An assessment of recently published gene expression data analyses: reporting experimental design and statistical factors

BACKGROUND: The analysis of large-scale gene expression data is a fundamental approach to functional genomics and the identification of potential drug targets. Results derived from such studies cannot be trusted unless they are adequately designed and reported. The purpose of this study is to assess current practices on the reporting of experimental design and statistical analyses in gene expression-based studies. METHODS: We reviewed hundreds of MEDLINE-indexed papers involving gene expression data analysis, which were published between 2003 and 2005. These papers were examined on the basis of their reporting of several factors, such as sample size, statistical power and software availability. RESULTS: Among the examined papers, we concentrated on 293 papers consisting of applications and new methodologies. These papers did not report approaches to sample size and statistical power estimation. Explicit statements on data transformation and descriptions of the normalisation techniques applied prior to data analyses (e.g. classification) were not reported in 57 (37.5%) and 104 (68.4%) of the methodology papers respectively. With regard to papers presenting biomedical-relevant applications, 41(29.1 %) of these papers did not report on data normalisation and 83 (58.9%) did not describe the normalisation technique applied. Clustering-based analysis, the t-test and ANOVA represent the most widely applied techniques in microarray data analysis. But remarkably, only 5 (3.5%) of the application papers included statements or references to assumption about variance homogeneity for the application of the t-test and ANOVA. There is still a need to promote the reporting of software packages applied or their availability. CONCLUSION: Recently-published gene expression data analysis studies may lack key information required for properly assessing their design quality and potential impact. There is a need for more rigorous reporting of important experimental factors such as statistical power and sample size, as well as the correct description and justification of statistical methods applied. This paper highlights the importance of defining a minimum set of information required for reporting on statistical design and analysis of expression data. By improving practices of statistical analysis reporting, the scientific community can facilitate quality assurance and peer-review processes, as well as the reproducibility of results

Risky decision-making and the intensity of opioid drug dependency in early phase of methadone maintenance protocol

Several studies show positive effect of MMT on decision-making in substance dependents, but severity of the disorder has been ignored by most of them. This study used Iowa Gambling Task(IGT) to find correlation between severity of the disorders in early phase of MMT and risky decision-making in three groups of subjects (mild, sever, control). The study shows no significant difference among groups in risky decision-making, which might be related to the effect of opioid on cognitive functions independent of the severity of the disorder, and stabilization in MMT can repair deficit in decision making shortly during the early phase

Evaluation of the quality of life in epileptic children of Shiraz, Southern Iran

Introduction: People  suffer chronic disease like epilepsy are highly prone to debilitating changes in factors that affect the quality of life such as physical capacity, self-esteem, relationships with others and fulfillment of their daily life activities.  In this study, we decided to evaluate the quality of life in children with epilepsy in Shiraz, South Iran. Methods: Epileptic patients  referred to epilepsy clinic of Shiraz University of Medical Sciences and had no first time episode of seizures in the previous 6 months and no febrile-seizure were included in the study. Patients were evaluated using the standard KIDSCREEN-27 questionnaire. Data were analyzed using the statistical software SPSS 21, Man Whitney and Chi-square tests and reported in terms of descriptive statistics. The  significance level was considered less than 0.05. Results: In this case-control study, 229 children with epilepsy were compared with a control group of 400 normal individuals. The mean age  was 12.44±3.16 and 12.10±2.69 years. The tonic-clonic seizure had the highest prevalence . Being a boy, older age and having more seizures per year were associated with lower quality of life; in general, epileptic children had significantly lower QOL compared to normal cases. Conclusion: In general, epileptic children had an overall lower QOL while factors such as older age, male gender, and higher number of seizures over the years reduced the quality of life of these patients. 

Readmission Risk Factors in Patients of General Surgery Wards in Shiraz Hospitals: Applying LACE Index as a Predictive Indicator

Background: Today, the effective use of limited health care resources is increasingly regarded. Reduction of the readmission is one of the key tools can improve health outcomes and considered as one of the control levers that reduces health costs. Identifying the causes of readmission to the hospital helps to utilize hospital beds and facilities a more efficiently.Methods: This case-control study had been conducted in general surgery (GS) wards in 2011-2012. Using chisquare test, t-test, and multiple regressions, we studied risk factors associated with readmission in both groups of case and control. Finally, the predictive power of the Length of stay, Acuity of illness, Co morbidity of the patient, Emergency (LACE) index was evaluated using receiver operating characteristic (ROC) curve.Results: About 20% of patients in GS wards were admitted within 30 days. There is a significant difference between the two groups in the following variables: age, sex, length of hospital stay, marital status, discharge season, congestive heart failure, diabetes and renal failure. The rate of readmission with LACE index which is compared with the ROC curve shows that it is significant (P < 0.001 and Kappa = 0.22).Conclusions: Awareness of the prevalence and risk factors of readmission is effective in planning and decision making for using hospital facilities efficiently. Identifying patients at risk of readmission and erforming training plan, ischarging and following up medical programs can reduce the rate of readmission and costs of hospital. Predicting readmission can be very effective but identifying an effective index is very difficult

