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opencc-zeroJul 2020View details →

HADDOCK screening against the COVID-19 RNA dependent RNA polymerase (RdRp)

The novel coronavirus (SARS-CoV-2) that has emerged from Wuhan, China in December 2019 has spread to almost all countries in the world causing a dramatic number of deaths. The current absence of antiviral treatment against the SARS-CoV-2 urges the scientific community to accelerate the drug discovery research process. One way to identify potential treatments and to be able to administer it swiftly is to focus on drug repurposing studies, i.e. to investigate the SARS-CoV-2 antiviral potential of drugs that have already been approved for human use. Proteins that are crucial for the survival and replication of the virus are the most attractive targets for such studies. Here we have focused on the SARS-CoV-2 RNA dependent RNA polymerase (RdRp) that plays an essential role in the virus replication process by screening ~2000 approved drugs (and 6 experimental ones) against this particular protein. This is one part of a multi-target screen emphasising the main protease (Mrpo), the RNA-dependent-RNA-polymerase (RdRp) and human ACE2. The other datasets can found at the following locations: <ul> <li><a href="https://zenodo.org/record/3929438">Mpro: Shape-based assay</a></li> <li><a href="https://zenodo.org/record/3929446">Mpro: Pharmacophore-based assay</a></li> <li><a href="https://zenodo.org/record/3929463">ACE2</a></li> </ul> More information about this screen along with interactive visualisations of the top compounds can be found on our website <a href="https://bonvinlab.org/covid/">bonvinlab.org</a>.

opencc-by-4.0Jul 2020View details →

Extended Data: Structure-dependence of the atomic-scale mechanisms of Pt electrooxidation and dissolution

Abstract: Platinum dissolution and restructuring due to surface oxidation are primary degradation mechanisms that limit the lifetime of Pt-based electrocatalysts for electrochemical energy conversion. Here, we studied well-defined Pt(100) and Pt(111) electrode surfaces by in situ high-energy surface X-ray diffraction, on-line inductively coupled plasma mass spectrometry, and density functional theory calculations, to elucidate the atomic-scale mechanisms of these processes. The locations of the extracted Pt atoms after Pt(100) oxidation reveal distinct differences from the Pt(111) case, which explains the different surface stability. The evolution of a specific stripe oxide structure on Pt(100) produces unstable surface atoms which are prone to dissolution and restructuring, leading to one order of magnitude higher dissolution rates. Contents of this repository: 1. SXRD data: The experiments for the acquisition of the raw SXRD data were performed at the the European Synchrotron Radiation Facility, Grenoble, France at the beamlines ID31 and ID03. We thank H. Isern and T. Dufrane for the help during the SXRD experiments. <ul> <li>tomo_tomo.spec is the file with the X-ray diffraction metadata for the CTR scans. It is a plain text file.</li> <li>Each HESXRD dataset is saved in a folder, which denotes the potential (e.g. 1V0.zip). The png-image files are previews of the corresponding dataset. The individual raw cbf files can be opened by pyMCA or silx. From python, the images can be accessed using the fabio library.</li> <li>calibration.zip contains the pyFAI calibration files and a list with indexed Bragg reflections for the UB matrix calculation</li> <li>CTRs_parameters.zip contains the averaged CTR structure factors used for the structual analysis as well as files with the atomic coordinates of the refined structural model.</li> <li>steps.zip contains the full datasets from the potential step experiments in Fig. 1e.</li> </ul> 2. DFT: <ul> <li>CONTCARs.zip contains the atomic coordinates of the optimized computational models.</li> </ul>

opencc-zeroJul 2020View details →

Spectral data and R modeling code from: Polarized light sensitivity in Pieris rapae is dependent on both color and intensity

This dataset provides supplementary spectral data and the R code underlying the spectral sensitivy moding of female Pieris rapae photoreceptors used in the manuscript "Polarized light sensitivity in Pieris rapae is dependent on both color and intensity".

opencc-zeroJul 2020View details →

Data from: Whole-organism behavioral profiling reveals a role for dopamine in state-dependent motor program coupling in C. elegans.

