cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12179715
title: Autophagy triggers CTSD (cathepsin D) maturation and localization inside cells to promote apoptosis

description: CTSD/CathD/CATD (cathepsin D) is a lysosomal aspartic protease. A distinguishing characteristic of CTSD is its dual functions of promoting cell proliferation via secreting a pro-enzyme outside the cells as a ligand, and promoting apoptosis via the mature form of this enzyme inside cells; however, the regulation of its secretion, expression, and maturation is undetermined. Using the lepidopteran insect <i>Helicoverpa armigera</i>, a serious agricultural pest, as a model, we revealed the dual functions and regulatory mechanisms of CTSD secretion, expression, and maturation. Glycosylation of asparagine 233 (N233) determined pro-CTSD secretion. The steroid hormone 20-hydroxyecdysone (20E) promoted CTSD expression. Macroautophagy/autophagy triggered CTSD maturation and localization inside midgut cells to activate CASP3 (caspase 3) and promote apoptosis. Pro-CTSD was expressed in the pupal epidermis and was secreted into the hemolymph to promote adult fat body endoreplication/endoreduplication, cell proliferation, and association. Our study revealed that the differential expression and autophagy-mediated maturation of CTSD in tissues determine its roles in apoptosis and cell proliferation, thereby determining the cell fates of tissues during lepidopteran metamorphosis. <b>Abbreviations:</b> 20E: 20-hydroxyecdysone; 3-MA: 3-methyladenine; ACTB/β-actin: actin beta; AKT: protein kinase B; ATG1: autophagy-related 1; ATG4: autophagy-related 4; ATG5: autophagy-related 5; ATG7: autophagy-related 7; ATG14: autophagy-related 14; BSA: bovine serum albumin; CASP3: caspase 3; CQ: choroquine; CTSD: cathepsin D; DAPI: 4′,6-diamidino-2-phenylindole; DMSO: dimethyl sulfoxide; DPBS: dulbecco’s phosphate-buffered saline; DsRNA: double-stranded RNA; EcR: ecdysone receptor; EcRE: ecdysone response element; EdU: 5-ethynyl-2´-deoxyuridine; G-m-CTSD: glycosylated-mautre-CTSD; G-pro-CTSD: glycosylated-pro-CTSD; HaEpi: <i>Helicoverpa armigera</i> epidermal cell line; HE staining: hematoxylin and eosin staining; IgG: immunoglobin G; IM: imaginal midgut; JH: juvenile hormone; Kr-h1: krueppel homologous protein 1; LM: larval midgut; M6P: mannose-6-phosphate; PBS: phosphate-buffered saline; PCD: programmed cell death; PNGase: peptide-N-glycosidase F; RFP: red fluorescent protein; RNAi: RNA interference; SDS-PAGE: sodium dodecyl sulfate-polyacrylamide gel electrophoresis; SYX17: syntaxin 17; USP1: ultraspiracle isoform 1.
DOI: 10.6084/m9.figshare.12703830.v1
title: Additional file 1 of Overexpression of the Transcription Factor Gene OsSTAP1 Increases Salt Tolerance in Rice

description: Additional file 1: Table S1. Cis-elements analysis of the OsSTAP1 promoter sequence. Table S2. List of the differentially expressed gene in the OsSTAP1 overexpression line compared with WT under normal growth conditions. Table S3. List of the differentially expressed gene in the OsSTAP1 overexpression line compared with WT under salt stress conditions. Table S4. The primers used in the present study. Table S5. The expression levels of 24 differentially expressed gene detected by transcriptome and qRT-PCR.
DOI: 10.6084/m9.figshare.14795138.v1
title: Additional file 1 of Genome-wide DNA methylation analysis in Chinese Chenghua and Yorkshire pigs

description: Additional file 1: Table S1. Summary of hypermethylation regions in CHP vs. YP.
DOI: 10.6084/m9.figshare.14795147
title: Additional file 3 of Genome-wide DNA methylation analysis in Chinese Chenghua and Yorkshire pigs

description: Additional file 3: Table S3. Summary of hypermethylation genes in CHP vs. YP.
DOI: 10.6084/m9.figshare.13228217.v1
title: In vitro study of the effects of DC electric fields on cell activities and gene expression in human choriocarcinoma cells

