cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7725020
title: Supplementary Material for: Amelioration of Uremic Toxin Indoxyl Sulfate-Induced Osteoblastic Calcification by SET Domain Containing Lysine Methyltransferase 7/9 Protein

description: <b><i>Background:</i></b> Vascular calcification (VC) is a very common phenomenon in patients with chronic kidney disease (CKD). It has been reported that some histone methylation play a role in VC as an epigenetic regulator. Indoxyl sulfate (IS) is a protein-bound uremic toxin that has been proven as one of the major risk factors of cardiovascular disease in CKD. SET domain containing lysine methyltransferase 7/9 (SET7/9) is one of the important histone methyltransferases. <b><i>Objectives:</i></b> This study aimed to determine the effect of IS on the expression of SET7/9 and the role of SET7/9 in IS-induced osteoblastic differentiation and calcification of vascular smooth muscle cells (VSMCs). <b><i>Methods:</i></b> VSMCs were incubated with various concentrations of IS for different durations to assess osteoblastic differentiation and expression of SET7/9. Western blot analysis and quantitative real-time polymerase chain reaction were performed to assess the protein and mRNA levels of SET7/9 respectively. The calcium content was measured to evaluate calcification. <b><i>Results:</i></b> Osteoblastic differentiation and calcification of VSMCs and downregulation of the expression of SET7/9 were observed after IS treatment. The autophagy was activated after treatment with IS, whereas the inhibition of the autophagy partially attenuated the effect of IS on both the stimulation of the expression of runt-related transcription factor 2 and calcium deposition. <b><i>Conclusions:</i></b> Our data demonstrated that SET7/9 downregulation and autophagy activation may be the key mechanism of IS-induced VC in CKD.
DOI: 10.6084/m9.figshare.7725092.v1
title: Visual Function in Mice Lacking GM3 Synthase

description: <b>Purpose</b>: Most complex gangliosides in vertebrates are formed from ganglioside GM3. GM3 deficiency in humans can result in epilepsy and visual impairment. To investigate whether a deficiency of GM3 is involved in visual function, ST3GAL5<sup>−/−</sup> mice with mutations in the ST3GAL5 gene-coded GM3 synthase were employed. <b>Materials and Methods</b>: Sixty mice were employed in this study. The glycosphingolipids of mice retinas were analyzed through high performance thin layer chromatography. The morphology of the optic nerves and retinas were evaluated by hematoxylin and eosin staining and immunohistochemical analysis using an anti-glial fibrillary acidic protein (GFAP) antibody. An electroretinogram (ERG) was applied on the eyes of 4, 9, 12, and 14-month-old mice. Also, visual evoked potential (VEP) was applied on 13-month-old mice. <b>Results</b>: The GM3 in the retinas was detected in ST3GAL5<sup>+/+</sup> mice but not ST3GAL5<sup>−/−</sup> mice. Also, GM1b and GD1α expressions and lactosylceramide accumulation were found in the ST3GAL5<sup>−/−</sup> mouse retinas. There was no significant difference in GFAP expression in the retinas or optic discs between ST3GAL5<sup>+/+</sup> and ST3GAL5<sup>−/−</sup> mice. Furthermore, the outcome of ERG and VEP analysis showed no disparity between the two strains in 13 and 14-month-old mice. <b>Conclusion</b>: In the eye, neither histopathological abnormalities nor abnormal functions of the retina were found in GM3-deficient mice. Differing from the situation in patients with GM3 deficiency, the lack of GM3 in mice did not lead to optic nerve atrophy.
DOI: 10.6084/m9.figshare.7725020.v1
title: Supplementary Material for: Amelioration of Uremic Toxin Indoxyl Sulfate-Induced Osteoblastic Calcification by SET Domain Containing Lysine Methyltransferase 7/9 Protein

