Effect of data normalization on fuzzy clustering of DNA microarray data

BACKGROUND: Microarray technology has made it possible to simultaneously measure the expression levels of large numbers of genes in a short time. Gene expression data is information rich; however, extensive data mining is required to identify the patterns that characterize the underlying mechanisms of action. Clustering is an important tool for finding groups of genes with similar expression patterns in microarray data analysis. However, hard clustering methods, which assign each gene exactly to one cluster, are poorly suited to the analysis of microarray datasets because in such datasets the clusters of genes frequently overlap. RESULTS: In this study we applied the fuzzy partitional clustering method known as Fuzzy C-Means (FCM) to overcome the limitations of hard clustering. To identify the effect of data normalization, we used three normalization methods, the two common scale and location transformations and Lowess normalization methods, to normalize three microarray datasets and three simulated datasets. First we determined the optimal parameters for FCM clustering. We found that the optimal fuzzification parameter in the FCM analysis of a microarray dataset depended on the normalization method applied to the dataset during preprocessing. We additionally evaluated the effect of normalization of noisy datasets on the results obtained when hard clustering or FCM clustering was applied to those datasets. The effects of normalization were evaluated using both simulated datasets and microarray datasets. A comparative analysis showed that the clustering results depended on the normalization method used and the noisiness of the data. In particular, the selection of the fuzzification parameter value for the FCM method was sensitive to the normalization method used for datasets with large variations across samples. CONCLUSION: Lowess normalization is more robust for clustering of genes from general microarray data than the two common scale and location adjustment methods when samples have varying expression patterns or are noisy. In particular, the FCM method slightly outperformed the hard clustering methods when the expression patterns of genes overlapped and was advantageous in finding co-regulated genes. Thus, the FCM approach offers a convenient method for finding subsets of genes that are strongly associated to a given cluster

Effects of whole body vibration training on body composition, skeletal muscle strength, and cardiovascular health

Whole body vibration training (WBVT) has been used as a supplement to conventional exercise training such as resistance exercise training to improve skeletal muscle strength, specifically, in rehabilitation field. Recently, this exercise modality has been utilized by cardiovascular studies to examine whether WBVT can be a useful exercise modality to improve cardiovascular health. These studies reported that WBVT has not only beneficial effects on muscular strength but also cardiovascular health in elderly and disease population. However, its mechanism underlying the beneficial effects of WBVT in cardiovascular health has not been well documented. Therefore, this review highlighted the impacts of WBVT on cardiovascular health, and its mechanisms in conjunction with the improved muscular strength and body composition in various populations

Outcomes of endovascular treatment for aortic pseudoaneurysm in Behcet's disease

ObjectiveTo evaluate the effectiveness of endovascular stent grafting for surgical management of aortic pseudoaneurysm in patients with Behcet's disease (BD).MethodsWe present a single-institution retrospective cohort of patients with aortic pseudoaneurysm and BD treated with aortic stent grafting. Computed tomography imaging was obtained preoperatively in all patients and once within 2 weeks postoperatively, and then annually. Clinical follow-up and erythrocyte sedimentation rate were used to follow BD activity. Immunosuppressant therapy was instituted prior to endovascular treatment unless a contraindication existed.ResultsFrom 1998 to 2012, 10 patients (eight male, two female; median age, 39) with BD and aortic pseudoaneurysm were treated with endovascular stent grafting at this institution. Ninety percent of these patients received immunosuppressive therapy before and after surgical treatment. The median follow-up period was 57 months (interquartile range, 43-72). The locations of the 12 pseudoaneurysms treated in this cohort were infrarenal abdominal aorta (seven), descending thoracic aorta (four), and aortic arch (one). Median pseudoaneurysm size was 4.5 cm (interquartile range, 3.4-5.9). At long-term follow-up, complete resolution of the aortic pseudoaneurysm was noted in all patients. No endoleaks occurred. Newly developed pseudoaneurysm at the distal margin of the stent graft was noted in one patient 17 months after the stent graft procedure. One patient required a subsequent stent graft placement for an expanding pseudoaneurysm of the subclavian artery. No patient deaths occurred during the follow-up period.ConclusionsEndovascular treatment of aortic pseudoaneurysm with stent-grafting in patients with BD is safe and effective with long-term durability

