A Parameterized Centrality Metric for Network Analysis

A variety of metrics have been proposed to measure the relative importance of nodes in a network. One of these, alpha-centrality [Bonacich, 2001], measures the number of attenuated paths that exist between nodes. We introduce a normalized version of this metric and use it to study network structure, specifically, to rank nodes and find community structure of the network. Specifically, we extend the modularity-maximization method [Newman and Girvan, 2004] for community detection to use this metric as the measure of node connectivity. Normalized alpha-centrality is a powerful tool for network analysis, since it contains a tunable parameter that sets the length scale of interactions. By studying how rankings and discovered communities change when this parameter is varied allows us to identify locally and globally important nodes and structures. We apply the proposed method to several benchmark networks and show that it leads to better insight into network structure than alternative methods.Comment: 11 pages, submitted to Physical Review

Least Upper Delay Bound for VBR Flows in Networks-on- Chip with Virtual Channels

Real-time applications such as multimedia and gaming require stringent performance guarantees, usually enforced by a tight upper bound on the maximum end-to-end delay. For FIFO multiplexed on-chip packet switched networks we consider worst-case delay bounds for Variable Bit-Rate (VBR) flows with aggregate scheduling, which schedules multiple flows as an aggregate flow. VBR Flows are characterized by a maximum transfer size, peak rate, burstiness, and average sustainable rate. Based on network calculus, we present and prove theorems to derive per-flow end-to-end Equivalent Service Curves (ESC) which are in turn used for computing Least Upper Delay Bounds (LUDBs) of individual flows. In a realistic case study we find that the end-to-end delay bound is up to 46.9% more accurate than the case without considering the traffic peak behavior. Likewise, results also show similar improvements for synthetic traffic patterns. The proposed methodology is implemented in C++ and has low run-time complexity, enabling quick evaluation for large and complex SoCs

The anti-bacterial iron-restriction defence mechanisms of egg white; the potential role of three lipocalin-like proteins in resistance against Salmonella

Salmonella enterica serovar Enteritidis (SE) is the most frequently-detected Salmonella in foodborne outbreaks in the European Union. Among such outbreaks, egg and egg products were identified as the most common vehicles of infection. Possibly, the major antibacterial property of egg white is iron restriction, which results from the presence of the iron-binding protein, ovotransferrin. To circumvent iron restriction, SE synthesise catecholate siderophores (i.e. enterobactin and salmochelin) that can chelate iron from host iron-binding proteins. Here, we highlight the role of lipocalin-like proteins found in egg white that could enhance egg-white iron restriction through sequestration of certain siderophores, including enterobactin. Indeed, it is now apparent that the egg-white lipocalin, Ex-FABP, can inhibit bacterial growth via its siderophore-binding capacity in vitro. However, it remains unclear whether ex-FABP performs such a function in egg white or during bird infection. Regarding the two other lipocalins of egg white (Cal-γ and α-1-glycoprotein), there is currently no evidence to indicate that they sequester siderophores

InterPro in 2019: improving coverage, classification and access to protein sequence annotations

The InterPro database (http://www.ebi.ac.uk/interpro/) classifies protein sequences into families and predicts the presence of functionally important domains and sites. Here, we report recent developments with InterPro (version 70.0) and its associated software, including an 18% growth in the size of the database in terms on new InterPro entries, updates to content, the inclusion of an additional entry type, refined modelling of discontinuous domains, and the development of a new programmatic interface and website. These developments extend and enrich the information provided by InterPro, and provide greater flexibility in terms of data access. We also show that InterPro's sequence coverage has kept pace with the growth of UniProtKB, and discuss how our evaluation of residue coverage may help guide future curation activities

Molecular signatures of the rediae, cercariae and adult stages in the complex life cycles of parasitic flatworms (Digenea: Psilostomatidae)

