cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21676469.v1
title: Geochronology and petrogenesis of the early Silurian Zeluo mafic-ultramafic intrusion, eastern Tibet: implications for the tectonic setting and evolution of the eastern Proto-Tethys Ocean

description: The Tibetan Plateau is a key region to understand the evolution of the Tethys Oceans. To better constrain the tectonic evolution of the Proto-Tethys Ocean on the western margin of the Yangtze plate, we present an integrated petrography, geochemistry, and zircon U-Pb-Lu-Hf isotope study on newly recognized early Silurian gabbro and serpentinite rocks from the eastern Yidun terrane of the Tibetan Plateau. Zircon U-Pb dating of the gabbro yields an Early Silurian age of 438.2 ± 2.8 Ma. Zircon ε<sub>Hf</sub>(t) values of 5.4 to 8.5 suggest a single-stage model age (T<sub>DM1</sub>) ranging from 729 to 858 Ma. The gabbros exhibit low total rare earth element abundances but are moderately enriched in the light rare earth elements and the large-ion lithophile elements (e.g. Rb, Ba, and Sr), and display representative negative high-field strength elemental anomalies for Nb, Ta, Zr, and Hf on spidergrams. The gabbro and serpentinites were derived from a depleted mantle-like source made of garnet-spinel lherzolite composition, from a sub-arc mantle wedge that was metasomatized by slab dehydration. Thus, the gabbro and serpentinites record an Early Silurian subduction event of the Proto-Tethys Ocean under the Yangtze plate. Furthermore, this study confirms that the Yidun terrane on the western margin of the Yangtze plate is underlined by a Precambrian crystalline basement.
DOI: 10.6084/m9.figshare.14329439.v1
title: Additional file 6 of High-dose rapamycin exerts a temporary impact on T. reesei RUT-C30 through gene trFKBP12

description: Additional file 6: Table S3. Transcriptional level of genes involved in (hemi)cellulase production in T. reesei RUT-C30.
DOI: 10.6084/m9.figshare.21152425
title: The annotation results of gene structure in yellow-throated marten genome

description: The annotation results of gene structure in yellow-throated marten genome
DOI: 10.6084/m9.figshare.21152425.v1
title: The annotation results of gene structure in yellow-throated marten genome

description: The annotation results of gene structure in yellow-throated marten genome
DOI: 10.6084/m9.figshare.11710287.v1
title: Datasets, comparative statistics, skews and phylogenetic analyses from Architectural instability, inverted skews and mitochondrial phylogenomics of Isopoda: outgroup choice affects the long-branch attraction artefacts

description: The majority strand of mitochondrial genomes of crustaceans usually exhibits negative GC skews. Most isopods exhibit an inversed strand asymmetry, believed to be a consequence of an inversion of the replication origin (ROI). Recently, we proposed that an additional ROI event in the common ancestor of Cymothoidae and Corallanidae families resulted in a double-inverted skew (negative GC), and that taxa with homoplastic skews cluster together in phylogenetic analyses (long-branch attraction, LBA). Herein, we further explore these hypotheses, for which we sequenced the mitogenome of <i>Asotana magnifica</i> (Cymothoidae), and tested whether our conclusions were biased by poor taxon sampling and inclusion of outgroups. (1) The new mitogenome also exhibits a double-inverted skew, which supports the hypothesis of an additional ROI event in the common ancestor of Cymothoidae and Corallanidae families. (2) It exhibits a unique gene order, which corroborates that isopods possess exceptionally destabilized mitogenomic architecture. (3) Improved taxonomic sampling failed to resolve skew-driven phylogenetic artefacts. (4) The use of a single outgroup exacerbated the LBA, whereas both the use of a large number of outgroups and complete exclusion of outgroups ameliorated it.
DOI: 10.6084/m9.figshare.21152455
title: The annotation results of repeated sequences in yellow-throated marten genome

description: The annotation results of repeated sequences in yellow-throated marten genome
DOI: 10.6084/m9.figshare.21152455.v1
title: The annotation results of repeated sequences in yellow-throated marten genome

description: The annotation results of repeated sequences in yellow-throated marten genome
DOI: 10.6084/m9.figshare.14936490
title: Additional file 1 of Computational analysis for identification of early diagnostic biomarkers and prognostic biomarkers of liver cancer based on GEO and TCGA databases and studies on pathways and biological functions affecting the survival time of liver cancer

