cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25442/hku.27060052
title: Supporting data for “<i>In vitro</i> co-culture CRISPR screen for kinase potentiating T cell-mediated cytotoxicity in hepatocellular carcinoma”

description: The overall response rate to immune checkpoint blockade (ICB) in hepatocellular carcinoma (HCC) patients remains suboptimal, highlighting the need for immediate efforts to identify resistance factors and develop synergistic strategies to enhance the antitumor activity of ICB. Cytotoxic T lymphocytes (CTLs) are the central effectors of anti-tumor immune response. Understanding the relationship between tumor intrinsic kinases and CTL-mediated cytotoxicity could reveal novel mechanisms in promoting immunotherapy efficacy. Here, we conducted a kinome knockout (KO) CRISPR screen in an <i>in vitro</i> tumor-T cell co-culture system to identify kinases in HCC cells that contribute to immune escape from cytotoxic T cell killing.Within the top depleted candidates, Tumor Immune Dysfunction and Exclusion (TIDE) analysis of The Cancer Genome Atlas (TCGA) HCC dataset revealed that higher suppressor of morphogenesis in genitalia 1 (SMG1) expression in patients predicted ICB resistance. Further bioinformatics analysis also showed that SMG1 expression is inversely associated with CTL signature, and patients with low SMG1 expression and high CTL signature have more favorable survival outcomes. <i>In vitro</i> proliferation assay and orthotopic transplantation of murine HCC cells in mice demonstrated that SMG1 depletion elicited immune-dependent tumor suppressive effect. Using single-cell RNA sequencing (scRNA-seq), we observed an increased proportion of effector CD8<sup>+</sup> T cells in SMG1-depleted tumors, which exhibited enhanced activation of T cell receptor (TCR) signaling pathway along pseudotime, indicating an enhanced T cell-mediated immune response in tumors following SMG1 inhibition.Additionally, we showed that SMG1 loss promoted MHC-I-mediated antigen presentation, while further investigation of the transcriptome profile following SMG1 knockout indicated dysregulation of alternative splicing (AS) in HCC cells. We also demonstrated that nonsense-mediated mRNA decay (NMD) inhibition can enhance T cell-mediated cytotoxic response, and NMD signature is associated with infiltration of CD8<sup>+ </sup>T cells in HCC. This suggested the potential of inhibiting SMG1 to promote antigen presentation, as well as disrupt AS and NMD coupled events to drive the generation of splicing-derived neoantigens, thereby augmenting anti-tumor immunity.
DOI: 10.25442/hku.27060052.v1
title: Supporting data for “<i>In vitro</i> co-culture CRISPR screen for kinase potentiating T cell-mediated cytotoxicity in hepatocellular carcinoma”

description: The overall response rate to immune checkpoint blockade (ICB) in hepatocellular carcinoma (HCC) patients remains suboptimal, highlighting the need for immediate efforts to identify resistance factors and develop synergistic strategies to enhance the antitumor activity of ICB. Cytotoxic T lymphocytes (CTLs) are the central effectors of anti-tumor immune response. Understanding the relationship between tumor intrinsic kinases and CTL-mediated cytotoxicity could reveal novel mechanisms in promoting immunotherapy efficacy. Here, we conducted a kinome knockout (KO) CRISPR screen in an <i>in vitro</i> tumor-T cell co-culture system to identify kinases in HCC cells that contribute to immune escape from cytotoxic T cell killing.Within the top depleted candidates, Tumor Immune Dysfunction and Exclusion (TIDE) analysis of The Cancer Genome Atlas (TCGA) HCC dataset revealed that higher suppressor of morphogenesis in genitalia 1 (SMG1) expression in patients predicted ICB resistance. Further bioinformatics analysis also showed that SMG1 expression is inversely associated with CTL signature, and patients with low SMG1 expression and high CTL signature have more favorable survival outcomes. <i>In vitro</i> proliferation assay and orthotopic transplantation of murine HCC cells in mice demonstrated that SMG1 depletion elicited immune-dependent tumor suppressive effect. Using single-cell RNA sequencing (scRNA-seq), we observed an increased proportion of effector CD8<sup>+</sup> T cells in SMG1-depleted tumors, which exhibited enhanced activation of T cell receptor (TCR) signaling pathway along pseudotime, indicating an enhanced T cell-mediated immune response in tumors following SMG1 inhibition.Additionally, we showed that SMG1 loss promoted MHC-I-mediated antigen presentation, while further investigation of the transcriptome profile following SMG1 knockout indicated dysregulation of alternative splicing (AS) in HCC cells. We also demonstrated that nonsense-mediated mRNA decay (NMD) inhibition can enhance T cell-mediated cytotoxic response, and NMD signature is associated with infiltration of CD8<sup>+ </sup>T cells in HCC. This suggested the potential of inhibiting SMG1 to promote antigen presentation, as well as disrupt AS and NMD coupled events to drive the generation of splicing-derived neoantigens, thereby augmenting anti-tumor immunity.
DOI: 10.15468/dl.p298nc
title: Occurrence Download

