Paradigm for diagnosing mycobacterial disease: direct detection and differentiation of Mycobacterium tuberculosis complex and non-tuberculous mycobacteria in clinical specimens using multiplex real-time PCR.

AIMS: Mycobacterium tuberculosis and non-tuberculous mycobacteria (NTM) are clinically different, and the rapid detection and differentiation of M. tuberculosis complex (MTBC) and NTM is crucial for patient management and infection control. Given the slow growth of most pathogenic mycobacteria, nucleic acid amplification assays are excellent tools for direct identification of mycobacteria in clinical specimens. Recently, a multiplex real-time PCR assay was developed that can directly detect 20 mycobacterial species in clinical specimens. Here, we evaluated the diagnostic performance of the assay for diagnosing mycobacterial disease under routine laboratory conditions. METHODS: A total of 3334 specimens collected from 1437 patients suspected of tuberculosis infection were subjected to acid-fast bacilli staining, conventional culture and the multiplex real-time PCR assay. To evaluate the sensitivity and specificity of the assay, the overall diagnosis of tuberculosis was defined by positive culture plus medical history, and the 2007 American Thoracic Society and Infectious Disease Society of America diagnostic criteria for NTM disease were applied. RESULTS: The sensitivity, specificity, positive predictive value and negative predictive value were 87.5%, 99.6%, 96.1% and 98.5%, respectively, for the detection of MTBC isolates and 53.3%, 99.9%, 95.2%, and 98.9%, respectively, for detecting NTM isolates. CONCLUSIONS: Thus, the assay can correctly differentiate between MTBC and NTM isolates in clinical specimens and would be a useful tool for the rapid differentiation of tuberculosis and NTM disease, despite its limited sensitivity for the diagnosis of NTM disease.

Continuous digital zooming using local self-similarity-based super-resolution for an asymmetric dual camera system.

This paper presents a digital zooming method using a super-resolution (SR) algorithm based on the local self-similarity between the wide- and tele-view images acquired by an asymmetric dual camera system. The proposed SR algorithm consists of four steps: (i) registration of an optically zoomed image to the wide-view image, (ii) restoration of the central region of the zoomed wide-view image, (iii) restoration of the boundary region of the zoomed wide-view image, and (iv) fusion of the results from steps (ii) and (iii). Since an asymmetric dual camera system acquires different-resolution images on the same scene due to the different optical specifications, the proposed method can restore the low-resolution wide-view image using the ideal high-frequency component estimated from the optically zoomed image. Experimental results demonstrate that the proposed method can provide significantly improved high-resolution wide-view images compared to existing single-image-based SR methods.

Intracellular delivery of molecules using microfabricated nanoneedle arrays.

Many bioactive molecules have intracellular targets, but have difficulty crossing the cell membrane to reach those targets. To address this difficulty, we fabricated arrays of nanoneedles to gently and simultaneously puncture 10(5) cells and thereby provide transient pathways for transport of molecules into the cells. The nanoneedles were microfabricated by etching silicon to create arrays of nanoneedles measuring 12 µm in height, tapering to a sharp tip less than 30 nm wide to facilitate puncture into cells and spaced 10 µm apart in order to have at least one nanoneedle puncture each cell in a confluent monolayer. These nanoneedles were used for intracellular delivery in two ways: puncture loading, in which nanoneedle arrays were pressed into cell monolayers, and centrifuge loading, in which cells in suspension were spun down onto nanoneedle arrays. The effects on intracellular uptake and cell viability were determined as a function of nanoneedle length and sharpness, puncture force and duration, and molecular weight of the molecule delivered. Under optimal conditions, intracellular uptake was seen in approximately 50 % of cells while maintaining high cell viability. Overall, this study provides a comparative analysis of intracellular delivery using nanoneedle arrays by two different loading methods over a range of operating parameters.

Direct identification of mycobacteria from liquid media using a triplex real-time PCR coupled with pyrosequencing method.

Culture in enriched broth, as well as on a solid medium, is recommended for primary isolation of mycobacteria. With the introduction of liquid mycobacterial culture methods, a substantial workload regarding the identification of culture-recovered mycobacterial species, particularly Mycobacterium tuberculosis complex (MTC), has been imposed on our laboratory. We thus developed a triplex, real-time PCR coupled with pyrosequencing assay that can directly identify mycobacterial species from liquid media, which can reduce the workload. In this assay, real-time PCR simultaneously detects MTC and Mycobacterium xenopi, and amplifies the region of 16S rRNA gene containing hypervariable region A for pyrosequencing analysis; subsequent, pyrosequencing identifies many other nontuberculous mycobacteria. The assay was evaluated using 333 DNA samples directly prepared from liquid media, including 24 reference strains and 309 clinical isolates. Three hundred and twenty-eight (98.5%) of the 333 samples were correctly identified. The remaining five were determined as indeterminate. In conclusion, this coupled assay would be an alternative method for rapid identification of mycobacteria directly from liquid media in a clinical laboratory with a high workload in regions where tuberculosis is endemic.

