cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.14921067
title: Submarine Groundwater Discharge Alters Benthic Community Composition and Functional Diversity on Coral Reefs

description: Abstract: Coral reefs experience numerous natural and anthropogenic environmental gradients that alter biophysical conditions and affect biodiversity. While many studies have focused on drivers of reef biodiversity using traditional diversity metrics (e.g., species richness, diversity, evenness), less is known about how environmental variability may influence functional diversity. In this study, we tested the impact of submarine groundwater discharge (SGD) on taxonomic and functional diversity metrics in Mo‘orea, French Polynesia. SGD is the expulsion of terrestrial fresh or recirculated seawater into marine environments and is associated with reduced temperatures, pH, and salinity and elevated nutrient levels. Using a regression approach along the SGD gradient, we found that taxon and functional-entity richness displayed unimodal relationships to SGD parameters, primarily nitrate + nitrite and phosphate variability, with peak richness at moderate SGD for stony coral and the full benthic community. Macroalgae showed this unimodal pattern for functional-entity but not taxonomic richness. Functional community composition (presence and abundance of functional entities) increased along the gradient, while taxonomic composition showed a nonlinear relationship to SGD-related parameters. SGD is a common feature of many coastal ecosystems globally and therefore may be more important to structuring benthic functional diversity than previously thought. Further, studying community shifts through a functional-trait lens may provide important insights into the roles of community functions on ecosystem processes and stability, leading to improved management strategies.

Keywords: biodiversity; coral reefs; functional diversity; nutrient enrichment; submarine groundwater discharge
DOI: 10.5281/zenodo.14921068
title: Submarine Groundwater Discharge Alters Benthic Community Composition and Functional Diversity on Coral Reefs

description: Abstract: Coral reefs experience numerous natural and anthropogenic environmental gradients that alter biophysical conditions and affect biodiversity. While many studies have focused on drivers of reef biodiversity using traditional diversity metrics (e.g., species richness, diversity, evenness), less is known about how environmental variability may influence functional diversity. In this study, we tested the impact of submarine groundwater discharge (SGD) on taxonomic and functional diversity metrics in Mo‘orea, French Polynesia. SGD is the expulsion of terrestrial fresh or recirculated seawater into marine environments and is associated with reduced temperatures, pH, and salinity and elevated nutrient levels. Using a regression approach along the SGD gradient, we found that taxon and functional-entity richness displayed unimodal relationships to SGD parameters, primarily nitrate + nitrite and phosphate variability, with peak richness at moderate SGD for stony coral and the full benthic community. Macroalgae showed this unimodal pattern for functional-entity but not taxonomic richness. Functional community composition (presence and abundance of functional entities) increased along the gradient, while taxonomic composition showed a nonlinear relationship to SGD-related parameters. SGD is a common feature of many coastal ecosystems globally and therefore may be more important to structuring benthic functional diversity than previously thought. Further, studying community shifts through a functional-trait lens may provide important insights into the roles of community functions on ecosystem processes and stability, leading to improved management strategies.

Keywords: biodiversity; coral reefs; functional diversity; nutrient enrichment; submarine groundwater discharge
DOI: 10.5281/zenodo.14302088
title: Tracing Datas of Train Ticket Benchmark - for TraceZip

description: We append the dataset collected from `otel-instrumented` middleware components.
DOI: 10.5281/zenodo.14302089
title: Tracing Datas of Train Ticket Benchmark - for TraceZip
DOI: 10.5281/zenodo.14885259
title: Tracing Datas of Train Ticket Benchmark - for TraceZip

description: We categorized spans by service-name.
DOI: 10.5281/zenodo.14921120
title: Tracing Datas of Train Ticket Benchmark - for TraceZip

description: We append the dataset collected from `otel-instrumented` middleware components.
DOI: 10.15468/dl.7fjrj9
title: Occurrence Download

description: A dataset containing 3501 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Micrurus tener Baird & Girard, 1853"
 ]
}

 The dataset includes 3501 records from 58 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004149-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.v4zkma
title: Occurrence Download

description: A dataset containing 7188 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Bradypus variegatus Schinz, 1825"
 ]
}

 The dataset includes 7188 records from 108 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004151-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.623dwn
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Issue is Continent derived from country",
 "TaxonKey is Moina macrocopa (Straus, 1820)"
 ]
}

