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opencc-by-4.0Oct 2021View details →

Archival bundle of the data used for "Predictive Auto-scaling with OpenStack Monasca" (UCC 2021)

This archive contains the data used for the paper Predictive Auto-scaling with OpenStack Monasca <a href="mailto:giacomo.lanciano@sns.it">Giacomo Lanciano</a>*, Filippo Galli, Tommaso Cucinotta, Davide Bacciu, Andrea Passarella 2021 IEEE/ACM 14th International Conference on Utility and Cloud Computing (UCC) <a href="https://doi.org/10.1145/3468737.3494104">10.1145/3468737.3494104</a> Follow the instructions provided in the <a href="https://github.com/giacomolanciano/UCC2021-predictive-auto-scaling-openstack">companion repo</a> to automatically download and decompress the archive. The following files are included: <table> <tbody> <tr> <td>File</td> <td>Description</td> </tr> <tr> <td> amphora-x64-haproxy.qcow2 </td> <td> Image used to create Octavia amphorae </td> </tr> <tr> <td> distwalk-{lin,mlp,rnn,stc}-<INCREMENTAL-ID>.log </td> <td> distwalk run log </td> </tr> <tr> <td> distwalk-{lin,mlp,rnn,stc}-<INCREMENTAL-ID>-pred.json </td> <td> Predictive metric data exported from Monasca DB </td> </tr> <tr> <td> distwalk-{lin,mlp,rnn,stc}-<INCREMENTAL-ID>-real.json </td> <td> Actual metric data exported from Monasca DB </td> </tr> <tr> <td> distwalk-{lin,mlp,rnn,stc}-<INCREMENTAL-ID>-times.csv </td> <td> Client-side response time for each request sent during a run </td> </tr> <tr> <td> model_dumps/* </td> <td> Dumps of the models and data scalers used for the validation </td> </tr> <tr> <td> predictor.log </td> <td> monasca-predictor log </td> </tr> <tr> <td> predictor-times.log </td> <td> monasca-predictor` log (timing info only) </td> </tr> <tr> <td> predictor-times-{lin,mlp,rnn}.{csv,log} </td> <td> monasca-predictor log (timing info only, group by predictor) </td> </tr> <tr> <td> super_steep_behavior.csv </td> <td> Dataset used to train MLP and RNN models </td> </tr> <tr> <td> test_behavior_02_distwalk-6t_last100.dat </td> <td> distwalk load trace </td> </tr> <tr> <td> ubuntu-20.04-min-distwalk.img </td> <td> Image used to create Nova instances for the scaling group </td> </tr> </tbody> </table> * contact author

opencc-by-4.0Oct 2021View details →

Data-base for : 'Partitioning carbon sources between wetland and well-drained ecosystems to a tropical first-order stream - Implications to carbon cycling at the watershed scale (Nyong, Cameroon)'

Dataset of carbon (pCO2, TA, DIC, DOC, POC) and ancillary parameters (water temperature, oxygen saturation, pH, specific conducitivity) in ground and surface waters of the Nyong watershed (Cameroon). The dataset covers one entire year (in 2016) and thus allows describing the varability of carbon and ancillary paramaters concentrations induced by seasons.

Developing National Identity Scale: As Indonesian Case

Background: National identity is an important concept to be developed, so it is necessary to have a measurement instrument with evidence of validity and reliability. Thus, the accuracy of the information obtained through the measurement of this instrument will be guaranteed.   Objective: This article aims to test the psychometric properties of the national identity scale to fulfil the standardization of good measurement.   Method: In this study, three analytical approaches were used: content validity involving eight subject matter experts (SME), confirmatory factor analysis (CFA), and reliability analysis. For the reliability and CFA approach, 300 students were used as samples taken through the convenience sampling technique.   Result: The analysis results show that out of the 20 items compiled in the content validity analysis, one item is inadequate because it has a below standard score on Aiken's coefficient of validity. This one item was revised again to be included in the tryout and data collection for the following analysis stage. The results of the CFA analysis show that the model and data are fit, and there are two inadequate items. At the same time, the contribution of the three factors on the national identity scale is significant. In the third analysis, it was found that adequate coefficient reliability affected the low standard error measurement (SEM).   Conclusion: Based on the analysis results, it can be concluded that the Indonesian national identity scale has fulfilled good psychometric properties. It can be proven from evidence validity based on content, confirmatory factor analysis (CFA), and reliability analysis.

