Find research datasets worth reusing

opencc-by-4.0Sep 2024View details →

Potential map generated by the RF spatial model to define ideal zones for the occurrence of high density of giant trees in the Amazon

The provided image is a theoretical map of giant tree density in the Amazon, generated from a spatial model based on the **Random Forest** algorithm. The map displays the spatial distribution of tree density, representing the number of trees taller than 60 meters per square kilometer (trees/km²). The model was developed using climatic, topographic, and soil variables to predict areas with higher concentrations of these giant trees. The areas are color-coded according to different density ranges, where: - Lighter shades indicate lower tree density (≤ 5 trees/km²), - Darker shades indicate higher density (up to 141 trees/km²). Biogeographic provinces within the Amazon biome, such as the **Guiana Shield**, **Xingu-Tapajós**, and **Roraima**, are highlighted, showing distinct density patterns across the Amazon region. This map is a valuable tool for understanding the spatial distribution of giant trees in the Amazon and plays a crucial role in conservation efforts and ecological monitoring in the region.

opencc-by-4.0Oct 2024View details →

Development of a High-Energy-Density Lithiated Silicon-Sulfur Full Cell with Enhanced Stability and Longevity

The raw materials for the draft: "Development of a High-Energy-Density Lithiated Silicon-Sulfur Full Cell with Enhanced Stability and Longevity"

opencc-by-4.0Nov 2024View details →

Production of Marine Shrimp Integrated with Tilapia at High Densities and in a Biofloc System: Choosing the Best Spatial Configuration

Dataset with experimental results.

opencc-by-4.0Nov 2024View details →

2D visco-elasto-plastic subduction models in the presence of a high density and viscosity continental block

Three main models with different rheological conditions and density are incorporated for an imposed intrusion between the upper and lower continental crust. Output files for a model with a crust without intrusions are also incorporated. The file contains data on the conditions of plate motion velocity, plate age, plate thickness in Excel (Input_Data_Age_Vel.xlsx), a table with the rheology used to reproduce different numerical models incorporating the intrusion (Table_S3.pdf), and a file High_density_materials.m showing the construction of the intrusion within the continental crust. High_density_materials.m m should be imposed on the original I2ELVIS code provided by Taras Gerya - ETH Zürich, Institut für Geophysik, Switzerland - email: taras.gerya@erdw.ethz.ch The file has the main time steps as a function of temperature, viscosity, density and rock composition into the folders. If you want to visualize them please run the following Script PLOT_OUTPUT_DATA.m where, str=string(2040), represent the time_step Files are organized in a matrix form, each folder has the grid_x :coordinate matrix,  gridy_: coordinate matrix,  matrix_temperature_, density and viscosity. To plot the Rock composition. mx and my, tracer coordinates in x-direction and y-direction matrix_markcom is  matrix tracers.   Model 1 (Time step= 10= 14.99 Ma, 120= 14 Ma, 310= 12 Ma, 670 = 9 Ma, 1120 = 6 Ma, 1620 = 3 Ma, 2040 = 0 Ma)   The temperature, viscosity, density, and rock composition for the PHS slab are shown in this animation for Model 1.  This model is reproduced under the conditions of plate motion velocity and age from Figure 3 with an initial dip angle for the weak zone of 20°.   The high density material between the upper and lower crust in the vicinity of the slab is not included in Model 1.  The model evolves over a period of the last 15 Myr and shows a shallow subduction.  Model 2 (Time step= 10= 14.99 Ma, 120= 14 Ma, 380= 12 Ma, 850 = 9 Ma, 1490 = 6 Ma, 2090 = 3 Ma, 2540 = 0 Ma) With high density block The temperature,  viscosity, density, and rock composition for the PHS slab are shown in this animation for Model 2. This model is reproduced under the conditions of plate motion velocity and age from Figure 3 with an initial dip angle for the weak zone of 20°.  The high density material between the upper and lower crust in the vicinity of the slab is included in Model 2. The model evolves over a period of the last 15 Myr and shows a steep subduction. Model 3 (Time step= 10= 14.99 Ma, 120= 14 Ma, 310= 12 Ma, 670 = 9 Ma, 1120 = 6 Ma, 1690 = 3 Ma, 2040 = 0 Ma) Without high density block and high viscosity The temperature, viscosity, density, and rock composition for the PHS slab are shown in this animation for Model 3. This model is reproduced under the conditions of plate motion velocity and age from Figure 3 with an initial dip angle for the weak zone of 20°.  The initial high viscosity material and without high density between the upper and lower crust in the vicinity of the slab is included in Model 3. The model evolves over a period of the last 15 Myr and shows subduction with a high dip angle.  Model4 (Time step= 10= 14.99 Ma, 120= 14 Ma, 330= 12 Ma, 770 = 9 Ma, 1190 = 6 Ma, 1640 = 3 Ma, 2040 = 0 Ma)    With high density block and high viscosity The temperature, viscosity, density, and rock composition for the PHS slab are shown in this animation for Model 4. This model is reproduced under the conditions of plate motion velocity and age from Figure 3 with an initial dip angle for the weak zone of 20°.  The high density and high viscosity material between the upper and lower crust in the vicinity of the slab is included in Model 4. The model evolves over a period of the last 15 Myr and shows a steep subduction

