cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25345/c5t14tz85
title: MassIVE Reanalysis RMSV000000675.160 - 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: NTERA2_PD] [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/f1gx490b
title: Stemflow reduction experiment of epiphytes, in Fushan experimental forest, Taiwan (2020-2021)

description: In this study, customary-made stemflow-manipulation devices were set up to explore how drought stress affect two epiphytes, Asplenium nidus and Haplopteris flexuosa, in the Fushan Experimental Forest of northern Taiwan for ten months. Using the devices, three levels of stemflow reduction were created, 0% (Control), 25% and 50%. We examined the traits indicative of plant growth condition, number of leaves and leaf area, and drought stress, SLA, LDMC, thickness of leaves and cuticle and δ13C, and nutrients of leaves to explore the effects of the treatments.
DOI: 10.25345/c5t14tz9n
title: MassIVE Reanalysis RMSV000000366.104 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000086387 A Quantitative Proteome Map of the Human Body, TMT10 MS3 [Mixture: 16] [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/f1h41pws
title: Great-tailed grackle serial reversal learning data for post hoc analyses

description: These are the input data for the article "Behavioral flexibility is manipulatable and it improves flexibility and problem solving in a new context: post-hoc analyses of the components of behavioral flexibility". The data were collected to understand behavioral flexibility in great-tailed grackles. There are simulated data to test the approach and the observed data from a set of grackles in Arizona. Behavioral flexibility, adapting behavior to changing situations, is hypothesized to be related to adapting to new environments and geographic range expansions. However, flexibility is rarely directly tested in a way that allows insight into how flexibility works. Research on great-tailed grackles, a bird species that has rapidly expanded their range into North America over the past 140 years, shows that grackle flexibility is manipulatable using colored tube reversal learning and that flexibility is generalizable across contexts multi-access box). Here, we use these grackle results to conduct a set of posthoc analyses using a model that breaks down performance on the reversal learning task into different components. We show that the rate of learning to be attracted to an option (phi) is a stronger predictor of reversal performance than the rate of deviating from learned attractions that were rewarded (lambda). This result was supported in simulations and in the data from the grackles: learning rates in the manipulated grackles doubled by the end of the manipulation compared to control grackles, while the rate of deviation slightly decreased. Grackles with intermediate rates of deviation in their last reversal, independently of whether they had gone through the serial reversal manipulation, solved fewer loci on the plastic and wooden multi-access boxes, and those with intermediate learning rates in their last reversal were faster to attempt a new locus on both multi-access boxes. These findings provide additional insights into how grackles changed their behavior when conditions changed. Their ability to rapidly change their learned associations validates that the manipulation had an effect on the cognitive ability we think of as flexibility.
DOI: 10.25345/c5t14v005
title: MassIVE Reanalysis RMSV000000609.2 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080256 CHPP chr 1,8,20 proteome dataset using the HCC cell lines of Hep3B and MHCC97H, instrument is AB5600, part 3 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: 10.25345/c5t14v01n
title: MassIVE Reanalysis RMSV000000355.8921 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, GPI [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/f1h70d7m
title: Census of flowering annuals in the open and associated with Larrea tridentata, Mojave Desert, April 2019

description: Larrea tridentata is a well known facilitator of annuals in arid ecosystems. We surveyed the annual flowering community associated with 100 Larrea tridentata and paired open areas in the Mojave Desert three times over the course of the flowering season of 2019. Only annual species that were flowering in the area were identified. Plant density, species richness and flowering density was recorded for each shrub. A total of 15 annual species across 6 families and 14 genera were recorded.This dataset has three files:1. flowering_censuses_2019 contains the annual community data (e.g. density, richness, and floral density)2. ShrubInfo contains the characteristics of each shrub (e.g. size and location)3. code2.R contains code related to the presentation and analysis of the data.
DOI: 10.25345/c5t14v024
title: MassIVE MSV000091188 - GNPS_202302022022060820211207_ISP4vs.1,2-PG_Streptomyces.
title: metabolomics data for Streptomyces samples of fermentation broth in different culture mediums of ISP4 vs. 1,2-PG
DOI: 10.25345/c5t43j66p
title: MassIVE MSV000089766 - GNPS_Cryptoglena_skujai_in_Af6_and _EG:JM
title: Solvent extracts of axenic Cryptoglena skujai grown in Af6 and EG:JM media
DOI: 10.5063/f1hm56wb
title: Dataset of the rhizosphere microbiome and coffee bean fermentation in the Castillo-Tambo and Borbón varieties in the Popayán-Colombia plateau

