cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12123720.v3
title: A monolayer hiPSC culture system for autophagy/mitophagy studies in human dopaminergic neurons

description: Macroautophagy/autophagy cytoplasmic quality control pathways are required during neural development and are critical for the maintenance of functional neuronal populations in the adult brain. Robust evidence now exists that declining neuronal autophagy pathways contribute to human neurodegenerative diseases, including Parkinson disease (PD). Reliable and relevant human neuronal model systems are therefore needed to understand the biology of disease-vulnerable neural populations, to decipher the underlying causes of neurodegenerative disease, and to develop assays to test therapeutic interventions <i>in vitro</i>. Human induced pluripotent stem cell (hiPSC) neural model systems can meet this demand: they provide a renewable source of material for differentiation into regional neuronal sub-types for functional assays; they can be expanded to provide a platform for screening, and they can potentially be optimized for transplantation/neurorestorative therapy. So far, however, hiPSC differentiation protocols for the generation of ventral midbrain dopaminergic neurons (mDANs) – the predominant neuronal sub-type afflicted in PD – have been somewhat restricted by poor efficiency and/or suitability for functional and/or imaging-based <i>in vitro</i> assays. Here, we describe a reliable, monolayer differentiation protocol for the rapid and reproducible production of high numbers of mDANs from hiPSC in a format that is amenable for autophagy/mitophagy research. We characterize these cells with respect to neuronal differentiation and macroautophagy capability and describe qualitative and quantitative assays for the study of autophagy and mitophagy in these important cells. <b>Abbreviations:</b> AA: ascorbic acid; ATG: autophagy-related; BDNF: brain derived neurotrophic factor; CCCP: carbonyl cyanide m-chlorophenylhydrazone; dbcAMP: dibutyryl cAMP; DAN: dopaminergic neuron; DAPI: 4ʹ,6-diamidino-2-phenylindole; DAPT: N-[N-(3,5-difluorophenacetyl)-L-alanyl]-sphenylglycine; DLG4/PSD95: discs large MAGUK scaffold protein 4; DMEM: Dulbecco’s modified eagle’s medium; EB: embryoid body; ECAR: extracellular acidification rate; EGF: epidermal growth factor; FACS: fluorescence-activated cell sorting; FCCP: arbonyl cyanide p-triflouromethoxyphenylhydrazone; FGF: fibroblast growth factor; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GDNF: glia cell derived neurotrophic factor; hiPSC: human induced pluripotent stem cell; LAMP2A: lysosomal associated membrane protein 2A; LT-R: LysoTracker Red; MAP1LC3: microtubule associated protein 1 light chain 3; mDAN: midbrain dopaminergic neuron; MEF: mouse embryonic fibroblast; MT-GR: MitoTracker Green; MT-R: MitoTracker Red; NAS2: normal SNCA2; NEM: neuroprogenitor expansion media; NR4A2/NURR1: nuclear receptor subfamily group A member 2; OA: oligomycin and antimycin A; OCR: oxygen consumption rate; PD: Parkinson disease; SHH: sonic hedgehog signaling molecule; SNCA/α-synuclein: synuclein alpha; TH: tyrosine hydroxylase; VTN: vitronectin.
DOI: 10.6084/m9.figshare.26053234
title: Ancient developmental genes underlie evolutionary novelties in walking fish

description: Scripts and data for "Ancient developmental genes underlie evolutionary novelties in walking fish" by Herbert et al. 2024.
DOI: 10.6084/m9.figshare.12024480
title: Nucleoporin TPR (translocated promoter region, nuclear basket protein) upregulation alters MTOR-HSF1 trails and suppresses autophagy induction in ependymoma

