cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28426942
title: Finding a needle in the haystack: ADME and pharmacokinetics/pharmacodynamics characterization and optimization towards orally available bifunctional protein degraders

description: Degraders are an increasingly important sub-modality of small molecules as illustrated by an ever-expanding number of publications and clinical candidate molecules in human trials. Nevertheless, their preclinical optimization of ADME and PK/PD properties has remained challenging. Significant research efforts are being directed to elucidate the underlying principles and to derive rational optimization strategies. In this review, the authors summarize currently best practices in terms of in vitro assays and in vivo experiments. Furthermore, the authors collate and comment on the current understanding of optimal physicochemical characteristics and their impact on absorption, distribution, metabolism, and excretion properties, including the current knowledge of drug–rug interactions. Finally, the authors describe the pharmacokinetic prediction and Pharmacokinetic/Pharmacodynamic -concepts unique to degraders and how to best implement these in research projects. Despite many recent advances in the field, continued research will further our understanding of rational design regarding degrader optimization. Machine-learning and computational approaches will become increasingly important once larger, more robust datasets become available. Furthermore, tissue-targeting approaches (particularly regarding the central nervous system will be increasingly studied to elucidate efficacious drug regimens that capitalize on the catalytic mode of action. Finally, additional specialized approaches (e.g. covalent degraders, LOVdegs) can further enrich the field and offer interesting alternative approaches.
DOI: 10.15468/dl.uj9n7b
title: Occurrence Download

description: A dataset containing 17089 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Caragana arborescens Lam.)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Geometry POLYGON((-180 -90,180 -90,180 90,-180 90,-180 -90))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1945"
 ]
}

 The dataset includes 17089 records from 269 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002594-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f62dyj
title: Occurrence Download

description: A dataset containing 329 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Selaginella plana (Desv. ex Poir.) Hieron.)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Geometry POLYGON((-180 -90,180 -90,180 90,-180 90,-180 -90))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1945"
 ]
}

 The dataset includes 329 records from 40 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002633-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j5qpdh
title: Occurrence Download

description: A dataset containing 32125 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Calendula officinalis L.)",
 "BasisOfRecord is one of (Machine Observation, Human Observation, Observation, Literature Occurrence)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 32125 records from 281 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002634-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e2rus7
title: Occurrence Download

description: A dataset containing 1202 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Selaginella uncinata (Desv. ex Poir.) Spring)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Geometry POLYGON((-180 -90,180 -90,180 90,-180 90,-180 -90))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1945"
 ]
}

 The dataset includes 1202 records from 67 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002597-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.28518833
title: IJGIS manuscript data and code

description: Data and Codes for Reproducing Findings in the Responsible GIScience Manuscript.To be more specific, this repository contains data and code for reproducing Figure 3 in the manuscript.
DOI: 10.15468/dl.jr4d3r
title: Occurrence Download

description: A dataset containing 742 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Selaginella willdenowii (Desv.) Baker)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Geometry POLYGON((-180 -90,180 -90,180 90,-180 90,-180 -90))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1945"
 ]
}

 The dataset includes 742 records from 51 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002636-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wrwp58
title: Occurrence Download

description: A dataset containing 2327 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Selenicereus undatus (Haw.) D.R.Hunt)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Geometry POLYGON((-180 -90,180 -90,180 90,-180 90,-180 -90))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1945"
 ]
}

 The dataset includes 2327 records from 129 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002598-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.6462712
title: AMPredictor - Dataset

description: The entire dataset for the running of AMPredictor, including contact maps and ESM-1b based embeddings. This antimicrobial peptide dataset is from PepVAE.
DOI: 10.15468/dl.nubb38
title: Occurrence Download

description: A dataset containing 5372 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Sempervivum globiferum L.)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Geometry POLYGON((-180 -90,180 -90,180 90,-180 90,-180 -90))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1945"
 ]
}

 The dataset includes 5372 records from 105 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002599-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dsz3be
title: Occurrence Download

description: A dataset containing 226438 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Odocoileus virginianus (Zimmermann, 1780))",
 "BasisOfRecord is one of (Machine Observation, Human Observation, Observation, Literature Occurrence)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 226438 records from 202 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002595-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ky7ubm
title: Occurrence Download

description: A dataset containing 188260 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Centaurea nigra L.)",
 "BasisOfRecord is one of (Machine Observation, Human Observation, Observation, Literature Occurrence)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 188260 records from 883 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002635-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.12585820
title: Dataset accompanying: "Applying and Validating Coulomb Rate-and-State Seismicity Models in Acoustic Emission Experiments")

description: Dataset accompanying: "Applying and Validating Coulomb Rate-and-State Seismicity Models in Acoustic Emission Experiments" by Heimisson, Naderloon, Chandra and Barnhoorn.

