cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25442/hku.26790016
title: Supporting data for “Functional genome-wide CRISPR screen in human gastric organoids reveals drivers of anoikis resistance”

description: "Proliferation assay" includes the record of cell counts and doubling time of organoids assessed by proliferation assay. "ROCK inhibitor withdrawal assay" includes the record of cell viability assays in ROCK inhibitor withdrawal assays. "Spheroid formation assay" includes the calculations of fold changes in cell number assessed by spheroid formation assays. "Collagen assay" includes the record of cell viability assays in collagen assays. "RNA_log2TPM" describes gene expression levels of in-house clinical samples by RNA-seq (in Log2TPM). "Sanger sequencing files" includes raw Sanger sequencing files of DNA of organoids with gene knockouts. "Western blot raw images" includes raw images of western blots.
DOI: 10.25442/hku.26790016.v1
title: Supporting data for “Functional genome-wide CRISPR screen in human gastric organoids reveals drivers of anoikis resistance”

description: "Proliferation assay" includes the record of cell counts and doubling time of organoids assessed by proliferation assay. "ROCK inhibitor withdrawal assay" includes the record of cell viability assays in ROCK inhibitor withdrawal assays. "Spheroid formation assay" includes the calculations of fold changes in cell number assessed by spheroid formation assays. "Collagen assay" includes the record of cell viability assays in collagen assays. "RNA_log2TPM" describes gene expression levels of in-house clinical samples by RNA-seq (in Log2TPM). "Sanger sequencing files" includes raw Sanger sequencing files of DNA of organoids with gene knockouts. "Western blot raw images" includes raw images of western blots.
DOI: 10.15468/dl.5mdxh5
title: Occurrence Download

description: A dataset containing 4503 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Salix babylonica L.",
 "Year 2014-2024"
 ]
}

 The dataset includes 4503 records from 247 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0114610-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25442/hku.26796178
title: Supporting data for "The functional role of tumour-derived small extracellular vesicles and particles in reshaping hepatocellular carcinoma tumour microenvironment".

description: This work consists of two research projects. The first project presented in Chapter 3 was recently submitted, which is entitled “Small extracellular vesicle-derived NAMPT induces SLC27A4-mediated glycolysis to promote hepatocellular carcinoma”. The second project presented in Chapter 4 was also submitted lately, which is entitled “Identification of novel molecular markers and exploration of exomeres’ oncogenic role in hepatocellular carcinoma
DOI: 10.25442/hku.26796178.v1
title: Supporting data for "The functional role of tumour-derived small extracellular vesicles and particles in reshaping hepatocellular carcinoma tumour microenvironment".

description: This work consists of two research projects. The first project presented in Chapter 3 was recently submitted, which is entitled “Small extracellular vesicle-derived NAMPT induces SLC27A4-mediated glycolysis to promote hepatocellular carcinoma”. The second project presented in Chapter 4 was also submitted lately, which is entitled “Identification of novel molecular markers and exploration of exomeres’ oncogenic role in hepatocellular carcinoma
DOI: 10.5281/zenodo.13639493
title: A Universal Database of Surface Ligands for Quantum Dots

description: We introduce a public database of organic molecules, derived by an advanced filtering of the PUBCHEM database, with the aim of building a subset of surface ligands candidates that are potentially suitable to passivate the surface of any colloidal QD. For each ligand in the database, we additionally provide relevant chemical and physical properties, from the boiling and melting points to more specific properties that account for the interactions with the solvent and amongst ligands themselves at the QD surface.

 

The “smiles to filter” scanning process, excluding (or including) a set of molecules based on structural characteristics like their functional groups was performed using the Python-based library Flamingo. The estimation of COSMO-RS (COnductor-like Screening MOdel for Realistic Solvents) [2] properties was carried out by the Fast Sigma program implemented in AMS (Amsterdam Modelling Suite) [3]. The calculations were automatized and managed via the Compound Attachment Tools (CAT) [4] and sister packages nano-CAT and data-CAT. The calculations of the cone angle are currently performed via the nano-CAT code and preceded by a biased conformational search implemented in CAT and by a geometry optimization at the DFTB level of theory with the GFN1-xTB parameter set [5] using AMS and will be progressively added to the dataset as they become available.

