cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25345/c53m2d
title: MassIVE MSV000084266 - TMT10 controlled mixtures - SILAC HeLa UPS1, acquired using MS2-only strategy
title: The controlled mixtures were prepared to evaluate the ability of our proposed approach when dealing with the complicated design, e.g. multiple TMT mixtures with technical replicates. 500, 333, 250, and 62.5 fmol UPS1 peptides were spiked-into 50 g SILAC HeLa peptides in duplicate. It produced a dilution series corresponding to 1, 0.667, 0.5, and 0.125 of the highest UPS1 peptide amount (500 fmol). In addition, a reference sample was generated by pooling all four diluted UPS1 peptide samples (286.5 fmol) and combined with 50 g of SILAC HeLa in duplicate. These 10 replicates were labeled with TMT10-plex reagents and mixed together to pass LC-MS/MS analysis. The procedure was repeated to generate a total of five such controlled mixtures. To assess technical variability, three technical replicates were prepared for each mixture. Totally there are 15 MS runs from 5 TMT mixtures. LC-MS/MS was performed using an EASY-nLC 1200 ultrahigh pressure liquid chromatography (UHPLC) connected to an Orbitrap Fusion Lumos Tribrid and equipped with an EASY-spray source (Thermo Fisher Scientific, San Jose, CA). The same samples for MSV000084264 (or PXD0015258) are used. The data were acquired using MS2-only strategies.
DOI: 10.25345/c5gt04
title: MassIVE MSV000084263 - A Triple Knockout (TKO) Proteomics Standard for Diagnosing Ion Interference in Isobaric Labeling Experiments
title: Isobaric labeling is a powerful strategy for quantitative mass spectrometry-based proteomic investigations. A complication of such analyses has been the co-isolation of multiple analytes of similar mass-to-charge resulting in the distortion of relative protein abundance measurements across samples. When properly implemented, triple-stage mass spectrometry and synchronous precursor selection (SPS-MS3) can reduce the occurrence of this phenomena, referred to as ion interference. However, no diagnostic tool is available currently to rapidly and accurately assess ion interference. To address this need, we developed a multiplexed TMT-based standard, termed the triple knockout (TKO). This standard is comprised of three yeast proteomes in triplicate, each from a strain deficient in a highly abundant protein (Met6, Pfk2, or Ura2). The relative abundance patterns of these proteins, which can be inferred from dozens of peptide measurements, are representative of ion interference in peptide quantification. We expect no signal in channels where the protein is knocked out, permitting maximum sensitivity for measurements of ion interference against a null background. Here, we emphasize the need to investigate further ion interference-generated ratio distortion and promote the TKO standard as a tool to investigate such issues. [dataset license: CC0 1.0 Universal (CC0 1.0)] Joao A. Paulo provided the raw file to Manuel Tzouros (Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, Switzerland)
DOI: 10.25739/x2wc-yj71
title: The relevance of dominance and functional annotations to predict agronomic traits in hybrid maize

description: Supporting data for analyses of hybrid panels in “The relevance of dominance and functional annotations to predict agronomic traits in hybrid maize” (bioRxiv: https://www.biorxiv.org/content/10.1101/745208v1). This study examined within-locus complementation and enrichment of genetic effects by functional classes in maize. We based our analyses on a diverse panel of inbred lines crossed with two testers representative of the major heterotic groups in the United States (1,106 hybrids), as well as a collection of 24 biparental populations crossed with a single tester (1,640 hybrids). We assayed these hybrids for more than 12 millions SNP markers, and evaluated them for three agronomic traits: days to silking, plant height and grain yield.
DOI: 10.25345/c5c08z
title: MassIVE MSV000084264 - TMT10 controlled mixtures - SILAC HeLa UPS1, acquired using SPS-MS3
title: The controlled mixtures were prepared to evaluate the ability of our proposed approach when dealing with the complicated design, e.g. multiple TMT mixtures with technical replicates. 500, 333, 250, and 62.5 fmol UPS1 peptides were spiked-into 50 g SILAC HeLa peptides in duplicate. It produced a dilution series corresponding to 1, 0.667, 0.5, and 0.125 of the highest UPS1 peptide amount (500 fmol). In addition, a reference sample was generated by pooling all four diluted UPS1 peptide samples (286.5 fmol) and combined with 50 g of SILAC HeLa in duplicate. These 10 replicates were labeled with TMT10-plex reagents and mixed together to pass LC-MS/MS analysis. The procedure was repeated to generate a total of five such controlled mixtures. To assess technical variability, three technical replicates were prepared for each mixture. Totally there are 15 MS runs from 5 TMT mixtures. LC-MS/MS was performed using an EASY-nLC 1200 ultrahigh pressure liquid chromatography (UHPLC) connected to an Orbitrap Fusion Lumos Tribrid and equipped with an EASY-spray source (Thermo Fisher Scientific, San Jose, CA). The data was acquired using an MS2/MS3 (also called multinotch MS3 or Synchronous Precursor Selection, SPS).
DOI: 10.5281/zenodo.3383005
title: Suansu 250 concepts wordlist