description: Additional file 1: Supplement Table 1. The differentially expressed genes of GSE25097
DOI: 10.6084/m9.figshare.14936493
title: Additional file 2 of Computational analysis for identification of early diagnostic biomarkers and prognostic biomarkers of liver cancer based on GEO and TCGA databases and studies on pathways and biological functions affecting the survival time of liver cancer

description: Additional file 2: Supplement Table 2. TCGA the differentially expressed genes
DOI: 10.6084/m9.figshare.14936490.v1
title: Additional file 1 of Computational analysis for identification of early diagnostic biomarkers and prognostic biomarkers of liver cancer based on GEO and TCGA databases and studies on pathways and biological functions affecting the survival time of liver cancer

description: Additional file 1: Supplement Table 1. The differentially expressed genes of GSE25097
DOI: 10.6084/m9.figshare.21152479
title: The annotation results of gene function in yellow-throated marten genome

description: The annotation results of gene function in yellow-throated marten genome
DOI: 10.6084/m9.figshare.21152479.v1
title: The annotation results of gene function in yellow-throated marten genome

description: The annotation results of gene function in yellow-throated marten genome
DOI: 10.6084/m9.figshare.21152482
title: chromosome-level genome assembly of the yellow-throated marten

description: chromosome-level genome assembly of the yellow-throated marten
DOI: 10.6084/m9.figshare.21152482.v1
title: chromosome-level genome assembly of the yellow-throated marten

description: chromosome-level genome assembly of the yellow-throated marten
DOI: 10.6084/m9.figshare.23244437
title: Novel chromobox 2 inhibitory peptide decreases tumor progression

description: The Polycomb Repressor Complex 1 (PRC1) is an epigenetic regulator of differentiation and development, consisting of multiple subunits including RING1, BMI1, and Chromobox. The composition of PRC1 dictates its function and aberrant expression of specific subunits contributes to several diseases including cancer. Specifically, the reader protein Chromobox2 (CBX2) recognizes the repressive modifications including histone H3 lysine 27 tri-methylation (H3K27me3) and H3 lysine 9 dimethylation (H3K9me2). CBX2 is overexpressed in several cancers compared to the non-transformed cell counterparts, it promotes both cancer progression and chemotherapy resistance. Thus, inhibiting the reader function of CBX2 is an attractive and unique anti-cancer approach. Compared with other CBX family members, CBX2 has a unique A/T-hook DNA binding domain that is juxtaposed to the chromodomain (CD). Using a computational approach, we constructed a homology model of CBX2 encompassing the CD and A/T hook domain. We used the model as a basis for peptide design and identified blocking peptides that are predicted to directly bind the CD and A/T-hook regions of CBX2. These peptides were tested in vitro and in vivo models. The CBX2 blocking peptide significantly inhibited both 2D and 3D growth of ovarian cancer cells, downregulated a CBX2 target gene, and blunted tumor growth in vivo.
DOI: 10.6084/m9.figshare.14329442.v1
title: Additional file 7 of High-dose rapamycin exerts a temporary impact on T. reesei RUT-C30 through gene trFKBP12

description: Additional file 7: Table S4. Transcriptional level of DEGs related to “Biosynthesis of secondary metabolites” in T. reesei RUT-C30.
DOI: 10.6084/m9.figshare.14329468
title: Additional file 1 of Phenome-wide investigation of the causal associations between childhood BMI and adult trait outcomes: a two-sample Mendelian randomization study

description: Additional file 1. This file provides the details of Supplementary tables S1-S17.
DOI: 10.6084/m9.figshare.25211209
title: On stratified flow over a topographic ridge in a rotating annulus

