cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21277265.v1
title: Health economic analysis of vaccine options for the polio eradication endgame: 2022-2036

description: Multiple vaccine options are available for polio prevention and risk management. Integrated global risk, economic, and poliovirus transmission modeling provides a tool to explore the dynamics of ending all use of one or more poliovirus vaccines to simplify the polio eradication endgame. With global reported cases of poliomyelitis trending higher since 2016, we apply an integrated global model to simulate prospective vaccine policies and strategies for OPV-using countries starting with initial conditions that correspond to the epidemiological poliovirus transmission situation at the beginning of 2022. Abruptly ending all OPV use in 2023 and relying only on IPV to prevent paralysis with current routine immunization coverage would lead to expected reestablished endemic transmission of poliovirus types 1 and 2, and approximately 150,000 expected cases of poliomyelitis per year. Alternatively, if OPV-using countries restart trivalent OPV (tOPV) use for all immunization activities and end IPV use, the model shows the lowest anticipated annual polio cases and lowest costs. Poor global risk management and coordination of OPV cessation remain a critical failure mode for the polio endgame, and national and global decision makers face difficult choices due to multiple available polio vaccine options and immunization strategies.
DOI: 10.6084/m9.figshare.19361756
title: Phosphatidic acid suppresses autophagy through competitive inhibition by binding GAPC (glyceraldehyde-3-phosphate dehydrogenase) and PGK (phosphoglycerate kinase) proteins

description: Macroautophagy/autophagy is a finely-regulated process in which cytoplasm encapsulated within transient organelles termed autophagosomes is delivered to lysosomes or vacuoles for degradation. Phospholipids, particularly phosphatidic acid (PA) that functions as a second messenger, play crucial and differential roles in autophagosome formation; however, the underlying mechanism remains largely unknown. Here we demonstrated that PA inhibits autophagy through competitive inhibition of the formation of ATG3 (autophagy-related)-ATG8e and ATG6-VPS34 (vacuolar protein sorting 34) complexes. PA bound to GAPC (glyceraldehyde-3-phosphate dehydrogenase) or PGK (phosphoglycerate kinase) and promoted their interaction with ATG3 or ATG6, which further attenuated the interactions of ATG3-ATG8e or ATG6-VPS34, respectively. Structural and mutational analyses revealed the mechanism of PA binding with GAPCs and PGK3, and that GAPCs or ATG8e competitively interacted with ATG3, and PGK3 or VPS34 competitively interacted with ATG6, at the same binding interface. These results elucidate the molecular mechanism of how PA inhibits autophagy through binding GAPC or PGK3 proteins and expand the understanding of the functional mode of PA, demonstrating the importance of phospholipids in plant autophagy and providing a new perspective for autophagy regulation by phospholipids. <b>Abbreviation:</b> ATG: autophagy-related; BiFC: bimolecular fluorescence complementation; co-IP: co-immunoprecipitation; Con A: concanamycin A; ER: endoplasmic reticulum; EZ: elongation zone; FRET-FLIM: fluorescence resonance energy transfer with fluorescence lifetime imaging microscopy; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GST: glutathione S-transferase; MDC: monodansylcadaverine; MZ: meristem zone; PA: phosphatidic acid; PAS: phagophore assembly site; PC: phosphatidylcholine; PE: phosphatidylethanolamine; PGK3: phosphoglycerate kinase; PtdIns3K: phosphatidylinositol 3-kinase; PLD: phospholipase D; TEM: transmission electron microscopy; TOR: target of rapamycin; VPS34: vacuolar protein sorting 34; WT: wild type; Y2H: yeast two-hybrid.
DOI: 10.6084/m9.figshare.19361756.v1
title: Phosphatidic acid suppresses autophagy through competitive inhibition by binding GAPC (glyceraldehyde-3-phosphate dehydrogenase) and PGK (phosphoglycerate kinase) proteins

