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opencc-by-4.0Jul 2023View details →

Appendix for the paper "Assessment of Aging and Rejuvenation for Resiliency in Heterogeneous Network Clusters"

Appendix for the paper "Alberto Avritzer, Andrea Janes, Andrea Marin, Andre van Hoorn, Matteo Camilli, Catia Trubiani, Daniel S. Menasché: Assessment of Aging and Rejuvenation for Resiliency in Heterogeneous Network Clusters" This repository contains the complete set of charts for all core machines (in the paper, figures 3-8 contain only the results of one machine) and the collected data for each strategy. Contents The files contained in this appendix are: <ul> <li>18 files of the format "experiment(strategy)(granularity).pdf, where "strategy" goes from -1 to 4 and granularity is one of i, dc, or dp (see table I in the paper).</li> <li>18 files of the format "output-(strategy)(granularity).csv, with the same format as the files above, containing the raw data.</li> </ul>

opencc-zeroJul 2023View details →

Data from: Soil nutrient heterogeneity alters productivity and diversity of experimental plant communities under multiple global change factors

Plant communities in nature are often challenged by multiple global change factors (GCFs) and also ubiquitously encountered with soil nutrient heterogeneity. So far, however, we know little about the interactive effect of multiple GCFs and soil nutrient heterogeneity on plant communities. We conducted an outdoor mesocosm experiment in which a plant community was either grown in heterogeneous soils consisting of high- and low-nutrient patches, or in homogeneous soils where the same amount of nutrients was evenly distributed. These plant communities were exposed to none (control), single, or a combination of two or four GCFs (i.e., drought, nitrogen deposition, microplastic and cadmium). Biomass of the plant community exposed to drought and nitrogen deposition were greater in heterogeneous than in homogeneous soils, but evenness of the plant community exposed to microplastics was lower. Increasing the number of GCFs increased community biomass more in heterogeneous than in homogeneous soils, but it generally reduced community evenness, independent of soil nutrient heterogeneity. These contrasting responses were related to changing competitive hierarchies and root foraging responses under different treatments. Our results suggest that soil nutrient heterogeneity can alter community productivity and diversity via changing competitive interactions of the component species, depending on both the identity and the number of GCFs acting on the community. These results have important implications for the maintenance of ecosystem functions and services under rapid and complex ongoing global changes.

opencc-zeroAug 2023View details →

Data from: Beyond the case study: Characterizing natural floodplain heterogeneity in the United States

As river channels move across the valley floor, they create diverse topography including natural levees, cutoff meanders, secondary channels, and floodplain wetlands. These features increase the spatial heterogeneity of the floodplain. Many studies indicate that this heterogeneity strongly influences habitat abundance and diversity, storage of flood waters and excess nitrate or phosphate, and other floodplain functions. However, no one has systematically measured floodplain heterogeneity across multiple rivers and different geographic regions. We measured the heterogeneity of natural floodplains at 14 sites in the continental United States using metrics developed by landscape ecologists. We find that natural floodplains have distinctive heterogeneity signatures that relate to drainage area, the size of the floodplain, and other characteristics. The data included here are the original field data associated with 14 of the field sites, including GPS locations of floodplain transects, floodplain patches, sediment cores, and large wood; and delineated floodplain shapefiles.

opencc-zeroAug 2023View details →

Heterogeneous microgeographic genetic structure of the common cockle (Cerastoderma edule) in the Northeast Atlantic Ocean: biogeographic barriers and environmental factors

Knowledge of genetic structure at the finest level is essential for conservation of genetic resources. Despite no visible barriers limiting gene flow, significant genetic structure has been shown in marine species. The common cockle (Cerastoderma edule) is a bivalve of great commercial and ecological value inhabiting the Northeast Atlantic Ocean. Previous population genomics studies demonstrated significant structure both across the Northeast Atlantic, but also within small geographic areas, highlighting the need to investigate fine-scale structuring. Here, we analysed two geographic areas that could represent opposite models of structure for the species: 1) the SW British Isles region, highly fragmented due to biogeographic barriers, and 2) Galicia (NW Spain), a putative homogeneous region. 9,250 SNPs genotyped by 2b-RAD on 599 individuals from 22 natural beds were used for the analysis. The entire SNP dataset mostly confirmed previous observations related to genetic diversity and differentiation, however, neutral and divergent SNP outlier datasets enabled disentangling physical barriers from abiotic environmental factors structuring both regions. While Galicia showed a homogeneous structure, the SW British Isles region was split into four reliable genetic regions related to oceanographic features and abiotic factors, such as sea surface salinity and temperature. The information gathered supports specific management policies of cockle resources in SW British and Galician regions also considering their particular socio-economic characteristics; further, these new data will be added to those recently reported in the Northeast Atlantic to define sustainable management actions across the whole distribution range of the species.