Animal behaviors are commonly organized into long-lasting states that coordinately impact the generation of diverse motor outputs such as feeding, locomotion, and grooming. However, the neural mechanisms that coordinate these diverse motor programs remain poorly understood. Here, we examine how the distinct motor programs of the nematode C. elegans are coupled together across behavioral states. We describe a new imaging platform that permits automated, simultaneous quantification of each of the main C. elegans motor programs over hours or days. Analysis of these whole-organism behavioral profiles shows that the motor programs coordinately change as animals switch behavioral states. Utilizing genetics, optogenetics, and calcium imaging, we identify a new role for dopamine in coupling locomotion and egg-laying together across states. These results provide new insights into how the diverse motor programs throughout an organism are coordinated and suggest that neuromodulators like dopamine can couple motor circuits together in a state-dependent manner.

opencc-by-4.0Jul 2020View details →

Physics in Precision-Dependent Normal Neighborhoods

This dataset is associated with "Physics in Precision-Dependent Normal Neighborhoods", Bruno Hoegl, Stefan Hofmann, and Maximilian Koegler (2020) [https://arxiv.org/abs/2007.15717] It includes mathematica 11.0.1.0 notebooks to allow for the replication of figures 2 and 3 as well as equations (26), (29), and (31).

Data from: Are skyline plot-based demographic estimates overly dependent on smoothing prior assumptions?

In Bayesian phylogenetics, the coalescent process provides an informative framework for inferring changes in the effective size of a population from a phylogeny (or tree) of sequences sampled from that population. Popular coalescent inference approaches such as the Bayesian Skyline Plot, Skyride and Skygrid all model these population size changes with a discontinuous, piecewise-constant function but then apply a smoothing prior to ensure that their posterior population size estimates transition gradually with time. These prior distributions implicitly encode extra population size information that is not available from the observed coalescent data i.e. the tree. Here we present a novel statistic, Ω, to quantify and disaggregate the relative contributions of the coalescent data and prior assumptions to the resulting posterior estimate precision. Our statistic also measures the additional mutual information introduced by such priors. Using Ω we show that, because it is surprisingly easy to over-parametrise piecewise-constant population models, common smoothing priors can lead to overconfident and potentially misleading inference, even under robust experimental designs. We propose Ω as a useful tool for detecting when posterior estimate precision is overly reliant on prior choices.

Data from: Age-dependent changes in infidelity in Seychelles warblers

Extra-pair paternity (EPP) is often linked to male age in socially monogamous vertebrates, i.e. older males are more likely to gain EPP and less likely to be cuckolded. However, whether this occurs because males improve at gaining paternity as they grow older, or because 'higher quality' males that live longer are preferred by females, has rarely been tested, despite being central to our understanding of the evolutionary drivers of female infidelity. Moreover, how extra-pair reproduction changes with age within females has received even less attention. Using 18 years of longitudinal data from an individually-marked population of Seychelles warblers (Acrocephalus sechellensis), we found considerable within-individual changes in extra-pair reproduction in both sexes, i.e. an early-life increase and a late-life decline. Furthermore, males were cuckolded less as they aged. Our results indicate that in this species age-related patterns of extra-pair reproduction are determined by within-individual changes with age, rather than differences among individuals in longevity. These results challenge the hypothesis – based on longevity reflecting intrinsic quality – that the association between male age and EPP is due to females seeking high quality paternal genes for offspring. Importantly, EPP accounted for up to half of male reproductive success, emphasising the male fitness benefits of this reproductive strategy. Finally, the occurrence of post-peak declines in extra-pair reproduction provides explicit evidence of senescence in infidelity in both males and females.