opencc-zeroFeb 2023View details →

Patterns of frequency and density dependence are highly variable in diverse annual flowering plant communities

Applications of ecological theory to natural communities often assume that competitive, negative density-dependent processes are the only type of interaction important for diversity maintenance. Recent advances suggest that positive interactions within trophic levels (e.g. plant-plant) may also affect plant coexistence. Though positive plant-plant interactions theoretically might result in positive or nonmonotonic frequency or density dependence (FD/DD), less is known about how commonly these patterns occur, or which ecological processes might result in such patterns in natural plant communities. In this study, we test for signals of variable frequency and density dependence in annual flowering plant communities in Western Australia and search for evidence that interactions among plants during flowering might induce positive or nonmonotonic FD/DD in flowering plants. Using four common annual wildflower species, we ask if plant fecundity exhibits positive or nonmonotonic FD/DD and if pollinator-mediated plant-plant interactions during flowering change patterns of FD/DD relative to pollinator-independent plant interactions. Three species exhibited nonmonotonic (hump-shaped) density dependence, and only one species experienced strictly negative density dependence. Each species exhibited a different pattern of frequency dependence (positive, negative, weakly nonmonotonic, and no detectable frequency dependence). Pollinator-mediated plant-plant interactions during flowering induced both nonmonotonic density dependence and negative frequency dependence in one species. Importantly, the extent of variation in FD/DD observed in our study brings into question the dominance of negative density and frequency dependence in theory, suggesting instead that demographic responses of plants to their communities fall along a continuum of possible density- and frequency-dependent patterns.

opencc-by-4.0Feb 2023View details →

Dataset for: Supplementation of seasonal natural resources with year-round anthropogenic resources by coyotes in natural fragments within a high-density urban area.

Dataset for: Supplementation of seasonal natural resources with year-round anthropogenic resources by coyotes in natural fragments within a high-density urban area.  (Pending publication in Wildlife Biology as of 02/24/2023)

opencc-by-4.0Mar 2023View details →

Data for manuscript "Adaptive Ensemble Refinement of Protein Structures in High Resolution Electron Microscopy Density Maps with Radical Augmented Molecular Dynamics Flexible Fitting"

