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.     

Elevated monoclonal and polyclonal serum immunoglobulin free light chain as prognostic factors in B‐ and T‐cell non‐Hodgkin lymphoma

The serum immunoglobulin free light chain (FLC) assay quantitates free kappa (κ) and lambda (λ) light chains. FLC elevations in patients with diffuse large B‐cell lymphoma (DLBCL), Hodgkin lymphoma (HL), and chronic lymphocytic leukemia (CLL) are associated with an inferior survival. These increases in FLC can be monoclonal (as in myeloma) or polyclonal. The goal was to estimate the frequency of these elevations within distinct types of B‐cell and T‐cell non‐Hodgkin lymphoma (NHL) and whether the FLC measurements are associated with event‐free survival (EFS). We studied serum for FLC abnormalities using normal laboratory reference ranges to define an elevated κ or λ FLC. Elevations were further classified as polyclonal or monoclonal. Four hundred ninety‐two patients were studied: 453 B‐cell and 34 T‐cell NHL patients. Twenty‐nine % (142/453) of patients had an elevated FLC of which 10% were monoclonal elevations. Within B‐cell NHL, FLC abnormalities were most common in lymphoplasmacytic (79%), mantle cell (68%), and lymphomas of mucosa associated lymphoid tissue (31%); they were least common in follicular (15%). The hazard ratio (HR) for EFS in all patients was 1.41 (95% CI; 1.11–1.81); in all B‐cell NHL the HR was 1.44 (95% CI 1.11–1.96); in all T‐cell NHL the HR was 1.17 (95% CI 0.55–2.49). FLC abnormalities predicted an inferior OS (HR = 2.75, 95% CI: 1.93–3.90, P < 0.0001). The serum FLC assay is useful for prognosis in both B‐cell and T‐cell types of NHL. In B‐cell NHL further discrimination between a monoclonal and polyclonal elevation may be helpful and should be analyzed in prospective clinical trials. Am. J. Hematol. 89:1116–1120, 2014. © 2014 Wiley Periodicals, Inc.     

A simple bactericidal antibody test for sero-diagnosis of typhoid fever

Serum samples were collected from 24 confirmed cases of typhoid fever, 15 clinically suspected cases and 23 normal healthy controls. The convalescent sera were obtained in 13 of the 24 confirmed typhoid cases. In all, 13 paired sera, 11 acute phase only, 15 clinically suspected and 23 normal serum samples were tested for eliciting bactericidal antibodies to Salmonella typhi. In addition, the Widal test was also performed for comparison. All the 24 acute phase sera as well as 13 convalescent sera were found to be positive by bactericidal antibody test (titre 1:80 or above). Of 15 clinically suspected cases, 5 were positive whereas one of the 23 normal controls sera gave a false positive reaction. In contrast, the Widal test could detect only one of the 24 cases in the acute stage, but all 13 cases showed antibodies at a diagnostic titre level during the convalescent stage. None of the 15 clinically suspected cases or 23 normal controls were positive by the Widal test. The feasibility of using a bactericidal antibody test in sero-diagnosis of typhoid fever is discussed.     

Carried meningococci in the Czech Republic: a diverse recombining population

Population and evolutionary analyses of pathogenic bacteria are frequently hindered by sampling strategies that concentrate on isolates from patients with invasive disease. This is especially so for the gram-negative diplococcus Neisseria meningitidis, a cause of septicemia and meningitis worldwide. Meningococcal isolate collections almost exclusively comprise organisms originating from patients with invasive meningococcal disease, although this bacterium is a commensal inhabitant of the human nasopharynx and very rarely causes pathological effects. In the present study, molecular biology-based techniques were used to establish the genetic relationships of 156 meningococci isolated from healthy young adults in the Czech Republic during 1993. None of the individuals sampled had known links to patients with invasive disease. Multilocus sequence typing (MLST) showed that the bacterial population was highly diverse, comprising 71 different sequence types (STs) which were assigned to 34 distinct complexes or lineages. Three previously identified hyperinvasive lineages were present: 26 isolates (17%) belonged to the ST-41 complex (lineage 3); 4 (2.6%) belonged to the ST-11 (electrophoretic type [ET-37]) complex, and 1 (0.6%) belonged to the ST-32 (ET-5) complex. The data were consistent with the view that most nucleotide sequence diversity resulted from the reassortment of alleles by horizontal genetic exchange.     

