cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22857062.v1
title: Epigenome wide association study in peripheral blood of pregnant women identifies potential metabolic pathways related to gestational diabetes

description: Gestational diabetes mellitus (GDM) increases the risk of developing metabolic disorders in both pregnant women and their offspring. Factors such as nutrition or the intrauterine environment may play an important role, through epigenetic mechanisms, in the development of GDM. The aim of this work is to identify epigenetic marks involved in the mechanisms or pathways related to gestational diabetes. A total of 32 pregnant women were selected, 16 of them with GDM and 16 non-GDM. DNA methylation pattern was obtained from Illumina Methylation Epic BeadChip, from peripheral blood samples at the diagnostic visit (26–28 weeks). Differential methylated positions (DMPs) were extracted using ChAMP and limma package in R 2.9.10, with a threshold of FDR &lt;0.05, deltabeta &gt;|5|% and B &gt;0. A total of 1.141 DMPs were found, and 714 were annotated in genes. A functional analysis was performed, and we found 23 genes significantly related to carbohydrate metabolism. Finally, a total of 27 DMPs were correlated with biochemical variables such as glucose levels at different points of oral glucose tolerance test, fasting glucose, cholesterol, HOMAIR and HbA1c, at different visits during pregnancy and postpartum. Our results show that there is a differentiated methylation pattern between GDM and non-GDM. Furthermore, the genes annotated to the DMPs could be implicated in the development of GDM as well as in alterations in related metabolic variables.
DOI: 10.5281/zenodo.7942294
title: Data sets for temperature rise due to frictional heat generation during a sliding contact between an elastic particle and a rigid substrate

description: This dataset contains essential data from the Finite Element Method model predicting heat generation due to friction during the sliding contact between an elastic particle and a rigid substrate. Part of this data was processed and presented in an article under review for journal publication. The following is the description of the data files and the associated Figure in the original paper. 'Temp_CoeffFric_01_055.xlsx' data for temperature evolution for the nodes in the contacts and along the particle radius for various friction coefficient values (0.1-0.55). 'Temp_Load_001_01.xlsx' data for temperature evolution for the nodes in the contacts and along the particle radius for various normal load values (0.01-0.1 N). 'Temp_Vel_02_1.xlsx' data for temperature evolution for the nodes in the contacts and along the particle radius for various sliding velocity values (0.2-1 m/s). 'Temp_TC_5_100.xlsx' data for temperature evolution for the nodes in the contacts and along the particle radius for various thermal conductivity values. (i.e. 5-100 W/m K). 'Temp_HC_100_1600.xlsx' data for temperature evolution for the nodes in the contacts and along the particle radius for various thermal conductivity values. (i.e. 100-1600 J/kg K).
DOI: 10.5281/zenodo.7942293
title: Data sets for temperature rise due to frictional heat generation during a sliding contact between an elastic particle and a rigid substrate

description: This dataset contains essential data from the Finite Element Method model predicting heat generation due to friction during the sliding contact between an elastic particle and a rigid substrate. Part of this data was processed and presented in an article under review for journal publication. The following is the description of the data files and the associated Figure in the original paper. 'Temp_CoeffFric_01_055.xlsx' data for temperature evolution for the nodes in the contacts and along the particle radius for various friction coefficient values (0.1-0.55). 'Temp_Load_001_01.xlsx' data for temperature evolution for the nodes in the contacts and along the particle radius for various normal load values (0.01-0.1 N). 'Temp_Vel_02_1.xlsx' data for temperature evolution for the nodes in the contacts and along the particle radius for various sliding velocity values (0.2-1 m/s). 'Temp_TC_5_100.xlsx' data for temperature evolution for the nodes in the contacts and along the particle radius for various thermal conductivity values. (i.e. 5-100 W/m K). 'Temp_HC_100_1600.xlsx' data for temperature evolution for the nodes in the contacts and along the particle radius for various thermal conductivity values. (i.e. 100-1600 J/kg K).
DOI: 10.5517/ccdc.csd.cc251x6c
title: CCDC 1997832: Experimental Crystal Structure Determination

description: Related Article: Raffaella Mancuso, Ida Ziccarelli, Matteo Brindisi, Cosimo D. Altomare, Luca Frattaruolo, Aurelia Falcicchio, Nicola Della Ca’, Anna Rita Cappello, Bartolo Gabriele|2021|Catalysts|11|227|doi:10.3390/catal11020227
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc251x7d
title: CCDC 1997833: Experimental Crystal Structure Determination

