cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3630767_d13.v1
title: Additional file 10: Table S2. of Survey of cryptic unstable transcripts in yeast

description: Divergent gene-CUT pairs enriched for metabolic process genes. A total of 698 divergent gene-CUT pairs were identified in S288c. The subset of genes in these gene-CUT pairs are enriched for various metabolic processing gene ontologies (GO). P-values are based on the hypergeometric test after Holm-Bonferroni correction using the default background from YeastMine http://yeastmine.yeastgenome.org . The total number of genes in each GO category is listed far right. Table S3. Strains used in this study. A table describing the genotype and mating type of strains used in this study. Table S4. Summary of RNA-seq Read Mapping Results. A table summarizing the read mapping results for each RNA-seq library used in this study. Reported values for total mapped reads corresponds to all uniquely mapped reads after rRNA read removal. Table S5. Fold change conversion to discrete values. The Matlab HMM Toolkit only accepts discrete emission values. Per nucleotide rrp6Δ/WT fold change values were converted to a discrete value according to the table above. Table S6. HMM emission probabilities. The HMM emission probability for each discrete rrp6Δ/WT RNA-seq fold change value (see Table S3) for states 1–10. Because states 2–10 have the same emission probabilities we only show a single iteration of these emission probabilities for simplification. Table S7. HMM transition probabilities. The HMM transition probabilities for states 1–10. Movement through the HM is unidirectional and only two transition probabilities exist for each state. (XLSX 19 kb)
DOI: 10.15468/dl.9y4y6h
title: Occurrence Download

description: A dataset containing 1927 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Leptoseris mycetoseroides Wells, 1954"
 ]
}

 The dataset includes 1927 records from 48 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037868-241126133413365/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.c.3630821_d4.v1
title: Additional file 8: Table S2. of Exploration of hydroxymethylation in Kagami-Ogata syndrome caused by hypermethylation of imprinting control regions

description: Primer sequences utilized in BS/oxBS pyrosequencing and cloning-based sequencing. (XLSX 9.68 kb)
DOI: 10.17863/cam.7267
title: Data for Surface-Selective Direct 17O DNP NMR of CeO2 Nanoparticles

description: This includes the FIDs and processed spectra of all NMR experiments published in the paper "Surface-Selective Direct 17O DNP NMR of CeO2 Nanoparticles". Specifically, this is 17O DNP and ssNMR spectra of CeO2 nanoparticles and nanorods as well as 17O DNP build-up curves. Please see the paper for more details.
DOI: 10.6084/m9.figshare.c.3630842_d6.v1
title: MOESM6 of The cohesin-associated protein Wapal is required for proper Polycomb-mediated gene silencing

description: Additional file 6: Table S5. All statistically significant altered gene sets from GSEA analysis after Wapal depletion.
DOI: 10.6084/m9.figshare.c.3630857_d1.v1
title: Additional file 1: of A pilot study of marking accuracy and mental workload as measures of OSCE examiner performance

description: Response time data, OSCE Scores of subjects, Max available scores and Expert scores. Response Time Data – Unique Identifier, Subject Number, Date, Time, Response time in seconds, Phase (1 = listening, 2 = rating video), Video = number of video being rated. OSCE Scores – Unique identifier, Scenario (CVS = cardiovascular exam, Comm = Communication Skills, P = Borderline Pass, G = Good performance), Subject Number, Attempt (number 1–4), Item on Checklist, Score as recorded by subject. OSCE Max Scores available – Unique Idenifier, Subject (blank), Attempt (not relevant here), Item on Checklist, Score – Max score available. Expert Scores – Agreed scores for each item on checklist for each of the four videos used, Unique identifier, Scenario as previously, Subject (blank), Attempt (not relevant here), Item on Checklist, Agreed Score. (XLSX 158 kb)
DOI: 10.6084/m9.figshare.c.3630842_d8.v1
title: MOESM14 of The cohesin-associated protein Wapal is required for proper Polycomb-mediated gene silencing

description: Additional file 14: Table S3. Normalized microarray expression data.
DOI: 10.6084/m9.figshare.c.3630866_d2.v1
title: Additional file 3: Table S2. of Prediction of response to anti-EGFR antibody-based therapies by multigene sequencing in colorectal cancer patients

description: Genetic changes found in all CRC samples. (XLSX 34 kb)
DOI: 10.17863/cam.97061
title: Research Data Supporting "Delayed parabolic oxidation via transient thermal exposures on a polycrystalline nickel-based superalloy"