description: This dataset presents lexical data on Suansu (Glottocode: suan1234), a previously undocumented and unreported<br> Tibeto-Burman language spoken in North East India (25.4333° N, 94.5803° E). The datasheet comprises 250 lexical entries in Suansu (in broad IPA transcription) with English translation. The wordlist is based entirely on the Concepticon wordlist. Data is based on original fieldwork and it has been collected in Pune (Maharashtra, India), in November 2018. IPA transcription needs further stabilisation.<br> Data collector: Jessica Katiuscia Ivani (University of Kiel) The material in this file may be freely quoted, copied, or reproduced for non-commercial purposes. If used, a citation is required.
description: {"references": ["List, Johann Mattis & Greenhill, Simon & Rzymski, Christoph & Schweikhard, Nathanael & Forkel, Robert (eds.) 2019. Concepticon 2.1.0. Jena: Max Planck Institute for the Science of Human History."]}
DOI: 10.5281/zenodo.3383006
title: Suansu 250 concepts wordlist

description: This dataset presents lexical data on Suansu (Glottocode: suan1234), a previously undocumented and unreported<br> Tibeto-Burman language spoken in North East India (25.4333° N, 94.5803° E). The datasheet comprises 250 lexical entries in Suansu (in broad IPA transcription) with English translation. The wordlist is based entirely on the Concepticon wordlist. Data is based on original fieldwork and it has been collected in Pune (Maharashtra, India), in November 2018. IPA transcription needs further stabilisation.<br> Data collector: Jessica Katiuscia Ivani (University of Kiel) The material in this file may be freely quoted, copied, or reproduced for non-commercial purposes. If used, a citation is required.
description: {"references": ["List, Johann Mattis & Greenhill, Simon & Rzymski, Christoph & Schweikhard, Nathanael & Forkel, Robert (eds.) 2019. Concepticon 2.1.0. Jena: Max Planck Institute for the Science of Human History."]}
DOI: 10.17632/4hgvh5ngs4.1
title: Data for: Enhanced Dielectric Response and Thermal Conduction in Copper Nanoparticles Embedded Polyaniline Nanofibers

description: The file contains all the data related to experiments mentioned in the manuscript.
DOI: 10.25345/c5zt0g
title: MassIVE MSV000084267 - ClpX, activated by SSB, is required for DNA replication in Mycobacterium tuberculosis
title: The ClpP1P2 proteolytic complex is essential in Mycobacterium tuberculosis (Mtb). ClpP1P2 mediated proteolysis by ClpP1P2 requires an associated ATPase, either ClpX or ClpC1. Here, we seek to define the unique contributions of the ClpX ATPase to mycobacterial growth. We formally demonstrate that ClpX is essential for mycobacterial growth and to understand its essential functions, we identify ClpX-His-interacting proteins by pulldown and tandem mass spectrometry. We find an unexpected association between ClpX and proteins involved in DNA replication, and confirm a physical association between ClpX and the essential DNA maintenance protein Single-Stranded DNA Binding protein (SSB). Although pure SSB is not degraded by ClpXP1P2, it instead enhances ATPase hydrolysis by ClpX and degradation of the model substrate GFP-SsrA by ClpXP1P2. This activation of ClpX is mediated by the C-terminal tail of SSB that had previously been implicated in the activation of other ATPases associated with DNA replication. Consistent with the predicted interactions, depletion of ClpX perturbs DNA replication. These data reveal that ClpX serves a necessary function in DNA replication and identify the first activator of ClpX in mycobacteria.
DOI: 10.17632/kh837ypv2k.1
title: Data for: Correlative FLIM-Confocal-Raman mapping applied to plant lignin composition and autofluorescence.