description: Physiological electric fields (EFs), as one of the environmental cues influencing both normal and tumor cells, have profound effects on tumor cell malignancy potential. The cellular responses to EFs by choriocarcinoma cells and their underlying mechanisms are unknown. In this study, the migration/motility, cell cycle progression and proliferation of choriocarcinoma cells in electric field culture showed that choriocarcinoma cells migrated cathodally in an applied EF, and EF stimulation influenced cell cycle progression through G2/M arrest and therefore induced a reduction in cellular proliferation. The transcriptome of choriocarcinoma cells subjected to EF stimulation (150 mV/mm) was analyzed using RNA sequencing (RNA-Seq), and the results were verified by reverse transcription quantitative polymerase chain reaction. A Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that ErbB and HIF-1 signaling pathways that are involved in cell migration/motility, cell cycle progression and proliferation were significantly altered in cells treated with an EF of 150 mV/mm compared with control cells, and in addition, the downstream pathways of these signaling pathways such as AKT and P42/P44 MAPK (ERK1/2) showed primary activation by Western blotting. This study’s results suggest that an applied EF is an effective cue in regulating cellular phenotypes of choriocarcinoma cells and that transcriptional analysis contributes to the understanding of the mechanism of EF-guided cell functions.
DOI: 10.6084/m9.figshare.14795153
title: Additional file 5 of Genome-wide DNA methylation analysis in Chinese Chenghua and Yorkshire pigs

description: Additional file 5: Table S5. Summary of Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis in CHP vs. YP.
DOI: 10.6084/m9.figshare.13154069
title: Metadata record for the manuscript: Glembatumumab vedotin for patients with metastatic, gpNMB over-expressing, triplenegative breast cancer (“METRIC”): A Randomized Multicenter Study

description: <b>Summary</b>

This
metadata record provides details of the data supporting the claims of the
related manuscript: “Glembatumumab vedotin for patients with metastatic, gpNMB
over-expressing, triplenegative breast cancer (“METRIC”): A Randomized
Multicenter Study”.

The
related study evaluated whether glembatumumab vedotin (a gpNMB-specific
monoclonal antibody conjugated to the potent cytotoxin monomethyl auristatin E)
would improve progression-free survival compared to capecitabine in
gpNMB-overexpressing triple-negative breast cancer (TNBC).

 

<b>Data
access</b>

The data are are available from the company which funded the study--Celldex Therapeutics, Inc (https://www.celldex.com/)--on reasonable request for a period of 3 years following publication. After this period Celldex does not commit to making the data available as the compound has been discontinued from development.<br>

The
data, along with details of the figures and tables in the manuscript that they
underlie, are as follows:

Figure 2: CDX011-04_ADEF.sas;
CDX011-04_ADEFI.sas; CDX011-04_ADTTE.sas

Figure 3: CDX011-04_ADEF.sas;
CDX011-04_ADEFI.sas

Figure 4: CDX011-04_ADEFI.sas;
CDX011-04_ADTTE.sas

Table 1: CDX011-04_ADSL.sas;
CDX011-04_ADMH.sas

Table 2: CDX011-04_ADEF.sas;
CDX011-04_ADEFI.sas; CDX011-04_ADTTE.sas

Table 3: CDX011-04_RawPK.xls

Table 4: CDX011-04_ADAE.sas

Supplemental
Table 1: CDX011-04_ADCM.sas

Supplemental
Table 2: CDX011-04_ADEF.sas; CDX011-04_ADEFI.sas; CDX011-04_ADTTE.sas

 

For
all data requests please contact Celldex at: info@celldex.com 
<b>Name of Institutional
Review Board or ethics committee that approved the study </b>

The study was conducted
at 120 sites in the United States, Canada, Australia, United Kingdom, France,
Spain, Belgium, Germany, and Italy. The study was conducted at each of the
participating institutions according to the Declaration of Helsinki and Good
Clinical Practice Guidelines, after approval by local institutional/ethics review
boards.

 

<b>Clinical trial registry URL</b>

https://www.clinicaltrials.gov/ct2/show/NCT01997333?term=NCT#01997333&draw=2&rank=1

