cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/csvdrr4d68.1
title: The Abinit project: Impact, environment and recent developments

description: Abinit is a material- and nanostructure-oriented package that implements density-functional theory (DFT) and many-body perturbation theory (MBPT) to find, from first principles, numerous properties including total energy, electronic structure, vibrational and thermodynamic properties, different dielectric and non-linear optical properties, and related spectra. In the special issue to celebrate the 40th anniversary of CPC, published in 2009, a detailed account of Abinit was included [Gonze et al. (2009)], and has been amply cited. The present article comes as a follow-up to this 2009 publication. It includes an analysis of the impact that Abinit has had, through for example the bibliometric indicators of the 2009 publication. Links with several other computational materials science projects are described. This article also covers the new capabilities of Abinit that have been implemented during the last three years, complementing a recent update of the 2009 article published in 2016. Physical and technical developments inside the abinit application are covered, as well as developments provided with the Abinit package, such as the multibinit and a-tdep projects, and related Abinit organization developments such as AbiPy . The new developments are described with relevant references, input variables, tests, and tutorials.
DOI: 10.5281/zenodo.3604333
title: Behavioural Simulator Matsim Input Data

description: Behavioural simulator requires 4 input data files. Each file contains the following information: 1. Network.xml file contains road network information based on no of lanes, speed limits, vehicle access details derived from open street maps. 2. Plan.xml file contains synthetic population along with activity-travel information. These activity-travel patterns are output generated from activity-based models. 3. Schedules.xml file have information about public transport schedules with stops details, timetables etc drived from GTFS data 4. Vehicels.xml file is comprised of Public Transport Fleet information e.g no of buses.
DOI: 10.5519/qd.229ugcp8
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (0 records)
DOI: 10.17037/data.00001531
title: TB Fast Track dataset

description: The TB Fast Track dataset was produced as part of an open-label, pragmatic cluster-randomised trial, with primary health clinics as the unit of randomisation, conducted in South Africa. The dataset consists of three data tables: a "baseline" table that lists participant characteristics measured at enrolment; an "outcomes" table containing details of primary and secondary outcomes; and a "I-sputumresults" table that lists sputum results from specimen collected at enrolment (intervention arm only). These data underpin analysis reported in a Lancet HIV 2020 paper.
DOI: 10.17632/bwzdv623xn.1
title: Compartive proteome, transcriptome and co-expression network data set of six plant species

description: Proteome: MS data was searched with the MaxQuant software (version 1.5.7.5). Searches were performed against the following UniProt protein sequence databases (v20150827): Medicago truncatula, Arabidopsis thaliana, Solanum tuberosum, Oryza sativa, Physcomitrella patens, and Zea mays. Searches used the default precursor mass tolerances (20 ppm first search and 4.5 ppm main search) and a product mass tolerance of 0.35 Da. The in silico digest was set to specific tryptic cleavage and a maximum of two missed cleavages. The fixed modification specified were carbamidomethylation of cysteine residues, and variable modifications were oxidation of methionine and acetylation of protein N-terminus. Peptides and proteins groups were both filtered to a 1% FDR. Label-free quantification was performed within MaxQuant using MaxLFQ. Protein groups were screened for "Reverse" and "Contaminant" identifications. The final protein levels are the LFQ intensity values. Transcriptome: The compendia of transcriptomic datasets for 6 plant species were created using publicly available RNA-seq dataset from Sequence Read Archive. We used the Curse and Prose suite (http://bioinformatics.psb.ugent.be/webtools/Curse/) to construct these expression compendia. First, we searched for datasets corresponding to "RNA-seq" and "Transcriptome analysis" for each species, and manually excluded the experiments which contained mutant, knock-out, and transgenic lines by curating the metadata in the Curse interface. We passed the chosen experiments and genomic sequence files to the Prose tool, which downloads data, performs quality control, and quantifies transcript expression to normalized TPM values. To change the transcript level expression to gene level, we summed up the multiple values of transcript expression for one gene. Co-expression network: We defined a species-specific graph as a fully-connected weighted graph, where the weight corresponds to the Gaussian kernel-based similarity between two gene expression profiles. First, we collected genes that are defined in the orthogroups of 6 species in the previous step (see method in the paper). Then we generated a distance matrix by calculating the pairwise Euclidean distance between two genes of the transcriptome compendium, and finally we transformed it to the similarity matrix using the Gaussian kernel to map the nearer distance to higher similarity.
DOI: 10.5281/zenodo.3604332
title: Behavioural Simulator Matsim Input Data

