cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11913969.v1
title: Applications of the Fractional-Random-Weight Bootstrap

description: For several decades, the resampling based bootstrap has been widely used for computing confidence intervals (CIs) for applications where no exact method is available. However, there are many applications where the resampling bootstrap method cannot be used. These include situations where the data are heavily censored due to the success response being a rare event, situations where there is insufficient mixing of successes and failures across the explanatory variable(s), and designed experiments where the number of parameters is close to the number of observations. These three situations all have in common that there may be a substantial proportion of the resamples where it is not possible to estimate all of the parameters in the model. This article reviews the fractional-random-weight bootstrap method and demonstrates how it can be used to avoid these problems and construct CIs in a way that is accessible to statistical practitioners. The fractional-random-weight bootstrap method is easy to use and has advantages over the resampling method in many challenging applications.
DOI: 10.5281/zenodo.10669847
title: Optimal Beam Shapes: Fact or Fantasy?

description: Raw data associated with a paper submission."Optimal Beam Shapes: Fact or Fantasy?" submitted to Additive Manufacturing Letters.

Contained are all the Matlab scripts used for the simulations, as well as csv's of any data plotted in graphs.
DOI: 10.6084/m9.figshare.7195436
title: Intraplate extension of the Indochina plate deduced from 26 to 24 Ma A-type granites and tectonic implications

description: In recent years, abundant Cenozoic potassic magmatic rocks from eastern Tibet and the Indochina Block have been studied extensively; however, until now, knowledge of Cenozoic A-type granites from the interior of the Indochina Block has been limited. U–Pb zircon ages for six samples of the Salei granite pluton within the Indochina Block range from 26 to 24 Ma. <i>In situ</i> Lu–Hf and Sr–Nd isotope data indicate that the Salei pluton was sourced mostly from Mesoproterozoic basement rocks of the Indochina Block, mixed with a small volume of juvenile crust derived from the underplated mantle. Whole-rock major element geochemistry indicates that the six samples are peraluminous high-K calc-alkaline granites. The trace and rare earth element patterns are typical of within-plate A-type granites. In combination with previous research, the present results suggest that the late Oligocene Salei granite formed from the convective removal of thickened lower continental lithospheric mantle. Moreover, the presence of 26<b>–</b>24 Ma A-type granites in the Indochina Block indicates within-plate extension in the interior of the block during the late Oligocene.
DOI: 10.6084/m9.figshare.16625186
title: Additional file 5 of Mapping the evolving landscape of super-enhancers during cell differentiation

description: Additional file 5: Table S4. Summary of the evolving signals of enhancers during differentiation for each interrogated system.
DOI: 10.6084/m9.figshare.8247758
title: PHB2 (prohibitin 2) promotes PINK1-PRKN/Parkin-dependent mitophagy by the PARL-PGAM5-PINK1 axis

description: Mitophagy, which is a conserved cellular process for selectively removing damaged or unwanted mitochondria, is critical for mitochondrial quality control and the maintenance of normal cellular physiology. However, the precise mechanisms underlying mitophagy remain largely unknown. Prior studies on mitophagy focused on the events in the mitochondrial outer membrane. PHB2 (prohibitin 2), which is a highly conserved membrane scaffold protein, was recently identified as a novel inner membrane mitophagy receptor that mediates mitophagy. Here, we report a new signaling pathway for PHB2-mediated mitophagy. Upon mitochondrial membrane depolarization or misfolded protein aggregation, PHB2 depletion destabilizes PINK1 in the mitochondria, which blocks the mitochondrial recruitment of PRKN/Parkin, ubiquitin and OPTN (optineurin), leading to an inhibition of mitophagy. In addition, PHB2 overexpression directly induces PRKN recruitment to the mitochondria. Moreover, PHB2-mediated mitophagy is dependent on the mitochondrial inner membrane protease PARL, which interacts with PHB2 and is activated upon PHB2 depletion. Furthermore, PGAM5, which is processed by PARL, participates in PHB2-mediated PINK1 stabilization. Finally, a ligand of PHB proteins that we synthesized, called FL3, was found to strongly inhibit PHB2-mediated mitophagy and to effectively block cancer cell growth and energy production at nanomolar concentrations. Thus, our findings reveal that the PHB2-PARL-PGAM5-PINK1 axis is a novel pathway of PHB2-mediated mitophagy and that targeting PHB2 with the chemical compound FL3 is a promising strategy for cancer therapy. AIFM1: apoptosis inducing factor mitochondria associated 1; ATP5F1A/ATP5A1: ATP synthase F1 subunit alpha; BAF: bafilomycin A<sub>1</sub>; CALCOCO2/NDP52: calcium binding and coiled-coil domain 2; CCCP: chemical reagent carbonyl cyanide m-chlorophenyl hydrazine; FL3: flavaglines compound 3; HSPD1/HSP60: heat shock protein family D (Hsp60) member 1; LC3B/MAP1LC3B: microtubule associated protein 1 light chain 3 beta; MEF: mouse embryo fibroblasts; MPP: mitochondrial-processing peptidase; MT-CO2/COX2: mitochondrially encoded cytochrome c oxidase II; MTS: mitochondrial targeting sequence; OA: oligomycin and antimycin A; OPTN: optineurin; OTC: ornithine carbamoyltransferase; PARL: presenilin associated rhomboid like; PBS: phosphate-buffered saline; PGAM5: PGAM family member 5, mitochondrial serine/threonine protein phosphatase; PHB: prohibitin; PHB2: prohibitin 2; PINK1: PTEN induced kinase 1; PRKN/Parkin: parkin RBR E3 ubiquitin protein ligase; Roc-A: rocaglamide A; TOMM20: translocase of outer mitochondrial membrane 20; TUBB: tubulin beta class I.
DOI: 10.6084/m9.figshare.8247758.v1
title: PHB2 (prohibitin 2) promotes PINK1-PRKN/Parkin-dependent mitophagy by the PARL-PGAM5-PINK1 axis

