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464 results for “high density”
FAB 1: Forests and Biodiversity Experiment - High density diversity experiment: carbon budget data
This data represents changes in above and belowground C pools in young stands six years after the initiation of the Forests and Biodiversity experiment (FAB1) in 2013, consisting of high density plots of one, two, five, or 12 tree species planted in a common garden. Trees were planted to represent a range of native functional diversity, including needle-leaf conifer and broadleaf deciduous species as well as ectomycorrhizal and arbuscular mycorrhizal species. We quantified the effects of species richness, phylogenetic diversity, and functional diversity on aboveground C accumulation, as well as on soil C accumulation, fine root C, and soil aggregation. To assess the role of the microbial community in mediating these effects, we further compared changes in soil C pools to phospholipid fatty acids (PLFAs) profiles collected in 2016.
Dataset of "Black Titanium Oxide/Activated TaS2 Flakes Photoelectrode for Plasmon Assisted Hydrogen Evolution at Neutral pH at High Current Density"
<p>Nanotubular structure of black titania with sputtered gold and incorporation of 3R-TaS2 self-activated flakes for high current density and neutral pH usage for hydrogen evolution reaction. Dataset consists of electrochemical data (LSV, EIS, CA), x-ray difractograms, Raman spectra, SEM images with EDX mapping, UV-vis spectra, DEMS records, ICP-MS records, XPS spectra and compositional analysis and BET records.</p>
High-Throughput Density Functional Theory Screening of Double Transition Metal MXene Precursors
<p>This dataset contains density functional theory results on a set of double-transition metal MXene precursors</p>
Predator effects on metamorphosis: The effects of scaring versus thinning at high prey densities.
Organisms with complex life cycles face the challenge of when to switch between habitats and foraging strategies over ontogeny in ways that improve their fitness. Metamorphosis is a well-studied life history event in animals and ecologists have spent decades trying to understand how the size at and time to metamorphosis are altered by natural stressors such as competition and predation. The challenges in interpreting the effects of predators on metamorphic decisions include the need to compare predator species that pose different levels of risk, compare the roles of predators inducing fear versus thinning of the density of prey, and examine prey life history traits and behavior over ontogeny. We addressed these challenges in a mesocosm experiment in which we introduced a high initial density of hatchling Northern Leopard Frogs (Rana pipiens) and exposed them to three different species of caged predators (to induce three different levels of fear), three rates of hand-thinning (to mimic the thinning effect of each predator), or three species of lethal predators (to cause induction and thinning). Under these initial high densities, we found that caged predators had no effects on tadpole activity, growth, and development. This outcome was likely due to the high density of tadpoles causing high competition, which can inhibit anti-predator responses. High rates of hand thinning caused decreased tadpole activity, greater mass, and faster development. Interestingly, lethal predators caused phenotypic changes that were largely in line with the hand thinning effects alone. These results suggest that at high initial prey densities, the thinning process of predation appears plays a much more important role in prey metamorphosis than induction from predatory chemical cues.
Invert species counts and density along transects on the high marsh along Rowley River tidal creeks associated with long term fertilization experiments, Rowley, MA.
At PIE, mummichog (Fundulus heteroclitus) use the spring-cycle high tides to access the flooded high marsh platform and consume invertebrate prey. Invertebrate surveys were conducted before and after spring tides that flooded the high marsh area to determine the effect of mummichog predation that occurs on the high marsh during the flood events and to assess the impact of low marsh geomorphology on top-down control by mummichog. These data were included in part of the study "Cross-habitat access modifies the ‘trophic relay’ in New England saltmarsh ecosystems” (Lesser et al. 2021) as well as a part of a NEU Three Seas Master's thesis.
High-marsh epifauna densities within references and ice-rafted sediment deposits, Rowley, MA.
