cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.15832008
title: Disease-related blood-based differential methylation in cystic fibrosis and its representation in lung cancer revealed a regulatory locus in <i>PKP3</i> in lung epithelial cells

description: Cystic fibrosis (CF) is a monogenic disease, characterized by massive chronic lung inflammation. The observed variability in clinical phenotypes in monozygotic CF twins is likely associated with the extent of inflammation. This study sought to investigate inflammation-related aberrant DNA methylation in CF twins and to determine to what extent acquired methylation changes may be associated with lung cancer. Blood-based genome-wide DNA methylation analysis was performed to compare the DNA methylomes of monozygotic twins, from the European CF Twin and Sibling Study with various degrees of disease severity. Putatively inflammation-related and differentially methylated positions were selected from a large lung cancer case-control study and investigated in blood by targeted bisulphite next-generation-sequencing. An inflammation-related locus located in the <i>Plakophilin-3</i> (<i>PKP3</i>) gene was functionally analysed regarding promoter and enhancer activity in presence and absence of methylation using luciferase reporter assays. We confirmed in a unique cohort that monozygotic twins, even if clinically discordant, have only minor differences in global DNA methylation patterns and blood cell composition. Further, we determined the most differentially methylated positions, a high proportion of which are blood cell-type-specific, whereas others may be acquired and thus have potential relevance in the context of inflammation as lung cancer risk factors. We identified a sequence in the gene body of <i>PKP3</i> which is hypermethylated in blood from CF twins with severe phenotype and highly variably methylated in lung cancer patients and controls, independent of known clinical parameters, and showed that this region exhibits methylation-dependent promoter activity in lung epithelial cells.
DOI: 10.6084/m9.figshare.13734232
title: Adiposity associated DNA methylation signatures in adolescents are related to leptin and perinatal factors

description: Epigenetics links perinatal influences with later obesity. We identifed differentially methylated CpG (dmCpG) loci measured at 17 years associated with concurrent adiposity measures and examined whether these were associated with hsCRP, adipokines, and early life environmental factors. Genome-wide DNA methylation from 1192 Raine Study participants at 17 years, identified 29 dmCpGs (Bonferroni corrected p &lt; 1.06E-07) associated with body mass index (BMI), 10 with waist circumference (WC) and 9 with subcutaneous fat thickness. DmCpGs within Ras Association (RalGDS/AF-6), Pleckstrin Homology Domains 1 (<i>RAPH1</i>), Musashi RNA-Binding Protein 2 (<i>MSI2</i>), and solute carrier family 25 member 10 (<i>SLC25A10</i>) are associated with both BMI and WC. Validation by pyrosequencing confirmed these associations and showed that <i>MSI2</i> , <i>SLC25A10</i> , and <i>RAPH1</i> methylation was positively associated with serum leptin. These were also associated with the early environment; <i>MSI2</i> methylation (β = 0.81, p = 0.0004) was associated with pregnancy maternal smoking, <i>SLC25A10</i> (CpG2 β = 0.12, p = 0.002) with pre- and early pregnancy BMI, and <i>RAPH1</i> (β = −1.49, p = 0.036) with gestational weight gain. Adjusting for perinatal factors, methylation of the dmCpGs within <i>MSI2, RAPH1,</i> and <i>SLC25A10</i> independently predicted BMI, accounting for 24% of variance. <i>MSI2</i> methylation was additionally associated with BMI over time (17 years old β = 0.026, p = 0.0025; 20 years old β = 0.027, p = 0.0029) and between generations (mother β = 0.044, p = 7.5e-04). Overall findings suggest that DNA methylation in <i>MSI2</i>, <i>RAPH1</i>, and <i>SLC25A10</i> in blood may be robust markers, mediating through early life factors.
DOI: 10.6084/m9.figshare.13734232.v1
title: Adiposity associated DNA methylation signatures in adolescents are related to leptin and perinatal factors

