cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25442/hku.25496881
title: Supporting data for "New chemical probes for chemoproteomic profiling and redox biology investigation"

description: Emerging evidence presented the significance of cellular redox signalling in regulating protein expression and activity, hence modulating cancer proliferation and metastasis.<br>The signalling was mediated by redox-active species that induce reversible redox modifications on amino acid residues, such as cysteine Oxidative post-translational modification (OxiPTM). This led to dynamic regulation of cellular events, including survival, proliferation, and metastasis.<br>Yet, the underlying molecular mechanism of many redox signalling pathways remained undetermined. The transient and short-lived characteristics of redox species and the corresponding redox modification challenged the capture of the signalling process and recognition of the associated protein targets.<br>The thesis presented the synthesis and application of two chemical probes incorporated with the chemoproteomic approach to study cellular redox signalling from two perspectives: (1) the cysteine OxiPTM upon ROS stimulation and (2) the superoxide-induced proximity modification of proteins associated with superoxide biology.<br>
DOI: 10.25442/hku.25496881.v1
title: Supporting data for "New chemical probes for chemoproteomic profiling and redox biology investigation"

description: Emerging evidence presented the significance of cellular redox signalling in regulating protein expression and activity, hence modulating cancer proliferation and metastasis.<br>The signalling was mediated by redox-active species that induce reversible redox modifications on amino acid residues, such as cysteine Oxidative post-translational modification (OxiPTM). This led to dynamic regulation of cellular events, including survival, proliferation, and metastasis.<br>Yet, the underlying molecular mechanism of many redox signalling pathways remained undetermined. The transient and short-lived characteristics of redox species and the corresponding redox modification challenged the capture of the signalling process and recognition of the associated protein targets.<br>The thesis presented the synthesis and application of two chemical probes incorporated with the chemoproteomic approach to study cellular redox signalling from two perspectives: (1) the cysteine OxiPTM upon ROS stimulation and (2) the superoxide-induced proximity modification of proteins associated with superoxide biology.<br>
DOI: 10.15468/dl.a3j256
title: Occurrence Download

description: A dataset containing 873 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Omonadus formicarius (Goeze, 1777))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 873 records from 90 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025464-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25442/hku.25711212
title: Supporting data for "Investigating Biodiversity Dynamics and Anthropogenic Impacts in Coastal Ecosystems: Insights from Molecular Ecology Approaches"

description: To develop efficient survey methods that maximize sampling efforts to address gaps in contemporary biodiversity, environmental DNA (eDNA) metabarcoding and underwater visual census (UVC) surveys were compared in characterizing marine fish diversity across environmental gradients. eDNA recorded 90 putative species never recorded in UVC, with a few prospective new species to the territorial waters. Importantly, each survey method featured a distinct species profile, with 32.3% and 39.6% species found exclusively by UVC and eDNA respectively, highlighting the importance of complementing both UVC and eDNA metabarcoding survey for a complete overview of local biodiversity.I then looked into two major anthropogenic threats to the contemporary ecosystem, namely overexploitation and non-native species introduction. Here, I developed a novel species-specific quantitative PCR (qPCR) assay to detect occurrence of Hong Kong Grouper <i>Epinephelus akaara</i> through non-invasive environmental water samples. This endangered species suffers from overfishing, where monitoring will provide crucial insights for its conservation and management amidst dwindling populations. The designed qPCR assay offered high sensitivity and specificity to target species, but only 6.81% of water samples collected spatially and temporally across Hong Kong detected the species at a concentration below limit of detection, implying rarity in Hong Kong nowadays. Overall, the designed assay is a promising tool in documenting endangered species for species management and conservation.On the other hand, by utilizing gut content DNA metabarcoding, the dietary niche and prey composition of the hybrid grouper (TGGG) introduced from religious mercy release were assessed. In comparison with four local grouper species, TGGG exhibited six unique prey taxa, and displayed significant lower mean number of pray taxa. TGGG also revealed a significantly different diet composition, indicating diet transitioning and acquiring new feeding behavior. Such high taxonomic resolution analysis on the diet of released artificial hybrids demonstrates how local trophic dynamics could be impacted by release of animals through religious practices.Finally, I examine the role of interspecific genetic admixture in past speciation processes of <i>Epinephelus</i> spp under highly connected marine environment through whole genome resequencing. Results revealed rapid speciation rates were accompanied by multiple episodes of introgression events between ancestral lineages during speciation processes, with genetic admixture ranging from 1.67% to 6.78% were detected between species pairs of a subclade lineage. It is apparent the genetic admixture occurred between two lineages that preferred different habitats and water depths. This study provides novel insights into the genetic exchanges and evolutionary dynamics shaping the biodiversity of serranid fishes in the region.
DOI: 10.25442/hku.25711212.v1
title: Supporting data for "Investigating Biodiversity Dynamics and Anthropogenic Impacts in Coastal Ecosystems: Insights from Molecular Ecology Approaches"

