Find research datasets worth reusing

opencc-by-4.0Aug 2023View details →

Supplementary data for "Structural, biochemical, and computational characterization of sulfonamides as bimetallic peptidase inhibitors"

Supplementary data for "Structural, biochemical, and computational characterization of sulfonamides as bimetallic peptidase inhibitors" Coordinates, schemes, NCI density visualization in VMD, and PyMOL sessions for the Figures in the publication are provided.

opencc-zeroDec 2023View details →

Data from: Two male-killing Wolbachia from Drosophila birauraia that are closely related but distinct in genome structure

<a>Insects </a>harbour diverse maternally inherited bacteria and viruses, some of which have evolved to kill the male progeny of their hosts (male killing: MK). The fly species Drosophila biauraria carries a maternally transmitted MK-inducing partiti-like virus, but it was unknown if it carries other MK-inducing endosymbionts. Here, we identified two male-killing Wolbachia strains (wBiau1 and wBiau2) from D. biauraria and compared their genomes to elucidate their evolutionary processes. The two strains were genetically closely related but had exceptionally different genome structures with considerable rearrangements compared with combinations of other Wolbachia strains. Despite substantial changes in the genome structure, the two Wolbachia strains did not experience gene losses that would disrupt the male-killing expression or persistence in the host population. The two Wolbachia-infected matrilines carried distinct mitochondrial haplotypes, suggesting that wBiau1 and wBiau2 have invaded D. biauraria independently and undergone considerable genome changes owing to unknown selective pressures in evolutionary history. This study demonstrated the presence of three male-killers from two distinct origins in one fly species and highlighted the diverse and rapid genome evolution of MK Wolbachia in the host.

opencc-zeroDec 2023View details →

Data for: A novel and enhanced calibration of the tilting weir as a flow measurement structure

To achieve reliable and equitable water distribution it is necessary to accurately estimate the volumetric discharge of water flow through rivers and canals. One such method of accomplishing this is by using hydraulic structures, such as the tilting weir. This structure not only can be used to measure the discharge of water on a continuous basis, but also allows for regulating the water level upstream of the structure. Presently, tilting weirs are often used to control water levels, but the literature on their utilization as flow measurement structures has remained sparse. This study presents a thorough analysis of laboratory experiments on scaled models of tilting weirs, where the flow depth upstream of the structure (i.e., head) and the inclination angle are used to calibrate an equation to estimate the discharge to a high degree of accuracy. Operational guidelines to ensure minimum uncertainty in measurement are also given. The data published here include head and discharge measurements for all experiments conducted, including information on the experimental location, date, and model dimensions. Publication of this data is intended to allow other researchers to verify the calibration procedure laid out in the primary article, and as a comparative dataset for future calibrations.

opencc-zeroDec 2023View details →

Data from: Seasonal variability drives differences in the structure of the calanoid copepod community in two contrasting regions of the Gulf of Mexico

Calanoid copepods (CC) are key contributors to the biological carbon pump and pelagic trophic dynamics. The deep-water regions of Perdido and the Bay of Campeche in the western and southern Gulf of Mexico (GM), respectively, differ in hydrography and productivity, leading to potential differences in copepod biomass and community structure. Zooplankton (0-200 m) were collected from the shelf edge to the deep-water region during the winter and summer autumn 2016. Calanoids contributed 38-60% of total zooplankton biomass and 55-70% of overall copepod abundance. The Bay of Campeche had the highest total zooplankton biovolume (287±120 ml 1000 m-3) and total mean copepod abundance (CC and non-calanoids ~146,000 ind. 1000 m-3) during summer-autumn, likely resulting from cross-shelf nutrient transport fueling local productivity. Adult females dominated calanoid numerical abundance (43-50%), thus suggesting a high reproductive potential. Cluster analysis showed differences between seasons (~40% dissimilarity) but not regions. Environmental conditions explained 22% of the variability in community composition; the winter assemblage was significantly related to oxygen concentrations, whereas the summer-autumn community was related to warmer conditions and higher integrated chlorophyll-a concentrations. The CC community responded to seasonal changes more than regionally related hydrographic differences, with likely implications for organic matter cycling and export.