description: Mitophagy, which is a conserved cellular process for selectively removing damaged or unwanted mitochondria, is critical for mitochondrial quality control and the maintenance of normal cellular physiology. However, the precise mechanisms underlying mitophagy remain largely unknown. Prior studies on mitophagy focused on the events in the mitochondrial outer membrane. PHB2 (prohibitin 2), which is a highly conserved membrane scaffold protein, was recently identified as a novel inner membrane mitophagy receptor that mediates mitophagy. Here, we report a new signaling pathway for PHB2-mediated mitophagy. Upon mitochondrial membrane depolarization or misfolded protein aggregation, PHB2 depletion destabilizes PINK1 in the mitochondria, which blocks the mitochondrial recruitment of PRKN/Parkin, ubiquitin and OPTN (optineurin), leading to an inhibition of mitophagy. In addition, PHB2 overexpression directly induces PRKN recruitment to the mitochondria. Moreover, PHB2-mediated mitophagy is dependent on the mitochondrial inner membrane protease PARL, which interacts with PHB2 and is activated upon PHB2 depletion. Furthermore, PGAM5, which is processed by PARL, participates in PHB2-mediated PINK1 stabilization. Finally, a ligand of PHB proteins that we synthesized, called FL3, was found to strongly inhibit PHB2-mediated mitophagy and to effectively block cancer cell growth and energy production at nanomolar concentrations. Thus, our findings reveal that the PHB2-PARL-PGAM5-PINK1 axis is a novel pathway of PHB2-mediated mitophagy and that targeting PHB2 with the chemical compound FL3 is a promising strategy for cancer therapy. AIFM1: apoptosis inducing factor mitochondria associated 1; ATP5F1A/ATP5A1: ATP synthase F1 subunit alpha; BAF: bafilomycin A<sub>1</sub>; CALCOCO2/NDP52: calcium binding and coiled-coil domain 2; CCCP: chemical reagent carbonyl cyanide m-chlorophenyl hydrazine; FL3: flavaglines compound 3; HSPD1/HSP60: heat shock protein family D (Hsp60) member 1; LC3B/MAP1LC3B: microtubule associated protein 1 light chain 3 beta; MEF: mouse embryo fibroblasts; MPP: mitochondrial-processing peptidase; MT-CO2/COX2: mitochondrially encoded cytochrome c oxidase II; MTS: mitochondrial targeting sequence; OA: oligomycin and antimycin A; OPTN: optineurin; OTC: ornithine carbamoyltransferase; PARL: presenilin associated rhomboid like; PBS: phosphate-buffered saline; PGAM5: PGAM family member 5, mitochondrial serine/threonine protein phosphatase; PHB: prohibitin; PHB2: prohibitin 2; PINK1: PTEN induced kinase 1; PRKN/Parkin: parkin RBR E3 ubiquitin protein ligase; Roc-A: rocaglamide A; TOMM20: translocase of outer mitochondrial membrane 20; TUBB: tubulin beta class I.
DOI: 10.6084/m9.figshare.8247764
title: TGFB1-induced autophagy affects the pattern of pancreatic cancer progression in distinct ways depending on SMAD4 status

