TY - JOUR A1 - Nowicki, Sophie A1 - Bindschadler, Robert A. A1 - Abe-Ouchi, Ayako A1 - Aschwanden, Andy A1 - Bueler, Ed A1 - Choi, Hyeungu A1 - Fastook, Jim A1 - Granzow, Glen A1 - Greve, Ralf A1 - Gutowski, Gail A1 - Herzfeld, Ute A1 - Jackson, Charles A1 - Johnson, Jesse A1 - Khroulev, Constantine A1 - Larour, Eric A1 - Levermann, Anders A1 - Lipscomb, William H. A1 - Martin, Maria A. A1 - Morlighem, Mathieu A1 - Parizek, Byron R. A1 - Pollard, David A1 - Price, Stephen F. A1 - Ren, Diandong A1 - Rignot, Eric A1 - Saito, Fuyuki A1 - Sato, Tatsuru A1 - Seddik, Hakime A1 - Seroussi, Helene A1 - Takahashi, Kunio A1 - Walker, Ryan A1 - Wang, Wei Li T1 - Insights into spatial sensitivities of ice mass response to environmental change from the SeaRISE ice sheet modeling project II Greenland JF - Journal of geophysical research : Earth surface N2 - The Sea-level Response to Ice Sheet Evolution (SeaRISE) effort explores the sensitivity of the current generation of ice sheet models to external forcing to gain insight into the potential future contribution to sea level from the Greenland and Antarctic ice sheets. All participating models simulated the ice sheet response to three types of external forcings: a change in oceanic condition, a warmer atmospheric environment, and enhanced basal lubrication. Here an analysis of the spatial response of the Greenland ice sheet is presented, and the impact of model physics and spin-up on the projections is explored. Although the modeled responses are not always homogeneous, consistent spatial trends emerge from the ensemble analysis, indicating distinct vulnerabilities of the Greenland ice sheet. There are clear response patterns associated with each forcing, and a similar mass loss at the full ice sheet scale will result in different mass losses at the regional scale, as well as distinct thickness changes over the ice sheet. All forcings lead to an increased mass loss for the coming centuries, with increased basal lubrication and warmer ocean conditions affecting mainly outlet glaciers, while the impacts of atmospheric forcings affect the whole ice sheet. KW - Greenland KW - ice-sheet KW - sea-level KW - model KW - ensemble Y1 - 2013 U6 - https://doi.org/10.1002/jgrf.20076 SN - 2169-9003 VL - 118 IS - 2 SP - 1025 EP - 1044 PB - American Geophysical Union CY - Washington ER - TY - JOUR A1 - Seebens, Hanno A1 - Essl, Franz A1 - Dawson, Wayne A1 - Fuentes, Nicol A1 - Moser, Dietmar A1 - Pergl, Jan A1 - Pysek, Petr A1 - van Kleunen, Mark A1 - Weber, Ewald A1 - Winter, Marten A1 - Blasius, Bernd T1 - Global trade will accelerate plant invasions in emerging economies under climate change JF - Global change biology N2 - Trade plays a key role in the spread of alien species and has arguably contributed to the recent enormous acceleration of biological invasions, thus homogenizing biotas worldwide. Combining data on 60-year trends of bilateral trade, as well as on biodiversity and climate, we modeled the global spread of plant species among 147 countries. The model results were compared with a recently compiled unique global data set on numbers of naturalized alien vascular plant species representing the most comprehensive collection of naturalized plant distributions currently available. The model identifies major source regions, introduction routes, and hot spots of plant invasions that agree well with observed naturalized plant numbers. In contrast to common knowledge, we show that the 'imperialist dogma,' stating that Europe has been a net exporter of naturalized plants since colonial times, does not hold for the past 60 years, when more naturalized plants were being imported to than exported from Europe. Our results highlight that the current distribution of naturalized plants is best predicted by socioeconomic activities 20 years ago. We took advantage of the observed time lag and used trade developments until recent times to predict naturalized plant trajectories for the next two decades. This shows that particularly strong increases in naturalized plant numbers are expected in the next 20 years for emerging economies in megadiverse regions. The interaction with predicted future climate change will increase invasions in northern temperate countries and reduce them in tropical and (sub) tropical regions, yet not by enough to cancel out the trade-related increase. KW - alien vascular plants KW - bioinvasion KW - climate warming KW - global spread KW - imperialist dogma KW - model KW - network of plant invasion Y1 - 2015 U6 - https://doi.org/10.1111/gcb.13021 SN - 1354-1013 SN - 1365-2486 VL - 21 IS - 11 SP - 4128 EP - 4140 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Kumar, Kevin K. A1 - Goodwin, Cody R. A1 - Uhouse, Michael A. A1 - Bornhorst, Julia A1 - Schwerdtle, Tanja A1 - Aschner, Michael A. A1 - McLean, John A. A1 - Bowman, Aaron B. T1 - Untargeted metabolic profiling identifies interactions between Huntington's disease and neuronal manganese status JF - Metallomics N2 - Manganese (Mn) is an essential micronutrient for development and function of the nervous system. Deficiencies in Mn transport have been implicated in the pathogenesis of Huntington's disease (HD), an autosomal dominant neurodegenerative disorder characterized by loss of medium spiny neurons of the striatum. Brain Mn levels are highest in striatum and other basal ganglia structures, the most sensitive brain regions to Mn neurotoxicity. Mouse models of HD exhibit decreased striatal Mn accumulation and HD striatal neuron models are resistant to Mn cytotoxicity. We hypothesized that the observed modulation of Mn cellular transport is associated with compensatory metabolic responses to HD pathology. Here we use an untargeted metabolomics approach by performing ultraperformance liquid