Find research datasets worth reusing

Drop Everything? Analyzing Developer Response to Fix a High Severity Dependency

Although using third-party libraries has become prevalent in contemporary software development, prior work are all in agreement that developers struggle to update their dependencies. They often acknowledge that due to the migration effort, priority and other issues cause lags in the adoption process. On the other hand, with a vulnerability that has showstopping potential, we expect developers to drop everything! to fix the risk. In this new idea paper, we explore a case study of when Log4JShell, which has the highest ever reported severity of 10. Our goal is to analyze the developer response in relation to how fast they migrated to a safer version, and what were the information discussed while fixing this severe vulnerability.

openapache2.0Feb 2022View details →

The artifact for the paper "Demystifying the Dependency Challenge in Kernel Fuzzing" in ICSE 2022 Technical Tracks.

This artifact is for the paper "Demystifying the Dependency Challenge in Kernel Fuzzing" in ICSE 2022 Technical Tracks. More detail and update please refer to https://github.com/ZHYfeng/Dependency.

opencc-zeroFeb 2022View details →

Data from: Harvest and density-dependent predation drive long-term population decline in a northern ungulate

The relative effect of top-down versus bottom-up forces in regulating and limiting wildlife populations is an important theme in ecology. Untangling these effects is critical for a basic understanding of trophic dynamics and effective management. We examined the drivers of moose (Alces alces) population growth by integrating two independent sources of observations within a hierarchical Bayesian population model. This analysis used one of the largest existing spatiotemporal datasets on ungulate population dynamics globally. We documented a 20% population decline over the period examined. Moose population growth was negatively density-dependent. Although the mechanisms producing density-dependent suppression of population growth could not be determined, the relatively low densities at which moose populations were documented suggests it could be due primarily to density-dependent predation. Predation primarily limited population growth, except at low density, where it was regulating. Harvest appeared to be largely additive and contributed to population declines. Our results, highlight how population dynamics are context dependent and vary strongly across gradients in climate, forest type, and predator abundance. These results help clarify long-standing questions in population ecology and highlight the complex relationships between natural and human-caused mortality in driving ungulate population dynamics.

Acoustic propulsion of nano- and microcones: dependence on particle size, acoustic energy density, and sound frequency

Supplementary data for the following manuscript: Johannes Voß, Raphael Wittkowski, "Acoustic propulsion of nano- and microcones: dependence on particle size, acoustic energy density, and sound frequency".

Propulsion of nano- and microcones by a traveling ultrasound wave: dependence on orientation and aspect ratio of the particles

Supplementary data for the following manuscript: Johannes Voß, Raphael Wittkowski, "Propulsion of nano- and microcones by a traveling ultrasound wave: dependence on orientation and aspect ratio of the particles"

Acoustic propulsion of nano- and microcones: dependence on the viscosity of the surrounding fluid

Supplementary data for the following manuscript: Johannes Voß, Raphael Wittkowski, "Acoustic propulsion of nano- and microcones: dependence on the viscosity of the surrounding fluid".

Cyclin F drives proliferation through SCF-dependent degradation of the retinoblastoma-like tumor suppressor p130/RBL2

Cell cycle gene expression programs fuel proliferation and are universally dysregulated in cancer. The retinoblastoma (RB)-family of proteins, RB1, RBL1/p107, and RBL2/p130, coordinately represses cell cycle gene expression, inhibiting proliferation, and suppressing tumorigenesis. Phosphorylation of RB-family proteins by cyclin-dependent kinases is firmly established. Like phosphorylation, ubiquitination is essential to cell cycle control, and numerous proliferative regulators, tumor suppressors, and oncoproteins are ubiquitinated. However, little is known about the role of ubiquitin signaling in controlling RB-family proteins. A systems genetics analysis of CRISPR/Cas9 screens suggested the potential regulation of the RB-network by cyclin F, a substrate recognition receptor for the SCF family of E3 ligases. We demonstrate that RBL2/p130 is a direct substrate of SCFcyclin F. We map a cyclin F regulatory site to a flexible linker in the p130 pocket domain, and show that this site mediates binding, stability, and ubiquitination. Expression of a mutant version of p130, which cannot be ubiquitinated, severely impaired proliferative capacity and cell cycle progression. Consistently, we observed reduced expression of cell cycle gene transcripts, as well a reduced abundance of cell cycle proteins, analyzed by quantitative, iterative immunofluorescent imaging. These data suggest a key role for SCFcyclin F in the CDK-RB network and raise the possibility that aberrant p130 degradation could dysregulate the cell cycle in human cancers.

