cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.14847386
title: EXPLORING PHRASEOLOGICAL UNITS AND IDIOMS THAT EXPRESS CHARACTER TRAITS
DOI: 10.15468/dl.h6wy34
title: Occurrence Download

description: A dataset containing 60 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Helvella elastica Bull."
 ]
}

 The dataset includes 60 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023133-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9s9jar
title: Occurrence Download

description: A dataset containing 26 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Craugastor megalotympanum (Shannon & Werler, 1955)"
 ]
}

 The dataset includes 26 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023144-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2yhw6v
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-54.45138 -29.81909,-45.80329 -29.81909,-45.80329 -20.8374,-54.45138 -20.8374,-54.45138 -29.81909))",
 "TaxonKey is Brycon amazonicus (Spix & Agassiz, 1829)"
 ]
}

 The dataset includes 6 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023139-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wbbc36
title: Occurrence Download

description: A dataset containing 2608 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Craugastor mexicanus (Brocchi, 1877)"
 ]
}

 The dataset includes 2608 records from 58 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023145-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.chy3tb
title: Occurrence Download

description: A dataset containing 1694 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Compilación de fonoteca de referencia de murciélagos insectívoros de México: Fase I"
 ]
}

 The dataset includes 1694 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023146-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.28385981.v1
title: Data for 'Dynamical patterns and nonreciprocal effective interactions in an active-passive mixture through exact hydrodynamic analysis'

description: Data from stochastic particle simulations and PDE simulations used to produce the figures in the paper "Dynamical patterns and nonreciprocal effective interactions in an active-passive mixture through exact hydrodynamic analysis". This data has been generated using the code in the GitHub repository https://github.com/jimmmmason/Active-Passive-Lattice-Gas
DOI: 10.5281/zenodo.14847387
title: THE IMPORTANCE OF CUSTOMS AND TRADITIONS IN LANGUAGE ACQUISITION
DOI: 10.5281/zenodo.14847388
title: THE IMPORTANCE OF CUSTOMS AND TRADITIONS IN LANGUAGE ACQUISITION
DOI: 10.15468/dl.qvfa2v
title: Occurrence Download

description: A dataset containing 762 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Craugastor montanus (Taylor, 1942)"
 ]
}

 The dataset includes 762 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023148-250127130748423/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/10716922
title: BOS Kemdikbud
DOI: 10.5281/zenodo.14847393
title: MODERN IRRIGATION TECHNOLOGIES ARE THE NEED OF THE HOUR
DOI: 10.5281/zenodo.14847394
title: MODERN IRRIGATION TECHNOLOGIES ARE THE NEED OF THE HOUR
DOI: 10.25573/serc.28373957
title: NASA Blue Methane Field Monitoring for Louisiana and the Chesapeake Bay, 2019-2021

description: The purpose of the study was to collect data on both tidal wetland methane emissions and the processes that drive and interact with them, from two sites, to fit and validate improved near-term forecasting models. The study consists of two focal sites, the Smithsonian Environmental Research Center (SERC) and the Louisiana Universities Marine Consortium (LUMCON). Both sites are previously well studied, are microtidal, and have intermediate salinities. SERC is located on the Rhode River, a tributary of the Chesapeake Bay. LUMCON is located in Terrebonne Parish on the U.S. Gulf Coast.Each site consisted of 3 sub-sites referred to throughout as LUM1, 2, and 3 for LUMCON, and Mud, Hog, and Kirk, for SERC, referring to local names of Muddy Creek, Hog Island, and Kirkpatrick marsh. Each subsite, contained four nested plots. Plots were clustered so that pairs of plots pairs of pairs (1 and 2) were located 15 meters apart and pairs within were located 1.5 m apart (indicated by A and B). Fluxes, porewater concentrations of important biogeochemical constituents, plant biomass, and phenology, were measured approximately monthly. Salinity and water level were monitored within wetland wells continuously.
DOI: 10.25573/serc.28373957.v1
title: NASA Blue Methane Field Monitoring for Louisiana and the Chesapeake Bay, 2019-2021