description: Behavioural simulator requires 4 input data files. Each file contains the following information: 1. Network.xml file contains road network information based on no of lanes, speed limits, vehicle access details derived from open street maps. 2. Plan.xml file contains synthetic population along with activity-travel information. These activity-travel patterns are output generated from activity-based models. 3. Schedules.xml file have information about public transport schedules with stops details, timetables etc drived from GTFS data 4. Vehicels.xml file is comprised of Public Transport Fleet information e.g no of buses.
DOI: 10.5066/p945w4c4
title: Liquid water content of summertime coastal California fog events, San Mateo County

description: Measurements of liquid water content (LWC) of coastal fog events were collected using specialized fog water collection units during the hot dry summer season (July to September) and continued through the winter. These data were assembled to explore the potential of fog water collection as a water resource for Midpeninsula Regional Open Space District public lands in San Mateo County, California. Simultaneous meteorological measurements were collected for four variables: wind, temperature, humidity, and solar radiation. The dataset includes ~12,000 records for two summers (2016 and 2017) at two sites. One site was a grassland near the MROSD Skyline Field Office (SFO) and the other in a Douglas forest clearing at the MROSD North Purisima (NPUR) trailhead. The fog water collecting experiment also compared six mesh for collection efficiency, three coated with NBD-Nano hydrophobic formulation and three left uncoated. Each mesh was affixed to standard 1.00 m2 frames. The three mesh types were coated or left uncoated. They were 1) double-layer 35% shade coefficient Raschel; 2) stainless steel 0.02 in, 49% shade coeffient wire mesh, and 3) FogHaTin, a 3-dimensional specialty textile weave. The data show that the highest collection, 67 litres, came during the fog event of August 14, 2017 at SFO. The NBD coated FogHaTin mesh collected the most water (14 l) from that fog event and the uncoated metal collecting the least (12 l). The total collected from all 18 fog events that occurred during the 8/4 - 9/20/2017 period was 171.34 l at SFO and at 44.95 l at NPUR.
DOI: 10.17034/ff74c4c1-dbf5-4413-9e93-274904338147
title: A General-Purpose Colourimetric Air pressure Indicator

description: Data underpinning A General-Purpose Colourimetric Air pressure Indicator
DOI: 10.24414/h5pn-7n71
title: BMAN20

description: semi-analytical model to predict the precession and nutations of a rigid Mars
DOI: 10.17034/f8fd1290-99c7-4bda-b960-99498c4c15d3
title: Photonic efficiency and selectivity study of M (M = Pt, Pd, Au and Ag)/TiO2 photocatalysts for methanol reforming in the gas phase

description: Data underpinning Photonic efficiency and selectivity study of M (M = Pt, Pd, Au and Ag)/TiO2 photocatalysts for methanol reforming in the gas phase
DOI: 10.17632/3g73zffjbg.1
title: Data for: Wastewater treatment plant effluent inputs induce large biogeochemical changes during low flows in an intermittent stream but small changes in day-night patterns

description: This data set includes stream discharge, stream physicochemistry, and in-stream net uptake rates for ammonium, nitrite, nitrate, dissolved inorganic nitrogen and soluble reactive phosphorus. The data set contains data from 8 sampling campaigns which were conducted at two reaches located upstream and downstream of a wastewater treatment plant in la Tordera stream (Catalonia, NE Spain) during the water year 2016-2017. During each sampling date, water measurements and sample collection was repeated during daytime and nighttime. In-stream net nutrient uptake velocity (Vf) was calculated following standard nutrient spiraling procedures. Daily photosynthetically active radiation during the period of study is also provided. More details about data collection and data analysis can be found in the material and methods section of the paper: "Wastewater treatment plant effluent inputs induce large biogeochemical changes during low flows in an intermittent stream but small changes in day-night patterns" by Bernal et al.
DOI: 10.17632/64wgnk2svg.1
title: Basic data of infrastructure externalities

