Streaming covariance selection with applications to adaptive querying in sensor networks

Sensor networks can be naturally represented as graphical models, where the edge set encodes the presence of sparsity in the correlation structure between sensors. Such graphical representations can be valuable for information mining purposes as well as for optimizing bandwidth and battery usage with minimal loss of estimation accuracy. We use a computationally efficient technique for estimating sparse graphical models which fits a sparse linear regression locally at each node of the graph via the Lasso estimator. Using a recently suggested online, temporally adaptive implementation of the Lasso, we propose an algorithm for streaming graphical model selection over sensor networks. With battery consumption minimization applications in mind, we use this algorithm as the basis of an adaptive querying scheme. We discuss implementation issues in the context of environmental monitoring using sensor networks, where the objective is short-term forecasting of local wind direction. The algorithm is tested against real UK weather data and conclusions are drawn about certain tradeoffs inherent in decentralized sensor networks data analysis. © 2010 The Author. Published by Oxford University Press on behalf of The British Computer Society. All rights reserved.

Simulating dynamic covariance structures for testing the adaptive behavior of variable selection algorithms (Invited Paper)

Variable selection for regression is a classical statistical problem, motivated by concerns that too large a number of covariates may bring about overfitting and unnecessarily high measurement costs. Novel difficulties arise in streaming contexts, where the correlation structure of the process may be drifting, in which case it must be constantly tracked so that selections may be revised accordingly. A particularly interesting phenomenon is that non-selected covariates become missing variables, inducing bias on subsequent decisions. This raises an intricate exploration-exploitation tradeoff, whose dependence on the covariance tracking algorithm and the choice of variable selection scheme is too complex to be dealt with analytically. We hence capitalise on the strength of simulations to explore this problem, taking the opportunity to tackle the difficult task of simulating dynamic correlation structures. © 2008 IEEE.

Temporally adaptive estimation of logistic classifiers on data streams

Modern technology has allowed real-time data collection in a variety of domains, ranging from environmental monitoring to healthcare. Consequently, there is a growing need for algorithms capable of performing inferential tasks in an online manner, continuously revising their estimates to reflect the current status of the underlying process. In particular, we are interested in constructing online and temporally adaptive classifiers capable of handling the possibly drifting decision boundaries arising in streaming environments. We first make a quadratic approximation to the log-likelihood that yields a recursive algorithm for fitting logistic regression online. We then suggest a novel way of equipping this framework with self-tuning forgetting factors. The resulting scheme is capable of tracking changes in the underlying probability distribution, adapting the decision boundary appropriately and hence maintaining high classification accuracy in dynamic or unstable environments. We demonstrate the scheme's effectiveness in both real and simulated streaming environments. © Springer-Verlag 2009.

Collective Cell Migration: Leadership, Invasion and Segregation

A number of biological processes, such as embryo development, cancer metastasis or wound healing, rely on cells moving in concert. The mechanisms leading to the emergence of coordinated motion remain however largely unexplored. Although biomolecular signalling is known to be involved in most occurrences of collective migration, the role of physical and mechanical interactions has only been recently investigated. In this paper, a versatile framework for cell motility is implemented in-silico in order to study the minimal requirements for the coordination of a group of epithelial cells. We find that cell motility and cell-cell mechanical interactions are sufficient to generate a broad array of behaviours commonly observed in vitro and in vivo. Cell streaming, sheet migration and susceptibility to leader cells are examples of behaviours spontaneously emerging from these simple assumptions, which might explain why collective effects are so ubiquitous in nature. This analysis provides also new insights into cancer metastasis and cell sorting, suggesting in particular that collective invasion might result from an emerging coordination in a system where single cells are mechanically unable to invade.

ZnO thin film surface acoustic wave based lab-on-a-chip

Lab-on-a-chip (LOC) is one of the most important microsystem applications with promise for use in microanalysis, drug development, diagnosis of illness and diseases etc. LOC typically consists of two main components: microfluidics and sensors. Integration of microfluidics and sensors on a single chip can greatly enhance the efficiency of biochemical reactions and the sensitivity of detection, increase the reaction/detection speed, and reduce the potential cross-contamination, fabrication time and cost etc. However, the mechanisms generally used for microfluidics and sensors are different, making the integration of the two main components complicated and increases the cost of the systems. A lab-on-a-chip system based on a single surface acoustic wave (SAW) actuation mechanism is proposed. SAW devices were fabricated on nanocrystalline ZnO thin films deposited on Si substrates using sputtering. Coupling of acoustic waves into a liquid induces acoustic streaming and motion of droplets. A streaming velocity up to ∼ 5cm/s and droplet pumping speeds of ∼lcm/s were obtained. It was also found that a higher order mode wave, the Sezawa wave is more effective in streaming and transportation of microdroplets. The ZnO SAW sensor has been used for prostate antigen/antibody biorecognition systems, demonstrated the feasibility of using a single actuation mechanism for lab-on-a-chip applications. © 2010 Materials Research Society.

Microfluidics based on ZnO/nanocrystalline diamond surface acoustic wave devices.

