cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25345/c5ng4gv93
title: MassIVE Reanalysis RMSV000000389.4 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080812/PXD004927 [4 out of 24] [launched by cfca6e4ba8934e65aa11617b56091339]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.6084/m9.figshare.17122301.v1
title: Supplementary Material for: Evolutionary and allometric insights into anuran auditory sensitivity and morphology

description: As species change through evolutionary time, the neurological and morphological structures that underly behavioral systems typically remain coordinated. This is especially important for communication systems, in which these structures must remain coordinated both within and between senders and receivers for successful information transfer. The acoustic communication of anurans (“frogs”) offers an excellent system to ask when and how such coordination is maintained, and to allow researchers to dissociate allometric effects from independent correlated evolution. Anurans constitute one of the most speciose groups of vocalizing vertebrates and females typically rely on vocalizations to localize males for reproduction. Here, we compile and compare data on various aspects of auditory morphology, hearing sensitivity and call dominant frequency across 81 species of anurans. We find robust, phylogenetically independent scaling effects of body size for all features measured. Furthermore, after accounting for body size, we find preliminary evidence that morphological evolution beyond allometry can correlate with hearing sensitivity and dominant frequency. These data provide foundational results regarding constraints imposed by body size on communication systems and motivate further data collection and analysis using comparative approaches across the numerous anuran species.
DOI: 10.25345/c5hq3s25c
title: MassIVE Reanalysis RMSV000000362.9 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000081607 Confetti, ArgC-GluC-LysC HCD [launched by cfca6e4ba8934e65aa11617b56091339]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.5281/zenodo.6372330
title: Matched Oxford Nanopore Technologies and Bisulfite Sequencing of the GM24385 Cell Line

description: One of the most widespread genomic modifications is 5-methylcytosine (5mC), which most frequently occurs at CpG dinucleotides. Compared to whole-genome bisulfite sequencing, the traditional method of 5mC detection, nanopore technology can offer many advantages such as simplicity of sample prep and subsequent analysis. In order to demonstrate the utility and convenience of Oxford Nanopore Technologies’ sequencing platform for performing detection and analysis of 5mC, we have sequenced the HG002 Genome in a Bottle Sample GM24385 with both traditional bisulfite sequencing and using nanopore sequencing. Both technologies, old and new, were applied to the same sample from a single DNA extraction. <em>Bisulfite sequencing</em> Bisulfite sequencing was performed by a commercial provider and processed with the commonly used bismark package to obtain the proportion of reads displaying methylation at CpG sites throughout the whole genome. <em>Nanopore sequencing</em> Nanopore sequencing was performed using the same sample of GM24385 material sent for bisulfite sequencing. Sequencing was performed on the MinION platform, across multiple flowcells, as part of ongoing platform development activities. The sequencing was not performed explicitly for the analysis presented here; we are making available all sequencing runs undertaken with this sample for the benefit of the community. <em>Data Access</em> Data is available as part of the Registry of Open Data on AWS: https://registry.opendata.aws/ont-open-data/. This dataset can be accessed through the S3 prefix: s3://ont-open-data/gm24385_mod_2021.09/ <em>Further Information</em> https://labs.epi2me.io/gm24385-5mc/ https://labs.epi2me.io/gm24385-5mc-remora
DOI: 10.5281/zenodo.6372329
title: Matched Oxford Nanopore Technologies and Bisulfite Sequencing of the GM24385 Cell Line

