results from up to six different outlier identification methods. There is an</b>R<b>package OutliersO3 implementing the plot. The article is illustrated with outlier analyses of German demographic and economic data. Supplementary materials for this article are available online.</b>
DOI: 10.6084/m9.figshare.7792115.v1
title: Multivariate Outliers and the O3 Plot

description: <b>Identifying and dealing with outliers is an important part of data analysis. A new visualization, the O3 plot, is introduced to aid in the display and understanding of patterns of multivariate outliers. It uses the results of identifying outliers for every possible combination of dataset variables to provide insight into why particular cases are outliers. The O3 plot can be used to compare the results from up to six different outlier identification methods. There is an</b>R<b>package OutliersO3 implementing the plot. The article is illustrated with outlier analyses of German demographic and economic data. Supplementary materials for this article are available online.</b>
DOI: 10.6084/m9.figshare.7791881
title: Effects of <i>Kigelia africana</i> (Lam.) Benth. fruits extract on the development and maturation of the reproductive system in immature male rats

description: In the present study, we investigated the effects of <i>Kigelia africana</i> (Lam.) Benth. fruits ethanolic extract in prepubertal male rats, to evaluate the influence of the extract on the reproductive system and on pubertal development. Experiments were conducted using the rodent pubertal male assay. The plant extract, analyzed by TLC, HPLC-PDA and HPLC-ESI-MS, was administered orally at doses of 200, 400 and 800 mg/kg b.w. from post-natal date 21 to post-natal day 53. Age at puberty onset, body growth, development of sexual organs exposure to plant extract or positive control were examined. Results obtained indicate that <i>Kigelia</i> extract, at all doses tested, significantly anticipates puberty and increases body growth and sexual organs development. These effects appears to be due to stimulation of the secretion of androgenic hormones by the compounds found in its extract and scientifically support some of its traditional uses in disorders of the male reproductive system.
DOI: 10.23725/yhyc-7237
title: NWD248150.freeze5.v1.vcf.gz

description: TOPMed: NWD248150.freeze5.v1.vcf.gz <br>File: VCF file
DOI: 10.23725/yrtq-1h93
title: NWD858072.b38.irc.v1.cram.crai

description: TOPMed: NWD858072.b38.irc.v1.cram.crai <br>File: CRAI index file
DOI: 10.23725/z9rz-s107
title: NWD773724.b38.irc.v1.cram.crai

description: TOPMed: NWD773724.b38.irc.v1.cram.crai <br>File: CRAI index file
DOI: 10.23725/zb0w-ja97
title: NWD177101.freeze5.v1.vcf.gz

description: TOPMed: NWD177101.freeze5.v1.vcf.gz <br>File: VCF file