Find research datasets worth reusing

Disentangling the relative contributions of factors determining seed physical defence: a global-scale data synthesis

Physical defence investment in seeds varies greatly among plant species and is affected by many potential factors. However, the relative importance of influential factors has not yet been systematically evaluated. Here, we compiled a global database of the seed coat ratio (SCR), a proxy of seed physical defence, for 1,357 species. Using partial R2 calculation that can estimate the reduction in explained variance of a given factor after removing it from a full model containing all the other factors, we disentangled the relative contributions of seven factors commonly used to explain variation in the SCR. Seed desiccation response and phylogeny explained a large amount of SCR variation among species, with a partial R2lik value of 13.31% and 10.62%, respectively. Seed dormancy, plant growth form, seed mass, climate region, and fruit type showed little power to explain SCR variation, although they are often cited in the literature as potential factors. Our results highlight the important roles of seed desiccation response and phylogeny in shaping interspecific variation in the SCR. These findings provide a detailed interpretation of both evolutionary and ecological patterns underlying the physical defence mechanisms and allocation strategies of plant seeds.

Throughfall exclusion and fertilization effects on tropical dry forest tree plantations, a large-scale experiment

Across tropical ecosystems, global environmental change is causing drier climatic conditions and increased nutrient deposition. Such changes represent large uncertainties due to unknown interactions between drought and nutrient availability in controlling ecosystem net primary productivity (NPP). Using a large-scale manipulative experiment, we studied for 4 years whether nutrient availability affects the individual and integrated responses of aboveground and belowground ecosystem processes to throughfall exclusion in 30-year-old mixed plantations of tropical dry forest tree species in Guanacaste, Costa Rica. We used a factorial design with four treatments: control, fertilization (F), drought (D), and drought + fertilization (D + F). While we found that a 13 %–15 % reduction in soil moisture only led to weak effects in the studied ecosystem processes, NPP increased as a function of F and D + F. The relative contribution of each biomass flux to NPP varied depending on the treatment, with woody biomass being more important for F and root biomass for D + F and D. Moreover, the F treatment showed modest increases in maximum canopy cover. Plant functional type (i.e., N fixation or deciduousness) and not the experimental manipulations was the main source of variation in tree growth. Belowground processes also responded to experimental treatments, as we found a decrease in nodulation for F plots and an increase in microbial carbon use efficiency 25 for F and D plots. Our results emphasize that nutrient availability, more so than modest reductions in soil moisture, limits ecosystem processes in tropical dry forests and that soil fertility interactions with other aspects of drought intensity (e.g., vapor pressure deficit) are yet to be explored.

Reversing declines in farmland birds: how much agri-environment provision is needed at farm and landscapes scales?

1) Agri-environment schemes (AES) are the primary policy mechanism for addressing farmland biodiversity declines across Europe. Despite previous studies on the impacts of AES on biodiversity, there is little empirical evidence on the scale of provision required to reverse declines. 2) Across three regions of lowland England with contrasting farm systems (arable, pastoral, mixed) we estimated avian Population Growth Rates (PGRs) on farmland with high AES provision ('higher-tier': average bird-friendly option cover = 7.4%), low AES provision ('lower-tier': 2.3%), and no bird-friendly AES ('no AES'). Ten-year PGRs were derived for 24 species and three multi-species groups comprising farmland-associated species ('farmland birds'), species of conservation concern ('priority birds'), and species restricted to farmland ('specialist birds'). We used PGRs to simulate the proportion of the regional farmland landscape that would have to be assigned to higher- and lower-tier agreements to stabilise or increase populations. 3) In the arable and pastoral regions, 13/23 and 13/22 species respectively had more positive PGRs under higher-tier AES than on no AES farmland (none had more negative PGRs), compared to 4/22 (positive) and 1/22 (negative) in the mixed region. Only 2-4 species per region exhibited more positive PGRs under lower-tier AES compared to no AES farmland. 4) Multi-species PGRs in the arable and pastoral regions increased from no AES (strong decline), to lower-tier (decline or stability) to higher-tier (moderate or strong increase). There was no overall AES effect in the mixed region. 5) To increase regional farmland bird populations by 10% over 10-years, 47% and 26% of the farmed landscape would need to be devoted to higher-tier agreements in arable and pastoral landscapes respectively. This falls to 34% and 17% when higher-tier is targeted at localities supporting higher abundances of target species, and to 29% and 10% when 30% of the farmed landscape is also devoted to lower-tier. Priority and specialist birds require higher provision levels. 6) Policy implications. Where farmland bird recovery is an AES objective, farms should prioritise higher-tier agreement delivery over lower-tier. Farmland bird responses to AES provision are likely to vary regionally but careful targeting will reduce the amount needed in the landscape.