Size-dependent predation and intraspecific inhibition of an estuarine snail feeding on oysters

Predator outbreaks have increased in the past two decades in many ecosystems and are predicted to become more common with climate change. During these outbreaks, predator densities increase rapidly, and can cause large reductions in prey populations or shifts in prey size structure. However, unexpected interactions may occur at high predator densities, necessitating a mechanistic understanding of how increased predator density affects predator-prey dynamics. In the northern Gulf of Mexico, outbreaks of southern oyster drill (Stramonita haemastoma, Linnaeus, 1767) occur during high salinity events, and can greatly reduce eastern oyster (Crassostrea virginica, Gmelin, 1791) populations. A large outbreak of drills occurred from 2013—2015 in Apalachicola Bay, FL which corresponded with an oyster fishery collapse in that bay. To improve our mechanistic understanding of predation during such a high-density outbreak, laboratory experiments based on field observations were used to quantify the prey size selection by drills and the drill functional response, as a function of drill abundance. Drills fed on medium-sized oysters (50-75 mm) more often than small and larger-sized oysters, and often formed aggregations during feeding events. However, despite this aggregative response, there was a negative relationship between per capita feeding rates and drill abundance. Indeed, the Crowley-Martin functional response model had the most parsimonious fit to the data, suggesting that predator-predator inhibition reduced attack rates and increased handling times. Due to an increase in regional drought conditions and water usage in the southeastern United States, drill outbreaks will likely increase in frequency and duration. A greater understanding of how predation rates change with predator densities during outbreaks will improve predictions of oyster mortality, and strengthen the scientific framework for oyster fishery decisions.

opencc-by-4.0Aug 2020View details →

Density-dependent natural selection mediates harvest-induced trait changes

Rapid life-history changes caused by size-selective harvesting are often interpreted as a response to direct harvest selection against a large body size. However, similar trait changes may result from a harvest-induced relaxation of natural selection for a large body size via density-dependent selection. Here, we show evidence of such density-dependent selection favouring large-bodied individuals at high population densities, in replicated pond populations of medaka fish. Harvesting, in contrast, selected medaka directly against a large body size and, in parallel, decreased medaka population densities. Five years of harvesting were enough for harvested and unharvested medaka populations to inherit the classically-predicted trait differences, whereby harvested medaka grew slower and matured earlier than unharvested medaka. We demonstrate that this life-history divergence was not driven by direct harvest selection for a smaller body size in harvested populations, but by density-dependent natural selection for a larger body size in unharvested populations.

An age-dependent ovulatory strategy explains the evolution of dizygotic twinning in humans

Dizygotic twinning, the simultaneous birth of siblings when multiple ova are released, is an evolutionary paradox. Twin bearing mothers often have elevated fitness1-5; but despite twinning being heritable6, twin births only occur at low frequencies in human populations7. We resolve this paradox by showing that twinning and non-twinning are not competing strategies, instead dizygotic twinning is the outcome of an adaptive conditional ovulatory strategy of switching from single to double ovulation with increasing age. This conditional strategy when coupled with the well-known decline in fertility as women age, maximizes reproductive success and explains the increase and subsequent decrease in twinning rate with maternal age that is observed across human populations8-10. We show that the most successful ovulatory strategy would be to always double ovulate as an insurance against early fetal loss, but to never bear twins. This finding supports the hypothesis that twinning is a byproduct of selection for double ovulation rather than twinning.

Demographic analysis of invasible habitat fraction identifies context-dependent roles of resource availability and biotic resistance in determining invasion success

Theories of plant invasions predict that plant communities should be more easily invaded when resources increase and/or competition decreases. We tested this with an experimentally introduced plant population by manipulating precipitation and resident community biomass. We used a spatially-explicit demographic approach to develop a new population-level metric of invasibility that quantifies the invasible habitat fraction (IHF) across the landscape. The existing community was essentially uninvasible (median IHF ≈ 0%), but experimental manipulations greatly increased the range of outcomes, with maximum observed IHF values over 50%. However, changes in invasibility were often context-dependent, resulting in some outcomes that aligned with existing theory, and others that were not readily predicted. Moreover, variation in invasibility was often driven by specific sets of invader demographic vital rates. Removing competitors revealed the capacity for strong biotic resistance, but this interacted with precipitation such that little biotic resistance was detected under drought conditions. Adding precipitation typically had little positive effect on invasibility, and moderate drought relief led to relatively high invasibility. However, the latter was driven to a large extent by interactions with mammal herbivory that otherwise inhibited invasion in one year. Synthesis. Our findings show that interactions between abiotic and biotic factors, as well as legacy effects, can strongly mediate invasibility. This study also highlights the importance of incorporating spatial heterogeneity into population-level assessments of invasion, as initial population declines do not necessarily indicate resistance to invasion.

