Find research datasets worth reusing

opencc-zeroMar 2023View details →

Data for: Heavy metal pollution impacts soil bacterial community structure and antimicrobial resistance at the Birmingham 35th Avenue Superfund Site

The data in this archive are the results of a study on the impact of heavy metals (HMs) on the soil microbiota of an urban Superfund site in Alabama. HMs are known to modify bacterial communities both in the laboratory and in situ. Consequently, soils in HM-contaminated sites such as the U.S. Environmental Protection Agency (EPA) Superfund sites are predicted to have altered ecosystem functioning, with potential ramifications for the health of organisms, including humans, that live nearby. Further, several studies have shown that heavy metal-resistant (HMR) bacteria often also display antimicrobial resistance (AMR), and therefore HM-contaminated soils could potentially act as reservoirs that could disseminate AMR genes into human-associated pathogenic bacteria. To explore this possibility, topsoil samples were collected from six public locations in the zip code 35207 (the home of the North Birmingham 35th Avenue Superfund Site) and in six public areas in the neighboring zip code, 35214. 35027 soils had significantly elevated levels of the HMs As, Mn, Pb, and Zn, and sequencing of the V4 region of the bacterial 16S rRNA gene revealed that elevated HM concentrations correlated with reduced microbial diversity and altered community structure. While there was no difference between zip codes in the proportion of total culturable HMR bacteria, bacterial isolates with HMR almost always also exhibited AMR. Metagenomes inferred using PICRUSt2 also predicted significantly higher mean relative frequencies in 35207 for several AMR genes related to both specific and broad-spectrum AMR phenotypes. Together, these results support the hypothesis that chronic HM pollution alters the soil bacterial community structure in ecologically meaningful ways and may also select for bacteria with increased potential to contribute to AMR in human disease.

opencc-by-4.0Mar 2023View details →

Supplementary data and code to "An assessment of quaternary structure functionality in homomer protein complexes" by G. Abrusan and C. Foguet, https://doi.org/10.1093/molbev/msad070

Scripts and high-level data to reproduce the figures and supplementary figures of "An assessment of quaternary structure functionality in homomer protein complexes" by G. Abrusan and C. Foguet, https://doi.org/10.1093/molbev/msad070

opencc-by-4.0Apr 2023View details →

Data and code for "Tuning the lattice thermal conductivity in van-der-Waals structures through rotational (dis)ordering"

This record contains neuroevolution potential (NEP) models for C, BN, and MoS2 that have been constructed to model the potential energy surfaces of these materials in the presence of interlayer rotations. It also contains databases with the results from density functional theory calculations that were used for constructing the NEP models. Databases The <code>*.db</code> files are databases with the results from density functional theory (DFT) calculations. These are sqlite databases in ase format, see <a href="https://wiki.fysik.dtu.dk/ase/tutorials/tut06_database/database.html">here</a> for more information. The <code>demo-database-access.py</code> script illustrates the most basic access. Models The neuroevolution potential (NEP) models described in the publication can be found in the <code>nep-*.txt</code> files. They can be used in conjunction with the <a href="https://gpumd.org">GPUMD package</a>. The <a href="https://calorine.materialsmodeling.org">calorine package</a> provides a Python interface to GPUMD. Primitive structures Several primitive structures in extended xyz format can be found in the <code>*.xyz</code> files. These structures have been relaxed using the NEP models included here. The <code>demo-for-using-structures-and-models.py</code> script illustrates how to access the structures and models.

opencc-by-4.0May 2023View details →

Simulation data and code used for the publication in Magn. Reson. "Time-domain proton-detected local-field NMR for molecular structure determination in complex lipid membranes"

Simulation data used in the publication Magn. Reson.  "Time-domain proton-detected local-field NMR for molecular structure determination in complex lipid membranes". The simulation data set, and the code developed to generate such data, are included. Details in the published paper

opencc-zeroApr 2023View details →

Data from: A brain-wide analysis maps structural evolution to distinct anatomical modules