Remote insolation forcing of orbital-scale South Asian summer monsoon variability

CESM simulation data for the manuscript "Remote insolation forcing of orbital-scale South Asian summer monsoon variability", which has been submitted to Geophysical Research Letters.

Inter-rating reliability of the Swiss Easy-Read Integrated Palliative Care Outcome Scale for People with Dementia

# Brief project overview This is Data coming out of the IPOS-Dem project, a Stepped-wedge Cluster Randomised Trial (SW-CRT). Please make shure to check out the SW-CRT protocol for more details at <a href="http://www.doi.org/10.1111/jan.14953">https://www.doi.org/10.1111/jan.14953</a>. A detailed description of the reliability study published based on this data is availiable at <a href="http://www.doi.org/10.1371/journal.pone.0286557">https://www.doi.org/10.1371/journal.pone.0286557</a>.   We are currently working on our main study (SW-CRT) analysis. While we remain dedicated to open science, our priority is to ensure the utmost integrity of our ongoing research. I am pleased to inform you that we anticipate the final trial results to be published by Fall-Winter of 2023. Upon completion, our anonymized full dataset will be made accessible at <a href="https://doi.org/10.5281/zenodo.4008427">https://doi.org/10.5281/zenodo.4008427</a>. Interested parties seeking early access are encouraged to reach out to the first author directly. Furthermore, we are committed to enhancing the transparency and reproducibility of our research, and as such, we will provide the code for the full analysis at <a href="https://doi.org/10.5281/zenodo.4008429">https://doi.org/10.5281/zenodo.4008429</a>. # Contributors Frank Spichiger, Andrea Koppitz, Thomas Volken, André Meichtry ## Repository overview |-- readme.md |-- documentation     |--readme.md     |--IPOS-Dem-Reliability_data-dictionary.html     |--IPOS-Dem-Reliability_sociodemographics_data-dictionary.html |-- data      |-- readme.md     |--data.csv     |--sd_overall.csv |-- analysis     |--readme.md     |--scripts         |--MainAnalysis.rmd         |--S1_ClusterwiseSDs.rmd         |--S2_Item_Characteristics.rmd # Applicable instructions The R markdown files were generated using R 4.2.2 in RStudio 2023.06.0 for MacOS X you can run them using free software but will need to install R, Rstudio and the packages introduced at the beginning of the files we used. # Additional resources - Main study protocol: <a href="https://www.doi.org/10.1111/jan.14953">https://www.doi.org/10.1111/jan.14953</a> - IPOS-Dem translation and adaption: <a href="https://www.doi.org/10.1186/s41687-022-00420-7">https://www.doi.org/10.1186/s41687-022-00420-7</a> - Pos-Pal consortium with more information on the measure: <a href="https://www.pos-pal.org">https://www.pos-pal.org</a>

Fine-scale intraspecific niche partitioning in a highly mobile, marine megafauna species: implications for ecology and conservation

A species may partition its realized ecological niche along bionomic and/or scenopoetic axes due to intraspecific competition for limited resources. How partitioning manifests depends on resource needs and availability by and for the partitioning groups. Here we demonstrate the utility of analyzing short- and long-term stable carbon and nitrogen isotope ratios from imperiled marine megafauna to elucidate realized niche partitioning in these species. We captured 113 loggerhead (Caretta caretta) sea turtles at a high-use area near Crystal River, Florida, between 2016–2022, comprising 53 subadults, 10 adult males, and 50 adult females. Isotopic analyses indicated that loggerheads partition their realized ecological niche by life stage, along a scenopoetic axis. Most adults likely forage and reside in shallow areas of the study site, with most subadults displaying habitat switching between deeper locations to forage and shallower locations to rest. Some subadults, like adults, also forage and reside in shallow areas, and may display behaviors to avoid intraspecific competition. Analysis of stable isotopes with different turnover rates was critical for this characterization of intraspecific niche partitioning in loggerhead turtles, which has direct implications for ongoing research and conservation efforts for this and other imperiled species.

