A CRISP-DM-based Methodology for Assessing Agent-based Simulation Models using Process Mining

Agent-based simulation (ABS) models are potent tools for analyzing complex systems. However, understanding and validating ABS models can be a significant challenge. To address this challenge, cutting-edge data-driven techniques offer sophisticated capabilities for analyzing the outcomes of ABS models. One such technique is process mining, which encompasses a range of methods for discovering, monitoring, and enhancing processes by extracting knowledge from event logs. However, applying process mining to event logs derived from ABSs is not trivial, and deriving meaningful insights from the resulting process models adds an additional layer of complexity. Although process mining is invaluable in extracting insights from ABS models, there is a lack of comprehensive methodological guidance for its application in ABS evaluation in the research landscape. In this paper, we propose a methodology, based on the CRoss-Industry Standard Process for Data Mining (CRISP-DM) methodology, to assess ABS models using process mining techniques. We incorporate process mining techniques into the stages of the CRISP-DM methodology, facilitating the analysis of ABS model behaviors and their underlying processes. We demonstrate our methodology using an established agent-based model, Schelling model of segregation. Our results show that our proposed methodology can effectively assess ABS models through produced event logs, potentially paving the way for enhanced agent-based model validity and more insightful decision-making

Advancing presence and changes in body size of brown shrimp <i>Crangon crangon</i> on intertidal flats in the western Dutch Wadden Sea, 1984–2018

Upon settlement after a pelagic larval phase, brown shrimp Crangon crangon depend on intertidal flats. During low as well as high tide the young brown shrimp play roles as predators of meiofauna and as prey for fish and birds. Unlike the biol- ogy of the commercially important adults, knowledge on these juveniles remains sketchy. Here we provide an analysis of 35 years (1984–2018) of brown shrimp monitoring in May–June on intertidal flats in the westernmost Dutch Wadden Sea. Intertidal shrimp densities were sampled bi-weekly at three stations during low tide, using sampling corers. We show that over this 35-year period the appearance of shrimp on mudflats advanced by 12 days (− 0.34 days yr−1). Simultaneously, densities on 7 May increased by more than 2.4 times, from 28 shrimp m−2 in 1984 to 69 shrimp m−2 in 2018. Across years, mean shrimp length decreased from 12.6 to 10.7 mm, but length in early May did not change. The advancement in settle- ment and the increasing shrimp densities correlated with increases in the seawater temperatures in April more than during earlier times of the year. We propose four interpretations of these changes: (1) shrimp settle on the mudflat when they reach a certain ‘threshold’ length, (2) settlement of shrimp is controlled by a critical period of ‘threshold’ temperature sensitivity, (3) timing of shrimp settlement is a response to food availability on mudflats or (4) a direct response to inferred predation pressure. The different interpretations will lead to different scenarios of change in a warming world

Offshore Landward Motion Shortly After a Subduction Earthquake Implies Rapid Relocking of the Shallow Megathrust

Geodetic observations after large subduction earthquakes reflect multiple postseismic processes, including megathrust relocking. The timing of relocking and the observational constraints on it are unclear. Relocking was inferred to explain some observed landward motion that occurs within months. It was also considered unable to explain other, greater landward motion, including that off the coast of Japan beginning weeks after the 2011 Tohoku earthquake, attributed to postseismic relaxation. We use generic, 3D numerical models to show that relocking, particularly of the shallow interface, is needed for postseismic relaxation to produce landward motion on the tip of the overriding plate. We argue that this finding is consistent with previous simulations that implicitly relock the megathrust where afterslip is not included. We conclude that the Tohoku megathrust relocked within less than 2 months of the earthquake. This suggests that the shallow megathrust probably behaves as a true, unstably sliding asperity

Growth, maturity, and diet of the pearl whipray (<i>Fontitrygon margaritella</i>) from the Bijagós Archipelago, Guinea-Bissau

The pearl whipray Fontitrygon margaritella (Compagno & Roberts, 1984) is a common elasmobranch in coastal western African waters. However, knowledge on their life-history and trophic ecology remains limited. Therefore, we aimed to determine the growth, maturity and diet of F. margaritella from the Bijagós Archipelago in Guinea-Bissau. Growth was modelled with: von Bertalanffy, Gompertz and logistic functions. Model selection revealed no model significantly outperformed another. The sampled age ranged from less than 1 to 7 years (1.8 ± 1.9 cm, mean ± standard deviation) and size (disc width) ranged from 12.2 to 30.6 cm (18.7 ± 5.2 cm). Size-at-maturity was estimated at 20.3 cm (95% CI [18.8–21.8 cm]) for males and 24.3 cm for females (95% CI [21.9–26.5 cm]), corresponding ages of 2.2 and 3.9 years. The diet differed significantly among young-of-the-year (YOY), juveniles and adults (p = 0.001). Diet of all life stages consisted mainly of crustaceans (27.4%, 28.5%, 33.3%) and polychaetes (12.5%, 26.7%, 20.3%), for YOY, juveniles and adults respectively. This study shows that F. margaritella is relatively fast-growing, matures early and experiences ontogenetic diet shifts. These results contribute to status assessments and conservation efforts of F. margaritella and closely related species

