cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25582/data.2023-01.2712402/2305018
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2710680/2305019
title: Data for EMSL Project 51287 from January 2023
DOI: 10.6084/m9.figshare.22802858
title: Gene Signatures for myeloid and T_NK

description: File “Gene Signatures for myeloid and T_NK” provided gene signatures curated from literature to evaluate functions of myeloid and T/NK subclusters.
DOI: 10.25582/data.2023-02.2733070/2305020
title: Data for EMSL Project 51287 from February 2023
DOI: 10.6084/m9.figshare.14414256
title: Complexity of <i>Gaeumannomyces</i> species causing take-all root rot of St. Augustinegrass in Texas

description: <i>Gaeumannomyces graminis</i> var. <i>graminis</i> (<i>Ggg</i>) has been the etiological agent of take-all root rot (TARR) in St. Augustinegrass (<i>Stenotaphrum secundatum</i>) and root decline of the other warm-season turfgrasses. Seventy-five <i>Ggg</i> isolates were obtained from St. Augustinegrass in central and east Texas. Evaluation of colony morphologies on potato dextrose agar (PDA) within 2 wk and follow-up multilocus phylogenic analyses revealed three phenotypic groups associated with different <i>Gaeumannomyces</i> species: (i) <i>G. floridanus</i>, highly melanized with round colony formation; (ii) <i>G. arxii</i>, none to slightly melanized with round colony formation; and (iii) <i>G. graminicola</i>, highly melanized with irregular colony formation. Further examination with representative isolates from each group revealed that their phenotypic characterizations supported the distinctive genetic groups within <i>Ggg</i> associated with St. Augustinegrass TARR. <i>Gaeumannomyces floridanus</i> isolates grew faster at warmer temperature (30 C) than <i>G. arxii</i> or <i>G. graminicola</i>. Pathogenicity assays using rice seedlings indicated that <i>G. floridanus</i> was more aggressive in disease symptom development than <i>G. arxii</i> or <i>G. graminicola</i>. A multilocus phylogeny reconstruction supported that most of <i>Gaeumannomyces</i> isolates tested in this study were separated into three phylogenetically distinct groups: <i>G. floridanus, G. arxii</i>, and <i>G</i>. graminicola. The resolution of intravarietal complexities of causal fungi of TARR is important for proper diagnostics and management strategies for TARR in St. Augustinegrass and other root-decline diseases in warm-season turfgrasses.
DOI: 10.25582/data.2023-01.2706116/2305021
title: Data for EMSL Project 51287 from January 2023
DOI: 10.6084/m9.figshare.14414256.v1
title: Complexity of <i>Gaeumannomyces</i> species causing take-all root rot of St. Augustinegrass in Texas

description: <i>Gaeumannomyces graminis</i> var. <i>graminis</i> (<i>Ggg</i>) has been the etiological agent of take-all root rot (TARR) in St. Augustinegrass (<i>Stenotaphrum secundatum</i>) and root decline of the other warm-season turfgrasses. Seventy-five <i>Ggg</i> isolates were obtained from St. Augustinegrass in central and east Texas. Evaluation of colony morphologies on potato dextrose agar (PDA) within 2 wk and follow-up multilocus phylogenic analyses revealed three phenotypic groups associated with different <i>Gaeumannomyces</i> species: (i) <i>G. floridanus</i>, highly melanized with round colony formation; (ii) <i>G. arxii</i>, none to slightly melanized with round colony formation; and (iii) <i>G. graminicola</i>, highly melanized with irregular colony formation. Further examination with representative isolates from each group revealed that their phenotypic characterizations supported the distinctive genetic groups within <i>Ggg</i> associated with St. Augustinegrass TARR. <i>Gaeumannomyces floridanus</i> isolates grew faster at warmer temperature (30 C) than <i>G. arxii</i> or <i>G. graminicola</i>. Pathogenicity assays using rice seedlings indicated that <i>G. floridanus</i> was more aggressive in disease symptom development than <i>G. arxii</i> or <i>G. graminicola</i>. A multilocus phylogeny reconstruction supported that most of <i>Gaeumannomyces</i> isolates tested in this study were separated into three phylogenetically distinct groups: <i>G. floridanus, G. arxii</i>, and <i>G</i>. graminicola. The resolution of intravarietal complexities of causal fungi of TARR is important for proper diagnostics and management strategies for TARR in St. Augustinegrass and other root-decline diseases in warm-season turfgrasses.
DOI: 10.25582/data.2023-01.2710658/2305022
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2709516/2305023
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2708959/2305024
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2711429/2305025
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2708735/2305026
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2707535/2305027
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-02.2732617/2305028
title: Data for EMSL Project 51287 from February 2023
DOI: 10.25582/data.2023-01.2710238/2305029
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2710466/2305030
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2710661/2305031
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2706019/2305032
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2708628/2305033
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2710817/2305034
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2711119/2305035
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-02.2733327/2305036
title: Data for EMSL Project 51287 from February 2023
DOI: 10.25582/data.2023-01.2712146/2305037
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2707718/2305038
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2709679/2305039
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2710138/2305040
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2710916/2305041
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2712244/2305042
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2709687/2305043
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2710687/2305044
title: Data for EMSL Project 51287 from January 2023
DOI: 10.6084/m9.figshare.14938760
title: An innovative, highly efficient and expertise-free mechanism reduction method: important species identification through species’ participation in element fluxes

