Improving the prediction accuracy in classification using the combined data sets by ranks of gene expressions

<p>Abstract</p> <p>Background</p> <p>The information from different data sets experimented under different conditions may be inconsistent even though they are performed with the same research objectives. More than that, even when the data sets were generated from the same platform, the data agreement may be affected by the technical variation among the laboratories. In this case, it is necessary to use the combined data set after adjusting the differences between such data sets, for detecting the more reliable information.</p> <p>Results</p> <p>The proposed method combines data sets posterior to the discretization of data sets based on the ranks of the gene expression ratios, and the statistical method is applied to the combined data set for predictive gene selection. The efficiency of the proposed method was evaluated using five colon cancer related data sets, which were experimented using cDNA microarrays with different RNA sources, and one experiment utilized oligonucleotide arrays. NCI-60 cell lines data sets were used, which were performed with two different platforms of cDNA microarrays and Affymetrix HU6800 oligonucleotide arrays. The combined data set by the proposed method predicted the test data sets more accurately than the separated data sets did. The biological significant genes were detected from the combined data set, which were missed on the separated data sets.</p> <p>Conclusion</p> <p>By transforming gene expressions using ranks, the proposed method is not influenced by systematic bias among chips and normalization method. The method may be especially more useful to find predictive genes from data sets which have different scale in gene expressions.</p

Functional Characterization of Siberian Wild Rye Grass \u3cem\u3eEsHSP 16.9\u3c/em\u3e Gene Conferring Diverse Stress Tolerance in Prokaryotic Cells

Siberian wild rye (Elymus sibiricus L.) is a perennial, caespitose, and self-pollinating grass indigenous to Northern Asia and also is widely distributed from Northern Europe to Japan. The plant shows strong environmental adaptability with tolerance to drought and cold; thus, it is often used as forage resources (Yan et al., 2007). Environmental stresses caused by global warming are acknowledged to be as a serious issue in agriculture due to reductions of crop productivity (Ahuja et al., 2010). Genetic natural breeding of Siberian wild rye would potentially increase the productivity of forage crops; however, genetic studies on this grass have yet to be conducted. Heat shock proteins (Hsps) are the well characterized stress inducible proteins playing as molecular chaperones in prokaryotes and eukaryotes. We have also identified two differently localized small Hsps: rice chloroplastic and alfalfa mitochondrial Hsps confer tolerance to oxidative and heat stresses in tall fescue and to salinity and arsenic stresses in E. coli, tobacco, and tall fescue, respectively (Lee et al., 2012a; Lee et al., 2012b). Here, we cloned the small Hsp16.9 gene from various heat stress-induced fragments in Siberian wild rye using differentially expressed gene (DEG) analysis. We examined the mRNA expression of EsHsp16.9, in vitro molecular chaperone activity and in vivo stress tolerance by using a prokaryotic system against diverse environmental stresse

The biological significance of non-enzymatic reaction of menadione with plasma thiols: enhancement of menadione-induced cytotoxicity to platelets by the presence of blood plasma

AbstractTo test the hypothesis that the non-enzymatic reaction of quinones with thiols in plasma can generate reactive oxygens (ROS), thereby leading to potentiated cellular toxicity, we have studied the effect of a representative quinone compound, menadione, on plasma isolated from rats. The experimental results are as follows: (1) menadione generated ROS via non-enzymatic reaction with protein thiols in plasma; (2) the presence of plasma increased menadione-induced cytotoxicity to platelets; (3) pretreatment of plasma with a thiol-depleting agent significantly suppressed menadione-induced ROS and cytotoxicity. These results suggest that the non-enzymatic reaction of menadione with plasma thiols could be an important process in quinone-induced cellular toxicity

Constitutive Activation of STAT5A Promotes Human Hematopoietic Stem Cell Self-Renewal and Erythroid Differentiation

Activation of the transcription factor signal transducer and activator of transcription (STAT)5 is involved in various aspects of hematopoiesis, affecting cell proliferation, differentiation, and cell survival. Constitutive activation of STAT5 has also been associated with leukemic transformation. We overexpressed the constitutively active mutant STAT5A(1*6) in human cord blood CD34+ cells and evaluated the effects on the hematopoietic potential of stem cells in a variety of in vitro and in vivo systems. The observed phenotypic changes were correlated with differential gene expression patterns induced by STAT5A(1*6). Our data indicate that a persistent activation of STAT5A in human hematopoietic stem and progenitor cells results in their enhanced self-renewal and diverts differentiation to the erythroid lineage

