Find research datasets worth reusing

opencc-zeroSep 2020View details →

The benefit of kidney transplantation versus remaining on the waitlist depends on patients' baseline comorbidities: a retrospective study

Background: Patients with end-stage renal disease present comorbidities that increase mortality risk on the waitlist and after kidney transplantation. This study aimed to determine the impact of baseline comorbidities on the risk of death after kidney transplantation compared to remaining on the waitlist. Methods: Records of waitlisted patients were retrospectively analyzed. Multivariable time-dependent Cox-regression model was used to determine the initial and the lowest relative hazard-risk of death (HRD) after exposure to kidney transplantation. Results: 1692 patients were included in the study. Patients without comorbidities had the relative HRD 3-fold higher, immediately after kidney transplantation, but it reduced progressively, reaching equality to waitlist at 75 days and a HRD of 0.28 thereafter (p<0.001). Patients with Diabetes and coronary artery disease had an initial relative HRD of 2.41 (p=0.009) and 2.68 (p=0.009) and matched to the waitlist at 175 and 200 days, respectively. Patients with peripheral vascular disease, had an initial relative HRD 3.6-fold in the first 240 days (p=0.008) and patients with congestive heart failure a relative HRD of 7.47 (p=0.07). Both declined rapidly, reaching equality at 110 days. Finally, all comorbidities, except cerebrovascular disease, presented lower HRD on long-term follow-up. Conclusions: This study shows that the time and the range of relative HRD between kidney transplantation and waitlist varies depending upon the patients´ baseline comorbidities.

opencc-zeroSep 2020View details →

Data and code from: Growth strategies of a model picoplankter depend on social milieu and pCO2

Aquatic microbial primary producers exist in genetically diverse populations, but are often studied as single lineages, so that interpreting single lineage studies relies critically on understanding how microbial growth differs with social milieu. The properties of lineages grown alone often fail to predict the growth of these same lineages in the presence of conspecifics, and this discrepancy points towards an opportunity to improve our understanding of how multilineage assemblages of a species are shaped. We demonstrate that different lineages of a marine picoplankter modulate their lineage growth rate in response to the presence of non-self conspecifics, even when resource competition is effectively absent. This explains why growth rates of lineages in isolation do not reliably predict their growth rates in mixed culture, or the lineage composition of assemblages. The diversity of growth strategies observed are thus consistent with lineage-specific energy-allocation that depends on social milieu. Since lineage growth is only one of many traits determining fitness in natural assemblages, we propose that in all but the poorest quality environments where allocating maximum energy to growth is the only viable strategy, we should expect intraspecific variation in growth strategies, with more strategies possible in ameliorated environments, such as high CO2 for many marine picoplankton.

opencc-zeroOct 2020View details →

Data from: Scale-dependent intraspecific competition of Taurus cedar (Cedrus libani A. Rich.) saplings in the Southern Turkey

Better understanding of the competitive interaction at the early development stages of the stand is crucial to help schedule silvicultural treatments for young stands and for the better management of the future stands. We used scale-dependent analysis to improve our understanding of sapling dynamics in the pure Taurus cedar (Cedrus libani A. Rich.) stands in Southern Turkey. Using data from nine plots established at the western Taurus Mountains; diameter, height and crown radii of saplings were compared, and spatial point pattern analyses were performed. We found significant differences for the mean diameter and height, and crown radii of saplings among the plots. Univariate pair correlation function showed that sapling pattern was regular only at small scales (r < 0.4 m) but was predominantly random. Bivariate pair correlation function revealed no evidence of spatial interaction between tall saplings and short saplings. Univariate mark correlation function revealed that strong intraspecific competition was detected at small scales (up to 0.55m). This distance is reasonable for the juvenile age tending of Taurus cedar saplings and should be under consideration during silvicultural treatments to use the site productivity more efficiently.

opencc-zeroOct 2020View details →

Data from: Landscape-dependent effects of varietal mixtures on insect pest control and implications for farmer profits

