All in One: Encoding spatio-temporal big data in XML, JSON, and RDF without information loss

Baumann P., Hirschorn E., Maso J., Merticariu V., Misev D. (2018) All in One: Encoding spatio-temporal big data in XML, JSON, and RDF without information loss. Proceedings - 2017 IEEE International Conference on Big Data, Big Data 2017. 2018-January: 1-10.
Link
Doi: 10.1109/BigData.2017.8258326

Abstract:

With the unprecedented availability of continuously observed and generated data there is a likewise unprecedented potential for new and timely insights; yet, benefits are not fully leveraged as of today. The plethora of formats in combination with heterogeneous services remains is an obstacle-e.g., image services prefer binary formats, SPARQL endpoints like to think in RDF triples, and browsers integrate JSON data smoothly. We propose a model-based multi-encoding approach for overcoming the limitations of individual formats while still supporting their use. Concretely, this approach is being followed by the OGC Coverage Implementation Schema (CIS) standard which establishes a concrete, interoperable data model unifying n-D spatiotemporal regular and irregular grids, point clouds, and meshes. We describe how independence from data formats is achieved, in particular for three practically relevant formats-XML, JSON, and RDF-, thereby fostering integration of hitherto rather separate application domains. © 2017 IEEE.

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On the influence of water conductivity, pH and climate on bryophyte assemblages in Catalan semi-natural springs

Bes M., Corbera J., Sayol F., Bagaria G., Jover M., Preece C., Viza A., Sabater F., Fernández-Martínez M. (2018) On the influence of water conductivity, pH and climate on bryophyte assemblages in Catalan semi-natural springs. Journal of Bryology. : 1-10.
Link
Doi: 10.1080/03736687.2018.1446484

Abstract:

Bryophytes are some of the most sensitive biological indicators of environmental change. Springs have a significant presence of bryophytes and so are ideal habitats for studying their relationship with the environment. We tested whether bryophyte assemblages can be explained with macro-, meso- and micro-ecological variables (i.e. seasonal climate, altitude, water pH and conductivity) sampling bryophytes from 198 semi-natural springs distributed along montane regions in the north-eastern Iberian Peninsula. We tested the influence of environmental variables on bryophyte assemblages in springs using sparse Partial Least Squares. Our results show that variability in bryophyte assemblages is explained by seasonal climate (temperature and precipitation from winter, spring, summer and autumn and temperature and precipitation seasonality), altitude and water conductivity. The results obtained by the present study will be useful for predicting bryophyte diversity in springs using simple and easy to obtain variables such as climate, water pH and conductivity. © British Bryological Society 2018

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The microbial cycling of phosphorus on long-term fertilized soil: Insights from phosphate oxygen isotope ratios

Bi, Q.-F., Zheng, B.-X., Lin, X.-Y., Li, K.-J., Liu, X.-P., Hao, X.-L., Zhang, H., Zhang, J.-B., Jaisi, D.P., Zhu, Y.-G. (2018) The microbial cycling of phosphorus on long-term fertilized soil: Insights from phosphate oxygen isotope ratios. Chemical Geology. 483: 56-64.
Link
Doi: 10.1016/j.chemgeo.2018.02.013

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Plant functional trait change across a warming tundra biome

Bjorkman A.D., Myers-Smith I.H., Elmendorf S.C., Normand S., Rüger N., Beck P.S.A., Blach-Overgaard A., Blok D., Cornelissen J.H.C., Forbes B.C., Georges D., Goetz S.J., Guay K.C., Henry G.H.R., HilleRisLambers J., Hollister R.D., Karger D.N., Kattge J., Manning P., Prevéy J.S., Rixen C., Schaepman-Strub G., Thomas H.J.D., Vellend M., Wilmking M., Wipf S., Carbognani M., Hermanutz L., Lévesque E., Molau U., Petraglia A., Soudzilovskaia N.A., Spasojevic M.J., Tomaselli M., Vowles T., Alatalo J.M., Alexander H.D., Anadon-Rosell A., Angers-Blondin S., Beest M., Berner L., Björk R.G., Buchwal A., Buras A., Christie K., Cooper E.J., Dullinger S., Elberling B., Eskelinen A., Frei E.R., Grau O., Grogan P., Hallinger M., Harper K.A., Heijmans M.M.P.D., Hudson J., Hülber K., Iturrate-Garcia M., Iversen C.M., Jaroszynska F., Johnstone J.F., Jørgensen R.H., Kaarlejärvi E., Klady R., Kuleza S., Kulonen A., Lamarque L.J., Lantz T., Little C.J., Speed J.D.M., Michelsen A., Milbau A., Nabe-Nielsen J., Nielsen S.S., Ninot J.M., Oberbauer S.F., Olofsson J., Onipchenko V.G., Rumpf S.B., Semenchuk P., Shetti R., Collier L.S., Street L.E., Suding K.N., Tape K.D., Trant A., Treier U.A., Tremblay J.-P., Tremblay M., Venn S., Weijers S., Zamin T., Boulanger-Lapointe N., Gould W.A., Hik D.S., Hofgaard A., Jónsdóttir I.S., Jorgenson J., Klein J., Magnusson B., Tweedie C., Wookey P.A., Bahn M., Blonder B., van Bodegom P.M., Bond-Lamberty B., Campetella G., Cerabolini B.E.L., Chapin F.S., III, Cornwell W.K., Craine J., Dainese M., de Vries F.T., Díaz S., Enquist B.J., Green W., Milla R., Niinemets Ü., Onoda Y., Ordoñez J.C., Ozinga W.A., Penuelas J., Poorter H., Poschlod P., Reich P.B., Sandel B., Schamp B., Sheremetev S., Weiher E. (2018) Plant functional trait change across a warming tundra biome. Nature. 562: 57-62.
Link
Doi: 10.1038/s41586-018-0563-7

