Find research datasets worth reusing

Data from: Species loss drives ecosystem function in experiments, but in nature the importance of species loss depends on dominance

Aim: Decades of experimental research have conclusively shown a positive relationship between species richness and ecosystem function. However, authoritative reviews find no consensus on how species loss affects function in natural communities. We analyse experimental and observational data in an identical way and test whether they produce similar results. Location: North America and Europe (experimental communities); global (natural communities). Time period: Experimental communities: 1998–2013; natural communities: 1982–2018. Major taxa studied: Experimental communities: temperate grassland plants; natural communities: temperate grassland plants, tropical forest trees, kelp forest producers and native bees. Methods: We used an approach inspired by the Price equation to analyse 129 datasets from experimental and natural communities worldwide. We tested how the effects of species loss on ecosystem function varied with dominance and the nonrandomness of species loss and, in turn, how these two factors differed between experiments and observations. Results: Studies carried out in experimental and natural communities reached different conclusions regarding the effects of species loss. First, species loss had greater effects on ecosystem function in experiments than in nature. Second, the importance of species loss was negatively correlated with dominance in nature because as dominance increased, lost species were increasingly those contributing little to ecosystem function. Although experimental and natural communities exhibited similar levels of dominance, an analogous relationship was not possible in experiments because the order of species loss was randomized by design. Main conclusions: Species loss was sometimes, but not always, the major driver of loss of function in nature. Variation in the importance of species loss was not messy and context dependent; instead, it was predicted by functional dominance. Although results from experimental and natural communities were similar in several key ways, they differed in that species loss was a consistent predictor of ecosystem function in experiments and not in nature.

opencc-by-4.0Oct 2020View details →

Blood oxygenation level dependent magnetic resonance imaging and diffusion weighted MRI imaging for benign and malignant breast cancer discrimination

We uploaded the daset releatet t the manuscript: Fusco R, Granata V, Pariante P, Cerciello V, Siani C, Di Bonito M, Valentino M, Sansone M, Botti G, Petrillo A. Blood oxygenation level dependent magnetic resonance imaging and diffusion weighted MRI imaging for benign and malignant breast cancer discrimination. Magn Reson Imaging. 2021 Jan;75:51-59. doi: 10.1016/j.mri.2020.10.008. Epub 2020 Oct 17. PMID: 33080334.

Uptake of nitrogen forms by diploid and triploid white poplar depends on seasonal carbon use strategy and elevated summer ozone

This dataset contains data from an experiment described in the paper: "Miaomiao Wang, Guolei Li, Zhaozhong Feng, Yong Liu, Yansen Xu, Mercedes Uscola. Uptake of nitrogen forms by diploid and triploid white poplar depends on seasonal carbon use strategy and elevated summer ozone. Journal of Experimental Botany, erab317, https://doi.org/10.1093/jxb/erab317". In the study, we investigated the mechanisms of N forms acquisition in response to developmental phase allowing us to analyze the plasticity in N forms preferences due to internal plant N demands that are modified by growth rates. As a second objective we evaluate the effects of O3 enriched atmosphere during summer on the N forms uptake rates, which is a major air pollutant harmful to terrestrial vegetation and to human health. Main results of the experiments are that (1) Both ploidy levels had the physiological capacity to absorb intact glycine, and differed in growth, C and N acquisition patterns and N forms preferences. (2) Diploid, with six times higher RGR in spring than in summer, but similar absolute growth between seasons, showed plasticity on N forms preferences in response to seasons, shifting from no preferences in spring to strong preference on NO3- in summer. (3) Triploid, with only two times higher RGR in spring than in summer, but strongly higher absolute growth in summer than in spring, showed no plasticity among N forms in response to season and an overall preference for NO3-. (4) In response to O3, both ploidy levels decreased their NO3- uptake rates as a consequence of C acquisition reduction. However, while diploid was not able to modify its preferences among N forms, and therefore decreased total N uptake rate, triploid was able to compensate the reduction in NO3- uptake by increasing NH4+ and glycine acquisition, further decreasing the cost of N uptaken metabolism. (5) The different plasticity on N forms preferences across seasons and in response to elevated O3 between ploidy levels was attributed to different C and N use strategy among nutrients functions in plants, i.e. mass growth, N uptake and metabolism and nutrient reserve, including repair or detoxication in response to O3. Those strategies are deeply explored in the discussion.

