pSLIP: SVM based protein subcellular localization prediction using multiple physicochemical properties

BACKGROUND: Protein subcellular localization is an important determinant of protein function and hence, reliable methods for prediction of localization are needed. A number of prediction algorithms have been developed based on amino acid compositions or on the N-terminal characteristics (signal peptides) of proteins. However, such approaches lead to a loss of contextual information. Moreover, where information about the physicochemical properties of amino acids has been used, the methods employed to exploit that information are less than optimal and could use the information more effectively. RESULTS: In this paper, we propose a new algorithm called pSLIP which uses Support Vector Machines (SVMs) in conjunction with multiple physicochemical properties of amino acids to predict protein subcellular localization in eukaryotes across six different locations, namely, chloroplast, cytoplasmic, extracellular, mitochondrial, nuclear and plasma membrane. The algorithm was applied to the dataset provided by Park and Kanehisa and we obtained prediction accuracies for the different classes ranging from 87.7% – 97.0% with an overall accuracy of 93.1%. CONCLUSION: This study presents a physicochemical property based protein localization prediction algorithm. Unlike other algorithms, contextual information is preserved by dividing the protein sequences into clusters. The prediction accuracy shows an improvement over other algorithms based on various types of amino acid composition (single, pair and gapped pair). We have also implemented a web server to predict protein localization across the six classes (available at )

Scalable and variable bit rate speech coding based on multi-band excitation model

The Multi-band Excitation (MBE) model, first proposed by Daniel Griffin at MIT, is a speech model which uses harmonic sinusoidal representation to produce intelligible and high quality synthesized speech at low bit rates. A novel model based on the existing MBE concept and denoted as the Auditory Masking Multi-band Excitation (AMMBE) model is presented in this thesis. It exploits auditory masking characteristics to improve the perceptual quality of the synthesized speech.Master of Engineerin

Challenges of a maturing economy : a case study on Singapore

As the environment is constantly changing, Singapore will need to response to the challenges ahead. To compete successfully, two critical questions need to be addressed : • What are the challenges faced by Singapore in the 21st century? • What are the strategies available to cope successfully in view of these challenges? The first part of this study reviews the development of the Singapore economy, based on two basis -- time and sector. The second part of the study is devoted to the various challenges faced by Singapore in the next lap, namely, competition from other developing countries, market saturation, demographic changes of the Singapore population, slower economic growth faced by Singapore, strengthening of the Singapore dollar and relocation of companies formerly based in Singapore to other nearby countries. The third part of the study focus on the various opportunities and strategies available to Singapore. Lastly, it is hoped that our study will help others to develop a better understanding of the constraints faced and the opportunities available to Singapore as she becomes an advenced developing nation in 1996.BUSINES

LIPID TUMOUR PROFILE

US20110021451A1Published Applicatio

Entropic criteria for protein folding derived from recurrences: Six residues patch as the basic protein word

10.1016/j.febslet.2006.07.076FEBS Letters580204861-4864FEBL

Combinatorial hypofractionated radiotherapy and pembrolizumab in anaplastic thyroid cancer

Objective: Anaplastic thyroid cancer (ATC) is an aggressive disease associated with poor outcomes and resistance to therapies. Our study aim was to evaluate the activity of a combinatorial regimen of sandwich sequencing of pembrolizumab immunotherapy and hypofractionated radiotherapy (RT). Methods: In this case series, patients with ATC received hypofractionated RT (QUAD-shot) and intravenous pembrolizumab 200 mg every 3–4 weeks. Pembrolizumab was continued until disease progression or up till 24 months. Concurrent lenvatinib treatment was allowed. Primary endpoint was best overall response (BOR) and progression-free survival (PFS). Additionally, we performed immune profiling of circulating T cells in a responder to investigate the immune response to our combinatorial treatment. Results: At median follow-up of 32.6 months (IQR: 26.4–38.8), of a cohort of five patients, BOR was 80%; with two complete responses (CR) and two partial responses (PR). Patients who achieved CR remained disease-free at last follow-up. Median PFS was 7.6 months (IQR: 6.2–NR), and 1-year PFS and overall survival rate was 40% (95% CI: 13.7– 100) for both. Treatment was well-tolerated, with mostly grade 1–2 adverse events. Immune profiling of one partial responder revealed an increase in activated CD4 and CD8 T cells post-QUAD-shot RT, which was further enhanced during the maintenance phase of pembrolizumab. Conclusion: Herein, we report a case series of five patients with ATC, with two long-term survivors who were treated with surgical debulking followed by QUAD-shot RT and pembrolizumab, possibly due to synergy of local and systemic treatments in activating anti-tumour immunogenic cytotoxicity. This regimen warrants further investigation in a larger cohort of patients

Toward one step analysis of cellular lipidomes using liquid chromatography coupled with mass spectrometry: Application to Saccharomyces cerevisiae and Schizosaccharomyces pombe lipidomics

10.1039/b913353dMolecular BioSystems661008-101