description: An innovative kinetic mechanism reduction method, Species’ Participation in Element Fluxes (SPEF), is developed in this study. It utilises species’ participation in element fluxes to evaluate the importance of the species during the combustion process. The SPEF method has two main benefits: (1) it targets at C, H and O elements instead of pre-selected target species and has only one variable threshold on species importance, which makes it feasible to obtain satisfactory skeletal mechanisms for researchers even without any mechanism reduction expertise; (2) it shows significantly low time complexity, which helps to achieve high computational efficiency in the reduction process. Three mechanisms with different sizes were reduced and utilised to investigate the reduction capability of the SPEF method. It has been observed that the reduction performance of the SPEF method is competitive with other widely used directed relation graph with error propagation (DRGEP), path flux analysis (PFA) and global pathway selection (GPS) methods. The effectiveness of the SPEF method was further demonstrated by extensively validating the SPEF-reduced mechanisms against the detailed mechanisms. In addition to the application to static reduction, this method could also be easily utilised for dynamic reduction to save computational efforts in reactive flow simulation while retaining satisfactory accuracy. An example was given by integrating the SPEF method into the KIVA4 code package to dynamically reduce chemical mechanisms in 3-D engine simulations. It has been proved that even for 3-D engine simulations with a highly compact mechanism, computational cost can still be saved in a considerable scale using the SPEF method.
DOI: 10.25582/data.2023-01.2706051/2305045
title: Data for EMSL Project 51287 from January 2023
DOI: 10.6084/m9.figshare.14938760.v1
title: An innovative, highly efficient and expertise-free mechanism reduction method: important species identification through species’ participation in element fluxes

description: An innovative kinetic mechanism reduction method, Species’ Participation in Element Fluxes (SPEF), is developed in this study. It utilises species’ participation in element fluxes to evaluate the importance of the species during the combustion process. The SPEF method has two main benefits: (1) it targets at C, H and O elements instead of pre-selected target species and has only one variable threshold on species importance, which makes it feasible to obtain satisfactory skeletal mechanisms for researchers even without any mechanism reduction expertise; (2) it shows significantly low time complexity, which helps to achieve high computational efficiency in the reduction process. Three mechanisms with different sizes were reduced and utilised to investigate the reduction capability of the SPEF method. It has been observed that the reduction performance of the SPEF method is competitive with other widely used directed relation graph with error propagation (DRGEP), path flux analysis (PFA) and global pathway selection (GPS) methods. The effectiveness of the SPEF method was further demonstrated by extensively validating the SPEF-reduced mechanisms against the detailed mechanisms. In addition to the application to static reduction, this method could also be easily utilised for dynamic reduction to save computational efforts in reactive flow simulation while retaining satisfactory accuracy. An example was given by integrating the SPEF method into the KIVA4 code package to dynamically reduce chemical mechanisms in 3-D engine simulations. It has been proved that even for 3-D engine simulations with a highly compact mechanism, computational cost can still be saved in a considerable scale using the SPEF method.
DOI: 10.6084/m9.figshare.19657367
title: Plin5 inhibits proliferation and migration of vascular smooth muscle cell through interacting with PGC-1α following vascular injury