Data from: Development of common leaf-footed bug pests depends on the presence and identity of their environmentally-acquired symbionts

Many beneficial symbioses between bacteria and their terrestrial arthropod hosts are vertically transmitted from mother to offspring, ensuring the progeny acquire necessary partners. Unusually, in several families of coreoid and lygeoid bugs (Hemiptera), nymphs must instead ingest the beneficial symbiont, Burkholderia (sensu lato), from the environment early in development. We studied the effects of Burkholderia on development of two species of leaf-footed bug (Coreidae) in the genus Leptoglossus, L. zonatus and L. phyllopus. We found no evidence for vertical transmission of the symbiont, but found stark differences in performance between symbiotic and aposymbiotic individuals. Symbiotic nymphs grew more rapidly, were approximately four times more likely to survive to adulthood than aposymbiotic bugs, and were two times larger. These findings suggest that Burkholderia is an obligate symbiont for Leptoglossus species. We also tested for variation in fitness effects conferred by four symbiont isolates representing different species within Burkholderia's insect-associated Stinkbug Beneficial and Environmental (SBE) clade. While three isolates conferred similar benefits to hosts, nymphs associated with the fourth isolate grew more slowly and weighed significantly less as adults. The effects of the four isolates were similar for both Leptoglossus species. This work indicates that both Burkholderia acquisition and isolate identity play critical roles in the growth and development of Leptoglossus. Importance Leptoglossus zonatus and L. phyllopus are important polyphagous pests and both species have been well-studied, but generally without regard to their dependance on a bacterial symbiont. Our results indicate that the central role of Burkholderia in the biology of these insects, as well as in other leaf-footed bugs, should be considered in future studies of coreid life history, ecology and pest management. Our work suggests acquisition of Burkholderia is critical for the growth and development of Leptoglossus species. Further, we found that there was variation in performance outcomes according to symbiont identity, even among members of the Stinkbug Beneficial and Environmental clade. This suggests that although environmental acquisition of a symbiont can provide extraordinary flexibility in partner associations, it also carries a risk if the partner is sub-optimal.

Context dependent fitness costs of reproduction despite stable body mass costs in an Arctic herbivore

1. The cost of reproduction on demographic rates is often assumed to operate through changing body condition. Several studies have found that reproduction depresses body mass more if the current conditions are severe, such as high population densities or adverse weather, than under benign environmental conditions. However, few studies have investigated the association between the fitness and body mass costs of reproduction. 2. Using 25 years of individual-based capture-recapture data from Svalbard reindeer (Rangifer tarandus platyrhynchus), we built a novel Bayesian state-space model that jointly estimated inter-annual change in mass, annual reproductive success, and survival, while accounting for incomplete observations. The model allowed us to partition the differential effects of intrinsic and extrinsic factors on both non-reproductive mass change and the body mass cost of reproduction and to quantify their consequences on demographic rates. 3. Contrary to our expectation, the body mass cost of reproduction (mean = 5.8 kg) varied little between years (CV = 0.08) whereas the between-year variation in body mass changes, that were independent of the previous year's reproductive state, varied substantially (CV = 0.4) in relation to autumn temperature and the amount of rain-on-snow in winter. This mass loss led to a cost of reproduction on the next reproduction, which was amplified by the same environmental covariates, from a 10% reduction in reproductive success in benign years, to a 50% reduction in harsh years. The reproductive mass loss also resulted in a small reduction in survival. 4. Our results show how demographic costs of reproduction, driven by inter-annual fluctuations in individual body condition, result from the balance between body mass costs of reproduction and body mass changes that are independent of previous reproductive state. We illustrate how a strong context dependent fitness cost of reproduction can occur, despite a relatively fixed body mass cost of reproduction. This suggests that female reindeer display a very conservative energy allocation strategy, either aborting their reproductive attempt at an early stage or weaning at a relatively constant cost. Such a strategy might be common in species living in a highly stochastic food limited environment.

