cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25345/c5t43jc01
title: MassIVE Reanalysis RMSV000000675.77 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000090571 Chemical phosphoproteomics reveals kinase network topologies associated to genotypes and phenotypes of cancer cells [Cohort: HL60_NU7441] [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/f1qf8r9m
title: Water chemistry at tea plantation in Taiwan

description: Occult deposition is deposition of pollutants by direct contact with mist or cloud. The total quantity of fog water is in general much less than that of rain water, however, concentrations in cloud water could be very high. This is because the formation of fog is close to the ground where concentration of air pollutants is high and the per unit volume surface of fog is much higher than that of rain. Due to higher concentrations, the contribution of chemical deposition from fog often exceeds its contribution on water input and its effects on ecosystem cannot be neglected. Cloud forest in Taiwan is also important for tea plantation. In addition to precipitation, fog is another important pathway of atmospheric deposition in tea plantations. As global tea consumption is increasing, tea plantations are expanding and more nitrogen fertilizers are used to increase yields, which could directly or indirectly influence ecosystems. Through collection and analyses of rainfall, fog, throughfall, and stream water, this study aims to evaluate the impacts of atmospheric deposition on nutrient input-output of tea plantations in northern Taiwan. The abundance order of all ions was Cl- &gt; Na+ &gt; SO42- &gt; K+ &gt; NO3- &gt;NH4+ &gt;Ca2+ &gt;Mg2+ in rainwater and Na+&gt;Cl- &gt;NO3- &gt;Mg2+ &gt;SO42- &gt; Ca2+ &gt; NH4+ &gt; K+ in fog water. Cl- and Na+ were the most abundant ions in both fog and rain water, indicating strong oceanic influences on water chemistry. The concentrations of all ions were much higher in fog water and the ratio to fog and rain was K+ (2.11) &lt; NH4+ (5.59) &lt; SO42- (6.99) &lt; Ca2+ (9.25) &lt; Cl- (9.26) &lt; NO3- (10.3) &lt; Na+ (14.2) &lt; Mg2+ (22.2) &lt; DON (46.9), which lies between sites with (mostly were larger than 10) and without (less than 5) major emission, possibly because the study site is close to big cities but the surroundings are well covered with forest. Results from principal component analysis indicates that agriculture influence is the main factor for explaining variance of K+ and NH4+ concentrations in fog water but not rain water. The result indicates that fog was more affected by local air pollution.
DOI: 10.25345/c5t43jc1h
title: MassIVE Reanalysis RMSV000000369.39 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080757/PXD002619 [9 out of 24] [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/c5t43jc20
title: MassIVE Reanalysis RMSV000000444.26 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080868/PXD003523 [5 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/f1qn656j
title: Avian biodiversity data from Global Biodiversity Information Facility for the Central Desert Ecological Sites of California

description: Bird observations at different spatial scales at several sites and regions across deserts in California. All data pulled from GBIF.
DOI: 10.25345/c5t43jc3g
title: MassIVE Reanalysis RMSV000000592.74 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000083508 29 tissues, ovary Trypsin_HCD_QExactiveplus [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/c5t43jc4z
title: MassIVE MSV000091157 - Blood and urine multi-omics analysis of the impact of e-vaping, smoking and cessation. From exposome to molecular responses
title: Cigarette smoking is a major cause of preventable morbidity and mortality. While quitting smoking is the best option, switching from cigarettes to non-combustible alternatives (NCAs) such as e-vapor products is a viable harm reduction approach for smokers who would otherwise continue to smoke. A key challenge for the clinical assessment of NCAs is that self-reported product use can be unreliable, compromising the proper evaluation of their risk reduction potential. In this cross-sectional study with 205 healthy volunteers, we combined comprehensive exposure characterization with in-depth multi-omics profiling to compare effects across four study groups: cigarette smokers (CS), e-vapor users (EV), former smokers (FS) and never smokers (NS). Multi-omics analyses included metabolomics, transcriptomics, DNA methylomics, proteomics, and lipidomics. Comparison of the molecular effects between CS and NS recapitulated several previous observations, such as increases in inflammatory markers in CS. Generally, FS and EV demonstrated intermediate molecular effects between the NS and CS groups. Stratification of the FS and EV by combustion exposure markers suggested that this positioning on the scale between CS and NS was partially driven by non-compliance / dual use. Overall, this study highlights the importance of in-depth exposure characterization before biological effect characterization for any NCA assessment study.
DOI: 10.5063/f1qr4vjk
title: Alaskan commercial salmon fishing statistical areas, 2017

