cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21550649
title: Comparison of global DNA methylation analysis by whole genome bisulfite sequencing and the Infinium Mouse Methylation BeadChip using fresh and fresh-frozen mouse epidermis

description: Until recently, studying the murine methylome was restricted to sequencing-based methods. In this study we compared the global DNA methylation levels of hairless mouse epidermis using the recently released Infinium Mouse Methylation BeadChip from Illumina and whole genome bisulphite sequencing (WGBS). We also studied the effect of sample storage conditions by using fresh and fresh-frozen epidermis. The DNA methylation levels of 123,851 CpG sites covered by both the BeadChip and WGBS were compared. DNA methylation levels obtained with WGBS and the BeadChip were strongly correlated (Pearson correlation r = 0.984). We applied a threshold of 15 reads for the WGBS methylation analysis. Even at a threshold of 10 reads, we observed no substantial difference in DNA methylation levels compared with that obtained with the BeadChip. The DNA methylation levels from the fresh and the fresh-frozen samples were strongly correlated when analysed with both the BeadChip (r = 0.999) and WGBS (r = 0.994). We conclude that the two methods of analysis generally work equally well for studies of DNA methylation of mouse epidermis and find that fresh and fresh-frozen epidermis can generally be used equally well. The choice of method will depend on the specific study’s aims and the available resources in the laboratory.
DOI: 10.6084/m9.figshare.21550649.v1
title: Comparison of global DNA methylation analysis by whole genome bisulfite sequencing and the Infinium Mouse Methylation BeadChip using fresh and fresh-frozen mouse epidermis

description: Until recently, studying the murine methylome was restricted to sequencing-based methods. In this study we compared the global DNA methylation levels of hairless mouse epidermis using the recently released Infinium Mouse Methylation BeadChip from Illumina and whole genome bisulphite sequencing (WGBS). We also studied the effect of sample storage conditions by using fresh and fresh-frozen epidermis. The DNA methylation levels of 123,851 CpG sites covered by both the BeadChip and WGBS were compared. DNA methylation levels obtained with WGBS and the BeadChip were strongly correlated (Pearson correlation r = 0.984). We applied a threshold of 15 reads for the WGBS methylation analysis. Even at a threshold of 10 reads, we observed no substantial difference in DNA methylation levels compared with that obtained with the BeadChip. The DNA methylation levels from the fresh and the fresh-frozen samples were strongly correlated when analysed with both the BeadChip (r = 0.999) and WGBS (r = 0.994). We conclude that the two methods of analysis generally work equally well for studies of DNA methylation of mouse epidermis and find that fresh and fresh-frozen epidermis can generally be used equally well. The choice of method will depend on the specific study’s aims and the available resources in the laboratory.
DOI: 10.6084/m9.figshare.21781498.v1
title: Non-pathogenic microbiota accelerate age-related CpG Island methylation in colonic mucosa

description: DNA methylation is an epigenetic process altered in cancer and ageing. Age-related methylation drift can be used to estimate lifespan and can be influenced by extrinsic factors such as diet. Here, we report that non-pathogenic microbiota accelerate age-related methylation drift in the colon when compared with germ-free mice. DNA methylation analyses showed that microbiota and IL10KO were associated with changes in 5% and 4.1% of CpG sites, while mice with both factors had 18% alterations. Microbiota, IL10KO, and their combination altered 0.4%, 0.4%, and 4% of CpG island methylation, respectively. These are comparable to what is seen in colon cancer. Ageing changes were accelerated in the IL10KO mice with microbiota, and the affected genes were more likely to be altered in colon cancer. Thus, the microbiota affect DNA methylation of the colon in patterns reminiscent of what is observed in ageing and colorectal cancer.
DOI: 10.6084/m9.figshare.21813773.v1
title: Identification and comparison of m6A modifications in glioblastoma non-coding RNAs with MeRIP-seq and Nanopore dRNA-seq

