Find research datasets worth reusing

opencc-by-4.0Aug 2020View details →

Data for paper "Micromechanical modeling of MXene-polymer composites"

Data for paper “Micromechanical modeling of MXene-polymer composites” <a href="https://doi.org/10.1016/j.carbon.2020.02.070">https://doi.org/10.1016/j.carbon.2020.02.070</a> M_M_MX_P_C_data.xlsx is the data represented in the paper. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 777810.

Data from: Contrasting effects of host identity, plant community, and local species pool on the composition and colonisation levels of arbuscular mycorrhizal fungal community in a temperate grassland

Arbuscular mycorrhizal fungi (AMF) are important plant symbionts, but we know little about the effects of plant taxonomic identity or functional group on the AMF community composition. To examine effects of the surrounding plant community, of host, and of the AMF pool on the AMF community in plant roots, we manipulated plant community composition in a long-term field experiment. Within four types of manipulated grassland plots, seedlings of eight grassland plant species were planted for 12 weeks, and AMF in their roots were quantified. Additionally, we characterised the AMF community of individual plots (as their AMF pool) and quantified plot abiotic conditions. The largest determinant of AMF community composition was the pool of available AMF, varying at metre scale due to changing soil conditions. The second strongest predictor was the host functional group. The differences between grasses and dicotyledonous forbs in AMF community variation and diversity were much larger than the differences among species within those groups. High cover of forbs in the surrounding plant community had a strong positive effect on AMF colonisation intensity in grass hosts. Using a manipulative field experiment enabled us to demonstrate direct causal effects of plant host and surrounding vegetation.

Data from: Biological stoichiometry of oleaginous microalgal lipid synthesis: The role of N:P supply ratios and growth rate on microalgal elemental and biochemical composition

Biological Stoichiometry is an ecological framework connecting the balance of elements to the functioning of organisms. Here, we applied this framework to study the relationships between carbon:nitrogen:phosphorus (C:N:P) ratios and synthesis of industrial high value biochemicals in the highly oleaginous alga Tetradesmus bernardii. We expected an increase in protein content with increasing cellular N content and decreasing C:N stoichiometry, and an increase in lipid content with increasing C:N and C:P stoichiometry. We tested these hypotheses by exposing T. bernardii to N and P limitation at a range of N:P supply ratios in chemostats set at low and high dilution rates. Following expectations, the cellular protein content increased with the N content, and decreased with cellular C:N ratios across all treatments. Carbohydrates and lipids largely followed the relative availability of C and increased under both N and P limitation, with higher C:N and C:P ratios. Specifically, lipid content increased by 100–125% upon N and P limitation, with a shift towards more neutral lipids at the cost of glycolipids and phospholipids. Generally, we observed a re-allocation of cellular C from protein to carbohydrates upon modest N limitation, and towards lipids under P and severe N limitation. Our results demonstrate stoichiometrically predictable patterns of industrially valuable compounds in an oleaginous microalga.

opencc-by-4.0Aug 2020View details →

The evaluation dataset of the AI composition recognition competition, CSMT2020

The evaluation dataset contains 4000 MIDI files with exact configurations of development dataset with two exceptions: 1) A number of melodies composed by human composers are added, some of which are published, and some of which are composed for this competition. The music style of the human composed melodies are the same as the styles of music in the training set. This was confirmed by musicologists. 2) There are a number of melodies generated by algorithms with minor algorithmic or parameter changes compared to the algorithms in the development dataset. The development dataset: <a href="https://zenodo.org/record/3944685#.Xza9DegzY2x">https://zenodo.org/record/3944685#.Xza9DegzY2x</a> The website of the challenge: <a href="http://www.csmcw-csmt.cn/data/2020/ai-composition-recognition2020/">http://www.csmcw-csmt.cn/data/2020/ai-composition-recognition2020</a> (Chinese instruction) <a href="https://ai-composition-recognition2020.github.io/english.html">https://ai-composition-recognition2020.github.io/english.html</a> (English instruction)

opennotspecifiedJun 2020View details →

FIGURE 4 in Quantifying vertebrate zoogeographical regions of Australia using geospatial turnover in the species composition of mammals, birds, reptiles and terrestrial amphibians

FIGURE 4. The zoogeographical regions proposed by Cracraft (1991, thick black lines) and superimposed over the three clusters found in this study.