High-Throughput Screening of Acyl-CoA Thioesterase I Mutants Using a Fluid Array Platform

Screening target microorganisms from a mutated recombinant library plays a crucial role in advancing synthetic biology and metabolic engineering. However, conventional screening tools have several limitations regarding throughput, cost, and labor. Here, we used the fluid array platform to conduct high-throughput screening (HTS) that identified Escherichia coli ???TesA thioesterase mutants producing elevated yields of free fatty acids (FFAs) from a large (106) mutant library. A growth-based screening method using a TetA-RFP fusion sensing mechanism and a reporter-based screening method using high-level FFA producing mutants were employed to identify these mutants via HTS. The platform was able to cover >95% of the mutation library, and it screened target cells from many arrays of the fluid array platform so that a post-analysis could be conducted by gas chromatography. The ???TesA mutation of each isolated mutant showing improved FFA production in E. coli was characterized, and its enhanced FFA production capability was confirmed

Changes in medical care due to the absence of internal medicine physicians in emergency departments

Objective Especially in emergency departments (EDs), a lack of internal medicine (IM) residents in charge causes difficulties in medical care and ED overcrowding. Thus, protocols without IM residents in EDs is needed. This study aimed to investigate changes in medical care when emergency medicine residents replaced the roles of IM residents. Methods This study was conducted at a single-site ED of a university medical center. The study group contained patients admitted to the IM department between September and December 2015, during which IM residents were absent in the ED. The control group contained patients admitted to the IM department between September and December 2014, during which IM residents were present in the ED. Changes in medical care between the presence and absence of IM residents in the ED were studied by comparing admission rates from the ED, length of ED stay, duration of hospitalization, and concordance of diagnoses between admission and discharge by the IM department. Results The study group contained 2,341 patients; the control group contained 2,215 patients. Admission rates from the ED increased by 53.4% (95% confidence interval [CI], P<0.001); lengths of stay decreased by 15.1% (95% CI, P<0.001); and durations of hospitalization in the pulmonology department decreased by 38.4% (95% CI, P=0.001). Concordance of diagnoses between admission and discharge decreased by 14.2% in the cardiology department (95% CI, P=0.021). Conclusion Lengths of stay were reduced without critical declines in diagnostic concordance rates when emergency medicine physicians, instead of IM residents in the ED, decided upon admissions of IM patients

PAGaN I: Multi-Frequency Polarimetry of AGN Jets with KVN

Active Galactic Nuclei (AGN) with bright radio jets offer the opportunity to study the structure of and physical conditions in relativistic outflows. For such studies, multi-frequency polarimetric very long baseline interferometric (VLBI) observations are important as they directly probe particle densities, magnetic field geometries, and several other parameters. We present results from first-epoch data obtained by the Korean VLBI Network (KVN) within the frame of the Plasma Physics of Active Galactic Nuclei (PAGaN) project. We observed seven radio-bright nearby AGN at frequencies of 22, 43, 86, and 129 GHz in dual polarization mode. Our observations constrain apparent brightness temperatures of jet components and radio cores in our sample to $>10^{8.01}$ K and $>10^{9.86}$ K, respectively. Degrees of linear polarization $m_{L}$ are relatively low overall: less than 10%. This indicates suppression of polarization by strong turbulence in the jets. We found an exceptionally high degree of polarization in a jet component of BL Lac at 43 GHz, with $m_{L} \sim$ 40%. Assuming a transverse shock front propagating downstream along the jet, the shock front being almost parallel to the line of sight can explain the high degree of polarization.Comment: 14 pages, 17 figures, 4 tables. To appear in JKAS (received 2015 July 27; accepted 2015 October 25). Note the PAGaN II companion paper by J. Oh et a