Find research datasets worth reusing

opencc-by-4.0Nov 2022View details →

Magnaporthe oryzae transposable elements manuscript additional datasets

Additional datasets for manuscript on transposable elements in Magnaporthe oryzae.  <ul> <li>analysis_files.tar.gz - contains selected analysis files generated by scripts in this GitHub repository: <a href="https://github.com/annenakamoto/moryzae_tes">https://github.com/annenakamoto/moryzae_tes</a>. File names correspond to those in the scripts.</li> <li>FungGAP_out.tar.gz - contains gene prediction outputs for all genomes used</li> <li>OrthoFinder_out.tar.gz - contains output from OrthoFinder, run on proteomes of all genomes used</li> <li>tabular_data_for_figures.tar.gz - contains tabular data used to generate figures</li> <li>visualization_files.tar.gz - contains bed and seg files used to visualize all genes, SCOs, effectors, TEs, solo LTRs, and GC content in each representative genome</li> </ul>

opencc-zeroNov 2022View details →

The first African record of Isothecium algarvicum in Kroumiria (Tunisia), a relictual element of the Neogene flora?

Isothecium algarvicum W. E. Nicholson & Dixon, was discovered in Tunisia, which constitutes the first report of this Macaronesianoceanic species in Africa. Three distinct populations were observed in ravines in the humid Meso-Mediterranean vegetation belt of Kroumiria. The Tunisian material is fully described, with particular attention to alar and supra-alar cells, prorate cells and other morphological characteristics. The density and size of the prorate cells appear to be a robust diagnostic characteristic for the separation of Isothecium algarvicum, I. alopecuroides and I. myosuroides. Detailed analysis of the forest habitat reveals a uniquely rich environment. The origin of a possibly relict species with Macaronesian-oceanic affinities is discussed.

Major element chemistry from supraglacial debris at Khumbu Glacier

An Excel spreadsheet containing raw XRF measurements of 34 major elements in sand samples from source tributaries and the compound tongue of Khumbu Glacier. Samples collected in the field between 1-15 May 2018 and measured in laboratory conditions.

Folk children's songs with tragic elements

The database collects the results of manual content analysis, formal analysis of the lyrics and musical analysis of the scores of a corpus of 506 Spanish children's folk songs identified as tragic by a previous analysis.

Major and trace element composition of IODP Site U1429 and Yellow River sediments and simulated rainfall changes in East-Southeast Asia during past 300 ka

This dataset includes major and trace element composition of IODP Site U1429 and Yellow River surface sediments. They are all analyzed based on the clay-sized fractions. It also includes the data of simulated rainfall changes in the northern and southern China, as well as in Southeast Asia during past 300 ka.

opencc-zeroDec 2022View details →

Data from: Whiskers provide time-series of toxic and essential trace elements, Se:Hg molar ratios, and stable isotope values of an apex Antarctic predator, the leopard seal

In an era of rapid environmental change and increasing human presence, researchers need efficient tools for tracking contaminants to monitor the health of Antarctic flora and fauna. Here, we examined the utility of leopard seal whiskers as a biomonitoring tool that reconstructs time-series of significant ecological and physiological biomarkers. Leopard seals (Hydrurga leptonyx) are a sentinel species in the Western Antarctic Peninsula due to their apex predator status and top-down effects on several Antarctic species. However, there are few data on their contaminant loads. We analyzed leopard seal whiskers (n = 18 individuals, n = 981 segments) collected during 2018–2019 field seasons to acquire longitudinal profiles of non-essential (Hg, Pb, and Cd) and essential (Se, Cu, and Zn) trace elements, stable isotope (ẟ15N and ẟ13C) values and to assess Hg risk with Se:Hg molar ratios. Whiskers provided between 46 and 286 cumulative days of growth with a mean ~125 days per whisker (n = 18). Adult whiskers showed variability in non-essential trace elements over time that could partly be explained by changes in diet. Whisker Hg levels were insufficient (<20 ppm) to consider most seals being at "high" risk for Hg toxicity. Nevertheless, maximum Hg concentrations observed in this study were greater than that of leopard seal hair measured two decades ago. However, variation in the Se:Hg molar ratios over time suggest that Se may detoxify Hg burden in leopard seals. Overall, we provide evidence that the analysis of leopard seal whiskers allows for the reconstruction of time-series ecological and physiological data and can be valuable for opportunistically monitoring the health of the leopard seal population and their Antarctic ecosystem during climate change.

