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opencc-by-4.0Jun 2021View details →

Tectonic and magmatic evolution of NE Cathaysia Block controls sediment geochemical heterogeneity of rivers in SE China

The supplementary data of the manuscript: Tectonic and magmatic evolution of NE Cathaysia Block controls sediment geochemical heterogeneity of rivers in SE China

opencc-by-4.0Oct 2022View details →

Burn severity data from: The heterogeneity of burn severity affects bird density in an abandoned mountain landscape of the Atlantic-Mediterranean transition

[Abstract] Fire regimes in mountain landscapes of southern Europe have been shifting from their baselines due to the accumulation of fuel fostered by long-standing rural abandonment and fire exclusion policies. Understanding the role of fire on biodiversity is paramount to implement adequate management to mitigate the impacts of altered fire regimes and land abandonment on biodiversity. Here, we explored to what extent the spatiotemporal variation in burn severity has affected bird abundance of a mountain abandoned landscape located in the Atlantic-Mediterranean transition (NW Iberia). We took advantage of: (1) satellite images of Sentinel 2 and Landsat missions to compute burn severity indicators from 2010 to 2020, and (2) standardized bird surveys carried out over 206 point-counts along the breeding season of 2021. Bird abundance models were built from burn severity metrics together with well-known fire regime attributes (% of burnt area and time since fire). Our results showed that the spatiotemporal variation of burn severity significantly correlated with the abundance of the 39% of the modeled species, supporting the role of pyro-diversity in driving bird populations in our region. The burnt area also explained abundance patterns for 28% of species. Time since fire only correlated with the abundance of 3 species. Our findings confirm the importance of incorporating burn severity indicators into the toolkit of decision makers to anticipate the response of birds to fire management. [Dataset Description] For each year between 2010 and 2020, we used a pair of satellite images, one before (April - July) and one after (September - November) the fire season. In order to use the best available information, we selected different satellites along the study period: for years 2010 and 2011, we used Landsat 5 imagery, whereas for 2012 we used Landsat 7, since Landsat 5 imagery was not useful due to high cloudiness. Since its launch in 2013, we shifted to Landsat 8 data, and finally to Sentinel 2 data from 2015 onwards. For each of these images we calculated the Normalized Burn Ratio (NBR), which is the normalized ratio between near infrared (NIR) and short wave infrared (SWIR) radiation (Eq. 1). NIR and SWIR bands of satellite sensors respond in opposite ways to burned vegetation, allowing to identify burned areas. NBR =(NIR - SWIR) / (NIR +SWIR) (1) To obtain a quantitative measure of change for each year, we calculated the dNBR by subtracting the NBR of the post-fire season image from the NBR of the pre-fire season image (Eq. 2). Finally, dNBR values were used as an estimate for fire severity. dNBR = NBRprefire- NBRpostfire (2)

opencc-zeroOct 2022View details →

No seasonal curtailment of the Eurasian Skylark's (Alauda arvensis) breeding season in German heterogeneous farmland

The lack of suitable nesting sites is one key driver behind the farmland bird crisis in Europe. Winter cereals become impenetrable for ground-breeding birds like the Eurasian Skylark (Alauda arvensis), curtailing breeding time. Stable Skylark populations depend on multiple breeding attempts per year; thus, the widespread cultivation of winter cereals has strongly contributed to their tremendous decline. Crop diversification is thought to be a potential measure to counteract this development. Therefore, we explored how individual Skylarks respond to the decreasing suitability of winter cereals as nesting habitat in heterogeneous but otherwise conventionally managed farmland. Our study focused on: i) the degree to which Skylarks prematurely cease nesting activity, switch nesting habitats, or breed on linear structures like tramlines. Additionally, we analyzed: ii) if nest success decreases throughout the breeding season and iii) how often Skylarks make a successful breeding attempt per year. We radio-tagged 28 adults in a German population during April 2018 and 2019, tracked half of them for more than 3 months, and measured their breeding success. Additionally, we monitored nests of untagged pairs, resulting in 96 nests found. None, except one tagged individual, stopped breeding activity before July 1st. Home ranges were mainly stable, but Skylarks switched nesting habitats away from winter cereals to crops like sugar beet or set-aside. High-risk nesting sites like corn and linear structures played a minor role in breeding. Overall, Mayfield logistic regressions revealed no seasonal decrease in nest success, and tagged Skylarks had sufficient time to make 1.5 – 1.8 breeding attempts, of which 0.8 were successful. We suggest that heterogeneous farmland in our study area, which enabled diversely composed home ranges, prevented a curtailment of the breeding season. Thus, our study reinforces the need for crop diversification which gives Skylarks a chance to survive in modern farmland.

