Find research datasets worth reusing

Data published in manuscript "Effects of reversal of water flow in an Arctic floodplain river on fluvial emissions of CO2 and CH4" by Castro-Morales et al.

This data is published in the manuscript: Castro-Morales, K., Canning, A., Körtzinger, A., Göckede, M., Küsel, K., et al. (2022). Effects of reversal of water flow in an Arctic floodplain river on fluvial emissions of CO2 and CH4. Journal of Geophysical Research: Biogeosciences, 127, e2021JG006485. <a href="https://doi.org/10.1029/2021JG006485">https://doi.org/10.1029/2021JG006485</a>. The data contains the water properties and gases data measured at a site in Ambolikha River, meteorological data measured at an eddy covariance tower located in the neighbor floodplain, and data from the analysis of dissolved organic matter in river water samples. The data was collected between 26 June, 2019 and 02 August, 2019. This folder contains four data files and the file "README_Data_access_Castro-Morales_etal_Ambolikha_River.txt" should be read before accessing the data. The authors recommend downloading Version 2.0 because it is the most up to date data. For questions contact the main and corresponding author Dr. Karel Castro-Morales at: karel.castro.morales@uni-jena.de

Datasets for "Dynamo effect in unstirred self-gravitating turbulence"

<pre>This directory contains an index.html file with links to the run directories with secondary data for Table I of the paper "Dynamo effect in unstirred self-gravitating turbulence" by Axel Brandenburg and Evangelia Ntormousi. If anything turns out to be incomplete, please email brandenb@nordita.org. </pre>

openother-openDec 2021View details →

Erratum: Constraints on dark matter-nucleon effective couplings in the presence of kinematically distinct halo substructures using the DEAP-3600 detector [Phys. Rev. D 102, 082001 (2020)]

Corrections to the results from O3 operator in <a href="https://journals.aps.org/prd/abstract/10.1103/PhysRevD.102.082001">Phys. Rev. D 102, 082001</a>. "Constraints on dark matter-nucleon effective couplings in the presence of kinematically distinct halo substructures using the DEAP-3600 detector".

opencc-zeroDec 2021View details →

Simulated treatment effects on bird communities inform landscape‐scale dry conifer forest management

Human land use and climate change have increased forest density and wildfire risk in dry conifer forests of western North America, threatening various ecosystem services, including habitat for wildlife. Government policy supports active management to restore historical structure and ecological function. Information on potential contributions of restoration to wildlife habitat can allow assessment of tradeoffs with other ecological benefits when prioritizing treatments. We predicted avian responses to simulated treatments representing alternative scenarios to inform landscape‐scale forest management planning along the Colorado Front Range. We used data from the Integrated Monitoring in Bird Conservation Regions program to inform a hierarchical multispecies occupancy model relating species occupancy and richness with canopy cover at two spatial scales. We then simulated changes in canopy cover (remotely sensed in 2018) under three alternative scenarios, (1) a "fuels reduction" scenario representing landscape‐wide 30% reduction in canopy cover, (2) a "restoration" scenario representing more nuanced, spatially variable treatments targeting historical conditions, and (3) a reference, no‐change scenario. Model predictions showed areas of potential gains and losses for species richness, richness of ponderosa pine forest habitat specialists, and the ratio of specialists to generalists at two (1 km2 and 250 m2) spatial scales. Under both fuels reduction and restoration scenarios, we projected greater gains than losses for species richness. Surprisingly, despite restoration more explicitly targeting ecologically relevant historical conditions, fuels reduction benefited bird species richness over a greater spatial extent than restoration, particularly in the lower montane life zone. These benefits reflected generally positive species associations with moderate canopy cover promoted more consistently under the fuels reduction scenario. In practice, contemporary forest management is likely to lie somewhere between the fuels reduction and restoration scenarios represented here. Therefore, our results inform where and how active forest management can best support avian diversity. Although our study raises questions regarding the value of including landscape‐scale heterogeneity as a management objective, we do not question the value of targeting finer-scale heterogeneity (i.e., stand and treatment level). Rather, our results combined with those from previous work clarify the scale at which targeting structural heterogeneity and historical reference conditions can promote particular ecosystem services.

opencc-by-4.0Nov 2021View details →

High-fidelity simulation of the effects of street trees, green roofs and green walls on the distribution of thermal exposure in Prague-Dejvice

Archive with PALM simulation results. All data were used in paper <a href="https://doi.org/10.1016/j.buildenv.2022.109484">https://doi.org/10.1016/j.buildenv.2022.109484</a>

opencc-zeroDec 2020View details →

Ecological specialization, rather than the island effect, explains morphological diversification in an ancient radiation of geckos