Dataset supporting publications: "Discrete Element Modelling of Rock Drilling" and "Towards Discrete Element Modelling of Rock Drilling"

Dataset supporting publications: Paper - “Discrete Element Modelling of Rock Drilling” and Thesis - “Towards Discrete Element Modelling of Rock Drilling” (both publications available in Zenodo: <a href="https://zenodo.org/record/7274081#.Y2JoCXbMJPY">paper</a>, <a href="https://zenodo.org/record/5901677#.Y2s51HaZO3B">thesis</a>) Dataset used: Wear test datasets as described in T2.3.1 for the improvement of drilling efficiency via the selection of optimal drill bits (D5), Mechanical properties rock/soil (D29), Datasets resultant from numerical simulations of the drilling operation in T7.2-5 (D33) Percussive rotary drilling is recognized as the most efficient method for hard rock drilling. Despite clear advantages over conventional rotary methods, there are still some uncertainties associated with percussive drilling. For geothermal applications, drilling accounts for a large portion of the total cost. Specifically, the wear of drill bits when drilling in hard rock is a predominant cost factor and drilling parameters are often based on the experience of the field operator. Within the framework of the H2020 project GEOFIT, numerical simulations of percussive drilling are performed in order to evaluate the rock drilling process and gain insight about the trade-off between wear and Rate of Penetration (ROP). In the simulations, the rock material was represented by the Bonded Discrete Element Method (BDEM), the drill bit by the Finite Element Method (FEM), the drilling fluid by the Particle Finite Element Method (PFEM) and the abrasive wear on the surface of the drill bit was represented by Archard’s wear law. The drilling simulations were conducted for two rock materials; a sedimentary rock material corresponding to what was found when drilling at the GEOFIT pilot site in Aran Islands, Ireland, and a harder reference rock similar to granite. The results show that, at a drill bit impact force of 10 kN, the ROP in the sedimentary rock was 6.3 times faster than for granite. When increasing the impact force to 40 and 50 kN, however, the ROP for the sedimentary rock is only 1.9 and 1.6 times faster, respectively. Furthermore, the wear rate decreased with increased impact force when drilling in the granite rock. For the sedimentary rock, however, the loading resulting in the best trade-off between abrasive wear and ROP was the second highest loading of 40 kN, which suggests that an increase in impact energy may increase the rate of penetration but may not be economically motivated.

opencc-zeroJan 2023View details →

Does long-term soil warming affect microbial element limitation? A test by short-term assays of microbial growth responses to labile C, N and P additions

Increasing global temperatures have been reported to accelerate soil carbon (C) cycling but also to promote nitrogen (N) and phosphorus (P) dynamics in terrestrial ecosystems. However, warming can differentially affect ecosystem C, N and P dynamics, potentially intensifying elemental imbalances between soil resources, plants and soil microorganisms. Here we investigated the effect of long-term soil warming on microbial resource limitation, based on measurements of microbial growth (18O incorporation into DNA) and respiration after C, N and P amendments. Soil samples were taken from two soil depths (0–10, 10–20 cm) in control and warmed (>14 yrs warming, +4°C) plots in the Achenkirch soil warming experiment. Soils were amended with combinations of glucose-C, inorganic/organic N and inorganic/organic P in a full factorial design, followed by incubation at their respective mean field temperatures for 24 hours. Soil microbes were generally C-limited, exhibiting 1.8-fold to 8.8-fold increases in microbial growth upon C addition. Warming consistently caused soil microorganisms to shift from being predominately C limited to become C-P co-limited. This P limitation possibly was due to increased abiotic P immobilization in warmed soils. Microbes further showed stronger growth stimulation under combined glucose and inorganic nutrient amendments compared to organic nutrient additions. This may be related to a prolonged lag phase in organic N (glucosamine) mineralization and utilization compared to glucose. Soil respiration strongly positively responded to all kinds of glucose-C amendments, while responses of microbial growth were less pronounced in many of these treatments. This highlights that respiration – though easy and cheap to measure – is not a good substitute of growth when assessing microbial element limitation. Overall, we demonstrate a significant shift in microbial element limitation in warmed soils, from C to C-P co-limitation, with strong repercussions on the linkage between soil C, N and P cycles under long-term warming.

opencc-by-4.0Jan 2023View details →

The Anthropocene and the Sustainable Development Goals: Key elements in geography higher education? Study Dataset.

