cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5286/isis.e.rb1920434-1
title: Quantum dots with deuterated oleic acid shells and their functionalisation with singlet fission ligands

description: Our research aims to develop plastic films that change the colour of the light that passes through them, not by absorbing certain wavelengths of light, as a simple colour filter would, but by converting light of one wavelength to another without losing any energy. Such a film, applied to a silicon solar cell, could make it up to 30% more efficient. To do this we need to make semiconductor nanocrystals, coat them with a very thin layer of an organic semiconductor so the two materials are in molecular contact. Then we have to disperse these tiny composite nanoparticles in a clear plastic film, as evenly as possible and without clumping. Small angle neutron scattering allows to pick out the shapes of the composite nanoparticles and their component parts, and the way they interact each other, helping us to design routes to make these "photon multiplier" films.
DOI: 10.5286/isis.e.rb2000052-1
title: Elucidation of dynamic structural characteristics of γ-Na3PS4 plastic crystal through neutron-PDF

description: We aim to further clarify the atomic scale structure of a novel phase of the Na3PS4 solid ion conductor. This phase appears to possess ideal properties to be used as a solid electrolyte for applications such as next-generation batteries. These properties include superionic, liquid-like mobility of Na+ ions with extremely low resistance while maintaining a solid nature that can lead to solid-state batteries with increased safety and performance. Understanding the intricacies of this material can lead to fundamental advances in materials science as well as practical breakthroughs in battery technology.
DOI: 10.7284/107926
title: TSG (Thermosalinograph) data collected during research cruise MGL1216 using a Sea-Bird SBE-21 instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/107927
title: Winch data collected during research cruise MGL1216 using a Lebus CTD instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7477772
title: Data set for Belvedere et al., 2019. Late Jurassic globetrotters compared: A closer look at large and giant theropod tracks of North Africa and Europe. Journal of African Earth Sciences

description: Orginal 3D models (.ply) and point coulds of the tracks scaled at FL=1 m (.asc) used for the morphological comparisons in Belvedere et al., 2019. Late Jurassic globe trotters compared. A closer look at large and gigantic theropod tracks of North Africa and Europe. Journal of African Earth Sciences.
DOI: 10.7284/112220
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise MGL1218 using a Hawaii UHDAS instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/112218
title: Multibeam Echosounder data collected during research cruise MGL1218 using a Kongsberg EM122 instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7477751
title: Data from Ocean acidification and warming affect skeletal mineralization in a marine fish

description: Data set used for analyses
DOI: 10.7284/112219
title: Singlebeam Echosounder data collected during research cruise MGL1218 using a Knudsen 3260 instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7477715
title: Supplementary Material for: lncRNA MEG3 Suppresses the Tumorigenesis of Hemangioma by Sponging miR-494 and Regulating PTEN/ PI3K/AKT Pathway

description: <b><i>Background/Aims:</i></b> Dysregulation of long noncoding RNAs (lncRNAs) is associated with the proliferation and metastasis in a variety of cancers, of which lncRNA maternally expressed gene 3 (MEG3) has been indicated as a tumor suppressor in multiple malignancies. However, the underlying mechanisms by which MEG3 contributes to human hemangiomas (HAs) remain undetermined. <b><i>Methods:</i></b> qRT-PCR analysis was performed to examine the expression levels of MEG3 and VEGF in proliferating or involuting phase HAs. MTT, colony formation assay, flow cytometry analysis and a subcutaneous xenograft tumor model were conducted to assess the effects of MEG3 on the HAs tumorigenesis. The interaction between MEG3 and miRNAs or their downstream pathways was evidenced by bioinformatic analysis, luciferase report assays, RNA immunoprecipitation (RIP) assay. and Western blot analysis. <b><i>Results:</i></b> The expression of MEG3 was substantially decreased and had a negative correlation with VEGF expression in proliferating phase HAs, as compared with the involuting phase HAs and normal skin tissues. Ectopic expression of MEG3 suppressed cell proliferation, colony formation and induced cycle arrest <i>in vitro</i> and <i>in vivo</i>, followed by the downregulation of VEGF and cyclinD1, but knockdown of MEG3 reversed these effects. Furthermore, MEG3 was verified to act as a sponge of miR-494 in HAs cells, and miR-494 counteracted MEG3-caused anti-proliferative effects by regulating PTEN/PI3K/AKT pathway, and exhibited the negative correlation with MEG3 and PTEN expression in proliferating phase HAs. <b><i>Conclusion:</i></b> Our findings suggested that lncRNA MEG3 inhibited HAs tumorigenesis by sponging miR-494 and regulating PTEN/PI3K/AKT pathway.
DOI: 10.6084/m9.figshare.7477715.v1
title: Supplementary Material for: lncRNA MEG3 Suppresses the Tumorigenesis of Hemangioma by Sponging miR-494 and Regulating PTEN/ PI3K/AKT Pathway