The tar file contains the input files for RADICAL augmented MDFF implementation (R-MDFF) for two protein systems, Adenylate Kinase (ADK) and Carbon Monoxide Dehydrogenase (CODH). These examples demonstrate the implementation of R-MDFF using RADICAL-Cybertools to flexibly fit biomolecules in cryo-EM density maps with on-the-fly decision making. All molecular simulations were performed using CUDA enabled NAMD 2.14 installed on OLCF Summit HPC resource. The CHARMM36 force field parameters were used for the proteins. Synthetic density maps were prepared at 1.8, 3 and 5 Å for ADK and 1.8 and 3 Å for CODH using VMD 1.9.3 software installed on OLCF Summit HPC resource. During the analysis stage, the cross correlation coefficients between density maps and atomic model were computed using VMD 1.9.3 on Summit HPC as part of the R-MDFF workflow. The source code is publicly available on GitHub: <a href="https://github.com/radical-collaboration/MDFF-EnTK">https://github.com/radical-collaboration/MDFF-EnTK </a> The preprint of this research is submitted on bioRxiv, doi: <a href="https://doi.org/10.1101/2021.12.07.471672">https://doi.org/10.1101/2021.12.07.471672 </a> To obtain maximum compression of the data, the tar command used to generate this tarball was: <pre><code class="language-bash">GZIP=-9 tar --exclude='last.pdb' --exclude='*last_from_prev_iter.pdb' --exclude='*old' --exclude='*log' --exclude='*coor' --exclude='*vel' --exclude='*xsc' --exclude='*dcd' --exclude='lastframepdbs_fix' --exclude='*out' --exclude='*sl' --exclude='*rs' --exclude='*prof' --exclude='*err' --exclude='*dx' --exclude='*grid.pdb' --exclude='*txt' -cvzf rmdffv2.tar.gz rmdff-zenodo/</code></pre>

opencc-zeroApr 2023View details →

High population density and large body mass lead to increased reproductive success

Although population density and phenotype are known to alter the mating strategies of individuals, their impacts on reproductive success have not been fully investigated. We examined genetic mating system variation (number of mating partners), reproductive success (offspring number) and sperm competition intensity (sires per litter) in semi-natural populations of Brandt's voles (Lasiopodomys brandtii) under low-, medium- and high-densities. We used 12 microsatellite genetic markers and parentage assignment of 3,516 voles, with the aim of identifying the number of mating partners and offspring produced by founder individuals. We provided strong evidence that individuals with more mating partners experienced increased reproductive success, as measured by the production of more offspring, compared with individuals that had fewer mating partners. Further, we found that large males had more mating partners (especially in high-population density enclosures) and also produced more offspring relative to smaller males. A high density of founder individuals led to more sires per litter but greater paternity share across litters (reduced paternity skew). Our results suggest that a polygamous mating system and increased body size should be favored by natural selection, and density-dependent variation in mating strategy would be sufficient to stabilize reproductive fitness under unfavorable conditions such as high founding density.

opencc-zeroApr 2023View details →

Data from: Supplementation of seasonal natural resources with year-round anthropogenic resources by coyotes in natural fragments within a high-density urban area

Coyotes (Canis latrans) in urban landscapes provide important food web functions and ecological services but can also trigger human-wildlife conflict when their diet includes anthropogenic resources or domestic pets. As adaptable omnivores, coyotes adjust their diet to their environment, routinely switching among food items to accommodate spatial and seasonal differences in availability. To evaluate coyotes' potential impacts within the food web of urban Long Beach, California where human-wildlife conflict involving coyotes may occur, we analyzed 115 scat samples collected once every two weeks from two open space fragments inside the urban matrix. We hypothesized that differences in scat composition would correlate with seasonal and site differences, with greater use of anthropogenic resources during the dry season supplementing lower prey availability, and greater consumption of wild mammal prey during the wet season when rabbits and small mammals reproduce. We found coyote diet was predominately composed of natural prey and vegetation year-round. Mammals made up more of the coyote diet in the wet season than the dry, while arthropods and vegetation occurred more in dry season scats. Coyotes relied on rabbits as their main prey year-round across all sites. Domestic cats (Felis catus) were the third most common individual prey species found in coyote scats; we did not find evidence of domestic dog (Canis lupus familiaris) consumption. The overall frequency of mammalian remains did not differ across sites but did differ across sites for other prey types. While there is a potential for human-wildlife conflict in coyote's consumption of feral or domestic cats, coyotes may also be providing an ecological service by reducing cats in natural habitat fragments.