description: <b><i>Background:</i></b> Vascular calcification (VC) is a very common phenomenon in patients with chronic kidney disease (CKD). It has been reported that some histone methylation play a role in VC as an epigenetic regulator. Indoxyl sulfate (IS) is a protein-bound uremic toxin that has been proven as one of the major risk factors of cardiovascular disease in CKD. SET domain containing lysine methyltransferase 7/9 (SET7/9) is one of the important histone methyltransferases. <b><i>Objectives:</i></b> This study aimed to determine the effect of IS on the expression of SET7/9 and the role of SET7/9 in IS-induced osteoblastic differentiation and calcification of vascular smooth muscle cells (VSMCs). <b><i>Methods:</i></b> VSMCs were incubated with various concentrations of IS for different durations to assess osteoblastic differentiation and expression of SET7/9. Western blot analysis and quantitative real-time polymerase chain reaction were performed to assess the protein and mRNA levels of SET7/9 respectively. The calcium content was measured to evaluate calcification. <b><i>Results:</i></b> Osteoblastic differentiation and calcification of VSMCs and downregulation of the expression of SET7/9 were observed after IS treatment. The autophagy was activated after treatment with IS, whereas the inhibition of the autophagy partially attenuated the effect of IS on both the stimulation of the expression of runt-related transcription factor 2 and calcium deposition. <b><i>Conclusions:</i></b> Our data demonstrated that SET7/9 downregulation and autophagy activation may be the key mechanism of IS-induced VC in CKD.
DOI: 10.7284/122191
title: GNSS (Global Navigation Satellite System) data collected during research cruise AR5 using a C&C C-Nav 3050 instrument system onboard the platform RV Neil Armstrong

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7724999
title: RawData_Blanchart_et_al.2019 ASE

description: Raw data of the experimental study performed by the team Blanchart et al. 2019 at the University of Antananarivo Laboratory of Radio-Isotopes concerning the role of dual fertilization of silicon and earthworms on rice growth and nutrition and tolerance against the disease Pyricularia oryzae growing on a poor tropical soil.<br>
DOI: 10.6084/m9.figshare.7724987
title: Epigenetic activation of <i>POTE</i> genes in ovarian cancer

description: The <i>POTE</i> gene family consists of 14 homologous genes localized to autosomal pericentromeres, and a sub-set of <i>POTEs</i> are cancer-testis antigen (CTA) genes. <i>POTE</i>s are over-expressed in epithelial ovarian cancer (EOC), including the high-grade serous subtype (HGSC), and expression of individual <i>POTEs</i> correlates with chemoresistance and reduced survival in HGSC. The mechanisms driving <i>POTE</i> overexpression in EOC and other cancers is unknown. Here, we investigated the role of epigenetics in regulating <i>POTE</i> expression, with a focus on DNA hypomethylation. Consistent with their pericentromeric localization, <i>Pan-POTE</i> expression in EOC correlated with expression of the pericentromeric repeat <i>NBL2</i>, which was not the case for non-pericentromeric CTAs. <i>POTE</i> genomic regions contain <i>LINE-1</i> (L1) sequences, and <i>Pan-POTE</i> expression correlated with both global and <i>POTE</i>-specific L1 hypomethylation in EOC. Analysis of individual <i>POTEs</i> using RNA-seq and DNA methylome data from fallopian tube epithelia (FTE) and HGSC revealed that <i>POTEs C, E, and F</i> have increased expression in HGSC in conjunction with DNA hypomethylation at 5’ promoter or enhancer regions. Moreover, <i>POTEs C/E/F</i> showed additional increased expression in recurrent HGSC in conjunction with 5’ hypomethylation, using patient-matched samples. Experiments using decitabine treatment and DNMT knockout cell lines verified a functional contribution of DNA methylation to <i>POTE</i> repression, and epigenetic drug combinations targeting histone deacetylases (HDACs) and histone methyltransferases (HMTs) in combination with decitabine further increased <i>POTE</i> expression. In summary, several alterations of the cancer epigenome, including pericentromeric activation, global and locus-specific <i>L1</i> hypomethylation, and locus-specific 5’ CpG hypomethylation, converge to promote <i>POTE</i> expression in ovarian cancer.
DOI: 10.7284/122297
title: Gyrocompass data collected during research cruise AR5 using a Sperry NAVIGAT X MK 1 instrument system onboard the platform RV Neil Armstrong