description: A dataset containing 1405728 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is one of (Corvus corax Linnaeus, 1758, Corvus corax kamtschaticus Dybowski, 1883, Corvus corax clarionensis Rothschild & Hartert, 1902, Corvus corax sinuatus Wagler, 1829, Corvus corax tingitanus Irby, 1874, Corvus corax richardsoni Miller & Griscom, Corvus corax principalis Ridgway, 1887, Corvus corax canariensis Hartert & O.Kleinschmidt, 1901, Corvus corax principalis Ridgway, 1887, Corvus corax corax, Corvus corax varius Brünnich, 1764, Corvus corax laurencei Hume, 1873, Corvus corax tibetanus Hodgson, 1849, Corvus corax hispanus Hartert & O.Kleinschmidt, 1901, Corvus corax corax, Pithecops corvus corax Fruhstorfer, 1919)",
 "Year is greater than or equal to 2000",
 "CoordinateUncertaintyInMeters is less than 5001"
 ]
}

 The dataset includes 1405728 records from 1010 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038718-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21951/nationalhydropowermap_fy20/1634829
title: The 2020 National Hydropower Map, Version 1: A Visualization of the Geospatial Distribution and Characteristics of Operational Hydropower Plants in the United States in 2020

description: This map poster uses Oak Ridge National Laboratory’s Existing Hydropower Assets Plant Dataset FY20 to visualize the geospatial distribution and characteristics of existing hydropower plants in the United States.
DOI: 10.21951/nationalhydropowermap_fy18/1643695
title: The 2018 National Hydropower Map, Version 1

description: This map poster uses Oak Ridge National Laboratory’s 2018 Existing Hydropower Assets Plant Dataset to visualize the geospatial distribution and characteristics of existing hydropower plants in the United States.
DOI: 10.21951/nationalhydropowermap_fy14/1644026
title: The 2014 National Hydropower Map, Version 1

description: This map poster uses Oak Ridge National Laboratory’s 2014 Existing Hydropower Assets Plant Dataset to visualize the geospatial distribution and characteristics of existing hydropower plants in the United States.
DOI: 10.21951/nationalhydropowermap_fy16/1644027
title: The 2016 National Hydropower Map, Version 1

description: This map poster uses Oak Ridge National Laboratory’s 2016 Existing Hydropower Assets Plant Dataset to visualize the geospatial distribution and characteristics of existing hydropower plants in the United States.
DOI: 10.21951/themmapseries_fy20/1668717
title: Thematic Map Series: U.S. Hydropower and Fish Species of Conservation Concern

description: This thematic map series provides the distribution of selected fish species across hydropower plants within the US.
DOI: 10.25442/hku.27041863
title: Supporting data for “Advanced Label-free Imaging Modalities Empowered by Novel Fiber-based Methodology”

description: The research dataset for the thesis titled "Advanced Label-free Imaging Modalities Empowered by Novel Fiber-based Methodology" comprises a comprehensive collection of raw data, figures, codes, and supplementary materials essential for the in-depth analysis and interpretation of the experimental results. The dataset encompasses a diverse range of imaging modalities enabled by innovative fiber-based techniques, providing a rich source of information for understanding the novel methodologies employed in label-free imaging. The dataset is structured to facilitate reproducibility and further exploration of the findings presented in the thesis, offering researchers a valuable resource for advancing knowledge in the field of advanced imaging technologies.
DOI: 10.25442/hku.27041863.v1
title: Supporting data for “Advanced Label-free Imaging Modalities Empowered by Novel Fiber-based Methodology”

description: The research dataset for the thesis titled "Advanced Label-free Imaging Modalities Empowered by Novel Fiber-based Methodology" comprises a comprehensive collection of raw data, figures, codes, and supplementary materials essential for the in-depth analysis and interpretation of the experimental results. The dataset encompasses a diverse range of imaging modalities enabled by innovative fiber-based techniques, providing a rich source of information for understanding the novel methodologies employed in label-free imaging. The dataset is structured to facilitate reproducibility and further exploration of the findings presented in the thesis, offering researchers a valuable resource for advancing knowledge in the field of advanced imaging technologies.
DOI: 10.21951/nationalhydropowermap_fy22/1877924
title: The 2022 National Hydropower Map
DOI: 10.25442/hku.27021910
title: Supporting data for "Sleep-wake state discrepancy: correlates and implications for treatment"

