cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24265774.v1
title: CDK6 Inhibits De Novo Lipogenesis in White Adipose Tissues but not in the Liver

description: Increased de novo lipogenesis (DNL) in white adipose tissue (WAT) is associated with insulin sensitivity. Under both normal chow diet (NCD) and high fat diet (HFD), mice expressing a kinase inactive Cdk6 allele (Cdk6K43M, K43M) displays an increase in DNL in visceral WAT as compared to WT mice, accompanied by markedly increased lipogenic transcriptional factor CHREBP and lipogenic enzymes in WAT but not in the liver. Treatment of WT mice under HFD by CDK6 inhibitors recapitulates the phenotypes observed in K43M mice. Mechanistically, CDK6 is found to phosphorylate AMPK leading to phosphorylation and inactivation of acetyl-CoA carboxylase, a key enzyme in DNL. CDK6 is also found to phosphorylate CHREBP thus preventing its entry into the nucleus. Ablation of RUNX1 in K43M mature adipocytes reverses most of the phenotypes observed in K43M mice. These results demonstrate a role of CDK6 in DNL and a novel strategy to alleviate metabolic syndromes.
DOI: 10.18419/darus-3242/22
title: package-info.java

description: :unav
DOI: 10.18419/darus-3242/29
title: WebsiteExportQS.java

description: :unav
DOI: 10.18419/darus-3242/34
title: package-info.java

description: :unav
DOI: 10.6084/m9.figshare.23615119.v1
title: Pan-precancer and cancer DNA methylation profiles revealed significant tissue specificity of interrupted biological processes in tumorigenesis

description: DNA methylation (DNAme) alterations are known to initiate from the precancerous stage of tumorigenesis. Herein, we investigated the global and local patterns of DNAme perturbations in tumorigenesis by analysing the genome-wide DNAme profiles of the cervix, colorectum, stomach, prostate, and liver at precancerous and cancer stages. We observed global hypomethylation in tissues of both two stages, except for the cervix, whose global DNAme level in normal tissue was lower than that of the other four tumour types. For alterations shared by both stages, there were common hyper-methylation (sHyperMethyl) and hypo-methylation (sHypoMethyl) changes, of which the latter type was more frequently identified in all tissues. Biological pathways interrupted by sHyperMethyl and sHypoMethyl alterations demonstrated significant tissue specificity. DNAme bidirectional chaos indicated by the enrichment of both sHyperMethyl and sHypoMethyl changes in the same pathway was observed in most tissues and was a common phenomenon, particularly in liver lesions. Moreover, for the same enriched pathways, different tissues may be affected by distinct DNAme types. For the PI3K−Akt signalling pathway, sHyperMethyl enrichment was observed in the prostate dataset, but sHypoMethyl enrichment was observed in the colorectum and liver datasets. Nevertheless, they did not show an increased possibility in survival prediction of patients in comparison with other DNAme types. Additionally, our study demonstrated that gene-body DNAme changes of tumour suppressor genes and oncogenes may persist from precancerous lesions to the tumour. Overall, we demonstrate the tissue specificity and commonality of cross-stage alterations in DNA methylation profiles in multi-tissue tumorigenesis.
DOI: 10.6084/m9.figshare.24265774
title: CDK6 Inhibits De Novo Lipogenesis in White Adipose Tissues but not in the Liver

description: Increased de novo lipogenesis (DNL) in white adipose tissue (WAT) is associated with insulin sensitivity. Under both normal chow diet (NCD) and high fat diet (HFD), mice expressing a kinase inactive Cdk6 allele (Cdk6K43M, K43M) displays an increase in DNL in visceral WAT as compared to WT mice, accompanied by markedly increased lipogenic transcriptional factor CHREBP and lipogenic enzymes in WAT but not in the liver. Treatment of WT mice under HFD by CDK6 inhibitors recapitulates the phenotypes observed in K43M mice. Mechanistically, CDK6 is found to phosphorylate AMPK leading to phosphorylation and inactivation of acetyl-CoA carboxylase, a key enzyme in DNL. CDK6 is also found to phosphorylate CHREBP thus preventing its entry into the nucleus. Ablation of RUNX1 in K43M mature adipocytes reverses most of the phenotypes observed in K43M mice. These results demonstrate a role of CDK6 in DNL and a novel strategy to alleviate metabolic syndromes.
DOI: 10.18419/darus-3242
title: QSDB - a graphical Quorum Sensing Database: VANTED add-on source code