description: The raw synchrotron and thermo-gravimetric analysis data described in the manuscript are enclosed in this dataset as Microsoft Excel Worksheets (.xlsx). In addition, scanning electron micrographs (.tif files) obtained for RR1000 are provided. Energy dispersive X-ray spectroscopy data are also included (.oip file) with the relevant data files (.dat) and can be opened using the proprietary Oxford Instruments AZtec software.
DOI: 10.6084/m9.figshare.c.3630842_d14.v1
title: MOESM15 of The cohesin-associated protein Wapal is required for proper Polycomb-mediated gene silencing

description: Additional file 15: Table S4. List of all primers used.
DOI: 10.15468/dl.c2zssp
title: Occurrence Download

description: A dataset containing 25485 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Myiodynastes luteiventris P.L.Sclater, 1859"
 ]
}

 The dataset includes 25485 records from 88 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037869-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dnbeuh
title: Occurrence Download

description: A dataset containing 19639 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Myiopagis viridicata (Vieillot, 1817)"
 ]
}

 The dataset includes 19639 records from 61 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037870-241126133413365/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.c.3630914_d2.v1
title: Additional file 3: of Mitochondrial heteroplasmy in vertebrates using ChIP-sequencing data

description: Heteroplasmy detection algorithm and analysis in Python. (ZIP 115 kb)
DOI: 10.17863/cam.54726
title: Research data supporting: "Quantifying photon recycling in solar cells and light emitting diodes: absorption and emission are always key"

description: Figure 1 plots the number of photon recycling events per initial excitation versus photoluminescence quantum efficiency and escape probability, calculated from equation 6 given in manuscript. Figures 2 and 3 model photon recycling in methylammonium lead iodide solar cells. Figure 2 shows the number of photon recycling at maximum power point events versus; thickness (with no charge trapping); charge trapping rate (for a 500nm film); and as a fucntion of front transmission and back reflection coefficients (for a 500nm film). The inset in Figure 2a shows corresponding information to 2a, but at open circuit. Figure 3 shows number of photon recycling events versus efficiency, both as a function of charge trapping rate for a 500nm film, for a film which interacts with a 2*pi hemisphere and 2.5 degrees solid angle about the sun in a) and c) respectively. b) shows the current-voltage curves for some situations described in a) (for no charge trapping, 500nm film). Figure 4 models photon recycling in caesium lead bromide light emittiong diodes. Figure 4: a shows the number of photon recycling events versus thickness (with no charge trapping); b shows the number of photon recycling events versus voltage for different charge trapping rates (for a 100nm film); c the number of photon recycling events versus front transmission and back reflection coefficients (for a 100nm thick film and no charge trapping). Figure 4d presents normalised photoluminescence for three absorption models considered; and e and f the number of photon recycling events versus emitted light (luminous emittance or luminance respectively) both as a function of voltage, for three different emittance models considered, for emission into a 2*pi hemisphere (e) or 2.5 degree solid angle (f), both for a 100nm thin film.
DOI: 10.6084/m9.figshare.c.3630914_d3.v1
title: Additional file 2: of Mitochondrial heteroplasmy in vertebrates using ChIP-sequencing data

description: Supplementary tables S1â  S4. Table S1. Detected heteroplasmies of excluded individuals. Table S2. Detected heteroplasmies. Table S3. Sanger sequencing and pyrosequencing validation results. Table S4. Additional details for each file. Table S5. Raw pyrosequencing data. (XLS 352 kb)
DOI: 10.6084/m9.figshare.c.3630926_d2.v1
title: Additional file 1: Table S1. of The evolutionary scope and neurological disease linkage of yeast-prion-like proteins in humans

description: Gene Ontology (GO) process category enrichments for the NQP and prion prediction data sets from human (the same sets that are analyzed in TablesÂ 1, 2, 3 and 4). These are derived using the website GOrilla [52]. (TXT 3Â kb)
DOI: 10.17863/cam.90061
title: Dataset of Springer Nature Group related journals.