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7724987.v1
title: Epigenetic activation of <i>POTE</i> genes in ovarian cancer

description: The <i>POTE</i> gene family consists of 14 homologous genes localized to autosomal pericentromeres, and a sub-set of <i>POTEs</i> are cancer-testis antigen (CTA) genes. <i>POTE</i>s are over-expressed in epithelial ovarian cancer (EOC), including the high-grade serous subtype (HGSC), and expression of individual <i>POTEs</i> correlates with chemoresistance and reduced survival in HGSC. The mechanisms driving <i>POTE</i> overexpression in EOC and other cancers is unknown. Here, we investigated the role of epigenetics in regulating <i>POTE</i> expression, with a focus on DNA hypomethylation. Consistent with their pericentromeric localization, <i>Pan-POTE</i> expression in EOC correlated with expression of the pericentromeric repeat <i>NBL2</i>, which was not the case for non-pericentromeric CTAs. <i>POTE</i> genomic regions contain <i>LINE-1</i> (L1) sequences, and <i>Pan-POTE</i> expression correlated with both global and <i>POTE</i>-specific L1 hypomethylation in EOC. Analysis of individual <i>POTEs</i> using RNA-seq and DNA methylome data from fallopian tube epithelia (FTE) and HGSC revealed that <i>POTEs C, E, and F</i> have increased expression in HGSC in conjunction with DNA hypomethylation at 5’ promoter or enhancer regions. Moreover, <i>POTEs C/E/F</i> showed additional increased expression in recurrent HGSC in conjunction with 5’ hypomethylation, using patient-matched samples. Experiments using decitabine treatment and DNMT knockout cell lines verified a functional contribution of DNA methylation to <i>POTE</i> repression, and epigenetic drug combinations targeting histone deacetylases (HDACs) and histone methyltransferases (HMTs) in combination with decitabine further increased <i>POTE</i> expression. In summary, several alterations of the cancer epigenome, including pericentromeric activation, global and locus-specific <i>L1</i> hypomethylation, and locus-specific 5’ CpG hypomethylation, converge to promote <i>POTE</i> expression in ovarian cancer.
DOI: 10.6084/m9.figshare.7724999.v2
title: RawData_Blanchart_et_al.2019 ASE

description: Raw data of the experimental study performed by the team Blanchart et al. 2019 at the University of Antananarivo Laboratory of Radio-Isotopes concerning the role of dual fertilization of silicon and earthworms on rice growth and nutrition and tolerance against the disease Pyricularia oryzae growing on a poor tropical soil.<br>
DOI: 10.7284/122301
title: Multibeam Echosounder data collected during research cruise AR5 using a Kongsberg EM122 instrument system onboard the platform RV Neil Armstrong

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.5281/zenodo.8075063
title: Source code: Bilateral human laryngeal motor cortex in perceptual decision of lexical tone and voicing of consonant

description: Source code (and data) for the paper <em>Bilateral Human Laryngeal Motor Cortex in Perceptual Decision of Lexical Tone and Voicing of Consonant</em>. Exp1_datacollection.zip:code for data collection in Experiment 1. Exp2_datacollection.zip: code for data collection in Experiment 2. codes_for_dataprocess.zip:data processing code and source data. Exp1 and Exp2 collection codes are provided for reference, but for practice, due to copyright and software environment issues, please contact Baishen (liangbs@psych.ac.cn, liangbs95@gmail.com) for technical assistant.
DOI: 10.5281/zenodo.8103223
title: Source code: Bilateral human laryngeal motor cortex in perceptual decision of lexical tone and voicing of consonant

description: Source code (and data) for the paper <em>Bilateral Human Laryngeal Motor Cortex in Perceptual Decision of Lexical Tone and Voicing of Consonant</em>. Exp1_datacollection.zip:code for data collection in Experiment 1. Exp2_datacollection.zip: code for data collection in Experiment 2. codes_for_dataprocess.zip:data processing code and source data. Exp1 and Exp2 collection codes are provided for reference, but for practice, due to copyright and software environment issues, please contact Baishen (liangbs@psych.ac.cn, liangbs95@gmail.com) for technical assistant.
DOI: 10.5281/zenodo.8214407
title: Source code: Bilateral human laryngeal motor cortex in perceptual decision of lexical tone and voicing of consonant

description: Source code (and data) for the paper <em>Bilateral Human Laryngeal Motor Cortex in Perceptual Decision of Lexical Tone and Voicing of Consonant</em>. Exp1_datacollection.zip:code for data collection in Experiment 1. Exp2_datacollection.zip: code for data collection in Experiment 2. codes_for_dataprocess.zip:data processing code and source data. Exp1 and Exp2 collection codes are provided for reference, but for practice, due to copyright and software environment issues, please contact Baishen (liangbs@psych.ac.cn, liangbs95@gmail.com) for technical assistant.
DOI: 10.6084/m9.figshare.23856591
title: <b>利用高渗透率可再生能源实现Data_Dynamic网络改造</b><b>与无功电压调节协同优化</b>