Following a historic bomb cyclone (Winter Storm Grayson) in January of 2018, a large volume of ice-rafted sediment was patchily deposited on the surface of salt marshes in the Great Marsh, MA. In May of 2018, twenty patches of ice-rafted sediments and paired reference sites (i.e., no sediment deposition) were delineated. In May 2018, August 2018, and August 2019, samples were collected to examine how ice-rafted sediments affected vegetation, infauna, and epifauna recovery over time. This specific dataset focuses on epifauna species counts, with the primary species including: Melampus bidentatus, Littorophiloscia vittata, and Orchestia grillus. This dataset is complete and please see our publication (https://doi.org/10.1007/s12237-021-01023-z) for more information.
High-marsh infauna densities within references and ice-rafted sediment deposits, Rowley, MA.
Following a historic bomb cyclone (Winter Storm Grayson) in January of 2018, a large volume of ice-rafted sediment was patchily deposited on the surface of salt marshes in the Great Marsh, MA. In May of 2018, twenty patches of ice-rafted sediments and paired reference sites (i.e., no sediment deposition) were delineated. In May 2018, August 2018, and August 2019, samples were collected to examine how ice-rafted sediments affected vegetation, infauna, and epifauna recovery over time. This specific dataset focuses on infauna species counts, with the primary species including: mites, Manayunkia aestuarina, and Cernosvitotviella immota. This dataset is complete and please see our publication (https://doi.org/10.1007/s12237-021-01023-z) for more information.
CO excitation, molecular gas density and interstellar radiation field in local and high-redshift galaxies
<p>This dataset includes the SED fitting figures and full sample table produced in the study of Liu et al. (2020, ApJ). Two example figures are shown in the Figure 1 of the paper. And selected columns of the full sample table is shown in the Table 1 of the paper. </p> <p> </p>
A machine learning-based high-precision density functional method for drug-like molecules
<h2><strong>Models</strong></h2><p>The repo contains the models and test datasets for our aticles. The energy unit is in <strong>Hartree,</strong> The coordinate unit is in<strong> Bohr.</strong></p><p><strong>## DeePHF</strong></p><p>you need first prepare the `dm_eig.npy` in data_test and do predict `l_e_delta.npy`, you can use</p><p>```</p><p>deepks test -m model.pth -o test/test -d data_test/* -D dm_eig -G</p><p>```</p><p><strong>## DeePKS</strong></p><p>first you should prepare the `atom.npy`, and `energy.npy` in data_test. you can test the datasets by command. </p><p>```</p><p>deepks scf scf_input.yaml -m model.pth -s data_test -d test_out</p><p>```</p><p><strong># Datasets</strong></p><p>All datasets only have `atom.npy` and `energy.npy`. The coordinate unit is `bohr`, and energy unit is `Hartree`.</p><p><strong>## small molecules torsion</strong></p><p>Contains 62 small molecules with 36 conformation for each under CCSD(T)/def2-TZVP.</p><p><br> </p><p>[1] B. D. Sellers, N. C. James, A. Gobbi, A comparison of quantum and molecular mechanical methods to estimate strain energy in druglike fragments, Journal of chemical information and modeling 57 (6) (2017) 1265–127</p><p><br> </p><p><strong>## MPCONF91</strong></p><p>Contains 6 molecules with 91 conformations under LNO-CCSD(T)/def2-TZVP.</p><p><br> </p><p>[1] J. Rezac, D. Bím, O. Gutten, L. Rulisek, Toward accurate conformational energies of smaller peptides and medium-sized macrocycles: Mpconf196 benchmark energy data set, Journal of chemical theory and computation 14 (3) (2018) 1254–1</p><p><br> </p><p><strong>## torsionNet206</strong></p><p>Contains 206 molecules with 4494 conformations under CCSD(T)/def2-TZVP.</p><p><br> </p><p>[1] B. K. Rai, V. Sresht, Q. Yang, R. Unwalla, M. Tu, A. M. Mathiowetz,G. A. Bakken, Torsionnet: A deep neural network to rapidly predict small-molecule torsional energy profiles with the accuracy of quantum mechanics, Journal of Chemical Information and Modeling 62 (4) (2022) 785–80</p><p><br> </p><p><strong>## Out-of-plane bending</strong></p><p>Contains 242 molecules with 3315 conformations under CCSD(T)/def2-TZVP.