cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7533943
title: Multiplexed histology of COVID-19 post-mortem lung samples - CONTROL CASE 3 FOV1

description: <strong>Image-based data set of a post-mortem lung sample from a COVID-19 donor (CONTROL CASE 3 FOV1)</strong> Each image shows the same field of view (FOV), sequentially stained with the depicted fluorescence-labelled antibodies, including surface proteins, intracellular proteins and transcription factors. Images contain 2024 x 2024 pixels and are generated using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have been normalized and intensities adjusted.
description: Funding: Deutsche Forschungsgemeinschaft HA5354/10-1, SPP1937 (HA5354/8-2) and TRR130 P17 and C01 (to Anja Hauser)
description: {"references": ["Mothes, R. and Pascual-Reguant, A. et al. Local CCL18 and CCL21 expand lung fibrovascular niches and recruit lymphocytes, leading to tertiary lymphoid structure formation in prolonged COVID-19. medRxiv 2022.03.24.22272768 (2022) doi:10.1101/2022.03.24.22272768."]}
DOI: 10.5281/zenodo.7520240
title: Multiplexed histology of COVID-19 post-mortem lung samples - PROLONGED CASE 2 FOV2

description: <strong>Image-based data set of a post-mortem lung sample from a COVID-19 donor (PROLONGED CASE 2 FOV2)</strong> Each image shows the same field of view (FOV), sequentially stained with the depicted fluorescence-labelled antibodies, including surface proteins, intracellular proteins and transcription factors. Images contain 2024 x 2024 pixels and are generated using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have been normalized and intensities adjusted.
description: Funding: Deutsche Forschungsgemeinschaft HA5354/10-1, SPP1937 (HA5354/8-2) and TRR130 P17 and C01 (to Anja Hauser)
description: {"references": ["Mothes, R. and Pascual-Reguant, A. et al. Local CCL18 and CCL21 expand lung fibrovascular niches and recruit lymphocytes, leading to tertiary lymphoid structure formation in prolonged COVID-19. medRxiv 2022.03.24.22272768 (2022) doi:10.1101/2022.03.24.22272768."]}
DOI: 10.5281/zenodo.7533942
title: Multiplexed histology of COVID-19 post-mortem lung samples - CONTROL CASE 3 FOV1

description: <strong>Image-based data set of a post-mortem lung sample from a COVID-19 donor (CONTROL CASE 3 FOV1)</strong> Each image shows the same field of view (FOV), sequentially stained with the depicted fluorescence-labelled antibodies, including surface proteins, intracellular proteins and transcription factors. Images contain 2024 x 2024 pixels and are generated using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have been normalized and intensities adjusted.
description: Funding: Deutsche Forschungsgemeinschaft HA5354/10-1, SPP1937 (HA5354/8-2) and TRR130 P17 and C01 (to Anja Hauser)
description: {"references": ["Mothes, R. and Pascual-Reguant, A. et al. Local CCL18 and CCL21 expand lung fibrovascular niches and recruit lymphocytes, leading to tertiary lymphoid structure formation in prolonged COVID-19. medRxiv 2022.03.24.22272768 (2022) doi:10.1101/2022.03.24.22272768."]}
DOI: 10.5281/zenodo.7525811
title: Multiplexed histology of COVID-19 post-mortem lung samples - CONROL CASE 3 FOV2

description: <strong>Image-based data set of a post-mortem lung sample from a COVID-19 donor (CONTROL CASE 3 FOV2)</strong> Each image shows the same field of view (FOV), sequentially stained with the depicted fluorescence-labelled antibodies, including surface proteins, intracellular proteins and transcription factors. Images contain 2024 x 2024 pixels and are generated using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have been normalized and intensities adjusted.
description: Funding: Deutsche Forschungsgemeinschaft HA5354/10-1, SPP1937 (HA5354/8-2) and TRR130 P17 and C01 (to Anja Hauser)
DOI: 10.5281/zenodo.7525810
title: Multiplexed histology of COVID-19 post-mortem lung samples - CONROL CASE 3 FOV2

