cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21655849
title: Induction of significant neutralizing antibodies against SARS-CoV-2 by a highly attenuated pangolin coronavirus variant with a 104nt deletion at the 3'-UTR

description: SARS-CoV-2 related coronaviruses (SARS-CoV-2r) from Guangdong and Guangxi pangolins have been implicated in the emergence of SARS-CoV-2 and future pandemics. We previously reported the culture of a SARS-CoV-2r GX_P2V from Guangxi pangolins. Here we report the GX_P2V isolate rapidly adapted to Vero cells by acquiring two genomic mutations: an alanine to valine substitution in the nucleoprotein and a 104-nucleotide deletion in the hypervariable region (HVR) of the 3′-terminus untranslated region (3′-UTR). We further report the characterization of the GX_P2V variant (renamed GX_P2V(short_3UTR)) in <i>in vitro</i> and <i>in vivo</i> infection models. In cultured Vero, BGM and Calu-3 cells, GX_P2V(short_3UTR) had similar robust replication kinetics, and consistently produced minimum cell damage. GX_P2V(short_3UTR) infected golden hamsters and BALB/c mice but was highly attenuated. Golden hamsters infected intranasally had a short duration of productive infection in pulmonary, not extrapulmonary, tissues. These productive infections induced neutralizing antibodies against pseudoviruses of GX_P2V and SARS-CoV-2. Collectively, our data show that the GX_P2V(short_3UTR) is highly attenuated in <i>in vitro</i> and <i>in vivo</i> infection models. Attenuation of the variant is likely partially due to the 104-nt deletion in the HVR in the 3′-UTR. This study furthers our understanding of pangolin coronaviruses pathogenesis and provides novel insights for the design of live attenuated vaccines against SARS-CoV-2.
DOI: 10.6084/m9.figshare.16412982.v1
title: Zircon and monazite U-Pb ages of the Mashan Complex of the Jiamusi Block of NE China: a link to Gondwana?

description: The tectonic affinities of the microcontinents in the eastern Central Asian Orogenic Belt of NE China, particularly the Jiamusi Block, have been hotly debated in the last decade. The Mashan Complex, which is the oldest exposed basement of the Jiamusi Block and consists of khondalitic rocks (felsic granulite, marble, and graphite schist) and orthogneisses, is the key geological unit to look into the tectonic affinity of the Jiamusi Block. In this study, we carried out LA-ICP-MS U-Pb dating on zircon and monazite minerals from the granitic gneisses in the Mashan Complex, to constrain the affinity of the Jiamusi Block. Magmatic zircons from two granitic gneisses yielded weighted mean <sup>206</sup>Pb/<sup>238</sup>U ages of 517 ± 7 Ma and 527 ± 4 Ma, respectively, which are interpreted as the protolith ages. These age data verify a late Pan-African magmatic event in the Jiamusi Block. Metamorphic zircons from one granitic gneiss gave a weighted mean <sup>206</sup>Pb/<sup>238</sup>U age of 510 ± 3 Ma, which constrained the metamorphic time of the Mashan Complex. This metamorphic age is further supported by monazite dating results – the monazites from three granitic gneiss samples yielded weighted mean <sup>206</sup>Pb/<sup>238</sup>U ages of 489 ± 3 Ma, 498 ± 3 Ma, and 500 ± 3 Ma, respectively, which represented the metamorphic recrystallization ages of these monazites. These data consistently indicate a regional metamorphic event immediately after the late Pan-African magmatism in the Jiamusi Block. Our new data, combined with previously published late Pan-African geochronological data from the Jiamusi Block, support that the Jiamusi Block has an affinity to the Gondwana.
DOI: 10.6084/m9.figshare.13791484
title: T-box transcription factor TBX1, targeted by microRNA-6727-5p, inhibits cell growth and enhances cisplatin chemosensitivity of cervical cancer cells through AKT and MAPK pathways