description: Interactions between the rotating stratified oceanic and atmospheric flows and topography play a fundamental role in Earth's climate. Here we use laboratory experiments in a differentially-heated rotating annulus to explore stratified flow-topography interactions in a dynamical regime of strong background geostrophic turbulence. A localised small-scale topographic ridge is differentially-rotated at a range of angular velocities around the base of the annulus to impose a relative velocity between the stratified fluid and the small ridge. Considering the idealised setup of the laboratory configuration, the experiments exhibit rich dynamics that include, but are not limited to, lee waves, internal bores, baroclinic instabilities, boundary currents, large-scale gyres, blocking, and geostrophic eddies. Despite the complicated nature of the circulations, several bulk properties and features of the system are able to be characterised globally by relatively simple parameters. We find that the most useful parameter for describing the flows is the internal Froude number (Frn), which is the ratio between the imposed ridge velocity and the internal wave phase speed in the stratified fluid. Standing features that are predominantly barotropic and stationary relative to the ridge are only able to occur when the imposed ridge velocity is less than the internal wave phase speed (|Frn|&lt;1). This implies that the flow-topography interactions leading to stationary dynamics are primarily internal stratified processes, which steer the flow and shape the background geostrophic turbulence such that it can support standing barotropic features.
DOI: 10.6084/m9.figshare.25211209.v1
title: On stratified flow over a topographic ridge in a rotating annulus

description: Interactions between the rotating stratified oceanic and atmospheric flows and topography play a fundamental role in Earth's climate. Here we use laboratory experiments in a differentially-heated rotating annulus to explore stratified flow-topography interactions in a dynamical regime of strong background geostrophic turbulence. A localised small-scale topographic ridge is differentially-rotated at a range of angular velocities around the base of the annulus to impose a relative velocity between the stratified fluid and the small ridge. Considering the idealised setup of the laboratory configuration, the experiments exhibit rich dynamics that include, but are not limited to, lee waves, internal bores, baroclinic instabilities, boundary currents, large-scale gyres, blocking, and geostrophic eddies. Despite the complicated nature of the circulations, several bulk properties and features of the system are able to be characterised globally by relatively simple parameters. We find that the most useful parameter for describing the flows is the internal Froude number (Frn), which is the ratio between the imposed ridge velocity and the internal wave phase speed in the stratified fluid. Standing features that are predominantly barotropic and stationary relative to the ridge are only able to occur when the imposed ridge velocity is less than the internal wave phase speed (|Frn|&lt;1). This implies that the flow-topography interactions leading to stationary dynamics are primarily internal stratified processes, which steer the flow and shape the background geostrophic turbulence such that it can support standing barotropic features.
DOI: 10.6084/m9.figshare.25211207
title: Smoothed particle hydrodynamics approach for modelling submerged granular flows and the induced water wave generation

description: In this study, we develop a Smoothed Particle Hydrodynamics (SPH) 2D-model for simulating fully submerged granular flows and their arising water waves. The granular particles are characterised by a non-Newtonian flow pattern, following a Casson constitutive law, generalised by applying the infinitesimal strain theory to avoid numerical singularities inherited from the original law. The implementation of this rheological model on the weakly compressible viscous Navier-Stokes equations enables the simultaneous modelling of the motion of granular flows and their resulting water waves, establishing a monolithic representation of fluid-structure coupling. The novelty of this model lies in the numerical continuity of the generalised rheological model based mainly on the yield stress criterion, which is computed purely from the mechanical properties of granular materials, including internal friction, cohesion, and viscosity coefficients. The proposed SPH model is validated through two benchmarks available in the literature, representing a submarine landslide along an inclined plane and an immersed granular column collapse. The outcomes of our study illustrate the effectiveness of the proposed model in accurately predicting the motions of submerged granular masses and their resulting water waves, which is crucial for accurately predicting the behaviour of underwater landslides and other natural hazards.
DOI: 10.6084/m9.figshare.25211207.v1
title: Smoothed particle hydrodynamics approach for modelling submerged granular flows and the induced water wave generation

description: In this study, we develop a Smoothed Particle Hydrodynamics (SPH) 2D-model for simulating fully submerged granular flows and their arising water waves. The granular particles are characterised by a non-Newtonian flow pattern, following a Casson constitutive law, generalised by applying the infinitesimal strain theory to avoid numerical singularities inherited from the original law. The implementation of this rheological model on the weakly compressible viscous Navier-Stokes equations enables the simultaneous modelling of the motion of granular flows and their resulting water waves, establishing a monolithic representation of fluid-structure coupling. The novelty of this model lies in the numerical continuity of the generalised rheological model based mainly on the yield stress criterion, which is computed purely from the mechanical properties of granular materials, including internal friction, cohesion, and viscosity coefficients. The proposed SPH model is validated through two benchmarks available in the literature, representing a submarine landslide along an inclined plane and an immersed granular column collapse. The outcomes of our study illustrate the effectiveness of the proposed model in accurately predicting the motions of submerged granular masses and their resulting water waves, which is crucial for accurately predicting the behaviour of underwater landslides and other natural hazards.
DOI: 10.6084/m9.figshare.23244437.v1
title: Novel chromobox 2 inhibitory peptide decreases tumor progression