description: <strong>Image-based data set of a post-mortem lung sample from a COVID-19 donor (CONTROL CASE 3 FOV2)</strong> Each image shows the same field of view (FOV), sequentially stained with the depicted fluorescence-labelled antibodies, including surface proteins, intracellular proteins and transcription factors. Images contain 2024 x 2024 pixels and are generated using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have been normalized and intensities adjusted.
description: Funding: Deutsche Forschungsgemeinschaft HA5354/10-1, SPP1937 (HA5354/8-2) and TRR130 P17 and C01 (to Anja Hauser)
DOI: 10.6084/m9.figshare.21084829.v15
title: List of native-alien populations in South Africa.csv

description: Native-alien population is defined as a population that is within a country to which the species is native and founded by individuals moved by direct human agency (or substantial indirect human agency) over a biogeographical barrier to an area beyond the species’ native range (Nelufule et al. 2022). <br> Reference Nelufule T, Robertson MP, Wilson JRU, Faulkner KT (2022) Native-alien populations—an apparent oxymoron that requires specific conservation attention. <em>NeoBiota</em> 74: 57–74, https://doi.org/10.3897/neobiota.74.81671
DOI: 10.5281/zenodo.7547717
title: Druglike molecule datasets for drug discovery

description: <strong>Background</strong><br> Trnasformer-based AI models have shown outstanding performance in identifying druggable candidate molecules. In most cases, models are trained on a massive amount of database of molecular information to capture the latent meaning of a given molecule. However, the desirable properties of candidate molecules include the feasibility of synthesizing them, low toxicity, and high druggability. In this study, we injected prior knowledge of the desirable properties of molecules during the training process. <strong>Methods</strong><br> Using the PubChem database (100 M), we filtered druglike molecules based on the quantity of drug-likeliness (QED) score and the Pfizer rule. With this dataset of drug-like molecules, we trained both the molecular representation model (chemBERTa) and the molecular generation models (MolGPT). The molecular representation model was evaluated by fine-tuning the results on the MoleculeNet benchmark datasets, and the molecular generation model was evaluated based on the generated samples (10 K). <strong>Results</strong><br> Training with druglike molecules enabled the generation of molecules with desirable properties without any conditioning. Although the molecular representation learning model was not remarkable, however, its performance in predicting clinical toxicology exceeded that of conventional molecular representation models. <strong>Conclusion</strong><br> By training based on a dataset of druglike molecules, our approach enables molecular representation models to predict clinical toxicity more precisely. Furthermore, it enables the molecule generation model to generate molecules with desirable druglike properties without any conditional generation procedures.<br> ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- import pickle with open("druglike_molecules_QED.pkl", "rb") as f: data = pickle.load(f)
DOI: 10.5281/zenodo.7547716
title: Druglike molecule datasets for drug discovery

description: <strong>Background</strong><br> Trnasformer-based AI models have shown outstanding performance in identifying druggable candidate molecules. In most cases, models are trained on a massive amount of database of molecular information to capture the latent meaning of a given molecule. However, the desirable properties of candidate molecules include the feasibility of synthesizing them, low toxicity, and high druggability. In this study, we injected prior knowledge of the desirable properties of molecules during the training process. <strong>Methods</strong><br> Using the PubChem database (100 M), we filtered druglike molecules based on the quantity of drug-likeliness (QED) score and the Pfizer rule. With this dataset of drug-like molecules, we trained both the molecular representation model (chemBERTa) and the molecular generation models (MolGPT). The molecular representation model was evaluated by fine-tuning the results on the MoleculeNet benchmark datasets, and the molecular generation model was evaluated based on the generated samples (10 K). <strong>Results</strong><br> Training with druglike molecules enabled the generation of molecules with desirable properties without any conditioning. Although the molecular representation learning model was not remarkable, however, its performance in predicting clinical toxicology exceeded that of conventional molecular representation models. <strong>Conclusion</strong><br> By training based on a dataset of druglike molecules, our approach enables molecular representation models to predict clinical toxicity more precisely. Furthermore, it enables the molecule generation model to generate molecules with desirable druglike properties without any conditional generation procedures.<br> ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- import pickle with open("druglike_molecules_QED.pkl", "rb") as f: data = pickle.load(f)
DOI: 10.6084/m9.figshare.21084829.v16
title: List of native-alien populations in South Africa.csv