description: <b><i>Background/Aims:</i></b> Dysregulation of long noncoding RNAs (lncRNAs) is associated with the proliferation and metastasis in a variety of cancers, of which lncRNA maternally expressed gene 3 (MEG3) has been indicated as a tumor suppressor in multiple malignancies. However, the underlying mechanisms by which MEG3 contributes to human hemangiomas (HAs) remain undetermined. <b><i>Methods:</i></b> qRT-PCR analysis was performed to examine the expression levels of MEG3 and VEGF in proliferating or involuting phase HAs. MTT, colony formation assay, flow cytometry analysis and a subcutaneous xenograft tumor model were conducted to assess the effects of MEG3 on the HAs tumorigenesis. The interaction between MEG3 and miRNAs or their downstream pathways was evidenced by bioinformatic analysis, luciferase report assays, RNA immunoprecipitation (RIP) assay. and Western blot analysis. <b><i>Results:</i></b> The expression of MEG3 was substantially decreased and had a negative correlation with VEGF expression in proliferating phase HAs, as compared with the involuting phase HAs and normal skin tissues. Ectopic expression of MEG3 suppressed cell proliferation, colony formation and induced cycle arrest <i>in vitro</i> and <i>in vivo</i>, followed by the downregulation of VEGF and cyclinD1, but knockdown of MEG3 reversed these effects. Furthermore, MEG3 was verified to act as a sponge of miR-494 in HAs cells, and miR-494 counteracted MEG3-caused anti-proliferative effects by regulating PTEN/PI3K/AKT pathway, and exhibited the negative correlation with MEG3 and PTEN expression in proliferating phase HAs. <b><i>Conclusion:</i></b> Our findings suggested that lncRNA MEG3 inhibited HAs tumorigenesis by sponging miR-494 and regulating PTEN/PI3K/AKT pathway.
DOI: 10.7284/112235
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise MGL1302 using a Hawaii UHDAS instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7477706
title: Supplementary Material for: Shikimic Acid Inhibits Osteoclastogenesis in Vivo and in Vitro by Blocking RANK/TRAF6 Association and Suppressing NF-κB and MAPK Signaling Pathways

description: <b><i>Background/Aims:</i></b> Bone homeostasis is associated with the balance between bone-resorbing osteoclasts and bone-forming osteoblasts. Unbalanced bone homeostasis as a result of reduced osteogenesis or excessive osteoclastogenesis can lead to disorders such as osteoporosis, Paget’s disease, and rheumatoid arthritis. Shikimic acid is a cyclohexanecarboxylic acid, reported to exhibit pharmacological properties including anti-inflammatory and antioxidant activities. However, its effects on bone homeostasis remain unknown. <b><i>Methods:</i></b> First, the <i>in vitro</i> MTT cell viability assay was performed. Tartrate-resistant acid phosphatase (TRAP) and actin ring formation assays, as well as immunofluorescence staining were then performed to evaluate osteoclastogenesis. Potential signaling pathways were characterized by western blotting and verified in overexpression experiments. Related factors were examined by western blotting, reverse transcription polymerase chain reaction, electrophoretic mobility shift assay, and co-immunoprecipitation. Ovariectomized mice were used for the <i>in vivo</i> study. <b><i>Results:</i></b> TRAP staining showed that shikimic acid significantly inhibited osteoclastogenesis and pit resorption in bone marrow monocytes and RAW264.7 cells, and actin ring formation assays showed that shikimic acid suppressed the bone resorption function of osteoclasts. Furthermore, shikimic acid inhibited the receptor activator of nuclear factor-κB RANK/tumor necrosis factor receptor-associated factor 6 (TRAF6) association, suppressed nuclear factor-κB and mitogen-activated protein kinase signaling pathways, and downregulated nuclear factor of activated T-cell cytoplasmic 1. The expression of osteoclastogenesis biomarkers, including TRAF6, calcitonin receptor, TRAP, cathepsin K, and matrix metalloproteinase-9, was inhibited. <i>In vivo,</i> shikimic acid also significantly ameliorated bone loss and prevented osteoclastogenesis in ovariectomized mice. <b><i>Conclusion:</i></b> Shikimic acid inhibited osteoclastogenesis and osteoclast function by blocking RANK ligand-induced recruitment of TRAF6, as well as downstream signaling pathways <i>in vitro</i>. Shikimic acid also reduced ovariectomy-induced osteoclastogenesis and bone loss <i>in vivo</i>.
DOI: 10.6084/m9.figshare.7477697
title: Supplementary Material for: The Motion of An <b><i>Inv</i></b> Nodal Cilium: a Realistic Model Revealing Dynein-Driven Ciliary Motion with Microtubule Mislocalization