description: Children with ependymoma have high mortality rates because ependymoma is resistant to conventional therapy. Genomic and transcriptomic studies have identified potential targets as significantly altered genes in ependymoma patients. Although several candidate oncogenes in ependymoma were recently reported, the detailed mechanisms for the roles of these candidate oncogenes in ependymoma progression remain unclear. Here, we report an oncogenic role of the nucleoporin TPR (translocated promoter region, nuclear basket protein) in regulating <i>HSF1</i> (heat shock transcription factor 1) mRNA trafficking, maintaining MTORC1 activity to phosphorylate ULK1, and preventing macroautophagy/autophagy induction in ependymoma. High expression of TPR were associated with increased <i>HSF1</i> and <i>HSPA/HSP70</i> expression in ependymoma patients. In an ependymoma mouse xenograft model, MTOR inhibition by rapamycin therapeutically suppressed TPR expression and reduced tumor size <i>in vivo</i>. Together, these results suggest that TPR may act as a biomarker for ependymoma, and pharmacological interventions targeting TPR-HSF1-MTOR may have therapeutic potential for ependymoma treatment. <b>Abbreviations</b>: ATG: autophagy related; BECN1: beclin 1; BSA: bovine serum albumin; CQ: chloroquine; DMSO: dimethyl sulfoxide; GEO: gene expression omnibus; GFP: green fluorescence protein; HSF1: heat shock transcription factor 1; HSPA/HSP70: heat shock protein family A (Hsp70); LMNB1: lamin B1; MAP1LC3B/LC3B: microtubule-associated protein 1 light chain 3 beta; MAPK: mitogen-activated protein kinase; MAPK8/JNK: mitogen-activated protein kinase 8; MTORC1: mechanistic target of rapamycin kinase complex 1; NPC: nuclear pore complex; NUP: nucleoporin; PBS: phosphate-buffered saline; q-PCR: quantitative real time PCR; SDS: sodium dodecyl sulfate; SQSTM1: sequestosome 1; STED: stimulated emission depletion microscopy; STX17: syntaxin 17; TCGA: the cancer genome atlas; TPR: translocated promoter region, nuclear basket protein; ULK1: unc-51 like autophagy activating kinase 1.
DOI: 10.6084/m9.figshare.12024480.v3
title: Nucleoporin TPR (translocated promoter region, nuclear basket protein) upregulation alters MTOR-HSF1 trails and suppresses autophagy induction in ependymoma

description: Children with ependymoma have high mortality rates because ependymoma is resistant to conventional therapy. Genomic and transcriptomic studies have identified potential targets as significantly altered genes in ependymoma patients. Although several candidate oncogenes in ependymoma were recently reported, the detailed mechanisms for the roles of these candidate oncogenes in ependymoma progression remain unclear. Here, we report an oncogenic role of the nucleoporin TPR (translocated promoter region, nuclear basket protein) in regulating <i>HSF1</i> (heat shock transcription factor 1) mRNA trafficking, maintaining MTORC1 activity to phosphorylate ULK1, and preventing macroautophagy/autophagy induction in ependymoma. High expression of TPR were associated with increased <i>HSF1</i> and <i>HSPA/HSP70</i> expression in ependymoma patients. In an ependymoma mouse xenograft model, MTOR inhibition by rapamycin therapeutically suppressed TPR expression and reduced tumor size <i>in vivo</i>. Together, these results suggest that TPR may act as a biomarker for ependymoma, and pharmacological interventions targeting TPR-HSF1-MTOR may have therapeutic potential for ependymoma treatment. <b>Abbreviations</b>: ATG: autophagy related; BECN1: beclin 1; BSA: bovine serum albumin; CQ: chloroquine; DMSO: dimethyl sulfoxide; GEO: gene expression omnibus; GFP: green fluorescence protein; HSF1: heat shock transcription factor 1; HSPA/HSP70: heat shock protein family A (Hsp70); LMNB1: lamin B1; MAP1LC3B/LC3B: microtubule-associated protein 1 light chain 3 beta; MAPK: mitogen-activated protein kinase; MAPK8/JNK: mitogen-activated protein kinase 8; MTORC1: mechanistic target of rapamycin kinase complex 1; NPC: nuclear pore complex; NUP: nucleoporin; PBS: phosphate-buffered saline; q-PCR: quantitative real time PCR; SDS: sodium dodecyl sulfate; SQSTM1: sequestosome 1; STED: stimulated emission depletion microscopy; STX17: syntaxin 17; TCGA: the cancer genome atlas; TPR: translocated promoter region, nuclear basket protein; ULK1: unc-51 like autophagy activating kinase 1.
DOI: 10.15468/dl.3xpdwd
title: Occurrence Download

description: A dataset containing 7474 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Spondias mombin L."
 ]
}