Large-scale restoration of species-rich dry grasslands on arable land: Environmental filtering drives successful species establishment over a period of 10 years

Sowing of regionally specific seed mixtures on former arable land is increasingly used to restore species-rich grasslands, but it often faces important obstacles in environmental conditions and colonisation from preserved surrounding grasslands. Long-term landscape scale studies, which explore the processes governing plant establishment from seed mixtures and later colonisation from the surrounding landscape are scarce. We studied the species and functional trait composition of 32 grasslands restored 1–11 years before the first sampling by sowing regional seed mixtures in the White Carpathian Mts (SE Czech Republic). We compared them with 23 well-preserved permanent grasslands in their surroundings. In each grassland we estimated plant species cover in three plots of 25 m2, in restored grasslands in 2009, 2014 and 2019, in permanent grasslands in 2009. The species composition of the restored grasslands converged towards the permanent grasslands due to expansion of dry grassland species and retreat of mesic grassland and weed species. The majority (60–71%) of the vegetation cover of restored grasslands was formed by sown species, while the species number was mainly determined by colonising unsown species (61–63%). The species number of restored grasslands remained lower than that in permanent grasslands. Functional trait composition (Community Weighted Mean) of the sown seed mixtures, permanent grasslands and restored grasslands overlapped in all three samplings. With increasing grassland age, species with resource-retaining traits of low specific leaf area and high leaf dry matter content, lower stature, higher seed mass, and lower capacity for clonal reproduction expanded. Functional trait diversity of the plots was mostly lower than expected by null model randomisations of community, which indicates strong environmental filtering. Comparison of newly colonising species and extinct species indicated that mainly species with traits similar to the rest of the community are able to colonise the grasslands successfully. Synthesis and applications. Sowing of regionally specific seed mixtures was successful and demonstrated to be a fast way of grassland restoration, particularly in terms of functional trait composition. The resulting species diversity depended on the colonisation processes, which are controlled by the functional composition of the local communities.

Large-scale changes in macrobenthic biodiversity driven by mangrove afforestation

<ol> <li>Large-scale anthropogenic mangroves have been constructed in coastal regions worldwide, but our understanding of their ecological effects is limited. In particular, the question of whether and how anthropogenic mangroves influence biodiversity patterns remains elusive.</li> <li>Here, we investigated the influence of large-scale anthropogenic mangroves on biodiversity patterns of mangrove macrobenthos. Specifically, we measure and seek to explain differences in species richness, abundance, assemblage composition, and distance-decay effect before and after the construction of anthropogenic mangroves.</li> <li>We surveyed assemblages of gastropod, bivalve and crab species over a wide latitudinal extent (24–28°N) in subtropical China. For each, we calculated species richness, abundance, assemblage composition, and distance-decay relationship before and after the construction of anthropogenic mangroves.</li> <li> After the large-scale anthropogenic mangroves, we found species richness of gastropods, bivalves and crabs increased by 23.81%, 100% and 20%, respectively. The distance-decay effects of gastropods and bivalves decreased by 25% and 91.43%, while that of crabs remained virtually unchanged, indicating that large-scale monospecific planting changed spatial processes of macrobenthos (e.g., dispersal limitation). With mangrove plantation, compositional similarity of crab and bivalve assemblages increased by 28.57% and 38.46%, suggesting that large-scale monospecific planting exacerbates biotic homogenization. Altogether, these results indicate that large-scale anthropogenic habitats increase the diversity of mangrove macrobenthos and change taxonomic compositions by reducing distance-decay effects. </li> <li> Synthesis and applications. We emphasize that afforestation of coastal wetlands can drive major changes in benthonic communities. Monitoring and assessing the ecological effects of the anthropogenic habitats for the presence of functional faunas will be important in determining the future coastal restoration and maintaining economic aquaculture. Quantifying those effects in terms of regional biodiversity composition enables management decisions about habitat restoration to be based upon macro-evidence rather than wishful thinking or untested intuition even or a one-sided local perspective. </li> </ol>

opencc-zeroDec 2022View details →

Data from: Dominant species determine grazing effects on the stability of herbaceous community production at multiple scales in drylands

