cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.2tafh4
title: Occurrence Download

description: A dataset containing 277444 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pistacia lentiscus"
 ]
}

 The dataset includes 277444 records from 488 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044019-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25442/hku.29958179
title: <b>Supporting data for "SARS-CoV-2: Immune Response Elicited by Vaccines and Infection"</b>

description: The COVID-19 pandemic highlighted the critical role of vaccines in reducing morbidity and mortality. However, vaccine efficacy is influenced by host-specific factors, waning immunity, and the emergence of immune-evasive viral variants. This thesis investigates these dynamics through four independent cohort studies, evaluating the immunogenicity, durability, and real-world performance of the BNT162b2 (mRNA) and CoronaVac (inactivated virus) vaccines, along with booster regimens.The cohorts included (1) a primary vaccination cohort for longitudinal profiling of antibody responses; (2) Hospitalized patient<b> </b>cohort to study post-vaccination infections; and (3) an updated vaccine booster cohort to assess XBB.1.5 mRNA boosting.We methodologically employed iFlash RBD-neutralizing antibody (NAb) assays, iFlash-SARS-CoV-2 IgG-S assay, live virus microneutralization (vMN), and intracellular cytokine staining to comprehensively profile humoral and cellular immune responses against SARS-CoV-2 variants.
DOI: 10.25442/hku.29958179.v1
title: <b>Supporting data for "SARS-CoV-2: Immune Response Elicited by Vaccines and Infection"</b>

description: The COVID-19 pandemic highlighted the critical role of vaccines in reducing morbidity and mortality. However, vaccine efficacy is influenced by host-specific factors, waning immunity, and the emergence of immune-evasive viral variants. This thesis investigates these dynamics through four independent cohort studies, evaluating the immunogenicity, durability, and real-world performance of the BNT162b2 (mRNA) and CoronaVac (inactivated virus) vaccines, along with booster regimens.The cohorts included (1) a primary vaccination cohort for longitudinal profiling of antibody responses; (2) Hospitalized patient<b> </b>cohort to study post-vaccination infections; and (3) an updated vaccine booster cohort to assess XBB.1.5 mRNA boosting.We methodologically employed iFlash RBD-neutralizing antibody (NAb) assays, iFlash-SARS-CoV-2 IgG-S assay, live virus microneutralization (vMN), and intracellular cytokine staining to comprehensively profile humoral and cellular immune responses against SARS-CoV-2 variants.
DOI: 10.25442/hku.29966428
title: Supporting data for "Tropical Spider Communities in a Rural-to-Urban Landscape"

description: Spiders (order <i>Araneae</i>) are the most diverse and densely distributed predators in tropical ecosystems, serving critical ecological functions and services. The diversity and abundance of these organisms are highly influenced by environmental conditions. These characteristics can be significantly influenced by changes in habitat quality resulting from fragmentation and alterations to trophic webs.Forest habitats serve as reservoirs of biodiversity, facilitating species dispersal and are therefore expected to harbour high biodiversity. While modern urbanisation is transforming natural habitats into cities, it introduces various environmental challenges, such as the urban heat island effect (UHI). These changes result in drastically altered conditions in urban environments, which are expected to impact the diversity and abundance of the spider community. Previous studies conducted in temperate cities indicate that urban thermal patterns shape the distribution of spider species and shift the spider community structures. However, there is limited research on the urban diversity of tropical spiders, and a knowledge gap remains on their adaptation to urban environments.In my work, I test the theoretical framework exploring the role of environmental backgrounds in the structure and physiology of spider communities. For this, I contrasted the diversity of spiders in rural and urban areas, testing the hypothesis of the heat island effect as the main driver of differences in spider communities. In addition, I assessed the thermal plasticity of spiders from different habitats and evolutionary histories, evaluating the effects of ecological and evolutionary backgrounds on their physiological potentials.
DOI: 10.25442/hku.29966428.v1
title: Supporting data for "Tropical Spider Communities in a Rural-to-Urban Landscape"

