cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.4716273
title: Geomorphology model (ArcGIS Pro version), input datasets and legend symbology files

description: Original model developed in 2016-17 in ArcGIS by Henk Pieter Sterk (www.rfase.org), with minor updates in 2021 by Stacy Shinneman and Henk Pieter Sterk. Model used to generate publication results: Hierarchical geomorphological mapping in mountainous areas. 2021. Matheus G.G. De Jong, Henk Pieter Sterk, Stacy Shinneman & Arie C. Seijmonsbergen. Journal of Maps This model creates tiers (columns) of geomorphological features (Tier 1, Tier 2 and Tier 3) in the landscape of Vorarlberg, Austria, each with an increasing level of detail. The input dataset needed to create this 'three-tier-legend' is a geomorphological map of Vorarlberg with a Tier 3 category (e.g. 1111, for glacially eroded bedrock). The model then automatically adds Tier 1, Tier 2 and Tier 3 categories based on the Tier 3 code in the 'Geomorph' field. The model replaces the input file with an updated shapefile of the geomorphology of Vorarlberg, now including three tiers of geomorphological features. Python script files and .lyr symbology files are also provided here.
description: We also created an online storymap (https://arcg.is/Xjvy4) of all three tiers for both areas, which scales automatically as the user zooms in and out between scales to show how the data are dynamically visualized in a GIS.
DOI: 10.5281/zenodo.4716272
title: Geomorphology model (ArcGIS Pro version), input datasets and legend symbology files

description: Original model developed in 2016-17 in ArcGIS by Henk Pieter Sterk (www.rfase.org), with minor updates in 2021 by Stacy Shinneman and Henk Pieter Sterk. Model used to generate publication results: Hierarchical geomorphological mapping in mountainous areas. 2021. Matheus G.G. De Jong, Henk Pieter Sterk, Stacy Shinneman & Arie C. Seijmonsbergen. Journal of Maps This model creates tiers (columns) of geomorphological features (Tier 1, Tier 2 and Tier 3) in the landscape of Vorarlberg, Austria, each with an increasing level of detail. The input dataset needed to create this 'three-tier-legend' is a geomorphological map of Vorarlberg with a Tier 3 category (e.g. 1111, for glacially eroded bedrock). The model then automatically adds Tier 1, Tier 2 and Tier 3 categories based on the Tier 3 code in the 'Geomorph' field. The model replaces the input file with an updated shapefile of the geomorphology of Vorarlberg, now including three tiers of geomorphological features. Python script files and .lyr symbology files are also provided here.
description: We also created an online storymap (https://arcg.is/Xjvy4) of all three tiers for both areas, which scales automatically as the user zooms in and out between scales to show how the data are dynamically visualized in a GIS.
DOI: 10.5281/zenodo.4716264
title: Roles and problems of stroke caregivers: A qualitative study in Yogyakarta, Indonesia

description: <strong>Background</strong>: Caregivers play a central role in post-stroke patients care. However, the role of and problems managed by caregivers have not been widely studied, particularly in Indonesia. This study aims to explore the roles and problems of caregivers in post- stroke patients’ care. <strong>Method</strong>: This was a qualitative study. Caregivers of post-stroke patients from the homecare clinic of Dr Sardjito General Hospital were purposely selected during January 2017 to June 2018. Focus group discussions were conducted to explore the roles and problems of caregiving. <strong>Results</strong>: Themes related to caregivers’ roles were: connecting patients with medical personnel and other family members, maintaining patients’ health conditions by fulfilling basic needs and assisting rehabilitation, as well as maintaining patients’ psychological conditions by encouraging conversation, telling jokes, or recreation. On the other hand, themes related to caregivers’ problems were: lack of knowledge caused by education inadequacy, underappreciated and unconcerned family, suboptimal service including limited physiotherapy and pharmacy resource, and unthorough administration, lack of communication, physical limitations and burnout, as well as uncooperative patients. <strong>Conclusions: </strong>Caregivers play essential roles as communicators and help to maintain patient's health conditions. Common problems are related to a lack of knowledge about strokes and a lack of attention from family. Understanding the roles and problems of caregivers may help facilitate better management and increase the quality of life for both patients and their caregivers.
DOI: 10.5281/zenodo.4716263
title: Roles and problems of stroke caregivers: A qualitative study in Yogyakarta, Indonesia