Dynamics of the African Plate 75 Ma: From Plate Kinematic Reconstructions to Intraplate Paleo-Stresses

Plate reconstruction studies show that the Neotethys Ocean was closing due to the convergence of Africa and Eurasia toward the end of the Cretaceous. The period around 75 Ma reflects the onset of continental collision between the two plates as convergence continued to be taken up mostly by subduction of the Neotethys slab beneath Eurasia. The Owen transform plate boundary in the northeast accommodated the fast northward motion of the Indian plate relative to the African plate. The rest of the plate was surrounded by mid-ocean ridges. Africa was experiencing continent-wide rifting related to northeast-southwest extension. We aim to quantify the forces and paleostresses that may have driven this continental extension. We use the latest plate kinematic reconstructions in a grid search to estimate horizontal gravitational stresses (HGSs), plate boundary forces, and the plate's interaction with the asthenosphere. The contribution of dynamic topography to HGSs is based on recent mantle convection studies. We model intraplate stresses and compare them with the strain observations. The fit to observations favors models where dynamic topography amplitudes are smaller than 300 m. The results also indicate that the net pull transmitted from slab to the surface African plate was low. To put this into context, we notice that available tectonic reconstructions show fragmented subduction zones and various colliding micro-continents along the northern margin of the African plate around this time. We therefore interpret a low net pull as resulting from either a small average slab length or from the micro-continents' resistance to subduction

Artilysation' of endolysin λSa2lys strongly improves its enzymatic and antibacterial activity against streptococci

Endolysins constitute a promising class of antibacterials against Gram-positive bacteria. Recently, endolysins have been engineered with selected peptides to obtain a new generation of lytic proteins, Artilysins, with specific activity against Gram-negative bacteria. Here, we demonstrate that artilysation can also be used to enhance the antibacterial activity of endolysins against Gram-positive bacteria and to reduce the dependence on external conditions. Art-240, a chimeric protein of the anti-streptococcal endolysin λSa2lys and the polycationic peptide PCNP, shows a similar species specificity as the parental endolysin, but the bactericidal activity against streptococci increases and is less affected by elevated NaCl concentrations and pH variations. Time-kill experiments and time-lapse microscopy demonstrate that the killing rate of Art-240 is approximately two-fold higher compared to wildtype endolysin λSa2lys, with a reduction in viable bacteria of 3 log units after 10min. In addition, lower doses of Art240 are required to achieve the same bactericidal effect

Optimizing the use of InSAR observations in data assimilation problems to estimate reservoir compaction

Hydrocarbon production may cause subsidence as a result of the pressure reduction in the gas-producing layer and reservoir compaction. To analyze the process of subsidence and estimate reservoir parameters, we use a particle method to assimilate Interferometric synthetic-aperture radar (InSAR) observations of surface deformation with a conceptual model of reservoir. As example, we use an analytical model of the Groningen gas reservoir based on a geometry representing the compartmentalized structure of the subsurface at the reservoir depth. The efficacy of the particle method becomes less when the degree of freedom is large compared to the ensemble size. This degree of freedom, in turn, varies because of spatial correlation in the observed field. The resolution of the InSAR data and the number of observations affect the performance of the particle method. In this study, we quantify the information in a Sentinel-1 SAR dataset using the concept of Shannon entropy from information theory. We investigate how to best capture the level of detail in model resolved by the InSAR data while maximizing their information content for a data assimilation use. We show that incorrect representation of the existing correlations leads to weight collapse when the number of observation increases, unless the ensemble size growths. However, simulations of mutual information show that we could optimize data reduction by choosing an adequate mesh given the spatial correlation in the observed subsidence. Our approach provides a means to achieve a better information use from available InSAR data reducing weight collapse without additional computational cost

The Lectin Receptor Kinase LecRK-I.9 Is a Novel Phytophthora Resistance Component and a Potential Host Target for a RXLR Effector