opencc-by-4.0Sep 2021View details →

The effect of S427F mutation on RXRα activity depends on its dimeric partner

Simulations for RXRa-RARa can be found at: https://repo.vi-seem.eu/handle/21.15102/VISEEM-169  Below are the datasets of the MD simulations RXRα-RXRα and RXRα-PPARγ for the paper: "The effect of S427F mutation on RXRα activity depends on its dimeric partner", Galdadas et al, 2021, Chemical Science. RXRs are nuclear receptors acting as transcription regulators that control key cellular processes in all tissues. All type II nuclear receptors require RXRs for transcriptional activity by forming heterodimeric complexes. Recent whole-exome sequencing studies have identified the RXRα S427F hotspot mutation in 5% of the bladder cancer patients, which is always located at the interface of RXRα with its obligatory dimerization partners. Here, we show that mutation of S427 deregulates transcriptional activity of RXRα dimers, albeit with diverse allosteric mechanisms of action depending on its dimeric partner. S427F acts by allosteric mechanisms, which range from inducing the collapse of the binding pocket to allosteric stabilization of active co-activator competent RXRα states. Unexpectedly, RXR S427F heterodimerization leads to either loss- or gain-of-function complexes, in both cases likely compromising its tumor suppressor activity. This is the first report of a cancer-associated single amino acid substitution that affects the function of the mutant protein variably depending on its dimerization partner.

opencc-by-4.0Oct 2021View details →

Facilitating load-dependent queueing analysis through factorization

Dataset for the experiments reported in the IFIP PERFORMANCE 2021 paper "Facilitating load-dependent queueing analysis through factorization" by G. Casale, P.G. Harrison, H.W. Ong.

opencc-by-4.0Sep 2021View details →

A neural circuit linking two sugar sensors regulates satiety-dependent fructose drive in Drosophila (raw data)

This is the raw numerical data used in Musso et al., 2021, A neural circuit linking two sugar sensors regulates satiety-dependent fructose drive in Drosophila.

opencc-zeroOct 2021View details →

All-trans retinoic acid induces synaptopodin-dependent metaplasticity in mouse dentate granule cells

Previously we showed that the vitamin A metabolite all-trans retinoic acid (atRA) induces synaptic plasticity in acute brain slices prepared from the mouse and human neocortex (Lenz et al., 2021). Depending on the brain region studied, distinct effects of atRA on excitatory and inhibitory neurotransmission have been reported. Here, we used intraperitoneal injections of atRA (10 mg/kg) in adult C57BL/6J mice to study the effects of atRA on excitatory and inhibitory neurotransmission in the mouse fascia dentate – a brain region implicated in memory acquisition. No major changes in synaptic transmission were observed in the ventral hippocampus while a significant increase in both sEPSC frequencies and synapse numbers were evident in the dorsal hippocampus 6 hours after atRA administration. The intrinsic properties of hippocampal dentate granule cells were not significantly different and hippocampal transcriptome analysis revealed no essential neuronal changes upon atRA treatment. In light of these findings, we tested for the metaplastic effects of atRA, i.e., for its ability to modulate synaptic plasticity expression in the absence of major changes in baseline synaptic strength. Indeed, in vivo long-term potentiation (LTP) experiments demonstrated that systemic atRA treatment improves the ability of dentate granule cells to express LTP. The plasticity-promoting effects of atRA were not observed in synaptopodin-deficient mice, therefore, extending our previous results regarding the relevance of synaptopodin in atRA-mediated synaptic strengthening in the mouse prefrontal cortex. Taken together, our data show that atRA mediates synaptopodin-dependent metaplasticity in mouse dentate granule cells.

opencc-by-4.0Oct 2021View details →

Time Dependent Analysis of Rat Microglial Markers in Traumatic Brain Injury Reveals Dynamics of Distinct Cell Subpopulations