Fine-scale spatial patterns of wildlife disease are common and understudied

1. All parasites are heterogeneous in space, yet little is known about the prevalence and scale of this spatial variation, particularly in wild animal systems. To address this question, we sought to identify and examine spatial dependence of wildlife disease across a wide range of systems. 2. Conducting a broad literature search, we collated 31 such datasets featuring 89 replicates and 71 unique host-parasite combinations, only 51% of which had previously been used to test spatial hypotheses. We analysed these datasets for spatial dependence within a standardised modelling framework using Bayesian linear models, and we then meta-analysed the results to identify generalised determinants of the scale and magnitude of spatial autocorrelation. 3. We detected spatial autocorrelation in 48/89 model replicates (54%) across 21/31 datasets (68%), spread across parasites of all groups. Even some very small study areas (under 0.01km2) exhibited substantial spatial variation. 4. Despite the common manifestation of spatial variation, our meta-analysis was unable to identify host-, parasite-, or sampling-level determinants of this heterogeneity across systems. Parasites of all transmission modes had easily detectable spatial patterns, implying that structured contact networks and susceptibility effects are potentially as important in spatially structuring disease as are environmental drivers of transmission efficiency. 5. Our findings demonstrate that fine-scale spatial patterns of infection manifest frequently and across a range of wild animal systems, and many studies are able to investigate them – whether or not the original aim of the study was to examine spatially varying processes. Given the widespread nature of these findings, studies should more frequently record and analyse spatial data, facilitating development and testing of spatial hypotheses in disease ecology. Ultimately, this may pave the way for an a priori predictive framework for spatial variation in novel host-parasite systems.

opencc-zeroDec 2021View details →

Large-scale eDNA metabarcoding survey reveals marine biogeographic break and transitions over tropical north-western Australia

Aim: Environmental DNA (eDNA) metabarcoding has demonstrated its applicability as a highly sensitive biomonitoring tool across small spatial and temporal scales in marine ecosystems. However, it has rarely been tested across large spatial scales, or biogeographical barriers. Here, we scale up marine eDNA metabarcoding, test its ability to detect a major marine biogeographic break, and evaluate its use as a regional biomonitoring tool in Australia. Location: North-western Australia (NWA) Methods: We applied metabarcoding assays targeting the mitochondrial 16S rRNA and CO1 genes to 284 surface seawater eDNA samples collected from 71 mid-shelf, inshore, coastal and nearshore estuarine sites over 700 km of the NWA coastline. Results: Metabarcoding detected a wide range of bony fish (404 taxa), elasmobranchs (44) and aquatic reptiles (5). We detected bioregional and depth differentiation within inshore bony fish communities. These findings support the presence of a marine biogeographic break, which is purported to occur in the vicinity of Cape Leveque, demarcating the border between the Kimberley and Canning bioregions. Inshore bony fish and elasmobranch communities, as well as coastal bony assemblages, were additionally found to differ between the South and North Kimberley regions suggesting previously unrecognised subregional differentiation among these taxa. The overall compositional data has been used to update distribution information for a number of endangered, elusive and data-deficient taxa, including sawfish (family: Pristidae), northern river shark (Glyphis garricki) and wedgefish (genus: Rhynchobatus). Main conclusions: eDNA metabarcoding demonstrated a high level of sensitivity that was able to discern fine-scale patterns across the large-scale, remote and oceanographically complex region of North-western Australia. Importantly, this study highlights the potential of integrating broad-scale eDNA metabarcoding alongside other baseline surveys and long-term monitoring approaches, which are crucial for the sustainable management and conservation of marine biodiversity in this unique marine region.

Disentangling effects of climate and land use on biodiversity and ecosystem services – a multi-scale experimental design

1. Climate and land-use change are key drivers of environmental degradation in the Anthropocene, but too little is known about their interactive effects on biodiversity and ecosystem services. Long-term data on biodiversity trends are currently lacking. Furthermore, previous ecological studies have rarely considered climate and land use in a joint design, did not achieve variable independence or lost statistical power by not covering the full range of environmental gradients. 2. Here, we introduce a multi-scale space-for-time study design to disentangle effects of climate and land use on biodiversity and ecosystem services. The site selection approach coupled extensive GIS-based exploration and correlation heatmaps with a crossed and nested design covering regional, landscape and local scales. Its implementation in Bavaria (Germany) resulted in a set of study plots that maximize the potential range and independence of environmental variables at different spatial scales. 3. Stratifying the state of Bavaria into five climate zones (reference period 1981–2010) and three prevailing land-use types, i.e. near-natural, agriculture and urban, resulted in 60 study regions (5.8x5.8 km quadrants) covering a mean annual temperature gradient of 5.6–9.8 °C and a spatial extent of ~310x310 km. Within these regions, we nested 180 study plots located in contrasting local land-use types, i.e. forests, grasslands, arable land or settlement (local climate gradient 4.5–10 °C). This approach achieved low correlations between climate and land use (proportional cover) at the regional and landscape scale with |r≤0.33| and |r≤0.29|, respectively. Furthermore, using correlation heatmaps for local plot selection reduced potentially confounding relationships between landscape composition and configuration for plots located in forests, arable land and settlements. 4. The suggested design expands upon previous research in covering a significant range of environmental gradients and including a diversity of dominant land-use types at different scales within different climatic contexts. It allows independent assessment of the relative contribution of multi-scale climate and land use on biodiversity and ecosystem services. Understanding potential interdependencies among global change drivers is essential to develop effective restoration and mitigation strategies against biodiversity decline, especially in expectation of future climatic changes. Importantly, this study also provides a baseline for long-term ecological monitoring programs.

