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opencc-zeroJan 2024View details →

Butterfly community composition within a tropical urban landscape is influenced by habitat type and temperature

The specific factors that influence spatial community or population dynamics are often elusive, and even less known is the impact of tropical urban landscapes on diverse species community assemblages. To address this knowledge gap, we used a survey data set with 510 fruit‐feeding butterflies comprising 20 species across two heterogeneous habitats within a city in Nigeria. Next, we constructed generalised linear mixed models to understand the differential responses of the butterfly community to changes in environmental conditions across habitats. Butterfly species community assemblages significantly differed between the two urban habitats, with butterfly species significantly higher in the savannah woodland compared with the gallery forest due to the optimal daily temperatures of the savannah woodland. However, butterfly richness was lower in the gallery forest due to extreme environmental conditions. This study highlights that butterfly community changes in tropical urban landscapes are possibly responding to local microclimates and spatial heterogeneity across habitats. For evidence‐based conservation management of tropical butterfly biodiversity, there would be a need for a long‐term, extensive and systematic insect monitoring programme for butterflies across disturbed and undisturbed fragmented habitats harbouring diverse insect species.

opencc-by-4.0Jul 2023View details →

Datasets of mineral composition and geochronological result of Barrovian metamorphic sequence rocks in the Ailao Shan massif

This file includes the supporting information of the manuscript titled“Thermal and physical properties of Barrovian metamorphic sequence rocks in the Ailao Shan-Red River shear zone, and implications for crustal channel flow”

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

Dataset for "Cascading effects of mammal host community composition on tick vector occurrence at the urban human-wildlife interface"

Dataset for the following paper: Cascading effects of mammal host community composition on tick vector occurrence at the urban human-wildlife interface Jonathan Bastard *, Nichar Gregory *, Maria Pilar Fernandez, Michaela Mincone, Olivia Card, Sara Kross, Maria Diuk-Wasser * These authors contributed equally.

opencc-zeroFeb 2024View details →

Data from: Gut microbiota composition and functionality are associated with REM sleep duration and continuous glucose levels

Context: Sleep disruption is associated with poorer glucose metabolic control and altered gut microbiota in animal models. Objective: We aimed to evaluate the possible links among REM sleep duration, continuous glucose levels, and gut microbiota composition. Design: This is an observational, prospective, real-life, cross-sectional case-control study. Setting: Tertiary Hospital recruiting healthy volunteers. Patients or Other Participants: One-hundred and eighteen (60 with obesity), middle-aged (39.1-54.8) subjects. Intervention(s): Glucose variability and REM sleep duration were assessed by 10-day continuous glucose monitoring (CGM) (Dexcom G6®) and wrist-actigraphy (Fitbit Charge 3®), respectively Main Outcome Measure(s):. Glucose variability was evaluated through standard deviation (SD), coefficient of variation (CV), and interquartile range (IQR). The percentage of time in range (% TIR), 126-139 mg/dL (TIR2), and 140-199 mg/dL (TIR3) were calculated. Shotgun metagenomics sequencing was applied to study gut microbiota taxonomy and functionality. Results: Increased glycemic variability (SD, CV, and IQR) was observed among subjects with obesity in parallel to increased % TIR2 and % TIR3. REM sleep duration was independently associated with the % TIR3 (β=-0.339; p<0.001) and glucose variability (SD, β=-0.350; p<0.001). Microbial taxa from Christensenellaceae family (Firmicutes phylum) were positively associated with REM sleep and negatively with glucose continuous monitoring levels, while bacteria from Enterobacteriacea family and bacterial functions involved in iron metabolism showed opposite associations. Conclusions: Decreased REM sleep duration was independently associated with a worse glucose profile. The associations of species from Christensenellaceae and Enterobacteriaceae families with REM sleep duration and continuous glucose values suggest an integrated picture of metabolic health.