Data from: Intraspecific variation in host plant traits mediates taxonomic and functional composition of local insect herbivore communities

Host plant phenotypic traits affect the structure of the associated consumer community and mediate species interactions. We compare herbivore assemblages from the canopy of the phenotypically variable tree Metrosideros polymorpha on Hawai'i Island. Multiple distinct varieties of M. polymorpha frequently co‐occur, with variation in morphological traits. Using this system, we identify host and insect traits that underlie patterns of herbivore abundance and quantify the strength of host‐insect trait interactions. The dataset includes host plant phenotypic traits (specific leaf area, leaf water content, foliar nutrients, trichome presence), as well as collection information. The dataset also contains the herbivorous insect community associated with this host plant, their abundances and life history traits. R code for analyses in this article is also included.

Dark septate endophytes and arbuscular mycorrhizal fungi (Paris-morphotype) affect the stable isotope composition of 'classically' non-mycorrhizal plants

The vast majority of terrestrial plants exchange nutrients with fungal partners forming different mycorrhizal types. The minority of plants considered as non-mycorrhizal, however, are not necessarily free of any fungi, but are frequently colonized by elusive fungal endophytes, such as dark septate endophytes (DSE) or fine root endophytes (FRE). While a functional role of FRE in improvement of nutrient gain was recently elucidated, the function of DSE is still in discussion and was here addressed for 36 plant species belonging to the families Equisetaceae, Cypereaceae and Caryophyllaceae. Molecular and microscopic staining approaches were conducted to verify the presence of DSE in the investigated species. Stable isotope natural abundances of the elements carbon, nitrogen, hydrogen and oxygen and total nitrogen concentrations were analyzed for the respective species of the target plant families and accompanying mycorrhizal and non-mycorrhizal (Brassicaceae) plant species. Staining approaches confirmed the presence of DSE in all investigated species within the families Equisetaceae, Cyperaceae and Caryophyllaceae. A co-colonization with Paris-type arbuscular mycorrhiza (AM) was occasionally found by staining and molecular approaches in species of the Equisetaceae. Species of the Equisetaceae, Cyperaceae and Caryophyllaceae were significantly 15N-enriched in comparison to accompanying plants. In addition, a significant 13C and 2H enrichment and increased total nitrogen concentrations were found for representatives of the Equisetaceae. The 15N-enrichment found here for representatives of Equisetaceae, Cyperaceae and Caryophyllaceae provides evidence for a functional role of the ubiquitous DSE fungi. DSE fungi obviously provide access to 15N-enriched soil organic compounds probably in exchange for organic carbon compounds from plant photosynthesis. As indicated by additional 13C- and 2H-enrichments, representatives of the Equisetaceae apparently gain simultaneously organic carbon compounds from their AM fungi of the Paris-morphotype. Thus, species of the Equisetaceae have to be considered as partially, or in case of the achlorophyllous fertile Equisetum arvense, as fully mycoheterotrophic at least in some stages of their life cycle. So far mostly underappreciated fungi classified as DSE are suggested to occupy an ecologically relevant role similar to mycorrhizae and the occurrence of simultaneous functions of DSE and AM fungi in Equisetaceae is proposed.