</p><p><br> </p><p>[1] X. Yang, C. Liu, P. Ren, High order ab initio valence force field with chemical pattern based parameter assignment., Journal of Computational Biophysics and Chemistry 21 (4) (2021) 43</p><p><br><br> </p><p><strong>## DrugBank-T</strong></p><p>Contains 165 molecules with 1155 conformations under CCSD(T)/def2-TZVP.</p><p><br> </p><p>[1] V. Law, C. Knox, Y. Djoumbou, T. Jewison, A. C. Guo, Y. Liu, A. Maciejewski, D. Arndt, M. Wilson, V. Neveu, et al., Drugbank</p><p>4.0: shedding new light on drug metabolism, Nucleic acids research 42 (D1) (2014) D1091–D1097 </p><p>[2] Z. Qiao, M. Welborn, A. Anandkumar, F. R. Manby, T. F. Miller III, Orbnet: Deep learning for quantum chemistry using symmetry adapted atomic-orbital features, The Journal of chemical physics 153 (12) (2020) 124111</p><p><strong>## Notice</strong></p><p>if you use above datasets, please cite the original articals too</p>
Root phytohormone levels of mangrove seedlings grown in soils of low and high bulk density
<p>These data contain information on root traits and concentrations of multiple hormones in root tissue of two mangrove species grown under low and high soil bulk density conditions. Inhibitors were used to assess the role of the phytohormone ethylene.</p> <h2>Description of the data and file structure</h2> <p>The root trait file contains total root length (cm), mean root length (cm), root dry weight (g), and root number data for two mangrove species (Avicennia marina, Rhizophora stylosa) grown under two different soil bulk densities: 0.2 and 1.0 g cm^-3. Treatment refers to the application of ethylene inhibitors (CoCl2: cobalt chloride, AIB: aminoisobutyric acid, control).</p> <p>The phytohormone file contains the root tissue concentrations (all in ng g^-1) for multiple hormones (ABA: abscisic acid, ACC: 1-aminocyclopropane-1-carboxylic acid, GAx: gibberellins, IAA: indole-3-acetic acid, iP: isopentenyl adenine, JA: jasmonic acid, SA: salicylic acid, tZ: cytokinin <em>trans</em>-zeatin) of two mangrove species (Avicennia marina, Rhizophora stylosa) grown under two different soil bulk densities: 0.2 and 1.0 g cm^-3. Treatment refers to the application of ethylene inhibitors (CoCl2: cobalt chloride, AIB: aminoisobutyric acid, control).</p> <p> </p> <p> </p>
Impact of the PSR J0740+6620 radius constraint on the properties of high-density matter: Neutron star equation of state posterior samples
<p>Equation of state posterior samples associated with Legred et al., "Impact of the PSR J0740+6620 radius constraint on the properties of high-density matter," Phys. Rev. D 104, 063003 (2021); doi:10.1103/PhysRevD.104.063003</p> <p> </p> <p>Three sets of 1e4 samples from the posterior distribution over equations of state are provided. These sets are drawn from the posterior conditioned on different combinations of radio pulsar observations, gravitational wave data, and NICER x-ray measurements. The data release contains the equation of state table and the corresponding table of neutron star observables for each sample. The posterior distributions one can generate from these samples approximate those plotted in Figs. 1-6 of the accompanying paper.</p> <p> </p> <p>Refer to the readme for usage information.</p>
Impact of the PSR J0740+6620 radius constraint on the properties of high-density matter : Weighted Monte Carlo samples for neutron star observables
<p>This data release contains weighted Monte Carlo samples associated with</p> <p>Legred, Chatziioannou, Essick, Han, and Landry, 2021</p> <p>"Impact of PSR J0740+6620 radius constraint on the properties of high-density matter"</p> <p>Phys. Rev. D 104, 063003;</p> <p>doi:10.1103/PhysRevD.104.063003</p> <p> </p> <p> </p> <p> </p> <p> </p>
Supplementary materials for "TUJI1 Dataset: Multi-device dataset for indoor localization with high measurement density"
<p>Supplementary materials for "TUJI1 Dataset: Multi-device dataset for indoor localization with high measurement density"</p> <p> </p> <p>For more information please refer to the data descriptor available at: https://www.sciencedirect.com/science/article/pii/S2352340924003251</p> <p>Please cite as:</p> <p>Klus, L., Klus, R., Lohan, E.S., Nurmi, J., Granell, C., Valkama, M., Talvitie, J., Casteleyn, S. and Torres-Sospedra, J., 2024. TUJI1 Dataset: Multi-device dataset for indoor localization with high measurement density. <em>Data in Brief</em>, p.110356.</p> <p> </p>
