An integrated approach to feature selection and classification for microarray data with outlier detection

postprintThe 8th Annual International Conference on Computational Systems Bioinformatics (CSB 2009), Stanford University, 10-13 August 2009

An integrated approach for identifying wrongly labeled samples when performing classification in microarray data

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Gene selection in microarray data analysis for brain cancer classification

Cancer classification has been one of the most challenging tasks in clinical diagnosis. At present cancer classification is done mainly by looking through the cells' morphological differences, which do not always give a clear distinction of cancer subtypes. Unfortunately, this may have a significant impact on the final outcome of whether a patient could be cured effectively. Microarray technology can play an important role on diagnosing which type of disease one is carrying. The gene selection process is critical for developing gene markers for faster and more accurate diagnosis. In this paper, we develop a method using pairwise data comparisons instead of the one-over-the-rest approach used nowadays. Results are evaluated using available clustering techniques including hierarchical clustering and k-means clustering. Using pairwise comparison, the best accuracy achieved is 95% while it is only 83% when using one-over-the-rest approach. ©2006 IEEE.published_or_final_versio

Histiocytic sarcoma simulating immune thrombocytopenic purpura

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E2F1 Downregulation by Arsenic Trioxide in Lung Adenocarcinoma

Lung cancer is one of the most common cancers worldwide. Arsenic trioxide (ATO) has been approved by the U.S. Food and Drug Administration for the treatment of acute promyelocytic leukemia. Nonetheless preliminary data have suggested potential activity of ATO in solid tumors including lung cancer. This study aimed to examine the underlying mechanisms of ATO in the treatment of lung adenocarcinoma. Using a panel of 7 lung adenocarcinoma cell lines, the effects of ATO treatment on cell viability, expression of E2F1 and its downstream targets, phosphatidylserine externalization, mitochondrial membrane depolarization and alteration of apoptotic/anti-apoptotic factors were studied. Tumor growth inhibition in vivo was investigated using a nude mouse xenograft model. ATO decreased cell viability with clinically achievable concentrations (8 uM) in all cell lines investigated. This was accompanied by reduced expression of E2F1, cyclin A2, skp2, c-myc, thymidine kinase and ribonucleotide reductase M1, while p-c-Jun was upregulated. Cell viability was significantly decreased with E2F1 knockdown. Treatment with ATO resulted in phosphatidylserine externalization in H23 cells and mitochondrial membrane depolarization in all cell lines, associated with truncation of Bid, downregulation of Bcl-2, upregulation of Bax and Bak, caspase-9 and caspase-3 activation and PARP cleavage. Using a H358 xenograft model, the tumor growth was suppressed in the ATO treatment group during 8 days of treatment, associated with downregulation of E2F1 and upregulation of truncated Bid and cleaved caspase-3. In conclusion, ATO has potent in vitro and in vivo activity in lung adenocarcinoma, partially mediated through E2F1 downregulation and apoptosis.published_or_final_versio

Feasibility and potentials of online support for stress management among secondary school teachers

Teachers' work-related stress is a widespread problem. Few studies have used online communications to provide support to teachers, and these were mainly focused on novice teachers. Here, we performed an exploratory study to examine whether the use of online forums by secondary school teachers in Hong Kong could provide social support to manage work-related stress. Following 7 days of forum use, content analysis and post-intervention evaluations were carried out to examine the anonymous communications of 75 secondary school teachers who participated in one of five online discussion forums. Consensus on the coding and categorization of the data was reached among three experienced researchers in qualitative analyses. The online forums were well received by the participants. Most participants reported that they received support from the forum and considered it useful for stress management. These results suggest that online support can be used for stress management among secondary school teachers. Further studies on using online approaches as stress management tools are warranted. Copyright © 2010 John Wiley & Sons, Ltd.preprin

Combination of SAHA and bortezomib up-regulates CDKN2A and CDKN1A and induces apoptosis of Epstein-Barr virus-positive Wp-restricted Burkitt lymphoma and lymphoblastoid cell lines

Epstein-Barr virus (EBV) latent proteins exert anti-apoptotic effects on EBV-transformed lymphoid cells by down-regulating BCL2L11 (BIM), CDKN2A (p16(INK4A) ) and CDKN1A (p21(WAF1) ). However, the potential therapeutic effects of targeting these anti-apoptotic mechanisms remain unexplored. Here, we tested both in vitro and in vivo effects of the combination of histone deacetylase (HDAC) and proteasome inhibitors on the apoptosis of six endemic Burkitt lymphoma (BL) lines of different latency patterns (types I and III and Wp-restricted) and three lymphoblastoid cell lines (LCLs). We found that the combination of HDAC and proteasome inhibitors (e.g. SAHA/bortezomib) synergistically induced the killing of Wp-restricted and latency III BL and LCLs but not latency I BL cells. The synergistic killing was due to apoptosis, as evidenced by the high percentage of annexin V positivity and strong cleavage of PARP1 (PARP) and CASP3 (caspase-3). Concomitantly, SAHA/bortezomib up-regulated the expression of CDKN2A and CDKN1A but did not affect the level of BCL2L11 or BHRF1 (viral homologue of BCL2). The apoptotic effects were dependent on reactive oxygen species generation. Furthermore, SAHA/bortezomib suppressed the growth of Wp-restricted BL xenografts in nude mice. This study provides the rationale to test the novel application of SAHA/bortezomib on the treatment of EBV-associated Wp-restricted BL and post-transplant lymphoproliferative disorder.postprin

Does staged removal of lower third molars pose unnecessary re-operations to patients?

Comment in Journal of Oral and Maxillofacial Surgery Feb 2010, v. 68 n. 2, p. 442-446; Author's reply on 2011, v. 68 n. 11, p. 2925-2926postprin

A cluster analysis of patterns of objectively measured physical activity in Hong Kong

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