Find research datasets worth reusing

Data for "Invertebrate Activities in Wetland Sediments Influence Oxygen and Nutrient Dynamics at the Sediment-Water Interface"

Code and data for a project looking at how bioturbation by two benthic invertebrate taxa influence oxygen and nutrient dynamics a coastal freshwater wetland along Lake Erie, located in Ohio, USA. Article is titled "Invertebrate Activities in Wetland Sediments Influence Oxygen and Nutrient Dynamics at the Sediment-Water Interface" and is published in Wetlands.

Raw data for: Platicon dynamics in photonic molecules

This dataset includes the raw data and  Python scripts to plot the figures included in the paper  "Platicon states in photonic molecules". The dataset for "Active feedback stabilization of super-efficient microcombs in photonic molecules" is available in:  <a href="../records/10908341">https://zenodo.org/records/10908341</a>

opencc-zeroSep 2023View details →

Data from: Coinfection with chytrid genotypes drives divergent infection dynamics reflecting regional distribution patterns

By altering the abundance, diversity, and distribution of species — and their pathogens — globalization may inadvertently select for more virulent pathogens. In Brazil's Atlantic Forest, a hotspot of amphibian biodiversity, the global trade has facilitated the co-occurrence of previously isolated enzootic and panzootic lineages of the pathogenic amphibian-chytrid (Batrachochytrium dendrobatidis, 'Bd') and generated new virulent recombinant genotypes ('hybrid'). Epidemiological data indicate that amphibian declines are most severe in hybrid zones, suggesting that coinfections are causing more severe infections or selecting for higher virulence. We investigated how coinfections involving these genotypes shaped virulence and transmission. Overall, coinfection favored the more virulent and competitively superior panzootic genotype, despite dampening its transmission potential and overall virulence. However, for the least virulent and least competitive genotype, coinfection increased both overall virulence and transmission. Thus, by integrating experimental and epidemiological data, our results provide a mechanistic insight into how globalization can select for, and propel, the emergence of introduced hypervirulent lineages, such as the globally distributed panzootic lineage of Bd.

Dynamic rupture of the 2021 MW 7.4 Maduo earthquake

The dataset includes the figures and data in the article "Dynamic rupture of the 2021 MW 7.4 Maduo earthquake: An intra-block event controlled by fault geometry".

Molecular dynamics simulations of hyaluronan octamer–tetrapeptide mixtures

To cite: Riopedre-Fernandez, M.; Biriukov, D.; Dračínský, M.; Martinez-Seara, H. Hyaluronan-arginine enhanced and dynamic interaction emerges from distinctive molecular signature due to electrostatics and side-chain specificity. Carbohydr. Polym. 2024, 325, 121568. DOI: <a href="https://doi.org/10.1016/j.carbpol.2023.121568">10.1016/j.carbpol.2023.121568</a> MD simulations of hyaluronan octamer (HA8) with tetrapeptides. Simulation files and molecular topologies are provided. Tetrapeptides simulated: tetraarginine (R4), tetralysine (K4), tetraalanine (A4), tetraproline (P4), tetraglycine (G4), arginine-lysine-arginine-lysine (RKRK), and tetraglutamic acid (E4). Two force fields were compared: CHARMM (version charmm36-jul2020.ff.tgz from <a href="http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs">http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs</a>) and prosECCo75 (<a href="https://gitlab.com/sparkly/prosecco/prosECCo75">https://gitlab.com/sparkly/prosecco/prosECCo75</a>). Each simulation contained one hyaluronan polymer, one tetrapeptide, CHARMM-specific TIP3P water, and potassium counterions (standard "K" model in CHARMM and "K_s" model in prosECCo75) when necessary. We also additionally performed: (i) reference simulations with only hyaluronan octamer and potassium counterions; (ii) reference simulations with only R4 or K4 peptide and chloride counterions; (iii) simulations with two peptides (R4, K4, or G4) and two hyaluronan octamers. Simulations were done in Gromacs. Length - at least 1 µs, prolonged till 2 µs for prosECCo75 systems with R4, K4, or G4 peptides. Temperature - 300 K. For peer-reviewing process, extracted PDB configurations (a configuration every 10 ns of 2 μs simulations excluding the first 100 ns of equilibration) from selected systems were separately uploaded to <a href="http://doi.org/10.5281/zenodo.8423276">http://doi.org/10.5281/zenodo.8423276</a>