description: A comprehensive study was conducted to investigate the microbial biodiversity and associated functional roles of microorganisms in the fermentation process of washed coffee in Colombia, utilizing the Borbón and Castillo coffee varieties as model systems. DNA sequencing techniques were employed to evaluate the soil microbial biota and their contribution to fermentation. The study aimed to analyze the potential benefits of these microorganisms, including enhanced productivity and the requirement for identifying rhizospheric bacterial species to optimize such benefits.
DOI: 10.25345/c5t43j675
title: MassIVE MSV000089974 - LncRNA LIMp27 regulates the DNA damage response through p27 in p53-defective cancer cells
title: P53 inactivation occurs in about 50% of human cancers, where p53-driven p21 activity is devoid and p27 becomes essential for the establishment of the G1/S checkpoint upon DNA damage. Here, we show that the E2F1-responsive lncRNA LIMp27 selectively represses p27 expression and contributes to proliferation, tumorigenicity, and treatment resistance in p53-defective colon adenocarcinoma (COAD) cells. LIMp27 competes with p27 mRNA for binding to cytoplasmically localized hnRNA0, which otherwise stabilizes p27 mRNA leading to cell cycle arrest at the G0/G1 phase. In response to DNA damage, LIMp27 is upregulated in both wild-type and p53-mutant COAD cells, whereas cytoplasmic hnRNPA0 is only increased in p53-mutant COAD cells due to translocation from the nucleus. Moreover, high LIMp27 expression is associated with poor survival of p53-mutant but not wild-type p53 COAD patients. These results uncover a lncRNA mechanism that promotes p53-defective cancer pathogenesis and suggest that LIMp27 may constitute a target for the treatment of such cancers.
DOI: 10.5063/f1ht2mrf
title: Geolocations of all Ephedra californica shrubs at key ecological areas within the San Joaquin Desert.

description: The geolocation of all Ephedra californica shrubs withing key ecological areas within the San Joaquin Desert. All shrubs have been geolocated via the Google earth satellite.
DOI: 10.25345/c5t43j68n
title: MassIVE MSV000090152 - Test_Seseli tortuosum (Apiaceae) root extract
title: Analyses of Seseli tortuosum (Apiaceae) root methanol extracts. Plants were collected in Turkey. Dried plant material was extracted with Methanol. Both positive/negative ionization mode analyses. LC-MS/MS performed in a Thermo scientific HPLC, mass spectrometer (ion trap) equipped with an ESI source. Auto MSn mode for exploratory analysis.
DOI: 10.25345/c5t43j694
title: MassIVE Reanalysis RMSV000000668.87 - CCMS ProteoCarta Maestro reanalysis of Mus musculus from Mass spectrometry-based draft of the mouse proteome (Cell_line_8028) [launched by fb749713ee06486fa322870abe44395d]
title: CCMS ProteoCarta open modification search for modified peptide variants (Maestro) reanalysis of Mus musculus (Cell_line_8028) (MSV000089856/PXD030983).
DOI: 10.5063/f1hx1b4q
title: The effect of shrub density on animal abundance in Panoche, Southern California

description: The following data was collected during the 2019 field season in the Carrizo Plain National Monument in Southern California, United States. 16 Cameras were deployed at varying shrub densities ranging from no shrub individuals to a high number of individuals (11-12 shrubs). These cameras were deployed in 1 of our major site. Cameras were not rotated and were deployed for a total of 27 continuous days. All animals in each photo were recorded as well as their behaviour, time of photo, and local density.
DOI: 10.25345/c5t43j707
title: MassIVE Reanalysis RMSV000000668.448 - CCMS ProteoCarta ModDecode reanalysis of Mus musculus from Mass spectrometry-based draft of the mouse proteome (Male_White_adipose_tissue_phosphoproteome) [launched by ab1ddc566e8244bd975da925e6cb9107]
title: CCMS ProteoCarta peptidoform interpretation (ModDecode) of Maestro open modification search results for Mus musculus (Male_White_adipose_tissue_phosphoproteome) from MSV000089856/PXD030983.
DOI: 10.5063/f1j38qzq
title: A set of Keyhole Markup Language polygons to describe site-level ecoregional differences in the plants and animals of Central California Deserts.

