OEMC D2.1 Report "Stakeholder Committee and Open- Earth-Monitor Design" workshop

This deliverable of the Open-Earth-Monitor project describes the approach taken to compile and categorize the project's stakeholders, and provides recommendations for the future stakeholder interactions based on the results of a survey from the OEMC design workshop, which took place during the project's kick-off meeting in July, 2022

Quo vadis, smallholder forest landscape?: An introduction to the LPB-RAP model

The impacts of the Anthropocene on climate and biodiversity pose societal and ecological problems that may only be solved by ecosystem restoration. Local to regional actions are required, which need to consider the prevailing present and future conditions of a certain landscape extent. Modeling approaches can be of help to support management efforts and to provide advice to policy making. We present stage one of the LaForeT-PLUC-BE model (Landscape Forestry in the Tropics–PCRaster Land Use Change–Biogeographic & Economic model; in short: LPB) and its thematic expansion module RAP (Restoration Areas Potentials). LPB-RAP is a high-resolution pixel-based scenario tool that relies on a range of explicit land use types (LUTs) to describe various forest types and the environment. It simulates and analyzes future landscape configurations under consideration of climate, population and land use change long-term. Simulated Land Use Land Cover Change (LULCC) builds on dynamic, probabilistic modeling incorporating climatic and anthropogenic determinants as well as restriction parameters to depict a sub-national regional smallholder-dominated forest landscape. The model delivers results for contrasting scenario settings by simulating without and with potential Forest and Landscape Restoration (FLR) measures. FLR potentials are depicted by up to five RAP-LUTs. The model builds on user-defined scenario inputs, such as the Shared Socioeconomic Pathways (SSP) and Representative Concentration Pathways (RCP). Model application is here exemplified for the SSP2-RCP4.5 scenario in the time frame 2018–2100 on the hectare scale in annual resolution using Esmeraldas province, Ecuador, as a case study area. The LPB-RAP model is a novel, heuristic Spatial Decision Support System (SDSS) tool for smallholder-dominated forest landscapes, supporting near-time top-down planning measures with long-term bottom-up modeling. Its application should be followed up by FLR on-site investigations and stakeholder participation across all involved scales

NeuralHydrology -- Interpreting LSTMs in Hydrology

Despite the huge success of Long Short-Term Memory networks, their applications in environmental sciences are scarce. We argue that one reason is the difficulty to interpret the internals of trained networks. In this study, we look at the application of LSTMs for rainfall-runoff forecasting, one of the central tasks in the field of hydrology, in which the river discharge has to be predicted from meteorological observations. LSTMs are particularly well-suited for this problem since memory cells can represent dynamic reservoirs and storages, which are essential components in state-space modelling approaches of the hydrological system. On basis of two different catchments, one with snow influence and one without, we demonstrate how the trained model can be analyzed and interpreted. In the process, we show that the network internally learns to represent patterns that are consistent with our qualitative understanding of the hydrological system.Comment: Pre-print of published book chapter. See journal reference and DOI for more inf

First GIS analysis of modern stone tools used by wild chimpanzees (Pan troglodytes verus) in Bossou, Guinea, West Africa

Stone tool use by wild chimpanzees of West Africa offers a unique opportunity to explore the evolutionary roots of technology during human evolution. However, detailed analyses of chimpanzee stone artifacts are still lacking, thus precluding a comparison with the earliest archaeological record. This paper presents the first systematic study of stone tools used by wild chimpanzees to crack open nuts in Bossou (Guinea-Conakry), and applies pioneering analytical techniques to such artifacts. Automatic morphometric GIS classification enabled to create maps of use wear over the stone tools (anvils, hammers, and hammers/anvils), which were blind tested with GIS spatial analysis of damage patterns identified visually. Our analysis shows that chimpanzee stone tool use wear can be systematized and specific damage patterns discerned, allowing to discriminate between active and passive pounders in lithic assemblages. In summary, our results demonstrate the heuristic potential of combined suites of GIS techniques for the analysis of battered artifacts, and have enabled creating a referential framework of analysis in which wild chimpanzee battered tools can for the first time be directly compared to the early archaeological record.Leverhulme Trust [IN-052]; MEXT [20002001, 24000001]; JSPS-U04-PWS; FCT-Portugal [SFRH/BD/36169/2007]; Wenner-Gren Foundation for Anthropological Researc

Comparison of Different Methods of Automated Landform Classification at the Drainage Basin Scale: Examples from the Southern Italy