description: The Polycomb Repressor Complex 1 (PRC1) is an epigenetic regulator of differentiation and development, consisting of multiple subunits including RING1, BMI1, and Chromobox. The composition of PRC1 dictates its function and aberrant expression of specific subunits contributes to several diseases including cancer. Specifically, the reader protein Chromobox2 (CBX2) recognizes the repressive modifications including histone H3 lysine 27 tri-methylation (H3K27me3) and H3 lysine 9 dimethylation (H3K9me2). CBX2 is overexpressed in several cancers compared to the non-transformed cell counterparts, it promotes both cancer progression and chemotherapy resistance. Thus, inhibiting the reader function of CBX2 is an attractive and unique anti-cancer approach. Compared with other CBX family members, CBX2 has a unique A/T-hook DNA binding domain that is juxtaposed to the chromodomain (CD). Using a computational approach, we constructed a homology model of CBX2 encompassing the CD and A/T hook domain. We used the model as a basis for peptide design and identified blocking peptides that are predicted to directly bind the CD and A/T-hook regions of CBX2. These peptides were tested in vitro and in vivo models. The CBX2 blocking peptide significantly inhibited both 2D and 3D growth of ovarian cancer cells, downregulated a CBX2 target gene, and blunted tumor growth in vivo.
DOI: 10.6084/m9.figshare.20098816
title: Additional file 2 of Patterns of human social contact and mask wearing in high-risk groups in China

description: Additional file 2: Table S1. Characteristics and number of contacts of participants stratified by provinces and occupations.
DOI: 10.6084/m9.figshare.20098816.v1
title: Additional file 2 of Patterns of human social contact and mask wearing in high-risk groups in China

description: Additional file 2: Table S1. Characteristics and number of contacts of participants stratified by provinces and occupations.
DOI: 10.6084/m9.figshare.20098745
title: Additional file 2 of First case report of complete paternal isodisomy of chromosome 10 harbouring a novel variant in COL17A1 that causes junctional epidermolysis bullosa intermediate

description: Additional file 2. Table of identified variants annotated as pathogenic/likely pathogenic for the trio.
DOI: 10.5281/zenodo.10652949
title: Ermua Municipality Diagnosis Dataset

description: This dataset contains the information used in the  drOp project (Digitally enabled social district renovation processes for age-friendly environments driving social innovation and local economic development. Num.101080025) to build a multidimensional characterization of Ermua and the Santa Ana neighbourhood through relevant indicators, and its visualisation in a Geographic Information System (GIS) by analysing statistical data, as well as other urban and social data available
DOI: 10.5281/zenodo.10652950
title: Ermua Municipality Diagnosis Dataset

description: This dataset contains the information used in the  drOp project (Digitally enabled social district renovation processes for age-friendly environments driving social innovation and local economic development. Num.101080025) to build a multidimensional characterization of Ermua and the Santa Ana neighbourhood through relevant indicators, and its visualisation in a Geographic Information System (GIS) by analysing statistical data, as well as other urban and social data available
DOI: 10.6084/m9.figshare.11710287
title: Datasets, comparative statistics, skews and phylogenetic analyses from Architectural instability, inverted skews and mitochondrial phylogenomics of Isopoda: outgroup choice affects the long-branch attraction artefacts

description: The majority strand of mitochondrial genomes of crustaceans usually exhibits negative GC skews. Most isopods exhibit an inversed strand asymmetry, believed to be a consequence of an inversion of the replication origin (ROI). Recently, we proposed that an additional ROI event in the common ancestor of Cymothoidae and Corallanidae families resulted in a double-inverted skew (negative GC), and that taxa with homoplastic skews cluster together in phylogenetic analyses (long-branch attraction, LBA). Herein, we further explore these hypotheses, for which we sequenced the mitogenome of <i>Asotana magnifica</i> (Cymothoidae), and tested whether our conclusions were biased by poor taxon sampling and inclusion of outgroups. (1) The new mitogenome also exhibits a double-inverted skew, which supports the hypothesis of an additional ROI event in the common ancestor of Cymothoidae and Corallanidae families. (2) It exhibits a unique gene order, which corroborates that isopods possess exceptionally destabilized mitogenomic architecture. (3) Improved taxonomic sampling failed to resolve skew-driven phylogenetic artefacts. (4) The use of a single outgroup exacerbated the LBA, whereas both the use of a large number of outgroups and complete exclusion of outgroups ameliorated it.
DOI: 10.6084/m9.figshare.6991715
title: Early Assessment of Right Ventricular Function in Systemic Lupus Erythematosus Patients using Strain and Strain Rate Imaging

