Inferring efficient operating rules in multireservoir water resource systems: A review

[EN] Coordinated and efficient operation of water resource systems becomes essential to deal with growing demands and uncertain resources in water-stressed regions. System analysis models and tools help address the complexities of multireservoir systems when defining operating rules. This paper reviews the state of the art in developing operating rules for multireservoir water resource systems, focusing on efficient system operation. This review focuses on how optimal operating rules can be derived and represented. Advantages and drawbacks of each approach are discussed. Major approaches to derive optimal operating rules include direct optimization of reservoir operation, embedding conditional operating rules in simulation-optimization frameworks, and inferring rules from optimization results. Suggestions on which approach to use depend on context. Parametrization-simulation-optimization or rule inference using heuristics are promising approaches. Increased forecasting capabilities will further benefit the use of model predictive control algorithms to improve system operation. This article is categorized under: Engineering Water > Water, Health, and Sanitation Engineering Water > MethodsThe study has been partially funded by the ADAPTAMED project (RTI2018-101483-B-I00) from the Ministerio de Ciencia, Innovacion Universidades (MICINN) of Spain, and by the postdoctoral program (PAID-10-18) of the Universitat Politecnica de Valencia (UPV).Macian-Sorribes, H.; Pulido-Velazquez, M. (2019). Inferring efficient operating rules in multireservoir water resource systems: A review. Wiley Interdisciplinary Reviews Water. 7(1):1-24. https://doi.org/10.1002/wat2.1400S12471Aboutalebi, M., Bozorg Haddad, O., & Loáiciga, H. A. (2015). Optimal Monthly Reservoir Operation Rules for Hydropower Generation Derived with SVR-NSGAII. 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Engineering Emergence: A Survey on Control in the World of Complex Networks

Complex networks make an enticing research topic that has been increasingly attracting researchers from control systems and various other domains over the last two decades. The aim of this paper was to survey the interest in control related to complex networks research over time since 2000 and to identify recent trends that may generate new research directions. The survey was performed for Web of Science, Scopus, and IEEEXplore publications related to complex networks. Based on our findings, we raised several questions and highlighted ongoing interests in the control of complex networks.publishedVersio

Modeling And Identification Of Differentially Regulated Genes Using Transcriptomics And Proteomics Data

Photosynthetic organisms are complex dynamical systems, showing a remarkable ability to adapt to different environmental conditions for their survival. Mechanisms underlying the coordination between different cellular processes in these organisms are still poorly understood. In this dissertation we utilize various computational and modeling techniques to analyze transcriptomics and proteomics data sets from several photosynthetic organisms. We try to use changes in expression levels of genes to study responses of these organisms to various environmental conditions such as availability of nutrients, concentrations of chemicals in growth media, and temperature. Three specific problems studied here are transcriptomics modifications in photosynthetic organisms under reduction-oxidation: redox) stress conditions, circadian and diurnal rhythms of cyanobacteria and the effect of incident light patterns on these rhythms, and the coordination between biological processes in cyanobacteria under various growth conditions. Under redox stresses caused by high light treatments, a strong transcriptomic level response, spread across many biological processes, is discovered in the cyanobacterium Synechocystis sp. PCC 6803. Based on statistical tests, expression levels of about 20% of genes in Synechocystis 6803 are identified as significantly affected due to influence of high light. Gene clustering methods reveal that these responses can mainly be classified as transient and consistent responses, depending on the duration of modified behaviors. Many genes related to energy production as well as energy utilization are shown to be strongly affected. Analysis of microarray data under two stress conditions, high light and DCMU treatment, combined with data mining and motif finding algorithms led to a discovery of novel transcription factor, RRTF1 that responds to redox stresses in Arabidopsis thaliana. Time course transcriptomics data from Cyanothece sp. ATCC 51142 have shown strong diurnal rhythms. By combining multiple experimental conditions and using gene classification algorithms based on Fourier scores and angular distances, it is shown that majority of the diurnal genes are in fact light responding. Only about 10% of genes in the genome are categorized as being circadian controlled. A transcription control model based on dynamical systems is employed to identify the interactions between diurnal genes. A phase oscillator network is proposed to model the behavior of different biological processes. Both these models are shown to carry biologically meaningful features. To study the coordination between different biological processes to various environment and genetic modifications, an interaction model is derived using Bayesian network approach, combining all publicly available microarray data sets for Synechocystis sp. PCC 6803. Several novel relationships between biological processes are discovered from the model. Model is used to simulate several experimental conditions, and the response of the model is shown to agree with the experimentally observed behaviors

Integrative methods for reconstruction of dynamic networks in chondrogenesis

Application of human mesenchymal stem cells represents a promising approach in the field of regenerative medicine. Specific stimulation can give rise to chondrocytes, osteocytes or adipocytes. Investigation of the underlying biological processes which induce the observed cellular differentiation is essential to efficiently generate specific tissues for therapeutic purposes. Upon treatment with diverse stimuli, gene expression levels of cultivated human mesenchymal stem cells were monitored using time series microarray experiments for the three lineages. Application of gene network inference is a common approach to identify the regulatory dependencies among a set of investigated genes. This thesis applies the NetGenerator V2.0 tool, which is capable to deal with multiple time series data, which investigates the effect of multiple external stimuli. The applied model is based on a system of linear ordinary differential equations, whose parameters are optimised to reproduce the given time series datasets. Several procedures in the inference process were adapted in this new version in order to allow for the integration of multiple datasets. Network inference was applied on in silico network examples as well as on multi-experiment microarray data of mesenchymal stem cells. The resulting chondrogenesis model was evaluated on the basis of several features including the model adaptation to the data, total number of connections, proportion of connections associated with prior knowledge and the model stability in a resampling procedure. Altogether, NetGenerator V2.0 has provided an automatic and efficient way to integrate experimental datasets and to enhance the interpretability and reliability of the resulting network. In a second chondrogenesis model, the miRNA and mRNA time series data were integrated for the purpose of network inference. One hypothesis of the model was verified by experiments, which demonstrated the negative effect of miR-524-5p on downstream genes