description: The add-on had been designed for the VANTED framework and used to create QSDB Database's collection of clickable networks. Each network is laid out according to SBGN standards, showing quorum sensing and quorum quenching interactions between organisms and signaling molecules. This data set constitutes the source code of the add-on, developed to visualise the SBGN graphs of the QSDB Database using as input tabular aggregated data collected from existing literature. Paper abstract: The human microbiome is largely shaped by the chemical interactions of its microbial members, which includes cross-talk via shared signals or quenching of the signalling of other species. Quorum sensing is a process that allows microbes to coordinate their behaviour in dependence of their population density and to adjust gene expression accordingly. We present the Quorum Sensing Database (QSDB), a comprehensive database of all published sensing and quenching relations between organisms and signalling molecules of the human microbiome, as well as an interactive web interface that allows browsing the database, provides graphical depictions of sensing mechanisms as Systems Biology Graphical Notation diagrams and links to other databases. Database URL: QSDB (Quorum Sensing DataBase) is freely available via an interactive web interface and as a downloadable csv file at http://qsdb.org.
DOI: 10.18419/darus-3242/13
title: NodeCluster.java

description: :unav
DOI: 10.6084/m9.figshare.11555751.v2
title: A Stochastic Second-Order Generalized Estimating Equations Approach for Estimating Association Parameters

description: Design and analysis of cluster randomized trials (CRTs) must take into account the intraclass correlation coefficient (ICC), which quantifies the correlation among outcomes from the same cluster. Second-order generalized estimating equations (GEE2) provide a statistically robust way in estimating this quantity and other association parameters. However, GEE2 becomes computationally infeasible as cluster sizes grow. This article proposes a stochastic variant to fitting GEE2 which alleviates reliance on parameter starting values and provides substantially faster speeds and higher convergence rates than the widely used deterministic Newton–Raphson method. We also propose new estimators for the ICC which account for informative missing outcome data through the use of GEE2, for which we incorporate a “second-order” inverse probability weighting scheme and “second-order” doubly robust estimating equations that guard against partial model misspecification. Our proposed methods are evaluated through simulations and applied to data from a CRT in Bangladesh evaluating the effect of different marketing interventions on the use of hygienic latrines. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.22954151.v1
title: 300 years of sclerosponge thermometry shows global warming has exceeded 1.5oC

description: Sr/Ca temperature anomalies compared to HadSST4 global and U-series dating information
DOI: 10.6084/m9.figshare.24492043
title: Avoiding ecosystem and social impacts of hydropower, wind, and solar in Southern Africa’s low-carbon electricity system

description: Data to accompany paper entitled, "Avoiding ecosystem and social impacts of hydropower, wind, and solar in Southern Africa’s low-carbon electricity system"

Includes source data as CSVs and GIS data of reservoir footprints

For help interpreting the hydropowerPortfolio csvs, see the supporting information table S4

For help interpreting the non-hydropower CSVs:
- ccap = no (normal) carbon cap
- ccap_low = low carbon cap 
- costs_emissions = total system costs (USD) and GHG emissions of all scenarios 
- capacity_generation = capacity (GW) and generation (TWh)
- diffFromBaseLine = difference from baseline for capacity and generation
- percentagechangeFromBaseline = differences expressed as percentages
- rawValues = new capacity (GW) additions and total generation (TWh)
DOI: 10.6084/m9.figshare.11556153.v1
title: Data from Numerical simulation on fracturing behaviour of hard roofs at different levels during extra-thick coal seam mining

description: Data supported the article
DOI: 10.6084/m9.figshare.14702262
title: Additional file 4 of Mvda is required for zebrafish early development