The repository contains seven zip files for flow cytometry data for rat microglia following Controlled cortical impact (CCI) collected at seven time points: 3 hours, 1 day, 2 days, 7 days 14 days, 21 days and 28 days. Each file contains 24 CSV files converted from the raw fcs file and text files that contain meta data about the file. Each file name depicts the information of whether it is Panel A (M1 in the file name) or Panel B (M2 in the file name) measurement and whether the measurement was conducted on the ipsilateral (ipsi) or contralateral (contra) side of the CCI, or sham conducted on the ipsilateral (ipsi) or contralateral (contra) sides. Below is the description of the columns of each file: <table> <tbody> <tr> <td> File column name </td> <td> Original name </td> <td> Panel A (M1) context </td> <td> PAnel B (M2) context </td> <td> Description </td> </tr> <tr> <td> F0 </td> <td> FSC-A </td> <td> FSC-A </td> <td> FSC-A </td> <td> Forward scattering Area </td> </tr> <tr> <td> F1 </td> <td> FSC-H </td> <td> FSC-H </td> <td> FSC-H </td> <td> Forward scattering Height </td> </tr> <tr> <td> F2 </td> <td> FSC-W </td> <td> FSC-W </td> <td> FSC-W </td> <td> Forward scattering Width </td> </tr> <tr> <td> F3 </td> <td> SSC-A </td> <td> SSC-A </td> <td> SSC-A </td> <td> Side scattering area </td> </tr> <tr> <td> F4 </td> <td> FITC-A </td> <td> FITC-A </td> <td> FITC-A </td> <td> Fluorescein isothiocyanate </td> </tr> <tr> <td> F5 </td> <td> PE-A </td> <td> CD32 </td> <td> CD200R </td> <td> Protein expression </td> </tr> <tr> <td> F6 </td> <td> PerCP-Cy5-5-A </td> <td> - </td> <td> CD163 </td> <td> Protein expression </td> </tr> <tr> <td> F7 </td> <td> PE-Cy7-A </td> <td> CD11 </td> <td> CD11 </td> <td> Protein expression </td> </tr> <tr> <td> F8 </td> <td> BV421-A </td> <td> P2Y12 </td> <td> P2Y12 </td> <td> Protein expression </td> </tr> <tr> <td> F9 </td> <td> BV510-A </td> <td> - </td> <td> - </td> <td> Dye  </td> </tr> <tr> <td> F10 </td> <td> Alexa Fluor 647-A </td> <td> CD86 </td> <td> RT1B </td> <td> Protein expression </td> </tr> <tr> <td> F11 </td> <td> APC-Cy7-A </td> <td> CD45 </td> <td> CD45 </td> <td> Protein expression </td> </tr> <tr> <td> F12 </td> <td> Event Time </td> <td> Event Time </td> <td> Event Time </td> <td>Event Time</td> </tr> </tbody> </table>

opencc-zeroDec 2018View details →

Supplementary material 1 from: Antoł A, Czarnoleski M (2018) Size dependence of offspring production in isopods: a synthesis. In: Hornung E, Taiti S, Szlavecz K (Eds) Isopods in a Changing World. ZooKeys 801: 337-357. https://doi.org/10.3897/zookeys.801.23677

Table S1 : Explanation note: Results of the literature search for reports of at least one of the following relationships in isopods: clutch size vs female size, offspring size vs female size, offspring size vs clutch size.

opencc-by-4.0Nov 2022View details →

Spatial scale-dependent dilution effects of biodiversity on plant diseases in grasslands

This study was conducted at the Gansu Gannan Grassland Ecosystem National Observation and Research Station of Lanzhou University (33°40'N, 101°52'E, 3540 m a.s.l.), which is located on the eastern edge of the Qinghai-Tibetan Plateau.

opencc-by-4.0Nov 2022View details →

Dataset related to article "Dose-Dependent Impairment of the Immune Response to the Moderna-1273 mRNA Vaccine by Mycophenolate Mofetil in Patients with Rheumatic and Autoimmune Liver Diseases"