Intraspecific plant diversity can significantly impact insect herbivore populations in natural systems. Yet, its role as an insect pest control strategy in agriculture has received less attention, and little is known about which crop traits are important to herbivores in different landscape contexts. Moreover, empirical economic analyses on the cost-effectiveness of varietal mixtures is lacking. We used varietal mixtures of Brassica oleracea crops on working farms to examine how two metrics of intraspecific crop diversity—varietal richness and number of plant colors (color richness)—affect crop damage and the incidence and abundance of two insect pest species, Pieris rapae and Phyllotreta spp. We evaluated the context-dependency of varietal mixtures by sampling early and late season plantings of B. oleracea crops in farms across a gradient of landscape composition. We developed crop budgets and used a net present value analysis to assess the impact of varietal mixtures on input and labor costs, crop revenues, and profit. We found context-dependent effects of varietal mixtures on both pests. In early season plantings, color richness did not affect Phyllotreta spp. populations. However, increasing varietal richness reduced Phyllotreta spp. incidence in simple landscapes dominated by cropland, but this trend was reversed in complex landscapes dominated by natural habitats. In late season plantings, color richness reduced the incidence and abundance of P. rapae larvae, but only in complex landscapes where their populations were highest. Varietal richness had the same effect on P. rapae larvae as color richness. Unexpectedly, we consistently found lower pest pressure and reduced crop damage in simple landscapes. Although varietal mixtures did not affect crop damage, increasing color richness corresponded with increased profits, due to increased revenue and a marginal reduction in labor and input costs. We demonstrate varietal mixtures can significantly impact pest populations, and this effect can be mediated by intraspecific variation in crop color. However, the strength and direction of these effects vary by season, landscape composition, and pest species. The association between varietal color richness and profitability indicates farmers could design mixtures to enhance economic returns. We recommend additional research on the benefits of intraspecific trait variation for farmers.

openmit-licenseOct 2020View details →

Scale and Space Dependent Horizontal Eddy Diffusivity at the Global Surface Ocean

Sea surface temperature (SST) and idealized temperature tracer based estimates of horizontal diffusivity at the ocean surface. See https://doi.org/10.5281/zenodo.4126315 for the code to reproduce these estimates. There are two files which include the following KxKy_SST_MITGCM_025.nc SST based estimates are based on 35 years of satellite SST data (1982-2017) and we have divided the data in 30 chuncks, both using a 5 year and 10 year sub-sampling. The 'ens' dimension marks these chuncks whereas 'lat' and 'lon' mark the two Cartesian directions (latitude and longitude). Note that 'ens' can be also viewed as time. There are two fields 'Kx' and 'Ky' for each dataset ('SST' for the OI-SST based estimates or 'MITGCM' for the tracer simulation based estimates) and length of sub-sampling. 'Kx' is the diffusivity in 'lon' direction whereas 'Ky' is the diffusivity in 'lat' direction. Data is given at 0.25° resolution, but the effective resolution is twice that i.e. 0.5°. K_SST_MITGCM_2deg.nc Scale dependent estimate of the diffusivity magnitude i.e. \(K= \sqrt{K_xK_y}\) . As for the other data, here as well the estimates are done using 5 year and 10 year sub-sampling, and all the data is interpolated to a common 2° by 2° global grid. The coordinate 'dg' defines the scale in degrees. Note that again the effective resolution of the estimates is twice the 'dg'.

opencc-by-4.0Oct 2020View details →

Dependence of Skull Surface Wave Propagation on Coupling Methods under Bone Conduction: Support material

Objectives: This study is aimed at the quantitative investigation of skull bone surface wave propagation dependence on different coupling methods of the bone conduction hearing aid (BCHA). Design: Experiments were conducted on five Thiel embalmed whole head cadaver specimens. The electromagnetic actuators from a commercial BCHA (Baha® Cordelle and Power) were used to provide stepped sine stimulus in the range of 0.1-10 kHz. Osseous pathways were sequentially activated by a BCHA mounted on a 5-Newton steel headband on Mastoid, on a percutaneously implanted screw (Baha® Connect), and transcutaneously with a Baha® Attract at bone anchored hearing aid (BAHA) location.  Surface motion was quantified by sequentially measuring ~200 points on the skull surface via a three-dimensional laser Doppler vibrometer (3D LDV) system. Results: The stimulation area undergoes deformations at a lower frequency range than the whole head does (less than 500Hz versus more than 1 kHz). Stiffer coupling (Connect versus Headband) appears to lead to earlier onset and faster transition, with frequency, to local deformations and wave motion. Conclusion: For stimulation with the headband at the mastoid, the sound wave travelling across the head does not exactly origin from the site of  stimulation. Potentially, because the skull vibration is influenced by the dynamic mechanical properties of skull plates.

