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Many roads to convergence

Science, Vol. 361, No. 6398. (13 July 2018), pp. 125-126,


Many plants form specialized symbiotic root structures, called nodules, that harbor beneficial associations with nitrogen-fixing bacteria in the genera Rhizobium or Frankia (see the photo). How this nitrogen-fixing root nodule (NFN) symbiosis arose repeatedly during plant evolution is an age-old mystery: It shows signatures of convergence (the repeated emergence of similarity during evolution) yet builds on similar gene sets in phylogenetically distant plants. On page 144 of this issue, Griesmann et al. (1) sequenced the genomes of 10 plant species to ...


Archetypical patterns and trajectories of land systems in Europe

Regional Environmental Change (2015), pp. 1-18,


Assessments of land-system change have dominantly focused on conversions among broad land-use categories, whereas intensity changes within these categories have received less attention. Considering that both modes of land change typically result in diverse patterns and trajectories of land-system change, there is a need to develop approaches to reduce this complexity. Using Europe as a case study, we applied a clustering approach based on self-organising maps and 12 land-use indicators to map (1) land-system archetypes for the year 2006, defined as ...


Climate twins - An attempt to quantify climatological similarities

IFIP Advances in Information and Communication Technology In Environmental Software Systems. Frameworks of eEnvironment, Vol. 359 (2011), pp. 428-436,


As climate change appears, strategies and actions will be necessary to cope with its effects on environment and society in the coming decades. Current climate conditions can be observed everywhere in the world but future climate conditions can only be estimated through climate simulations which produce huge amounts of quantitative data. This data leads to statements like “temperature increase is expected to exceed 2.6°C” or similar and remain fuzzy to non-experts in climate research. The Climate Twins application is designed to ...


Partial distance correlation with methods for dissimilarities

The Annals of Statistics, Vol. 42, No. 6. (December 2014), pp. 2382-2412,


Distance covariance and distance correlation are scalar coefficients that characterize independence of random vectors in arbitrary dimension. Properties, extensions and applications of distance correlation have been discussed in the recent literature, but the problem of defining the partial distance correlation has remained an open question of considerable interest. The problem of partial distance correlation is more complex than partial correlation partly because the squared distance covariance is not an inner product in the usual linear space. For the definition of partial ...


(INRMM-MiD internal record) List of keywords of the INRMM meta-information database - part 37

(February 2014)
Keywords: inrmm-list-of-tags   sequoia-sempervirens   sequoiadendron-giganteum   serbia   serbian-spruce   serendipity   serotinous-pine   service-as-a-software-substitute   service-tree   services   sesia-apiformis   sex-ratio   shade-tolerance   shake   shallow-soil   shape-index   shape-semantics   sharka-disease   short-rotation-forestry   short-term-vs-long-term   shrubs   si   sicily   sieve   sieve-parameter-training-architecture   sigma-pi-networks   silent-faults   silo-thinking   silver-bullet   silver-fir   silver-fir-decline   silvical-characteristics   silvics   silviculture   similarity   simple-sequence-repeats   simulation   single-nucleotide-polymorphism   sismic-hazard   site-quality   sitka-spruce   situational-awareness   size-asymmetry   slash-management   slavery   slope   slope-stability   slovakia   slovenia   slovenian-alps   smoke   smooth-transition   smyrnium-perfoliatum   snow   snow-avalances   so2   soc   social-engineering-risk   social-learning   social-media   social-system   society   socratea-exorrhiza   sodium   soft-constraint   soft-systems-approach   softw   software-control   software-engineering   software-errors   software-evolution   software-evolvability   software-libraries   software-patents   software-quality   software-security   software-uncertainty   software-validity   software-verification   soil   soil-carbon   soil-compactation   soil-conditions   soil-erosion   soil-evolution   soil-fertility   soil-food   soil-formation   soil-hydrophobicity   soil-loss   soil-microbial-properties   soil-moisture   soil-pollution   soil-resources   soil-restoration   soil-sealing   soil-stabilization   soil-thickness   soil-vs-vegetation  


List of indexed keywords within the transdisciplinary set of domains which relate to the Integrated Natural Resources Modelling and Management (INRMM). In particular, the list of keywords maps the semantic tags in the INRMM Meta-information Database (INRMM-MiD). [\n] The INRMM-MiD records providing this list are accessible by the special tag: inrmm-list-of-tags ( ). ...