description: This dataset compiles the identifying details of Springer Nature Group published journals. This covers journals published by Springer Nature, Nature Portfolio, Palgrave Macmillan, Springer, BioMed Central, and Scientific American, It accounts for both current (as of Oct. 22) and archived journals. It compiles identifiers of each journal where possible: Title, Alternative title, eBook and Print ISSN, Title ID, Active years, Primary language, Publisher and imprint, Access type, Default licence and Platform URL. In particular aid for Springer Negotiations of 2022/23, it identifies the ISSN used via UnSub.org (and Jisc) for relevant journals, a URL link to the editorial board of current journals, and a subject area has also been assigned to each journal. This dataset is designed to further aid data analysis by universitites in preparations for the Springer Negotiations 2022/23 (following the success of the Elsevier Negotiations in 2021/22). Further information and sources can be found in the attached ReadMe file. Both CSV and XLSX files contain the same data in two different formats.
DOI: 10.17863/cam.57308
title: Data supporting "Time Limited Self-Organised Criticality in the High Rate Deformation of Face Centred Cubic Metals"

description: Data set containing the underpinning measurements on face centred cubic metal deformation that were used in the publication "Time Limited Self-Organised Criticality in the High Rate Deformation of Face Centred Cubic Metals".
DOI: 10.6084/m9.figshare.c.3630935_d5.v1
title: Additional file 8: of Effect of concomitant use of memantine on mortality and efficacy outcomes of galantamine-treated patients with Alzheimerâ  s disease: post-hoc analysis of a randomized placebo-controlled study

description: Investigators and institutional review boards/independent ethics committees. (XLSX 24Â kb)
DOI: 10.25420/britishmuseum.28008389
title: The production of ceramic tiles

description: José and Jesuíta make ceramic tiles, like the ones that will be used to cover the house under construction, camera 1
DOI: 10.25420/britishmuseum.28008389.v1
title: The production of ceramic tiles

description: José and Jesuíta make ceramic tiles, like the ones that will be used to cover the house under construction, camera 1
DOI: 10.17863/cam.7944
title: Research data supporting "Extracting Crystal Chemistry from Amorphous Carbon Structures"

description: Original data regarding structures and properties of the carbon allotropes discussed in the associated publication. Furthermore, the potential files for the underlying Gaussian approximation potential (GAP) model are provided.
DOI: 10.6084/m9.figshare.c.3631055_d3.v1
title: Additional file 3: of Convergent evolution of hemoglobin switching in jawed and jawless vertebrates

description: Analyses of individual sequence datasets. (XLSX 51 kb)
DOI: 10.17863/cam.48786
title: Data supporting "Microscale diffusiophoresis of proteins"

description: The device used for experiments is created with the autoCAD file "diffusiophoresis_device.dwg". The results are in the folder "Experiments" and consist of tiff stacks with an accompanying metadata json file. The simulations are created by COMSOL with the "diffusiophoresis.mph" File and the results are saved in the "Simulations" folder. All the processing can be done with the scripts located at https://github.com/impact27/diffusiophoresis (https://doi.org/10.5281/zenodo.3635473)
DOI: 10.6084/m9.figshare.c.3631070_d8.v1
title: Additional file 2: of Host-induced aneuploidy and phenotypic diversification in the Sudden Oak Death pathogen Phytophthora ramorum

description: Details of P. ramorum isolates used in this study. Other names, source, geographical location, year of isolation and contact scientists for isolates are shown. (XLSX 48 kb)
DOI: 10.17863/cam.66056
title: Research data supporting "Observation of first and second sound in a BKT superfluid"

description: The 'Figure' folders contain the source data (density distribution, time trace, response spectra, sound speeds, superfluid density) for data points shown in the corresponding figures in the manuscript. The readme files provided include the necessary information to interpret and use the data.
DOI: 10.17863/cam.95244
title: Research data supporting "MOVPE studies of zincblende GaN on 3C-SiC/Si (001)"

description: The MOVPE growth of two different sample series has been studied. In Sample Series A the epilayer growth temperature was varied at a constant V/III-ratio of 76 and a reactor pressure of 300 Torr. In Sample Series B the V-to-III ratio during the epilayer growth was varied at a constant temperature and a pressure of 300 Torr. For each sample series, a separate Text Document (.txt file) with the following information has been deposited: - AFM data: RMS roughness - AFM data: Feature size parallel and perpendicular to the miscut direction - XRD phase analysis - XRD w-Rocking curves FWHM A detailed description on how these data were collected is given in the associated research article.
DOI: 10.17863/cam.14291
title: Research data supporting "Real-time spectroscopic analysis enabling the full and safe consumption of fluoroform during nucleophilic trifluoromethylation in flow."