opencc-zeroApr 2023View details →

Data for: Invasive brown widow spiders avoid parasitism despite high densities

Invasive species are sometimes less susceptible to natural enemies compared to native species, but the mechanism is often unclear. Here we tested two potential mechanisms for lower parasitism of invasive species: density-dependent parasitism and preference for human-dominated habitats. We investigated how variation in host density and habitat type affect egg sac parasitism in two widow spider species (family Theridiidae). We compared parasitism on the egg sac of the brown widow, Latrodectus geometricus, an urban invasive species, and the white widow, L. pallidus, a species native to Israel. To investigate variation in host and parasitoid density, we measured nearest-neighbor distance between spider webs and parasitism rates in 16 sites, and in a single site monthly throughout a year. In L. pallidus, denser sites were more heavily parasitized (up to 55%) and parasitism rate increased with population density throughout the season. Extremely dense L. geometricus populations, however, had very low rates of parasitism (0-5%). We then conducted an egg sac transplant experiment in human-dominated and natural habitats. We found no parasitism of either species in the human-dominated habitat, compared to 30% parasitism of both species in the natural habitat. In addition, we found evidence for higher predation of L. pallidus than of L. geometricus egg sacs, particularly in the natural habitat. These combined results suggest that the human-dominated habitats inhabited by L. geometricus have a lower abundance of predators and parasites. We conclude that lower parasitism and predation in human-dominated habitats could contribute to the invasion success of L. geometricus.

opencc-by-4.0May 2023View details →

Field Application of a High-Power Density Electromagnetic Energy Harvester to Power Wireless Sensors in Transportation Infrastructures

Traffic-induced vibration of transportation infrastructures is a reliable source of kinetic energy, which can be harvested to power conventional monitoring sensors and peripherals installed on bridges, thereby reducing some dependence on non-renewable energy. The highway statistics shows that the average daily vehicles miles travelled in the US is more than 5 billion. This is a massive source of kinetic energy that lies unused in the national transportation network. This study focuses on the design and field testing of a high-power density electromagnetic energy harvester (EMEH) to convert such a kinetic energy into electrical energy for powering ubiquitous sensors installed on transportation infrastructures. The principal investigators have been investigating the design of the EMEH using analytical and finite element simulations, as well as, its laboratory prototype fabrication and testing in the first phase. The proposed EMEH utilizes the innovative concept of creating planar array of large number of small permanent magnets through certain optimization criteria to achieve strong and focused magnetic field in a particular orientation. The proposed EMEH has a compact design, such that it can be integrated into the power circuit of wireless sensor nodes (WSNs) and installed at suitable part of a transportation infrastructure without elaborate wiring. It is capable of continuously charging the rechargeable battery of a WSN, thereby extending the lifespan of the monitoring system, almost, indefinitely. For the next phase of this research, the principal investigators propose the development and field implementation of a larger scale and more compact version of the EMEH with a minimum of 500 mW output power to be installed on selected transportation infrastructures for the evaluation of its energy harvesting efficiency and capability to derive different types of monitoring sensors and peripherals. Three different highway bridges with different fundamental frequencies, ideally between 2Hz to 8Hz, will be selected for the field testing of the EMEH. An acceleration sensor will be used to record the traffic-induced vibration of each bridge during a normal daily traffic that after signal processing is used to measure the fundamental frequency of that bridge. The dynamic characteristics of the proposed EMEH (i.e. tip mass and spring stiffness) will be modified to put it into a resonant condition with the bridge by matching their natural frequencies. The output power will be monitored and used to continuously charge a rechargeable battery powering a wireless sensor. The focus is on the feasibility of the proposed EMEH to power sensors that are used to regularly monitor the structural integrity of materials and components of highway bridges such as acceleration and temperature sensors.

opencc-by-4.0Jun 2023View details →

Complex Whistler-Mode Wave Features Created by a High Density Plasma Duct in the Magnetosphere

Raytracing simulation trajectories (from "DenRay" code) for modeling an RBSP observation of a duct-like structure in the magnetosphere. The data is saved in MATLAB's '.mat' format. it contains the following variables: x: x- position of rays z: z- position of rays kx: x-component of whistler mode wavevector kz: x-component of whistler mode wavevector t: vector of times along ray trajectory The dataset includes 10,000 rays and 859 time steps per ray. Please contact Vijay Harid (vijay.harid@ucdenver.edu) for specifics on the simulation.

