Find research datasets worth reusing

opencc-by-4.0Feb 2020View details →

Dataset to perform COMBINE analysis using HSP90

AMBER topology (hsp90_amber_topology_files.zip) and coordinate (hsp90_amber_coordinate_files.zip) files for a set of 70 HSP90-inhibitor complexes. In addition, bash scripts and input files to help one to prepare a system for COMBINE analysis and run it.

opencc-zeroJan 2021View details →

Data from: Combining climate, land use change and dispersal to predict the distribution of endangered species with limited vagility

Aim: Many rare species are dispersal-limited and minimal land use and climate changes can impact their colonization capacity. Most ecological niche models predict the distribution of species under future climate and land use change scenarios without incorporating specie-specific dispersal abilities. Here we investigated the effect of climate and land use change on low vagile species accounting for their dispersal capacity and defined accessible areas in the future. Location: Europe. Taxon: Saproxylic beetles. Methods: We used the current (2007-2012) occurrences of six endangered saproxylics to develop ecological niche models using current climate and land use conditions. We projected species distributions under four future climate and land use change scenarios to estimate their potential occurrences. Finally, accounting for species-specific dispersal, we limited their distributions to accessible areas in 2040-50. Results: Without accounting for dispersal abilities we found a strong and positive impact of climate change on the distribution of Cerambix cerdo, Cucujus cinnaberinus, Morimus funereus and Rosalia alpina and a positive effect of land use change on the distribution of Lucanus cervus and Osmoderma eremita. When species-specific dispersal was included, we found a strong and positive impact of land use change on the distribution of all the species. In this case climate change had a lower but positive effect on the distribution of C. cerdo, C. cinnaberinus, L. cervus and R. alpina, and a negative effect on the distribution of O. eremita. Main conclusion: We found that climate change would promote the expansion of saproxylic beetles only in the unrealistic case of unlimited dispersal. Accounting for dispersal abilities, the expansion of our species would be mainly conditioned by the effect of land use change. Thus, we encourage researchers to combine climate and land use change with dispersal when projecting species distribution under future scenarios to accurately identify areas with fundamental species-specific resources.

opencc-zeroDec 2018View details →

Data from: Assessing combinability of phylogenomic data using Bayes Factors

With the rapid reduction in sequencing costs of high-throughput genomic data, it has become commonplace to use hundreds of genes to infer phylogeny of any study system. While sampling a large number of genes has given us a tremendous opportunity to uncover previously unknown relationships and improve phylogenetic resolution, it also presents us with new challenges when the phylogenetic signal is confused by differences in the evolutionary histories of sampled genes. Given the incorporation of accurate marginal likelihood estimation methods into popular Bayesian software programs, it is natural to consider using the Bayes Factor (BF) to compare different partition models in which genes within any given partition subset share both tree topology and edge lengths. We explore using marginal likelihood to assess data subset combinability when data subsets have varying levels of phylogenetic discordance due to deep coalescence events among genes (simulated within a species tree), and compare the results with our recently-described phylogenetic informational dissonance index (D) estimated for each data set. BF effectively detects phylogenetic incongruence, and provides a way to assess the statistical significance of D values. We use BFs to assess data combinability using an empirical data set comprising 56 plastid genes from the green algal order Volvocales. We also discuss the potential need for calibrating BFs and demonstrate that BFs used in this study are correctly calibrated.

opencc-zeroDec 2014View details →

Data from: Combined use of GPS and accelerometry reveals fine scale three-dimensional foraging behaviour in the short-tailed shearwater

Determining the foraging behaviour of free-ranging marine animals is fundamental for assessing their habitat use and how they may respond to changes in the environment. However, despite recent advances in bio-logging technology, collecting information on both at-sea movement patterns and activity budgets still remains difficult in small pelagic seabird species due to the constraints of instrument size. The short-tailed shearwater, the most abundant seabird species in Australia (ca 23 million individuals), is a highly pelagic procellariiform. Despite its ecological importance to the region, almost nothing is known about its at-sea behaviour, in particular, its foraging activity. Using a combination of GPS and tri-axial accelerometer data-loggers, the fine scale three-dimensional foraging behaviour of 10 breeding individuals from two colonies was investigated. Five at-sea behaviours were identified: (1) resting on water, (2) flapping flight, (3) gliding flight, (4) foraging (i.e., surface foraging and diving events), and (5) taking-off. There were substantial intra- and inter- individual variations in activity patterns, with individuals spending on average 45.8% (range: 17.1–70.0%) of time at sea resting on water and 18.2% (range: 2.3–49.6%) foraging. Individuals made 76.4 ± 65.3 dives (range: 8–237) per foraging trip (mean duration 9.0 ± 1.9 s), with dives also recorded during night-time. With the continued miniaturisation of recording devices, the use of combined data-loggers could provide us with further insights into the foraging behaviour of small procellariiforms, helping to better understand interactions with their prey.

