TY - JOUR A1 - Kumar, Rohini A1 - Hesse, Fabienne A1 - Rao, P. Srinivasa A1 - Musolff, Andreas A1 - Jawitz, James A1 - Sarrazin, Francois A1 - Samaniego, Luis A1 - Fleckenstein, Jan H. A1 - Rakovec, Oldrich A1 - Thober, S. A1 - Attinger, Sabine T1 - Strong hydroclimatic controls on vulnerability to subsurface nitrate contamination across Europe JF - Nature Communications N2 - Subsurface contamination due to excessive nutrient surpluses is a persistent and widespread problem in agricultural areas across Europe. The vulnerability of a particular location to pollution from reactive solutes, such as nitrate, is determined by the interplay between hydrologic transport and biogeochemical transformations. Current studies on the controls of subsurface vulnerability do not consider the transient behaviour of transport dynamics in the root zone. Here, using state-of-the-art hydrologic simulations driven by observed hydroclimatic forcing, we demonstrate the strong spatiotemporal heterogeneity of hydrologic transport dynamics and reveal that these dynamics are primarily controlled by the hydroclimatic gradient of the aridity index across Europe. Contrasting the space-time dynamics of transport times with reactive timescales of denitrification in soil indicate that similar to 75% of the cultivated areas across Europe are potentially vulnerable to nitrate leaching for at least onethird of the year. We find that neglecting the transient nature of transport and reaction timescale results in a great underestimation of the extent of vulnerable regions by almost 50%. Therefore, future vulnerability and risk assessment studies must account for the transient behaviour of transport and biogeochemical transformation processes. KW - travel time distributions KW - groundwater vulnerability KW - flux tracking KW - transit-time KW - water age KW - nitrogen KW - model KW - dynamics KW - pollution KW - patterns Y1 - 2020 U6 - https://doi.org/10.1038/s41467-020-19955-8 SN - 2041-1723 VL - 11 IS - 1 SP - 1 EP - 10 PB - Nature Publishing Group UK CY - London ER - TY - JOUR A1 - Botero, David A1 - Monk, Jonathan A1 - Rodriguez Cubillos, Maria Juliana A1 - Rodriguez Cubillos, Andres Eduardo A1 - Restrepo, Mariana A1 - Bernal-Galeano, Vivian A1 - Reyes, Alejandro A1 - Gonzalez Barrios, Andres A1 - Palsson, Bernhard O. A1 - Restrepo, Silvia A1 - Bernal, Adriana T1 - Genome-scale metabolic model of Xanthomonas phaseoli pv. manihotis BT - an approach to elucidate pathogenicity at the metabolic level JF - Frontiers in genetics N2 - Xanthomonas phaseoli pv. manihotis (Xpm) is the causal agent of cassava bacterial blight, the most important bacterial disease in this crop. There is a paucity of knowledge about the metabolism of Xanthomonas and its relevance in the pathogenic process, with the exception of the elucidation of the xanthan biosynthesis route. Here we report the reconstruction of the genome-scale model of Xpm metabolism and the insights it provides into plant-pathogen interactions. The model, iXpm1556, displayed 1,556 reactions, 1,527 compounds, and 890 genes. Metabolic maps of central amino acid and carbohydrate metabolism, as well as xanthan biosynthesis of Xpm, were reconstructed using Escher (https://escher.github.io/) to guide the curation process and for further analyses. The model was constrained using the RNA-seq data of a mutant of Xpm for quorum sensing (QS), and these data were used to construct context-specific models (CSMs) of the metabolism of the two strains (wild type and QS mutant). The CSMs and flux balance analysis were used to get insights into pathogenicity, xanthan biosynthesis, and QS mechanisms. Between the CSMs, 653 reactions were shared; unique reactions belong to purine, pyrimidine, and amino acid metabolism. Alternative objective functions were used to demonstrate a trade-off between xanthan biosynthesis and growth and the re-allocation of resources in the process of biosynthesis. Important features altered by QS included carbohydrate metabolism, NAD(P)(+) balance, and fatty acid elongation. In this work, we modeled the xanthan biosynthesis and the QS process and their impact on the metabolism of the bacterium. This model will be useful for researchers studying host-pathogen interactions and will provide insights into the mechanisms of infection used by this and other Xanthomonas species. KW - Xanthomonas