cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21354183.v1
title: Example eHealth monitoring and evaluation indicators and their operationalization tools

description: In order to demonstrate how the eHealth interventions’ performance can be measured at each stage of the results chain in the reference model, suggestions and best practices provided in various eHealth evaluation literature<sup>13,16–20,22,28,30</sup> were synthesized and used to develop a set of example indicators and their respective operationalization tools
DOI: 10.34729/t6ne-7k29
title: Harmonized SHARE COVID, Version A
DOI: 10.5281/zenodo.7185249
title: Calculated structures of РТТА-nLi and Cartesian coordinates

description: The file contains quantum-chemical calculations of the interaction of PTTA oligomers with different numbers of lithium atoms. And also investigated the data of interaction in the presence of two solvents: dimethyl carbonate (DMC) and tetraglyme (G4). The file contains calculated structures and cartesian coordinates of complex PTTA4[Li<sup>+</sup>(DMC)<sub>2</sub>] and products of reductive metallation of PTTA2 oligomer with 8 Li atoms and with 12 Li atoms. Calculated structures of the ion pairs [Li<sup>+</sup>(DMC)<sub>4</sub>] [PF<sub>6</sub><sup>-</sup>] and [Li<sup>+</sup>G4] [PF<sub>6</sub><sup>-</sup>]. Calculated structures of complexes PTTA4[Li<sup>+</sup>(DMC)<sub>2</sub>] [PF<sub>6</sub><sup>-</sup>], PTTA4[Li<sup>+</sup>G4] [PF<sub>6</sub><sup>-</sup>] and PTTA4{[Li<sup>+</sup>(DMC)<sub>2</sub>] [PF<sub>6</sub><sup>-</sup>]}<sub>2</sub>. Calculated structures of complexes (PTTA3)<sub>3</sub>[Li<sup>+</sup>(DMC)<sub>2</sub>] [PF<sub>6</sub><sup>-</sup>] and (PTTA3)<sub>3</sub> [Li<sup>+</sup>G4] [PF<sub>6</sub><sup>-</sup>]. Calculated specific metalation energies DЕ<sub>n </sub> of PTTA2 oligomer. Calculated structures of the isomers РТТА2(Li)<sub>2</sub> with Li atoms coordinated at (N,N), (O,O), (O,N) and (N,O) chelate knot. Calculated structures of РТТА2(Li)<sub>4</sub>, РТТА2(Li)<sub>6</sub> and dimers [PTTA2(Li<sub>4</sub>)]<sub>2</sub> and [PTTA2(Li<sub>6</sub>)]<sub>2</sub>.
description: This work was supported by the Ministry of Education and Science of the Russian Federation, project no. AAAA-A19-119111390022-2.
DOI: 10.5281/zenodo.7185248
title: Calculated structures of РТТА-nLi and Cartesian coordinates

description: The file contains quantum-chemical calculations of the interaction of PTTA oligomers with different numbers of lithium atoms. And also investigated the data of interaction in the presence of two solvents: dimethyl carbonate (DMC) and tetraglyme (G4). The file contains calculated structures and cartesian coordinates of complex PTTA4[Li<sup>+</sup>(DMC)<sub>2</sub>] and products of reductive metallation of PTTA2 oligomer with 8 Li atoms and with 12 Li atoms. Calculated structures of the ion pairs [Li<sup>+</sup>(DMC)<sub>4</sub>] [PF<sub>6</sub><sup>-</sup>] and [Li<sup>+</sup>G4] [PF<sub>6</sub><sup>-</sup>]. Calculated structures of complexes PTTA4[Li<sup>+</sup>(DMC)<sub>2</sub>] [PF<sub>6</sub><sup>-</sup>], PTTA4[Li<sup>+</sup>G4] [PF<sub>6</sub><sup>-</sup>] and PTTA4{[Li<sup>+</sup>(DMC)<sub>2</sub>] [PF<sub>6</sub><sup>-</sup>]}<sub>2</sub>. Calculated structures of complexes (PTTA3)<sub>3</sub>[Li<sup>+</sup>(DMC)<sub>2</sub>] [PF<sub>6</sub><sup>-</sup>] and (PTTA3)<sub>3</sub> [Li<sup>+</sup>G4] [PF<sub>6</sub><sup>-</sup>]. Calculated specific metalation energies DЕ<sub>n </sub> of PTTA2 oligomer. Calculated structures of the isomers РТТА2(Li)<sub>2</sub> with Li atoms coordinated at (N,N), (O,O), (O,N) and (N,O) chelate knot. Calculated structures of РТТА2(Li)<sub>4</sub>, РТТА2(Li)<sub>6</sub> and dimers [PTTA2(Li<sub>4</sub>)]<sub>2</sub> and [PTTA2(Li<sub>6</sub>)]<sub>2</sub>.
description: This work was supported by the Ministry of Education and Science of the Russian Federation, project no. AAAA-A19-119111390022-2.
DOI: 10.5281/zenodo.7220160
title: Low Frequency Ambient Noise Dynamics and Trends: Cape Leeuwin, Australia

