@article{BoteroMonkRodriguezCubillosetal.2020, author = {Botero, David and Monk, Jonathan and Rodriguez Cubillos, Maria Juliana and Rodriguez Cubillos, Andres Eduardo and Restrepo, Mariana and Bernal-Galeano, Vivian and Reyes, Alejandro and Gonzalez Barrios, Andres and Palsson, Bernhard O. and Restrepo, Silvia and Bernal, Adriana}, title = {Genome-scale metabolic model of Xanthomonas phaseoli pv. manihotis}, series = {Frontiers in genetics}, volume = {11}, journal = {Frontiers in genetics}, publisher = {Frontiers Media}, address = {Lausanne}, issn = {1664-8021}, doi = {10.3389/fgene.2020.00837}, pages = {19}, year = {2020}, abstract = {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.}, language = {en} } @article{BryantDaviesSoletal.2022, author = {Bryant, Seth and Davies, Evan and Sol, David and Davis, Sandy}, title = {The progression of flood risk in southern Alberta since the 2013 flood}, series = {Journal of flood risk management}, volume = {15}, journal = {Journal of flood risk management}, number = {3}, publisher = {Wiley-Blackwell}, address = {Oxford}, issn = {1753-318X}, doi = {10.1111/jfr3.12811}, pages = {18}, year = {2022}, abstract = {After a century of semi-restricted floodplain development, Southern Alberta, Canada, was struck by the devastating 2013 Flood. Aging infrastructure and limited property-level floodproofing likely contributed to the \$4-6 billion (CAD) losses. Following this catastrophe, Alberta has seen a revival in flood management, largely focused on structural protections. However, concurrent with the recent structural work was a 100,000+ increase in Calgary's population in the 5 years following the flood, leading to further densification of high-hazard areas. This study implements the novel Stochastic Object-based Flood damage Dynamic Assessment (SOFDA) model framework to quantify the progression of the direct-damage flood risk in a mature urban neighborhood after the 2013 Flood. Five years of remote-sensing data, property assessment records, and inundation simulations following the flood are used to construct the model. Results show that in these 5 years, vulnerability trends (like densification) have increased flood risk by 4\%; however, recent structural mitigation projects have reduced overall flood risk by 47\% for this case study. These results demonstrate that the flood management revival in Southern Alberta has largely been successful at reducing flood risk; however, the gains are under threat from continued development and densification absent additional floodproofing regulations.}, language = {en} } @article{BoehnkeKrehlMoermannetal.2022, author = {B{\"o}hnke, Denise and Krehl, Alice and Moermann, Kai and Volk, Rebekka and L{\"u}tzkendorf, Thomas and Naber, Elias and Becker, Ronja and Norra, Stefan}, title = {Mapping urban green and its ecosystem services at microscale-a methodological approach for climate adaptation and biodiversity}, series = {Sustainability / Multidisciplinary Digital Publishing Institute (MDPI)}, volume = {14}, journal = {Sustainability / Multidisciplinary Digital Publishing Institute (MDPI)}, number = {15}, publisher = {MDPI}, address = {Basel}, issn = {2071-1050}, doi = {10.3390/su14159029}, pages = {26}, year = {2022}, abstract = {The current awareness of the high importance of urban green leads to a stronger need for tools to comprehensively represent urban green and its benefits. A common scientific approach is the development of urban ecosystem services (UES) based on remote sensing methods at the city or district level. Urban planning, however, requires fine-grained data that match local management practices. Hence, this study linked local biotope and tree mapping methods to the concept of ecosystem services. The methodology was tested in an inner-city district in SW Germany, comparing publicly accessible areas and non-accessible courtyards. The results provide area-specific [m(2)] information on the green inventory at the microscale, whereas derived stock and UES indicators form the basis for comparative analyses regarding climate adaptation and biodiversity. In the case study, there are ten times more micro-scale green spaces in private courtyards than in the public space, as well as twice as many trees. The approach transfers a scientific concept into municipal planning practice, enables the quantitative assessment of urban green at the microscale and illustrates the importance for green stock data in private areas to enhance decision support in urban development. Different aspects concerning data collection and data availability are critically discussed.}, language = {en} } @article{ChandraKruegelEngbert2020, author = {Chandra, Johan and Kr{\"u}gel, Andr{\´e} and Engbert, Ralf}, title = {Experimental test of Bayesian saccade targeting under reversed reading direction}, series = {Attention, Perception, \& Psychophysics}, volume = {82}, journal = {Attention, Perception, \& Psychophysics}, publisher = {Springer}, address = {New York, NY}, issn = {1943-393X}, doi = {10.3758/s13414-019-01814-4}, pages = {1230 -- 1240}, year = {2020}, abstract = {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.}, language = {en} } @article{FuerstenbergAlfesKearney2021, author = {F{\"u}rstenberg, Nils and Alfes, Kerstin and Kearney, Eric}, title = {How and when paradoxical leadership benefits work engagement}, series = {Journal of occupational and organizational psychology / British Psychological Society}, volume = {94}, journal = {Journal of occupational and organizational psychology / British Psychological Society}, number = {3}, publisher = {Wiley}, address = {Hoboken}, issn = {0963-1798}, doi = {10.1111/joop.12344}, pages = {672 -- 705}, year = {2021}, abstract = {Paradoxical leadership behaviour (PLB) represents an emerging leadership construct that can help leaders deal with conflicting demands. In this paper, we report three studies that add to this nascent literature theoretically, methodologically, and empirically. In Study 1, we validate an effective short-form measure of global PLB using three different samples. In Studies 2 and 3, we draw on the job demands-resources model to propose that paradoxical leaders promote