description: The dataset contains the data of a series of 4 thesis studies (chapter 2, 3, 4, 5). Chapter 2 is a cross-sectional study exploring the association between arousal and sleep-wake state discrepancy among healthy adults. Chapter 3 is a case-control study investigating the relationship between sleep-related factors and sleep-wake state discrepancy among youths with insomnia. Chapter 4 is a systematic review and meta-analysis of randomized controlled trials aiming to examine the effect of cognitive behavioral therapy for insomnia on sleep-wake state discrepancy. Chapter 5 is a secondary analysis of a randomized controlled trial examining the effect of CBT-I on SWSD among youths with insomnia. Detailed descriptions of variable names can be found in the README file.
DOI: 10.25442/hku.27021910.v1
title: Supporting data for "Sleep-wake state discrepancy: correlates and implications for treatment"

description: The dataset contains the data of a series of 4 thesis studies (chapter 2, 3, 4, 5). Chapter 2 is a cross-sectional study exploring the association between arousal and sleep-wake state discrepancy among healthy adults. Chapter 3 is a case-control study investigating the relationship between sleep-related factors and sleep-wake state discrepancy among youths with insomnia. Chapter 4 is a systematic review and meta-analysis of randomized controlled trials aiming to examine the effect of cognitive behavioral therapy for insomnia on sleep-wake state discrepancy. Chapter 5 is a secondary analysis of a randomized controlled trial examining the effect of CBT-I on SWSD among youths with insomnia. Detailed descriptions of variable names can be found in the README file.
DOI: 10.25442/hku.27019207
title: Supporting data for "REPONSES TO FOOD, NOVELTY AND ACTIVITY IN CAPTIVE ASIAN ELEPHANTS (<i>ELEPHAS MAXIMUS</i>)"

description: The overarching goal of this thesis is to characterise and quantify elephant behavioural and physiological responses in different settings. Chapter 2 highlights the importance of training within the context of captive animal welfare and performance. In this chapter we explore the methodology and its limitations for further food-based chapters (Chapters 3 & 4) by providing insight into captive Asian elephant olfactory capabilities and behavioural (latency) indicators of training success within an experimental setting. Chapter 3 examines the impact of sensory modality on Asian elephant behaviour in a foraging context. Using an experimental setting we measure and quantify specific food-based behaviours, when we limit elephants’ sensory abilities to three treatments: vision, olfaction and vision and olfaction simultaneously. In the same experiment elephants were also exposed to novel and familiar food items (within each sensory treatment) to explore the the neophilic/ neophobic behavioural responses of elephants within a foraging context. Chapter 4 evaluates neophobic / neophilic food-based behavioural responses at greater depth and characterises the food preferences of elephants. Here we use a similar experimental design to Chapter 3, presenting elephants with an array of novel and familiar food items without sensory constraints. Chapter 5 quantifies the impact of exercise on the temperature of different elephant body regions. Using thermography, we assessed the temperature changes of elephants (before and after exercise) undertaking two different forms of exercise; regular eco-tourism activities such as walks with tourists through Chitwan National Park (Nepal), which elephants undertake daily during lodge opening times (Sept-May) and an irregular activity; an elephant polo tournament (on an ad-hoc basis but always in December).<br>
DOI: 10.25442/hku.27019207.v1
title: Supporting data for "REPONSES TO FOOD, NOVELTY AND ACTIVITY IN CAPTIVE ASIAN ELEPHANTS (<i>ELEPHAS MAXIMUS</i>)"

description: The overarching goal of this thesis is to characterise and quantify elephant behavioural and physiological responses in different settings. Chapter 2 highlights the importance of training within the context of captive animal welfare and performance. In this chapter we explore the methodology and its limitations for further food-based chapters (Chapters 3 & 4) by providing insight into captive Asian elephant olfactory capabilities and behavioural (latency) indicators of training success within an experimental setting. Chapter 3 examines the impact of sensory modality on Asian elephant behaviour in a foraging context. Using an experimental setting we measure and quantify specific food-based behaviours, when we limit elephants’ sensory abilities to three treatments: vision, olfaction and vision and olfaction simultaneously. In the same experiment elephants were also exposed to novel and familiar food items (within each sensory treatment) to explore the the neophilic/ neophobic behavioural responses of elephants within a foraging context. Chapter 4 evaluates neophobic / neophilic food-based behavioural responses at greater depth and characterises the food preferences of elephants. Here we use a similar experimental design to Chapter 3, presenting elephants with an array of novel and familiar food items without sensory constraints. Chapter 5 quantifies the impact of exercise on the temperature of different elephant body regions. Using thermography, we assessed the temperature changes of elephants (before and after exercise) undertaking two different forms of exercise; regular eco-tourism activities such as walks with tourists through Chitwan National Park (Nepal), which elephants undertake daily during lodge opening times (Sept-May) and an irregular activity; an elephant polo tournament (on an ad-hoc basis but always in December).<br>
DOI: 10.25442/hku.27098779
title: Supporting data for “Prevalence, Risk Factors, Treatment of Heart Failure and associated Cardiovascular and Non-?Cardiovascular Outcomes”.

