cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5552656
title: Variability measures for clinical trials at baseline and at the end of study

description: Data from 208 parallel clinical trials with quantitative outcome published in years 2004, 2007, 2010 and 2013. The main collected variables are: title; link to PubMed abstract; type of outcome (measured or scored); type of intervention (pharmacological or not); type of measure (automatic or assessed); if the main endpoint was significant; the standard deviations of the main outcome in both arms at the baseline and at the end of the study.<br>
DOI: 10.6084/m9.figshare.5552602
title: Bayesian Multivariate Distributional Regression With Skewed Responses and Skewed Random Effects

description: The normal and the <i>t</i> distribution are classical tools for building random effects regression models where both can be used for the specification of either the conditional response distribution or the random effects distribution. However, the underlying assumption of symmetry can be questionable in many applications. We, therefore, propose regression models where the skew-normal and skew-<i>t</i> distribution are considered for both the response and the random effects specification and embed these models in the framework of distributional regression such that regression predictors can be specified for all distributional parameters. The distributional regression framework also allows us to consider multivariate versions of the skew-normal and the skew-<i>t</i> distribution. For Bayesian inference, we adapt iteratively weighted least-square proposals within Markov chain Monte Carlo simulations such that they can also facilitate the inclusion of nonnormal random effects specifications. Model choice is based on the Watanabe–Akaike information criterion, in particular, to differentiate between skew and nonskew distributional specifications in a number of simulation studies. Finally, to illustrate their practical applicability, the developed models are applied to a study on cholesterol levels originating from the Framingham Heart Study and a dataset from the Demographic and Health Surveys on undernutrition among children in Nigeria. Supplementary material for this article is available online.
DOI: 10.6084/m9.figshare.5552602.v1
title: Bayesian Multivariate Distributional Regression with Skewed Responses and Skewed Random Effects

description: The normal and the t distribution are classical tools for building random effects regression models where both can be used for the specification of either the conditional response distribution or the random effects distribution. However, the underlying assumption of symmetry can be questionable in many applications. We, therefore, propose regression models where the skew-normal and skew-t distribution are considered for both the response and the random effects specification and embed these models in the framework of distributional regression such that regression predictors can be specified for all distributional parameters. The distributional regression framework also allows us to consider multivariate versions of the skew-normal and the skew-t distribution. For Bayesian inference, we adapt iteratively weighted least squares proposals within Markov chain Monte Carlo simulations such that they can also facilitate the inclusion of non-normal random effects specifications. Model choice is based on the Watanabe-Akaike information criterion, in particular, to differentiate between skew and non-skew distributional specifications in a number of simulation studies. Finally, to illustrate their practical applicability, the developed models are applied to a study on cholesterol levels originating from the Framingham Heart Study and a dataset from the Demographic and Health Surveys on undernutrition among children in Nigeria.
DOI: 10.6084/m9.figshare.5552596
title: Least Ambiguous Set-Valued Classifiers With Bounded Error Levels

description: In most classification tasks, there are observations that are ambiguous and therefore difficult to correctly label. Set-valued classifiers output sets of plausible labels rather than a single label, thereby giving a more appropriate and informative treatment to the labeling of ambiguous instances. We introduce a framework for multiclass set-valued classification, where the classifiers guarantee user-defined levels of coverage or confidence (the probability that the true label is contained in the set) while minimizing the ambiguity (the expected size of the output). We first derive oracle classifiers assuming the true distribution to be known. We show that the oracle classifiers are obtained from level sets of the functions that define the conditional probability of each class. Then we develop estimators with good asymptotic and finite sample properties. The proposed estimators build on existing single-label classifiers. The optimal classifier can sometimes output the empty set, but we provide two solutions to fix this issue that are suitable for various practical needs. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.5552584
title: GC-FID data of biocatalytic esterification reactions & NMR data of lignin characterization

description: Tabulated chromatographic data (GC-FID) from butyl butyrate esterification reactions. 13C and 31P NMR data from pine kraft lignin (BIOPIVA 100) and cationic pine kraft lignin. A list of sample code identifiers with their descriptions is available upon request from the author.<br>
DOI: 10.6084/m9.figshare.5552596.v2
title: Least Ambiguous Set-Valued Classifiers With Bounded Error Levels