Surface acoustic wave (SAW) devices with 64 μm wavelength were fabricated on a zinc oxide (ZnO) film deposited on top of an ultra-smooth nanocrystalline diamond (UNCD) layer. The smooth surface of the UNCD film allowed the growth of the ZnO film with excellent c-axis orientation and low surface roughness, suitable for SAW fabrication, and could restrain the wave from significantly dissipating into the substrate. The frequency response of the fabricated devices was characterized and a Rayleigh mode was observed at ∼65.4 MHz. This mode was utilised to demonstrate that the ZnO/UNCD SAW device can be successfully used for microfluidic applications. Streaming, pumping, and jetting using microdroplets of 0.5 and 20 μl were achieved and characterized under different powers applied to the SAW device, focusing more on the jetting behaviors induced by the ZnO SAW.

Thylakoid terminal oxidases are essential for the cyanobacterium Synechocystis sp. PCC 6803 to survive rapidly changing light intensities.

Cyanobacteria perform photosynthesis and respiration in the thylakoid membrane, suggesting that the two processes are interlinked. However, the role of the respiratory electron transfer chain under natural environmental conditions has not been established. Through targeted gene disruption, mutants of Synechocystis sp. PCC 6803 were generated that lacked combinations of the three terminal oxidases: the thylakoid membrane-localized cytochrome c oxidase (COX) and quinol oxidase (Cyd) and the cytoplasmic membrane-localized alternative respiratory terminal oxidase. All strains demonstrated similar growth under continuous moderate or high light or 12-h moderate-light/dark square-wave cycles. However, under 12-h high-light/dark square-wave cycles, the COX/Cyd mutant displayed impaired growth and was completely photobleached after approximately 2 d. In contrast, use of sinusoidal light/dark cycles to simulate natural diurnal conditions resulted in little photobleaching, although growth was slower. Under high-light/dark square-wave cycles, the COX/Cyd mutant suffered a significant loss of photosynthetic efficiency during dark periods, a greater level of oxidative stress, and reduced glycogen degradation compared with the wild type. The mutant was susceptible to photoinhibition under pulsing but not constant light. These findings confirm a role for thylakoid-localized terminal oxidases in efficient dark respiration, reduction of oxidative stress, and accommodation of sudden light changes, demonstrating the strong selective pressure to maintain linked photosynthetic and respiratory electron chains within the thylakoid membrane. To our knowledge, this study is the first to report a phenotypic difference in growth between terminal oxidase mutants and wild-type cells and highlights the need to examine mutant phenotypes under a range of conditions.

Sensors based on SAW and FBAR technologies

Over the last few years a number of sensing platforms are being investigated for their use in drug development, microanalysis or medical diagnosis. Lab-on-a-chip (LOC) are devices integrating more than one laboratory functions on a single device chip of a very small size, and typically consist of two main components: microfluidic handling systems and sensors. The physical mechanisms that are generally used for microfluidics and sensors are different, hence making the integration of these components difficult and costly. In this work we present a lab-on-a-chip system based on surface acoustic waves (for fluid manipulation) and film bulk acoustic resonators (for sensing). Coupling surface acoustic waves into liquids induces acoustic streaming and motion of micro-droplets, whilst it is well-known that bulk acoustic waves can be used to fabricate microgravimetric sensors. Both technologies offer exceptional sensitivity and can be fabricated from piezoelectric thin films deposited on Si substrates, reducing the fabrication time/cost of the LOC devices. © 2013 SPIE.

Nonautonomous contact guidance signaling during collective cell migration.

Directed migration of groups of cells is a critical aspect of tissue morphogenesis that ensures proper tissue organization and, consequently, function. Cells moving in groups, unlike single cells, must coordinate their migratory behavior to maintain tissue integrity. During directed migration, cells are guided by a combination of mechanical and chemical cues presented by neighboring cells and the surrounding extracellular matrix. One important class of signals that guide cell migration includes topographic cues. Although the contact guidance response of individual cells to topographic cues has been extensively characterized, little is known about the response of groups of cells to topographic cues, the impact of such cues on cell-cell coordination within groups, and the transmission of nonautonomous contact guidance information between neighboring cells. Here, we explore these phenomena by quantifying the migratory response of confluent monolayers of epithelial and fibroblast cells to contact guidance cues provided by grooved topography. We show that, in both sparse clusters and confluent sheets, individual cells are contact-guided by grooves and show more coordinated behavior on grooved versus flat substrates. Furthermore, we demonstrate both in vitro and in silico that the guidance signal provided by a groove can propagate between neighboring cells in a confluent monolayer, and that the distance over which signal propagation occurs is not significantly influenced by the strength of cell-cell junctions but is an emergent property, similar to cellular streaming, triggered by mechanical exclusion interactions within the collective system.

Integrated ZnO surface acoustic wave microfluidic components for biosensor

This paper describes the novel nanocrystalline film ZnO surface acoustic wave devices, which demonstrate their great potential for the portable disease diagnostic system with integrated functions of microfluidic transport, mixing and biosensing. The devices can be easily integrated with electronic control circuitry and fabricated with low temperature process on Si, glass or even polymer substrates. The liquid convection and internal streaming patterns was easily induced by acoustic wave at signal voltages. With further increase in applied voltage to above 20V, the liquid droplet was pushed forward. Immunoreaction-based bio-detection PSA/ACT, all based on SAW devices on thin film piezoelectric ZnO on Si substrate was demonstrated. © 2009 CBMS.