description: The purpose of the study was to collect data on both tidal wetland methane emissions and the processes that drive and interact with them, from two sites, to fit and validate improved near-term forecasting models. The study consists of two focal sites, the Smithsonian Environmental Research Center (SERC) and the Louisiana Universities Marine Consortium (LUMCON). Both sites are previously well studied, are microtidal, and have intermediate salinities. SERC is located on the Rhode River, a tributary of the Chesapeake Bay. LUMCON is located in Terrebonne Parish on the U.S. Gulf Coast.Each site consisted of 3 sub-sites referred to throughout as LUM1, 2, and 3 for LUMCON, and Mud, Hog, and Kirk, for SERC, referring to local names of Muddy Creek, Hog Island, and Kirkpatrick marsh. Each subsite, contained four nested plots. Plots were clustered so that pairs of plots pairs of pairs (1 and 2) were located 15 meters apart and pairs within were located 1.5 m apart (indicated by A and B). Fluxes, porewater concentrations of important biogeochemical constituents, plant biomass, and phenology, were measured approximately monthly. Salinity and water level were monitored within wetland wells continuously.
DOI: 10.34740/kaggle/dsv/10716938
title: Zanskar's GeoGym
DOI: 10.5281/zenodo.14847400
title: TAKRORIY EKINLAR VA ULARGA QO'LLANILGAN ORGANO-MA'DAN KOMPOSTLARNI PAXTA HOSILIGA TA'SIRI
DOI: 10.5281/zenodo.14847401
title: TAKRORIY EKINLAR VA ULARGA QO'LLANILGAN ORGANO-MA'DAN KOMPOSTLARNI PAXTA HOSILIGA TA'SIRI
DOI: 10.6084/m9.figshare.21121917
title: cAMP-Protein kinase A and stress-activated MAP kinase signaling mediate transcriptional control of autophagy in fission yeast during glucose limitation or starvation

description: Macroautophagy/autophagy is an essential adaptive physiological response in eukaryotes induced during nutrient starvation, including glucose, the primary immediate carbon and energy source for most cells. Although the molecular mechanisms that induce autophagy during glucose starvation have been extensively explored in the budding yeast <i>Saccharomyces cerevisiae</i>, little is known about how this coping response is regulated in the evolutionary distant fission yeast <i>Schizosaccharomyces pombe</i>. Here, we show that <i>S. pombe</i> autophagy in response to glucose limitation relies on mitochondrial respiration and the electron transport chain (ETC), but, in contrast to <i>S. cerevisiae</i>, the AMP-activated protein kinase (AMPK) and DNA damage response pathway components do not modulate fission yeast autophagic flux under these conditions. In the presence of glucose, the cAMP-protein kinase A (PKA) signaling pathway constitutively represses <i>S. pombe</i> autophagy by downregulating the transcription factor Rst2, which promotes the expression of respiratory genes required for autophagy induction under limited glucose availability. Furthermore, the stress-activated protein kinase (SAPK) signaling pathway, and its central mitogen-activated protein kinase (MAPK) Sty1, positively modulate autophagy upon glucose limitation at the transcriptional level through its downstream effector Atf1 and by direct <i>in vivo</i> phosphorylation of Rst2 at S292. Thus, our data indicate that the signaling pathways that govern autophagy during glucose shortage or starvation have evolved differently in <i>S. pombe</i> and uncover the existence of sophisticated and multifaceted mechanisms that control this self-preservation and survival response.
DOI: 10.6084/m9.figshare.21084761.v1
title: Apicoplast biogenesis mediated by ATG8 requires the ATG12–ATG5-ATG16L and SNAP29 complexes in <i>Toxoplasma gondii</i>

