An efficient statistical feature selection approach for classification of gene expression data

Classification of gene expression data plays a significant role in prediction and diagnosis of diseases. Gene expression data has a special characteristic that there is a mismatch in gene dimension as opposed to sample dimension. All genes do not contribute for efficient classification of samples. A robust feature selection algorithm is required to identify the important genes which help in classifying the samples efficiently. In order to select informative genes (features) based on relevance and redundancy characteristics, many feature selection algorithms have been introduced in the past. Most of the earlier algorithms require computationally expensive search strategy to find an optimal feature subset. Existing feature selection methods are also sensitive to the evaluation measures. The paper introduces a novel and efficient feature selection approach based on statistically defined effective range of features for every class termed as ERGS (Effective Range based Gene Selection). The basic principle behind ERGS is that higher weight is given to the feature that discriminates the classes clearly. Experimental results on well-known gene expression datasets illustrate the effectiveness of the proposed approach. Two popular classifiers viz. Nave Bayes Classifier (NBC) and Support Vector Machine (SVM) have been used for classification. The proposed feature selection algorithm can be helpful in ranking the genes and also is capable of identifying the most relevant genes responsible for diseases like leukemia, colon tumor, lung cancer, diffuse large B-cell lymphoma (DLBCL), prostate cancer.

A New Selection Measure for Classification Using Decision Trees

The paper proposes a new selection measure for classification using decision trees for Data mining. Various algorithms have been proposed in the past for classification using decision trees viz. ID3, CART, SLIQ, etc. Selection measures like the Gain, Gain ratio, and Gini index have been proposed in these algorithms. However, none of the selection measures developed so far take into account the balancing of trees. This paper proposes a new selection measure which also takes into account the balancing of trees that will facilitate in improving the classification accuracy. The performance of the original SLIQ algorithm, C5 and the algorithm using the new selection measure (which takes into account the accuracy as well as the balance factor) was measured on the basis of the classification accuracy. Three real life data sets were chosen for this purpose.

Aesthetic evolution and its infusion in consumer durable

This paper explores some aspects of aesthetics, its qualities and attributes in case of a consumer durable and the association of some attributes and quality with one another. Attempt is also made to understand the extent to which these play a role in designing a consumer durable. The attribute beauty, quality, feel and experience emerged important, whereas in the case of qualities of aesthetics beauty, order and symmetry, definitions, form proportion, finishing and unity of various parts emerged important. Amongst attributes, feel and experience has the highest association with other attributes of aesthetics. The correlation between qualities of aesthetics established that there is association between all the qualities of aesthetics, which confirms interrelationship with each other.

Prognostic significance of biologic factors in squamous cell carcinoma of the esophagus

BACKGROUND

Esophageal carcinoma is one of the most lethal tumors. Therefore, it is important to identify prognostic factors for patients with this disease. The objective of this study was to clarify the relation between clinicopathologic and biologic factors in esophageal carcinoma and to determine the prognostic significance of different biologic factors.

METHODS

DNA ploidy pattern, Ki-67 labeling index (LI), and cyclin D1 and p53 protein expression were examined and detailed pathologic examinations were conducted on tumors from 53 patients (46 males and 7 females with a mean age of 66 years [range, 47-85 years]) with surgically resected esophageal squamous cell carcinoma and the prognostic value of these factors was evaluated.

RESULTS

Of the 53 esophagus carcinomas examined, 26 (49%) were classified as DNA diploid. The mean Ki-67 LI was 45 +/- 4. 9% (range, 10.5-86.1%). p53 expression was detected in 38 of the carcinomas (71.7%) and cyclin D1 expression was detected in 35 (66%). Various prognostic factors were examined using the Cox stepwise regression model, four of which were found to correlate with overall survival: tumor size (P = 0.0346), lymph node status (P = 0.0384), Ki-67 LI (P = 0.0161), and p53 expression (P = 0.001). Lower Ki-67 LI and a lower rate of p53 expression were detected in the long term survival group (> 3 years) compared with the short term survival group (P = 0.00045 and P = 0.0023, respectively).

CONCLUSIONS

The biologic factors of Ki-67 LI and p53 expression, as well as clinicopathologic factors, may be used as independent prognostic factors for patients with esophageal carcinoma. However, the results of the current study do not support cyclin D1 expression as a prognostic factor.

Prognostic significance of biologic factors in squamous cell carcinoma of the esophagus

BACKGROUND

Esophageal carcinoma is one of the most lethal tumors. Therefore, it is important to identify prognostic factors for patients with this disease. The objective of this study was to clarify the relation between clinicopathologic and biologic factors in esophageal carcinoma and to determine the prognostic significance of different biologic factors.

