cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7488/ds/1691
title: Comparison of amine-impregnated mesoporous carbon with microporous activated carbon and 13X zeolite for biogas purification
title: Biogas manuscript_raw data

description: Three materials were directly compared for their potential for biogas purification: 13X zeolite, microporous activated carbon and mesoporous activated carbon impregnated with polyethyleneimine. The amine-impregnated material showed the highest selectivity for CO2 over CH4 but this should be balanced by the higher operating temperature required. All three materials could be used for biogas purification. See Gibson et al. for further details: https://doi.org/10.1007/s10934-017-0387-0 .
description: 3 excel files (each contains 3-12 separate sheets) in 1 zip archive: * "Biogas_N2&CO2 Isotherms vs T.csv.xlsx"; * "Biogas_liqN2 isotherms.xlsx"; * "Biogas_breakthrough MS vs time.xlsx"
DOI: 10.7488/ds/2457
title: Pulse-shaped two-photon excitation of a fluorescent base analogue approaches single-molecule sensitivity

description: These data are associated with the paper "Pulse-shaped two-photon excitation of a fluorescent base analogue approaches single-molecule sensitivity", Rachel S. Fisher, David Nobis, Anders F. Füchtbauer, Mattias Bood, Morten Grøtli, L. Marcus Wilhelmsson, Anita C. Jones and Steven W. Magennis. Fluorescent nucleobase analogues (FBAs) have many desirable features in comparison to extrinsic fluorescent labels, but they are yet to find application in ultrasensitive detection. Many of the disadvantages of FBAs arise from their short excitation wavelengths (often in the ultraviolet), making two-photon excitation a potentially attractive approach. Pentacyclic adenine (pA) is a recently developed FBA that has an exceptionally high two-photon brightness. We have studied the two-photon-excited fluorescence properties of pA and how they are affected by incorporation in DNA. We find that pA is more photostable under two-photon excitation than via resonant absorption. When incorporated in an oligonucleotide, pA has a high two-photon cross section and emission quantum yield, varying with sequence context, resulting in the highest reported brightness for such a probe. The use of a two-photon microscope with ultrafast excitation and pulse shaping has allowed the detection of pA-containing oligonucleotides in solution with a limit of detection of ~ 5 molecules, demonstrating that practical single-molecule detection of FBAs is now within reach.
DOI: 10.7488/ds/365
title: Data associated with manuscript: Methylene blue not ferrocene: optimal reporters for electrochemical detection of protease activity

description: Optimisation and evaluation of an electrochemical biosensor for protease activity employing self-assembled monolayers. A platform for detecting proteases in a clinically-relevant range is reported.
description: Data associated to manuscript. Includes set of tables containing the data used for obtaining figures and results.
DOI: 10.7488/ds/3168
title: Data for publication "Determination of Void Fraction in Wet-Gas Vertical Flows via Differential Pressure Measurement"

description: This data set is for publication "Determination of Void Fraction in Wet-Gas Vertical Flows via Differential Pressure Measurement". The measurement of void fraction in multiphase flow is important for a wide range of industrial processes. Existing methods for void fraction measurement require intrusive, expensive and potentially hazardous equipments which constrict the flow, adding both capital and operational costs. Two phase flow experiments were carried out at the National Engineering Laboratory (NEL) to measure void fraction via pressure drop in a vertical pipe. Additional experiments are carried out at Spirax Sarco Inc. to validate the efficacy of the method on steam/water flow mixtures at high temperature and pressure, in gas mass fraction range between 0.17 and 0.95 and void fraction range between 0.75 and 1.0. The void fraction calculated by the presented differential pressure (dP) method is confirmed via established correlations. The work demonstrates the efficacy of a low cost, non-intrusive method to determine void fraction in two phase flow over a wide range of flow conditions.
DOI: 10.7488/ds/3221
title: Impact of surface nanostructure and wettability on interfacial ice physics

description: LAMMPS data file and input script required to setup and run simulations carried out in the paper: Nikiforidis, Datta, Borg and Pillai, 'Impact of surface nanostructure and wettability on interfacial ice physics', Journal of Chemical Physics.
DOI: 10.7488/ds/3272
title: Forest Canopy Nitrogen Uptake experiments data