description: Related Article: Raffaella Mancuso, Ida Ziccarelli, Matteo Brindisi, Cosimo D. Altomare, Luca Frattaruolo, Aurelia Falcicchio, Nicola Della Ca’, Anna Rita Cappello, Bartolo Gabriele|2021|Catalysts|11|227|doi:10.3390/catal11020227
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2bzydp
title: CCDC 2174693: Experimental Crystal Structure Determination

description: Related Article: Xiao-qin Wu, Ze-yu Yang, Xiao-jie Sang, Xin-xin Tian, Xuehong Wei|2022|Dalton Trans.|51|16861|doi:10.1039/d2dt02049a
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2ckj6p
title: CCDC 2191582: Experimental Crystal Structure Determination

description: Related Article: Raffaella Mancuso, Patrizio Russo, Melania Lettieri, Domenico Santandrea, Corrado Cuocci, Bartolo Gabriele|2022|Adv.Synth.Catal.|364|3917|doi:10.1002/adsc.202200958
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2ckj8r
title: CCDC 2191584: Experimental Crystal Structure Determination

description: Related Article: Raffaella Mancuso, Patrizio Russo, Melania Lettieri, Domenico Santandrea, Corrado Cuocci, Bartolo Gabriele|2022|Adv.Synth.Catal.|364|3917|doi:10.1002/adsc.202200958
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2cq8n1
title: CCDC 2196153: Experimental Crystal Structure Determination

description: Related Article: Jacob O. Rothbaum, Alessandro Motta, Yosi Kratish, Tobin J. Marks|2023|Chemical Science|14|3247|doi:10.1039/D2SC06442A
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2cq8s5
title: CCDC 2196157: Experimental Crystal Structure Determination

description: Related Article: Jacob O. Rothbaum, Alessandro Motta, Yosi Kratish, Tobin J. Marks|2023|Chemical Science|14|3247|doi:10.1039/D2SC06442A
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2cq8t6
title: CCDC 2196158: Experimental Crystal Structure Determination

description: Related Article: Jacob O. Rothbaum, Alessandro Motta, Yosi Kratish, Tobin J. Marks|2023|Chemical Science|14|3247|doi:10.1039/D2SC06442A
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2fdpcx
title: CCDC 2246519: Experimental Crystal Structure Determination

description: Related Article: Xiao-qin Wu, Ze-yu Yang, Xiao-jie Sang, Xin-xin Tian, Xuehong Wei|2022|Dalton Trans.|51|16861|doi:10.1039/d2dt02049a
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5281/zenodo.7942322
title: Datasheets affiliated with thesis "Understanding the adaptive capacity in Populus tremuloides, a keystone North American tree species"

description: These datasheets are included in the unpublished thesis chapters of the doctoral thesis "Understanding the adaptive capacity in <em>Populus tremuloides</em>, a keystone North American tree species".
DOI: 10.5281/zenodo.7942321
title: Datasheets affiliated with thesis "Understanding the adaptive capacity in Populus tremuloides, a keystone North American tree species"

description: These datasheets are included in the unpublished thesis chapters of the doctoral thesis "Understanding the adaptive capacity in <em>Populus tremuloides</em>, a keystone North American tree species".
DOI: 10.25345/c5cv4c25x
title: MassIVE MSV000091966 - The Cancer Testes Antigen, HORMAD1, is a Tumor-Specific Replication Fork Protection Factor
title: LUM1_986119- HORMAD1 IP Mass spec on H1395 cells Biological Replicate 1 LUM1_986120- IgG Rabbit CTRL IP Mass spec on H1395 cells Biological Replicate 1 LUM1_986121- HORMAD1 IP Mass spec on H1395 cells Biological Replicate 2 LUM1_986122- IgG Rabbit CTRL IP Mass spec on H1395 cells Biological Replicate 2 LUM1_S12053- Untreated CTRL IgG Rabbit IP Mass spec on A549 Cells Biological Replicate 1 LUM1_S12054- Untreated HORMAD1 IP Mass spec on A549 Cells Biological Replicate 1
DOI: 10.21227/50qj-9k55
title: Embedding Imputation

description: The datasets are used to test an embedding imputation model. There are two different experiments: finance and mobile applications.
DOI: 10.5281/zenodo.7791980
title: Map of the global wildland-urban interface