description: Data in the file collected on CDARS includes but not limited to: diagnoses,demographic data, drug prescriptions, procedures, laboratory tests, visits to emergency department as well as episodes of hospital visits since 1993. International Classification of Diseases, both Ninth (ICD-9) and Tenth Revision(ICD-10) were used to determine diagnostic data. Previous studies have proved that CDARS has a high coding accuracy, which enables it to be a reliable data source while conducting high-quality epidemiological research. To protect identity, records of patients are anonymized.<br><br>
DOI: 10.25442/hku.27098779.v1
title: Supporting data for “Prevalence, Risk Factors, Treatment of Heart Failure and associated Cardiovascular and Non-?Cardiovascular Outcomes”.

description: Data in the file collected on CDARS includes but not limited to: diagnoses,demographic data, drug prescriptions, procedures, laboratory tests, visits to emergency department as well as episodes of hospital visits since 1993. International Classification of Diseases, both Ninth (ICD-9) and Tenth Revision(ICD-10) were used to determine diagnostic data. Previous studies have proved that CDARS has a high coding accuracy, which enables it to be a reliable data source while conducting high-quality epidemiological research. To protect identity, records of patients are anonymized.<br><br>
DOI: 10.15468/dl.w726az
title: Occurrence Download

description: A dataset containing 8536 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is one of (Auriparus flaviceps (Sundevall, 1850), Auriparus flaviceps lamprocephalus Oberholser, 1897, Auriparus flaviceps hidalgensis A.R.Phillips, 1986, Auriparus flaviceps acaciarum Grinnell, 1931, Auriparus flaviceps flaviceps, Auriparus flaviceps sinaloae A.R.Phillips, 1986, Auriparus flaviceps ornatus (Lawrence, 1851))",
 "Year is greater than or equal to 2000",
 "CoordinateUncertaintyInMeters is less than 5001"
 ]
}

 The dataset includes 8536 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038727-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5439/2377035
title: 60varanarap75km (c1)

description: 60varanarap75km
DOI: 10.15468/dl.7wcgbt
title: Occurrence Download

description: A dataset containing 125 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dyscophus insularis Grandidier, 1872"
 ]
}

 The dataset includes 125 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038728-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vynacn
title: Occurrence Download

description: A dataset containing 2229 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is one of (Polioptila melanura Lawrence, 1857, Polioptila melanura californica Brewster, 1881, Polioptila melanura margaritae Ridgway, 1904, Polioptila melanura melanura, Polioptila melanura curtata van Rossem, 1932, Polioptila melanura pontilis Van Rossem, 1931, Polioptila melanura lucida Van Rossem, 1931)",
 "Year is greater than or equal to 2000",
 "CoordinateUncertaintyInMeters is less than 5001"
 ]
}

 The dataset includes 2229 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038729-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wztk9s
title: Occurrence Download

description: A dataset containing 4262 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cheilinus undulatus Rüppell, 1835"
 ]
}

 The dataset includes 4262 records from 109 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038730-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.txxcp9
title: Occurrence Download

description: A dataset containing 8875 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "DatasetKey is one of (Especies silvestres de nopales mexicanos, Digitalización y Sistematización de las Colecciones Biológicas Nacionales del Instituto de Biología, UNAM (Plantas vasculares))",
 "TaxonKey is Opuntia Mill."
 ]
}

 The dataset includes 8875 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038731-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.d2fe5g
title: Occurrence Download

description: A dataset containing 9308 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is one of (Phainopepla nitens (Swainson, 1838), Phainopepla nitens nitens, Phainopepla nitens lepida Van Tyne, 1925)",
 "Year is greater than or equal to 2000",
 "CoordinateUncertaintyInMeters is less than 5001"
 ]
}

 The dataset includes 9308 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038732-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3vv53h
title: Occurrence Download

description: A dataset containing 1536 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Elachistocleis bicolor (Guérin-Méneville, 1838)"
 ]
}

 The dataset includes 1536 records from 49 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038733-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xq5g25
title: Occurrence Download

description: A dataset containing 2763 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is one of (Icterus parisorum Bonaparte, 1838)",
 "Year is greater than or equal to 2000",
 "CoordinateUncertaintyInMeters is less than 5001"
 ]
}

 The dataset includes 2763 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038734-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.