cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25345/c5sx64j9d
title: MassIVE Reanalysis RMSV000000355.8400 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, TPRG1L [launched by dab8bba1f45f4e4082f7fa74fbbf30fb]
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/c5sx64k0h
title: MassIVE Reanalysis RMSV000000355.8788 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ACVR2A [launched by dab8bba1f45f4e4082f7fa74fbbf30fb]
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: 10.5063/f18914bj
title: A list of ecological study sites within Central California Drylands

description: Plant-animal ecological interaction research within The Central California Drylands spatial summary list. Data provided describe primary site identifiers with geospatial data for joins to detailed site-level ecological research.
DOI: 10.25345/c5sx64k10
title: MassIVE Reanalysis RMSV000000681.15 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000084248 Proteogenomics Connects Somatic Mutations to Signalling in Breast Cancer [Notes: Phosphoproteome, Mixture: TCGA_AO-A12D_AN-A04A_BH-A0AV_117C_P_BI_20130322_H-PM] [launched by 31fc25a7c92347c2b9f58f8f26be259f]
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/c5sx64k2g
title: MassIVE Reanalysis RMSV000000594.2 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000083971 Proteome analysis of the MO3.13 cell line from human oligodendrocytes [launched by 31fc25a7c92347c2b9f58f8f26be259f]
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: 10.5063/f18c9tp1
title: Decomposition and nitrogen mineralization in five common urban habitat types across seven college campuses in Southern California (January-May 2019)

description: Urban landscaping conversions can alter decomposition processes and soil respiration, making it difficult to forecast regional CO2 emissions. Here we explore rates of initial mass loss and net nitrogen (N) mineralization in natural and four common urban landcovers (water -wise, water-wise with mulch, shrub, and lawn) from sites across seven Colleges in southern California. To better understand decomposition processes in surface soils across various urban habitats, we measured rates of leaf litter decomposition and nitrogen (N) mineralization between 28 January and 17 May 2019, for two dominant native trees of the southern California region: coastal live oak (Quercus agrifolia Neé, “oak”) and western sycamore (Platanus racemosa L., “sycamore”) in natural and urbanized land-covers at seven college campuses in southern California. At each college, we placed litter bags in five landcover types that typify southern California urban landscapes: (1) lawns, dominated by non-native grasses and high water inputs; (2) hedge/shrub environments, defined by at least 75% cover of non-native shrubs with water inputs; (3) water-wise gardens (no mulch), which consist of native or non-native plants with reduced water inputs but no mulch; (4) water-wise (with mulch) gardens, with native or non-native plants, reduced water inputs and a mulch (most often mixed wood chips) covered soil; and (5) natural areas, receiving no water subsidies often dominated by native shrubs or non-native annuals.
DOI: 10.25345/c5sx64k3z
title: MassIVE Reanalysis RMSV000000499.5 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080764/PXD004668 [3 out of 3] [launched by 31fc25a7c92347c2b9f58f8f26be259f]
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: 10.5063/f18k77jh
title: Data: Repeatability of performance within and across contexts measuring behavioral flexibility

description: Research into animal cognitive abilities is increasing quickly and often uses methods where behavioral performance on a task is assumed to represent variation in the underlying cognitive trait. However, because these methods rely on behavioral responses as a proxy for cognitive ability, it is important to validate that the task structure does, in fact, target the cognitive trait of interest rather than non-target cognitive, personality, or motivational traits (construct validity). One way to validate that task structure elicits performance based on the target cognitive trait is to assess the temporal and contextual repeatability of performance. In other words, individual performance is likely to represent an inherent trait when it is consistent across time and across similar or different tasks that theoretically test the same trait. Here we assessed the temporal and contextual repeatability of the cognitive trait behavioral flexibility in great-tailed grackles. For temporal repeatability, we quantified the number of trials to form a color preference after each of multiple color reversals on a serial reversal learning task. For contextual repeatability, we then compared performance on this task to the latency to switch solutions on two different multi-access boxes. We found that the number of trials to form a preference in reversal learning was repeatable across serial reversals and the latency to switch a preference was repeatable across reversal learning and the multi-access box contexts. This supports the idea that reversal learning and solution switching on multi-access boxes similarly reflect the inherent trait of behavioral flexibility.
DOI: 10.25345/c5sx64k4f
title: MassIVE Reanalysis RMSV000000384.37 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000081563 HeLa proteome, Tissue_Colon_46_fractions [launched by 31fc25a7c92347c2b9f58f8f26be259f]
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/c5sx64k5x
title: MassIVE Reanalysis RMSV000000433.22 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080836/PXD003700 [13 out of 14] [launched by 31fc25a7c92347c2b9f58f8f26be259f]
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: 10.5063/f18p5xx0
title: The role of climate change and niche shifts in divergent range dynamics of a sister-species pair

