TIME-BASED FORM TRANSFORMATION WITH FOLDING SPACE

Design activity could be treated as state transition computationally. In stepwise processing, in-between form-states are not easily observed. However, in this research time-based concept is introduced and applied in order to bridge the gap. In architecture, folding is one method of form manipulation and architects also want to search for alternatives by this operation. Besides, folding operation has to be defined and parameterized before time factor is involved as a variable of folding. As a result, time-based transformation provides sequential form states and redirects design activity

A neural network-based approach in predicting consumers' intentions of purchasing insurance policies

Insurance is a crucial mechanism used to lighten the financial burden as it provides protection against financial losses resulting from unexpected events. Insurers adopt various approaches, such as machine learning, to attract the uninsured. By using machine learning, a company is able to tap into the wealth of information of its potential customers. The main objective of this study is to apply artificial neural networks (ANNs) to predict the propensity of consumers to purchase an insurance policy by using the dataset from the Computational Intelligence and Learning (CoIL) Challenge 2000. In addition, this study also aims to identify factors that affect the propensity of customers to purchase insurance policies via feature selection. The dataset is pre-processed with feature construction and three feature selection methods, which are the neighbourhood component analysis (NCA), sequential forward selection (SFS) and sequential backward selection (SBS). Sampling techniques are carried out to address the issue of imbalanced class distributions. The results obtained are found to be comparable with the top few entries of the CoIL Challenge 2000, which shows the efficiency of the proposed model in predicting consumers’ intention of purchasing insurance policies

Prediction of B-cell Linear Epitopes with a Combination of Support Vector Machine Classification and Amino Acid Propensity Identification

Epitopes are antigenic determinants that are useful because they induce B-cell antibody production and stimulate T-cell activation. Bioinformatics can enable rapid, efficient prediction of potential epitopes. Here, we designed a novel B-cell linear epitope prediction system called LEPS, Linear Epitope Prediction by Propensities and Support Vector Machine, that combined physico-chemical propensity identification and support vector machine (SVM) classification. We tested the LEPS on four datasets: AntiJen, HIV, a newly generated PC, and AHP, a combination of these three datasets. Peptides with globally or locally high physicochemical propensities were first identified as primitive linear epitope (LE) candidates. Then, candidates were classified with the SVM based on the unique features of amino acid segments. This reduced the number of predicted epitopes and enhanced the positive prediction value (PPV). Compared to four other well-known LE prediction systems, the LEPS achieved the highest accuracy (72.52%), specificity (84.22%), PPV (32.07%), and Matthews' correlation coefficient (10.36%)

Protein-ligand binding region prediction (PLB-SAVE) based on geometric features and CUDA acceleration

[[abstract]]Background Protein-ligand interactions are key processes in triggering and controlling biological functions within cells. Prediction of protein binding regions on the protein surface assists in understanding the mechanisms and principles of molecular recognition. In silico geometrical shape analysis plays a primary step in analyzing the spatial characteristics of protein binding regions and facilitates applications of bioinformatics in drug discovery and design. Here, we describe the novel software, PLB-SAVE, which uses parallel processing technology and is ideally suited to extract the geometrical construct of solid angles from surface atoms. Representative clusters and corresponding anchors were identified from all surface elements and were assigned according to the ranking of their solid angles. In addition, cavity depth indicators were obtained by proportional transformation of solid angles and cavity volumes were calculated by scanning multiple directional vectors within each selected cavity. Both depth and volume characteristics were combined with various weighting coefficients to rank predicted potential binding regions. Results Two test datasets from LigASite, each containing 388 bound and unbound structures, were used to predict binding regions using PLB-SAVE and two well-known prediction systems, SiteHound and MetaPocket2.0 (MPK2). PLB-SAVE outperformed the other programs with accuracy rates of 94.3% for unbound proteins and 95.5% for bound proteins via a tenfold cross-validation process. Additionally, because the parallel processing architecture was designed to enhance the computational efficiency, we obtained an average of 160-fold increase in computational time. Conclusions In silico binding region prediction is considered the initial stage in structure-based drug design. To improve the efficacy of biological experiments for drug development, we developed PLB-SAVE, which uses only geometrical features of proteins and achieves a good overall performance for protein-ligand binding region prediction. Based on the same approach and rationale, this method can also be applied to predict carbohydrate-antibody interactions for further design and development of carbohydrate-based vaccines. PLB-SAVE is available at http://save.cs.ntou.edu.tw.[[booktype]]電子

Functional pathway mapping analysis for hypoxia-inducible factors

Background: Hypoxia-inducible factors (HIFs) are transcription factors that play a crucial role in response to hypoxic stress in living organisms. The HIF pathway is activated by changes in cellular oxygen levels and has significant impacts on the regulation of gene expression patterns in cancer cells. Identifying functional conservation across species and discovering conserved regulatory motifs can facilitate the selection of reference species for empirical tests. This paper describes a cross-species functional pathway mapping strategy based on evidence of homologous relationships that employs matrix-based searching techniques for identifying transcription factorbinding sites on all retrieved HIF target genes. Results: HIF-related orthologous and paralogous genes were mapped onto the conserved pathways to indicate functional conservation across species. Quantitatively measured HIF pathways are depicted in order to illustrate the extent of functional conservation. The results show that in spite of the evolutionary process of speciation, distantly related species may exhibit functional conservation owing to conservative pathways. The novel terms OrthRate and ParaRate are proposed to quantitatively indicate the flexibility of a homologous pathway and reveal the alternative regulation of functional genes. Conclusion: The developed functional pathway mapping strategy provides a bioinformatics approach for constructing biological pathways by highlighting the homologous relationships between various model species. The mapped HIF pathways were quantitatively illustrated and evaluated by statistically analyzing their conserved transcription factor-binding elements