opencc-zeroNov 2022View details →

Time-dependent benefits of camouflage strategies on heterogeneous backgrounds

Background-matching camouflage is a well-established strategy to reduce detection, but implementing this on heterogeneous backgrounds is challenging. For prey with fixed colour patterns, solutions include specialising on a particular visual microhabitat or adopting a compromise or generalist appearance, matching multiple backgrounds imperfectly. Existing studies suggest both approaches can succeed, but most consider relatively simple scenarios, where artificial prey appear against two backgrounds differing in a single visual characteristic. Here, we used computer-based search tasks with human participants to test the relative benefits of specialising and generalising for complex targets, displayed on either two or four types of naturalistic backgrounds. Overall, across two background types, specialisation was beneficial, though its success varied with search duration, such that generalist targets could outperform specialists in the first seconds of each search event. Against four different backgrounds, the initial cost to specialisation was greater, so specialists and generalists ultimately experienced similar survival. Generalists performed better when their patterning was a compromise between backgrounds that were more similar to each other than when backgrounds were more different, with similarity in luminance more relevant than pattern differences. Time-dependence in the relative success of these strategies suggests that predator search behaviour may affect optimal camouflage in real-world situations.

opencc-zeroNov 2022View details →

Pooling robustness in distance sampling: Avoiding bias when there is unmodelled heterogeneity

Data from a two-visit line transect survey of four songbird species gathered in spring 2004. Study area size was 33.2 ha of woodland and parkland on the Montrave Estate near Leven in Fife, Scotland.

opencc-zeroNov 2022View details →

Spatial heterogeneity in benthic foraminiferal assemblages track regional impacts of paleoenvironmental change across Cretaceous OAE2

The impact of global climate events on local ecosystems can vary spatially. Understanding this heterogeneity can illuminate which environments will be most impacted and the proximal drivers of ecosystem responses. Cenomanian-Turonian marine deposits of the Western Interior Seaway (WIS) record paleoceanographic changes associated with transgression and the onset of Oceanic Anoxic Event 2 (OAE2). They provide an ideal setting to study basinwide paleoecological responses during a global perturbation. Here, we integrate benthic foraminiferal assemblages from before, during, and after OAE2 via multivariate ordination analysis to examine spatial patterns in faunal responses across the western United States on a common scale and to interrogate a previously defined faunal marker used for basin-wide correlation, the Benthonic Zone (BZ). We identify oxygenation and organic matter quality as primary and secondary controls of variation across the 10 stratigraphic records and use this variation to infer paleoenvironmental changes. Stratigraphic trends reveal, in contrast to previous studies, deoxygenation at the onset of OAE2. They also reveal temporal patterns in oxygenation and productivity consistent with the gradual northward migration of a southern water mass into the WIS. This spatial heterogeneity hinders the use of the BZ in biostratigraphy because assemblages change in response to diachronous environmental change, and thus timing of the BZ with respect to OAE2 is not consistent across the basin. Our study demonstrates that regional processes can overshadow ecosystem responses to global events and underscores the importance of considering how changes in the position of water masses impact the expression of global biogeochemical perturbations.

opencc-by-4.0Dec 2021View details →

Areography, environmental heterogeneity and spatial models explain patterns of past and present diversity in Edraianthus (Campanulaceae)