opencc-by-4.0Feb 2021View details →

Specimens from Brand et al. 2021, "Large-scale phylogenomics of the genus Macrostomum (Platyhelminthes) reveals cryptic diversity and novel sexual traits"

The deposited folders contain image and video material of free-living flatworm specimens that were documented in vivo. These data support the following publication: Jeremias N. Brand, Gudrun Viktorin, R. Axel W. Wiberg, Christian Beisel, Lukas Schärer. Large-scale phylogenomics of the genus Macrostomum (Platyhelminthes) reveals cryptic diversity and novel sexual traits. Molecular Phylogenetics and Evolution. Volume 166. 2022. <a href="https://doi.org/10.1016/j.ympev.2021.107296">https://doi.org/10.1016/j.ympev.2021.107296</a> For more information about these specimens see also http://macrostomorpha.info.

Termite trait data from: Continental-scale shifts in termite diversity and nesting and feeding strategies

Typically, termites are treated as a single guild, which ignores important internal diversity, including diverse feeding and nesting traits. These termite traits are crucial for both ecosystem-level fluxes and trophic webs, with implications for vertebrate species. Despite their ecological importance, the large-scale distribution of termite feeding and nesting traits and the relationship with termite diversity is largely unknown. We investigated whether functional diversity, species richness, and feeding (wood, litter, grass, dung) and nesting trait (aboveground mound, belowground nest, inside tree or outside tree nest) distributions of termites were climatically control. To address this gap, we assembled a continental-scale database of termite traits and occurrence in Australia and modelled termite nesting and feeding traits in response to macroclimate. Functional richness and evenness increased primarily with temperature. Australia showed multiple hotspots of termite diversity with each hotspot showing a distinct guild composition. The large-scale distribution of nesting traits showed that aboveground nesting species were the most common nesting guild in the dry and wet tropics while belowground nesting dominated in seasonally cold arid environments, demonstrating a strong climatic control on nesting strategy. Given their large biomass and many interactions with other species, the macro-ecology of termite traits may be especially important in predicting shifts in other species' distributions at continental and global scales.

Fine-scale spatial segregation in a pelagic seabird driven by differential use of tidewater glacier fronts

<div class="WordSection1"> In colonially breeding marine predators, individual movements and colonial segregation are influenced by seascape characteristics. Tidewater glacier fronts are important features of the Arctic seascape and are often described as foraging hotspots. Albeit their documented importance for wildlife, little is known about their structuring effect on arctic predator movements and space use. In this study, we tested the hypothesis that tidewater glacier fronts can influence marine bird foraging patterns and drive spatial segregation among adjacent colonies. We analysed movements of black-legged kittiwakes (Rissa tridactyla) in a glacial fjord by tracking breeding individuals from five colonies. Although breeding kittiwakes were observed to travel up to ca. 280 km from the colony, individuals were more likely to use glacier fronts located closer to their colony and rarely used glacier fronts located farther away than 18 km. Such variation in the use of glacier fronts created fine-scale spatial segregation among the four closest (ca. 7 km distance on average) kittiwake colonies. Overall, our results support the hypothesis that spatially predictable foraging patches like glacier fronts can have strong structuring effects on predator movements and can modulate the magnitude of intercolonial spatial segregation in central-place foragers. </div>

R scripts for "Using LiDAR to assess the influence of fine-scale habitat structure on the abundance of the bearded reedling (Panurus biarmicus)"

Dataset which contains R scripts and R package SDMaps used for data preparation and modelling in the methodology described in my MSc thesis "Using LiDAR to assess the influence of fine-scale habitat structure on the abundance of the bearded reedling (Panurus biarmicus)". The project involved creating Species Distribution Models to test whether and how fine-scale habitat structure - in the form of LiDAR derived variable - influences the relative abundance of the bearded reedling in the Netherlands, beyond other variables such as land use, soil type and climate data. These scripts can serve as an example of how the SDMaps package can be used to build Species Distribution Models that include LiDAR derived variables, and to replicate some of the methodologies described in the thesis. The SDMaps package contains an installation guide, manual, tutorial and examples.