In this work, we tested the reliability of two different methods of automated landform classification (ACL) in three geological domains of the southern Italian chain with contrasting morphological features. ACL maps deriving from the TPI-based (topographic position index) algorithm are strictly dependent to the search input parameters and they are not able to fully capture landforms of different size. Geomorphons-based classification has shown a higher potential and can represent a powerful method of ACL, although it should be improved with the introduction of additional DEM-based parameters for the extraction of landform classe

Spatial risk assessment of hydrological extremities : Inland excess water hazard, Szabolcs-Szatmár-Bereg Country, Hungary

Inland excess water hazard was regionalized and digitally mapped using auxiliary spatial environmental information for a county in Eastern Hungary. Quantified parameters representing the effect of soil, geology, groundwater, land use and hydrometeorology on the formulation of inland excess water were defined and spatially explicitly derived. The complex role of relief was characterized using multiple derivatives computed from a DEM. Legacy maps displaying inland excess water events were used as a reference dataset. Regression kriging was applied for spatial inference with the correlation between environmental factors and inundation determined using multiple linear regressions. A stochastic factor derived through kriging the residual was added to the regression results,thus producing the final inundation hazard map. This may be of use for numerous landrelated activities

African soil properties and nutrients mapped at 30 m spatial resolution using two-scale ensemble machine learning

Soil property and class maps for the continent of Africa were so far only available at very generalised scales, with many countries not mapped at all. Thanks to an increasing quantity and availability of soil samples collected at field point locations by various government and/or NGO funded projects, it is now possible to produce detailed pan-African maps of soil nutrients, including micro-nutrients at five spatial resolutions. In this paper we describe production of a 30 m resolution Soil Information System of the African continent using, to date, the most comprehensive compilation of soil samples (N ≈ 150, 000) and Earth Observation data. We produced predictions for soil pH, organic carbon (C) and total nitrogen (N), total carbon, effective Cation Exchange Capacity (eCEC), extractable—phosphorus (P), potassium (K), calcium (Ca), magnesium (Mg), sulfur (S), sodium (Na), iron (Fe), zinc(Zn)—silt, clay and sand, stone content, bulk density and depth to bedrock, at three depths (0, 20 and 50 cm) and using 2-scale 3D Ensemble Machine Learning framework implemented in the mlr (Machine Learning in R) package. As covariate layers we used 250 m resolution (MODIS, PROBA-V and SM2RAIN products), and 30 m resolution (Sentinel-2, Landsat and DTM derivatives) images. Our fivefold spatial Cross-Validation results showed varying accuracy levels ranging from the best performing soil pH (CCC = 0.900) to more poorly predictable extractable phosphorus (CCC = 0.654) and sulphur (CCC = 0.708) and depth to bedrock. Sentinel-2 bands SWIR (B11, B12), NIR (B09, B8A), Landsat SWIR bands, and vertical depth derived from 30 m resolution DTM, were the overall most important 30 m resolution covariates. Climatic data images—SM2RAIN, bioclimatic variables and MODIS Land Surface Temperature—however, remained as the overall most important variables for predicting soil chemical variables at continental scale. This publicly available 30-m Soil Information System of Africa aims at supporting numerous applications, including soil and fertilizer policies and investments, agronomic advice to close yield gaps, environmental programs, or targeting of nutrition interventions

Assessment of the olfactory function in Italian patients with type 3 von Willebrand disease caused by a homozygous 253 Kb deletion involving VWF and TMEM16B/ANO2.

Type 3 Von Willebrand disease is an autosomal recessive disease caused by the virtual absence of the von Willebrand factor (VWF). A rare 253 kb gene deletion on chromosome 12, identified only in Italian and German families, involves both the VWF gene and the N-terminus of the neighbouring TMEM16B/ANO2 gene, a member of the family named transmembrane 16 (TMEM16) or anoctamin (ANO). TMEM16B is a calcium-activated chloride channel expressed in the olfactory epithelium. As a patient homozygous for the 253 kb deletion has been reported to have an olfactory impairment possibly related to the partial deletion of TMEM16B, we assessed the olfactory function in other patients using the University of Pennsylvania Smell Identification Test (UPSIT). The average UPSIT score of 4 homozygous patients was significantly lower than that of 5 healthy subjects with similar sex, age and education. However, 4 other members of the same family, 3 heterozygous for the deletion and 1 wild type, had a slightly reduced olfactory function indicating that socio-cultural or other factors were likely to be responsible for the observed difference. These results show that the ability to identify odorants of the homozygous patients for the deletion was not significantly different from that of the other members of the family, showing that the 253 kb deletion does not affect the olfactory performance. As other genes may compensate for the lack of TMEM16B, we identified some predicted functional partners from in silico studies of the protein-protein network of TMEM16B. Calculation of diversity for the corresponding genes for individuals of the 1000 Genomes Project showed that TMEM16B has the highest level of diversity among all genes of the network, indicating that TMEM16B may not be under purifying selection and suggesting that other genes in the network could compensate for its function for olfactory ability

