Supporting differentiated classes of resilience in multilayer networks

Services provided over telecommunications networks typically have different resilience requirements and networks need to be able to support different levels of resilience in an efficient manner. This dissertation investigates the problem of supporting differentiated classes of resilience in multilayer networks, including the most stringent resilience class required by critical services. We incorporate an innovative technique of embedding a subnetwork, termed the spine, with comparatively higher availability values at the physical layer. The spine lays a foundation for differentiation between multiple classes of flows that can be leveraged to achieve both high resilience and differentiation. The aim of this research is mainly to explore, design, and evaluate the proposed spine concept model in multilayer networks. The dissertation has four major parts. First, we explore the spine concept through numerical analysis of simple topologies illustrating the potential benefits and the cost considerations of the spine. We develop heuristics algorithms to find suitable spines for a network based on the structural properties of the network topology. Second, an optimization problem is formulated to determine the spine. The problem encompasses estimates of link availability improvements, associated costs, and a total budget. Third, we propose a crosslayer mapping and spine-aware routing design problem with protection given mainly at the lower layer. The problem is designed to transfer lower layer differentiation capability to the upper layer network and flows. We provide two joint routing-mapping optimization formulations and evaluate their performance in a multilayer scenario. Fourth, the joint routing-mapping problem is redesigned with protection given in the upper network layer instead. This will create two isolated logical networks; one mapped to the spine and the other is mapped freely on the network. Flows are assigned a path or path-pair based on their class of resilience. This approach can provide more routing options yielding different availability levels. The joint routing-mapping design problems are formulated as Integer Linear Programming (ILP) models. The goal is to achieve a wider range of availability values across layers and high availability levels for mission-critical services without the need to use higher order protection configurations. The proposed models are evaluated with extensive numerical results using real network topologies

The Importance of Cerebellar Connectivity on Simulated Brain Dynamics

The brain shows a complex multiscale organization that prevents a direct understanding of how structure, function and dynamics are correlated. To date, advances in neural modeling offer a unique opportunity for simulating global brain dynamics by embedding empirical data on different scales in a mathematical framework. The Virtual Brain (TVB) is an advanced data-driven model allowing to simulate brain dynamics starting from individual subjects’ structural and functional connectivity obtained, for example, from magnetic resonance imaging (MRI). The use of TVB has been limited so far to cerebral connectivity but here, for the first time, we have introduced cerebellar nodes and interconnecting tracts to demonstrate the impact of cerebro-cerebellar loops on brain dynamics. Indeed, the matching between the empirical and simulated functional connectome was significantly improved when including the cerebro-cerebellar loops. This positive result should be considered as a first step, since issues remain open about the best strategy to reconstruct effective structural connectivity and the nature of the neural mass or mean-field models generating local activity in the nodes. For example, signal processing is known to differ remarkably between cortical and cerebellar microcircuits. Tackling these challenges is expected to further improve the predictive power of functional brain activity simulations, using TVB or other similar tools, in explaining not just global brain dynamics but also the role of cerebellum in determining brain states in physiological conditions and in the numerous pathologies affecting the cerebro-cerebellar loop

Transcriptional Regulation of Sorghum Stem Composition : Key Players Identified Through Co-expression Gene Network and Comparative Genomics Analyses

