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opencc-by-4.0Apr 2022View details →

Indicator values for the many-body localization of the Heisenberg spin chain at various energies, system sizes and disorder magnitude

This data set accompanies the preprint Scalable approach to many-body localization via quantum data (arXiv: <a href="https://arxiv.org/abs/2202.08853">2202.08853</a>) and its code, available at <a href="https://github.com/GreschAl/MBLlearning">GitHub</a>. It consists of the numerically obtained indicator values for the many-body localization for the Heisenberg model (see preprint for details and background) for various values of the energy density \(\epsilon = 0.05, 0.1, \dots, 0.9, 0.95\) and for chain lengths \(L = 10, 12, 14\). For each tuple \((\epsilon,L)\), there exist two files, representing the training and the test set, respectively. Each such file contains various values of the disorder parameter \(h = 0.5, 1, \dots, 14.5, 15\) with \(N = 1000\ (100)\) sampled realizations of the disorder vector for each \(h\) for the training (test) set, followed by the three calculated values of the three indicators. The data is automatically processable by the code provided in the GitHub repository.

opencc-zeroMay 2022View details →

Chronogram or phylogram for ancestral state estimation? Model-fit statistics indicate the branch lengths underlying a binary character's evolution: R scripts and simulated trees

All R scripts used in this study, and the set of simulated phylogenetic trees used in the study. 1. Modern methods of ancestral state estimation (ASE) incorporate branch length information, and it has been demonstrated that ASEs are more accurate when conducted on the branch lengths most correlated with a character's evolution; however, a reliable method for choosing between alternate branch length sets for discrete characters has not yet been proposed. 2. In this study, we simulate paired chronograms and phylograms, and generate binary characters that evolve in correlation with one of these. We then investigate (1) the effect of alternate branch lengths on ASE error, and (2) whether phylogenetic signal statistics and/or model-fit statistic can be used to select the branch lengths most correlated with a binary character. 3. In agreement with previous studies, we find that ASEs are more accurate when conducted on the branch lengths most correlated with the character. Phylogenetic signal statistics show limited utility for selecting the correct branch lengths, but model-fit statistics are found to be more accurate, with the correct branch lengths generally returning greater model-fit (lower AICc and BIC values). Using this method to choose between alternate branch length sets is more accurate when tree and character properties are more favorable for model optimization, and when shape differences between alternate phylogenies are greater. 4. Our results indicate that researchers conducting ASEs on discrete characters should carefully consider which branch lengths are appropriate, and, in the absence of other evidence, we suggest estimating model-fit values over alternate branch length sets and evolutionary models and choosing the branch length/model combination that returns better model fit.

opencc-by-4.0May 2022View details →

Plant–insect interactions from the mid-Cretaceous at Puy-Puy (Aquitaine Basin, western France) indicates preferential herbivory for angiosperms amid a forest of ferns, gymnosperms, and angiosperms

The nine in-text figures and table below (Appendices S1–S10), and the additional text and excel files attached, provide the raw data, summaries of the raw data, rarefaction analyses, and nonmetric multidimensional scale analyses (NMDS) that support the discussions of the main text. The raw data and their summaries of provide for each plant species or morphotype values important for assessment of their herbivory: percentage of specimens herbivorized, damage type (DT) richness, DT frequency, DT host-plant specificity, herbivorized surface area as a proportion of total surface area, and feeding event occurrences. The rarefaction analyses furnished evaluations of whether the number of samples was sufficient, given the surface area covered by those samples. For comparison, the number of samples was rarified to the number of DTs in those samples. Lastly, two NMDS analyses produced the relationships between the plant orders present in the plant assemblage and their interactive functional feeding groups (FFGs). A separate NMDS analysis shows the association between the three most herbivorized species and their FFGs.