Figure 5 in Medium and large sized mammals and the effect of habitat heterogeneity from a Caatinga shrubby forest at Serra de Santa Catarina, Paraíba, Brazil

Figure 5. Non-metric Multidimensional Scaling of medium-large mammal community structure according to different phytophysiognomies (a) and presence of water bodies (b), recorded in the Serra de Santa Catarina, Northeast Brazil, between August 2012 and November 2014. The ANOSIM (one-way) analysis showed no difference between phytophysiognomies (R = 0.1124, p> 0.05) and a significant difference between the presence of water bodies (R = 0.3907, p <0.05).

Figure 4 in Medium and large sized mammals and the effect of habitat heterogeneity from a Caatinga shrubby forest at Serra de Santa Catarina, Paraíba, Brazil

Figure 4. Average of abundance of medium-large mammal species according to different phytophysiognomies (a) and presence of water bodies (b), recorded in the Serra de Santa Catarina, Northeast Brazil, between August 2012 and November 2014. The Mann-Whitney analysis showed no difference between both phytophysiognomies (U = 29.5, p> 0.05) and presence of water bodies (U = 48.5, p> 0.05).

Figure 2 in Medium and large sized mammals and the effect of habitat heterogeneity from a Caatinga shrubby forest at Serra de Santa Catarina, Paraíba, Brazil

Figure 2. Different habitats analyzed in Serra de Santa Catarina, Paraíba, Brazil. A = Arboreal; B = Shrub; C = Arboreal-shrub; D = Water spot with a capuchin monkey in the foreground.

Figure 1 in Medium and large sized mammals and the effect of habitat heterogeneity from a Caatinga shrubby forest at Serra de Santa Catarina, Paraíba, Brazil

Figure 1. Study area, the Serra de Santa Catarina, extreme West of Paraíba state, northeastern Brazil. In light gray Caatinga biome and in dark gray Atlantic Forest Biome; in green, Serra de Santa Catarina limits.

Figure 3 in Medium and large sized mammals and the effect of habitat heterogeneity from a Caatinga shrubby forest at Serra de Santa Catarina, Paraíba, Brazil

Figure 3. Rarefaction curve for camera-trap sampling to medium-large mammal species of the Serra de Santa Catarina, Paraíba, northeastern Brazil, sampled between August 2012 and November 2014. Observed richness (S = 10 ± 1.76) has no significant difference to estimated richness (S = 12.97 ± 1.7) through the non-parametric Jackknife 1. Sample unit were defined as days with effective records in different camera-traps.

opencc-zeroSep 2023View details →

Data from: Microbial activity contributes to spatial heterogeneity of wetland methane fluxes

The emission of methane from wetlands is spatially heterogeneous, as concurrently measured surface fluxes can vary by orders of magnitude within the span of a few meters. Despite extensive study and the climatic significance of these greenhouse gas emissions, it remains unclear what drives these large within-site variations, creating a knowledge-gap that impedes a mechanistic understanding of wetland fluxes. While geophysical variables including water table depth (WTD) and soil temperature are known to correlate with CH4 flux, measurable variance in these parameters declines as spatial and temporal scales become finer. Here, we leveraged depth-stratified gene abundance and gene expression measurements of methanogenesis and methanotrophy to investigate CH4 flux variance at an ombrotrophic peat bog. Our results show that the flux variance was strongly correlated to methanogen abundance and that peat depth also exerted significant control over CH4 flux, methanogen abundance, and the relationship between the two. Correlations between CH4 flux and either WTD or soil temperature were absent or minimal. These findings suggest that microbial factors likely underlie localized variance in wetland CH4 flux, and that a greater reliance on biological predictors could improve our ability to understand wetland methane fluxes at finer scales than is currently possible.

openmit-licenseApr 2024View details →

A comparative benchmarking and evaluation framework for heterogeneous network-based drug repositioning methods

This repository contains all the datasets used for benchmarking drug repositioning methods based on heterogeneous networks, including drug-drug similarity, disease-disease similarity, and drug-disease associations. The repository consists of: <ol> <li>Name or keyword information for drugs and diseases information contained in the dataset</li> <li>Inputs needed for different drug repositioning methods: multiple drug similarity matrices,multiple disease similarity matrices, and drug-disease associations matrices.</li> </ol>     <blockquote> Please cite us : Yinghong Li, Yinqi Yang, Zhuohao Tong, Yu Wang, Qin Mi, Mingze Bai, Guizhao Liang, Bo Li, Kunxian Shu, A comparative benchmarking and evaluation framework for heterogeneous network-based drug repositioning methods, Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae172, <a href="https://doi.org/10.1093/bib/bbae172">https://doi.org/10.1093/bib/bbae172</a> </blockquote>

opencc-zeroSep 2023View details →

Data for: Genomic signals of local adaptation across climatically heterogenous habitats in an invasive tropical fruit fly (Bactrocera tryoni)