Most sorghum biomass accumulates in stem secondary cell walls (SCW). As sorghum stems are used as raw materials for various purposes such as feed, energy and fiber reinforced polymers, identifying the genes responsible for SCW establishment is highly important. Taking advantage of studies performed in model species, most of the structural genes contributing at the molecular level to the SCW biosynthesis in sorghum have been proposed while their regulatory factors have mostly not been determined. Validation of the role of several MYB and NAC transcription factors in SCW regulation in Arabidopsis and a few other species has been provided. In this study, we contributed to the recent efforts made in grasses to uncover the mechanisms underlying SCW establishment. We reported updated phylogenies of NAC and MYB in 9 different species and exploited findings from other species to highlight candidate regulators of SCW in sorghum. We acquired expression data during sorghum internode development and used co-expression analyses to determine groups of co-expressed genes that are likely to be involved in SCW establishment. We were able to identify two groups of co-expressed genes presenting multiple evidences of involvement in SCW building. Gene enrichment analysis of MYB and NAC genes provided evidence that while NAC SECONDARY WALL THICKENING PROMOTING FACTOR NST genes and SECONDARY WALL-ASSOCIATED NAC DOMAIN PROTEIN gene functions appear to be conserved in sorghum, NAC master regulators of SCW in sorghum may not be as tissue compartmentalized as in Arabidopsis. We showed that for every homolog of the key SCW MYB in Arabidopsis, a similar role is expected for sorghum. In addition, we unveiled sorghum MYB and NAC that have not been identified to date as being involved in cell wall regulation. Although specific validation of the MYB and NAC genes uncovered in this study is needed, we provide a network of sorghum genes involved in SCW both at the structural and regulatory levels

Identification of Biomarkers Controlling Cell Fate In Blood Cell Development

A blood cell lineage consists of several consecutive developmental stages starting from the pluri- or multipotent stem cell to a state of terminal differentiation. Despite their importance for human biology, the regulatory pathways and gene networks that govern these differentiation processes are not yet fully understood. This is in part due to challenges associated with delineating the interactions between transcription factors (TFs) and their corresponding target genes. A possible step forward in this case is provided by the increasing amount of expression data, as a basis for linking differentiation stages and gene activities. Here, we present a novel hierarchical approach to identify characteristic expression peak patterns that global regulators excert along the differentiation path of cell lineages. Based on such simple patterns, we identified cell state-specific marker genes and extracted TFs that likely drive their differentiation. Integration of the mean expression values of stage-specific “key player” genes yielded a distinct peaking pattern for each lineage that was used to identify further genes in the dataset which behave similarly. Incorporating the set of TFs that regulate these genes led to a set of stage-specific regulators that control the biological process of cell fate. As proof of concept, we considered two expression datasets covering key differentiation events in blood cell formation of mice

Energy Management Systems for Smart Electric Railway Networks: A Methodological Review

Energy shortage is one of the major concerns in today’s world. As a consumer of electrical energy, the electric railway system (ERS), due to trains, stations, and commercial users, intakes an enormous amount of electricity. Increasing greenhouse gases (GHG) and CO2 emissions, in addition, have drawn the regard of world leaders as among the most dangerous threats at present; based on research in this field, the transportation sector contributes significantly to this pollution. Railway Energy Management Systems (REMS) are a modern green solution that not only tackle these problems but also, by implementing REMS, electricity can be sold to the grid market. Researchers have been trying to reduce the daily operational costs of smart railway stations, mitigating power quality issues, considering the traction uncertainties and stochastic behavior of Renewable Energy Resources (RERs) and Energy Storage Systems (ESSs), which has a significant impact on total operational cost. In this context, the first main objective of this article is to take a comprehensive review of the literature on REMS and examine closely all the works that have been carried out in this area, and also the REMS architecture and configurations are clarified as well. The secondary objective of this article is to analyze both traditional and modern methods utilized in REMS and conduct a thorough comparison of them. In order to provide a comprehensive analysis in this field, over 120 publications have been compiled, listed, and categorized. The study highlights the potential of leveraging RERs for cost reduction and sustainability. Evaluating factors including speed, simplicity, efficiency, accuracy, and ability to handle stochastic behavior and constraints, the strengths and limitations of each optimization method are elucidated

Digitalisation of Development and Supply Networks: Sequential and Platform-Driven Innovations

