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opencc-by-4.0Jan 2023View details →

Baseline data for Citizen Energy Responsible Behaviour in 27 Member States

This dataset contains all the information on the levels that each country in Europe should have in the labelling system to assess citizens energy behaviours fully described in the document AURORA D1.1 Near-Zero Emissions Citizens Label https://doi.org/10.5281/zenodo.7594879 The zip file contains one document for each member state. Reference values are extracted from the same datasources individuated in D1.1 for the 5 selected countries fully described in the document.

Fitness and niche differences are both important in explaining responses of plant diversity to nutrient addition

Plant species loss due to eutrophication is a common phenomenon in temperate perennial grasslands. It occurs in a non-random fashion and is usually explained by increased competitive size asymmetry between co-occurring winner (tall species with optima in productive habitats) and loser species (small-statured plants typical for unproductive habitats). It remains unclear why nutrient addition decreases diversity in communities consisting of losers only, whereas it has little effect on winner-only communities. Here, I used the framework of modern coexistence theory to explore fertilization-driven changes in fitness and niche differences between different combinations of field-identified winner (W) and loser (L) species. I experimentally estimated competition parameters for plant species pairs constructed from a pool of eight species, including pairs of species from the same (WW, LL) and different species categories (LW) grown for approximately two years in control and fertilized conditions. Concurrently, I also followed plant species diversity in mesocosm communities constructed from the same species pool (four-species communities including winners, losers, or both) exposed to control and nutrient addition. I found that nutrient addition can reduce but, unexpectedly, also promote species coexistence depending on the type of species pairs. Whereas nutrient addition eroded coexistence of losers with winners, but also with other losers, treatment had the opposite effect on the persistence of winner species. Fertilization induced large fitness differences between species in loser-winner and loser-loser combinations, but had little effect on the fitness differences of species within the winner-winner combination. In addition, the persistence of winner pairs was promoted by larger niche differences compared to loser species, irrespective of soil nutrients. The differences in how nutrient addition modified coexistence at the pairwise level were reflected by differences in evenness of multispecies communities assembled from the corresponding species categories. These results suggest that the effect of eutrophication on plant species richness cannot simply be explained by an increased competitive asymmetry. To fully understand the effect of fertilization on the diversity of temperate grasslands, interspecific and intraspecific interactions should be explored while considering differences in species' ecological optima.

Sex and background risk influence responses to acute predation risk in Trinidadian guppies

Intraspecific sex differences in morphology, physiology, and behaviour are widespread among taxa. However, despite their fundamental importance, they have been relatively understudied in the context of risk assessment. For instance, with Trinidadian guppies (Poecilia reticulata), there has been a bias towards the exclusive use of females, as males are thought to be less responsive to acute predation threats. However, there is little empirical evidence supporting this assumption. Moreover, the antipredator behaviour of male guppies has been unexplored, perhaps resulting in the over-generalization of female behaviour to both sexes in previous studies. Here, we conducted laboratory experiments involving wild-caught and laboratory-reared guppies. In Experiment 1, shoals of either male or female guppies from a high predation population were tested for their response to alarm cues, novel odour, or a water control. We found that while female shoals exhibited strong antipredator responses to alarm cues and neophobic responses to novel odour, male shoals exhibited only a weak response to alarm cues and no evidence of neophobia. In Experiment 2, we exposed male and female guppies to high or low predation risk and then tested individuals for their responses to alarm cues, novel odour, or a water control. Regardless of background risk, males did not respond to any stimulus. In contrast, low-risk females exhibited antipredator responses toward alarm cues and those from high background risk displayed neophobia. Our results suggest that females are more cautious when encountering an acute predation risk, highlighting the importance of accounting for both sexes in studies on predation.

Similar transcriptomic responses to early and late drought stresses produce divergent phenotypes in sunflower (Helianthus annuus L.)