description: Data supporting FOREST CANOPY NITROGEN UPTAKE CAN SUPPLY ENTIRE FOLIAR DEMAND (Ferarretto et al. 2022, Functional Ecology) Contact person: Richard K F Nair, rnair@bgc-jena.mpg.de These datasets contain ecohydrology N fluxes for a set of experiments investigating N processing by forest canopies at Griffin Forest, Scotland These data were previously used in the PhD thesis Ferarretto 2020, 'Nitrogen fluxes in forests from atmospheric deposition to soil: use of water flux monitoring and stable isotopes to close gaps in nitrogen transfers': https://era.ed.ac.uk/handle/1842/38004 Data collection was funded by Elizabeth Sinclair Irvine Bequest and Centenary Agroforestry 89 Fund of the School of GeoSciences (University of Edinburgh), Forest Research UK and the UK Natural Environment Research Council (NERC) through grant NE/G00725X/1 and a Life Sciences Mass Spectrometry Facility (LSMSF) award. This dataset consists of a readme file and three files corresponding to the three experiments described in the paper.
description: This dataset consists of three files corresponding to the three experiments described in the paper FOREST CANOPY NITROGEN UPTAKE CAN SUPPLY ENTIRE FOLIAR DEMAND (Ferarretto et al. 2022, Functional Ecology) Contact person: Richard K F Nair, rnair@bgc-jena.mpg.de **ecohydrology.csv** This file contains data relating to the ecohydrological budget part of the paper. **canopy.csv** This file contains data relating to the canopy fertilisation experiment **branch.csv** This file contains data relating to the branch fertilisation experiment **readme,txt** file explains the contents of the three data files
DOI: 10.7488/ds/3104
title: Variations in tephra stratigraphy created by small-scale surface features in sub-polar landscapes - Dataset from paper

description: This is the dataset used is the Thompson et al paper ‘Variations in tephra stratigraphy created by small-scale surface features in sub-polar landscapes’ The data is separated into the relevant folders, with grain size data for H1947 and G2011 (from a combination of laser diffracted measurements and sieved), as well as thickness measurements and control thickness measurements. Details about the control measurements sites can be found in the supplementary information of the paper. Details about the rest of the data are presented in both the manuscript and the supplementary information.
DOI: 10.7488/ds/2408
title: Carbon losses from deforestation and widespread degradation offset by extensive growth in African woodlands

description: Data associated with the publication: McNicol, IM, Ryan, CMR & Mitchard ETA (2018) Carbon losses from deforestation and widespread degradation offset by extensive growth in African woodlands. Nature Communications, DOI: 10.1038/s41467-018-05386-z. Each layer has been aggregated from its original 25 m resolution to 100 m. The original files are available from the authors on request. The metadata for each layer is included as a separate file. ### Paper abstract ### Land use carbon fluxes are major uncertainties in the global carbon cycle. This is because carbon stocks, the extent of deforestation and degradation, and biomass growth remain poorly resolved, particularly in the densely populated savannas which dominate the tropics. Here we quantify changes in aboveground woody carbon stocks from 2007–2010 in the world’s largest savanna—the southern African woodlands. Degradation is widespread, affecting 17.0% of the wooded area, and is the source of 55% of biomass loss (−0.075 PgC yr−1). Deforestation losses are lower (−0.038 PgC yr−1), despite deforestation rates being 5× greater than existing estimates. Gross carbon losses are therefore 3–6x higher than previously thought. Biomass gains occurred in 48% of the region and totalled +0.12 PgC yr−1. Region-wide stocks are therefore stable at ~5.5 PgC. We show that land cover in African woodlands is highly dynamic with globally high rates of degradation and deforestation, but also extensive regrowth.
DOI: 10.7488/ds/2970
title: Biorobot log data for visual navigation with transverse oscillating route following (TORF)