Brain anatomy is highly variable and it is widely accepted that anatomical variation impacts brain function and ultimately behavior. The structural complexity of the brain, including differences in volume and shape, presents an enormous barrier to define how variability underlies differences in function. In this study, we sought to investigate the evolution of brain anatomy in relation to brain region volume and shape across the brain of a single species with variable genetic and anatomical morphs. We generated a high-resolution brain atlas for the blind Mexican cavefish and coupled the atlas with automated computational tools to directly assess variability in brain region shape and volume across all populations. We measured the volume and shape of every neuroanatomical region of the brain and assessed correlations between anatomical regions in surface fish, cavefish, and surface to cave F2 hybrids, whose phenotypes span the range of surface to cave. We find that dorsal regions of the brain are contracted in cavefish, while ventral regions have expanded. This trend is true for both volume and shape, suggesting that these two parameters share developmental mechanisms necessary for remodeling the entire brain. Given the high conservation of brain anatomy and function among vertebrate species, we expect these data to reveal generalized principles of brain evolution and show that Astyanax provides a system for functionally determining basic principles of brain evolution by utilizing the independent genetic diversity of different morphs, to test how genes influence early patterning events to drive brain-wide anatomical evolution.

opencc-by-4.0May 2023View details →

Experimental and Simulation Data for "Hierarchical structure formation by crystal growth-front instabilities during ice templating" (2023) PNAS

<pre>Experimental and Simulation Data for: "Hierarchical structure formation by crystal growth-front instabilities during ice templating" by Kaiyang Yin, Kaihua Ji, Louise Strutzenberg Littles, Rohit Trivedi, Alain Karma, Ulrike G.K. Wegst (2023) PNAS, DOI: 10.1073/pnas.2210242120. </pre>

opencc-by-4.0May 2023View details →

Data from: Fatigue crack propagation in AA5083 structures additively manufactured via multi-layer friction surfacing

This dataset contains the data for the publication " Fatigue crack propagation in AA5083 structures additively manufactured via multi-layer friction surfacing"

opencc-zeroJun 2023View details →

Data for: Age structure eliminates the impact of coinfection on epidemic dynamics in a freshwater zooplankton system

Parasites often coinfect host populations, and, by interacting within hosts, might change the trajectory of multi-parasite epidemics. However, host-parasite interactions often change with host age, raising the possibility that within-host interactions between parasites might also change, influencing the spread of disease. We measured how heterospecific parasites interacted within zooplankton hosts and how host age changed these interactions. We then parameterized an epidemiological model to explore how age-effects altered the impact of coinfection on epidemic dynamics. In our model, we found that in populations where epidemiologically relevant parameters did not change with age, the presence of a second parasite altered epidemic dynamics. In contrast, when parameters varied with host age (based on our empirical measures), there was no longer a difference in epidemic dynamics between singly and coinfected populations, indicating that variable age structure within a population eliminates the impact of coinfection on epidemic dynamics. Moreover, infection prevalence of both parasites was lower in populations where epidemiologically relevant parameters changed with age. Given that host-population age structure changes over time and space, these results indicate that age-effects are important for understanding epidemiological processes in coinfected systems and that studies focused on a single age group could yield inaccurate insights.

Accompanying data for the paper "Reduced order modeling of geometrically nonlinear rotating structures using the direct parametrisation of invariant manifolds"