Data from: Fire history and plant community composition outweigh decadal multi-factor global change as drivers of microbial composition in an annual grassland

Soil microbial communities regulate and respond to key biogeochemical cycles and influence plant community patterns. However, microbial communities also respond to disturbance events, motivating an assessment of the relative roles of decadal multi-factor global change, disturbance, and plant community structure on microbial community responses. We used high-throughput amplicon sequencing to characterize the diversity and composition of bacterial and fungal communities in bulk soil (0–7 cm) collected in 2014 from the Jasper Ridge Global Change Experiment, a full-factorial field experiment in which ambient and elevated levels of nitrogen deposition (+7 g N m-2 yr-1 calcium nitrate), CO2 concentration (+275 ppm), temperature (+1–2 ºC), and precipitation (+50% volume with +3 weeks duration) were applied to a California annual grassland from 1998 to 2014. We used linear mixed-effects modeling to test for the effects of global change on microbial diversity (observed richness, Shannon index). We also used generalized dissimilarity modeling (GDM) to study controls on compositional dissimilarity in fungal and bacterial communities. Bacterial community composition was best explained by exposure to fires in 2003 and 2011, whereas fungal community composition was best explained by plant community composition. The richness of fungi increased under elevated nitrogen deposition; bacterial diversity metrics decreased under warmer temperatures. Interactions between global change factors were statistically insignificant or weak. Synthesis. Our results indicate that even on decadal timescales, the effects of fire history and plant community composition on bacterial and fungal community composition, respectively, outweigh the effects of multi-factor global change. Furthermore, global change factors have mostly additive effects on microbial diversity patterns. Our results show that highly variable mediators such as fire history and plant community composition limit the generalizability of soil microbial responses to long-term global change.

Data from: Decreasing predation rates and shifting predator compositions along a land-use gradient in Madagascar's vanilla landscapes

1. Land-use change is the main driver of deforestation and land degradation resulting in the loss of biodiversity and ecosystem functioning in north-eastern Madagascar. Vanilla, the region's main cash crop, is grown in agroforestry systems and may provide an opportunity for the conservation of biodiversity and ecosystem functioning. 2. We used dummy caterpillars to assess predation rates and predator communities along a land-use gradient including unburned old-growth and forest fragments, herbaceous and woody fallows after shifting cultivation with fire usage, as well as rice paddies. The studied vanilla agroforests were either forest-derived or fallow-derived. Besides land-use type, we considered the effects of land-use history (unburned/burned), plot-level parameters and the landscape composition to conclude on management recommendations. 3. Old-growth forest and forest fragments exhibited highest predation rates, which decreased with land-use intensity. Overall, predation was higher in unburned land-use types than in more open, previously burned habitats and rice paddies. High stem and vegetation densities were positively related to predation rates, but decreased with land-use intensity. High forest cover in the surrounding landscape led to higher predation rates, while local structural parameters remained more important. 4. The predator community was arthropod-dominated across all land-use types with ants responsible for between 33 % and 69 % of all predation events. Overall predator composition in old-growth and forest fragments differed from all other land-use types. Predation by Gryllacrididae (Orthoptera) was lower in all land-use types, including forest-derived vanilla, than in old-growth forest and forest fragments, where they were important contributors to total predation. Vertebrate predation was low throughout. Synthesis and applications: Forested habitats feature higher predation rates and different predator compositions than other land-use systems. Maintaining or restoring tree- and understory-rich vanilla agroforestry represents a viable tool in landscape conservation programmes as it has the potential to contribute to the conservation of predation as an important ecosystem function in both forest- and fallow-derived agroforests. However, vanilla agroforestry has limited value in conserving forest-specialised predator communities. While the establishment of tree-rich agroforests on former fallow land is favourable for conservation ecosystem functioning, further forest transformation should be <a>avoided</a>.

Data from: Seabirds vary responses to supplemental food under dynamic natural prey availability and feeding aggregation composition