opencc-by-4.0Nov 2020View details →

EMPA, temperature-dependent Raman, FTIR data and breakdown temperature of phlogopite

This dataset contains all new data corresponding to figures in the manuscript and the supporting information, including EMPA, temperature-dependent FTIR, Raman data, and breakdown temperature from previous studies and this study.

opencc-by-4.0Nov 2020View details →

EMPA, temperature-dependent Raman, FTIR data and breakdown temperature of phlogopite

opencc-zeroDec 2019View details →

Data from: Density-dependent space use affects interpretation of camera trap detection rates

Camera-traps (CTs) are an increasingly popular tool for wildlife survey and monitoring. Estimating relative abundance in unmarked species is often done using detection rate as an index of relative abundance, which assumes a positive linear relationship with true abundance. This assumption may be violated if movement behavior varies with density, but the degree to which movement is density-dependent across taxa is unclear. The potential confounding of population-level relative abundance indices by movement depends on how regularly, and by what magnitude, movement rate and home-range size vary with density. We conducted a systematic review and meta-analysis to quantify relationships between movement rate, home range size, and density, across terrestrial mammalian taxa. We then simulated animal movements and CT sampling to test the effect of contrasting movement scenarios on CT detection rates. Overall, movement rate and home range size were negatively correlated with density and positively correlated with one another. The strength of the relationships varied significantly between taxa and populations. In simulations, detection rates were related to true abundance but underestimated change, particularly for slower moving species with small home ranges. In situations where animal space use changes markedly with density, we estimate that up to thirty percent of a true change in abundance may be missed due to the confounding effect of movement, making trend estimation more difficult. The common assumption that movement remains constant across densities is therefore violated across a wide range of mammal species. When studying unmarked species using CT detection rates, researchers and managers should consider that such indices of relative abundance reflect both density and movement. Practitioners interpreting changes in detection rates should be aware that observed differences may be biased low relative to true changes in abundance, and that further information on animal movement may be required to make robust inferences on population trends.

opencc-zeroDec 2019View details →

Dietary stress increases the total opportunity for sexual selection and modifies selection on condition-dependent traits

Although it is often expected that adverse environmental conditions depress the expression of condition-dependent sexually-selected traits, the full consequences of environmental change for the action of sexual selection, in terms of the opportunity for total sexual selection and patterns of phenotypic selection, are unknown. Here we show that dietary stress in guppies, Poecilia reticulata, reduces the expression of several sexually-selected traits and increases the opportunity for total sexual selection (standardized variance in reproductive success) in males. Furthermore, our results show that dietary stress modulates the relative importance of precopulatory (mating success) and postcopulatory (relative fertilization success) sexual selection, and that the form of multivariate sexual selection (linear vs. nonlinear) depends on dietary regime. Overall, our results are consistent with a pattern of heightened directional selection on condition-dependent sexually-selected traits under environmental stress, and underscore the importance of sexual selection in shaping adaptation in a changing world.

opencc-by-4.0Dec 2020View details →

Cerebellar Purkinje cells can differentially modulate coherence between sensory and motor cortex depending on region and behavior

Dataset belonging to "Cerebellar Purkinje cells can differentially modulate coherence between sensory and motor cortex depending on region and behavior" (https://doi.org/10.1073/pnas.2015292118)

Data from: A condition-dependent male sexual signal predicts adaptive predator-induced plasticity in offspring

The possibility that sexual selection promotes adaptive evolution in variable environments remains controversial. In particular, where the scale of environmental variation results in parents and their offspring experiencing different environmental conditions, such variation is expected to break down associations between adult sexual traits and adaptive offspring traits. However, when adaptive offspring plasticity in nonsexual traits acts as an indirect benefit of mate choice, then mate choice for males that produce more plastic offspring could promote adaptation to variable environments. This hypothesis assumes that male sexual signals predict offspring plasticity, which has rarely been tested. To test this assumption, we used spadefoot toads (Spea multiplicata) to investigate whether variation in male sexual signals predicts the expression of tadpole tail-fin plasticity in response to predation cues. Such plasticity has been shown to be adaptive in numerous amphibian taxa. We found that condition-dependent male call characteristics predicted offspring plasticity. Generally, both phenotypic plasticity and female mate choice are ubiquitous in nature; therefore, adaptive associations between male sexual signals and offspring plasticity such as the one reported here might be common.