Cultivated sunflower (Helianthus annuus L.) exhibits numerous phenotypic and transcriptomic responses to drought. However, the ways in which these responses vary with differences in drought timing and severity are insufficiently understood. We used phenotypic and transcriptomic data to evaluate the response of sunflower to drought scenarios of different timing and severity in a common garden experiment. Using a semi-automated outdoor high-throughput phenotyping platform, we grew six oilseed sunflower lines under control and drought conditions. Our results reveal that similar transcriptomic responses can have disparate phenotypic effects when triggered at different developmental time points. Leaf transcriptomic responses, however, share similarities despite timing and severity differences (e.g., 523 differentially expressed genes (DEGs) were shared across all treatments), though increased severity elicits greater differences in expression, particularly during vegetative growth. Across treatments, DEGs were highly enriched for genes related to photosynthesis and plastid maintenance. A co-expression analysis identified a single module (M8) enriched in all drought stress treatments. Genes related to drought, temperature, proline biosynthesis, and other stress responses were overrepresented in this module. In contrast to transcriptomic responses, phenotypic responses were largely divergent between early and late drought. Early-stressed sunflowers responded to drought with reduced overall growth, but became highly water-acquisitive during recovery irrigation, resulting in overcompensation (higher aboveground biomass and leaf area) and a greater overall shift in phenotypic correlations, whereas late-stressed sunflowers were smaller and more water use-efficient. Taken together, these results suggest that drought stress at an earlier growth stage elicits a change in development that enables greater uptake and transpiration of water during recovery, resulting in higher growth rates despite similar initial transcriptomic responses.

Spore germination and gametophore development of mosses in response to competition

Interactions between moss species in their earliest growth stages have received little attention. To what extent interspecific competition or priority effects influence spore germination, protonemal development, and gametophore emergence is unknown. We evaluated such effects in pairwise interaction between six common bryophyte species: Atrichum undulatum, Bryum argenteum, Ceratodon purpureus, Funaria hygrometrica, Hypnum cupressiforme, and Leptobryum pyriforme. Interspecific interactions were assessed in vitro. Spores were sterilized and sown on agar plates in three treatments: 1) as single species cultures (controls), 2) as pairwise species cultures inoculated simultaneously, and 3) with a time lag of 20 days between species. Data on time needed for spore germination, germination rate, the time needed for gametophore differentiation, number of gametophores per germinated spore and average diameter of colonies were collected. We also performed spore germination tests in single-species cultures at the start and end of the study, as well as tests for density-dependency at spore germination and gametophore formation.

Nighttime geomagnetic response to jumps of solar wind dynamic pressure: A possible cause of Québec blackout in March 1989

This contains the original simulation data used by the paper 'Nighttime geomagnetic response to jumps of solar wind dynamic pressure:  A possible cause of Québec blackout in March 1989', which will appear in Space Weather. The data were obtained by the global MHD simulation (REPPU). Each sav file (IDL saveset format) contains the physical variables in the ionosphere at each grid point (mlt*mlat: 321*221, starting at 0 MLT and -90 MLAT) for Run 02n, 30n, 30s, 33n, and 33s, including <ul> <li>MHD time series ('time' in minutes),</li> <li>field-aligned current ('fac1' in A/m2),</li> <li>electric potential ('pot' in V),</li> <li>ionospheric conductivities ('ss11', 'ss12', and 'ss22' in S).</li> </ul> The sav file can be opened by IDL. By typing, for example, IDL> restore,'run02n.sav' you can load the file to the memory of IDL. Type 'help' to confirm the variables that are loaded.

The Aedes aegypti RNA interference response against Zika virus in the context of co-infection with dengue and chikungunya viruses

This is the corresponding data of the Publication in Plos Neglected tropical diseases. Zika virus (ZIKV) is a mosquito-borne human-pathogenic arbovirus of the Flaviviridae family, genus Flavivirus. Other arboviruses, including dengue (DENV) or chikungunya (CHIKV) virus, can occur in the same regions as ZIKV and are also transmitted by Aedes aegypti. Notably, it has been shown that these viruses can co-infect this mosquito, andco-transmission occurs. Such processes may add to the serious public health issues already linked to those pathogens. Arbovirus infections in mosquitoes are controlled through an immune response called RNA interference (RNAi). It is however unknown whether immune responses changs when a mosquito is exposed to a co-infection of ZIKV with either DENV or CHIKV. In this study, we provide evidence that ZIKV co-infections with CHIKV or DENV are similarly well controlled by RNAi as single infections. These findings give new insights into the dynamics of arboviral co-infections in mosquito vectors that increase our understanding of co-infection scenarios during arbovirus outbreaks.