Genetic diversity, population structure, and linkage disequilibrium among tropical quality protein maize (QPM) lines assessed with high-density SNP markers
<p>The study of genetic diversity (GD), population structure, and linkage disequilibrium (LD) provides a better understanding of the genetic relationships between individuals in a population which can be utilized in crop research and improvement. Genotyping-by-sequencing (GBS) was used to detect and genotype single nucleotide polymorphisms (SNPs) in a collection of 74 quality protein maize (QPM) lines and further to characterize their genetic diversity, population structure, and linkage disequilibrium. A total of 235,214 high-quality SNPs were used for different genetic analyses except for structure analysis where 11,950 SNPs were used. Analysis of molecular variance (AMOVA) based on these SNPs revealed high genetic heterozygosity among the five populations with 1% of the total genetic variation present among the subpopulations and 99% of the variation among individuals within the populations. Population structure analysis using Bayesian-based clustering revealed that the 74 lines could be clustered into four groups. However, neighbor-joining trees indicate the lines are grouped into three major clusters. Further analysis using principal component analyses (PCA) clustered the genotypes into five groups which are concordant with the groups based on pedigree information. Higher genetic diversity was detected in population 1 with a GD value of 0.484 and the lowest in population 5 (0.396) and overall, with a mean of 0.434. The LD pattern in the quality protein maize was investigated and we observed a relatively rapid LD decay of 3.53kb and 10.66kb at r<sup>2</sup> =0.2 and r<sup>2</sup>= 0.1, respectively. Our findings provide important information for future Linkage mapping studies, genome-wide association analyses, and marker-assisted selective breeding of maize as well as genomic prediction-based selection in tropical germplasm.</p>
Sapling Census:FAB 1: Forests and Biodiversity Experiment - High density diversity experiment
A forest biodiversity experiment (FAB) focused on trees of our region investigates the consequences of multiple dimensions of tree diversity for soil, food webs, plant communities and ecosystems. FAB is designed to unravel effects of three forms of biological diversity: species richness (SR), functional diversity (FD), and phylogenetic diversity (PD). We define FD as the representation of multiple traits of leaves, roots, seeds, and the whole organism that are correlated with species positions along gradients of resource supply, growth, and decomposition. PD is the representation of evolutionary lineages measured as the genetic distances between species. While PD and FD are often correlated, convergent evolution and adaptive differentiation can decouple them. When functional traits that drive specific ecosystem functions are not phylogenetically conserved, PD and FD may give contrasting predictions. SR, PD, and FD are not independent, and we posit that PD may help explain SR effects, and FD may help explain both PD and SR effects. Thus FAB is designed to examine the separate and combined effects of all three components of diversity for multiple ecosystem functions and to distinguish between ???sampling??? and ???complementarity??? effects of biodiversity. Due to the long lag between planting tree seedlings and determining effects of tree composition and diversity on ecosystem functioning, fewer experiments have been established to elucidate the role of biodiversity in the functioning of forest ecosystems than grassland experiments. FAB will contribute to this gap and is a member of the IDENT and TreeDiv network of forest biodiversity experiments (www.treedivnet.ugent.be). Hypotheses: 1. PD, FD, and SR will all contribute to increased productivity, stability, and diversity of other trophic levels (herbivores, predators, parasitoids, soil microbes, soil flora and fauna) as well as to greater soil C sequestration. 2. Because PD incorporates both the number of species a
High-marsh invertebrate densities for Rowley River tidal creeks associated with long term fertilization experiments, Rowley and Ipswich, MA.
