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Lucas P. Medeiros Stefano Allesina Vasilis Dakos George Sugihara Serguei Saavedra 《Ecology letters》2023,26(1):170-183
Managing ecological communities requires fast detection of species that are sensitive to perturbations. Yet, the focus on recovery to equilibrium has prevented us from assessing species responses to perturbations when abundances fluctuate over time. Here, we introduce two data-driven approaches (expected sensitivity and eigenvector rankings) based on the time-varying Jacobian matrix to rank species over time according to their sensitivity to perturbations on abundances. Using several population dynamics models, we demonstrate that we can infer these rankings from time-series data to predict the order of species sensitivities. We find that the most sensitive species are not always the ones with the most rapidly changing or lowest abundance, which are typical criteria used to monitor populations. Finally, using two empirical time series, we show that sensitive species tend to be harder to forecast. Our results suggest that incorporating information on species interactions can improve how we manage communities out of equilibrium. 相似文献
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Mihalis N. Mindrinos William H. Petri Vasilis K. Galanopoulos Mary F. Lombard Lukas H. Margaritis 《Development genes and evolution》1980,189(3):187-196
Summary TheDrosophila chorion contains an endogenous peroxidase activity which remains inactive until late stage 14 when it catalyzes the crosslinking of the chorionic proteins. Using explanted follicles developing in vitro, premature, but otherwise normal crosslinking can be induced with hydrogen peroxide and normal crosslinking can be prevented with peroxidase inhibitors. Inhibition or premature activation of the shell peroxidase allows characterization of chorionic filament specific proteins and establishes new criteria for the identification of eggshell components. 相似文献
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Steffen E. Eikenberry Vasilis Z. Marmarelis 《Journal of computational neuroscience》2013,34(1):163-183
We propose a new variant of Volterra-type model with a nonlinear auto-regressive (NAR) component that is a suitable framework for describing the process of AP generation by the neuron membrane potential, and we apply it to input-output data generated by the Hodgkin–Huxley (H–H) equations. Volterra models use a functional series expansion to describe the input-output relation for most nonlinear dynamic systems, and are applicable to a wide range of physiologic systems. It is difficult, however, to apply the Volterra methodology to the H–H model because is characterized by distinct subthreshold and suprathreshold dynamics. When threshold is crossed, an autonomous action potential (AP) is generated, the output becomes temporarily decoupled from the input, and the standard Volterra model fails. Therefore, in our framework, whenever membrane potential exceeds some threshold, it is taken as a second input to a dual-input Volterra model. This model correctly predicts membrane voltage deflection both within the subthreshold region and during APs. Moreover, the model naturally generates a post-AP afterpotential and refractory period. It is known that the H–H model converges to a limit cycle in response to a constant current injection. This behavior is correctly predicted by the proposed model, while the standard Volterra model is incapable of generating such limit cycle behavior. The inclusion of cross-kernels, which describe the nonlinear interactions between the exogenous and autoregressive inputs, is found to be absolutely necessary. The proposed model is general, non-parametric, and data-derived. 相似文献
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Dong Song Haonan Wang Catherine Y. Tu Vasilis Z. Marmarelis Robert E. Hampson Sam A. Deadwyler Theodore W. Berger 《Journal of computational neuroscience》2013,35(3):335-357
One key problem in computational neuroscience and neural engineering is the identification and modeling of functional connectivity in the brain using spike train data. To reduce model complexity, alleviate overfitting, and thus facilitate model interpretation, sparse representation and estimation of functional connectivity is needed. Sparsities include global sparsity, which captures the sparse connectivities between neurons, and local sparsity, which reflects the active temporal ranges of the input-output dynamical interactions. In this paper, we formulate a generalized functional additive model (GFAM) and develop the associated penalized likelihood estimation methods for such a modeling problem. A GFAM consists of a set of basis functions convolving the input signals, and a link function generating the firing probability of the output neuron from the summation of the convolutions weighted by the sought model coefficients. Model sparsities are achieved by using various penalized likelihood estimations and basis functions. Specifically, we introduce two variations of the GFAM using a global basis (e.g., Laguerre basis) and group LASSO estimation, and a local basis (e.g., B-spline basis) and group bridge estimation, respectively. We further develop an optimization method based on quadratic approximation of the likelihood function for the estimation of these models. Simulation and experimental results show that both group-LASSO-Laguerre and group-bridge-B-spline can capture faithfully the global sparsities, while the latter can replicate accurately and simultaneously both global and local sparsities. The sparse models outperform the full models estimated with the standard maximum likelihood method in out-of-sample predictions. 相似文献