 The dataset includes 16 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004150-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7wn6b7
title: Occurrence Download

description: A dataset containing 44511 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Mexico, United States of America, Canada)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Bombus vosnesenskii Radoszkowski, 1862",
 "Year 1950-2025"
 ]
}

 The dataset includes 44511 records from 47 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004152-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qz6vm9
title: Occurrence Download

description: A dataset containing 104 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Caenolestes caniventer Anthony, 1921"
 ]
}

 The dataset includes 104 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004153-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14917558
title: Upload the data used in the study

description: 上传实验中使用的数据
DOI: 10.5281/zenodo.14917559
title: Upload the data used in the study

description: 上传实验中使用的数据
DOI: 10.6084/m9.figshare.26176576
title: HLH-30/TFEB mediates sexual dimorphism in immunity in <i>Caenorhabditis elegans</i>

description: Sexual dimorphism affects various biological functions, including immune responses. However, the mechanisms by which sex alters immunity remain largely unknown. Using <i>Caenorhabditis elegans</i> as a model species, we showed that males exhibit enhanced immunity against various pathogenic bacteria through the upregulation of HLH-30 (Helix Loop Helix 30/TFEB (transcription factor EB)), a transcription factor crucial for macroautophagy/autophagy. Compared with hermaphroditic <i>C. elegans</i>, males displayed increased activity of HLH-30/TFEB, which contributed to enhanced antibacterial immunity. <i>atg-2</i> (AuTophaGy (yeast Atg homolog) 2) upregulated by HLH-30/TFEB mediated increased immunity in male <i>C. elegans</i>. Thus, the males appear to be equipped with enhanced HLH-30/TFEB-mediated autophagy, which increases pathogen resistance, and this may functionally prolong mate-searching ability with reduced risk of infection. <b>Abbreviations:</b><i>atg-2</i>: AuTophaGy (yeast Atg homolog) 2; FUDR: 5-fluoro-2’-deoxyuridine; GSEA: gene set enrichment analysis; HLH-30: Helix Loop Helix 30; <i>LC3</i>: microtubule associated protein 1 light chain 3; NGM: nematode growth media; RNA-seq: RNA sequencing; SEM: standard error of the mean; TFEB: transcription factor EB; WT: wild-type
DOI: 10.6084/m9.figshare.26176576.v2
title: HLH-30/TFEB mediates sexual dimorphism in immunity in <i>Caenorhabditis elegans</i>

description: Sexual dimorphism affects various biological functions, including immune responses. However, the mechanisms by which sex alters immunity remain largely unknown. Using <i>Caenorhabditis elegans</i> as a model species, we showed that males exhibit enhanced immunity against various pathogenic bacteria through the upregulation of HLH-30 (Helix Loop Helix 30/TFEB (transcription factor EB)), a transcription factor crucial for macroautophagy/autophagy. Compared with hermaphroditic <i>C. elegans</i>, males displayed increased activity of HLH-30/TFEB, which contributed to enhanced antibacterial immunity. <i>atg-2</i> (AuTophaGy (yeast Atg homolog) 2) upregulated by HLH-30/TFEB mediated increased immunity in male <i>C. elegans</i>. Thus, the males appear to be equipped with enhanced HLH-30/TFEB-mediated autophagy, which increases pathogen resistance, and this may functionally prolong mate-searching ability with reduced risk of infection. <b>Abbreviations:</b><i>atg-2</i>: AuTophaGy (yeast Atg homolog) 2; FUDR: 5-fluoro-2’-deoxyuridine; GSEA: gene set enrichment analysis; HLH-30: Helix Loop Helix 30; <i>LC3</i>: microtubule associated protein 1 light chain 3; NGM: nematode growth media; RNA-seq: RNA sequencing; SEM: standard error of the mean; TFEB: transcription factor EB; WT: wild-type
DOI: 10.6084/m9.figshare.26176576.v1
title: HLH-30/TFEB mediates sexual dimorphism in immunity in <i>caenorhabditis elegans</i>

