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opencc-zeroDec 2021View details →

Eavesdropping micropredators as dynamic limiters of sexual signal elaboration and intrasexual competition

To thoroughly understand the drivers of dynamic signal elaboration requires assessing the direct and indirect effects of naturally interacting factors. Here, we use structural equation modeling (SEM) to test multivariate data from in situ observations of sexual signal production against a model of causal processes hypothesized to drive signal elaboration. We assess direct and indirect effects, and relative impacts, of male-male competition and attacks by eavesdropping frog-biting midges (Diptera: Corethrellidae) on call elaboration of male túngara frogs (Engystomops pustulosus). We find that the intensity of attacks by these micropredator flies drives the extent to which frogs elaborate their calls, likely due to a temporal trade-off between signaling and anti-micropredator defense. Micropredator attacks appear to dynamically limit a male's call rate and complexity and consequently dampen the effects of intrasexual competition. In accounting for naturally interacting drivers of signal elaboration, this study presents a counterpoint to the mechanisms traditionally thought to drive sexual selection in this system. Moreover, the results shed light on the relatively unexamined and potentially influential role of eavesdropping micropredators in the evolution of sexual communication systems.

opencc-by-4.0Jan 2021View details →

Hybridization dynamics and extensive introgression in the Daphnia longispina species complex: new insights from a high-quality Daphnia galeata reference genome

Supplementary data for the Genome Biology and Evolution paper <a href="http://dx.doi.org/10.1093/gbe/evab267">10.1093/gbe/evab267</a>

opencc-zeroDec 2021View details →

Integrating dynamic processes into waterfowl conservation prioritization tools

Aim: Traditional approaches for including species' distributions in conservation planning have presented them as long-term averages of variation. Like these approaches, the main waterfowl conservation targeting tool in the United States Prairie Pothole Region (US PPR) is based primarily on long-term averaged distributions of breeding pairs. While this tool has supported valuable conservation, it does not explicitly consider spatiotemporal changes in spring wetland availability and does not assess wetland availability during the brood rearing period. We sought to develop a modeling approach and targeting tool that incorporated these types of dynamics for breeding waterfowl pairs and broods. This goal also presented an opportunity for us to compare predictions from a traditional targeting tool based on long-term averages to predictions from spatiotemporal models. Such a comparison facilitated tests of the underlying assumption that this traditional targeting tool could provide an effective surrogate measure for conservation objectives such as brood abundance and climate refugia. Location: US PPR Methods: We developed spatiotemporal models of waterfowl pair and brood abundance within the PPR of the US. We compared the distributions predicted by these models and assessed similarity with the averaged pair data that is used to develop the current waterfowl targeting tool. Results: Results demonstrated low similarity and correlation between the averaged pair data and spatiotemporal brood and pair models. The spatiotemporal pair model distributions served as better surrogates for brood abundance than the averaged pair data. Main conclusions: Our study underscored the contributions that the current targeting tool has made to waterfowl conservation but also suggested that conservation plans in the region would benefit from the consideration of inter- and intra-annual dynamics. We suggested that using only the averaged pair data and derived products might result in the omission of 46-98% of important pair and brood habitat, respectively, from conservation plans.

Role of internal loop dynamics in antibiotic permeability of outer membrane porins

Representative structures for Markov State models for wild type and mutants of OmpF "Coupling of internal loop dynamics and antibiotic permeation in outer membrane porins"

Raw data for "Condensates in RNA repeat sequences are heterogeneously organized and exhibit reptation dynamics"

This is the raw data for the paper "Condensates in RNA repeat sequences are heterogeneously organized and exhibit reptation dynamics". There are 5 directories. Three correspond to the CAG repeats with different length (20, 31 and 47). The "scramble47" directory stores data for the scrambled sequence. "Electrostatics" has data for the electrostatics run (see details in Extended Data Fig. 9). Each directory of CAG contains multiple sub-directories corresponding to different concentrations.

opencc-by-4.0Oct 2021View details →

Dynamics in a stellar convective layer and at its boundary: Comparison of five 3D hydrodynamics codes