description: These are the raw data in their original filetypes as follows: Lignin_LASX_Leica.lif = The confocal images showing lignin autofluorescence in the WT and lignin mutant. The data were created in Leica LAS X software and additionally contain all the metadata describing the imaging parameters. The .lif file can additionally be read in Fiji/ImageJ. Lignin_FLIM.sptw.zip = ZIP archive of the SymPhoTime 64 workspace containing all the FLIM data of the same regions as the above confocal images taken in LAS X. Can be read by SymPhoTime software (Picoquant). WT.wdf and cad2_6_mutant.wdf = Original Raman mapping data .wdf files taken on a Renishaw InVia Raman microscope using WiRE 4 software. The data have been baseline subtracted. There are two files - one of a map of WT, the other is the lignin mutant. FLIM_Raman_replicates = ZIP archive of the SymPhoTime 64 workspace containing FLIM biological replicates labelled WT1, WT2 and WT3 for WT and cad_1, cad_2 for mutant. Also contains associated original Raman data (as .wdf files) taken on a Renishaw InVia Raman microscope using WiRE 4 software. The data have been baseline subtracted. Note WT1 represents a FLIM dataset that was taken without associated Raman mapping as a control experiment for FLIM with no prior Raman illumination.
DOI: 10.17632/76ks3yn5w8.1
title: Data for: Modeling of PANDA Isolation Condenser experiments with MELCOR and Apros

description: MELCOR input of a PANDA Isolation Condenser experiment
DOI: 10.3886/e111663
title: Supporting You in Supporting Youth: National Online Survey for Transition Service Providers

description: The Supporting You in Supporting Youth (SYSY) survey was developed in collaborationwith Youth MOVE National to answer the research question, "What are the trainingneeds and preferences of service providers who serve young people with mental healthdifficulties?“ The survey was also used to explore preferred training modalities, tounderstand the major barriers to participating in training, and to gain findings to guidedevelopment of training resources to improve supports to young people. It includes 22items that are demographic questions and quantitative rating scales to collect serviceproviders’ views on (a) the importance of and their personal need for, training inspecific competencies and skills; (b) barriers to their accessing training; and, (c) theirpreferences for specific training modalities. The survey was implemented as a cross-sectional online survey conducted from June 23-July 24, 2017.
description: Response Rates: 100%
description: web-based survey~~
description: Service providers who serve young people with mental healthdifficultiesSmallest Geographic Unit: State
description: Convenience sampling. <br><br>See publication for full sampling description.:<br>Jivanjee, P., Grover, L., Thorp, K., Masselli, B., Bergan, J., & Brennan, E. M. (2019).Training needs of peer and non-peer transition service providers: Results of a nationalsurvey. Journal of Behavioral Health Services & Research. Available online: https://doi-org.proxy.lib.pdx.edu/10.1007/s11414-019-09667-3
DOI: 10.3886/e111663v1
title: Supporting You in Supporting Youth: National Online Survey for Transition Service Providers

description: The Supporting You in Supporting Youth (SYSY) survey was developed in collaborationwith Youth MOVE National to answer the research question, "What are the trainingneeds and preferences of service providers who serve young people with mental healthdifficulties?“ The survey was also used to explore preferred training modalities, tounderstand the major barriers to participating in training, and to gain findings to guidedevelopment of training resources to improve supports to young people. It includes 22items that are demographic questions and quantitative rating scales to collect serviceproviders’ views on (a) the importance of and their personal need for, training inspecific competencies and skills; (b) barriers to their accessing training; and, (c) theirpreferences for specific training modalities. The survey was implemented as a cross-sectional online survey conducted from June 23-July 24, 2017.
description: Response Rates: 100%
description: web-based survey~~
description: Service providers who serve young people with mental healthdifficultiesSmallest Geographic Unit: State
description: Convenience sampling. <br><br>See publication for full sampling description.:<br>Jivanjee, P., Grover, L., Thorp, K., Masselli, B., Bergan, J., & Brennan, E. M. (2019).Training needs of peer and non-peer transition service providers: Results of a nationalsurvey. Journal of Behavioral Health Services & Research. Available online: https://doi-org.proxy.lib.pdx.edu/10.1007/s11414-019-09667-3
DOI: 10.3886/e111567
title: Implementation of the SunSmart program and population sun protection behaviour in Melbourne Australia