Dataset and R-scripts to the manuscript: Beyond salinity: plants show divergent responses to soil ion composition

Dataset and R-scripts to the article: Pätsch R., Midolo G., Dítě Z., Dítě, D., Wagner, V., Pavonič, M., Danihelka, J., Preislerová Z., Ćuk M., Stroh H.G., Tóth T., Chytrá H., Chytrý M. (2024) Beyond salinity: plants show divergent responses to soil ion composition. Global Evology and Biogeography, 00, e13821. <a href="https://doi.org/10.1111/geb.13821%E2%80%8B" target="_blank" rel="noopener">https://doi.org/10.1111/geb.13821</a>

Oxygen driving hydrogen into the inner core: Implications for the Earth's core composition

Dataset for "Oxygen driving hydrogen into the inner core: Implications for the Earth’s core composition" Including two sheets for raw data: Free Energies (21 records) and PVTX data (30 records).

opencc-by-4.0Mar 2022View details →

Engineering the Compositional Architecture of Core-Shell Upconverting Lanthanide-Doped Nanoparticles for Optimal Luminescent Donor in Resonance Energy Transfer: The Effects of Energy Migration and Storage

Förster Resonance Energy Transfer (FRET) between single molecule donor (D) and acceptor (A) is well understood from fundamental perspective and is widely applied in biology, biotechnology, medical diagnostics and bio-imaging. However, the reliability of molecular FRET measurements can be affected by numerous artefacts which eventually hamper quantitative and reliable analysis, mostly due to issues with the donor and acceptor molecules. Lanthanide doped upconverting nanoparticles (UCNPs) have demonstrated their suitability as alternative donor species. Nevertheless, while they solved most disadvantageous features of organic donor molecules, such as photo-bleaching, spectral cross-excitation and emission bleed-through, the fundamental understanding and practical realizations of bio-assays with UCNP donors remain challenging. Among others, the actual donor ions in individual donor UCNPs are the numerous activator ions randomly distributed in the nanoparticle at various distances to acceptors anchored on the nanoparticle surface. Further, the power dependent, complex energy transfer upconversion and energy migration between sensitizing and activating lanthanide ions within UCNPs complicate the decay based analysis of D-A interaction. In this work, the assessment of designed virtual core-shell nanoparticle (VNP) models led us to the new designs of UCNPs, such as …@Er, Yb@Er, Yb@YbEr, which were experimentally evaluated as donor nanoparticles and compared to the simulations. Moreover, the specific properties of lanthanide-based upconversion motivated us to analyze not only steady-state luminescence and luminescence decay responses of both the UNCP donor and the sensitized acceptor, but also the effects of their luminescence rise kinetics upon RET was discussed in newly proposed disparity measurements. The presented studies help to understand the role of energy-transfer and energy migration between lanthanide ion dopants (due to their concentration and spatial distribution) and how the architecture of core-shell UCNPs affects their performance as FRET donors to organic acceptor dyes.

Data from: Forest bees benefit from compositionally diverse broadleaf canopies

Data from: Forest bees benefit from compositionally diverse broadleaf canopies 2024. Forest Ecology and Management 566: 122051. <a title="Persistent link using digital object identifier" href="https://doi.org/10.1016/j.foreco.2024.122051" target="_blank" rel="noreferrer noopener">https://doi.org/10.1016/j.foreco.2024.122051</a>   Clayton R. Traylor1,2, Michael D. Ulyshen3, Don C. Bragg4, Joseph V. McHugh1   1 Department of Entomology, University of Georgia, Athens, GA 30602, USA 2 Department of Biology, Temple University, Philadelphia, PA 19122, USA 3 Southern Research Station, USDA Forest Service, Athens, GA 30602, USA 4 Southern Research Station, USDA Forest Service, Monticello, AR, 71656, USA   Corresponding author: Clayton R. Traylor ( <a href="mailto:clayton.r.traylor@gmail.com">clayton.r.traylor@gmail.com</a> ) Abstract Forests provide critical habitats for pollinating insects, including forest-dependent and habitat generalist species, yet it is unknown how these assemblages are shaped by overstory tree composition. We sampled bees in closed canopy plots in the southeastern United States representing a continuum of forest age and tree composition, from younger conifer-dominated forests to older forests dominated by deciduous broadleaf trees. Species-specific responses of bees to forest composition, and the influence of their traits on responses, were estimated using a joint species distribution model. Additionally, we investigated species richness trends of nesting, sociality, and phenological trait groups. Forest composition greatly influenced bee species occurrence: 48 % of species had positive relationships with the diversity of insect-pollinated broadleaf trees and 46 % had negative relationships with the proportion of conifer basal area. Bee species with early phenological activity drove these responses and richness patterns supported these trends. Our results indicate that phenology is an important factor determining bee species’ forest dependency and sensitivity to forest composition in this region. We conclude that diverse broadleaf forests are crucial to maintaining bee diversity by providing floral resources that support forest-dependent species even in closed canopy conditions. Conifer forests can also provide valuable habitat to bee pollinators when restored to open canopy conditions. However, because no traits are indicative of conifer forest dependency and bee species respond to understory flora rather than tree attributes, open conifer forests may more strongly favor habitat generalists than forest specialists.