Density (individuals per m2) of epibenthic invertebrate (on the surface such as snails and amphipods) for Rowley River tidal creeks associated with long term fertilization experiments, Rowley and Ipswich, MA. The TIDE project aims to simulate eutrophication on a large scale by the addition of NO3- aiming to reach 70μM concentrations from May to September every year during the growing season. Marsh fertilization from 2004 - 2016 at Sweeney Creek and 2005, and 2009-2016 at Clubhead Creek. Nutrient enrichment ended in 2016.
High density SNP genotypes (Infinium Human CytoSNP-850K v1.2 BeadChip) of ERAP2-WT and ERAP2-KO Birdshot LCL
<p>SNP genotype data was performed on DNA isolated from WT and CRISPR-Cas9 edited LCLs (ERAP2-KO) according to standard procedures using the Infinium Human CytoSNP-850K v1.2 BeadChip (Illumina, San Diego, CA, USA). SNP-array results and data analysis were carried out using NxClinical software v5.1 (BioDiscovery, Los Angeles, CA, USA). Human genome build Feb. 2009 GRCh37/hg19 was used. </p>
Resting-State High-Density EEG using EGI GES 300 with 256 Channels of Healthy Elders, People with Subjective and Mild Cognitive Impairment and Alzheimer's Disease
<p>This repository contains Matlab files including 4 samples of resting-state EEG recording for Alzheimer's Disease (AD), Mild Cognitive Impairment (MCI), Subjective Cognitive Decline (SCD), and Healthy Controls (HC) using the HD-EEG EGI GES 300.</p> <p><strong>[AD: i108, MCI: i100, SCD: i090, HC: s055]</strong></p> <p> </p> <p><strong>Participants & Settings</strong></p> <p>In total 230 participants have been recruited from the memory and dementia clinic of the Greek Association of Alzheimer’s Disease and Related Disorders (GAADRD) and the 1st Department of Neurology, U.H. AHEPA, Aristotle University of Thessaloniki, Greece.</p> <p>The full dataset includes:</p> <p><strong>Healthy Controls Elders (60+ years old)</strong>: 33 participants</p> <p><strong>Subjective Cognitive Decline:</strong> 34 participants</p> <p><strong>Mild Cognitive Impairment</strong>: 79 participants</p> <p><strong>Alzheimer's Disease</strong>: 48 participants</p> <p><strong>Healthy Young (25-40 years old):</strong> 36 participants</p> <p>The study was carried out in accordance with the Declaration of Helsinki and received approval by the Scientific and Ethics Committee of GAADRD (No56_27/11/2016), and written informed consent was obtained from all participants prior to their participation in the study. The diagnosis of AD was conducted by a neuropsychiatrist according to their medical history, neuropsychological performance, structural magnetic resonance imaging (MRI), and clinical and neurological examinations.</p> <p>Participants with AD fulfilled the National Institute of Neurological and Communication Disorders and Stroke/Alzheimer’s Disease and Related Disorders Association (NINCDS-ADRDA) criteria for probable AD, as well as the Diagnostic and Statistical Manual of Mental Disorders (DSM-V) criteria for dementia of Alzheimer’s type (American Psychological Association, 1994). On the other hand, the MCI participants fulfilled the Petersen criteria, while the SCD group met International Working Group-2 guidelines and the recent National Institute on Aging-Alzheimer’s Association workgroups on diagnostic guidelines for Alzheimer’s disease (NI-AA), as well as the SCD-I Working Group instructions. </p> <p><strong>Resting-State EEG Recording</strong></p> <p>Fifteen-minute resting EEG activity was recorded for all the participants. For the whole duration of the resting state EEG recording, participants were advised to keep themselves relaxed as much as possible, close their eyes and open them after the researcher’s demand, sit still, minimize blinking or mouth movements and let their mind wander. The experimental procedure was monitored by a research assistant aiming to identify cases of horizontal eye movements, continued blinking, or excessive movement by visually inspecting the EEG traces during the experiment. More specifically, an EEG was registered for both resting conditions (eyes open, EO and eyes closed, EC) for at least 2–3 min for each period.