What Google Maps can do for Biomedical Data Dissemination: Examples and a Design Study

Background: Biologists often need to assess whether unfamiliar datasets warrant the time investment required for more detailed exploration. Basing such assessments on brief descriptions provided by data publishers is unwieldy for large datasets that contain insights dependent on specific scientific questions. Alternatively, using complex software systems for a preliminary analysis may be deemed as too time consuming in itself, especially for unfamiliar data types and formats. This may lead to wasted analysis time and discarding of potentially useful data. Results: We present an exploration of design opportunities that the Google Maps interface offers to biomedical data visualization. In particular, we focus on synergies between visualization techniques and Google Maps that facilitate the development of biological visualizations which have both low-overhead and sufficient expressivity to support the exploration of data at multiple scales. The methods we explore rely on displaying pre-rendered visualizations of biological data in browsers, with sparse yet powerful interactions, by using the Google Maps API. We structure our discussion around five visualizations: a gene co-regulation visualization, a heatmap viewer, a genome browser, a protein interaction network, and a planar visualization of white matter in the brain. Feedback from collaborative work with domain experts suggests that our Google Maps visualizations offer multiple, scale-dependent perspectives and can be particularly helpful for unfamiliar datasets due to their accessibility. We also find that users, particularly those less experienced with computer use, are attracted by the familiarity of the Google Maps API. Our five implementations introduce design elements that can benefit visualization developers. Conclusions: We describe a low-overhead approach that lets biologists access readily analyzed views of unfamiliar scientific datasets. We rely on pre-computed visualizations prepared by data experts, accompanied by sparse and intuitive interactions, and distributed via the familiar Google Maps framework. Our contributions are an evaluation demonstrating the validity and opportunities of this approach, a set of design guidelines benefiting those wanting to create such visualizations, and five concrete example visualizations.

Reverse Engineering of Modified Genes by Bayesian Network Analysis Defines Molecular Determinants Critical to the Development of Glioblastoma

In this study we have identified key genes that are critical in development of astrocytic tumors. Meta-analysis of microarray studies which compared normal tissue to astrocytoma revealed a set of 646 differentially expressed genes in the majority of astrocytoma. Reverse engineering of these 646 genes using Bayesian network analysis produced a gene network for each grade of astrocytoma (Grade I–IV), and ‘key genes’ within each grade were identified. Genes found to be most influential to development of the highest grade of astrocytoma, Glioblastoma multiforme were: COL4A1, EGFR, BTF3, MPP2, RAB31, CDK4, CD99, ANXA2, TOP2A, and SERBP1. All of these genes were up-regulated, except MPP2 (down regulated). These 10 genes were able to predict tumor status with 96–100% confidence when using logistic regression, cross validation, and the support vector machine analysis. Markov genes interact with NFkβ, ERK, MAPK, VEGF, growth hormone and collagen to produce a network whose top biological functions are cancer, neurological disease, and cellular movement. Three of the 10 genes - EGFR, COL4A1, and CDK4, in particular, seemed to be potential ‘hubs of activity’. Modified expression of these 10 Markov Blanket genes increases lifetime risk of developing glioblastoma compared to the normal population. The glioblastoma risk estimates were dramatically increased with joint effects of 4 or more than 4 Markov Blanket genes. Joint interaction effects of 4, 5, 6, 7, 8, 9 or 10 Markov Blanket genes produced 9, 13, 20.9, 26.7, 52.8, 53.2, 78.1 or 85.9%, respectively, increase in lifetime risk of developing glioblastoma compared to normal population. In summary, it appears that modified expression of several ‘key genes’ may be required for the development of glioblastoma. Further studies are needed to validate these ‘key genes’ as useful tools for early detection and novel therapeutic options for these tumors.

Effect of Pavement-Vehicle Interaction on Highway Fuel Consumption and Emission

Vehicle fuel consumption and emission are two important effectiveness measurements of sustainable transportation development. Pavement plays an essential role in goals of fuel economy improvement and greenhouse gas (GHG) emission reduction. The main objective of this dissertation study is to experimentally investigate the effect of pavement-vehicle interaction (PVI) on vehicle fuel consumption under highway driving conditions. The goal is to provide a better understanding on the role of pavement in the green transportation initiates. Four study phases are carried out. The first phase involves a preliminary field investigation to detect the fuel consumption differences between paired flexible-rigid pavement sections with repeat measurements. The second phase continues the field investigation by a more detailed and comprehensive experimental design and independently investigates the effect of pavement type on vehicle fuel consumption. The third study phase calibrates the HDM-IV fuel consumption model with data collected in the second field phase. The purpose is to understand how pavement deflection affects vehicle fuel consumption from a mechanistic approach. The last phase applies the calibrated HDM-IV model to Florida’s interstate network and estimates the total annual fuel consumption and CO2 emissions on different scenarios. The potential annual fuel savings and emission reductions are derived based on the estimation results. Statistical results from the two field studies both show fuel savings on rigid pavement compared to flexible pavement with the test conditions specified. The savings derived from the first phase are 2.50% for the passenger car at 112km/h, and 4.04% for 18-wheel tractor-trailer at 93km/h. The savings resulted from the second phase are 2.25% and 2.22% for passenger car at 93km/h and 112km/h, and 3.57% and 3.15% for the 6-wheel medium-duty truck at 89km/h and 105km/h. All savings are statistically significant at 95% Confidence Level (C.L.). From the calibrated HDM-IV model, one unit of pavement deflection (1mm) on flexible pavement can cause an excess fuel consumption by 0.234-0.311 L/100km for the passenger car and by 1.123-1.277 L/100km for the truck. The effect is more evident at lower highway speed than at higher highway speed. From the network level estimation, approximately 40 million gallons of fuel (combined gasoline and diesel) and 0.39 million tons of CO2 emission can be saved/reduced annually if all Florida’s interstate flexible pavement are converted to rigid pavement with the same roughness levels. Moreover, each 1-mile of flexible-rigid conversion can result in a reduction of 29 thousand gallons of fuel and 258 tons of CO2 emission yearly.