[1] Kim S et al., Nucleic Acids Res., 49(D1):D1388–D1395, 2021.

[2] Klamt A. et al., J. Phys. Chem., 99(7) : 2224–2235, 1995.

[3] te Velde G. et al., J. Comput. Chem., 22(9): 931–967, 2001.

[4] van Beek B. et al., J. Chem. Inf. Model. 2022, 62, 22, 5525–5535.

[5] Grimme S. et al., J. Chem. Theory Comput., 13(5):1989–2009, 2017.
DOI: 10.5281/zenodo.13639494
title: A Universal Database of Surface Ligands for Quantum Dots

description: We introduce a public database of organic molecules, derived by an advanced filtering of the PUBCHEM database, with the aim of building a subset of surface ligands candidates that are potentially suitable to passivate the surface of any colloidal QD. For each ligand in the database, we additionally provide relevant chemical and physical properties, from the boiling and melting points to more specific properties that account for the interactions with the solvent and amongst ligands themselves at the QD surface.

 

The “smiles to filter” scanning process, excluding (or including) a set of molecules based on structural characteristics like their functional groups was performed using the Python-based library Flamingo. The estimation of COSMO-RS (COnductor-like Screening MOdel for Realistic Solvents) [2] properties was carried out by the Fast Sigma program implemented in AMS (Amsterdam Modelling Suite) [3]. The calculations were automatized and managed via the Compound Attachment Tools (CAT) [4] and sister packages nano-CAT and data-CAT. The calculations of the cone angle are currently performed via the nano-CAT code and preceded by a biased conformational search implemented in CAT and by a geometry optimization at the DFTB level of theory with the GFN1-xTB parameter set [5] using AMS and will be progressively added to the dataset as they become available.

[1] Kim S et al., Nucleic Acids Res., 49(D1):D1388–D1395, 2021.

[2] Klamt A. et al., J. Phys. Chem., 99(7) : 2224–2235, 1995.

[3] te Velde G. et al., J. Comput. Chem., 22(9): 931–967, 2001.

[4] van Beek B. et al., J. Chem. Inf. Model. 2022, 62, 22, 5525–5535.

[5] Grimme S. et al., J. Chem. Theory Comput., 13(5):1989–2009, 2017.
DOI: 10.34740/kaggle/dsv/9307217
title: Met Office Historical Station Data
DOI: 10.15468/dl.rhs5gu
title: Occurrence Download

description: A dataset containing 8374 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Salix fragilis L.",
 "Year 2014-2024"
 ]
}

 The dataset includes 8374 records from 333 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0114611-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34740/kaggle/dsv/9307218
title: Health Workforce Shortage Areas
DOI: 10.25442/hku.26728339
title: Supporting data for "Competition Dysfunction: Unravelling Structural Competition Problems and Reconstructing Lost Competition in the Indian Digital Landscape".