description: Epigenetics links perinatal influences with later obesity. We identifed differentially methylated CpG (dmCpG) loci measured at 17 years associated with concurrent adiposity measures and examined whether these were associated with hsCRP, adipokines, and early life environmental factors. Genome-wide DNA methylation from 1192 Raine Study participants at 17 years, identified 29 dmCpGs (Bonferroni corrected p &lt; 1.06E-07) associated with body mass index (BMI), 10 with waist circumference (WC) and 9 with subcutaneous fat thickness. DmCpGs within Ras Association (RalGDS/AF-6), Pleckstrin Homology Domains 1 (<i>RAPH1</i>), Musashi RNA-Binding Protein 2 (<i>MSI2</i>), and solute carrier family 25 member 10 (<i>SLC25A10</i>) are associated with both BMI and WC. Validation by pyrosequencing confirmed these associations and showed that <i>MSI2</i> , <i>SLC25A10</i> , and <i>RAPH1</i> methylation was positively associated with serum leptin. These were also associated with the early environment; <i>MSI2</i> methylation (β = 0.81, p = 0.0004) was associated with pregnancy maternal smoking, <i>SLC25A10</i> (CpG2 β = 0.12, p = 0.002) with pre- and early pregnancy BMI, and <i>RAPH1</i> (β = −1.49, p = 0.036) with gestational weight gain. Adjusting for perinatal factors, methylation of the dmCpGs within <i>MSI2, RAPH1,</i> and <i>SLC25A10</i> independently predicted BMI, accounting for 24% of variance. <i>MSI2</i> methylation was additionally associated with BMI over time (17 years old β = 0.026, p = 0.0025; 20 years old β = 0.027, p = 0.0029) and between generations (mother β = 0.044, p = 7.5e-04). Overall findings suggest that DNA methylation in <i>MSI2</i>, <i>RAPH1</i>, and <i>SLC25A10</i> in blood may be robust markers, mediating through early life factors.
DOI: 10.6084/m9.figshare.15832008.v2
title: Disease-related blood-based differential methylation in cystic fibrosis and its representation in lung cancer revealed a regulatory locus in <i>PKP3</i> in lung epithelial cells

description: Cystic fibrosis (CF) is a monogenic disease, characterized by massive chronic lung inflammation. The observed variability in clinical phenotypes in monozygotic CF twins is likely associated with the extent of inflammation. This study sought to investigate inflammation-related aberrant DNA methylation in CF twins and to determine to what extent acquired methylation changes may be associated with lung cancer. Blood-based genome-wide DNA methylation analysis was performed to compare the DNA methylomes of monozygotic twins, from the European CF Twin and Sibling Study with various degrees of disease severity. Putatively inflammation-related and differentially methylated positions were selected from a large lung cancer case-control study and investigated in blood by targeted bisulphite next-generation-sequencing. An inflammation-related locus located in the <i>Plakophilin-3</i> (<i>PKP3</i>) gene was functionally analysed regarding promoter and enhancer activity in presence and absence of methylation using luciferase reporter assays. We confirmed in a unique cohort that monozygotic twins, even if clinically discordant, have only minor differences in global DNA methylation patterns and blood cell composition. Further, we determined the most differentially methylated positions, a high proportion of which are blood cell-type-specific, whereas others may be acquired and thus have potential relevance in the context of inflammation as lung cancer risk factors. We identified a sequence in the gene body of <i>PKP3</i> which is hypermethylated in blood from CF twins with severe phenotype and highly variably methylated in lung cancer patients and controls, independent of known clinical parameters, and showed that this region exhibits methylation-dependent promoter activity in lung epithelial cells.
DOI: 10.6084/m9.figshare.16571376
title: DNA methylome-based validation of induced sputum as an effective protocol to study lung immunity: construction of a classifier of pulmonary cell types

description: Flow cytometry is a classical approach used to define cell types in peripheral blood. While DNA methylation signatures have been extensively employed in recent years as an alternative to flow cytometry to define cell populations in peripheral blood, this approach has not been tested in lung-derived samples. Here, we compared bronchoalveolar lavage with a more cost-effective and less invasive technique based on sputum induction and developed a DNA methylome-based algorithm that can be used to deconvolute the cell types in such samples. We analysed the DNA methylome profiles of alveolar macrophages and lymphocytes cells isolated from the pulmonary compartment. The cells were isolated using two different methods, sputum induction and bronchoalveolar lavage. A strong positive correlation between the DNA methylome profiles of cells obtained with the two isolation methods was found. We observed the best correlation of the DNA methylomes when both isolation methods captured cells from the lower parts of the lungs. We also identified unique patterns of CpG methylation in DNA obtained from the two cell populations, which can be used as a signature to discriminate between the alveolar macrophages and lymphocytes by means of open-source algorithms. We validated our findings with external data and obtained results consistent with the previous findings. Our analysis opens up a new possibility to identify different cell populations from lung samples and promotes sputum induction as a tool to study immune cell populations from the lung.
DOI: 10.6084/m9.figshare.16571376.v2
title: DNA methylome-based validation of induced sputum as an effective protocol to study lung immunity: construction of a classifier of pulmonary cell types