description: Additional file 4: Table S1. qRT-PCR primers for zebrafish. The primer sequences for qRT-PCR.
DOI: 10.6084/m9.figshare.14702262.v1
title: Additional file 4 of Mvda is required for zebrafish early development

description: Additional file 4: Table S1. qRT-PCR primers for zebrafish. The primer sequences for qRT-PCR.
DOI: 10.6084/m9.figshare.14702271
title: Additional file 1 of Radiographic features and prognosis of early- and late-onset non-small cell lung cancer immune checkpoint inhibitor-related pneumonitis

description: Additional file 1.
DOI: 10.6084/m9.figshare.14702271.v1
title: Additional file 1 of Radiographic features and prognosis of early- and late-onset non-small cell lung cancer immune checkpoint inhibitor-related pneumonitis

description: Additional file 1.
DOI: 10.6084/m9.figshare.4216518
title: Carboniferous porphyry Cu (-Au) mineralization of the West Junggar region, NW China: the Shiwu example

description: The West Junggar region, located in the Central Asian Orogenic Belt (CAOB), is characterized by extensive Carboniferous magmatism and porphyry Cu (-Au) deposits. The Shiwu porphyry Cu-Au deposit, located in the east of the Barluk Mountains, the West Junggar region, is not only a newly discovered deposit but also a representative porphyry Cu-Au deposit in this area. The volcanic rocks (including andesite and tuff) and intrusive rocks (including diorite, quartz diorite, quartz diorite porphyry, and tonalite porphyry) occurred in the Shiwu area and the mineralization associated with the quartz diorite porphyry. The secondary ion mass spectrometry (SIMS) zircon U–Pb ages of quartz diorite porphyry and tonalite porphyry are 310.4 ± 2.3 Ma and 310.1 ± 2.4 Ma, respectively, indicating that the Shiwu deposit is related to the Late Carboniferous magmatism. Intrusive rocks, which were characterized by the enrichment of large ion lithophile elements (LILEs) and pronounced negative high field strength elements (HFSEs), belong to the calc-alkaline or tholeiitic series. Their (<sup>87</sup>Sr/<sup>86</sup>Sr)<sub>i</sub>, (<sup>143</sup>Nd/<sup>144</sup>Nd)<sub>I</sub>, and <i>ε</i>Nd(<i>t</i>) values range from 0.703569 to 0.704311, 0.512488 to 0.512512, and 4.9 to 5.3, respectively. Volcanic rocks, which belong to the calc-alkaline series, have similar geochemical features as the intrusive rocks, and their (<sup>87</sup>Sr/<sup>86</sup>Sr)<sub>i</sub>, (<sup>143</sup>Nd/<sup>144</sup>Nd)<sub>i</sub>, and <i>ε</i>Nd(<i>t</i>) values, respectively, are 0.703704–0.704071, 0.512520–0.512542, and 5.49–5.92. These characters indicate that the igneous rocks in the Shiwu area derived dominantly from the mantle and formed in an island arc setting. These characters also further confirmed that the Barluk Mountains is still in an island arc setting in the Late Carboniferous and the accretionary orogenesis can exist until 310 Ma at least.
DOI: 10.6084/m9.figshare.4216518.v1
title: Carboniferous porphyry Cu (-Au) mineralization of the West Junggar region, NW China: the Shiwu example

