cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7937/k9/tcia.2016.jgnihep5
title: The Cancer Genome Atlas Lung Adenocarcinoma Collection (TCGA-LUAD)

description: The Cancer Genome Atlas Lung Adenocarcinoma (TCGA-LUAD) data collection is part of a larger effort to build a research community focused on connecting cancer phenotypes to genotypes by providing clinical images matched to subjects from The Cancer Genome Atlas (TCGA). Clinical, genetic, and pathological data resides in the Genomic Data Commons (GDC) Data Portal while the radiological data is stored on The Cancer Imaging Archive (TCIA). Matched TCGA patient identifiers allow researchers to explore the TCGA/TCIA databases for correlations between tissue genotype, radiological phenotype and patient outcomes. Tissues for TCGA were collected from many sites all over the world in order to reach their accrual targets, usually around 500 specimens per cancer type. For this reason the image data sets are also extremely heterogeneous in terms of scanner modalities, manufacturers and acquisition protocols. In most cases the images were acquired as part of routine care and not as part of a controlled research study or clinical trial.
DOI: 10.15468/dl.grp6pc
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (, , , , , , , , , , , , , , , , , , , Amiiformes, , , , , , , , , , , , , , , , , , , , )",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Geometry POLYGON((109.5 20.15,117.25 20.15,117.25 24,109.5 24,109.5 20.15))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003199-260129131611470/datasets/export for details.
DOI: 10.15468/dl.hbmmre
title: Occurrence Download

description: A dataset containing 5157 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Thalassiosira pseudonana"
 ]
}

 The dataset includes 5157 records from 62 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003200-260129131611470/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.31220326
title: <b>SUPPLEMENTAL MATERIALS</b>

description: The types of PKW based on crest overhang and associated geometric and hydraulic characteristics are summarized with full specifications are given below.Type-A Piano Key Weir, the upstream and downstream overhangs are kept equal to maintain a constant crest length and identical nappe development conditions. This allows the study to isolate the effect of internal key geometry on flow separation and energy conversion, which governs discharge efficiency in CFD analysis. In Type-B, only the outlet key overhang is present, which is kept constant in the model to maintain a uniform nappe detachment condition at the exit. This allows the study to isolate the effect of inlet-to-outlet flow contraction, shear development, and momentum amplification, which control discharge efficiency in CFD simulations. In <b>Type-C PKW, o</b>nly the <b>inlet key overhang</b> is provided and retained unchanged to ensure consistent upstream pressure distribution and boundary-layer initiation. This enables assessment of the influence of <b>flow entry alignment, separation suppression, and energy preservation within the key system</b>, which dictate hydraulic efficiency. For Type-D PKW, no overhangs exist on either side, eliminating geometric extension of the crest and preventing nappe aeration enhancement from overhang effects. Therefore, the analysis focuses purely on <b>core-flow acceleration, pressure build-up, and vortex dissipation inside the keys</b>, which govern hydraulic performance under submerged flow regimes.
DOI: 10.6084/m9.figshare.31220326.v1
title: <b>SUPPLEMENTAL MATERIALS</b>

description: The types of PKW based on crest overhang and associated geometric and hydraulic characteristics are summarized with full specifications are given below.Type-A Piano Key Weir, the upstream and downstream overhangs are kept equal to maintain a constant crest length and identical nappe development conditions. This allows the study to isolate the effect of internal key geometry on flow separation and energy conversion, which governs discharge efficiency in CFD analysis. In Type-B, only the outlet key overhang is present, which is kept constant in the model to maintain a uniform nappe detachment condition at the exit. This allows the study to isolate the effect of inlet-to-outlet flow contraction, shear development, and momentum amplification, which control discharge efficiency in CFD simulations. In <b>Type-C PKW, o</b>nly the <b>inlet key overhang</b> is provided and retained unchanged to ensure consistent upstream pressure distribution and boundary-layer initiation. This enables assessment of the influence of <b>flow entry alignment, separation suppression, and energy preservation within the key system</b>, which dictate hydraulic efficiency. For Type-D PKW, no overhangs exist on either side, eliminating geometric extension of the crest and preventing nappe aeration enhancement from overhang effects. Therefore, the analysis focuses purely on <b>core-flow acceleration, pressure build-up, and vortex dissipation inside the keys</b>, which govern hydraulic performance under submerged flow regimes.
DOI: 10.15468/dl.wvpkts
title: Occurrence Download