opencc-zeroJun 2022View details →

Close kin dyads indicate intergenerational dispersal and barriers

The movement of individuals through continuous space is typically constrained by dispersal ability and dispersal barriers. A range of approaches have been developed to investigate these. Kindisperse is a new approach that infers intergenerational dispersal (σ) from close kin dyads, and appears particularly useful for investigating taxa that are difficult to observe individually. This study, focusing on the mosquito Aedes aegypti, shows how the same close kin data can also be used for barrier detection. We empirically demonstrate this new extension of the method using genome-wide sequence data from 266 Ae. aegypti. First, we use the spatial distribution of full-sib dyads collected within one generation to infer past movements of ovipositing female mosquitoes. These dyads indicated the relative barrier strengths of two roads, and performed favourably against alternative genetic methods for detecting barriers. The difference in variance between the sib and first cousin spatial distributions was used to infer movement over the past two generations, providing estimates of intergenerational dispersal (σ = 81.5-197.1 m.gen-1/2) and density (ρ = 833-4864 km-2). Dispersal estimates showed general agreement with those from mark-release-recapture studies. Barriers, σ, ρ, and neighbourhood size (331-526) can inform forthcoming releases of dengue-suppressing Wolbachia bacteria into this mosquito population.

opencc-zeroJun 2022View details →

Great tits (Parus major) flexibly learn that herbivore-induced plant volatiles indicate prey location – an experimental evidence with two tree species

1. When searching for food, great tits (Parus major) can use herbivore-induced plant volatiles (HIPVs) as an indicator of arthropod presence. Their ability to detect HIPVs was shown to be learned, and not innate, yet the flexibility and generalization of learning remains unclear. 2. We studied if, and if so how, naïve and trained great tits (Parus major) discriminate between herbivore-induced and non-induced saplings of Scotch elm (Ulmus glabra) and cattley guava (Psidium cattleyanum). We chemically analysed the used plants and showed that their HIPVs differed significantly and overlapped only in a few compounds. 3. Birds trained to discriminate between herbivore-induced and non-induced saplings preferred the herbivore-induced saplings of the plant species they were trained to. Naïve birds did not show any preferences. Our results indicate that the attraction of great tits to herbivore-induced plants is not innate, rather it is a skill that can be acquired through learning, one tree species at a time. 4. We demonstrate that the ability to learn to associate HIPVs with food reward is flexible, expressed to both tested plant species, even if the plant species has not coevolved with the bird species (i.e. guava). Our results imply that the birds are not capable of generalising HIPVs among tree species but suggest that they either learn to detect individual compounds or associate whole bouquets with food rewards.

Neutron and LIBS data behind figures in Gabriel et al. (2022). On an extensive late hydrologic event in Gale crater as indicated by water-rich fracture halos. JGR-Planets.

This repository contains datasets that allow for the reproduction of certain figures and analysis by Gabriel et al. (2022), a peer-reviewed journal article accepted in the Journal of Geophysical Research: Planets. Below are brief descriptions of the datasets.   File: TGabriel_JGR-P_DAN_Passive_NoMobility_Raw_Data_sol350-400_FigureS10.txt Description: These are raw neutron counts from the thermal and epithermal neutron detectors as part of the Dynamic Albedo of Neutrons instrument. Only data from rover stops for sols 350 to 400 are included. Data from rover stops allows them to be readily colocated rover localization data, which includes 'site' and 'drive' numbers that are specific to each stop. File: TGabriel_JGR-P_DAN_Passive_NoMobility_Raw_Data_sol900-1500_Figure5.txt Description: This is similar data to the product above, however for the sol range 900 to 1500.   File: TGabriel_JGR-P_DAN_Passive_withMobility_Raw_Data_sol350-420_FigureS13.txt Description: This is similar data to the products above, however the dataset includes passive neutron count rates acquired while the rover was traversing, smoothed over 3 meters of lateral distance traveled. This dataset allows for the analysis of environments that may be present between rover stops, and thus not detected in 'no mobility' datasets.   TGabriel_JGR-P_Kukri_CCAM_MajorOxideComposition_FigureS19TableS1.xlsx Description: This is the result of the Major Oxide Quantification pipeline developed by the ChemCam instrument team (sPDL Tool v2.0, 25 July 2015) as run by William Rapin. Additional H quantification in Figure S19 of Gabriel et al. (2022) is not included in this dataset, but is provided in the manuscript.

