Search for: All records

A source generates time-stamped update packets that are sent to a server and then forwarded to a monitor. This occurs in the presence of an adversary that can infer information about the source by observing the output process of the server. The server wishes to release updates in a timely way to the monitor but also wishes to minimize the information leaked to the adversary. We analyze the trade-off between the age of information (AoI) and the maximal leakage for systems in which the source generates updates as a Bernoulli process. For a time slotted system in which sending an update requires one slot, we consider three server policies: (1) Memoryless with Bernoulli Thinning (MBT): arriving updates are queued with some probability and head-of-line update is released after a geometric holding time; (2) Deterministic Accumulate-and-Dump (DAD): the most recently generated update (if any) is released after a fixed time; (3) Random Accumulate-and-Dump (RAD): the most recently generated update (if any) is released after a geometric waiting time. We show that for the same maximal leakage rate, the DAD policy achieves lower age compared to the other two policies but is restricted to discrete age-leakage operating points.

To better understand tick ecology in Virginia and the increasing Lyme disease incidence in western Virginia, a comparative phenological study was conducted in which monthly collections were performed at twelve sampling locations in southwestern Virginia (high Lyme disease incidence) and 18 equivalent sampling locations in southeastern Virginia (low Lyme disease incidence) for one year. In western Virginia, we also explored the effect of elevation on collection rates of Ixodes scapularis Say (Acari: Ixodidae) and Amblyomma americanum (L.) (Acari: Ixodidae). In total, 35,438 ticks were collected (33,106 A. americanum; 2,052 I. scapularis; 134 Ixodes affinis Neumann [Acari: Ixodidae]; 84 Dermacentor variabilis [Say] [Acari: Ixodidae]; 49 Dermacentor albipictus [Packard] [Acari: Ixodidae]; 10 Haemaphysalis leporispalustris [Packard] [Acari: Ixodidae]; 2 Ixodes brunneus Koch [Acari: Ixodidae]; 1 Haemaphysalis longicornis Neumann [Acari: Ixodidae]). Within southwestern Virginia, Ixodes scapularis collection rates were not influenced by elevation, unlike A. americanum which were collected more frequently at lower elevations (e.g., below 500 m). Notably, I. scapularis larvae and nymphs were commonly collected in southwestern Virginia (indicating that they were questing on or above the leaf litter) but not in southeastern Virginia. Questing on or above the leaf litter is primarily associated with northern populations of I. scapularis. Thesemore »findings may support the hypothesis that I. scapularis from the northeastern United States are migrating into western Virginia and contributing to the higher incidence of Lyme disease in this region. This comparative phenological study underscores the value of these types of studies and the need for additional research to further understand the rapidly changing tick-borne disease dynamics in Virginia.

« less

Abstract Molecular interactions are studied as independent networks in systems biology. However, molecular networks do not exist independently of each other. In a network of networks approach (called multiplex), we study the joint organization of transcriptional regulatory network (TRN) and protein–protein interaction (PPI) network. We find that TRN and PPI are non-randomly coupled across five different eukaryotic species. Gene degrees in TRN (number of downstream genes) are positively correlated with protein degrees in PPI (number of interacting protein partners). Gene–gene and protein–protein interactions in TRN and PPI, respectively, also non-randomly overlap. These design principles are conserved across the five eukaryotic species. Robustness of the TRN–PPI multiplex is dependent on this coupling. Functionally important genes and proteins, such as essential, disease-related and those interacting with pathogen proteins, are preferentially situated in important parts of the human multiplex with highly overlapping interactions. We unveil the multiplex architecture of TRN and PPI. Multiplex architecture may thus define a general framework for studying molecular networks. This approach may uncover the building blocks of the hierarchical organization of molecular interactions.

A source node forwards fresh status updates as a point process to a network of observer nodes. Within the network of observers, these updates are forwarded as point processes from node to node. Each node wishes its knowledge of the source to be as timely as possible. In this network, timeliness at each node is measured by an age of information metric: how old is the timestamp of the freshest received update. This work extends a method for evaluating the average age at each node in the network when nodes forward updates using a memoryless gossip protocol. This method is then demonstrated by age analysis for a simple network.

