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September 2016

Interval estimation of small tail probabilities—applications in food safety

Benjamin Kedem, Lemeng Pan, Wen Zhou, Carlos A. Coelho

This article introduces a new statistical idea: repeated out-of-sample fusion. Often in food safety and bio-surveillance it is desirable to estimate the probability that a contaminant or a function thereof exceeds an unsafe high threshold. The probability or chance in question is very small. To estimate such a probability, we need information about large values. In many cases, the data do not contain information about exceedingly large contamination levels, which ostensibly renders the problem insolvable. A solution is suggested whereby more information about small tail probabilities is obtained by repeatedly combining the real data with computer-generated data. This method provides short yet reliable interval estimates based on moderately large samples. An example is provided in terms of lead exposure data.

Statistics in Medicine (Impact factor 1.99) 17 February 2016, DOI: 10.1002/sim.6921  A PDF of the article can be downloaded here.


Bifurcation Analysis of Cardiac Alternans using Delta-Decidability

M.A. Islam, G. Byrne, S. Kong, E.M. Clarke, R. Cleaveland, F. Fenton, R. Grosu, and S. Smolka

Image: Bifurcation analysis of alternans with respect to four parameters of the MS model.

To the best of our knowledge, this analysis represents the first formal verification of non-trivial dynamics in a numerical cardiac-cell model.

The paper presents a bifurcation analysis of electrical alternans in the two-current Mitchell-Schaeffer (MS) cardiac-cell model using the theory of delta-decidability over the reals. Electrical alternans is a phenomenon characterized by a variation in the successive Action Potential Durations (APDs) generated by a single cardiac cell or tissue. Alternans are known to initiate re-entrant waves and are an important physiological indicator of an impending life-threatening arrhythmia such as ventricular fibrillation. The bifurcation analysis the researchers perform determines, for each control parameter tau of the MS model, the bifurcation point in the range of tau such that a small perturbation to this value results in a transition from alternans to non-alternans behavior.

14th International Conference, CMSB 2016, Cambridge, UK, September 21-23, 2016, Proceedings. A PDF of the paper can be downloaded here. Also available as a chapter in Computational Methods in Systems Biology, Vol. 9859 of the series Lecture Notes in Computer Science, by Springer.


Inferring Cortical Variability from Local Field Potentials

Y. Cui, L. Liu, J.M. McFarland, C.C. Pack, D.A. Butts

Image: Improvements in model performance were greater for neurons that were less stimulus locked.

The responses of sensory neurons can be quite different to repeated presentations of the same stimulus. Here, we demonstrate a direct link between the trial-to-trial variability of cortical neuron responses and network activity that is reflected in local field potentials (LFPs). Our results identify signatures of network activity related to the variability of cortical neuron responses, and suggest their central role in sensory cortical function.

The Journal of Neuroscience, April 6, 2016, 36(14): 4121– 4135. A PDF of the paper can be downloaded here.


New science at the meso frontier: Dense nanostructure architectures for electrical energy storage

Gary Rubloff and Sang Bok Lee

Image: Nanostructured electrodes for enhanced power, shown here in discharge. (a) Conventional planar electrodes. (b) Heterogeneous nanowire electrodes. (c) Integrated ion storage and electron current collecting materials comprise heterogeneous nanoelectrodes.

We examine the scientific challenges and opportunities presented at the mesoscale in the context of employing nanostructures for electrical energy storage. In order to capitalize on the power–energy and charge/discharge cycling stability that nanostructures offer, massive assemblies of nanostructures in networks must be organized into dense mesoscale architectures. With a fairly wide variety of architectures already demonstrated and more expected, the essential questions are whether regular or random 3-D arrangements are favorable, which embodiments should show best performance, and at what dimensional scaling? Dense packing raises challenging new questions about ion available and transport in highly confined electrolyte nanoenvironments, as well as designs to balance ion transport in electrolyte and electron transport in electrodes over distances long compared to nanostructure characteristic dimensions. Architectures and dimensional scaling present important issues of defects, statistical outliers, and their dynamic evolution, which in turn control degradation and failure phenomena. These considerations promise a rich set of mesoscale scientific challenges crucial to exploiting storage nanostructures in mesoscale architectures for energy storage.

Current Opinion in Solid State and Materials Science, Vol. 19, Issue 4, August 2015, 227-234. A PDF of the paper can be downloaded here.