A Data-facilitated Numerical Method for Richards Equation to Model Water Flow Dynamics in Soil Dataset

This dataset contains the reference solutions used for training the two neural networks in 1-, 2- and 3-D cases for the article:"A Data-facilitated Numerical Method for Richards Equation to Model Water Flow Dynamics in Soil" by Zeyuan Song and Zheyu Jiang, submitted to the journal Water Resources Research.  This dataset which describes the relationship between the pressure head and number of particles used to train two MLPs in D-GRW based solvers consists of three files, i.e., 1-, 2- and 3-D case study. There are two parts, original reference solutions and reference solutions, corresponding to the original solutions generated by coarse mesh solvers and solutions after data augmentation process, respectively.The dataset is generated by GRW based solvers and simulation results (e.g., Celia's finite difference method). Original reference solutions admit GRW proportionality assumption. We initialize the number of particles by multiplying the initial condition and 1E10.

Airflow dynamics and aeolian sand transport across a beach-climbing dune-clifftop dune system

This study presents an analysis of wind flow and sediment transport from the beach, up a 50m high, long (130m), steep (mean slope 26°) climbing dune and across a 1.5 m high max, 85 m long and 17.5 m wide clifftop dune 30km south of Dakhla in Morocco, NW Africa during highly oblique incident wind conditions. Multiple 2D sonic and cup/vane anemometers and sand traps were utilised for measurements. Flow steering was significant on the upper climbing dune. Flow deceleration occurred near the dune toe, and topographic forcing of flow was considerable on the upper slopes of the climbing dune. Near-surface flow steadiness (CVU1, CVU0.25) on the climbing dune straight slope segment was low and constant The distance upslope over which the airflow reached the speed comparable to that on the beach increases as the incident wind speed increases. The greatest flow acceleration and speed-up was observed at the cliff edge reaching 250% at 1m height and 220% at 0.25m height for the lowest incident wind speed class (4-5 m/s). The sand transport rate declined from the beach to the climbing dune toe and lower slope, but at the uppermost section of the climbing dune was 4 times higher than at the beach for the 7-8m/s incident wind speed. Sand in aeolian transport was generally finer than surface sand with mean grain size increasing up the slope. A comparison of the sand transport data collected with sand transport models, and the effects of slope on aeolian transport are also examined.

opencc-by-4.0May 2023View details →

Introduction to HPC: molecular dynamics simulations with GROMACS: log files

Introduction to HPC: molecular dynamics simulations with GROMACS: log files corresponding to the exercises 1.X 2.X 3.X

opencc-by-4.0Dec 2022View details →

Future land cover and land cover dynamic trajectories in China under anthropogenic and climate forcing in 8 SSP-RCP scenarios

The projection of future land cover in 21st century in China and land cover dynamic trajectories in 8 SSP-RCP scenarios

Deep Learning-based 3D single-cell imaging analysis pipeline for quantifying cell-cell interaction dynamics in the tumor microenvironment

These are 3D live-cell imaging datasets of gastric tumor organoids in co-culture with primary human Natural Killer (NK) cells. The datasets were analyzed by a new, deep learning-based 3D image analysis software tool, SiQ-3D, which we developed and presented in the paper titled "Deep Learning-based 3D single-cell imaging analysis pipeline for quantifying cell-cell interaction dynamics in the tumor microenvironment". Interested users can download the SiQ-3D software code from GitHub (https://github.com/simonlbd1/SiQ-3D) or Code Ocean (https://codeocean.com/capsule/6676007/tree/v2), analyze the 3D image datasets locally, and cross-check the results with the SiQ-3D quantified results that we provided here.

opencc-by-3.0-usOct 2023View details →

Temporal Dynamics of Attitude Decisions: A Test of the Iterative Reprocessing Model using Event-related Potentials

Experimental instructions, stimulus procedures and stimuli, single trial EEG data, decoding program

opencc-by-4.0May 2023View details →

Microscopic insights to spin transport–driven ultrafast magnetization dynamics in a Gd/Fe bilayer

Datasets for the publication "Microscopic insights to spin transport–driven ultrafast magnetization dynamics in a Gd/Fe bilayer" published in Sci. Adv. 9,eade0286 (2023).