description: This empirical study is qualitative in nature. It consists of personal interviews of four different target groups/stakeholders i.e., consumers, third-party sellers, start-ups, and Competition Commission of India 'CCI' officials. The target groups were interviewed about their understanding of competitiveness of e-commerce segment in India with the objective to identify if statutorily non-dominant e-commerce platforms act as gatekeepers and needs to be regulated. More specifically, the objective is to identify if underneath the appearance of statutorily non-dominant structure of e-commerce platforms lie a new dimension of market power that suggests a deeper problem, perhaps even a more alarming form of concentration of power which requires antitrust intervention.<b>Adherence to legal and ethical requirements: </b>Prior to undertaking this empirical research, the approval of Human Research Ethics Committee (HREC) was obtained. Thus, the data collection is in compliance of legal and ethical requirements.<b>Methodology and techniques of data collection: </b>Structured interview was chosen as the most appropriate means of data collection. This format allowed for more considered and reflective responses due to technicality of questions<b>. </b>Purposive sampling, networked introductions, and the snowball method were used. For instance, third party sellers and start-ups were chosen via networked introductions and snowball method. The consumers were chosen through purposive sampling method. CCI officials were chosen via purposive sampling method.Following supporting data files have been submitted:Questionnaire: Four different sets of questionnaires have been submitted which corresponds to separate sets of respondents i.e., consumers, start-ups, third-party sellers and CCI officials. Broadly, the objective is to learn the understanding of different respondents about the competitiveness of e-commerce segment in India and to identify if few e-commerce platforms are increasingly becoming ‘systemic’ digital gatekeepers by controlling access to the market for users even below the point of dominance. Audio recordings of interviews: It contains the audio recording of the interview of the respondents, wherever available.Summary document: It contains summary details of the respondents which include type of respondent, occupation of respondent, mode of interview, date of interview, duration of interview.<br>
DOI: 10.25442/hku.26728339.v1
title: Supporting data for "Competition Dysfunction: Unravelling Structural Competition Problems and Reconstructing Lost Competition in the Indian Digital Landscape".

description: This empirical study is qualitative in nature. It consists of personal interviews of four different target groups/stakeholders i.e., consumers, third-party sellers, start-ups, and Competition Commission of India 'CCI' officials. The target groups were interviewed about their understanding of competitiveness of e-commerce segment in India with the objective to identify if statutorily non-dominant e-commerce platforms act as gatekeepers and needs to be regulated. More specifically, the objective is to identify if underneath the appearance of statutorily non-dominant structure of e-commerce platforms lie a new dimension of market power that suggests a deeper problem, perhaps even a more alarming form of concentration of power which requires antitrust intervention.<b>Adherence to legal and ethical requirements: </b>Prior to undertaking this empirical research, the approval of Human Research Ethics Committee (HREC) was obtained. Thus, the data collection is in compliance of legal and ethical requirements.<b>Methodology and techniques of data collection: </b>Structured interview was chosen as the most appropriate means of data collection. This format allowed for more considered and reflective responses due to technicality of questions<b>. </b>Purposive sampling, networked introductions, and the snowball method were used. For instance, third party sellers and start-ups were chosen via networked introductions and snowball method. The consumers were chosen through purposive sampling method. CCI officials were chosen via purposive sampling method.Following supporting data files have been submitted:Questionnaire: Four different sets of questionnaires have been submitted which corresponds to separate sets of respondents i.e., consumers, start-ups, third-party sellers and CCI officials. Broadly, the objective is to learn the understanding of different respondents about the competitiveness of e-commerce segment in India and to identify if few e-commerce platforms are increasingly becoming ‘systemic’ digital gatekeepers by controlling access to the market for users even below the point of dominance. Audio recordings of interviews: It contains the audio recording of the interview of the respondents, wherever available.Summary document: It contains summary details of the respondents which include type of respondent, occupation of respondent, mode of interview, date of interview, duration of interview.<br>
DOI: 10.25442/hku.26550379
title: Supporting data for Molecular mechanisms of PARP inhibitor sensitivity in FANCM-Deficient cells