description: <b><i>Background/Aims:</i></b> Nodal cilia that rotate in the ventral node play an important role in establishing left-right asymmetry during embryogenesis; however, <i>inv</i> mutant cilia present abnormal movement and induce laterality defects. The mechanism of their motility, which is regulated by dynein activation and microtubule arrangement, has not been fully understood. This study analyzed the dynein-triggered ciliary motion in the abnormal ultrastructure of the <i>inv</i> mutant, aiming to quantitatively evaluate the influence of microtubule mislocalization on the movement of the cilium. <b><i>Methods:</i></b> We established a realistic 3-D model of an <i>inv</i> mutant cilium with an ultrastructure based on tomographic datasets generated by ultra-high voltage electron microscopy. The time-variant activation of the axonemal dynein force was simulated by pairs of point loads and embedded at dynein-mounted positions between adjacent microtubule doublets in this mathematical model. Utilizing the finite element method and deformable grid, the motility of the mutant cilium that is induced by various dynein activation hypotheses was investigated and compared to experimental observation. <b><i>Results:</i></b> The results indicate that for the <i>inv</i> mutant, simulations of the ciliary movement with the engagement of dyneins based on the distance-controlled pattern in the partially activation scenario are broadly consistent with the observation; the shortening of the microtubules induces smaller movement amplitudes, while the angles of the mislocalized microtubules affect the pattern of the ciliary movement, and during the ciliary movement, the microtubules swing and twist in the mutant ciliary body. <b><i>Conclusion:</i></b> More generally, this study implies that dynein engagement is sensitive to subtle geometric changes in the axoneme, and thus, this geometry greatly influences the integrity of a well-formed ciliary rotation.
DOI: 10.6084/m9.figshare.7477682
title: Whole genome alignment file of 368 Yersinia pestis isolates

description: Whole genome alignment file of 368 <i>Yersinia pestis</i> isolates.
DOI: 10.7284/112231
title: GNSS (Global Navigation Satellite System) data collected during research cruise MGL1302 using a C&C C-Nav 3050 instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7477682.v1
title: Whole genome alignment file of 368 Yersinia pestis isolates

description: Whole genome alignment file of 368 <i>Yersinia pestis</i> isolates.
DOI: 10.7284/112233
title: GNSS (Global Navigation Satellite System) data collected during research cruise MGL1302 using a C&C C-Nav 2000 instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7477601
title: Circulating miRs-183-5p, -206-3p and -381-3p may serve as novel biomarkers for 4,4’-methylene diphenyl diisocyanate exposure