description: To develop efficient survey methods that maximize sampling efforts to address gaps in contemporary biodiversity, environmental DNA (eDNA) metabarcoding and underwater visual census (UVC) surveys were compared in characterizing marine fish diversity across environmental gradients. eDNA recorded 90 putative species never recorded in UVC, with a few prospective new species to the territorial waters. Importantly, each survey method featured a distinct species profile, with 32.3% and 39.6% species found exclusively by UVC and eDNA respectively, highlighting the importance of complementing both UVC and eDNA metabarcoding survey for a complete overview of local biodiversity.I then looked into two major anthropogenic threats to the contemporary ecosystem, namely overexploitation and non-native species introduction. Here, I developed a novel species-specific quantitative PCR (qPCR) assay to detect occurrence of Hong Kong Grouper <i>Epinephelus akaara</i> through non-invasive environmental water samples. This endangered species suffers from overfishing, where monitoring will provide crucial insights for its conservation and management amidst dwindling populations. The designed qPCR assay offered high sensitivity and specificity to target species, but only 6.81% of water samples collected spatially and temporally across Hong Kong detected the species at a concentration below limit of detection, implying rarity in Hong Kong nowadays. Overall, the designed assay is a promising tool in documenting endangered species for species management and conservation.On the other hand, by utilizing gut content DNA metabarcoding, the dietary niche and prey composition of the hybrid grouper (TGGG) introduced from religious mercy release were assessed. In comparison with four local grouper species, TGGG exhibited six unique prey taxa, and displayed significant lower mean number of pray taxa. TGGG also revealed a significantly different diet composition, indicating diet transitioning and acquiring new feeding behavior. Such high taxonomic resolution analysis on the diet of released artificial hybrids demonstrates how local trophic dynamics could be impacted by release of animals through religious practices.Finally, I examine the role of interspecific genetic admixture in past speciation processes of <i>Epinephelus</i> spp under highly connected marine environment through whole genome resequencing. Results revealed rapid speciation rates were accompanied by multiple episodes of introgression events between ancestral lineages during speciation processes, with genetic admixture ranging from 1.67% to 6.78% were detected between species pairs of a subclade lineage. It is apparent the genetic admixture occurred between two lineages that preferred different habitats and water depths. This study provides novel insights into the genetic exchanges and evolutionary dynamics shaping the biodiversity of serranid fishes in the region.
DOI: 10.15468/dl.86g77u
title: Occurrence Download

description: A dataset containing 671 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Ampithoe valida S.I.Smith, 1873)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 671 records from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025465-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25442/hku.25712946
title: Supporting data for "Photoresponsive Nanomedicines for Cancer Stemness-targeted Combination Therapy"

description: The dataset includes figures, synthesis method, data analysis of nanoparticle characterization, in vitro and in vivo studies against cancer.In project 1, figures and data for molecular self-assembly based on photosensitizer, cell study and animal experiments were included. In project 2, figures and data for synthesis of photoresponsive nanocarrier, nanoparticle characterization, in vitro and in vivo studies against orthotopic mouse breast cancer were presented. In project 3, figures and data for synthesis of light-activatable prodrug, nanoparticle characterization, in vitro and in vivo studies against subcutaneous mouse colon cancer were included.
DOI: 10.25442/hku.25712946.v1
title: Supporting data for "Photoresponsive Nanomedicines for Cancer Stemness-targeted Combination Therapy"

description: The dataset includes figures, synthesis method, data analysis of nanoparticle characterization, in vitro and in vivo studies against cancer.In project 1, figures and data for molecular self-assembly based on photosensitizer, cell study and animal experiments were included. In project 2, figures and data for synthesis of photoresponsive nanocarrier, nanoparticle characterization, in vitro and in vivo studies against orthotopic mouse breast cancer were presented. In project 3, figures and data for synthesis of light-activatable prodrug, nanoparticle characterization, in vitro and in vivo studies against subcutaneous mouse colon cancer were included.
DOI: 10.25442/hku.25720086
title: Supporting data for "Deciphering and characterization of genetic architecture in complex diseases"

description: All the data and analytical codes utilized in the study are stored on the HKU CPOS server. Accessing paths have been described in the README file.
DOI: 10.25442/hku.25720086.v1
title: Supporting data for "Deciphering and characterization of genetic architecture in complex diseases"