Abstract:

The tundra is warming more rapidly than any other biome on Earth, and the potential ramifications are far-reaching because of global feedback effects between vegetation and climate. A better understanding of how environmental factors shape plant structure and function is crucial for predicting the consequences of environmental change for ecosystem functioning. Here we explore the biome-wide relationships between temperature, moisture and seven key plant functional traits both across space and over three decades of warming at 117 tundra locations. Spatial temperature–trait relationships were generally strong but soil moisture had a marked influence on the strength and direction of these relationships, highlighting the potentially important influence of changes in water availability on future trait shifts in tundra plant communities. Community height increased with warming across all sites over the past three decades, but other traits lagged far behind predicted rates of change. Our findings highlight the challenge of using space-for-time substitution to predict the functional consequences of future warming and suggest that functions that are tied closely to plant height will experience the most rapid change. They also reveal the strength with which environmental factors shape biotic communities at the coldest extremes of the planet and will help to improve projections of functional changes in tundra ecosystems with climate warming. © 2018, Springer Nature Limited.

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Tundra Trait Team: A database of plant traits spanning the tundra biome

Bjorkman A.D., Myers-Smith I.H., Elmendorf S.C., Normand S., Thomas H.J.D., Alatalo J.M., Alexander H., Anadon-Rosell A., Angers-Blondin S., Bai Y., Baruah G., te Beest M., Berner L., Björk R.G., Blok D., Bruelheide H., Buchwal A., Buras A., Carbognani M., Christie K., Collier L.S., Cooper E.J., Cornelissen J.H.C., Dickinson K.J.M., Dullinger S., Elberling B., Eskelinen A., Forbes B.C., Frei E.R., Iturrate-Garcia M., Good M.K., Grau O., Green P., Greve M., Grogan P., Haider S., Hájek T., Hallinger M., Happonen K., Harper K.A., Heijmans M.M.P.D., Henry G.H.R., Hermanutz L., Hewitt R.E., Hollister R.D., Hudson J., Hülber K., Iversen C.M., Jaroszynska F., Jiménez-Alfaro B., Johnstone J., Jorgensen R.H., Kaarlejärvi E., Klady R., Klimešová J., Korsten A., Kuleza S., Kulonen A., Lamarque L.J., Lantz T., Lavalle A., Lembrechts J.J., Lévesque E., Little C.J., Luoto M., Macek P., Mack M.C., Mathakutha R., Michelsen A., Milbau A., Molau U., Morgan J.W., Mörsdorf M.A., Nabe-Nielsen J., Nielsen S.S., Ninot J.M., Oberbauer S.F., Olofsson J., Onipchenko V.G., Petraglia A., Pickering C., Prevéy J.S., Rixen C., Rumpf S.B., Schaepman-Strub G., Semenchuk P., Shetti R., Soudzilovskaia N.A., Spasojevic M.J., Speed J.D.M., Street L.E., Suding K., Tape K.D., Tomaselli M., Trant A., Treier U.A., Tremblay J.-P., Tremblay M., Venn S., Virkkala A.-M., Vowles T., Weijers S., Wilmking M., Wipf S., Zamin T. (2018) Tundra Trait Team: A database of plant traits spanning the tundra biome. Global Ecology and Biogeography. 27: 1402-1411.
Link
Doi: 10.1111/geb.12821

Abstract:

Motivation: The Tundra Trait Team (TTT) database includes field-based measurements of key traits related to plant form and function at multiple sites across the tundra biome. This dataset can be used to address theoretical questions about plant strategy and trade-offs, trait–environment relationships and environmental filtering, and trait variation across spatial scales, to validate satellite data, and to inform Earth system model parameters. Main types of variable contained: The database contains 91,970 measurements of 18 plant traits. The most frequently measured traits (> 1,000 observations each) include plant height, leaf area, specific leaf area, leaf fresh and dry mass, leaf dry matter content, leaf nitrogen, carbon and phosphorus content, leaf C:N and N:P, seed mass, and stem specific density. Spatial location and grain: Measurements were collected in tundra habitats in both the Northern and Southern Hemispheres, including Arctic sites in Alaska, Canada, Greenland, Fennoscandia and Siberia, alpine sites in the European Alps, Colorado Rockies, Caucasus, Ural Mountains, Pyrenees, Australian Alps, and Central Otago Mountains (New Zealand), and sub-Antarctic Marion Island. More than 99% of observations are georeferenced. Time period and grain: All data were collected between 1964 and 2018. A small number of sites have repeated trait measurements at two or more time periods. Major taxa and level of measurement: Trait measurements were made on 978 terrestrial vascular plant species growing in tundra habitats. Most observations are on individuals (86%), while the remainder represent plot or site means or maximums per species. Software format: csv file and GitHub repository with data cleaning scripts in R; contribution to TRY plant trait database (www.try-db.org) to be included in the next version release. © 2018 The Authors Global Ecology and Biogeography Published by John Wiley & Sons Ltd

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Invasive oaks escape pre-dispersal insect seed predation and trap enemies in their seeds

Bogdziewicz M., Bonal R., Espelta J.M., Kalemba E.M., Steele M.A., Zwolak R. (2018) Invasive oaks escape pre-dispersal insect seed predation and trap enemies in their seeds. Integrative Zoology. 13: 228-237.
Link
Doi: 10.1111/1749-4877.12285

Abstract:

Species introduced to habitats outside their native range often escape control by their natural enemies. Besides competing with native species, an alien species might also affect the native herbivores by introducing a new source of different quality food. Here, we describe the case of northern red oak (Quercus rubra) invasion in Europe. We collected data on insect (moth Cydia spp. and weevil Curculio spp.) seed predation of northern red oak in its native (USA, North America) and invasive (Poland, Europe) range, as well as for sessile oaks (Quercus petrea) in Europe. We also evaluated the quality of acorns as hosts for weevil larvae by collecting infested acorns and measuring weevil developmental success, and quantifying acorn traits such as seed mass, tannins, lipids and protein concentration. We used DNA barcoding to identify insects to the species level. The predation by moths was similar and very low in both species and in both ranges. However, red oaks escape pre-dispersal seed predation by weevils in Europe. Weevil infestation rates of northern red oak acorns in their invasive range were 10 times lower than that of sessile oaks, and also 10 times lower than that of red oaks in North America. Furthermore, even when weevils oviposited into northern red oaks, the larvae failed to develop, suggesting that the exotic host created a trap for the insect. This phenomenon might gradually decrease the local abundance of the seed predator, and further aid the invasion. © 2017 International Society of Zoological Sciences, Institute of Zoology/Chinese Academy of Sciences and John Wiley & Sons Australia, Ltd

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Effectiveness of predator satiation in masting oaks is negatively affected by conspecific density

Bogdziewicz M., Espelta J.M., Muñoz A., Aparicio J.M., Bonal R. (2018) Effectiveness of predator satiation in masting oaks is negatively affected by conspecific density. Oecologia. 186: 983-993.
Link
Doi: 10.1007/s00442-018-4069-7

Abstract:

Variation in seed availability shapes plant communities, and is strongly affected by seed predation. In some plant species, temporal variation in seed production is especially high and synchronized over large areas, which is called ‘mast seeding’. One selective advantage of this phenomenon is predator satiation which posits that masting helps plants escape seed predation through starvation of predators in lean years, and satiation in mast years. However, even though seed predation can be predicted to have a strong spatial component and depend on plant densities, whether the effectiveness of predator satiation in masting plants changes according to the Janzen-Connell effect has been barely investigated. We studied, over an 8-year period, the seed production, the spatiotemporal patters of weevil seed predation, and the abundance of adult weevils in a holm oak (Quercus ilex) population that consists of trees interspersed at patches covering a continuum of conspecific density. Isolated oaks effectively satiate predators, but this is trumped by increasing conspecific plant density. Lack of predator satiation in trees growing in dense patches was caused by re-distribution of insects among plants that likely attenuated them against food shortage in lean years, and changed the type of weevil functional response from type II in isolated trees to type III in trees growing in dense patches. This study provides the first empirical evaluation of the notion that masting and predator satiation should be more important in populations that start to dominate their communities, and is consistent with the observation that masting is less frequent and less intense in diverse forests. © 2018, The Author(s).

