Find research datasets worth reusing

opencc-by-4.0Feb 2023View details →

Modeled wintertime sea ice drift, sea ice thickness, dynamic sea surface height and sea ice drift budget terms in the Arctic

Modeled wintertime sea ice drift, sea ice thickness, dynamic sea surface height and sea ice drift budget terms in the Arctic between 1981 and 2020.

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-by-4.0Feb 2023View details →

A quantitative autonomous bioluminescence reporter system with a wide dynamic range for Plant Synthetic Biology

This data set includes: Luminescence (NeoLuc Luminescence), Fluorescence (eGFP) , NeoLuc/eGFP ratios, Area Under The Curve of NeoLuc/eGFP ratios, Normalized Area Under The Curve of Neoluc/eGFP (FBP-RTAs), Firefly Luciferase luminescence (FLuc), Renilla Luciferase luminescence (RLuc), FLuc/RLuc ratios and Normalized  FLuc/RLuc values of all experiments in this work.

opencc-by-4.0Feb 2023View details →

Materials to accompany "Dynamic Theologies: the Ruthwell Cross from an Irish perspective" (2023) by Éamonn Ó Carragáin

Materials to accompany "Dynamic Theologies: the Ruthwell Cross from an Irish perspective" by Éamonn Ó Carragáin.

Short-term, but not long-term grooming reciprocity in a species with high fission-fusion dynamics

Reciprocity allows animals to balance the costs and benefits of cooperative interactions by switching roles over time. Reciprocity can be based on two different processes: partner control and partner choice. Although not mutually exclusive, the relative roles of the two processes remain debated. We investigated grooming reciprocity in wild Geoffroy's spider monkeys (Ateles geoffroyi), a species with low grooming rates and reduced opportunities for group members to interact due to a high degree of fission-fusion dynamics. We assessed separately the roles of partner control and partner choice in grooming exchanges and investigated the factors affecting reciprocity. We found short-term reciprocity based on partner-control with reciprocation occurring within 401 s after receiving grooming. In contrast, we did not find evidence for long-term reciprocity based on partner choice. Short-term reciprocity based on partner control was not affected by kinship, whereas reduced time spent together in the same subgroup increased the probability of short-term grooming reciprocation. Our results suggest the opportunity to interact is a potent modulator of reciprocity. In species characterized by a high degree of fission-fusion dynamics and low grooming rates, short-term reciprocation based on partner control can be favoured at the expense of partner choice.

Supplementary Tables and Datasets for publication: Spatial and finely tuned temporal metagenomics of river compartments reveals viral community dynamics in an urban stream

This is a data dump of the tables, genomes, and .faa files that were too large to submit as part of the publication titled: Spatial and finely tuned temporal metagenomics of river compartments reveals viral community dynamics in an urban stream   Files here include: -Fasta file containing 1230 vMAGs. -Zip file containing individual fasta files for 125 MAGs -Annotations output for DRAM and DRAM-v for all MAGs and vMAGs -.faa proteins file for the full Freshwater / Wastewater / TARA Oceans dataset that was used for vContact2 biogeography analyses

Data for: Charting the spatial dynamics of early SARS-CoV-2 transmission in Washington state

All code and data necessary to reproduce results and figures in the publication "Charting the spatial dynamics of early SARS-CoV-2 transmission in Washington state".

opencc-by-4.0May 2023View details →

Effects of increasing phosphorus rate on microbial dynamics and soil available P under a Lixisol soil in Zimbabwe