description: The most prominent RNA modification – N6-methyladenosine (m6A) – affects gene regulation and cancer progression. The extent and effect of m6A on long non-coding RNAs (lncRNAs) is, however, still not clear. The most established method for m6A detection is methylated RNA immunoprecipitation and sequencing (MeRIP-seq). However, Oxford Nanopore Technologies recently developed direct RNA-seq (dRNA-seq) method, allowing m6A identification at higher resolution and in its native form. We performed whole transcriptome sequencing of the glioblastoma cell line U87-MG with both MeRIP-seq and dRNA-seq. For MeRIP-seq, m6A peaks were identified using nf-core/chipseq, and for dRNA-seq – EpiNano pipeline. MeRIP-seq analysis revealed <i>5086</i> lncRNAs transcripts, while dRNA-seq identified 336 lncRNAs transcripts from which 556 and 198 were found to be m6A modified, respectively. While 24 lncRNAs with m6A overlapped between two methods. Gliovis database analysis revealed that the expression of the major part of identified overlapping lncRNAs was associated with glioma grade or patient survival prognosis. We found that the frequency of m6A occurrence in lncRNAs varied more than 9-fold throughout the provided list of 24 modified lncRNAs. The highest m6A frequency was detected in <i>MIR1915HG, THAP9-AS1, MALAT1, NORAD1</i>, and <i>NEAT1 (</i>49–88nt), while <i>MIR99AHG, SNHG3, LOXL1-AS1, ILF3-DT</i> showed the lowest m6A frequency (445–261nt). Taken together, (1) we provide a high accuracy list of 24 m6A modified lncRNAs of U87-MG cells; (2) we conclude that MeRIP-seq is more suitable for an initial m6A screening study, due to its higher lncRNA coverage, whereas dRNA-seq is most useful when more in-depth analysis of m6A quantity and precise location is of interest. <b>Abbreviations:</b> (dRNA-seq) direct RNA-seq, (GBM) glioblastoma, (LGG) low-grade glioma, (lncRNAs) long non-coding RNAs, (m6A) N6-methyladenosine, (MeRIP-seq) methylated RNA immunoprecipitation and sequencing, (ncRNA) non-coding RNA, (ONT) Oxford Nanopore Technologi; Lietuvos Mokslo Taryba
DOI: 10.6084/m9.figshare.21819471.v1
title: Comparison between indicine and taurine cattle DNA methylation reveals epigenetic variation associated to differences in morphological adaptive traits

description: Indicine and taurine subspecies present distinct morphological traits as a consequence of environmental adaptation and artificial selection. Although the two subspecies have been characterized and compared at genome-wide level and at specific loci, their epigenetic diversity has not yet been explored. In this work, Reduced Representation Bisulphite Sequencing (RRBS) profiling of the taurine Angus (A) and indicine Nellore (N) cattle breeds was applied to identify methylation differences between the two subspecies. Genotyping by sequencing (GBS) of the same animals was performed to detect single nucleotide polymorphisms (SNPs) at cytosines in CpG dinucleotides and remove them from the differential methylation analysis. A total of 660,845 methylated cytosines were identified within the CpG context (CpGs) across the 10 animals sequenced (5 N and 5 A). A total of 25,765 of these were differentially methylated (DMCs). Most DMCs clustered in CpG stretches nearby genes involved in cellular and anatomical structure morphogenesis. Also, sequences flanking DMC were enriched in SNPs compared to all other CpGs, either methylated or unmethylated in the two subspecies. Our data suggest a contribution of epigenetics to the regulation and divergence of anatomical morphogenesis in the two subspecies relevant for cattle evolution and sub-species differentiation and adaptation.
DOI: 10.6084/m9.figshare.21710650
title: Circulating miRNAs in the first trimester and pregnancy complications: a systematic review