description: All the data and analytical codes utilized in the study are stored on the HKU CPOS server. Accessing paths have been described in the README file.
DOI: 10.15468/dl.hmnfup
title: Occurrence Download

description: A dataset containing 284 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Ampithoe longimana Smith, 1873)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 284 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025467-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.smaygw
title: Occurrence Download

description: A dataset containing 3194 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Omonadus floralis (Linnaeus, 1758))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 3194 records from 184 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025466-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25442/hku.25721457
title: Supporting data for "Coronary artery disease biomarker discovery using computational omics approaches"

description: Metabolomic and lipidomic analysis in CAD using 33 mice. Plaque tissue were collected using the Multi-ABLE method and was analysed and processed using the multi-ABLE pipeline. Uploaded data includes the input data for multi-ABLE, processed data and the code to processed the data. Full data and methodology is published at https://doi.org/10.1016/j.isci.2023.106881.Proteomic analysis in CAD using 1004 samples. Plasma proteins were collected under the BioHEART study and is analysed using LC-MS. DIA-NN is used to process the LC-MS raw data. Uploaded data includes processed data and the code to generate the figures in the chapter.CITE-seq data in CAD using 51 samples. PBMC of 51 samples were collected under the BioHEART study and is analysed using CITE-seq. scClassify and Seurat is used to process and annotate the raw data. Uploaded data includes processed data and the code to generate those figures in the chapter which does not requires raw data.<br>
DOI: 10.25442/hku.25721457.v1
title: Supporting data for "Coronary artery disease biomarker discovery using computational omics approaches"

description: Metabolomic and lipidomic analysis in CAD using 33 mice. Plaque tissue were collected using the Multi-ABLE method and was analysed and processed using the multi-ABLE pipeline. Uploaded data includes the input data for multi-ABLE, processed data and the code to processed the data. Full data and methodology is published at https://doi.org/10.1016/j.isci.2023.106881.Proteomic analysis in CAD using 1004 samples. Plasma proteins were collected under the BioHEART study and is analysed using LC-MS. DIA-NN is used to process the LC-MS raw data. Uploaded data includes processed data and the code to generate the figures in the chapter.CITE-seq data in CAD using 51 samples. PBMC of 51 samples were collected under the BioHEART study and is analysed using CITE-seq. scClassify and Seurat is used to process and annotate the raw data. Uploaded data includes processed data and the code to generate those figures in the chapter which does not requires raw data.<br>
DOI: 10.15468/dl.v43xa6
title: Occurrence Download

description: A dataset containing 184 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Ampithoe pollex Kunkel, 1910)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 184 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025468-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.esv6vm
title: Occurrence Download

description: A dataset containing 28 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Anthicus crinitus La Ferté-Sénectère, 1849)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 28 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025469-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25442/hku.25729386
title: Supporting data for "Polymeric Microcapsules for Self-healing Application in Geotechnical Engineering"

description: This research designed and synthesized polymeric microcapsules by matching shell and cargo systems suitable for self-healing purposes in geotechnical applications. The research result demonstrated the microcapsules application in soil hydrophobicity recovery, enhanced soil remediation, soil strength recovery, and the arrest for soil desiccation cracking. The support data_Folder1 contains data for the chapter on soil hydrophobicity recovery. The support data_Folder2 contains data for the chapters on enhanced soil remediation. The support data_Folder3 and 4 contain data for the chapters on soil strength recovery. The support data_Folder5 contains data for the chapters on soil desiccation cracking. It includes the conceptual diagram, experiment process, microscopic, and SEM images in jpeg/tif format, the data for microcapsule characteristics, such as size, TGA analysis, and FTIR analysis, and the data for microcapsule performance assessment.
DOI: 10.25442/hku.25729386.v1
title: Supporting data for "Polymeric Microcapsules for Self-healing Application in Geotechnical Engineering"

description: This research designed and synthesized polymeric microcapsules by matching shell and cargo systems suitable for self-healing purposes in geotechnical applications. The research result demonstrated the microcapsules application in soil hydrophobicity recovery, enhanced soil remediation, soil strength recovery, and the arrest for soil desiccation cracking. The support data_Folder1 contains data for the chapter on soil hydrophobicity recovery. The support data_Folder2 contains data for the chapters on enhanced soil remediation. The support data_Folder3 and 4 contain data for the chapters on soil strength recovery. The support data_Folder5 contains data for the chapters on soil desiccation cracking. It includes the conceptual diagram, experiment process, microscopic, and SEM images in jpeg/tif format, the data for microcapsule characteristics, such as size, TGA analysis, and FTIR analysis, and the data for microcapsule performance assessment.
DOI: 10.25442/hku.25731156
title: <i>Supporting data for “</i><b>FASN inhibition complements PD-L1 checkpoint blockade by suppressing palmitoylation of MHC-I in hepatocellular carcinoma</b><i>”.</i>