BACKGROUND: Parasitic flatworms (Trematoda: Digenea) represent one of the most remarkable examples of drastic morphological diversity among the stages within a life cycle. Which genes are responsible for extreme differences in anatomy, physiology, behavior, and ecology among the stages? Here we report a comparative transcriptomic analysis of parthenogenetic and amphimictic generations in two evolutionary informative species of Digenea belonging to the family Psilostomatidae. METHODS: In this study the transcriptomes of rediae, cercariae and adult worm stages of Psilotrema simillimum and Sphaeridiotrema pseudoglobulus, were sequenced and analyzed. High-quality transcriptomes were generated, and the reference sets of protein-coding genes were used for differential expression analysis in order to identify stage-specific genes. Comparative analysis of gene sets, their expression dynamics and Gene Ontology enrichment analysis were performed for three life stages within each species and between the two species.RESULTS: Reference transcriptomes for P. simillimum and S. pseudoglobulus include 21,433 and 46,424 sequences, respectively. Among 14,051 orthologous groups (OGs), 1354 are common and specific for two analyzed psilostomatid species, whereas 13 and 43 OGs were unique for P. simillimum and S. pseudoglobulus, respectively. In contrast to P. simillimum, where more than 60% of analyzed genes were active in the redia, cercaria and adult worm stages, in S. pseudoglobulus less than 40% of genes had such a ubiquitous expression pattern. In general, 7805 (36.41%) and 30,622 (65.96%) of genes were preferentially expressed in one of the analyzed stages of P. simillimum and S. pseudoglobulus, respectively. In both species 12 clusters of co-expressed genes were identified, and more than a half of the genes belonging to the reference sets were included into these clusters. Functional specialization of the life cycle stages was clearly supported by Gene Ontology enrichment analysis.CONCLUSIONS: During the life cycles of the two species studied, most of the genes change their expression levels considerably, consequently the molecular signature of a stage is not only a unique set of expressed genes, but also the specific levels of their expression. Our results indicate unexpectedly high level of plasticity in gene regulation between closely related species. Transcriptomes of P. simillimum and S. pseudoglobulus provide high quality reference resource for future evolutionary studies and comparative analyses

A graph theoretic modeling for securing link layer in mobile ad hoc networks

The increased usage of wireless ad-hoc networks (MANET), which is a collection of wireless mobile nodes that form a dynamic network without the need for infrastructure or centralized points, in many different applications has opened the door for many security challenges. In recent years, securing and protecting communications between mobile nodes in MANETs have become an active research field. The vast majority has only focused on providing authenticity of the route and mostly ignored the availability of malicious nodes in the environment. The aim of this work is to explore the effectiveness of malicious nodes in MANETs considering the Request-to-Send (RTS) / Clear-to-Send (CTS) protocol. It is assumed that a certain node is not listening to any RTS messages until it has a specific number of nodes within its range, and, it will have a fixed period of time before it replies a CTS message. In this paper, specific attention was paid to the security issues of a mobile ad hoc network. We propose a graph theoretic model that satisfies the basic mobility requirements of a MANET and define a mathematic analysis for the model in order to show the effectiveness of a malicious node in this network.Mnar Saeed Alnaghes, Fayez Gebal

Performance analysis of server-side spam control strategies based on layer-3 classification

Two server-side e-mail service strategies that utilize a layer-3 e-mail classification technique are presented. Based on layer-3 classification scores, the class of an e-mail can be estimated with minimal processing during normal reassembly on e-mail servers with a high accuracy. Non-spam e-mails are queued in a fast queue, whereas spam e-mails are queued in a slower queue. The non-spam queue is served with higher service capacity than the spam one. Two e-mail service strategies are analyzed using a priority queue model. The first service strategy assigns fixed service capacities to both queues. The second service strategy serves the spam queue based on the occupancies of both queues. We model these two strategies using discrete-time Markov chain analysis. The behavior and performance of the proposed service strategies are analyzed under different e-mail traffic loads. Our models show that non-spam e-mails can be delivered under small delay, as compared to the current strategy that uses a single queue approach. The proposed strategies exhibit delay and loss probability orders of magnitude smaller than the ones for the single queue approach, even under heavy e-mail loading and high spam to non-spam prior. Servicing e-mails by predicting an e-mail's class has two-fold advantages. First speeding up non-spam e-mail services and delivery at the expense of longer spam queuing delay, and second protecting e-mail servers in the events of spam attacks and high e-mail traffic