description: Flow cytometry is a classical approach used to define cell types in peripheral blood. While DNA methylation signatures have been extensively employed in recent years as an alternative to flow cytometry to define cell populations in peripheral blood, this approach has not been tested in lung-derived samples. Here, we compared bronchoalveolar lavage with a more cost-effective and less invasive technique based on sputum induction and developed a DNA methylome-based algorithm that can be used to deconvolute the cell types in such samples. We analysed the DNA methylome profiles of alveolar macrophages and lymphocytes cells isolated from the pulmonary compartment. The cells were isolated using two different methods, sputum induction and bronchoalveolar lavage. A strong positive correlation between the DNA methylome profiles of cells obtained with the two isolation methods was found. We observed the best correlation of the DNA methylomes when both isolation methods captured cells from the lower parts of the lungs. We also identified unique patterns of CpG methylation in DNA obtained from the two cell populations, which can be used as a signature to discriminate between the alveolar macrophages and lymphocytes by means of open-source algorithms. We validated our findings with external data and obtained results consistent with the previous findings. Our analysis opens up a new possibility to identify different cell populations from lung samples and promotes sputum induction as a tool to study immune cell populations from the lung.
DOI: 10.6084/m9.figshare.16571376.v1
title: DNA methylome-based validation of induced sputum as an effective protocol to study lung immunity: construction of a classifier of pulmonary cell types

description: Flow cytometry is a classical approach used to define cell types in peripheral blood. While DNA methylation signatures have been extensively employed in recent years as an alternative to flow cytometry to define cell populations in peripheral blood, this approach has not been tested in lung-derived samples. Here, we compared bronchoalveolar lavage with a more cost-effective and less invasive technique based on sputum induction and developed a DNA methylome-based algorithm that can be used to deconvolute the cell types in such samples. We analysed the DNA methylome profiles of alveolar macrophages and lymphocytes cells isolated from the pulmonary compartment. The cells were isolated using two different methods, sputum induction and bronchoalveolar lavage. A strong positive correlation between the DNA methylome profiles of cells obtained with the two isolation methods was found. We observed the best correlation of the DNA methylomes when both isolation methods captured cells from the lower parts of the lungs. We also identified unique patterns of CpG methylation in DNA obtained from the two cell populations, which can be used as a signature to discriminate between the alveolar macrophages and lymphocytes by means of open-source algorithms. We validated our findings with external data and obtained results consistent with the previous findings. Our analysis opens up a new possibility to identify different cell populations from lung samples and promotes sputum induction as a tool to study immune cell populations from the lung.
DOI: 10.5281/zenodo.6607081
title: 500-yr Projections of Thwaites Glacier, Antarctica, with MALI, including glacial isostatic adjustment: no elastic displacement

description: This archive contains a subset of results reproducing the material presented in the manuscript "Stabilizing effect of bedrock uplift on retreat of Thwaites Glacier, Antarctica, at centennial timescales" by Cameron Book, et al. This archive only includes results for the simulations with elastic displacement in the GIA model disabled. These results are briefly discussed in the first paragraph of section 'Factors controlling feedbacks between glacier retreat and bedrock uplift'. The main results from the manuscript are in a separate archive. Questions should be directed to Matt Hoffman (mhoffman@lanl.gov). This archive contains the following directories: |-- N1_no_elastic<br> |-- N2_no_elastic<br> |-- N3_no_elastic<br> `-- N4_no_elastic The individual runs have the following corresponence to the manuscript, but<br> with the elastic displacement disabled:<br> N1=TYP<br> N2=BEST2<br> N3=VLV-THIN<br> N4=VLV Within each run directory, are the following model output files:<br> globalStats.nc: MALI global, scalar time-series<br> output_*.nc: MALI spatial output fields, separated by century
DOI: 10.5281/zenodo.6607705
title: 500-yr Projections of Thwaites Glacier, Antarctica, with MALI, including glacial isostatic adjustment