description: Spiders (order <i>Araneae</i>) are the most diverse and densely distributed predators in tropical ecosystems, serving critical ecological functions and services. The diversity and abundance of these organisms are highly influenced by environmental conditions. These characteristics can be significantly influenced by changes in habitat quality resulting from fragmentation and alterations to trophic webs.Forest habitats serve as reservoirs of biodiversity, facilitating species dispersal and are therefore expected to harbour high biodiversity. While modern urbanisation is transforming natural habitats into cities, it introduces various environmental challenges, such as the urban heat island effect (UHI). These changes result in drastically altered conditions in urban environments, which are expected to impact the diversity and abundance of the spider community. Previous studies conducted in temperate cities indicate that urban thermal patterns shape the distribution of spider species and shift the spider community structures. However, there is limited research on the urban diversity of tropical spiders, and a knowledge gap remains on their adaptation to urban environments.In my work, I test the theoretical framework exploring the role of environmental backgrounds in the structure and physiology of spider communities. For this, I contrasted the diversity of spiders in rural and urban areas, testing the hypothesis of the heat island effect as the main driver of differences in spider communities. In addition, I assessed the thermal plasticity of spiders from different habitats and evolutionary histories, evaluating the effects of ecological and evolutionary backgrounds on their physiological potentials.
DOI: 10.25442/hku.29972056
title: Supporting data for "The role of adipocyte fatty acid binding protein in sepsis-induced myocardial dysfunction"

description: This study aims to investigate the role and the underlying mechanism of A-FABP in the regulation of sepsis-induced myocardial dysfunction (SIMD). Mice were subjected to lipopolysaccharide (LPS) injection or cecum ligation and puncture (CLP) surgery to establish sepsis murine model. Echocardiographic assessment was performed to evaluate the heart function. The therapeutic potential of A-FABP neutralizing antibody 6H2 in mitigating SIMD was investigated. In conclusion, sepsis-induced A-FABP promotes neutrophil infiltration into the myocardium, thereby exacerbating cardiac dysfunction. Neutralization of A-FABP with the monoclonal antibody 6H2 may represent a novel therapeutic approach for attenuating sepsis-associated cardiac impairment.
DOI: 10.25442/hku.29972056.v1
title: Supporting data for "The role of adipocyte fatty acid binding protein in sepsis-induced myocardial dysfunction"

description: This study aims to investigate the role and the underlying mechanism of A-FABP in the regulation of sepsis-induced myocardial dysfunction (SIMD). Mice were subjected to lipopolysaccharide (LPS) injection or cecum ligation and puncture (CLP) surgery to establish sepsis murine model. Echocardiographic assessment was performed to evaluate the heart function. The therapeutic potential of A-FABP neutralizing antibody 6H2 in mitigating SIMD was investigated. In conclusion, sepsis-induced A-FABP promotes neutrophil infiltration into the myocardium, thereby exacerbating cardiac dysfunction. Neutralization of A-FABP with the monoclonal antibody 6H2 may represent a novel therapeutic approach for attenuating sepsis-associated cardiac impairment.
DOI: 10.5281/zenodo.17082271
title: MANIFESTATIONS OF CANDIDIASIS (THRUSH) IN THE ORAL CAVITY
DOI: 10.5281/zenodo.17082272
title: MANIFESTATIONS OF CANDIDIASIS (THRUSH) IN THE ORAL CAVITY
DOI: 10.25442/hku.29947178
title: Supporting data for "Evaluation of feasibility of cell-free DNA analysis as non- invasive diagnostic test on sarcomas"

description: Sarcoma encompasses a heterogeneous group of malignancies that originate from mesenchymal cells. These tumours are broadly classified into two main categories, namely soft tissue sarcomas and bone sarcomas. There are over 100 recognized subtypes, each exhibits variability in clinical presentation and therapeutic management. Currently, definitive diagnosis is established through histopathological evaluation of tissue obtained via tissue biopsy, which is an invasive procedure associated with potential risks and complications. The collected cellular material is then examined microscopically by pathologists to assess for the presence of malignancy and subtyping.It is postulated that cancerous cells undergoing apoptosis and necrosis release DNA fragments into the bloodstream, which are referred to as circulating tumour DNA (ctDNA). ctDNA is increasingly recognized as a valuable biomarker for cancer detection and monitoring, hence giving rise to a method collectively termed liquid biopsy. This approach has been well-established in the screening and surveillance of various malignancies. Based on these findings, there is growing interest in evaluating the applicability of liquid biopsy for the diagnosis of sarcoma. This study is organized into two primary sections. The first section examines the diagnostic potential of liquid biopsy for atypical lipomatous tumours/well-differentiated liposarcomas (ALT/WDLPS) and dedifferentiated liposarcoma (DDLPS). The second section extends the investigation to other sarcoma subtypes, with focuses on genetic variants detection and the application of cell-free DNA (cfDNA) fragmentomics.
DOI: 10.25442/hku.29947178.v1
title: Supporting data for "Evaluation of feasibility of cell-free DNA analysis as non- invasive diagnostic test on sarcomas"