Estimating where and how animals travel: An optimal framework for path reconstruction from autocorrelated tracking data

C.H. Fleming, W.F. Fagan, T. Mueller, K.A. Olson, P. Leimgruber, and J.M. Calabrese

Image: Occurrence distributions for a fisher, as calculated with the OUF and BM models.

Our paper introduces kriging as a general purpose method for reconstructing animal movement paths from incompletely sampled track data.

An animal’s trajectory is a fundamental object of interest in movement ecology, as it directly informs a range of topics from resource selection, to energy expenditure and behavioral states. However, optimally inferring the mostly unobserved movement path and its dynamics from a limited sample of telemetry observations is a key unsolved problem. The field of geostatistics has focused significant attention on a mathematically analogous problem that has a statistically optimal solution coined after its inventor Krige. Kriging revolutionized geostatistics and is now the gold standard for interpolating between a limited number of autocorrelated spatial point observations. Here we translate Kriging for use with animal movement data. Our Kriging formalism encompasses previous methods to estimate animal’s trajectories—the Brownian bridge and continuous-time correlated random walk library—as special cases, informs users as to when these previous methods are appropriate and provides a more general method when they are not. We demonstrate the capabilities of Kriging on a case study with Mongolian gazelles where, compared to the Brownian bridge, Kriging with a more optimal model was 10% more precise in interpolating locations and 500% more precise in estimating occurrence areas.

Ecology, Vol. 19, Issue 4, August 2015, 227-234. A PDF of the paper can be downloaded here.


Autoinducer-2 analogs and electric fields—an antibiotic-free bacterial biofilm combination treatment

Sowmya Subramanian, Konstantinos Gerasopoulos, Min Guo, Herman O. Sintim, William E. Bentley, Reza Ghodssi

Image: (a) Schematic of the macroscale experimental setup. (b) Photograph of electroporation cuvette with glass chip/coupon placed inside it.

Bacterial biofilms are a common cause of chronic medical implant infections. Treatment and eradication of biofilms by conventional antibiotic therapy has major drawbacks including toxicity and side effects associated with high-dosage antibiotics. Additionally, administration of high doses of antibiotics may facilitate the emergence of antibiotic resistant bacteria. There is an urgent need for the development of treatments that are not based on conventional antibiotic therapies.

We present a novel bacterial biofilm combination treatment independent of traditional antibiotics, by using low electric fields in combination with small molecule inhibitors of bacterial quorum sensing – autoinducer-2 analogs. We investigate the effect of this treatment on mature Escherichia coli biofilms by application of an alternating and offset electric potential in combination with the small molecule inhibitor for 24 h using both macro and micro-scale devices. Crystal violet staining of the macro-scale biofilms shows a 46 % decrease in biomass compared to the untreated control. We demonstrate enhanced treatment efficacy of the combination therapy using a high-throughput polydimethylsiloxane-based microfluidic biofilm analysis platform. This microfluidic flow cell is designed to reduce the growth variance of in vitro biofilms while providing an integrated control, and allows for a more reliable comparison and evaluation of new biofilm treatments on a single device. Our results suggest that the antibiotic-free combination treatment described here may provide an effective alternative to traditional antibiotic therapies against bacterial biofilm infections. Use of this combination treatment in the medical and environmental fields would alleviate side effects associated with high-dosage antibiotic therapies, and reduce the rise of antibiotic-resistant bacteria.

Biomed Microdevices (2016) 18:95. A PDF of the paper can be downloaded here.


Bidirectional Resonant DC–DC Step-Up Converters for Driving High-Voltage Actuators in Mobile Microrobots

Yichao Tang and Alireza Khaligh

Image: Proposed bidirectional resonant dc-dc converters for driving EAP actuators.

Electroactive polymer (EAP) actuators have been investigated to convert electrical energy into mechanical deformation in autonomous microrobots. The use of dielectric EAP actuators comes with several challenges to address requirements such as high excitation voltages, explicit driving signals, and low conversion efficiency. External bulky and heavy power sources are used to generate and provide required excitation voltages. The development of a miniature, high voltage gain, and highly efficient power electronic interface is required to overcome such challenges and enable autonomous operation of miniature robots. In this paper, a bidirectional single-stage resonant dc-dc step-up converter is introduced and developed to efficiently drive high-voltage EAP actuators in mobile microrobots. The converter utilizes resonant capacitors and a coupled inductor as a soft-switched LC network to step up low input voltage.

IEEE Transactions on Power Electronics, Vol. 31, No. 1. A PDF of the paper can be downloaded here.