opencc-by-4.0Dec 2012View details →

Fig. 1 in Scale-Morphometry Study To Discriminate Gibel Carp (Carassius Gibelio) Populations In The Balaton-Catchment (Hungary)

Fig. 1. Overlooking map of sampling areas

Data for "Can Regenerative Agriculture increase national soil carbon stocks? Simulated country-scale adoption of reduced tillage, cover cropping, and ley-arable integration using RothC"

R code and supplementary data for soil carbon simulations: "Can Regenerative Agriculture increase national soil carbon stocks? Simulated country-scale adoption of reduced tillage, cover cropping, and ley-arable integration using RothC-26.3"

Data supporting the study "The evolution of surface structure during atmospheric ageing of nano-scale coatings of an organic surfactant aerosol proxy" by Milsom et al.

Reduced neutron reflectometry (NR) data associated with the study "The evolution of surface structure during atmospheric ageing of nano-scale coatings of an organic surfactant aerosol proxy" by Milsom et al.. One folder contains the raw data for fitted parameters obtained from NR curves and supporting figure 3 in the study. The other contains a set of sub-folders which have reduced NR data along with python scripts which were used to create and fit the interfacial model to the data. Fitting bounds for each parameter are found in these scripts.

Multi-Scale Computational Screening to Accelerate Discovery of IL/COF Composites for Flue Gas Separation

Covalent organic frameworks (COFs) have emerged as novel adsorbents and membranes for gas separation. Incorporation of ionic liquids (ILs) into COFs is important to exceed the current performance limits of COFs. However, synthesis and testing of a nearly unlimited number of IL/COF combinations are simply impractical. Herein, we used a multi-scale computational screening approach combining COnductor-like Screening MOdel for Realistic Solvents (COSMO-RS) method, Grand Canonical Monte Carlo (GCMC), molecular dynamics (MD) simulations, and density functional theory (DFT) calculations to unlock both the adsorption- and membrane-based CO2/N2 separation performances of IL/COF composites. Several adsorbent and membrane performance assessment metrics including selectivity, working capacity, regenerability, adsorbent performance score, and permeability were computed. Our results revealed that IL-incorporation into COFs significantly improved CO2/N2 adsorption selectivities (from 12 to 26) and adsorbent performance scores (from 3.7 to 12 mol/kg). By performing DFT calculations, the nature of the interactions between CO2, N2, COFs and their IL-incorporated composites were evaluated. The high CO2 selectivity of IL/COF composites was attributed to the cooperative intermolecular effects induced by the COF and the IL. Finally, IL/COF membranes were studied, and results showed that they achieve significantly higher CO2 permeabilities (2.4 104-9.4 105 Barrer) than polymeric and zeolite membranes and comparable selectivities (up to 15.7), which hold great promise to replace conventional materials in membrane-based flue gas separation applications. Our results will be useful in accelerating experimental efforts to design new IL/COF composites that can achieve high-performance CO2 separation.

opencc-zeroDec 2021View details →

Counterintuitive scaling between population abundance and local density: implications for modelling transmission of infectious diseases in bat populations

1. Models of host-pathogen interactions help to explain infection dynamics in wildlife populations and to predict and mitigate the risk of zoonotic spillover. Insights from models inherently depend on the way contacts between hosts are modelled, and crucially, how transmission scales with animal density. 2. Bats are important reservoirs of zoonotic disease and are among the most gregarious of all mammals. Their population structures can be highly heterogenous, underpinned by ecological processes across different scales, complicating assumptions regarding the nature of contacts and transmission. Although models commonly parameterise transmission using metrics of total abundance, whether this is an ecologically representative approximation of host-pathogen interactions is not routinely evaluated. 3. We collected a 13-month dataset of tree-roosting Pteropus spp. from 2,522 spatially referenced trees across eight roosts to empirically evaluate the relationship between total roost abundance and tree-level measures of abundance and density – the scale most likely to be relevant for virus transmission. We also evaluate whether roost features at different scales (roost-level, subplot-level, tree-level) are predictive of these local density dynamics. 4. Roost-level features were not representative of tree-level abundance (bats per tree) or tree-level density (bats per m2 or m3), with roost-level models explaining minimal variation in tree-level measures. Total roost abundance itself was either not a significant predictor (tree-level 3-D density) or only weakly predictive (tree-level abundance). 5. This indicates that basic measures, such as total abundance of bats in a roost, may not provide adequate approximations for population dynamics at scales relevant for transmission, and that alternative measures are needed to compare transmission potential between roosts. From the best candidate models, the strongest predictor of local population structure was tree density within roosts, where roosts with low tree density had a higher abundance but lower density of bats (more spacing between bats) per tree. 6. Together, these data highlight unpredictable and counterintuitive relationships between total abundance and local density. More nuanced modelling of transmission, spread and spillover from bats likely requires alternative approaches to integrating contact structure in host-pathogen models, rather than simply modifying the transmission function.