Sustainable provision of critical ecosystem services in drylands is reliant on their stability under anthropogenic disturbances. Livestock grazing and shrub encroachment are the primary drivers of disturbance that impact their biodiversity and production dynamics. However, the effects of grazing on the stability at multiple scales, particularly following the transition from grass-dominated to shrub-encroached drylands, is still largely unexplored. Here, we conducted comparable sheep-grazing experiments in two types of drylands (grass-dominated vs. shrub-encroached grasslands) on the Mongolia Plateau to explore the effects of grazing and shrub encroachment on biodiversity and stability at multiple scales. We examined how grazing affected the temporal stability of aboveground biomass in herbaceous communities in both grass-dominated and shrub-encroached grasslands, through two potential mechanisms: insurance effects and changes in the population-level stability of individual species. We found that an increase in sheep grazing intensity had significant and negative effects on insurance effects by decreasing both species asynchrony and spatial asynchrony but it had no effects on population stability, consequently leading to reductions in herbaceous community stability of the grasslands. However, grazing-increased insurance effects canceled out grazing-decreased population stability, contributing to no changes in the community stability of shrub-encroached grasslands. Likely, because grazing-induced reductions in the relative abundance of the dominant species were more noticeable in shrub-encroached grasslands than that of in grasslands. Moreover, the grazing-decreased abundance of dominant species was directly correlated to increases in insurance effects in shrub-encroached grasslands but not in grasslands, despite the positive relationships between population stability and the relative abundance of the dominant species in both grass-dominated and shrub-encroached drylands. Synthesis and applications. Our results indicate that grazing can decrease the stability of herbaceous production in drylands, but this negative effect is attenuated with the transition from grasslands to shrub-encroached grasslands, suggesting that grazing effects on herbaceous community stability can be altered by shrub encroachment in drylands. Furthermore, the stability of dominant grasses plays a crucial role in stabilizing herbaceous communities, and should be considered in promoting sustainable ecosystem functioning and services in drylands.

Stability of the next-to-tribimaximal mixings under radiative corrections with the variation of SUSY breaking scale in MSSM

<pre>We analyse the radiative stability of the next-to-tribimaximal mixings ($NTBM$) with the variation of SUSY breaking scale ($m_S$) in MSSM, for both normal and inverted hierarchical cases at the fixed input value of seesaw scale $M_R = 10^{15}$ GeV and $\tan \beta = 30$. All the neutrino oscillation parameters receive varying radiative corrections irrespective of the $m_S$ values at the electroweak scale, which are all within $3\sigma$ range of the latest global fit data. NH case is found to be more stable than IH case for all four cases.</pre>

Stability of the next-to-tribimaximal mixings under radiative corrections with the variation of SUSY breaking scale in MSSM

Large-scale exploration of nitrogen utilization efficiency in Asia region for rice crop: variation patterns and determinants

Improving rice nitrogen utilization efficiency (NUtE) is imperative to maximizing future food productivity while minimizing environmental threats, yet knowledge of its variation and the underlying regulatory factors is still lacking. Here, we integrated a dataset with 21,571 data compiled by available data from peer-reviewed literature and a large-scale field survey to address this knowledge gap. The overall results revealed great variations in rice NUtE, which were mainly associated with human activities, climate conditions and rice variety. Specifically, N supply rate, temperature and precipitation were the foremost determinants of rice NUtE, and NUtE responses to climatic change differed among rice varieties. Further prediction highlighted the improved rice NUtE with the increasing latitude or longitude. The indica and hybrid rice exhibited higher NUtE in low-latitude regions compared to japonica and inbred rice, respectively. Collectively, our results evaluated the primary drivers of rice NUtE variations and predicted the geographical responses of NUtE in different varieties. Linking the global variations in rice NUtE with environmental factors and geographical adaptability provides valuable agronomic and ecological insights into the regulation of rice NUtE.