Data from: Associations between testosterone and immune activity in alligators depend on bacteria species and temperature

Males often use elaborate sexual traits to enhance reproduction, but can experience trade-offs between investment in these traits and other physiological needs. The immunocompetence handicap hypothesis (ICHH) postulates that testosterone supports development of sexual traits while also suppressing immunity. While the ICHH implicates testosterone-mediated immunosuppression as a key mechanism of honest signaling in males, conflicting patterns across studies suggest that testosterone-immunity interactions are complex. In this study, we test the ICHH in free-ranging alligators and examine how intrinsic (steroid hormone levels) and extrinsic (temperature) factors modulate testosterone-immunity relationships. Specifically, we quantified simultaneous effects of testosterone and dehydroepiandrosterone (DHEA) on killing capacity of plasma against three bacteria species at two challenge temperatures. We found that DHEA was important in predicting the effects of testosterone on killing capacity. Further, testosterone-mediated effects were dependent on both temperature and bacteria species. Our results highlight the context dependency of interactions between testosterone and immunity, and illustrate the importance of evaluating the ICHH in natural systems to identify key intrinsic and extrinsic factors mediating testosterone-immunity trade-offs.

Which enemies mediate distance- and density-dependent mortality of tree seeds and seedlings? A meta-analysis of fungicide, insecticide, and exclosure studies

Conspecific negative distance- and density-dependence is believed to be one of the most important mechanisms controlling forest community assembly and species diversity globally. SoilPlant pathogens, and insect and mammalian herbivores, are the most common natural enemy types that have been implicated in this phenomenon, but their relative importancegeneral effects at different plant life stages isare still unclear. Here, we conduct a meta-analysis of studies that involved robust manipulative experiments, using fungicides, insecticides, and exclosures, to assess the contributions of different natural enemy types to distance- and density-dependent effects at seed and seedling stages. We found that natural enemies cause stronger distance- and density-dependent mortality caused by natural enemies was most likely at the seedling stage than the seed stage. Fungicide treatments can change significantand was greater at higher mean annual temperatures. Seedling mortality was significantly weakened when fungi were removed. By contrast, negative distance- and density-dependent mortality to non-significance at the seedling stage. Negative conspecific distance- and density-dependence is not a general pattern at the seed stage. High seed mass reduced distance- and density-dependent mortality. Seed studies excluding only large mammals found significant negative conspecific distance-dependent mortality, but exclusion of all mammals resulted in a non-significant mortality.effect of conspecifics. Our study suggests that soilplant pathogens are a major cause of distance- and density-dependent mortality at the seedling stage, althoughwhile the impacts of herbivores on seedlings have been understudied. At the seed stage, large and small mammals respectively weaken and enhance negative conspecific distance-dependent mortality. Future research should identify specific agents of mortality, investigate the interactions among different enemy types, and assess how global change drivers may affect the dynamics of natural enemies and thus influence the strength of conspecific distance- and density-dependence.

opencc-by-4.0Aug 2020View details →

Energy-dependent protein folding: modeling how a protein folding machine may work

MD trajectories of all-atom MD simulations for peptides P1-P5.

Data from: Cholesterol and ORP1L dependent clustering of dynein on endolysosmes in cells 2 revealed by super resolution microscopy

The sub-cellular positioning of endolysosomes is crucial for regulating their function. Particularly, the positioning of endolysosomes between the cell periphery versus the peri-nuclear region impacts autophagy, mTOR (mechanistic target of rapamycin) signaling and other processes. The mechanisms that regulate the positioning of endolysosomes at these two locations are still being uncovered. Here, using quantitative super-resolution microscopy in intact cells, we show that the retrograde motor dynein forms nano-clusters on endolysosomal membranes containing 1-2 dyneins, with an average of ~3 nanoclusters per endolysosome. These data suggest that a very small number of dynein motors (1-6) drive endolysosome motility inside cells. Surprisingly, dynein nano-clusters are slightly larger on peripheral endolysosomes having higher cholesterol levels compared to peri-nuclear ones. By perturbing endolysosomal membrane cholesterol levels, we show that dynein copy number within nano-clusters is influenced by the amount of endolysosomal cholesterol while the total number of nano-clusters per endolysosome is independent of cholesterol. Finally, we show that the dynein adapter protein ORP1L (Oxysterol Binding Protein Homologue) regulates the number of dynein motors within nano-clusters in response to cholesterol levels. We propose a new model by which endolysosomal transport and positioning is influenced by the cholesterol sensing adapter protein ORP1L, which influences dynein's copy number within nano-clusters.