description: The advent of immune checkpoint inhibitors (ICIs) has revolutionized the treatment approach for hepatocellular carcinoma (HCC). However, patients with lowered major histocompatibility complex class I (MHC-I) expression continue to exhibit resistance to ICIs, and there are limited targets available for enhancing MHC-I levels. In this study, we discovered that inhibiting fatty acid synthase (FASN), either genetically or pharmacologically, elevated HCC cells' MHC-I levels. The cytotoxicity of CD8+ T lymphocytes that are specific to the antigens was activated and antigen presentation was strengthened by this increase in MHC-I. Mechanistically, FASN inhibition decreased MHC-I's palmitoylation, which in turn inhibited lysosome degradation of MHC-I. We identified the palmitoyltransferase DHHC3 as a direct binder of MHC-I, exerting a negative regulation on the levels of MHC-I protein. The lack of<i> Fasn</i> increased MHC-I levels in an orthotopic HCC mice model and facilitate CD8+ T lymphocytes infiltrating the tumor and eliminating cancer cells. Moreover, combining anti-PD-L1 antibody with two different FASN inhibitors, orlistat and TVB-2640, effectively inhibited the growth of tumors in vivo. Furthermore, it was shown that a higher percentage of cytotoxic CD8+ T cells was connected with decreased expression of FASN by multiplex immunohistochemistry of human HCC samples and bioinformatic analysis of TCGA data. The discovery of FASN as a negative regulator of MHC-I offers a rationale for combining FASN inhibitors with immunotherapy for the treatment of HCC.
DOI: 10.25442/hku.25731156.v1
title: <i>Supporting data for “</i><b>FASN inhibition complements PD-L1 checkpoint blockade by suppressing palmitoylation of MHC-I in hepatocellular carcinoma</b><i>”.</i>

description: The advent of immune checkpoint inhibitors (ICIs) has revolutionized the treatment approach for hepatocellular carcinoma (HCC). However, patients with lowered major histocompatibility complex class I (MHC-I) expression continue to exhibit resistance to ICIs, and there are limited targets available for enhancing MHC-I levels. In this study, we discovered that inhibiting fatty acid synthase (FASN), either genetically or pharmacologically, elevated HCC cells' MHC-I levels. The cytotoxicity of CD8+ T lymphocytes that are specific to the antigens was activated and antigen presentation was strengthened by this increase in MHC-I. Mechanistically, FASN inhibition decreased MHC-I's palmitoylation, which in turn inhibited lysosome degradation of MHC-I. We identified the palmitoyltransferase DHHC3 as a direct binder of MHC-I, exerting a negative regulation on the levels of MHC-I protein. The lack of<i> Fasn</i> increased MHC-I levels in an orthotopic HCC mice model and facilitate CD8+ T lymphocytes infiltrating the tumor and eliminating cancer cells. Moreover, combining anti-PD-L1 antibody with two different FASN inhibitors, orlistat and TVB-2640, effectively inhibited the growth of tumors in vivo. Furthermore, it was shown that a higher percentage of cytotoxic CD8+ T cells was connected with decreased expression of FASN by multiplex immunohistochemistry of human HCC samples and bioinformatic analysis of TCGA data. The discovery of FASN as a negative regulator of MHC-I offers a rationale for combining FASN inhibitors with immunotherapy for the treatment of HCC.
DOI: 10.25442/hku.25745661
title: <i>Supporting data for</i> "<i>Emerging Computational Approaches For Predictive Nanomaterial Design And Redox Mechanism Exploration Toward Efficient Electrocatalysis</i><i>"</i>

description: Computational techniques play a critical role in the design and optimization of electrocatalysts, offering invaluable insights into their structure-function relationships and catalytic mechanisms for various electrocatalytic reactions. By employing density functional theory (DFT) calculation, researchers can analyze the electronic structure, explore the reaction mechanism, predict material properties, and identify promising catalyst candidates with enhanced activity, selectivity, and stability. The main idea of this thesis is utilizing emerging computational approaches to explore redox mechanism and predict nanomaterials design toward efficient electrocatalysis.Here, in this dataset, it contains the nanomaterials structure optimized by DFT calculations. The DFT calculated energy for each structure. Then training data and the testing data of machine learning model were included in this dataset. Finally, the constructed Wulff constructions, phase diagrams and free energy diagrams were all included in this dataset.