Novel and simple transformation algorithm for combining microarray data sets

<p>Abstract</p> <p>Background</p> <p>With microarray technology, variability in experimental environments such as RNA sources, microarray production, or the use of different platforms, can cause bias. Such systematic differences present a substantial obstacle to the analysis of microarray data, resulting in inconsistent and unreliable information. Therefore, one of the most pressing challenges in the field of microarray technology is how to integrate results from different microarray experiments or combine data sets prior to the specific analysis.</p> <p>Results</p> <p>Two microarray data sets based on a 17k cDNA microarray system were used, consisting of 82 normal colon mucosa and 72 colorectal cancer tissues. Each data set was prepared from either total RNA or amplified mRNA, and the difference of RNA source between these two data sets was detected by ANOVA (Analysis of variance) model. A simple integration method was introduced which was based on the distributions of gene expression ratios among different microarray data sets. The method transformed gene expression ratios into the form of a reference data set on a gene by gene basis. Hierarchical clustering analysis, density and box plots, and mixture scores with correlation coefficients revealed that the two data sets were well intermingled, indicating that the proposed method minimized the experimental bias. In addition, any RNA source effect was not detected by the proposed transformation method. In the mixed data set, two previously identified subgroups of normal and tumor were well separated, and the efficiency of integration was more prominent in tumor groups than normal groups. The transformation method was slightly more effective when a data set with strong homogeneity in the same experimental group was used as a reference data set.</p> <p>Conclusion</p> <p>Proposed method is simple but useful to combine several data sets from different experimental conditions. With this method, biologically useful information can be detectable by applying various analytic methods to the combined data set with increased sample size.</p

The Clinical Usefulness of 18F-FDG PET/CT for the Evaluation of Lymph Node Metastasis in Periorbital Malignancies

PURPOSE: Surgical treatment of malignancies in the oral cavity and subsequent radiotherapy often result in an oral condition unfavorable for prosthodontic rehabilitation. This study assessed the quality of life related to oral function in edentulous head and neck cancer patients following oncology treatment of malignancies in the lower region of the oral cavity. MATERIALS AND METHODS: Patients treated between 1990 and 2000 with surgery and radiotherapy for a squamous cell carcinoma in the oral cavity who were edentulous in the mandible and had been treated with a conventional, non-implant-retained denture received an invitation for a clinical check-up (clinical assessment, questionnaires regarding oral function and quality of life). RESULTS: Sixty-seven of the 84 patients who fulfilled the inclusion criteria were willing to participate in the study. The mean irradiation dosage that these patients had received in the oral region was 61.8 +/- 5.4 Gy. Half of the patients (n=33) were not very satisfied with their prostheses; they wore their mandibular prostheses at most a few hours per day. It was concluded from the clinical assessment that two thirds of the patients (n 4) could benefit from an implant-retained mandibular denture. Analyses of the questionnaires revealed no significant associations between functional assessments, quality of life, and parameters such as size of the primary tumor, location of the primary tumor, and different treatment regimes. Despite cancer treatment, the patients reported a rather good general quality of life. CONCLUSIONS: Sequelae resulting from radiotherapy probably dominate oral function and quality of life after oncology treatment. In two thirds of the patients, improvement of oral function and related quality of life would be expected with the use of an implant-retained mandibular denture

Subscapular and Pectoralis Major Sparing Deltopectoral Approach for Reverse Total Shoulder Arthroplasty

In reverse ball shoulder replacement, surgery is usually performed using a deltopectoral approach or an anterosuperior transdeltoid approach. The deltopectoral approach is to incise the pectoralis major to upper 1/3 to 1/2, and subscapularis tendon should be removed at the lesser tuberosity of the humerus. This approach has the problem of breaking the shoulder deltoid instead of incising the rotator cuff. Therefore, we report a detailed procedure of reverse ball shoulder replacement using approach without incision of the pectoralis major muscle and subscapularis muscle

Treatment of instability with scapular notching and glenoid component loosing by partial mixed different implant revision

In general, reverse shoulder arthroplasty revision is performed using the same implant for both the humerus and glenoid components. However, the authors of the present case used different implants from what was used previously for treating instability with scapular notching and glenoid aseptic loosening and report the case