description: PARP inhibitors (PARPis) display significant anticancer activity in tumors carrying mutations in BRCA1/BRCA2 or other genes required for homologous recombination (HR). However, how other DNA repair proteins are involved in PARPi-induced lethality remains unclear. Here, we show that FANCM-depleted cells, but not FANCB-depleted cells, are hypersensitive to PARPi, indicating that FANCM promotes PARPi resistance independent of the core FA complex. FANCM-depleted cells are HR-proficient and FANCM acts independently of BRCA1 in response to PARPi. Importantly, we show that FANCM-depleted cells display an elevated level of DNA damage in the second S phase after PARPi exposure due to an increased formation of ssDNA gaps behind replication forks in the first S phase. Strikingly, FANCM-depleted cells also exhibit reduced DNA resection of collapsed forks in the second S phase, resulting in chromosome fusion and chromatin bridges in the following mitosis. Our results lead us to propose a model in which FANCM plays a dual role in repairing PARPi-induced lesions. PARP1 trapping induced by PARPi inhibits the processing of unligated Okazaki fragments. FANCM prevents the formation of ssDNA gaps by counteracting 53BP1, which has been shown to inhibit Okazaki fragment processing. In the second S phase, collisions of the replication forks with ssDNA gaps lead to fork collapse and one-ended DSBs. Another role of FANCM is to facilitate the repair of the collapsed forks via HR as it promotes the resection of DSBs at collapsed forks by counteracting 53BP1, an inhibitor of resection. In the absence of FANCM, resection is inhibited by 53BP1, and error-prone repair via NHEJ will be promoted to repair the collapse forks, leading to structural chromosomal instability such as radial chromosomes and chromatin bridges. This project provides the potential to extend the license for use beyond BRAC-deficient tumors, expand indications beyond breast and ovarian cancers, and enhance the efficacy of PARPi combination therapy.
DOI: 10.25442/hku.26550379.v1
title: Supporting data for Molecular mechanisms of PARP inhibitor sensitivity in FANCM-Deficient cells

description: PARP inhibitors (PARPis) display significant anticancer activity in tumors carrying mutations in BRCA1/BRCA2 or other genes required for homologous recombination (HR). However, how other DNA repair proteins are involved in PARPi-induced lethality remains unclear. Here, we show that FANCM-depleted cells, but not FANCB-depleted cells, are hypersensitive to PARPi, indicating that FANCM promotes PARPi resistance independent of the core FA complex. FANCM-depleted cells are HR-proficient and FANCM acts independently of BRCA1 in response to PARPi. Importantly, we show that FANCM-depleted cells display an elevated level of DNA damage in the second S phase after PARPi exposure due to an increased formation of ssDNA gaps behind replication forks in the first S phase. Strikingly, FANCM-depleted cells also exhibit reduced DNA resection of collapsed forks in the second S phase, resulting in chromosome fusion and chromatin bridges in the following mitosis. Our results lead us to propose a model in which FANCM plays a dual role in repairing PARPi-induced lesions. PARP1 trapping induced by PARPi inhibits the processing of unligated Okazaki fragments. FANCM prevents the formation of ssDNA gaps by counteracting 53BP1, which has been shown to inhibit Okazaki fragment processing. In the second S phase, collisions of the replication forks with ssDNA gaps lead to fork collapse and one-ended DSBs. Another role of FANCM is to facilitate the repair of the collapsed forks via HR as it promotes the resection of DSBs at collapsed forks by counteracting 53BP1, an inhibitor of resection. In the absence of FANCM, resection is inhibited by 53BP1, and error-prone repair via NHEJ will be promoted to repair the collapse forks, leading to structural chromosomal instability such as radial chromosomes and chromatin bridges. This project provides the potential to extend the license for use beyond BRAC-deficient tumors, expand indications beyond breast and ovarian cancers, and enhance the efficacy of PARPi combination therapy.
DOI: 10.15468/dl.jzrq2q
title: Occurrence Download

description: A dataset containing 757 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Cyatheaceae"
 ]
}

 The dataset includes 757 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0114612-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25442/hku.26536777
title: Supporting data for "Mitochondrial protein Coiled-Coil-Helix-Coiled-coil-Helix Domain 10 (CHCHD10) as a novel contributor to heart failure through controlling microtubule organization"