Links<ul><li>isSupplementTo publication-article <a href="https://doi.org/10.46298/jtcam.10430">https://doi.org/10.46298/jtcam.10430</a></li><li>isSupplementedBy software <a href="https://archive.softwareheritage.org/swh:1:dir:97292192b4790c2af01e25f4694d024561c5638c;origin=https://github.com/MORFEproject/MORFEInvariantManifold.jl;visit=swh:1:snp:cbd3f3eaf0dc99efb1d6bed706c3b4c3b67a1077;anchor=swh:1:rev:f56492ccd78890ee2b82970ae8941d6e39c0c147">https://archive.softwareheritage.org/swh:1:dir:97292192b4790c2af01e25f4694d024561c5638c;origin=https://github.com/MORFEproject/MORFEInvariantManifold.jl;visit=swh:1:snp:cbd3f3eaf0dc99efb1d6bed706c3b4c3b67a1077;anchor=swh:1:rev:f56492ccd78890ee2b82970ae8941d6e39c0c147</a></li></ul>Language<ul><li>English</li></ul>License<ul><li>Creative Commons Attribution 4.0</li></ul>Contributions<ul><li>Adrien MARTIN carried out the main part of study, defined the examples, performed the numerical simulations and drafted the manuscript;</li><li>Andrea OPRENI and Alessandra VIZZACCARO developed the methodology and built the main parts of the Julia code implementing the reduction method;</li><li>Andrea OPRENI developed the first version of the HBFEM code which has been updated for rotation in collaboration with Adrien MARTIN;</li><li>Marielle DEBEURRE performed all the simulations shown in Appendix C related to the Timoshenko beam model with continuation;</li><li>Loïc SALLES supervised the work, discussed applications to blades, and helped in designing and understanding the twisted plate model;</li><li>Attilio FRANGI supervised the work and help in the development of the methodology;</li><li>Olivier THOMAS helped in all discussions related to the comparisons with the thin beam example and wrote Appendix C;</li><li>Cyril TOUZE supervised the work, carried out most of the writing and developed the methodology;</li></ul>All authors read and approved the final manuscript.Data collection: period and details<ul><li>Datasets produced between September and December 2022</li></ul>Funding sources<ul><li>Funding from AID (Agence de l'Innovation de Défense), project REMODEL, contract number 2020 65 0057 ENSTA</li></ul>Data structure and information<ul><li>README.md: Contains the general information concerning this dataset</li></ul>Figures<ul><li>fig_1: description of the rotating beam</li><li>fig_2(a,b,c,d): Linear characteristics of the rotating cantilever beam</li><li>fig_3(a,b): FRC of the rotating cantilever beam around 1F mode</li><li>fig_4: Convergence of the non-autonomous part of DPIM for the 1F mode</li><li>fig_5(a,b,c,d,e,f): Interpolation of the coefficients of the autonomous ROM</li><li>fig_6(a,c): Hardening/softening behaviour of the rotating beam; fig 6b is a zoom on fig 6a</li><li>fig_7(a,b,c): Comparisons of FRCs obtained from interpolated ROMs with FOM solution</li><li>fig_8a: FRC of the rotating cantilever beam around 2F mode; fig 8b is a zoom of fig 8a</li><li>fig_9(a,b,c,d): fig 9 a-b-c : geometry of the blade and some modes and static displacements; fig 9d : Campbell diagram of the blade</li><li>fig_10: FRC of the twisted plate</li><li>fig_11(a,b,c): Computing time and convergence analysis with respect to mesh refinement for the fan blade</li></ul>fig_12(a,b,c,d): FRC of interpolated ROMs with increasing degrees compared to reference solutionfig_A_1: Campbell diagram of the beam : impact of Coriolis effects<ul><li>fig_C_3(a,b,c,d,e,f,g,h,i): Comparison of the results on the beam studied between DPIM and article from Thomas for 1F and 2F modes</li><li>fig_C_2(a, b): Comparison of the results on the beam studied between : DPIM, article from Thomas and results from Debeurre</li></ul>

Data for "Symbiotic nutrient exchange enhances the long-term survival of cassiosomes, the autonomous stinging-cell structures of Cassiopea"

Raw data linked to the publication "Symbiotic nutrient exchange enhances the long-term survival of cassiosomes, the autonomous stinging-cell structures of Cassiopea". NanoSIMS data and data from the survival experiments are available as individual tabs in the excel file.

opencc-zeroJun 2023View details →

Data for: Environmental responses of fruiting fungal communities are phylogenetically structured