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Julie Chaumeil Mariann Micsinai Panagiotis Ntziachristos Ludovic Deriano Joy M.-H. Wang Yanhong Ji Elphege P. Nora Matthew J. Rodesch Jeffrey A. Jeddeloh Iannis Aifantis Yuval Kluger David G. Schatz Jane A. Skok 《Cell reports》2013,3(2):359-370
Highlights? RAG-dependent monoallelic loop formation is linked to monoallelic RAG cleavage ? RAG enrichment, cleavage, and higher-order loop formation occur at the 3′ end of Tcra ? Looping out is a determinant of directed RAG targeting ? ATM-mediated control of looping out is linked to the maintenance of genome stability 相似文献
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Regime shifts of Mediterranean forest carbon uptake and reduced resilience driven by multidecadal ocean surface temperatures 总被引:1,自引:0,他引:1
Jofre Carnicer Cristina Domingo‐Marimon Miquel Ninyerola Jesus Julio Camarero Ana Bastos Jorge Lpez‐Parages Laura Blanquer Beln Rodríguez‐Fonseca Timothy M. Lenton Vasilis Dakos Montserrat Ribas Emilia Gutirrez Josep Peuelas Xavier Pons 《Global Change Biology》2019,25(8):2825-2840
The mechanisms translating global circulation changes into rapid abrupt shifts in forest carbon capture in semi‐arid biomes remain poorly understood. Here, we report unprecedented multidecadal shifts in forest carbon uptake in semi‐arid Mediterranean pine forests in Spain over 1950–2012. The averaged carbon sink reduction varies between 31% and 37%, and reaches values in the range of 50% in the most affected forest stands. Regime shifts in forest carbon uptake are associated with climatic early warning signals, decreased forest regional synchrony and reduced long‐term carbon sink resilience. We identify the mechanisms linked to ocean multidecadal variability that shape regime shifts in carbon capture. First, we show that low‐frequency variations of the surface temperature of the Atlantic Ocean induce shifts in the non‐stationary effects of El Niño Southern Oscillation (ENSO) on regional forest carbon capture. Modelling evidence supports that the non‐stationary effects of ENSO can be propagated from tropical areas to semi‐arid Mediterranean biomes through atmospheric wave trains. Second, decadal changes in the Atlantic Multidecadal Oscillation (AMO) significantly alter sea–air heat exchanges, modifying in turn ocean vapour transport over land and land surface temperatures, and promoting sustained drought conditions in spring and summer that reduce forest carbon uptake. Third, we show that lagged effects of AMO on the winter North Atlantic Oscillation also contribute to the maintenance of long‐term droughts. Finally, we show that the reported strong, negative effects of ocean surface temperature (AMO) on forest carbon uptake in the last decades are unprecedented over the last 150 years. Our results provide new, unreported explanations for carbon uptake shifts in these drought‐prone forests and review the expected impacts of global warming on the profiled mechanisms. 相似文献
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Lisa Rizzetto Daniela C. Ifrim Silvia Moretti Noemi Tocci Shih-Chin Cheng Jessica Quintin Giorgia Renga Vasilis Oikonomou Carlotta De Filippo Tobias Weil Bastiaan A. Blok Marcello S. Lenucci Manuel A. S. Santos Luigina Romani Mihai G. Netea Duccio Cavalieri 《The Journal of biological chemistry》2016,291(15):7961-7972
The immune system is essential to maintain the mutualistic homeostatic interaction between the host and its micro- and mycobiota. Living as a commensal, Saccharomyces cerevisiae could potentially shape the immune response in a significant way. We observed that S. cerevisiae cells induce trained immunity in monocytes in a strain-dependent manner through enhanced TNFα and IL-6 production upon secondary stimulation with TLR ligands, as well as bacterial and fungal commensals. Differential chitin content accounts for the differences in training properties observed among strains, driving induction of trained immunity by increasing cytokine production and direct antimicrobial activity both in vitro and in vivo. These chitin-induced protective properties are intimately associated with its internalization, identifying a critical role of phagosome acidification to facilitate microbial digestion. This study reveals how commensal and passenger microorganisms could be important in promoting health and preventing mucosal diseases by modulating host defense toward pathogens and thus influencing the host microbiota-immune system interactions. 相似文献