description: Sarcoma encompasses a heterogeneous group of malignancies that originate from mesenchymal cells. These tumours are broadly classified into two main categories, namely soft tissue sarcomas and bone sarcomas. There are over 100 recognized subtypes, each exhibits variability in clinical presentation and therapeutic management. Currently, definitive diagnosis is established through histopathological evaluation of tissue obtained via tissue biopsy, which is an invasive procedure associated with potential risks and complications. The collected cellular material is then examined microscopically by pathologists to assess for the presence of malignancy and subtyping.It is postulated that cancerous cells undergoing apoptosis and necrosis release DNA fragments into the bloodstream, which are referred to as circulating tumour DNA (ctDNA). ctDNA is increasingly recognized as a valuable biomarker for cancer detection and monitoring, hence giving rise to a method collectively termed liquid biopsy. This approach has been well-established in the screening and surveillance of various malignancies. Based on these findings, there is growing interest in evaluating the applicability of liquid biopsy for the diagnosis of sarcoma. This study is organized into two primary sections. The first section examines the diagnostic potential of liquid biopsy for atypical lipomatous tumours/well-differentiated liposarcomas (ALT/WDLPS) and dedifferentiated liposarcoma (DDLPS). The second section extends the investigation to other sarcoma subtypes, with focuses on genetic variants detection and the application of cell-free DNA (cfDNA) fragmentomics.
DOI: 10.25442/hku.29977267
title: Supporting data for Thesis "Deciphering the Roles of Somatic XPD Mutations in Bladder Cancer"

description: This dataset was to characterize clinical and molecular associations of XPD‑mutant bladder tumors and to validate mechanistic consequences experimentally. Major results include impaired DNA‑repair and altered oxidative‑stress/glutathione metabolism, APOBEC‑associated mutagenesis that preferentially targets CTCF binding sites and perturbs TAD boundaries, and enhanced sensitivity of XPD‑deficient cells to ferroptosis. The resource supports discovery, reanalysis, and method development aimed at biomarker evaluation and translational hypothesis testing in BLCA.The data are organized by Chapters, including differential expression results from TCGA BLCA (DESeq2), experimental validation datasets from engineered cell lines (ROS, cell‑cycle, viability, colony‑formation, slot‑blot), CTCF binding‑site mutation and chromatin‑structure analyses (bedtools, FIMO, deepTools outputs and BED/TSV files), and computational pathology/machine‑learning artifacts (CLAM model checkpoints, prediction CSVs, attention weights, and HoVerNet segmentation outputs). Files using TCGA raw data may require access credentials.
DOI: 10.25442/hku.29977267.v1
title: Supporting data for Thesis "Deciphering the Roles of Somatic XPD Mutations in Bladder Cancer"

description: This dataset was to characterize clinical and molecular associations of XPD‑mutant bladder tumors and to validate mechanistic consequences experimentally. Major results include impaired DNA‑repair and altered oxidative‑stress/glutathione metabolism, APOBEC‑associated mutagenesis that preferentially targets CTCF binding sites and perturbs TAD boundaries, and enhanced sensitivity of XPD‑deficient cells to ferroptosis. The resource supports discovery, reanalysis, and method development aimed at biomarker evaluation and translational hypothesis testing in BLCA.The data are organized by Chapters, including differential expression results from TCGA BLCA (DESeq2), experimental validation datasets from engineered cell lines (ROS, cell‑cycle, viability, colony‑formation, slot‑blot), CTCF binding‑site mutation and chromatin‑structure analyses (bedtools, FIMO, deepTools outputs and BED/TSV files), and computational pathology/machine‑learning artifacts (CLAM model checkpoints, prediction CSVs, attention weights, and HoVerNet segmentation outputs). Files using TCGA raw data may require access credentials.
DOI: 10.25442/hku.29960018
title: <b>Supporting Data for</b> "The Role of MicroRNAs in the Viral Pathogenesis of H5N1 Influenza Virus Infection"