METHODS

DNA ploidy pattern, Ki-67 labeling index (LI), and cyclin D1 and p53 protein expression were examined and detailed pathologic examinations were conducted on tumors from 53 patients (46 males and 7 females with a mean age of 66 years [range, 47-85 years]) with surgically resected esophageal squamous cell carcinoma and the prognostic value of these factors was evaluated.

RESULTS

Of the 53 esophagus carcinomas examined, 26 (49%) were classified as DNA diploid. The mean Ki-67 LI was 45 +/- 4. 9% (range, 10.5-86.1%). p53 expression was detected in 38 of the carcinomas (71.7%) and cyclin D1 expression was detected in 35 (66%). Various prognostic factors were examined using the Cox stepwise regression model, four of which were found to correlate with overall survival: tumor size (P = 0.0346), lymph node status (P = 0.0384), Ki-67 LI (P = 0.0161), and p53 expression (P = 0.001). Lower Ki-67 LI and a lower rate of p53 expression were detected in the long term survival group (> 3 years) compared with the short term survival group (P = 0.00045 and P = 0.0023, respectively).

CONCLUSIONS

The biologic factors of Ki-67 LI and p53 expression, as well as clinicopathologic factors, may be used as independent prognostic factors for patients with esophageal carcinoma. However, the results of the current study do not support cyclin D1 expression as a prognostic factor.

Iron overload in patients with chronic hepatitis C: a clinicopathologic study

Recent studies suggest that increased hepatic iron may impair the response to interferon therapy in patients with chronic hepatitis C. We reviewed the records and liver biopsies of 72 patients with chronic hepatitis C to determine the prevalence of iron overload and to evaluate whether there is a correlation between serum and hepatic iron concentrations and activity of liver disease. Patients with other causes of liver disease or iron overload were excluded. Necroinflammatory activity and fibrosis were evaluated using modified Knodell score. Hepatic iron was assessed using Brissot's grading system. Increased serum iron and ferritin levels were found in 29% and 43% patients, respectively. Hepatic iron grades 0, I, II, III, and IV were present in 37%, 35%, 25%, 3%, and 0% of patients, respectively. A significant correlation was found between hepatic iron grade and serum ferritin (P = .0001). There was no correlation between hepatic iron grade and histological activity index or fibrosis score. In summary, we found a high proportion of patients with chronic hepatitis C had mild to moderate increase in hepatic iron content even when patients with alcoholism and recurrent transfusions were excluded. However, very few patients had severely increased iron load.

Alkaptonuria and renal failure: a case report and review of the literature

In alkaptonuric ochronosis, the absence of homogentisic acid oxidase results in the accumulation of homogentisic acid in the body. Associated renal failure is rare and usually occurs in the later stages of the disease. We report a 19-yr-old girl who presented initially with severe renal failure, without family or past history of illness. There was no significant proteinuria or hematuria. No clinical evidence of pigmentation such as skin and subcutaneous cartilages was noted. However, pigment deposits were identified in the renal biopsy specimens obtained within a week after admission and another after a month. Two months later the peritoneal dialysis fluid and skin progressively darkened, suggesting ochronosis. This was confirmed by the detection of homogentisic acid in the serum and urine. The patient expired in renal failure. Renal biopsy tissues showed diffuse chronic tubulo-interstitial disease characterized by widespread tubular atrophy, interstitial fibrosis, and a moderate degree of inflammation. Many tubular cells contained brown, coarsely granular ochronotic pigment (OP) and a few pigment casts were in the lumina. Similar deposits were also in the interstitium and within histiocytes. Ultrastructural studies of the glomeruli revealed small sparse OP deposits in the visceral and parietal epithelial cells, mesangial cells, and rare extracellular and basement membrane deposits. The tubulointerstitial changes were varied: atrophy and dilatation of tubules, varying degrees of lysosomal OP and degeneration of tubular cells, casts containing OP with crystalline material, histiocytes distended with OP, and free interstitial pigment deposition.(ABSTRACT TRUNCATED AT 250 WORDS)

First seizure in adults: to treat or not to treat

A double-blind trial was done in 228 patients with one single seizure 2 weeks before coming to the author. One group was given sodium valproate, the other group placebo. The duration of therapy was 12 months. The results of this trial show that a person with a single seizure has epilepsy and should be treated with sodium valproate.