Direct and legacy-mediated drought effects on plant performance are species-specific and depend on soil community composition

Droughts affect plant communities, but their impacts may be mediated by soil biota. Soil communities may ameliorate drought stress, and droughts may leave legacies of altered soil communities that may affect future plant growth. However, it is not yet understood which groups of soil biota in particular affect plant performance under drought, nor which groups contribute to drought-legacy effects on future plant growth. We hypothesized that increasing soil-community complexity ameliorates drought stress and that drought-legacy effects are species-specific and soil-community-dependent. To test these hypotheses, we performed a two-phase experiment with six grassland species. In the first phase, we examined plant performance under drought and ambient conditions, in soils inoculated with a sterilized inoculum, or increasingly complex soil communities created by wet-sieving through 20-, 40-, and 200-µm mesh sieves. In the second phase, we examined drought-legacy effects on conspecific plant performance. We separately analysed plant performance in both phases, and integrated data from both phases using structural equation models. Drought effects on first-phase root biomass depended on soil inoculum, and this interaction differed among plant species, while effects on shoot biomass differed among species, but did not depend on inoculum. Only one species experienced drought-stress-ameliorating effects of soil biota. Drought-legacy effects on plant performance were positive, but depended on soil inoculum in case of root biomass, and on soil inoculum and species identity in case of shoot biomass. Drought-legacy effects were often mediated by first-phase biomass. In some species this effect was independent of inoculum, suggesting an abiotic legacy effect. In others, low first-phase biomass corresponded with high second-phase performance in presence of the most complex soil community. We conclude that drought-legacy effects on plant performance were soil-community-dependent but positive, suggesting that plants establishing after drought may benefit from increased nutrient availability and more positive impacts of soil biota.

Data from: Host sex modulates the energetics of pathogen proliferation and its dependence on environmental resources

Sex differences in immunity are predicted to underlie much of the frequently observed sex differences in the prevalence or severity of infection. We propose the additional hypothesis that differences in the ability of males and females to acquire and use resources will also affect how readily a pathogen can convert host energy into transmission stages, thereby contributing to sex differences in infection dynamics. To test this we manipulated the resource environment of male and female Daphnia magna by altering the availability of food and then exposed hosts to a bacterial pathogen. We measured the production of transmission spores and virulence via the reduction in life span, together with feeding rates and changes in mass-independent metabolic rate, as a measure of the intake and expenditure of energy during infection. When raised in the presence of high resource levels, females more readily allowed for resources in the environment to be translated to pathogen exploitation, as represented by increased spore production, greater virulence, and higher energy use. In contrast, the traits of infected males were robust to changes in resource availability. High food availability thus exaggerated the degree of sexual dimorphism observed between the sexes. It also modified the relationship between host energy use, virulence, and pathogen spore production for each sex. These results suggest that a host's resource environment can affect how a male or female is exploited by a pathogen and may thus be an additional factor driving sex-specific patterns of disease susceptibility or severity.

Figures S1–S10 from: Shoman ME, Abd El-Hafeez AA, Khobrani M, Assiri AA, Al Thagfan SS, Othman EM, Ibrahim ARN (2022) Molecular docking and dynamic simulations study for repurposing of multitarget coumarins against SARS-CoV-2 main protease, papain-like protease and RNA-dependent RNA polymerase. Pharmacia 69(1): 211-226. https://doi.org/10.3897/pharmacia.69.e77021

Molecular docking and Dynamic simulations study for repurposing of multitarget Coumarins against SARS-CoV-2 main protease, papain like protease and RNA-Dependent RNA polymerase.

Negative frequency dependent selection maintains shell banding polymorphisms in two marine snails (Littorina fabalis and L. saxatilis)

The presence of shell bands is common in gastropods. The marine snails, Littorina fabalis and L. saxatilis, are both polymorphic for this trait. Such polymorphism would be expected to be lost by the action of genetic drift or directional selection, but it appears to be widespread at relatively constant frequencies. This suggests it is maintained by balancing selection on the trait or on a genetically linked trait. Using long time-series of empirical data, we compared potential effects of genetic drift and negative frequency-dependent selection, in the two species. The contribution of genetic drift to changes in the frequency of bands in L. fabalis was estimated using the effective population size estimated from microsatellite data, while the effect of genetic drift in L. saxatilis were derived from previously published study. Frequency-dependent selection was assessed comparing the cross-product estimator of fitness with the frequency of the polymorphism across years using a regression analysis. Both studied species showed patterns of negative frequency-dependent selection. In addition, in L. fabalis, contributions from genetic drift could explain some of the changes in banding frequency. Overdominance and heterogeneous selection did not fit well to our data. The possible biological explanations resulting on the maintenance of the banding polymorphism are discussed.