</p> <p><strong>EEG Data Acquisition</strong></p> <p>The EEG data were collected by using the EGI 300 Geodesic EEG system (GES 300, CERTH-ITI, Thessaloniki, Greece) with a 256-channel HydroCel Geodesic Sensor Net (HCGSN) and a sampling rate of 250 Hz (EGI Eugene, OR). Moreover, the researcher placed the electrodes in accordance with the 256 HCGSN adult 1.0 montage system, while the signals were recorded relative to a vertex reference electrode (Cz), with AFz as the ground electrode with the electrodes’ impedance below 50 kΩ throughout the experimental procedure, as recommended for the high-input impedance amplifier. In detail, the HD-EEG data were analyzed offline in order to detect any artifact, as well as to conduct pre-processing (filtering, segmentation, bad channel replacement) using Net Station 4.3 software (EGI). HD-EEG data were initially filtered with a 5th-order bandpass Butterworth IIR filter of 0.3–30 Hz. Once the segmentation was completed, the detection of artifacts was performed by using the Net Station artifact detection tool for the automatic detection of excessive eye blinking and movement. Afterward, the signals were baseline corrected using 200 msec before the start of the experiment period and average re-referenced to transform them into reference-independent values.</p> <p> </p> <p><strong>Full Dataset Access</strong></p> <p>More information about the sample dataset and access to the full dataset can be available after request via e-mail:</p> <p><strong>Ioulietta Lazarou</strong> BSc, MSc, PhD candidate</p> <p>Neuropsychologist - Clinical Research Associate </p> <p>Centre for Research and Technology Hellas (CERTH), Information Technologies Institute (ITI)</p> <p>6th km Charilaou-Thermi Road, P.O. Box 60361, 57001 Thermi-Thessaloniki, Greece</p> <p>E-mail: <a href="mailto:iouliettalaz@iti.gr">iouliettalaz@iti.gr</a></p>
Evolution under pH stress and high population densities leads to increased density-dependent fitness in the protist Tetrahymena thermophila
<p>Abiotic stress is a major force of selection that organisms are constantly facing. While the evolutionary effects of various stressors have been broadly studied, it is only more recently that the relevance of interactions between evolution and underlying ecological conditions, that is, eco-evolutionary feedbacks, have been highlighted. Here, we experimentally investigated how populations adapt to pH-stress under high population densities. Using the protist species <em>Tetrahymena thermophila</em>, we studied how four different genotypes evolved in response to stressfully low pH conditions and high population densities. We found that genotypes underwent evolutionary changes, some shifting up and others shifting down their intrinsic rates of increase (<em>r<sub>0</sub></em>). Overall, evolution at low pH led to the convergence of <em>r<sub>0</sub></em> and intraspecific competitive ability (<em>α</em>) across the four genotypes. Given the strong correlation between <em>r<sub>0</sub></em> and <em>α</em>, we argue that this convergence was a consequence of selection for increased density-dependent fitness at low pH under the experienced high density conditions. Increased density-dependent fitness was either attained through increase in <em>r<sub>0</sub></em> , or decrease of <em>α</em>, depending on the genetic background. In conclusion, we show that demography can influence the direction of evolution under abiotic stress.</p> <p> </p>
High density genotypes of French Sheep populations
<p>Genotypes of 27 French sheep populations on the Illumina Ovine HD SNP chip.</p> <p>Dataset and results are presented in the preprint:</p> <p><strong>High density genome scan for selection signatures in French sheep reveals allelic heterogeneity and introgression at adaptive loci. </strong>Christina Marie Rochus, Flavie Tortereau, Florence Plisson-Petit, Gwendal Restoux, Carole Moreno-Romieux, Gwenola Tosser-Klopp, Bertrand Servin. bioRxiv 103010; doi: https://doi.org/10.1101/103010</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.