description: data of load and branch
DOI: 10.6084/m9.figshare.23856591.v1
title: <b>利用高渗透率可再生能源实现Data_Dynamic网络改造</b><b>与无功电压调节协同优化</b>

description: data of load and branch
DOI: 10.48366/r604175
title: Crop mapping and field area estimation from Multispectral Satellite Remote Sensing data

description: Crop mapping and field area estimation using multispectral satellite remote sensing data involve using satellite imagery to identify different types of crops and accurately measure the area they occupy in a given area. This comparison will benefit Precision Agriculture, Yield Prediction, Land Use Planning, Food Security and Risk Assessment.
DOI: 10.5517/ccdc.csd.cc2c4yn4
title: CCDC 2179506: Experimental Crystal Structure Determination

description: Related Article: Sofie M. P. Vanden Broeck, Nikolaos V. Tzouras, Marina Saab, Kristof Van Hecke, Busra Dereli, Ida Ritacco, Luigi Cavallo, Georgios C. Vougioukalakis, Pierre Braunstein, Steven P. Nolan, Andreas A. Danopoulos, Catherine S. J. Cazin|2023|Dalton Trans.|52|9908|doi:10.1039/D3DT02086J
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2c4yp5
title: CCDC 2179507: Experimental Crystal Structure Determination

description: Related Article: Sofie M. P. Vanden Broeck, Nikolaos V. Tzouras, Marina Saab, Kristof Van Hecke, Busra Dereli, Ida Ritacco, Luigi Cavallo, Georgios C. Vougioukalakis, Pierre Braunstein, Steven P. Nolan, Andreas A. Danopoulos, Catherine S. J. Cazin|2023|Dalton Trans.|52|9908|doi:10.1039/D3DT02086J
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2c4yq6
title: CCDC 2179508: Experimental Crystal Structure Determination

description: Related Article: Sofie M. P. Vanden Broeck, Nikolaos V. Tzouras, Marina Saab, Kristof Van Hecke, Busra Dereli, Ida Ritacco, Luigi Cavallo, Georgios C. Vougioukalakis, Pierre Braunstein, Steven P. Nolan, Andreas A. Danopoulos, Catherine S. J. Cazin|2023|Dalton Trans.|52|9908|doi:10.1039/D3DT02086J
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2c4yr7
title: CCDC 2179509: Experimental Crystal Structure Determination

description: Related Article: Sofie M. P. Vanden Broeck, Nikolaos V. Tzouras, Marina Saab, Kristof Van Hecke, Busra Dereli, Ida Ritacco, Luigi Cavallo, Georgios C. Vougioukalakis, Pierre Braunstein, Steven P. Nolan, Andreas A. Danopoulos, Catherine S. J. Cazin|2023|Dalton Trans.|52|9908|doi:10.1039/D3DT02086J
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6084/m9.figshare.23855835
title: The phylogenetic reconstruction of the Neotropical cycad genus <i>Ceratozamia</i> (Zamiaceae) reveals disparate patterns of niche evolution

description: MIG-seq data of 145 samples of most <i>Ceratozamia</i> species are included in a compressed file. Also, the PC1, PC2 scores of niche variation for each evaluated species, and the input and output files of the phylogenetic analyses of three filtering steps (Step1, Step2 and Step3) are included.
DOI: 10.6084/m9.figshare.23855835.v1
title: The phylogenetic reconstruction of the Neotropical cycad genus <i>Ceratozamia</i> (Zamiaceae) reveals disparate patterns of niche evolution

description: MIG-seq data of 145 samples of most <i>Ceratozamia</i> species are included in a compressed file. Also, the PC1, PC2 scores of niche variation for each evaluated species, and the input and output files of the phylogenetic analyses of three filtering steps (Step1, Step2 and Step3) are included.
DOI: 10.5281/zenodo.8214462
title: The Antarctic sea ice reconstruction (CMST-South) based on the optimized Data Assimilation System for the Southern Ocean