Markedly disturbed sleep in medically refractory compared to controlled epilepsy - a clinical and polysomnography study

PurposeTo evaluate sleep disturbances or sleep related events and their characteristics among patients with medically refractory epilepsy, compared to those with controlled epilepsy.MethodsIn a prospective case-controlled study, patients of medically refractory and controlled epilepsy were recruited and history pertaining to epilepsy and sleep related events and Epworth sleepiness scores were recorded and all patients underwent over night polysomnography.ResultsAmong 40 patients, 20 with medically refractory (Group 1) and 20 with controlled epilepsy (Group 2) (median age 18, range 10–35 years), the self reported sleep parameters in Group 1 patients were found to be significantly different as compared to Group 2, in terms of the duration of night time sleep, day time sleep, day time nap frequency, total sleep hours per day, excessive daytime sleepiness (EDS)(45% vs. 15%) and average sleep hours over the week prior to polysomnography. On PSG, Group 1 patients showed significantly less total sleep time [340.4 min (147–673) vs. 450.3 min (330–570)] with delayed sleep latency and REM latency, poor sleep efficiency [80.45 (40.5–98.0) vs. 95.45 (88.4–99.7)] and frequent arousals and wake after sleep onset (WASO) compared to Group 2 patients. Four patients (20%) in Group 1 compared to none in Group 2 were found to have mild obstructive sleep apnea.ConclusionsOur results indicate that medically refractory epilepsy patients believe that they spend more time sleeping, in contrast to the documented shorter sleep duration on polysomnography. This difference between perceived and actual sleep seems, by their data, to arise mainly from sleep fragmentation, disturbed architecture and the interesting finding of associated sleep apnea among the medically refractory epilepsy patients.     

Clinical profile of psychogenic non-epileptic seizures in adults: A study of 63 cases

Aims:

To evaluate clinical profile and short-term outcome of psychogenic non-epileptic seizures (PNES) in Indian adult population.

Setting and Design:

A prospective observational study, conducted at tertiary teaching institute at New Delhi.

Materials and Methods:

Sixty-three patients with confirmed PNES were enrolled. The diagnosis was based on witnessing the event during video-electroencephalography (Video-EEG) monitoring. A detailed clinical evaluation was done including evaluation for coexistent anxiety or depressive disorders. Patients were divided into two groups on the basis of excessive or paucity of movements during PNES attacks. Patients were followed-up to 12 months for their PNES frequency.

Statistical Analysis:

Means and standard deviations were calculated for continuous variables. Chi-square and Students t-test were used to compare categorical and continuous variables respectively.

Results:

The mean age at onset of PNES was 25.44 years; with F:M ratio of 9.5:1. Coexistent epilepsy was present in 13 (20.63%) cases. Twenty-two patients (44%) with only PNES (n = 50) had received antiepileptic drugs. Out of 63 patients of PNES 24 (38.1%) had predominant motor phenomenon, whereas 39 (61.9%) had limp attacks. The common features observed were pre-ictal headache, ictal eye closure, jaw clenching, resistant behavior, ictal weeping, ictal vocalization, and unresponsiveness during episodes. Comorbid anxiety and depressive disorders was seen in 62.3% and 90.16% patients, respectively. Short-term (6-12 months) outcome of 45 patients was good (seizure freedom in 46.66% and >50% improvement in 24.44% cases).

Conclusion:

PNES is common, but frequently misdiagnosed and treated as epileptic seizures. A high index of suspicion is required for an early diagnosis. Proper disclosure of diagnosis and management of the psychiatric comorbidities can improve their outcome.

Limitation:

Limited sample size and change in seizures frequency as the only parameter for the assessment of the outcome are the two major limitations of our study.