description: A dataset containing 234 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Discoclaoxylon hexandrum",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 234 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003201-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18402749
title: Electron density and molecular electrostatic potential of benzene
DOI: 10.5281/zenodo.18402748
title: Electron density and molecular electrostatic potential of benzene
DOI: 10.5281/zenodo.18439294
title: SuperDARN data in netCDF format (2008-Nov)

description: 2008-Nov SuperDARN radar data in netCDF format. These files were produced using version 3.0 of the public FitACF algorithm, using the AACGM v2 coordinate system. Cite this dataset if using our data in a publication.


The RST is available here: https://github.com/SuperDARN/rst



The research enabled by SuperDARN is due to the efforts of teams of scientists and engineers working in many countries to build and operate radars, process data and provide access, develop and improve data products, and assist users in interpretation.
Users of SuperDARN data and data products are asked to acknowledge this support in presentations and publications.
A brief statement on how to acknowledge use of SuperDARN data is provided below.




Users are also asked to consult with a SuperDARN PI prior to submission of work intended for publication.
A listing of radars and PIs with contact information can be found here:
(SuperDARN Radar Overview)



Recommended form of acknowledgement for the use of SuperDARN data:



'The authors acknowledge the use of SuperDARN data. SuperDARN is a collection of radars funded by national scientific funding agencies of Australia, Canada, China, France, Italy, Japan, Norway, South Africa, United Kingdom and the United States of America.'
DOI: 10.5281/zenodo.6579187
title: SuperDARN data in netCDF format (2008-Nov)

description: 2008-Nov SuperDARN radar data in netCDF format. These files were produced using version 3.0 of the public FitACF algorithm, using the AACGM v2 coordinate system. Cite this dataset if using our data in a publication.


The RST is available here: https://github.com/SuperDARN/rst



The research enabled by SuperDARN is due to the efforts of teams of scientists and engineers working in many countries to build and operate radars, process data and provide access, develop and improve data products, and assist users in interpretation.
Users of SuperDARN data and data products are asked to acknowledge this support in presentations and publications.
A brief statement on how to acknowledge use of SuperDARN data is provided below.




Users are also asked to consult with a SuperDARN PI prior to submission of work intended for publication.
A listing of radars and PIs with contact information can be found here:
(SuperDARN Radar Overview)



Recommended form of acknowledgement for the use of SuperDARN data:



'The authors acknowledge the use of SuperDARN data. SuperDARN is a collection of radars funded by national scientific funding agencies of Australia, Canada, China, France, Italy, Japan, Norway, South Africa, United Kingdom and the United States of America.'
DOI: 10.15468/dl.qnjjg6
title: Occurrence Download

description: A dataset containing 1055 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Discocleidion rufescens",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 1055 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003202-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6shqq5
title: Occurrence Download

description: A dataset containing 559 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Discoglypremna caloneura",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 559 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003203-260129131611470/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.29552111
title: Ultrahigh resolution nanoimprint patterning of quantum dot light-emitting diodes via capillary self-assembly

description: We realise pixels as small as sub-100 nm with ultrahigh pixel resolution up to 169,333 pixels-per-inch (PPI) over an electroluminescent area of 4 mm2. Benefiting from the closely packed light-emitting QD monolayers, our nano-QLEDs exhibit minimal performance degradation upon reducing the pixel size. Notably, the smallest red, green and blue nano-QLEDs maintain average external quantum efficiencies (EQEs) of 17.0%, 10.5% and 5.7%, respectively.
DOI: 10.6084/m9.figshare.29552111.v1
title: Ultrahigh resolution nanoimprint patterning of quantum dot light-emitting diodes via capillary self-assembly