description: <strong>Background</strong>: Caregivers play a central role in post-stroke patients care. However, the role of and problems managed by caregivers have not been widely studied, particularly in Indonesia. This study aims to explore the roles and problems of caregivers in post- stroke patients’ care. <strong>Method</strong>: This was a qualitative study. Caregivers of post-stroke patients from the homecare clinic of Dr Sardjito General Hospital were purposely selected during January 2017 to June 2018. Focus group discussions were conducted to explore the roles and problems of caregiving. <strong>Results</strong>: Themes related to caregivers’ roles were: connecting patients with medical personnel and other family members, maintaining patients’ health conditions by fulfilling basic needs and assisting rehabilitation, as well as maintaining patients’ psychological conditions by encouraging conversation, telling jokes, or recreation. On the other hand, themes related to caregivers’ problems were: lack of knowledge caused by education inadequacy, underappreciated and unconcerned family, suboptimal service including limited physiotherapy and pharmacy resource, and unthorough administration, lack of communication, physical limitations and burnout, as well as uncooperative patients. <strong>Conclusions: </strong>Caregivers play essential roles as communicators and help to maintain patient's health conditions. Common problems are related to a lack of knowledge about strokes and a lack of attention from family. Understanding the roles and problems of caregivers may help facilitate better management and increase the quality of life for both patients and their caregivers.
DOI: 10.5281/zenodo.4716261
title: Geomorphology model (ArcMap version), input datasets and legend symbology files

description: Original model developed in 2016-17 in ArcGIS by Henk Pieter Sterk (www.rfase.org), with minor updates in 2021 by Stacy Shinneman and Henk Pieter Sterk. Model used to generate publication results: Hierarchical geomorphological mapping in mountainous areas. 2021. Matheus G.G. De Jong, Henk Pieter Sterk, Stacy Shinneman & Arie C. Seijmonsbergen. Journal of Maps This model creates tiers (columns) of geomorphological features (Tier 1, Tier 2 and Tier 3) in the landscape of Vorarlberg, Austria, each with an increasing level of detail. The input dataset needed to create this 'three-tier-legend' is a geomorphological map of Vorarlberg with a Tier 3 category (e.g. 1111, for glacially eroded bedrock). The model then automatically adds Tier 1, Tier 2 and Tier 3 categories based on the Tier 3 code in the 'Geomorph' field. The model replaces the input file with an updated shapefile of the geomorphology of Vorarlberg, now including three tiers of geomorphological features. Python script files and .lyr symbology files are also provided here.
description: We also created an online storymap (https://arcg.is/Xjvy4) of all three tiers for both areas, which scales automatically as the user zooms in and out between scales to show how the data are dynamically visualized in a GIS.
DOI: 10.5281/zenodo.4716260
title: Geomorphology model (ArcMap version), input datasets and legend symbology files

description: Original model developed in 2016-17 in ArcGIS by Henk Pieter Sterk (www.rfase.org), with minor updates in 2021 by Stacy Shinneman and Henk Pieter Sterk. Model used to generate publication results: Hierarchical geomorphological mapping in mountainous areas. 2021. Matheus G.G. De Jong, Henk Pieter Sterk, Stacy Shinneman & Arie C. Seijmonsbergen. Journal of Maps This model creates tiers (columns) of geomorphological features (Tier 1, Tier 2 and Tier 3) in the landscape of Vorarlberg, Austria, each with an increasing level of detail. The input dataset needed to create this 'three-tier-legend' is a geomorphological map of Vorarlberg with a Tier 3 category (e.g. 1111, for glacially eroded bedrock). The model then automatically adds Tier 1, Tier 2 and Tier 3 categories based on the Tier 3 code in the 'Geomorph' field. The model replaces the input file with an updated shapefile of the geomorphology of Vorarlberg, now including three tiers of geomorphological features. Python script files and .lyr symbology files are also provided here.
description: We also created an online storymap (https://arcg.is/Xjvy4) of all three tiers for both areas, which scales automatically as the user zooms in and out between scales to show how the data are dynamically visualized in a GIS.
DOI: 10.18434/m32262
title: NIST STEP to X3D Translator (STP2X3D)
DOI: 10.5281/zenodo.4716268
title: LOXL3 Silencing Affected Mitochondria Localization and Protein Recycling in U87MG Glioma Cells