Mechanism of PP2A-mediated IKKβ dephosphorylation: a systems biological approach

BACKGROUND: Biological effects of nuclear factor-kappaB (NF kappaB) can differ tremendously depending on the cellular context. For example, NF kappaB induced by interleukin-1 (IL-1) is converted from an inhibitor of death receptor induced apoptosis into a promoter of ultraviolet-B radiation (UVB)-induced apoptosis. This conversion requires prolonged NF kappaB activation and is facilitated by IL-1 + UVB-induced abrogation of the negative feedback loop for NF kappaB, involving a lack of inhibitor of kappaB (I kappaB alpha) protein reappearance. Permanent activation of the upstream kinase IKK beta results from UVB-induced inhibition of the catalytic subunit of Ser-Thr phosphatase PP2A (PP2Ac), leading to immediate phosphorylation and degradation of newly synthesized I kappaB alpha. RESULTS: To investigate the mechanism underlying the general PP2A-mediated tuning of IKK beta phosphorylation upon IL-1 stimulation, we have developed a strictly reduced mathematical model based on ordinary differential equations which includes the essential processes concerning the IL-1 receptor, IKK beta and PP2A. Combining experimental and modelling approaches we demonstrate that constitutively active, but not post-stimulation activated PP2A, tunes out IKK beta phosphorylation thus allowing for I kappaB alpha resynthesis in response to IL-1. Identifiability analysis and determination of confidence intervals reveal that the model allows reliable predictions regarding the dynamics of PP2A deactivation and IKK beta phosphorylation. Additionally, scenario analysis is used to scrutinize several hypotheses regarding the mode of UVB-induced PP2Ac inhibition. The model suggests that down regulation of PP2Ac activity, which results in prevention of I kappaB alpha reappearance, is not a direct UVB action but requires instrumentality. CONCLUSION: The model developed here can be used as a reliable building block of larger NF kappa B models and offers comprehensive simplification potential for future modeling of NF kappa B signaling. It gives more insight into the newly discovered mechanisms for IKK deactivation and allows for substantiated predictions and investigation of different hypotheses. The evidence of constitutive activity of PP2Ac at the IKK complex provides new insights into the feedback regulation of NF kappa B, which is crucial for the development of new anti-cancer strategies

SILKNOWViz: Spatio-temporal data ontology viewer

Interactive visualization of spatio-temporal data is a very active area that has experienced remarkable advances in the last decade. This is due to the emergence of fields of research such as big data and advances in hardware that allow better analysis of information. This article describes the methodology followed and the design of an open source tool, which in addition to interactively visualizing spatio-temporal data that are represented in an ontology, allows the definition of what to visualize and how to do it. The tool allows selecting, filtering and visualizing in a graphical way the entities of the ontology with spatiotemporal data, as well as the instances related to them. The graphical elements used to display the information are specified on the same ontology, extending the VISO graphic ontology, used for mapping concepts to graphic objects with RDFS/OWL Visualization Language (RVL). This extension contemplates the data visualization on rich real-time 3D environments, allowing different modes of visualization according to the level of detail of the scene, while also emphasizing the treatment of spatio-temporal data, very often used in cultural heritage models. This visualization tool involves simple visualization scenarios and high interaction environments that allow complex comparative analysis. It combines traditional solutions, like hypercube or time-animations with innovative data selection methods.Interactive visualization of spatio-temporal data is a very active area that has experienced remarkable advances in the last decade. This is due to the emergence of fields of research such as big data and advances in hardware that allow better analysis of information. This article describes the methodology followed and the design of an open source tool, which in addition to interactively visualizing spatio-temporal data that are represented in an ontology, allows the definition of what to visualize and how to do it. The tool allows selecting, filtering and visualizing in a graphical way the entities of the ontology with spatiotemporal data, as well as the instances related to them. The graphical elements used to display the information are specified on the same ontology, extending the VISO graphic ontology, used for mapping concepts to graphic objects with RDFS/OWL Visualization Language (RVL). This extension contemplates the data visualization on rich real-time 3D environments, allowing different modes of visualization according to the level of detail of the scene, while also emphasizing the treatment of spatio-temporal data, very often used in cultural heritage models. This visualization tool involves simple visualization scenarios and high interaction environments that allow complex comparative analysis. It combines traditional solutions, like hypercube or time-animations with innovative data selection methods