Identifying set-wise differential co-expression in gene expression microarray data

<p>Abstract</p> <p>Background</p> <p>Previous differential coexpression analyses focused on identification of differentially coexpressed gene pairs, revealing many insightful biological hypotheses. However, this method could not detect coexpression relationships between pairs of gene sets. Considering the success of many set-wise analysis methods for microarray data, a coexpression analysis based on gene sets may elucidate underlying biological processes provoked by the conditional changes. Here, we propose a differentially coexpressed gene sets (dCoxS) algorithm that identifies the differentially coexpressed gene set pairs between conditions.</p> <p>Results</p> <p>dCoxS is a two-step analysis method. In each condition, dCoxS measures the interaction score (IS), which represents the expression similarity between two gene sets using Renyi relative entropy. When estimating the relative entropy, multivariate kernel density estimation was used to model gene-gene correlation structure. Statistical tests for the conditional difference between the ISs determined the significance of differential coexpression of the gene set pair. Simulation studies supported that the IS is a representative measure of similarity between gene expression matrices. Single gene coexpression analysis of two publicly available microarray datasets detected no significant results. However, the dCoxS analysis of the datasets revealed differentially coexpressed gene set pairs related to the biological conditions of the datasets.</p> <p>Conclusion</p> <p>dCoxS identified differentially coexpressed gene set pairs not found by single gene analysis. The results indicate that set-wise differential coexpression analysis is useful for understanding biological processes induced by conditional changes.</p

Mastoid Obliteration with Silicone Blocks after Canal Wall Down Mastoidectomy

ObjectivesTo evaluate the usefulness of silicone blocks as graft material for mastoid cavity obliteration in the prevention of problematic mastoid cavities after canal wall down mastoidectomies.MethodsRetrospective evaluation of 20 patients who underwent mastoid obliteration with silicone blocks between 2002 and 2009 at the Chonnam National University Hospital. The cases consisted of 17 patients with chronic otitis media with cholesteatoma and 3 patients with adhesive otitis media. The postoperative follow-up period was an average 49 months (range, 6 to 90 months). The surgical technique used at our institution composed four major steps: First, the canal wall down mastoidectomy was performed and the middle ear procedure was completed. The silicone blocks were used to fill up the mastoidectomized cavity. Then, a cortical bone pate was used to cover the surface of the silicone blocks. Finally, temporalis fascia and a split musculoperiosteal flap were used to surround the bone pate for reinforcement of the reconstructed canal wall. We examined postoperative success rate and hearing outcomes.ResultsIn 19 cases (95%), the reconstructed canal wall maintained a cylindrical shape and the ear drum healed without perforation. In only 1 case (5%), the reconstructed canal wall was destroyed with ear drum perforation. The mean improvement in air-bone gap was about 12 dB (P<0.05), and the mean improvement in air-conduction was about 16 dB (P<0.05).ConclusionWe suggest that silicone blocks could be valuable resources as graft materials for mastoid obliteration after canal wall down mastoidectomies

Hepatocellular carcinoma with characteristic mucin production: a case report

We present a unique case of hepatocellular carcinoma with mucin-producing gland formation. A 53-year-old man with hepatitis B infection presented with weight loss for the past month. Computed tomography demonstrated a 10 × 9.8 cm mass in the right hepatic lobe accompanied by cirrhotic changes in the hepatic parenchyma. Right hepatectomy was performed, and the tumor cut surface showed a poorly-circumscribed, white to pink tumor with numerous nodules and extensive necrosis. Microscopically, the tumor was composed of thick trabeculae and large, irregularly-shaped islands, both of which were filled with pleomorphic eosinophilic hepatoid cells or gland-forming columnar cells with mucin production. Those cells were immunoreactive for cytokeratin 19 in both the trabeculae and the glands. In some tumor cells, limited immunoreactivity for cytokeratin 7, epithelial membrane antigen and carcinoembryonic antigen was noted. The cells forming thick trabeculae were focally positive for hepatocyte paraffin 1 and alpha-fetoprotein. We suggest that this tumor shows bidirectional differentiation into hepatocytes and cholangiocytes, supporting the concepts that human hepatocarcinogenesis can be based on transformation of progenitor cells which can imply divergent differentiation

Genetic evaluation of domestic walnut cultivars trading on Korean tree markets using microsatellite markers