description: Abnormal proliferation and migration of vascular smooth muscle cell (VSMC) is a hallmark of vascular neointima hyperplasia. Perilipin 5 (Plin5), a regulator of lipid metabolism, is also confirmed to be involved in vascular disorders, such as microvascular endothelial dysfunction and atherosclerosis. To investigate the regulation and function of plin5 in the phenotypic alteration of VSMC, -an animal model of vascular intima hyperplasia was established in C57BL/6 J and <i>Plin5</i> knockdown <i>(Plin5</i><sup>±</sup>) mice by wire injure. Immunohistochemical staining was used to analyze neointima hyperplasia in artery. Ki-67, dihydroethidium immunofluorescence staining and wound healing assay were used to measure proliferation, reactive oxygen species (ROS) generation and migration of VSMC, respectively. Plin5 was downregulated in artery subjected to vascular injury and in VSMC subjected to platelet-derived growth factor (PDGF)-BB. Plin5 knockdown led to accelerated neointima hyperplasia, excessive proliferation and migration of VSMC after injury. In vitro, we observed increased ROS content in VSMC isolated from <i>Plin5</i><sup>±</sup> mice. Antioxidative N-acetylcysteine (NAC) inhibited VSMC proliferation and migration induced by PDGF-BB or plin5 knockdown. More importantly, plin5-peroxlsome proliferator-activated receptor-γ coactivator (PGC)-1α interaction was also attenuated in VSMC after knockdown of plin5. Overexpression of PGC-1α suppressed PDGF-BB-induced ROS generation, proliferation, and migration in VSMC isolated from <i>Plin5</i><sup>±</sup> mice. These data suggest that plin5 serves as a potent regulator of VSMC proliferation, migration, and neointima hyperplasia by interacting with PGC-1α and affecting ROS generation.
DOI: 10.6084/m9.figshare.19657367.v1
title: Plin5 inhibits proliferation and migration of vascular smooth muscle cell through interacting with PGC-1α following vascular injury

description: Abnormal proliferation and migration of vascular smooth muscle cell (VSMC) is a hallmark of vascular neointima hyperplasia. Perilipin 5 (Plin5), a regulator of lipid metabolism, is also confirmed to be involved in vascular disorders, such as microvascular endothelial dysfunction and atherosclerosis. To investigate the regulation and function of plin5 in the phenotypic alteration of VSMC, -an animal model of vascular intima hyperplasia was established in C57BL/6 J and <i>Plin5</i> knockdown <i>(Plin5</i><sup>±</sup>) mice by wire injure. Immunohistochemical staining was used to analyze neointima hyperplasia in artery. Ki-67, dihydroethidium immunofluorescence staining and wound healing assay were used to measure proliferation, reactive oxygen species (ROS) generation and migration of VSMC, respectively. Plin5 was downregulated in artery subjected to vascular injury and in VSMC subjected to platelet-derived growth factor (PDGF)-BB. Plin5 knockdown led to accelerated neointima hyperplasia, excessive proliferation and migration of VSMC after injury. In vitro, we observed increased ROS content in VSMC isolated from <i>Plin5</i><sup>±</sup> mice. Antioxidative N-acetylcysteine (NAC) inhibited VSMC proliferation and migration induced by PDGF-BB or plin5 knockdown. More importantly, plin5-peroxlsome proliferator-activated receptor-γ coactivator (PGC)-1α interaction was also attenuated in VSMC after knockdown of plin5. Overexpression of PGC-1α suppressed PDGF-BB-induced ROS generation, proliferation, and migration in VSMC isolated from <i>Plin5</i><sup>±</sup> mice. These data suggest that plin5 serves as a potent regulator of VSMC proliferation, migration, and neointima hyperplasia by interacting with PGC-1α and affecting ROS generation.
DOI: 10.25582/data.2023-02.2732239/2305046
title: Data for EMSL Project 51287 from February 2023
DOI: 10.25582/data.2023-01.2708200/2305047
title: Data for EMSL Project 51287 from January 2023
DOI: 10.6084/m9.figshare.23851695
title: #GlobalCollembola - full sample-level database