Data from: Urbanisation and agricultural intensification modulate plant-pollinator network structure and robustness

Land use change is a major pressure on pollinator abundance, diversity, and plant-pollinator interactions. Far less is known about how land use alters the structure of plant-pollinator networks and their robustness to plant-pollinator coextinctions. We analyzed the structure of plant-pollinator networks sampled in 12 landscapes along an urbanisation and agricultural intensity gradient, from early spring to late summer 2021, and used a stochastic coextinction model to correlate plant-pollinator coextinction risk with network structure (species and network-level metrics) and landscape context. Networks in intensively managed (i.e. agricultural and urban) landscapes had a lower risk of initiating a coextinction cascade, while networks in less-intensively managed landscapes may be less robust. Network structure modulated the frequency and severity of coextinctions and species loss, while the strength of species interactions increased robustness. Urban networks were more species-rich and symmetrical due to the high diversity of ornamental plants, while intensively managed agricultural landscapes had smaller, more tightly connected, and nested networks. Network structure modulated the frequency of extinctions, which was decreased by greater linkage density, interaction asymmetry, and interaction dependence in the networks, while once an extinction occurred, nestedness and linkage density propagated the degree of the coextinction cascade and species loss. At the species level, species strength was inversely correlated with extinction risk, implying that generalist species with a high number of interactions with specialists had the lowest extinction risk.

Data from: Same places, same stories? Genomics reveals similar structuring and demographic patterns for four Pocillopora coral species in the southwestern Indian Ocean

Aim Efficiently protecting species requires knowing their ecological, life history and reproductive traits. This is particularly decisive for scleractinian corals, key components of coral reefs, which are experiencing critical declines. Yet their connectivity remains insufficiently documented. Here, we focused on four distinct species of the coral genus Pocillopora found in diverse habitats of the southwestern Indian Ocean and presenting various reproductive strategies. We aimed to understand whether these traits affect species connectivity. Location Archipelagos and islands of the southwestern Indian Ocean. Taxon Pocillopora spp. Methods We used target-capture to collect single-nucleotide polymorphisms (SNPs) from over a thousand colonies sampled across nine localities. From the ca. 1,400 SNPs retained per species, Bayesian clustering methods, networks and demographic inferences were applied to first infer the population genetic structure and connectivity of each species, then the demographic history of each population. Results All four Pocillopora species exhibited almost the same genetic structuring pattern, reflecting the sampled ecoregions (Madagascar and surrounding islands vs. Mascarene Islands). However, the genetic differentiation was stronger ( FST about 10 times higher) for P. acuta, the species inhabiting more enclosed habitats, such as lagoons and shallow waters, and reproducing mainly asexually. Similarly, all populations, except those from P. acuta, showed a signature of population expansion ca. 100,000 years ago, following the penultimate glacial period. Main conclusions These results indicate reduced gene flow between Madagascar and the Mascarenes, probably linked to currents, suggesting distinct connectivity networks that should be considered independently when setting up conservation plans. In addition, shared demographic histories reflect that populations from these species have probably met the same environmental constraints and reacted similarly, something that should be considered in light of the ongoing rapid climate change.

Data from: Compromise docking power evaluation of liganded crystal structures of Mpro SARS-CoV-2

A set of 406 liganded SARS-CoV-2 Mpro crystal structures originally downloaded from RCSB PBD database is provided. Ligand and protein files are processed and corrected for various types of structural errors and are provided in pdbqt and mol2 formats for immediate use in molecular docking programs AutoDock, AutoDock Vina, and PLANTS. Data are utilized in calculations of newly defined compromise docking power to monitor the performance of above-mentioned software. The provided dataset can also be used for benchmarking of other software and molecular docking protocols on liganded SARS-CoV-2 Mpro systems.