Island colonists are often assumed to experience higher levels of phenotypic diversification than continental taxa. However, empirical evidence has uncovered exceptions to this 'island effect'. Here, we tested this pattern using the geckos of the genus Pristurus from continental Arabia and Africa and the Socotra Archipelago. Using a recently published phylogeny and an extensive morphological dataset, we explore the differences in phenotypic evolution between Socotran and continental taxa. Moreover, we reconstructed ancestral habitat occupancy to examine if ecological specialization is correlated with morphological change, comparing phenotypic disparity and trait evolution between habitats. We found a heterogeneous outcome of island colonization. Namely, only one of the three colonization events resulted in a body size increase. However, in general, Socotran species do not present higher levels or rates of morphological diversification than continental groups. Instead, habitat specialization explains better the body size and shape evolution in Pristurus . Particularly, the colonization of ground habitats appears as the main driver of morphological change, producing the highest disparity and evolutionary rates. Additionally, arboreal species show very similar body size and head proportions. These results reveal a determinant role of ecological mechanisms in morphological evolution and corroborate the complexity of ecomorphological dynamics in continent–island systems.

CESM model results - Effect of nitrogen limitation and soil processes on Holocene greening of the Sahara

The model results are made in EAPL, Yonsei University, South Korea (https://eapl.yonsei.ac.kr). The purpose of the simulations were to find out the effect of nitrogen limitation and soil processes on Holocene greening of the Sahara. CESM model v1.2 was used for this simulation.

opencc-by-4.0Nov 2021View details →

Final project report: The Side Effects of Forced Online Distance Education (FODE)

The outbreak of COVID-19 forced most universities into distance education. Three didacticians and researchers from the University of Maribor, Slovenia: Kosta Dolenc, Mateja Ploj Virtič and Andrej &Scaron;orgo formed a self-initiated initiative project group during the COVID-19 epidemic and started the project with the working title: The Side Effects of Forced Online Distance Education (FODE). The aim of the project, was to investigate the response of university teachers and students to the new situation.

Detection of neurofilament light chain with label-free electrolyte-gated organic field-effect transistors

The uploaded data include i) transfer curves registered at every NF-L concentration; ii) transfer curves for control experiments; iii) raw AFM data acquired after electrode incubation in 0 M, 1 pM, 100 pM and 10 nM [NF-L]. Electrical measurements were acquired in 50 mM PBS, pH 7.4 under static conditions. Anti-NF-L antibodies were immobilized on the gate electrode through cys-Protein G. The gate surface has been subsequently passivated through 11-mercaptoundecyl-triethylene glycol SAM.

Inner filter effect correction for fluorescence measurements in microplates (ZINFE and NINFE) - experimental data

Experimental data for the paper entitled Inner Filter Effect Correction for Fluorescence Measurements in Microplates Using Variable Vertical Axis Focus (https://doi.org/10.1021/acs.analchem.2c01031). Separate datasets are provided for data with background correction, without background correction, and absorbance-corrected data. All results were obtained using the online calculator service written in Javascript: https://ninfe.science (version 15.9.2021.). For additional details please visit: https://glymech.pharma.hr//GlyMech.html.

Cumulative effects doubled the drought impacts for one-fifth of ecosystems exposed to recurrent droughts during Australia's Millennium Drought

Drought-induced vegetation declines have been reported across the globe and may have widespread implications for ecosystem composition, structure, and functions. Thus, it is critical to maximizing our understanding of how vegetation has responded to recent drought extremes. To date, most drought assessments have focused on the impact of a single drought event, emphasizing the importance of drought intensity for vegetation responses. However, drought timing, duration, and repeat exposure may all be important aspects of ecosystem response with the potential for non-linear effects. Cumulative effects are one such phenomenon, representing the additional decline due to repeated or prolonged exposure to drought, and indicating gradual loss of ecosystem resistance. This study quantifies the frequency and magnitude of cumulative effects among Australian ecosystems as they responded to the Millennium Drought. Three distinct biophysical variables derived from satellite remote sensing were analyzed, including fraction of photosynthetically absorbed radiation, photosynthetic vegetation cover, and canopy density derived from passive microwave data. While cumulative effects were detected in only 20% or less of the landscape exposed to repeat or long-duration drought, they approximately doubled drought impacts in the areas where they occurred. Cultivated lands and grasslands were the most susceptible to cumulative effects from recurrent droughts. Despite being relatively infrequent in forests and savannas, cumulative effects from repeated or long-duration drought caused larger additional declines in these ecosystems. Overall, our study demonstrates that the temporal sequence of drought events can strongly influence the magnitude of drought impacts, which provides important insights into modeling vegetation response to recurrent drought events