description: Most pregnancy complications originate with early placentation. MicroRNAs (miRNAs) may play an important role in placentation and function as biomarkers of future pregnancy complications. We summarized from the literature all first trimester circulating miRNAs associated with pregnancy complications of placental origin and further identified the miRNAs which have the most evidence as potential early biomarkers for pregnancy complications. We conducted a systematic review following PRISMA reporting guidelines (PROSPERO CRD42020183421). We identified all first trimester serum or plasma miRNAs associated with a pregnancy complication of placental origin (preeclampsia, intrauterine growth restriction (IUGR), gestational hypertension, preterm delivery) and the number of times those miRNAs were identified, as a measure of replication. Twenty-one studies examined 118 unique miRNAs, and 87 were associated with at least one pregnancy complication; preeclampsia was the most common. Seven miRNAs were significantly associated with a pregnancy complication in at least two studies: miR-125b, miR-518b, miR-628-3p, miR-365a-3p, miR-520h, miR-374a-5p, miR-191-5p. Few miRNAs were associated with more than one pregnancy complication: miR-518b and miR-520h with preeclampsia and gestational hypertension, miR-374a-5p and miR-191-5p with preterm birth and preeclampsia. Our systematic review suggests seven miRNAs as potential biomarkers of pregnancy complications. These complications are thought to originate with early placental defects and these miRNAs may also be biomarkers of placental pathology. First-trimester biomarkers of pregnancy complications can facilitate early detection and interventions.
DOI: 10.6084/m9.figshare.21710650.v1
title: Circulating miRNAs in the first trimester and pregnancy complications: a systematic review

description: Most pregnancy complications originate with early placentation. MicroRNAs (miRNAs) may play an important role in placentation and function as biomarkers of future pregnancy complications. We summarized from the literature all first trimester circulating miRNAs associated with pregnancy complications of placental origin and further identified the miRNAs which have the most evidence as potential early biomarkers for pregnancy complications. We conducted a systematic review following PRISMA reporting guidelines (PROSPERO CRD42020183421). We identified all first trimester serum or plasma miRNAs associated with a pregnancy complication of placental origin (preeclampsia, intrauterine growth restriction (IUGR), gestational hypertension, preterm delivery) and the number of times those miRNAs were identified, as a measure of replication. Twenty-one studies examined 118 unique miRNAs, and 87 were associated with at least one pregnancy complication; preeclampsia was the most common. Seven miRNAs were significantly associated with a pregnancy complication in at least two studies: miR-125b, miR-518b, miR-628-3p, miR-365a-3p, miR-520h, miR-374a-5p, miR-191-5p. Few miRNAs were associated with more than one pregnancy complication: miR-518b and miR-520h with preeclampsia and gestational hypertension, miR-374a-5p and miR-191-5p with preterm birth and preeclampsia. Our systematic review suggests seven miRNAs as potential biomarkers of pregnancy complications. These complications are thought to originate with early placental defects and these miRNAs may also be biomarkers of placental pathology. First-trimester biomarkers of pregnancy complications can facilitate early detection and interventions.
DOI: 10.6084/m9.figshare.21819471
title: Comparison between indicine and taurine cattle DNA methylation reveals epigenetic variation associated to differences in morphological adaptive traits

description: Indicine and taurine subspecies present distinct morphological traits as a consequence of environmental adaptation and artificial selection. Although the two subspecies have been characterized and compared at genome-wide level and at specific loci, their epigenetic diversity has not yet been explored. In this work, Reduced Representation Bisulphite Sequencing (RRBS) profiling of the taurine Angus (A) and indicine Nellore (N) cattle breeds was applied to identify methylation differences between the two subspecies. Genotyping by sequencing (GBS) of the same animals was performed to detect single nucleotide polymorphisms (SNPs) at cytosines in CpG dinucleotides and remove them from the differential methylation analysis. A total of 660,845 methylated cytosines were identified within the CpG context (CpGs) across the 10 animals sequenced (5 N and 5 A). A total of 25,765 of these were differentially methylated (DMCs). Most DMCs clustered in CpG stretches nearby genes involved in cellular and anatomical structure morphogenesis. Also, sequences flanking DMC were enriched in SNPs compared to all other CpGs, either methylated or unmethylated in the two subspecies. Our data suggest a contribution of epigenetics to the regulation and divergence of anatomical morphogenesis in the two subspecies relevant for cattle evolution and sub-species differentiation and adaptation.
DOI: 10.6084/m9.figshare.22181713
title: Table S19

description: Table S19. Expression matrix of C.papaya generated by GetExpressionMatrix.py module
DOI: 10.6084/m9.figshare.22181713.v1
title: Table S19

description: Table S19. Expression matrix of C.papaya generated by GetExpressionMatrix.py module
DOI: 10.6084/m9.figshare.22180840
title: RNA-seq

description: Quantified RNA-seq results of Arabidopsis (control vs heat).
DOI: 10.6084/m9.figshare.22180840.v1
title: RNA-seq