description: In most classification tasks, there are observations that are ambiguous and therefore difficult to correctly label. Set-valued classifiers output sets of plausible labels rather than a single label, thereby giving a more appropriate and informative treatment to the labeling of ambiguous instances. We introduce a framework for multiclass set-valued classification, where the classifiers guarantee user-defined levels of coverage or confidence (the probability that the true label is contained in the set) while minimizing the ambiguity (the expected size of the output). We first derive oracle classifiers assuming the true distribution to be known. We show that the oracle classifiers are obtained from level sets of the functions that define the conditional probability of each class. Then we develop estimators with good asymptotic and finite sample properties. The proposed estimators build on existing single-label classifiers. The optimal classifier can sometimes output the empty set, but we provide two solutions to fix this issue that are suitable for various practical needs. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.5552596.v1
title: Least Ambiguous Set-Valued Classifiers with Bounded Error Levels

description: In most classification tasks there are observations that are ambiguous and therefore difficult to correctly label. Set-valued classifiers output sets of plausible labels rather than a single label, thereby giving a more appropriate and informative treatment to the labeling of ambiguous instances. We introduce a framework for multiclass set-valued classification, where the classifiers guarantee user-defined levels of coverage or confidence (the probability that the true label is contained in the set) while minimizing the ambiguity (the expected size of the output). We first derive oracle classifiers assuming the true distribution to be known. We show that the oracle classifiers are obtained from level sets of the functions that define the conditional probability of each class. Then we develop estimators with good asymptotic and finite sample properties. The proposed estimators build on existing single-label classifiers. The optimal classifier can sometimes output the empty set, but we provide two solutions to fix this issue that are suitable for various practical needs.
DOI: 10.6084/m9.figshare.5552479
title: Simulations of two-state smFRET dynamics

description: Simulations of single molecule FRET on freely 3D diffusing molecules, with two different FRET values and with intrinsic transition dynamics.
DOI: 10.6084/m9.figshare.5552434
title: Supplemental data file 1.xls

description: Dataset of study as published in Molecular Oncology
DOI: 10.6084/m9.figshare.5552434.v1
title: Supplemental data file 1.xls

description: Dataset of study as published in Molecular Oncology
DOI: 10.6084/m9.figshare.5552479.v3
title: Simulations of two-state smFRET dynamics

description: Simulations of single molecule FRET on freely 3D diffusing molecules, with two different FRET values and with intrinsic transition dynamics.
DOI: 10.6084/m9.figshare.5550331
title: Relación migración, religión, educación

description: Relación migración, religión, educación in Latin America
DOI: 10.6084/m9.figshare.5551585
title: Mikado v1.0.1

description: Version 1.0.1 of Mikado, used for the analyses in the paper.<br>
DOI: 10.6084/m9.figshare.5552479.v2
title: Simulation Results

description: Simulations of single molecule FRET on freely 3D diffusing molecules, with two different FRET values and with intrinsic transition dynamics.
DOI: 10.6084/m9.figshare.5550319
title: Source data for "Single excitatory axons form clustered synapses onto CA1 pyramidal cell dendrites" by Bloss, Cembrowski, Karsh, Colonell, Fetter, and Spruston (2018).

description: These are the raw data from Bloss et al. (2018) titled "Single excitatory axons from clustered synapses onto CA1 pyramidal cell dendrites." <br>For the raw data, each sheet within the Excel file corresponds to a Figure or Supplementary Figure.
DOI: 10.6084/m9.figshare.5550319.v1
title: Source data for "Single excitatory axons form clustered synapses onto CA1 pyramidal cell dendrites" by Bloss, Cembrowski, Karsh, Colonell, Fetter, and Spruston (2018).

description: These are the raw data from Bloss et al. (2018) titled "Single excitatory axons from clustered synapses onto CA1 pyramidal cell dendrites." <br>For the raw data, each sheet within the Excel file corresponds to a Figure or Supplementary Figure.
DOI: 10.6084/m9.figshare.5551585.v1
title: Mikado v1.0.1

description: Version 1.0.1 of Mikado, used for the analyses in the paper.<br>
DOI: 10.6084/m9.figshare.5550298
title: Nexus File of Phylogenetic Matrix from A new rhynchocephalian (Reptilia: Lepidosauria) from the Late Jurassic of Solnhofen (Germany) and the origin of the marine Pleurosauridae