opencc-by-4.0Jun 2022View details →

Figure 4 Mandible and p4 comparison for several European amphycionids. The red circle indicates the p4 in A new gigantic carnivore (Carnivora, Amphicyonidae) from the late middle Miocene of France

Figure 4 Mandible and p4 comparison for several European amphycionids. The red circle indicates the p4 position on the mandible. Modified from Dehm (1950), Kuss (1965), Bergounioux & Crouzel (1973), Viranta (1996), Peigné & Heizmann (2003), Peigné et al. (2008), Nagel, Stefen & Morlo (2009), Morales et al. (2021a) and Morales et al. (2021b). NMB TD1162 (Heizmannocyon steinheimensis), NMB SO4377 (Megamphicyon giganteus). The scale bar is five cm for the mandibles. The p4 are not to scale. Full-size DOI: 10.7717/peerj.13457/fig-4

Multi-Annual Indicative Programmes EU for Sub-Saharan Africa (2014-2021-2027)

This dataset is the result of the analysis of all 44 Multi-Annual Indicative Programmes (MIPs) for the period 2021-2027 of the European Union (EU) for Sub-Saharan Africa in which the EU implements its bilateral programmes. In addition, hitherto, 5 of the 29 National Indicative Programmes (NIPs) for the period 2014-2020, which are the of the predecessors of the MIPs, have been analyzed. In the following months, an updated dataset including the remaining 24 NIPs(2014-2020) can be expected. The documents have been examined from a financial perspective, and provide the following information: European Development Finance Institutions (EDFI) Activity: - Which European (and International) Development Finance Institutions are mentioned (/active) in which Sub-Saharan African (SSA) country. Member State (MS) Activity: - Which European Member States (MS) are mentioned (/ active) in which SSA country. - Which other international actors are mentioned in which SSA country. Budgets: - How much funding does each SSA country receive of the NDICI (2021) or EDF (2014) budget. - How much funding is attributed to which financial instrument; specifically Team Europa Initiatives (TEIs) and the External Action Guarantee (EAG). - Which concrete other numbers have been mentioned per actor (selected EU member states and development banks). Budgets comparison - A preliminary comparison, however not the same time period (!). The budgets in the 2021-2027 MIPs mentioned are those for the first period and are for the timer frame 2021-2024. The budgets in the 2014-2020 NIPs are for the full term. Instruments: - Which (financial) instruments are mentioned (/will be used) in which SSA country; specifically micro loans, blending, guarantees, technical assistance, Public-Private Partnerships (PPPs), and others. - For the 2021-2027 MIPs: Does the SSA country receive a Team Europe Initiative? If yes, how many, and which actors are involved in the TEI. Policy Priorities - What are the three EU policy priorities per SSA country.

DATASET: What is the best scale for implementing anaerobic digestion according to environmental and economic indicators?

DATASET: What is the best scale for implementing anaerobic digestion according to environmental and economic indicators? Journal of Water Process Engineering, Volume 35, June 2020, 101235 https://doi.org/10.1016/j.jwpe.2020.101235

Integrated Statistical Indicators from Scottish Linked Open Government Data

Integrated statistical indicators that were retrieved from the official Scottish data portal in order to facilitate the exploitation of Machine Learning methods in Open Government Data. Data include 60 statistical indicators from seven categories such as health and social care, housing, and crime and justice. The indicators refer to the 6,976 “2011 data zones” of Scotland, while the year of reference is 2015. Data are ready to be used by the research community, students, policy makers, and journalists and give rise to plenty of social, business, and research scenarios that can be solved using Machine Learning technologies and methods.