description: We realise pixels as small as sub-100 nm with ultrahigh pixel resolution up to 169,333 pixels-per-inch (PPI) over an electroluminescent area of 4 mm2. Benefiting from the closely packed light-emitting QD monolayers, our nano-QLEDs exhibit minimal performance degradation upon reducing the pixel size. Notably, the smallest red, green and blue nano-QLEDs maintain average external quantum efficiencies (EQEs) of 17.0%, 10.5% and 5.7%, respectively.
DOI: 10.6084/m9.figshare.30795083
title: A conveyor-belt magneto-optical trap of CaF

description: This dataset contains all the data used for generating the plots shown in the paper
DOI: 10.6084/m9.figshare.30795083.v1
title: A conveyor-belt magneto-optical trap of CaF

description: This dataset contains all the data used for generating the plots shown in the paper
DOI: 10.6084/m9.figshare.30787619
title: Breaking Dense Integration Limits: Inverse-Designed Lithium Niobate Multimode Photonic Circuits

description: This dataset is derived from the data provided in the main text and Supplementary Information of the manuscript “Breaking Dense Integration Limits: Inverse-Designed Lithium Niobate Multimode Photonic Circuits” by Han et al., submitted to Nature Communications.
DOI: 10.6084/m9.figshare.30787619.v1
title: Breaking Dense Integration Limits: Inverse-Designed Lithium Niobate Multimode Photonic Circuits

description: This dataset is derived from the data provided in the main text and Supplementary Information of the manuscript “Breaking Dense Integration Limits: Inverse-Designed Lithium Niobate Multimode Photonic Circuits” by Han et al., submitted to Nature Communications.
DOI: 10.6084/m9.figshare.26981620
title: 13.5 ka Australian summer monsoon index (AuSMI) reconstructed from Bromfield Swamp, northeastern Australia

description: Five hydrlogical related proxies, Rb/Sr, Al/Ca, Ti/Ca, mean grain size and organic content obtained from the lacustrine sediments in Bromfield Swamp, northeastern Australia were shown in this dataset. The AuSM index reconstructed by those five proxies through principal component analysis was also given. It covered the past 13.5 kyr, reflecting the Australian summer monsoon variations during that period.
DOI: 10.6084/m9.figshare.26981620.v1
title: 13.5 ka Australian summer monsoon index (AuSMI) reconstructed from Bromfield Swamp, northeastern Australia

description: Five hydrlogical related proxies, Rb/Sr, Al/Ca, Ti/Ca, mean grain size and organic content obtained from the lacustrine sediments in Bromfield Swamp, northeastern Australia were shown in this dataset. The AuSM index reconstructed by those five proxies through principal component analysis was also given. It covered the past 13.5 kyr, reflecting the Australian summer monsoon variations during that period.
DOI: 10.6084/m9.figshare.30581027
title: Optical heterostructure in a two-dimensional organic crystal

description: The original data of all measurements in the main text and Supplementary Information, except for the optical photographs.
DOI: 10.6084/m9.figshare.30581027.v1
title: Optical heterostructure in a two-dimensional organic crystal

description: The original data of all measurements in the main text and Supplementary Information, except for the optical photographs.
DOI: 10.15468/dl.d5guev
title: Occurrence Download

description: A dataset containing 93 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ditaxis fasciculata",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 93 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003204-260129131611470/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.28924694
title: Structural visualization of the molecular evolution of CRISPR-Cas9

description: cryo-EM maps and models
DOI: 10.6084/m9.figshare.28924694.v1
title: Structural visualization of the molecular evolution of CRISPR-Cas9

description: cryo-EM maps and models
DOI: 10.5281/zenodo.18439538
title: Microalgal Colony Blot: a simple and rapid method for direct detection of recombinant protein production in microalgae colonies

description: Supporting Data for

Microalgal colony blot: a simple and rapid method for direct detection of recombinant proteins in microalgae

Torres-Tiji Y., Fields F., Mayfield S. P. (2025)PLOS ONE



Contents

Plasmid Sequences

GenBank (.gbk) and SnapGene (.dna) formats are provided for all plasmids.





mCloverGFP expression plasmid (.gbk, .dna)Ble-mCloverGFP fusion expression vector used for primary screening




ICAM1 expression plasmid (.gbk, .dna)Ble-ICAM1 fusion expression vector (FLAG-tagged)




CtxB-RBD expression plasmid (.gbk, .dna)Cholera toxin subunit B fused to SARS-CoV-2 spike protein RBD




RBD-mClover secreted expression plasmid (.gbk, .dna)RBD-mClover fusion with secretion signal




RBD-mClover ER-retained expression plasmid (.gbk, .dna)RBD-mClover fusion with ER retention signal





Flow Cytometry Data

Flow cytometry standard (.fcs, version 3.0) files acquired on a CytoFLEX (Beckman Coulter) using CytExpert 2.4.