opencc-zeroDec 2012View details →

Data from: Tracing horizontal Wolbachia movements among bees (Anthophila): a combined approach using multilocus sequence typing data and host phylogeny

The endosymbiotic bacterium Wolbachia enhances its spread via vertical transmission by generating reproductive effects in its hosts, most notably cytoplasmic incompatibility (CI). Additionally, frequent interspecific horizontal transfer is evident from a lack of phylogenetic congruence between Wolbachia and its hosts. The mechanisms of this lateral transfer are largely unclear. To identify potential pathways of Wolbachia movements, we performed multilocus sequence typing of Wolbachia strains from bees (Anthophila). Using a host phylogeny and ecological data, we tested various models of horizontal endosymbiont transmission. In general, Wolbachia strains seem to be randomly distributed among bee hosts. Kleptoparasite-host associations among bees as well as other ecological links could not be supported as sole basis for the spread of Wolbachia. However, cophylogenetic analyses and divergence time estimations suggest that Wolbachia may persist within a host lineage over considerable timescales and that strictly vertical transmission and subsequent random loss of infections across lineages may have had a greater impact on Wolbachia strain distribution than previously estimated. Although general conclusions about Wolbachia movements among arthropod hosts cannot be made, we present a framework by which precise assumptions about shared evolutionary histories of Wolbachia and a host taxon can be modelled and tested.

opencc-zeroNov 2015View details →

Crack nucleation using combined crystal plasticity modelling, HR-DIC and HR-EBSD in a superalloy containing non-metallic inclusions under fatigue

The uploaded data are required to reproduce the experimental results in the paper.  To replicate figure 4, both GID.mat and thermal_E11.mat should be loaded into matlab.  To replicate figure 6, strain_11.mat should be uploaded. Then fDIC_GB.m should be executed.  If the reader has further questions, please contact Tiantian Zhang at tiantian.zhang08@imperial.ac.uk or tzhang6@wpi.edu

opencc-by-nc-4.0Aug 2016View details →

Software used in research based on combined surveys

The combined results of five surveys run by the Software Sustainability Institute, which were run between 2014 to 2016. The data relate to 1261 survey participants who were asked “What software do you use in your research?”. The data are described here: https://www.software.ac.uk/blog/2016-08-13-quick-and-dirty-analysis-software-being-used-research-python-matlab-and-r

FIGURE 4 in Combined approach using morphology and ITS-sequences for description of three new species of Macrocheles (Acari: Macrochelidae)

FIGURE 4. Phylogenetic tree of seven Macrocheles species (14 individuals) and two outgroup species using PAUP*4b10 with Branch and Bound. Bootstrap values (=50%) from analyses with 1000 replications are plotted.

FIGURE 3 in Combined approach using morphology and ITS-sequences for description of three new species of Macrocheles (Acari: Macrochelidae)

FIGURE 3. Macrocheles ovoidalis sp. nov. Female. (a) dorsal shield; (b) ventral idiosoma; (c) epistome; (d) chelicera. Scale bar = 500 Μm for 3a, 300 Μm for 3b, 50 Μm for 3c, 30 Μm for 3d.

FIGURE 2 in Combined approach using morphology and ITS-sequences for description of three new species of Macrocheles (Acari: Macrochelidae)

FIGURE 2. Macrocheles bertrandi sp. nov. Female. (a) dorsal shield; (b) ventral idiosoma; (c) epistome; (d) chelicera. Scale bar = 500 Μm for 2a, 300 Μm for 2b, 50 Μm for 2c, 2d.

FIGURE 1 in Combined approach using morphology and ITS-sequences for description of three new species of Macrocheles (Acari: Macrochelidae)

FIGURE 1. Macrocheles lumareti sp. nov. Female. (a) dorsal shield; (b) ventral idiosoma; (c) epistome; (d) chelicera. Scale bar = 500 Μm for 1a, 1b, 50 Μm for 1c, 1d.

opencc-by-4.0Feb 2024View details →

Agricultural land use (raster) : National-scale crop type maps for Germany from combined time series of Sentinel-1, Sentinel-2 and Landsat data (2017 to 2021)