Supplementary materials for the paper "Dynamics in a stellar convective layer and at its boundary: Comparison of five 3D hydrodynamics codes". The data contained in the .tar.gz archives can be read and visualised using the Jupyter notebooks available on the CoCoPy repository (<a href="https://github.com/robert-andrassy/CoCoPy">https://github.com/robert-andrassy/CoCoPy</a>) and on the CoCo Hub (<a href="https://www.ppmstar.org/coco">https://www.ppmstar.org/coco</a>). The four parts of the archive 2D-slices.tar.gz need to be concatenated using the standard Unix tool "cat" before decompression. Two minor bugs affecting the 1D profiles are corrected in this version. Everything else is the same as in Version 1.

opencc-zeroDec 2021View details →

Data from: Emerging experience-dependent dynamics in primary somatosensory cortex reflect behavioral adaptation

Behavioral experience and flexibility are crucial for survival in a constantly changing environment. Despite evolutionary pressures to develop adaptive behavioral strategies in a dynamically changing sensory landscape, the underlying neural correlates have not been well explored. Here, we use genetically encoded voltage imaging to measure signals in primary somatosensory cortex (S1) during sensory learning and behavioral adaptation in the mouse. In response to changing stimulus statistics, mice adopt a strategy that modifies their detection behavior in a context dependent manner as to maintain reward expectation. Surprisingly, neuronal activity in S1 shifts from simply representing stimulus properties to transducing signals necessary for adaptive behavior in an experience dependent manner. Our results suggest that neuronal signals in S1 are part of an adaptive framework that facilitates flexible behavior as individuals gain experience, which could be part of a general scheme that dynamically distributes the neural correlates of behavior during learning.

Self-Limiting Earthquake Dynamics and Spatio-Temporal Clustering of Seismicity Enabled by Off-Fault Plasticity

Earthquakes are among nature’s deadliest and costliest hazards. Physics-based simulations are essential for overcoming the lack of data and elucidating the complex patterns of earthquakes. Enabled by a novel numerical scheme, this work discovers a new mechanism for regulating earthquake dynamics that emerges due to the co-evolution of fault slip and fault zone plasticity. It enables transition from periodic events to fully irregular sequences of earthquakes. The impact of plasticity on earthquake source characteristics goes beyond its limited contribution to the overall energy budget, emphasized in earlier studies, to underscore its crucial role on the redistribution of stresses that self-limits earthquake growth and leads to clustering of seismicity. This work highlights the need for characterizing the fault zone mechanical response beyond their elastic properties to better inform seismic hazard models.

Comparative analysis of patient-specific aortic dissections through computational fluid dynamics suggests increased likelihood of degeneration in partially thrombosed aorta

Aortic dissection is a life-threatening cardiovascular disease associated with high rates of morbidity and mortality, especially in medically under-served communities. It compromises the hemodynamics of the arteries that originate from the aorta, and its outcomes include visceral ischemia and aortic rupture in the acute phase and aneurysmatic degeneration in the chronic phase. Understanding patients’ blood flow patterns is pivotal for non-invasive evidence-based treatment as they greatly influence both the disease onset and its outcome. In this paper, we combine diagnostic imaging techniques and computational fluid dynamics to analyze the flow patterns of three aorta dissections (fully perfused, partially thrombosed, and fully thrombosed), and compare them to a healthy aorta. Besides flow kinematics, we focus on time averaged wall shear stress and oscillatory shear index that are recognized risk factors for aneurysm and rupture. Our analysis shows that partially thrombosed dissection is the most prone to false lumen degeneration. In all dissections, the arteries connected to the false lumen are generally poorly supplied with blood. Further, both true and false lumens present higher turbulence levels than the healthy aorta, and critical stagnation points. Mesh sensitivity and a thorough comparison against literature data together support the methodology robustness.