description: Nexus File of Character Matrix Used in Assessing the Phylogenetic Relationships of Vadasaurus herzogi
DOI: 10.6084/m9.figshare.5550217
title: Hundred nanosecond molecular dynamics simulation of the G domain of K-Ras4B

description: This is a one hundred nanosecond simulation of the G domain of K-Ras4B (UNIPROT:P01116-2, residues 1-166). The simulation was generated using GROMACS v.4.6.5 with the AMBER99SB-ILDN forcefield (altered following doi:10.1002/jcc.10262, see References), TIP3P water and 0.15 M salt. The leap-frog integrator with 2 fs timestep was used. A v-rescale thermostat was used at 310 K, with two energy groups (protein+GTP+MG and water+salt) and a time constant of 0.1 ps. PME was used with a tolerance of 1e-5 for the coulomb interactions and a cutoff was used for the VdW interactions, both with a cutoff of 1.1 nm. A Parrinello-rahman barostat was applied with a reference pressure of 1 bar and a time constant of 1 ps. For more information take a look at md.mdp. Coordinates were saved every 1 nanosecond and waters were stripped, resulting in a trajectory of 101 snapshots. <br>The initial model was made using the G-domain of GppNHp bound H-Ras (PDB ID: 4EFL). The protein was converted using MODELLER v9.16(doi:10.1002/cpbi.3 , see References) and GppNHp was converted to GTP by hand.<br><br><br>
DOI: 10.6084/m9.figshare.5550175
title: Raw data used for 3D printing

description: We use these data in paper "A Frame of 3D Printing Data Generation Method Extracted from CT Data".<br>
DOI: 10.6084/m9.figshare.5550298.v1
title: Nexus File of Phylogenetic Matrix from A new rhynchocephalian (Reptilia: Lepidosauria) from the Late Jurassic of Solnhofen (Germany) and the origin of the marine Pleurosauridae

description: Nexus File of Character Matrix Used in Assessing the Phylogenetic Relationships of Vadasaurus herzogi
DOI: 10.6084/m9.figshare.5550217.v1
title: Hundred nanosecond molecular dynamics simulation of the G domain of K-Ras4B

description: This is a one hundred nanosecond simulation of the G domain of K-Ras4B (UNIPROT:P01116-2, residues 1-166). The simulation was generated using GROMACS v.4.6.5 with the AMBER99SB-ILDN forcefield (altered following doi:10.1002/jcc.10262, see References), TIP3P water and 0.15 M salt. The leap-frog integrator with 2 fs timestep was used. A v-rescale thermostat was used at 310 K, with two energy groups (protein+GTP+MG and water+salt) and a time constant of 0.1 ps. PME was used with a tolerance of 1e-5 for the coulomb interactions and a cutoff was used for the VdW interactions, both with a cutoff of 1.1 nm. A Parrinello-rahman barostat was applied with a reference pressure of 1 bar and a time constant of 1 ps. For more information take a look at md.mdp. Coordinates were saved every 1 nanosecond and waters were stripped, resulting in a trajectory of 101 snapshots. <br>The initial model was made using the G-domain of GppNHp bound H-Ras (PDB ID: 4EFL). The protein was converted using MODELLER v9.16(doi:10.1002/cpbi.3 , see References) and GppNHp was converted to GTP by hand.<br><br><br>
DOI: 10.4225/03/59f7341c81c5d
title: Black Tide

