Adaptive thresholds to detect differentially expressed genes in microarray data

To detect changes in gene expression data from microarrays, a fixed threshold for fold difference is used widely. However, it is not always guaranteed that a threshold value which is appropriate for highly expressed genes is suitable for lowly expressed genes. In this study, aiming at detecting truly differentially expressed genes from a wide expression range, we proposed an adaptive threshold method (AT). The adaptive thresholds, which have different values for different expression levels, are calculated based on two measurements under the same condition. The sensitivity, specificity and false discovery rate (FDR) of AT were investigated by simulations. The sensitivity and specificity under various noise conditions were greater than 89.7% and 99.32%, respectively. The FDR was smaller than 0.27. These results demonstrated the reliability of the method

Inter-Species Differences of Co-expression of Neighboring Genes in Eukaryotic Genomes

Background: There is increasing evidence that gene order within the eukaryotic genome is not random. In yeast and worm, adjacent or neighboring genes tend to be co-expressed. Clustering of co-expressed genes has been found in humans, worm and fruit flies. However, in mice and rats, an effect of chromosomal distance (CD) on co-expression has not been investigated yet. Also, no cross-species comparison has been made so far. We analyzed the effect of CD as well as normalized distance (ND) using expression data in six eukaryotic species: yeast, fruit fly, worm, rat, mouse and human. Results: We analyzed 24 sets of expression data from the six species. Highly co-expressed pairs were sorted into bins of equal sized intervals of CD, and a co-expression rate (CoER) in each bin was calculated. In all datasets, a higher CoER was obtained in a short CD range than a long distance range. These results show that across all studied species, there was a consistent effect of CD on co-expression. However, the results using the ND show more diversity. Intra- and inter-species comparisons of CoER reveal that there are significant differences in the co-expression rates of neighboring genes among the species. A pair-wise BLAST analysis finds 8 – 30 % of the highly co-expressed pairs are duplic ated genes. Conclusion: We confirmed that in the six eukaryotic species, there was a consistent tendency that neighboring genes are likely to be co-expressed. Results of pair-wised BLAST indicate a significant effect of non-duplicated pairs on co-expression. A comparison of CD and ND suggests the dominant effect of CD

Lower Expression of Genes near microRNA in C. elegans Germline

Background: MicroRNAs (miRNAs) are recently discovered short non-protein-coding RNA molecules. miRNAs are increasingly implicated in tissue-specific transcriptional control and particularly in development. Because there is mounting evidence for the localized component of transcriptional control, we investigated if there is a distance-dependent effect of miRNA. Results: We analyzed gene expression levels around the 84 of 113 know miRNAs for which there are nearby gene that were measured in the data in two independent C. elegans expression data sets. The expression levels are lower for genes in the vicinity of 59 of 84 (71%) miRNAs as compared to genes far from such miRNAs. Analysis of the genes with lower expression in proximity to the miRNAs reveals increased frequency matching of the 7 nucleotide "seed"s of these miRNAs. Conclusion: We found decreased messenger RNA (mRNA) abundance, localized within a 10 kb of chromosomal distance of some miRNAs, in C. elegans germline. The increased frequency of seed matching near miRNA can explain, in part, the localized effects

Purely excitonic lasing in ZnO microcrystals: Temperature-induced transition between exciton-exciton and exciton-electron scattering

Since the seminal observation of room-temperature laser emission from ZnO thin films and nanowires, numerous attempts have been carried out for detailed understanding of the lasing mechanism in ZnO. In spite of the extensive efforts performed over the last decades, the origin of optical gain at room temperature is still a matter of considerable discussion. In this work, we show that a ZnO film consisting of well-packed micrometer-sized ZnO crystals exhibits purely excitonic lasing at room temperature without showing any symptoms of electron-hole plasma emission, even under optical excitation more than 25 times above the excitonic lasing threshold. The lasing mechanism is shifted from the exciton-exciton scattering to the exciton-electron scattering with increasing temperature from 3 to 150 K. The exciton-electron scattering process continues to exist with further increasing temperature from 150 to 300 K. Thus, we present distinct experimental evidence that the room-temperature excitonic lasing is achieved not by exciton-exciton scattering, as has been generally believed, but by exciton-electron scattering. We also argue that the long carrier diffusion length and the low optical loss nature of the micrometer-sized ZnO crystals, as compared to those of ZnO nanostructures, plays a key role in showing room-temperature excitonic lasing