Scale dependence in functional equivalence and difference in the soil microbiome

Climatic history can shape the functioning of soil microbial communities and thus rates of ecosystem processes such as organic matter decomposition. For example, broad spatial scale differences in climatic history, such as contrasting precipitation regimes, have been shown to generate unique microbial functional responses to contemporary moisture conditions. Yet it is an open question as to whether local differences in soil microclimate similarly influence the functional potential of decomposer communities. Here, we use a multi-scale approach within and among two temperate forest field sites to investigate this question. Soils from fifty-four microsites, that vary in their soil moisture climate-regimes, were used as inocula for a common leaf litter (Quercus rubra) in a controlled, laboratory microcosm study. Microcosms were placed under dry, mesic and wet lab-moisture conditions and the rate of carbon (C) mineralization of the litter was measured over 202 days. Our results reveal differences in decomposition rates under controlled conditions that highlight broad-scale functional differences between the soil communities at each site. Specifically, we found that C mineralization differed by as much as two-fold for soil communities when compared between the sites. Our results also show that functional differences of soil communities are observable within one site but not the other. In the site where local-scale functional legacies were apparent, the historical soil moisture microclimate-regimes generated as much as an 89% change in C mineralization rates of the leaf litter under the same contemporary, lab-imposed moisture conditions. A similar pattern was not observable in the other site; instead, laboratory moisture conditions explained almost all variation in C mineralization. Our findings confirm those from prior studies where regional-scale moisture-regime differences shape microbial function, and extends this prior work by providing evidence that pronounced local-scale differences in soil moisture microclimate-regimes can generate microbial functional legacies.

Prey and predator density-dependent interactions under different water volumes

Predation is a critical ecological process that directly and indirectly mediates population stabilities, as well as ecosystem structure and function. The strength of interactions between predators and prey may be mediated by multiple density-dependences concerning numbers of predators and prey. In temporary wetland ecosystems in particular, fluctuating water volumes may alter predation rates through differing search space and prey encounters rates. Using a functional response approach, we examined the influence of predator and prey densities on interaction strengths of the temporary pond specialist copepod Lovenula raynerae preying on cladoceran prey, Daphnia pulex, under contrasting water volumes. Further, using a population dynamic modelling approach, we quantified multiple predator effects across differences in prey density and water volume. Predators exhibited Type II functional responses under both water volumes, with significant antagonistic multiple predator effects (i.e. antagonisms) exhibited overall. The strengths of antagonistic interactions were, however, enhanced under reduced water volumes and at intermediate prey densities. These findings indicate important biotic and abiotic contexts that mediate predator-prey dynamics, whereby multiple predator effects are contingent on both prey density and search area characteristics. In particular, reduced search areas (i.e., water volumes) under intermediate prey densities could enhance antagonisms by heightening predator-predator interference effects.

Reward-dependent selection of feedback gains impact rapid motor decisions

Target reward influences motor planning strategies through modulation of movement vigor. Considering current theories of sensorimotor control suggesting that movement planning consists in selecting a goal-directed control strategy, we sought to investigate the influence of reward on feedback control. Here we explored this question in three human reaching experiments. First, we altered the explicit reward associated with the goal target and found an overall increase in feedback gains for higher target rewards, highlighted by larger velocities, feedback responses to external loads, and background muscle activity. Then, we investigated whether the differences in target rewards across multiple goals impacted rapid motor decisions during movement. We observed idiosyncratic switching strategies dependent on both target rewards and, surprisingly, the feedback gains at perturbation onset: the more vigorous movements were less likely to switch to a new goal following perturbations. To gain further insight into a causal influence of the feedback gains on rapid motor decisions, we demonstrated that biasing the baseline activity and reflex gains by means of a background load evoked a larger proportion of target switches in the direction opposite to the background load associated with lower muscle activity. Together, our results demonstrate an impact of target reward on feedback control and highlight the competition between movement vigor and flexibility.

opencc-zeroApr 2022View details →

Wide-range viscoelastic compression forces in microfluidics to probe cell-dependent nuclear structural and mechanobiological responses