Community patch‐dynamics governs direct and indirect nutrient recycling by aggregated animals across spatial scales

Animals can have pervasive effects on ecosystems as they modify their biogeochemical and physical environments. In particular, when animals occur in high densities these effects can result in dramatic changes in the physical environment and biogeochemical hotspots or hot moments. While most research to date has focused on the direct role of animals in biogeochemical cycles, few have examined how animals indirectly influence biogeochemical cycles across scales. Freshwater mussels occur as spatially heterogeneous, dense and species-rich aggregations in many river ecosystems worldwide. Here we examined how mussel communities (1) directly influence the flux of particulate and dissolved nutrients and (2) indirectly effect the flux of N2 production, via denitrification, across a gradient of mussel biomass and differences in community composition at the patch- (0.25 m2) and stream reach-scales (60-80 m). We combined measurements of ammonia (N) and soluble reactive phosphorous (P) excretion and C, N, and P biodeposition rates for ten species with biomass and distribution estimates for seven mixed-species aggregations to quantify direct mussel contributions to biogeochemical cycling and the spatial heterogeneity of their impact. Additionally, we sampled sediments at a fine spatial scale to determine how mussel biomass and richness influence potential denitrification (indirect flux) rates at the patch- and reach-scales. We predicted that increasing mussel biomass would lead to greater direct and indirect fluxes of nutrients, manifesting in heterogeneous nutrient redistribution within and among stream reaches. We also predicted that variation in community composition would result in differential nutrient excretion and egestion stoichiometries. Our results indicate that mussel aggregations directly influence soluble and particulate nutrient fluxes with community composition, particularly phylogenetic tribe composition, controlling the stoichiometry. Mussel aggregations also indirectly influenced nutrient fluxes as greater mussel biomass and species richness resulted in higher denitrification rates as mediated by their interactions with the sediments and enhancement of nutrient availability. Our results underscore the importance of patchy communities in acting as biogeochemical control points.

Artificial size selection experiment reveals telomere length dynamics and fitness consequences in a wild passerine

Telomere dynamics could underlie life-history trade-offs among growth, size, and longevity, but our ability to quantify such processes in natural, unmanipulated populations is limited. We investigated how 4 years of artificial selection for either larger or smaller tarsus length, a proxy for body size, affected early-life telomere length (TL) and several components of fitness in two insular populations of wild house sparrows over a study period of 11 years. The artificial selection was expected to shift the populations away from their optimal body size and increase the phenotypic variance in body size. Artificial selection for larger individuals caused TL to decrease, but there was little evidence that TL increased when selecting for smaller individuals. There was a negative correlation between nestling TL and tarsus length under both selection regimes. Males had longer telomeres than females and there was a negative effect of harsh weather on TL. We then investigated whether changes in TL might underpin fitness effects due to the deviation from the optimal body size. Mortality analyses indicated disruptive selection on TL because both short and long early-life telomeres tended to be associated with the lowest mortality rates. In addition, there was a tendency for a negative association between TL and annual reproductive success, but only in the population where body size was increased experimentally. Our results suggest that natural selection for optimal body size in the wild may be associated with changes in TL during growth, which is known to be linked to longevity in some bird species.

Tree dynamic response and survival in a category-5 tropical cyclone: The case of super typhoon Trami

In the future with climate change, we expect more forest and tree damage due to the increasing strength and changing trajectories of tropical cyclones (TCs). However, to date, we have limited information to estimate likely damage levels, and nobody has ever measured exactly how forest trees behave mechanically during a TC. In 2018, a category-5 TC destroyed trees in our ongoing research plots, in which we were measuring tree movement and wind speed in two different tree spacing plots. We found damaged trees in only the wider spaced plot. Here, we present how trees dynamically respond to strong winds during a TC. Sustained strong winds obviously trigger the damage to trees and forests but inter-tree spacing is also a key factor because the level of support from neighboring trees modifies the effective "stiffness" against the wind both at the single tree and whole forest stand level.