This record contains data related to article “Dose-Dependent Impairment of the Immune Response to the Moderna-1273 mRNA Vaccine by Mycophenolate Mofetil in Patients with Rheumatic and Autoimmune Liver Diseases” The purpose of this study was to evaluate the efficacy and safety of the Moderna-1273 mRNA vaccine for SARS-CoV-2 in patients with immune-mediated diseases under different treatments. Anti-trimeric spike protein antibodies were tested in 287 patients with rheumatic or autoimmune diseases (10% receiving mycophenolate mofetil, 15% low-dose glucocorticoids, 21% methotrexate, and 58% biologic/targeted synthetic drugs) at baseline and in 219 (76%) 4 weeks after the second Moderna-1273 mRNA vaccine dose. Family members or caretakers were enrolled as the controls. The neutralizing serum activity against SARS-CoV-2-G614, alpha, and beta variants in vitro and the cytotoxic T cell response to SARS-CoV-2 peptides were determined in a subgroup of patients and controls. Anti-SARS-CoV-2 antibody development, i.e., seroconversion, was observed in 69% of the mycophenolate-treated patients compared to 100% of both the patients taking other treatments and the controls (p &lt; 0.0001). A dose-dependent impairment of the humoral response was observed in the mycophenolate-treated patients. A daily dose of &gt;1 g at vaccination was a significant risk factor for non-seroconversion (ROC AUC 0.89, 95% CI 0.80-98, p &lt; 0.0001). Moreover, in the seroconverted patients, a daily dose of &gt;1 g of mycophenolate was associated with significantly lower anti-SARS-CoV-2 antibody titers, showing slightly reduced neutralizing serum activity but a comparable cytotoxic response compared to other immunosuppressants. In non-seroconverted patients treated with mycophenolate at a daily dose of &gt;1 g, the cytotoxic activity elicited by viral peptides was also impaired. Mycophenolate treatment affects the Moderna-1273 mRNA vaccine immunogenicity in a dose-dependent manner, independent of rheumatological disease. .

opencc-zeroDec 2022View details →

Interactions with soil fungi alter density-dependence and neighborhood effects in a locally abundant dipterocarp species

Seedling recruitment can be strongly affected by the composition of nearby plant species. At the neighborhood scale (on the order of tens of meters), adult conspecifics can modify soil chemistry and presence of host microbes (pathogens and mutualists) across their combined canopy area or rooting zones. At local or small spatial scales (on the order of one to few meters), conspecific seed or seedling density can influence the strength of intraspecific light and resource competition and also modify the density-dependent spread of natural enemies such as pathogens or invertebrate predators. Intrinsic correlation between proximity to adult conspecifics (i.e. recruitment neighborhood) and local seedling density, arising from dispersal, make it difficult to separate the independent and interactive factors that contribute to recruitment success. Here, we present a field experiment in which we manipulated both the recruitment neighborhood and seedling density to explore how they interact to influence the growth and survival of Dryobalanops aromatica, a dominant ectomycorrhizal tree species in a Bornean tropical rainforest. First, we found that both local seedling density and recruitment neighborhood had effects on performance of D. aromatica seedlings, though the nature of these impacts varied between growth and survival. Second, we did not find strong evidence that the effect of density on seedling survival is dependent on the presence of conspecific adult trees. However, accumulation of mutualistic fungi beneath conspecifics adults does facilitate establishment of D. aromatica seedlings. In total, our results suggest that recruitment near adult conspecifics was not associated with a performance cost and may have weakly benefitted recruiting seedlings. Positive effects of conspecifics may be a factor facilitating the regional hyperabundance of this species. Synthesis: Our results provide support for the idea that dominant species in diverse forests may escape the localized recruitment suppression that limits abundance in rarer species.

opencc-zeroNov 2022View details →

Data and code from: The functional trait distinctiveness of plant species is scale dependent