The cell nucleus plays a critical role in mechanosensing and mechanotransduction processes, by adaptive changes of its envelope composition to external biophysical stimuli such as substrate rigidity and tensile forces. Current measurement approaches lack of precise control in stress application on nuclei, thus significantly impairing a complete mechanobiological study of cells. Here, we present a contactless microfluidic approach capable to exert a wide-range of viscoelastic compression forces (10-103 μN) -as an alternative to adhesion-related techniques- to induce cell-specific mechano-structural and biomolecular changes. We succeed in monitoring substantial nuclear modifications in Lamin A/C expression and coverage, diffusion processes of probing molecules, YAP shuttling, chromatin re-organization and cGAS pathway activation. As a result, high compression forces lead to a nuclear reinforcement (e.g. up to +20% in Lamin A/C coverage) or deconstruction (e.g. down to -45% in Lamin A/C coverage with a 30% reduction of chromatin condensation state parameter) up to cell death. We demonstrate how wide-range compression on suspended cells can be used as a tool to investigate nuclear mechanobiology and to define specific nuclear signatures for cell mechanical phenotyping.

opencc-zeroApr 2022View details →

A test of frequency dependent selection in the evolution of a generalist phenotype

A solitary population of consumers frequently evolves to the middle of a resource gradient and an intermediate mean phenotype compared to a sympatric pair of competing species that diverge to either side via character displacement. The forces governing the distribution of phenotypes in these allopatric populations, however, are little investigated. Theory predicts that the intermediate mean phenotype of the generalist should be maintained by negative frequency dependent selection, whereby alternate extreme phenotypes are favored because they experience reduced competition for resources when rare. However, the theory makes assumptions that are not always met, and alternative explanations for an intermediate phenotype are possible. We provide a test of this prediction in a mesocosm experiment using threespine stickleback that are ecologically and phenotypically intermediate between the more specialized stickleback species that occur in pairs. We manipulated the frequency distribution of phenotypes in two treatments and then measured effects on a focal intermediate population. We found a slight frequency-dependent effect on survival in the predicted direction but not on individual growth rates. This result suggests that frequency dependent selection might be a relatively weak force across the range of phenotypes within an intermediate population and we suggest several general reasons why this might be so. We propose that allopatric populations might often be maintained at an intermediate phenotype instead by stabilizing or fluctuating directional selection.

opencc-zeroApr 2022View details →

Community composition of bacteria isolated from Swiss banknotes varies depending on collection environment

Humans interact constantly with surfaces and associated microbial communities in the environment. The factors shaping the composition of these communities are poorly understood: some proposed explanations emphasize the influence of local habitat conditions (niche-based explanations), while others point to geographic structure and the distance among sampled locations (dispersal-based explanations). However, the relative roles of these different drivers for microbial community assembly on human-associated surfaces are not clear. Here, we used a combination of sampling, sequencing (16S rRNA) and culturing to show that the composition of banknote-associated bacterial communities varies depending on the local collection environment. Using banknotes collected from various locations and types of shops across Switzerland, we found taxonomic diversity dominated by families such as Pseudomonadaceae and Staphylococcaceae, but with banknote samples from particular types of shops (especially butcher shops) having distinct community structure. By contrast, we found no evidence of geographic structure: similarity of community composition did not decrease with increasing distance among sampled locations. These results show that microbial communities associated with banknotes, one of the most commonly encountered and exchanged human-associated surfaces, can reflect the local environmental conditions (in this case, the type of shop), and the signal for this type of variation was stronger than that for geographic structure among the locations sampled here.

opencc-by-4.0May 2022View details →

Data of event list of cold and hot patches for manuscript "The Dependence of Cold and Hot Patches on Local Plasma Transport and Particle Precipitation in Northern Hemisphere Winter"

A database of 4,634 cold patches (high density and low electron temperature) and 4,700 hot patches (high density and high electron temperature) from Defense Meteorological Satellite Program F16 in 2005-2018 winter months.

opencc-by-4.0May 2022View details →

Not All Dependencies are Equal: An Empirical Study on Production Dependencies in NPM

This dataset contains the data and scripts we used to conduct our study on production dependencies in npm.  js_projects.zip contains 100 JavaScript projects mined from GitHub in November 2021.  data_and_scripts.zip contains data on all installed dependencies from the 100 JavaScript projects and the scripts to process the data and obtain the results for our study. See the README file for more details.