Our study aims to shed light on distribution patterns and the relationship between species diversity and environmental heterogeneity of 17 Edraianthus taxa. We examined present-day and past distribution (Last Glacial Maximum) by applying ecological niche modelling. The environmental space occupied by the taxa was analysed using niche comparison methods. The results support the idea that the central and southern Dinaric Alps represent a centre of diversity and endemism in the western Balkan Peninsula. Edraianthus diversity is best explained by topographic (slope) and bioclimatic predictors (maximum temperature of warmest month, precipitation seasonality, precipitation of warmest quarter, precipitation of coldest quarter), suggesting that mountain areas with the most diversified relief have higher diversity. Niche modelling results suggest considerable range dynamics during the climatically unstable Quaternary. Thermophitic and lowland taxa responded with longitudinal shifts to ecologically suitable areas farther south, while high mountain taxa responded mainly with elevational shifts. The greatest niche similarity is found among phylogenetically closely related taxa and among ecologically similar and often sympatric taxa. The least similarity was observed in species with marked differences in habitat elevation and in more geographically isolated species. Our results suggest that the extent of range and niche overlap varied among some taxa throughout their evolutionary history, which may have led to diversification at both allopatric and sympatric levels. The correlation between the genetic diversity of the most widespread taxon and the richness of taxa could be a consequence of past and present contacts. On the other hand, alternate periods of isolation may have favoured the emergence of taxa that are reproductively isolated and ecologically specialised.

opencc-zeroDec 2022View details →

Songbirds of the Americas show uniform morphological evolution despite heterogeneous diversification

Studying the relationship between diversification and functional trait evolution among broadly co-occurring clades can shed light on interactions between ecology and evolutionary history. However, evidence from many studies is compromised because of their focus at overly broad geographic or narrow phylogenetic scales. We addressed these limitations by studying 46 independent, biogeographically-delimited clades of songbirds that dispersed from the Eastern Hemisphere into the Americas and assessed 1) whether diversification has varied through time and/or among clades within this assemblage, 2) the extent of heterogeneity in clade-specific morphological trait disparity, and 3) whether morphological disparity among these clades is consistent with a uniform diversification model. We found equivalent support for constant rates of birth-death and density-dependent speciation processes, with notable outliers having significantly fewer or more species than expected given their age. We also found substantial variation in morphological disparity among these clades, but that variation was broadly consistent with uniform evolutionary rates, despite the existence of diversification outliers. These findings indicate relatively continuous, ongoing morphological diversification within all clades, arguing against conceptual models of adaptive radiation. Additionally, they suggest surprisingly consistent diversification among the majority of these clades, despite tremendous variance in colonization history, habitat valences, and trophic specializations that exist among continental clades of organisms.

opencc-zeroDec 2022View details →

Urbanization drives geographically heterogeneous freshwater salinization in the northeastern United States

Rising trends in freshwater salinity, collectively termed the Freshwater Salinization Syndrome (FSS), constitute a global environmental concern. Given that the FSS has been observed in diverse settings, key questions regarding the causes, trend magnitudes, and consequences remain. Prior work hypothesized that FSS is driven by state factors, such as human-centered land use change, geology, and climate. Here, we identify the fundamental overriding factors driving FSS within the northeastern United States and quantify the diversity of FSS severity within the region. Specifically, we analyzed decadal-scale trends in specific conductance (a salinity proxy) for 333 lotic sites over four decades. Next, we quantified potential variables driving the rising or falling trends, including impervious surface cover (ISC), winter temperature and precipitation, watershed size, and ambient conductance. Temperature and ISC were considered the most likely candidates for predicting FSS severity because road salts have previously emerged as the fundamental regional driver.Most (62.5%) sites exhibited patterns of significantly increasing conductance; thus, the overall regional state reflects advancing FSS. However, others exhibited an absence of change (28.8%) or decreasing values (8.7%), and slope magnitude did change with latitude. Linear modeling demonstrated that two variables—ISC and watershed size—constitute the best predictors of long-termconductance trends and that an intercept not significantly different than zero suggests that the FSS does not reign in the absence of urbanization. We also detected areas with consistently decreasing trends despite moderate ISC. Therefore, within the region, advancing urbanization causes the typical condition of advancing FSS, but heterogeneity also exists.