chromatography-ion mobility-mass spectrometry (UPLC-IM-MS) on control and HD immortalized mouse striatal neurons to identify metabolic disruptions under three Mn exposure conditions, low (vehicle), moderate (non-cytotoxic) and high (cytotoxic). Our analysis revealed lower metabolite levels of pantothenic acid, and glutathione (GSH) in HD striatal cells relative to control cells. HD striatal cells also exhibited lower abundance and impaired induction of isobutyryl carnitine in response to increasing Mn exposure. In addition, we observed induction of metabolites in the pentose shunt pathway in HD striatal cells after high Mn exposure. These findings provide metabolic evidence of an interaction between the HD genotype and biologically relevant levels of Mn in a striatal cell model with known HD by Mn exposure interactions. The metabolic phenotypes detected support existing hypotheses that changes in energetic processes underlie the pathobiology of both HD and Mn neurotoxicity. KW - hallervorden-spatz-syndrome KW - mobility-mass spectrometry KW - energy-metabolism KW - coenzyme-a KW - model KW - neurotoxicity KW - glutathione KW - database KW - cells KW - neurodegeneration Y1 - 2015 U6 - https://doi.org/10.1039/C4MT00223G SN - 1756-591X SN - 1756-5901 VL - 7 SP - 363 EP - 370 PB - RSC Publ. CY - Cambridge ER - TY - JOUR A1 - Schutt, Heiko Herbert A1 - Wichmann, Felix A. T1 - An image-computable psychophysical spatial vision model JF - Journal of vision N2 - A large part of classical visual psychophysics was concerned with the fundamental question of how pattern information is initially encoded in the human visual system. From these studies a relatively standard model of early spatial vision emerged, based on spatial frequency and orientation-specific channels followed by an accelerating nonlinearity and divisive normalization: contrast gain-control. Here we implement such a model in an image-computable way, allowing it to take arbitrary luminance images as input. Testing our implementation on classical psychophysical data, we find that it explains contrast detection data including the ModelFest data, contrast discrimination data, and oblique masking data, using a single set of parameters. Leveraging the advantage of an image-computable model, we test our model against a recent dataset using natural images as masks. We find that the model explains these data reasonably well, too. To explain data obtained at different presentation durations, our model requires different parameters to achieve an acceptable fit. In addition, we show that contrast gain-control with the fitted parameters results in a very sparse encoding of luminance information, in line with notions from efficient coding. Translating the standard early spatial vision model to be image-computable resulted in two further insights: First, the nonlinear processing requires a denser sampling of spatial frequency and orientation than optimal coding suggests. Second, the normalization needs to be fairly local in space to fit the data obtained with natural image masks. Finally, our image-computable model can serve as tool in future quantitative analyses: It allows optimized stimuli to be used to test the model and variants of it, with potential applications as an image-quality metric. In addition, it may serve as a building block for models of higher level processing. KW - model KW - spatial vision KW - image-computable KW - psychophysics Y1 - 2017 U6 - https://doi.org/10.1167/17.12.12 SN - 1534-7362 VL - 17 PB - Association for Research in Vision and Opthalmology CY - Rockville ER - TY - JOUR A1 - Volkert, Dorothee A1 - Kiesswetter, Eva A1 - Cederholm, Tommy A1 - Donini, Lorenzo M. A1 - Egiseer, Doris A1 - Norman, Kristina A1 - Schneider, Stephane M. A1 - Stroebele-Benschop, Nanette A1 - Torbahn, Gabriel A1 - Wirth, Rainer A1 - Visser, Marjolein T1 - Development of a Model on Determinants of Malnutrition in Aged Persons BT - A MaNuEL Project JF - Gerontology and Geriatric Medicine N2 - In older persons, the origin of malnutrition is often multifactorial with a multitude of factors involved. Presently, a common understanding about potential causes and their mode of action is lacking, and a consensus on the theoretical framework on the etiology of malnutrition does not exist. Within the European Knowledge Hub "Malnutrition in the Elderly (MaNuEL)," a model of "Determinants of Malnutrition in Aged Persons" (DoMAP) was developed in a multistage consensus process with live meetings and written feedback (modified Delphi process) by a multiprofessional group of 33 experts in geriatric nutrition. DoMAP consists of three triangle-shaped levels with malnutrition in the center, surrounded by the three principal conditions through which malnutrition develops in the innermost level: low intake, high requirements, and impaired nutrient bioavailability. The middle level consists of factors directly causing one of these conditions, and the outermost level contains factors indirectly causing one of the three conditions through the direct factors. The DoMAP model may contribute to a common understanding about the multitude of factors involved in the etiology of malnutrition, and about potential causative mechanisms. It may serve as basis for future research and may also be helpful in clinical routine to identify persons at increased risk of malnutrition. KW - older persons KW - malnutrition KW - determinants KW - etiology KW - model Y1 - 2019 U6 - https://doi.org/10.1177/2333721419858438 SN - 2333-7214 VL - 5 PB - Sage Publ. CY - Thousand Oaks 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 - 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 - 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 - 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 -