Soil phosphorus (P) deficiency is a major challenge to the attainment of food security in most parts of sub-Saharan Africa, including Zimbabwe, where farmers largely depend on local organic nutrient resources in cropping. A greenhouse study was conducted to evaluate the  influence of  increasing inorganic P fertilizer rates (16, 26 and 36 kg P ha-1) on microbial dynamics, soil P pools and maize P uptake. using soils collected  from a long-term (16 seasons) maize-monocropped field experiment where organic nutrient resources of different qualty namely Crotalaria juncea (high quality), Calliandra Calothyrus (medium quality), cattle manure ( variable quality), maize stover and Pinus patula sawdust ( both low quality) were applied at 4 t C ha-1 with 16 kg P ha-1 at the start of every season, a 3 x 6 factorial experiment was established by adding single super phosphate (8.5% P) as a basal fertilizer. Maize was used as the test crop and the experiment was conducted at Soil Productivity Research Laboratory in Zimbabwe. Using Pokovskays agar medium and serial dilution methods, phsophate-solubilizing microbes were monitored forthnightly from day 1 to 57 after maize planting. Ninetten (19) fungal and forty-two (42) bacterial colonies were identified  over the study period, Fungi dominated bacteria on dayone, wth Aspergillus niger showing 20-98% abundance that depended on organic resources quality. Overall, a microbial explosion bulge characterized sucession on day 29 which coincided with a  significant (P< 0.05) increase in diversity (H') and soil available P. Increasing P rate to 26 kg ha-1 amplified the explosion bulge under medium-high quality resources while under the control the bulge emerged earlier on day 15. Mucor and Bacillus had peak abundance on day 43 and 57, respectively, across treatments regardless of P rates. Treatment and P rate had a significant (P< 0.01) effect on microbial P. Bacteria were more rsponsive to added P than fungi. Increasing P to 36 kg P ha-1 also stimulated an earlier bulge under maize stover on day 15. Addition of P alone, without supplying complementary nutrients such as nitrogen,did not have a positive effect on maize P uptake. Farmers need to co-apply medium-high quality organic resources with high fertilzier P rates to increase microbial diversity, soil available P and maize growth on sandy soils (Lixisols). Our results suggest the need to recondiser existing P fertilizer recommendations, currently pegged at between 26 and 30 kg P ha-1, for maize production on sandy soils as well develop new fertilizer formulations to intensify crop production in Zimbabwe.

opencc-by-4.0Jan 2022View details →

DeLTA 2.0: A deep learning pipeline for quantifying single-cell spatial and temporal dynamics

Datasets associated with https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009797

Effect of Single-Residue Mutations on CTCF Binding to DNA: Insights from Molecular Dynamics Simulations

Supplementary dataset for manuscript "Effect of Single-Residue Mutations on CTCF Binding to DNA: Insights from Molecular Dynamics Simulations".

Movie of the molecular dynamics simulation of a crucial step in the activation of the STING protein

STING (stimulator of interferon genes) is a homodimer protein involved in regulation of the innate immune system and plays a role in antitumor immunity by inducing the production of cytokines. Activation of STING stems from binding of endogenous cyclic dinucleotides (CDNs), which induce a conformational change to initiate signaling. The MP4 movie shows a molecular dynamics simulation of a crucial step of the activation process.

Movie of the molecular dynamics simulation of the opening and closing of the Cullin-RING protein complex

Heterobifunctional degraders, which consist of two separate protein binding moieties (the warhead and the E3-ligand) joined by a linker, are a class of molecules that "induce proximity" between a target protein of interest (POI) and a E3 ubiquitin ligase. This induced proximity can lead to ubiquitination of the POI and its subsequent proteosomal degradation through a complex machinery of proteins. TPD present a novel approach to drug protein targets, since a single degrader molecule can induce catalytic degradation of the POI and potentially offer an avenue to eliminate targets traditionally labeled as undruggable by classical therapeutic strategies. Here we probe the conformational landscape of the full CRL macromolecular assembly and present a MP4 trajectory movie showing the molecular dynamics simulation of the large-scale conformational change during the opening and closing of the Cullin-RING protein complex.

opencc-by-4.0Jun 2022View details →

Retrieving accurate precipitable water vapor based on GNSS multi-antenna PPP with an ocean-based dynamic experiment

GNSS-derived PWVs during a 4-day shipborne experiment are included in this repository. There are four solutions with four different processing strategies, namely PPP without constraints (Conventional), with baseline length constraint only (Bl), with common ZTD constraint only (Com), and with both baseline length and common ZTD constraints (Bl+Com). The suffix 'Smooth' in the file names represents the PWV results after backward smoothing.

Data for: Morphological covariance and onset of foot prehensility as indicators of integrated evolutionary dynamics in the herons (Ardeidae)

The ultimate form an organism attains is based, in part, on the rate and timing of developmental trajectories and on compensatory relationships between morphological traits. For example, there is often an inverse correlation between the relative size of an organism's head and the length of its legs. Avian examples with disproportionately small heads and long legs include ostriches (Struthionidae), flamingos (Phoenicopteridae), cranes (Gruidae), stilts (Recurvirostridae), and storks (Ciconiidae). To determine whether a possible compensatory relationship exists between relative head size and hind-limb length in a typically long-legged family of birds—the Ardeidae—we measured skull dimensions (length, width, and height of cranium, and total skull length, including culmen) and skeletal hind-limb dimensions (femur, tibiotarsus, and tarsometatarsus) of the 12 North American species (north of Mexico) and of 12 additional taxa, including the morphologically divergent Agamia and Cochlearius. Our analyses reveal a negative allometric relationship between head size and leg length. For example, Ardea species exhibit the smallest relative head sizes and the longest legs, while Butorides, Nycticorax, Nyctanassa, and Cochlearius have among the largest heads relative to hind-limb length. Furthermore, both positive and negative allometries occur in paired comparisons between the three hind-limb bones, resulting in tall morphotypes having disproportionately short femurs while small morphotypes exhibit long femurs; this relationship has implications for foraging behavior. Moreover, long legs of Ardea apparently derive from an extended growth period, or hypermorphosis, while relatively short legs of Butorides result from growth truncation. The latter are thus morphologically paedomorphic features that, paradoxically, permit a functional precociality of the hind limbs: early onset of prehensile ability of the feet for grasping branches, which nestlings retain into adulthood, later expressed in foraging mode. This developmentally accelerated prehensile function in small species may be attributed, in part, to selection for predator avoidance in the early nestling stage.