description: Native-alien population is defined as a population that is within a country to which the species is native and founded by individuals moved by direct human agency (or substantial indirect human agency) over a biogeographical barrier to an area beyond the species’ native range (Nelufule et al. 2022). <br> Reference Nelufule T, Robertson MP, Wilson JRU, Faulkner KT (2022) Native-alien populations—an apparent oxymoron that requires specific conservation attention. <em>NeoBiota</em> 74: 57–74, https://doi.org/10.3897/neobiota.74.81671
DOI: 10.6084/m9.figshare.7770383
title: Cell lineage-specific genome-wide DNA methylation analysis of patients with paediatric-onset systemic lupus erythematosus

description: Patients with paediatric-onset systemic lupus erythematosus (SLE) often present with more severe clinical courses than adult-onset patients. Although genome-wide DNA methylation (DNAm) profiling has been performed in adult-onset SLE patients, parallel data on paediatric-onset SLE are not available. Therefore, we undertook a genome-wide DNAm study in paediatric-onset SLE patients across multiple blood cell lineages. The DNAm profiles of four purified immune cell lineages (CD4 + T cells, CD8 + T cells, B cells and neutrophils) and whole blood were compared in 16 Chinese patients with paediatric-onset SLE and 13 healthy controls using the Illumina HumanMethylationEPIC BeadChip. Comparison of DNAm in whole blood and within each independent cell lineage identified a consistent pattern of loss of DNAm at 21 CpG sites overlapping 15 genes, which represented a robust, disease-specific DNAm signature for paediatric-onset SLE in our cohort. In addition, cell lineage-specific changes, involving both loss and gain of DNAm, were observed in both novel genes and genes with well-described roles in SLE pathogenesis. This study also highlights the importance of studying DNAm changes in different immune cell lineages rather than only whole blood, since cell type-specific DNAm changes facilitated the elucidation of the cell type-specific molecular pathophysiology of SLE.
DOI: 10.6084/m9.figshare.7861346.v2
title: Locus-specific DNA methylation prediction in cord blood and placenta

description: DNA methylation is known to be responsive to prenatal exposures, which may be a part of the mechanism linking early developmental exposures to future chronic diseases. Many studies use blood to measure DNA methylation, yet we know that DNA methylation is tissue specific. Placenta is central to fetal growth and development, but it is rarely feasible to collect this tissue in large epidemiological studies; on the other hand, cord blood samples are more accessible. In this study, based on paired samples of both placenta and cord blood tissues from 169 individuals, we investigated the methylation concordance between placenta and cord blood. We then employed a machine-learning-based model to predict locus-specific DNA methylation levels in placenta using DNA methylation levels in cord blood. We found that methylation correlation between placenta and cord blood is lower than other tissue pairs, consistent with existing observations that placenta methylation has a distinct pattern. Nonetheless, there are still a number of CpG sites showing robust association between the two tissues. We built prediction models for placenta methylation based on cord blood data and documented a subset of 1,012 CpG sites with high correlation between measured and predicted placenta methylation levels. The resulting list of CpG sites and prediction models could help to reveal the loci where internal or external influences may affect DNA methylation in both placenta and cord blood, and provide a reference data to predict the effects on placenta in future study even when the tissue is not available in an epidemiological study.
DOI: 10.6084/m9.figshare.7770383.v3
title: Cell lineage-specific genome-wide DNA methylation analysis of patients with paediatric-onset systemic lupus erythematosus