description: The main content of "Basic data of infrastructure externalities" is the raw data used in the literature review.
DOI: 10.17632/64wgnk2svg.2
title: Basic data of infrastructure externalities

description: The main content of "Basic data of infrastructure externalities" is the raw data used in the literature review.
DOI: 10.17632/k2xv3yss8m.1
title: Production of enzymes via solid state fermentation from cereals

description: The database contains 487 quantified enzymes production examples using cereals as a substrate in 209 experiments (some experiment include several enzymes). It covers both single (cereal) and mixed substrates (cereal plus other substrates) from food waste and agri-industrial residues. Main substrates are wheat (53 experiments), rice (22 experiments) and corn (22 experiments). The most common enzymes are xylanase, CMCase, FPase. The dataset consists of separated columns with details on the organisms; yield; unit; incubation time; pretreatment; nutritive or inducing supplement; optimization method; and other parameters and details, with references to scientific articles. The database was structured in a way that makes it possible to filter any parameter (for example it is possible to select only rice stray as substrates, only xylanase, only certain units to make a more appropriate data comparison, only yield above a certain number, and combination of such parameters.). Each experiment includes data on the reference in the last column. The full reference list is in the last sheet of the dataset. The file includes an introduction to the database with a description of each column and abbreviations. This database was produced as part of the research for “The review of enzyme production from cereal residues via solid state fermentation with fungi” Joseph Bourgine1, Dominika Alexa Teigiserova2,3, Marianne Thomsen2,3* 1 University Nantes, Department of Process and Bioprocess Engineering, Rue Christian Pauc, CS 50609, 44300 Nantes, France 2 Research Group on EcoIndustrial System Analysis, Department of Environmental Science, Aarhus University, Frederiksborgvej 399, Postboks 358, DK-4000, Roskilde, Denmark 3 Aarhus University Centre for Circular Bioeconomy *Corresponding Author email: mth@envs.au.dk The research was performed as part of the Horizon 2020 project DECISIVE (Decentralised valorisation of biowaste) under grant agreement N° 689229. The work was further supported by Aarhus University Centre for Circular Bioeconomy and Aarhus University Graduate School of Science and Technology.
DOI: 10.17632/pf86xs7ybk.1
title: Data on the effects of filters, storage conditions, and chlorination in fluorescence and absorbance wastewater measurements

description: Data in this repository contain raw fluorescence and UV absorbance measurements of wastewater organic matter related to different wastewater qualities, including primary, secondary and tertiary wastewater effluents, and a wastewater-impacted surface water. Samples stored under different conditions were analyzed at different time of storage over a testing period of 21 days. Surface water and wastewater samples were stored filtered (0.7 μm) and unfilterd at different temperature (i.e.; room temperature, 4 °C, and -20 °C). The repository contains also fluorescence and UV absorbance raw data of chlorinated wastewater effluents. Furthermore, data in the repository include fluorescence and UV absorbance spectra of blank samples obtained filtering Milli-Q water by glass microfiber filters (0.7 μm), polyvinylidene fluoride (PVDF) membrane filters (0.45 μm), cellulose nitrate membrane filters (0.45 μm), and by polyether sulfone (PES) syringe filters (0.45 μm). Ultraviolet light absorbance was analyzed using a Shimadzu UV-1800 spectrophotometer (Kyoto, Japan). Absorbance spectra were measured from 200 to 800 nm at 1 nm intervals in a 1 cm quartz cuvette with Milli-Q water used as a blank. Fluorescence data were collected using a Shimadzu RF-5301PC fluorescence spectrophotometer (Kyoto, Japan) with the scanning range from excitation wavelength 220 nm to 450 nm at an interval of 5 nm, and emission wavelength from 250 nm to 580 nm at the interval of 1 nm. Excitation and emission slit widths were both set at 5 nm.
DOI: 10.5281/zenodo.3604334
title: weecology/forecasts 2020-01-10