description: Here, we present a global, spatially-explicit database on springtail communities that includes 249,912 occurrences from 44,999 samples and 2,990 sites. These data are mainly raw sample-level records at the species level collected predominantly from private archives of the authors that were quality-controlled and taxonomically-standardised. Despite covering all continents, most of the sample-level data come from the European continent (82.5% of all samples) and represent four habitats: woodlands (57.4%), grasslands (14.0%), agrosystems (13.7%) and scrublands (9.0%). We included sampling by soil layers, and across seasons and years, representing temporal and spatial within-site variation in springtail communities. We also provided data use and sharing guidelines and R code to facilitate the use of the database by other researchers. The database will be further expanded to include underrepresented regions and linked with trait data.
DOI: 10.25582/data.2023-02.2733153/2305048
title: Data for EMSL Project 51287 from February 2023
DOI: 10.25582/data.2023-02.2732224/2305049
title: Data for EMSL Project 51287 from February 2023
DOI: 10.25582/data.2023-02.2732628/2305050
title: Data for EMSL Project 51287 from February 2023
DOI: 10.25582/data.2023-01.2709549/2305051
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2710144/2305052
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2706033/2305053
title: Data for EMSL Project 51287 from January 2023
DOI: 10.6084/m9.figshare.13890277
title: The synaptic marker neurogranin as a disease state biomarker in Alzheimer’s disease: a systematic review and meta-analysis

description: <b>Objective:</b> Synaptic degeneration is the pathologic foundation of cognitive decline in the Alzheimer’s disease (AD) continuum. We aimed to determine whether cerebrospinal fluid (CSF) synaptic marker neurogranin (Ng) is a disease state or a disease stage biomarker in the AD continuum. <b>Methods:</b> Studies comparing CSF Ng levels among AD, mild cognitive impairment (MCI) and healthy participants were included. Studies were eligible if the correlation between CSF Ng levels and Mini-Mental Status Examination (MMSE) scores was investigated. <b>Results:</b> Twenty-one studies met our inclusion criteria (<i>n</i> = 4515). The magnitude of effect sizes was more apparent in AD (standardized mean difference [SMD] = 1.72; 95% confidence interval [CI] = 1.23–2.22), than in MCI (SMD = 0.82; 95% CI = 0.29–1.34) compared to control populations. These results suggest that CSF Ng can discriminate AD and MCI from control populations, implying that synaptic degeneration worsens as patients progress from MCI to AD. However, there was a very weak correlation between CSF Ng levels and MMSE scores (<i>r</i> = −0.15; 95% CI = −0.21–-0.08) among the whole populations, suggesting that an increment of CSF Ng is best considered a biological evidence of disease state in the AD continuum. <b>Conclusion:</b> Our study provides evidence that the synaptic marker CSF Ng can be used as a disease state biomarker for the AD continuum. Because synaptic degeneration is a distinct pathologic event from amyloid deposition and neurofibrillary tangle formation, CSF Ng may provide an important supplementation to the AT(N) biomarker system to reveal the sequence of neuropathology.
DOI: 10.25582/data.2023-01.2707193/2305054
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2708733/2305055
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2710871/2305056
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2710899/2305057
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2711069/2305058
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2709547/2305059
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2710192/2305060
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2706142/2305061
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-02.2733181/2305062
title: Data for EMSL Project 51287 from February 2023
DOI: 10.6084/m9.figshare.14414729
title: Supplemental Tables-Sleep Habit.pdf