description: <b>Background:</b> Occupational exposure to the most widely used diisocyanate, 4,4’-methylene diphenyl diisocyanate (MDI), is a cause of occupational asthma (OA). Early recognition of MDI exposure and sensitization is essential for the prevention of MDI-OA. <b>Objective:</b> Identify circulating microRNAs (miRs) as novel biomarkers for early detection of MDI exposure and prevention of MDI-OA. <b>Materials and methods:</b> Female BALB/c mice were exposed to one of three exposure regimens: dermal exposure to 1% MDI in acetone; nose-only exposure to 4580 ± 1497 μg/m<sup>3</sup> MDI-aerosol for 60 minutes; or MDI dermal exposure/sensitization followed by MDI-aerosol inhalation challenge. Blood was collected and miRCURY™ miRs qPCR Profiling Service was used to profile circulate miRs from dermally exposed mice. Candidate miRs were identified and verified from mice exposed to three MDI-exposure regimens by TaqMan<sup>®</sup> miR assays. <b>Results:</b> Up/down-regulation patterns of circulating mmu-miRs-183-5p, -206-3p and -381-3p were identified and verified. Circulating mmu-miR-183-5p was upregulated whereas mmu-miRs-206-3p and -381-3p were downregulated in mice exposed via all three MDI exposure regimens. <b>Discussion and conclusion:</b> Upregulation of circulating miR-183-5p along with downregulation of circulating miRs-206-3p and -381-3p may serve as putative biomarkers of MDI exposure and may be considered as potential candidates for validation in exposed human worker populations.
DOI: 10.6084/m9.figshare.7477589
title: Amyloid properties of the yeast cell wall protein Toh1 and its interaction with prion proteins Rnq1 and Sup35

description: Amyloids are non-branching fibrils that are composed of stacked monomers stabilized by intermolecular β-sheets. Some amyloids are associated with incurable diseases, whereas others, functional amyloids, regulate different vital processes. The prevalence and significance of functional amyloids in wildlife are still poorly understood. In recent years, by applying new approach of large-scale proteome screening, a number of novel candidate amyloids were identified in the yeast <i>Saccharomyces cerevisiae</i>, many of which are localized in the yeast cell wall. In this work, we showed that one of these proteins, Toh1, possess amyloid properties. The Toh1-YFP hybrid protein forms detergent-resistant aggregates in the yeast cells while being expressed under its own <i>P<sub>TOH1</sub></i> or inducible <i>P<sub>CUP1</sub></i> promoter. Using bacterial system for generation of extracellular amyloid aggregates C-DAG, we demonstrated that the N-terminal Toh1 fragment, containing amyloidogenic regions predicted <i>in silico</i>, binds Congo Red dye, manifests ‘apple-green’ birefringence when examined between crossed polarizers, and forms amyloid-like fibrillar aggregates visualized by TEM. We have established that the Toh1(20–365)-YFP hybrid protein fluorescent aggregates are co-localized with a high frequency with Rnq1C-CFP and Sup35NM-CFP aggregates in the yeast cells containing [<i>PIN<sup>+</sup></i>] and [<i>PSI<sup>+</sup></i>] prions, and physical interaction of these aggregated proteins was confirmed by FRET. This is one of a few known cases of physical interaction of non-Q/N-rich amyloid-like protein and Q/N-rich amyloids, suggesting that interaction of different amyloid proteins may be determined not only by similarity of their primary structures but also by similarity of their secondary structures and of conformational folds.
DOI: 10.7284/112234
title: Gravimeter data collected during research cruise MGL1302 using a Bell BGM-3 instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7477589.v1
title: Amyloid properties of the yeast cell wall protein Toh1 and its interaction with prion proteins Rnq1 and Sup35

description: Amyloids are non-branching fibrils that are composed of stacked monomers stabilized by intermolecular β-sheets. Some amyloids are associated with incurable diseases, whereas others, functional amyloids, regulate different vital processes. The prevalence and significance of functional amyloids in wildlife are still poorly understood. In recent years, by applying new approach of large-scale proteome screening, a number of novel candidate amyloids were identified in the yeast <i>Saccharomyces cerevisiae</i>, many of which are localized in the yeast cell wall. In this work, we showed that one of these proteins, Toh1, possess amyloid properties. The Toh1-YFP hybrid protein forms detergent-resistant aggregates in the yeast cells while being expressed under its own <i>P<sub>TOH1</sub></i> or inducible <i>P<sub>CUP1</sub></i> promoter. Using bacterial system for generation of extracellular amyloid aggregates C-DAG, we demonstrated that the N-terminal Toh1 fragment, containing amyloidogenic regions predicted <i>in silico</i>, binds Congo Red dye, manifests ‘apple-green’ birefringence when examined between crossed polarizers, and forms amyloid-like fibrillar aggregates visualized by TEM. We have established that the Toh1(20–365)-YFP hybrid protein fluorescent aggregates are co-localized with a high frequency with Rnq1C-CFP and Sup35NM-CFP aggregates in the yeast cells containing [<i>PIN<sup>+</sup></i>] and [<i>PSI<sup>+</sup></i>] prions, and physical interaction of these aggregated proteins was confirmed by FRET. This is one of a few known cases of physical interaction of non-Q/N-rich amyloid-like protein and Q/N-rich amyloids, suggesting that interaction of different amyloid proteins may be determined not only by similarity of their primary structures but also by similarity of their secondary structures and of conformational folds.
DOI: 10.6084/m9.figshare.7477601.v2
title: Circulating miRs-183-5p, -206-3p and -381-3p may serve as novel biomarkers for 4,4’-methylene diphenyl diisocyanate exposure

