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opencc-by-4.0Jul 2022View details →

Fig. 6 in Taxonomic implications of describing a new species of Loimia (Annelida, Terebellidae) with two size-dependent morphotypes

Fig. 6. Loimia davidi sp. nov., paratype MNCN 16.01/19140. A. Alimbate capillary chaeta. B. Unilimbate capillary chaeta. C. Position of the thoracic uncini from segment 10. D. Single thoracic uncinus from segment 10 (thorax). E. Single abdominal uncinus from segment 22 (abdomen).

opencc-by-4.0Jul 2022View details →

Fig. 7 in Taxonomic implications of describing a new species of Loimia (Annelida, Terebellidae) with two size-dependent morphotypes

Fig. 7. Loimia gigantea (Montagu, 1819), ARC-Loimia-IND2. A. Dorsolateral section of thoracic neuropodium 12, showing the uncinal growing zone (black arrow). B. View of entire abdominal neuropodium 4. C. Detail of the uncinal arrangement of abdominal neuropodium 4. D. Uncinus from thoracic neuropodium 8. E. Uncinus from abdominal neuropodium 4.

Recovered frog populations coexist with endemic Batrachochytrium dendrobatidis despite load-dependent mortality

Novel infectious diseases, particularly those caused by fungal pathogens, pose considerable risks to global biodiversity. The amphibian chytrid fungus (Batrachochytrium dendrobatidis, Bd) has demonstrated the scale of the threat, having caused the greatest recorded loss of vertebrate biodiversity attributable to a pathogen. Despite catastrophic declines on several continents, many affected species have experienced population recoveries after epidemics. However, the potential ongoing threat of endemic Bd in these recovered or recovering populations is still poorly understood. We investigated the threat of endemic Bd to frog populations that recovered after initial precipitous declines, focusing on the endangered rainforest frog Mixophyes fleayi. We conducted extensive field surveys over four years at three independent sites in eastern Australia. First, we compared Bd infection prevalence and infection intensities within frog communities to reveal species-specific infection patterns. Then, we analyzed capture-recapture data of M. fleayi to estimate the impact of Bd infection intensity on apparent mortality rates and Bd infection dynamics. We found that M. fleayi had lower infection intensities than sympatric frogs across the three sites, and cleared infections at higher rates than they gained infections throughout the study period. By incorporating time-varying individual infection intensities, we show that healthy M. fleayi populations persist despite increased apparent mortality associated with infrequent high Bd loads. Infection dynamics were influenced by environmental conditions, with Bd prevalence, infection intensity, and rates of gaining infection associated with lower temperatures and increased rainfall. However, mortality remained constant year-round despite these fluctuations in Bd infections, suggesting major mortality events did not occur over the study period. Together, our results demonstrate that while Bd is still a potential threat to recovered populations of M. fleayi, high rates of clearing infections and generally low average infection loads likely minimize mortality caused by Bd. Our results are consistent with pathogen resistance contributing to the coexistence of M. fleayi with endemic Bd. We emphasize the importance of incorporating infection intensity into disease models rather than infection status alone. Similar population and infection dynamics likely exist within other recovered amphibian-Bd systems around the globe, promising longer-term persistence in the face of endemic chytridiomycosis.

Data to reproduce: Cultural diffusion dynamics depend on behavioral production rules

This repository contains data to reproduce the manuscript titled "Cultural diffusion dynamics depend on behavioural production rules". These RDAs contain simulation data, as well as inference data from NBDA and EWA analyses. They are intended to be used with the analysis code found at <a href="http://www.github.com/michaelchimento/acquisition_production_abm" rel="noopener">www.github.com/michaelchimento/acquisition_production_abm</a>.

Supplementary material and supplementary data files for: Handling logical character dependency in phylogenetic inference: Extensive performance testing of assumptions and solutions using simulated and empirical data