opencc-by-4.0Dec 2021View details →

Multi-Scale Representation Learning on Proteins

Protein-ligand structures from PDBBind (v2019), and protein structures from the enzyme dataset as described in the paper: "Multi-Scale Representation Learning on Proteins" with associated code at https://github.com/vsomnath/holoprot. Paper Abstract Proteins are fundamental biological entities mediating key roles in cellular function and disease. This paper introduces a multi-scale graph construction of a protein – HoloProt – connecting surface to structure and sequence. The surface captures coarser details of the protein, while sequence as primary component and structure – comprising secondary and tertiary components – capture finer details. Our graph encoder then learns a multi-scale representation by allowing each level to integrate the encoding from level(s) below with the graph at that level. We test the learned representation on different tasks, (i.) ligand binding affinity (regression), and (ii.) protein function prediction (classification). On the regression task, contrary to previous methods, our model performs consistently and reliably across different dataset splits, outperforming all baselines on most splits. On the classification task, it achieves a performance close to the top-performing model while using 10x fewer parameters. To improve the memory efficiency of our construction, we segment the multiplex protein surface manifold into molecular superpixels and substitute the surface with these superpixels at little to no performance loss.

opencc-by-4.0Jul 2023View details →

1D-1V Vlasov-Poisson Simulations of Mutual Impedance Experiments in the presence of small-scale and large-scale plasma inhomogeneities - PART 3

PART 1 IS FOUND AT  https://doi.org/10.5281/zenodo.8118023 PART 2 IS FOUND AT  https://doi.org/10.5281/zenodo.8119090   ===================================================================================================== Author        :     L. Bucciantini Date         :    05/07/2023 Laboratory    :    CNRS-LPC2E, Orléans (France) ===================================================================================================== Dear reader, we thank you for your interest in our dataset. In this document, we describe what you will find in it. In case you need help with using the dataset, or if you are interested in mutual impedance experiments, do not hesitate to contact our team in Orléans (pierre.henri@cnrs-orleans.fr, pierre.henri@oca.eu) ===================================================================================================== Topic: This dataset contains the outputs of numerical simulations performed to assess the impact of plasma inhomogeneities on the diagnostic performance of mutual impedance experiments. Numerical model: The outputs are obtained from a numerical model based on the solution of the 1D-1V Vlasov-Poisson system of equations. The scheme used to solve the model is the one developed by Mangeney et al. (2002),  A Numerical Scheme for the Integration of the Vlasov-Maxwell System of Equations. Journal of Computational Physics, (doi: https://doi.org/10.1006/jcph.2002.7071). The 1D-1V Vlasov-Poisson version of this model is described in Henri, et al. (2010), Vlasov-Poisson simulations of electrostatic parametric instability for localized Langmuir wave packets in the solar wind, Journal of Geophysical Research (Space Physics), 115, 6106 (2010) ----------------------------------------------------------------------------------------------------- What is inside the dataset: The dataset is composed of 7 different mutual impedance measurements, each corresponding to one directory (see below). The measurements (i.e. directory) correspond to small-scale plasma inhomogeneities at different positions with respect to the mutual impedance antennas, or to a large-scale plasma inhomogeneity. Each directory contains a number of folders. Each folder corresponds to the emission of a signal at different frequency. ----------------------------------------------------------------------------------------------------- List of directories: (Note : each directory corresponds to one mutual impedance measurement) L        :    These outputs correspond to one mutual impedance measurement in                 small antenna emission amplitude, which corresponds to a linear                 plasma response to the emission. s_xx     :    Each of these outputs corresponds to one mutual impedance measurement in correspondance of         a small-scale plasma inhomogeneity at xx Debye lengths of distance from the emitting antenna          ----------------------------------------------------------------------------------------------------- List of folders inside the directories: Folders begin with the name "000" and have increasing index. Inside the same directory, each folder represents a different simulation used to build the same mutual impedance measurement. ------------------------------------------------------------------------------------------------------ List of files inside the folders: density_e.npz        :    electron density inside the box, in function of time (tempo) density_p.npz        :    ion density inside the box, in function of time (tempo) E.npz            :    electric field in the box, in function of time (tempo) qrho.npz        :    electric potential in the box, in function of time (tempo) qrho_imposed.npz    :    electric charge imposed at the emitting antennas, in function of time (tempo) tempo.npz        :    time-vector for density, electric field, electric potential and charge vectors TEST_Luca.dat        :    parameters describing the characteristics of the simulated plasma box [ Note : the previous files can be opened as follows import numpy as np vector_file_name = np.load('file_name.npz') # Use these for the .npz files characteristics_of_the_box = np.genfromtxt('TEST_Luca.dat',skip_header=1) ] ------------------------------------------------------------------------------------------------------- Characteristics of the simulated plasma box (TEST_Luca.dat) nx        :    amount of spatial grid points xl        :    physical size of the spatial box, expressed in Debye length tt_w        :    time resolution for ion and electron density, electric field, electric potential and charge rap_m          :    ion-to-electron mass ratio R_p        :    ion-to-electron temperature ratio dt        :    time step used to evolve in time the numerical simulation emission    :    emission frequency power        :    amplitude of the electric charge imposed at the emitting antennas (Note : all parameters not listed here but present inside the TEST_Luca.dat file correspond to additional     functionalities of the model. For the use of this dataset, they can be discarded.)

