Find research datasets worth reusing

Figure 4. A in New data on the mitochondrial genome of Nematocera (lower Diptera): features, structures and phylogenetic implications

Figure 4. A LIGROOVE analysis for four datasets. The mean similarity score between sequences is represented by a coloured square, based on ALIGROOVE scores ranging from minus one, indicating a large difference in sequence composition from the remainder of the dataset (red coloration), to plus one, indicating similarity to all other comparisons (blue coloration).

Figure 3 in New data on the mitochondrial genome of Nematocera (lower Diptera): features, structures and phylogenetic implications

Figure 3. Structures of AT-rich regions in three nematoceran species. The location and copy number of tandem repeat units are displayed by blue ovals. The non-repeat regions are indicated by red boxes. A, structure of AT-rich region in Plecia sp. B, structure of AT-rich region in Protaxymyia sp. C, structure of AT-rich region in Bradysia sp.

Figure 2 in New data on the mitochondrial genome of Nematocera (lower Diptera): features, structures and phylogenetic implications

Figure 2. Relative synonymous codon usage (RSCU) and number of amino acids in protein-coding genes (PCGs) of the mitogenomes of eight nematoceran species. Leu1 = Leu (CUN); Leu2 = Leu (UUR); Ser1 = Ser (AGN); Ser2 = Ser (UCN).

Figure 1 in New data on the mitochondrial genome of Nematocera (lower Diptera): features, structures and phylogenetic implications

Figure 1. Mitochondrial genomes of eight nematoceran species sequenced in this study. The circular maps were drawn with GENEIOUS v.10.2.2 (http://www.geneious.com/). The transcriptional direction is indicated by arrows.

Figure 6 in New data on the mitochondrial genome of Nematocera (lower Diptera): features, structures and phylogenetic implications

Figure 6. Bayesian tree of Nematocera based on PCGRNA with heterogeneous models CAT+GTR in PhyloBayes. Circles indicate that posterior probabilities = 100%. Squares indicate that posterior probabilities = 50–94%. Other posterior probabilities (95–99%) are given above the branches. Multiple sampling of different species from a single family, in addition to outgroups and Brachycera, are collapsed into triangles.

opencc-by-4.0Jan 2023View details →

Data for Structural Features of Interfacial Water Predict the Hydrophobicity of Chemically Heterogeneous Surfaces

Scripts, raw and processed data, Jupyter notebooks, and force field files for the simulations performed in: B. C. Dallin, A. S. Kelkar, and R. C. Van Lehn. “Structural Features of Interfacial Water Predict the Hydrophobicity of Chemically Heterogeneous Surfaces.” Chemical Science 2023.

opencc-by-4.0Nov 2022View details →

Data for "Machine-learning-aided atomic structure identification of interfacial ionic hydrates from AFM images"

Dataset for Neural Network training and testing of paper entitled "Machine-learning-aided atomic structure identification of interfacial ionic hydrates from AFM images" (<a href="https://doi.org/10.1093/nsr/nwac282">https://doi.org/10.1093/nsr/nwac282</a>). Each file contains named-dependent simulated AFM Images at different tip height and corresponding atomic structure file in POSCAR format. (See detailed description in the manuscript <a href="https://doi.org/10.1093/nsr/nwac282">https://doi.org/10.1093/nsr/nwac282</a>)

opencc-by-4.0Jan 2023View details →

MODES DATA - vertical structure functions

MODES DATA - vertical structure functions (VSF)

opencc-by-4.0Jan 2023View details →

Experimental and Computational data related to research on ``Investigating the Electronic Structure of Prospective Water-splitting Oxide BaCe0.25Mn0.75O3−δ Before and After Thermal Reduction''

Data files and gnuplot scripts for the figures included in the submission titled ``Investigating the Electronic Structure of Prospective Water-splitting Oxide BaCe0.25Mn0.75O3−δ Before and After Thermal Reduction''

opencc-zeroJan 2023View details →

Data from: Distinctive microbial community and genome structure in coastal seawater from a human-made port and nearby offshore island in northern Taiwan facing the Northwestern Pacific Ocean