Artemisia pollen dataset for exploring the potential ecological indicators in deep time

To cover the maximum range of Artemisia pollen morphological variation, we provide a pollen dataset of 36 species from 9 clades and 3 outgroups of Artemisia constrained by the phylogenetic framework, containing 4018 original pollen photographs under LM and SEM, 9360 pollen morphological trait measurements, together with their 30858 source plant occurrences, and corresponding environmental factors. Here, we attempt to decipher the underlying causes of the long-standing disagreement in the palynological community on the correlation between Artemisia pollen and aridity by using this pollen dataset to recognize the different ecological implications of Artemisia pollen types. The Artemisia pollen dataset as designed is open and expandable for new pollen data from Artemisia worldwide in order to better serve the global environment assessment and refined reconstruction of vegetation in the geological past.

opencc-by-4.0Apr 2021View details →

Maps and R code from: Marginality indices for biodiversity conservation in forest trees

This dataset provides the raster map of marginality indices for eight European tree species as described in the article "Marginality indices for biodiversity conservation in forest tree". It also provided the R code to compute the marginality indices. The eight species are the following: <ul> <li>Abies alba Mill. (silver fir)</li> <li>Fagus sylvatica L. (European beech)</li> <li>Picea abies (L.) H.Karst. (Norway spruce) </li> <li>Pinus halepensis Mill. (Aleppo pine)</li> <li>Pinus nigra J.F.Arnold (black pine)</li> <li>Pinus pinaster Aiton (maritime pine) </li> <li>Pinus pinea L. (stone pine)</li> <li>Pinus sylvestris L. (Scots pine)</li> </ul> For each species, a 7z archive of a multi-layered image of the raster maps of the marginality indices is given. Each image has 12 layers: <ul> <li>Layer 1: distribution map of the species</li> <li>Layer 2: map of the probability of being marginal according to the Maxent model using eight marginality indices and countries as predictors</li> <li>Layer 3: map of the environmental marginality index, defined as the z-transform of the suitability of each location as predicted by a species distribution model using climatic variables as predictors</li> <li>Layer 4: map of the segmented distribution according to morphological spatial pattern analysis</li> <li>Layer 5: map of the area index</li> <li>Layer 6: map of the gravity index</li> <li>Layer 7: map of the centroid index</li> <li>Layer 8: map of the edge index</li> <li>Layer 9: map of the isolation index</li> <li>Layer 10: map of the second nearest core index</li> <li>Layer 11: map of the north/south index</li> <li>Layer 12: map of the east/west index</li> </ul>

opencc-zeroDec 2021View details →

Data from: Different taxonomic and functional indices complement the understanding of herb-layer community assembly patterns in a southern-limit temperate forest

The efficient conservation of vulnerable ecosystems in the face of global change requires a complete understanding of how plant communities respond to various environmental factors. We aim to demonstrate that a combined use of different approaches, traits, and indices representing each of the taxonomic and functional characteristics of plant communities will give complementary information on the factors driving vegetation assembly patterns. We analyzed variation across an environmental gradient in taxonomic and functional composition, richness, and diversity of the herb-layer of a temperate beech-oak forest that was located in northern Spain. We measured species cover and four functional traits: leaf dry matter content (LDMC), specific leaf area (SLA), leaf size, and plant height. We found that light is the most limiting resource influencing herb-layer vegetation. Taxonomic changes in richness are followed by equivalent functional changes in the diversity of leaf size but by opposite responses in the richness of SLA. Each functional index is related to different environmental factors even within a single trait (particularly for LDMC and leaf size). To conclude, each characteristic of a plant community is influenced by different and even contrasting factors or processes. Combining different approaches, traits, and indices simultaneously will help us understand how plant communities work.

opencc-zeroSep 2022View details →

Congruence among multiple indices of habitat preference for species facing human-induced rapid environmental change: A case study using the Brewer's sparrow