While foraging, a predator can feed solitarily or in a group. The net energy gain of joining a group is predicted to vary with prey patch quality, species-specific prey capture behavior and the size and species composition of the predator group. In coastal Newfoundland, Canada, capelin (Mallotus villosus), a key forage fish, migrates inshore to spawn during the summer, resulting in a dramatic shift in prey availability. During July-August, 2015-2017, we examined the numerical and behavioral responses of procellarid (Great Shearwater Ardenna gravis, Sooty Shearwater A. grisea, Northern Fulmar Fulmarus glacialis) and gull species (Herring Gull Larus argentatus, Great Black-backed Gull L. marinus) to fish offal under varying capelin availability as well as flock size and composition using an at-sea experiment on the northeast Newfoundland coast. The experiment consisted of providing a offal every 30 s (10-min experimental period), along with 10-min control periods before and after. We recorded the species-specific number of birds on the water, the number of birds simultaneously attempting to capture offal, and the number of successful attempts ('foraging success'). The number of birds on the water was lower during high capelin availability for all species, except for Northern Fulmar. The number of conspecifics simultaneously attempting increased with the number of conspecifics on the water, but plateaued at different numbers (4-17) for each species. The species-specific proportion of successful attempts (i.e. 'foraging success') varied with flock size and composition (i.e. number of conspecifics, heterospecifics, species). Foraging success of Herring Gulls and fulmars were moderately affected by flock size and composition, suggesting that they may be dominant competitors. Findings suggest that seabirds rely more heavily on supplemental food sources, such as fisheries discards and offal, when natural prey availability declines, potentially resulting in a higher risk of by-catch during fisheries activities as forage fish stocks decline.

opencc-by-4.0Aug 2019View details →

Dataset (.esg files) of a multiphase aggregate representative of a lower mantle composition compressed at High P/T in an R rDAC

A collection of .esg files for use in the software package Materials Analysis Using Diffraction (MAUD; Lutterotti et al., 1997). Seven files are included, spanning the range used in data analysis. All are post-conversion from San Carlos olivine. Files are named in the following format: MPBrgFp: Stands for Multiphase, primary phases bridgmanite and ferropericlase ###: Number of the diffraction pattern taken during the experiment ##GPa: Approximate temperature, rounded to the nearest whole number. This is to cross-correlate .esg files with experimental Pt pressures cited within the paper.

Supplementary material 1 from: Huang J, Guo Z, Tang S, Ren W, Chu G, Wang L, Zhao L, Yu R, Xu Y, Ding Y, Zang R (2020) Floristic composition and plant diversity in distribution areas of native species congeneric with Betula halophila in Xinjiang, northwest China. Nature Conservation 42: 1-17. https://doi.org/10.3897/natureconservation.42.54735

Figure S1. The correlation between environmental variables in distribution areas of five congeneric species with Betula halophila

opencc-by-4.0Aug 2020View details →

Raw data for "Are bioplastics and plant-based materials safer than conventional plastics? In vitro toxicity and chemical composition"

This upload contains the raw data files from FTIR analysis (csv format) and the non-target chemical analysis (UPLC-QTOF-MS/MS, positive ionization, MSE acquisition, Waters raw format) associated with our publication "Are bioplastics and plant-based materials safer than conventional plastics? In vitro toxicity and chemical composition" published in Environment International (https://doi.org/10.1016/j.envint.2020.106066). You will find all methodological details there.

Cellulose nanocrystals/graphene oxide composite for the adsorption and removal of levofloxacin hydrochloride antibiotic from aqueous solution

<a name="_Hlk33498008">Residual antibiotics in water are often persistent organic pollutants. </a><a name="_Hlk32994933">The purpose of this study was </a>to prepare a <a name="_Hlk32132836">cellulose nanocrystals/graphene oxide composite</a> (CNCs-GO) with a three-dimensional structure for the removal of the antibiotic levofloxacin hydrochloride (Levo-HCl) in water by adsorption. The Scanning Electron Microscope (SEM), Fourier Transform Infrared (FT-IR), Energy dispersive spectroscopy (EDS), X-ray Photoelectron Spectroscopy (XPS) and other characterization methods were used to study the physical structure and chemical properties of the CNCs-GO. The three-dimensional structure of the composite material rendered a high <a name="_Hlk32994964">surface area and electrostatic </a>attraction, resulting in an increased adsorption capacity of the CNCs-GO for Levo-HCl. Based on the Box–Behnken design, the effects of different factors on the removal of Levo-HCl by the CNCs-GO were explored. The composite material exhibited good antibiotic adsorption capacity, with a removal percentage exceeding 80.1% at an optimal pH of 4, adsorbent dosage of 1.0 g L⁻1, initial pollutant concentration of 10.0 mg L⁻1, and contact time of 4 h. The adsorption isotherm was well fitted by the Sips model, and kinetics studies demonstrated that the adsorption process conformed to a quasi-second-order kinetics model. Consequently, the as-synthesized CNCs-GO demonstrate good potential for the effective removal of antibiotics such as levofloxacin hydrochloride from aqueous media.