description: Cervical cancer (CC) is the fourth most common cancers among women worldwide. T-box transcription factor 1 (TBX1), a member of the T-box family, has anti-tumor effects in some types of cancer, but its role in CC is yet unknown. The aim of this study is to investigate the functions and underlying mechanisms of TBX1 in CC. Online database UALCAN showed that TBX1 was down-regulated in CC tissues compared with normal tissues and patients with lower TBX1 expression level had a poor prognosis. TBX1 overexpression significantly decreased the proliferation, migration, and invasion of Hela and SiHa cells. Conversely, cell apoptosis and chemosensitivity to cisplatin were promoted in TBX1-overexpressing CC cells. Moreover, up-regulation of TBX1 inhibited both AKT and MAPK signaling pathways. Furthermore, dual luciferase report assay indicated that TBX1 could directly bind to miR-6727-5p. In addition, TBX1 expression was inhibited by miR-6727-5p mimic and up-regulated by miR-6727-5p inhibitor. Knockdown of TBX1 reversed the inhibitory effect of the miR-6727-5p inhibitor on CC cells. This study demonstrates that TBX1, a target gene of miR-6727-5p, acts as a tumor suppressor in CC, indicating that TBX1 may be a new target for CC therapy.
DOI: 10.6084/m9.figshare.21656071
title: Spatiotemporal changes in microtubule dynamics during dendritic morphogenesis

description: Dendritic morphogenesis requires dynamic microtubules (MTs) to form a coordinated cytoskeletal network during development. Dynamic MTs are characterized by their number, polarity and speed of polymerization. Previous studies described a correlation between anterograde MT growth and terminal branch extension in <i>Drosophila</i> dendritic arborization (da) neurons, suggesting a model that anterograde MT polymerization provides a driving force for dendritic branching. We recently found that the Ste20-like kinase Tao specifically regulates dendritic branching by controlling the number of dynamic MTs in a kinase activity-dependent fashion, without affecting MT polarity or speed. This finding raises the interesting question of how MT dynamics affects dendritic morphogenesis, and if Tao kinase activity is developmentally regulated to coordinate MT dynamics and dendritic morphogenesis. We explored the possible correlation between MT dynamics and dendritic morphogenesis together with the activity changes of Tao kinase in C1da and C4da neurons during larval development. Our data show that spatiotemporal changes in the number of dynamic MTs, but not polarity or polymerization speed, correlate with dendritic branching and Tao kinase activity. Our findings suggest that Tao kinase limits dendritic branching by controlling the abundance of dynamic MTs and we propose a novel model on how regulation of MT dynamics might influence dendritic morphogenesis.
DOI: 10.6084/m9.figshare.12218765.v1
title: Additional file 7 of Analysis of DNA methylation profiles during sheep skeletal muscle development using whole-genome bisulfite sequencing

description: Additional file 7. The list of DMGs enriched for muscle development-related KEGG terms.
DOI: 10.6084/m9.figshare.12218750.v1
title: Additional file 4 of Analysis of DNA methylation profiles during sheep skeletal muscle development using whole-genome bisulfite sequencing

description: Additional file 4. Information of DMRs in the Fetus group and the Adult group.
DOI: 10.6084/m9.figshare.12218759.v1
title: Additional file 5 of Analysis of DNA methylation profiles during sheep skeletal muscle development using whole-genome bisulfite sequencing

description: Additional file 5. Information about the COG, GO and KEGG analyses of DMGs. DMGs: Differential methylation genes.
DOI: 10.6084/m9.figshare.13273091
title: Carboniferous isotope stratigraphy

description: Age-updated geochemical data used to build the figures.
DOI: 10.6084/m9.figshare.13273091.v1
title: Carboniferous isotope stratigraphy

description: Age-updated geochemical data used to build the figures.
DOI: 10.25545/qwozwh/2ovhyo
title: Supplementary+Data+4+-+Heron+H-73.pdf

description: :unav
DOI: 10.25545/qwozwh/an7mfq
title: Supplementary+Data+1+-+Bandol-1.pdf

description: :unav
DOI: 10.25545/qwozwh/olfdce
title: Supplementary+Data+2+-+East+Wolverine+G-37.pdf

description: :unav
DOI: 10.25545/qwozwh/xk20wn
title: Supplementary+Data+5+-+DSDP+Site+547B.pdf

description: :unav
DOI: 10.25545/qwozwh
title: Supplementary Data Files accompanying “Re-evaluation of the Mesozoic–Cenozoic biostratigraphy of the Laurentian Subbasin of the Scotian Basin, offshore eastern Canada” (Weston et al., 2023)