description: Cancer Council Victoria's Sun Protection Survey (SPS) has provided comprehensive data to assess the prevalence of sun-related knowledge, attitudes, behaviours and sunburn among the population in Victoria since 1987. These data have been used to inform and evaluate the implementation of SunSmart, the long-running skin cancer prevention program in Victoria. The surveys were conducted on behalf on Cancer Council Australia as part of a larger national survey in the later years (2003-2017). Essentially equivalent methods were used across all survey years. The methods described here pertain to the data prepared for a manuscript entitled "Implementation of the SunSmart program and population sun protection behaviour in Melbourne Australia". The study used a cross-sectional (observational) design, recruiting on a weekly basis a representative sample of Victorian adolescents (14-17 years) and adults (18-69 years) to telephone interviews during the summer months. Survey data for 14 summers between 1987 and 2017 are available for analysis. The detailed measures focus on respondents' activities, behaviour and sunburn on the weekend or public holiday prior to the respondents' interview. Interviews were held within two to four days of the reported behaviour to minimise recall bias. The behavioural measures which focused on a specific time and location enabled linkage with weather and UV records for Melbourne on the dates relevant to the respondents' reported behaviour. The specific data appended were: (i) the 3pm temperature and mean UV Index between 11am-3pm (DST) for the weekend date; and (ii) the number of days of rainfall (1mm or more), number of days of heavy cloud cover (6 oktas or more), and median 3pm temperature over the past month.
description: Population-based weights based on the estimated resident population of Melbourne by age and sex.
description: telephone interview~~
description: Quotas were used to ensure the sample was proportional to the population by age and sex, while younger respondents were oversampled in some years.
DOI: 10.3886/e111567v2
title: Implementation of the SunSmart program and population sun protection behaviour in Melbourne Australia

description: Cancer Council Victoria's Sun Protection Survey (SPS) has provided comprehensive data to assess the prevalence of sun-related knowledge, attitudes, behaviours and sunburn among the population in Victoria since 1987. These data have been used to inform and evaluate the implementation of SunSmart, the long-running skin cancer prevention program in Victoria. The surveys were conducted on behalf on Cancer Council Australia as part of a larger national survey in the later years (2003-2017). Essentially equivalent methods were used across all survey years. The methods described here pertain to the data prepared for a manuscript entitled "Implementation of the SunSmart program and population sun protection behaviour in Melbourne Australia". The study used a cross-sectional (observational) design, recruiting on a weekly basis a representative sample of Victorian adolescents (14-17 years) and adults (18-69 years) to telephone interviews during the summer months. Survey data for 14 summers between 1987 and 2017 are available for analysis. The detailed measures focus on respondents' activities, behaviour and sunburn on the weekend or public holiday prior to the respondents' interview. Interviews were held within two to four days of the reported behaviour to minimise recall bias. The behavioural measures which focused on a specific time and location enabled linkage with weather and UV records for Melbourne on the dates relevant to the respondents' reported behaviour. The specific data appended were: (i) the 3pm temperature and mean UV Index between 11am-3pm (DST) for the weekend date; and (ii) the number of days of rainfall (1mm or more), number of days of heavy cloud cover (6 oktas or more), and median 3pm temperature over the past month.
description: Population-based weights based on the estimated resident population of Melbourne by age and sex.
description: telephone interview~~
description: Quotas were used to ensure the sample was proportional to the population by age and sex, while younger respondents were oversampled in some years.
DOI: 10.21227/305k-cy43
title: Analytic Geomagnetic and Geoelectric Fields