Logical character dependency is a major conceptual and methodological problem in phylogenetic inference of morphological datasets, as it violates the assumption of character independence that is common to all phylogenetic methods. It is more frequently observed in higher-level phylogenies or in datasets characterizing major evolutionary transitions, as these represent parts of the tree of life where (primary) anatomical characters either originate or disappear entirely. As a result, secondary traits related to these primary characters become "inapplicable" across all sampled taxa in which that character is absent. Various solutions have been explored over the last three decades to handle character dependency, such as alternative character coding schemes and, more recently, new algorithmic implementations. However, the accuracy of the proposed solutions, or the impact of character dependency across distinct optimality criteria, has never been directly tested using standard performance measures. Here, we utilize simple and complex simulated morphological datasets analyzed under different maximum parsimony optimization procedures and Bayesian inference to test the accuracy of various coding and algorithmic solutions to character dependency. This is complemented by empirical analyses using a recoded dataset on palaeognathid birds. We find that in small, simulated datasets, absent coding performs better than other popular coding strategies available (contingent and multistate), whereas in more complex simulations (larger datasets controlled for different tree structure and character distribution models) contingent coding is favored more frequently. Under contingent coding, a recently proposed weighting algorithm produces the most accurate results for maximum parsimony. However, Bayesian inference outperforms all parsimony-based solutions to handle character dependency due to fundamental differences in their optimization procedures—a simple alternative that has been long overlooked. Yet, we show that the more primary characters bearing secondary (dependent) traits there are in a dataset, the harder it is to estimate the true phylogenetic tree, regardless of the optimality criterion, owing to a considerable expansion of the tree parameter space.

opencc-by-4.0Aug 2022View details →

MyD88-TLR4-dependent choroid plexus activation precedes perilesional inflammation and secondary brain edema in a mouse model of intracerebral hemorrhage

Supplementary data and code of the article "MyD88-TLR4-dependent choroid plexus activation precedes perilesional inflammation and secondary brain edema in a mouse model of intracerebral hemorrhage".

opencc-by-4.0Aug 2022View details →

The hydro-mechanical properties of fracture intersections: pressure dependant permeability and effective stress law

The present repository includes the raw permeability data presented in the manuscript submitted for publication in Journal of Geophysical Research: Solid Earth entitled The hydro-mechanical properties of fracture intersections: pressure-dependant permeability and effective stress law. The repository is presented as compressed folders named after the Figures of the manuscript where the data is presented.

opencc-by-4.0Sep 2022View details →

Data set for "The ion-ion recombination coefficient α: comparison of temperature- and pressure-dependent parameterisations for the troposphere and stratosphere"

The uploaded data are related to the publication "The ion–ion recombination coefficient \(\alpha\): comparison of temperature- and pressure-dependent parameterisations for the troposphere and stratosphere" in Atmospheric Chemistry and Physics (ACP). The data are the same as shown in the figures of the publication. The naming of the uploaded files indicates the figure (e.g., "Fig_2" indicates Figure 2 of the publication).

Data from: Density-dependence produces spurious relationships among demographic parameters in a harvested species

1. Harvest of wild organisms is an important component of human culture, economy, and recreation, but can also put species at risk of extinction. Decisions that guide successful management actions therefore rely on the ability of researchers to link changes in demographic processes to the anthropogenic actions or environmental changes that underlie variation in demographic parameters. 2. Ecologists often use population models or maximum sustained yield curves to estimate the impacts of harvest on wildlife and fish populations. Applications of these models usually focus exclusively on the impact of harvest and often fail to consider adequately other potential, often collinear, mechanistic drivers of the observed relationships between harvest and demographic rates. In this study, we used an integrated population model and long-term data (1973-2016) to examine the relationships among hunting and natural mortality, the number of hunters, habitat conditions, and population size of blue-winged teal (Spatula discors), an abundant North American dabbling duck with a relatively fast-paced life history strategy. 3. Over the last two and a half decades of the study, teal abundance tripled, hunting mortality probability increased slightly (< 0.02), and natural mortality probability increased substantially (> 0.1) at greater population densities. We demonstrate strong density-dependent effects on natural mortality and fecundity as population density increased, indicative of compensatory harvest mortality and compensatory natality. Critically, an analysis that only assessed the relationship between survival and hunting mortality would spuriously indicate depensatory hunting mortality due to multicollinearity between abundance, natural mortality, and hunting mortality. 4. Our findings demonstrate that models that only consider the direct effect of hunting on survival or natural mortality can fail to accurately assess the mechanistic impact of hunting on population dynamics due to multicollinearity among demographic drivers. This multicollinearity limits inference and may have strong impacts on applied management actions globally.

opencc-zeroSep 2022View details →

Temperature-dependent evolutionary speed shapes the evolution of biodiversity patterns across tetrapod radiations