Data sets for "Dynamical bulk-boundary correspondence and dynamical quantum phase transitions in higher-order topological insulators"

Data sets for the return rates and Loschmidt eigenvalues for the paper "Dynamical bulk-boundary correspondence and dynamical quantum phase transitions in higher-order topological insulators". Included are data for both bulk calculations and finite open systems labelled OBC. Data files are named with the quench parameters, see the article for details.

Molecular dynamics simulations of hyaluronan octamer–tetrapeptide mixtures (PDB configurations)

Extracted PDB configurations from MD simulations of hyaluronan octamer (HA8) with R4 and K4 tetrapeptides. Simulated explicit water was removed for clarity. See <a href="https://doi.org/10.5281/zenodo.8028600">10.5281/zenodo.8028600</a> for more details about simulated systems.

Data on: Projecting spatiotemporal dynamics of severe fever with thrombocytopenia syndrome in the mainland of China

This dataset is the data used in the paper of Global change biology entitled "Projecting spatiotemporal dynamics of severe fever with thrombocytopenia syndrome in the mainland of China". We use an integrated multi-model, multi-scenario framework to assess the impact of global climate change on SFTS disease in the mainland of China. The SFTS incidence in three time periods (2030-2039, 2050-2059, 2080-2089) is predicted to be increased as compared to the 2010s in the context of various RCPs. The projected spatiotemporal dynamics of SFTS will be heterogeneous across provinces. Notably, we predict possible outbreaks in Xinjiang and Yunnan in the future, where only sporadic cases have been reported previously. These findings highlight the need for population awareness of SFTS in endemic regions, and enhanced monitoring in potential risk areas.

Data from: Integrating variation in bacterial-fungal co-occurrence network with soil carbon dynamics

Bacteria and fungi are core microorganisms in diverse ecosystems, and their cross-kingdom interactions are considered key determinants of microbiome structure and ecosystem functioning. However, how bacterial-fungal interactions mediate soil organic carbon (SOC) dynamics remains largely unexplored in the context of artificial forest ecosystems. Here, we characterized soil bacterial and fungal communities in four successive planting of Eucalyptus and compared them to a neighboring evergreen broadleaf forest. Carbon (C) mineralization combined with five C-degrading enzymatic activities was investigated to determine the effects of successive planting of Eucalyptus on SOC dynamics. Our results indicated that successive planting of Eucalyptus significantly altered the diversity and structure of soil bacterial and fungal communities and increased the negative bacterial-fungal associations. The bacterial diversity significantly decreased in all Eucalyptus plantations compared to the evergreen forest, while the fungal diversity showed the opposite trend. The ratio of negative bacterial-fungal associations increased with successive planting of Eucalyptus due to the decrease in SOC, ammonia nitrogen (NH4+−N), nitrate nitrogen (NO3−−N), and available phosphorus (AP). Structural equation modeling indicated that the potential cross-kingdom competition, based on the ratio of negative bacterial-fungal correlations, was significantly negatively associated with the diversity of total bacteria and keystone bacteria, thereby increasing C-degrading enzymatic activities and C mineralization. Synthesis and applications: Our results highlight the regulatory role of the negative bacterial-fungal association in enhancing the correlation between bacterial diversity and C mineralization. This suggests that promoting short-term successive planting in the management of Eucalyptus plantations can mitigate the impact of this association on SOC decomposition. Taken together, our study advances the understanding of bacterial-fungal negative associations to mediate carbon mineralization in Eucalyptus plantations, giving us a new insight into SOC cycling dynamics in artificial forests.

Dynamic social interactions and keystone species shape the diversity and stability of mixed-species biofilms – an example from dairy isolates - Dataset