Data for: Phylogenetic structure of body shape in a diverse inland ichthyofauna

Body shape is a fundamental metric of animal diversity affecting critical behavioral and ecological dynamics and conservation status, yet previously available methods capture only a fraction of total body-shape variance. Here we use structure-from-motion (SFM) 3D photogrammetry to generate digital 3D models of adult fishes from the Lower Mississippi Basin, one of the most diverse temperate-zone freshwater faunas on Earth, and 3D geometric morphometrics to capture morphologically distinct shape variables, interpreting principal components as growth fields. The mean body shape in this fauna resembles plesiomorphic teleost fishes, and the major dimensions of body-shape disparity are similar to those of other fish faunas worldwide. Major patterns of body-shape disparity are structured by phylogeny, with nested clades occupying distinct portions of the morphospace, most of the morphospace occupied by multiple distinct clades, and one clade (Acanthomorpha) accounting for over half of the total body shape variance. In contrast to previous studies, variance in body depth (59.4%) structures overall body-shape disparity more than does length (31.1%), while width accounts for a non-trivial (9.5%) amount of the total body-shape disparity.

opencc-by-4.0Jan 2024View details →

Data for "Heat treatment and fiber drawing effect on the matrix structure and fluorescence lifetime of Er- and Tm-doped silica optical fibers"

Includes data for absorption and attenuation measurements and calculations, profiles of refractive index and concentrations, TEM images, XRD patters, and data for fluorescence decay curves presented in the graphs.

Data for: Melt electrowriting enabled 3D liquid crystal elastomer structures for cross-scale actuators and temperature field sensors

Liquid crystal elastomers have garnered significant attention due to their remarkable capability to undergo reversible strains and shape transformations under various stimuli. Early studies on LCE primarily focused on limited shape changes of macrostructures or quasi-3D microstructures. However, fabricating complex cross-scale LCE-based 3D structures still remains challenging. Here, we report a compatible method, the Melt-Electrohydrodynamic (Melt-EHD) 3D printing, to create LCE-based microfiber actuators and various 3D actuators across micrometer to centimeter scales, showcasing their actuation to thermal airflow stimulus. By controlling printing parameters, microfiber actuators with different diameters (5 μm~70 μm), and tunable properties including actuation strain (10%~55%), actuation stress (0~0.6 MPa), and large work density (~160J/kg) have been demonstrated. Under dynamic thermal airflow stimulus at 15 Hz, the microfiber actuators lift weights over 3500 times heavier than themselves. These 3D structures were obtained by depositing LCE microfibers along pre-programmed paths, including various gradient-responsive elementary structural units, 1 mm-sized microgripper, and various large area 3D lattice structures. In addition, by integrating a Deep Learning model, we have demonstrated, for the first time, large area (≥ centimeter scale), real-time (24 Hz sampling frequency), high-precision (~95%) LCE grid based spatial temperature field sensors with a spatial resolution of only 4 mm.

Data from: multidimensional beta-diversity across local and regional scales in a Chinese subtropical forest: the role of forest structure

Beta-diversity, or the spatio-temporal variation in community composition, can be partitioned into turnover and nestedness components in a multidimensional framework. Forest structure, including comprehensive characteristics of vertical and horizontal complexity, strongly affects species composition and its spatial variation. However, the effects of forest structure on beta-diversity patterns in multidimensional and multiple-scale contexts are poorly understood. Here, we assessed beta-diversity at local (a 20-ha forest dynamics plot) and regional (a plot network composed of 19 1-ha plots) scales in a Chinese subtropical evergreen broad-leaved forest. We then evaluated the relative importance of forest structure, topography, and spatial structure on beta-diversity and its turnover and nestedness components in taxonomic, functional, and phylogenetic dimensions at local and regional scales. We derived forest structural parameters from both unmanned aerial vehicle light detection and ranging (UAV LiDAR) data and plot inventory data. Turnover component dominated total beta-diversity for all dimensions at the two scales. With the exception of some components (taxonomic and functional turnover at the local scale; functional nestedness at the regional scale), environmental factors (i.e., topography and forest structure) contributed more than pure spatial variation. Explanations of forest structure for beta-diversity and its component patterns at the local scale were higher than those at the regional scale. The joint effects of spatial structure and forest structure influenced component patterns in all dimensions (except for functional turnover) to some extent at the local scale, while pure forest structure influenced taxonomic and phylogenetic nestedness patterns to some extent at the regional scale. Our results highlight the importance and scale dependence of forest structure in shaping multidimensional beta-diversity and its component patterns. Clearly, further studies need to link forest structure directly to ecological processes (e.g., asymmetric light competition and disturbance dynamics) and explore its roles in biodiversity maintenance.