Corrigendum to "Modelling soil erosion at European scale: towards harmonization and reproducibility" published in Nat. Hazards Earth Syst. Sci.,15, 225-245, 2015

Natural Hazards and Earth System Science, Vol. 15, No. 2. (16 February 2015), pp. 291-291,


[Excerpt] Two editorial mistakes were found in the article. Both refer to Eq. (2), p. 231 (whose correct version was published in the discussion paper, p. 2652). [\n] The first mistake is related to the operator Ω, which was wrongly rendered with a summation operator (Σ). The editorial notation mistake is also evident by considering the semantics of the RDS (relative distance similarity) statistics. As explained in de Rigo et al. (2013) and Bosco et al. (2013), RDS is defined in [0, 1]. Therefore, a summation operator whose arguments are quantities ...


Studying evolving software ecosystems based on ecological models

In Evolving Software Systems (2014), pp. 297-326,


Research on software evolution is very active, but evolutionary principles, models and theories that properly explain why and how software systems evolve over time are still lacking. Similarly, more empirical research is needed to understand how different software projects co-exist and co-evolve, and how contributors collaborate within their encompassing software ecosystem. In this chapter, we explore the differences and analogies between natural ecosystems and biological evolution on the one hand, and software ecosystems and software evolution on the other hand. The aim is to learn from research in ...


A comparative study of rainfall erosivity estimation for southern Italy and southeastern Australia

Hydrological Sciences Journal, Vol. 44, No. 1. (1 February 1999), pp. 3-24,


Abstract In this paper, using Sicilian and Australian rainfall intensity data, a comparison between different estimators (modified Fournier index F, FF index) of the rainfall erosivity factor in the USLE was made. The relationship between the modified Fournier index and the mean annual rainfall, P, was theoretically derived. The K constant, linking the FF index and P, and its cumulative distribution function (CDF) were used to establish hydrological similitude among different geographical regions of southern Italy and southeastern Australia. To predict ...


Development of indicators reflecting criteria of spatial differentiation - 1.6. Natural assets environmental indicators



[Excerpt] In the task sharing established at the Preparatory Meeting of the Study Programme on European Spatial Planning (SPESP), Brussels, 7 December 1998, it was agreed that the Work Group in charge of the development of theme 1.6, Indicators on Natural Assets, would be made up of the National Focal Points (NFP’s) of Spain and Denmark. Furthermore, it was planned that the work would be carried out in close collaboration with the European Environment Agency (EEA), given the obvious relationship of this organisation with the theme under study. Apart ...


Predicting future forest ranges using array-based geospatial semantic modelling

IEEE Earthzine, Vol. 7, No. 2. (2014), 827545,


Studying the impacts of climate change requires looking at a multitude of variables across a broad range of sectors . Information on the variables involved is often unevenly available or offers different uncertainties, and a lack of uniform terminology and methods further complicates the process of analysis, resulting in communication gaps when research enterprises span different sectors. For example, models designed by experts in one given discipline might assume conventions in language or oversimplify cross-disciplinary links in a way that is ...

Visual summary


Competitive interactions between forest trees are driven by species' trait hierarchy, not phylogenetic or functional similarity: implications for forest community assembly

Ecology Letters, Vol. 15, No. 8. (August 2012), pp. 831-840,


The relative importance of competition vs. environmental filtering in the assembly of communities is commonly inferred from their functional and phylogenetic structure, on the grounds that similar species compete most strongly for resources and are therefore less likely to coexist locally. This approach ignores the possibility that competitive effects can be determined by relative positions of species on a hierarchy of competitive ability. Using growth data, we estimated 275 interaction coefficients between tree species in the French mountains. We show that ...


The influence of phylogenetic relatedness on species interactions among freshwater green algae in a mesocosm experiment

Journal of Ecology, Vol. 102, No. 5. (September 2014), pp. 1288-1299,


1. A long-standing hypothesis in ecology and evolutionary biology is that closely related species are more ecologically similar to each other and therefore compete more strongly than distant relatives do. A recent hypothesis posits that evolutionary relatedness may also explain the prevalence of mutualisms, with facilitative interactions being more common among distantly related species. Despite the importance of these hypotheses for understanding the structure and function of ecological communities, experimental tests to determine how evolutionary relatedness influences competition ...


