A core genetic module : the Mixed Feedback Loop

The so-called Mixed Feedback Loop (MFL) is a small two-gene network where protein A regulates the transcription of protein B and the two proteins form a heterodimer. It has been found to be statistically over-represented in statistical analyses of gene and protein interaction databases and to lie at the core of several computer-generated genetic networks. Here, we propose and mathematically study a model of the MFL and show that, by itself, it can serve both as a bistable switch and as a clock (an oscillator) depending on kinetic parameters. The MFL phase diagram as well as a detailed description of the nonlinear oscillation regime are presented and some biological examples are discussed. The results emphasize the role of protein interactions in the function of genetic modules and the usefulness of modelling RNA dynamics explicitly.Comment: To be published in Physical Review

Evaluation of Few-View Reconstruction Parameters for Illicit Substance Detection using Fast-Neutron Transmission Spectroscopy

We have evaluated the performance of an illicit substance detection system that performs image reconstruction using the Maximum Likelihood algebraic reconstruction algorithm, a few number of projections, and relatively coarse projection and pixel resolution. This evaluation was done using receiver operator curves and simulated data from the fast-neutron transmission spectroscopy system operated in a mode to detect explosives in luggage. The results show that increasing the number of projection angles is more important than increasing the projection resolution, the reconstructed pixel resolution, or the number of iterations in the Maximum Likelihood algorithm. A 100% detection efficiency with essentially no false positives is possible for a square block of RDX explosive, a projection resolution of 2 cm, a reconstructed pixel size of 2x2 cm, and five projection angles. For rectangular shaped explosives more angles are required to obtain the same system performance

Evaluating Local Community Methods in Networks

We present a new benchmarking procedure that is unambiguous and specific to local community-finding methods, allowing one to compare the accuracy of various methods. We apply this to new and existing algorithms. A simple class of synthetic benchmark networks is also developed, capable of testing properties specific to these local methods.Comment: 8 pages, 9 figures, code included with sourc

Bacterial biofilm formation on indwelling urethral catheters

Urethral catheters are the most commonly deployed medical devices and used to manage a wide range of conditions in both hospital and community care settings. The use of long-term catheterization, where the catheter remains in place for a period &gt;28 days remains common, and the care of these patients is often undermined by the acquisition of infections and formation of biofilms on catheter surfaces. Particular problems arise from colonization with urease-producing species such as Proteus mirabilis, which form unusual crystalline biofilms that encrust catheter surfaces and block urine flow. Encrustation and blockage often lead to a range of serious clinical complications and emergency hospital referrals in long-term catheterized patients. Here we review current understanding of bacterial biofilm formation on urethral catheters, with a focus on crystalline biofilm formation by P. mirabilis, as well as approaches that may be used to control biofilm formation on these devices. Significance and Impact of the Study: Urinary catheters are the most commonly used medical devices in many healthcare systems, but their use predisposes to infection and provide ideal conditions for bacterial biofilm formation. Patients managed by long-term urethral catheterization are particularly vulnerable to biofilm-related infections, with crystalline biofilm formation by urease producing species frequently leading to catheter blockage and other serious clinical complications. This review considers current knowledge regarding biofilm formation on urethral catheters, and possible strategies for their control.</p

Collective decision-making on triadic graphs

Many real-world networks exhibit community structures and non-trivial clustering associated with the occurrence of a considerable number of triangular subgraphs known as triadic motifs. Triads are a set of distinct triangles that do not share an edge with any other triangle in the network. Network motifs are subgraphs that occur significantly more often compared to random topologies. Two prominent examples, the feedforward loop and the feedback loop, occur in various real-world networks such as gene-regulatory networks, food webs or neuronal networks. However, as triangular connections are also prevalent in communication topologies of complex collective systems, it is worthwhile investigating the influence of triadic motifs on the collective decision-making dynamics. To this end, we generate networks called Triadic Graphs (TGs) exclusively from distinct triadic motifs. We then apply TGs as underlying topologies of systems with collective dynamics inspired from locust marching bands. We demonstrate that the motif type constituting the networks can have a paramount influence on group decision-making that cannot be explained solely in terms of the degree distribution. We find that, in contrast to the feedback loop, when the feedforward loop is the dominant subgraph, the resulting network is hierarchical and inhibits coherent behavior

