Parameter determination of support vector machine and feature selection using simulated annealing approach

Support vector machine (SVM) is a novel pattern classification method that is valuable in many applications. Kernel parameter setting in the SVM training process, along with the feature selection, significantly affects classification accuracy. The objective of this study is to obtain the better parameter values while also finding a subset of features that does not degrade the SVM classification accuracy. This study develops a simulated annealing (SA) approach for parameter determination and feature selection in the SVM, termed SA-SVM.To measure the proposed SA-SVM approach, several datasets in UCI machine learning repository are adopted to calculate the classification accuracy rate. The proposed approach was compared with grid search which is a conventional method of performing parameter setting, and various other methods. Experimental results indicate that the classification accuracy rates of the proposed approach exceed those of grid search and other approaches. The SA-SVM is thus useful for parameter determination and feature selection in the SVM.     

Secretome analysis of novel IgE-binding proteins from Penicillium citrinum

The Penicillium genus of fungi is a frequently reported cause of allergic reactions. However, only a limited number of allergens have been reported. In Penicillium spp., many allergens show higher IgE-binding activity in culture filtrate extracts than in cellular extracts. In order to investigate the IgE-reactive profile of mold-sensitized patients, secreted IgE-reactive proteins from Penicillium citrinum were identified by 2-DE, serum immunoblotting, and nanoLC-MS/MS. Among the IgE-reactive spots, one known allergen, Pen c 13, and four novel allergens were identified. The cDNAs coding for Pen c 32 and Pen c 30 were cloned using designed primers based on nanoLC-MS/MS analysis. The amino acid sequences of Pen c 32 and Pen c 30 were, respectively, found to have extensive similarity with those of pectate lyases and catalases from various fungi. Native Pen c 30 was shown to have catalase activity and to bind to serum IgE from 48% of mold-allergic patients and induced immediate type skin reactions in a sensitized patient. Here, we present a proteome approach which resulted in the identification of four novel secreted allergens. These novel allergens might be useful in allergy diagnosis and in the treatment of mold-allergic disorders.     

Overexpression and elevated plasma level of tumor-associated antigen 90K/Mac-2 binding protein in colorectal carcinoma

The cancer cell secretome may contain potentially useful biomarkers. Previously, we have analyzed the colorectal carcinoma (CRC) cell secretome. In this study, tumor‐associated antigen 90K (TAA90K)/Mac‐2 binding protein (Mac‐2BP), one of the CRC cell secreted proteins, was chosen for evaluation as a potential CRC biomarker because its mRNA level was also found to be significantly elevated in CRC tissues and in a more metastatic CRC cell line from the analysis of two public domain array‐based datasets. Immunohistochemical analysis of 241 CRC specimens showed that TAA90K/Mac‐2BP was positively detected in 52.7% of the tumors, but weakly or not detected in over 95% of the adjacent nontumor epithelial cells. The plasma TAA90K/Mac‐2BP levels were significantly higher in CRC patients (N = 280) versus healthy controls (N = 147) (7.77 ± 3.49 vs. 5.72 ± 2.67 μg/mL, p<0.001). Moreover, combination of TAA90K/Mac‐2BP and carcinoembryonic antigen (CEA) could outperform CEA alone in discriminating CRC patients from healthy persons in this case‐control study. Our results collectively indicate that analysis of cancer cell secretome is a feasible strategy for identifying cancer biomarker candidates, and the TAA90K/Mac‐2BP may be a potential CRC biomarker.     

A well-based reverse-phase protein array applicable to extracts from formalin-fixed paraffin-embedded tissue

Proteomic analysis of formalin-fixed paraffin-embedded (FFPE) tissue offers significant diagnostic utility but is complicated due to the high level of covalently crosslinked proteins arising from formalin fixation. To address these challenges, we developed a reliable protein extraction method for FFPE tissue, based on heat-induced antigen retrieval within a pressure cooker. The protein extraction yield from archival FFPE tissue section is approximately 90% of that recovered from frozen tissue. This method demonstrates preservation of immunoreactivity and recovery of full-length proteins by Western blotting. Additionally, we developed a well-based RP protein array platform utilizing an electrochemiluminescence detection system. Protein samples derived from FFPE tissue by means of laser capture dissection, with as few as 500 shots demonstrate measurable signal differences for different proteins. The lysates coated to the array plate, remain stable over 1?month at room temperature. Theses data suggest that this new protein-profiling platform coupled with the protein extraction method can be used for molecular profiling analysis in FFPE tissue, and contribute to the validation and development of biomarkers in clinical studies.     