description: The datasets collected here were used to generate species distribution models for the great-tailed grackle (Quiscalus mexicanus) and boat-tailed grackle (Quiscalus major) as part of publication by Summers et al. 2022. The publication abstract is included below.Species ranges are set by limitations in climate tolerances, habitat use, and dispersal abilities. Understanding the factors governing species range dynamics remains a challenge that is ever more important in our rapidly changing world. Species ranges can shift if environmental changes affect available habitat, or if the habitat breadth or connectivity of a species changes. The ability of a species to rapidly expand their geographic range through changes in their habitat breadth, also known as niche shifts, has been linked to behavioral flexibility, the ability to change behavior when circumstances change. We tested how changes in habitat availability, habitat breadth, or habitat connectivity contributed to divergent range dynamics in a sister-species pair. The highly behaviorally flexible great-tailed grackle (Quiscalus mexicanus) has expanded its range northward from Texas to South Dakota in the past 40 years, while its closest relative, the boat-tailed grackle (Quiscalus major), has remained tied to the coasts of the Atlantic Ocean and the Gulf of Mexico. We created species distribution and connectivity models trained on citizen science data from 1970-1979 and 2010-2019 to determine how suitable habitat ranges,habitat breadth, and range-wide connectivity have changed for both species. We found that the two species occupy distinct habitats and that the habitat of the great-tailed grackle has shifted to include a larger breadth of urban, arid environments farther from natural water sources. Meanwhile, the boat-tailed grackle has remained limited to warm, wet, coastal environments. We found no evidence that changes in habitat connectivity affected the ranges of either species. Overall, our results suggest that a change in habitat breadth drove the rapid range expansion of the great-tailed grackle, while climate change shaped minor shifts in the available range of the boat-tailed grackle. The expansion in habitat breadth of the great-tailed grackle is consistent with observations that species with high behavioral flexibility can rapidly expand their geographic range by using human-altered habitat. This investigation identifies how opposite responses to anthropogenic change drive divergent range dynamics, elucidating the factors that have and will continue to shape species ranges.
DOI: 10.25345/c5sx64k6d
title: MassIVE Reanalysis RMSV000000384.44 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000081563 HeLa proteome, HeLa_Trypsin_39_fractions [launched by 31fc25a7c92347c2b9f58f8f26be259f]
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/c5sx64k7w
title: MassIVE Reanalysis RMSV000000677.63 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000081738 Pharmacoproteomic characterisation of human colon and rectal cancer - CRC65 Full Proteomes [Cohort: P012580] [launched by 31fc25a7c92347c2b9f58f8f26be259f]
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: 10.5063/f1930rmf
title: TBEP Up in the Air and Down in the Water_Nitrogen Data, Tampa Bay Watershed Florida 2021 to 2022

description: Data is being collected on nitrogen forms and concentrations in atmospheric wet deposition, stormwater runoff and throughfall from the urban tree canopy. Sampling sites are Pinellas and Hillsborough Counties Florida. Data includes nitrate stable isotope analysis of wet deposition and stormwater, as well as cell count data from a bioassay of wet deposition, stormwater, and throughfall with Karenia brevis and Pyrodinium bahamense.
DOI: 10.25345/c5t14tt10
title: MassIVE MSV000089589 - Comparative proteomics of Adult Paragominus kellikotti excretion/secretion products released in vitro or present in the lung cyst nodule
title: The aims of this study were to study ESPs to improve understanding of parasite-host interactions and to support the discovery of novel diagnostic or therapeutic targets. We used tandem mass-spectrometry to characterize the secretome of adult P. kellicotti flukes and to compare ESPs released during in vitro culture with parasite cyst fluid proteins (CFPs) which correspond to ESPs released by adult flukes in vivo. We also compared these results to the global proteome of soluble, somatic protein (SSP) extracts of whole adult flukes.
DOI: 10.5063/f19885gc
title: List or Research Questions developed as part of The Future of Synthesis in Ecology and Environmental Science Virtual workshop (February 17th & 18th, 2021)

description: Here is the list of research questions and themes that we, as members of the research community, developed to begin to prioritize the future synthesis needs in ecology and environmental science. To develop these priorities, we convened a virtual workshop at the National Center for Ecological Analysis and Synthesis (NCEAS) on Feb 17-18, 2021, with 127 participants across career stages, institutions, backgrounds, and geographies which were selected through an application process (see Halpern et al. 2022, Appendix S1). Participants were drawn from ecology and environmental sciences and largely identified as natural scientists. We asked workshop participants to anonymously identify key synthesis questions in ecology and environmental science, and the challenges and innovations needed to answer those questions. Participants proposed ideas or questions in pre-workshop brainstorming sessions; added and upvoted questions online; and worked in breakout teams during the workshop to refine upvoted questions into lists of top three questions. These final lists were then grouped into themes by the 12-person steering committee and discussed at length by the workshop participants.
DOI: 10.25345/c5t14tt2g
title: MassIVE MSV000089797 - Endophytic Fungus Pure Culture (Costa Rica)
title: extract of pure culture broth, first collection (PI: Giselle Tamayo-Castillo, Priscila Chaverri, Ph.D. candidate Efrain Escudero)
DOI: 10.25345/c5t14tt3z
title: MassIVE MSV000090183 - Lab_8_Untargeted_Metabolomics_Tubingen_Summer_School
title: Algae bloom simulation Lab 8 for the course Untargeted Metabolomics Summer School 2022
DOI: 10.5063/f19c6vvv
title: A GBIF endangered species diversity analysis of burn sites in the Southwestern, USA