Graph Metrics for Temporal Networks

Temporal networks, i.e., networks in which the interactions among a set of elementary units change over time, can be modelled in terms of time-varying graphs, which are time-ordered sequences of graphs over a set of nodes. In such graphs, the concepts of node adjacency and reachability crucially depend on the exact temporal ordering of the links. Consequently, all the concepts and metrics proposed and used for the characterisation of static complex networks have to be redefined or appropriately extended to time-varying graphs, in order to take into account the effects of time ordering on causality. In this chapter we discuss how to represent temporal networks and we review the definitions of walks, paths, connectedness and connected components valid for graphs in which the links fluctuate over time. We then focus on temporal node-node distance, and we discuss how to characterise link persistence and the temporal small-world behaviour in this class of networks. Finally, we discuss the extension of classic centrality measures, including closeness, betweenness and spectral centrality, to the case of time-varying graphs, and we review the work on temporal motifs analysis and the definition of modularity for temporal graphs.Comment: 26 pages, 5 figures, Chapter in Temporal Networks (Petter Holme and Jari Saram\"aki editors). Springer. Berlin, Heidelberg 201

Bada Bang, Bada Boom: Dispersal of fall migrating cormorants to protect sportfish on Oneida Lake, New York

The interior population of double-crested cormorants (Phalacrocorax auritus) continues to increase. As a result, conflicts between human interests and cormorants have intensified. The impacts of nesting, roosting, and migrating cormorants include predation at aquaculture facilities, interspecific competition with rare species including common terns {Sterna hirundo), and impacts to private property. In addition, heightened public and scientific debate regarding cormorant impacts on sportfish has accelerated the need for effective, socially acceptable methods for managing local conflicts. In 1998 and 1999, USDA, APHIS, Wildlife Services; the New York State Department of Environmental Conservation; and USGS, New York Fish and Wildlife Research Cooperative collaborated on a pilot project to investigate prospective methods and strategies for reducing predation of yellow perch (Perca flavescens) and walleye (Stizostedion vitreum) by fall migrating cormorants on Oneida Lake, New York. The goal of the cooperative program was to reduce stopover time, thereby reducing predation on fish stocks by migrating cormorants. A lakewide integrated non-lethal harassment and roost management program was initiated to disperse local and migrating cormorants from September to October each year. A variety of methods were used to manage cormorants including: electronic guards, propane cannons, mylar tape, human effigies, pyrotechnics, and dispersing birds with a boat. Harassment was focused on birds loafing on the water as well as day and night roosting sites (8 day and 2 night roosts). A total of 52,840 cormorants was dispersed (in many cases individual birds were harassed multiple times) using 1,518 pyrotechnics and 649 staff hours on the lake during the 2 years of the program. Surveys documented a 61%-98% reduction of the cormorants population on Oneida Lake compared to mean counts during the same time period from 1995-1997. Estimated total annual fish consumption by cormorants was reduced by 30% in 1998. Some off-site impacts of the program were seen with increased flocks of cormorants documented on nearby lakes

Bursty egocentric network evolution in Skype

In this study we analyze the dynamics of the contact list evolution of millions of users of the Skype communication network. We find that egocentric networks evolve heterogeneously in time as events of edge additions and deletions of individuals are grouped in long bursty clusters, which are separated by long inactive periods. We classify users by their link creation dynamics and show that bursty peaks of contact additions are likely to appear shortly after user account creation. We also study possible relations between bursty contact addition activity and other user-initiated actions like free and paid service adoption events. We show that bursts of contact additions are associated with increases in activity and adoption - an observation that can inform the design of targeted marketing tactics.Comment: 7 pages, 6 figures. Social Network Analysis and Mining (2013

Little-Parks effect and multiquanta vortices in a hybrid superconductor--ferromagnet system

Within the phenomenological Ginzburg-Landau theory we investigate the phase diagram of a thin superconducting film with ferromagnetic nanoparticles. We study the oscillatory dependence of the critical temperature on an external magnetic field similar to the Little-Parks effect and formation of multiquantum vortex structures. The structure of a superconducting state is studied both analytically and numerically.Comment: 7 pages, 1 figure. Submitted to J. Phys.: Condens. Mat

Spectral plots and the representation and interpretation of biological data

It is basic question in biology and other fields to identify the char- acteristic properties that on one hand are shared by structures from a particular realm, like gene regulation, protein-protein interaction or neu- ral networks or foodwebs, and that on the other hand distinguish them from other structures. We introduce and apply a general method, based on the spectrum of the normalized graph Laplacian, that yields repre- sentations, the spectral plots, that allow us to find and visualize such properties systematically. We present such visualizations for a wide range of biological networks and compare them with those for networks derived from theoretical schemes. The differences that we find are quite striking and suggest that the search for universal properties of biological networks should be complemented by an understanding of more specific features of biological organization principles at different scales.Comment: 15 pages, 7 figure