Accurate evaluations of habitat preference are key to understanding optimal conditions for wildlife survival and reproduction. Habitat selection, however, usually is evaluated using a single index of preference, and congruence among multiple, relevant indices of preference is examined rarely. We assessed the concordance between patterns of habitat preference using three different indices of breeding site preference in a migratory songbird. Specifically, we compared the chronology of territorial establishment, pair formation, and reproductive initiation of the Brewer's sparrow (Spizella breweri) along a gradient of surface disturbance associated with natural gas development in Wyoming, USA during 2019. We expected all three indices to demonstrate a preference for breeding sites with less surface disturbance, where reproductive success typically is higher. By contrast, all indices suggested suboptimal preference with respect to surface disturbance, with some discrepancy among them. The chronology of settlement and pairing did not vary across the disturbance gradient, whereas nest initiation tended to occur earlier at sites with more disturbance. If the pattern of suboptimal selection of breeding sites that we identified is generalizable across other populations of migratory birds affected by energy development, the resultant lower fitness in those areas may exacerbate population declines. Our results suggest that traditional, single-index approaches to the study of habitat selection, if chosen carefully, may provide adequate inference on habitat preferences. Different metrics, however, can lead to at least subtle differences in patterns of habitat selection. The simultaneous examination of multiple indices of preference across a diversity of systems would help clarify the contexts under which preference metrics can become decoupled.

opencc-by-4.0Dec 2022View details →

Disturbance indicator values for European plants

We report a data set of disturbance indicator values identifying mean optima along gradients of natural and anthropogenic disturbance for 6,382 vascular plant species based on the analysis of 736,366 European vegetation plots and using an expert-based characterization of disturbance regimes in 236 habitat types. The indicator values presented here are crucial for integrating disturbance niche optima in large-scale assessments of vegetation and macroecological studies. The data set contains five main continuous indicator values for European plants: disturbance severity, disturbance frequency, mowing frequency, grazing pressure and soil disturbance. The first two indicators are provided separately for the whole community and the herb layer. Reference: Midolo, G., Herben, T., Axmanová, I., Marcenò, C., Pätsch, R., Bruelheide, H., Karger D.N., Aćić, S., Bergamini, A., Bergmeier, E., Biurrun, I., Bonari, G., Čarni, A., Chiarucci, A., De Sanctis, M., Demina, O., Dengler, J., Dziuba, T., Fanelli, G., Garbolino, E., Giusso del Galdo, G., Goral, F., Güler, B., Hinojos-Mendoza, G., Jansen, F., Jiménez-Alfaro, B., Lengyel, A., Lenoir, J., Pérez-Haase, A., Pielech, R., Prokhorov, V., Ra&scaron;omavičius, V., Ruprecht, E., Rusina, S., &Scaron;ilc, U., &Scaron;kvorc, Ž., Stancic, Z., Tatarenko, I., & Chytrý, M. (2022). Disturbance indicator values for European plants. Global Ecology and Biogeography (Accepted for publication)

opencc-zeroSep 2022View details →

Direct and indirect phenotypic effects on sociability indicate potential to evolve

The decision to leave or join a group is important as group size influences many aspects of organisms' lives and their fitness. This tendency to socialise with others, sociability, should be influenced by genes carried by focal individuals (direct genetic effects) and by genes in partner individuals (indirect genetic effects), indicating the trait's evolution could be slower or faster than expected. However, estimating these genetic parameters is difficult. Here, in a laboratory population of the cockroach Blaptica dubia, I estimate phenotypic parameters for sociability: repeatability (R) and repeatable influence (RI), which indicate whether direct and indirect genetic effects respectively are likely. I also estimate the interaction coefficient (Ψ), which quantifies how strongly a partner's trait influences the phenotype of the focal individual and is key in models for the evolution of interacting phenotypes. Focal individuals were somewhat repeatable for sociability across a three-week period (R = 0.080), and partners also had marginally consistent effects on focal sociability (RI = 0.053). The interaction coefficient was non-zero, although in the opposite sign for the sexes; males preferred to associate with larger individuals (Ψmale = -0.129) while females preferred to associate with smaller individuals (Ψfemale = 0.071). Individual sociability was consistent between dyadic trials and in social networks of groups. These results provide phenotypic evidence that direct and indirect genetic effects have limited influence on sociability, with perhaps the most evolutionary potential stemming from heritable effects of the body mass of partners. Sex-specific interaction coefficients may produce sexual conflict and the evolution of sexual dimorphism in social behaviour.