<br>
DOI: 10.6084/m9.figshare.22141127.v1
title: Adaptive Endpoints Selection with Application in Rare Disease

description: In rare diseases, there are many unanswered questions that are critical to clinical development. Among them, one important question is how to choose primary endpoints that translate into meaningful improvement of health outcomes for patients while maximizing trial probability of success at the same time. A natural history study is often recommended by regulatory agencies, following this, traditional approach has dampened enthusiasm for many drug developers because it entails much higher cost and longer timeline. We propose to use an innovative design that allows adaptation on primary endpoint(s) so that learning stage of the disease can be done within the pivotal trial itself through a subset of patients (i.e. informational cohort). The overall family wise error rate (FWER) will be controlled through the use of combination test following partition test principle. A case example in patients with Pompe disease is used to show that the proposed innovative design maintains robust power across treatment effect scenarios while traditional fixed design bears the high risk of failure due to incorrect endpoint selection. Even if multiple endpoints can be included as primary, the proposed innovative design can still improve power over traditional designs by optimizing alpha allocations in cases with differential treatment effects.
DOI: 10.6084/m9.figshare.14795138
title: Additional file 1 of Genome-wide DNA methylation analysis in Chinese Chenghua and Yorkshire pigs

description: Additional file 1: Table S1. Summary of hypermethylation regions in CHP vs. YP.
DOI: 10.6084/m9.figshare.14795141
title: Additional file 2 of Genome-wide DNA methylation analysis in Chinese Chenghua and Yorkshire pigs

description: Additional file 2: Table S2. Summary of hypomethylation regions in CHP vs. YP.
DOI: 10.15468/dl.d3vnyx
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cyathea thysanolepis (Barrington) A.R.Sm."
 ]
}

 The dataset includes 16 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0230563-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hyns37
title: Occurrence Download

description: A dataset containing 55199 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Danaus plexippus (Linnaeus, 1758)"
 ]
}

 The dataset includes 55199 records from 163 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008820-180131172636756/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.eqvqeu
title: Occurrence Download

description: A dataset containing 712 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Stylidium schoenoides DC."
 ]
}

 The dataset includes 712 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043745-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gp5eze
title: Occurrence Download

description: A dataset containing 82622 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON ((5.475 51.975,5.525 51.975,5.525 52.025,5.475 52.025,5.475 51.975))",
 "DatasetKey is Observation.org, Nature data from around the World",
 "TaxonKey is Animalia"
 ]
}

 The dataset includes 82622 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0306278-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.raqjmx
title: Occurrence Download

description: A dataset containing 39991 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Prunus persica (L.) Stokes"
 ]
}

 The dataset includes 39991 records from 594 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0246451-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e9fxen
title: Occurrence Download

description: A dataset containing 118 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Ctenopoma nigropannosum Reichenow, 1875"
 ]
}

 The dataset includes 118 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0294207-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gsjy71
title: Occurrence Download

description: A dataset containing 28334 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Costa Rica",
 "HasCoordinate is true",
 "TaxonKey is Amphibia",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 28334 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008820-180730143533302/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8z6msj
title: Occurrence Download

description: A dataset containing 11218 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON ((5.475 51.425,5.525 51.425,5.525 51.475,5.475 51.475,5.475 51.425))",
 "DatasetKey is Observation.org, Nature data from around the World",
 "TaxonKey is Animalia"
 ]
}

 The dataset includes 11218 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0306290-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w9a8w7
title: Occurrence Download

description: A dataset containing 221 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Scinax boulengeri (Cope, 1887)"
 ]
}

 The dataset includes 221 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0265878-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.lks5jd
title: Occurrence Download

description: A dataset containing 226 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "MediaType is Image",
 "TaxonKey is Danaus gilippus (Cramer, 1775)"
 ]
}

 The dataset includes 226 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008820-180824113759888/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.shvwj6
title: Occurrence Download

description: A dataset containing 1620 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pinus koraiensis Siebold & Zucc."
 ]
}

 The dataset includes 1620 records from 116 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0294209-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h368j7
title: Occurrence Download

description: A dataset containing 2080 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Canadian Museum of Nature Herbarium",
 "PublishingOrg is a41250f0-7c3e-11d8-a19c-b8a03c50a862",
 "TaxonKey is Juncus L."
 ]
}

 The dataset includes 2080 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0289742-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ujr44r
title: Occurrence Download

description: A dataset containing 183 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hyoscyamus pusillus L.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 183 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0262482-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xe2kq6
title: Occurrence Download

description: A dataset containing 23137165 species occurrences available in GBIF matching the query:
{
 "Country" : [
 "is Mexico"
 ]
}

 The dataset includes 23137165 records from 3091 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0316206-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15156/bio/sh3261532.08fu
title: SH3261532.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh2105833.08fu
title: SH2105833.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh2105834.08fu
title: SH2105834.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh2105835.08fu
title: SH2105835.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh3261533.08fu
title: SH3261533.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.