Spatial patterns in neighbourhood effects on woody plant selection and bark stripping by deer in a lowland alluvial forest

This dataset presents the incidence of bark stripping (present or not) and its intensity by two deer species mapped over all woody individuals ≥ 1 cm diameter at breast height (DBH). Stripping intensity was measured as the maximal percentage of the stripped stem circumference at the part of the stem with the horizontally widest stripping wound. A four-hectare square research plot is located in the Ran&scaron;purk old-growth forest reserve in the south-eastern part of the Czech Republic (N48°40´, E16°56´). Several treefalls damaged the fence around the reserve in late autumn 2017, allowing fallow deer (Dama dama L.) and red deer (Cervus elaphus L.) to enter the reserve from the deer enclosure. The number of fallow deer and red deer individuals in the reserve was unknown, and likely fluctuated over time as they could enter and leave the reserve at any time. Data were collected in July 2018, ca 9–10 months after the fence was damaged. Although the fence was not fixed at the time of data collection (deer could still enter and leave the reserve), stripping wounds were not fresh and were likely received between late autumn 2017 and early spring 2018. The datasets includes tree and shrub individuals that fell within species-specific DBH range (susceptible individuals). The range was defined for each tree and shrub species as DBHmin ≤ DBH ≤ DBHmax, where DBHmin and DBHmax are DBH of the smallest and largest stripped individuals. Individuals smaller and larger than this range were excluded from analyses, because small and large individuals may be relatively less often stripped. Woody species with ≥ 70 individuals are presented, because stochasticity does not allow meaningful spatial point pattern analyses with fewer individuals per species. Data contains the x and y coordinates of each individual in a local coordinate system, the woody species, its code, diameter at breast height, the incidence of stripping (present = 1 or not = 0), and the intensity of stripping (%).

opencc-by-4.0Sep 2021View details →

Datasets for "Effects of the COVID-19 Pandemic on Authors and Reviewers of American Geophysical Union Journals"

These files include summary data on demographics of people submitting journal articles and reviewing manuscripts submitted to American Geophysical Union (AGU) journals. The date range is January 2018 through February 2021, divided by two years before the pandemic and during the pandemic ("year grouping"): March 2018- February 2019; March 2019- February 2020, and March 2020- February 2021 ("year of the COVID-19 pandemic"). Author-related files only include demographics of the submitting, or "corresponding" author. These datasets supplement the under-review manuscript and pre-print submission to ESSOAr (Earth and Space Science Open Archive) "Effects of the COVID-19 Pandemic on Authors and Reviewers of American Geophysical Union Journals."

opencc-by-4.0Jun 2021View details →

Forest cover and connectivity have pervasive effects on the maintenance of evolutionary distinct interactions in seed dispersal networks

This Data set contain 29 table of weighted interaction network between plants (columns) and frugivore birds from the Brazilian Atlantic Forest used in the manuscript "Forest cover and connectivity have pervasive effects on the maintenance of evolutionary distinct interactions in seed dispersal networks" published in Oikos Journal.

Revisiting the cumulative effects of drought on global gross primary productivity based on new long-term series data (1982-2018)

Aim: Drought has broad and deep impacts on vegetation. Studies on the effects of drought on vegetation have been conducted over years. However, global-scale and long-term (>30 years) studies on the cumulative effect of drought are still lacking. Thus, combining a new satellite based gross primary productivity (GPP) and multi-timescale Standardized Precipitation Evapotranspiration Index datasets, we investigated the cumulative effect of drought on global vegetation GPP. Location: Global. Time period: 1982 – 2018 (37 years). Major taxa studied: Forests and grasslands. Method: Based on correlation analysis framework, we investigated the cumulative effect duration of drought on global vegetation GPP. Meanwhile, the variability of this cumulative effect across different elevation gradients and climatic zones was analyzed using variance analysis.

opencc-zeroJan 2022View details →

Incorporating effects of age on energy dynamics predicts non-linear maternal allocation patterns in iteroparous animals