description: Quantified RNA-seq results of Arabidopsis (control vs heat).
DOI: 10.5281/zenodo.7679724
title: Modeled wintertime sea ice drift, sea ice thickness, dynamic sea surface height and sea ice drift budget terms in the Arctic

description: Modeled wintertime sea ice drift, sea ice thickness, dynamic sea surface height and sea ice drift budget terms in the Arctic between 1981 and 2020.
DOI: 10.5281/zenodo.7679723
title: Modeled wintertime sea ice drift, sea ice thickness, dynamic sea surface height and sea ice drift budget terms in the Arctic

description: Modeled wintertime sea ice drift, sea ice thickness, dynamic sea surface height and sea ice drift budget terms in the Arctic between 1981 and 2020.
DOI: 10.25919/f1pm-rq13
title: Light Change Dataset

description: Light Change Dataset is a new benchmark dataset for evaluation of background subtraction methods under large illumination change. The data was collected in the Robotics Innovation Centre Building, Queensland Centre for Advanced Technologies, Brisbane, Australia. The dataset has four videos with over 2000 manual annotations.
DOI: 10.6084/m9.figshare.11634372
title: Mainland China SSP Population Grids

description: Mainland China SSP Population Grids ~100m (Taiwan, Hong Kong and Macau are nodata regions). To reduce the size, the original population estimates have been formatted in integer type. The 2015 base-year population map has been adjusted using the national statistics of total population. <br> Please cite the following paper if using this dataset: Chen, Y., Li, X., Huang, K., Luo, M., & Gao, M. (2020). High‐resolution gridded population projections for China under the shared socioeconomic pathways. <em>Earth's Future</em>, <em>8</em>(6), e2020EF001491.
DOI: 10.6084/m9.figshare.11634372.v1
title: Mainland China SSP Population Grids

description: Mainland China SSP Population Grids ~100m (Taiwan, Hong Kong and Macau are nodata regions). To reduce the size, the original population estimates have been formatted in integer type.
DOI: 10.6084/m9.figshare.21164335
title: Building Form Simulation

description: The zip file contains the (sample) data and code for the manuscript BAE-D-22-01728. <br> The "Urban land use change simulation" folder includes the code and the data for the historical simulation and the ssp simulations of urban land use change in Guangzhou-Foshan. <br> The "Building height prediction" folder includes the code and the data for the prediction of cell-level building height in Panyu for three urban land use categories: residential, commercial, and industrial. <br> The "Building generation (sample data)" folder includes the CGA script and the sample data for the simulation of building objects using CityEngine. <br> For any technical questions, please contact Mingwei Feng (fengmw@mail2.sysu.edu.cn) or Yimin Chen (chenym49@mail.sysu.edu.cn). <br> Please cite the following paper if using the code and data: Chen, Y., & Feng, M. (2022). Urban form simulation in 3D based on cellular automata and building objects generation. <em>Building and Environment</em>, <em>226</em>, 109727.
DOI: 10.25442/hku.22180726
title: Supporting data for "Interventions on tobacco industry denormalisation and alternative smoking products on Hong Kong primary school students"

description: My thesis contains 3 trials (Chapters 3-5): Chapter 3 examines the immediate effects of a 2 A4-page colourful tobacco industry denormalisation (TID) worksheet on Primary 4-6 students’ TID belief, general attitudes towards smoking, support for tobacco control measures and susceptibility to using cigarettes and electronic cigarettes (ECs). Chapter 4 firstly examines the immediate effects (T1) of the 2 A4-page colourful alternative smoking products (ASP) worksheet on Primary 4-6 students’ ASP-related knowledge, TID belief, perceived risks and acceptability of ASPs, and susceptibility to using ASPs. Then, the feasibility of conducting a 1-month online booster session and a 1-month online follow-up assessment (T1) of the intervention is also explored. Chapter 5 examines the immediate effects (T1) of a TID-tailored video and a 2 A4-page colourful TID worksheet on Primary 4-6 students’ TID belief, ASP-related knowledge, perceived risks and acceptability of ASPs, general views on the tobacco industry and susceptibility to using ASPs. The feasibility of conducting a 2-week on-site booster session (T2) and the 1- (T3) and 3-month (T4) on-site follow-up assessments are also included.
DOI: 10.25442/hku.22180726.v1
title: Supporting data for "Interventions on tobacco industry denormalisation and alternative smoking products on Hong Kong primary school students"