description: RNAseq data of LOXL3-siRNA and NTC-siRNA U87MG cells.
DOI: 10.5281/zenodo.4716267
title: LOXL3 Silencing Affected Mitochondria Localization and Protein Recycling in U87MG Glioma Cells

description: RNAseq data of LOXL3-siRNA and NTC-siRNA U87MG cells.
DOI: 10.5281/zenodo.4716300
title: ArcGIS Map packages with geomorphological and geographical datasets used to generate maps for Dunza-Tschengla study area in Vorarlberg, Austria

description: Map packages for use in ArcGIS Pro or ArcMap containing three-tiered geomorphological data and geographical datasets such as rivers and hillshading. Datasets were used to generate figures for publication: Hierarchical geomorphological mapping in mountainous areas. 2021. Matheus G.G. De Jong, Henk Pieter Sterk, Stacy Shinneman & Arie C. Seijmonsbergen. Journal of Maps. All data is in MGI Austria GK West projected coordinate system (EPSG: 31254) and was clipped to the study area.
description: We also created an online storymap (https://arcg.is/Xjvy4) of all three tiers for both areas, which scales automatically as the user zooms in and out between scales to show how the data are dynamically visualized in a GIS.
DOI: 10.5281/zenodo.4716299
title: ArcGIS Map packages with geomorphological and geographical datasets used to generate maps for Dunza-Tschengla study area in Vorarlberg, Austria

description: Map packages for use in ArcGIS Pro or ArcMap containing three-tiered geomorphological data and geographical datasets such as rivers and hillshading. Datasets were used to generate figures for publication: Hierarchical geomorphological mapping in mountainous areas. 2021. Matheus G.G. De Jong, Henk Pieter Sterk, Stacy Shinneman & Arie C. Seijmonsbergen. Journal of Maps. All data is in MGI Austria GK West projected coordinate system (EPSG: 31254) and was clipped to the study area.
description: We also created an online storymap (https://arcg.is/Xjvy4) of all three tiers for both areas, which scales automatically as the user zooms in and out between scales to show how the data are dynamically visualized in a GIS.
DOI: 10.6084/m9.figshare.14475705
title: Analysis of the ratio of um to of in the earlier vs. later component texts of Sturlunga saga

description: Quantitative/ statistical analysis of <i>Sturlunga saga</i> to verify the claim of Einar Ól. Sveinsson in <i>Dating the Icelandic Sagas </i>that the component texts reflect their relative ages based on the ratio of the particles um and of.
DOI: 10.6084/m9.figshare.14475705.v1
title: Analysis of the ratio of um to of in the earlier vs. later component texts of Sturlunga saga

description: Quantitative/ statistical analysis of <i>Sturlunga saga</i> to verify the claim of Einar Ól. Sveinsson in <i>Dating the Icelandic Sagas </i>that the component texts reflect their relative ages based on the ratio of the particles um and of.
DOI: 10.5519/qd.wj0ppkid
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (710 records)
DOI: 10.6084/m9.figshare.12851690
title: Genome-wide DNA methylation alteration in prenatally stressed Brahman heifer calves with the advancement of age

description: Possible phenotypic impairments associated with maternal stress during gestation in beef cattle may be explained by epigenetic effects. This study examined the impact of prenatal transportation stress on DNA methylation of lymphocytes of Brahman cows over the first 5 years of life. Methylation analysis through reduced representation bisulphite sequencing was conducted on DNA from lymphocytes from 28 paired samples from 6 prenatally stressed (PNS) and 8 control (Control) females obtained initially when they were 28 days of age and 5 years of age. There were 14,386 CpG (C = cytosine; p = phosphate; G = guanine) sites differentially methylated (<i>P</i> P
DOI: 10.6084/m9.figshare.12851690.v1
title: Genome-wide DNA methylation alteration in prenatally stressed Brahman heifer calves with the advancement of age

description: Possible phenotypic impairments associated with maternal stress during gestation in beef cattle may be explained by epigenetic effects. This study examined the impact of prenatal transportation stress on DNA methylation of lymphocytes of Brahman cows over the first 5 years of life. Methylation analysis through reduced representation bisulphite sequencing was conducted on DNA from lymphocytes from 28 paired samples from 6 prenatally stressed (PNS) and 8 control (Control) females obtained initially when they were 28 days of age and 5 years of age. There were 14,386 CpG (C = cytosine; p = phosphate; G = guanine) sites differentially methylated (<i>P</i> P
DOI: 10.6084/m9.figshare.12851696
title: In silico structural analysis of sequences containing 5-hydroxymethylcytosine reveals its potential as binding regulator for development, ageing and cancer-related transcription factors