description: Macroautophagy/autophagy is a finely-regulated process in which cytoplasm encapsulated within transient organelles termed autophagosomes is delivered to lysosomes or vacuoles for degradation. Phospholipids, particularly phosphatidic acid (PA) that functions as a second messenger, play crucial and differential roles in autophagosome formation; however, the underlying mechanism remains largely unknown. Here we demonstrated that PA inhibits autophagy through competitive inhibition of the formation of ATG3 (autophagy-related)-ATG8e and ATG6-VPS34 (vacuolar protein sorting 34) complexes. PA bound to GAPC (glyceraldehyde-3-phosphate dehydrogenase) or PGK (phosphoglycerate kinase) and promoted their interaction with ATG3 or ATG6, which further attenuated the interactions of ATG3-ATG8e or ATG6-VPS34, respectively. Structural and mutational analyses revealed the mechanism of PA binding with GAPCs and PGK3, and that GAPCs or ATG8e competitively interacted with ATG3, and PGK3 or VPS34 competitively interacted with ATG6, at the same binding interface. These results elucidate the molecular mechanism of how PA inhibits autophagy through binding GAPC or PGK3 proteins and expand the understanding of the functional mode of PA, demonstrating the importance of phospholipids in plant autophagy and providing a new perspective for autophagy regulation by phospholipids. <b>Abbreviation:</b> ATG: autophagy-related; BiFC: bimolecular fluorescence complementation; co-IP: co-immunoprecipitation; Con A: concanamycin A; ER: endoplasmic reticulum; EZ: elongation zone; FRET-FLIM: fluorescence resonance energy transfer with fluorescence lifetime imaging microscopy; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GST: glutathione S-transferase; MDC: monodansylcadaverine; MZ: meristem zone; PA: phosphatidic acid; PAS: phagophore assembly site; PC: phosphatidylcholine; PE: phosphatidylethanolamine; PGK3: phosphoglycerate kinase; PtdIns3K: phosphatidylinositol 3-kinase; PLD: phospholipase D; TEM: transmission electron microscopy; TOR: target of rapamycin; VPS34: vacuolar protein sorting 34; WT: wild type; Y2H: yeast two-hybrid.
DOI: 10.6084/m9.figshare.19354996
title: Targeting lipophagy in macrophages improves repair in multiple sclerosis

description: Foamy macrophages containing abundant intracellular myelin remnants are an important pathological hallmark of multiple sclerosis. Reducing the intracellular lipid burden in foamy macrophages is considered a promising therapeutic strategy to induce a phagocyte phenotype that promotes central nervous system repair. Recent research from our group showed that sustained intracellular accumulation of myelin-derived lipids skews these phagocytes toward a disease-promoting and more inflammatory phenotype. Our data now demonstrate that disturbed lipophagy, a selective form of autophagy that helps with the degradation of lipid droplets, contributes to the induction of this phenotype. Stimulating autophagy using the natural disaccharide trehalose reduced the lipid load and inflammatory phenotype of myelin-laden macrophages. Importantly, trehalose was able to boost remyelination in the <i>ex vivo</i> brain slice model and the <i>in vivo</i> cuprizone-induced demyelination model. In summary, our results provide a molecular rationale for impaired metabolism of myelin-derived lipids in macrophages, and identify lipophagy induction as a promising treatment strategy to promote remyelination. <b>Abbreviations:</b> Baf: bafilomycin a1; BMDM: bone marrow-derived macrophage; CD68: CD68 antigen; CNS: central nervous system; LD: lipid droplet; LIPE/HSL: lipase, hormone sensitive; LPS: lipopolysaccharide; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; MBP: myelin basic protein; MGLL: monoglyceride lipase; MS: multiple sclerosis; NO: nitric oxide; NOS2/iNOS: nitric oxide synthase 2, inducible; ORO: oil red o; PNPLA2: patatin-like phospholipase domain containing 2; PLIN2: perilipin 2; TEM: transmission electron microscopy; TFEB: transcription factor EB; TOH: trehalose.
DOI: 10.15129/74ad4a0a-b8d6-476e-9525-dd6d293e27a7
title: Rotating Disk Electrode (RDE) & UoS Disk Origin Files with Modelling Results

description: Origin files with the analysis of modelling results obtained by the RDE and scaled-up UoS disk models created in COMSOL Multiphysics for the project.
DOI: 10.5281/zenodo.7274507
title: List of Paris Bibles in the World

description: This dataset was built in the context of the Paris Bible Project (https://parisbible.github.io/). It lists libraries, archives and museums holding manuscripts of medieval Latin Bibles known as Paris Bibles, as well as relevant metadata.
DOI: 10.5281/zenodo.7274506
title: List of Paris Bibles in the World

description: This dataset was built in the context of the Paris Bible Project (https://parisbible.github.io/). It lists libraries, archives and museums holding manuscripts of medieval Latin Bibles known as Paris Bibles, as well as relevant metadata.
DOI: 10.5066/p9h9m79k
title: Genetically informed seed transfer zones for Astragalus lonchocarpus, Cleome serrulata, and Heliomeris multiflora across the Colorado Plateau and adjacent regions