description: This archive contains model code, results, and analysis scripts for<br> reproducing the material presented in the manuscript "Stabilizing effect of<br> bedrock uplift on retreat of Thwaites Glacier, Antarctica, at centennial<br> timescales" by Cameron Book, et al. Questions should be directed to Matt<br> Hoffman (mhoffman@lanl.gov). This archive contains the following directories: |-- MALI_code<br> |-- PIGL_control<br> |-- analysis<br> |-- control<br> |-- run_setup<br> |-- N1<br> |-- N2<br> |-- N3<br> |-- N4<br> `-- PIGL_N3 <br> 'MALI_code' is a snapshot of the MALI repository used for these simulations,<br> commit 454e0fc8bf384bee1c1560d6c3eaa5fae43bfdda.<br> This commit is present in an older MALI repository that is no longer<br> maintained, at https://github.com/MPAS-Dev/MPAS-Model<br> MALI is currently maintained on Github at https://github.com/MALI-Dev/E3SM<br> Building MALI requires the Albany multiphysics library, which is available<br> at https://github.com/sandialabs/Albany. The simulations presented use Albany<br> master from March 5, 2021. 'analysis' contains the scripts used to process the model output and produce<br> the figures and results presented in the manuscript. Filepaths will have to<br> be adjusted to your local layout. 'run_setup' is a directory of files and scripts necessary to reproduce the<br> model simulations presented. The GIA model giapy is in the file<br> 'giascript.py'. giapy can also be found on Github at https://github.com/skachuck/giapy 'control' is the control run with the GIA model disabled. It corresponds to<br> the run labeled CTRL in the manuscript. 'PIGL_control' is the control run using the high melt forcing. It corresponds<br> to the run labeled HM-CTRL in the manuscript. The five run directories included here (N1-N4, PIGL_N3) are the standard<br> ensemble described in the manuscript. (There is a separate archive for the<br> runs briefly mentioned that exclude the elastic response of the lithosphere.)<br> The individual runs have the following correspondence to the manuscript:<br> N1=TYP<br> N2=BEST2<br> N3=VLV-THIN<br> N4=VLV<br> PIGL_N3=HM-VLV-THIN<br> Within each run directory, are the following model output files:<br> globalStats.nc: MALI global, scalar time-series<br> iceload_all.nc: Thwaites Glacier ice load on the GIA grid<br> output_*.nc: MALI spatial output fields, separated by century<br> uplift_GIA_all.nc: GIA output on GIA grid
DOI: 10.5281/zenodo.6607706
title: 500-yr Projections of Thwaites Glacier, Antarctica, with MALI, including glacial isostatic adjustment

description: This archive contains model code, results, and analysis scripts for<br> reproducing the material presented in the manuscript "Stabilizing effect of<br> bedrock uplift on retreat of Thwaites Glacier, Antarctica, at centennial<br> timescales" by Cameron Book, et al. Questions should be directed to Matt<br> Hoffman (mhoffman@lanl.gov). This archive contains the following directories: |-- MALI_code<br> |-- PIGL_control<br> |-- analysis<br> |-- control<br> |-- run_setup<br> |-- N1<br> |-- N2<br> |-- N3<br> |-- N4<br> `-- PIGL_N3 <br> 'MALI_code' is a snapshot of the MALI repository used for these simulations,<br> commit 454e0fc8bf384bee1c1560d6c3eaa5fae43bfdda.<br> This commit is present in an older MALI repository that is no longer<br> maintained, at https://github.com/MPAS-Dev/MPAS-Model<br> MALI is currently maintained on Github at https://github.com/MALI-Dev/E3SM<br> Building MALI requires the Albany multiphysics library, which is available<br> at https://github.com/sandialabs/Albany. The simulations presented use Albany<br> master from March 5, 2021. 'analysis' contains the scripts used to process the model output and produce<br> the figures and results presented in the manuscript. Filepaths will have to<br> be adjusted to your local layout. 'run_setup' is a directory of files and scripts necessary to reproduce the<br> model simulations presented. The GIA model giapy is in the file<br> 'giascript.py'. giapy can also be found on Github at https://github.com/skachuck/giapy 'control' is the control run with the GIA model disabled. It corresponds to<br> the run labeled CTRL in the manuscript. 'PIGL_control' is the control run using the high melt forcing. It corresponds<br> to the run labeled HM-CTRL in the manuscript. The five run directories included here (N1-N4, PIGL_N3) are the standard<br> ensemble described in the manuscript. (There is a separate archive for the<br> runs briefly mentioned that exclude the elastic response of the lithosphere.)<br> The individual runs have the following correspondence to the manuscript:<br> N1=TYP<br> N2=BEST2<br> N3=VLV-THIN<br> N4=VLV<br> PIGL_N3=HM-VLV-THIN<br> Within each run directory, are the following model output files:<br> globalStats.nc: MALI global, scalar time-series<br> iceload_all.nc: Thwaites Glacier ice load on the GIA grid<br> output_*.nc: MALI spatial output fields, separated by century<br> uplift_GIA_all.nc: GIA output on GIA grid
DOI: 10.34740/kaggle/dsv/4124402
title: 2021 World Population (updated daily)
DOI: 10.5281/zenodo.7024885
title: TikTok dataset - Current affairs on TikTok. Virality and entertainment for digital natives