description: Sexual dimorphism affects various biological functions, including immune responses. However, the mechanisms by which sex alters immunity remain largely unknown. Using <i>Caenorhabditis elegans</i> as a model species, we showed that males exhibit enhanced immunity against various pathogenic bacteria through the upregulation of HLH-30 (Helix Loop Helix 30/TFEB (transcription factor EB), a transcription factor crucial for macroautophagy/autophagy. Compared with hermaphroditic <i>C. elegans</i>, males displayed increased activity of HLH-30/TFEB, which contributed to enhanced antibacterial immunity. <i>atg-2</i> (AuTophaGy (yeast Atg homolog) 2) upregulated by HLH-30/TFEB mediated increased immunity in male <i>C. elegans</i>. Thus, the males appear to be equipped with enhanced HLH-30/TFEB-mediated autophagy, which increases pathogen resistance, and this may functionally prolong mate-searching ability with reduced risk of infection.
DOI: 10.6084/m9.figshare.26824892
title: USP8 promotes intracellular infection by enhancing ESCRT-mediated membrane repair, limiting xenophagy, and reducing oxidative stress

description: The host ESCRT-machinery repairs damaged endolysosomal membranes. If damage persists, selective macroautophagy/autophagy clears the damaged compartment. <i>Mycobacterium tuberculosis</i> (Mtb) is an intracellular pathogen that damages the phagosomal membrane and targets ESCRT-mediated repair as part of its virulence program. The E3 ubiquitin ligases PRKN and SMURF1 promote autophagic capture of damaged, Mtb-containing phagosomes. Because ubiquitination is a reversible process, we anticipated that host deubiquitinases (DUBs) would also be involved. Here, we screened all predicted mouse DUBs for their role in ubiquitin targeting and control of intracellular Mtb. We show that USP8 (ubiquitin specific peptidase 8) colocalizes with intracellular Mtb, recognizes phagosomal membrane damage, and is required for ESCRT-dependent membrane repair. Furthermore, we show that USP8 regulates the NFE2L2/NRF2-dependent antioxidant signature. Taken together, our study demonstrates a central role of USP8 in promoting Mtb intracellular growth by promoting phagosomal membrane repair, limiting ubiquitin-driven selective autophagy, and reducing oxidative stress. <b>Abbreviation:</b> BMDMs: bone marrow-derived macrophages; CFUs: colony-forming units; DUB: deubiquitinase; ESCRT: endosomal sorting complexes required for transport; LLOMe: L-leucyl-L-leucine methyl ester; MFI: mean fluorescence intensity; MOI: multiplicity of infection; Mtb: <i>Mycobacterium tuberculosis</i>; NFE2L2/NRF2: nuclear factor, erythroid derived 2, like 2; PMA: phorbol 12-myristate 13-acetate; ROS: reactive oxygen species; USP8: ubiquitin specific peptidase 8
DOI: 10.6084/m9.figshare.26824892.v2
title: USP8 promotes intracellular infection by enhancing ESCRT-mediated membrane repair, limiting xenophagy, and reducing oxidative stress

description: The host ESCRT-machinery repairs damaged endolysosomal membranes. If damage persists, selective macroautophagy/autophagy clears the damaged compartment. <i>Mycobacterium tuberculosis</i> (Mtb) is an intracellular pathogen that damages the phagosomal membrane and targets ESCRT-mediated repair as part of its virulence program. The E3 ubiquitin ligases PRKN and SMURF1 promote autophagic capture of damaged, Mtb-containing phagosomes. Because ubiquitination is a reversible process, we anticipated that host deubiquitinases (DUBs) would also be involved. Here, we screened all predicted mouse DUBs for their role in ubiquitin targeting and control of intracellular Mtb. We show that USP8 (ubiquitin specific peptidase 8) colocalizes with intracellular Mtb, recognizes phagosomal membrane damage, and is required for ESCRT-dependent membrane repair. Furthermore, we show that USP8 regulates the NFE2L2/NRF2-dependent antioxidant signature. Taken together, our study demonstrates a central role of USP8 in promoting Mtb intracellular growth by promoting phagosomal membrane repair, limiting ubiquitin-driven selective autophagy, and reducing oxidative stress. <b>Abbreviation:</b> BMDMs: bone marrow-derived macrophages; CFUs: colony-forming units; DUB: deubiquitinase; ESCRT: endosomal sorting complexes required for transport; LLOMe: L-leucyl-L-leucine methyl ester; MFI: mean fluorescence intensity; MOI: multiplicity of infection; Mtb: <i>Mycobacterium tuberculosis</i>; NFE2L2/NRF2: nuclear factor, erythroid derived 2, like 2; PMA: phorbol 12-myristate 13-acetate; ROS: reactive oxygen species; USP8: ubiquitin specific peptidase 8
DOI: 10.6084/m9.figshare.26824892.v1
title: USP8 PROMOTES INTRACELLULAR INFECTION by ENHANCING ESCRT-MEDIATED MEMBRANE REPAIR, LIMITING XENOPHAGY, and REDUCING OXIDATIVE STRESS