ChatGPT responses to questions from Vetala_Tales-Arthur_Ryder-Twenty_Two_Goblins

ChatGPT (GPT-4 & GPT-3.5) responses to Vetala-questions from stories (paraphrased) selected from Twenty-Two Goblins by Arthur W. Ryder based on Vetala Tales composed in Sanskrit in the 11th century Data for preprint: Goblin's Challenge to ChatGPT: Exploring AI's Dilemma Resolution and Mentalization through Riddle Tales https://ssrn.com/abstract=4476837 OR https://dx.doi.org/10.2139/ssrn.4476837 Authors:  Kunal Bhattacharya (ORCID: 0000-0002-4943-3814) Aalto University School of Science, Finland,  kunal.bhattacharya@aalto.fi   Anjan K. Nandi (ORCID: 0000-0002-7859-4596) Edukorus Knowledge Services, Kolkata, India anjanandi@gmail.com *Ry- denotes the story number in Ryder’s adaptation (J.M. Dent & Sons Ltd., London, 1917 available at https://www.gutenberg.org/ebooks/2290)  *Pe- N. M. Penzer. The Ocean of Story, being C. H. Tawney’s translation of Somadeva’s Katha Sarit Sagara, volumes VI-VII. Chas. J. Sawyer, London, 1924-26 Stories selected:  Ry1, Ry2, Ry3, Ry5, Ry6, Ry7, Ry10, Ry11, Ry12, Ry13, Ry17, & Pe10  ChatGPT sessions conducted in the first two weeks of May, 2023.

Data for: Antibiotic-degrading resistance changes bacterial community structure via species-specific responses

Some bacterial resistance mechanisms degrade antibiotics, potentially protecting neighbouring susceptible cells from antibiotic exposure. We do not yet understand how such effects influence bacterial communities of more than two species, which are typical in nature. Here, we used experimental multispecies communities to test the effects of clinically important pOXA-48-plasmid-encoded resistance on community-level responses to antibiotics. We found that resistance in one community member reduced antibiotic inhibition of other species, but some benefitted more than others. Further experiments with supernatants and pure-culture growth assays showed the susceptible species profiting most from detoxification were those that grew best at degraded antibiotic concentrations (greater than zero, but lower than the starting concentration). This pattern was also observed on agar surfaces, and the same species also showed relatively high survival compared to most other species during the initial high-antibiotic phase. By contrast, we found no evidence of a role for higher-order interactions or horizontal plasmid transfer in community-level responses to detoxification in our experimental communities. Our findings suggest carriage of an antibiotic-degrading resistance mechanism by one species can drastically alter community-level responses to antibiotics, and the identities of the species that profit most from antibiotic detoxification are predicted by their intrinsic ability to survive and grow at changing antibiotic concentrations.

A phenomics approach reveals interspecific differences in integrated developmental responses to chronic elevated temperatures

Raw data for publication 'A phenomics approach reveals interspecific differences in integrated developmental responses to chronic elevated temperatures', Journal of Experimental Biology (2023) 226, jeb245612. doi:10.1242/jeb.245612. Developmental_Event_Timings.csv - Raw data for the timings of development of Lymnaea stagnalis, Radix balthica and Physella acuta maintained at 20 and 25C, recorded by manual observation from video of developing embryos. Data are recorded as absolute timings, and relative timings normalised between the 4-cell stage and hatching.  EPT_Data.csv - Time series of frequency specific EPT data binned at 0.1Hz increments for embryos of Lymnaea stagnalis, Radix balthica and Physella acuta maintained at 20 and 25C, normalised by relative developmental time.  EPT_data_by_physiological_window.csv - Frequency specific EPT data binned at 0.1Hz increments, and averaged across 4 key physiological windows in development (ciliary driven rotation, muscular crawling, cardiovascular function and radula function) for embryos of Lymnaea stagnalis, Radix balthica and Physella acuta maintained at 20 and 25C.  Total_energy_data.csv - Time series of total energy data for embryos of Lymnaea stagnalis, Radix balthica and Physella acuta maintained at 20 and 25C, normalised by relative developmental time.