opencc-by-4.0Jan 2024View details →

Data from: Polymerization of renewable itaconic acid in deep eutectic monomers: Effect of the quaternary ammonium cation structure

The upload contains data associated with the publication, including raw data in the original file format whenever possible. Dataset content: NMR, rheology, UVVIS, FTIR, real time photo-FTIR as well as physicochemical properties of the investigated systems. This work was financially supported by the Lead Agency bilateral a Czech-Polish project provided by the Czech Science Foundation (21-07004K) and National Science Center Poland (CEUS-UNISONO project grant no. 2020/02/Y/ST5/00021).

opencc-by-4.0Feb 2024View details →

A data set on_Electrical and colloidal properties of hydrogenated nanodiamonds: effects of structure, composition and size

The data set to paper:  Electrical and colloidal properties of hydrogenated nanodiamonds: effects of structure, composition and size Stepan Stehlik1,2*, Ondrej Szabo2, Ekaterina Shagieva2, Daria Miliaieva2, Alexander Kromka2, Zuzana Nemeckova3, Jiri Henych3, 4, Jan Kozempel5, Evgeny Ekimov6, Bohuslav Rezek7 1 New Technologies – Research Centre, University of West Bohemia, Univerzitní 8, 306 14, Pilsen, Czechia 2 Institute of Physics of the Czech Academy of Sciences, Cukrovarnická 10, 162 00 Prague 6, Czechia 3 Institute of Inorganic Chemistry of the Czech Academy of Sciences, 250 68 Husinec-Řež, Czechia 4 Faculty of Environment, Jan Evangelista Purkyně University in Ústí nad Labem, Pasteurova 3632/15, 400 96 Ústí nad Labem, Czechia 5 Department of Nuclear Chemistry, Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague, Břehová 7, Prague 1, 115 19, Czechia 6 Vereshchagin Institute for High Pressure Physics, Russian Academy of Sciences, Moscow 108840, Russia 7 Faculty of Electrical Engineering, Czech Technical University in Prague, Technická 2, 166 27 Prague, Czechia *principal investigator: stehlik@fzu.cz Data manager: Jan Jaro&scaron;: Jan.Jaros2@vut.cz Date of data collection: 1. 6. 2020 - 18. 1. 2024 All the data showed in the pictures are provided in X-Y format with described sample. Always, the respective Figure to which the data belong is provided in high resolution.  The data are in the following formats:  Figure 1: tiff, csv Figure 2: tiff, csv Figure 3: tiff, csv Figure 4: tiff, csv Figure 5: tiff, csv Figure 6: tiff Data acquistion methods and conditions and data processing is provided in the Experimental part in the publication: DOI:10.1016/j.cartre.2024.100327

opencc-zeroFeb 2024View details →

Data from: Heat stress conditions affect the social network structure of free‐ranging sheep

Extreme weather conditions, like heatwave events, are becoming more frequent with climate change. Animals often modify their behaviour to cope with environmental changes and extremes. During heat stress conditions, individuals change their spatial behaviour and increase the use of shaded areas to assist with thermoregulation. Here, we suggest that for social species, these behavioural changes and ambient conditions have the potential to influence an individual's position in its social network, and the social network structure as a whole. We investigated whether heat stress conditions (quantified through the temperature humidity index) and the resulting use of shaded areas, influence the social network structure and an individual's connectivity in it. We studied this in free‐ranging sheep in the arid zone of Australia, GPS‐tracking all 48 individuals in a flock. When heat stress conditions worsened, individuals spent more time in the shade and the network was more connected (higher density) and less structured (lower modularity). Furthermore, we then identified the behavioural change that drove the altered network structure and showed that an individual's shade use behaviour affected its social connectivity. Interestingly, individuals with intermediate shade use were most strongly connected (degree, strength, betweenness), indicating their importance for the connectivity of the social network during heat stress conditions. Heat stress conditions, which are predicted to increase in severity and frequency due to climate change, influence resource use within the ecological environment. Importantly, our study shows that these heat stress conditions also affect the animal's social environment through the changed social network structure. Ultimately, this could have further flow on effects for social foraging and individual health since social structure drives information and disease transmission.