Legacy effects of anthropogenic disturbances modulate dynamics in the world's coral reefs

Rapidly changing conditions alter disturbance patterns, highlighting the need to better understand how the transition from pulse disturbances to more persistent stress will impact ecosystem dynamics. We conducted a global analysis of the impacts of eleven types of disturbances on reef integrity using the rate of change of coral cover as a measure of damage. Then, we evaluated how the magnitude of the damage due to thermal stress, cyclones, and diseases varied among tropical Atlantic and Indo-Pacific reefs and whether the cumulative impact of thermal stress and cyclones was able to modulate the responses of reefs to future events. We found that reef damage largely depends on the condition of a reef before a disturbance, disturbance intensity, and biogeographic region, regardless of the type of disturbance. Changes in coral cover after thermal stress events were largely influenced by the cumulative stress of past disturbances and did not depend on disturbance intensity or initial coral cover, which suggests that an ecological memory is present within coral communities. In contrast, the effect of cyclones (and likely other physical impacts) was primarily modulated by the initial reef condition and did not appear to be influenced by previous impacts. Our findings also underscore that coral reefs can recover if stressful conditions decrease, yet the lack of action to reduce anthropogenic impacts and greenhouse gas emissions continues to trigger reef degradation. We uphold that evidence-based strategies can guide managers to make better decisions to prepare for future disturbances.

Impact of urea fertilization rates on nitrogen dynamics, productivity, and profitability from Ugandan sugarcane plantations

All the datasets contained in the zipped file have all the different variables written out in full with the appropriate units defined in brackets [].

Animal data associated with: Pattern dynamics and stochasticity of the brain rhythms

Our current understanding of brain rhythms is based on quantifying their instantaneous or time-averaged characteristics. What remains unexplored, is the actual structure of the waves–their shapes and patterns over finite timescales. The data published here are used to study brain wave patterning in different physiological contexts using two independent approaches: the first is based on quantifying stochasticity relative to the underlying mean behavior, and the second assesses "orderliness'' of the waves' features. The corresponding measures capture the waves' characteristics and abnormal behaviors, such as atypical periodicity or excessive clustering, and demonstrate coupling between the patterns' dynamics and the animal's location, speed, and acceleration. Specifically, patterns of θ, γ, and ripple waves recorded in mice hippocampi and observed speed-modulated changes of the wave's cadence, an antiphase relationship between orderliness and acceleration, as well as spatial selectiveness of patterns, are derived from the data. The results offer a complementary–mesoscale–perspective on brain wave structure, dynamics, and functionality.

Data for: Optimal inference of molecular interaction dynamics in FRET microscopy

Intensity-based time-lapse fluorescence resonance energy transfer (FRET) microscopy has been a major tool for investigating cellular processes, converting otherwise unobservable molecular interactions into fluorescence time series. However, inferring the molecular interaction dynamics from the observables remains a challenging inverse problem, particularly when measurement noise and photobleaching are nonnegligible—a common situation in single-cell analysis. The conventional approach is to process the time-series data algebraically, but such methods inevitably accumulate the measurement noise and reduce the signal-to-noise ratio (SNR), limiting the scope of FRET microscopy. Here, we introduce an alternative probabilistic approach, B-FRET, generally applicable to standard 3-cube FRET-imaging data. Based on filtering theory, B-FRET implements a statistically optimal way to infer molecular interactions and thus drastically improves the SNR. We validate B-FRET using simulated data and then apply it to real data, including the notoriously noisy in vivo FRET time series from individual bacterial cells to reveal signaling dynamics otherwise hidden in the noise.

Dataset from publication: Long-term changes in bloom dynamics of Southern and Central Baltic cold-water phytoplankton

This data set contains the output of the numerical ocean model GETM used in the publication "Long-term changes in bloom dynamics of Southern and Central Baltic cold-water phytoplankton"