followers' work engagement by simultaneously fostering follower goal clarity and work autonomy. The results of survey data from Studies 2 and 3 largely confirm our model. Specifically, our findings show that PLB is positively associated with follower goal clarity and work autonomy, and that PLB exerts an indirect effect on work engagement via these variables. Moreover, our results support a hypothesized interaction effect of goal clarity and work autonomy to predict followers' work engagement, as well as a conditional indirect effect of PLB on work engagement via the interactive effect. We discuss the practical implications for leaders and organizations. Practitioner points To effectively engage followers in their work, leaders should create work environments in which followers know exactly what to do (i.e., have high goal clarity), but at the same time can determine on their own how to do their work (i.e., have high work autonomy) To foster both goal clarity and work autonomy, leaders should combine communal (e.g., other-centred, flexibility-providing) and agentic aspects of leadership (e.g., maintaining decision control and enforcing performance standards). HR departments should design leadership trainings that help leaders to combine seemingly opposing, yet ultimately synergistic behaviours.}, language = {en} } @article{KumarGoodwinUhouseetal.2015, author = {Kumar, Kevin K. and Goodwin, Cody R. and Uhouse, Michael A. and Bornhorst, Julia and Schwerdtle, Tanja and Aschner, Michael A. and McLean, John A. and Bowman, Aaron B.}, title = {Untargeted metabolic profiling identifies interactions between Huntington's disease and neuronal manganese status}, series = {Metallomics}, volume = {7}, journal = {Metallomics}, publisher = {RSC Publ.}, address = {Cambridge}, issn = {1756-591X}, doi = {10.1039/C4MT00223G}, pages = {363 -- 370}, year = {2015}, abstract = {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.}, language = {en} } @article{KumarHesseRaoetal.2020, author = {Kumar, Rohini and Hesse, Fabienne and Rao, P. Srinivasa and Musolff, Andreas and Jawitz, James and Sarrazin, Francois and Samaniego, Luis and Fleckenstein, Jan H. and Rakovec, Oldrich and Thober, S. and Attinger, Sabine}, title = {Strong hydroclimatic controls on vulnerability to subsurface nitrate contamination across Europe}, series = {Nature Communications}, volume = {11}, journal = {Nature Communications}, number = {1}, publisher = {Nature Publishing Group UK}, address = {London}, issn = {2041-1723}, doi = {10.1038/s41467-020-19955-8}, pages = {1 -- 10}, year = {2020}, abstract = {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.}, language = {en} } @article{LevyMussackBrunneretal.2020, author = {Levy, Jessica and Mussack, Dominic and Brunner, Martin and Keller, Ulrich and Cardoso-Leite, Pedro and Fischbach, Antoine}, title = {Contrasting classical and machine learning approaches in the estimation of value-added scores in large-scale educational data}, series = {Frontiers in psychology}, volume = {11}, journal = {Frontiers in psychology}, publisher = {Frontiers Research Foundation}, address = {Lausanne}, issn = {1664-1078}, doi = {10.3389/fpsyg.2020.02190}, pages = {18}, year = {2020}, abstract = {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.}, language = {en} } @article{MillesDammhahnJeltschetal.2022, author = {Milles, Alexander Benedikt and Dammhahn, Melanie and Jeltsch, Florian and Schl{\"a}gel, Ulrike and Grimm, Volker}, title = {Fluctuations in density-dependent selection drive the evolution of a pace-of-life syndrome within and between populations}, series = {The American naturalist : a bi-monthly journal devoted to the advancement and correlation of the biological sciences}, volume = {199}, journal = {The American naturalist : a bi-monthly journal devoted to the advancement and correlation of the biological sciences}, number = {4}, publisher = {Univ. of Chicago Press}, address = {Chicago}, issn = {0003-0147}, doi = {10.1086/718473}, pages = {E124 -- E139}, year = {2022}, abstract = {The pace-of-life syndrome (POLS) hypothesis posits that suites of traits are correlated along a slow-fast continuum owing to life history trade-offs. Despite widespread adoption, environmental conditions driving the emergence of POLS remain unclear. A recently proposed conceptual framework of POLS suggests that a slow-fast continuum should align to fluctuations in density-dependent selection. We tested three key predictions made by this framework with an ecoevolutionary agent-based population model. Selection acted on responsiveness (behavioral trait) to interpatch resource differences and the reproductive investment threshold (life history trait). Across environments with density fluctuations of different magnitudes, we observed the emergence of a common axis of trait covariation between and within populations (i.e., the evolution of a POLS). Slow-type (fast-type) populations with high (low) responsiveness and low (high) reproductive investment threshold were selected at high (low) population densities and less (more) intense and frequent density fluctuations. In support of the predictions, fast-type populations contained a higher degree of variation in traits and were associated with higher intrinsic reproductive rate (r(0)) and higher sensitivity to intraspecific competition (gamma), pointing to a universal trade-off. While our findings support that POLS aligns with density-dependent selection, we discuss possible mechanisms that may lead to alternative evolutionary pathways.}, language = {en} } @article{MunyaevSmirnovKostinetal.2020, author = {Munyaev, Vyacheslav O. and Smirnov, Lev A. and Kostin, Vasily A. and Osipov, Grigory V. and Pikovskij, Arkadij}, title = {Analytical approach to synchronous states of globally coupled noisy rotators}, series = {New journal of physics : the open-access journal for physics}, volume = {22}, journal = {New journal of physics : the open-access journal for physics}, number = {2}, publisher = {IOP Publ. Ltd.}, address = {Bristol}, issn = {1367-2630}, doi = {10.1088/1367-2630/ab6f93}, pages = {14}, year = {2020}, abstract = {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.}, language = {en} }