cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1342054.v2
title: Touch as techne: rethinking digitality

description: This article introduces <i>Pulse Project</i> (2011–), a doctoral performance research project that engages in critical discourse between art and science through the creation of digital soundscapes that weave together artistic, medical, technological, ancient and modern methodologies. Pulse ‘reading’, case histories, notations of pulses and programming soundscape compositions are all used together as methods for exploring the cultural encounter between artist, participants and diverse medical practices. <i>Pulse Project</i> seeks to provide an examination of the means with which the temporal materiality of touch can be used together with audio programming to form a translation and synthesis of different ecologies and disciplines, e.g. medicine and art, Eastern and Western practices, touch and digitality, etc. Drawing upon my experience as a clinical acupuncturist (with training in biomedicine), I use Chinese pulse diagnostics together with SuperCollider (an audio synthesis programming language) to inform the composition process of each soundscape. In this way, <i>Pulse Project</i> interrogates the aesthetic and philosophical axioms underpinning contemporary medicine, technology and cognitive embodiment through the exploration of their corollary ‘others’—traditional Chinese medicine and music theory—in order to generate a fresh approach to embodiment and soundscape composition.
DOI: 10.6084/m9.figshare.1342054.v1
title: Touch as techne: rethinking digitality

description: This article introduces <i>Pulse Project</i> (2011–), a doctoral performance research project that engages in critical discourse between art and science through the creation of digital soundscapes that weave together artistic, medical, technological, ancient and modern methodologies. Pulse ‘reading’, case histories, notations of pulses and programming soundscape compositions are all used together as methods for exploring the cultural encounter between artist, participants and diverse medical practices. <i>Pulse Project</i> seeks to provide an examination of the means with which the temporal materiality of touch can be used together with audio programming to form a translation and synthesis of different ecologies and disciplines, e.g. medicine and art, Eastern and Western practices, touch and digitality, etc. Drawing upon my experience as a clinical acupuncturist (with training in biomedicine), I use Chinese pulse diagnostics together with SuperCollider (an audio synthesis programming language) to inform the composition process of each soundscape. In this way, <i>Pulse Project</i> interrogates the aesthetic and philosophical axioms underpinning contemporary medicine, technology and cognitive embodiment through the exploration of their corollary ‘others’—traditional Chinese medicine and music theory—in order to generate a fresh approach to embodiment and soundscape composition.
DOI: 10.6084/m9.figshare.1342592.v2
title: Perceptual decision making EEG - subject 1

description: Participants decided on the direction of randomly moving dots. The events.mat file contains information about the behavior, while the other datafiles are the EEG time series, separately for each channel. See also the dataset containing the matlab scripts. Due to the size of the data, every subject becomes a new dataset.
DOI: 10.6084/m9.figshare.1342036.v1
title: Interoperability for Data Repositories. Metadata-based procedures for Retrieving Data for Display or Mining Utilising Persistent (data-DOI) Identifiers.

description: In the spirit of the Joint Declaration of Data Citation Principles, we present three flexible solutions for enabling machine-access to repository-based scientific data, given knowledge of the persistent identifier (DOI) of the dataset. Data from published chemical datasets will be retrieved by these methods for visualisation by clicking any of the buttons in the demonstrator.
DOI: 10.6084/m9.figshare.1341924
title: New Structures, 1890 Seattle

description: This project is a tabular version of the list of new buildings listed in the January 1, 1891 <em>Seattle Post-Intelligencer</em> from the previous year. My friend Curt Fischer and I cleaned up the Library of Congress' OCR of three pages and restructured it in a table. The transcription proejct is done. However, <strong>a future iteration</strong> of this table will include the current street names as well as addresses for known structures and wikipedia links for the major buildings that still exist today. The 1890 date is significant because of the number of buildings replaced by the 1889 Great Fire in downtown, as well as Seattle's continued suburban expansion. The pages are available for free on the Library of Congress Chronicling America site, after the Washington State Library completed a project to scan, OCR and post them. The OCR struggles with blurry 19th century type at times, though. I have links to the original text on my site ba-kground.com.
DOI: 10.6084/m9.figshare.1341967
title: ThetaW in 5Kb interval in Africa an Middle East and Zscores outliers in Africa and Middle East

description: ANGSD (Neilson et al. 2012) was used to calculate thetaW in 5kb window in Africa samples vs Middle East samples and outlier candidate selective regions were highlited using a Z-score statitics.
DOI: 10.6084/m9.figshare.1342026
title: Bophelo! Project January 2009 - October 2010