description: These five files are supplementary data that accompanies the publication for which the full citation is given below. Abstract: We use new and existing nannofossil, palynological, and microfossil biostratigraphic data in conjunction with lithologic and geophysical logs from four wells to establish a series of sequence-stratigraphic events in the Mesozoic–Cenozoic of the Laurentian Subbasin of offshore Newfoundland, eastern Canada. Well biostratigraphic events are integrated with reflection seismic in the area to correlate regional seismic stratigraphic surfaces. The four wells are: Bandol-1, Emerillon C-56, East Wolverine G-37, and Heron H-73. We extend the event stratigraphic scheme previously developed for the Scotian Margin, offshore Nova Scotia, into new areas to the east along the southern Grand Banks, where we recognize four new well-log sequence stratigraphic events, and we modify the definition of a previously recognized regional surface. The new and modified regional surfaces are the Early Albian Unconformity, the Late Bathonian Maximum Flooding Surface (MFS), the Late Bajocian MFS (renamed from Bathonian/Bajocian MFS), the Bajocian/Toarcian Unconformity, and the Late Pliensbachian MFS. We recognize the “Avalon Unconformity” and “Base-Tertiary Unconformity” of previous studies as amalgamations of multiple smaller-scale unconformities and refine their age in the studied wells. A major improvement over our earlier Scotian Margin event schemes is the extension of the event stratigraphy into the Early Jurassic using a suite of marine biostratigraphic markers. We compare the Early Jurassic event scheme to Deep Sea Drilling Project Site 547B on the conjugate Moroccan Margin to better constrain potential source rock intervals and the early history of the central Atlantic Ocean.
DOI: 10.25545/qwozwh/c2apyj
title: Supplementary+Data+3+-+Emerillon+C-56.pdf

description: :unav
DOI: 10.6084/m9.figshare.24807519
title: Supplementary Information;Supplementary Movie;Supplementary Figures from Kinematics and dynamics of non-developable origami

description: Non-developable origami is a unique type of origami structures that cannot be unfolded into a flat sheet without stretching. In this work, we study the kinematics and dynamics of such origami, theoretically, numerically and experimentally, considering rigid panels and stretchable creases. Unlike developable origami, we find that non-developable origami exhibits distinct folding angle relationships, leading to several separate branches in its kinematic configuration space with snap-through and locking behaviours. By modelling the creases as stretchable torsional springs, we derive a dynamic model to analyse the deployment of non-developable origami structures, from single-vertex origami to origami chains. Our dynamic model unveils the snap-through behaviour between the two kinematics branches of the single-vertex non-developable origami structure, which further validated by experiments with excellent agreement. We believe that our kinematic and dynamic framework of non-developable origami will greatly expand the current design space of origami structures and guide the design of novel origami actuators.
DOI: 10.6084/m9.figshare.24807519.v1
title: Supplementary Information;Supplementary Movie;Supplementary Figures from Kinematics and dynamics of non-developable origami

description: Non-developable origami is a unique type of origami structures that cannot be unfolded into a flat sheet without stretching. In this work, we study the kinematics and dynamics of such origami, theoretically, numerically and experimentally, considering rigid panels and stretchable creases. Unlike developable origami, we find that non-developable origami exhibits distinct folding angle relationships, leading to several separate branches in its kinematic configuration space with snap-through and locking behaviours. By modelling the creases as stretchable torsional springs, we derive a dynamic model to analyse the deployment of non-developable origami structures, from single-vertex origami to origami chains. Our dynamic model unveils the snap-through behaviour between the two kinematics branches of the single-vertex non-developable origami structure, which further validated by experiments with excellent agreement. We believe that our kinematic and dynamic framework of non-developable origami will greatly expand the current design space of origami structures and guide the design of novel origami actuators.
DOI: 10.6084/m9.figshare.16419179
title: Nano-CuO causes cell damage through activation of dose-dependent autophagy and mitochondrial lncCyt b-AS/ND5-AS/ND6-AS in SH-SY5Y cells

description: Metal copper oxide nanoparticles (nano-CuO) are under mass production and have been widely utilized in many fields including catalysis, gas sensors, semiconductor materials, etc. The broad applications of nano-CuO have increased the possibility of risk to incidental exposure to the environment, and therefore, an in-depth investigation of their effects on live cells is required. This study investigated the impact of the nano-CuO on SH-SY5Y cells, and findings showed that the ratio of LC3-II/LC3-I was significantly increased in SH-SY5Y cells when the cells were treated with nano-CuO. However, if the autophagy inhibitor Bafilomycin A1 (Baf A1) was co-treated, the ratio of LC3-II/LC3-I was further improved. These outcomes might indicate that autophagy flux was permanently elevated by adding nano-CuO. Further results found highly activated levels of long noncoding RNAs (lncRNAs) under nano-CuO treatment. The data illustrate a mechanism that nano-CuO can promote autophagy and activate lncCyt b-AS/ND5-AS/ND6-AS in SH-SY5Y cells and have critical implications for nanoparticle biomedical applications.
DOI: 10.13012/b2idb-7963044_v1
title: Data for Unsupervised Sinogram Inpainting for Nanoparticle Electron Tomography (UsiNet) for missing wedge correction