description: One of the most widespread genomic modifications is 5-methylcytosine (5mC), which most frequently occurs at CpG dinucleotides. Compared to whole-genome bisulfite sequencing, the traditional method of 5mC detection, nanopore technology can offer many advantages such as simplicity of sample prep and subsequent analysis. In order to demonstrate the utility and convenience of Oxford Nanopore Technologies’ sequencing platform for performing detection and analysis of 5mC, we have sequenced the HG002 Genome in a Bottle Sample GM24385 with both traditional bisulfite sequencing and using nanopore sequencing. Both technologies, old and new, were applied to the same sample from a single DNA extraction. <em>Bisulfite sequencing</em> Bisulfite sequencing was performed by a commercial provider and processed with the commonly used bismark package to obtain the proportion of reads displaying methylation at CpG sites throughout the whole genome. <em>Nanopore sequencing</em> Nanopore sequencing was performed using the same sample of GM24385 material sent for bisulfite sequencing. Sequencing was performed on the MinION platform, across multiple flowcells, as part of ongoing platform development activities. The sequencing was not performed explicitly for the analysis presented here; we are making available all sequencing runs undertaken with this sample for the benefit of the community. <em>Data Access</em> Data is available as part of the Registry of Open Data on AWS: https://registry.opendata.aws/ont-open-data/. This dataset can be accessed through the S3 prefix: s3://ont-open-data/gm24385_mod_2021.09/ <em>Further Information</em> https://labs.epi2me.io/gm24385-5mc/ https://labs.epi2me.io/gm24385-5mc-remora
DOI: 10.25345/c5cz32804
title: MassIVE Reanalysis RMSV000000366.5 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000086387 A Quantitative Proteome Map of the Human Body, TMT10 MS3 [Mixture: 24] [launched by cfca6e4ba8934e65aa11617b56091339]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.5519/qd.6ozc4x41
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (76538 records)
DOI: 10.6073/pasta/ea22c735ddfe17c595ccca978a87d109
title: Plant Community and Ecosystem Responses to Long-term Fertilization & Disturbance at the Kellogg Biological Station, Hickory Corners, MI (1989 to 2019)

description: Dataset AbstractThis work is part of the long-term sampling and monitoring of successional dynamics in abandoned fields – and responses to N-fertilization. Data from this research has been, and will continue to, contribute to LTER cross-site analysis of plant community dynamics, diversity-productivity, and responses to fertilization and disturbance.N-fertilized and tilled (disturbed) microplots are located in the NW corner of all treatment 7 (early successional communities) on the LTER main site. Experimental treatments are: 1) Nitrogen addition vs. no nitrogen addition and 2) Annual disturbance vs. undisturbedoriginal data source http://lter.kbs.msu.edu/datasets/60
DOI: 10.48370/ofd/qbiuq8/nrn7tm
title: Rhizophagus parallelicolis.jpg

description: :unav
DOI: 10.48370/ofd/qbiuq8
title: Rhizophagus parallelocollis (Gyllenhal, 1827), C-579

description: Coleoptera collection
DOI: 10.25345/c5862bf6p
title: MassIVE Reanalysis RMSV000000367.2 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080859/PXD001205 [4 out of 5] [launched by cfca6e4ba8934e65aa11617b56091339]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c54f1mn2j
title: MassIVE Reanalysis RMSV000000388.3 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080701/PXD000612 [8 out of 27] [launched by cfca6e4ba8934e65aa11617b56091339]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c50p0wt98
title: MassIVE Reanalysis RMSV000000386.3 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080864/PXD003708 [7 out of 15] [launched by cfca6e4ba8934e65aa11617b56091339]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5w08wk7c
title: MassIVE Reanalysis RMSV000000372.2 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080782/PXD002601 [4 out of 4] [launched by cfca6e4ba8934e65aa11617b56091339]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5r785s43
title: MassIVE Reanalysis RMSV000000390.2 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080274/PXD002389 [2 out of 4] [launched by cfca6e4ba8934e65aa11617b56091339]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5mg7g00c
title: MassIVE Reanalysis RMSV000000400.2 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080749/PXD003187 [4 out of 8] [launched by cfca6e4ba8934e65aa11617b56091339]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5gq6r554
title: MassIVE Reanalysis RMSV000000388.4 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080701/PXD000612 [16 out of 27] [launched by cfca6e4ba8934e65aa11617b56091339]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5bz61c1c
title: MassIVE Reanalysis RMSV000000383.2 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080854/PXD003811 [1 out of 10] [launched by cfca6e4ba8934e65aa11617b56091339]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c57659j7x
title: MassIVE Reanalysis RMSV000000415.2 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080794/PXD001339 [2 out of 5] [launched by cfca6e4ba8934e65aa11617b56091339]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c53f4kr48
title: MassIVE Reanalysis RMSV000000397.2 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000088434 LOPIT-DC subcellular map of U-2 OS cells [BioReplicate: REP3_SET2] [launched by cfca6e4ba8934e65aa11617b56091339]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5zs2kh0n
title: MassIVE Reanalysis RMSV000000396.2 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080848/PXD002214 [11 out of 21] [launched by cfca6e4ba8934e65aa11617b56091339]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5v11vp7p
title: MassIVE Reanalysis RMSV000000394.2 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080843/PXD003790 [3 out of 6] [launched by cfca6e4ba8934e65aa11617b56091339]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5q814w3x
title: MassIVE Reanalysis RMSV000000393.2 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080833/PXD001608 [6 out of 6] [launched by cfca6e4ba8934e65aa11617b56091339]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.5281/zenodo.1492197
title: A benchmark dataset of herbarium specimen images with label data: Summary