Beyond the local abundance of species, their functional trait distinctiveness is now recognized as a key driver of community dynamics and ecosystem functioning. Yet, since the functional distinctiveness of a species is always relative to a given species pool, a species distinct at the regional scale might not necessarily be distinct at the local or community scale, and reciprocally. To assess the importance of scale (i.e the definition of a species pool) when quantifying the functional distinctiveness of species, and how it might distort the ecological conclusions derived from it, we quantified trait distinctiveness of 1,350 plant species at regional, local, and community scales over ca. 88 000 grassland plots in France. We measured differences in functional distinctiveness of species between regional, local and community scales and tested the influence of environmental predictors (climate and nitrogen input) and contexts (environmental distinctiveness, frequency, and heterogeneity) on these variations. In line with theoretical expectations, we found large variations of functional distinctiveness (in particular between regional and community scales) for many species, with a general tendency of lower distinctiveness at smaller scales. We also showed that nitrogen input – a key aspect of high land use intensity – and environmental frequency partly explained the differences between local and regional scales only. These results suggest the role played by environmental filtering on species' distinctiveness at the local scale, but the determinant of distinctiveness variations at the community scale still needs to be elucidated. Our study provides robust empirical evidence that measures of ecological originality are strongly scale-dependent. We urge ecologists to carefully consider the scale at which they measure distinctiveness, as ignoring scale dependencies could lead to biased (or even entirely wrong) conclusions when not considered at the scale of interest for the respective research question.

opencc-by-4.0Oct 2022View details →

Derived data for: 'Modelling the Time-Dependent Magnetic Fields that BepiColombo will use to Probe Down into Mercury's Mantle'

Derived data for the manuscript entitled 'Modelling the Time-Dependent Magnetic Fields that BepiColombo will use to Probe Down into Mercury’s Mantle'.

opencc-by-4.0Nov 2021View details →

Giving Back: Contributions Congruent to Library Dependency Changes in a Software Ecosystem

Abstract:  Widespread adoption of third-party libraries for contemporary software development has led to the creation of large inter-dependency networks, where sustainability issues of a single library can have widespread network effects. Maintainers of these libraries are often overworked, relying on the contributions of volunteers to sustain these libraries. To understand these contributions, in this work, we leverage socio-technical techniques to introduce and formalise dependency-contribution congruence (DC congruence) at both ecosystem and library level, i.e., to understand the degree and origins of contributions congruent to dependency changes, analyze whether they contribute to library dormancy (i.e., a lack of activity), and investigate similarities between these congruent contributions compared to typical contributions. We conduct a large-scale empirical study to measure the DC congruence for the NPM ecosystem using 1.7 million issues, 970 thousand pull requests (PR), and over 5.3 million commits belonging to 107,242 NPM libraries. We find that the most congruent contributions originate from contributors who can only submit (not commit) to both a client and library. At the project level, we find that DC congruence shares an inverse relationship with the likelihood that a library becomes dormant, i.e., the lower the DC congruence, the more likely the project becomes dormant. Finally, by comparing source code of contributions, we find statistical differences in file path and added lines in source code of congruent contributions when compared to typical contributions. Our work has implications to encourage and sustain dependency change congruent contributions, especially to support library maintainers in sustaining their projects. Data Description: Datasets and source code related to (a) the ecosystem-level and package-level DC congruence results, (b) the metric data for our survival model analysis, and (c) the file path and source code similarities between contribution types. For each folder, it includes a text file to describe file details.

opencc-by-4.0Dec 2022View details →

Age dependent incidence rates (2)

Figure 4 shows the sex-specific logarithmic incidence depending on age (50 to 90 years) for the period from 2011 to 2019. Across all evaluated years we found both, an age-dependent, exponential increase in the incidence rates for both sexes and a distinct increase in incidences in the young age groups of women (about tenfold increase in incidences up to 2019) . Up to the age of about 70 years, men show a higher incidence rate for long-term care than women in 2011. For people older than 70 years, the ratio changes, with a higher incidence of needing long-term care for women than for men. This point of intersection of the incidence rates was evident in all plots of the time course (table 2). We see a left shift, to younger age groups, between 2011 and 2019 and from this age (intersection point) onwards the incidence for women exceeds that of men. In addition to that, the incidence in the scenario with higher mortality rate ratios (scenario 1) is always above the curve from the scenario with lower mortality rate ratios (scenario 2). We also see that the gap between the incidences increases with age.

opencc-by-4.0Dec 2022View details →

Age dependent incidence rates (1)

Figure 3 shows an increasing incidence rate dependent on age. Additionally we see increasing incidence rates from 2011 to 2019, with bigger steps between the incidences in younger age groups.