description: The wildland-urban interface (WUI) is where buildings and wildland vegetation meet or intermingle. It is where human-environmental conflicts and risks are concentrated, including the loss of houses and lives to wildfire, habitat loss and fragmentation, and the spread of zoonotic diseases. However, a global analysis of the WUI has been lacking. This dataset features a global, 10 m resolution map of the wildland-urban interface that was developed in a recent study by the authors of this dataset (see corresponding publication). <strong>Temporal extent</strong> The data contains data representative for ca. 2020. <strong>Data format and units</strong> The data are organized in tiles of 100 km x 100 km and follow the EQUI7 tiling grid and projection system. The images are compressed GeoTiff files (*.tif). There is a mosaic in GDAL Virtual format (*.vrt), which can readily be opened in most Geographic Information Systems. Please consider the generation of image pyramids before using *.vrt files. The raster dataset contains Wildland-urban interface (WUI) data (one layer), 10 m spatial resolution, 8 discrete classes: 1 - Forest/Shrubland/Wetland-dominated Intermix WU 2 - Forest/Shrubland/Wetland-dominated Interface WUI 3 - Grassland-dominated Intermix WUI 4 - Grassland -dominated Interface WUI 5 - Non-WUI: Forest/Shrub/Wetland-dominated 6 - Non-WUI: Grassland-dominated 7 - Non-WUI: Urban 8 - Non-WUI: Other In addition, the data contain tabular data on WUI area, population and biomass in the WUI, as well as wildfire area and people affected by wildfire in the WUI per world region, country, subnational administrative unit and biome. The data also contain the key algorithm for WUI mapping (also accessible here: https://github.com/franzschug/global_wildland_urban_interface). <strong>Further information</strong> For further information, please see the publication or contact Franz Schug (fschug@wisc.edu). Visit the website of SILVIS lab, University of Wisconsin-Madison (https://silvis.forest.wisc.edu/) to learn more about the Wildland-Urban Interface. The data can be interactively visualizes in a web viewer here: <strong>Corresponding publication</strong> Schug, Franz<sup>*</sup>; Bar-Massada, Avi; Carlson, Amanda R.; Cox, Heather; Hawbaker, Todd J.; Helmers, David; Hostert, Patrick; Kaim, Dominik; Kasraee, Neda K.; Martinuzzi, Sebastián; Mockrin, Miranda H.; Pfoch, Kira A.; Radeloff, Volker C. The global Wildland-Urban Interface and wildfires near people (in review). <strong>Funding</strong> This research was funded by the NASA Land Cover and Land Use Change Program under agreement 80NSSC21K0310.
DOI: 10.6084/m9.figshare.22209925
title: Milk glycan metabolism by intestinal bifidobacteria: insights from comparative genomics

description: Bifidobacteria are early colonizers of the human neonatal gut and provide multiple health benefits to the infant, including inhibiting the growth of enteropathogens and modulating the immune system. Certain <i>Bifidobacterium</i> species prevail in the gut of breastfed infants due to the ability of these microorganisms to selectively forage glycans present in human milk, specifically human milk oligosaccharides (HMOs) and <i>N</i>-linked glycans. Therefore, these carbohydrates serve as promising prebiotic dietary supplements to stimulate the growth of bifidobacteria in the guts of children suffering from impaired gut microbiota development. However, the rational formulation of milk glycan-based prebiotics requires a detailed understanding of how bifidobacteria metabolize these carbohydrates. Accumulating biochemical and genomic data suggest that HMO and <i>N</i>-glycan assimilation abilities vary remarkably within the <i>Bifidobacterium</i> genus, both at the species and strain levels. This review focuses on the delineation and genome-based comparative analysis of differences in respective biochemical pathways, transport systems, and associated transcriptional regulatory networks, providing a foundation for genomics-based projection of milk glycan utilization capabilities across a rapidly growing number of sequenced bifidobacterial genomes and metagenomic datasets. This analysis also highlights remaining knowledge gaps and suggests directions for future studies to optimize the formulation of milk-glycan-based prebiotics that target bifidobacteria.
DOI: 10.6084/m9.figshare.22209925.v1
title: Milk glycan metabolism by intestinal bifidobacteria: insights from comparative genomics