Through their ephemeral reproductive structures (fruiting bodies), ectomycorrhizal forest soil fungi provide a resource for a plethora of organisms. Thus, resolving what biotic and abiotic factors determine the occurrence and abundance of fruiting bodies is fundamental for understanding the dynamics of forest trophic networks. While the influence of abiotic factors such as moisture and temperature on fungal fruiting are relatively well established, little is known about how these processes interact with the evolutionary history of fungal species to determine when, where, and in which abundance fungal fruiting bodies will emerge. A specific knowledge gap relates to whether species' responses to their environment are phylogenetically structured. Here, we ask whether related fungal taxa respond similarly to climatic factors and forest habitat characteristics, and whether such correlated responses will affect the assembly of fungal fruiting communities. To resolve these questions, we fitted joint species distribution models combining data on the species composition and abundance of fungal fruiting bodies, environmental variation, and phylogenetic relationships among fungal taxa. Our results show that both site-level forest characteristics (dominant tree species and forest age) and climatic factors related to phenology (effective heat sum) greatly influence the occurrence and abundance of fruiting bodies. More importantly, while different fungal species responded unequally to their shared environment, there was a strong phylogenetic signal in their responses, so that related fungal species tended to fruit under similar environmental conditions. Thus, not only are fruiting bodies short-lived and patchily distributed, but the availability of similar resources will be further aggregated in time and space. These strong constraints on resource availability for fungus-associated taxa highlight the potential of fungus-based networks as a model system for studies on the ecology and evolution of resource–consumer relations in ephemeral systems of high spatiotemporal patchiness.

opencc-zeroJun 2023View details →

National forest inventory data for a size-structured forest population model

In forest communities, light competition is a key process for community assembly. Species' differences in seedling and sapling tolerance to shade cast by overstory trees is thought to determine species composition at late-successional stages. Most forests are distant from these late-successional equilibria, impeding a formal evaluation of their potential species composition. To extrapolate competitive equilibria from short-term data, we therefore introduce the JAB model, a parsimonious dynamic model with interacting size-structured populations, which focuses on sapling demography including the tolerance to overstory competition. We apply the JAB model to a two-"species" system from temperate European forests, i.e. the shade-tolerant species Fagus sylvatica L. and the group of all other competing species. Using Bayesian calibration with prior information from external Slovakian national forest inventory (NFI) data, we fit the JAB model to short timeseries from the German NFI. We use the posterior estimates of demographic rates to extrapolate that F. sylvatica will be the predominant species in 94% of the competitive equilibria, despite only predominating in 24% of the initial states. We further simulate counterfactual equilibria with parameters switched between species to assess the role of different demographic processes for competitive equilibria. These simulations confirm the hypothesis that the higher shade-tolerance of F. sylvatica saplings is key for its long-term predominance. Our results highlight the importance of demographic differences in early life stages for tree species assembly in forest communities.

Data from: Biochemical, structural and dynamical characterizations of the lactate dehydrogenase from Selenomonas ruminantium provide information about an intermediate evolutionary step prior to complete allosteric regulation acquisition in the super family of lactate and malate dehydrogenases.

This data accompanies the paper entitled Biochemical, structural and dynamical characterizations of the lactate dehydrogenase from Selenomonas ruminantium provide information about an intermediate evolutionary step prior to complete allosteric regulation acquisition in the super family of lactate and malate dehydrogenases. The zip archive contains the results of molecular dynamics simulations of the 2 systems investigated in the paper: S. rum and T. mar LDHs. The systems have been simulated at 315 K for S. rum and 340 K for T. mar. Final configurations of the proteins after productions are provided for all the systems in GRO Gromos87 format. Trajectories with the positions of the proteins every 100 ps are provided for all the systems in XTC gromacs format.

opencc-zeroDec 2022View details →

Inferring the evolutionary model of community-structuring traits with convolutional kitchen sinks: Code and data

When communities are assembled through processes such as filtering or limiting similarity acting on phylogenetically conserved traits, the evolutionary signature of those traits may be reflected in patterns of community membership. We show how the model of trait evolution underlying community-structuring traits can be inferred from community membership data using both a variation of a traditional eco-phylogenetic metric--the mean pairwise distance (MPD) between taxa--and a recent machine learning tool, Convolutional Kitchen Sinks (CKS). Both methods perform well across a range of phylogenetically informative evolutionary models, but CKS outperforms MPD as tree size increases. We demonstrate CKS by inferring the evolutionary history of freeze tolerance in angiosperms. Our analysis is consistent with a late burst model of freeze tolerance, suggesting it evolved recently. We suggest that data ordered on phylogenies such as trait values, species interactions, or community presence/absence are good candidates for CKS modeling because the generative models produce structured differences between neighboring points that CKS is well-suited for. We introduce the R package kitchen to perform CKS for generic application of the technique.