Evolutionary history and the strength of species interactions: testing the phylogenetic limiting similarity hypothesis

Ecology, Vol. 95, No. 5. (May 2014), pp. 1407-1417,


A longstanding concept in community ecology is that closely related species compete more strongly than distant relatives. Ecologists have invoked this “limiting similarity hypothesis” to explain patterns in the structure and function of biological communities and to inform conservation, restoration, and invasive-species management. However, few studies have empirically tested the validity of the limiting similarity hypothesis. Here we report the results of a laboratory microcosm experiment in which we used a model system of 23 common, co-occurring North American freshwater green ...


Is the C-terminal insertional signal in Gram-negative bacterial outer membrane proteins species-specific or not?

BMC Genomics, Vol. 13, No. 1. (26 September 2012), 510,


BACKGROUND:In Gram-negative bacteria, the outer membrane is composed of an asymmetric lipid bilayer of phopspholipids and lipopolysaccharides, and the transmembrane proteins that reside in this membrane are almost exclusively beta-barrel proteins. These proteins are inserted into the membrane by a highly conserved and essential machinery, the BAM complex. It recognizes its substrates, unfolded outer membrane proteins (OMPs), through a C-terminal motif that has been speculated to be species-specific, based on theoretical and experimental results from only two species, Escherichia coli and ...


Clustering by fast search and find of density peaks

Science, Vol. 344, No. 6191. (26 June 2014), pp. 1492-1496,


[Abstract] Cluster analysis is aimed at classifying elements into categories on the basis of their similarity. Its applications range from astronomy to bioinformatics, bibliometrics, and pattern recognition. We propose an approach based on the idea that cluster centers are characterized by a higher density than their neighbors and by a relatively large distance from points with higher densities. This idea forms the basis of a clustering procedure in which the number of clusters arises intuitively, outliers are automatically spotted and excluded ...


Cellular‐Automata Models Applied to Natural Hazards

Computing in Science & Engineering, Vol. 2, No. 3. (01 May 2000), pp. 42-51,


The concept of self‐organized criticality evolved from studies of three simple cellular‐automata models: the forest‐fire, slider‐block, and sandpile models. Each model is associated with natural hazards, which have frequency‐size statistics that are well approximated by power‐law distributions. These distributions have important implications for probabilistic hazard assessments. ...


Pruning of memories by context-based prediction error

Proceedings of the National Academy of Sciences, Vol. 111, No. 24. (17 June 2014), pp. 8997-9002,


[Significance] Forgetting is often considered to be bad, but selective forgetting of unreliable information can have the positive side effect of reducing mental clutter, thereby making it easier to access our most important memories. Prior studies of forgetting have focused on passive mechanisms (decay, interference) or on effortful inhibition by cognitive control. Here we report the discovery of an active mechanism for forgetting that weakens memories selectively and without burdening the conscious mind. Specifically, we show that the brain automatically generates ...


Unifying niche shift studies: insights from biological invasions

Trends in Ecology & Evolution, Vol. 29, No. 5. (7 August 2014), pp. 260-269,


[Highlights] [::] We propose a unifying framework for assessing niche shifts from empirical data. [::] We base it on a review of studies of niche changes during biological invasions. [::] It decomposes niche changes and accounts for environmental availability and analogy. [::] This unifying framework allows proper comparison of existing and future niche studies. [::] It can also guide management under global change and the design of niche change experiments. [Summary] Assessing whether the climatic niche of a species may change ...


Towards the reproducibility in soil erosion modelling: a new pan-European soil erosion map

In Wageningen conference on applied soil science : 'Soil Science in a Changing World' (February 2011),


Soil erosion by water is a widespread phenomenon throughout Europe and has the potentiality, with his on-site and off-site effects, to affect water quality, food security and floods. Despite the implementation of numerous and different models to estimate soil erosion by water in Europe, there is still a lack of harmonization of assessment methodologies. Very often, different approaches give soil erosion rates significantly different and even when the same model is applied to the same region the results may be different. ...