We draw from an eight-year dataset of 98 organisational entities involved in pre-competitive innovation networks across the UK pharmaceutical sector. These data map into three networks that are representative of: (i) a product development-led sequential pathway that begins with digitalised product development, followed by digitalisation of supply networks, (ii) a supply network-led sequential pathway that starts with digitalised supply networks, followed by digitalisation of product development, and (iii) a parallel — platform-driven — pathway that enables simultaneous digitalisation of development, production, and supply networks. We draw upon extant literature to assess these network structures along three dimensions — strategic intent, the integrative roles of nodes with high centrality, and innovation performance. We conduct within-case and cross-case analyses to postulate 10 research propositions that compare and contrast modalities for sequential and platform-based digitalisation involving collaborative innovation networks. With sequential development, our propositions are congruent with conventional pathways for mitigating innovation risks through modular moves. On the other hand, we posit that platform-based design rules, rather than modular moves, mitigate the risks for parallel development pathways, and lead to novel development and delivery mechanisms

Strategies for engineering microbial communities

Understanding how microbes assemble into communities is a fundamental open question in biology, with applications to human health, environmental sustainability, and metabolic engineering. Although it is known that the competition and exchange of nutrients (i.e., metabolic interactions) shape microbial community structure and dynamics, the ability to reliably predict the metabolic interactions and their effect on microbial communities is still being studied. This dissertation investigates how metabolism and environment shape microbial communities through the use of mathematical models, based on linear programming (LP) and mixed integer linear programming (MILP) methods. The first system I studied is a synthetic microbial consortium composed of two species, Cellulomonas fimi and Yarrowia lipolytica, hypothesized to be able to jointly transform cellulose into biofuel precursors. I combined experimental data and flux balance analysis (FBA) to test our capacity to predict metabolic interactions between the two organisms, and explored a proof-of-concept method to monitor the growth dynamics of this coculture. I next explored the possibility of generalizing the design of synthetic communities through the implementation of a computational method that can design division of labor strategies. The algorithm finds consortia of engineered bacterial strains that can survive by exchanging with each other specific nutrients. By distributing functions, microbial consortia can perform tasks that are impossible for individual species to accomplish alone. In addition to highlighting the trade-off between metabolic self-reliance and mutualistic exchange, this approach suggests how division of labor may arise in Escherichia coli monocultures. While mechanistic models are helpful for studying metabolism in microbes and microbial communities, it is interesting to ask whether increasingly cheaper high-throughput phenotypic data, can help achieve similar goals. To address this question, I developed a computational approach to investigate the relationship between growth profiles and microbial species, based on the identification of growth conditions that can best represent the whole dataset. This approach can help engineer microbial communities by identifying microbes that are more likely to engage in cross-feeding, rather than competition, based on their phenotypic profiles. In general, this dissertation demonstrates how different types of metabolic modeling approaches, both mechanism-based and data-driven, can be used to predict metabolic interactions between members of microbial consortia, and to help engineer novel synthetic communities

Gendering Human Rights Violations: The case of interpersonal violence: Final Report 2004-2007

Three years of project work are hardly enough to declare that a radical change has taken place in the overall understanding of violence in interpersonal relationships. However, it is fair to say that a new basis for conceptualising and using knowledge on violence has been laid by this Coordination Action on Human Rights Violations (CAHRV). The final report of CAHRV details on the objectives, methodology and scope of the project. But what is the value of this type of project for the European Union? How does this project contribute to the overall policy objectives of the EU

An expert system for project controls in construction management

In this paper, I describe an expert project control system for construction management. The purpose of the project is to develop methods and strategies for expert system based planning, scheduling, chronicling and analysis for construction management. Planning defines the actions required to accomplish a goal? scheduling links the plan into a frame of time? chronicling is monitoring job performance and analysis defines reevaluation of the plan as conditions change. Conditions are modeled as constraints and will be coded as rules. As conditions change, constraints must be dynamically modified by the system to accommodate the changes. The research is a combination of three related areas: a. Domain dependent hierarchical planning techniques. b. Model-based planning/scheduling techniques developed for the job-shop environment. c. Expert construction planning/scheduling techniques