 The dataset includes 7474 records from 393 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017657-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13768874
title: data_set for "Time-resolved sensing of electromagnetic fields with single-electron interferometry"
DOI: 10.5281/zenodo.12795284
title: data_set for "Time-resolved sensing of electromagnetic fields with single-electron interferometry"
DOI: 10.5281/zenodo.12795285
title: data_set for "Time-resolved sensing of electromagnetic fields with single-electron interferometry"
DOI: 10.5281/zenodo.13768560
title: data_set for "Time-resolved sensing of electromagnetic fields with single-electron interferometry"
DOI: 10.15468/dl.9kgavz
title: Occurrence Download

description: A dataset containing 17596 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gelsemiaceae"
 ]
}

 The dataset includes 17596 records from 297 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017658-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zcmcqh
title: Occurrence Download

description: A dataset containing 158861 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Global soil organisms",
 "Country is Sweden"
 ]
}

 The dataset includes 158861 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017609-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5zq2hu
title: Occurrence Download

description: A dataset containing 2881053 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is EOD – eBird Observation Dataset",
 "Country is Sweden"
 ]
}

 The dataset includes 2881053 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017610-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7ujrzm
title: Occurrence Download

description: A dataset containing 749781 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Xeno-canto - Bird sounds from around the world"
 ]
}

 The dataset includes 749781 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017606-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fq2uzp
title: Occurrence Download

description: A dataset containing 109544 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lindsaeaceae"
 ]
}

 The dataset includes 109544 records from 611 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017604-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qt7wqj
title: Occurrence Download

description: A dataset listing the 4024377 species recorded in GBIF matching the query:
{ }

 The dataset's 4024377 records were derived from 76368 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017628-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13768858
title: FRACTESUS_KIT_SA508Cl3_KJc_MCT_-45_28

description: Fractesus project. Fracture test mini-CT. Raw data SA508Cl3. KIT.
DOI: 10.5281/zenodo.13768859
title: FRACTESUS_KIT_SA508Cl3_KJc_MCT_-45_28

description: Fractesus project. Fracture test mini-CT. Raw data SA508Cl3. KIT.
DOI: 10.15468/dl.jspqwf
title: Occurrence Download

description: A dataset containing 2425 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Senegalia macrostachya (Rchb. ex DC.) Kyal. & Boatwr."
 ]
}

 The dataset includes 2425 records from 72 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017663-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x558f6
title: Occurrence Download

description: A dataset containing 178 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "TaxonKey is Iochroma fuchsioides (Kunth) Miers"
 ]
}

 The dataset includes 178 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017664-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wvxq8b
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Portugal",
 "TaxonKey is Liparis montagui (Donovan, 1804)"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017665-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.q4zxwj
title: Occurrence Download

description: A dataset containing 12470 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pterocarpus erinaceus Poir."
 ]
}

 The dataset includes 12470 records from 160 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017667-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xbxr27
title: Occurrence Download

description: A dataset containing 10080 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "PublishingCountry is Colombia",
 {
 "and" : [
 "Country is Colombia",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 }
 ]
 },
 "DatasetKey is one of (Influencia de los productos de un incendio forestal sobre la germinación de cuatro especies potencialmente invasoras en un Bosque Altoandino disturbado)"
 ]
}

 The dataset includes 10080 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017670-240906103802322/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.27037849
title: Dataset Structural Equation Model - Catfolis et al.

description: Forests provide crucial habitats for nature and people, but also harbor organisms, such as ticks, that can act as vectors for pathogens. Consequently, understanding how forest management practices influence host-parasite-pathogen interactions is essential for promoting both forest biodiversity conservation and nature’s contributions to people. Therefore, this study investigates the complex relationships between forest structural complexity, body condition, and tick infestation probability in a common forest bird, the great tit (Parus major), across 19 forests in the Flemish Ardennes, Belgium. Using Structural Equation Modeling (SEM), we first integrated multiple phenotypic health proxies into a single overall condition index. Subsequently, we assessed how variations in forest structural complexity impact the condition of forest birds and their chances of contracting ticks. Our findings revealed that birds in a better physiological condition, primarily driven by lower levels of cellular stress (indicated by longer telomeres) are more likely to carry ticks. This may be due to ticks preferring healthier and more nutritious hosts and/or condition-linked differences in bird behavior (e.g. foraging), resulting in higher contact rates with ticks. While forest structural complexity did not significantly affect the birds' overall body condition, it was responsible for an increased tick infestation probability. Specifically, forests with higher structural complexity were associated with increased densities of questing nymphs, thereby elevating the risk of tick infestation in birds. Our study highlights the multifaceted role of forest structure in shaping host-parasite dynamics. These insights are valuable for developing forest management practices that balance the enhancement of ecological health with the mitigation of health risks posed by tick-borne diseases.
DOI: 10.15468/dl.hxr329
title: Occurrence Download

description: A dataset listing the 4024197 species recorded in GBIF matching the query:
{
 "OccurrenceStatus" : [
 "is Present"
 ]
}