In plants, an active defense against biotrophic pathogens is dependent on a functional continuum between the cell wall (CW) and the plasma membrane (PM). It is thus anticipated that proteins maintaining this continuum also function in defense. The legume-like lectin receptor kinase LecRK-I.9 is a putative mediator of CW-PM adhesions in Arabidopsis and is known to bind in vitro to the Phytophthora infestans RXLR-dEER effector IPI-O via a RGD cell attachment motif present in IPI-O. Here we show that LecRK-I.9 is associated with the plasma membrane, and that two T-DNA insertions lines deficient in LecRK-I.9 (lecrk-I.9) have a ‘gain-of-susceptibility’ phenotype specifically towards the oomycete Phytophthora brassicae. Accordingly, overexpression of LecRK-I.9 leads to enhanced resistance to P. brassicae. A similar ‘gain-of-susceptibility’ phenotype was observed in transgenic Arabidopsis lines expressing ipiO (35S-ipiO1). This phenocopy behavior was also observed with respect to other defense-related functions; lecrk-I.9 and 35S-ipiO1 were both disturbed in pathogen- and MAMP-triggered callose deposition. By site-directed mutagenesis, we demonstrated that the RGD cell attachment motif in IPI-O is not only essential for disrupting the CW-PM adhesions, but also for disease suppression. These results suggest that destabilizing the CW-PM continuum is one of the tactics used by Phytophthora to promote infection. As countermeasure the host may want to strengthen CW-PM adhesions and the novel Phytophthora resistance component LecRK-I.9 seems to function in this process

A tsunami generated by a strike-slip event.: constraints from GPS and SAR data on the 2018 Palu earthquake

A devastating tsunami struck Palu Bay in the wake of the 28 September 2018 Mw = 7.5 Palu earthquake (Sulawesi, Indonesia). With a predominantly strike-slip mechanism, the question remains whether this unexpected tsunami was generated by the earthquake itself, or rather by earthquake-induced landslides. In this study we examine the tsunami potential of the co-seismic deformation. To this end, we present a novel geodetic dataset of GPS and multiple SAR-derived displacement fields to estimate a 3D co-seismic surface deformation field. The data reveal a number of fault bends, conforming to our interpretation of the tectonic setting as a transtensional basin. Using a Bayesian framework, we provide robust finite fault solutions of the co-seismic slip distribution, incorporating several scenarios of tectonically feasible fault orientations below the bay. These finite fault scenarios involve large co-seismic uplift ( > 2 m) below the bay due to thrusting on a restraining fault bend that connects the offshore continuation of two parallel onshore fault segments. With the co-seismic displacement estimates as input we simulate a number of tsunami cases. For most locations for which video-derived tsunami waveforms are available our models provide a qualitative fit to leading wave arrival times and polarity. The modeled tsunamis explain most of the observed runup. We conclude that co-seismic deformation was the main driver behind the tsunami that followed the Palu earthquake. Our unique geodetic dataset constrains vertical motions of the sea floor, and sheds new light on the tsunamigenesis of strike-slip faults in transtensional basins

A Tsunami Generated by a Strike-Slip Event: Constraints From GPS and SAR Data on the 2018 Palu Earthquake

A devastating tsunami struck Palu Bay in the wake of the 28 September 2018 Mw = 7.5 Palu earthquake (Sulawesi, Indonesia). With a predominantly strike-slip mechanism, the question remains whether this unexpected tsunami was generated by the earthquake itself, or rather by earthquake-induced landslides. In this study we examine the tsunami potential of the co-seismic deformation. To this end, we present a novel geodetic data set of Global Positioning System and multiple Synthetic Aperture Radar-derived displacement fields to estimate a 3D co-seismic surface deformation field. The data reveal a number of fault bends, conforming to our interpretation of the tectonic setting as a transtensional basin. Using a Bayesian framework, we provide robust finite fault solutions of the co-seismic slip distribution, incorporating several scenarios of tectonically feasible fault orientations below the bay. These finite fault scenarios involve large co-seismic uplift (>2 m) below the bay due to thrusting on a restraining fault bend that connects the offshore continuation of two parallel onshore fault segments. With the co-seismic displacement estimates as input we simulate a number of tsunami cases. For most locations for which video-derived tsunami waveforms are available our models provide a qualitative fit to leading wave arrival times and polarity. The modeled tsunamis explain most of the observed runup. We conclude that co-seismic deformation was the main driver behind the tsunami that followed the Palu earthquake. Our unique geodetic data set constrains vertical motions of the sea floor, and sheds new light on the tsunamigenesis of strike-slip faults in transtensional basins