cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25442/hku.24794517.v1
title: Supporting data for the thesis "<b>Transcriptional Plasticity and Environmental Change in Marine Fishes</b>"

description: This dissertation focuses on transcriptional plasticity and its regulation in marine fishes in response to changes in their environment. Several factors that influence plastic responses such as environmental stability, parental experiences, and the presence of genetic variation for plasticity are studied. Additionally, this thesis also explores molecular processes underlying the mutualistic relationship between the anemone and anemonefish.
DOI: 10.25442/hku.24844530
title: Supporting data for "The Roles of Src Homology 3 Domain Binding Kinase 1 in Lipid Metabolism"

description: The function and molecular mechanisms of a novel kinase protein Src Homology 3 Domain Binding Kinase 1 (SBK1）in the liver under fasting conditions. The supporting data was collected from different experiments. Gene expression profiling in tissues was performed using RNA sequencing, microarray, and real-time PCR. Activation of intracellular signaling pathways was determined by Western blotting. Dual-luciferase assay was used to characterize the promoter and responsive element activities. FAO in cells and tissues was measured using <sup>14</sup>C-palmitate oxidation. Protein-protein interactions were investigated by GST pull-down and immunoprecipitation.
DOI: 10.25442/hku.24844530.v1
title: Supporting data for "The Roles of Src Homology 3 Domain Binding Kinase 1 in Lipid Metabolism"

description: The function and molecular mechanisms of a novel kinase protein Src Homology 3 Domain Binding Kinase 1 (SBK1）in the liver under fasting conditions. The supporting data was collected from different experiments. Gene expression profiling in tissues was performed using RNA sequencing, microarray, and real-time PCR. Activation of intracellular signaling pathways was determined by Western blotting. Dual-luciferase assay was used to characterize the promoter and responsive element activities. FAO in cells and tissues was measured using <sup>14</sup>C-palmitate oxidation. Protein-protein interactions were investigated by GST pull-down and immunoprecipitation.
DOI: 10.25442/hku.24872235
title: <i>Supporting data for “</i> Evaluating the capabilities of POU (Pit-Oct-Unc) transcription factors to engage epigenetically silenced chromatin<i>”</i>

description: This is the dataset used for the PhD thesis entitled <i>“</i>Evaluating the capabilities of POU (Pit-Oct-Unc) transcription factors to engage epigenetically silenced chromatin<i>”</i>.Pioneer transcription factors (TFs) bind to and activate epigenetically silenced chromatin, making them critical regulators of cell fate. Oct4 of the Pit-Oct-Unc (POU) TF family is essential to establishing and maintaining pluripotency. Oct4 binds to silenced chromatin, such as methylated DNA or DNA compacted by nucleosome core particles (NCPs). Significant gaps remain to accurately define the unique traits of pioneer TFs to differentiate them from collaborating non-pioneering TFs. Furthermore, the mechanism behind how Oct4 asserts its function on methylated DNA remains elusive. Here, Oct4's interaction with a methylated DNA element called “CpGpal” was examined. We then compared Oct4 and Brn2's binding to methylated DNA and nucleosome core particles (NCPs) through biochemical and structural analyses. Through this comparison, we aim to uncover whether differential engagement with methylated DNA and NCPs could contribute to their contrasting biological functions.Furthermore, the evaluation of POU factors and their partners was further explored from a molecular evolution perspective. POU and their interactions with Sox factors are crucial to regulating stemness in mammals. To investigate the evolutionary conservation of biochemical properties in unicellular relatives of animals, we compared Sox and POU TFs from choanoflagellates and filastereans to their mammalian counterparts.
DOI: 10.25442/hku.24872235.v1
title: <i>Supporting data for “</i> Evaluating the capabilities of POU (Pit-Oct-Unc) transcription factors to engage epigenetically silenced chromatin<i>”</i>

description: This is the dataset used for the PhD thesis entitled <i>“</i>Evaluating the capabilities of POU (Pit-Oct-Unc) transcription factors to engage epigenetically silenced chromatin<i>”</i>.Pioneer transcription factors (TFs) bind to and activate epigenetically silenced chromatin, making them critical regulators of cell fate. Oct4 of the Pit-Oct-Unc (POU) TF family is essential to establishing and maintaining pluripotency. Oct4 binds to silenced chromatin, such as methylated DNA or DNA compacted by nucleosome core particles (NCPs). Significant gaps remain to accurately define the unique traits of pioneer TFs to differentiate them from collaborating non-pioneering TFs. Furthermore, the mechanism behind how Oct4 asserts its function on methylated DNA remains elusive. Here, Oct4's interaction with a methylated DNA element called “CpGpal” was examined. We then compared Oct4 and Brn2's binding to methylated DNA and nucleosome core particles (NCPs) through biochemical and structural analyses. Through this comparison, we aim to uncover whether differential engagement with methylated DNA and NCPs could contribute to their contrasting biological functions.Furthermore, the evaluation of POU factors and their partners was further explored from a molecular evolution perspective. POU and their interactions with Sox factors are crucial to regulating stemness in mammals. To investigate the evolutionary conservation of biochemical properties in unicellular relatives of animals, we compared Sox and POU TFs from choanoflagellates and filastereans to their mammalian counterparts.
DOI: 10.25442/hku.24885510
title: Supporting data for "HARNESSING METAL-FREE PHOTOCATALYSTS FOR RENEWABLE HYDROGEN AND HYDROGEN PEROXIDE".