description: Geomagnetic field variations produce geoelectric fields that can affect the operation of technological networks at the Earth’s surface, including power systems, pipelines, phone cables and railway circuits. To assess the geomagnetic hazard to this technology, it is necessary to model the geomagnetically induced currents (GIC) produced in these systems during geomagnetic disturbances. This requires use of geomagnetic data with appropriate Earth conductivity models to calculate the geoelectric fields that drive GIC. To provide a way of testing geoelectric field calculation software, we provide a benchmark test case by defining a synthetic geomagnetic field variation and deriving exact analytic expressions for the Earth response based on both uniform and layered Earth conductivity models. These are then used to provide exact analytic expressions for the geoelectric fields that would be produced by the synthetic geomagnetic field variation. The synthetic geomagnetic data can be used as input to numerical geoelectric field calculation software, the output of which can be tested by comparison with the analytically-generated geoelectric fields.
DOI: 10.21227/gnev-dd52
title: Analytic Geomagnetic and Geoelectric Fields

description: Geomagnetic field variations produce geoelectric fields that can affect the operation of technological networks at the Earth’s surface, including power systems, pipelines, phone cables and railway circuits. To assess the geomagnetic hazard to this technology, it is necessary to model the geomagnetically induced currents (GIC) produced in these systems during geomagnetic disturbances. This requires use of geomagnetic data with appropriate Earth conductivity models to calculate the geoelectric fields that drive GIC. To provide a way of testing geoelectric field calculation software, we provide a benchmark test case by defining a synthetic geomagnetic field variation and deriving exact analytic expressions for the Earth response based on both uniform and layered Earth conductivity models. These are then used to provide exact analytic expressions for the geoelectric fields that would be produced by the synthetic geomagnetic field variation. The synthetic geomagnetic data can be used as input to numerical geoelectric field calculation software, the output of which can be tested by comparison with the analytically-generated geoelectric fields.
DOI: 10.25345/c57949
title: MassIVE MSV000084265 - Reproducible Workflow for Multiplexed Deep-Scale Proteome and Phosphoproteome Analysis of Tumor Tissues by Liquid Chromatography-Mass Spectrometry
title: &lt;p&gt;Mertins P, Tang LC, Krug K, Clark DJ, Gritsenko MA, Chen L, Clauser KR, Clauss TR, Shah P, Gillette MA, et al., &lt;a href='https://www.nature.com/articles/s41596-018-0006-9' target='_blank'&gt;Nat Protoc. 2018 Jul 9. doi: 10.1038/s41596-018-0006-9&lt;/a&gt;&lt;/p&gt;&lt;p&gt;Here we present an optimized workflow for global proteome and phosphoproteome analysis of tissues or cell lines that uses isobaric tags (TMT (tandem mass tags)10) for multiplexed analysis and relative quantification, and provides 3x higher throughput than iTRAQ (isobaric tags for absolute and relative quantification)-4-based methods with high intra and inter-laboratory reproducibility. The workflow was systematically characterized and benchmarked across three independent laboratories using two distinct breast cancer subtypes from patient-derived xenograft models to enable assessment of proteome and phosphoproteome depth and quantitative reproducibility. Each plex consisted of ten samples, each being 300 ug of peptide derived from &lt;50 mg of wet-weight tissue. Of the 10,000 proteins quantified per sample, we could distinguish 7,700 human proteins derived from tumor cells and 3100 mouse proteins derived from the surrounding stroma and blood. The maximum deviation across replicates and laboratories was &lt;7%, and the inter-laboratory correlation for TMT ratio-based comparison of the two breast cancer subtypes was r &gt; 0.88. The maximum deviation for the phosphoproteome coverage was &lt;24% across laboratories, with an average of &gt;37,000 quantified phosphosites per sample and differential quantification correlations of r &gt; 0.72. The full procedure, including sample processing and data generation, can be completed within 10 d for ten tissue samples, and 100 samples can be analyzed in ~4 months using a single LC-MS/MS instrument. The high quality, depth, and reproducibility of the data obtained both within and across laboratories should enable new biological insights to be obtained from mass spectrometry-based proteomics analyses of cells and tissues together with proteogenomic data integration.&lt;/p&gt; &lt;ul&gt;&lt;li&gt;Dataset imported into MassIVE from &lt;a href="https://cptac-data-portal.georgetown.edu/cptac/s/S036"&gt;https://cptac-data-portal.georgetown.edu/cptac/s/S036&lt;/a&gt; on 08/30/19&lt;/li&gt;&lt;/ul&gt;