opencc-zeroDec 2022View details →

Heterogeneity in the abyssal plains: A case study in the Bering Sea

The abyssal plains are vast areas without large-scale topography that occupy much of the ocean floor. Ecological research in these superficially homogenous regions benefits increasingly from non-destructive visual sampling of epifaunal organisms with imaging technology. We analysed images from ultra high-definition towed camera transects at depths around 3500 m across three stations 100–130 km apart in the Bering Sea to ask whether the density and distribution of visible epifauna indicated any substantial heterogeneity. We identified 71 different megafaunal taxa, of which 24 occurred at only one station. Measurements of the two most abundant faunal elements, the holothurian Elpidia minutissima and xenophyophores, indicated significant differences in local densities and patchy aggregations that were strikingly dissimilar among stations. One station was dominated by xenophyophores, one was relatively depauperate in both target taxa as well as other identified megafauna, and the third station was dominated by Elpidia. This is an unexpected level of variation at relatively small spatial scales (~100 km), within comparable transects in a well-mixed oceanic basin, reinforcing the emerging view that abyssal habitats contain landscape heterogeneity at similar spatial scales to terrestrial continental realms.

opencc-zeroJan 2023View details →

Soil microbial community shifts explain habitat heterogeneity in two Haloxylon species from a nutrient perspective

Haloxylon ammodendron and Haloxylon persicum (as sister taxa) are dominant shrubs in the Gurbantunggut Desert. The former grows in inter-dune lowlands while the latter in sand dunes. However, little information is available regarding the possible role of soil microorganisms in their habitat heterogeneity from a nutrient perspective in deserts. Rhizosphere is the interface of plant-microbe-soil interactions and fertile islands usually occur around the roots of desert shrubs. Given this, we applied quantitative real-time PCR combined with MiSeq amplicon sequencing to compare their rhizosphere effects on microbial abundance and community structures at three soil depths (0–20, 20–40, and 40–60 cm). The rhizosphere effects on microbial activity (respiration) and soil properties had also been estimated. The rhizospheres of both shrubs exerted significant positive effects on microbial activity and abundance (e.g. eukarya, bacteria and nitrogen-fixing microbes). The rhizosphere effect of H. ammodendron on microbial activity and abundance of bacteria and nitrogen-fixing microbes was greater than that of H. persicum. However, the fertile island effect of H. ammodendron was weaker than that of H. persicum. Moreover, there existed distinct differences in microbial community structure between the two rhizosphere soils. Soil-available nitrogen, especially nitrate nitrogen was shown to be a driver of microbial community differentiation among rhizosphere and non-rhizosphere soils in the desert. In general, the rhizosphere of H. ammodendron recruited more copiotrophs (e.g. Firmicutes, Bacteroidetes and Proteobacteria), nitrogen-fixing microbes and ammonia-oxidizing bacteria, and with stronger microbial activities. This helps it maintain a competitive advantage in relatively nutrient-rich lowlands. H. persicum relied more on fungi, actinomycetes, archaea (including ammonia-oxidizing archaea) and eukarya, with higher nutrient use efficiency, which help it adapt to the harsher dune crests. This study provides insights into the microbial mechanisms of habitat heterogeneity in two Haloxylon species in the poor desert soil.

opencc-zeroJan 2023View details →

Alpine climate and soils heterogeneity data and simulation results

We developed metrics of climatic and edaphic heterogeneity, using principal components analyses and the shoelace algorithm, and added elevation range. We applied commonality analysis to partition the unique and shared explanation of the observed vascular plant species richness among selected metrics. A simulation was developed to separate the relative importance of area and heterogeneity at different extents and representations of spatial nestedness, and the heterogeneity – effective area tradeoff was evaluated by altering spatial discreteness. The simulations revealed that heterogeneity was consistently more important, but less so among smaller areas. This qualitative pattern was maintained regardless of whether and how nestedness was represented. The heterogeneity – effective area tradeoff occurred in a few simulations of more discrete habitats.