KW - Xpm KW - cassava bacterial blight KW - genome-scale metabolic KW - model KW - quorum sensing Y1 - 2020 U6 - https://doi.org/10.3389/fgene.2020.00837 SN - 1664-8021 VL - 11 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Vogt-Vincent, Noam A1 - Lippold, Jörg A1 - Kaboth-Bahr, Stefanie A1 - Blaser, Patrick T1 - Ice-rafted debris as a source of non-conservative behaviour for the epsilon Nd palaeotracer BT - insights from a simple model JF - Geo-marine letters : an international journal of marine geology N2 - Neodymium isotopic composition (epsilon Nd) has enjoyed widespread use as a palaeotracer, principally because it behaves quasi-conservatively in the modern ocean. However, recent bottom water epsilon Nd reconstructions from the eastern North Atlantic are difficult to interpret under assumptions of conservative behaviour. The observation that this apparent departure from conservative behaviour increases with enhanced ice-rafted debris (IRD) fluxes has resulted in the suggestion that IRD leads to the overprinting of bottom water epsilon Nd through reversible scavenging. In this study, a simple water column model successfully reproduces epsilon Nd reconstructions from the eastern North Atlantic at the Last Glacial Maximum and Heinrich Stadial 1, and demonstrates that the changes in scavenging intensity required for good model-data fit is in good agreement with changes in the observed IRD flux. Although uncertainties in model parameters preclude a more definitive conclusion, the results indicate that the suggestion of IRD as a source of non-conservative behaviour in the epsilon Nd tracer is reasonable and that further research into the fundamental chemistry underlying the marine neodymium cycle is necessary to increase confidence in assumptions of conservative epsilon Nd behaviour in the past. KW - Neodymium isotopes KW - epsilon Nd KW - ice-rafted debris KW - IRD KW - last glacial KW - maximum KW - LGM KW - Heinrich event KW - Palaeoceanography KW - Paleoceanography KW - model KW - reversible scavenging KW - conservative KW - ocean circulation KW - atlantic KW - meridional overturning circulation KW - geochemical cycling Y1 - 2020 U6 - https://doi.org/10.1007/s00367-020-00643-x SN - 0276-0460 SN - 1432-1157 VL - 40 IS - 3 SP - 325 EP - 340 PB - Springer CY - Berlin ER - TY - JOUR A1 - Munyaev, Vyacheslav O. A1 - Smirnov, Lev A. A1 - Kostin, Vasily A. A1 - Osipov, Grigory V. A1 - Pikovskij, Arkadij T1 - Analytical approach to synchronous states of globally coupled noisy rotators JF - New journal of physics : the open-access journal for physics N2 - We study populations of globally coupled noisy rotators (oscillators with inertia) allowing a nonequilibrium transition from a desynchronized state to a synchronous one (with the nonvanishing order parameter). The newly developed analytical approaches resulted in solutions describing the synchronous state with constant order parameter for weakly inertial rotators, including the case of zero inertia, when the model is reduced to the Kuramoto model of coupled noise oscillators. These approaches provide also analytical criteria distinguishing supercritical and subcritical transitions to the desynchronized state and indicate the universality of such transitions in rotator ensembles. All the obtained analytical results are confirmed by the numerical ones, both by direct simulations of the large ensembles and by solution of the associated Fokker-Planck equation. We also propose generalizations of the developed approaches for setups where different rotators parameters (natural frequencies, masses, noise intensities, strengths and phase shifts in coupling) are dispersed. KW - coupled rotators KW - synchronization transition KW - hysteresis KW - Kuramoto KW - model KW - noisy systems Y1 - 2020 U6 - https://doi.org/10.1088/1367-2630/ab6f93 SN - 1367-2630 VL - 22 IS - 2 PB - IOP Publ. Ltd. CY - Bristol ER - TY - JOUR A1 - Levy, Jessica A1 - Mussack, Dominic A1 - Brunner, Martin A1 - Keller, Ulrich A1 - Cardoso-Leite, Pedro A1 - Fischbach, Antoine T1 - Contrasting classical and machine learning approaches in the estimation of value-added scores in large-scale educational data JF - Frontiers in psychology N2 - There is no consensus on which statistical model estimates school value-added (VA) most accurately. To date, the two most common statistical models used for the