Psocodea Phylogenomic dataset from: Phylogenomics of parasitic and non-parasitic lice (Insecta: Psocodea): combining sequence data and Exploring compositional bias solutions in Next Generation Datasets

This dataset includes all alignments used for the phylogenomic analysis of Psocodea. In this dataset, includes all result files of phylogenomic analyses completed. This includes maximum likelihood, astral, MCMCtree, quartet sampling, and all gene trees. Any relevant input files are included, and any materials are available upon request. The insect order Psocodea is a diverse lineage comprising both parasitic (Phthiraptera) and non-parasitic members (Psocoptera). The extreme age and ecological diversity of the group may be associated with major genomic changes, such as base compositional biases expected to affect phylogenetic inference. Divergent morphology between parasitic and non-parasitic members has also obscured the origins of parasitism within the order. We conducted a phylogenomic analysis on the order Psocodea utilizing both transcriptome and genome sequencing to obtain a data set of 2,370 orthologous genes. All phylogenomic analyses, including both concatenated and coalescent methods suggest a single origin of parasitism within the order Psocodea, resolving conflicting results from previous studies. This phylogeny allows us to propose a stable ordinal level classification scheme that retains significant taxonomic names present in historical scientific literature and reflects the evolution of the group as a whole. A dating analysis, with internal nodes calibrated by fossil evidence, suggests an origin of parasitism that predates the K-Pg boundary. Nucleotide compositional biases are detected in third and first codon positions and result in the anomalous placement of the Amphientometae as sister to Psocomorpha when all nucleotide sites are analyzed. Likelihood-mapping and quartet sampling methods demonstrate that base compositional biases can also have an effect on quartet-based methods.

Personality composition determines social learning pathways within shoaling fish

In shaping how individuals explore their environment and interact with others, personality may mediate both individual and social learning. Yet increasing evidence indicates that personality expression is contingent on social context, suggesting that group personality composition may be key in determining how individuals learn about their environment. Here, we used recovery latency following simulated predator attacks to identify Trinidadian guppies (Poecilia reticulata) that acted in a consistently bold or shy manner. We then employed network-based diffusion analysis to track the spread of a novel foraging behaviour through groups containing different proportions of bold and shy fish. Informed associates promoted learning to a greater extent in bold individuals, but only within groups composed predominately of bold fish. As the proportion of shy fish within groups increased, bold individuals instead emerged as especially effective demonstrators that facilitated learning in others. Individuals were also more likely to learn overall within shy-dominated groups than in bold-dominated ones. We demonstrate that how individuals learn is conditional on group personality composition, indicating that selection may favour traits enabling individuals to better match their behavioural phenotype to their social environment.

Rainfall pulses mediate long-term plant community compositional dynamics in a semi-arid rangeland