Spring tropical cyclones modulate near-surface isotopic compositions of atmospheric water vapour at Kathmandu, Nepal

All these data have been published in a ACP paper. If you use these data in any conditions, please cite the following publicaiton: Adhikari, N., Gao, J., Zhao, A., Xu, T., Chen, M., Niu, X., and Yao, T.: Spring tropical cyclones modulate near-surface isotopic compositions of atmospheric water vapour at Kathmandu, Nepal, EGUsphere, https://doi.org/10.5194/egusphere-2023-2186, 2023.

opencc-zeroDec 2023View details →

Data from: Geography and ecology shape the phylogenetic composition of Amazonian tree communities

Aim: Amazonia hosts more tree species, from numerous evolutionary lineages both young and ancient, than any other biogeographic region. Previous studies have shown that tree lineages colonised multiple edaphic environments and dispersed widely across Amazonia, leading to a hypothesis, which we test, that lineages should not be strongly associated with either geographic regions or edaphic forest types. Location: Amazonia. Taxon: Angiosperms (Magnoliids; Monocots; Eudicots). Methods: Data for the abundance of 5,082 tree species in 1,989 plots were combined with a mega-phylogeny. We applied evolutionary ordination to assess how phylogenetic composition varies across Amazonia. We used variation partitioning and Moran's eigenvector maps (MEM) to test and quantify the separate and joint contributions of spatial and environmental variables to explain the phylogenetic composition of plots. We tested the indicator value of lineages for geographic regions and edaphic forest types and mapped associations onto the phylogeny. Results: In the terra firme and várzea forest types, phylogenetic composition varies by geographic region, but the igapó and white-sand forest types retain a unique evolutionary signature regardless of region. Overall, we find that soil chemistry, climate, and topography explain 24% of the variation in phylogenetic composition, with 79% of that variation being spatially structured (R 2 = 19% overall for combined spatial/environmental effects). Phylogenetic composition also shows substantial spatial patterns not related to the environmental variables we quantified (R 2 = 28%). A greater number of lineages were significant indicators of geographic regions than forest types. Main conclusions: Numerous tree lineages, including some ancient ones (>66 Ma), show strong associations with geographic regions and edaphic forest types of Amazonia. This shows that specialization on specific edaphic environments has played a long-standing role in the evolutionary assembly of Amazonian forests. Furthermore, many lineages, even those that have dispersed across Amazonia, dominate within a specific region, likely because of phylogenetically conserved niches for environmental conditions that are prevalent within regions.

Research Data - Dose and Compositional Dependence of Irradiation-Induced Property Change in FeCr

Research data and associated processing and plotting scripts for the article: Song et al., 'Dose and compositional dependence of irradiation-induced property change in FeCr', Journal of Nuclear Materials, 154998, 2024 <a title="Persistent link using digital object identifier" href="https://doi.org/10.1016/j.jnucmat.2024.154998" target="_blank" rel="noreferrer noopener">https://doi.org/10.1016/j.jnucmat.2024.154998</a>

opencc-zeroDec 2023View details →

Stem decomposition of temperate tree species is determined by stem traits and fungal community composition during early stem decay