description: These data were compiled to provide seed transfer and native plant materials development guidance to managers and practitioners across the Colorado Plateau and in adjacent regions. This data release contains empirical seed transfer zones derived from molecular genetic data for Cleome serrulata (syn. Peritoma serrulata), Heliomeris multiflora, and Astragalus lonchocarpus. These species show distinct population structure (i.e., genetic differentiation) across their ranges; as such, seed transfer zones reflect both patterns of genetic differentiation and information on each species' unique adaptations to climatic gradients. These shapefile data may support successful restoration outcomes if, for example, seed transfer follows seed transfer zones depicted herein and/or composite seed strategies for native plant materials development utilize seed transfer zones when determining which seed accessions may be combined. The ultimate goal of these seed transfer zones is to protect natural patterns of genetic variation and maximize (or at least better understand) species' adaptations to local environmental conditions. This work was funded by the Bureau of Land Management's Colorado Plateau Native Plant Program.
DOI: 10.6084/m9.figshare.21299958.v2
title: Depth data

description: HD NLOS depth maps were captured by TOF camera using relay wall of polypropylene plastic plate, PMMA plate and ceramic tile. <strong>See readme.xls for file descriptions.</strong>
DOI: 10.6084/m9.figshare.21440424.v1
title: Luminex Corporation_Amnis_ISEVxTech_DATA.zip

description: <strong>ISEVxTech rEV Characterization Study</strong> The purpose of the study is to highlight the utility that each assay/platform can provide for the research community and demonstrate what is achievable by the manufacturer. It is clear from the EV literature that orthogonal measurements of EVs is recommended and it is our aim to demonstrate the concordance and utility of data acquired from different platforms that work in complementary ways. Simultaneously, the organizers are aiming to promote reporting transparency, along with standard data analysis and reporting. This study will kick-start an open ISEV Task Force standardization study, with the sponsor company data setting a benchmark for their platforms / assays. <br> <strong>This data was acquired in CellStream and ImageStream imaging flow cytometry systems using recombinant GFP-EVs.</strong> <br> <strong>Copyright 2022 Luminex Corporation, a DiaSorin Company. For research use only. </strong>
DOI: 10.6084/m9.figshare.21454497
title: Luminex Corporation_Amnis_ISEVxTech_raw calibrated FCS files

description: <strong>Files are now part of Luminex ISEVxTech data</strong>
DOI: 10.6084/m9.figshare.21454497.v3
title: Luminex Corporation_Amnis_ISEVxTech_raw calibrated FCS files

description: <strong>ISEVxTech rEV Characterization Study</strong> The purpose of the study is to highlight the utility that each assay/platform can provide for the research community and demonstrate what is achievable by the manufacturer. It is clear from the EV literature that orthogonal measurements of EVs is recommended and it is our aim to demonstrate the concordance and utility of data acquired from different platforms that work in complementary ways. Simultaneously, the organizers are aiming to promote reporting transparency, along with standard data analysis and reporting. This study will kick-start an open ISEV Task Force standardization study, with the sponsor company data setting a benchmark for their platforms / assays. <br> <strong>This data was acquired in CellStream and ImageStream imaging flow cytometry systems using recombinant GFP-EVs. This data set contains raw calibrated data. Calibration performed in FCS Express.</strong> <br> <strong>Copyright 2022 Luminex Corporation, a DiaSorin Company. For research use only. </strong>
DOI: 10.6084/m9.figshare.21454497.v4
title: Luminex Corporation_Amnis_ISEVxTech_raw calibrated FCS files

description: <strong>Files are now part of Luminex ISEVxTech data</strong>
DOI: 10.25452/figshare.plus.19629864.v1
title: RNA-seq Titration Results supporting "Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously"