description: The productive use of toxic waste materials derived from industrial processes is one of the main goals of the modern chemical research to increase the sustainability of the large scale production. Here we devise a simple and robust strategy for the utilization of trifluoromethane, obtained in large quantities from Teflon manufacture, and the conversion of this greenhouse gas into valuable perfluorinated compounds. The generation of the trifluoromethyl carbanion and its direct and complete consumption through trapping with a number of electrophiles were achieved by a fully contained flow reactor setup. The adoption of modern in-line analytical tools, such as portable FT-IR and NMR devices, allowed the accurate reagent dosage with considerable benefits in terms of controlling the environmental impact during this continuous process. The advantages of the method, with respect to the batch procedure, will be discussed and demonstrated experimentally.
DOI: 10.6084/m9.figshare.c.3631142_d1.v1
title: Additional file 6: Table S5. of Transcriptome sequencing of gingival biopsies from chronic periodontitis patients reveals novel gene expression and splicing patterns

description: The GO term analysis of genes of up- and down-regulated genes in periodontitis. This excel file contains the list of the differentially expressed genes, categorized according to the GO terms. (XLSX 21Â kb)
DOI: 10.17863/cam.78150
title: Research data supporting "MineSweeper: A “Clean Sweep” for Drop-In Use-After-Free Prevention"

description: Contains the MineSweeper implementation, an allocator extension implemented on top of JeMalloc to mitigate use-after-free attacks, together with scripts to evaluate its running time and memory overheads on the SPEC CPU2006 benchmarks.
DOI: 10.25378/janelia.24256027
title: Manual organelle segmentations (crop212) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of (jrc_sum159-4)

description: <b>This acquisition is part of the CellMap 2024 Segmentation Challenge</b><br><br>- <b>Challenge DOI:</b> https://doi.org/10.25378/janelia.c.7456966<br><br>- <b>Challenge Website:</b> https://cellmapchallenge.janelia.org/<br><br><b>Annotation description</b>: Dense segmentations of extracellular space, plasma membrane, vesicle membrane, endosome membrane, vesicle lumen, endoplasmic reticulum lumen, endoplasmic reticulum membrane, lysosome lumen, lysosome membrane, endosome lumen, cytosol, lysosome, endosome, vesicle, endoplasmic reticulum, cell, endoplasmic reticulum membrane collective in jrc_sum159-4 using Amira 3D 2021.1, Classic Segmentation Workroom and the 'Using Amira to manually segment organelles in vEM for machine learning V.3' annotation protocol.<br><br><b>Annotation ID</b>: crop212<br><br><b>Primary Annotator</b>: Alyson Petruncio<br><br><b>Annotation protocol</b>: Using Amira to manually segment organelles in vEM for machine learning V.3 (http://dx.doi.org/10.17504/protocols.io.bp2l61rb5vqe/v3)<br><br><b>Software</b>: Amira 3D 2021.1, Classic Segmentation Workroom<br><br><b>Annotated voxel size (nm)</b>: 4 x 4 x 4 (x, y, z)<br><br><b>Annotated data dimensions (µm)</b>: 1.6 x 1.6 x 1.6 (x, y, z)<br><br><b>Annotated data offset (nm)</b>: 45246 x 4270 x 27398 (x, y, z)<br><br><b>Classes annotated</b>: extracellular space, plasma membrane, vesicle membrane, endosome membrane, vesicle lumen, endoplasmic reticulum lumen, endoplasmic reticulum membrane, lysosome lumen, lysosome membrane, endosome lumen, cytosol, lysosome, endosome, vesicle, endoplasmic reticulum, cell, endoplasmic reticulum membrane collective<br><br><b>Dataset URL</b>: s3://janelia-cosem-datasets/jrc_sum159-4/jrc_sum159-4.zarr/recon-1/labels/groundtruth/crop212<br><br><b>Source (EM) dataset ID</b>: jrc_sum159-4<br><br><b>Source (EM) voxel size (nm)</b>: 8 x 8 x 8 (x, y, z)<br><br><b>Source (EM) data dimensions (µm)</b>: 95 x 8.5 x 47.8 (x, y, z)<br><br><b>Source (EM) DOI</b>: https://doi.org/10.25378/janelia.20134103<br><br><b>Visualization website</b>: https://openorganelle.janelia.org/datasets/jrc_sum159-4<br><br><b>Publication:</b> <i>CellMap Segmentation Challenge,</i> 2024.<br><br><b>The CellMap Project Team during this time consisted of:</b> David Ackerman, Davis Bennett, Marley Bryant, Hannah Nguyen, Grace Park, Alyson Petruncio, Alannah Post, Jacquelyn Price, Diana Ramirez, Jeff Rhoades, Rebecca Vorimo, Aubrey Weigel, Marwan Zouinkhi, Yurii Zubov.<br><br><b>The CellMap Project Team Steering Committee during this time consisted of:</b> Misha Ahrens, Christopher Beck, Teng-Leong Chew, Daniel Feliciano, Jan Funke, Harald Hess, Wyatt Korff, Jennifer Lippincott-Schwartz, Zhe J. Liu, Kayvon Pedram, Stephan Preibisch, Stephan Saalfeld, Ronald Vale, and Aubrey Weigel.
DOI: 10.25378/janelia.24256027.v1
title: Manual organelle segmentations (crop212) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of (jrc_sum159-4)