Local adaptation plays a key role in the successful establishment of pest populations in new environments by enabling them to tolerate novel biotic and abiotic conditions experienced outside their native range. However, the genomic underpinnings of such adaptive responses remain unclear, especially for agriculturally important pests. We investigated population genomic signatures in the tropical/subtropical Queensland fruit fly, Bactrocera tryoni, which has an expanded range encompassing temperate and arid zones in Australia, and tropical zones in the Pacific Islands. Using reduced representation sequencing data from 28 populations, we detected allele frequency shifts associated with the native/invasive status of populations and identified environmental factors that have likely driven population differentiation. We also determined that precipitation, temperature, and geographic variables explain allelic shifts across the distribution range of B. tryoni. We found spatial heterogeneity in signatures of local adaptation across various climatic conditions in invaded areas. Specifically, disjunct invasive populations in the tropical Pacific Islands and arid zones of Australia were characterised by multiple significantly differentiated single nucleotide polymorphisms (SNPs), some of which were associated with genes with well-understood function in environmental stress (e.g., heat and desiccation) response. However, invasive populations in southeast Australian temperate zones showed higher gene flow with the native range and lacked a strong local adaptive signal. These results suggest that population connectivity with the native range has differentially affected local adaptive patterns in different invasive populations. Overall, our findings provide insights into the evolutionary underpinnings of invasion success of an important horticultural pest in climatically distinct environments.

opencc-by-4.0Sep 2023View details →

Data set for "Protracted localization of metamorphism and deformation in a heterogeneous lower-crustal shear zone"

Electron micro probe raw data used in the publication: "Protracted localization of metamorphism and deformation in a heterogeneous lower-crustal shear zone" (Zertani et al., 2023). Zertani, S., Menegon, L., Pennacchioni, G., Buisman, I., Corfu, F., Jamtveit, B. (2023). Protracted localization of metamorphism and deformation in a heterogeneous lower-crustal shear zone. Journal of Structural Geology, 104960. https://doi.org/10.1016/j.jsg.2023.104960

opencc-zeroSep 2023View details →

A global synthesis and meta-analysis of the environmental heterogeneity effects on the freshwater biodiversity

In this study, we aimed to synthesize the global knowledge about the relationship between spatial Environmental Heterogeneity (EH) and freshwater biodiversity (i.e., taxonomic and functional diversity, and their respective α and β components). Through a systematic review, we integrated results from 98 studies, published in 33 different countries, about the role of spatial EH – biodiversity relationship in freshwater ecosystems. Following the PRISMA-ecoevol criteria, we generated a dataset with 276 observations of the effect of EH – biodiversity relationship. For the meta-analysis, we extracted the effect size from 74 studies that effectively tested the effect of EH over any metric of biodiversity. Through this subset, we provided 242 individual effect sizes with their respective variances and sample sizes.

opencc-by-4.0Jul 2023View details →

Smartphone and smartwatch inertial measurements from heterogeneous subjects for human activity recognition.

This repository contains the dataset and contents described in the "Dataset of inertial measurements of smartphones and smartwatches for human activity recognition" data article.<blockquote>Matey-Sanz, M., Casteleyn, S., & Granell, C. (2023). Dataset of inertial measurements of smartphones and smartwatches for human activity recognition. Data in Brief, 109809.</blockquote>

opencc-zeroOct 2023View details →

Root-centric β diversity reveals functional homogeneity while phylogenetic heterogeneity in a subtropical forest