description: A large survey of over 10,000 individuals working in the Namibian formal sector from 2009 to 2010 including health behavior, risk assessment, demographic information, and biomedical assessment. The survey including the codes for results is part of the file set.
DOI: 10.6084/m9.figshare.1341967.v1
title: ThetaW in 5Kb interval in Africa an Middle East and Zscores outliers in Africa and Middle East

description: ANGSD (Neilson et al. 2012) was used to calculate thetaW in 5kb window in Africa samples vs Middle East samples and outlier candidate selective regions were highlited using a Z-score statitics.
DOI: 10.6084/m9.figshare.1341924.v2
title: New Structures, 1890 Seattle

description: This project is a tabular version of the list of new buildings listed in the January 1, 1891 <em>Seattle Post-Intelligencer</em> from the previous year. My friend Curt Fischer and I cleaned up the Library of Congress' OCR of three pages and restructured it in a table. The transcription proejct is done. However, <strong>a future iteration</strong> of this table will include the current street names as well as addresses for known structures and wikipedia links for the major buildings that still exist today. The 1890 date is significant because of the number of buildings replaced by the 1889 Great Fire in downtown, as well as Seattle's continued suburban expansion. The pages are available for free on the Library of Congress Chronicling America site, after the Washington State Library completed a project to scan, OCR and post them. The OCR struggles with blurry 19th century type at times, though. I have links to the original text on my site ba-kground.com.
DOI: 10.6084/m9.figshare.1342026.v4
title: Bophelo! Project January 2009 - October 2010

description: A large survey of over 10,000 individuals working in the Namibian formal sector from 2009 to 2010 including health behavior, risk assessment, demographic information, and biomedical assessment. The survey including the codes for results is part of the file set.
DOI: 10.6084/m9.figshare.1340978
title: MMP9 DATS MDA-MB-231

description: The effect of DATS on mRNA lever in MDA-MB-231 cell
DOI: 10.6084/m9.figshare.1340586
title: DADS MTT HS 578T

description: The effect of DADS on HS 578T cell
DOI: 10.6084/m9.figshare.1342026.v3
title: Bophelo! Project January 2009 - October 2010

description: A large survey of over 10,000 individuals working in the Namibian formal sector from 2009 to 2010 including health behavior, risk assessment, demographic information, and biomedical assessment. The survey including the codes for results is part of the file set.
DOI: 10.6084/m9.figshare.1340585
title: DATS HS 578T

description: The effect of DATS on HS 578T
DOI: 10.6084/m9.figshare.1340586.v1
title: DADS MTT HS 578T

description: The effect of DADS on HS 578T cell
DOI: 10.6084/m9.figshare.1340582
title: DAS HS 578T

description: The effect of DAS on HS 578T
DOI: 10.6084/m9.figshare.1340584
title: Luciferase reporter gene

description: The effect of DATS on MDA-MB-231 cell NF-KB Luciferase activity
DOI: 10.6084/m9.figshare.1340581
title: DADS HS 578T

description: The effect of DADS on HS 578T
DOI: 10.6084/m9.figshare.1340580
title: DATS MDA-MB-231 MTT

description: The effect of DATS on MDA-MB-231
DOI: 10.6084/m9.figshare.1340584.v1
title: Luciferase reporter gene

description: The effect of DATS on MDA-MB-231 cell NF-KB Luciferase activity
DOI: 10.6084/m9.figshare.1340576
title: DATS HS 578T MTT

description: The effect of DATS on HS 578T cell
DOI: 10.6084/m9.figshare.1340580.v1
title: DATS MDA-MB-231 MTT

description: The effect of DATS on MDA-MB-231
DOI: 10.6084/m9.figshare.1340581.v1
title: DADS HS 578T

description: The effect of DADS on HS 578T
DOI: 10.6084/m9.figshare.1340574
title: DAS MDA-MB-231 MTT

description: The effect of DAS on MDA-MB-231 cell
DOI: 10.6084/m9.figshare.1340576.v1
title: DATS HS 578T MTT

description: The effect of DATS on HS 578T cell
DOI: 10.6084/m9.figshare.1340978.v1
title: MMP9 DATS MDA-MB-231

description: The effect of DATS on mRNA lever in MDA-MB-231 cell
DOI: 10.6084/m9.figshare.1340570
title: DATS MMP PCR mRNA

description: The effect of DATS on mmp9 mRNA in MDA-MB-231 cell
DOI: 10.6084/m9.figshare.1340572
title: DADS MDA-MB-231 MTT

description: The effect of DADS on MDA-MB-231 cell
DOI: 10.6084/m9.figshare.1340477
title: wound healing DATS