description: This project aims to explore how EV-derived miRNAs contribute to the pathogenesis of the HPAI H5N1 virus, and evaluate their potential as therapeutic options for HPAI virus infection.<br>The Chapter 4 dataset addresses Research Objective 1, focusing on immune regulation by targeted miRNA mimics. The processed data was analyzed using GraphPad Prism software. The Prism files of each figure were included in the dataset, with the figure number indicated in the file header.The Chapter 5 dataset addresses Research Objective 2, examining immune regulation by targeted miRNA inhibitors. The processed data was analyzed using GraphPad Prism software. The Prism files of each figure were included in the dataset, with the figure number indicated in the file header.The Chapter 6 dataset covers the Research Objective 3, investigating downstream signaling molecules. Data from the nCounter detection platform were summarized in excel format files, and the file were further analyzed using R.<br>
DOI: 10.25442/hku.29960018.v1
title: <b>Supporting Data for</b> "The Role of MicroRNAs in the Viral Pathogenesis of H5N1 Influenza Virus Infection"

description: This project aims to explore how EV-derived miRNAs contribute to the pathogenesis of the HPAI H5N1 virus, and evaluate their potential as therapeutic options for HPAI virus infection.<br>The Chapter 4 dataset addresses Research Objective 1, focusing on immune regulation by targeted miRNA mimics. The processed data was analyzed using GraphPad Prism software. The Prism files of each figure were included in the dataset, with the figure number indicated in the file header.The Chapter 5 dataset addresses Research Objective 2, examining immune regulation by targeted miRNA inhibitors. The processed data was analyzed using GraphPad Prism software. The Prism files of each figure were included in the dataset, with the figure number indicated in the file header.The Chapter 6 dataset covers the Research Objective 3, investigating downstream signaling molecules. Data from the nCounter detection platform were summarized in excel format files, and the file were further analyzed using R.<br>
DOI: 10.25442/hku.29987065
title: Supporting data for "Illegal trade network, remote sensing and genomic approaches to tropical hardwood conservation in Africa and Asia"

description: This metadata contains supporting data for my PhD thesis titled "Illegal trade network, remote sensing and genomic approaches to tropical hardwood conservation in Africa and Asia".In Chapter 2, I did a social network analysis on timber seizure records involving China from 2012 - 2022 to identify conservation hotspots and species. The seizure records were aggregated by myself from open accessed media, press releases and court cases, and were uploaded in this metadata.Chapter 3 quantified the extent of conflict impacts, using the Anglophone crisis in Cameroon as a case study, on forest change and target tree species. I used remote sensing for a supervised random forest classification of target regions in Cameroon, and did overlap analyses between forest change and conflict events, as well as species occurrences and conflict events. The Google Earth Engine codes were used for the supervised random forest classification. The R codes and tree species list were used for obtaining tree occurrence data from GBIF. These outputs were overlapped with conflict events downloaded from ACLED at different buffering distances to understand the extent of conflict impacts.Chapter 4 was a population genetics study on a tree species, <i>Microberlinia bisulcata</i>, the African Zebrawood/Zingana. It compared the genetic diversity, gene flow and population structure across (i) the wild, Ebo forest population, (ii) a nursery population and (iii) two cultivated populations. The uploaded dataset contained the species list and their corresponding sampling populations, and their inline and index barcodes for the demultiplexing of pooled sequences into individual sequences. Sequences from the three pools of ddRADseq libraries generated by Illumina Novaseq 6000 2*150 bp were uploaded.
DOI: 10.25442/hku.29987065.v1
title: Supporting data for "Illegal trade network, remote sensing and genomic approaches to tropical hardwood conservation in Africa and Asia"