Root-centric studies have revealed fast taxonomic turnover across root neighborhoods, but how such turnover is accompanied by changes in species functions and phylogeny (i.e. β diversity), which can reflect the degree of community-wide biotic homogenization, remains largely unknown, hindering better inference of below-ground assembly rules, community structuring, and ecosystem processes. We collected 2480 root segments from 625 0–30 cm soil profiles in a subtropical forest in China. Root segments were identified into 143 species with DNA-barcoding with six root morphological and architectural traits measured per species. By using the mean pairwise (Dpw) and mean nearest neighbor distance (Dnn) to quantify species ecological differences, we tested the non-random functional and phylogenetic turnover of root neighborhoods that would lend more support to deterministic over stochastic community assembly processes, examined the distance-decay pattern of β diversity, and finally partitioned β diversity into geographical and environmental components to infer their potential drivers of environmental filtering, dispersal limitation, and biotic interactions. We found that functional turnover was often lower than expected given the taxonomic turnover, whereas phylogenetic turnover was often higher than expected. Both functional and phylogenetic Dpw (e.g. interfamily species) turnover exhibited a distance-decay pattern, likely reflecting limited dispersal or abiotic filtering that leads to the spatial aggregation of specific plant lineages. Conversely, phylogenetic Dnn (e.g. intrageneric species) exhibited an inverted distance-decay pattern, likely reflecting strong biotic interactions among spatially and phylogenetically close species leading to phylogenetic divergence. While the spatial distance was generally a better predictor of β diversity than environmental distance, the joint effect of environmental and spatial distance usually overrode their respective pure effects. These findings suggest that root neighborhood functional homogeneity may somewhat increase forest resilience after disturbance by exhibiting an insurance effect. Likewise, root neighborhood phylogenetic heterogeneity may enhance plant fitness by hindering the transmission of host-specific pathogens through root networks or by promoting interspecific niche complementarity not captured by species functions. Our study highlights the potential role of root-centric β diversity in mediating community structures and functions largely ignored in previous studies.

opencc-zeroOct 2023View details →

Data from: Promoting plant diversity and habitat heterogeneity through vineyard terracing

Questions: Viticulture on steep slopes has shaped landscape and biodiversity in many regions, but insufficient profitability has led to management cessation and shrub encroachment. A solution to maintain cultivation economically viable could be vineyard terracing. We aimed to identify the potential of terracing to enhance plant diversity and habitat heterogeneity in vineyards, analyse effects of management intensity on vineyard vegetation, and assess how plant communities change after vineyard abandonment. Location: Wine-growing region of the Upper Middle Rhine Valley in Hesse (50.042342°N, 7.814533°E) and Rhineland-Palatinate (50.119139°N, 7.719275°E), Germany. Methods: We recorded vascular plant species and local vineyard parameters in vertically oriented vineyards with vegetated and tilled open inter-rows, in terraced vineyards with tilled terrace inter-rows and extensively managed embankments and in vineyard fallows in a total of 45 study sites. We used plant species richness, Ellenberg indicator values and Grime's strategy types to describe how traits and ecological requirements respond to distinct vineyard management. Results: Plant species richness and composition were determined by management-derived disturbance intensities. Extensively managed embankments had a distinct plant community, the highest plant species richness, more perennial and indicator species, and lower nitrogen indicator values compared to inter-rows. In contrast, highly disturbed open and terrace inter-rows revealed plant communities associated with annuals and ruderals, but species richness did not differ between terrace inter-rows and embankments. Plant communities of fallows were completely different with lower plant diversity. Conclusions: Our results highlight the potential of terraced vineyards for plant diversity with nutrient-poor, extensively managed embankments providing conditions that have become rare in modern agricultural systems. A long environmental gradient from terrace inter-rows to embankments created habitat heterogeneity at a narrow space. In contrast, intensive inter-row management in vertically oriented vineyards hampers high plant diversity and abandonment fosters the spread of woody species at the expanse of plant diversity.

opencc-zeroOct 2023View details →

Environmental heterogeneity on landslide slopes affects the long-term recoveries of forest ecosystem components

Landslides are a common disturbance in mountainous areas of the world. Transporting and accumulating landslide debris, i.e., disturbance legacies, such as coarse woody debris (CWD), vegetation patches, and surface soils, generate a heterogeneous environment along slopes (zones), which are suggested to affect forest recovery. However, the long-term changes in forest ecosystems after landslides remain unknown, particularly zone-dependent change patterns. We aimed to reveal the differences in the changes in live trees, understory vegetation, CWD, and soils among zones by surveying forests with landslide ages (years since the landslide) ranging from 3 to 74 years and reference stands. The increase in live tree aboveground biomass occurred at a faster rate at the lower part of the slopes where the disturbance legacies were rich and surface soils were stabilized due to the smaller slope angle. Chronological patterns of understory vegetation amounts were determined by the differences in disturbance legacy richness and the timing of subsequent canopy closure. The amounts and decay-class diversity of CWD were determined by the differences in legacy richness and mortality through stand development. These zone-dependent chronological changes influenced litter production and determined the recovery rates of surface soil carbon and nitrogen stocks. The increase in the dominance rates of forest herbaceous species was faster in the lower part of the slopes due to the faster surface soil development and canopy closure. Our results illustrate that long-term forest ecosystem succession and recovery after landslides occurs more rapidly at the lower parts than at the upper parts of slopes.