opencc-by-4.0Oct 2022View details →

Leveraging IoT Data Stream for Near-Real-Time Calibration of City-Scale Microscopic Traffic Simulation

This repository includes input and output data of the methodology presented in the <a href="https://arxiv.org/abs/2210.17315">paper</a> for generating a calibrated dynamic microscopic traffic simulation. <ul> <li>The input data includes the network, initial normalized origin-destination matrix, and hourly traffic counts from stationary city sensors.</li> <li>The output is a 24-hour calibrated microscopic traffic simulation for the city of Tartu, Estonia.</li> </ul> All source codes are available at <a href="https://github.com/Khoshkhah/NRTCalib">https://github.com/Khoshkhah/NRTCalib</a>.

Fig. 6 in The coccid-tending ant genus Acropyga Roger and its obligate associated myrmecophilous scale insect genus Eumyrmococcus Silvestri new to Italy (Hymenoptera: Formicidae; Hemiptera: Xenococcidae)

Fig. 6 – Acropyga paleartica, male: head, frontal view (Scale bar: 0.5 mm).

Fig. 5 in The coccid-tending ant genus Acropyga Roger and its obligate associated myrmecophilous scale insect genus Eumyrmococcus Silvestri new to Italy (Hymenoptera: Formicidae; Hemiptera: Xenococcidae)

Fig. 5 – Acropyga paleartica, male: body, lateral view (Scale bar: 1 mm).

Fig. 3 in The coccid-tending ant genus Acropyga Roger and its obligate associated myrmecophilous scale insect genus Eumyrmococcus Silvestri new to Italy (Hymenoptera: Formicidae; Hemiptera: Xenococcidae)

Fig. 3 – Acropyga paleartica, gyne: body, lateral view (Scale bar: 1 mm).

Fig. 2 in The coccid-tending ant genus Acropyga Roger and its obligate associated myrmecophilous scale insect genus Eumyrmococcus Silvestri new to Italy (Hymenoptera: Formicidae; Hemiptera: Xenococcidae)

Fig. 2 – Acropyga paleartica, known distribution.

Fig. 1 in The coccid-tending ant genus Acropyga Roger and its obligate associated myrmecophilous scale insect genus Eumyrmococcus Silvestri new to Italy (Hymenoptera: Formicidae; Hemiptera: Xenococcidae)

Fig. 1 – An Acropyga paleartica gyne carring one Eumyrmococcus corynthiacus female.