Biodiversity varies predictably with environmental energy around the globe, but the underlying mechanisms remain incompletely understood. The evolutionary speed hypothesis predicts that environmental energy shapes variation in speciation rates through temperature- or life history-dependent rates of evolution. To test whether variation in evolutionary speed can explain the relationship between energy and biodiversity in birds, mammals, amphibians, and reptiles, we simulated diversification over 65 million years of geological and climatic change with a spatially explicit eco-evolutionary simulation model. We modeled four distinct evolutionary scenarios in which speciation-completion rates were dependent on temperature (M1), life history (M2), temperature and life history (M3), or were independent of temperature and life-history (M0). To assess the agreement between simulated and empirical data, we performed model selection by fitting supervised machine learning models to multidimensional biodiversity patterns. We show that a model with temperature-dependent rates of speciation (M1) consistently had the strongest support. In contrast to statistical inferences, which showed no general relationships between temperature and speciation rates in tetrapods, we demonstrate how process-based modeling can disentangle the causes behind empirical biodiversity patterns. Our study highlights how environmental energy has played a fundamental role in the evolution of biodiversity over deep time.

opencc-by-4.0Sep 2022View details →

[Supplementary material] Automated Code Generation for Inter-parameter Dependencies in REST APIs

This is the supplementary material of the paper entitled  Automated Code Generation for Inter-parameter Dependencies in REST APIs.

opencc-by-4.0Aug 2022View details →

Nanoscale Shape-Dependent Histone Modifications

Recent observations suggest a role for complex nanoscale particulate shape in regulation of specific immune-related cellular and in vivo processes. We suspect that cellular recognition of nanostructure architecture could involve non-molecular inputs, including cellular transduction of nanoscale spatially resolved stresses induced by complex shape. Here we report nanoscale shape-dependent control of the cellular epigenome. ChIP-Seq sequencing datasets are provided.

opencc-zeroOct 2022View details →

Data from: Sex-dependent effects of parental age on offspring fitness in a cooperatively breeding bird

Parental age can have considerable effects on offspring phenotypes and health. However, intergenerational effects may also have longer-term effects on offspring fitness. Few studies have investigated parental age effects on offspring fitness in natural populations while also testing for sex- and environment-specific effects. Further, longitudinal parental age effects may be masked by population-level processes such as the selective disappearance of poor-quality individuals. Here, we used multi-generational data collected on individually marked Seychelles warblers (Acrocephalus sechellensis) to investigate the impact of maternal and paternal age on offspring lifespan and lifetime reproductive success. We found negative effects of maternal age on female offspring lifespan and lifetime reproductive success, which were driven by within-mother effects. There was no difference in annual reproductive output of females born to older versus younger mothers, suggesting that the differences in offspring lifetime reproductive success were driven by effects on offspring lifespan. In contrast, there was no association between paternal age and female offspring lifespan or either maternal or paternal age and male offspring lifespan. Lifetime reproductive success, but not annual reproductive success, of male offspring increased with maternal age, but this was driven by between-mother effects. No paternal age effects were found on female offspring's lifetime reproductive success but there was a positive between-father effect on male offspring's lifetime reproductive success. We did not find strong evidence for environment-dependent parental age effects. Our study provides evidence for parental age effects on the lifetime fitness of offspring and shows that such effects can be sex-dependent. These results add to the growing literature indicating the importance of intergenerational effects on long-term offspring performance and highlight that these effects can be an important driver of variation in longevity and fitness in the wild.

opencc-zeroOct 2022View details →

Data from: Single cell transcriptomics shows dose-dependent disruption of hepatic zonation by TCDD in mice

2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) dose-dependently induces the development of hepatic fat accumulation and inflammation with fibrosis in mice initially in the portal region. Conversely, differential gene and protein expression is first detected in the central region. To further investigate cell-specific and spatially resolved dose-dependent changes in gene expression elicited by TCDD, single-nuclei RNA sequencing and spatial transcriptomics were used for livers of male mice gavaged with TCDD every 4 days for 28 days. The proportion of 11 cell (sub)types across 131,613 nuclei dose-dependently changed with 68% of all portal and central hepatocyte nuclei in control mice being overtaken by macrophages following TCDD treatment. We identified 368 (portal fibroblasts) to 1,339 (macrophages) differentially expressed genes. Spatial analyses revealed initial loss of portal identity that eventually spanned the entire liver lobule with increasing dose. Induction of R-spondin 3 (Rspo3) and pericentral Apc, suggested dysregulation of the Wnt/β-catenin signaling cascade in zonally resolved steatosis. Collectively, the integrated results suggest disruption of zonation contributes to the pattern of TCDD-elicited NAFLD pathologies.