description: <b>Background:</b> Occupational exposure to the most widely used diisocyanate, 4,4’-methylene diphenyl diisocyanate (MDI), is a cause of occupational asthma (OA). Early recognition of MDI exposure and sensitization is essential for the prevention of MDI-OA. <b>Objective:</b> Identify circulating microRNAs (miRs) as novel biomarkers for early detection of MDI exposure and prevention of MDI-OA. <b>Materials and methods:</b> Female BALB/c mice were exposed to one of three exposure regimens: dermal exposure to 1% MDI in acetone; nose-only exposure to 4580 ± 1497 μg/m<sup>3</sup> MDI-aerosol for 60 minutes; or MDI dermal exposure/sensitization followed by MDI-aerosol inhalation challenge. Blood was collected and miRCURY™ miRs qPCR Profiling Service was used to profile circulate miRs from dermally exposed mice. Candidate miRs were identified and verified from mice exposed to three MDI-exposure regimens by TaqMan<sup>®</sup> miR assays. <b>Results:</b> Up/down-regulation patterns of circulating mmu-miRs-183-5p, -206-3p and -381-3p were identified and verified. Circulating mmu-miR-183-5p was upregulated whereas mmu-miRs-206-3p and -381-3p were downregulated in mice exposed via all three MDI exposure regimens. <b>Discussion and conclusion:</b> Upregulation of circulating miR-183-5p along with downregulation of circulating miRs-206-3p and -381-3p may serve as putative biomarkers of MDI exposure and may be considered as potential candidates for validation in exposed human worker populations.
DOI: 10.6084/m9.figshare.7477601.v1
title: Circulating miRs-183-5p, -206-3p and -381-3p may serve as novel biomarkers for 4,4’-methylene diphenyl diisocyanate exposure

description: <b>Background:</b> Occupational exposure to the most widely used diisocyanate, 4,4’-methylene diphenyl diisocyanate (MDI), is a cause of occupational asthma (OA). Early recognition of MDI exposure and sensitization is essential for the prevention of MDI-OA. <b>Objective:</b> Identify circulating microRNAs (miRs) as novel biomarkers for early detection of MDI exposure and prevention of MDI-OA. <b>Materials and methods:</b> Female BALB/c mice were exposed to one of three exposure regimens: dermal exposure to 1% MDI in acetone; nose-only exposure to 4580 ± 1497 μg/m<sup>3</sup> MDI-aerosol for 60 minutes; or MDI dermal exposure/sensitization followed by MDI-aerosol inhalation challenge. Blood was collected and miRCURY™ miRs qPCR Profiling Service was used to profile circulate miRs from dermally exposed mice. Candidate miRs were identified and verified from mice exposed to three MDI-exposure regimens by TaqMan<sup>®</sup> miR assays. <b>Results:</b> Up/down-regulation patterns of circulating mmu-miRs-183-5p, -206-3p and -381-3p were identified and verified. Circulating mmu-miR-183-5p was upregulated whereas mmu-miRs-206-3p and -381-3p were downregulated in mice exposed via all three MDI exposure regimens. <b>Discussion and conclusion:</b> Upregulation of circulating miR-183-5p along with downregulation of circulating miRs-206-3p and -381-3p may serve as putative biomarkers of MDI exposure and may be considered as potential candidates for validation in exposed human worker populations.
DOI: 10.7284/112226
title: Gyrocompass data collected during research cruise MGL1302 using a Kongsberg Simrad GC80 instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/112232
title: INS (Inertial Navigation System) data collected during research cruise MGL1302 using a Kongsberg Seapath 200 instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition