First Responder Pathogen Detection System (FiRPaDS) Investigator: Bhaskar DasGupta, Computer Science, UIC with other investigators outside UIC Prime Grant Support: NSF CAREER IIS and DBI Problem Statement and Motivation Technical Approach Key Achievements and Future Goals Need to identify unknown virus sequences during events such as epidemic or biological warfare We only have a database of known virus sequences Few complications of the real-world problem: Sequence has mutated (possibly maliciously) Impossibility to obtain entire DNA sequence Sample may be contaminated and/or contains mixture of sequences. Rapid amplification of the collected genetic material, e.g., via degenerate oligonucleotide primer based multiplex PCR A pathogen fingerprinting and/or barcoding component built around universal DNA tag arrays Rapid and robust computational procedures to compute barcodes that produces short signatures of sequences Two possible approaches to design FiRPaDS: Target based FiRPaDS Primer based FiRPaDS Developed efficient barcoding algorithms using combinatorial techniques Software available from Will extend barcoding approaches for more complicated scenarios such as mixture of samples Will generate an efficient solution for a combinatorial or graph-theoretic formulation for the degenerate multiplexed PCR minimization problem Will investigate applications of universal DNA tag arrays for helpful coordination with barcoding or fingerprinting steps

Virtual Reality and Robots in Stroke Recovery Investigators: Robert V. Kenyon, Computer Science; James L. Patton, RIC Prime Grant Support: NIH, NIDRRMission: To evaluate the utility of simple robotic devices for providing rehabilitation therapy after hemispheric stroke. The integration of virtual reality and robot technology increases flexibility in training for patients recovering from stroke. Promoting innovative techniques to train the nervous system for the recovery of functional movement. Technical Approach: Key Achievements and Future Goals: Personal Augmented Reality Immersive System (PARIS): Virtual and physical objects seen by user. Robotic systems: PHANToM, Haptic Master, WAM: These back-drivable robots provide force to the subject only when commanded to do so. Software integration: Real-time interactivity requires rapid communication between the different components of the rehabilitation system and must contain consistent representations of what the user should feel and see. The robot’s control must quickly communicate with the display control so that graphics are synchronized with the robot’s state. This system provides a platform for exploring how the nervous system controls movements, teaches new movements, explores novel strategies for training and rehabilitation, assesses and tracks functional recovery, and tests and challenges existing theories of rehabilitation. Such a system will determine the necessary levels of quality for future design cycles and related technology. Future designs will lead the way to new modes of clinical practice and to the commercialization of such systems. PROJECT: Development Of A Robotic System With An Augmented Reality Interface For Rehabilitation Of Brain Injured Individuals

Computational Tools for Population Biology Tanya Berger-Wolf, Computer Science, UIC; Daniel Rubenstein, Ecology and Evolutionary Biology, Princeton; Jared Saia, Computer Science, U New Mexico Supported by NSF Technical Approach Collect explicitly dynamic social data: sensor collars on animals, disease logs, synthetic population simulations, cellphone and communications Represent a time series of observation snapshots as a layered graph. Questions about persistence and strength of social connections and about criticality of individuals and times can be answered using standard and novel graph connectivity algorithms Validate theoretical predictions derived from the abstract graph representation by simulations on collected data and controlled experiments on real populations Key Achievements and Future Goals A formal computational framework for analysis of dynamic social interactions Valid and tested computational criteria for identifying Individuals critical for spreading processes in a population Times of social and behavioral transition Implicit communities of individuals Preliminary results on Grevy’s zebra and wild donkeys data show that addressing dynamics of the population produces more accurate conclusions Extend and test our framework and computational tools to other problems and other data Problem Statement and Motivation Of the three existing species of zebra, one, the Grevy's zebra, is endangered while another, the plains zebra, is extremely abundant. The two species are similar in almost all but one key characteristic: their social organization. Finding patterns of social interaction within a population has applications from epidemiology and marketing to conservation biology and behavioral ecology. One of the intrinsic characteristics of societies is their continual change. Yet, there are few analysis methods that are explicitly dynamic. Our goal is to develop a novel conceptual and computational framework to accurately describe the social context of an individual at time scales matching changes in individual and group activity. Zebra with a sensor collar A snapshot of zebra population and the corresponding abstract representation

Signal Transduction Network Inference from Experimental Evidence Investigators: Bhaskar DasGupta, CS, UIC with other researchers outside UIC Primary Grant Support: NSF CAREER IIS Problem Statement and Motivation Technical Approach Key Achievements and Future Goals Understanding of many signaling processes is limited to the knowledge of the signal(s) and of key mediators' positive or negative effects on the whole process. Need methods for synthesizing indirect information into a consistent network that maintains all observed causal relationships. distill experimental conclusions into qualitative regulatory relations between cellular components of the type “A promotes (inhibits) B”, or “C promotes (inhibits) the process through which A promotes (inhibits) B”. direct biochemical interactions are marked as such. assume that a three-node indirect inference corresponds to an intersection of two paths (A  B and C  B) in the interaction network, i. e., we assume that C activates an unknown pseudo-vertex of the AB path. Using techniques from combinatorial optimization we find the sparsest graph, both in terms of pseudo vertex numbers and non-critical edge numbers, that is consistent with all reachability relationships between real vertices. developed efficient algorithms for the entire network synthesis procedure. validated the procedure by applying it to experimental results for abscisic acid-induced stomatal closure and comparing the results with the manually curated network. our graph sparsification procedure returns solutions close to optimal for randomly generated networks with a structure similar to those observed in transcriptional regulatory and signal transduction networks. An implementation of the graph synthesis procedure is available from synthesis/

A Test of the Leibowitz Hypothesis J. E. Barton 1, R.V. Kenyon 2, T.E. Cohn 1 1 University of California, 2 University of Illinois at Chicago Technical Approach Key Achievements Our experiment used a 3D Virtual Environment to display different sized textured spheres approaching an observer at different speeds. Our experiments show that speed perception is a function of object size, as hypothesized by Leibowitz. We hypothesize that subjects inaccurately estimated the large sphere’s size and distance as smaller and closer, but use the actual expansion rate information for this sphere. This lead them to incorrectly estimate the sphere’s approach speed as slower than it really is and maybe at important factor in collisions between small and large vehicles. Why do some people deliberately drive through railroad crossings and into the path of oncoming trains, even when warning signals are flashing? Are they seeking the ultimate thrill or is there something amiss in their judgment about the danger of crossing? Leibowitz observed that landing jumbo jets appeared to move more slowly than smaller counterparts, even though the former were traveling much faster. He speculated that this might be a contributing factor in railroad crossing accidents, and hypothesized that this misperception was the result of the way in which the visual system interprets the cues at hand. Proportion of times subjects perceived the smaller sphere to be approaching faster (P 5 ). Except for large sphere speeds of 10 and 15 m/sec where the smaller sphere was greater than then equal to the large sphere speed, respectively, the smaller sphere was always slower than the larger sphere, as the Correct response [red filled circles and dotted line] indicates. Thick dashed line shows chance level of response. Asterisks indicate response significantly less than the proportion for the next lower speed.