description: This landing page contains a CSV file compiling all data associated with herbarium specimens that are part of this dataset, as they could be found on GBIF, JACQ or FinBIF. A CSV file with and without Darwin Core extension data is available, as some CSV readers have trouble with the JSON format that is used for those extensions. In addition, DOI's of the individual specimens uploaded to Zenodo and direct links to the different files (JPEG, TIFF, JSON, PNG) are also included. Index of these added variables: - persistentID: Persistent Identifier of the collection specimen. Data uploaded as part of this dataset will not be kept in sync with changes at the collection's repository. Hence, this URI will always point to the most up to date information known about the herbarium specimen. - jpegURL, tiffURL, jsonURL: URL's pointing straight to the respective image and data files themselves, to facilitate (selective) batch downloads. - pngSegAllURL and pngSegSelURL: Segmented overlays of the herbarium specimens indicating the location of different labels and reference material on the sheet ("All") and their content ("Sel"). More information can be found in the paper (in prep) associated with this data publication and the individual depositions themselves. - DOI: The DOI of the deposition of images and data of these specimens on Zenodo. DOI's point to the most up-to-date version of these depositions at the time of the publication of this CSV file. As a rule, this CSV file will be updated should any changes happen to any of the depositions. - jpegURL2, tiffURL2: A few herbarium sheets had labels on the back and consisted therefore of two scans. As a rule, the label scans are in this category.
DOI: 10.5281/zenodo.6368368
title: Attentional Modulations of Alpha Power Are Sensitive to the Task-relevance of Auditory Spatial Information

description: The topographical distribution of oscillatory power in the alpha band is known to vary depending on the current focus of spatial attention. Here, we investigated to what extend univariate and multivariate measures of post-stimulus alpha power are sensitive to the required spatial specificity of a task. To this end, we varied the perceptual load and the spatial demand in an auditory search paradigm. A centrally presented sound at the beginning of each trial indicated the to-be-localized target sound. This spatially unspecific pre-cue was followed by a sound array, containing either two (low perceptual load) or four (high perceptual load) simultaneously presented lateralized sound stimuli. In separate task blocks, participants were instructed either to report whether the target was located on the left or the right side of the sound array (low spatial demand) or to indicate the exact target location (high spatial demand). Univariate alpha lateralization magnitude was neither affected by perceptual load nor by spatial demand. However, an analysis of onset latencies revealed that alpha lateralization emerged earlier in low (vs. high) perceptual load trials as well as in low (vs. high) spatial demand trials. Finally, we trained a classifier to decode the specific target location based on the multivariate alpha power scalp topography. A comparison of decoding accuracy in the low and high spatial demand conditions suggests that the amount of spatial information present in the scalp distribution of alpha-band power increases as the task demands a higher degree of spatial specificity. Altogether, the results offer new insights into how the dynamic adaption of alpha-band oscillations in response to changing task demands is associated with post-stimulus attentional processing.
description: This repository contains the raw EEG data files (in EEGLAB format, i.e., .set files and .fdt files) that already include all relevant condition and trial information in the EEG.event structure. In addition, the raw behavioral data files (response times relative to trial onset and registered button press) are provided. The analysis scripts associated with this dataset can be found here: https://osf.io/a8f6y/. Please see the README file in the OSF repository for further information regarding the shared datasets. The data are shared under the following licence: CC BY-NC-SA 4.0 (https://creativecommons.org/licenses/by-nc-sa/4.0/)