description: My thesis contains 3 trials (Chapters 3-5): Chapter 3 examines the immediate effects of a 2 A4-page colourful tobacco industry denormalisation (TID) worksheet on Primary 4-6 students’ TID belief, general attitudes towards smoking, support for tobacco control measures and susceptibility to using cigarettes and electronic cigarettes (ECs). Chapter 4 firstly examines the immediate effects (T1) of the 2 A4-page colourful alternative smoking products (ASP) worksheet on Primary 4-6 students’ ASP-related knowledge, TID belief, perceived risks and acceptability of ASPs, and susceptibility to using ASPs. Then, the feasibility of conducting a 1-month online booster session and a 1-month online follow-up assessment (T1) of the intervention is also explored. Chapter 5 examines the immediate effects (T1) of a TID-tailored video and a 2 A4-page colourful TID worksheet on Primary 4-6 students’ TID belief, ASP-related knowledge, perceived risks and acceptability of ASPs, general views on the tobacco industry and susceptibility to using ASPs. The feasibility of conducting a 2-week on-site booster session (T2) and the 1- (T3) and 3-month (T4) on-site follow-up assessments are also included.
DOI: 10.25442/hku.22100132
title: Supporting data for “SELECTIVE NITRATE ELECTROVALORIZATION INTO AMMONIA ON NON-PRECIOUS METAL CATALYSTS FOR SUSTAINABLE RESOURCIFICATION”

description: The dataset can be divided into three parts. First is electrocatalysts preparation and characterization. The material characterization can further support the success of catalyst preparation. Second is electrochemical measurement for different reactions in different experimental conditions. The electrochemical tests reveal the excellent performance of these catalysts toward a variety of reactions. The third part is product detection. Several methods are utilized to determine the product generation which can investigate the capability of product selectivity of dfferent catalysts. <br>
DOI: 10.25442/hku.22100132.v1
title: Supporting data for “SELECTIVE NITRATE ELECTROVALORIZATION INTO AMMONIA ON NON-PRECIOUS METAL CATALYSTS FOR SUSTAINABLE RESOURCIFICATION”

description: The dataset can be divided into three parts. First is electrocatalysts preparation and characterization. The material characterization can further support the success of catalyst preparation. Second is electrochemical measurement for different reactions in different experimental conditions. The electrochemical tests reveal the excellent performance of these catalysts toward a variety of reactions. The third part is product detection. Several methods are utilized to determine the product generation which can investigate the capability of product selectivity of dfferent catalysts. <br>
DOI: 10.5281/zenodo.7662295
title: Cadmium does not affect post-hatching maternal care or early offspring development in earwigs.

description: Dataset and R script used in the study focusing on the effects of cadmium ingestion on post-hatching maternal care and early offspring development in the European earwig.
DOI: 10.5281/zenodo.7388841
title: Cadmium does not affect post-hatching maternal care or early offspring development in earwigs.

description: Dataset and R script used in the study focusing on the effects of cadmium ingestion on post-hatching maternal care and early offspring development in the European earwig.
DOI: 10.34740/kaggle/ds/2361978
title: Electric & Alternative Fuel Vehicles US [2023]
DOI: 10.5281/zenodo.7226828
title: Zenodo package for Mao et al. ApJS, 2022, 263, 35

description: The supplementary materials here contain input files to reproduce the AUTOSTRUCTURE and R-matrix calculations, data files and python3 notebooks to reproduce figures in the paper. ADS link: https://ui.adsabs.harvard.edu/abs/2022ApJS..263...35M/abstract
DOI: 10.5281/zenodo.7226812
title: Zenodo package for Mao et al. ApJS, 2022, 263, 35

description: The supplementary materials here contain input files to reproduce the AUTOSTRUCTURE and R-matrix calculations, data files and python3 notebooks to reproduce figures in the paper. ADS link: https://ui.adsabs.harvard.edu/abs/2022ApJS..263...35M/abstract
DOI: 10.34740/kaggle/ds/2375714
title: Electric & Alternative Fuel Charging Stations 2023