description: The host ESCRT-machinery repairs damaged endolysosomal membranes. If damage persists, selective macroautophagy/autophagy clears the damaged compartment. <i>Mycobacterium tuberculosis</i> (Mtb) is an intracellular pathogen that damages the phagosomal membrane and targets ESCRT-mediated repair as part of its virulence program. The E3 ubiquitin ligases PRKN and SMURF1 promote autophagic capture of damaged, Mtb-containing phagosomes. Because ubiquitination is a reversible process, we anticipated that host deubiquitinases (DUBs) would also be involved. Here, we screened all predicted mouse DUBs for their role in ubiquitin targeting and control of intracellular Mtb. We show that USP8 (ubiquitin specific peptidase 8) colocalizes with intracellular Mtb, recognizes phagosomal membrane damage, and is required for ESCRT-dependent membrane repair. Furthermore, we show that USP8 regulates the NFE2L2/NRF2-dependent antioxidant signature. Taken together, our study demonstrates a central role of USP8 in promoting Mtb intracellular growth by promoting phagosomal membrane repair, limiting ubiquitin-driven selective autophagy, and reducing oxidative stress.
DOI: 10.6084/m9.figshare.26824890
title: Function of CSNK2/CK2 selectively affects the endoplasmic reticulum and the Golgi apparatus in mtor-mediated autophagy induction

description: Selective macroautophagy/autophagy of the endoplasmic reticulum, known as reticulophagy/ER-phagy, is essential to maintain ER homeostasis. We recently showed that members of the autophagy receptor family RETREG/FAM134 are regulated by phosphorylation-dependent ubiquitination. In an unbiased screen we had identified several kinases downstream of MTOR with profound impact on reticulophagy flux, including ATR and CSNK2/CK2. Inhibition of CSNK2 by SGC-CK2-1 prevented regulatory ubiquitination of RETREG1/FAM134B and RETREG3/FAM134C upon autophagy activation as well as the formation of high-density RETREG1- and RETREG3-clusters. Here we report on additional resource data of global proteomics upon CSNK2 and ATR inhibition, respectively. Our data suggests that the function of CSNK2 is mainly limited to the ER/reticulophagy and Golgi/Golgiphagy, while ATR inhibition by VE-822 affects the vast majority of organelles/selective autophagy pathways. <b>Abbreviation:</b> ATRi: ATR inhibitor VE-822; CSNK2i: CSNK2 inhibitor SGC-CK2-1; ER: endoplasmic reticulum
DOI: 10.6084/m9.figshare.26824890.v1
title: Function of CSNK2/CK2 selectively affects the endoplasmic reticulum and the Golgi apparatus in mtor-mediated autophagy induction

description: Selective macroautophagy/autophagy of the endoplasmic reticulum, known as reticulophagy/ER-phagy, is essential to maintain ER homeostasis. We recently showed that members of the autophagy receptor family RETREG/FAM134 are regulated by phosphorylation-dependent ubiquitination. In an unbiased screen we had identified several kinases downstream of MTOR with profound impact on reticulophagy flux, including ATR and CSNK2/CK2. Inhibition of CSNK2 by SGC-CK2-1 prevented regulatory ubiquitination of RETREG1/FAM134B and RETREG3/FAM134C upon autophagy activation as well as the formation of high-density RETREG1- and RETREG3-clusters. Here we report on additional resource data of global proteomics upon CSNK2 and ATR inhibition, respectively. Our data suggests that the function of CSNK2 is mainly limited to the ER/reticulophagy and Golgi/Golgiphagy, while ATR inhibition by VE-822 affects the vast majority of organelles/selective autophagy pathways. <b>Abbreviation:</b> ATRi: ATR inhibitor VE-822; CSNK2i: CSNK2 inhibitor SGC-CK2-1; ER: endoplasmic reticulum
DOI: 10.15468/dl.5nsfk8
title: Occurrence Download

description: A dataset containing 40850 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Dasypus novemcinctus Linnaeus, 1758"
 ]
}