Walnut (Juglans regia L.) is regarded as a healthy food because of its high nutritional composition and various health benefits. Although several walnut cultivars are being actively traded for domestic plantation or ornament in Korea, no particular effort has been made to evaluate genetic quality management of walnut cultivars in domestic tree markets. In this study, as an effort to evaluate the status of walnut seedling trade, we collected walnut seedlings of diverse cultivars from domestic tree markets and several locations in Korea and performed genotype analysis for the collections using microsatellite markers (76 individuals belonging to eight domestic cultivars). We used 12 markers that were previously reported to be informative and polymorphic in walnuts. The number of alleles that was detected from the collections using these markers ranged from 6 to 16, with heterozygosity values ranging from 0.03 to 0.75. Dendrogram revealed that the domestic walnut cultivars trading on tree markets could be genotypically distinguished from various foreign cultivars. However, genotyping data also showed that individual plants belonging to identical cultivars were sporadically distributed on the dendrogram, indicating that walnut cultivars trading on domestic tree markets seem to be poorly managed.Keywords: Walnut (Juglans regia L.), microsatellite markers, tree market, seedling trade, domestic cultivars, foreign cultivars, cultivar managementAfrican Journal of Biotechnology Vol. 11(29), pp. 7366-7374, 10 April, 201

Herbal Extracts That Reduce Ocular Oxidative Stress May Enhance Attentive Performance in Humans

We used herbal extracts in this study to investigate the effects of blue-light-induced oxidative stress on subjects’ attentive performance, which is also associated with work performance. We employed an attention network test (ANT) to measure the subjects’ work performance indirectly and used herbal extracts to reduce ocular oxidative stress. Thirty-two subjects participated in either an experimental group (wearing glasses containing herbal extracts) or a control group (wearing glasses without herbal extracts). During the ANT experiment, we collected electroencephalography (EEG) and electrooculography (EOG) data and measured button responses. In addition, electrocardiogram (ECG) data were collected before and after the experiments. The EOG results showed that the experimental group exhibited a reduced number of eye blinks per second during the experiment and faster button responses with a smaller variation than did the control group; this group also showed relatively more sustained tension in their ECG results. In the EEG analysis, the experimental group had significantly greater cognitive processing, with larger P300 and parietal 2–6 Hz activity, an orienting effect with neural processing of frontal area, high beta activity in the occipital area, and an alpha and beta recovery process after the button response. We concluded that reducing blue-light-induced oxidative stress with herbal extracts may be associated with reducing the number of eye blinks and enhancing attentive performance

Cavernous Hemangioma of the Tympanic Membrane

Cavernous hemangioma seems to most frequently arise in the posterior portion of the external auditory canal. However, they rarely occur in the tympanic membrane. A 49-year-old male patient was referred for evaluation of right-sided pulsatile tinnitus that he'd experienced for the previous 2 years. Temporal bone computerized tomography showed an isolated soft tissue mass just lateral to the tympanic membrane. There was no evidence of bony erosion or middle ear invasion. The patient underwent excision of the mass using a postauricular approach. The mass was removed en bloc and the defect of the tympanic membrane was repaired by tympanoplasty type I. There was no recurrence after 1 year of follow-up

The impact of sequential versus single anastomoses on flow characteristics and mid-term patency of saphenous vein grafts in coronary bypass grafting

ObjectiveTo assess the influence of bypass grafting technique on the flow characteristics and mid-term patency of saphenous vein coronary bypass grafts.MethodsIn the present study, 309 patients who underwent either sequential (group A, N = 84 grafts) or individual (group B, N = 244 grafts) saphenous vein coronary bypass grafting between February 2002 and September 2007 were investigated. Individual bypassing only was performed in 212 patients, and sequential bypassing only was performed in 78 patients. The remaining 19 patients received both. A total of 436 distal anastomoses were performed with 328 saphenous vein grafts. The intraoperative flow characteristics and the graft patency were assessed with the transit time flow meter and serial multi-detector computed tomography coronary angiograms, respectively.ResultsGroup A showed a higher mean flow compared with group B at 49.4 ± 27.4 mL/min versus 37.1 ± 20.1 mL/min, respectively (P = .001). The mean flow increased linearly as the number of anastomoses increased per graft (P < .001). Graft patency at 3 years was 93.3% ± 3.4% in group A and 86.5% ± 3.1% in group B (P = .048). After adjustment for baseline characteristics, group A showed a tendency for superior mid-term patency than group B (hazard ratio 0.362; 95% confidence interval, 0.129–1.017; P = .0538).ConclusionsSequential bypass grafts were associated with higher mean flows and superior mid-term patency compared with individual grafts. These findings suggest the more favorable results of sequential bypass grafting to be attributed to the enhanced flow hemodynamics