opencc-by-4.0Aug 2022View details →

Data and code for the article "Advancing Fine Branch Biomass Estimation with LiDAR and Structural Models"

This is the repository for the data and code to reproduce the article "Advancing Fine Branch Biomass Estimation with LiDAR and Structural Models". Summary: ·  Background and Aims Lidar is a promising tool for fast and accurate measurements of trees. There are several approaches to estimate aboveground woody biomass using lidar point clouds. One of the most widely used methods involves fitting geometric primitives (e.g. cylinders) to the point cloud, thereby reconstructing both the geometry and topology of the tree. However, current algorithms are not suited for accurate estimation of the volume of finer branches, because of the unreliable point dispersions from e.g. beam footprint compared to the structure diameter. ·  Methods We propose a new method that couples point cloud-based skeletonization and multi-linear statistical modelling based on structural data to make a model (structural model) that accurately estimates the aboveground woody biomass of trees from high-quality lidar point clouds, including finer branches. The structural model was tested at segment, axis, and branch level, and compared to a cylinder fitting algorithm and to the pipe model theory. ·  Key Results The model accurately predicted the biomass with 1.6% nRMSE at the segment scale from a k-fold cross-validation. It also gave satisfactory results when up-scaled to the branch level with a significantly lower error (13% nRMSE) and bias (-5%) compared to conventional cylinder fitting to the point cloud (nRMSE: 92%, bias: 82%), or using the pipe model theory (nRMSE: 31%, bias: -27%). The model was then applied to the whole-tree scale and showed that the sampled trees had more than 1.7km of structures on average and that 96% of that length was coming from the twigs (i.e. <5 cm diameter). Our results showed that neglecting twigs can lead to a significant underestimation of tree aboveground woody biomass (-21%). ·  Conclusions The structural model approach is an effective method that allows a more accurate estimation of the volumes of smaller branches from lidar point clouds. This method is versatile but requires manual measurements on branches for calibration. Nevertheless, once the model is calibrated, it can provide unbiased and large-scale estimations of tree structure volumes, making it an excellent choice for accurate 3D reconstruction of trees and estimating standing biomass.

opencc-zeroMar 2024View details →

Data from: The neck as a keystone structure in avian macroevolution and mosaicism

Background The origin of birds from non-avian theropod dinosaur ancestors required a comprehensive restructuring of the body plan to enable the evolution of powered flight. One of the proposed key mechanisms that allowed birds to acquire flight and modify the associated anatomical structures into diverse forms is mosaic evolution, which describes the parcelization of phenotypic traits into separate modules that evolve with heterogeneous tempo and mode. Avian mosaicism has been investigated with a focus on the cranial and appendicular skeleton, and as such we don't understand the role of the axial column in avian macroevolution. The long, flexible neck of extant birds lies between the cranial and pectoral modules and represents an opportunity to study the contribution of the axial skeleton to avian mosaicism. Results Here we use 3D geometric morphometrics in tandem with phylogenetic comparative methods to provide, to our knowledge, the first integrative analysis of avian neck evolution in context with the head and wing and to interrogate how the interactions between these anatomical systems have influenced macroevolutionary trends across a broad sample of extant birds. We find that the neck is integrated with both the head and the forelimb. These patterns of integration are variable across clades and only specific ecological groups exhibit either head-neck or neck-forelimb integration. Finally, we find that ecological groups that display head-neck and neck-forelimb integration tend to display significant shifts in the rate of neck morphological evolution. Conclusions Combined, these results suggest that the interaction between trophic ecology and head-neck-forelimb mosaicism influences the evolutionary variance of the avian neck. By linking together the biomechanical functions of these distinct anatomical systems, the cervical vertebral column serves as a keystone structure in avian mosaicism and macroevolution.

opencc-zeroMar 2024View details →

Calling structural variants with confidence from short-read data in wild bird populations