description: Patients with paediatric-onset systemic lupus erythematosus (SLE) often present with more severe clinical courses than adult-onset patients. Although genome-wide DNA methylation (DNAm) profiling has been performed in adult-onset SLE patients, parallel data on paediatric-onset SLE are not available. Therefore, we undertook a genome-wide DNAm study in paediatric-onset SLE patients across multiple blood cell lineages. The DNAm profiles of four purified immune cell lineages (CD4 + T cells, CD8 + T cells, B cells and neutrophils) and whole blood were compared in 16 Chinese patients with paediatric-onset SLE and 13 healthy controls using the Illumina HumanMethylationEPIC BeadChip. Comparison of DNAm in whole blood and within each independent cell lineage identified a consistent pattern of loss of DNAm at 21 CpG sites overlapping 15 genes, which represented a robust, disease-specific DNAm signature for paediatric-onset SLE in our cohort. In addition, cell lineage-specific changes, involving both loss and gain of DNAm, were observed in both novel genes and genes with well-described roles in SLE pathogenesis. This study also highlights the importance of studying DNAm changes in different immune cell lineages rather than only whole blood, since cell type-specific DNAm changes facilitated the elucidation of the cell type-specific molecular pathophysiology of SLE.
DOI: 10.6084/m9.figshare.7861346
title: Locus-specific DNA methylation prediction in cord blood and placenta

description: DNA methylation is known to be responsive to prenatal exposures, which may be a part of the mechanism linking early developmental exposures to future chronic diseases. Many studies use blood to measure DNA methylation, yet we know that DNA methylation is tissue specific. Placenta is central to fetal growth and development, but it is rarely feasible to collect this tissue in large epidemiological studies; on the other hand, cord blood samples are more accessible. In this study, based on paired samples of both placenta and cord blood tissues from 169 individuals, we investigated the methylation concordance between placenta and cord blood. We then employed a machine-learning-based model to predict locus-specific DNA methylation levels in placenta using DNA methylation levels in cord blood. We found that methylation correlation between placenta and cord blood is lower than other tissue pairs, consistent with existing observations that placenta methylation has a distinct pattern. Nonetheless, there are still a number of CpG sites showing robust association between the two tissues. We built prediction models for placenta methylation based on cord blood data and documented a subset of 1,012 CpG sites with high correlation between measured and predicted placenta methylation levels. The resulting list of CpG sites and prediction models could help to reveal the loci where internal or external influences may affect DNA methylation in both placenta and cord blood, and provide a reference data to predict the effects on placenta in future study even when the tissue is not available in an epidemiological study.
DOI: 10.6084/m9.figshare.7861346.v1
title: Locus-specific DNA methylation prediction in cord blood and placenta

description: DNA methylation is known to be responsive to prenatal exposures, which may be a part of the mechanism linking early developmental exposures to future chronic diseases. Many studies use blood to measure DNA methylation, yet we know that DNA methylation is tissue specific. Placenta is central to fetal growth and development, but it is rarely feasible to collect this tissue in large epidemiological studies; on the other hand, cord blood samples are more accessible. In this study, based on paired samples of both placenta and cord blood tissues from 169 individuals, we investigated the methylation concordance between placenta and cord blood. We then employed a machine-learning-based model to predict locus-specific DNA methylation levels in placenta using DNA methylation levels in cord blood. We found that methylation correlation between placenta and cord blood is lower than other tissue pairs, consistent with existing observations that placenta methylation has a distinct pattern. Nonetheless, there are still a number of CpG sites showing robust association between the two tissues. We built prediction models for placenta methylation based on cord blood data and documented a subset of 1,012 CpG sites with high correlation between measured and predicted placenta methylation levels. The resulting list of CpG sites and prediction models could help to reveal the loci where internal or external influences may affect DNA methylation in both placenta and cord blood, and provide a reference data to predict the effects on placenta in future study even when the tissue is not available in an epidemiological study.
DOI: 10.6084/m9.figshare.7731587
title: Maternal pre-pregnancy obesity, offspring cord blood DNA methylation, and offspring cardiometabolic health in early childhood: an epigenome-wide association study