description: In apicomplexan parasites, the macroautophagy/autophagy machinery is repurposed to maintain the plastid-like organelle apicoplast. Previously, we showed that in <i>Toxoplasma</i> and <i>Plasmodium</i>, ATG12 interacts with ATG5 in a non-covalent manner, in contrast to the covalent interaction in most organisms. However, it remained unknown whether apicomplexan parasites have functional orthologs of ATG16L1, a protein that is essential for the function of the covalent ATG12–ATG5 complex <i>in vivo</i> in other organisms. Furthermore, the mechanism used by the autophagy machinery to maintain the apicoplast is unclear. We report that the ATG12–ATG5-ATG16L complex exists in <i>Toxoplasma gondii</i> (Tg). This complex is localized on isolated structures at the periphery of the apicoplast dependent on TgATG16L. Inducible depletion of TgATG12, TgATG5, or TgATG16L caused loss of the apicoplast and affected parasite growth. We found that a putative soluble N-ethylmaleimide sensitive factor attachment protein receptor (SNARE) protein, synaptosomal-associated protein 29 (TgSNAP29, Qbc SNARE), is required to maintain the apicoplast in <i>T. gondii</i>. TgSNAP29 depletion disrupted TgATG8 localization at the apicoplast. Additionally, we identified a putative ubiquitin-interacting motif-docking site (UDS) of TgATG8. Mutation of the UDS site abolished TgATG8 localization on the apicoplast but not lipidation. These findings suggest that the TgATG12–TgATG5-TgATG16L complex is required for biogenesis of the apicoplast, in which TgATG8 is translocated to the apicoplast via vesicles in a SNARE -dependent manner in <i>T. gondii</i>. <b>Abbreviations</b>: AID: auxin-inducible degron; CCD: coiled-coil domain; HFF: human foreskin fibroblast; IAA: indole-3-acetic acid; LAP: LC3-associated phagocytosis; NAA: 1-naphthaleneacetic acid; PtdIns3P: phosphatidylinositol-3-phosphate; SNARE: soluble N-ethylmaleimide sensitive factor attachment protein receptor; UDS: ubiquitin-interacting motif-docking site; UIM: ubiquitin-interacting motif.
DOI: 10.6084/m9.figshare.21121917.v1
title: cAMP-Protein Kinase A and Stress-Activated MAP Kinase signaling mediate transcriptional control of autophagy in fission yeast during glucose limitation or starvation

description: Macroautophagy/autophagy is an essential adaptive physiological response in eukaryotes induced during nutrient starvation, including glucose, the primary immediate carbon and energy source for most cells. Although the molecular mechanisms that induce autophagy during glucose starvation have been extensively explored in the budding yeast <i>Saccharomyces cerevisiae</i>, little is known about how this coping response is regulated in the evolutionary distant fission yeast <i>Schizosaccharomyces pombe</i>. Here, we show that <i>S. pombe</i> autophagy in response to glucose limitation relies on mitochondrial respiration and the electron transport chain (ETC), but, in contrast to <i>S. cerevisiae</i>, the AMP-activated protein kinase (AMPK) and DNA damage response pathway components do not modulate fission yeast autophagic flux under these conditions. In the presence of glucose, the cAMP-protein kinase A (PKA) signaling pathway constitutively represses <i>S. pombe</i> autophagy by downregulating the transcription factor Rst2, which promotes the expression of respiratory genes required for autophagy induction under limited glucose availability. Furthermore, the stress-activated protein kinase (SAPK) signaling pathway, and its central mitogen-activated protein kinase (MAPK) Sty1, positively modulate autophagy upon glucose limitation at the transcriptional level through its downstream effector Atf1 and by direct <i>in vivo</i> phosphorylation of Rst2 at S292. Thus, our data indicate that the signaling pathways that govern autophagy during glucose shortage or starvation have evolved differently in <i>S. pombe</i> and uncover the existence of sophisticated and multifaceted mechanisms that control this self-preservation and survival response.
DOI: 10.6084/m9.figshare.21121917.v2
title: cAMP-Protein kinase A and stress-activated MAP kinase signaling mediate transcriptional control of autophagy in fission yeast during glucose limitation or starvation

description: Macroautophagy/autophagy is an essential adaptive physiological response in eukaryotes induced during nutrient starvation, including glucose, the primary immediate carbon and energy source for most cells. Although the molecular mechanisms that induce autophagy during glucose starvation have been extensively explored in the budding yeast <i>Saccharomyces cerevisiae</i>, little is known about how this coping response is regulated in the evolutionary distant fission yeast <i>Schizosaccharomyces pombe</i>. Here, we show that <i>S. pombe</i> autophagy in response to glucose limitation relies on mitochondrial respiration and the electron transport chain (ETC), but, in contrast to <i>S. cerevisiae</i>, the AMP-activated protein kinase (AMPK) and DNA damage response pathway components do not modulate fission yeast autophagic flux under these conditions. In the presence of glucose, the cAMP-protein kinase A (PKA) signaling pathway constitutively represses <i>S. pombe</i> autophagy by downregulating the transcription factor Rst2, which promotes the expression of respiratory genes required for autophagy induction under limited glucose availability. Furthermore, the stress-activated protein kinase (SAPK) signaling pathway, and its central mitogen-activated protein kinase (MAPK) Sty1, positively modulate autophagy upon glucose limitation at the transcriptional level through its downstream effector Atf1 and by direct <i>in vivo</i> phosphorylation of Rst2 at S292. Thus, our data indicate that the signaling pathways that govern autophagy during glucose shortage or starvation have evolved differently in <i>S. pombe</i> and uncover the existence of sophisticated and multifaceted mechanisms that control this self-preservation and survival response.
DOI: 10.6084/m9.figshare.21084761
title: Apicoplast biogenesis mediated by ATG8 requires the ATG12–ATG5-ATG16L and SNAP29 complexes in <i>Toxoplasma gondii</i>