Pollution in human-made fishing ports caused by petroleum from boats, dead fish, toxic chemicals, and effluent poses a challenge to the organisms in seawater. To decipher the impact of pollution on the microbiome, we collected surface water from a fishing port and a nearby offshore island in northern Taiwan facing the Northwestern Pacific Ocean. By employing 16S rRNA gene amplicon sequencing and whole-genome shotgun sequencing, we discovered that Rhodobacteraceae, Vibrionaceae, and Oceanospirillaceae emerged as the dominant species in the fishing port, where we found many genes harboring the functions of antibiotic resistance (ansamycin, nitroimidazole, and aminocoumarin), metal tolerance (copper, chromium, iron and multimetal), virulence factors (chemotaxis, flagella, T3SS1), carbohydrate metabolism (biofilm formation and remodeling of bacterial cell walls), nitrogen metabolism (denitrification, N2 fixation, and ammonium assimilation), and ABC transporters (phosphate, lipopolysaccharide, and branched-chain amino acids). The dominant bacteria at the nearby offshore island (Alteromonadaceae, Cryomorphaceae, Flavobacteriaceae, Litoricolaceae, and Rhodobacteraceae) were partly similar to those in the South China Sea and the East China Sea. Furthermore, we inferred that the microbial community network of the cooccurrence of dominant bacteria on the offshore island was connected to dominant bacteria in the fishing port by mutual exclusion. By examining the assembled microbial genomes collected from the coastal seawater of the fishing port, we revealed four genomic islands containing large gene-containing sequences, including phage integrase, DNA invertase, restriction enzyme, DNA gyrase inhibitor, and antitoxin HigA-1. In this study, we provided clues for the possibility of genomic islands as the units of horizontal transfer and as the tools of microbes for facilitating adaptation in a human-made port environment.

opencc-zeroFeb 2023View details →

Data for: From rivers to ocean basins: The role of ocean barriers and philopatry in the genetic structuring of a cosmopolitan coastal predator

The Bull Shark (Carcharhinus leucas) faces varying levels of exploitation around the world due to its coastal distribution. Information regarding population connectivity is crucial to evaluate its conservation status and local fishing impacts. In this study, we sampled 922 putative Bull Sharks from 19 locations in the first global assessment of population structure of this cosmopolitan species. Using a recently developed DNA-capture approach (DArTcap), samples were genotyped for 3,400 nuclear markers. Additionally, full mitochondrial genomes of 384 Indo-Pacific samples were sequenced. Reproductive isolation was found between and across ocean basins (eastern Pacific, western Atlantic, eastern Atlantic, Indo-West Pacific) with distinct island populations in Japan and Fiji. Bull Sharks appear to maintain gene flow using shallow coastal waters as dispersal corridors, whereas large oceanic distances and historical land-bridges act as barriers. Females tend to return to the same area for reproduction, making them more susceptible to local threats and an important focus for management actions. Given these behaviours, the exploitation of Bull Sharks from insular populations, such as Japan and Fiji, may instigate local decline that cannot readily be replenished by immigration, which can in turn affect ecosystem dynamics and functions. These data also supported the development of a genetic panel to ascertain the population of origin, which will be useful in monitoring the trade of fisheries products and assessing population-level impacts of this harvest.

opencc-by-4.0Oct 2022View details →

Data and Code from "Structure-based prediction of Ras-effector binding affinities and design of 'branchegetic' interface mutations"

Data, data generation and data analysis for manuscript "Structure-based prediction of Ras-effector binding affinities and design of ‘branchegetic’ interface mutations", currently available as a preprint <a href="https://doi.org/10.1101/2022.09.04.506480">here</a>. Contains the following directories: <ul> <li>01_models: Contains all scripts for model generation and selection, as well as some of the generated and selected models. <ul> <li>01_inputs: The different inputs for the homology modelling pipeline. This includes AlphaFold single and complex templates, PDB templates and sequence alignments.</li> <li>02_validation: Model generation and initial selection for validation models, based on AF2 single models and PDB complex models.</li> <li>03_production1: Model generation and initial selection for Ras effector complexes, based on AF2 single models and PDB complex models.</li> <li>04_production2: Model generation and initial selection for Ras effector complexes, based on AF2 single models and AF2 complex models.</li> <li>05_selection_optics: Code and analysis for selection by unsupervised learning using OPTICS.</li> </ul> </li> <li>02_selected_models: The three representative models selected for each complex.</li> <li>03_affinity_prediction: Contains code and data for the prediction of binding affinities for Ras effector complexes.</li> <li>04_branch_pruning: Contains code and data for branch pruning analysis.</li> <li>05_systems_analysis: Contains code and data for the analysis of Ras effector systems based on affinities derived from affinity prediction and branch pruning analysis.</li> <li>06_visualization: Information on where in the raw data the panels for the figures in the manuscript can be found.</li> </ul>