description: The West Junggar region, located in the Central Asian Orogenic Belt (CAOB), is characterized by extensive Carboniferous magmatism and porphyry Cu (-Au) deposits. The Shiwu porphyry Cu-Au deposit, located in the east of the Barluk Mountains, the West Junggar region, is not only a newly discovered deposit but also a representative porphyry Cu-Au deposit in this area. The volcanic rocks (including andesite and tuff) and intrusive rocks (including diorite, quartz diorite, quartz diorite porphyry, and tonalite porphyry) occurred in the Shiwu area and the mineralization associated with the quartz diorite porphyry. The secondary ion mass spectrometry (SIMS) zircon U–Pb ages of quartz diorite porphyry and tonalite porphyry are 310.4 ± 2.3 Ma and 310.1 ± 2.4 Ma, respectively, indicating that the Shiwu deposit is related to the Late Carboniferous magmatism. Intrusive rocks, which were characterized by the enrichment of large ion lithophile elements (LILEs) and pronounced negative high field strength elements (HFSEs), belong to the calc-alkaline or tholeiitic series. Their (<sup>87</sup>Sr/<sup>86</sup>Sr)<sub>i</sub>, (<sup>143</sup>Nd/<sup>144</sup>Nd)<sub>I</sub>, and <i>ε</i>Nd(<i>t</i>) values range from 0.703569 to 0.704311, 0.512488 to 0.512512, and 4.9 to 5.3, respectively. Volcanic rocks, which belong to the calc-alkaline series, have similar geochemical features as the intrusive rocks, and their (<sup>87</sup>Sr/<sup>86</sup>Sr)<sub>i</sub>, (<sup>143</sup>Nd/<sup>144</sup>Nd)<sub>i</sub>, and <i>ε</i>Nd(<i>t</i>) values, respectively, are 0.703704–0.704071, 0.512520–0.512542, and 5.49–5.92. These characters indicate that the igneous rocks in the Shiwu area derived dominantly from the mantle and formed in an island arc setting. These characters also further confirmed that the Barluk Mountains is still in an island arc setting in the Late Carboniferous and the accretionary orogenesis can exist until 310 Ma at least.
DOI: 10.6084/m9.figshare.6882032
title: Model of AlN substrate;Tersoff potential;Cfg files of finally deposited AlN film from Molecular dynamics simulation of AlN deposition: temperature and N : Al ratio effects

description: 10800aln.data;AlN.tersoff
DOI: 10.18167/dvn1/eeul8t
title: A survey of spontaneous species and cover crop communities in an experimental banana fallow in Guadeloupe: densities and functional traits

description: This dataset was obtained from a vegetation survey conducted on an experimental improved fallow preceding a banana crop, in Guadeloupe, French West indies. In this experiment, 8 treatments that correspond to a combination of two practices (soil tillage and cover crop species) were tested on 5 blocks (repetitions). For each modality, one sown cover crop species (among three species tested) was combined with one soil tillage modality (among two modalities tested) to test the effect of these practices on the sponatenous vegetation. The spontaneous vegetation and the cover crops were monitored (species determination, densities/m²) on permanent quadrats (25cm x 25cm) each month for 12 months. Nine aboveground traits were measured at flowering peaks on the 12 most abundant species. Dynamic of height over the 12 months and some global descriptors of the community (biomass, cover rate) were also measured. For details on variables measurements, see the related published papers.
DOI: 10.6084/m9.figshare.7886558
title: Pex13 and Pex14, the key components of the peroxisomal docking complex, are required for peroxisome formation, host infection and pathogenicity-related morphogenesis in <i>Magnaporthe oryzae</i>

description: Peroxisomes are ubiquitous organelles in eukaryotic cells that fulfill multiple important metabolisms. Pex13 and Pex14 are key components of the peroxisomal docking complex in yeasts and mammals. In the present work, we functionally characterized the homologues of Pex13 and Pex14 (Mopex13 and Mopex14) in the rice blast fungus <i>Magnaporthe oryzae</i>. Mopex13 and Mopex14 were peroxisomal membrane distributed and were both essential for the maintenance of Mopex14/17 on the peroxisomal membrane. Mopex13 and Mopex14 interacted with each other, and with Mopex14/17 and peroxisomal matrix protein receptors. Disruption of Mopex13 and Mopex14 resulted in a cytoplasmic distribution of peroxisomal matrix proteins and the Woronin body protein Hex1. In the ultrastructure of Δmopex13 and Δmopex14 cells, peroxisomes were detected on fewer occasions, and the Woronin bodies and related structures were dramatically affected. The Δmopex13 and Δmopex14 mutants were reduced in vegetative growth, conidial generation and mycelial melanization, in addition, Δmopex13 showed reduced conidial germination and appressorial formation and abnomal appressorial morphology. Both Δmopex13 and Δmopex14 were deficient in appressorial turgor and nonpathogenic to their hosts. The infection failures in Δmopex13 and Δmopex14 were also due to their reduced ability to degrade fatty acids and to endure reactive oxygen species and cell wall-disrupting compounds. Additionally, Mopex13 and Mopex14 were required for the sexual reproduction of the fungus. These data indicate that Mopex13 and Mopex14, as key components of the peroxisomal docking complex, are indispensable for peroxisomal biogenesis, fungal development and pathogenicity in the rice blast fungus.
DOI: 10.6084/m9.figshare.7886558.v2
title: Pex13 and Pex14, the key components of the peroxisomal docking complex, are required for peroxisome formation, host infection and pathogenicity-related morphogenesis in <i>Magnaporthe oryzae</i>