Please reference the following publication if the data is used:Heimisson, E.R., Naderloo, M., Chandra, D. and Barnhoorn, A., 2024. Applying and validating Coulomb rate-and-state seismicity models in acoustic emission experiments. Tectonophysics, p.230574. https://doi.org/10.1016/j.tecto.2024.230574
DOI: 10.5281/zenodo.12585821
title: Dataset accompanying: "Applying and Validating Coulomb Rate-and-State Seismicity Models in Acoustic Emission Experiments")

description: Dataset accompanying: "Applying and Validating Coulomb Rate-and-State Seismicity Models in Acoustic Emission Experiments" by Heimisson, Naderloon, Chandra and Barnhoorn.

Please reference the following publication if the data is used:Heimisson, E.R., Naderloo, M., Chandra, D. and Barnhoorn, A., 2024. Applying and validating Coulomb rate-and-state seismicity models in acoustic emission experiments. Tectonophysics, p.230574. https://doi.org/10.1016/j.tecto.2024.230574
DOI: 10.6084/m9.figshare.27896377
title: tRNA-derived RNAs in human milk extracellular vesicles and associations with breastfeeding variables and maternal diet

description: To describe tDRs in human milk EVs and their associations with maternal body mass index, age, dietary indices, breastfeeding frequency, season and time of milk collection in a Latina population. We sequenced small RNAs from EVs from 109 mature human milk samples collected at 1 month after delivery in the Southern California Mother’s Milk Study. We grouped tDRs using hierarchical clustering and clusters were compared across tDR characteristics. We analyzed associations of tDRs with intrinsic maternal variables (body mass index, age), maternal nutrition (caloric intake, Healthy Eating Index, Dietary Inflammatory Index), and variables related to feeding and milk collection (breastfeeding frequency, season and time of milk collection) using negative binomial models. We identified 338 tDRs expressed in 90% or more of milk EV samples, of which 113 were identified in all samples. tDR-1:26-Gly-CCC-1-M4 accounted for most reads (79%). Pathway analysis revealed a wide array of biological processes and disease mechanisms across the four tDR clusters. tDRs were associated with season of collection, time of collection, breastfeeding frequency, and the dietary inflammatory index. tDRs are abundant in milk EVs and may be sensitive to maternal diet, seasonality, time of day, and breastfeeding frequency. Human milk contains important nutrients and molecules that help to protect the infant from disease and ensure proper development. Small pieces of RNA that originate from transfer RNA molecules are enriched in human milk, particularly in compartments that exist outside of the cell and can be easily move from cell to cell. These small RNAs – referred to as tRNA-derived RNAs (or tDRs) – have gene silencing functions which may implicate them in health and development. Additionally, small RNAs like tDRs can survive digestion by the infant’s stomach when encapsulated in these extracellular compartments, meaning that they can be fully transferred from mom to baby. However, tDRs have not yet been characterized in human milk. In this study, we measured tDRs in mature milk samples from a cohort of mothers. We characterized these tDRs and tested their associations with several maternal characteristics, dietary variables, and variables related to milk collection and breastfeeding. We found that tDRs were readily identifiable and were associated with several tested variables, including maternal diet, seasonality, time of day, and breastfeeding frequency.
DOI: 10.6084/m9.figshare.27896377.v1
title: tRNA-derived RNAs in human milk extracellular vesicles and associations with breastfeeding variables and maternal diet