Habitat and not topographic heterogeneity constrains the range sizes of African mammals

Aim: The extinction risks of species are influenced by their geographical range sizes, as species with smaller ranges are more likely to go extinct following disturbance events. Theoretically, heterogeneous landscapes can maintain small-ranged species, because they facilitate the coexistence of taxa that are each constrained to distinct abiotic conditions. However, we do not fully understand whether this process is more attributable to variation in habitat types (habitat heterogeneity) or physical elevations (topographic heterogeneity) across landscapes. Here, we compare the influences of habitat versus topographic heterogeneity on mammalian range sizes in Africa. Location: Africa. Taxon: Mammalia. Methods: We built a phylogenetic generalized least squares model to predict the range sizes of 1033 mammalian species from their functional traits and abiotic conditions. We assessed how the performance of the model changed when we incorporated measures of the local habitat and, separately, topographic heterogeneity that species experience. Results: Habitat and topographic heterogeneity are weakly correlated across Africa (ρ = 0.14). Habitat heterogeneity is inversely related to range size (model coefficient = −0.88). Incorporating habitat heterogeneity significantly decreased the model's AICc, increased its likelihood and increased the proportion of variance that is explained in the range sizes of species. Conversely, topographic heterogeneity is not significantly related to range size and had no impact on the model's AICc, likelihood or predictive performance. This contrast between habitat and topographic heterogeneity is particularly prevalent in carnivorous mammalian clades. Results at multiple spatial resolutions differed minimally. Main Conclusions: Our findings advance ecological theory by demonstrating that a landscape's variation in habitats, and not in elevations, relates inversely with mammalian range size and therefore facilitates the coexistence of small-ranged mammals. Conservation efforts in regions of high habitat heterogeneity will be critical to prevent extinctions in Africa's biodiverse mammalian species.

opencc-zeroJan 2023View details →

nRCFV: A sequence, taxon and character state-normalised metric for the pre-reconstruction evaluation of compositional heterogeneity

Motivation Compositional heterogeneity – when the proportions of nucleotides and amino acids are not broadly similar across the dataset – is a cause of a great number of phylogenetic artefacts. Whilst a variety of methods can identify it post-hoc, few metrics exist to quantify compositional heterogeneity prior to the computationally intensive task of phylogenetic tree reconstruction. Here we assess the efficacy of one such existing, widely used, metric: Relative Composition Frequency Variability (RCFV), using both real and simulated data. Results Our results show that RCFV can be biased by sequence length, the number of taxa, and the number of possible character states within the dataset. However, we also find that missing data does not appear to have an appreciable value on RCFV. We discuss the theory behind this and the consequences of this for the future of the usage of the RCFV value and propose a new metric, nRCFV, which accounts for these biases. Alongside this, we present a new software that easily calculates both RCFV and nRCFV, called nRCFV_Reader. Availability and Implementation nRCFV has been implemented in RCFV_Reader, available at: <a href="https://github.com/JFFleming/RCFV_Reader">https://github.com/JFFleming/RCFV_Reader</a>. Both our simulation and real data are available in this dataset.

Fijian sea krait behavior relates to fine‐scale environmental heterogeneity in old‐growth coastal forest: The importance of integrated land–sea management for protecting amphibious animals

Here the data for "Fijian sea krait behaviour relates to fine-scale environmental heterogeneity in old growth forest: the importance of integrated land-sea management for protecting amphibious animals" by Lowe, C., Keppel, G., Waqa, K., Peters, S., Fisher, R.N., Scanlon, A., Osborne-Naikatini, T, and Thomas-Moko, N is provided. This article investigates the habitat of Yellow Lipped Sea Kraits, Laticauda colubrina, in the terrestrial realm on Leluvia Island, a small, topographically flat atoll in Fiji with coastal forest. The investigation uses concurrent microclimate measurements and behaviour surveys, as well as vegetation surveys, and the data collected for these analyses are provided here. Microclimates were significantly related to canopy cover, leaf litter depth, and distance from the high-water mark (HWM). Sea kraits were almost exclusively observed in coastal forest within 30 m of the HWM. Sloughing of skins only occurred within crevices of mature or dying trees. Resting L. colubrina were significantly more likely to occur at locations with higher mean diurnal temperatures, lower leaf litter depths, and shorter distances from the HWM. On Leleuvia, behaviour of L. colubrina therefore relates to environmental heterogeneity created by old-growth coastal forests, particularly canopy cover and crevices in mature and dead tree trunks. The importance of healthy coastal habitats, both terrestrial and marine, for L. colubrina suggests it could be a good flagship species for advocating integrated land-sea management. Furthermore, our study highlights the importance of coastal forests and topographically flat atolls for biodiversity conservation. Effective conservation management of amphibious species that utilise land- and seascapes is therefore likely to require a holistic approach that incorporates connectivity among ecosystems and environmental heterogeneity at all relevant scales.