Data for: Genomic variation across Chinook salmon populations reveals effects of a duplication on migration alleles and supports fine scale structure

Distribution of ecotypic variation in natural populations is influenced by neutral and adaptive evolutionary forces that are challenging to disentangle without understanding of genomic architecture for phenotypic traits. This study provides a high-resolution portrait of genomic variation in Chinook salmon (Oncorhynchus tshawytscha) with emphasis on a region of major effect for ecotypic variation in migration timing. With a filtered dataset of ~13 million SNPs from low coverage whole genome resequencing of 53 populations (3,566 barcoded individuals), we contrasted patterns of genomic variation within and among major lineages and examined the extent of a selective sweep at a major effect region underlying migration timing (GREB1L/ROCK1). Allele frequency variation in GREB1L/ROCK1 was highly correlated with mean migration timing for early- and late-run populations within each of the lineages (r2 between 0.58–0.95; P < 0.001). However, the extent of selection within the genomic region controlling migration timing was much narrower in one lineage (interior stream-type) compared to the other two major lineages which corresponded to the breadth of phenotypic variation in migration timing observed among lineages. Evidence of a duplicated block within GREB1L/ROCK1 may be responsible for reduced recombination in this portion of the genome and contributes to phenotypic variation within and across lineages. Lastly, SNP positions across GREB1L/ROCK1 were assessed for their utility in discriminating migration timing among lineages, and we recommend multiple markers nearest the duplication to provide highest accuracy in conservation applications such as those that aim to protect early migrating Chinook salmon. These results highlight the need to investigate variation throughout the genome and the effects of structural variants on ecologically relevant phenotypic variation in natural species.

Data set from: Phylogenetic structure of alien plant species pools from European donor habitats

Aim. Many plant species native to Europe have naturalized worldwide. We tested whether the phylogenetic structure of the species pools of European habitats is related to the proportion of species from each habitat that have naturalized outside Europe (habitat's donor role) and whether the donated species are more phylogenetically related to each other than expected by chance. Location. Europe (native range), the rest of the World (invaded range). Time period. Last c. 100 years. Major taxa studied. Angiospermae. Methods. We selected 33 habitats in Europe and analyzed their species pools, including 9,636 plant species, of which 2,293 have naturalized outside Europe. We assessed the phylogenetic structure of each habitat as the difference between the observed and expected mean pairwise phylogenetic distance (MPD) for (a) the whole species pool and (b) subgroups of species that have naturalized outside Europe and those that have not. We used generalized linear models to test for the effects of the phylogenetic structure and the level of human influence on the habitats' donor role. Results. Habitats strongly to moderately influenced by humans often showed phylogenetically clustered species pools. Within the clustered species pools, those species that have naturalized outside Europe showed a random phylogenetic structure. Species pools of less human-influenced natural habitats varied from phylogenetically clustered to overdispersed, with donated naturalized species also often showing random patterns within the species pools. Donor roles in both habitat groups increased with increasing MPD within habitats. Main conclusions. European human-influenced habitats donate closely related species that often naturalize in disturbed habitats outside their native range. Natural habitats donate species from different lineages with various ecological strategies that allow them to succeed in different habitats in the invaded range. However, in most cases, the naturalized species donated are phylogenetically random subsets of the donor habitats' species pools. Aim. Many plant species native to Europe have naturalized worldwide. We tested whether the phylogenetic structure of the species pools of European habitats is related to the proportion of species from each habitat that have naturalized outside Europe (habitat's donor role) and whether the donated species are more phylogenetically related to each other than expected by chance. Location. Europe (native range), the rest of the World (invaded range). Time period. Last c. 100 years. Major taxa studied. Angiospermae. Methods. We selected 33 habitats in Europe and analyzed their species pools, including 9,636 plant species, of which 2,293 have naturalized outside Europe. We assessed the phylogenetic structure of each habitat as the difference between the observed and expected mean pairwise phylogenetic distance (MPD) for (a) the whole species pool and (b) subgroups of species that have naturalized outside Europe and those that have not. We used generalized linear models to test for the effects of the phylogenetic structure and the level of human influence on the habitats' donor role. Results. Habitats strongly to moderately influenced by humans often showed phylogenetically clustered species pools. Within the clustered species pools, those species that have naturalized outside Europe showed a random phylogenetic structure. Species pools of less human-influenced natural habitats varied from phylogenetically clustered to overdispersed, with donated naturalized species also often showing random patterns within the species pools. Donor roles in both habitat groups increased with increasing MPD within habitats. Main conclusions. European human-influenced habitats donate closely related species that often naturalize in disturbed habitats outside their native range. Natural habitats donate species from different lineages with various ecological strategies that allow them to succeed in different habitats in the invaded range. However, in most cases, the naturalized species donated are phylogenetically random subsets of the donor habitats' species pools.