description: Quantitative of wound healing experiments
DOI: 10.6084/m9.figshare.1340574.v1
title: DAS MDA-MB-231 MTT

description: The effect of DAS on MDA-MB-231 cell
DOI: 10.6084/m9.figshare.1340568
title: DATS MMP2 PCR

description: The effect of DATS on mmp2 mRNA in MDA-MB-231 cell
DOI: 10.6084/m9.figshare.1340572.v1
title: DADS MDA-MB-231 MTT

description: The effect of DADS on MDA-MB-231 cell
DOI: 10.6084/m9.figshare.1340469
title: migration DATS MDA-MB-231

description: The effect of DATS on migraion in MDA-MB-231 cell
DOI: 10.6084/m9.figshare.1340473
title: DATS mmp2/9 Enzyme activity

description: The effect of DATS on mmp2/9 Enzyme activity
DOI: 10.6084/m9.figshare.1340568.v1
title: DATS MMP2 PCR

description: The effect of DATS on mmp2 mRNA in MDA-MB-231 cell
DOI: 10.6084/m9.figshare.1340473.v1
title: DATS mmp2/9 Enzyme activity

description: The effect of DATS on mmp2/9 Enzyme activity
DOI: 10.6084/m9.figshare.1340570.v2
title: DATS MMP PCR mRNA

description: The effect of DATS on mmp9 mRNA in MDA-MB-231 cell
DOI: 10.6084/m9.figshare.1340468
title: migration HS 578T DATS

description: The effect of DATS on migration in HS 578T
DOI: 10.6084/m9.figshare.1340570.v1
title: DATS MMP PCR mRNA

description: The effect of DATS on mmp9 mRNA in MDA-MB-231 cell
DOI: 10.6084/m9.figshare.1340468.v1
title: migration HS 578T DATS

description: The effect of DATS on migration in HS 578T
DOI: 10.6084/m9.figshare.1340107
title: Northern royal albatross demography, JAGS model

description: Files necessary to run the Bayesian multi-state capture-recapture model to analyse the demography of northern royal albatross at Taiaroa Head, New Zealand. The model is used for the article at https://peerj.com/preprints/712/, submitted for peer-reviewed publication. The files consist of: - <strong>model.bug</strong> - the Bayesian multi-state capture-recapture model, written in the BUG language, - <strong>data.txt</strong> - Data, in R raw format (readable in R using the source function), -<strong> inits.txt</strong> - Initialisation values for the model, - <strong>jags.cmd</strong> - JAGS command file to run the model, containing the names of the parameters to monitor, and to specify the length of the burnin period and of the total number of iterations. To run the model, assuming that JAGS is installed, simply run "jags jags.cmd". The data consist of 11 objects: - <strong>age</strong>: matrix of 355 x 23 values being the age in years for all 355 individuals and 23 years. - <strong>atcol</strong>: matrix of 355 x 23 values, with 1 indicating that an individual was at the colony, 0 otherwise, in each of the 23 years. - <strong>bsucc</strong>: matrix of 355 x 23 values, with 2 if an individual produced a fledgling, 1 otherwise, for each of the 23 years. - <strong>firstcap:</strong> vector of 355 values, representing the first year each individual was seen during the studied period, with 1 being the start of the period (1988-89). - <strong>k.R</strong><strong></strong>: minimum recruitment age, single value. - <strong>k.B</strong>: minimum age at first reproduction, single value. - <strong>N</strong>: number of individuals, single value. - <strong>sex</strong>: vector of 355 values, containing the gender of each individual: 1 for female, 2 for male, NA for unknown. - <strong>state</strong>: matrix of 355 x 23 values, being the state of each individual each year: 1: breeding adult, 2: non-breeding adult, 3: pre-breeder, 4: juvenile, 5: dead, NA: unknown. - <strong>T</strong>: number of years considered in the dataset, single value. - <strong>Tstar</strong>: maximum individual age in the dataset, single value.
DOI: 10.6084/m9.figshare.1340107.v1
title: Files to run JAGS model

description: Files necessary to run the Bayesian multi-state capture-recapture model to analyse the demography of northern royal albatross at Taiaroa Head, New Zealand. The model is used for the article at https://peerj.com/preprints/712/, submitted for peer-reviewed publication. The files consist of: - <strong>model.bug</strong> - the Bayesian multi-state capture-recapture model, written in the BUG language, - <strong>data.txt</strong> - Data, in R raw format (readable in R using the source function), -<strong> inits.txt</strong> - Initialisation values for the model, - <strong>jags.cmd</strong> - JAGS command file to run the model, containing the names of the parameters to monitor, and to specify the length of the burnin period and of the total number of iterations. To run the model, assuming that JAGS is installed, simply run "jags jags.cmd".
DOI: 10.6084/m9.figshare.1340062
title: Research Data Spring project pitches