Data from: Habitat heterogeneity determines species richness on small habitat islands in a fragmented landscape

Aim: The small-island effect (SIE), as an exception to the species-area relationship, has received much attention in true island systems. However, the prevalence and related patterns of the SIE have not been well evaluated in habitat island systems. Here, we aimed to identify the existence of SIE for habitat islands in fragmented landscapes and determine the key factors influencing species richness on small habitat islands. Location: Inner Mongolia Autonomous Region, China. Taxon: Vascular plants. Methods: Based on 78 grassland fragments in fragmented landscapes of the agro-pastoral ecotone of northern China, we used piecewise regression, path analysis, and null models to investigate the SIE of the species-area relationship. We then used a multi-model selection to evaluate the impacts of four influencing factors (instability, isolation, habitat heterogeneity, and surrounding productivity) on species richness (including habitat specialists and generalists) on small habitat islands within the range of SIE. Results: We found an obvious threshold of 5.1 ha in the species-area relationship, below which habitat island area had no direct and indirect effects on species richness. Small habitat islands (< 5.1 ha) host a lower percentage of habitat specialists and a higher percentage of generalists. On small habitat islands, species richness was positively affected by habitat heterogeneity while negatively affected by instability and isolation. Habitat heterogeneity had the strongest effect on species richness, positively affecting specialist richness while negatively affecting generalist richness. Main conclusions: There is a SIE in fragmented landscapes of the agro-pastoral ecotone of northern China, which should be considered in biodiversity conservation. Habitat heterogeneity had a key role in determining the pattern of species richness, especially for small islands. Habitat specialists and generalists had different SIE-related patterns. Our study highlights the importance of considering different ecological groups of species to improve our understanding of the SIE in fragmented habitats.

Plant functional traits predict heterogeneous distributional shifts in response to climate change

Climate change is causing the rapid redistribution of vegetation as plant species move to track their climatic optima. Despite a global trend of upward movement in latitude and elevation, there is extensive heterogeneity among species and locations, with few emerging generalizations. Greater generalization may be achieved by considering multidimensional changes in species' distributions as well as incorporating ecologically relevant functional traits into studies of range shifts. To better understand how recent changes in climate are influencing the elevational distribution of plant species and how species' functional traits mediate distributional changes, we resampled a 2,438-meter elevation transect spanning a distance of 16 kilometers which encompasses desert scrub, pinyon-juniper woodland, chaparral, and coniferous forest plant communities. Over the last 42 years, total perennial cover and species' average cover increased at lower elevations and decreased at higher elevations while the average elevational leading-edge increased 116 m and the elevational rear edge decreased 84 m. Notably, these changes were mediated by species' functional traits, where species exhibiting more conservative traits (lower SLA, greater δ13C, larger seed mass) and taller height shifted upward in their leading-edge range limit, average elevation, and trailing edge range limit, while declining in abundance at the median and trailing edge of their range. Species possessing more acquisitive traits (higher SLA, lower δ13C, smaller seed mass) and shorter height shifted downward and increased in abundance at their trailing edge, with increases in their total range size. Our results provide clear evidence that heterogeneous range dynamics under recent climate change can be generalized by considering ecologically relevant plant functional traits, and how they respond to localized climate exposure. Further, by documenting changes across a steep ecological gradient comprising a large aridity gradient, we show divergent patterns for plants occupying contrasting positions along the global spectrum of plant form and function, which provides critical insight into how trait-mediated changes under increasing aridity will impact ecosystem functioning.

opencc-by-4.0Feb 2023View details →

Data for Whole-cell modeling of E. coli colonies enables quantification of single-cell heterogeneity in the antibiotic response