description: Participants in Alaska commercial fisheries are required to report the statistical area where their harvest occurs. In combination with reports on the harvest species, poundage and etc., these data are useful to analyze and visualize spatial patterns in harvest. This data set defines the current valid statistical areas that may be used on ADF&G fish tickets for salmon and miscellaneous finfish. This data set should NOT be used for navigation or for determining compliance with ADF&G Commercial Fishing Regulations. Please consult the ADF&G Commercial Fisheries Regulations for the official definitions of regulatory boundaries. NOTE: These data attempt to depict statistical area boundaries as used for management during a specific time period. In some cases, statistical area boundaries used in practice may differ from those described in regulations, reports, maps, and other aids. Up to date published layers and historical areas can be found on Commercial Fishing GIS Data Downloads section on the ADF&G website (http://www.adfg.alaska.gov/index.cfm?adfg=maps.commercial_fishing_gis). This project received funding under award NA15NMF4270272 from NOAA Fisheries Service, in cooperation with the Saltonstall-Kennedy Grant Program.
DOI: 10.25345/c5t727k71
title: MassIVE MSV000089558 - GNPS_Maternal_Infant_Mouse_Antibiotics
title: Metabolomics of fecal and serum of mouse dams treated with antibiotics and their infants.
DOI: 10.5063/f1r49p7g
title: A meta-analysis of shrub density as a predictor of animal abundance

description: Facilitative interactions between shrub and animal species can shape the structure and composition of various ecosystems. Here, we tested whether the density of woody plants such as shrubs can be used to predict the local abundance of animal populations in a meta-analysis. Keyword searches on ISI Web of Science using the “density”, “facil*”, “shrub*”, and “animal*” returned 753 studies. Full-text review for shrub density, animal abundance or density, and sampling effort in total number of days resulted in a total of 113 independent observations that reported shrub density and animal abundance. shrub density positively predicted estimated animal abundance locally particularly in desert and grassland ecosystems. Shrub density can be used as an effective measure in predicting local animal abundances for wildlife biology and ecological research.
DOI: 10.25345/c5t727k8h
title: MassIVE MSV000089943 - Palaeoproteomic data for domesticated equids (horse and donkey) collagen for Zooarchaeology by Mass Spectrometry (ZooMS)
title: The dataset is for identification of MALDI markers for peptide mass fingerprinting of bone collagen for species identification using ZooMS for horse and donkey using chymotrypsin. Corresponding MALDI data can be found through Zenodo at 10.5281/zenodo.6878868. This dataset contains: - raw files - peak list files - results files for the proteome search and for collagen marker identification - database for the collagen marker identification - csv file with information about the sample numbers. More information about the extraction and digestion can be found at the linked manuscript.
DOI: 10.25345/c5t727k90
title: MassIVE Reanalysis RMSV000000668.54 - CCMS ProteoCarta MS-GF+ reanalysis of Mus musculus from Mass spectrometry-based draft of the mouse proteome (Cell_line_8248) [launched by 148d2da0ae3046aeb7af52e0653a7b24]
title: CCMS ProteoCarta database search (MSGF+) reanalysis of Mus musculus (Cell_line_8248) (MSV000089856/PXD030983).
DOI: 10.5063/f1r78cp7
title: Mountain Birdwatch: 2010-2022