Iteroparous parents face a trade-off between allocating current resources to reproduction versus maximizing survival to produce further offspring. Optimal allocation varies across age, and follows a hump-shaped pattern across diverse taxa, including mammals, birds and invertebrates. This non-linear allocation pattern lacks a general theoretical explanation, potentially because most studies focus on offspring number rather than quality and do not incorporate uncertainty or age-dependence in energy intake or costs. Here, we develop a life history model of maternal allocation in iteroparous animals. We identify the optimal allocation strategy in response to stochasticity when energetic costs, feeding success, energy intake, and environmentally-driven mortality risk are age-dependent. As a case study, we use tsetse, a viviparous insect that produces one offspring per reproductive attempt and relies on an uncertain food supply of vertebrate blood. Diverse scenarios generate a hump-shaped allocation: when energetic costs and energy intake increase with age; and also when energy intake decreases, and energetic costs increase or decrease. Feeding success and mortality risk have little influence on age-dependence in allocation. We conclude that ubiquitous evidence for age-dependence in these influential traits can explain the prevalence of non-linear maternal allocation across diverse taxonomic groups.

Fortran code used in 'A fractal model for effective excess charge density in variably saturated fractured rocks'

This code is uploaded to support the research study 'A fractal model for effective excess charge density in variably saturated fractured rocks' by L. Guarracino and  D. Jougnot (submitted to JGR: Solid Earth, 2021). Files: a) Fortran source code (qvfrac.f) for estimating the effective excess charge density in fractured rocks. The calculation is based on model equations described in the research study. b) Input data (network1.dat) to calculate the effective excess charge density for fracture network 1 described in Section 3 (Figure 5a).

opencc-zeroJan 2022View details →

Pollution induces epigenetic effects that are stably transmitted across multiple generations

It has been hypothesised that the effects of pollutants on phenotypes can be passed to subsequent generations through epigenetic inheritance, affecting populations long after the removal of a pollutant. But there is still little evidence that pollutants can induce persistent epigenetic effects in animals. Here we show that low doses of commonly used pollutants induce genome-wide differences in cytosine methylation in the freshwater crustacean Daphnia pulex. Uniclonal populations were either continually exposed to pollutants or switched to clean water, and methylation was compared to control populations that did not experience pollutant exposure. While some direct changes to methylation were only present in the continually exposed populations, others were present in both the continually exposed and switched to clean water treatments, suggesting that these modifications had persisted for seven months (> 15 generations). We also identified modifications which were only present in the populations that had switched to clean water, indicating a long-term legacy of pollutant exposure distinct from the persistent effects. Pollutant-induced differential methylation tended to occur at sites that were highly methylated in controls. Modifications that were observed in both continually and switched treatments were highly methylated in controls and showed reduced methylation in the treatments. On the other hand, modifications found just in the switched treatment tended to have lower levels of methylation in the controls and showed increase methylation in the switched treatment. In a second experiment we confirmed that sub-lethal doses of the same pollutants generate effects on life-histories for at least three generations following the removal of the pollutant. Our results demonstrate that even low doses of pollutants can induce transgenerational epigenetic effects that are stably transmitted over many generations. Persistent effects are likely to influence phenotypic development, which could contribute to the rapid adaptation, or extinction, of populations confronted by anthropogenic stressors.

opencc-by-4.0Feb 2022View details →

Viroplant Project - Microcosm studies on the effect of bacteriophages used as plant protection products on soil microbial communities

This file contains the description, data and DNA analyses on the effect of bacteriophages with a potential to be used as plant protecction products on the structure and function of soil microbial communities. The objective was to evaluate two different microcsom incubation systems with phages and microbial cells from soil, or soil itself and to analyses in a time dependent manner how the phages affect the natural soil microbiomes. The microbial communities were quantified with qPCR and their diversity analyzed with PCR amplified 16S rRNA gene sequences. Bioinformatic analyses were used to evaluate microbial community responses

Natural variation in Drosophila shows weak pleiotropic effects

Pleiotropy is the phenomenon that a gene affects multiple phenotypes. The extent of pleiotropy is still disputed, mainly because of power issues. A further challenge is that empirical tests of pleiotropy are restricted to a small subset of all possible phenotypes. To overcome these limitations, we propose a new measurement of pleiotropy, which integrates across many phenotypes and multiple generations to improve power. We infer pleiotropy from the fitness cost imposed by frequency changes of pleiotropic loci. Mixing Drosophila simulans populations, which adapted independently to the same new environment using different sets of genes we show that the adaptive frequency changes have been accompanied by measurable fitness costs. Unlike previous studies characterizing the molecular basis of pleiotropy, we show that many loci, each with weak effects, contribute to genome-wide pleiotropy. We propose that the costs of pleiotropy were reduced by the modular architecture of gene expression, which facilitated adaptive gene expression changes with low impact on other functions.