Comprehensive characterisation of structural variation in natural populations has only become feasible in the last decade. To investigate the population genomic nature of structural variation (SV), reproducible and high-confidence SV callsets are first required. We created a population-scale reference of the genome-wide landscape of structural variation across 33 Nordic house sparrows (Passer domesticus) individuals. To produce a consensus callset across all samples using short-read data, we compare heuristic-based quality filtering and visual curation (Samplot/PlotCritic and Samplot-ML) approaches. We demonstrate that curation of SVs is important for reducing putative false positives and that the time invested in this step outweighs the potential costs of analysing short-read discovered SV datasets that include many potential false positives. We find that even a lenient manual curation strategy (e.g. applied by a single curator) can reduce the proportion of putative false positives by up to 80%, thus enriching the proportion of high-confidence variants. Crucially, in applying a lenient manual curation strategy with a single curator, nearly all (>99%) variants rejected as putative false positives were also classified as such by a more stringent curation strategy using three additional curators. Furthermore, variants rejected by manual curation failed to reflect the expected population structure from SNPs, whereas variants passing curation did. Combining heuristic-based quality-filtering with rapid manual curation of structural variants in short-read data can therefore become a time- and cost-effective first step for functional and population genomic studies requiring high-confidence SV callsets.

opencc-by-4.0Mar 2024View details →

Data of "Sustainable and imperceptible augmentation of living structures with organic bioelectronic fibres"

Functional and sensory augmentation of living structures, such as the human skin and plant epidermis, offers vast opportunities for biology-machine interface, wearable health, and environmental monitoring. However, current sensor and electronic formats could be obstructive to their hosts’ inherent sensations or physiological changes. Challenges are also faced in widening the augmentation of living structures without drastically increasing the global environmental and ecological burdens. Here, we demonstrate imperceptibly augmented living systems, through in situ tethering of poly (3,4-ethylenedioxythiophene) : polystyrene sulfonate (PEDOT:PSS)-based organic bioelectronic fibres. Customising fibre tether patterns and modalities enable applications from biopotential acquisition and skin-gated organic electrochemical transistors, to augmented touch and plant interfaces. The open networks formed by the intrinsically substrate-free fibres provide a biomorphic interface, while supporting direct rigid-to-flexible coupling with microelectronics and e-textiles. We further demonstrate conceptual fibre formats for on-demand device repair, upgrade, and recycle, or for enhancing electromechanical stability against touch. Our work may unfold bioelectronic interfaces that are simultaneously biologically-adaptable, sustainable, and created with unprecedented freedom.

opencc-zeroMar 2024View details →

Data from: Genomic diversity and structure of a Neotropical microendemic fig tree

Genetic diversity is a key component of evolution and unraveling factors that promote genetic differentiation in space and time is a central question in evolutionary biology. One of the most diverse and ecologically important tree genera in tropical forests worldwide is Ficus (Moraceae). It has been suggested that, given the great dispersal capacity of pollinating fig wasps (Chalcidoidea; Agaonidae), the spatial genetic structure, particularly in monoecious fig species, should be weak. However, no studies have addressed the factors that determine the genetic structure of Ficus species in regions of high geological, geographic, and climatic complexity, such as the Mexican Transition Zone. Using nuclear single nucleotide polymorphisms (5,311 SNPs) derived from low-coverage whole genomes and 17 populations, we analyzed the population genomics of Ficus pringlei to characterize neutral and adaptive genetic variation and structure and its association with geographic barriers such as the Trans-Mexican Volcanic Belt, environmental heterogeneity, and wind connectivity. From genomic data of 71 individuals, high genetic diversity, and the identification of three genomic lineages were recorded (North, South, and Churumuco). The results suggest that genetic variation is primarily determined by climatic heterogeneity. Ficus pringlei populations from the north and south of the Trans-Mexican Volcanic Belt also exhibited minimal genetic differentiation (FST= 0.021), indicating that this mountain range may not act as an insurmountable barrier to gene flow. Wind connectivity is also highlighted in structuring putative adaptive genetic variation, underscoring the intricate complexity of the various factors influencing genetic variation in the species. This study provides information on the possible mechanisms underlying the genetic variation of endemic species of the tropical dry forest of Western Mexico, such as F. pringlei.