Data associated to the article "Effects of fluoride salt addition to the physico-chemical properties of the MgCl2-NaCl-KCl heat transfer fluid : a molecular dynamics study"

Contains input file and data used to generate the figures of the article: Effects of fluoride salt addition to the physico-chemical properties of the MgCl2-NaCl-KCl heat transfer fluid : a molecular dynamics study Weiguang Zhou, Yanping Zhang, Mathieu Salanne https://chemrxiv.org/engage/chemrxiv/article-details/618e903a2bf8a950c7d98e5d The files data.inpt and runtime.inpt are used to simulate the system using the software MetalWalls The files MgNaKCl.txt, MgNaKClF01.txt, MgNaKClF05.txt, MgNaKClF10.txt, MgNaKClF20.txt contain the computed densities, viscosities and thermal conductivities at various temperatures for several compositions (provided in the header of the files)

Frequency multiplication by collective nanoscale spin wave dynamics

This dataset contains all primary data used in the manuscript.

Direct observation of a dynamical glass transition in a nanomagnetic artificial Hopfield network

Source files used to produce the publication "Direct observation of a dynamical glass transition in a nanomagnetic artificial Hopfield network."

Supplementary Movies: "Probing the dynamics of Streptococcus pyogenes Cas9 endonuclease bound to sgRNA complex using hydrogen-deuterium exchange mass spectrometry"

Movies related to the article "Probing the dynamics of Streptococcus pyogenes Cas9 endonuclease bound to sgRNA complex using hydrogen-deuterium exchange mass spectrometry" in the International Journal of Molecular Science. "MD_Movie_Cas9_sgRNA_DNA" is the video of SpCas9-sgRNA-DNA complex behavior during 50 ns molecular dynamics simulation. In this movie, SpCas9 protein domains are shown in the following colors: REC lobe (green), CTD (blue), RuvC (pink), L-I-II (yellow), Arg (violet), and HNH (orange). RNA presented in cyan, and DNA -in dark blue. Movies "SpCas9_HeatMap" and "SpCas9-sgRNA_HeatMap" show the hydrogen exchange levels superimposed onto the protein structure obtained from MD trajectories. Relative uptake level presented at the time points of 10 s, 30 s, 1 min, 2 min, 5 min, 10 min, 30 min, 60 min, 120 min, 240 min, 360 min, and 480 min. The exchange scale is shown in a rainbow color scheme, where blue corresponds to the minimum uptake, while red corresponds to the highest observed uptake.

A patch-dynamic metacommunity perspective on the persistence of mutualistic and antagonistic bipartite networks

The structure of interactions between species within a community plays a key role in maintaining biodiversity. Previous studies have found that the effects of these structures might substantially differ depending on interaction type, for example, a highly connected and nested architecture stabilizes mutualistic communities, while the stability of antagonistic communities is enhanced in modular and weakly connected structures. Here we show that, when network dynamics are modelled using a patch-dynamic metacommunity framework, the qualitative differences between antagonistic and mutualistic systems disappear, with nestedness and modularity interacting to promote metacommunity persistence. However, the interactive effects are significantly weaker in antagonistic metacommunities. Our model also predicts an increase in connectance, nestedness and modularity over time in both types of interaction, except in antagonistic networks where nestedness declines. At steady state, we find a strong negative correlation between nestedness and modularity in both mutualistic and antagonistic metacommunities. These predictions are consistent with the structural trends found in a large dataset of real-world antagonistic and mutualistic communities.

Water residence time and temperature drive the dynamics of dissolved organic matter in Alpine lakes in the Tibetan Plateau