description: 3D data workflow RDM Administration Analytics Enabling complex analysis of large scale digital collections Develop a DataVault Filling the digital preservation gap Collaboration for Research Enhancement by Active Metadata Use semantic desktop to capture contextual research data Software re-use, repurposing and reproducibility Unlocking the UK’s thesis data through persistent identifiers Using Alfresco for management of research data An Intelligent Data Cleaning Software Tool for Research Data Giving researchers credit for their data Cloud Work Bench Open Source Database-as-a-Service with Data Publishing Pushing Database Wiki out of the nest DAF Case Bank Extending the Organisational Profile Document (OPD) to cover RDM Sound Matters: a framework for use and re-use of sound Standards MetaProject Distributed Knowledge Sharing Platform for RDM A consortial approach to building and integrated RDM system - "small and specialist" Project pitches for the following ideas:
DOI: 10.6084/m9.figshare.1340078.v1
title: Comprehensive Analysis of the Ubiquitinome during Oncogene-Induced Senescence in Human Fibroblasts

description: Oncogene-induced senescence (OIS) is an important tumor suppression mechanism preventing uncontrolled proliferation in response to aberrant oncogenic signalling. The profound functional and morphological remodelling of the senescent cell involves extensive changes. In particular, alterations in protein ubiquitination during senescence have not been systematically analysed previously. Here, we report the first global ubiquitination profile of primary human cells undergoing senescence. We employed a well-characterized <i>in vitro</i> model of OIS, primary human fibroblasts expressing oncogenic RAS. To compare the ubiquitinome of RAS-induced OIS and controls, ubiquitinated peptides were enriched by immune affinity purification and subjected to liquid chromatography tandem mass spectrometry (LC-MS/MS). We identified 4,472 ubiquitination sites, with 397 sites significantly changed (&gt; 3 standard deviations) in senescent cells. In addition, we performed mass spectrometry analysis of total proteins in OIS and control cells to account for parallel changes in both protein abundance and ubiquitin levels that did not affect the percentage of ubiquitination of a given protein. Pathway analysis revealed that the OIS-induced ubiquitinome alterations mainly affected three signalling networks: eIF2 signalling, eIF4/p70S6K signaling, and mTOR signalling. Interestingly, the majority of the changed ubiquitinated proteins in these pathways belong to the translation machinery. This includes several translation initiation factors (eIF2C2, eIF2B4, eIF3I, eIF3L, eIF4A1) and elongation factors (eEF1G, eEF1A) as well as 40S (RPS4X, RPS7, RPS11 and RPS20) and 60S ribosomal subunits (RPL10, RPL11, RPL18 and RPL35a). In addition, we observed enriched ubiquitination of aminoacyl-tRNA ligases (isoleucyl-, glutamine-, and tyrosine-tRNA ligase), which provide the amino acid-loaded tRNAs for protein synthesis. These results suggest that ubiquitination affects key components of the translation machinery to regulate protein synthesis during OIS. Our results thus point towards ubiquitination as a hitherto unappreciated regulatory mechanism during OIS.
DOI: 10.6084/m9.figshare.1340062.v1
title: Research Data Spring project pitches

description: 3D data workflow RDM Administration Analytics Enabling complex analysis of large scale digital collections Develop a DataVault Filling the digital preservation gap Collaboration for Research Enhancement by Active Metadata Use semantic desktop to capture contextual research data Software re-use, repurposing and reproducibility Unlocking the UK’s thesis data through persistent identifiers Using Alfresco for management of research data An Intelligent Data Cleaning Software Tool for Research Data Giving researchers credit for their data Cloud Work Bench Open Source Database-as-a-Service with Data Publishing Pushing Database Wiki out of the nest DAF Case Bank Extending the Organisational Profile Document (OPD) to cover RDM Sound Matters: a framework for use and re-use of sound Standards MetaProject Distributed Knowledge Sharing Platform for RDM A consortial approach to building and integrated RDM system - "small and specialist" Project pitches for the following ideas:
DOI: 10.6084/m9.figshare.1340023
title: RNAseq_dolores

description: RNAseq analysis of teosinte in late Holocene conditions
DOI: 10.6084/m9.figshare.1340078.v2
title: Comprehensive analysis of the ubiquitinome during oncogene-induced senescence in human fibroblasts