Intersexual differences in density-dependent dispersal and their evolutionary drivers

Dispersal is well recognised as a major driver of evolutionary processes in local populations. Nevertheless, dispersal abilities should also be perceived as a life history trait, being subject to evolutionary changes in response to various drivers. Empirical studies investigating these drivers rarely consider that they may influence male and female dispersal differently. The purpose of our study was to document intersexual differences in density-dependent emigration from local habitat patches. As a model system we used a metapopulation of Maculinea (Phengaris) teleius butterfly, in which densities of both sexes vary greatly throughout the flying season. Following intensive mark-release-recapture surveys, the parameters and predictors of dispersal were analysed with the Virtual Migration model and the multi-state recapture model. The emigration rate in males was substantially higher in the early season, especially at smaller habitat patches. With the proportion of females increasing with the season progression, males became reluctant to emigrate from their natal patches. In turn, higher female emigration in the later part of the season was most strongly associated with female tendency to reduce intraspecific competition experienced by their offspring. Our findings provide evidence for the impact of reproductive strategies on dispersal in both sexes. The difference in reproductive strategies of males and females explain sex-biased dispersal in different parts of the season, which carries important implications for metapopulation functioning.

opencc-by-4.0Aug 2020View details →

How do auroral substorms depend on Earth's dipole magnetic moment?

This contains the original simulation data used by the paper 'How do auroral substorms depend on Earth's dipole magnetic moment?', which will appear in Journal of Geophysical Research - Space Physics. The data were obtained by the global MHD simulation (REPPU) with Level 6.  Each VTK file (Visualization Tookkit format) contains the physical variables in the magnetosphere at the expansion onset for Run 1, 2, 3, 4, and 5, including <ul> <li>plasma pressure (P in nPa),</li> <li>velocity vector (V in km/s),</li> <li>current density vector (J in nA/m2),</li> <li>magnetic field vector (B in nT).</li> </ul> The VTK file can be opened by the software VisIT, or paraview.  Each sav file (IDL saveset format) contains the physical variables in the ionosphere at the expansion onset for Run 1, 2, 3, 4, and 5, including <ul> <li>time ('tim' in minutes),</li> <li>magnetic latitude ('lat' in deg),</li> <li>magnetic local time ('mlt' in hour),</li> <li>field-aligned current ('fac' in A/m2),</li> <li>electric potential ('pot' in V),</li> <li>ionospheric conductivities ('s11', 's12', and 's22' in S).</li> </ul> The sav file can be opened by IDL. By typing  IDL> restore,'tablei-run1.sav' you can load the file to the memory of IDL. Type 'help' to confirm the variables that are loaded.

Data from: Functional richness shows spatial scale dependency in Pheidole ant assemblages from Neotropical savannas

There is a growing recognition that spatial scale is important for understanding ecological processes shaping community membership, but empirical evidence on this topic is still scarce. Ecological processes such as environmental filtering can decrease functional differences among species and promote functional clustering of species assemblages, whereas interspecific competition can do the opposite. These different ecological processes are expected to take place at different spatial scales, with competition being more likely at finer scales and environmental filtering most likely at coarser scales. We used a comprehensive dataset on species assemblages of a dominant ant genus, Pheidole, in the Cerrado (savanna) biodiversity hotspot to ask how functional richness relate to species richness gradients and whether such relationships vary across spatial scales. Functional richness of Pheidole assemblages decreased with increasing species richness, but such relationship did not vary across different spatial scales. Species were more functionally dissimilar at finer spatial scales, and functional richness increased less than expected with increasing species richness. Our results indicate a tighter packing of the functional volume as richness increases and point out to a primary role for environmental filtering in shaping membership of Pheidole assemblages in Neotropical savannas.