description: <b>This acquisition is part of the CellMap 2024 Segmentation Challenge</b><br><br>- <b>Challenge DOI:</b> https://doi.org/10.25378/janelia.c.7456966<br><br>- <b>Challenge Website:</b> https://cellmapchallenge.janelia.org/<br><br><b>Annotation description</b>: Dense segmentations of extracellular space, plasma membrane, vesicle membrane, endosome membrane, vesicle lumen, endoplasmic reticulum lumen, endoplasmic reticulum membrane, lysosome lumen, lysosome membrane, endosome lumen, cytosol, lysosome, endosome, vesicle, endoplasmic reticulum, cell, endoplasmic reticulum membrane collective in jrc_sum159-4 using Amira 3D 2021.1, Classic Segmentation Workroom and the 'Using Amira to manually segment organelles in vEM for machine learning V.3' annotation protocol.<br><br><b>Annotation ID</b>: crop212<br><br><b>Primary Annotator</b>: Alyson Petruncio<br><br><b>Annotation protocol</b>: Using Amira to manually segment organelles in vEM for machine learning V.3 (http://dx.doi.org/10.17504/protocols.io.bp2l61rb5vqe/v3)<br><br><b>Software</b>: Amira 3D 2021.1, Classic Segmentation Workroom<br><br><b>Annotated voxel size (nm)</b>: 4 x 4 x 4 (x, y, z)<br><br><b>Annotated data dimensions (µm)</b>: 1.6 x 1.6 x 1.6 (x, y, z)<br><br><b>Annotated data offset (nm)</b>: 45246 x 4270 x 27398 (x, y, z)<br><br><b>Classes annotated</b>: extracellular space, plasma membrane, vesicle membrane, endosome membrane, vesicle lumen, endoplasmic reticulum lumen, endoplasmic reticulum membrane, lysosome lumen, lysosome membrane, endosome lumen, cytosol, lysosome, endosome, vesicle, endoplasmic reticulum, cell, endoplasmic reticulum membrane collective<br><br><b>Dataset URL</b>: s3://janelia-cosem-datasets/jrc_sum159-4/jrc_sum159-4.zarr/recon-1/labels/groundtruth/crop212<br><br><b>Source (EM) dataset ID</b>: jrc_sum159-4<br><br><b>Source (EM) voxel size (nm)</b>: 8 x 8 x 8 (x, y, z)<br><br><b>Source (EM) data dimensions (µm)</b>: 95 x 8.5 x 47.8 (x, y, z)<br><br><b>Source (EM) DOI</b>: https://doi.org/10.25378/janelia.20134103<br><br><b>Visualization website</b>: https://openorganelle.janelia.org/datasets/jrc_sum159-4<br><br><b>Publication:</b> <i>CellMap Segmentation Challenge,</i> 2024.<br><br><b>The CellMap Project Team during this time consisted of:</b> David Ackerman, Davis Bennett, Marley Bryant, Hannah Nguyen, Grace Park, Alyson Petruncio, Alannah Post, Jacquelyn Price, Diana Ramirez, Jeff Rhoades, Rebecca Vorimo, Aubrey Weigel, Marwan Zouinkhi, Yurii Zubov.<br><br><b>The CellMap Project Team Steering Committee during this time consisted of:</b> Misha Ahrens, Christopher Beck, Teng-Leong Chew, Daniel Feliciano, Jan Funke, Harald Hess, Wyatt Korff, Jennifer Lippincott-Schwartz, Zhe J. Liu, Kayvon Pedram, Stephan Preibisch, Stephan Saalfeld, Ronald Vale, and Aubrey Weigel.
DOI: 10.6084/m9.figshare.c.3631157_d1.v1
title: Additional file 1: of Reluctance to care for patients with HIV or hepatitis B / C in Japan

description: Supporting raw data. (XLSX 50 kb)
DOI: 10.17863/cam.17255
title: Research data supporting "Resolving the rapid water absorption of porous functionalised calcium carbonate powder compacts by terahertz pulsed imaging"

description: The dataset includes the liquid penetration depth (extracted from the terahertz reflection measurements) as a function of time. Each file holds the data of either 5 or 6 different measurements. The time is given by the acquisition rate (15 Hz) of the used terahertz system.