description: Data files and code for : Low Frequency Ambient Noise Dynamics and Trends: Cape Leeuwin, Australia R version 4.X used for plots and analysis. Packages: entropy, foreach, rEDM Plots.R : Create plots for manuscript. MI.R : Evaluate lagged Mutual Information of random data segments CCM.R : Convergent cross mapping of Ambient Noise with teleconnections EMM_Surrogate.R : Evaluate CCM significance with randomized surrogates Python 3.X used for plots and analysis. Packages: pandas, matplotlib, emd, pyEDM Figure5,py Figure14.py : Create plots for manuscript EMD.py : Compute empirical mode decompositions
DOI: 10.5281/zenodo.7220159
title: Low Frequency Ambient Noise Dynamics and Trends: Cape Leeuwin, Australia

description: Data files and code for : Low Frequency Ambient Noise Dynamics and Trends: Cape Leeuwin, Australia R version 4.X used for plots and analysis. Packages: entropy, foreach, rEDM Plots.R : Create plots for manuscript. MI.R : Evaluate lagged Mutual Information of random data segments CCM.R : Convergent cross mapping of Ambient Noise with teleconnections EMM_Surrogate.R : Evaluate CCM significance with randomized surrogates Python 3.X used for plots and analysis. Packages: pandas, matplotlib, emd, pyEDM Figure5,py Figure14.py : Create plots for manuscript EMD.py : Compute empirical mode decompositions
DOI: 10.5281/zenodo.7220854
title: Phanerozoic global climatic fields simulated using the mixed-layer general circulation model FOAM

description: These files contain the output of Phanerozoic global climate simulations conducted using the “slab” mixed-layer ocean-atmosphere general circulation model FOAM. They are available every 20 Myrs between 540 Ma and 0 Ma, both included. Boundary conditions were adapted to best match each time slice. Continental reconstructions were taken from Scotese and Wright (https://www.earthbyte.org/paleodem-resource-scotese-and-wright-2018/). We defined pCO2 after the proxy data compilation of Foster et al. (doi:10.1038/ncomms14845) when available and Krause et al. (dot:10.1038/s41467-018-06383-y) for older time slices. Solar luminosity followed Gough et al. (doi:10.1007/BF00151270). Continental vegetation was set to Modern-like latitudinal bands between 0 Ma and 100 Ma (included), tropical evergreen, broad-leaved forest between 120 Ma and 360 Ma (included), tundra between 380 Ma and 440 Ma (included) and rocky desert afterwards. The orbital configuration was set to null eccentricity and minimum obliquity. The reader is referred to the associated paper for a full description of the model and boundary conditions. All model output file names use the following pattern: « [age]ebP2_solCgough1981_EccN_pCO2FosterKr_[model_component] _slab.nc", with [age], the age expressed in million years ago, and [model_component] being 'atmos' or 'coupl' (atmospheric component or coupler). For each time slice, the topography-bathymetry data used in FOAM is also provided (« Topobathy_[age]eb_postslarti_cor.nc »).
DOI: 10.5281/zenodo.7220853
title: Phanerozoic global climatic fields simulated using the mixed-layer general circulation model FOAM

description: These files contain the output of Phanerozoic global climate simulations conducted using the “slab” mixed-layer ocean-atmosphere general circulation model FOAM. They are available every 20 Myrs between 540 Ma and 0 Ma, both included. Boundary conditions were adapted to best match each time slice. Continental reconstructions were taken from Scotese and Wright (https://www.earthbyte.org/paleodem-resource-scotese-and-wright-2018/). We defined pCO2 after the proxy data compilation of Foster et al. (doi:10.1038/ncomms14845) when available and Krause et al. (dot:10.1038/s41467-018-06383-y) for older time slices. Solar luminosity followed Gough et al. (doi:10.1007/BF00151270). Continental vegetation was set to Modern-like latitudinal bands between 0 Ma and 100 Ma (included), tropical evergreen, broad-leaved forest between 120 Ma and 360 Ma (included), tundra between 380 Ma and 440 Ma (included) and rocky desert afterwards. The orbital configuration was set to null eccentricity and minimum obliquity. The reader is referred to the associated paper for a full description of the model and boundary conditions. All model output file names use the following pattern: « [age]ebP2_solCgough1981_EccN_pCO2FosterKr_[model_component] _slab.nc", with [age], the age expressed in million years ago, and [model_component] being 'atmos' or 'coupl' (atmospheric component or coupler). For each time slice, the topography-bathymetry data used in FOAM is also provided (« Topobathy_[age]eb_postslarti_cor.nc »).
DOI: 10.34808/j6x8-jt17
title: Spatial distribution of CO2, O2, CO, NO and temperature within a biowaste composting pile