Wild-type controlsWT1.fcs, WT2.fcs




High-expressing clonesH1.fcs, H2.fcs, H3.fcs




Medium-expressing clonesM1.fcs, M2.fcs, M3.fcs




Low-expressing clonesL1.fcs, L2.fcs, L3.fcs




Gated cell populations (.xlsx)Exported scale values for gated populations used in analysis



Acquisition settings (identical for all samples):





FL1 (GFP FITC): Gain 60; Ex 488 nm; Em 525/40 nm




FL3 (Auto APC): Gain 600; Ex 638 nm; Em 660/10 nm




FSC/SSC: Gain 500; Threshold 50,000 / 10,000





Original Blot Images

Uncropped, unadjusted original images provided in compliance with PLOS ONE data-availability requirements.





Figure 1





Panel A – original picture (.JPG)




Panel B – original picture (.JPG)




Panel C – original picture (.JPG)




Panel D – original picture (.JPG)Microalgal colony blot development time series






Figure 2





Original picture (.JPG)western blot validation of selected clones






Figure 5





Panel A – ICAM1 MCB algae original picture (.JPG)ICAM1-expressing colonies on plate




Panel B – ICAM1 MCB original picture (.JPG)ICAM1 microalgal colony blot




Panel C – RBD MCB algae original picture (.JPG)RBD-expressing colonies on plate




Panel D – RBD MCB original picture (.JPG)RBD microalgal colony blot




Panel E – MCB C. pacifica algae original picture (.JPG)C. pacifica colonies on plate




Panel F – MCB C. pacifica original picture (.JPG)C. pacifica microalgal colony blot






Figure S2





Anti-RBD western blot original picture (.JPG)




Anti-CtxB western blot original picture (.JPG)







File Formats





.gbk — GenBank format (SnapGene, Benchling, ApE, UGENE)




.dna — SnapGene format (annotations preserved; free viewer available)




.fcs — Flow Cytometry Standard 3.0 (FlowJo, CytExpert, FCS Express)




.xlsx — Microsoft Excel format




.JPG — JPEG image format





Contact

Corresponding author:Yasin Torres-Tiji

Colorado School of Mines / UC San Diego

yasin.torres-tiji@mines.edu/ytorrest@ucsd.edu
DOI: 10.5281/zenodo.18439537
title: Microalgal Colony Blot: a simple and rapid method for direct detection of recombinant protein production in microalgae colonies

description: Supporting Data for

Microalgal colony blot: a simple and rapid method for direct detection of recombinant proteins in microalgae

Torres-Tiji Y., Fields F., Mayfield S. P. (2025)PLOS ONE



Contents

Plasmid Sequences

GenBank (.gbk) and SnapGene (.dna) formats are provided for all plasmids.





mCloverGFP expression plasmid (.gbk, .dna)Ble-mCloverGFP fusion expression vector used for primary screening




ICAM1 expression plasmid (.gbk, .dna)Ble-ICAM1 fusion expression vector (FLAG-tagged)




CtxB-RBD expression plasmid (.gbk, .dna)Cholera toxin subunit B fused to SARS-CoV-2 spike protein RBD




RBD-mClover secreted expression plasmid (.gbk, .dna)RBD-mClover fusion with secretion signal




RBD-mClover ER-retained expression plasmid (.gbk, .dna)RBD-mClover fusion with ER retention signal





Flow Cytometry Data

Flow cytometry standard (.fcs, version 3.0) files acquired on a CytoFLEX (Beckman Coulter) using CytExpert 2.4.