The ability of bacteria to colonize and grow on different surfaces is an essential process for biofilm development. Here, we report the use of synthetic hydrogels with tunable stiffness and porosity to assess physical effects of the substrate on biofilm development. Using time-lapse microscopy to track the growth of expanding Serratia marcescens colonies, we find that biofilm colony growth can increase with increasing substrate stiffness, unlike what is found on traditional agar substrates. Using traction force microscopy-based techniques, we find that biofilms exert transient stresses correlated over length scales much larger than a single bacterium, and that the magnitude of these forces also increases with increasing substrate stiffness. Our results are consistent with a model of biofilm development in which the interplay between osmotic pressure arising from the biofilm and the poroelastic response of the underlying substrate controls biofilm growth and morphology.

ABSTRACT Myxococcus xanthus is a bacterium that lives on surfaces as a predatory biofilm called a swarm. As a growing swarm feeds on prey and expands, it displays dynamic multicellular patterns such as traveling waves called ripples and branching protrusions called flares. The rate at which a swarm expands across a surface, and the emergence of the coexisting patterns, are all controlled through coordinated cell movement. M. xanthus cells move using two motility systems known as adventurous (A) and social (S). Both are involved in swarm expansion and pattern formation. In this study, we describe a set of M. xanthus swarming genotype-to-phenotype associations that include both genetic and environmental perturbations. We identified new features of the swarming phenotype, recorded and measured swarm expansion using time-lapse microscopy, and compared the impact of mutations on different surfaces. These observations and analyses have increased our ability to discriminate between swarming phenotypes and provided context that allows us to identify some phenotypes as improbable outliers within the M. xanthus swarming phenome. IMPORTANCE Myxococcus xanthus grows on surfaces as a predatory biofilm called a swarm. In nature, a feeding swarm expands by moving over and consuming prey bacteria. In the laboratory, a swarm is createdmore »by spotting cell suspension onto nutrient agar in lieu of prey. The suspended cells quickly settle on the surface as the liquid is absorbed into the agar, and the new swarm then expands radially. An assay that measures the expansion rate of a swarm of mutant cells is the first, and sometimes only, measurement used to decide whether a particular mutation impacts swarm motility. We have broadened the scope of this assay by increasing the accuracy of measurements and introducing prey, resulting in new identifiable and quantifiable features that can be used to improve genotype-to-phenotype associations.« less

A source node updates its status as a point process and also forwards its updates to a network of observer nodes. Within the network of observers, these updates are forwarded as point processes from node to node. Each node wishes its knowledge of the source to be as timely as possible. In this network, timeliness is measured by a discrete form of age of information: each status change at the source is referred to as a version and the age at a node is how many versions out of date is its most recent update from the source. This work introduces a method for evaluating the average version age at each node in the network when nodes forward updates using a memoryless gossip protocol. This method is then demonstrated by version age analysis for a collection of simple networks. For gossip on a complete graph with symmetric updating rates, it is shown that each node has average age that grows as the logarithm of the network size.

We quantify, over inter-continental paths, the ageing of TCP packets, throughput and delay for different TCP congestion control algorithms containing a mix of loss-based, delay-based and hybrid congestion control algorithms. In comparing these TCP variants to ACP+, an improvement over ACP, we shed better light on the ability of ACP+ to deliver timely updates over fat pipes and long paths. ACP+ estimates the network conditions on the end-to-end path and adapts the rate of status updates to minimize age. It achieves similar average age as the best (age wise) performing TCP algorithm but at end-to-end throughputs that are two orders of magnitude smaller. We also quantify the significant improvements that ACP+ brings to age control over a shared multiaccess channel.

We consider updating strategies for a local cache which downloads time-sensitive files from a remote server through a bandwidth-constrained link. The files are requested randomly from the cache by local users according to a popularity distribution which varies over time according to a Markov chain structure. We measure the freshness of the requested time-sensitive files through their Age of Information (AoI). The goal is then to minimize the average AoI of all requested files by appropriately designing the local cache’s downloading strategy. To achieve this goal, the original problem is relaxed and cast into a Constrained Markov Decision Problem (CMDP), which we solve using a Lagrangian approach and Linear Programming. Inspired by this solution for the relaxed problem, we propose a practical cache updating strategy that meets all the constraints of the original problem. Under certain assumptions, the practical updating strategy is shown to be optimal for the original problem in the asymptotic regime of a large number of files. For a finite number of files, we show the gain of our practical updating strategy over the traditional square-root-law strategy (which is optimal for fixed non time-varying file popularities) through numerical simulations.