The document contains the Dataset of a study "The Anthropocene and the Sustainable Development Goals: Key elements in geography higher education? "

opencc-by-4.0Jan 2023View details →

1 PREHEALING: Design of concrete precast elements incorporating sustainable strategies for self-healing to increase their service life. Material characterization

This project deals with the analysis of the performance of concrete with internal curing aggregates (IC), low clinker cementitious materials and steel fibres, to be used in real applications in the field of precast industry. The low clinker cementitious material will be composed of clinker (C), metakaolin (MK) and limestone filler (LF) as powder material. In order to promote the sustainability of these products, a sustainable powder (SP) obtained from wood ash will be included. In addition, aggregates from coal bottom ash (CBA) will be used as internal curing water reservoirs. This section includes the characterization of these materials providing their main properties as particle size distribution, density or absorption, among others

opencc-by-nc-4.0Oct 2020View details →

Euclid in print, 1482–1703. A catalogue of the editions of the Elements and other Euclidean works

This catalogue lists, in intention, every edition of one or more works attributed to Euclid printed in any language down to the year 1703. It is intended to improve upon the previous Euclidean bibliographies of Riccardi, Duarte, Thomas-Stanford and Steck, which were compiled before the availability of digital catalogues. It was produced as part of the 2016–18 project 'Reading Euclid', based at the University of Oxford and funded by the Arts and Humanities Research Council of the UK.

opencc-by-4.0Jan 2023View details →

Baseline concentrations, spatial distribution and origin of trace elements in marine surface sediments of the northern Antarctic Peninsula

Supplementary data to article published in Marine Pollution Bulletin 187 (2023) 114501: https://doi. org/10.1016/j.marpolbul.2022.114501

opencc-by-4.0Feb 2023View details →

Dataset for 'A microscopic diffusion-induced discrete element model for swellable particles'

This dataset contains both numerical simulation data and experimental data describing the swelling behaviour of binary particle systems. Detailed study on the swelling behaviour is presented in a journal paper entitled "A microscopic diffusion-induced discrete element model for swellable particles ". We provide all the essential data in a single excel file with the description below: Dataset 1-Evolution of the radius of core zone obtained from experiments  (used in Fig.7c of the associated paper): Experimental data for the measured radius of core zone and associated standard deviation at various time. Dataset 2-Calibration procedures for the microscopic swelling model from DEM simulation (used in Fig8 of the associated paper). Dataset 3 - Evolutions of the normalised average diameter d/d_0 (used in Fig.9) obtained from experiments  and DEM simulations. Dataset 4 - Evolutions of normalised water concentration (used in Fig.10a) and Young’s modulus (used in Fig.10b) of the swollen particle obtained with different swelling models. Dataset 5 - Evolution of core zone obtained from DEM simulations with the microscopic swelling model (used in Fig.10b). Dataset 6 - Evolution of the height of the particle bed obtained from experiments and simulations (used in Fig.13 of the associated paper): Experimental data for the measured hight and associated standard deviation at various time, as well as the numerical data. Dataset 7 -Evolutions of  (a) The ratio of average normal contact force to the initial gravity of the dry particle (used in Fig.14a of the associated paper) and (b) the ratio of average normal contact force to the instantaneous gravity(used in Fig.14b of the associated paper) obtained from DEM simulations with the microscopic swelling model. Dataset 8 - Evolution of the dimensionless height of the bilayer particle bed and randomly mixed particle bed obtained from experiments and simulations (used in Fig.17 of the associated paper): Experimental data for the measured hight and associated standard deviation at various time, as well as the numerical data. Dataset 9 - Evolution of the dimensionless height of the pure SAP particle bed obtained from simulations with different water concentration in the liquid (used in Fig.18 of the associated paper): Dataset 10 -Evolution of dimensionless heights of SAP particle bed and (b) the dimensionless diameter of the particle obtained from DEM simulations during shrinkage with different water concentrations in the liquid (used in Fig.19 of the associated paper). Dataset 11 -Comparison of the dimensionless height of SAP particle bed, dimensionless diameter and the standard deviation of dimensionless diameter obtained from DEM simulations with different values of diffusivity for particle-particle diffusion (used in Fig.20 of the associated paper).