Wild-type controlsWT1.fcs, WT2.fcs




High-expressing clonesH1.fcs, H2.fcs, H3.fcs




Medium-expressing clonesM1.fcs, M2.fcs, M3.fcs




Low-expressing clonesL1.fcs, L2.fcs, L3.fcs




Gated cell populations (.xlsx)Exported scale values for gated populations used in analysis



Acquisition settings (identical for all samples):





FL1 (GFP FITC): Gain 60; Ex 488 nm; Em 525/40 nm




FL3 (Auto APC): Gain 600; Ex 638 nm; Em 660/10 nm




FSC/SSC: Gain 500; Threshold 50,000 / 10,000





Original Blot Images

Uncropped, unadjusted original images provided in compliance with PLOS ONE data-availability requirements.





Figure 1





Panel A – original picture (.JPG)




Panel B – original picture (.JPG)




Panel C – original picture (.JPG)




Panel D – original picture (.JPG)Microalgal colony blot development time series






Figure 2





Original picture (.JPG)western blot validation of selected clones






Figure 5





Panel A – ICAM1 MCB algae original picture (.JPG)ICAM1-expressing colonies on plate




Panel B – ICAM1 MCB original picture (.JPG)ICAM1 microalgal colony blot




Panel C – RBD MCB algae original picture (.JPG)RBD-expressing colonies on plate




Panel D – RBD MCB original picture (.JPG)RBD microalgal colony blot




Panel E – MCB C. pacifica algae original picture (.JPG)C. pacifica colonies on plate




Panel F – MCB C. pacifica original picture (.JPG)C. pacifica microalgal colony blot






Figure S2





Anti-RBD western blot original picture (.JPG)




Anti-CtxB western blot original picture (.JPG)







File Formats





.gbk — GenBank format (SnapGene, Benchling, ApE, UGENE)




.dna — SnapGene format (annotations preserved; free viewer available)




.fcs — Flow Cytometry Standard 3.0 (FlowJo, CytExpert, FCS Express)




.xlsx — Microsoft Excel format




.JPG — JPEG image format





Contact

Corresponding author:Yasin Torres-Tiji

Colorado School of Mines / UC San Diego

yasin.torres-tiji@mines.edu/ytorrest@ucsd.edu
DOI: 10.15468/dl.rc4c67
title: Occurrence Download

description: A dataset containing 67753 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Empetrum hermaphroditum"
 ]
}

 The dataset includes 67753 records from 350 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003182-260129131611470/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.28302140
title: Dataset for MMF nano-displacement detection

description: This dataset contains two sets of raw speckle data collected by the multimode fiber nano-displacement detection system:

1. Different detected patterns: This folder contains speckle fields with different displacements when detecting target's patterns changes (256×256 pixels, grayscale).

2. Wafer Detection Dataset: This folder contains speckle fields with different displacements of wafers detected with fiber probes (256×256 pixels, grayscale).
DOI: 10.6084/m9.figshare.28302140.v1
title: Dataset for MMF nano-displacement detection

description: This dataset contains two sets of raw speckle data collected by the multimode fiber nano-displacement detection system:

1. Different detected patterns: This folder contains speckle fields with different displacements when detecting target's patterns changes (256×256 pixels, grayscale).

2. Wafer Detection Dataset: This folder contains speckle fields with different displacements of wafers detected with fiber probes (256×256 pixels, grayscale).
DOI: 10.6084/m9.figshare.29175806
title: Cryo-EM structure of EBV gB prefusion construct C3-GT.

description: A 3.1 Å cryo-EM map and associated molecular structure of the prefusion EBV gB variant C3-GT.
DOI: 10.6084/m9.figshare.29175806.v1
title: Cryo-EM structure of EBV gB prefusion construct C3-GT.

description: A 3.1 Å cryo-EM map and associated molecular structure of the prefusion EBV gB variant C3-GT.
DOI: 10.6084/m9.figshare.29413124
title: raw data of the presented data in this papaer

description: raw data of the presented data in this papaer
DOI: 10.6084/m9.figshare.29413124.v1
title: raw data of the presented data in this papaer

description: raw data of the presented data in this papaer
DOI: 10.15468/dl.x8gfzv
title: Occurrence Download

description: A dataset containing 58 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ditta myricoides",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 58 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003205-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.