Data from simulations used to generate the figures in the paper Whole-cell modeling of E. coli colonies enables quantification of single-cell heterogeneity in the antibiotic response. To reproduce analyses, extract colony_data.zip in the data folder after cloning the vivarium-ecoli repository. The extracted folder contains the following items: <ul> <li>sim_dfs: a folder containing the CSV files that represent a subset of the raw simulation data used for downstream analyses.</li> <li>glc_10000_fluxome.csv: Each row represents a reaction in central carbon metabolism (in same order as listed in validation/ecoli/flat/toya_2010_central_carbon_fluxes.tsv). Each column represents a single time point for a single cell in a baseline glucose simulation (seed 10000). Each value is a flux (mmol/L/hr). Provided as input to ecoli/analysis/centralCarbonMetabolism.py script to reproduce fluxome validation plot.</li> <li>glc_10000_proteome_avgs.csv: Each row represents a protein monomer (in same order as sim_data.translation.monomer_data["id"] where sim_data is reconstruction/sim_data/kb/validationData.cPickle). Each column represents a cell in a baseline glucose simulation (seed 10000). Each row represents a protein monomer. Each value represents the average count of a given protein monomer for a given cell. Provided as input to ecoli/analysis/proteinCountsValidation.py script to reproduce proteome validation plot.</li> <li>glc_10000_expressome.csv: Each column represents a gene (with the exception of the final two metadata columns: "Time" and "Agent ID"). Each row represents a specific cell (agent) at a specific time in a baseline glucose simulation (seed 10000). Each value represents the number of new RNA transcripts for a given gene in a given cell at a given time. Provided as input to ecoli/analysis/antibiotics_colony/subgen_gene_plots/count_subgen.py script to calculate number of sub-generational genes among all genes and antibiotic response genes.</li> <li>glc_10000_total_mrna.json: Mapping of agent IDs for all cells in a baseline glucose simulation (seed 10000) to their average total mRNA count. Used by ecoli/analysis/antibiotics_colony/plot.py to generate Fig. 2C,D.</li> <li>jenner_2013.csv: Data extracted from Fig. 2C of <a href="https://doi.org/10.1073/pnas.1216691110">10.1073/pnas.1216691110</a>. Used by ecoli/analysis/antibiotics_colony/plot.py to generate Fig. S6A.</li> <li>olson_2006.csv: Data extracted from Fig. 2D of <a href="https://doi.org/10.1128%2FAAC.01499-05">10.1128/AAC.01499-05</a>. Used by ecoli/analysis/antibiotics_colony/plot.py to generate Fig. S6A.</li> <li>lysis_ratios.csv: Data extracted from Fig. 2 of <a href="https://doi.org/10.1099/00221287-31-3-339">10.1099/00221287-31-3-339</a>. Used by ecoli/analysis/antibiotics_colony/plot.py to generate Fig. 4N.</li> </ul>

opencc-by-4.0Mar 2023View details →

HADES: An NFV solution for energy-efficient placement and resource allocation in heterogeneous infrastructures. Study dataset

The publication and research associated with this dataset are currently under review in the Journal of Network and Computer Applications. In that research, we present HADES, an NFV solution for energy-efficient placement and resource allocation in heterogeneous infrastructures. HADES is an OSM (Open Source MANO)  extension that allows the configuration of virtual network functions and their subsequent resource allocation and deployment at the edge, minimizing energy consumption and ensuring the quality of service. This dataset contains the following: <ul> <li>1 CSV file with execution time results of the iTAREA module for (60) different problem sizes and (3) execution environments.</li> <li>1 CSV file with energy consumption results of HADES deployments and other 5 assignment policies: First-fit, Random-fit, Fastest-fit, Best-fit, and kube-scheduler (the Kubernetes’ assignment policy).</li> </ul> This work is supported by the European Union's H2020 research and innovation programme under grant agreement DAEMON 101017109 and by the projects co-financed by FEDER funds LEIA UMA18-FEDERJA-15 and IRIS PID2021-122812OB-I00 (MCI/AEI).