description: This thesis synthesizes and applies functional nonmetal-based photocatalysts generating renewable energy carriers under visible light. The photocatalytic performance of the synthesized photocatalysts could generate hydrogen or hydrogen peroxide effectively under visible irradiation, respectively.
DOI: 10.25442/hku.24885510.v1
title: Supporting data for "HARNESSING METAL-FREE PHOTOCATALYSTS FOR RENEWABLE HYDROGEN AND HYDROGEN PEROXIDE".

description: This thesis synthesizes and applies functional nonmetal-based photocatalysts generating renewable energy carriers under visible light. The photocatalytic performance of the synthesized photocatalysts could generate hydrogen or hydrogen peroxide effectively under visible irradiation, respectively.
DOI: 10.25442/hku.24901455
title: Supporting data for "Molecular and functional characterization of leptin receptor-positive mesenchymal stem cells in human endometrium"

description: Chapter 2 provides a single-cell dataset of cultured MCs.Chapter 3 is comprised of multiple functional assays, including colony-forming ability, in-vitro differentiation, immunochemistry, immunofluorescent staining, cell cycle analysis, etc.Chapter 4 established two in-vitro quiescent models: serum starvation-induced and activation of Notch signaling induced.
DOI: 10.25442/hku.24901455.v1
title: Supporting data for "Molecular and functional characterization of leptin receptor-positive mesenchymal stem cells in human endometrium"

description: Chapter 2 provides a single-cell dataset of cultured MCs.Chapter 3 is comprised of multiple functional assays, including colony-forming ability, in-vitro differentiation, immunochemistry, immunofluorescent staining, cell cycle analysis, etc.Chapter 4 established two in-vitro quiescent models: serum starvation-induced and activation of Notch signaling induced.
DOI: 10.25442/hku.24906834
title: <b><i>Supporting data for </i></b>"Unraveling Fertility Treatment Decisions: Working with Women Dealing with Unsuccessful In-vitro Fertilization"

description: This research aimed to explore the decision-making experience of women with failed IVF treatment and to investigate the effectiveness of a tailored psychosocial intervention for women following unsuccessful IVF treatment. The dataset includes both qualitative and quantitative data. The folder of qualitative data includes raw interview recordings, interview scripts, and ethical approval as required. The folder of quantitative data includes a cleaned dataset of an RCT study, the analysis results, intervention case notes, ethical approvals, informed consent, and questionnaires.
DOI: 10.25442/hku.24906834.v1
title: <b><i>Supporting data for </i></b>"Unraveling Fertility Treatment Decisions: Working with Women Dealing with Unsuccessful In-vitro Fertilization"

description: This research aimed to explore the decision-making experience of women with failed IVF treatment and to investigate the effectiveness of a tailored psychosocial intervention for women following unsuccessful IVF treatment. The dataset includes both qualitative and quantitative data. The folder of qualitative data includes raw interview recordings, interview scripts, and ethical approval as required. The folder of quantitative data includes a cleaned dataset of an RCT study, the analysis results, intervention case notes, ethical approvals, informed consent, and questionnaires.
DOI: 10.6084/m9.figshare.24802719
title: <b>Two-photon excitation fluorescence </b><b>microspectroscopy protocols for examining </b><b>fluorophores in fossil plants</b>