description: Archived forecasts for future analysis
DOI: 10.5281/zenodo.3604335
title: Matsim Simulation Results (disaggregated)

description: Matsim Simulation results at disaggregate level are based on the following 2 datasets files for each city i.e. Bologna, Hasselt and Vantaa. The details are as follows: 1. The plan.xml file contains the population together with activity-travel details containing trip route information. All these results are for the base cases. 2. Config.xml file contains parameters/details required to run Matsim simulation.
DOI: 10.5281/zenodo.3604336
title: Matsim Simulation Results (disaggregated)

description: Matsim Simulation results at disaggregate level are based on the following 2 datasets files for each city i.e. Bologna, Hasselt and Vantaa. The details are as follows: 1. The plan.xml file contains the population together with activity-travel details containing trip route information. All these results are for the base cases. 2. Config.xml file contains parameters/details required to run Matsim simulation.
DOI: 10.5519/qd.7zc5id3s
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (4494131 records)
DOI: 10.17632/9drxd9d8nx.1
title: Nektar++: Enhancing the capability and application of high-fidelity spectral/hp element methods

description: Nektar++ is an open-source framework that provides a flexible, high-performance and scalable platform for the development of solvers for partial differential equations using the high-order spectral/hp element method. In particular, Nektar++ aims to overcome the complex implementation challenges that are often associated with high-order methods, thereby allowing them to be more readily used in a wide range of application areas. In this paper, we present the algorithmic, implementation and application developments associated with our Nektar++ version 5.0 release. We describe some of the key software and performance developments, including our strategies on parallel I/O, on in situ processing, the use of collective operations for exploiting current and emerging hardware, and interfaces to enable multi-solver coupling. Furthermore, we provide details on a newly developed Python interface that enables a more rapid introduction for new users unfamiliar with spectral/hp element methods, C++ and/or Nektar++. This release also incorporates a number of numerical method developments – in particular: the method of moving frames (MMF), which provides an additional approach for the simulation of equations on embedded curvilinear manifolds and domains; a means of handling spatially variable polynomial order; and a novel technique for quasi-3D simulations (which combine a 2D spectral element and 1D Fourier spectral method) to permit spatially-varying perturbations to the geometry in the homogeneous direction. Finally, we demonstrate the new application-level features provided in this release, namely: a facility for generating high-order curvilinear meshes called NekMesh; a novel new AcousticSolver for aeroacoustic problems; our development of a ‘thick’ strip model for the modelling of fluid–structure interaction (FSI) problems in the context of vortex-induced vibrations (VIV). We conclude by commenting on some lessons learned and by discussing some directions for future code development and expansion.
DOI: 10.17632/n3xpw2txcm.1
title: Section 2.7 -Integrating high-resolution satellite images and topographic data for rangeland resources mapping in pastoral landscapes of eastern Africa

description: Stack Landsat images for three different dates. Pixel-wise timeseries trend analysis with PVI and downloadable R- script. Large slope coefficients of linear regression analysis indicate highly deciduous surfaces with highly dry-out dynamics and land surfaces that stay greener for most part of the season show slow dry-out dynamics.
DOI: 10.5281/zenodo.3604060
title: Supporting students in making informed data sharing decisions: from comprehension to consenting