description: A set of Keyhole Markup Language (KML) polygons were generated to describe site-level ecological differences in plant and animal communities within California Deserts. All polygons were acquired and generated with Google Earth satellite.
DOI: 10.25345/c5t43j71q
title: MassIVE MSV000090582 - Charge-detection Mass Spectrometry on AAV8 and AAV2
title: In this dataset, AAV2 and AAV8 particles either with a CMV-GFP transgene or without were subjected to charge-detection mass spectrometry. Single ions can be analyzed for intact mass of each particle.
DOI: 10.25345/c5t43j726
title: MassIVE Reanalysis RMSV000000354.5888 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, RASSF8 [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/f1jm2831
title: Benthic invertebrates in Oneida Lake, New York, 1956 to present

description: This dataset contains benthic invertebrate data from Ekman grab samples on Oneida Lake 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://www.cbfs.dnr.cornell.edu) 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 1956 to the present. This dataset contains counts of benthic invertebrates sampled since 1956 at three to seven locations per year on Oneida Lake in central New York state. Samples were collected using an Ekman sampler, and invertebrates were handpicked from samples and identified, taxonomic level varies. The dataset is comprised of a primary table with a summary of the data available organized by taxonomic groups defined in the taxonomy table. Fields also include year, depth category (shallow versus deep sites) and season. A third table contains latitude and longitude in decimal degrees for each site as well as the classification of each site as shallow or deep sites. This is a companion data set to the book Oneida Lake: Long-term dynamics of a managed ecosystem and its fisheries, edited by LG Rudstam, EL Mills, JR Jackson and DJ Stewart and published by the American Fisheries Society, Bethesda, Maryland. It is updated annually.
DOI: 10.25345/c5t43j73p
title: MassIVE Reanalysis RMSV000000354.6272 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, DYNC2LI1 [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/c5t43j745
title: MassIVE Reanalysis RMSV000000354.6480 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, G3BP2 [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/f1jq0zgh
title: Designcraft for Experiments: Balcony Birdwatching

description: A set of remote exercises exploring experimental design for the life sciences. A total of three independent labs were done to focus on different design principles, sampling techniques, and taxa. Exercises are described in full in this open access manual entitled Designcraft for experiments. Data were collected by students in a third-year biology course offering at York University in Toronto, ON, Canada. Students collected the data and published individual datasets to figshare with a CCBY4.0 licensing. Data were then compiled for each lab including balcony birdwatching, backyard bioblitz, and solo surveys. The provenance of each independent observation in the compiled data was recognized by attribution to the initials of the primary data author including citation via DOI and link to figshare.AttributionCJL designed the experiments.Students in course offering collected, innovated, and published individual, primary datasets.MZ, NG and CJL reviewed the compiled data.MetadataRecord-levelyear is the calendar year of work not termexperiment describes the three experimental options in designcraft booksource is either full experiment or pilot experimentrep is the replicate per experimental setlocation is the site name locallyhabitat is the ecological classificationdate is the calendar date for each observation
DOI: 10.25345/c5t43j75n
title: MassIVE Reanalysis RMSV000000354.6660 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, RPL18 [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/f1jw8cbf
title: The effect of shrub density on animal abundance in Carrizo Plain National Monument

description: The following data was collected during the 2019 field season in the Carrizo Plain National Monument in Southern California, United States. 16 Cameras were deployed at varying shrub densities ranging from no shrub individuals to a high number of individuals (11-12 shrubs). These cameras were deployed in 2 of our major sites. Cameras were not rotated and were deployed for a total of 27 continuous days. All animals in each photo were recorded as well as their behaviour, time of photo, and local density.
DOI: 10.25345/c5t43j764
title: MassIVE Reanalysis RMSV000000354.6867 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, PRKAG1 [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/c5t43j77m
title: MassIVE Reanalysis RMSV000000354.7252 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, PDLIM3 [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/f1k072qm
title: Streambank Erodibility, Soil Physical Properties and Environmental Conditions for Streams within the North Carolina Piedmont Region

description: The dataset contains streambank erodibility parameters measured in-situ with the Jet Erosion Test with corresponding soil physical properties and environmental conditions for 27 streambanks distributed across 11 streams within the North Carolina Piedmont Region. Site explanatory variables include date, county, watershed, latitude, longitude, cross section id and JET number. The erodibility parameters consist of the critical boundary shear stress and the coefficient of erodibility. The soil physical properties include median grain size, coefficient of uniformity, coefficient of curvature, geometric standard deviation, percent passing the #200 sieve, percent clay, percent sand, and bulk density The environmental conditions include soil temperature, electrical conductivity, soil moisture content and water temperature. The purpose of this data is to highlight the variability of streambank erodibility parameters relative to soil physical properties and changing environmental conditions.
DOI: 10.25345/c5t43j783
title: MassIVE Reanalysis RMSV000000354.7638 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, SIRPG [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/c5t43j79k
title: MassIVE Reanalysis RMSV000000354.8025 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, SIRPD [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.