The dataset contains maps of the main classes of agricultural land use (dominant crop types and other land use types) in Germany, which are produced annually at the Thünen Institute beginning with the year 2017 on the basis of satellite data. The maps cover the entire open landscape, i.e., the agriculturally used area (UAA) and e.g., uncultivated areas. The map was derived from time series of Sentinel-1, Sentinel-2, Landsat 8 and additional environmental data. Map production is based on the methods described in <a href="https://doi.org/10.1016/j.rse.2021.112831">Blickensdörfer et al. (2022)</a>. All optical satellite data were managed, pre-processed and structured in an analysis-ready data (ARD) cube using the open-source software <a href="https://force-eo.readthedocs.io/en/latest/">FORCE </a>- Framework for Operational Radiometric Correction for Environmental monitoring (Frantz, D., 2019), in which SAR and environmental data were integrated. The map extent covers all areas in Germany that are defined in the respective year as cropland, grassland, small woody features, heathland, peatland or unvegetated areas according to ATKIS Basis-DLM (Geobasisdaten: © GeoBasis-DE / BKG, 2020).  Version v201: Post-processing of the maps included a sieve filter as well as a ruleset for the reduction of non-plausible areas using the Basis-DLM and the digital terrain model of Germany (Geobasisdaten: © GeoBasis-DE / BKG, 2015). Version v202: Additional post-processing was performed to detect and mask additional non-plausible areas that were not adequately covered by the first post-processing (e.g., areas with sparse vegetation, montane forests) based on the &bdquo;Ökosystematlas Deutschland“ (© Statistisches Bundesamt, Deutschland, 2024). As a consequence, the current version includes a new class “Small woody features on other land”. Furthermore, the class "permanent grassland" was refined. Each pixel that was classified as "cultivated grassland" in at least five years (between 2017 and 2022) was translated to "permanent grassland" in the annual maps. The maps are available as cloud optimized GeoTiffs, which makes downloading the full dataset optional. All data can directly be accessed in QGIS, R, Python or any supported software of your choice using the provided URL to the datasets (right click on the respective data set --> “copy link address”). By doing so the entire map area or only the regions of interest can be accessed. QGIS legend files for data visualization can be downloaded separately. Class-specific accuracies for each year are provided in the respective tables. We provide this dataset "as is" without any warranty regarding the accuracy or completeness and exclude all liability.    References: Blickensdörfer, L., Schwieder, M., Pflugmacher, D., Nendel, C., Erasmi, S., & Hostert, P. (2022). Mapping of crop types and crop sequences with combined time series of Sentinel-1, Sentinel-2 and Landsat 8 data for Germany. Remote Sensing of Environment, 269, 112831. BKG, Bundesamt für Kartographie und Geodäsie (2015). Digitales Geländemodell Gitterweite 10 m. DGM10. https://sg.geodatenzentrum.de/web_public/gdz/dokumentation/deu/dgm10.pdf (last accessed: 28. April 2022). BKG, Bundesamt für Kartographie und Geodäsie (2020). Digitales Basis-Landschaftsmodell. https://sg.geodatenzentrum.de/web_public/gdz/dokumentation/deu/basis-dlm.pdf (last accessed: 28. April 2022). Frantz, D. (2019). FORCE—Landsat + Sentinel-2 Analysis Ready Data and Beyond. Remote Sensing, 11, 1124. Statistisches Bundesamt, Deutschland (2024). Ökosystematlas Deutschland https://oekosystematlas-ugr.destatis.de/ (last accessed: 08.02.2024). ___________________________________________________________________________ National-scale crop type maps for Germany from combined time series of Sentinel-1, Sentinel-2 and Landsat data (2017 to 2021) © 2024 by Schwieder, Marcel; Tetteh, Gideon Okpoti; Blickensdörfer, Lukas; Gocht, Alexander; Erasmi, Stefan;  licensed under CC BY 4.0.  Funding was provided by the German Federal Ministry of Food and Agriculture as part of the joint project “Monitoring der biologischen Vielfalt in Agrarlandschaften” (<a href="https://www.agrarmonitoring-monvia.de/en/">MonViA</a>, Monitoring of biodiversity in agricultural landscapes). The study was financially supported by the European Environment Agency and the European Union’s Horizon Europe Research and Innovation programme under Grant Agreement No 101060423 (LAMASUS).

opencc-zeroMar 2022View details →

Integrative taxonomic analysis to reveal the species status of Bombus flavidus, combining COI and nuclear sequencing, wing morphometrics and secretions used for mate attraction as well as patterns of color polymorphism