Systems analysis of inflammatory bowel disease based on comprehensive gene information

<p>Abstract</p> <p>Background</p> <p>The rise of systems biology and availability of highly curated gene and molecular information resources has promoted a comprehensive approach to study disease as the cumulative deleterious function of a collection of individual genes and networks of molecules acting in concert. These "human disease networks" (HDN) have revealed novel candidate genes and pharmaceutical targets for many diseases and identified fundamental HDN features conserved across diseases. A network-based analysis is particularly vital for a study on polygenic diseases where many interactions between molecules should be simultaneously examined and elucidated. We employ a new knowledge driven HDN gene and molecular database systems approach to analyze Inflammatory Bowel Disease (IBD), whose pathogenesis remains largely unknown.</p> <p>Methods and Results</p> <p>Based on drug indications for IBD, we determined sibling diseases of mild and severe states of IBD. Approximately 1,000 genes associated with the sibling diseases were retrieved from four databases. After ranking the genes by the frequency of records in the databases, we obtained 250 and 253 genes highly associated with the mild and severe IBD states, respectively. We then calculated functional similarities of these genes with known drug targets and examined and presented their interactions as PPI networks.</p> <p>Conclusions</p> <p>The results demonstrate that this knowledge-based systems approach, predicated on functionally similar genes important to sibling diseases is an effective method to identify important components of the IBD human disease network. Our approach elucidates a previously unknown biological distinction between mild and severe IBD states.</p

Comparison of the diagnostic value of 3 T MRI after intratympanic injection of GBCA, electrocochleography, and the glycerol test in patients with Meniere's disease

Conclusion. 3 T MRI after intratympanic injection of gadolinium-based contrast agent (GBCA) is more useful for the diagnosis of endolymphatic hydrops compared with the glycerol test and electrocochleography (ECoG). Objective: To investigate the relationship between 3 T MRI after intratympanic injection of GBCA, the glycerol test, and ECoG in patients with Meniere's disease (MD). Methods: A total of 20 patients with MD were evaluated. Diluted gadodiamide (a gadolinium-based contrast agent) was administered to the bilateral tympanic cavity by injection through the tympanic membrane. After 24 h, the endolymphatic hydrops was evaluated by a 3.0 T MR scanner. To investigate cochlear hydrops, the glycerol test and ECoG were carried out in all patients. Results: A positive result was observed in 11 patients (55%) in the glycerol test and in 12 patients (60%) by ECoG. The incidence of positive findings when evaluating the same patients with both the glycerol test and ECoG increased to 75%. Nineteen of 20 (95%) patients showed positive results for 3 T MRI.ArticleACTA OTO-LARYNGOLOGICA. 132(2):141-145 (2012)journal articl

Effect of Laughter Yoga on Pulmonary Rehabilitation in Patients with Chronic Obstructive Pulmonary Disease.

Objective: To evaluate the clinical usefulness of laughter yoga for patients with chronic obstructive pulmonary disease (COPD) in a pulmonary rehabilitation setting. Design: Pilot study, with randomization of participants. Setting: This study was conducted by the Yoshino-cho National Health Insurance Yoshino Hospital Department of Internal Medicine. Participants: Stable outpatients with COPD (7 men and 1 woman, age 64 to 84 years) participated in the pulmonary rehabilitation program during a 2-week period. Intervention : The patients were divided into two groups based on a sealed envelope randomization method. The laughter yoga group had a 10-min laughter yoga session before exercise training. Patients in both groups had exercise training, educational programs, lung physiotherapy, and nutrition counseling. Outcome Measures: Health-related quality of life using the St. George's Respiratory Questionnaire (SGRQ) and the Medical Research Council (MRC) Health Survey Short Form 36-item (SF-36), depression scores using the Self-rating Depression Scale (SDS), anxiety scores using State-Trait Anxiety Inventory (STAI), and spirometry, the 6-minute walk test and mMRC dyspnea scale results were evaluated before and at 2 weeks after the program in both groups. Results: There were significant improvements in the SGRQ impacts domain and the SF-36 general health domain in the laughter yoga group, while the SF-36 physical functioning domain significantly improved in the control group. SDS and STAI result did not significantly change in either group. Spirometry, the 6-minute walk test, and MRC dyspnea scale results did not significantly change in either group. Conclusion: Laughter yoga may improve the psychological quality of life in patients with COPD