description: Example data for https://github.com/chenlabUIUC/UsiNet
The data contains computer simulated and experimental tilting series (or sinograms) of gold nanoparticles.
Two training data examples are provided:
1. simulated_data.zip
2. experimental_data.zip
In each zip folder, we include an image_data.zip and a training_data.zip. The former is for viewing and only the latter is needed for model training. For more details, please refer to our GitHub repository.
DOI: 10.6084/m9.figshare.12218768.v1
title: Additional file 8 of Analysis of DNA methylation profiles during sheep skeletal muscle development using whole-genome bisulfite sequencing

description: Additional file 8. Muscle development -related DMGs target genes in muscle between Fetus and Adult Hu sheep.
DOI: 10.5281/zenodo.10649568
title: Transformation matrix results (.mat files) produced with the FSL FLIRT application (v6.0.5.1) within a reproducibilty study

description: This dataset contains transformation matrix results (.mat files) produced with the FSL FLIRT application (v6.0.5.1) within a reproducibilty study. The associated research paper will be linked to the dataset when published.

Inputs provided to the FSL FLIRT application correspond to the first part of the OASIS-I dataset (https://www.oasis-brains.org/), i.e. 148 brain scans from 39 healthy subjects (31 subjects × 4 scans + 8 subjects × 3 scans).

The three main folders of the output dataset correspond to:



different FSL FLIRT deployment strategies (folders Docker and Guix) and




the use of  Verificarlo through “fuzzy libmath" (v0.9.1) added to FSL Docker container (vnmd/fsl_6.0.5.1) for the evaluation of numerical stability (folder MCA)
DOI: 10.5281/zenodo.10649569
title: Transformation matrix results (.mat files) produced with the FSL FLIRT application (v6.0.5.1) within a reproducibilty study

description: This dataset contains transformation matrix results (.mat files) produced with the FSL FLIRT application (v6.0.5.1) within a reproducibilty study. The associated research paper will be linked to the dataset when published.

Inputs provided to the FSL FLIRT application correspond to the first part of the OASIS-I dataset (https://www.oasis-brains.org/), i.e. 148 brain scans from 39 healthy subjects (31 subjects × 4 scans + 8 subjects × 3 scans).

The three main folders of the output dataset correspond to:



different FSL FLIRT deployment strategies (folders Docker and Guix) and




the use of  Verificarlo through “fuzzy libmath" (v0.9.1) added to FSL Docker container (vnmd/fsl_6.0.5.1) for the evaluation of numerical stability (folder MCA)
DOI: 10.6084/m9.figshare.12218750
title: Additional file 4 of Analysis of DNA methylation profiles during sheep skeletal muscle development using whole-genome bisulfite sequencing

description: Additional file 4. Information of DMRs in the Fetus group and the Adult group.
DOI: 10.6084/m9.figshare.12218759
title: Additional file 5 of Analysis of DNA methylation profiles during sheep skeletal muscle development using whole-genome bisulfite sequencing

description: Additional file 5. Information about the COG, GO and KEGG analyses of DMGs. DMGs: Differential methylation genes.
DOI: 10.6084/m9.figshare.12218762.v1
title: Additional file 6 of Analysis of DNA methylation profiles during sheep skeletal muscle development using whole-genome bisulfite sequencing

description: Additional file 6. The list of DMGs enriched for muscle development-related top 20 GO terms.
DOI: 10.5281/zenodo.10642221
title: IODP Expedition 390C Elemental analysis (CHNS)

description: Fundamental elemental component (total carbon, hydrogen, nitrogen, and sulfur) fluctuations help define the origin, depositional environment, and diagenetic alteration of source materials. To determine C, H, N, and S, solid samples are reacted with a catalyst, separated by chromatography, and detected by thermal conductivity on a FlashEA 1112 CHNS elemental analyzer. Organic carbon can be directly measured on the elemental analyzer by acidification of the sample to drive off carbonate as carbon dioxide before analyzing. Total organic carbon on this report is measured rather than calculated.
DOI: 10.5281/zenodo.10642222
title: IODP Expedition 390C Elemental analysis (CHNS)