description: The dataset contains the color-coded isophlets illustrating the spatial distribution of gas concentrations (CO, CO2, O2 and NO) and the temperature in biowaste composting pile during 6 weeks of process. Four cross sections and two longitudinal cross sections (the left and right sides of the pile) were made using Surfer 10 software (Golden Software, Cracow, Poland).
A small subset (16 cross sections) illustrates the chimney effect in the pile and the temperature effect on CO distribution is presented in the manuscript: https://doi.org/10.3390/su11082340. The dataset contains 6 folders - one for each week of composting process (called: "1 tydzień", "2 tydzień", "3 tydzień", "4 tydzień", "5 tydzień" and "6 tydzień").
In each folder there are 5 graphic files in the .png extension with a resolution of 300 dpi, named: "CO" (spatial distribution of carbon monoxide), "CO2" (spatial distribution of carbon dioxide, example on the left), "NO" (spatial distribution of nitric oxide), "temp" (spatial distribution of temperature) and "tlen" (spatial distribution of oxygen).
For each of the views in the upper left corner there is a label with measurement point (left/right side of the pile or number of the cross-section). The scale with the unit (concentration in % or ppm, temperature in°C) is placed next to the label.
DOI: 10.6084/m9.figshare.20749609
title: Raw data and results - COVID trajectory project

description: This repository contains the raw data and results of the molecular analysis performed in our study.
DOI: 10.6084/m9.figshare.20749609.v2
title: Raw data and results - COVID trajectory project

description: This repository contains the raw data and results of the molecular analysis performed in our study.
DOI: 10.6084/m9.figshare.21354333
title: Endometriosis pregnancy experience qualitative

description: <em><strong>Endometriosis and pregnancy: the illusion of recovery.</strong></em>
DOI: 10.18715/ipgp.2021.kq136bzh/1
title: 2019-02-25_2020-05-10_MayobsRevosima_catalog.txt

description: 2019-02-25 – 2020-05-10 Mayobs Revosima catalog
DOI: 10.5282/ubm/data.326
title: Supplementary Datasets for the Paper "A heated rock crack captures and polymerizes primordial DNA and RNA"

description: Previous versions of this dataset: Dirscherl, Christina Felicitas and Braun, Dieter: Supplementary Datasets for the Paper "A heated rock crack captures and polymerizes primordial DNA and RNA". 2022. Open Data LMU. 10.5282/ubm/data.320 (deposited 12. Oct 2022 07:17) Dirscherl, Christina Felicitas and Braun, Dieter: Supplementary Datasets for the Paper "A Heated Rock Pore Promotes Primordial DNA and RNA Polymerization". 2022. Open Data LMU. 10.5282/ubm/data.296 (deposited 16. Mar 2022 08:55)
DOI: 10.5525/gla.researchdata.1348
title: Drone Authentication via Acoustic Fingerprint

description: This artifact consists of raw drone audio recordings and experiment code. Drone audio recordings include all the audio mentioned in Table 1. Additionally, the size of all raw drone audio recordings is about 2.9 gigabytes in the WAV format. Based on that, the experiment code can generate the four MFCC-based datasets: DS1, DS2, DS1N, and DS2N, which are mentioned in the paper. Furthermore, this code can reproduce all the experiment results in Sections 4 and 5 of our paper.
DOI: 10.6084/m9.figshare.16870689
title: Effects of electrospun fiber curcumin on bisphenol A exposed Caco-2 cells