 The dataset includes 40850 records from 473 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004154-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9s6hcz
title: Occurrence Download

description: A dataset containing 61756 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-142.78948 20.99390,-40.21052 20.99390,-40.21052 62.00610,-142.78948 62.00610,-142.78948 20.99390))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Bombus bimaculatus Cresson, 1863",
 "Year 1950-2025"
 ]
}

 The dataset includes 61756 records from 80 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004155-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rjh544
title: Occurrence Download

description: A dataset containing 61 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is one of (Antarctica, Oceania)",
 "Geometry POLYGON((168.92467 -52.67057,169.42003 -52.67057,169.42003 -52.41581,168.92467 -52.41581,168.92467 -52.67057))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Curculionidae"
 ]
}

 The dataset includes 61 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004156-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14912249
title: SUGGESTED PSEUDOPOTENTIALS for PBEsol v.1.0.0

description: This is pslibrary ver.1.0.0 based on "SUGGESTED PSEUDOPOTENTIALS". Pseudopotentials were generated with q-e-qe-6.3. Pseudopotentials for versions other than pslibrary ver.1.0.0 were obtained from THEOS pbesol.0.3.1.tgz and Quantum espresso pseudopotentials (pslibrary). The json data was constructed based on Standard solid-state pseudopotentials (SSSP).
DOI: 10.5281/zenodo.14912380
title: SUGGESTED PSEUDOPOTENTIALS for PBEsol v.1.0.0

description: This is pslibrary ver.1.0.0 based on "SUGGESTED PSEUDOPOTENTIALS". Pseudopotentials were generated with q-e-qe-6.3. Pseudopotentials for versions other than pslibrary ver.1.0.0 were obtained from THEOS pbesol.0.3.1.tgz and Quantum espresso pseudopotentials (pslibrary). The json data was constructed based on Standard solid-state pseudopotentials (SSSP).
DOI: 10.5281/zenodo.14912399
title: SUGGESTED PSEUDOPOTENTIALS for PBEsol v.1.0.0

description: This is pslibrary ver.1.0.0 based on "SUGGESTED PSEUDOPOTENTIALS". Pseudopotentials were generated with q-e-qe-6.3. Pseudopotentials for versions other than pslibrary ver.1.0.0 were obtained from THEOS pbesol.0.3.1.tgz and Quantum espresso pseudopotentials (pslibrary). The json data was constructed based on Standard solid-state pseudopotentials (SSSP).
DOI: 10.5281/zenodo.14921164
title: SUGGESTED PSEUDOPOTENTIALS for PBEsol v.1.0.0

description: This is pslibrary ver.1.0.0 based on "SUGGESTED PSEUDOPOTENTIALS". Pseudopotentials were generated with q-e-qe-6.3. Pseudopotentials for versions other than pslibrary ver.1.0.0 were obtained from THEOS pbesol.0.3.1.tgz and Quantum espresso pseudopotentials (pslibrary). The json data was constructed based on Standard solid-state pseudopotentials (SSSP).
DOI: 10.5281/zenodo.13323393
title: The impacts of permeable fluid-solid interfaces on dissolution patterns
DOI: 10.5281/zenodo.14835812
title: The impacts of intragranular porosity on mineral dissolution rates
DOI: 10.5281/zenodo.14921115
title: The impacts of intragranular porosity on mineral dissolution rates
DOI: 10.6084/m9.figshare.28478650
title: Additional file 1 of Hematological reference intervals for Danish crossbred Landrace Yorkshire Duroc (LYD) pigs used in biomedical research

description: Additional file 1. Estimated error (%) in the total platelet count. The number of single platelets and platelets in clumps were calculated in eight high power fields and an estimated error in the total platelet count was calculated as "number of platelets in clumps"/"total counted number of platelets".
DOI: 10.6084/m9.figshare.28478650.v1
title: Additional file 1 of Hematological reference intervals for Danish crossbred Landrace Yorkshire Duroc (LYD) pigs used in biomedical research

description: Additional file 1. Estimated error (%) in the total platelet count. The number of single platelets and platelets in clumps were calculated in eight high power fields and an estimated error in the total platelet count was calculated as "number of platelets in clumps"/"total counted number of platelets".
DOI: 10.6084/m9.figshare.28478653.v1
title: Additional file 2 of Hematological reference intervals for Danish crossbred Landrace Yorkshire Duroc (LYD) pigs used in biomedical research

description: Additional file 2. Quality controls. The mean value, standard deviation (SD) and the coefficient of variation (CV) of the quality controls.