Resolution of structural variation in diverse mouse genomes reveals chromatin remodeling due to transposable elements

Structural variant calls, RepeatMasker annotations, and genome assemblies of diverse mouse genomes.

Mechanisms of the reaction of elemental sulfur and polysulfides with cyanide and phosphines

Gaussian 16 output files for all computed structures for "Mechanisms of the reaction of elemental sulfur and polysulfides with cyanide and phosphines". Chemistry - A European Journal, 2023, e202203906. DOI: 10.1002/chem.202203906

opencc-by-4.0Jan 2022View details →

Targeted Surface Manipulation of Cu/Zn/Ag coatings and Ag/Cu particles based on Sacrificial Element Selection by Electrodeposition and Redox replacement

Dataset Targeted Surface Manipulation of Cu/Zn/Ag coatings and Ag/Cu particles based on Sacrificial Element Selection  by Electrodeposition and Redox replacement

opencc-zeroMar 2023View details →

Data from: Ultraconserved elements improve resolution of marmot phylogeny and offer insights into biogeographic history

Marmots (Marmota spp.) comprise a lineage of large-bodied ground squirrels that diversified rapidly in the Pleistocene, when the planet quickly transitioned to a drier, colder, and highly seasonal climate—particularly at high latitudes. Fossil evidence indicates the genus spread from North America, across Beringia, and into the European Alps over the course of only a few million years, beginning in the late Pliocene. Marmots are highly adapted to survive long and severely cold winters, and this likely favored their expansion and diversification over this time period. Previous phylogenetic studies have identified two major subgenera of marmots, but the timing of important speciation events and some species relationships have been difficult to resolve. Here we use ultraconserved elements and mitogenomes, with samples from all 15 extant species, to more precisely retrace how and when marmots came to inhabit a vast Holarctic range. Our results indicate marmots arose in North America in the mid Miocene (~16.3 Mya) and dispersed across the Bering Land Bridge in the late Pliocene (~3-4 Mya); in addition, our fossil-calibrated timeline is suggestive of the rise and spread of open grasslands as being particularly important to marmot diversification. The woodchuck (M. monax) and the Alaska marmot (M. broweri) are found to be more closely related to the Eurasian species than to the other North American species. Paraphyly is evident in the bobak marmot (M. bobak) and the hoary marmot (M. caligata), and in the case of the latter the data are highly suggestive of a second, cryptic species in the Cascade Mountains of Washington.

cultural heritage elements in Andalusia and demographic data sorted by urban category

Dataset concerning cultural heritage elements and demographic data in Andalusia at the municipality level, as they appear on SIMA (Sistema de Información Multiterritorial de Andalucía), March 2023. They have been sorted by urban category, depending on the number of inhabitants of each municipality: less than 1.000 inhabitants, 1.000 to 10.000 inhabitants, 10.000 to 100.000 inhabitants, and more than 100.000 inhabitants.

Massively Parallel Reporter Assays for High-Throughput In Vivo Analysis of Cis-Regulatory Elements

A library of 50 enhancers, each tested in three different lengths and with two different promoters (300 combinations), was packaged into AAV9 and delivered to newborn mice. Enhancers were selected from the VISTA Enhancer Browser of transgenic reporter data, and included 25 candidates active in the embryonic myocardium and 25 negative control candidates active in embryonic endothelium but not in myocardium. In the heart, AAV9 selectively transduces cardiomyocytes. After collecting ventricles at P28, the reporter transcripts were sequenced, and the frequency of each barcode was compared to its frequency in the viral pool DNA. Here we provide fastq files for each sample, an Excel spreadsheet (MPRA-Metadata.xls) containing annotation, and an Excel spreadsheet (MPRA-counts.xlsx) containing extracted barcode counts for each enhancer, as well as additional annotation and calculated enhancer activity.

Finite Element Analysis-Based Soft Robotic Modeling: Simulating a Soft Actuator in SOFA

This document represent a step by step guide for a simulation in SOFA framework of a cable driven soft robot.