description: This data accompanies the manuscript "Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously" by Foltz, Taroni, and Greene. Please refer to our github page. The file contains all results and outputs from the analysis pipeline as well as intermediate files (including models and normalized data) from one repeat (seed 3274). Abstract: Large compendia of gene expression data have proven valuable for the discovery of novel biological relationships. Historically, the majority of available RNA assays were run on microarray, while RNA-seq has become the platform of choice for many new experiments. The data structure and distributions between the platforms differ, making it challenging to combine them. Here we perform supervised and unsupervised machine learning evaluations, as well as differential expression analyses, to assess which normalization methods are best suited for combining microarray and RNA-seq data. We find that quantile and Training Distribution Matching normalization allow for supervised and unsupervised model training on microarray and RNA-seq data simultaneously. Nonparanormal normalization and z-scores are also appropriate for some applications, including differential expression analysis. We demonstrate that it is possible to perform effective cross-platform normalization and combine microarray and RNA-seq data for machine learning applications.
DOI: 10.5066/p9l4gtqx
title: Impervious Land Cover Raster Derived from the National Land Cover Dataset (NLCD) 2019 for South Carolina StreamStats

description: In cooperation with the South Carolina Department of Transportation, the U.S. Geological Survey prepared a geospatial raster dataset describing impervious surface in the SC StreamStats study area derived from the 30m resolution National Land Cover Dataset (NLCD) 2019. This layer, which covers the SC StreamStats study area, has been resampled from the source resolution to a scale of 30ft pixels and reprojected to the common projection of the other project data layers (SC State Plane NAD 1983 International Feet WKID 2273). It will be served as part of the SC StreamStats application (https://streamstats.usgs.gov) to describe delineated watersheds. The StreamStats application provides access to spatial analytical tools that are useful for water-resources planning and management, and for engineering and design purposes. The map-based interface can be used to delineate watershed areas, get basin characteristics and estimates of flow statistics, and more.
DOI: 10.15129/b505a527-7d51-4343-9cbc-8d964301ea27
title: Radius Vane Origin Files with Modelling Results

description: Origin files with the analysis of modelling results obtained by the Radius vane models created in COMSOL Multiphysics. Access to data restrcited due to Commercial constraints.
DOI: 10.6084/m9.figshare.21460026
title: ijms-Pericat-alldata.xlsx

description: Data from manuscript " Antiviral and Anti-Inflammatory Activities of Fluoxetine in a SARS-CoV-2 Infection Mouse Model" by Péricat David et al.
DOI: 10.6084/m9.figshare.21460026.v1
title: ijms-Pericat-alldata.xlsx

description: Data from manuscript " Antiviral and Anti-Inflammatory Activities of Fluoxetine in a SARS-CoV-2 Infection Mouse Model" by Péricat David et al.
DOI: 10.15129/29ac5d6e-9bed-4cbd-bffa-9865459a7739
title: Rotating Disk Electrode (RDE) Electrochemical Impedance Spectroscopy Experiments

description: This dataset contains raw electrochemical impedance spectroscopy data collected for a 1.000 Hz - 20000.00 Hz range of frequency, used for linear sweep voltammetry data correction in terms of ohmic drop.
DOI: 10.15129/681219d3-9912-4659-9406-50ca886a0321
title: Rotating Disk Electrode (RDE) Cyclic Voltammetry Experiments

description: Cyclic voltammetry measurements under various scan rates and stagnant conditions conducted to determine the electrochemical stability of the system.
DOI: 10.15129/3ebb0d68-637b-4451-bf45-372237dcd334
title: Rotating Disk Electrode (RDE) Deposition Experiments

description: Photographs of the nickel deposits developed in the laboratory-scale rotating disk electrode setup at various current densities, at 50 C and 1500 rpm. Refer to the "CV_Experiments" log under the "Rotating Disk Electrode (RDE) Experiments Logs" entry for detailed experimental parameters.
DOI: 10.6084/m9.figshare.21407213
title: Analysis of the complete plastidial genome of the newly highland papaya <i>Vasconcellea carvalhoae</i> (Caricaceae) from Peru

description: Especially in South American Andean communities, <i>Vasconcellea carvalhoae</i> D. Tineo & D.E. Bustamante 2020 is a significant highland papaya with agronomic promise. High-throughput sequencing of the holotype specimen of <i>V. carvalhoae</i> from Peru (KUELAP227) resulted in the assembly of its complete plastid genome (GenBank accession number ON764441). The plastid genome of this highland papaya is 158,723 bp and contains 130 genes. This plastid genome is similar in length, content, and organization to other members of Caricaceae, except for the absence of the pseudogene infA. Phylogenetic analyses of <i>V. carvalhoae</i> support its sistership to <i>V. pubescens</i>.
DOI: 10.6084/m9.figshare.21407213.v1
title: Analysis of the complete plastidial genome of the newly highland papaya <i>Vasconcellea carvalhoae</i> (Caricaceae) from Peru