description: Fundamental elemental component (total carbon, hydrogen, nitrogen, and sulfur) fluctuations help define the origin, depositional environment, and diagenetic alteration of source materials. To determine C, H, N, and S, solid samples are reacted with a catalyst, separated by chromatography, and detected by thermal conductivity on a FlashEA 1112 CHNS elemental analyzer. Organic carbon can be directly measured on the elemental analyzer by acidification of the sample to drive off carbonate as carbon dioxide before analyzing. Total organic carbon on this report is measured rather than calculated.
DOI: 10.6084/m9.figshare.12218762
title: Additional file 6 of Analysis of DNA methylation profiles during sheep skeletal muscle development using whole-genome bisulfite sequencing

description: Additional file 6. The list of DMGs enriched for muscle development-related top 20 GO terms.
DOI: 10.6084/m9.figshare.12218765
title: Additional file 7 of Analysis of DNA methylation profiles during sheep skeletal muscle development using whole-genome bisulfite sequencing

description: Additional file 7. The list of DMGs enriched for muscle development-related KEGG terms.
DOI: 10.6084/m9.figshare.12218768
title: Additional file 8 of Analysis of DNA methylation profiles during sheep skeletal muscle development using whole-genome bisulfite sequencing

description: Additional file 8. Muscle development -related DMGs target genes in muscle between Fetus and Adult Hu sheep.
DOI: 10.6084/m9.figshare.12219038.v1
title: Additional file 1 of Establishment and characterization of stable red, far-red (fR) and near infra-red (NIR) transfected canine prostate cancer cell lines

description: Additional file 1. Genes located in the chromosomal area chr16:18500001-59500001.
DOI: 10.5281/zenodo.10642219
title: IODP Expedition 390C Carbonates composite report

description: This composite report includes data from two analyses (total carbon from Elemental analysis [CHNS], and inorganic carbon from [Coulometer]). Each row combines the  CHNS and Coulometer data from measurements made on the same sample at the same time for a particular section and section offset (depth). If data do not exist for a particular expedition, the column does not appear. To identify individual samples and tests, see each separate data type (Elemental analysis and Coulometer). If the same sample was measured multiple times by any of the methods, results in the report will be combined on one line where possible. Each additional replicate result will be shown in subsequent rows and will be combined where possible. Report includes results for carbon forms: total, inorganic, calcium carbonate, and organic by difference, along with total hydrogen, nitrogen, and sulfur.
DOI: 10.5281/zenodo.10642220
title: IODP Expedition 390C Carbonates composite report

description: This composite report includes data from two analyses (total carbon from Elemental analysis [CHNS], and inorganic carbon from [Coulometer]). Each row combines the  CHNS and Coulometer data from measurements made on the same sample at the same time for a particular section and section offset (depth). If data do not exist for a particular expedition, the column does not appear. To identify individual samples and tests, see each separate data type (Elemental analysis and Coulometer). If the same sample was measured multiple times by any of the methods, results in the report will be combined on one line where possible. Each additional replicate result will be shown in subsequent rows and will be combined where possible. Report includes results for carbon forms: total, inorganic, calcium carbonate, and organic by difference, along with total hydrogen, nitrogen, and sulfur.
DOI: 10.6084/m9.figshare.21656071.v1
title: Spatiotemporal changes in microtubule dynamics during dendritic morphogenesis

description: Dendritic morphogenesis requires dynamic microtubules (MTs) to form a coordinated cytoskeletal network during development. Dynamic MTs are characterized by their number, polarity and speed of polymerization. Previous studies described a correlation between anterograde MT growth and terminal branch extension in <i>Drosophila</i> dendritic arborization (da) neurons, suggesting a model that anterograde MT polymerization provides a driving force for dendritic branching. We recently found that the Ste20-like kinase Tao specifically regulates dendritic branching by controlling the number of dynamic MTs in a kinase activity-dependent fashion, without affecting MT polarity or speed. This finding raises the interesting question of how MT dynamics affects dendritic morphogenesis, and if Tao kinase activity is developmentally regulated to coordinate MT dynamics and dendritic morphogenesis. We explored the possible correlation between MT dynamics and dendritic morphogenesis together with the activity changes of Tao kinase in C1da and C4da neurons during larval development. Our data show that spatiotemporal changes in the number of dynamic MTs, but not polarity or polymerization speed, correlate with dendritic branching and Tao kinase activity. Our findings suggest that Tao kinase limits dendritic branching by controlling the abundance of dynamic MTs and we propose a novel model on how regulation of MT dynamics might influence dendritic morphogenesis.