description: Oncogene-induced senescence (OIS) is an important tumor suppression mechanism preventing uncontrolled proliferation in response to aberrant oncogenic signaling. The profound functional and morphological remodelling of the senescent cell involves extensive changes. In particular, alterations in protein ubiquitination during senescence have not been systematically analyzed previously. Here, we report the first global ubiquitination profile of primary human cells undergoing senescence. We employed a well-characterized <i>in vitro</i> model of OIS, primary human fibroblasts expressing oncogenic RAS. To compare the ubiquitinome of RAS-induced OIS and controls, ubiquitinated peptides were enriched by immune affinity purification and subjected to liquid chromatography tandem mass spectrometry (LC-MS/MS). We identified 4,472 ubiquitination sites, with 397 sites significantly changed (&gt;3 standard deviations) in senescent cells. In addition, we performed mass spectrometry analysis of total proteins in OIS and control cells to account for parallel changes in both protein abundance and ubiquitin levels that did not affect the percentage of ubiquitination of a given protein. Pathway analysis revealed that the OIS-induced ubiquitinome alterations mainly affected 3 signaling networks: eIF2 signaling, eIF4/p70S6K signaling, and mTOR signaling. Interestingly, the majority of the changed ubiquitinated proteins in these pathways belong to the translation machinery. This includes several translation initiation factors (eIF2C2, eIF2B4, eIF3I, eIF3L, eIF4A1) and elongation factors (eEF1G, eEF1A) as well as 40S (RPS4X, RPS7, RPS11 and RPS20) and 60S ribosomal subunits (RPL10, RPL11, RPL18 and RPL35a). In addition, we observed enriched ubiquitination of aminoacyl-tRNA ligases (isoleucyl-, glutamine-, and tyrosine-tRNA ligase), which provide the amino acid-loaded tRNAs for protein synthesis. These results suggest that ubiquitination affects key components of the translation machinery to regulate protein synthesis during OIS. Our results thus point toward ubiquitination as a hitherto unappreciated regulatory mechanism during OIS.
DOI: 10.6084/m9.figshare.1340023.v1
title: RNAseq_dolores

description: RNAseq analysis of teosinte in late Holocene conditions
DOI: 10.6084/m9.figshare.1340020
title: Rationale and Implementation of a Bimodal Fitting Formula

description: Introduction<br>The effectiveness of cochlear implants has increased markedly over the past years. As a consequence, candidacy for implantation has been relaxed and more CI users have functionally useful contralateral hearing. Such bimodal users often report improved speech understanding, particularly in noisy situations, better tonal quality and improved lateralization of sound sources. The individual bimodal benefit, however, varies considerably. A potential reason for this is that conventional hearing aid fitting does not account for certain specific characteristics of bimodal listening. Of particular importance are: low-frequency audibility, spectral overlap of electric and acoustic stimulation, loudness balance, inter-aural tonotopy and (dynamic) synchronization of adaptive signal processing. While many of these requisites are highly individual and thus, may have to be addressed by individual fine-tuning, others might be accounted for, at least partially, by a prescriptive fitting formula specifically designed for bimodal listeners. Method<br>In order to improve the efficiency of bimodal fitting, a bimodal fitting formula is being developed that aims at accounting for the specific characteristics of bimodal listening. This formula can use any established fitting formula (e.g. DSL v5, NAL-RP) as a starting point. In the current implementation, Phonak’s proprietary formula (Adaptive Phonak Digital) is used. The importance of low-frequency audibility is addressed by maximizing effective audibility [1] based on the individual audiogram. Edge frequencies of Dead Regions can be either entered manually or are estimated automatically from the audiogram. As a second step, the static and dynamic behavior of the CI’s AGC has been approximated with the hearing aid’s compression system to account for loudness balance and dynamic synchronization between electric and acoustic hearing. This is accomplished by a special parameterization of channel-coupling, time constants, compression knee-points and compression ratios in the hearing aid. Results<br>Compared to conventional hearing fitting aid formulae, the novel bimodal fitting formula typically results in decreased gain at high frequencies and increased gain at low frequencies. Technical measurements using percentile analysis show that the dynamic behavior of the CI’s AGC can be approximated with the HA’s AGC nicely for speech signals. First results from studies using the bimodal fitting formula indicate that this formula can improve speech understanding in noise and provides a good starting point for individual fine-tuning.
DOI: 10.6084/m9.figshare.1340021
title: 2 Police Officers shot during Ferguson protest Co-Retweeted Network

description: The Co-Retweeted network of users tweeting about the two Ferguson police officers who were shot during a protest March 12, 2015.