389 research outputs found

    Methods for simultaneously identifying coherent local clusters with smooth global patterns in gene expression profiles

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    <p>Abstract</p> <p>Background</p> <p>The hierarchical clustering tree (HCT) with a dendrogram <abbrgrp><abbr bid="B1">1</abbr></abbrgrp> and the singular value decomposition (SVD) with a dimension-reduced representative map <abbrgrp><abbr bid="B2">2</abbr></abbrgrp> are popular methods for two-way sorting the gene-by-array matrix map employed in gene expression profiling. While HCT dendrograms tend to optimize local coherent clustering patterns, SVD leading eigenvectors usually identify better global grouping and transitional structures.</p> <p>Results</p> <p>This study proposes a flipping mechanism for a conventional agglomerative HCT using a rank-two ellipse (R2E, an improved SVD algorithm for sorting purpose) seriation by Chen <abbrgrp><abbr bid="B3">3</abbr></abbrgrp> as an external reference. While HCTs always produce permutations with good local behaviour, the rank-two ellipse seriation gives the best global grouping patterns and smooth transitional trends. The resulting algorithm automatically integrates the desirable properties of each method so that users have access to a clustering and visualization environment for gene expression profiles that preserves coherent local clusters and identifies global grouping trends.</p> <p>Conclusion</p> <p>We demonstrate, through four examples, that the proposed method not only possesses better numerical and statistical properties, it also provides more meaningful biomedical insights than other sorting algorithms. We suggest that sorted proximity matrices for genes and arrays, in addition to the gene-by-array expression matrix, can greatly aid in the search for comprehensive understanding of gene expression structures. Software for the proposed methods can be obtained at <url>http://gap.stat.sinica.edu.tw/Software/GAP</url>.</p

    Endoscopic Balloon Dilatation for Esophageal Strictures in Children Younger Than 6 Years: Experience in a Medical Center

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    Esophageal strictures in children may be caused by congenital anomaly, caustic agent or foreign body ingestion, complication of reflux esophagitis, and after esophageal surgery. Accidental ingestion of alkaline fluid is the most common cause of corrosive esophagitis in children in Taiwan. In this article, we studied 10 pediatric patients who had esophageal strictures and required endoscopic balloon dilatation (EBD) therapy under general anesthesia from January 2003 to June 2009. The median age of the studied children who received their first EBD treatment was 36.2 months (13.4–60.9 months), with a dilator size of 8.0mm (5–12 mm). The interval between injury and initial EBD was 3.0 months (1.3–60.8 months). The treatment duration averaged 16.7 months (3.0–69.3 months), with 13.5 (4–31) instances of EBD therapy per patient. The greater the length of stricture, the more number of times EBD was needed. In these cases, no severe complication was found after the procedure. The result indicated that EBD under general anesthesia was a safe and effective method to resolve the symptom of dysphagia and diet condition. Because of the limited number of study cases, long-term studies are required to further confirm the clinical effect of EBD under general anesthesia

    Lasing on nonlinear localized waves in curved geometry

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    The use of geometrical constraints opens many new perspectives in photonics and in fundamental studies of nonlinear waves. By implementing surface structures in vertical cavity surface emitting lasers as manifolds for curved space, we experimentally study the impacts of geometrical constraints on nonlinear wave localization. We observe localized waves pinned to the maximal curvature in an elliptical-ring, and confirm the reduction in the localization length of waves by measuring near and far field patterns, as well as the corresponding dispersion relation. Theoretically, analyses based on a dissipative model with a parabola curve give good agreement remarkably to experimental measurement on the transition from delocalized to localized waves. The introduction of curved geometry allows to control and design lasing modes in the nonlinear regime.Comment: 6 pages, 6 figure

    Effects of Angelica dahurica

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    The main objective of wound treatments is to restore the functional skin properties and prevent infection. Traditional Chinese medicine provides alternative anti-inflammatory, antimicrobial, and wound healing therapies. Both Angelica dahurica extract (AE) and Rheum officinale extract (RE) possess antimicrobial activity. In this study, AE and RE were applied in wound treatment to investigate their healing effects. Thirty Sprague-Dawley rats with dorsal full-thickness skin excision were divided into normal saline (NS), AE, RE, AE plus RE (ARE), and Biomycin (BM) groups. The treatment and area measurement of wounds were applied daily for 21 days. Wound biopsies and blood samples were obtained for histology examinations and cytokine analysis. Results showed that wound contraction in ARE group was significantly higher than that in NS and BM groups (P 0.05), and plasma TGF-β1 levels were significantly lower than those in the NS group on days 3-4 (P < 0.05). In conclusion, ARE accelerates wound healing during inflammation and proliferation phases