description: The purpose of this work was to develop a flying robot that can navigate using a bee-inspired visual route following approach. To this end we performed several missions in which an aerial robot with an onboard camera and processing unit flies along a predefined route and samples images of the ground. Thereafter, it tries to autonomously navigate back along the learned route by comparing the current view with the bank of views acquired on the learning flight. By centring an oscillatory flight path on the most familiar views, the biorobot can traverse the route without any additional information. See attached video (torf_operation_5x_speed.mp4) for a visual impression. This dataset contains all the data used to generate the figures in the associated publication. This includes information about the state of the robot and in some cases, the images acquired along the way. The data structures are defined in the attached “readme” file. The software used to generate this data is hosted at: https://github.com/jannsta1/torf
DOI: 10.7488/ds/3184
title: Recruiting Participants With Programming Skills: A Comparison of Four Crowdsourcing Platforms and a CS Student Mailing List

description: Reliably recruiting participants who have programming skills is an ongoing challenge for empirical studies involving software development technologies, often leading to the use of crowdsourcing platforms and computer science (CS) students. In this work, we use five existing survey instruments to explore the programming skills, privacy and security attitudes, and secure development self-efficacy of University CS student participants and participants from four crowdsourcing platforms (Appen, Clickworker, MTurk, and Prolific). We recruited 613 participants who claimed to have programming skills and assessed recruitment channels in regards to costs, quality, programming skills, and privacy/security attitudes. We find that 27% of crowdsourcing participants, 40% of self-reported developers from crowdsourcing participants, and 89% of CS students got all programming skill questions correct. CS students are the cheapest recruitment channel and rate themselves lower than crowdsourcing participants in terms of secure development self-efficacy. This dataset incudes the data from the 613 participants that we recruited for our study.
DOI: 10.7488/ds/2127
title: Scoping Statistical Analysis Support

description: The aim of this survey was to collect feedback about existing training programmes in statistical analysis for postgraduate researchers at the University of Edinburgh, as well as respondents’ preferred methods for training, and their requirements for new courses. The survey was circulated via e-mail to research staff and postgraduate researchers across three colleges of the University of Edinburgh: the College of Arts, Humanities and Social Sciences; the College of Science and Engineering; and the College of Medicine and Veterinary Medicine. The survey was conducted on-line using the Bristol Online Survey tool, March through July 2017. 90 responses were received. The Scoping Statistical Analysis Support project, funded by Information Services Innovation Fund, aims to increase visibility and raise the profile of the Research Data Service by: understanding how statistical analysis support is conducted across University of Edinburgh Schools; scoping existing support mechanisms and models for students, researchers and teachers; identifying services and support that would satisfy existing or future demand.
DOI: 10.7488/ds/97
title: A survey of undergraduate technology use and attitudes

description: An award from ELESIG (The Evaluation of Learners' Experience of eLearning Special Interest Group) provided an opportunity to continue the long and successful collection of information about how our students view ICT at the University of Edinburgh. The original work started in the 1990s but lapsed in recent years due to data collection issues. During the second semester in 2010-11, using a paper questionnaire, first and second years across the University were targetted. The findings raised a number of interesting points, for example: some students still find IT challenging; although laptop ownership is high, students do not seem to be planning to carry their laptops to the campus; Facebook appears to be used significantly for academic purposes.
description: Data files in SPSS and Excel format. Documentation in SPSS and Rich Text Format.
DOI: 10.7488/ds/3185
title: Bicontinuous Soft Solids with a Gradient in Channel Size Designed for Energy Storage Applications

description: Examples of bicontinuous interfacially jammed emulsion gels ("bijels") are presented with a designed gradient in the channel size along the sample. These samples are created by quenching binary fluids which have a gradient in particle concentration along the sample, since the channel size is determined by the local particle concentration. A gradient in local particle concentration is achieved using a two-stage loading process, with different particle volume fractions in each stage. Confocal microscopy and image analysis were used to quantitatively measure the channel size of the bijels. Bijels with a gradient in channel size of up to 2.8%/mm have been created. Such tailored soft materials could act as templates for energy materials optimised for both high ionic transport rates (high power) and high interfacial area (high energy density), potentially making them useful in novel energy applications.
description: See README.txt file in dataset for further information. Also see arXiv pre-print for further information.
DOI: 10.7488/ds/3263
title: Analysing and meta-analysing time-series data of microbial growth and gene expression from plate readers