Entangled Ecologies. Interactive Documentary between Living Archive, Responsible Witnessing and Relational Co-Creation

The videoessay is also accessible: <a href="https://trametrami.avinus.org/publikationen/3-2023">https://trametrami.avinus.org/publikationen/3-2023</a> Recent re-conceptualizations of participation as well as theories of digital transformation culture have shifted the notion of the archive seeing not so much as a static, institutional body but rather as a dynamic, living epistemic environments. Building on these approaches, this presentation discusses emerging phenomena in interactive documentary focusing on ecological emergency – seeing this crisis itself as a complex ecology of issues where images and conceptualization past, present and future meet. Taking paradigmatic projects addressing the issue of climate change – The Shore Line (2017) and Climate Witness Project (2019) – I suggest tentative answers to the question in which way i-docs can contribute to tackle complex change. Are there images from the past which help us to better cope with the present and to envision a more sustainable future? How can one raise awareness of immanent ecological risks when menace is almost invisible, unprecedented and un-imaginable? Is there a way to negotiate multifaceted entanglements through documentaries which are neither paralyzing ecodystopian narratives nor naive ecotopian success-stories? The hypothesis underlying my approach is that one possible solution resides in documentaries which are built on principles of pluri-perspectivity and polyphony to transcend dualisms and to build bridges leading from history to the forthcoming. Discourses from various traditions are brought into dialogue: theories of documentary film meet ecocriticism; network theory encounters reflections on the epistemic dimension of non-fiction; and concepts of co-creation and intervention are related to processes of witnessing, doing documentary and responsible action-taking.   more information: <a href="https://did.avinus.org/">https://did.avinus.org/</a> and <a href="https://trametrami.avinus.org/publikationen">https://trametrami.avinus.org/publikationen </a>

Data from: Serum metabolomics predicts treatment response in myasthenia gravis

High-dose prednisone is the primary initial therapy for myasthenia gravis (MG) but upwards of a third of patients do not respond to treatment. No biomarkers can predict clinical responsiveness to corticosteroid treatment. We conducted a discovery-based study to identify treatment responsive biomarkers in MG using sera obtained at study entry to the thymectomy clinical trial (MGTX), an NIH-sponsored randomized, controlled study of thymectomy plus prednisone versus prednisone alone. We applied ultra-performance liquid chromatography coupled with electro-spray quadrupole time of flight mass spectrometry to obtain comparative serum metabolomic and lipidomic profiles at study entry to correlate with treatment response at 6 months. Treatment response was assessed using validated outcome measures of minimal manifestation status (MMS), MG-Activities of Daily Living (MG-ADL), Quantitative MG (QMG) score, or a strictly defined composite measure of response. Increased levels of phospholipids were associated with treatment response as assessed by QMG, MMS, and the Responders classification, but all measures showed limited overlap in metabolomic profiles, in particular the MG-ADL. A panel including histidine, free fatty acid (13:0), γ-cholestenol and guanosine was highly predictive of the strictly defined treatment response measure. The AUC in Responders' prediction for these markers was 0.90. Pathway analysis suggests that xenobiotic metabolism could play a major role in treatment resistance. We have defined a metabolomic and lipidomic profile that can now undergo validation as treatment predictive markers for MG patients undergoing corticosteroid therapy. Distinct metabolomic profiles were appreciated for each outcome measure.