  1. Rusco, E., Montanarella, L., Bosco, C., 2008. Soil erosion: a main threats to the soils in Europe. In: Tóth, G., Montanarella, L., Rusco, E. (Eds.), Threats to Soil Quality in Europe. No. EUR 23438 EN in EUR - Scientific and Technical Research series. Office for Official Publications of the European Communities, pp. 37-45
  2. Casagrandi, R. and Guariso, G., 2009. Impact of ICT in Environmental Sciences: A citation analysis 1990-2007. Environmental Modelling & Software 24

Mapping land cover from detailed aerial photography data using textural and neural network analysis

International Journal of Remote Sensing, Vol. 28, No. 7. (1 April 2007), pp. 1625-1642,


Automated mapping of land cover using black and white aerial photographs, as an alternative method to traditional photo?interpretation, requires using methods other than spectral analysis classification. To this end, textural measurements have been shown to be useful indicators of land cover. In this work, a neural network model is proposed and tested to map historical land use/land cover (LUC) from very detailed panchromatic aerial photographs (5 m resolution) using textural measurements. The method is used to identify different land use and management ...


Numerical taxonomy

Nature, Vol. 193, No. 4818. (03 March 1962), pp. 855-860,


Recent years have seen a remarkable re-awakening of interest in taxonomy accompanied by a new freedom of ideas and concepts in this field. A number of authors, both in Great Britain and the United States, and in such diverse fields as zoology, botany, palontology and microbiology, have started thinking and working along similar lines quite independently. We do not attempt to review here all the growing technical literature on the subject, since this is listed in several other publications will therefore ...


Efficient Exact Edit Similarity Query Processing with the Asymmetric Signature Scheme

In Proceedings of the 2011 ACM SIGMOD International Conference on Management of Data (2011), pp. 1033-1044,


Given a query string Q, an edit similarity search finds all strings in a database whose edit distance with Q is no more than a given threshold t. Most existing method answering edit similarity queries rely on a signature scheme to generate candidates given the query string. We observe that the number of signatures generated by existing methods is far greater than the lower bound, and this results in high query time and index space complexities. In this paper, we show ...


Multiseed lossless filtration

Computational Biology and Bioinformatics, IEEE/ACM Transactions on, Vol. 2, No. 1. (January 2005), pp. 51-61,


We study a method of seed-based lossless filtration for approximate string matching and related bioinformatics applications. The method is based on a simultaneous use of several spaced seeds rather than a single seed as studied by Burkhardt and Kärkkäinen [1]. We present algorithms to compute several important parameters of seed families, study their combinatorial properties, and describe several techniques to construct efficient families. We also report a large-scale application of the proposed technique to the problem of oligonucleotide selection for an ...


Transposition invariant string matching

Journal of Algorithms, Vol. 56, No. 2. (August 2005), pp. 124-153,


Given strings and over an alphabet Σ⊆U, where U is some numerical universe closed under addition and subtraction, and a distance function d(A,B) that gives the score of the best (partial) matching of A and B, the transposition invariant distance is mint∈Ud(A+t,B), where A+t=(a1+t)(a2+t)...(am+t). We study the problem of computing the transposition invariant distance for various distance (and similarity) functions d, including Hamming distance, longest common subsequence (LCS), Levenshtein distance, and their versions where the exact matching condition is ...


Evidence for soft bounds in Ubuntu package sizes and mammalian body masses

Proceedings of the National Academy of Sciences, Vol. 110, No. 52. (24 December 2013), pp. 21054-21058,


[Significance] Not unlike a big city, a large software project grows in a complex way, involving many developers and even more users, but a predictive framework to understand these temporal patterns is lacking. We focus on software size and analyze the changes of the Ubuntu open source operating system, finding two quantitative laws. First, growth is driven by changes in scale rather than by addition–subtraction; second, evolution toward larger sizes between two consecutive releases is limited by bounds that depend on ...


Classification of Natural and Semi-natural Vegetation

In Vegetation Ecology (07 January 2013), pp. 28-70,


This chapter covers classification of natural and semi-natural vegetation, including classification frameworks, components of classification, project planning and data acquisition, data preparation and integration, community entitation, cluster assessment, community characterization and determination, classification integration, documentation, and future directions and challenges. ...