 The dataset's 4024197 records were derived from 76339 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017632-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hvshna
title: Occurrence Download

description: A dataset containing 629 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Trichiurus japonicus Temminck & Schlegel, 1844"
 ]
}

 The dataset includes 629 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017671-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f4n2cu
title: Occurrence Download

description: A dataset containing 342 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Arenaria bourgaei Hemsl."
 ]
}

 The dataset includes 342 records from 58 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045893-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rtj68w
title: Occurrence Download

description: A dataset containing 137 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON ((-81.4539297999999974 41.0510561999999979, -81.4539297999999974 41.0533771599999966, -81.4539297999999974 41.0550018300000019, -81.4539297999999974 41.0567425500000027, -81.4539297999999974 41.0581351299999966, -81.4539297999999974 41.0598758499999974, -81.4539297999999974 41.0626609999999985, -81.4508007700000007 41.0626609999999985, -81.4490625199999982 41.0626609999999985, -81.4468607200000037 41.0626609999999985, -81.4453542300000066 41.0626609999999985, -81.4419936000000035 41.0626609999999985, -81.4392123899999945 41.0626609999999985, -81.4358517600000056 41.0626609999999985, -81.4329544999999939 41.0626609999999985, -81.4329544999999939 41.0596437499999993, -81.4329544999999939 41.0581351299999966, -81.4329544999999939 41.0566265000000001, -81.4329544999999939 41.0543055400000014, -81.4329544999999939 41.0529129700000013, -81.4329544999999939 41.0510561999999979, -81.4349246900000026 41.0510561999999979, -81.4381694399999958 41.0510561999999979, -81.4400235800000019 41.0510561999999979, -81.4425730199999975 41.0510561999999979, -81.4443112799999938 41.0510561999999979, -81.4465130699999946 41.0510561999999979, -81.4492942800000037 41.0510561999999979, -81.4509166600000043 41.0510561999999979, -81.4539297999999974 41.0510561999999979))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1932",
 "BasisOfRecord is one of (Human Observation, Living Specimen, Observation, Specimen, Machine Observation)"
 ]
}

 The dataset includes 137 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0098814-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-65181
title: Redemption tidings, vol. 45, nos. 1-52, 2 Jan. - 25 Dec. 1969

description: [description english/roman)] Issued weekly.
DOI: 10.15468/dl.9cyf5b
title: Occurrence Download

description: A dataset containing 71 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Diaphus metopoclampus (Cocco, 1829)",
 "Year 1899-1950"
 ]
}

 The dataset includes 71 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005847-240202131308920/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sqsjfr
title: Occurrence Download

description: A dataset containing 3954 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Sceloporus spinosus Wiegmann, 1828"
 ]
}

 The dataset includes 3954 records from 72 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032250-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2jkyey
title: Occurrence Download

description: A dataset containing 1324 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Trillium albidum J.D.Freeman",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1324 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0073965-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-65249
title: Redemption tidings, vol. 45, nos. 1-52, 2 Jan. - 25 Dec. 1969

description: [description english/roman)] Issued weekly.
DOI: 10.15468/dl.8mxp36
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Eumorphometra hirsuta (Carpenter, 1888)"
 ]
}

 The dataset includes 12 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0067924-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ecjjba
title: Occurrence Download

description: A dataset containing 167 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Caligus elongatus von Nordmann, 1832"
 ]
}

 The dataset includes 167 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0114716-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7nf4zq
title: Occurrence Download

description: A dataset containing 1215 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Setaria liebmannii E.Fourn."
 ]
}

 The dataset includes 1215 records from 92 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0126995-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-65191
title: Redemption tidings, vol. 45, nos. 1-52, 2 Jan. - 25 Dec. 1969

description: [description english/roman)] Issued weekly.