1. Semi-arid rangelands, comprising more than 40% of the Earth's land surface, provide critical ecosystem services. Worldwide, these ecosystems are experiencing rapid degradation due to overgrazing and precipitation changes. However, how plants respond to these interacting factors remains relatively unexplored, and precisely which and how rainfall factors determine plant community dynamics in rangelands has not been well developed. 2. We used a long-term (1953‒2018) dataset from semi-arid rangeland to investigate coupled effects of grazing intensity and rainfall intensity (the total amount of precipitation) on different groups of plant cover (herbaceous, woody, and cacti plants) using linear mixed-effects models, redundancy analysis and structural equation models. We examined how rainfall intensity influenced plant cover dynamics according to pulse size (intensity over time) categories, which we analyzed at three scales: yearly, within the wet season only (June to September), and within the dry season only (October to May). 3. Plant community cover showed a humpbacked trend in the last six decades, mostly through changes in woody plants. Although both grazing intensity and rainfall presented similar humpbacked trends with plant community cover, our models demonstrated that the reduction of plant cover from the 1990s has been mainly caused by a decrease of rainfall rather than grazing intensity, particularly due to profound reductions of the intensity of relatively small rainfall pulses (e.g., 5.1 ~ 15 mm·day-1) during the dry season. Specifically, these small rainfall pulses can increase plant cover of all subgroups of woody and herbaceous species, thereby increasing plant community cover. Moreover, rainfall pulses during the wet season had negative effects on herbaceous species and positive effects on woody plants. These results suggest a phenological niche partitioning between woody plants and herbaceous in subtropical rangelands. 4. Synthesis and applications. Our results show how critical seasonal rainfall pulses are for regulating plant community compositional dynamics, which has significant implications for rangeland management and our ability to adapt and mitigate amplified climate influences in semi-arid ecosystems.

Community composition of arctic root-associated fungi mirrors host plant phylogeny

The number of plant species regarded as non-mycorrhizal increases at higher latitudes, and several plant species in the High-Arctic Archipelago Svalbard have been reported as non-mycorrhizal. We used the rRNA ITS2 and 18S gene markers to survey which fungi, as well as other micro-eukaryotes, were associated with roots of 31 arctic plant species not usually regarded as mycorrhizal in Svalbard. We assessed to what degree the root-associated fungi showed any host preference and whether the phylogeny of the plant hosts may mirror the composition of root-associated fungi. Fungal communities were largely structured according to host plant identity and to a less extent by environmental factors. We observed a positive relationship between the phylogenetic distance of host plants and the distance of fungal community composition between samples, indicating that the evolutionary history of the host plants plays a major role for which fungi colonize the plant roots. In contrast to the ITS2 marker, the 18S rRNA gene marker showed that chytrid fungi were prevalently associated with plant roots, together with a wide spectrum of amoeba-like protists and nematodes. Our study confirms that arbuscular mycorrhizal (AM) fungi are present also in arctic environments in low abundance.

opencc-by-4.0Oct 2020View details →

Recommending Composite Refactorings for Smell Removal: Heuristics and Evaluation

Short presentation for the paper entitled "Recommending Composite Refactorings for Smell Removal: Heuristics and Evaluation. Abstract. Structural degradation is the process in which quality attributes of a system are negatively impacted. When due attention is not paid to structural degradation, the source code may also become difficult to change. Code smells are recurring structures in the source code that may represent structural degradation. Hence, there are many catalogs and techniques for supporting the removal of code smells through refactoring recommendations, such as a Move Method or a Extract Method. Such recommendations usually consist of single refactorings. However, single refactorings are often not enough for completely removing certain smell occurrences. Moreover, recent studies show that developers most often apply composite refactorings -- i.e., sequences of two or more refactorings -- for removing code smells. Despite showing the importance of performing composite refactorings, existing studies do not provide information on which composite refactoring patterns are recurrent in practice. Therefore, in this work, we conducted an empirical study to extract data from multiple open source systems regarding the composite refactoring practice. This data helped us to find 35 recurring patterns that are effective in removing certain types of code smells. Based on such patterns, we propose a suite of new recommendation heuristics to help developers in applying effective composite refactorings. These heuristics are intended to remove three code smell types, namely Complex Class, Feature Envy, and God Class. After designing the heuristics, we evaluated their effectiveness through a quasi-experiment. This evaluation was conducted with 12 software developers and 9 smelly Java classes. Results indicate that developers considered our heuristics effective or partially effective in more than 93% of the cases. In addition, the evaluation helped us to identify multiple factors that contribute to the acceptance or rejection of the refactoring recommendations. Based on these factors we define new guidelines for the effective recommendation of smell-removal composite refactorings.