description: Curcumin; the major polyphenolic compound, isolated from <i>Curcuma longa</i> L.; loaded polyvinylpyrrolidone K90 fibers were prepared using electrospinning method. Effectiveness was tested on human colorectal adenocarcinoma cells with the presence of the endocrine disrupter Bisphenol A. Curcumin-loaded fibers were shown to have good physicochemical properties where excellent morphology of the electrospin fibers were formed. With the presence of 8 nM Bisphenol A, 17.37 mM fibers were found to inhibit proliferation in the cells in a dose-dependent manner. Fibers induced a significant increase in malondialdehyde by Thiobarbituric Acid Reactive Substances Assay compared to the control and this effect was supported by the presence of Bisphenol A. Western blot results indicate Super Oxide Dismutase-1 levels were increased by fiber, while Bisphenol A coincubated group resulted in a decrease. Fibers increased the expression of Estrogen Receptor 2, while Estrogen Receptor 1 expression did not change. Estrogen Receptor 2 expression was increased by coincubation with Bisphenol A; indicating a possible role of Estrogen Receptor 2 in the protective effects of fiber. This study presents that fiber had enhanced bioavailability and solubility with increased anticancer effect in human colon adenocarcinoma cells in presence of Bisphenol A; where involved mechanisms are antioxidant system and estrogen receptor expression.
DOI: 10.6084/m9.figshare.16870689.v1
title: Effects of electrospun fiber curcumin on bisphenol A exposed Caco-2 cells

description: Curcumin; the major polyphenolic compound, isolated from <i>Curcuma longa</i> L.; loaded polyvinylpyrrolidone K90 fibers were prepared using electrospinning method. Effectiveness was tested on human colorectal adenocarcinoma cells with the presence of the endocrine disrupter Bisphenol A. Curcumin-loaded fibers were shown to have good physicochemical properties where excellent morphology of the electrospin fibers were formed. With the presence of 8 nM Bisphenol A, 17.37 mM fibers were found to inhibit proliferation in the cells in a dose-dependent manner. Fibers induced a significant increase in malondialdehyde by Thiobarbituric Acid Reactive Substances Assay compared to the control and this effect was supported by the presence of Bisphenol A. Western blot results indicate Super Oxide Dismutase-1 levels were increased by fiber, while Bisphenol A coincubated group resulted in a decrease. Fibers increased the expression of Estrogen Receptor 2, while Estrogen Receptor 1 expression did not change. Estrogen Receptor 2 expression was increased by coincubation with Bisphenol A; indicating a possible role of Estrogen Receptor 2 in the protective effects of fiber. This study presents that fiber had enhanced bioavailability and solubility with increased anticancer effect in human colon adenocarcinoma cells in presence of Bisphenol A; where involved mechanisms are antioxidant system and estrogen receptor expression.
DOI: 10.6084/m9.figshare.19167900
title: Multi-tissue DNA methylation microarray signature is predictive of gene function

description: Background Transcriptional correlation networks derived from publicly available gene expression microarrays have been previously shown to be predictive of known gene functions, but less is known about the predictive capacity of correlated DNA methylation at CpG sites. Guilt-by-association co-expression methods can adapted for use with DNA methylation when a representative methylation value is created for each gene. We examine how methylation compares to expression in predicting Gene Ontology terms using both co-methylation and traditional machine learning approaches across different types of representative methylation values per gene. Methods We perform guilt-by-association gene function prediction with a suite of models called Methylation Array Network Analysis, using a network of correlated methylation values derived from over 24,000 samples. In generating the correlation matrix, the performance of different methods of collapsing probe-level data effect on the resulting gene function predictions was compared, along with the use of different regions surrounding the gene of interest. Results Using mean comethylation of a given gene to its annotated term had an overall highest prediction macro-AUC of 0.60 using mean gene body methylation, across all Gene Ontology terms. This was increased using the logistic regression approach with the highest macro-AUC of 0.82 using mean gene body methylation, compared to the naive predictor of 0.72. Conclusion Genes correlated in their methylation state are functionally related. Genes clustered in co-methylation space were enriched for chromatin state, PRC2, immune response, and development-related terms.
DOI: 10.6084/m9.figshare.19167900.v1
title: Multi-tissue DNA methylation microarray signature is predictive of gene function

description: Background Transcriptional correlation networks derived from publicly available gene expression microarrays have been previously shown to be predictive of known gene functions, but less is known about the predictive capacity of correlated DNA methylation at CpG sites. Guilt-by-association co-expression methods can adapted for use with DNA methylation when a representative methylation value is created for each gene. We examine how methylation compares to expression in predicting Gene Ontology terms using both co-methylation and traditional machine learning approaches across different types of representative methylation values per gene. Methods We perform guilt-by-association gene function prediction with a suite of models called Methylation Array Network Analysis, using a network of correlated methylation values derived from over 24,000 samples. In generating the correlation matrix, the performance of different methods of collapsing probe-level data effect on the resulting gene function predictions was compared, along with the use of different regions surrounding the gene of interest. Results Using mean comethylation of a given gene to its annotated term had an overall highest prediction macro-AUC of 0.60 using mean gene body methylation, across all Gene Ontology terms. This was increased using the logistic regression approach with the highest macro-AUC of 0.82 using mean gene body methylation, compared to the naive predictor of 0.72. Conclusion Genes correlated in their methylation state are functionally related. Genes clustered in co-methylation space were enriched for chromatin state, PRC2, immune response, and development-related terms.
DOI: 10.6084/m9.figshare.19698142
title: The effects of age, sex, weight, and breed on canid methylomes