description: Coiled-Coil-Helix-Coiled-coil-Helix Domain 10 (CHCHD10) is a mitochondrial protein located in the mitochondrial intermembrane space and has been identified as a regulator of mitochondrial oxidative phosphorylation (OXPHOS). We aimed to investigate the role of CHCHD10 in the heart and its underlying mechanisms in the pathogenesis of heart failure. Our findings discovered severe heart failure in cardiac CHCHD10-deficient mice, accompanied by pathological alterations of cardiac metabolism, mitochondrial dysfunction, and disruption of microtubule networks. In summary, these data suggested that cardiac CHCHD10 may play an important role in the maintenance of cardiac function.
DOI: 10.25442/hku.26536777.v1
title: Supporting data for "Mitochondrial protein Coiled-Coil-Helix-Coiled-coil-Helix Domain 10 (CHCHD10) as a novel contributor to heart failure through controlling microtubule organization"

description: Coiled-Coil-Helix-Coiled-coil-Helix Domain 10 (CHCHD10) is a mitochondrial protein located in the mitochondrial intermembrane space and has been identified as a regulator of mitochondrial oxidative phosphorylation (OXPHOS). We aimed to investigate the role of CHCHD10 in the heart and its underlying mechanisms in the pathogenesis of heart failure. Our findings discovered severe heart failure in cardiac CHCHD10-deficient mice, accompanied by pathological alterations of cardiac metabolism, mitochondrial dysfunction, and disruption of microtubule networks. In summary, these data suggested that cardiac CHCHD10 may play an important role in the maintenance of cardiac function.
DOI: 10.15468/dl.spgwcb
title: Occurrence Download

description: A dataset containing 1705952 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((144.104788634 -16.4712801589999, 145.278098325 -15.6825102299999, 145.329243869 -15.6016101039999, 145.350402807 -15.5304700419999, 145.357501946 -15.2747911409999, 145.354339959 -14.9826330339999, 145.352219836 -14.9527341119999, 145.349369822 -14.9466441599999, 142.35991794 -10.1154901919999, 142.328417584 -10.0814341859999, 142.326107537 -10.0800342399999, 142.124079852 -10.0157921349999, 142.123152649 -10.0161211349999, 142.066292592 -10.0415316209999, 142.065800825 -10.0424621739999, 141.591405885 -12.5630560319999, 141.466403877 -13.8705080429999, 141.466553919 -13.889228187, 141.468233813 -13.922528144, 141.524945955 -14.4864941179999, 141.564869957 -14.7353316079999, 141.588716805 -14.8538521409999, 141.60196693 -14.8851121039999, 141.605436857 -14.8928621819999, 141.62890686 -14.9447111289999, 141.783046041 -15.2445624939999, 141.784208261 -15.246634329, 141.796609623 -15.2649061999999, 141.820449946 -15.2995642049999, 141.821225602 -15.3005059849999, 142.276205362 -15.6304555819999, 142.926482806 -15.9640224799999, 143.839921823 -16.3644554989999, 144.104788634 -16.4712801589999))"
 ]
}

 The dataset includes 1705952 records from 505 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0114594-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25442/hku.26508031
title: Supporting data for Structure and Function of a Neuronal Amyloid Implicated in Memory Persistence During Aging

description: Investigation of the role of Orb2 protein in aging related memory through the changes in its amyloid structure during aging, affecting the translational profile at the synapse, thus the formation and maintenance of long-term memory. This dataset contains lab notes and the memory assay data of Drosophila, both wildtype of different ages and chaperone overexpression of specific ages
DOI: 10.25442/hku.26508031.v1
title: Supporting data for Structure and Function of a Neuronal Amyloid Implicated in Memory Persistence During Aging

description: Investigation of the role of Orb2 protein in aging related memory through the changes in its amyloid structure during aging, affecting the translational profile at the synapse, thus the formation and maintenance of long-term memory. This dataset contains lab notes and the memory assay data of Drosophila, both wildtype of different ages and chaperone overexpression of specific ages
DOI: 10.15468/dl.cuqs2g
title: Occurrence Download

description: A dataset containing 2385 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Sesbania punicea (Cav.) Benth.",
 "Year 2014-2024"
 ]
}

 The dataset includes 2385 records from 57 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0114613-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.