Candidate metastasis suppressor genes uncovered by array comparative genomic hybridization in a mouse allograft model of prostate cancer.

Background The purpose of this study was to identify candidate metastasis suppressor genes from a mouse allograft model of prostate cancer (NE-10). This allograft model originally developed metastases by twelve weeks after implantation in male athymic nude mice, but lost the ability to metastasize after a number of in vivo passages. We performed high resolution array comparative genomic hybridization on the metastasizing and non-metastasizing allografts to identify chromosome imbalances that differed between the two groups of tumors. Results This analysis uncovered a deletion on chromosome 2 that differed between the metastasizing and non-metastasizing tumors. Bioinformatics filters were employed to mine this region of the genome for candidate metastasis suppressor genes. Of the 146 known genes that reside within the region of interest on mouse chromosome 2, four candidate metastasis suppressor genes (Slc27a2, Mall, Snrpb, and Rassf2) were identified. Quantitative expression analysis confirmed decreased expression of these genes in the metastasizing compared to non-metastasizing tumors. Conclusion This study presents combined genomics and bioinformatics approaches for identifying potential metastasis suppressor genes. The genes identified here are candidates for further studies to determine their functional role in inhibiting metastases in the NE-10 allograft model and human prostate cancer.

Performance evaluation of an adaptive travel time prediction model

This paper presents a travel time prediction model and evaluates its performance and transferability. Advanced Travelers Information Systems (ATIS) are gaining more and more importance, increasing the need for accurate, timely and useful information to the travelers. Travel time information quantifies the traffic condition in an easy to understand way for the users. The proposed travel time prediction model is based on an efficient use of nearest neighbor search. The model is calibrated for optimal performance using Genetic Algorithms. Results indicate better performance by using the proposed model than the presently used naïve model.

Cluster-based network model for time-course gene expression data

We propose a model-based approach to unify clustering and network modeling using time-course gene expression data. Specifically, our approach uses a mixture model to cluster genes. Genes within the same cluster share a similar expression profile. The network is built over cluster-specific expression profiles using state-space models. We discuss the application of our model to simulated data as well as to time-course gene expression data arising from animal models on prostate cancer progression. The latter application shows that with a combined statistical/bioinformatics analyses, we are able to extract gene-to-gene relationships supported by the literature as well as new plausible relationships.

Integration of a road traffic noise model (ASJ) and traffic simulation (AVENUE) for a built-up area

A road traffic noise prediction model (ASJ MODEL-1998) has been integrated with a road traffic simulator (AVENUE) to produce the Dynamic areawide Road traffic NoisE simulator-DRONE. This traffic-noise-GIS based integrated tool is upgraded to predict noise levels in built-up areas. The integration of traffic simulation with a noise model provides dynamic access to traffic flow characteristics and hence automated and detailed predictions of traffic noise. The prediction is not only on the spatial scale but also on temporal scale. The linkage with GIS gives a visual representation to noise pollution in the form of dynamic areawide traffic noise contour maps. The application of DRONE on a real world built-up area is also presented.

Tactical driver lane change model using forward search

This paper describes the development and evaluation of a tactical lane change model using the forward search algorithm, for use in a traffic simulator. The tactical lane change model constructs a set of possible choices of near-term maneuver sequences available to the driver and selects the lane change action at the present time to realize the best maneuver plan. Including near term maneuver planning in the driver behavior model can allow a better representation of the complex interactions in situations such as a weaving section and high-occupancy vehicle (HOV) lane systems where drivers must weave across several lanes in order to access the HOV lanes. To support the investigation, a longitudinal control model and a basic lane change model were also analyzed. The basic lane change model is similar to those used by today's commonly-used traffic simulators. Parameters in all models were best-fit estimated for selected vehicles from a real-world freeway vehicle trajectory data set. The best-fit estimation procedure minimizes the discrepancy between the model vehicle and real vehicle's trajectories. With the best fit parameters, the proposed tactical lane change model gave a better overall performance for a greater number of cases than the basic lane change model.

RatSLAM : a hippocampal model for simultaneous localization and mapping

The work presents a new approach to the problem of simultaneous localization and mapping - SLAM - inspired by computational models of the hippocampus of rodents. The rodent hippocampus has been extensively studied with respect to navigation tasks, and displays many of the properties of a desirable SLAM solution. RatSLAM is an implementation of a hippocampal model that can perform SLAM in real time on a real robot. It uses a competitive attractor network to integrate odometric information with landmark sensing to form a consistent representation of the environment. Experimental results show that RatSLAM can operate with ambiguous landmark information and recover from both minor and major path integration errors.

Empirical investigation of interactive highway safety design model accident prediction algorithm : Rural intersections

One major gap in transportation system safety management is the ability to assess the safety ramifications of design changes for both new road projects and modifications to existing roads. To fulfill this need, FHWA and its many partners are developing a safety forecasting tool, the Interactive Highway Safety Design Model (IHSDM). The tool will be used by roadway design engineers, safety analysts, and planners throughout the United States. As such, the statistical models embedded in IHSDM will need to be able to forecast safety impacts under a wide range of roadway configurations and environmental conditions for a wide range of driver populations and will need to be able to capture elements of driving risk across states. One of the IHSDM algorithms developed by FHWA and its contractors is for forecasting accidents on rural road segments and rural intersections. The methodological approach is to use predictive models for specific base conditions, with traffic volume information as the sole explanatory variable for crashes, and then to apply regional or state calibration factors and accident modification factors (AMFs) to estimate the impact on accidents of geometric characteristics that differ from the base model conditions. In the majority of past approaches, AMFs are derived from parameter estimates associated with the explanatory variables. A recent study for FHWA used a multistate database to examine in detail the use of the algorithm with the base model-AMF approach and explored alternative base model forms as well as the use of full models that included nontraffic-related variables and other approaches to estimate AMFs. That research effort is reported. The results support the IHSDM methodology.

Interactions between human osteoblasts and prostate cancer cells in a novel 3D in vitro model

Cell-cell and cell-matrix interactions play a major role in tumor morphogenesis and cancer metastasis. Therefore, it is crucial to create a model with a biomimetic microenvironment that allows such interactions to fully represent the pathophysiology of a disease for an in vitro study. This is achievable by using three-dimensional (3D) models instead of conventional two-dimensional (2D) cultures with the aid of tissue engineering technology. We are now able to better address the complex intercellular interactions underlying prostate cancer (CaP) bone metastasis through such models. In this study, we assessed the interaction of CaP cells and human osteoblasts (hOBs) within a tissue engineered bone (TEB) construct. Consistent with other in vivo studies, our findings show that intercellular and CaP cell-bone matrix interactions lead to elevated levels of matrix metalloproteinases, steroidogenic enzymes and the CaP biomarker, prostate specific antigen (PSA); all associated with CaP metastasis. Hence, it highlights the physiological relevance of this model. We believe that this model will provide new insights for understanding of the previously poorly understood molecular mechanisms of bone metastasis, which will foster further translational studies, and ultimately offer a potential tool for drug screening. © 2010 Landes Bioscience.