description: The wealth of historical sea ice concentration (SIC) observations, coupled with their extensive spatial coverage, renders them indispensable for the reconstruction of long-term Antarctic sea ice variability. However, recent studies have pointed out the presence of significant uncertainties in certain aspects of Antarctic sea ice reanalyses obtained from assimilating SIC. Notably, while previous studies on ocean data assimilation have already demonstrated the significance of optimizing model-dependent parameters for assimilating oceanic observations, this aspect has received limited attention in current sea ice data assimilation studies. As a result, whether optimizing model-dependent parameters can enhance the effectiveness of assimilating SIC remains an open question. Thus, we address this gap by refining the model-dependent parameters of Data Assimilation System for the Southern Ocean (DASSO), including the development of a latitude-dependent localization scheme and the objective estimation of observation error variance of SIC which takes into account both measurement errors and representation errors. Here, the monthly anomalies in Antarctic sea ice extent and volume (1980 -2018) are uploaded which is produced by the optimized Data Assimilation System for the Southern Ocean (DASSO) with assimilating SIC. Besides, a 13-month moving mean is applied to monthly anomalies to focus on the low-frequency variability of Antarctic sea ice.
DOI: 10.5281/zenodo.8214461
title: The Antarctic sea ice reconstruction (CMST-South) based on the optimized Data Assimilation System for the Southern Ocean

description: The wealth of historical sea ice concentration (SIC) observations, coupled with their extensive spatial coverage, renders them indispensable for the reconstruction of long-term Antarctic sea ice variability. However, recent studies have pointed out the presence of significant uncertainties in certain aspects of Antarctic sea ice reanalyses obtained from assimilating SIC. Notably, while previous studies on ocean data assimilation have already demonstrated the significance of optimizing model-dependent parameters for assimilating oceanic observations, this aspect has received limited attention in current sea ice data assimilation studies. As a result, whether optimizing model-dependent parameters can enhance the effectiveness of assimilating SIC remains an open question. Thus, we address this gap by refining the model-dependent parameters of Data Assimilation System for the Southern Ocean (DASSO), including the development of a latitude-dependent localization scheme and the objective estimation of observation error variance of SIC which takes into account both measurement errors and representation errors. Here, the monthly anomalies in Antarctic sea ice extent and volume (1980 -2018) are uploaded which is produced by the optimized Data Assimilation System for the Southern Ocean (DASSO) with assimilating SIC. Besides, a 13-month moving mean is applied to monthly anomalies to focus on the low-frequency variability of Antarctic sea ice.
DOI: 10.5281/zenodo.8208562
title: Resolution Enhancement and Deblurring of Porous Media μ-CT Images based on Super Resolution Generative Adversarial Network

description: The above is the Data2 of Super Resolution Generative Adversarial Network based on High-Resolution Representation Learning.
DOI: 10.5281/zenodo.7347656
title: Spatially-regularized imputation of spatial transcriptomes from single-cell reference

description: Recent spatial transcriptomics technologies offer a lens of observing the spatial distribution of RNA transcripts in tissues, yet achieving a whole-genome-level spatial landscape remains technically challenging. Multiple computational methods hence have been proposed to impute missing genes from a single-cell reference dataset, while they lack mechanisms of explicitly encoding spatial patterns in their modeling.<br> <br> To fill the research gaps, we introduced a computational model, TransImp, that leverages a spatial auto-correlation metric as a regularization for imputing missing features in ST. Evaluation results from multiple platforms demonstrate that TransImp remarkably preserves the spatial patterns and achieves robust and state-of-the-art accuracy for imputing missing features, including both matched modality and unseen nascent RNAs. -------------------- This repository includes all the input data (data.tar.gz) and output data (output.tar.gz) for generating figures and tables in results.<br>
DOI: 10.5281/zenodo.7347655
title: Reliable imputation of spatial transcriptome with uncertainty estimation and spatial regularization

description: Imputation of missing features in spatial transcriptomics is urgently demanded due to technology limitations, while most existing computational methods suffer from moderate accuracy and cannot estimate the reliability of the imputation. <br> To fill the research gaps, we introduce a computational model, TransImp, that imputes the missing feature modality in spatial transcriptomics by mapping it from single-cell reference. Uniquely, we derived a set of attributes that can accurately predict imputation uncertainty, hence enabling us to select reliably imputed genes. Also, we introduced a spatial auto-correlation metric as a regularization to avoid overestimating spatial patterns. Multiple datasets from various platforms have demonstrated that our approach significantly improves the reliability of downstream analyses in detecting spatial variable genes and interacting ligand-receptor pairs. Therefore, TransImp offers a way towards a reliable spatial analysis of missing features for both matched and unseen modalities, e.g., nascent RNAs.