description: To describe tDRs in human milk EVs and their associations with maternal body mass index, age, dietary indices, breastfeeding frequency, season and time of milk collection in a Latina population. We sequenced small RNAs from EVs from 109 mature human milk samples collected at 1 month after delivery in the Southern California Mother’s Milk Study. We grouped tDRs using hierarchical clustering and clusters were compared across tDR characteristics. We analyzed associations of tDRs with intrinsic maternal variables (body mass index, age), maternal nutrition (caloric intake, Healthy Eating Index, Dietary Inflammatory Index), and variables related to feeding and milk collection (breastfeeding frequency, season and time of milk collection) using negative binomial models. We identified 338 tDRs expressed in 90% or more of milk EV samples, of which 113 were identified in all samples. tDR-1:26-Gly-CCC-1-M4 accounted for most reads (79%). Pathway analysis revealed a wide array of biological processes and disease mechanisms across the four tDR clusters. tDRs were associated with season of collection, time of collection, breastfeeding frequency, and the dietary inflammatory index. tDRs are abundant in milk EVs and may be sensitive to maternal diet, seasonality, time of day, and breastfeeding frequency. Human milk contains important nutrients and molecules that help to protect the infant from disease and ensure proper development. Small pieces of RNA that originate from transfer RNA molecules are enriched in human milk, particularly in compartments that exist outside of the cell and can be easily move from cell to cell. These small RNAs – referred to as tRNA-derived RNAs (or tDRs) – have gene silencing functions which may implicate them in health and development. Additionally, small RNAs like tDRs can survive digestion by the infant’s stomach when encapsulated in these extracellular compartments, meaning that they can be fully transferred from mom to baby. However, tDRs have not yet been characterized in human milk. In this study, we measured tDRs in mature milk samples from a cohort of mothers. We characterized these tDRs and tested their associations with several maternal characteristics, dietary variables, and variables related to milk collection and breastfeeding. We found that tDRs were readily identifiable and were associated with several tested variables, including maternal diet, seasonality, time of day, and breastfeeding frequency.
DOI: 10.6084/m9.figshare.27910505
title: Circular RNAs as multifaceted molecular regulators of vital activity and potential biomarkers of aging

description: Aging presents a significant challenge to health and social care systems due to the increasing proportion of the elderly population. The identification of reliable biomarkers to assess the progression of aging remains an unresolved question. Circular RNAs (circRNAs) are single-stranded covalently closed RNAs. They have been found to regulate various biological processes. CircRNAs are present in human biological fluids, are relatively stable, and accumulate with age, making them promising as biomarkers of aging. Current information on the expression of circRNAs in aging was analyzed using scientific databases. In this review, we have identified key stages in the study of circRNAs during aging and summarized the current understanding of their biogenesis. By focusing on the role of circRNAs in processes that contribute to aging – such as genomic stability, metabolism, cell death, and signaling pathways – we hypothesize that circRNAs may drive the aging process through their age-related accumulation and resultant deregulation. Examples of age-related differential expression of circRNAs in various species, including humans, are provided. This review highlights the importance of finding novel epigenetic biomarkers of aging, beyond the already identified molecules (circFOXO3, circRNA100783, circPVT1), and highlights circRNAs as a potential therapeutic target for the treatment of age-associated diseases.
DOI: 10.6084/m9.figshare.27910505.v1
title: Circular RNAs as multifaceted molecular regulators of vital activity and potential biomarkers of aging

description: Aging presents a significant challenge to health and social care systems due to the increasing proportion of the elderly population. The identification of reliable biomarkers to assess the progression of aging remains an unresolved question. Circular RNAs (circRNAs) are single-stranded covalently closed RNAs. They have been found to regulate various biological processes. CircRNAs are present in human biological fluids, are relatively stable, and accumulate with age, making them promising as biomarkers of aging. Current information on the expression of circRNAs in aging was analyzed using scientific databases. In this review, we have identified key stages in the study of circRNAs during aging and summarized the current understanding of their biogenesis. By focusing on the role of circRNAs in processes that contribute to aging – such as genomic stability, metabolism, cell death, and signaling pathways – we hypothesize that circRNAs may drive the aging process through their age-related accumulation and resultant deregulation. Examples of age-related differential expression of circRNAs in various species, including humans, are provided. This review highlights the importance of finding novel epigenetic biomarkers of aging, beyond the already identified molecules (circFOXO3, circRNA100783, circPVT1), and highlights circRNAs as a potential therapeutic target for the treatment of age-associated diseases.
DOI: 10.6084/m9.figshare.27874410
title: SNHG12 in cancer-associated fibroblast-derived extracellular vesicle induces macrophage-myofibroblast transition

description: To investigate mechanism of lncRNA SNHG12 induced macrophage-myofibroblast transition (MMT) in cancer-associated fibroblasts (CAFs)-derived extracellular vesicles (EVs) in non-small cell lung cancer (NSCLC). CAFs EVs were isolated from human NSCLC tissue and adjacent cancerous tissue (<i>n</i> = 3), and their morphology and particle size were evaluated. Macrophages and MMT cells with different phenotypes were detected, and the binding relationship of lncRNA SNHG12, miR-181a-5p, and Smad3 was verified. LncRNA SNHG12 derived from CAFs-EVs promoted the transformation of M2 macrophages into MMT. In addition, lncRNA-SNHG12 increased the expression of Smad3 which was significantly upregulated in MMT through sponge of miR-181a-5p. LncRNA SNHG12 derived from CAFs-EV induced MMT in NSCLC.
DOI: 10.6084/m9.figshare.27874410.v1
title: SNHG12 in cancer-associated fibroblast-derived extracellular vesicle induces macrophage-myofibroblast transition