Stable leaders pave the way for cooperation under time-dependent exploration rates

The exploration of different behaviors is part of the adaptation repertoire of individuals to new environments. Here, we explore how the evolution of cooperative behavior is affected by the interplay between exploration dynamics and social learning, in particular when individuals engage on the Prisoner's Dilemma along the edges of a social network. We show that when the population undergoes a transition from strong to weak exploration rates a decline in the overall levels of cooperation is observed. However, both constant and variable exploration rates are shown to be beneficial for cooperation as long as leaders (highly connected individuals) adopt lower exploration rates than followers (less connected individuals). This result suggests that noisy decision-making at the periphery of social networks may, in some cases, translate into major benefits at the population level.

Data for: Natural selection on adults has trait-dependent consequences for juvenile evolution in dragonflies

Although natural selection often varies across ontogeny, it remains unclear what conditions enable selection in one life-cycle stage to shape evolution in others. Organisms that undergo metamorphosis are useful for addressing this topic because, despite the dramatic life-history transition that separates their highly specialized life-cycle stages, the stages only exhibit evolutionary independence in some cases. Using a comparative study of dragonflies, we examined three conditions that are hypothesized to allow selection in one stage to affect evolution in others. First, contrary to predictions that life-cycle stages in lineages with less dramatic metamorphoses (e.g. hemimetabolous insects) do not evolve independently, we found that the evolution of larval body shape is not affected by selection on adult shape. Next, supporting the hypothesis that homologous and/or co-adapted structures do not evolve independently, selection for larger wings are associated with the evolution of a functionally co-adapted larval trait, the sheaths that store developing wing tissue. Finally, consistent with expectations of minimal stage-specific evolution in traits linked to a single biochemical pathway, species with more wing melanization have evolved weaker larval melanin immune defenses. Thus, even in organisms that undergo metamorphosis, some kinds of traits may have greater capacity for stage-specific evolution than others.

Context-dependent reproductive isolation: host plant variability drives fitness of hybrid herbivores

The role of divergent selection between alternative environments is well-recognized to promote reproductive isolation (RI) between lineages. However, most studies view each divergent environment as homogenous, thereby overlooking the potential role of within environment variation on RI between differentiating lineages. Here we test the importance of microenvironmental variation on RI using individual trees of two host plants each harboring locally adapted populations of the cynipid wasp, Belonocnema treatae. We compared the fitness surrogate (survival) of offspring from hybrid crosses with residents across individuals of each host plant Quercus virginiana and Q. geminata. We found evidence of weak hybrid inviability between host-associated lineages of B. treatae despite strong genomic differentiation. However, averaging across environments, masked great variation in hybrid fitness on individual trees, where hybrids performed worse than, equal to, or better than residents. Considering the environmental context of hybridization is thus critical to improving the predictability of divergence under variable selection.

Density-dependent individual variation in male attractiveness in a wild field cricket

Social environments modify a male's ability to attract females and thus affect its fitness. Theory implies that an individual's fitness should trade-off with its ability to cope with competition. Individuals are expected to solve this trade-off differently: some males should be more attractive at low but others instead at high density. This prediction has rarely been tested in the wild. We used an automated RFID-surveillance system to quantify for each hour of the day, over 30 days (i.e. almost the entire adult lifespan of our model organism), whether a male had attracted a female in its burrow. The data were collected across a range of naturally varying local densities in wild field crickets, G.campestris. We also estimated whether the shape of the relationship between attractiveness and density was under selection. At the population level, attractiveness increased from low to intermediate density, suggesting an Allee effect. Attractiveness subsequently declined at higher densities, for example, because of detrimental effects of increased competition. Opposite to expectations, males that were more attractive under low densities were also more attractive under higher densities. However, the increase in attractiveness with density varied among males, suggesting that Allee effects were individual-specific. Finally, selection was not acting on density-dependent attractiveness but males that lived longer acquired more mating partners. Our study reveals that social environments shape attractiveness in wild male insects, and imply the occurrence of individual-specific Allee effect that may be evolvable.