description: Whether deciding to participate in research or gain access to online applications, studies on consent suggest that individuals often do not read or fail to understand the text outlining the conditions they agree to when giving their consent. Limited comprehension related to the risks of big data and habituation may contribute to consent being given in a manner that counters the best interests of individuals (i.e. a privacy paradox). Are those asking students to use new technologies and share their data ethically responsible for helping students learn to make informed decisions regarding the sharing of their data? As educational technology researchers, we conducted a quasi-experimental study involving 127 undergraduate students in which we explored the effects on study enrollment of supporting students in making informed data sharing decisions. Prior to reading the consent form for a study involving the evaluation of a collaborative learning application, one group of participants was primed to consider data sharing risks whereas the other group was not. The primed group scored lower on a consent form comprehension quiz yet had higher enrollment rates and were more likely to cite trust as reasoning for enrolling in the study. The data set is composed by: ‘Classes’ spreadsheet: including the relation of flows, group of students, number of students, instructor id, day and time ‘Participants’ spreadsheet: including the relation of ID (of each participant), if s/he consented, group class, flow and language ‘Prior knowledge Survey’ spreadsheet: participant’s ID and ID, relevant prior knowledge questionnaire data (questions included). ‘Quiz data’ spreadsheet: participant’s ID, quiz data and survey data (questions included) PDF including: Table S1. Summary of participating classes Table S2. Consent form subsections and summaries Table S3. Consent form quiz questions, question types, and assigned points Table S4. Guiding questions in the prior knowledge questionnaire Table S5. Comparison of Flow A and Flow B quiz scores per question
DOI: 10.17632/r77sr2t5hz.1
title: Data from: Climate warming may affect the optimal timing of reproduction for migratory geese differently in the low and high Arctic

description: This data is connected to the research paper "Climate warming may affect the optimal timing of reproduction for migratory geese differently in the low and high Arctic". It includes data on timing of snow melt, and timing nest initiation and reproductive success of barnacle geese. Detailed information can be found in the README file. Please contact me before using these data.
DOI: 10.17632/znr5dy4x29.1
title: Adaptive introgression from indicine cattle into white cattle breeds from Central Italy

description: Genotype data in PLINK binary format associated with the following paper: Barbato et al., 2020. 'Adaptive introgression from indicine cattle into white cattle breeds from Central Italy' Scientific Reports. DOI: 10.1038/s41598-020-57880-4
DOI: 10.5281/zenodo.3604244
title: Metadata for the archive of JPG image files of Herbarium specimens from Columbia used in the BRAVO project.

description: An excel spreadsheet of the metadata to accompany the images in the file "Archive of JPG image files of Herbarium specimens from Columbia used in the BRAVO project". The metadata is information like (Family, genus, names, collector, coll_num, plot number, & location, identification of the material...) A majority of the metadata is also included on the "label" on the specimens in the images in the archive.
description: Robert Cubey (RBGE) Uploader only - data collated by Forrest Plots (www.forestplots.net/) and provided by TOLI herbarium (Ibagué, Tolima, Colombia) as part of the BRAVO project funded by British Council & The Newton Fund.
DOI: 10.5281/zenodo.3604243
title: Metadata for the archive of JPG image files of Herbarium specimens from Columbia used in the BRAVO project.

description: An excel spreadsheet of the metadata to accompany the images in the file "Archive of JPG image files of Herbarium specimens from Columbia used in the BRAVO project". The metadata is information like (Family, genus, names, collector, coll_num, plot number, & location, identification of the material...) A majority of the metadata is also included on the "label" on the specimens in the images in the archive.
description: Robert Cubey (RBGE) Uploader only - data collated by Forrest Plots (www.forestplots.net/) and provided by TOLI herbarium (Ibagué, Tolima, Colombia) as part of the BRAVO project funded by British Council & The Newton Fund.
DOI: 10.15784/601242
title: Basal Melt, Ice thickness and structure of the Ross Ice Shelf using airborne radar data

description: This dataset was produced for the manuscript \"Multi-decadal basal melt rates and structure of the Ross Ice Shelf, Antarctica using airborne ice penetrating radar\" by Das et al., 2020 in Journal of Geophysical Research-Earth Surface. It has total ice thickness, thickness of the LMI layer, strain induced thickness change, basal melt rates and the error estimate for basal melt rates.
DOI: 10.17632/fnzbxmkv83.1
title: Targeted vs untargeted MS2 data-dependent acquisition for automated peak annotation in LC-MS metabolomics