description: Unlike genomes, which are static throughout the lifespan of an organism, DNA methylomes are dynamic. To study these dynamics, we developed quantitative models that measure the effect of multiple factors on DNA methylomes including, age, sex, weight, and genetics. We conducted our study in canids, which prove to be an ideal species to assess epigenetic moderators due to their extreme variability in size and well-characterized genetic structure. We collected buccal swabs from 217 canids (207 domestic dogs and 10 grey wolves) and used targeted bisulphite sequencing to measure methylomes. We also measured genotypes at over one thousand single nucleotide polymorphisms (SNPs). As expected, we found that DNA methylomes are strongly associated with age, enabling the construction of epigenetic clocks. However, we also identify novel associations between methylomes and sex, weight, and sterilization status, leading to accurate models that predict these factors. Methylomes are also affected by genetics, and we observe multiple associations between SNP loci and methylated CpGs. Finally, we show that several factors moderate the relationship between epigenetic ages and real ages, such as body weight, which increases epigenetic ageing. In conclusion, we demonstrate that the plasticity of DNA methylomes is impacted by myriad genetics and physiological factors, and that DNA methylation biomarkers are accurate predictors of age, sex and sterilization status.
DOI: 10.6084/m9.figshare.19698142.v1
title: The effects of age, sex, weight, and breed on canid methylomes

description: Unlike genomes, which are static throughout the lifespan of an organism, DNA methylomes are dynamic. To study these dynamics, we developed quantitative models that measure the effect of multiple factors on DNA methylomes including, age, sex, weight, and genetics. We conducted our study in canids, which prove to be an ideal species to assess epigenetic moderators due to their extreme variability in size and well-characterized genetic structure. We collected buccal swabs from 217 canids (207 domestic dogs and 10 grey wolves) and used targeted bisulphite sequencing to measure methylomes. We also measured genotypes at over one thousand single nucleotide polymorphisms (SNPs). As expected, we found that DNA methylomes are strongly associated with age, enabling the construction of epigenetic clocks. However, we also identify novel associations between methylomes and sex, weight, and sterilization status, leading to accurate models that predict these factors. Methylomes are also affected by genetics, and we observe multiple associations between SNP loci and methylated CpGs. Finally, we show that several factors moderate the relationship between epigenetic ages and real ages, such as body weight, which increases epigenetic ageing. In conclusion, we demonstrate that the plasticity of DNA methylomes is impacted by myriad genetics and physiological factors, and that DNA methylation biomarkers are accurate predictors of age, sex and sterilization status.
DOI: 10.34740/kaggle/dsv/4346772
title: Elon Musk Tweets
DOI: 10.6084/m9.figshare.19169919.v1
title: Updates to data versions and analytic methods influence the reproducibility of results from epigenome-wide association studies

description: Biomedical research has grown increasingly cooperative through the sharing of consortia-level epigenetic data. Since consortia preprocess data prior to distribution, new processing pipelines can lead to different versions of the same dataset. Similarly, analytic frameworks evolve to incorporate cutting-edge methods and best practices. However, it remains unknown how different data and analytic versions alter the results of epigenome-wide analyses, which could influence the replicability of epigenetic associations. Thus, we assessed the impact of these changes using data from the Avon Longitudinal Study of Parents and Children (ALSPAC) cohort. We analysed DNA methylation from two data versions, processed using separate preprocessing and analytic pipelines, examining associations between seven childhood adversities or prenatal smoking exposure and DNA methylation at age 7. We performed two sets of analyses: (1) epigenome-wide association studies (EWAS); (2) Structured Life Course Modelling Approach (SLCMA), a two-stage method that models time-dependent effects. SLCMA results were also compared across two analytic versions. Data version changes impacted both EWAS and SLCMA analyses, yielding different associations at conventional p-value thresholds. However, the magnitude and direction of associations was generally consistent between data versions, regardless of p-values. Differences were especially apparent in analyses of childhood adversity, while smoking associations were more consistent using significance thresholds. SLCMA analytic versions similarly altered top associations, but time-dependent effects remained concordant. Alterations to data and analytic versions influenced the results of epigenome-wide analyses. Our findings highlight that magnitude and direction are better measures for replication and stability than p-value thresholds.