description: Bifidobacteria are early colonizers of the human neonatal gut and provide multiple health benefits to the infant, including inhibiting the growth of enteropathogens and modulating the immune system. Certain <i>Bifidobacterium</i> species prevail in the gut of breastfed infants due to the ability of these microorganisms to selectively forage glycans present in human milk, specifically human milk oligosaccharides (HMOs) and <i>N</i>-linked glycans. Therefore, these carbohydrates serve as promising prebiotic dietary supplements to stimulate the growth of bifidobacteria in the guts of children suffering from impaired gut microbiota development. However, the rational formulation of milk glycan-based prebiotics requires a detailed understanding of how bifidobacteria metabolize these carbohydrates. Accumulating biochemical and genomic data suggest that HMO and <i>N</i>-glycan assimilation abilities vary remarkably within the <i>Bifidobacterium</i> genus, both at the species and strain levels. This review focuses on the delineation and genome-based comparative analysis of differences in respective biochemical pathways, transport systems, and associated transcriptional regulatory networks, providing a foundation for genomics-based projection of milk glycan utilization capabilities across a rapidly growing number of sequenced bifidobacterial genomes and metagenomic datasets. This analysis also highlights remaining knowledge gaps and suggests directions for future studies to optimize the formulation of milk-glycan-based prebiotics that target bifidobacteria.
DOI: 10.6084/m9.figshare.22220985
title: Overview of physiological, biochemical, and regulatory aspects of nitrogen fixation in <i>Azotobacter vinelandii</i>

description: Understanding how Nature accomplishes the reduction of inert nitrogen gas to form metabolically tractable ammonia at ambient temperature and pressure has challenged scientists for more than a century. Such an understanding is a key aspect toward accomplishing the transfer of the genetic determinants of biological nitrogen fixation to crop plants as well as for the development of improved synthetic catalysts based on the biological mechanism. Over the past 30 years, the free-living nitrogen-fixing bacterium <i>Azotobacter vinelandii</i> emerged as a preferred model organism for mechanistic, structural, genetic, and physiological studies aimed at understanding biological nitrogen fixation. This review provides a contemporary overview of these studies and places them within the context of their historical development.
DOI: 10.6084/m9.figshare.22858931
title: An enriched maternal environment and stereotypies of sows differentially affect the neuro-epigenome of brain regions related to emotionality in their piglets

description: Epigenetic mechanisms are important modulators of neurodevelopmental outcomes in the offspring of animals challenged during pregnancy. Pregnant sows living in a confined environment are challenged with stress and lack of stimulation which may result in the expression of stereotypies (repetitive behaviours without an apparent function). Little attention has been devoted to the postnatal effects of maternal stereotypies in the offspring. We investigated how the environment and stereotypies of pregnant sows affected the neuro-epigenome of their piglets. We focused on the amygdala, frontal cortex, and hippocampus, brain regions related to emotionality, learning, memory, and stress response. Differentially methylated regions (DMRs) were investigated in these brain regions of male piglets born from sows kept in an enriched vs a barren environment. Within the latter group of piglets, we compared the brain methylomes of piglets born from sows expressing stereotypies vs sows not expressing stereotypies. DMRs emerged in each comparison. While the epigenome of the hippocampus and frontal cortex of piglets is mainly affected by the maternal environment, the epigenome of the amygdala is mainly affected by maternal stereotypies. The molecular pathways and mechanisms triggered in the brains of piglets by maternal environment or stereotypies are different, which is reflected on the differential gene function associated to the DMRs found in each piglets’ brain region . The present study is the first to investigate the neuro-epigenomic effects of maternal enrichment in pigs’ offspring and the first to investigate the neuro-epigenomic effects of maternal stereotypies in the offspring of a mammal.
DOI: 10.6084/m9.figshare.22858931.v1
title: An enriched maternal environment and stereotypies of sows differentially affect the neuro-epigenome of brain regions related to emotionality in their piglets

description: Epigenetic mechanisms are important modulators of neurodevelopmental outcomes in the offspring of animals challenged during pregnancy. Pregnant sows living in a confined environment are challenged with stress and lack of stimulation which may result in the expression of stereotypies (repetitive behaviours without an apparent function). Little attention has been devoted to the postnatal effects of maternal stereotypies in the offspring. We investigated how the environment and stereotypies of pregnant sows affected the neuro-epigenome of their piglets. We focused on the amygdala, frontal cortex, and hippocampus, brain regions related to emotionality, learning, memory, and stress response. Differentially methylated regions (DMRs) were investigated in these brain regions of male piglets born from sows kept in an enriched vs a barren environment. Within the latter group of piglets, we compared the brain methylomes of piglets born from sows expressing stereotypies vs sows not expressing stereotypies. DMRs emerged in each comparison. While the epigenome of the hippocampus and frontal cortex of piglets is mainly affected by the maternal environment, the epigenome of the amygdala is mainly affected by maternal stereotypies. The molecular pathways and mechanisms triggered in the brains of piglets by maternal environment or stereotypies are different, which is reflected on the differential gene function associated to the DMRs found in each piglets’ brain region . The present study is the first to investigate the neuro-epigenomic effects of maternal enrichment in pigs’ offspring and the first to investigate the neuro-epigenomic effects of maternal stereotypies in the offspring of a mammal.