description: Supplemental Tables for Sleep Habit of Women with Infertility
DOI: 10.25582/data.2023-01.2710679/2305063
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-02.2732542/2305064
title: Data for EMSL Project 51287 from February 2023
DOI: 10.25582/data.2023-01.2711139/2305065
title: Data for EMSL Project 51287 from January 2023
DOI: 10.6084/m9.figshare.19657694
title: An extraction from Trametes robiniophila Murr. (<i>Huaier</i>) inhibits non-small cell lung cancer proliferation via targeting to epidermal growth factor receptor

description: An extraction from Trametes robiniophila Murr. <i>(Huaier)</i> is a kind of natural fungus growing from the sophora japonica tree. <i>Huaier</i> is widely applied to cure the hepatocellular cancer (HCC). However, the medicinal fungus’ curative result on non-small-cell lung cancer (NSCLC) is not well elaborated. In this study, we applied <i>in vitro</i> experiments to study <i>Huaier’</i>s curative result on NSCLC. The potential <i>Huaier</i> targets were predicted using bioinformatics and validated by western blotting. We further elucidated the mechanism of <i>Huaier</i> targeting by molecular docking, kinase activity assay, CEllular Thermal Shift Assays (CETSAs). At last, <i>in vivo</i> curative result was verified further. <i>Huaier</i> weakened proliferation and promoted apoptosis of the NSCLC cell lines. According to bioinformatics, Epidermal Growth Factor Receptor (EGFR) may be the target of <i>Huaier</i>. Western blotting showed that <i>Huaier</i> can attenuate the activation of EGFR and we found that <i>Huaier</i> can dock to EGFR. <i>Huaier</i> significantly inhibited the tumor growth by weakening the expression of p-EGFR <i>in vivo</i>. This study offers a new idea for further understanding of <i>Huaier</i> and shows its potential as a therapeutic agent.
DOI: 10.6084/m9.figshare.19657694.v1
title: An extraction from Trametes robiniophila Murr. (<i>Huaier</i>) inhibits non-small cell lung cancer proliferation via targeting to epidermal growth factor receptor

description: An extraction from Trametes robiniophila Murr. <i>(Huaier)</i> is a kind of natural fungus growing from the sophora japonica tree. <i>Huaier</i> is widely applied to cure the hepatocellular cancer (HCC). However, the medicinal fungus’ curative result on non-small-cell lung cancer (NSCLC) is not well elaborated. In this study, we applied <i>in vitro</i> experiments to study <i>Huaier’</i>s curative result on NSCLC. The potential <i>Huaier</i> targets were predicted using bioinformatics and validated by western blotting. We further elucidated the mechanism of <i>Huaier</i> targeting by molecular docking, kinase activity assay, CEllular Thermal Shift Assays (CETSAs). At last, <i>in vivo</i> curative result was verified further. <i>Huaier</i> weakened proliferation and promoted apoptosis of the NSCLC cell lines. According to bioinformatics, Epidermal Growth Factor Receptor (EGFR) may be the target of <i>Huaier</i>. Western blotting showed that <i>Huaier</i> can attenuate the activation of EGFR and we found that <i>Huaier</i> can dock to EGFR. <i>Huaier</i> significantly inhibited the tumor growth by weakening the expression of p-EGFR <i>in vivo</i>. This study offers a new idea for further understanding of <i>Huaier</i> and shows its potential as a therapeutic agent.
DOI: 10.25582/data.2023-01.2707717/2305066
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2711370/2305067
title: Data for EMSL Project 51287 from January 2023
DOI: 10.34740/kaggle/dsv/7629025
title: CIDII Dataset
DOI: 10.25582/data.2023-01.2711147/2305068
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2709544/2305069
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2710324/2305070
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2710633/2305071
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2707186/2305072
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2710244/2305073
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2711035/2305074
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-02.2732510/2305075
title: Data for EMSL Project 51287 from February 2023
DOI: 10.25582/data.2023-01.2710811/2305076
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2710604/2305077
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2710722/2305078
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2712374/2305079
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2710770/2305080
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2711293/2305081
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2706068/2305082
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2706691/2305083
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2709973/2305084
title: Data for EMSL Project 51287 from January 2023