description: Mountain Birdwatch (MBW) is a long-term community science monitoring program for 10 bird and 1 mammal species that breed in high-elevation spruce-fir forests of the northeastern United States. Initiated in 2000 as Mountain Birdwatch 1.0, MBW 2.0 (years 2010 and onwards) provides the only region-wide source of population information on these high-elevation species. Each June, under the coordination of the Vermont Center for Ecostudies, volunteers perform repeated point counts at nearly 750 long-term fixed sampling sites along established hiking trails in Vermont, New Hampshire, Maine, and eastern New York (Catskills and Adirondacks). The primary emphasis was placed on Bicknell’s Thrush, a montane-fir specialist that breeds only in the Northeastern U.S. and adjacent portions of Canada. In 2010, the program underwent many positive changes to reemerge as Mountain Birdwatch 2.0. All of the sampling locations prior to 2010 were permanently retired, and new sampling locations were chosen using a generalized random tessellation stratified (GRTS) procedure. For more information see: https://vtecostudies.org/projects/mountains/mountain-birdwatch/ These data on KNB contain all of the point count for the 11 monitored species from 2010 to 2022 with the exception of data from 6 routes in Maine that occur on commercial timberlands. Our confidentiality agreements with those timber operations prevent us from sharing those data in a non-aggregated format.
DOI: 10.25345/c5t727m03
title: MassIVE Reanalysis RMSV000000668.263 - CCMS ProteoCarta MS-GF+ reanalysis of Mus musculus from Mass spectrometry-based draft of the mouse proteome (Male_Tongue_phosphoproteome) [launched by 148d2da0ae3046aeb7af52e0653a7b24]
title: CCMS ProteoCarta database search (MSGF+) reanalysis of Mus musculus (Male_Tongue_phosphoproteome) (MSV000089856/PXD030983).
DOI: 10.25345/c5t727m1k
title: MassIVE Reanalysis RMSV000000668.411 - CCMS ProteoCarta ModDecode reanalysis of Mus musculus from Mass spectrometry-based draft of the mouse proteome (Male_Urinary_bladder_proteome) [launched by ab1ddc566e8244bd975da925e6cb9107]
title: CCMS ProteoCarta peptidoform interpretation (ModDecode) of Maestro open modification search results for Mus musculus (Male_Urinary_bladder_proteome) from MSV000089856/PXD030983.
DOI: 10.5063/f1rf5sgf
title: Traits associated with fitness, flower visits per plant, single visit pollen deposition, pollinator abundance in San Diego County, USA (2018-2021)

description: This data set contains information regarding fitness traits following various pollination treatments on three native plants (Salvia apiana, Salvia mellifera, and Phacelia distans) in San Diego County, USA, for both maternal families and individual plants, the number of flower visits per plant for honey bees (Apis mellifera) and non-Apis flower visitors, the number of pollen grains deposited in a single visit by honey bees and non-Apis flower visitors, and pollinator abundance data (Apis or non-Apis) for the three plant species.This dataset was created in order to assess the geitonogamous visitation behavior of honey bees (not native to the USA) and non-Apis pollinators, and the fitness of zygotes produced by these two pollinator groups. With this dataset we were able to determine that honey bee pollination created zygotes of a lower fitness compared to outcrossing, and non-Apis pollinators.
DOI: 10.25345/c5t727m22
title: MassIVE MSV000090376 - Middle-Down Mass Spectrometry Reveals Activity-Modifying Phosphorylation Barcode in a Class C G Protein-Coupled Receptor
title: Supporting data files for "Middle-Down Mass Spectrometry Reveals Activity-Modifying Phosphorylation Barcode in a Class C G Protein-Coupled Receptor".
DOI: 10.5063/f1rj4gx6
title: Data: Is behavioral flexibility manipulatable and, if so, does it improve flexibility and problem solving in a new context?