description: To investigate mechanism of lncRNA SNHG12 induced macrophage-myofibroblast transition (MMT) in cancer-associated fibroblasts (CAFs)-derived extracellular vesicles (EVs) in non-small cell lung cancer (NSCLC). CAFs EVs were isolated from human NSCLC tissue and adjacent cancerous tissue (<i>n</i> = 3), and their morphology and particle size were evaluated. Macrophages and MMT cells with different phenotypes were detected, and the binding relationship of lncRNA SNHG12, miR-181a-5p, and Smad3 was verified. LncRNA SNHG12 derived from CAFs-EVs promoted the transformation of M2 macrophages into MMT. In addition, lncRNA-SNHG12 increased the expression of Smad3 which was significantly upregulated in MMT through sponge of miR-181a-5p. LncRNA SNHG12 derived from CAFs-EV induced MMT in NSCLC.
DOI: 10.6084/m9.figshare.27917052
title: Dynamic visualization of DNA methylation in cell cycle genes during iPSC cardiac differentiation

description: Existing analyses with conventional assays have generated significant insights into static states of DNA methylation but were unable to visualize the dynamics of epigenetic regulation. We utilized a genomic DNA methylation reporter (GMR) system carrying Snrpn minimal promoter and CpG regions of <i>Cdk1</i> (Cyclin-dependent kinase 1) or <i>Sox2</i> (SRY-Box Transcription Factor 2). Mouse Sox2 GMR iPSCs rapidly lost fluorescent reporter signal upon the induction of cardiac differentiation. Cdk1 GMR reporter signal was strong in undifferentiated iPSCs, and gradually decreased during cardiomyocyte differentiation. RT-qPCR and pyrosequencing demonstrated that the reduction of <i>Sox2</i> and <i>Cdk1</i> was regulated by hypermethylation of their promoters’ CpG regions during cardiac differentiation. The GMR reporter system can be useful for monitoring real-time epigenetic DNA modification at single-cell resolution. This research article introduces a genomics DNA methylation reporter (GMR) system that utilizes Snrpn gene’s mini-promoter along with regulatory regions (e.g. promoter or enhancer) of genes of interest, Cdk1, and Sox2. When mouse stem cells carrying the Sox2 or Cdk1 GMR were differentiated into heart muscle cells, the cells gradually lost their fluorescent reporter signal. Further testing with cell imaging, gene expression, and DNA methylation assays confirmed that these changes were due to increased methylation in specific DNA regions as the cells developed into heart cells. This system offers a way to track real-time changes in DNA methylation at the single-cell level.
DOI: 10.6084/m9.figshare.27917052.v1
title: Dynamic visualization of DNA methylation in cell cycle genes during iPSC cardiac differentiation

description: Existing analyses with conventional assays have generated significant insights into static states of DNA methylation but were unable to visualize the dynamics of epigenetic regulation. We utilized a genomic DNA methylation reporter (GMR) system carrying Snrpn minimal promoter and CpG regions of <i>Cdk1</i> (Cyclin-dependent kinase 1) or <i>Sox2</i> (SRY-Box Transcription Factor 2). Mouse Sox2 GMR iPSCs rapidly lost fluorescent reporter signal upon the induction of cardiac differentiation. Cdk1 GMR reporter signal was strong in undifferentiated iPSCs, and gradually decreased during cardiomyocyte differentiation. RT-qPCR and pyrosequencing demonstrated that the reduction of <i>Sox2</i> and <i>Cdk1</i> was regulated by hypermethylation of their promoters’ CpG regions during cardiac differentiation. The GMR reporter system can be useful for monitoring real-time epigenetic DNA modification at single-cell resolution. This research article introduces a genomics DNA methylation reporter (GMR) system that utilizes Snrpn gene’s mini-promoter along with regulatory regions (e.g. promoter or enhancer) of genes of interest, Cdk1, and Sox2. When mouse stem cells carrying the Sox2 or Cdk1 GMR were differentiated into heart muscle cells, the cells gradually lost their fluorescent reporter signal. Further testing with cell imaging, gene expression, and DNA methylation assays confirmed that these changes were due to increased methylation in specific DNA regions as the cells developed into heart cells. This system offers a way to track real-time changes in DNA methylation at the single-cell level.