description: Fluorescence emission is a common occurrence in plants and serves multiple functions, such as aiding photosynthesis, attracting pollinators and seed-dispersing mammals, warning insects of chemical defenses, and providing UV protection. Plant fluorescence can serve as an indicator of various physiological processes and provide valuable information about their health and vitality. While fluorescence microscopy has been widely used to study living plants, its application in quantifying the fluorescence of fossilized plants has been limited. Investigating the compounds responsible for fluorescence in fossil plants, whether from original fluorophores or formed during fossilization, can offer valuable insights into fluorescence in ancient plants and the fossilization processes. In this work, we utilized two-photon fluorescence microspectroscopy to spatially and spectrally resolve the fluorescence emitted by different fossil plants, including amber-embedded plants, leaf compression fossils, and silicified wood. The advanced micro-spectroscope utilized in this study, with its pixel-level spectral resolution and line-scan excitation capabilities, allowed us to collect comprehensive excitation and emission spectra with high sensitivity and minimal laser damage to the specimens. By applying linear spectral unmixing to the spectrally resolved fluorescence images, we could differentiate between (a) the matrix and (b) the original biological material or chemical products formed during fossilization. Our analysis suggests that the latter correspond to the durable tissues of the fossils, such as lignin and cellulose. Additionally, we observed potential signals from chlorophyll derivatives, although minerals could have contributed to this fingerprint. Combining this information with chemical analyses of the fossils will improve our understanding of the organic composition of fluorescent plant fossils and enhance the interpretation of fluorescence emission spectra. This research opens doors to exploring the ancient ecosystems and potentially understanding the ecological roles of fluorescence in plants throughout geological time. The findings may have broader implications in the field of paleobotany, offering insights into the evolution of fluorescence in plants and its relevance to ancient plant-animal interactions. Furthermore, the protocols developed as part of this work can be applied to analyze non-plant fossils and biological specimens as well.
DOI: 10.6084/m9.figshare.24802719.v2
title: <b>Two-photon excitation fluorescence </b><b>microspectroscopy protocols for examining </b><b>fluorophores in fossil plants</b>

description: Fluorescence emission is a common occurrence in plants and serves multiple functions, such as aiding photosynthesis, attracting pollinators and seed-dispersing mammals, warning insects of chemical defenses, and providing UV protection. Plant fluorescence can serve as an indicator of various physiological processes and provide valuable information about their health and vitality. While fluorescence microscopy has been widely used to study living plants, its application in quantifying the fluorescence of fossilized plants has been limited. Investigating the compounds responsible for fluorescence in fossil plants, whether from original fluorophores or formed during fossilization, can offer valuable insights into fluorescence in ancient plants and the fossilization processes. In this work, we utilized two-photon fluorescence microspectroscopy to spatially and spectrally resolve the fluorescence emitted by different fossil plants, including amber-embedded plants, leaf compression fossils, and silicified wood. The advanced micro-spectroscope utilized in this study, with its pixel-level spectral resolution and line-scan excitation capabilities, allowed us to collect comprehensive excitation and emission spectra with high sensitivity and minimal laser damage to the specimens. By applying linear spectral unmixing to the spectrally resolved fluorescence images, we could differentiate between (a) the matrix and (b) the original biological material or chemical products formed during fossilization. Our analysis suggests that the latter correspond to the durable tissues of the fossils, such as lignin and cellulose. Additionally, we observed potential signals from chlorophyll derivatives, although minerals could have contributed to this fingerprint. Combining this information with chemical analyses of the fossils will improve our understanding of the organic composition of fluorescent plant fossils and enhance the interpretation of fluorescence emission spectra. This research opens doors to exploring the ancient ecosystems and potentially understanding the ecological roles of fluorescence in plants throughout geological time. The findings may have broader implications in the field of paleobotany, offering insights into the evolution of fluorescence in plants and its relevance to ancient plant-animal interactions. Furthermore, the protocols developed as part of this work can be applied to analyze non-plant fossils and biological specimens as well.
DOI: 10.6084/m9.figshare.24802719.v1
title: <b>Fluorophores in fossil plants: investigation through two photon excitation fluorescence microspectroscopy</b>

description: Fluorescence emission is a common occurrence in plants and serves multiple functions, such as aiding photosynthesis, attracting pollinators and seed-dispersing mammals, warning insects of chemical defenses, and providing UV protection. Plant fluorescence can serve as an indicator of various physiological processes and provide valuable information about their health and vitality. While fluorescence microscopy has been widely used to study living plants, its application in quantifying the fluorescence of fossilized plants has been limited. Investigating the compounds responsible for fluorescence in fossil plants, whether from original fluorophores or formed during fossilization, can offer valuable insights into fluorescence in ancient plants and the fossilization processes. In this work, we utilized two-photon fluorescence microspectroscopy to spatially and spectrally resolve the fluorescence emitted by different fossil plants, including amber-embedded plants, leaf compression fossils, and silicified wood. The advanced micro-spectroscope utilized in this study, with its pixel-level spectral resolution and line-scan excitation capabilities, allowed us to collect comprehensive excitation and emission spectra with high sensitivity and minimal laser damage to the specimens. By applying linear spectral unmixing to the spectrally resolved fluorescence images, we could differentiate between (a) the matrix and (b) the original biological material or chemical products formed during fossilization. Our analysis suggests that the latter correspond to the durable tissues of the fossils, such as lignin and cellulose. Additionally, we observed potential signals from chlorophyll derivatives, although minerals could have contributed to this fingerprint. Combining this information with chemical analyses of the fossils will improve our understanding of the organic composition of fluorescent plant fossils and enhance the interpretation of fluorescence emission spectra. This research opens doors to exploring the ancient ecosystems and potentially understanding the ecological roles of fluorescence in plants throughout geological time. The findings may have broader implications in the field of paleobotany, offering insights into the evolution of fluorescence in plants and its relevance to ancient plant-animal interactions. Furthermore, the protocols developed as part of this work can be applied to analyze non-plant fossils and biological specimens as well.
DOI: 10.25442/hku.24911493
title: Supporting data for “Novel RNA Adjuvant for Intradermal Influenza and COVID-19 Vaccine”