Oxidation Temperature Effects on ZnO Thin Films Prepared from Zn Thin Films on Quartz Substrates.

We investigated the structural and optical properties of the ZnO thin films formed by oxidation of Zn thin films. Zn thin films were deposited by thermal evaporation and were then annealed from 300 to 800 degrees C to prepare ZnO thin films. We found that ZnO thin films were formed by thermal oxidation of Zn thin films at oxidation temperatures over 400 degrees C. The grain size of ZnO thin films increased with the oxidation temperature and the highest ZnO (002) intensity was obtained at 600 degrees C. In the PL spectra, the intensity of the near-band-edge peak increased with the oxidation temperatures until 400 degrees C. However, these values gradually decreased with a further increase in the oxidation temperatures over 400 degrees C. The transmittance of the ZnO thin films was more than 90% for the visible wavelength region, and the optical band gap was red-shifted with increase in the oxidation temperature.

Effects of substrate heating on the photovoltaic characteristics of dye-sensitized solar cells during two-step Ti film deposition by RF magnetron sputtering.

Nanoporous Ti metal film electrodes for use as photoanodes in dye-sensitized solar cells (DSSCs) were deposited directly on the nanoporous TiO2 layer using the two-step RF magnetron sputtering technique. The Ti film electrode replaces the transparent conducting oxide (TCO) layer. The effect of substrate heating during the deposition of the Ti film was studied to improve the porosity and columnar array of the film pores and the resulting cell efficiency. The porous Ti layer (-41 microm) with low sheet resistance (-1.7 omega/sq) was obtained by deposition at 250 degrees C. The porous Ti layer collects electrons from the TiO2 layer and allows the diffusion of I-/I3(-) through the holes. The DSSC efficiency (eta) using porous Ti layers with highly columnar structures was measured with the highest conversion efficiency of -5.77%; the other photovoltaic properties were ff: 0.76, V(oc): 0.72 V, and J(sc): 10.6 mA/cm2.

Detection abnormal pattern in activities of daily living using sequence alignment method.

As the aging is rapidly coming, the necessity of cares for old people increases. As requests for care services for patients requiring help of others increases, various systems for care services have been developed. For care services, recently, there have been developed technologies of tracking and monitoring daily activities of a person and recognizing the daily activities of the person by analyzing tracked data. Particularly, there have been developed systems for taking care of a person whose state should be periodically checked, such as patients or old persons. General care systems are good for tracking what activity the person executes, but limited to detecting what a person's state is, such as a normal or an abnormal state. So it is necessary to develop a new computational method to detect abnormal signs in a life pattern via changes of a sequence of activities of daily living.

Semi-automated clustering of gene expression data sets.

Clustering, as one of key analysis tools for gene expression data sets, attempts to discover groups of genes having similar expression patterns. In order to get a reasonable biological interpretation, it is desirable that a clustering result be accurate enough. However, conventional clustering methods do not always meet this demand since they require the exact tuning of input parameters and cluster centers for an acceptable quality of result. Through an intuitive user interaction, UI-Cluster solves the problem mentioned above, and yields better clustering results.

Finding the evidence for protein-protein interactions from PubMed abstracts.

MOTIVATION: Protein-protein interactions play critical roles in biological processes, and many biologists try to find or to predict crucial information concerning these interactions. Before verifying interactions in biological laboratory work, validating them from previous research is necessary. Although many efforts have been made to create databases that store verified information in a structured form, much interaction information still remains as unstructured text. As the amount of new publications has increased rapidly, a large amount of research has sought to extract interactions from the text automatically. However, there remain various difficulties associated with the process of applying automatically generated results into manually annotated databases. For interactions that are not found in manually stored databases, researchers attempt to search for abstracts or full papers. RESULTS: As a result of a search for two proteins, PubMed frequently returns hundreds of abstracts. In this paper, a method is introduced that validates protein-protein interactions from PubMed abstracts. A query is generated from two given proteins automatically and abstracts are then collected from PubMed. Following this, target proteins and their synonyms are recognized and their interaction information is extracted from the collection. It was found that 67.37% of the interactions from DIP-PPI corpus were found from the PubMed abstracts and 87.37% of interactions were found from the given full texts. AVAILABILITY: Contact authors.