description: This metadata contains supporting data for my PhD thesis titled "Illegal trade network, remote sensing and genomic approaches to tropical hardwood conservation in Africa and Asia".In Chapter 2, I did a social network analysis on timber seizure records involving China from 2012 - 2022 to identify conservation hotspots and species. The seizure records were aggregated by myself from open accessed media, press releases and court cases, and were uploaded in this metadata.Chapter 3 quantified the extent of conflict impacts, using the Anglophone crisis in Cameroon as a case study, on forest change and target tree species. I used remote sensing for a supervised random forest classification of target regions in Cameroon, and did overlap analyses between forest change and conflict events, as well as species occurrences and conflict events. The Google Earth Engine codes were used for the supervised random forest classification. The R codes and tree species list were used for obtaining tree occurrence data from GBIF. These outputs were overlapped with conflict events downloaded from ACLED at different buffering distances to understand the extent of conflict impacts.Chapter 4 was a population genetics study on a tree species, <i>Microberlinia bisulcata</i>, the African Zebrawood/Zingana. It compared the genetic diversity, gene flow and population structure across (i) the wild, Ebo forest population, (ii) a nursery population and (iii) two cultivated populations. The uploaded dataset contained the species list and their corresponding sampling populations, and their inline and index barcodes for the demultiplexing of pooled sequences into individual sequences. Sequences from the three pools of ddRADseq libraries generated by Illumina Novaseq 6000 2*150 bp were uploaded.
DOI: 10.15468/dl.bp4wvb
title: Occurrence Download

description: A dataset containing 97870943 species occurrences available in GBIF matching the query:
{
 "or" : [
 "InstitutionKey is 586ee56e-b0fe-4dff-b7f9-aeb104f3308a",
 "InstitutionKey is be5b9c72-e499-42b8-a5dc-c27505cf232e",
 "InstitutionKey is 6a6ac6c5-1b8a-48db-91a2-f8661274ff80",
 "InstitutionKey is 0e919a55-08d3-4bd2-aec1-200858fafd92",
 "InstitutionKey is 1d808a7c-1f9e-4379-9616-edb749ecf10e",
 "InstitutionKey is ab83e5ab-f4f7-4c9b-a1d5-eb779dfb9377",
 "InstitutionKey is fa252605-26f6-426c-9892-94d071c2c77f",
 "InstitutionKey is 1be3aa67-8f90-4309-92f4-bd55426a8c09",
 "InstitutionKey is 29acb160-1a5c-4c58-aba3-93093d60f642",
 "InstitutionKey is c40e8d01-a969-4fe0-b827-c69679ab42db",
 "InstitutionKey is 49fb6451-91b7-4af2-8cd3-354539a77589",
 "InstitutionKey is d2a27206-87ab-47ea-b5fc-d2e57054b688",
 "InstitutionKey is a9ab29d6-f380-4193-967f-15a64abc09e7",
 "InstitutionKey is 5ed4ae5a-4638-4c61-8af1-b476f64bc0a2",
 "InstitutionKey is 0360f257-7121-45f1-8947-14a3600e56af",
 "InstitutionKey is 3b896e03-901d-4cc7-ac2b-61e0469521b0",
 "InstitutionKey is e71f36f1-e271-4720-a604-3c5a1418e7aa",
 "InstitutionKey is 1cfca87c-083e-4d67-8e60-cb7d311f6058",
 "InstitutionKey is 4128c918-2aab-4610-8e72-d3aa6dfc48fc",
 "InstitutionKey is ab8b25c4-f95e-437b-82df-5aed3c9031ec",
 "InstitutionKey is 13edc77b-7023-4ddd-89c7-d883a480b294"
 ]
}

 The dataset includes 97870943 records from 4486 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043989-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nsmkwd
title: Occurrence Download

description: A dataset containing 284921 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Netta rufina (Pallas, 1773)",
 "BasisOfRecord is one of (Human Observation, Observation)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "HasGeospatialIssue is false",
 "Country is one of (Finland, Ireland, Sweden, Cyprus, Portugal, Netherlands, France, Bulgaria, Romania, Spain, Poland, Czechia, Malta, United Kingdom of Great Britain and Northern Ireland, Austria, Croatia, Slovenia, Slovakia, Germany, Denmark, Italy, Belgium, Gibraltar, Lithuania, Greece, Luxembourg, Latvia, Estonia, Hungary)"
 ]
}

 The dataset includes 284921 records from 796 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0034528-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.grmafh
title: Occurrence Download

description: A dataset containing 1400 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Pomaderris phylicifolia Lodd., Pomaderris phylirifolia Fenzl, Pomaderris phyllirioides DC.)"
 ]
}

 The dataset includes 1400 records from 53 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0034562-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.