We previously reported a bacterial four-species biofilm model comprising Stenotrophomonas rhizophila (SR), Bacillus licheniformis (BL), Microbacterium lacticum (ML), and Calidifontibacter indicus (CI) that were isolated from the surface of a dairy pasteuriser after cleaning and disinfection. These bacteria produced 3.13-fold more biofilm mass compared to the sum of biofilm masses in monoculture (<a href="https://doi.org/10.3389/fmicb.2023.1159434">https://doi.org/10.3389/fmicb.2023.1159434</a>). In a subsequent experiment we confirmed that the observed community synergy resulted from dynamic social interactions among various species pairs, encompassing commensalism, exploitation, and amensalism. M. lacticum appeared to be the keystone species as it increased the growth of all other species that led to the synergy in biofilm mass. Interactions among the other three species (in the absence of M. lacticum) also contributed towards the synergy in biofilm mass. Bacterial cell-free-supernatants were also investigated to assess the nature of the observed synergy. The first four sheets of the Excel file contain raw cell count data for the four species (SR, BL, ML, and CI), recorded every 4 h over a 24 h period on the surface of stainless steel (SS) in the presence of brain-heart-infusion (BHI) medium and skim-milk (SM). Data related to individual bacterial cell counts in various mixed-species biofilms are also presented. These biofilms were developed on SS in BHI for h.  Data related to bacterial biofilm masses in different mixed-species biofilm combinations are also presented, showcasing the effect of replacing one strain with its CFS. Species written in red indicate that their CFS was used, not their viable form.

Introduction to HPC: molecular dynamics simulations with GROMACS: output files - Devana

Introduction to HPC: molecular dynamics simulations with GROMACS: log files corresponding to the exercises 1.1, 1.2  2.1 3.1 and 3.2

Data from: Comparative genomics reveals the dynamic evolutionary history of cement protein genes of barnacles from intertidal to deep-sea hydrothermal vents

Thoracican barnacles are a diverse group of marine organisms for which the availability of genome assemblies is currently limited. In this study, we sequenced the genomes of two neolepadoid species (Ashinkailepas kermadecensis, Imbricaverruca yamaguchii) from hydrothermal vents, in addition to two intertidal species. Genome sizes ranged from 481.5 to 1054.6 Mb, with repetitive sequence contents of 21.2 to 50.7%. Concordance rates of orthologs and heterozygosity ratios were between 82.4 and 91.7% and between 1.1 and 2.6, respectively, indicating high genetic diversity and heterozygosity. Based on phylogenomic analyses, we revised the nomenclature of cement genes encoding cement proteins that are not homologous to any known proteins. The major cement gene, CP100A, was found in all thoracican species, including vent-associated neolepadoids, and was hypothesized to be essential for thoracican settlement. Duplicated genes, CP100B and CP100C, were found only in balanids, suggesting potential functional redundancy or acquisition of new functions associated with the calcareous base. An ancestor of CP52 genes was duplicated dynamically among lepadids, pollicipedids with multiple copies on a single scaffold, and balanids with multiple sequential repeats of the conserved regions, but no CP52 genes were found in neolepadoids, providing insights into cement gene evolution among thoracican lineages. This study enhances our understanding of the adhesion mechanisms of thoracicans in underwater environments. The newly sequenced genomes provide opportunities for studying their evolution and ecology, shedding light on their adaptation to diverse marine environments, and contributing to our knowledge of barnacle biology with valuable genomic resources for further studies in this field.

Neural and behavioral data from: A dynamic sequence of visual processing initiated by gaze shifts

Animals move their head and eyes as they explore and sample the visual scene. Previous studies have demonstrated neural correlates of head and eye movements in rodent primary visual cortex (V1), but the sources and computational roles of these signals are unclear. We addressed this by combining measurement of head and eye movements with high density neural recordings in freely moving mice. V1 neurons responded primarily to gaze shifts, where head movements are accompanied by saccadic eye movements, rather than to head movements where compensatory eye movements stabilize gaze. A variety of activity patterns immediately followed gaze shifts, including units with positive, biphasic, or negative responses, and together these responses formed a temporal sequence following the gaze shift. These responses were greatly diminished in the dark for the vast majority of units, replaced by a uniform suppression of activity, and were similar to those evoked by sequentially flashed stimuli in head-fixed conditions, suggesting that gaze shift transients represent the temporal response to the rapid onset of new visual input. Notably, neurons responded in a sequence that matches their spatial frequency preference, from low to high spatial frequency tuning, consistent with coarse-to-fine processing of the visual scene following each gaze shift. Recordings in foveal V1 of freely gazing head-fixed marmosets revealed a similar sequence of temporal response following a saccade, as well as the progression of spatial frequency tuning. Together, our results demonstrate that active vision in both mice and marmosets consists of a dynamic temporal sequence of neural activity associated with visual sampling.