description: Peroxisomes are ubiquitous organelles in eukaryotic cells that fulfill multiple important metabolisms. Pex13 and Pex14 are key components of the peroxisomal docking complex in yeasts and mammals. In the present work, we functionally characterized the homologues of Pex13 and Pex14 (Mopex13 and Mopex14) in the rice blast fungus <i>Magnaporthe oryzae</i>. Mopex13 and Mopex14 were peroxisomal membrane distributed and were both essential for the maintenance of Mopex14/17 on the peroxisomal membrane. Mopex13 and Mopex14 interacted with each other, and with Mopex14/17 and peroxisomal matrix protein receptors. Disruption of Mopex13 and Mopex14 resulted in a cytoplasmic distribution of peroxisomal matrix proteins and the Woronin body protein Hex1. In the ultrastructure of Δmopex13 and Δmopex14 cells, peroxisomes were detected on fewer occasions, and the Woronin bodies and related structures were dramatically affected. The Δmopex13 and Δmopex14 mutants were reduced in vegetative growth, conidial generation and mycelial melanization, in addition, Δmopex13 showed reduced conidial germination and appressorial formation and abnomal appressorial morphology. Both Δmopex13 and Δmopex14 were deficient in appressorial turgor and nonpathogenic to their hosts. The infection failures in Δmopex13 and Δmopex14 were also due to their reduced ability to degrade fatty acids and to endure reactive oxygen species and cell wall-disrupting compounds. Additionally, Mopex13 and Mopex14 were required for the sexual reproduction of the fungus. These data indicate that Mopex13 and Mopex14, as key components of the peroxisomal docking complex, are indispensable for peroxisomal biogenesis, fungal development and pathogenicity in the rice blast fungus.
DOI: 10.6084/m9.figshare.14702332
title: Additional file 1 of Detection of copy number variants in African goats using whole genome sequence data

description: Additional file 1 Supplementary Table 1 Genes in CNV with VST values above the 99th percentile for each comparison. Supplementary Table 2 List of CNVR by population. Supplementary Table 3 Summary of CNVR by population. Supplementary Table 4 List of global CNVR with frequency above 1%. Supplementary Table 5 Functional annotation and clustering analysis for global CNVR. Supplementary Table 6 Functional analysis for CNVR private to breeds and to populations. Supplementary Table 7 Sample processing details. Supplementary Table 8 Quality control details for the samples used in the study.
DOI: 10.6084/m9.figshare.14702332.v1
title: Additional file 1 of Detection of copy number variants in African goats using whole genome sequence data

description: Additional file 1 Supplementary Table 1 Genes in CNV with VST values above the 99th percentile for each comparison. Supplementary Table 2 List of CNVR by population. Supplementary Table 3 Summary of CNVR by population. Supplementary Table 4 List of global CNVR with frequency above 1%. Supplementary Table 5 Functional annotation and clustering analysis for global CNVR. Supplementary Table 6 Functional analysis for CNVR private to breeds and to populations. Supplementary Table 7 Sample processing details. Supplementary Table 8 Quality control details for the samples used in the study.
DOI: 10.7910/dvn/5dgfjb/iwwkbg
title: README.md

