Qualitative reasoning of dynamic gene regulatory interactions from gene expression data

<p>Abstract</p> <p>Background</p> <p>A gene regulatory relation often changes over time rather than being constant. But many gene regulatory networks available in databases or literatures are static in the sense that they are either snapshots of gene regulatory relations at a time point or union of successive gene regulations over time. Such static networks cannot represent temporal aspects of gene regulatory interactions such as the order of gene regulations or the pace of gene regulations.</p> <p>Results</p> <p>We developed a new qualitative method for representing dynamic gene regulatory relations and algorithms for identifying dynamic gene regulations from the time-series gene expression data using two types of scores. The identified gene regulatory interactions and their temporal properties are visualized as a gene regulatory network. All the algorithms have been implemented in a program called GeneNetFinder (<url>http://wilab.inha.ac.kr/genenetfinder/</url>) and tested on several gene expression data.</p> <p>Conclusions</p> <p>The dynamic nature of dynamic gene regulatory interactions can be inferred and represented qualitatively without deriving a set of differential equations describing the interactions. The approach and the program developed in our study would be useful for identifying dynamic gene regulatory interactions from the large amount of gene expression data available and for analyzing the interactions.</p

Field implementation feasibility study of cumulative travel-time responsive (CTR) traffic signal control algorithm

The cumulative travel-time responsive (CTR) algorithm determines optimal green split for the next time interval by identifying the maximum cumulative travel time (CTT) estimated under the connected vehicle environment. This paper enhanced the CTR algorithm and evaluated its performance to verify a feasibility of field implementation in a near future. Standard Kalman filter (SKF) and adaptive Kalman filter (AKF) were applied to estimate CTT for each phase in the CTR algorithm. In addition, traffic demand, market penetration rate (MPR), and data availability were considered to evaluate the CTR algorithm&apos;s performance. An intersection in the Northern Virginia connected vehicle test bed is selected for a case study and evaluated within vissim and hardware in the loop simulations. As expected, the CTR algorithm&apos;s performance depends on MPR because the information collected from connected vehicle is a key enabling factor of the CTR algorithm. However, this paper found that the MPR requirement of the CTR algorithm could be addressed (i) when the data are collected from both connected vehicle and the infrastructure sensors and (ii) when the AKF is adopted. The minimum required MPRs to outperform the actuated traffic signal control were empirically found for each prediction technique (i.e., 30% for the SKF and 20% for the AKF) and data availability. Even without the infrastructure sensors, the CTR algorithm could be implemented at an intersection with high traffic demand and 50-60% MPR. The findings of this study are expected to contribute to the field implementation of the CTR algorithm to improve the traffic network performance. © 2017 John Wiley &amp; Sons, Ltd.1

An ontology-based search engine for protein-protein interactions

<p>Abstract</p> <p>Background</p> <p>Keyword matching or ID matching is the most common searching method in a large database of protein-protein interactions. They are purely syntactic methods, and retrieve the records in the database that contain a keyword or ID specified in a query. Such syntactic search methods often retrieve too few search results or no results despite many potential matches present in the database.</p> <p>Results</p> <p>We have developed a new method for representing protein-protein interactions and the Gene Ontology (GO) using modified Gödel numbers. This representation is hidden from users but enables a search engine using the representation to efficiently search protein-protein interactions in a biologically meaningful way. Given a query protein with optional search conditions expressed in one or more GO terms, the search engine finds all the interaction partners of the query protein by unique prime factorization of the modified Gödel numbers representing the query protein and the search conditions.</p> <p>Conclusion</p> <p>Representing the biological relations of proteins and their GO annotations by modified Gödel numbers makes a search engine efficiently find all protein-protein interactions by prime factorization of the numbers. Keyword matching or ID matching search methods often miss the interactions involving a protein that has no explicit annotations matching the search condition, but our search engine retrieves such interactions as well if they satisfy the search condition with a more specific term in the ontology.</p

On The Method Of Stationary Phase

The method of stationary phase (MSP), which is an asymptotic method of integration, nevertheless yields general (nonasymptotic) results when applied to certain integrals involving the spherical function. In such cases one may drop the requirement of far-field or high frequency from the results. Copyright © 1973 by The Institute of Electrical and Electronics Engineers. Inc

Comparative Analysis of Gene Correlation Networks of Breast Cancer Patients Based on Mutations in TP53

Breast cancer is one of the most prevalent cancers in females, with more than 450,000 deaths each year worldwide. Among the subtypes of breast cancer, basal-like breast cancer, also known as triple-negative breast cancer, shows the lowest survival rate and does not have effective treatments yet. Somatic mutations in the TP53 gene frequently occur across all breast cancer subtypes, but comparative analysis of gene correlations with respect to mutations in TP53 has not been done so far. The primary goal of this study is to identify gene correlations in two groups of breast cancer patients and to derive potential prognostic gene pairs for breast cancer. We partitioned breast cancer patients into two groups: one group with a mutated TP53 gene (mTP53) and the other with a wild-type TP53 gene (wtTP53). For every gene pair, we computed the hazard ratio using the Cox proportional hazard model and constructed gene correlation networks (GCNs) enriched with prognostic information. Our GCN is more informative than typical GCNs in the sense that it indicates the type of correlation between genes, the concordance index, and the prognostic type of a gene. Comparative analysis of correlation patterns and survival time of the two groups revealed several interesting findings. First, we found several new gene pairs with opposite correlations in the two GCNs and the difference in their correlation patterns was the most prominent in the basal-like subtype of breast cancer. Second, we obtained potential prognostic genes for breast cancer patients with a wild-type TP53 gene. From a comparative analysis of GCNs of mTP53 and wtTP53, we found several gene pairs that show significantly different correlation patterns in the basal-like breast cancer subtype and obtained prognostic genes for patients with a wild-type TP53 gene. The GCNs and prognostic genes identified in this study will be informative for the prognosis of survival and for selecting a drug target for breast cancer, in particular for basal-like breast cancer. To the best of our knowledge, this is the first attempt to construct GCNs for breast cancer patients with or without mutations in the TP53 gene and to find prognostic genes accordingly

Comparative evaluation of fuel consumption estimation models

Increased fossil fuel consumptions present a huge environmental challenge to the world. In order to meet the consumers&apos; demands for transportation and at the same time to provide more fuel efficient vehicles, scientists are constantly searching for effective emissions and fuel consumption estimation models to protect the environment, especially to design more efficient control algorithms at traffic signalized intersections (e.g., eco-adaptive control) and promote environmentally friendly driving behaviors (e.g., eco-driving). The purpose of this research was to assess three existing fuel consumption estimation models using actual fuel consumption rates based on field measurements. The three models are the Virginia Tech Microscopic Energy and Emissions Model (VT-Micro), the Comprehensive Modal Emission Model (CMEM) and the Motor Vehicle Emission Simulator (MOVES) Model, and the field measured fuel consumptions are from instantaneous light duty vehicle (LDV) fuel consumption (FC) rate data collected by the Daegu Gyeongbuk Institute of Science and Technology of Korea (DGIST). Both the VT-Micro and the CMEM explained DGIST data reasonably well. All three models adequately tracked DGIST total fuel consumption over a fixed time interval