Scaling and multifractal fields in the solid earth and topography

Nonlinear Processes in Geophysics, Vol. 14, No. 4. (2 August 2007), pp. 465-502,


Starting about thirty years ago, new ideas in nonlinear dynamics, particularly fractals and scaling, provoked an explosive growth of research both in modeling and in experimentally characterizing geosystems over wide ranges of scale. In this review we focus on scaling advances in solid earth geophysics including the topography. To reduce the review to manageable proportions, we restrict our attention to scaling fields, i.e. to the discussion of intensive quantities such as ore concentrations, rock densities, susceptibilities, and magnetic and gravitational fields. ...


Deducing the USLE mathematical structure by dimensional analysis and self-similarity theory

Biosystems Engineering, Vol. 106, No. 2. (15 June 2010), pp. 216-220,


The Universal Soil Loss Equation (USLE) was originally deduced by a statistical analysis of a large data set of soil loss measurements. The multiplicative structure of the model has been criticised due to the considerable interdependence between the variables. Using the soil erosion representative variables and the reference condition adopted in the USLE, the aim of this paper was to apply dimensional analysis and self-similarity theory to deduce the functional relationship among the selected variables. The analysis yielded a multiplicative equation, ...


Coupling fuzzy modeling and neural networks for river flood prediction

Systems, Man, and Cybernetics, Part C: Applications and Reviews, IEEE Transactions on, Vol. 35, No. 3. (August 2005), pp. 382-390,


Over the last decade, neural network-based flood forecast systems have been increasingly used in hydrological research. Usually, input data of the network are composed by past measurements of flows and rainfalls, without providing a description of the saturation state of the basin, which, in contrast, plays a key role in the rainfall-runoff process. This paper couples neural networks and fuzzy logic in order to enrich the description of the basin saturation state for flood forecasting purposes. The basin state is assessed ...


Local Indicators of Spatial Association—LISA

Geographical Analysis, Vol. 27, No. 2. (1 September 1995), pp. 93-115,


The capabilities for visualization, rapid data retrieval, and manipulation in geographic information systems (GIS) have created the need for new techniques of exploratory data analysis that focus on the “spatial” aspects of the data. The identification of local patterns of spatial association is an important concern in this respect. In this paper, I outline a new general class of local indicators of spatial association (LISA) and show how they allow for the decomposition of global indicators, such as Moran's I, into ...


Towards the reproducibility in soil erosion modeling: a new pan-European soil erosion map

In Wageningen conference on applied soil science : 'Soil Science in a Changing World' (2011),


Soil erosion by water is a widespread phenomenon throughout Europe and has the potentiality, with his on-site and off-site effects, to affect water quality, food security and floods. Despite the implementation of numerous and different models to estimate soil erosion by water in Europe, there is still a lack of harmonization of assessment methodologies. Very often, different approaches give soil erosion rates significantly different and even when the same model is applied to the same region the results may be different. ...


  1. Rusco, E., Montanarella, L., Bosco, C., 2008. Soil erosion: a main threats to the soils in Europe. In: Tóth, G., Montanarella, L., Rusco, E. (Eds.), Threats to Soil Quality in Europe. No. EUR 23438 EN in EUR - Scientific and Technical Research series. Office for Official Publications of the European Communities, pp. 37-45
  2. Casagrandi, R. and Guariso, G., 2009. Impact of ICT in Environmental Sciences: A citation analysis 1990-2007. Environmental Modelling & Software 24
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Meta-information Database (INRMM-MiD).
This database integrates a dedicated meta-information database in CiteULike (the CiteULike INRMM Group) with the meta-information available in Google Scholar, CrossRef and DataCite. The Altmetric database with Article-Level Metrics is also harvested. Part of the provided semantic content (machine-readable) is made even human-readable thanks to the DCMI Dublin Core viewer. Digital preservation of the meta-information indexed within the INRMM-MiD publication records is implemented thanks to the Internet Archive.
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INRMM-MiD was experimentally established by the Maieutike Research Initiative in 2008 and then improved with the help of several volunteers (with a major technical upgrade in 2011). This new integrated interface is operational since 2014.