Bumble bees, due to their morphological monotony and color diversity, have presented difficulties with species delimitation. Recent bumble bee declines have made it ever more imperative to resolve the status of species to address conservation concerns. Some of the taxa found to be most threatened are the often-rare socially parasitic bumble bees, which have additional trophic requirements. Among the socially parasitic bumble bees, Bombus flavidus Eversmann has contentious species status. While multiple separate species allied with Bombus flavidus have been suggested, until recently, recognition of two species, a Nearctic Bombus fernaldae (Franklin) and Palearctic B. flavidus, was favoured. Limited genetic data, however, suggested that even these could be a single widespread species, B. flavidus. We addressed the species status of this lineage using an integrative taxonomic approach, combining COI and nuclear sequencing, wing morphometrics and secretions used for mate attraction. We also explore patterns of color polymorphism that have previously confounded taxonomy in this lineage. Our results support the conspecific status of Bombus fernaldae and Bombus flavidus, however, sampling specimens from across the range of these two taxa revealed a distinct population within this broader species confined to eastern North America. This makes the distribution of the social parasite B. flavidus the broadest of any bumble bee, broader than the known distribution of any non-parasitic bumble bee species. Analysis of color phenotypes revealed that color polymorphisms are retained across the range of the species, but may be influenced by local mimicry complexes. Following these results, Bombus flavidus Eversmann, 1852 is synonymized with Bombus fernaldae (Franklin, 1911) syn. nov. and a subspecific status, Bombus flavidus appalachiensis ssp. nov., is assigned to the distinct lineage ranging from the Appalachians to the eastern boreal regions of the United States and far southeastern Canada.

opencc-by-4.0Aug 2022View details →

Effect of Using Ethanol Extract of Artocarpus heterophyllus Leaves and Olea Europa Fruit Oil Combination on Facial Skin

The volunteers were applied to the clay mask once a week and then were observed before and after application, as follows: moisture, skin oil, skin texture, collagen, wrinkle, pigment, and sensitivity using a skin analyzer (Skin Observed System).

opencc-by-2.0Mar 2022View details →

Data for "Identification of Karst Spring Hydrographs Using Laboratory and Numerical Simulations Considering Combined Discrete-Continuum Approaches"

This is the dataset for "Identification of Karst Spring Hydrographs Using Laboratory and Numerical Simulations Considering Combined Discrete-Continuum Approaches”.

opennotspecifiedOct 2017View details →

FIGURE 8. 3 D in Contribution to the morphological description of the marine leech, Ozobranchus margoi (Apáthy) (Rhynchobdellida: Ozobranchidae) by using combined histology, micro-CT and SEM

FIGURE 8. 3 D volume renderings of O. margoi using the micro-CT technology. Contrast enhancement to expose the denser parts. A, dorsal view of the whole body until the posterior sucker (ps) enouncing the digestive system. From the posterior intestine (pi) two lateral post ceca are starting (pca). Four pairs of blind ending lateral diverticula (ld) are diverting from the posterior intestine that finally enlarge to form a sac-like structure. Arrows indicate the two lateral blind-ended sacks in the last sack of the posterior intestine. B, frontal view of the anterior sucker (as) showing the four lines of lateral columnar glands (gl) and a central gland-like structure separated from the other (arrow). Scale bar = 1 mm.

opennotspecifiedOct 2017View details →

FIGURE 7 in Contribution to the morphological description of the marine leech, Ozobranchus margoi (Apáthy) (Rhynchobdellida: Ozobranchidae) by using combined histology, micro-CT and SEM

FIGURE 7. Section images of O. margoi using the micro-CT technology. A, antero-coronal section in 3 D volume rendering of the dorsal part of the leech, showing the glands (gl) with the gland duct (gd) and the oesophagus (oe). Five pairs of blind sacs (bs) begins on both sides of the posterior crop (pc). B, transversal section with the ganglionic mass (gm) overcome by a glandlike structure (gls) and surrounding the proboscis (pr). C, transversal section on the oviducal bridge (ob) with the two ovaries arching ventrally and separating the anterior (ac) and posterior crop (pc). D, antero-coronal section of the leech showing the oesophagus (oe) and four pairs of testis (T) connected (cn) in two points with the body cavity. On both lateral sides there are five pairs of external gills (g). E, coronal section of the whole body showing the posterior crop (pc), a pair of testes (t) tied to the celomic cavity with two connections (cn), two lateral post ceca (pca) and three of the four central sacs of the posterior intestine. F, transversal section of the not branchiate segment of the urosome showing two ventrally located lateral post ceca (pca), one central expanded posterior intestine (pi) and a dorsally directed lateral diverticula (ld). G, transversal section in proximity of the posterior sucker (ps) showing the posterior intestine (pi) ending in a dorsal anus (da). Scale bar = 1 mm.