description: <sub>For trumpet and electronics.</sub><br>For Callum G'Froerer<br>Featuring prepared Biwa by Mitsuaki Matsumoto<br><br>Premiered at the 'Phenomena' program, Totally Huge New Music Festival, October 28, 2017, Perth Town Hall.<br>Also: 'The Relighting of the Sun' program, November 2, 2017 Abbotsford Convent, Melbourne, Australiia<br>Unerhörte Musik, Berlin. February 27, 2018.<br>​Die Skulptierte Trompete: PROGR Bern (Aula) (Waisenhausplatz 30 3011 Bern)<br>This work is part of a series of works for instrument and sub tones, but expands the idea of the subtone by adding additional concrete sounds. It reflects on the impact of the earthquake and subsequent tidal wave in Japan that occurred on the composer’s birthday in 2011. On a trip to Tokyo soon after the event, there was a lot of talk about water: radioactive water and a poisoned sea. As an island, lakes suddenly become more precious. This piece takes inspiration from water – depth, texture, reflection and the tension of it’s surface. The notation is this piece is derived from maps of Lake Biwa in Japan, and he electronics part features a Biwa, a traditional Japanese instrument, modified, prepared and amplified (performed by Mitsuaki Matsumoto) in addition to subtones.<br><br><strong>Performance Notes</strong><br>Each colour represents a different bell of the trumpet.<br>Green is the added bell, red is the original bell. All notes are subtones – except when the line is opaque, which represents breath only. A solid line is a single, unwavering sub tone. Orange means breathe in. The dynamic is never above medium soft.<br>Fine line under the colour indicates a mute, as marked.<br>Crosses mean tap superball stick on the bell, dots are tongue rams.<br>The electronics part is indicated in opaque pink, and plays through the ScorePlayer. This should be routed left channel to sub woofer, right channel to a single, normal range speaker. The part is provided as a erough guide for the performer only. There is a long tail of audio at the end, which should slowly fade out to end the piece.<br> <br>To perform this work, need to download the iPad app, the Decibel ScorePlayer which has many more features for performance. You can download the file for the player here. It has the audio part embedded in it, you will need to run mini jack out of the iPad into a sub woofer directly. You can also play the score from the video file, available from the composer. A digital or hard copy of the score is available from Material Press.<br><br>The work was also discussed in a paper by Dan O'Connor and Lindsay Vickery as part of the 2018 TENOR conference, available here. <br><br><br>
DOI: 10.25375/uct.5549944
title: Raw data_Geographic call variation in Rhinolphus clivosus.xlsx

description: The file provides data on the forearm length and resting frequency echolocation calls of individuals bats used in the analyses of the paper titled "Testing the Sensory Drive Hypothesis: geographic variation in echolocation frequencies of Geoffroy's horseshoe bat (Rhinolophidae: <i>Rhinolophus clivosus</i>)" published in Plos One in 2017.
DOI: 10.6084/m9.figshare.5549932
title: R code for the paper entitled "Accessibility maps as a tool to predict sampling bias in historical biodiversity occurrence records"

description: This file contains the R code for the analyses in the paper entitled "Accessibility maps as a tool to predict sampling bias in historical biodiversity occurrence records", by S. Monsarrat, A. Boshoff and G. Kerley
DOI: 10.6084/m9.figshare.5549917
title: Mapping of reads to genomes - (Item I)

description: <b>Additional Information to Figure 4: Coverage of bacterial i) reference genomes and ii) isolates by metagenomic reads from vitreous of endophthalmitis patients.</b> For each individual patient, the metagenomic shotgun reads for the most abundant microbial organism were extracted and mapped to the respective reference genome sequence in the database. For patients C1 and I7 a microbial organism could not be assigned confidently, and these patients are regarded as “sterile” endophthalmitis cases. <br>In the two cases where metagenomics analysis and culture results from the hospital were not identical (patients C5 and I3), we examined the reads for all organisms detected in the metagenomics analysis.<br>For the patients for which isolates were obtained and WGS generated, we mapped the respective metagenomic shotgun reads to these assemblies.<br>The most outer circle displays the genome sequence (including scaffolds and contigs). The orange and blue inner circles display the depth of mapped reads originating from the samples that were extracted with the QIA and UCP DNA extraction methods, respectively.<br><br><b>Reference</b> <b>Kirstahler P, Bjerrum SS, Friis-Møller A, </b><b>la Cour M, Aarestrup FM, Westh H., and Pamp SJ. (2018) </b>Genomics-Based Identification of Microorganisms in Human Ocular Body Fluid.<b> </b><b>Scientific Reports</b>, doi:10.1038/s41598-018-22416-4.
DOI: 10.6084/m9.figshare.5549905
title: DM-MSC

description: Effect of MSC treatment, serum insulin levels, of three experimental groups of BALB/C mice: the control group (healthy animals), the TIDM group (animals with induced diabetes) and the hAD-MSCs group (animals treated with hAD-MSC). Weight and blood glucose levels. Pancreatic histology tissue showed a reduction in the size of Langerhans islets, peroxidase immunohistochemistry for count of islets of Langerhans.
DOI: 10.6084/m9.figshare.5549932.v2
title: R code for the paper entitled "Accessibility maps as a tool to predict sampling bias in historical biodiversity occurrence records"