description: In apicomplexan parasites, the macroautophagy/autophagy machinery is repurposed to maintain the plastid-like organelle apicoplast. Previously, we showed that in <i>Toxoplasma</i> and <i>Plasmodium</i>, ATG12 interacts with ATG5 in a non-covalent manner, in contrast to the covalent interaction in most organisms. However, it remained unknown whether apicomplexan parasites have functional orthologs of ATG16L1, a protein that is essential for the function of the covalent ATG12–ATG5 complex <i>in vivo</i> in other organisms. Furthermore, the mechanism used by the autophagy machinery to maintain the apicoplast is unclear. We report that the ATG12–ATG5-ATG16L complex exists in <i>Toxoplasma gondii</i> (Tg). This complex is localized on isolated structures at the periphery of the apicoplast dependent on TgATG16L. Inducible depletion of TgATG12, TgATG5, or TgATG16L caused loss of the apicoplast and affected parasite growth. We found that a putative soluble N-ethylmaleimide sensitive factor attachment protein receptor (SNARE) protein, synaptosomal-associated protein 29 (TgSNAP29, Qbc SNARE), is required to maintain the apicoplast in <i>T. gondii</i>. TgSNAP29 depletion disrupted TgATG8 localization at the apicoplast. Additionally, we identified a putative ubiquitin-interacting motif-docking site (UDS) of TgATG8. Mutation of the UDS site abolished TgATG8 localization on the apicoplast but not lipidation. These findings suggest that the TgATG12–TgATG5-TgATG16L complex is required for biogenesis of the apicoplast, in which TgATG8 is translocated to the apicoplast via vesicles in a SNARE -dependent manner in <i>T. gondii</i>. <b>Abbreviations</b>: AID: auxin-inducible degron; CCD: coiled-coil domain; HFF: human foreskin fibroblast; IAA: indole-3-acetic acid; LAP: LC3-associated phagocytosis; NAA: 1-naphthaleneacetic acid; PtdIns3P: phosphatidylinositol-3-phosphate; SNARE: soluble N-ethylmaleimide sensitive factor attachment protein receptor; UDS: ubiquitin-interacting motif-docking site; UIM: ubiquitin-interacting motif.
DOI: 10.6084/m9.figshare.21170766
title: NLRC5 restricts dengue virus infection by promoting the autophagic degradation of viral NS3 through E3 ligase CUL2 (cullin 2)

description: NLRC5 has been reported to be involved in antiviral immunity; however, the underlying mechanism remains poorly understood. Here, we investigated the functional role of NLRC5 in the infection of a flavivirus, dengue virus (DENV). We found that the expression of NLRC5 was strongly induced by virus infection and IFNB or IFNG stimulation in different cell lines. Overexpression of NLRC5 remarkably suppressed DENV infection, whereas knockout of <i>NLRC5</i> led to a significant increase in DENV infection. Mechanistic study revealed that NLRC5 interacted with the viral nonstructural protein 3 (NS3) protease domain and mediated degradation of NS3 through a ubiquitin-dependent selective macroautophagy/autophagy pathway. We demonstrated that NLRC5 recruited the E3 ubiquitin ligase CUL2 (cullin 2) to catalyze K48-linked poly-ubiquitination of the NS3 protease domain, which subsequently served as a recognition signal for cargo receptor TOLLIP-mediated selective autophagic degradation. Together, we have demonstrated that NLRC5 exerted an antiviral effect by mediating the degradation of a multifunctional protein of DENV, providing a novel antiviral signal axis of NLRC5-CUL2-NS3-TOLLIP. This study expands our understanding of the regulatory network of NLRC5 in the host defense against virus infection.
DOI: 10.6084/m9.figshare.20839820.v1
title: Myeloid autophagy genes protect mice against fatal TNF- and LPS-induced cytokine storm syndromes