description: Especially in South American Andean communities, <i>Vasconcellea carvalhoae</i> D. Tineo & D.E. Bustamante 2020 is a significant highland papaya with agronomic promise. High-throughput sequencing of the holotype specimen of <i>V. carvalhoae</i> from Peru (KUELAP227) resulted in the assembly of its complete plastid genome (GenBank accession number ON764441). The plastid genome of this highland papaya is 158,723 bp and contains 130 genes. This plastid genome is similar in length, content, and organization to other members of Caricaceae, except for the absence of the pseudogene infA. Phylogenetic analyses of <i>V. carvalhoae</i> support its sistership to <i>V. pubescens</i>.
DOI: 10.6084/m9.figshare.21407268
title: The chloroplast genome of <i>Spiraea thunbergii</i> (Rosaceae)

description: <i>Spiraea thunbergii</i> (<i>S. thunbergia</i>) is a very common ornamental shrub in the garden, with important horticultural and economic value. In this study, we assembled the complete chloroplast (cp) genome of <i>S. thunbergia</i> into a typical quadripartite structure. The genome size and GC content of the <i>S. thunbergia</i> cp genome are 155,922 bp and 36.76%, respectively. It contains 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The phylogenetic tree supported that <i>S. thunbergii</i> is closely related to <i>Spiraea mongolica</i> in the Rosaceae family. The study will provide significant genomic resource for elucidating the phylogenetic relationship of <i>Spiraea</i>.
DOI: 10.6084/m9.figshare.21407268.v1
title: The chloroplast genome of <i>Spiraea thunbergii</i> (Rosaceae)

description: <i>Spiraea thunbergii</i> (<i>S. thunbergia</i>) is a very common ornamental shrub in the garden, with important horticultural and economic value. In this study, we assembled the complete chloroplast (cp) genome of <i>S. thunbergia</i> into a typical quadripartite structure. The genome size and GC content of the <i>S. thunbergia</i> cp genome are 155,922 bp and 36.76%, respectively. It contains 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The phylogenetic tree supported that <i>S. thunbergii</i> is closely related to <i>Spiraea mongolica</i> in the Rosaceae family. The study will provide significant genomic resource for elucidating the phylogenetic relationship of <i>Spiraea</i>.
DOI: 10.15129/70f02f4d-c017-408e-aa4f-3489c0726f05
title: Rotating Disk Electrode (RDE) Linear Sweep Voltammetry Experiments

description: Linear sweep voltammetry measurements under various scan rates, agitation conditions and applied current densities conducted n the laboratory-scale rotating disk electrode setup to determine the electrochemical behaviour of the system. Measurements for both nickel and nickel-cobalt systems are included. Refer to the "LSV_Experiments" log under the "Rotating Disk Electrode (RDE) Experiments Logs" entry for detailed experimental parameters.
DOI: 10.5517/ccdc.csd.ccwkxfr
title: CCDC 821575: Experimental Crystal Structure Determination

description: Related Article: Vladimir Sharutin|2016|CSD Communication|||
description: Related Article: Vladimir Viktorovich Sharutin, Olga Konstantinovna Sharutina, Vladislav Stanislavovich Senchurin|2012|Yuzhno-Ural'skii Gosudarst. Univ.Vestn. Ser.Khim.|9|46-24|
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/ccy99l3
title: CCDC 872885: Experimental Crystal Structure Determination

description: Related Article: T.V.Levenets,V.O.Koz'minykh,E.N.Koz'minykh|2013|Izv.Vyssh.Uchebn.Zaved.,Khim.Khim.Tek.||22|
description: Related Article: T.V.Levenets,V.O.Koz’minykh.A.O.Tolstikova|2013|Zh.Strukt.Khim.|54|192|
description: Related Article: Tatyana Vasilievna Levenets, Vladislav Olegovich Kozminykh, Alexandra Olegovna Tolstikova|2012|Yuzhno-Ural'skii Gosudarst. Univ.Vestn. Ser.Khim.|9|32-24|
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.cc115tgh
title: CCDC 958906: Experimental Crystal Structure Determination

description: Related Article: Anastasia Vladimirovna Rybakova, Pavel Aleksandrovich Slepukhin, Dmitry Gymnanovich Kim|2013|Yuzhno-Ural'skii Gosudarst. Univ.Vestn. Ser.Khim.|5|45-4|
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.