calculation of VA scores are two classical methods: linear regression and multilevel models. These models have the advantage of being relatively transparent and thus understandable for most researchers and practitioners. However, these statistical models are bound to certain assumptions (e.g., linearity) that might limit their prediction accuracy. Machine learning methods, which have yielded spectacular results in numerous fields, may be a valuable alternative to these classical models. Although big data is not new in general, it is relatively new in the realm of social sciences and education. New types of data require new data analytical approaches. Such techniques have already evolved in fields with a long tradition in crunching big data (e.g., gene technology). The objective of the present paper is to competently apply these "imported" techniques to education data, more precisely VA scores, and assess when and how they can extend or replace the classical psychometrics toolbox. The different models include linear and non-linear methods and extend classical models with the most commonly used machine learning methods (i.e., random forest, neural networks, support vector machines, and boosting). We used representative data of 3,026 students in 153 schools who took part in the standardized achievement tests of the Luxembourg School Monitoring Program in grades 1 and 3. Multilevel models outperformed classical linear and polynomial regressions, as well as different machine learning models. However, it could be observed that across all schools, school VA scores from different model types correlated highly. Yet, the percentage of disagreements as compared to multilevel models was not trivial and real-life implications for individual schools may still be dramatic depending on the model type used. Implications of these results and possible ethical concerns regarding the use of machine learning methods for decision-making in education are discussed. KW - value-added modeling KW - school effectiveness KW - machine learning KW - model KW - comparison KW - longitudinal data Y1 - 2020 U6 - https://doi.org/10.3389/fpsyg.2020.02190 SN - 1664-1078 VL - 11 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Omelʹchenko, Oleh E. T1 - Nonstationary coherence-incoherence patterns in nonlocally coupled heterogeneous phase oscillators JF - Chaos : an interdisciplinary journal of nonlinear science N2 - We consider a large ring of nonlocally coupled phase oscillators and show that apart from stationary chimera states, this system also supports nonstationary coherence-incoherence patterns (CIPs). For identical oscillators, these CIPs behave as breathing chimera states and are found in a relatively small parameter region only. It turns out that the stability region of these states enlarges dramatically if a certain amount of spatially uniform heterogeneity (e.g., Lorentzian distribution of natural frequencies) is introduced in the system. In this case, nonstationary CIPs can be studied as stable quasiperiodic solutions of a corresponding mean-field equation, formally describing the infinite system limit. Carrying out direct numerical simulations of the mean-field equation, we find different types of nonstationary CIPs with pulsing and/or alternating chimera-like behavior. Moreover, we reveal a complex bifurcation scenario underlying the transformation of these CIPs into each other. These theoretical predictions are confirmed by numerical simulations of the original coupled oscillator system. KW - chimera states KW - synchronization KW - networks KW - Kuramoto KW - populations KW - dynamics KW - bumps KW - model Y1 - 2020 U6 - https://doi.org/10.1063/1.5145259 SN - 1054-1500 SN - 1089-7682 VL - 30 IS - 4 PB - American Institute of Physics CY - Melville ER - TY - JOUR A1 - Wenz, Leonie A1 - Levermann, Anders A1 - Willner, Sven N. A1 - Otto, Christian A1 - Kuhla, Kilian T1 - Post-Brexit no-trade-deal scenario: short-term consumer benefit at the expense of long-term economic development JF - PLoS ONE N2 - After the United Kingdom has left the European Union it remains unclear whether the two parties can successfully negotiate and sign a trade agreement within the transition period. Ongoing negotiations, practical obstacles and resulting uncertainties make it highly unlikely that economic actors would be fully prepared to a “no-trade-deal” situation. Here we provide an economic shock simulation of the immediate aftermath of such a post-Brexit no-trade-deal scenario by computing the time evolution of more than 1.8 million interactions between more than 6,600 economic actors in the global trade network. We find an abrupt decline in the number of goods produced in the UK and the EU. This sudden output reduction is caused by drops in demand as customers on the respective other side of the Channel incorporate the new trade restriction into their decision-making. As a response, producers reduce prices in order to stimulate demand elsewhere. In the short term consumers benefit from lower prices but production value decreases with potentially severe socio-economic consequences in the longer term. KW - model KW - origins KW - chains KW - impact KW - costs Y1 - 2019 VL - 15 IS - 9 PB - PLOS CY - San Francisco ER - TY - JOUR A1 - Smirnov, Artem G. A1 - Kronberg, Elena A. A1 - Daly, Patrick W. A1 - Aseev, Nikita A1 - Shprits, Yuri Y. A1 - Kellerman, Adam C. T1 - Adiabatic Invariants Calculations for Cluster Mission: A Long-Term Product for Radiation Belts Studies JF - Journal of Geophysical Research: Space Physics N2 - The Cluster mission has produced a large data set of electron flux measurements in the Earth's magnetosphere since its launch in late 2000. Electron fluxes are measured using Research with Adaptive Particle Imaging Detector (RAPID)/Imaging Electron Spectrometer (IES) detector as a function of energy, pitch angle, spacecraft position, and time. However, no adiabatic invariants have been calculated for Cluster so far. In this paper we present a step-by-step guide to calculations of adiabatic invariants and conversion of the electron flux to phase space density (PSD) in these coordinates. The electron flux is measured in two RAPID/IES energy channels providing pitch angle distribution at energies 39.2-50.5 and 68.1-94.5 keV in nominal mode since 2004. A fitting method allows to expand the conversion of the differential fluxes to the range from 40 to 150 keV. Best data coverage for phase space density in adiabatic invariant coordinates can be obtained for values of second adiabatic invariant, K, similar to 10(2), and values of the first adiabatic invariant mu in the range approximate to 5-20 MeV/G. Furthermore, we describe the production of a new data product "LSTAR," equivalent to the third adiabatic invariant, available through the Cluster Science Archive for years 2001-2018 with 1-min resolution. The produced data set adds to the availability of observations in Earth's radiation belts region and can be used for long-term statistical purposes. KW - L-Asterisk KW - magnetosphere KW - electrons KW - model Y1 - 2019 VL - 125 IS - 2 PB - John Wiley & Sons, Inc. CY - New Jersey ER - TY - JOUR A1 - Chandra, Johan A1 - Krügel, André A1 - Engbert, Ralf T1 - Experimental test of Bayesian saccade targeting under reversed reading direction JF - Attention, Perception, & Psychophysics N2 - During reading, rapid eye movements (saccades) shift the reader's line of sight from one word to another for high-acuity visual information processing. While experimental data and theoretical models show that readers aim at word centers, the eye-movement (oculomotor) accuracy is low compared to other tasks. As a consequence, distributions of saccadic landing positions indicate large (i) random errors and (ii) systematic over- and undershoot of word centers, which additionally depend on saccade lengths (McConkie et al.Visual Research, 28(10), 1107-1118,1988). Here we show that both error components can be simultaneously reduced by reading texts from right to left in German language (N= 32). We used our experimental data to test a Bayesian model of saccade planning. First, experimental data are consistent with the model. Second, the model makes specific predictions of the effects of the precision of prior and (sensory) likelihood. Our results suggest that it is a more precise sensory likelihood that can explain the reduction of both random and systematic error components. KW - eye movements and reading KW - Bayesian modeling KW - eye-movement control KW - model KW - fixation KW - attention KW - words KW - swift Y1 - 2019 U6 - https://doi.org/10.3758/s13414-019-01814-4 SN - 1943-393X SN - 1943-3921 VL - 82 SP - 1230 EP - 1240 PB - Springer CY - New York, NY ER -