Dead trees are vital structural elements in forests playing key roles in the carbon and nutrient cycle. Stem traits and fungal community composition are both important drivers of stem decay, and thereby affect ecosystem functioning, but their relative importance for stem decomposition over time remains unclear. To address this issue, we used a common garden decomposition experiment in a Dutch larch forest hosting fresh logs from 13 common temperate tree species. In total 25 fresh wood and bark traits were measured as indicators of wood accessibility for decomposers, nutritional quality, and chemical or physical defense mechanisms. After one and four years of decay, we assessed the richness and composition of wood-inhabiting fungi using amplicon sequencing and determined the proportional wood density loss. Average proportional wood density loss for the first year was 18.5%, with further decomposition occurring at a rate of 4.3% yr-1 for the subsequent three years across tree species. Proportional wood density loss varied widely across tree species in the first year (8.7-24.8% yr-1) and subsequent years (0-11.3% yr-1). The variation was directly driven by initial wood traits during the first decay year, then later directly driven by bark traits and fungal community composition. Moreover, bark traits affected the composition of wood-inhabiting fungi and thereby indirectly affected decomposition rates. Specifically, traits promoting resource acquisition of the living tree, such as wide conduits that increase accessibility and high nutrient concentration, increased initial wood decomposition rates. Fungal community composition, but not fungal richness explained differences in wood decomposition after four years of exposure in the field, where fungal communities dominated by brown-rot and white-rot Basidiomycetes were linked to higher wood decomposition rate. Synthesis. Understanding what drives deadwood decomposition through time is important to understand the dynamics of carbon stocks. Here, using a tailor-made experimental design in a temperate forest setting, we have shown that stem trait variation is key to understanding the roles of these drivers; Initially, wood traits explained decomposition rates while subsequently, bark traits and fungal decomposer composition drove decomposition rates. These findings inform forest management with a view to selecting tree species to promote carbon storage.

opencc-by-4.0Nov 2023View details →

Thermal conductivity analysis of polymer-derived nano-composite via image-base structure reconstruction, computational homogenization and machine learning

This dataset includes supplementary data and utilities for validating simulation results and training machine learning models as outlined in the publication titled "Thermal Conductivity Analysis of Polymer-Derived Nanocomposite via Image-Based Structure Reconstruction, Computational Homogenization, and Machine Learning" (<a href="https://doi.org/10.1002/adem.202302021">Fathidoost, 2024</a>). This dataset containes the microstructure images (identified by particle diameters size \(D_1\) and \(D_2\) volume fraction \(V_\mathrm{f}\) and aspect ratio \(A_\mathrm{r}\)) (see Table 1) and their corresponding homogenized thermal conductivity. these images resemble the microstructure of the monolithic \(\mathrm{(Hf,Ta)C/SiC}\) ceramic following FAST sintering, the material system of this work (<a href="https://doi.org/10.1002/adem.202302021">Fathidoost, 2024</a>). White and black colors within the images represent distinct regions of the material system,  respectively referring to former powder particles (FPPs) and sinter necks (SNs), which is explained in this work. Table 1. Parameterized descriptors extracted from the mesoscale SEM image analysis <table> <tbody> <tr> <td>Param.</td> <td>Mean [unit]</td> <td>Std.</td> </tr> <tr> <td>\(D_{1}\)</td> <td>40, 50, 60 [μm]</td> <td>20%</td> </tr> <tr> <td>\(D_{2}\)</td> <td>20, 25, 26, 30, 33, 40 [μm]</td> <td>30%</td> </tr> <tr> <td>\(V_\mathrm{f}\)</td> <td>1.5, 2.0</td> <td>-</td> </tr> <tr> <td>\(A_\mathrm{r}\)</td> <td>35, 40, 45, 55, 60 [%]</td> <td>-</td> </tr> </tbody> </table> This dataset contains: <ul> <li>dataset.csv: containing a summary of data including the names of microstructure images, their corresponding geometric details, as well as the first and third principal components of two-point statistics for all images, along with the effective thermal conductivity of the corresponding microstructures. Further details can be found in the associated publication.</li> <li>microstructures_images.zip: containing binary cross-section images of the RVEs from synthetic microstructures。</li> <li>results.zip: contains all the simulation results based on digitized diffuse-interface microstructures, which can be opened by the post-processing software, such as ParaView.</li> </ul>

opencc-zeroMar 2024View details →

Variation in functional composition of reef fishes along a tropical to temperate gradient