description: Abstract Background: Right ventricular function is a crucial factor of the prognosis of systemic lupus erythematosus (SLE). Objectives: To evaluate the right ventricular function in SLE patients with different degrees of pulmonary hypertension (PH) by strain and strain rate imaging. Methods: A total of 102 SLE patients and 30 healthy volunteers were studied between October 2015 and May 2016. Patients were divided into three groups according to pulmonary artery systolic pressure (PASP) estimated by echocardiography: group control (A); PASP ≤ 30 mmHg (group B, n = 37); PASP 30-50 mmHg (mild PH; group C, n = 34); and PASP ≥ 50 mmHg (moderate-to-severe PH; group D, n = 31). Longitudinal peak systolic strain (ε) and strain rate (SR), including systolic strain rate (SRs), early diastolic strain rate (SRe) and late diastolic strain rate (SRa) were measured in the basal, middle and apical segments of the right ventricular free wall in participants by two-dimensional speckle tracking echocardiography (2D-STE) from the apical four-chamber view. A p &lt; 0.05 was set for statistical significance. Results: The parameters of ε, SRs, SRe, and SRa were significantly decreased in groups C and D compared with groups A and B. The ε of each segments was significantly lower in group D than in group C, while there were no differences in SRs, SRe and SRa between groups C and D. Conclusions: Strain and strain rate imaging could early detect the right ventricular dysfunction in SLE patients with PH, and provide important value for clinical therapy and prognosis of these patients. (Arq Bras Cardiol. 2018; [online].ahead print, PP.0-0)
DOI: 10.6084/m9.figshare.6991715.v1
title: Early Assessment of Right Ventricular Function in Systemic Lupus Erythematosus Patients using Strain and Strain Rate Imaging

description: Abstract Background: Right ventricular function is a crucial factor of the prognosis of systemic lupus erythematosus (SLE). Objectives: To evaluate the right ventricular function in SLE patients with different degrees of pulmonary hypertension (PH) by strain and strain rate imaging. Methods: A total of 102 SLE patients and 30 healthy volunteers were studied between October 2015 and May 2016. Patients were divided into three groups according to pulmonary artery systolic pressure (PASP) estimated by echocardiography: group control (A); PASP ≤ 30 mmHg (group B, n = 37); PASP 30-50 mmHg (mild PH; group C, n = 34); and PASP ≥ 50 mmHg (moderate-to-severe PH; group D, n = 31). Longitudinal peak systolic strain (ε) and strain rate (SR), including systolic strain rate (SRs), early diastolic strain rate (SRe) and late diastolic strain rate (SRa) were measured in the basal, middle and apical segments of the right ventricular free wall in participants by two-dimensional speckle tracking echocardiography (2D-STE) from the apical four-chamber view. A p &lt; 0.05 was set for statistical significance. Results: The parameters of ε, SRs, SRe, and SRa were significantly decreased in groups C and D compared with groups A and B. The ε of each segments was significantly lower in group D than in group C, while there were no differences in SRs, SRe and SRa between groups C and D. Conclusions: Strain and strain rate imaging could early detect the right ventricular dysfunction in SLE patients with PH, and provide important value for clinical therapy and prognosis of these patients. (Arq Bras Cardiol. 2018; [online].ahead print, PP.0-0)
DOI: 10.6084/m9.figshare.14936493.v1
title: Additional file 2 of Computational analysis for identification of early diagnostic biomarkers and prognostic biomarkers of liver cancer based on GEO and TCGA databases and studies on pathways and biological functions affecting the survival time of liver cancer

description: Additional file 2: Supplement Table 2. TCGA the differentially expressed genes