description: Tiktok network graph with 5,638 nodes and 318,986 unique links, representing up to 790,599 weighted links between labels, using Gephi network analysis software. Source of: Peña-Fernández, Simón, Larrondo-Ureta, Ainara, & Morales-i-Gras, Jordi. (2022). Current affairs on TikTok. Virality and entertainment for digital natives. Profesional De La Información, 31(1), 1–12. https://doi.org/10.5281/zenodo.5962655 Abstract: Since its appearance in 2018, TikTok has become one of the most popular social media platforms among digital natives because of its algorithm-based engagement strategies, a policy of public accounts, and a simple, colorful, and intuitive content interface. As happened in the past with other platforms such as Facebook, Twitter, and Instagram, various media are currently seeking ways to adapt to TikTok and its particular characteristics to attract a younger audience less accustomed to the consumption of journalistic material. Against this background, the aim of this study is to identify the presence of the media and journalists on TikTok, measure the virality and engagement of the content they generate, describe the communities created around them, and identify the presence of journalistic use of these accounts. For this, 23,174 videos from 143 accounts belonging to media from 25 countries were analyzed. The results indicate that, in general, the presence and impact of the media in this social network are low and that most of their content is oriented towards the creation of user communities based on viral content and entertainment. However, albeit with a lesser presence, one can also identify accounts and messages that adapt their content to the specific characteristics of TikTok. Their virality and engagement figures illustrate that there is indeed a niche for current affairs on this social network.
DOI: 10.5281/zenodo.7024884
title: TikTok dataset - Current affairs on TikTok. Virality and entertainment for digital natives

description: Tiktok network graph with 5,638 nodes and 318,986 unique links, representing up to 790,599 weighted links between labels, using Gephi network analysis software. Source of: Peña-Fernández, Simón, Larrondo-Ureta, Ainara, & Morales-i-Gras, Jordi. (2022). Current affairs on TikTok. Virality and entertainment for digital natives. Profesional De La Información, 31(1), 1–12. https://doi.org/10.5281/zenodo.5962655 Abstract: Since its appearance in 2018, TikTok has become one of the most popular social media platforms among digital natives because of its algorithm-based engagement strategies, a policy of public accounts, and a simple, colorful, and intuitive content interface. As happened in the past with other platforms such as Facebook, Twitter, and Instagram, various media are currently seeking ways to adapt to TikTok and its particular characteristics to attract a younger audience less accustomed to the consumption of journalistic material. Against this background, the aim of this study is to identify the presence of the media and journalists on TikTok, measure the virality and engagement of the content they generate, describe the communities created around them, and identify the presence of journalistic use of these accounts. For this, 23,174 videos from 143 accounts belonging to media from 25 countries were analyzed. The results indicate that, in general, the presence and impact of the media in this social network are low and that most of their content is oriented towards the creation of user communities based on viral content and entertainment. However, albeit with a lesser presence, one can also identify accounts and messages that adapt their content to the specific characteristics of TikTok. Their virality and engagement figures illustrate that there is indeed a niche for current affairs on this social network.