Data from: Genome duplication effects on functional traits and fitness are genetic context and species dependent: studies of synthetic polyploid Fragaria

PREMISE OF THE STUDY Divergence in functional traits and adaptive responses to environmental change underlies the ecological advantage of polyploid plants in the wild. While established polyploids may benefit from combined outcomes of genome doubling, hybridization and polyploidy-enabled adaptive evolution, it remains less clear whether genome doubling alone can drive ecological divergence or whether the outcome is genetically variable.METHODS Using synthetic, colchicine-induced, autotetraploid (4x) plants derived from self-pollinated diploid (2x) seeds, and their colchicine-treated but unconverted diploid (2x.nc) full sibs from two diploid wild strawberry taxa (Fragaria vesca ssp. vesca and F. vesca ssp. bracteata), we examined the effects of genome doubling on functional traits, heat stress tolerance and fitness components across taxa and maternal families (i.e. genetic families) within taxa.KEY RESULTS Comparisons between 2x and 2x.nc plants indicated a negligible effect of colchicine treatment on functional traits. Genome doubling increased stomatal length, and decreased stomatal density, specific leaf area and leaf vein density, recapitulating patterns observed in wild polyploid Fragaria. Trichome density, heat stress tolerance and relative growth rate were not significantly affected by genome doubling. Although a reduction in clonal reproduction was observed in response to genome doubling, this effect was strongly genetic family dependent.CONCLUSIONS The results suggest that genome doubling during incipient speciation alone can generate ecological divergence and variation among genetic lineages. This response potentially allows for rapid short-term evolutionary adaptation and fuels genomic diversity and independent origins of polyploidy.

Female fiddler crabs, Austruca lactea (Decapoda: Ocypodidae), adjust their rate of mate sampling based on remaining days until oviposition under a size-dependent temperature constraint

The rate of mate sampling is one of the critical components associated with the sampling costs in female mate choice. In ectotherms, environmental temperature generally constrains locomotion performance. In addition, females will adjust the mate sampling rate depending on their breeding schedule because of the risk of remaining unfertilized eggs or a loss of benefits related to mating, if they lost the opportunity to copulate. This study investigated how these effects influence the rate of female mate sampling in the temperate fiddler crab (Austruca lactea) in the field. The number of sampled males per searching duration formed a convex curve against environmental temperature. The optimal environmental temperature increased with the female body size. These results suggest that the mate sampling rate would be under a size-dependent temperature constraint, and sampling costs would be lower for larger females than smaller individuals under high-temperature conditions. Furthermore, when there were fewer remaining days, the mate sampling rate increased. Females would hasten the sampling rate to ensure a suitable burrow for breeding. Mate sampling rate in female A. lactea is therefore associated with environmental temperature, female body size, and remaining days until oviposition.

opencc-by-4.0Aug 2020View details →

DATA & CODE for "Substrate-dependent fish have shifted less in distribution under climate change"

Authors: Sarah M. Roberts*1, Andre M. Boustany2, Patrick N. Halpin1 Author affiliations: *1Marine Geospatial Ecology Lab, Nicholas School of the Environment and Earth Sciences, Duke University, Durham, NC 27708, US 2 Monterey Bay Aquarium, 886 Cannery Row, Monterey, CA 93940, USA This dataset and code run the necessary methods for the manuscript titled: "Substrate-dependent fish have shifted less in distribution under climate change. Substrate-dependent fish have shifted less in distribution under climate change" published in Nature Communications Biology. In order to run the code, you need to request data from <a href="https://oceanadapt.rutgers.edu/">https://oceanadapt.rutgers.edu/</a>. The download is free, I just don't have permission to publish their data. Software needed is Rstudio and R. This is the updated and current version.

opencc-by-4.0Sep 2020View details →

Data for GRL manuscript "Vertical Coordinate and Resolution Dependence of the Second Moment Turbulent Closure Models"