description: Macroautophagy/autophagy regulates inflammation via multiple mechanisms, including lysosomal degradation of specific cellular components. Certain autophagy gene “cassettes” also participate in non-canonical processes to mediate important biological activities. While select autophagy genes in myeloid cells have been implicated in protecting mice in models of cytokine storm syndromes (CSS), a more extensive genetic analysis of the autophagy pathway for this disorder has not been reported to date. We determined that multiple canonical autophagy genes in the myeloid compartment protected against fatal disease from both intravenous TNF and intraperitoneal LPS, with the notable exception that <i>Atg14</i> was dispensable for the latter. Serum cytokine analyses and genetic crosses further revealed distinct mechanisms contribute to the hypersensitivity of autophagy gene-deficient mice in these CSS models. Surprisingly, TNF was dispensable for the increased mortality of myeloid <i>5</i>-deficient mice challenged with LPS. Tissue-specific ablation of <i>Atg5</i> in cells expressing ITGAX/CD11c and LYZ2/LYSM, but not S100A8/MRP8, defined a myeloid subset that protected against TNF, while protection against LPS was conferred by <i>Atg5</i> in a distinct subset of LYZ2-expressing cells. Together, this study identifies autophagy gene sets and specific cell types that protect against fatal inflammation due to CSS, highlighting important differences in two commonly used murine models of the disorder. ATG5: autophagy related 5; ATG7: autophagy related 7; ATG14: autophagy related 14; ATG16L1: autophagy related 16-like 1 (S. cerevisiae); BECN1: beclin 1, autophagy related; CASP1: caspase 1; CASP4/CASP11: caspase 4, apoptosis-related cysteine peptidase; CIM: conditionally immortalized macrophage; CLP: cecal ligation and puncture; CSS: cytokine storm syndrome; DC: dendritic cell; IFNG/IFNγ: interferon gamma; IFNGR1: interferon gamma receptor 1; ip: intraperitoneal; iv: intravenous; IL12/p70: interleukin 12, p70 heterodimer; IL18: Interleukin 18; ITGAX/CD11c: integrin alpha X; LAP: LC3-associated phagocytosis; LPS: lipopolysaccharide; LYZ2/LYSM: lysozyme 2; MAP1LC3A/LC3: microtubule-associated protein 1 light chain 3 alpha; RB1CC1/FIP200: RB1-inducible coiled-coil 1; S100A8/MRP8: S100 calcium binding protein A8 (calgranulin A); TICAM1/TRIF: TIR domain containing adaptor molecule 1; TLR4: toll-like receptor 4; TNF: tumor necrosis factor.
DOI: 10.6084/m9.figshare.21170766.v2
title: NLRC5 restricts dengue virus infection by promoting the autophagic degradation of viral NS3 through E3 ligase CUL2 (cullin 2)

description: NLRC5 has been reported to be involved in antiviral immunity; however, the underlying mechanism remains poorly understood. Here, we investigated the functional role of NLRC5 in the infection of a flavivirus, dengue virus (DENV). We found that the expression of NLRC5 was strongly induced by virus infection and IFNB or IFNG stimulation in different cell lines. Overexpression of NLRC5 remarkably suppressed DENV infection, whereas knockout of <i>NLRC5</i> led to a significant increase in DENV infection. Mechanistic study revealed that NLRC5 interacted with the viral nonstructural protein 3 (NS3) protease domain and mediated degradation of NS3 through a ubiquitin-dependent selective macroautophagy/autophagy pathway. We demonstrated that NLRC5 recruited the E3 ubiquitin ligase CUL2 (cullin 2) to catalyze K48-linked poly-ubiquitination of the NS3 protease domain, which subsequently served as a recognition signal for cargo receptor TOLLIP-mediated selective autophagic degradation. Together, we have demonstrated that NLRC5 exerted an antiviral effect by mediating the degradation of a multifunctional protein of DENV, providing a novel antiviral signal axis of NLRC5-CUL2-NS3-TOLLIP. This study expands our understanding of the regulatory network of NLRC5 in the host defense against virus infection.