description: Pre-pregnancy obesity is an established risk factor for adverse sex-specific cardiometabolic health in offspring. Epigenetic alterations, such as in DNA methylation (DNAm), are a hypothesized link; however, sex-specific epigenomic targets remain unclear. Leveraging data from the Newborn Epigenetics Study (NEST) cohort, linear regression models were used to identify CpG sites in cord blood leukocytes associated with pre-pregnancy obesity in 187 mother-female and 173 mother-male offsprings. DNAm in cord blood was measured using the Illumina HumanMethylation450k BeadChip. Replication analysis was conducted among the Avon Longitudinal Study of Parents and Children (ALSPAC) cohort. Associations between pre-pregnancy obesity-associated CpG sites and offspring BMI z-score (BMIz) and blood pressure (BP) percentiles at 4–5-years of age were also examined. Maternal pre-pregnacy obesity was associated with 876 CpGs in female and 293 CpGs in male offspring (false discovery rate &lt;5%). Among female offspring, 57 CpG sites, including the top 18, mapped to the <i>TAPBP</i> gene (range of effect estimates: −0.83% decrease to 4.02% increase in methylation). CpG methylation differences in the <i>TAPBP</i> gene were also observed among males (range of effect estimates: −0.30% decrease to 2.59% increase in methylation). While technically validated, none of the <i>TAPBP</i> CpG sites were replicated in ALSPAC. In NEST, methylation differences at CpG sites of the <i>TAPBP</i> gene were associated with BMI z-score (cg23922433 and cg17621507) and systolic BP percentile (cg06230948) in female and systolic (cg06230948) and diastolic (cg03780271) BP percentile in male offspring. Together, these findings suggest sex-specific effects, which, if causal, may explain observed sex-specific effects of maternal obesity.
DOI: 10.6084/m9.figshare.7731587.v2
title: Maternal pre-pregnancy obesity, offspring cord blood DNA methylation, and offspring cardiometabolic health in early childhood: an epigenome-wide association study

description: Pre-pregnancy obesity is an established risk factor for adverse sex-specific cardiometabolic health in offspring. Epigenetic alterations, such as in DNA methylation (DNAm), are a hypothesized link; however, sex-specific epigenomic targets remain unclear. Leveraging data from the Newborn Epigenetics Study (NEST) cohort, linear regression models were used to identify CpG sites in cord blood leukocytes associated with pre-pregnancy obesity in 187 mother-female and 173 mother-male offsprings. DNAm in cord blood was measured using the Illumina HumanMethylation450k BeadChip. Replication analysis was conducted among the Avon Longitudinal Study of Parents and Children (ALSPAC) cohort. Associations between pre-pregnancy obesity-associated CpG sites and offspring BMI z-score (BMIz) and blood pressure (BP) percentiles at 4–5-years of age were also examined. Maternal pre-pregnacy obesity was associated with 876 CpGs in female and 293 CpGs in male offspring (false discovery rate &lt;5%). Among female offspring, 57 CpG sites, including the top 18, mapped to the <i>TAPBP</i> gene (range of effect estimates: −0.83% decrease to 4.02% increase in methylation). CpG methylation differences in the <i>TAPBP</i> gene were also observed among males (range of effect estimates: −0.30% decrease to 2.59% increase in methylation). While technically validated, none of the <i>TAPBP</i> CpG sites were replicated in ALSPAC. In NEST, methylation differences at CpG sites of the <i>TAPBP</i> gene were associated with BMI z-score (cg23922433 and cg17621507) and systolic BP percentile (cg06230948) in female and systolic (cg06230948) and diastolic (cg03780271) BP percentile in male offspring. Together, these findings suggest sex-specific effects, which, if causal, may explain observed sex-specific effects of maternal obesity.