Data for: Diversity and specialization responses to climate and land use differ between deadwood fungi and bacteria

This dataset contains data from a field study conducted in 2019 and described in the manuscript "Diversity and specialization responses to climate and land use differ between deadwood fungi and bacteria". To test the effects of land use and climate on diversity and community specialization (H2') of deadwood-inhabiting microbes, we exposed branches of four different tree species at 179 study sites, distributed over a spatial extent of 300 km x 300 km and 1000 m in elevation. Study sites were established in four local land-use types: forests, grasslands, arable sites, and settlements, embedded in near-natural, agricultural, or urban landscapes. We used negative-binomial generalized linear models for diversity and calculated community specialization on host trees by using the standardized two-dimensional Shannon entropy (H2') and beta-regression models. Our results show that host identity and hence specialization strongly exceed the effects of climate and land use for fungal but not bacterial communities. This suggests contrasting responses between microbial taxa to climate change and land-use intensification with further consequences on deadwood diversity interactions and hence decomposition processes.

opencc-by-4.0Jul 2023View details →

Coordinated drought responses determine the time to hydraulic failure in five temperate tree species differing in their degree of isohydry

This file contains variables of interest at tree level measured, calculated and presented in the study "Coordinated drought responses determine the time to hydraulic failure in five temperate tree species differing in their degree of isohydry".

Data from: African elephant dietary responses to odors of monoterpene mixtures and individual monoterpenes

The detoxification limitation hypothesis posits that, unless plant defense compounds interact synergistically or additively to increase their harmful effects, generalist herbivores will prefer consuming combinations of these compounds over singular compounds. Monoterpenes are odoriferous defense compounds that may be toxic to mammalian herbivores when ingested in sufficient quantities. Previous research has shown that the addition of individual monoterpenes to food sources reduces consumption by generalist mammalian herbivores. By using African elephants as a case study, we aimed to determine whether odors from monoterpene combinations (i.e., two or more monoterpenes) also deter generalist mammalian herbivory, and whether generalist herbivores prefer the odors of monoterpene combinations over individual monoterpenes. First, we tested whether the odor of monoterpene combinations that resemble the monoterpene profiles of a high-acceptability, intermediate-acceptability, and low-acceptability plant deter herbivory. We found that elephants preferred plants without the added odors of the monoterpene combinations. Second, we explored how elephants responded to individual monoterpenes found within the combinations compared to the combinations at the same set concentration, and found that the elephants did not always prefer the combinations over the individual monoterpenes. Moreover, the more diverse the combination, the less frequently it was preferred when compared to the individual monoterpene odors. Our results imply that generalist herbivores do not necessarily prefer combinations of plant chemical defenses at comparatively lower concentrations and that, consequently, the composition and diversity of monoterpene profiles in plants likely determine the efficacy of these compounds as an olfactory defense against mammalian herbivory.

opencc-by-4.0Feb 2023View details →

swu_dhe v1: Sectoral water use responses to droughts and heatwaves

These datasets enables the assessment of sectoral water use responses during droughts, heatwaves and compound events at global, regional and local scales. File names contain the spatial scale of the analysis, water dimension, water sector and period of analysis. Datasets show the median percentile of a sectoral water use (i.e., irrigation, domestic, thermoelectric, manufacturing, livestock) during an extreme event and a normal (non-extreme event) period. Files are in comma-separated values (csv) format for easy reading. In addition, mid-step calculation results, such us identified droughts, heatwaves and compound events, are also included. File names contain the periods of evaluation and input datasets used. These resulting datasets are in NetCDF (nc) format, with a resolution of 30 arcmin (gridded) at a global scale and at a monthly time step. Moreover, input files on sectoral water demands at local and regional scales are also included. Datasets included here allow the reproducibility of the analysis of sectoral water use responses during drought, heatwaves and compound events. Scripts used can be found on GitHub (https://doi.org/10.5281/zenodo.8122407).

