Proceedings of 2012 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB) on 9-12 May 2012 in San Diego, CA, USA. We use in silico evolution to study the generation of gene regulatory structures. A particular area of interest in evolutionary development (evo-devo) is the correspondence between gene regulatory sequences on the DNA (cis-regulatory modules, CRMs) and the spatial expression of the genes. We use computation to investigate the incorporation of new CRMs into the genome. Simulations allow us to characterize different cases of CRM to spatial pattern correspondence. Many of these cases are seen in biological examples; our simulations indicate relative advantages of the different scenarios. We find that, in the absence of specific constraints on the CRM-pattern correspondence, CRMs controlling multiple spatial domains tend to evolve very quickly. Genes constrained to a one-to-one CRM-pattern domain correspondence evolve more slowly. Of these, systems in which pattern domains appear in a particular order in evolution, as in insect segmentation mechanisms, take the longest time in in silico evolutionary searches. For biological cases of this type, it is likely that other selective advantages outweigh the time costs., Conference paper, Published.
The co-evolution of species with their genomic parasites (transposons) is thought to be one of the primary ways of rewiring gene regulatory networks (GRNs). We develop a framework for conducting evolutionary computations (EC) using the transposon mechanism. We find that the selective pressure of transposons can speed evolutionary searches for solutions and lead to outgrowth of GRNs (through co-option of new genes to acquire insensitivity to the attacking transposons). We test the approach by finding GRNs which can solve a fundamental problem in developmental biology: how GRNs in early embryo development can robustly read maternal signaling gradients, despite continued attacks on the genome by transposons. We observed co-evolutionary oscillations in the abundance of particular GRNs and their transposons, reminiscent of predator-prey or host-parasite dynamics., Peer-reviewed article, Published.
Understanding how genetic networks act in embryonic development requires a detailed and statistically significant dataset integrating diverse observational results. The fruit fly (Drosophila melanogaster) is used as a model organism for studying developmental genetics. In recent years, several laboratories have systematically gathered confocal microscopy images of patterns of activity (expression) for genes governing early Drosophila development. Due to both the high variability between fruit fly embryos and diverse sources of observational errors, some new nontrivial procedures for processing and integrating the raw observations are required. Here we describe processing techniques based on genetic algorithms and discuss their efficacy in decreasing observational errors and illuminating the natural variability in gene expression patterns. The specific developmental problem studied is anteroposterior specification of the body plan., Peer-reviewed article, Published.
Proceedings of 8th IAPR International Conference, PRIB 2013, Nice, France, June 17-20, 2013. Early fruit fly embryo development begins with the formation of a chemical blueprint that guides cellular movements and the development of organs and tissues. This blueprint sets the intrinsic spatial coordinates of the embryo. The coordinates are curvilinear from the start, becoming more curvilinear as cells start coherent movements several hours into development. This dynamic aspect of the curvature is an important characteristic of early embryogenesis: characterizing it is crucial for quantitative analysis and dynamic modeling of development. This presents a number of methodological problems for the elastic deformation of 3D and 4D data from confocal microscopy, to standardize images and follow temporal changes. The parameter searches for these deformations present hard optimization problems. Here we describe our evolutionary computation approaches to these problems. We outline some of the immediate applications of these techniques to crucial problems in Drosophila developmental biology., Conference paper, Published.
Precipitation is one of the most common moisture sources on which building designers focus. Water comes from both top down and bottom up. Although foundations are sometimes constructed out of pressure-treated lumber, generally they are constructed from poured concrete. In a wet climate zone, the foundation of a house is often under continuous contact with moisture, which is mainly caused by rundown rainwater, wet soil, a high water table, or a combination of all these factors. This causes rot growth and decay of the wood-frame structure as it sits constantly on the damp foundation concrete. In this research, moisture transfer between concrete and wood is investigated under three different scenarios: a case with direct wood and concrete contact and two cases with different moisture barriers between the two materials. The moisture barrier materials considered in this study are the damp-proofing layer and sill plate gasket. The moisture transfer processes in these three cases are investigated in a field experimental setting using a customized experimental setup for 1 year. The experimental data suggest that using damp proofing and a sill gasket helps restrict moisture transfer., Peer reviewed article, Published. Received: May 29, 2015; Accepted: December 09, 2015; Published online: February 24, 2016.
An experimental investigation of the sound absorption characteristics of vegetated roof substrates and plots has been completed. First, an impedance tube was used to measure the normal-incidence absorption coefficients of substrates and their constituents. Substrates provided significant sound absorption, with coefficients varying from 0.03 at 250 Hz to 0.89 at 2000 Hz. Absorption increased with the percentage of organic matter and decreased with moisture content and compaction. A multi-variable regression model was developed for predicting the absorption of substrates. Secondly, the sound absorption of vegetated roof plots was investigated using the spherical-decoupling method. An optimal method, validated in an anechoic chamber, was used to determine the diffuse-field absorption coefficients of unplanted and planted rooftop test plots. Sound absorption increased with increased substrate depth (without vegetation) and decreased with the addition of vegetation and plant establishment. The mean noise reduction coefficient of established vegetated roof plots, with distinctly different plant communities in substrate depths of 50–200 mm, ranged from 0.20 to 0.63 when evaluated over a two-year period. The results confirm that the sound absorption of vegetated roofs is a function of substrate depth, plant community establishment, and moisture content in the plants and substrate., Peer-reviewed article, Published. Received 4 March 2015, Revised 22 April 2015, Accepted 23 April 2015, Available online 1 May 2015.
This paper aims to study the effects of wind-driven rain load and vapor diffusion on the hygrothermal performance of wall systems in a wet and mild climate through a field experimental study. In the study, four test panels with a combination of vapor barrier and capillary break are manufactured, instrumented and installed in a field experimental facility. The wetting and drying potentials of the test panels in response to a predominately vapor diffusion and a wind-driven rain load are discussed based on the analysis of 15 months of measurement data. The experimental result shows that, in a yearly basis, the wetting and drying rates of a wall without a capillary break are about two times higher than that of the wall with a capillary break. While the wetting and drying rates are comparable in a wall system with a vapor barrier, the drying rate is 38% higher than the wetting rate in a wall with no vapor barrier. In general, a wall with no vapor barrier wets and also dries faster than a wall with a vapor barrier. For the wall types and climate considered in this paper, the wetting rates of walls with a predominately wetting mechanism of vapor diffusion and wind-drive rain load are comparable. In general, the experimental data suggest that even in a mild climate, vapor diffusion is a critical moisture load with comparable effect that wind-driven load induces., Peer-reviewed article, Published. Received 14 February 2015, Revised 10 May 2015, Accepted 11 May 2015, Available online 19 May 2015.
Recently, the amount of dredged soil material (DM) has been rapidly increasing in Korea due to four major river maintenance projects and new harbor construction. DM waste is mostly dumped into the ocean, while only a small part of it has been utilized for coastal reclaiming, or as filling and backfilling material. This study carried out physical and chemical tests to map out a specific plan for utilizing DM in a mortar mixture. The compressive strength tests and microstructure analysis using XRD and SEM of cement mortar contained DM were performed as a replacement for fine aggregate or as a filler material of mortar matrix. The study measured the impact of contaminants contained in DM and how silt and clay influenced the compressive strength of the mortar., Peer-reviewed article, Published. Received April 7th, 2011; revised May 16th, 2011; accepted June 1st, 2011.
Proceedings of the 8th International Symposium on Logical Formalizations of Commonsense Reasoning. Stanford, CA, 2007. Cryptographic protocols are structured sequences of messages that are used for exchanging information in a hostile environment. Many protocols have epistemic goals: a successful run of the protocol is intended to cause a participant to hold certain beliefs. As such, epistemic logics have been employed for the verification of cryptographic protocols. Although this approach to verification is explicitly concerned with changing beliefs, formal belief change operators have not been incorporated in previous work. In this preliminary paper, we introduce a new approach to protocol verification by combining a monotonic logic with a non-monotonic belief change operator. In this context, a protocol participant is able to retract beliefs in response to new information and a protocol participant is able to postulate the most plausible event explaining new information. Hence, protocol participants may draw conclusions from received messages in the same manner conclusions are drawn in formalizations of commonsense reasoning. We illustrate that this kind of reasoning is particularly important when protocol participants have incorrect beliefs., Conference paper, Published.