Data for: Ongoing and visually evoked activity in the zebrafish optic tectum and adjacent brain structures

The ongoing activity of neuronal populations represents an internal brain state that influences how sensory information is processed to control behaviour. Conversely, external sensory inputs perturb network dynamics, resulting in lasting effects that persist beyond the duration of the stimulus. However, the relationship between these dynamics and circuit architecture and their impact on sensory processing, cognition and behaviour are poorly understood. By combining cellular-resolution calcium imaging with mechanistic network modelling, we aimed to infer the spatial and temporal network interactions in the zebrafish optic tectum that shape its ongoing activity and state-dependent responses to visual input. We showed that a simple recurrent network architecture, wherein tectal dynamics are dominated by fast, short range, excitation countered by long-lasting, activity-dependent suppression, was sufficient to explain multiple facets of population activity including intermittent bursting, trial-to-trial sensory response variability and spatially-selective response adaptation. Moreover, these dynamics also predicted behavioural trends such as selective habituation of visually evoked prey-catching responses. Overall, we demonstrate that a mechanistic circuit model, built upon a uniform recurrent connectivity motif, can estimate the incidental state of a dynamic neural network and account for experience-dependent effects on sensory encoding and visually guided behaviour.

Data from: Contrasting patterns of disparity suggest differing constraints on the evolution of trilobite cephalic structures during the Cambrian 'explosion'

Trilobites are an abundant group of Palaeozoic euarthropods that appear abruptly in the fossil record c. 521 million years ago. Quantifying the development of morphological variation (or 'disparity') through time in fossil groups like trilobites is critical in understanding evolutionary radiations such as the Cambrian 'explosion'. Here, I use geometric morphometrics to quantify 'cumulative disparity' in functionally-important structures within the trilobite cephalon across their initial radiation during Cambrian Series 2. Overall cephalic disparity increased rapidly and attained a maximum within several million years. This pattern is dominated by the cephalic outline (in particular the genal spines), reflecting rapid, convergent expansion to the extremes of morphospace in a few early families. In contrast, removing the outline and focusing on structures such as the glabella and eye ridges (associated with feeding and vision, respectively) showed a more gradual increase in disparity, closer in line with taxonomic diversity and supporting the hypothesis of a relatively accurate trilobite fossil record. These contrasting patterns suggest that disparity in different structures was constrained in different ways, with extrinsic (ecological) factors likely having the biggest impact on overall disparity. It also implies that patterns of disparity in isolated substructures cannot necessarily be taken individually as representative of overall morphologies.

opencc-by-4.0Apr 2023View details →

Deciphering the structural dynamics in molten salt-promoted MgO-based CO2 sorbents and their role in the CO2 uptake. Open data access

Open data for publication "Deciphering the structural dynamics in molten salt-promoted MgO-based CO2 sorbents and their role in the CO2 uptake"

opencc-by-4.0Apr 2023View details →

Raw data for: Structure and assembly of a bacterial gasdermin pore

This repository contains raw data and code related to "Structure and assembly of a bacterial gasdermin pore" by Johnson et al. Included are molecular dynamics parameter files, structure files after energy minimization and equilibration steps, production trajectories, and code used for analysis. Trajectories are subsampled with every second frame of the original raw trajectories. This results in 1 frame / 2 ns for simulations of full 52-meric pores and 1 frame / 1 ns for all other simulations.     Contact information: Name: Stefan L. Schaefer Institution: Department of Theoretical Biophysics, Max Planck Institute of Biophysics Address: Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany Email: stefan.schaefer@biophys.mpg.de

opencc-by-4.0Oct 2022View details →

Source data belonged to "Establishing structure-property linkages for wicking time predictions in porous polymeric membranes using a data-driven approach"

This record contains all the necessary data to obtain the results of the study "Establishing structure-property linkages for wicking time predictions in porous polymeric membranes using a data-driven approach"