Data from: Quantum computation of frequency-domain molecular response properties using a three-qubit iToffoli gate

The quantum computation of molecular response properties on near-term quantum hardware is a topic of substantial interest. Computing these properties directly in the frequency domain is desirable, but the circuits require large depth if the typical hardware gate set consisting of single- and two-qubit gates is used. Here, we report the application of a high-fidelity multipartite gate, the iToffoli gate, to the computation of frequency-domain response properties of diatomic molecules. The iToffoli gate enables a ~50% reduction in circuit depth and ~40% reduction in circuit execution time compared to the traditional gate set. We show that the molecular properties obtained with the iToffoli gate exhibit comparable or better agreement with theory than those obtained with the native CZ gates. Our work is among the first demonstrations of the practical usage of a native multi-qubit gate in quantum simulation, with diverse potential applications to near-term quantum computation.

opencc-by-4.0Jul 2023View details →

Dataset: Recruitment responses of shade-tolerant and heliophilous trees in human-degraded areas: the necessity of knowing the recruitment autecology of species for making reforestation decisions

This repository contains the files associated with the following article: Johanna Croce, Ernesto I. Badano, Andrés Tálamo. Recruitment responses of shade-tolerant and heliophilous trees in human-degraded areas: the necessity of knowing the recruitment autecology of species for making reforestation decisions Submitted to Land Degradation & Development. The first Microsoft Excel file (Dataset 01 - Microclimate.xlsx) contains two sheets with the microclimatic data (average, maximum and minimum soil temperatures, and volumetric soil water content) measured in Cerro Chachapoyas and Cerro Fachacano. These measurements were performed on three plots of each trearment, including shrub-protected treatment with high shade, shrub-protected treatment with medium shade, sunny treatment with high herbaceous cover, sunny treatment with medium herbaceous cover and controls. The second Microsoft Excel file (Dataset 02 -Plant responses.xlsx Dataset 02 - Plant responses.xlsx) contains three sheets with the data used to estimate the seedling emergence rates, plant survival rates and net aboveground growth rates of the tree species, including Anadenanthera colubrina and Ceiba chodatii in Cerro Chachapoyas, and Jacaranda mimosifolia in Cerro Fachacano.

Snake-like bird hisses induce anti-predator responses in a frog

Mimicry is a fascinating natural phenomenon, yet the ecological role of vocal mimicry receives limited attention. Some snakes emit hissing calls and many birds perform such acoustic mimicry in order to deter potential predators. Here we hypothesize that snake-like hisses may evoke anti-predator responses in anuran species. We conducted sound playbacks to test how little torrent frogs (Amolops torrentis) varied their behaviors in response to white noise, snake hisses, and snake-like bird hisses. We found that snake hiss from sympatric king cobras (Ophiophagus hannah) could change calling behavior of little torrent frogs, while white noise and snake hiss from allopatric Gaboon vipers (Bitis gabonica) showed no influence. Calling frogs also had no response to white noise and great tit (Parus major) hisses, which had low acoustic similarity with snakes, while they decreased calling activity when exposed to zitting cisticola (Cisticola juncidis) hisses which had high acoustic similarity with snakes. In addition, more individuals cease calling during the playback of zitting cisticola hisses. These results suggest that both snake and snake-like hiss calls may evoke anti-predator responses in frog species. To our knowledge, this is the first study that attempts to reveal the effect of snake calls and avian vocal mimicry on anurans.

Rapid hyperthyroidism-induced adaptation of Salmonid fish in response to environmental pollution

The streams draining volcanic landscapes are often characterized by a complex of factors that negatively affect hydrobionts and lead to a decline of their populations. However, in a number of cases, hydrobionts ensure the resilience of populations througth a range of rapid adaptive changes. Here, we present both field and experimental data shedding light on the physiological basis of adaptation in populations of Dolly Varden charr (Salvelinus malma) differing in the duration of isolation in volcanic streams contaminated with heavy metals. The study reveals that isolated populations have a physiological phenotype that distinguishes them from the populations inhabiting clean waters. They are characterized by a hyperthyroid status accompanied by an increased metabolic rate, elevated activity of antioxidant enzymes, decreased ionic conductivity of tissues and reduced stored energetic reserves. The experimental data elucidate that hyperthyroidism is an adaptive characteristic enhancing the resistance to heavy metal contamination and shaping the evolution of these populations. The similarity of physiological, developmental and morphological changes in isolated populations suggests a common source and mechanisms underpinning their "evolutionary rescue". Thus, populations of S. malma trapped in volcanic streams represent a genuine case of a rapid neuroendocrine-driven adaptation to changing environmental stimuli.