description: Behavioral flexibility, the ability to adapt behavior to new circumstances, is thought to play an important role in a species' ability to successfully adapt to new environments and expand its geographic range. However, flexibility is rarely directly tested in species in a way that would allow us to determine how flexibility works to predict a species' ability to adapt their behavior to new environments. We use great-tailed grackles (Quiscalus mexicanus; a bird species) as a model to investigate this question because they have recently rapidly expanded their range into North America. We attempted to manipulate grackle flexibility using colored tube reversal learning to determine whether flexibility is generalizable across contexts (multi-access box), and what learning strategies grackles employ. We found that flexibility was manipulatable: birds in the manipulated group took fewer trials to pass criterion with increasing reversal number, and they reversed a color preference in fewer trials by the end of their serial reversals compared to control birds who had only one reversal. Birds that passed their last reversal faster were also more flexible (faster to switch between loci) and innovative (solved more loci) on a multi-access box. All grackles in the manipulated reversal learning group used one learning strategy (epsilon-decreasing: long exploration period) in all reversals and did not use the (epsilon-first strategy: quickly shift their preference), and none used a particular exploration or exploitation strategy earlier or later in their serial reversals. Understanding how flexibility causally relates to other traits will allow researchers to develop robust theory about what flexibility is and when to invoke it as a primary driver in a given context, such as a rapid geographic range expansion.
DOI: 10.25345/c5t727m3j
title: MassIVE MSV000090759 - Alternative polyadenylation alters protein dosage by switching between intronic and 3' UTR sites
title: Alternative polyadenylation (APA) creates distinct transcripts from the same gene by cleaving the pre-mRNA at poly(A) sites that can lie within the 3' UTR, introns, or exons. Most studies focus on APA within the 3' UTR, but here we show that CPSF6 insufficiency alters protein levels and causes a developmental syndrome by deregulating APA throughout the transcript. In neonatal humans and zebrafish larvae, CPSF6 insufficiency shifts poly(A) site usage between the 3'UTR and internal sites in a pathway-specific manner. Genes associated with neuronal function undergo mostly intronic APA, reducing their expression, while genes associated with heart and skeletal function mostly undergo 3' UTR APA and are upregulated. This suggests that, in healthy conditions, cells toggle between internal and 3'UTR APA to modulate protein expression.
DOI: 10.25345/c5t727m41
title: MassIVE Reanalysis RMSV000000354.6066 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ADRBK1 [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/c5t727m5h
title: MassIVE Reanalysis RMSV000000354.6450 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, PVRIG [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/c5t727m60
title: MassIVE Reanalysis RMSV000000354.6836 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, IFT74 [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/c5t727m7g
title: MassIVE Reanalysis RMSV000000354.7045 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, LRP2BP [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/f1s75ds5
title: Old Tampa Bay Philippe Park Wave Gauge Deployment

description: Living shoreline elements will be installed in 2023 to encompass the ~1000 m seawall in Philippe Park, Pinellas County, FL. The University of South Florida (USF) and the Tampa Bay Estuary Program (TBEP) are collaborating with Pinellas County to monitor the wave field in the vicinity of the seawall in Philippe Park. A pressure gauge array of 4 sensors has been assembled for deployment in shallow (nearshore) water. An initial deployment using a single sensor began July 1, 2022 and was recovered July 6, 2022. A second deployment using a single sensor began August 29, 2022 and was recovered September 9, 2022. The two files herein are for the two separate deployments that describe the wave field pre-installation of the living shoreline. Data were collected continuously at 4Hz using a RBR Concerto 3 data logger.
DOI: 10.25345/c5t727m8z
title: MassIVE Reanalysis RMSV000000354.7220 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, RNF115 [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/c5t727m9f
title: MassIVE Reanalysis RMSV000000354.7429 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, PPP6R2 [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/f1sf2tn8
title: The effect of shrubs on animals in Panoche Southern California

description: The following data was collected in Panoche hills in Southern California during the summer of 2019. 7 cameras were deployed facing shrub and open microsites and were rotated once. The cameras remained deployed for a total of 14 days.