The zipped directory contains data used for analysis and figures in the GRL manuscript "Vertical Coordinate and Resolution Dependence of the Second Moment Turbulent Closure Models" ### OSP observations: Air Temperature: airt50n145w_hr.ascii    Ocean Temperature: t50n145w_hr.ascii  Ocean Salinity: s50n145w_hr.ascii Total Heat Flux:  heatflux_papa.dat 10m Wind Speed: wspd_papa.dat u and v components of Stokes drift velocity hourly time series given on vertical grid vertical_grid_128: uvstk_papa.dat ### NCOM simulation results out_Model_LayerGrid.dat Model:   h15 - use harcourt (2015)     kc04 - use Kantha & Clayson (2004)   myl2p5 - use Mellor & Yamda (1982) level 2.5 Layer:   030, 040, 050, 080, 100 Grid:   s - uniform stretched grid   u - uniform grid   y - mixed layer enhanced grid The following variables are provied in all out_*.dat files as given in their headers  depth (m) tke (cm2/s2) dis (cm2/s3) tl (cm)  zkm (cm2/s)  zkh (cm2/s) T (C) S (psu) pd (kg/m3) z-mid (m) ### LES output Eddy viscosity computed using LES model   LES simulation with all foring - Km_les_AllForcing.dat   LES simulation without Stokes drift - Km_les_NoStk.dat   LES simulation without Heat Flux - Km_les_NoHF.dat

opencc-zeroOct 2020View details →

Data from: Ethanol abolishes vigilance-dependent astroglia network activation in mice by inhibiting norepinephrine release

This collection of data sets was obtained during a study of the effect of acute ethanol intoxication on vigilance-dependent astroglia network activation in mice. The main findings have been that ethanol inhibits astroglia activation by inhibiting vigilance-dependent norepinephrine release. This leads to a failure of activation of alpha1A-adrenergic receptors on astroglia. Further, this study has revealed that ethanol inhibition of cerebellar Bergmann glia Ca2+ activation does not account for ataxic motor behavior, but may rather contribute to cognitive deficits.

Grazing and climate change have site-dependent interactive effects on vegetation in Asian montane rangelands

1. Climate over Asian montane rangelands is changing faster than the global average, posing serious threats to the future of the region's livestock-based economies and cultures. Effects of climate change on rangeland vegetation likely depend on grazing by herbivores but the potential responses of vegetation to such changes in climate and grazing regimes remains unclear. 2. We examined vegetation responses to experimentally simulated climate change (warming, drought and increased rainfall) and grazing (clipping vegetation) between 2015-2018 at two mountain rangeland sites: Spiti valley, in the Indian Trans-Himalaya and Tost, in the Gobi-Altai Mountains in Mongolia. 3. Clipping and climate change manipulations interactively reduced vegetation cover and biomass but did not affect species richness. Treatment effects and their interactions varied between sites. In ungrazed plots, vegetation cover and biomass declined sharply in response to warming (18-35%) and drought (20-50%) at the two sites, and, surprisingly also declined slightly in response to increased rainfall (20%) at Tost. While the effects of climate treatments were largely similar in the grazed and ungrazed plots in Tost, they were larger in the ungrazed plots in Spiti. The decline in vegetation cover was driven by a decline in the cover of both forbs and grasses. 4. In combination, grazing and warming (Tost) or drought (Spiti) had sub-additive effects, i.e., the decrease in vegetation cover in response to grazing and warming/drought was less than the sum of their independent effects but greater than the effect of either manipulation alone. Of the two, warming had a greater effect than drought at the more arid site (Tost), while drought had a larger effect at the more mesic site (Spiti). Synthesis and applications. Our findings show that future changes in climate, including just over 1oC of warming, could undermine the sustainability of pastoral economies and the persistence of wildlife across Asian montane rangelands. Further, grazing by herbivores will play an important role in mediating rangeland responses to climate change; thus, pasture management in concert with local pastoralists will be crucial in mitigating the adverse effects of climate change on rangelands, pastoral livelihoods and wildlife populations.