opencc-zeroOct 2022View details →

Data From: Females alter their mate preferences depending on hybridization risk

Mating with another species is often maladaptive because it generally results in no or low-fitness offspring. When hybridization is sufficiently costly, individuals should avoid mating with heterospecifics even if it reduces their ability to mate with high-quality conspecifics that resemble heterospecifics. Here, we used spadefoot toads, Spea multiplicata, to evaluate whether females alter their preferences for conspecific male sexual signals (call rate) depending on heterospecific presence. When presented with conspecific signals against a background including both conspecific and heterospecific signals, females preferred male traits that were most dissimilar to heterospecifics—even though these signals are potentially associated with lower-quality mates. However, when these same females were presented with a background that included only conspecific signals, some females switched their preferences, choosing conspecific signals that were exaggerated and indicative of high-quality conspecific mates. Because only some females switched their preferences between these two chorus treatments, there was no population-level preference for exaggerated male signals in the absence of heterospecifics. Thus, hybridization risk can impact mate choice and thereby alter patterns of sexual selection. These results also emphasize that reproductive barriers between species (such as mate choice) can be context-dependent, with important implications for the origins and maintenance of species boundaries.

opencc-by-nc-4.0Sep 2017View details →

Dataset for "Secure and Dependable Multi-Cloud Network Virtualization"

Processed data from experiments using Sirius, the SUPERCLOUD network hypervisor Type of data: processed data Hardware/software used: We use one public (Amazon EC2 in Germany – Frankfurt) and one private (the private cloud is our datacenter in Portugal – Lisbon) clouds in the evaluation. In Amazon EC2 we use t2.medium as gateway VMs and t2.micro as normal VMs. The private cloud is based on a rack of Dell R420, with 2 Intel Xeon E5520 quad-core, 2.2 GHz, and 32 GB RAM. VirtualBox managed the VMs, which were configured with 1 CPU and 2GB RAM. The VMs run Ubuntu with Docker (1.13.1) and OvS (2.5.0). The containers were also based in Ubuntu. The hypervisor was hosted in the server of the private Datacenter. Data Format: Text files Source: Simulations and experiments Number of samples: 10 samples in each experiment Total size of samples: Time to create and destroy containers: 1KB Time to setup a virtual network: 1KB

opencc-by-4.0Jun 2010View details →

Figure 2: Variation of the shear stress depending on the speed rate 54-STUDIES TOWARDS OBTAINING A PHOTOPROTECTIVE DERMO-COSMETIC COMPLEX PRODUCT WITH NATURAL EXTRACTS OF INORGANIC AND ORGANIC SUBSTANCES

The evaluation of photodegradation was carried out through the variation of photoprotective factor of the studied product kept 60 minutes under UV radiation at 65±C. The tests revealed the preservation or even a slight increase in the SPF. The use of screen substances in the formulation of photoprotective products results in undesirable sensory characteristics: visible white ¯lm on the skin surface, unpleasant sensation, dry or oily skin after application.

opencc-by-4.0Jun 2010View details →

Figure 3: Viscosity variation depending on speed rate Table-STUDIES TOWARDS OBTAINING A PHOTOPROTECTIVE DERMO-COSMETIC COMPLEX PRODUCT WITH NATURAL EXTRACTS OF INORGANIC AND ORGANIC SUBSTANCES-

Microbiological characteristics The total number of aerobic germs and fungi was determined by the decimal dilution method or the multiple tube test. For identifying pathogenic species we have used speci¯c tests (table6). The evaluation of photodegradation was carried out through the variation of photoprotective factor of the studied product kept 60 minutes under UV radiation at 65±C. The tests revealed the preservation or even a slight increase in the SPF. The use of screen substances in the formulation of photoprotective products results in undesirable sensory characteristics: visible white ¯lm on the skin surface, unpleasant sensation, dry or oily skin after application.

opencc-by-4.0Sep 2010View details →

Figure 3: The dependencies ² 00 (log !¿¾). The values are normalized at ² 00 max-TOWARD THE PHYSICAL BASIS OF COMPLEX SYSTEMS: DIELECTRIC ANALYSIS OF POROUS SILICON NANOCHANNELS IN THE ELECTRICAL DOUBLE LAYER LENGTH RANGE

Fig.3. The conductivity relaxation occurs at lowing frequencies. The form of the ² 00 (!) = f(² 0 (!)) diagrams changes from a vertical line (a), to any deformate semicircles (b, c, d) having the angle to real axe below ¼ 2 , Fig.4. This behaviour denotes that the EDL is not an ideally capacitor, but also is not a disipative region, depending both on the EDL thickness and the frequency range of the applied ¯eld [7]. The composition (by thickness) of the EDL determines essentially the dielectric response of the interface system. Compared with experimental results, the dielectric pro¯le of this higher length scales model, can provides a more complet description of the solvent properties for a given electrode.