This dataset contains data from an investigation into the drivers on the spatial distribution of dissolved organic matter in alpine lakes in the Tibetan Plateau described in the paper: "Du Y., Chen F., Xiao K., Song C., He H., Zhang Q., Zhou Y., Jang K.-S., Zhang Y., Xing P., Liu Z., Zhang Y. and Lu Y. 2021. Water Residence Time and Temperature Drive the Dynamics of Dissolved Organic Matter in Alpine Lakes in the Tibetan Plateau, Global Biogeochemical Cycles 35(11), e2020GB006908". The primary objectives of the study were to: (i) evaluate the spatial variability of the amount, source, and composition of DOM from alpine lakes on the Tibetan Plateau, and (ii) determine the primary environmental controls and mechanisms responsible for the spatial variability. At first, we collected 35 water samples from 25 lakes distributed in the northwestern (33.1–33.6 °N, 78.9–80.4°E), central (30.5–31.9°N, 88.3–89.4°E) and southeastern (28.6–29.1 °N, 90.4–90.8°E) regions of the plateau. We characterized water chemistry and DOM composition in these lakes by measuring dissolved organic carbon (DOC) and DOM optical properties (i.e., absorbance and fluorescence spectroscopy). DOM compositions of three lakes of different water residence times (WRTs) were further analyzed using ultrahigh-resolution molecular techniques (i.e., electrospray ionization-assisted Fourier transform-ion cyclotron resonance mass spectrometry, ESI FT-ICR MS). Secondly, we collected the indices of climatic characteristics (i.e., mean annual temperature, mean annual precipitation, and mean annual irradiation period) and lake hydrology (i.e., catchment area, lake area, mean depth and water residence time) of the sampling lakes. Thirdly, we performed statistical analysis to determine the primary environmental control and predictors of the spatial variability in lacustrine DOM on the Tibetan Plateau. The statistical analyses included non-parametric Kruskal-Wallis with Dunn post hoc test, spearman's bivariate correlations, redundancy analysis, and linear regression models. Main results of this work are that (1) DOM in Tibetan alpine lakes is mediated more by in-lake production and transformations than by catchment inputs; (2) water residence time (WRT) of lakes and mean annual temperature (MAT) accounted for 30–59% of the spatial variance of the abundance of chromophoric DOM (CDOM) and fluorescent DOM (FDOM); (3) Alpine lakes on the Tibetan Plateau would play a more active and prominent role in regional and global carbon cycles in the face of climate change.

Data from: Watershed classification predicts streamflow regime and organic carbon dynamics in the Northeast Pacific Coastal Temperate Rainforest

Watershed classification has long been a key tool in the hydrological sciences, but few studies have been extended to biogeochemistry. We developed a combined hydro-biogeochemical classification for watersheds draining to the coastal margin of the Northeast Pacific coastal temperate rainforest (1,443,062 km2), including 2,695 small coastal rivers (SCR) and 10 large continental watersheds. We used cluster analysis to group SCR watersheds into 12 types, based on watershed properties. The most important variables for distinguishing SCR watershed types were evapotranspiration, slope, snowfall, and total precipitation. We used both streamflow and dissolved organic carbon (DOC) measurements from rivers (n = 104 and 90 watersheds respectively) to validate the classification. Watershed types corresponded with broad differences in streamflow regime, mean annual runoff, DOC seasonality, and mean DOC concentration. These links between watershed type and river conditions enabled the first region-wide empirical characterization of river hydro-biogeochemistry at the land-sea margin, spanning extensive ungauged and unsampled areas. We found very high annual runoff (mean > 3000 mm, n = 10) in three watershed types totaling 59,024 km2 and ranging from heavily glacierized mountain watersheds with high flow in summer to a rain-fed mountain watershed type with high flow in fall-winter. DOC hotspots (mean > 4 mg L-1, n = 14) were found in three other watershed types (48,557 km2) with perhumid rainforest climates and less-mountainous topography. We described four patterns of DOC seasonality linked to watershed hydrology, with fall-flushing being widespread. Hydro-biogeochemical watershed classification may be useful for other complex regions with sparse observation networks.

Laboratory evidence supporting a mechanical model describing the dynamic formation of fault damage asymmetry (data)

Data from the paper: Laboratory evidence supporting a mechanical model describing the dynamic formation of fault damage asymmetry This document includes the after-analysis data, where, the variable "Log2by3M" for the relative magnitude of AE events in the catalog, "M" for the coordinates of sensors, "Mechanical" for the raw mechanical loading information before synchronization, "Notch" for the coordinate of the notch on the beam, "QuaLoc" for the source location and time.