description: Pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive and lethal malignancies. Given that macroautophagy/autophagy activation is prevalent in PDAC, the dual roles of autophagy could be involved in PDAC heterogeneity. In this work, we demonstrated that TGFB1 induced autophagic flux through SMAD4-dependent or SMAD4-independent pathways based on a distinct genetic context. In SMAD4-positive PDAC cells, TGFB1-induced autophagy promoted proliferation and inhibited migration by decreasing the nuclear translocation of SMAD4. Conversely, TGFB1-induced autophagy inhibited proliferation and promoted migration in SMAD4-negative cells through the regulation of MAPK/ERK activation. TGFB1 expression also positively correlated with LC3B expression in PDAC specimens. A high level of LC3B was associated with unfavorable overall survival (OS) and disease-free survival (DFS) in SMAD4-negative PDAC patients, although LC3B could not predict OS and DFS for the 110 PDAC patients. Thus, TGFB1-induced autophagy contributed to the different patterns of PDAC progression. This knowledge can aid in improving our understanding of the molecular classification of PDAC and might guide the development of therapeutic strategies for PDAC, especially for SMAD4-negative PDAC. CDH1: cadherin 1; CDH2: cadherin 2; CI: combination index; CQ: chloroquine; DFS: disease-free survival; EMT: epithelial-to-mesenchymal transition; ERK: extracellular signal-regulated protein kinase; GFP: green fluorescent protein; IHC: immunohistochemistry; MAP1LC3B/LC3B: microtubule associated protein 1 light chain 3 beta; MAPK: mitogen-activated protein kinase; OS: overall survival; PBS: phosphate-buffered saline; PDAC: pancreatic ductal adenocarcinoma; RAP: rapamycin; RFP: red fluorescent protein; RT: room temperature; shRNA: short-hairpin RNA; SQSTM1: sequestosome 1; TCGA: The Cancer Genome Atlas; TEM: transmission electron microscopy; TGFB1: transforming growth factor beta 1; TMA: tissue microarray
DOI: 10.6084/m9.figshare.8247764.v1
title: TGFB1-induced autophagy affects the pattern of pancreatic cancer progression in distinct ways depending on SMAD4 status

description: Pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive and lethal malignancies. Given that macroautophagy/autophagy activation is prevalent in PDAC, the dual roles of autophagy could be involved in PDAC heterogeneity. In this work, we demonstrated that TGFB1 induced autophagic flux through SMAD4-dependent or SMAD4-independent pathways based on a distinct genetic context. In SMAD4-positive PDAC cells, TGFB1-induced autophagy promoted proliferation and inhibited migration by decreasing the nuclear translocation of SMAD4. Conversely, TGFB1-induced autophagy inhibited proliferation and promoted migration in SMAD4-negative cells through the regulation of MAPK/ERK activation. TGFB1 expression also positively correlated with LC3B expression in PDAC specimens. A high level of LC3B was associated with unfavorable overall survival (OS) and disease-free survival (DFS) in SMAD4-negative PDAC patients, although LC3B could not predict OS and DFS for the 110 PDAC patients. Thus, TGFB1-induced autophagy contributed to the different patterns of PDAC progression. This knowledge can aid in improving our understanding of the molecular classification of PDAC and might guide the development of therapeutic strategies for PDAC, especially for SMAD4-negative PDAC. CDH1: cadherin 1; CDH2: cadherin 2; CI: combination index; CQ: chloroquine; DFS: disease-free survival; EMT: epithelial-to-mesenchymal transition; ERK: extracellular signal-regulated protein kinase; GFP: green fluorescent protein; IHC: immunohistochemistry; MAP1LC3B/LC3B: microtubule associated protein 1 light chain 3 beta; MAPK: mitogen-activated protein kinase; OS: overall survival; PBS: phosphate-buffered saline; PDAC: pancreatic ductal adenocarcinoma; RAP: rapamycin; RFP: red fluorescent protein; RT: room temperature; shRNA: short-hairpin RNA; SQSTM1: sequestosome 1; TCGA: The Cancer Genome Atlas; TEM: transmission electron microscopy; TGFB1: transforming growth factor beta 1; TMA: tissue microarray
DOI: 10.6084/m9.figshare.17157014
title: Additional file 2 of Phytophthora infestans RXLR effector Pi04089 perturbs diverse defense-related genes to suppress host immunity

description: Additional file 2: Table S1 RNA sequence map information and expression profile.
DOI: 10.6084/m9.figshare.21351199
title: Additional file 7 of ELOVL gene family plays a virtual role in response to breeding selection and lipid deposition in different tissues in chicken (Gallus gallus)

description: Additional file 7: Table S5. Data sources for red jungle fowl and layers used in this study.
DOI: 10.6084/m9.figshare.17157029.v1
title: Additional file 6 of Phytophthora infestans RXLR effector Pi04089 perturbs diverse defense-related genes to suppress host immunity

description: Additional file 6: Table S5 DEGs triggered by flg22 in the Pi04089 transgenic line.
DOI: 10.6084/m9.figshare.17157026.v1
title: Additional file 5 of Phytophthora infestans RXLR effector Pi04089 perturbs diverse defense-related genes to suppress host immunity