    Antioxidant activity and growth inhibition of human colon cancer cells by crude and purified fucoidan preparations extracted from Sargassum cristaefolium

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    AbstractFucose-containing sulfated polysaccharides, also termed “fucoidans”, which are known to possess antioxidant, anticoagulant, anticancer, antiviral, and immunomodulating properties, are normally isolated from brown algae via various extraction techniques. In the present study, two methods (SC1 and SC2) for isolation of fucoidan from Sargassum cristaefolium were compared, with regard to the extraction yields, antioxidant activity, and inhibition of growth of human colon cancer cells exhibited by the respective extracts. SC1 and SC2 differ in the number of extraction steps and concentration of ethanol used, as well as the obtained sulfated polysaccharide extracts, namely, crude fucoidan preparation (CFP) and purified fucoidan preparation (PFP), respectively. Thin layer chromatography, Fourier transform infrared analysis, and measurements of fucose and sulfate contents revealed that the extracts were fucoidan. There was a higher extraction yield for CFP, which contained less fucose and sulfate but more uronic acid, and had weaker antioxidant activity and inhibition of growth in human colon cancer cells. In contrast, there was a lower extraction yield for PFP, which contained more fucose and sulfate but less uronic acid, and had stronger antioxidant activity and inhibition of growth in human colon cancer cells. Thus, since the difference in bioactive activities between CFP and PFP was not remarkable, the high extraction yield of SC1 might be favored as a method in industrial usage for extracting fucoidan

    Prevention and early management of carotid blowout syndrome for patients receiving head and neck salvage boron neutron capture therapy (BNCT)

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    Background/purpose The incidence rate of oral and pharyngeal cancers in Taiwan has increased gradually over the past few decades. The standard treatment strategy for oral and pharyngeal cancers includes surgery or radiotherapy, with concurrent chemotherapy in certain types of tumors. Unfortunately, in-field recurrence is sometimes inexorable. Furthermore, re-irradiation of the recurrence site may cause severe complications due to the tolerance of normal tissue to radiation therapy. One fatal complication is carotid blowout syndrome (CBS). Boron neutron capture therapy (BNCT) is a new modality of radiation therapy, which is also mentioned as targeted radiotherapy. It is a feasible treatment that has the potential to spare normal tissue from being damaged by irradiation while simultaneously treating the primary tumor. In this presentation, we will share our experience with BNCT in treating recurrent head and neck cancers, as well as the prevention and management of CBS. Materials and methods We evaluated 4 patients with head and neck cancers treated by BNCT in Taiwan. All patients had undergone surgery previously and had received postoperative concurrent chemoradiotherapy. Results The 4 patients in this study were diagnosed with head and neck malignancies. The median follow-up period after the first course of BNCT was 15.1 months. After BNCT, 2 patients developed impending CBS, and 1 of them died. The remaining 3 patients survived until the last date of follow-up. Conclusion Pre-BNCT carotid artery evaluation through computed tomography angiography and early intervention if necessary is crucial when treating patients with recurrent head and neck cancers by BNCT

    High ambient-contrast-ratio display using tandem reflective liquid crystal display and organic light-emitting device

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    A high ambient-contrast-ratio (A-CR) and large aperture-ratio display is conceptually demonstrated and experimentally validated by stacking a normally black reflective liquid crystal display (NB-RLCD) and an organic light-emitting device (OLED). Such a tandem device can be switched between the NB-RLCD mode and the OLED mode under bright and dark ambient light, respectively. The normally black characteristic of the RLCD also helps to boost the A-CR under OLED-mode operation. To obtain a better image quality in the RLCD mode, a bumpy and transmissive structure is used to eliminate the specular reflection and to increase the viewing angle performance that results in CR \u3e 2:1 over 55 degrees viewing cone. Besides, such a structure can also increase the external quantum efficiency of the OLED by 49.4%. In our experiments, regardless of the ambient intensity the A-CR is kept higher than 100:1
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