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Looking for variable molecular markers in the chestnut gall wasp Dryocosmus kuriphilus: First comparison across genes

Bonal R., Vargas-Osuna E., Mena J.D., Aparicio J.M., Santoro M., Martín A. (2018) Looking for variable molecular markers in the chestnut gall wasp Dryocosmus kuriphilus: First comparison across genes. Scientific Reports. 8: 0-0.
Link
Doi: 10.1038/s41598-018-23754-z

Abstract:

The quick spread of the chestnut gall wasp Dryocosmus kuriphilus in Europe constitutes an outstanding example of recent human-aided biological invasion with dramatic economic losses. We screened for the first time a set of five nuclear and mitochondrial genes from D. kuriphilus collected in the Iberian Peninsula, and compared the sequences with those available from the native and invasive range of the species. We found no genetic variability in Iberia in none of the five genes, moreover, the three genes compared with other European samples showed no variability either. We recorded four cytochrome b haplotypes in Europe; one was genuine mitochondrial DNA and the rest nuclear copies of mitDNA (numts), what stresses the need of careful in silico analyses. The numts formed a separate cluster in the gene tree and at least two of them might be orthologous, what suggests that the invasion might have started with more than one individual. Our results point at a low initial population size in Europe followed by a quick population growth. Future studies assessing the expansion of this pest should include a large number of sampling sites and use powerful nuclear markers (e. g. Single Nucleotide Polymorphisms) to detect genetic variability. © 2018 The Author(s).

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Satellite passive microwaves reveal recent climate-induced carbon losses in African drylands

Brandt M., Wigneron J.-P., Chave J., Tagesson T., Penuelas J., Ciais P., Rasmussen K., Tian F., Mbow C., Al-Yaari A., Rodriguez-Fernandez N., Schurgers G., Zhang W., Chang J., Kerr Y., Verger A., Tucker C., Mialon A., Rasmussen L.V., Fan L., Fensholt R. (2018) Satellite passive microwaves reveal recent climate-induced carbon losses in African drylands. Nature Ecology and Evolution. : 1-9.
Link
Doi: 10.1038/s41559-018-0530-6

Abstract:

The African continent is facing one of the driest periods in the past three decades as well as continued deforestation. These disturbances threaten vegetation carbon (C) stocks and highlight the need for improved capabilities of monitoring large-scale aboveground carbon stock dynamics. Here we use a satellite dataset based on vegetation optical depth derived from low-frequency passive microwaves (L-VOD) to quantify annual aboveground biomass-carbon changes in sub-Saharan Africa between 2010 and 2016. L-VOD is shown not to saturate over densely vegetated areas. The overall net change in drylands (53% of the land area) was −0.05 petagrams of C per year (Pg C yr−1) associated with drying trends, and a net change of −0.02 Pg C yr−1 was observed in humid areas. These trends reflect a high inter-annual variability with a very dry year in 2015 (net change, −0.69 Pg C) with about half of the gross losses occurring in drylands. This study demonstrates, first, the applicability of L-VOD to monitor the dynamics of carbon loss and gain due to weather variations, and second, the importance of the highly dynamic and vulnerable carbon pool of dryland savannahs for the global carbon balance, despite the relatively low carbon stock per unit area. © 2018 The Author(s)

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Satellite-Observed Major Greening and Biomass Increase in South China Karst During Recent Decade

Brandt M., Yue Y., Wigneron J.P., Tong X., Tian F., Jepsen M.R., Xiao X., Verger A., Mialon A., Al-Yaari A., Wang K., Fensholt R. (2018) Satellite-Observed Major Greening and Biomass Increase in South China Karst During Recent Decade. Earth's Future. 6: 1017-1028.
Link
Doi: 10.1029/2018EF000890

Abstract:

Above-ground vegetation biomass is one of the major carbon sinks and provides both provisioning (e.g., forestry products) and regulating ecosystem services (by sequestering carbon). Continuing deforestation and climate change threaten this natural resource but can effectively be countered by national conservation policies. Here we present time series (1999–2017) derived from complementary satellite systems to describe a phenomenon of global significance: the greening of South China Karst. We find a major increase in growing season vegetation cover from 69% in 1999 to 81% in 2017 occurring over ~1.4 million km2. Over 1999–2012, we report one of the globally largest increases in biomass to occur in the South China Karst region (on average +4% over 0.9 million km2), which accounts for ~5% of the global areas characterized with increases in biomass. These increases in southern China's vegetation have occurred despite a decline in rainfall (−8%) and soil moisture (−5%) between 1999 and 2012 and are derived from effects of forestry and conservation activities at an unprecedented spatial scale in human history (~20,000 km2 yr−1 since 2002). These findings have major implications for the provisioning of ecosystem services not only for the Chinese karst ecosystem (e.g., carbon storage, water filtration, and timber production) but also for the study of global carbon cycles. ©2018. The Authors.

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