description: In this project, we first established a mouse model with optimal virus inoculum and vaccine dosage to screen intradermal adjuvants. Next, we determined whether the combination of TLR9 and TLR7 agonists has superior adjuvant efficacy than TLR9 alone or TLR7 alone. Finally, we tested the efficacy of a novel RNA adjuvant, R266, an RNA derived from the 5’ untranslated region of the SARS-CoV-2 genomic sequence. R266 can improve the survival rate of mice infected with a lethal dose of influenza virus even when only one-sixth of the dose of previous influenza vaccines was immunized. We demonstrated the mechanism of R266 from B cell response and T cell response of mice and found that a powerful T cell response in the early stages of infection might be one key factor in increasing vaccine protection.In conclusion, we demonstrated that R266 could be used as a promising intradermal adjuvant to enhance the effectiveness of the influenza vaccine. Further detailed mechanisms of R266 are worth exploring, which will lay the foundation for future innovations in RNA adjuvants and vaccines.
DOI: 10.25442/hku.24911493.v1
title: Supporting data for “Novel RNA Adjuvant for Intradermal Influenza and COVID-19 Vaccine”

description: In this project, we first established a mouse model with optimal virus inoculum and vaccine dosage to screen intradermal adjuvants. Next, we determined whether the combination of TLR9 and TLR7 agonists has superior adjuvant efficacy than TLR9 alone or TLR7 alone. Finally, we tested the efficacy of a novel RNA adjuvant, R266, an RNA derived from the 5’ untranslated region of the SARS-CoV-2 genomic sequence. R266 can improve the survival rate of mice infected with a lethal dose of influenza virus even when only one-sixth of the dose of previous influenza vaccines was immunized. We demonstrated the mechanism of R266 from B cell response and T cell response of mice and found that a powerful T cell response in the early stages of infection might be one key factor in increasing vaccine protection.In conclusion, we demonstrated that R266 could be used as a promising intradermal adjuvant to enhance the effectiveness of the influenza vaccine. Further detailed mechanisms of R266 are worth exploring, which will lay the foundation for future innovations in RNA adjuvants and vaccines.
DOI: 10.5517/ccdc.csd.cc2gzwkx
title: CCDC 2293800: Experimental Crystal Structure Determination

description: Related Article: I Wayan  Dasna|2023|CSD Communication|||
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.cc2gzvfr
title: CCDC 2293765: Experimental Crystal Structure Determination

description: Related Article: I Wayan Dasna|2023|CSD Communication|||
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.cc2gzzjz
title: CCDC 2293892: Experimental Crystal Structure Determination

description: Related Article: Yi-Fan Wang|2023|CSD Communication|||
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.cc2gzzl1
title: CCDC 2293894: Experimental Crystal Structure Determination

description: Related Article: Vadim Zorin, Robin K. Harris, Dmitry S. Yufit, Judith A. K. Howard|2023|CSD Communication|||
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.cc2gzzv9
title: CCDC 2293902: Experimental Crystal Structure Determination

description: Related Article: Tobias Kruska, Marc Schmidtmann, Rüdiger Beckhaus|2023|CSD Communication|||
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.cc2h004p
title: CCDC 2293911: Experimental Crystal Structure Determination

description: Related Article: Michelle J. O'Mahony, AnnMarie C. O'Donoghue, Dmitry S. Yufit, Judith A. K. Howard|2023|CSD Communication|||
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.cc2h005q
title: CCDC 2293912: Experimental Crystal Structure Determination

description: Related Article: Katja Dralle, Marc Schmidtmann, Rüdiger Beckhaus|2023|CSD Communication|||
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: 10.5281/zenodo.10457145
title: Effects of Horizontal Resolution on Long-Range Equatorward Radiation of Near-inertial Internal Waves in Ocean General Circulation Models

description: Effects of Horizontal Resolution on Long-Range Equatorward Radiation of Near-inertial Internal Waves in Ocean General Circulation Models

 

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