Proceedings of 2016 14th Annual Conference on Privacy, Security and Trust (PST) in Auckland, New Zealand, 12-14 Dec. 2016. We address security vulnerabilities for a smart thermostat. As this kind of smart appliance is adopted in homes around the world, every user will be opening up a new avenue for cyber attack. Since these devices have known vulnerabilities and they are being managed by non-technical users, we anticipate that smart thermostats are likely to be targetted by unsophisticated attackers relying on publicly available exploits to take advantage of weakly protected devices. As such, in this paper, we take the role of a `script kiddy' and we assess the security of a smart thermostat by using Internet resources for attacks at both the physical level and the network level. We demonstrate that such attacks are unlikely to be effective without some additional social engineering to obtain user credentials. Moreover, we suggest that the vulnerability to attack can be further minimized by simply reducing the use of remote storage where possible., Conference paper
Proceedings of the AAAI Workshop on Artificial Intelligence for Cities, Austin, USA, 2015. The Smart Grid allows users to monitor power usage through the use of Smart Meter technology. In principle, this information can be used to modify usage habits in a way that reduces consumer costs as well as greenhouse emissions. However, in an urban environment, many users are restricted by the same constaints: they work during the day, and they are home at night. This creates spikes in power cost at peak usage times, and it may also lead to increased emissions in scenarios where sustainable resources are limited. An individual user can avoid these spikes by using an electric car as a storage device; it can be charged at the cheapest times, and then discharged to the home at the most expensive times. While this idea is intuitively appealing, it turns out that the benefits vary greatly depending on the storage algorithm used. In this paper, we describe the Power Storage Simulator, a tool for experimenting with storage algorithms to improve the efficiency of vehicle to grid systems. We suggest that this tool is also useful for educating power consumers about load balancing on the Smart Grid through an engaging, visual simulation., Conference paper, Published.
Background Previous evidence suggests the effects of task-specific therapy can be further enhanced when sensory stimulation is combined with motor practice. Sensory tongue stimulation is thought to facilitate activation of regions in the brain that are important for balance and gait. Improvements in balance and gait have significant implications for functional mobility for people with incomplete spinal cord injury (iSCI). The aim of this case study was to evaluate the feasibility of a lab- and home-based program combining sensory tongue stimulation with balance and gait training on functional outcomes in people with iSCI. Methods Two male participants (S1 and S2) with chronic motor iSCI completed 12 weeks of balance and gait training (3 lab and 2 home based sessions per week) combined with sensory tongue stimulation using the Portable Neuromodulation Stimulator (PoNS). Laboratory based training involved 20 minutes of standing balance with eyes closed and 30 minutes of body-weight support treadmill walking. Home based sessions consisted of balancing with eyes open and walking with parallel bars or a walker for up to 20 minutes each. Subjects continued daily at-home training for an additional 12 weeks as follow-up. Results Both subjects were able to complete a minimum of 83% of the training sessions. Standing balance with eyes closed increased from 0.2 to 4.0 minutes and 0.0 to 0.2 minutes for S1 and S2, respectively. Balance confidence also improved at follow-up after the home-based program. Over ground walking speed improved by 0.14 m/s for S1 and 0.07 m/s for S2, and skilled walking function improved by 60% and 21% for S1 and S2, respectively. Conclusions Sensory tongue stimulation combined with task-specific training may be a feasible method for improving balance and gait in people with iSCI. Our findings warrant further controlled studies to determine the added benefits of sensory tongue stimulation to rehabilitation training., Peer-reviewed article, Published. Received: 10 July 2013 ; Accepted: 2 June 2014 ; Published: 6 June 2014.