opencc-zeroAug 2023View details →

Data from: Electrical imaging of cortical and spinal axons using high-density microelectrode arrays

<div> <div> <div> Mammalian axons are specialized for transmitting action potentials to targets within the central and peripheral nervous system. A growing body of evidence suggests that, besides signal conduction, axons play essential roles in neural information processing, and their malfunctions are common hallmarks of neurodegenerative diseases. The technologies available to study axonal function and structure integrally limit the comprehension of axon neurobiology. Complementary-metal-oxide-semiconductor (CMOS) -based high-density microelectrode arrays (HD-MEAs) have been designed to record extracellular action potentials from neuronal cultures and allow tracking axonal signals across hundreds of microelectrodes. Thanks to a low-noise CMOS-design, HD-MEAs enable detection of APs across entire arbors of cortical axons. HD-MEAs provide noninvasive access to axonal action potentials and impose no constraints on the duration of the recording sessions. Here we present extracellular electrical activity recorded from rat's primary neurons using CMOS-based HD-MEA system (MaxWell Biosystems AG). Datasets comprise electrophysiological recordings obtained from primary motor and cortical neurons. Recorded signals were up-sampled to 200 kHz following the Whitaker-Shannon interpolation formula. Recorded signals were spike-sorted and spike-trigger averaged across an entire array (26400 electrodes). Such signal representation is referred to as 'axonal electrical image'. </div> </div> </div>

opencc-by-4.0Sep 2023View details →

The Genomic Reference Resource for African Cattle: genome sequences and high-density array variants.

The diversity in genome resources is fundamental to designing genomic strategies for local breed improvement and utilisation. These resources also support gene discovery and enhance our understanding of the mechanisms of resilience with applications beyond local breeds. We report here the genome sequences of 573 samples (198 new genomes) and high-density (HD) array genotyping of 1,082 samples (537 new samples) from indigenous African cattle populations. The new sequences have an average genome coverage of ~30X, three times higher than the average (~10X) of the over 300 sequences already in the public domain. Following variant quality checks, we identified approximately 32.4 million sequence variants and 661,943 HD autosomal variants mapped to the Bos taurus reference genome (ARS-UCD1.2).  The new datasets were generated as part of the Centre for Tropical Livestock Genetic and Health (CTLGH) Genomic Reference Resource for African Cattle (GRRFAC) initiative, which aspires to facilitate the generation of this livestock resource. We hope this resource will be utilised by the global scientific community and breeders for sustainable global livestock improvement.

opencc-zeroSep 2023View details →

Updated Pinus lambertiana high-density linkage maps

Sugar pine (Pinus lambertiana) is a five-needle pine of great economical and ecological importance in western North America. Genome-wide analyses in the species have been limited by the absence of a chromosome-scale reference genome. The genome of the species is one of the largest in any plant diploid species, with a size of 31 Gb, making assembly and annotation very challenging. Here we present high-density linkage maps that were used to help scaffolding a new chromosome-scale genome of sugar pine (assembly version 2.0, unpublished).

Effects of Pioglitazone on High-density Lipoprotein (HDL) Function in Persons With Diabetes

ClinicalTrials.gov study NCT01156597. IPD Sharing: Not stated. Countries: 1. Publications: 5.

controlledIPD-YESFeb 2026View details →

A Study Assessing Arrhythmia Mapping With a Globe-Shaped, High-Density, Multi-Electrode Mapping Catheter

ClinicalTrials.gov study NCT05373862. IPD Sharing: YES. Countries: 3. Publications: 15.

Substrate Ablation Guided by High Density Mapping in Atrial Fibrillation

ClinicalTrials.gov study NCT02093949. IPD Sharing: Not stated. Countries: 1. Publications: 1.

Study of Niacin on Endothelial Function in HIV-infected Subjects With Low High Density Lipoprotein Cholesterol Levels

ClinicalTrials.gov study NCT00986986. IPD Sharing: Not stated. Countries: 1. Publications: 1.

Tomato Consumption and High Density Lipoprotein-cholesterol

ClinicalTrials.gov study NCT01342666. IPD Sharing: Not stated. Countries: 1. Publications: 10.