description: The purpose of this dataset is to evaluate the impact of fires on endangered species biodiversity in California's southwest desert. Species data was downloaded from the Global Diversity Information Facility (GBIF). Wildland fires were downloaded from the National Interagency Fire Network
DOI: 10.25345/c5t14tt4f
title: MassIVE Reanalysis RMSV000000668.289 - CCMS ProteoCarta Maestro reanalysis of Mus musculus from Mass spectrometry-based draft of the mouse proteome (Male_Temporal_lobe_phosphoproteome) [launched by fb749713ee06486fa322870abe44395d]
title: CCMS ProteoCarta open modification search for modified peptide variants (Maestro) reanalysis of Mus musculus (Male_Temporal_lobe_phosphoproteome) (MSV000089856/PXD030983).
DOI: 10.25345/c5t14tt5x
title: MassIVE MSV000090407 - A2269_Citrus_limon_LC/MS_Dr.Heba_SH._Mohammed
title: LC/MS of Citrus limon plant sample Dr. Heba Sh. Mohammed_2022_A2269
DOI: 10.5063/f19k48pw
title: Global Ocean Health Index 2020 assessment

description: Scores from the 2020 global Ocean Health Index (OHI) assessment and accompanying data and models. The global Ocean Health Index assesses ocean health for 220 coastal countries and territories and has been conducted yearly since 2012. The Index describes how well we are sustainably managing 10 goals which represent the full suite of benefits that people want and need from the ocean. These goals include: artisanal fishing opportunity, biodiversity, carbon storage, clean waters, coastal livelihoods and economies, coastal protection, food provision, natural products, sense of place, and tourism and recreation. Each goal is given a score ranging from 0 to 100, and the full suite of goal scores are then averaged to obtain an overall index score for each region. Please see https://oceanhealthindex.org/ for additional resources and information.
DOI: 10.25345/c5t14tt6d
title: MassIVE MSV000090613 - Anticancer compounds from Annona muricata target protein glycosylation processes in lung cancer cells_proteomics
title: Treatment of A549 lung cancer cells with novel cytotoxic compounds isolated from Annona muricata. Mass spectrometry data was obtained for proteomics and glycoproteomics.
DOI: 10.5063/f19w0cz9
title: Geolocations of all Ephedra californica shrubs at key ecological areas within the the Kelso dunes.

description: The geolocation of all Ephedra californica shrubs within the Kelso dunes. All shrubs have been geolocated via the Google earth satellite.
DOI: 10.25345/c5t14tt7w
title: MassIVE MSV000090790 - The expression profiling under deletion of transcriptional regulator in Xcc
title: The Gammaproteobacterium Xanthomonas campestris pv. campestris (Xcc) B100 is the causal agent of black rot disease in a wide range of economically important crop plants. Additionally, Xcc is commercially relevant, due to the synthesis of an exopolysaccharide, xanthan. In this study, the effect that transcriptional regulator Crt1 exerts on the growth, virulence, as well as transcriptome and proteome profiles was investigated.
DOI: 10.25345/c5t14tt8c
title: MassIVE Reanalysis RMSV000000354.5919 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, CPEB1 [launched by 89f2bcaf3c714e3788b179581bc93515]
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: 10.5063/f1b27sr8
title: Phytoplankton in Oneida Lake, New York, 1975 to present

description: This dataset contains phytoplankton data from Oneida Lake from 1975 to present and is part of the collection Cornell Oneida Lake Data. The Cornell Biological Field Station (CBFS) serves as a primary field site for aquatic research at Cornell University (more information can be found at http://cbfs.dnr.cornell.edu/index.html) and is part of the Department of Natural Resources, College of Agriculture and Life Sciences ,Cornell University. The centerpiece of the station's research program is a 60-year database on the food web of Oneida Lake, New York, that has been collected with support from the Cornell University Brown Endowment and from the New York State Department of Environmental Conservation. The data are collected by personnel from the Cornell Biological Field Station and include limnology, benthos, zooplankton, phytoplankton, and fish survey data, primarily from Oneida Lake and spanning 1957 to the present. This data package contains results of phytoplankton surveys of Oneida Lake, New York divided in two series: 1975 - 1995 and 1996 to present. The primary tables give densities of phytoplankton taxa identified in samples collected from sites in Oneida Lake. Five of these sites are standard sites and used when stations are pooled. A derived table has the densities and biovolumes of each taxa averaged over the five standard stations (1975 to 1995 data). Supplemental tables provide explanations of the taxonomic codes used in the two primary tables as well as geographic coordinates and information for the sampling sites.
DOI: 10.25345/c5t14tt9v
title: MassIVE Reanalysis RMSV000000354.6097 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, FAM45A [launched by 89f2bcaf3c714e3788b179581bc93515]
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/c5t14tv0z
title: MassIVE Reanalysis RMSV000000354.6304 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, DIRAS3 [launched by 89f2bcaf3c714e3788b179581bc93515]
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.