Aims Transformations of species and functional compositions on subtropical reefs are ongoing due to poleward range shifts of some tropical species, with largely unknown consequences to ecosystem functioning. Trait-based approaches are powerful tools to quantify such changes. Here, we evaluated changes in the trait composition of coral-associated fish communities along a tropical to a temperate environmental gradient of ca.1400 km in southern Japan with abundance-weighted trait expression to assess how trait complexity changes with increasing latitude. Location Ryukyu Islands and southern Pacific coast of Japan Taxon Reef fish Methods We tested for shifts in trait space and functional redundancy, based on five morphological, life history, and behavioural traits: maximum length, pelagic larval duration, trophic level, substrate preference, and reproductive mode. Our trait database was coded with two approaches, first, by attributing a single value to each trait per species, and second, by fuzzy coding that allows more than one value per trait and hence considers some intraspecific trait variation. Results We found a reduction in specialist habitat traits (coral substrate preference, nesters, herbivores) and an increase in generalist traits (predators) with increasing latitude, along with a contraction in trait space from tropical to temperate reefs. Functional redundancy declined with increasing latitude. These trends were closely linked with latitudinal gradients in temperature, along with changes in other environmental factors such as turbidity and photosynthetically active radiation. Main Conclusion Functional turnover and contractions are thus likely due to the marginal conditions for coral-associated fishes at higher latitudes, favouring generalist species, whereas increased resources at lower latitudes favour high redundancy and niche partitioning. Accounting for intraspecific trait variation indicated the same trends but highlighted increased functional vulnerability across all sites. We show that trait complexity in coral-associated fish communities decreases from tropical to temperate reefs, highlighting the reduced functional scope that comes with marginal environmental conditions.

NSRC-Search: Efficient searching for similar protein sequences of non-standard amino acid composition

This research was funded by the National Science Centre in Poland (grant number 2021/41/N/ST6/01919)

Weekly Ground-based Measurements of NH3, HNO3, and Submicron Aerosol Composition from Greeley, Colorado

<div>This data was collected at the Weld County Tower in Greeley, Colorado, USA and used as part of the work submitted to JGR:Atmospheres titled "Inorganic Nitrogen Gas-Aerosol Partitioning in and around Animal Feeding Operations in Northeastern Colorado in Late Summer 2021."</div>

opencc-by-4.0Jul 2020View details →

Global data compilation of seawater, authigenic and detrital radiogenic neodymium isotope composition since the Last Glacial Maximum

The global radiogenic Neodymium isotope data compilation from: <div> <div>Du J., Haley B. A. and Mix A. C. (2020) Evolution of the Global Overturning Circulation since the Last Glacial Maximum based on marine authigenic neodymium isotopes. Quaternary Science Reviews 241, 106396.</div> </div>

opencc-zeroMar 2024View details →

Data from: Nutrient composition and functional constituents of daylily from different producing areas based on widely targeted metabolomics

Daylily is a functional food with high nutritional value in China. Datong (DT) in Shanxi Province is one of the four main production areas of daylily. Therefore, Linfen (LF), Lvliang (LL), and Yangquan (YQ) in Shanxi Province have also introduced daylily from DT. However, geographical and climatic conditions and producing patterns cause variations in the vegetable quality. In the present study, we determined the quality of daylilies from different producing areas and found that the nutrient composition of daylilies from different producing areas varied. The widely targeted metabolomics was performed, and the results showed that 1642 metabolites were found in daylily. The differential metabolites between DT and YQ, LL and LF were 557, 667, and 359, respectively. Notably, 9 metabolic pathways and 76 metabolite markers could be associated with daylily from different areas. This study provides a theoretical basis for the quality maintenance and health efficacy research of daylily.