COBALTO data set at large at CIEM large scale wave flume

The experiments carried out are framed within the COBLTO project (CTM2017-88036-R) and the doctoral thesis of Carlos Astudillo. A surrogate Posidonia meadow has been used to study the wave attenuation, velocity affections and changes in sediment transport due to the comparison of experiments with the meadow and the benchmark cases where the meadow was absent on the flume experiments. Two different wave conditions, high energy waves and low energy waves, have been considered. The case with higher energy was also repeated with a third configuration in which a meadow length of 5 m was also studied.

EnGRaiN : A Supervised Ensemble Learning Method for Recovery of Large-scale Gene Regulatory Networks

EnGRaiN is a supervised machine learning method to construct ensemble networks. To benefit from the typical accuracy advantages of supervised learning methods while taking into account the impossibility of knowing true networks for training, we devised a method that uses small training datasets of true positives and true negatives among gene pairs. The datasets used to evaluate the performance of EnGaiN include (i) simulated datasets generated from Yeast networks and (ii) A. thaliana gene expression datasets.

opencc-zeroDec 2021View details →

Scale dependence of drilling predation in the Holocene of the northern Adriatic Sea across benthic habitats and nutrient regimes

Predation has strongly shaped past and modern marine ecosystems, but the scale dependency of patterns in drilling predation, the most widely used proxy for predator-prey interactions in the fossil record, is a matter of debate. To assess the effects of spatial and taxonomic scale on temporal trends in the drilling frequencies (DF), we analyzed Holocene molluscan assemblages of different benthic habitats and nutrient regimes from the northern Adriatic shelf in a sequence stratigraphic context. Although it has been postulated that low predation pressures facilitated the development of high-biomass epifaunal communities in the eastern, relatively oligotrophic portion of the northern Adriatic shelf, DFs reaching up to 30-40% in the studied assemblage show that drilling predation levels are comparable to those typical of Late Cenozoic ecosystems. DFs tend to increase from the transgressive systems tract (TST) into the highstand systems tract (HST) at the local scale, reflecting an increase in water depth by 20-40 m and a shift from infralittoral to circalittoral habitats over the past 10,000 years. As transgressive deposits are thicker at shallower and highstand deposits are thicker at deeper locations, a regional increase in DFs from TST to HST is evident only when these differences are accounted for. The increase in DF towards the HST can be recognized at the level of total assemblages, classes and few abundant and widespread families, but it disappears at the level of genera and species because of their specific environmental requirements, leading to uneven or patchy distribution in space and time.

Scale growth data for analysis in Vollset et al. 2021

Scale samples of adult Atlantic salmon were compiled from 180 rivers in Norway, which comprise almost half of all Atlantic salmon rivers in Norway, during 1989-2016. The scales were collected by anglers when sport fishing in the various rivers. The back-calculation of fish length is based on the linear relationship between fish length and the diameter of the fish scale from the centre of the scale to the edge . We have focused on the average growth across four large geographic regions: South-western, south-western, middle-, and north Norway. In total, 52 371 Atlantic salmon were sampled by fishers. For each individual fish, the following data were used: length at capture (cm), back-calculated freshwater growth (cm), back-calculated early marine growth (cm), and smolt year, which is the year they migrated from the rivers as juveniles to the sea. Freshwater growth was defined as the distance from the centre of the scale to the end of the freshwater zone in the scale. Early marine growth, also termed post-smolt growth, was measured as the distance between the end of the freshwater zone and the end of the first winter at sea. Growth estimates from scales may be impacted by the size of the fish when they leave the rivers and enter the sea. To correct for this error, a relative growth estimate can be used where the early marine growth is divided by the freshwater growth of the individual, which we refer to as relative growth. Also, the timing of out-migration will vary by up to two months from north to south in Norway, meaning that the time to grow before winter is shorter for northern populations. Putative monthly growth estimates indicate that growth is limited from November, and we therefore calculate growth from day of out-migration to 31 October. Day of out migration was calculated according to using a model that explains out-migration data based on latitude, longitude, air temperature during winter, and river discharge. The estimated growth is called relative growth per day.