opencc-by-4.0Dec 2017View details →

Рис. 2–6. ÀетаΛи строения пауков семейства Gnaphosidae. 2 – Gnaphosa cumensis; 3 – G. cf.cumensis; 4 – Haplodrassus rugosus; 5–6 – Zelotes fuscus. 2–4 – паΛьпа самца, вентраΛьно; 5 – эпигина, вентраΛьно; 6 – эпигина, ΑорсаΛьно. Масштабные Λинейки 0.2 мм. Figs 2–6. Family Gnaphosidae, details of structure. 2 – Gnaphosa cumensis; 3 – G. cf. cumensis; 4 – Haplodrassus rugosus; 5–6 – Zelotes fuscus. 2–4 – male palp, ventral view; 5 – epigyne, ventral view; 6 – epigyne, dorsal view. Scale bars 0.2 mm. in New data on spiders (Aranei) of the Naurzum State Natural Reserve (Kostanay Region, Kazakhstan)

Рис. 2–6. ÀетаΛи строения пауков семейства Gnaphosidae. 2 – Gnaphosa cumensis; 3 – G. cf.cumensis; 4 – Haplodrassus rugosus; 5–6 – Zelotes fuscus. 2–4 – паΛьпа самца, вентраΛьно; 5 – эпигина, вентраΛьно; 6 – эпигина, ΑорсаΛьно. Масштабные Λинейки 0.2 мм. Figs 2–6. Family Gnaphosidae, details of structure. 2 – Gnaphosa cumensis; 3 – G. cf. cumensis; 4 – Haplodrassus rugosus; 5–6 – Zelotes fuscus. 2–4 – male palp, ventral view; 5 – epigyne, ventral view; 6 – epigyne, dorsal view. Scale bars 0.2 mm.

Primary data for: "Remotely sensed localised primary production anomalies predict the burden and community structure of infection in long-term rodent datasets"

Datasets

Data and codes from "How does dispersal shape the genetic structure of animal populations in European cities? A simulation approach"

Codes and data used for "Savary et al. How does dispersal shape the genetic structure of animal populations in European cities? A simulation approach".

Molecular dynamics simulation data 3: Structure of the connexin-43 gap junction channel in a putative closed state

Molecular dynamics data for the manuscript Qi C.*, Acosta-Gutierrez S.*, Lavriha P., Othman A., Lopez-Pigozzi D., Bayraktar E., Schuster D., Picotti P., Zamboni N., Bortolozzi M., Gervasio F.L., Korkhov V.M. Structure of the connexin-43 gap junction channel in a putative closed state. eLife (2023) <a href="https://doi.org/10.7554/eLife.87616.2">https://doi.org/10.7554/eLife.87616.2</a> The dataset includes: Production run gromacs trajectories for the Cx43 gap junction channel (500 mV)

Molecular dynamics simulation data 2: Structure of the connexin-43 gap junction channel in a putative closed state

Molecular dynamics data for the manuscript Qi C.*, Acosta-Gutierrez S.*, Lavriha P., Othman A., Lopez-Pigozzi D., Bayraktar E., Schuster D., Picotti P., Zamboni N., Bortolozzi M., Gervasio F.L., Korkhov V.M. Structure of the connexin-43 gap junction channel in a putative closed state. eLife (2023) <a href="https://doi.org/10.7554/eLife.87616.2">https://doi.org/10.7554/eLife.87616.2</a> The dataset includes: 1. The starting coordinates, topology, MD inputs 2. Production run gromacs trajectories for the Cx43 hemichannel

NMR and structure calculation data of the TccC3 toxin from Photorhabdus luminescens

NMR and structure calculation data of the protein TcART (a section of TccC3 from Photorhabdus luminescens) as presented in the publication Belyy, A., Lindemann, F., Roderer, D. et al. Mechanism of threonine ADP-ribosylation of F-actin by a Tc toxin. Nat Commun 13, 4202 (2022). https://doi.org/10.1038/s41467-022-31836-w and my thesis "A Structural View on Mechanisms of Bacterial Communal Life and Toxicity" submitted to the Free University Berlin (<a href="http://dx.doi.org/10.17169/refubium-41725">http://dx.doi.org/10.17169/refubium-41725</a>).