opencc-by-4.0Sep 2022View details →

Local Indicators of Climate Change Impacts reported by the Tuareg of Illizi (Algeria)

The dataset reports the Local Indicators of Climate Change Impacts mentioned during 19 interviews and 3 focus groups with members of the Tuareg community of Illizi (Algeria). The dataset includes reports events important to the local timeline and observations of atmospheric changes including seasonal, precipitation, temperature, and biodiversity changes.

opencc-by-4.0Feb 2022View details →

Text-fig. 1. Location of the study site. a: the location of Lühe Town, Yunnan, SW China; b: fossil bearing section, white arrow indicates the fossil collection stratum; c: geological map of fossil site. in Fraxinus L. (Oleaceae) Fruits From The Early Oligocene Of Southwest China And Their Biogeographic Implications

Text-fig. 1. Location of the study site. a: the location of Lühe Town, Yunnan, SW China; b: fossil bearing section, white arrow indicates the fossil collection stratum; c: geological map of fossil site.

opencc-by-4.0Dec 2021View details →

Text-fig. 12. Paramblypterus cf. rohani. Arrows indicate directio cranialis. a, b: photograph and drawing of four ridge scales in front of the dorsal fin base, locality Otovice "Chmelnice", P 80178, scale bars 5 mm; c: scale rows from the area between the pectoral and pelvic fins, outer surfaces of the scales bear fine ridges terminating as denticles on the posterior edge of the scales, locality Otovice "Chmelnice", NM-M 4916, scale bar 5 mm; d: isolated scale, from anterior area of the lateral side of the body, with denticulated posterior edge, locality Otovice "Chmelnice", P 30945, scale bar 2 mm; e: isolated scale from the pelvic area of the body, locality Otovice "Chmelnice", P 30945, scale bar 2 mm; f, g: drawing and photograph of the postcleithrum and the scales behind the pectoral girdle (the scales bear conspicuous ridges on their outer surface; well preserved large postcleithrum is without ridges.), locality Otovice "Chmelnice", NM-M 4915, scale bars 5 mm. Abbreviations: Cl – cleithrum, Pcl – postcleithrum, Scl – supracleithrum. in Actinopterygians Of The Broumov Formation (Permian) In The Czech Part Of The Intra-Sudetic Basin (The Czech Republic)

Text-fig. 12. Paramblypterus cf. rohani. Arrows indicate directio cranialis. a, b: photograph and drawing of four ridge scales in front of the dorsal fin base, locality Otovice "Chmelnice", P 80178, scale bars 5 mm; c: scale rows from the area between the pectoral and pelvic fins, outer surfaces of the scales bear fine ridges terminating as denticles on the posterior edge of the scales, locality Otovice "Chmelnice", NM-M 4916, scale bar 5 mm; d: isolated scale, from anterior area of the lateral side of the body, with denticulated posterior edge, locality Otovice "Chmelnice", P 30945, scale bar 2 mm; e: isolated scale from the pelvic area of the body, locality Otovice "Chmelnice", P 30945, scale bar 2 mm; f, g: drawing and photograph of the postcleithrum and the scales behind the pectoral girdle (the scales bear conspicuous ridges on their outer surface; well preserved large postcleithrum is without ridges.), locality Otovice "Chmelnice", NM-M 4915, scale bars 5 mm. Abbreviations: Cl – cleithrum, Pcl – postcleithrum, Scl – supracleithrum.