description: Responding to change is a fundamental property of life, making time-series data invaluable in biology. For microbes, plate readers are a popular, convenient means to measure growth and also gene expression using fluorescent reporters. Nevertheless, the difficulties of analysing the resulting data can be a bottleneck, particularly when combining measurements from different wells and plates. Here we present omniplate, a Python module that corrects and normalises plate-reader data, estimates growth rates and fluorescence per cell as function of time, calculates errors, exports in different formats, and enables meta-analysis of multiple plates. The software corrects for autofluorescence, the optical density's non-linear dependence on the number of cells, and the effects of the media. We use omniplate to measure the Monod relationship for growth of budding yeast in raffinose, showing that raffinose is a convenient carbon source for controlling growth rates. Using fluorescent tagging, we study yeast's glucose transport. Our results are consistent with the regulation of the hexose transporter (HXT) genes being approximately bipartite: the medium and high affinity transporters are regulated by both the high affinity glucose sensor Snf3 and the kinase complex SNF1 via the repressors Mth1, Mig1, and Mig2; the low affinity transporters are predominately regulated by the low affinity sensor Rgt2 via the co-repressor Std1. We thus demonstrate that omniplate is a powerful tool for exploiting the advantages offered by time-series data in revealing biological regulation.
description: Time-series data for strains of budding yeast growing in Tecan microplate readers in low fluorescence SC media with either glucose or raffinose as a carbon source. Pre-growth was in 2% pyruvate. Measurements are taken every five minutes and experiments run for approximately 20 hours. More information is in README.txt.
DOI: 10.7488/ds/3017
title: Synaptic proteome SQLite database

description: Genes encoding synaptic proteins are highly associated with neuronal disorders many of which show clinical co-morbidity. We integrated 58 published synaptic proteomic datasets that describe over 8,000 proteins and combined them with direct protein-protein interactions and functional metadata to build a network resource that reveals the shared and unique protein components that underpin multiple disorders. All the data are provided in a flexible and accessible format to encourage custom use.
description: See readme.txt file for information on data and files included in this dataset.
DOI: 10.6084/m9.figshare.22709506
title: ATRT cell lines bulk RNA-seq

description: Matrix of raw counts and matrix of TPM of bulk RNA-seq data from ATRT cell lines (CHLA02-02-ATRT and IC-032) treated with NOTCH inhibitor (DAPT gamma-secretase inhibitor) and DMSO (control) with 3 replicates. Data were pre-processed using an in-house pipeline developed at the Institut Curie Bioinformatics Core Facility (available at https://github.com/bioinfo-pf-curie/RNA-seq) and the human reference genome hg19. Except, the first column which contains the gene name, columns correspond to samples prefixed by the name of the cell line.
DOI: 10.6084/m9.figshare.22709506.v2
title: ATRT cell lines bulk RNA-seq

description: Matrix of raw counts and matrix of TPM of bulk RNA-seq data from ATRT cell lines (CHLA02-02-ATRT and IC-032) treated with NOTCH inhibitor (DAPT gamma-secretase inhibitor) and DMSO (control) with 3 replicates. Data were pre-processed using an in-house pipeline developed at the Institut Curie Bioinformatics Core Facility (available at https://github.com/bioinfo-pf-curie/RNA-seq) and the human reference genome hg19. Except, the first column which contains the gene name, columns correspond to samples prefixed by the name of the cell line.
DOI: 10.6084/m9.figshare.22709506.v1
title: ATRT cell lines bulk RNA-seq

description: Matrix of raw counts and matrix of TPM of bulk RNA-seq data from ATRT cell lines (CHLA02-02-ATRT and IC-032) treated with NOTCH inhibitor (DAPT gamma-secretase inhibitor) and DMSO (control) with 3 replicates. Data were pre-processed using an in-house pipeline developed at the Institut Curie Bioinformatics Core Facility (available at https://github.com/bioinfo-pf-curie/RNA-seq) and the human reference genome hg19. Except, the first column which contains the gene name, columns correspond to samples prefixed by the name of the cell line.
DOI: 10.3886/e164162v1-137380
title: Data and code for: Sundown Towns and Racial Exclusion: The Southern White Diaspora and the “Great Retreat”