description: The presence of 5-hydroxymethyl cytosine in DNA has been previously associated with ageing. Using in silico analysis of normal liver samples we presently observed that in 5-hydroxymethyl cytosine sequences, DNA methylation is dependent on the co-presence of G-quadruplexes and palindromes. This association exhibits discrete patterns depending on G-quadruplex and palindrome densities. DNase-Seq data show that 5-hydroxymethyl cytosine sequences are common among liver nucleosomes (<i>p</i> −16) and threefold more frequent than nucleosome sequences. Nucleosomes lacking palindromes and potential G-quadruplexes are rare in vivo (1%) and nucleosome occupancy potential decreases with increasing G-quadruplexes. Palindrome distribution is similar to that previously reported in nucleosomes. In low and mixed complexity sequences 5-hydroxymethyl cytosine is frequently located next to three elements: G-quadruplexes or imperfect G-quadruplexes with CpGs, or unstable hairpin loops (TCCCAY<sub>6</sub>TGGGA) mostly located in antisense strands or finally A-/T-rich segments near these motifs. The high frequencies and selective distribution of pentamer sequences (including TCCCA, TGGGA) probably indicate the positive contribution of 5-hydroxymethyl cytosine to stabilize the formation of structures unstable in the absence of this cytosine modification. Common motifs identified in all total 5-hydroxymethyl cytosine-containing sequences exhibit high homology to recognition sites of several transcription factor families: homeobox, factors involved in growth, mortality/ageing, cancer, neuronal function, vision, and reproduction. We conclude that cytosine hydroxymethylation could play a role in the recognition of sequences with G-quadruplexes/palindromes by forming epigenetically regulated DNA ‘springs’ and governing expansions or compressions recognized by different transcription factors or stabilizing nucleosomes. The balance of these epigenetic elements is lost in hepatocellular carcinoma.
DOI: 10.6084/m9.figshare.12888468.v1
title: Germline DNMT3A mutation in familial acute myeloid leukaemia

description: Acute myeloid leukaemia (AML) is a heterogeneous myeloid malignancy characterized by recurrent clonal events, including mutations in epigenetically relevant genes such as <i>DNMT3A, ASXL1, IDH1/2</i>, and <i>TET2</i>. Next-generation sequencing analysis of a mother and son pair who both developed adult-onset diploid AML identified a novel germline missense mutation <i>DNMT3A</i> p.P709S. The p.P709S protein-altering variant resides in the highly conserved catalytic DNMT3A methyltransferase domain. Functional studies demonstrate that the p.P709S variant confers dominant negative effects when interacting with wildtype <i>DNMT3A</i>. LINE-1 pyrosequencing and reduced representation bisulphite sequencing (RBBS) analysis demonstrated global DNA hypomethylation in germline samples, not present in the leukaemic samples. Somatic acquisition of <i>IDH2</i> p.R172K mutations, in concert with additional acquired clonal DNMT3A events in both patients at the time of AML diagnosis, confirms the important pathogenic interaction of epigenetically active genes, and implies a strong selection and regulation of methylation in leukaemogenesis. Improved characterization of germline mutations may enable us to better predict malignant clonal evolution, improving our ability to provide customized treatment or future preventative strategies.
DOI: 10.6084/m9.figshare.12851696.v2
title: In silico structural analysis of sequences containing 5-hydroxymethylcytosine reveals its potential as binding regulator for development, ageing and cancer-related transcription factors