description: This file contains the R code for the analyses in the paper entitled "Accessibility maps as a tool to predict sampling bias in historical biodiversity occurrence records", by S. Monsarrat, A. Boshoff and G. Kerley
DOI: 10.6084/m9.figshare.5549905.v1
title: DM-MSC

description: Effect of MSC treatment, serum insulin levels, of three experimental groups of BALB/C mice: the control group (healthy animals), the TIDM group (animals with induced diabetes) and the hAD-MSCs group (animals treated with hAD-MSC). Weight and blood glucose levels. Pancreatic histology tissue showed a reduction in the size of Langerhans islets, peroxidase immunohistochemistry for count of islets of Langerhans.
DOI: 10.6084/m9.figshare.5549932.v1
title: R code for the paper entitled "Accessibility maps as a tool to predict sampling bias in historical biodiversity occurrence records"

description: This file contains the R code for the analyses in the paper entitled "Accessibility maps as a tool to predict sampling bias in historical biodiversity occurrence records", by S. Monsarrat, A. Boshoff and G. Kerley
DOI: 10.21954/ou.rd.5549818
title: Digital Brain Switch project - pilot study

description: READ_ME_DigitalBrainSwitch_PilotStudy.txt<br>Digital Brain Switch (DBS; May 2013 – August 2015) was a project funded by the Engineering and Physical Sciences Research Council (EPSRC), which brought together computer science and social science. It was a collaboration between Lancaster University; The Open University; Royal Holloway, University of London; and University of Kent.<br>Data originates from a two year project examining the implications of digital technologies for work-life boundary management. Sample were 15 university students, 15 social entrepreneurs and 15 office workers across a range of institutions, organisations and contexts. Participants were recruited from a targeted invitation and all participated on a voluntary basis. Data consist of 45 week long video diaries consisting of instances of role transitions, textual transcription of simultaneous commentary and textual transcription of debriefing sessions. Additionally 45 hour long interview recordings and textual transcripts of further discussions of work-life issues, specifically work-life boundaries, work-life transitions and the effects of keeping video diaries. <br><br>Data were collected through hand held video cameras and recorded semi-structured interviews<br>Dataset contains sensitive personal information - restricted to project team only<br>This data set contains the pilot study's research data, in the following file 'DBS Pilot Study.zip', which contains the following data:<br>1. Consent Forms 2. Debrief interviews3. Pilot Participant Information pack4. Pilot Study Ethics5. Pilot video data6. DBS Pilot study data.nvp7. Pilot Data Analysis - thematic coding.pdf8. 'READ_ME_DigitalBrainSwitch_PilotStudy.txt' - a text file containing this description.<br><br>The project's research data is also archived on figshare at: 10.21954/ou.rd.5531911Supporting data is also archived on figshare at: 10.21954/ou.rd.5554840<br>Data record in Open Research Online: http://oro.open.ac.uk/46687/Project website: http://www.scc.lancs.ac.uk/research/projects/DBS/
DOI: 10.6084/m9.figshare.5549812
title: TW_1185_g_egg_60x

description: Original image stacks of Eocene Baltic amber inclusions, the type series for <br><br>Acari: Trombidiformes: Eleutherengona: Myobiidae: <br><br>Prohylomysobia erinaceophilus Sidorchuk and Bochkov in <br><br>Sidorchuk et al. 2017 Journal of Systematic Paleontology. In <br><br>Baltic amber piece, originally from the private collection of <br><br>Thomas Weiterchan, coll. # 1185 (TW 1185), housed by GPIH, <br><br>collection number 4597. Specimen number and microscopy <br><br>magnification indicated in file name.<br><br>Images are obtained with Nikon Eclipse 800 compound <br><br>microscope, mostly with 60x water immersion lens, Stacks of <br><br>images were obtained with a Nikon DS-Fi1 digital camera <br><br>(coded as "Vals" in th file names) or Nikon D7000 camera (see <br><br>filenames), color-, noise- and sharpness-enhanced with Adobe <br><br>Photoshop Lightroom 5.7.1. Combined images made with the aid <br><br>of Helicon Focus Pro 6.5.2, algorithm A, with subsequent <br><br>manual transfer of significant details taken from the <br><br>individual images, as necessary (_comb in the file names). <br><br>Scale bars are provided in the same collection: as a separate <br><br>folder for Vals camera and as additional files in the image <br><br>stacks from the Nikon D7000 camera.