Dynamic diamond anvil cell (dDAC): a novel device for studying the dynamic-pressure properties of materials

We have developed a unique device, a dynamic diamond anvil cell (dDAC), which repetitively applies a time-dependent load/pressure profile to a sample. This capability allows studies of the kinetics of phase transitions and metastable phases at compression (strain) rates of up to 500 GPa/s (approximately 0.16 s(-1) for a metal). Our approach adapts electromechanical piezoelectric actuators to a conventional diamond anvil cell design, which enables precise specification and control of a time-dependent applied load/pressure. Existing DAC instrumentation and experimental techniques are easily adapted to the dDAC to measure the properties of a sample under the varying load/pressure conditions. This capability addresses the sparsely studied regime of dynamic phenomena between static research (diamond anvil cells and large volume presses) and dynamic shock-driven experiments (gas guns, explosive, and laser shock). We present an overview of a variety of experimental measurements that can be made with this device.     

Mapping of user interfaces on electronic appliances

The purpose of this study was to investigate mapping of user interfaces on consumer electronic appliances. A digital clock with five different interface modes was chosen for the experiment. Forty elderly subjects (above 65 years) and 40 middle-aged subjects (45-64 years) participated in the study. Every subject had to complete three different tasks, namely time setting, alarm time setting and date setting. The researchers investigated what problems were encountered when performing these tasks and collected data such as operational time, the number of total inputs, subjective estimation and interview information. The findings of this study indicated that the interface modes had significant effects on operational time, the number of total inputs and subjective estimation. Finally, the study confirms that when the spatial relationship between buttons and display contents are clearly indicated, the operation is easier to complete.     

Building a portable data and information interoperability infrastructure-framework for a standard Taiwan Electronic Medical Record Template

Traditional electronic health record (EHR) data are produced from various hospital information systems. They could not have existed independently without an information system until the incarnation of XML technology. The interoperability of a healthcare system can be divided into two dimensions: functional interoperability and semantic interoperability. Currently, no single EHR standard exists that provides complete EHR interoperability. In order to establish a national EHR standard, we developed a set of local EHR templates. The Taiwan Electronic Medical Record Template (TMT) is a standard that aims to achieve semantic interoperability in EHR exchanges nationally. The TMT architecture is basically composed of forms, components, sections, and elements. Data stored in the elements which can be referenced by the code set, data type, and narrative block. The TMT was established with the following requirements in mind: (1) transformable to international standards; (2) having a minimal impact on the existing healthcare system; (3) easy to implement and deploy, and (4) compliant with Taiwan's current laws and regulations. The TMT provides a basis for building a portable, interoperable information infrastructure for EHR exchange in Taiwan.     

Robust measurement of ocular torsion using iterative Lucas-Kanade

We present a new method to measure ocular torsion using Lucas-Kanade method. After pixels of iris annulus around a pupil have been converted into Cartesian coordinates, 30 features on the iris was selected then the features were tracked using the iterative Lucas-Kanade algorithm to calculate torsional shift. The results show that a precision of the method is higher than those measured by a conventional cross-correlation and by a template matching method. The suggested method showed 0.03 degrees mean error with 0.15 degrees maximum error. Particularly, the method was robust to change of pupil size and misalignment of pupil location. Processing time was also fast enough to be implemented in a real-time system.     

Edge detection in a hexagonal-image processing framework

With processing power of computers and capabilities of graphics devices increasing rapidly, the time is ripe to reconsider using hexagonal sampling for computer vision in earnest. This paper reports on an investigation of edge detection in the context of hexagonally sampled images. It presents a complete framework for processing hexagonally sampled images which addresses four key aspects: conversion of square to hexagonally sampled images, storage, processing, and display of these images. Results from using edge detection on this framework show that (a) the computational requirement for processing a hexagonally sampled image is less than that for square sampled images, and (b) a better qualitative performance which is due to the compact and circular nature of the hexagonal lattice. This last point needs to be exploited in the development of edge detectors for hexagonally sampled images.