description: Abstract: "This paper studies the rise of sundown towns - places where Blacks and other minorities were excluded after dark - outside the South after 1890. We provide a new dataset on the timing of sundown town establishment using full count Census records. Using a shift-share instrumental variables approach, we show that the presence of Southern whites is causally related to the appearance of sundown towns, with lynchings and the establishment of KKK chapters as plausible mechanisms for racial exclusion."<br><br>This repository contains the replications files for "Sundown Towns and Racial Exclusion: The Southern White Diaspora and the “Great Retreat”"
DOI: 10.25345/c5513v580
title: MassIVE MSV000091813 - The human cerebrospinal fluid lipoproteome
title: Lipoproteins in human cerebrospinal fluid (CSF-Lps) were exchange labeled with a rhodamine-containing phospholipid and size distribution determined using a fluorescent lipoprotein profiler. CSF-Lps within each fraction were isolated using lipid removal agent. Lipid-bound proteins were digested directly off the resin, collected, and analyzed using bottom-up mass spectrometry (LC-MS/MS). Computational analysis of protein abundance and co-migration patterns were used to generate protein network maps and identify potential CSF-Lp subspecies.
DOI: 10.3886/e167024
title: Code for: Pay Transparency and the Gender Wage Gap: Evidence from Austria

description: This is the replication material for Pay Transparency and the Gender Wage Gap: Evidence from Austria, American Economic Journal: Economic Policy<br>We study the 2011 Austrian Pay Transparency Law, which requires firms above a size threshold to publish internal reports on the gender pay gap. Using an event-study design, we show that the policy had no discernible effects on male and female wages, thus leaving the gender wage gap unchanged. The effects are precisely estimated and we rule out that the policy narrowed the gender wage gap by more than 0.4 p.p.. Moreover, we do not find evidence for wage compression within establishments. We discuss several possible reasons why the reform did not reduce the gender wage gap.<br>
description: Austrian workers employed in a job subject to social security.
DOI: 10.3886/e167024v1
title: Code for: Pay Transparency and the Gender Wage Gap: Evidence from Austria

description: This is the replication material for Pay Transparency and the Gender Wage Gap: Evidence from Austria, American Economic Journal: Economic Policy<br>We study the 2011 Austrian Pay Transparency Law, which requires firms above a size threshold to publish internal reports on the gender pay gap. Using an event-study design, we show that the policy had no discernible effects on male and female wages, thus leaving the gender wage gap unchanged. The effects are precisely estimated and we rule out that the policy narrowed the gender wage gap by more than 0.4 p.p.. Moreover, we do not find evidence for wage compression within establishments. We discuss several possible reasons why the reform did not reduce the gender wage gap.<br>
description: Austrian workers employed in a job subject to social security.
DOI: 10.5281/zenodo.7869214
title: IRAS ML Predictions

description: Contained in this repository are the large files required for running the code in the following GitHub repository: https://github.com/zfried/IRAS_ML_Predictions fullDataset.csv contains all of the SMILES strings and length 70 feature vectors of the molecules used to train the mol2vec model. mol2vec_model_final_70.pkl is the trained mol2vec model that produces length 70 molecular feature vectors. prediction_molecules.csv contains all of the SMILES strings and length 89 feature vectors (including isotopic encoding) of the 84,863 molecules that are inputted into the trained model.
DOI: 10.5281/zenodo.7869213
title: IRAS ML Predictions

description: Contained in this repository are the large files required for running the code in the following GitHub repository: https://github.com/zfried/IRAS_ML_Predictions fullDataset.csv contains all of the SMILES strings and length 70 feature vectors of the molecules used to train the mol2vec model. mol2vec_model_final_70.pkl is the trained mol2vec model that produces length 70 molecular feature vectors. prediction_molecules.csv contains all of the SMILES strings and length 89 feature vectors (including isotopic encoding) of the 84,863 molecules that are inputted into the trained model.