description: The presence of 5-hydroxymethyl cytosine in DNA has been previously associated with ageing. Using in silico analysis of normal liver samples we presently observed that in 5-hydroxymethyl cytosine sequences, DNA methylation is dependent on the co-presence of G-quadruplexes and palindromes. This association exhibits discrete patterns depending on G-quadruplex and palindrome densities. DNase-Seq data show that 5-hydroxymethyl cytosine sequences are common among liver nucleosomes (<i>p</i> −16) and threefold more frequent than nucleosome sequences. Nucleosomes lacking palindromes and potential G-quadruplexes are rare in vivo (1%) and nucleosome occupancy potential decreases with increasing G-quadruplexes. Palindrome distribution is similar to that previously reported in nucleosomes. In low and mixed complexity sequences 5-hydroxymethyl cytosine is frequently located next to three elements: G-quadruplexes or imperfect G-quadruplexes with CpGs, or unstable hairpin loops (TCCCAY<sub>6</sub>TGGGA) mostly located in antisense strands or finally A-/T-rich segments near these motifs. The high frequencies and selective distribution of pentamer sequences (including TCCCA, TGGGA) probably indicate the positive contribution of 5-hydroxymethyl cytosine to stabilize the formation of structures unstable in the absence of this cytosine modification. Common motifs identified in all total 5-hydroxymethyl cytosine-containing sequences exhibit high homology to recognition sites of several transcription factor families: homeobox, factors involved in growth, mortality/ageing, cancer, neuronal function, vision, and reproduction. We conclude that cytosine hydroxymethylation could play a role in the recognition of sequences with G-quadruplexes/palindromes by forming epigenetically regulated DNA ‘springs’ and governing expansions or compressions recognized by different transcription factors or stabilizing nucleosomes. The balance of these epigenetic elements is lost in hepatocellular carcinoma.
DOI: 10.6084/m9.figshare.12888468
title: Germline DNMT3A mutation in familial acute myeloid leukaemia

description: Acute myeloid leukaemia (AML) is a heterogeneous myeloid malignancy characterized by recurrent clonal events, including mutations in epigenetically relevant genes such as <i>DNMT3A, ASXL1, IDH1/2</i>, and <i>TET2</i>. Next-generation sequencing analysis of a mother and son pair who both developed adult-onset diploid AML identified a novel germline missense mutation <i>DNMT3A</i> p.P709S. The p.P709S protein-altering variant resides in the highly conserved catalytic DNMT3A methyltransferase domain. Functional studies demonstrate that the p.P709S variant confers dominant negative effects when interacting with wildtype <i>DNMT3A</i>. LINE-1 pyrosequencing and reduced representation bisulphite sequencing (RBBS) analysis demonstrated global DNA hypomethylation in germline samples, not present in the leukaemic samples. Somatic acquisition of <i>IDH2</i> p.R172K mutations, in concert with additional acquired clonal DNMT3A events in both patients at the time of AML diagnosis, confirms the important pathogenic interaction of epigenetically active genes, and implies a strong selection and regulation of methylation in leukaemogenesis. Improved characterization of germline mutations may enable us to better predict malignant clonal evolution, improving our ability to provide customized treatment or future preventative strategies.
DOI: 10.6084/m9.figshare.12901100
title: Music-listening regulates human microRNA expression

description: Music-listening and performance have been shown to affect human gene expression. In order to further elucidate the biological basis of the effects of music on the human body, we studied the effects of music-listening on gene regulation by sequencing microRNAs of the listeners (Music Group) and their controls (Control Group) without music exposure. We identified upregulation of six microRNAs (hsa-miR-132-3p, hsa-miR-361-5p, hsa-miR-421, hsa-miR-23a-3p, hsa-miR-23b-3p, hsa-miR-25-3p) and downregulation of two microRNAs (hsa-miR-378a-3p, hsa-miR-16-2-3p) in Music Group with high musical aptitude. Some upregulated microRNAs were reported to be responsive to neuronal activity (miR-132, miR-23a, miR-23b) and modulators of neuronal plasticity, CNS myelination, and cognitive functions like long-term potentiation and memory. miR-132 plays a critical role in regulating TAU protein levels and is important for preventing tau protein aggregation that causes Alzheimer’s disease. miR-132 and <i>DICER</i>, upregulated after music-listening, protect dopaminergic neurons and are important for retaining striatal dopamine levels. Some of the transcriptional regulators (<i>FOS, CREB1, JUN, EGR1,</i> and <i>BDNF</i>) of the upregulated microRNAs were immediate early genes and top candidates associated with musical traits. <i>BDNF</i> and SNCA, co-expressed and upregulated in music-listening and music-performance, are both are activated by GATA2, which is associated with musical aptitude. Several miRNAs were associated with song-learning, singing, and seasonal plasticity networks in songbirds. We did not detect any significant changes in microRNA expressions associated with music education or low musical aptitude. Our data thereby show the importance of inherent musical aptitude for music appreciation and for eliciting the human microRNA response to music-listening.