description: Additional file 5: Table S4 DEGs triggered by flg22 in the E3 line.
DOI: 10.6084/m9.figshare.17157041.v1
title: Additional file 9 of Phytophthora infestans RXLR effector Pi04089 perturbs diverse defense-related genes to suppress host immunity

description: Additional file 9: Table S8 Primers used in this study.
DOI: 10.6084/m9.figshare.17157032
title: Additional file 7 of Phytophthora infestans RXLR effector Pi04089 perturbs diverse defense-related genes to suppress host immunity

description: Additional file 7: Table S6 Classification of common and specific genes in the flg22-treated Pi04089 transgenic line and control plants.
DOI: 10.6084/m9.figshare.21351205
title: Additional file 9 of ELOVL gene family plays a virtual role in response to breeding selection and lipid deposition in different tissues in chicken (Gallus gallus)

description: Additional file 9: Table S7. Gene specific primers used for qRT-PCR.
DOI: 10.6084/m9.figshare.16625258.v1
title: Additional file 5 of The stem rust fungus Puccinia graminis f. sp. tritici induces centromeric small RNAs during late infection that are associated with genome-wide DNA methylation

description: Additional file 5: Data S5. FASTA file of predicted Pgt siRNAs.
DOI: 10.15468/dl.v9yjck
title: Occurrence Download

description: A dataset containing 219768 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Occurrence evidence"
 ]
 },
 "CoordinateUncertaintyInMeters 0.0-1000.0",
 "Country is Spain",
 {
 "or" : [
 "Issue is Coordinate rounded",
 "Issue is Geodetic datum assumed WGS84",
 "Issue is Coordinate reprojected",
 "Issue is Country derived from coordinates",
 "Issue is Recorded date invalid",
 "Issue is References URI invalid",
 "Issue is Occurrence status inferred from individual count"
 ]
 },
 "OccurrenceStatus is Present",
 "TaxonKey is Pinus pinaster Aiton"
 ]
}

 The dataset includes 219768 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0364526-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vc42jf
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Rhynchosia ledermannii Harms"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0103156-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-57207
title: Redemption tidings, vol. 38, nos. 1-52, 5 Jan. - 28 Dec. 1962

description: [description english/roman)] Issued weekly. "A full gospel magazine" -- subtitle.
DOI: 10.15468/dl.sg5jtg
title: Occurrence Download

description: A dataset containing 19124 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Comoros",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 19124 records from 107 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0095745-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gapwxe
title: Occurrence Download

description: A dataset containing 46 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Raffenaldia platycarpa (Coss.) Stapf"
 ]
}

 The dataset includes 46 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0095749-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ks2wkr
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Raphionacme haeneliae Venter & R.L.Verh."
 ]
}

 The dataset includes 6 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0095748-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x28dc9
title: Occurrence Download

description: A dataset containing 69900 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Glareola pratincola (Linnaeus, 1766)"
 ]
}

 The dataset includes 69900 records from 294 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0095730-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ekpm9h
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Rhipidoglossum cuneatum (Summerh.) Garay"
 ]
}

 The dataset includes 13 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0095750-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.k698xg
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cinclidium stygium Sw.",
 "HasCoordinate is true",
 "Country is Iceland",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000",
 "CoordinateUncertaintyInMeters is less than 10000"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0095751-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ve4y6e
title: Occurrence Download

description: A dataset containing 637 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Raphionacme hirsuta (E.Mey.)"
 ]
}

 The dataset includes 637 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0095753-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8uqnue
title: Occurrence Download

description: A dataset containing 270 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Raffenaldia primuloides Godr."
 ]
}

 The dataset includes 270 records from 44 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0095752-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e722sd
title: Occurrence Download

description: A dataset containing 1384 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gleditsia japonica Miq."
 ]
}

 The dataset includes 1384 records from 125 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0095755-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ehj82w
title: Occurrence Download

description: A dataset containing 19814 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Cook Islands",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 19814 records from 81 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0095754-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8yvyvh
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cionura erecta (L.) Griseb.",
 "HasCoordinate is true",
 "Country is Iceland",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000",
 "CoordinateUncertaintyInMeters is less than 10000"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0095757-240321170329656/datasets/export for details.
DOI: 10.15468/dl.nee4a4
title: Occurrence Download

description: A dataset containing 66 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Rhipidoglossum curvatum (Rolfe) Garay"
 ]
}

 The dataset includes 66 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0095756-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ycegfm
title: Occurrence Download

description: A dataset containing 936 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ambystoma mexicanum (Shaw & Nodder, 1798)"
 ]
}

 The dataset includes 936 records from 60 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0095758-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vz5fdk
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Raphionacme inconspicua H.Huber"
 ]
}

 The dataset includes 3 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0095759-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.