description: description of how to read the data
DOI: 10.7910/dvn/5dgfjb/wu4k3w
title: data.parquet

description: Waveforms, dataset name, and p pick by analyst
DOI: 10.7910/dvn/5dgfjb/3byljn
title: README.md

description: A description of included files.
DOI: 10.7910/dvn/5dgfjb/xvx48h
title: data.parquet

description: Processed waveform files for picking
DOI: 10.6084/m9.figshare.12899846
title: Anterior BLA

description: Registered multiplexed smFISH images for 12 genes imaged across 3 separate rounds of imaging in an anterior coronal section of the BLA:<br><br><br>First Round Imaging: <i>Nr4a2, Otof, Cdh13, Rorb</i>Second Round Imaging: <i>Adamts, Prss23, Bdnf, Slc5a5</i>Third Round Imaging: <i>Slc17a7, Nnat, Negr1, Cplx1</i>
DOI: 10.6084/m9.figshare.12899846.v1
title: Anterior BLA

description: Registered multiplexed smFISH images for 12 genes imaged across 3 separate rounds of imaging in an anterior coronal section of the BLA:<br><br><br>First Round Imaging: <i>Nr4a2, Otof, Cdh13, Rorb</i>Second Round Imaging: <i>Adamts, Prss23, Bdnf, Slc5a5</i>Third Round Imaging: <i>Slc17a7, Nnat, Negr1, Cplx1</i>
DOI: 10.6084/m9.figshare.12899834.v1
title: Intermediate BLA

description: Registered multiplexed smFISH images for 12 genes imaged across 3 separate rounds of imaging in an intermediate coronal section of the BLA:<br><br><br>First Round Imaging: <i>Nr4a2, Otof, Cdh13, Rorb</i>Second Round Imaging: <i>Adamts, Prss23, Bdnf, Slc5a5</i>Third Round Imaging: <i>Slc17a7, Nnat, Negr1, Cplx1</i>
DOI: 10.6084/m9.figshare.12899834
title: Intermediate BLA

description: Registered multiplexed smFISH images for 12 genes imaged across 3 separate rounds of imaging in an intermediate coronal section of the BLA:<br><br><br>First Round Imaging: <i>Nr4a2, Otof, Cdh13, Rorb</i>Second Round Imaging: <i>Adamts, Prss23, Bdnf, Slc5a5</i>Third Round Imaging: <i>Slc17a7, Nnat, Negr1, Cplx1</i>
DOI: 10.6084/m9.figshare.12899828
title: Posterior BLA

description: Registered multiplexed smFISH images for 12 genes imaged across 3 separate rounds of imaging in a posterior coronal section of the BLA:<br><br><br>First Round Imaging: <i>Nr4a2, Otof, Cdh13, Rorb</i>Second Round Imaging: <i>Adamts, Prss23, Bdnf, Slc5a5</i>Third Round Imaging: <i>Slc17a7, Nnat, Negr1, Cplx1</i>
DOI: 10.6084/m9.figshare.12899783
title: Cell Size

description: Dataset of excitatory cells in the BLA segmented according to size (denoted by s<i>lc17a7</i> gene expression). Expression of lateral BLA marker gene <i>negr1</i> and basal BLA marker gene <i>cplx1 </i>used to distinguish differences in cell body size across the basal and lateral BLA (which were found to be significant).
DOI: 10.6084/m9.figshare.12899783.v1
title: Cell Size

description: Dataset of excitatory cells in the BLA segmented according to size (denoted by s<i>lc17a7</i> gene expression). Expression of lateral BLA marker gene <i>negr1</i> and basal BLA marker gene <i>cplx1 </i>used to distinguish differences in cell body size across the basal and lateral BLA (which were found to be significant).
DOI: 10.6084/m9.figshare.12659933.v2
title: Participant's Instrumented Gait Analysis Pre Post FES Cycling Therapy.xlsx

description: Instrumented gait analysis data calculated using the VICON motion capture system for patients who suffered a stroke. The data includes two conditions: baseline and post-intervention with a FES-Cycling system.