Using Rasch rating scale model to reassess the psychometric properties of the Persian version of the PedsQLTM 4.0 Generic Core Scales in school children

<p>Abstract</p> <p>Background</p> <p>Item response theory (IRT) is extensively used to develop adaptive instruments of health-related quality of life (HRQoL). However, each IRT model has its own function to estimate item and category parameters, and hence different results may be found using the same response categories with different IRT models. The present study used the Rasch rating scale model (RSM) to examine and reassess the psychometric properties of the Persian version of the PedsQL^TM4.0 Generic Core Scales.</p> <p>Methods</p> <p>The PedsQL^TM4.0 Generic Core Scales was completed by 938 Iranian school children and their parents. Convergent, discriminant and construct validity of the instrument were assessed by classical test theory (CTT). The RSM was applied to investigate person and item reliability, item statistics and ordering of response categories.</p> <p>Results</p> <p>The CTT method showed that the scaling success rate for convergent and discriminant validity were 100% in all domains with the exception of physical health in the child self-report. Moreover, confirmatory factor analysis supported a four-factor model similar to its original version. The RSM showed that 22 out of 23 items had acceptable infit and outfit statistics (<1.4, >0.6), person reliabilities were low, item reliabilities were high, and item difficulty ranged from -1.01 to 0.71 and -0.68 to 0.43 for child self-report and parent proxy-report, respectively. Also the RSM showed that successive response categories for all items were not located in the expected order.</p> <p>Conclusions</p> <p>This study revealed that, in all domains, the five response categories did not perform adequately. It is not known whether this problem is a function of the meaning of the response choices in the Persian language or an artifact of a mostly healthy population that did not use the full range of the response categories. The response categories should be evaluated in further validation studies, especially in large samples of chronically ill patients.</p

Health related quality of life of Iranian children with type 1 diabetes: reliability and validity of the Persian version of the PedsQL™ Generic Core Scales and Diabetes Module

<p>Abstract</p> <p>Background</p> <p>The aim of this study was to measure health related quality of life (HRQOL) in Iranian children with type 1 diabetes and to test the psychometric properties of the Persian version of the PedsQL™ 4.0 Generic Core Scales and the PedsQL™ 3.0 Diabetes Module.</p> <p>Methods</p> <p>Participants were 94 children and adolescents diagnosed with type 1 diabetes for at least 3 months in Shiraz, southern Iran. Convergent, discriminant, and construct validity of the PedsQL™ 4.0 Generic Core Scales and the PedsQL™ 3.0 Diabetes Module were assessed. Moreover, internal consistency was checked by Cronbach's alpha coefficient.</p> <p>Results</p> <p>Cronbach's α for the PedsQL™ 4.0 Generic Core Scales and the PedsQL™ 3.0 Diabetes Module was greater than 0.80 both in the child self-report and parent proxy-report. Both generic and disease-specific versions of the PedsQL showed excellent convergent and acceptable discriminant validity except for 'diabetes symptoms' subscale in the child self-report of the disease-specific module. Moreover, Iranian children with diabetes, as compared with other countries, had lower HRQOL scores.</p> <p>Conclusions</p> <p>While this study showed that the Persian version of the PedsQL™ 4.0 Generic Core Scales has good psychometric properties in children with type 1 diabetes, the PedsQL™ 3.0 Diabetes Module needs some modifications to be used as a disease-specific quality of life (QOL) measure. Also, more support should be provided for the care of Iranian children with diabetes.</p

DLQI scores in vitiligo: reliability and validity of the Persian version

BACKGROUND: The objective of this study was to translate and to test the reliability and validity of the 10-item Dermatology Life Quality Index (DLQI) questionnaire in Iranian patients with vitiligo. METHODS: Using a standard "forward-backward" translation procedure, the English language version of the questionnaire was translated into Persian (the Iranian official language) by two bilinguals. Seventy patients with vitiligo attending the Department of Dermatology, Saadi Hospital, Shiraz, Iran, were enrolled in this study. The reliability and internal consistency of the questionnaire were assessed by Cronbach's alpha coefficient and Spearman's correlation, respectively. Validity was performed using convergent validity. RESULTS: In all, seventy people entered into the study. The mean age of respondents was 28.3 (SD = 11.09) years. Scores on the DLQI ranged from 0 to 24 (mean ± SD, 7.05 ± 5.13). Reliability analysis showed satisfactory result (Cronbach's α coefficient = 0.77). There were no statistically significant differences between daily activity (DA) and personal relationship (PR) scale mean scores in generalized versus focal-segmental involvement in sufferers (P = 0.056, P = 0.053, respectively). There were also strong differences between the mean scores of the PR (personal relationship) scale with the involvement of covered only and covered/uncovered areas (P= 0.016) that was statistically significant in the second group. CONCLUSIONS: The study findings showed that the Persian version of the DLQI questionnaire has a good structural characteristic and is a reliable and valid instrument that can be used for measuring the effects of vitiligo on quality of life

A Simulation Study to Assess the Effect of the Number of Response Categories on the Power of Ordinal Logistic Regression for Differential Item Functioning Analysis in Rating Scales

Objective. The present study uses simulated data to find what the optimal number of response categories is to achieve adequate power in ordinal logistic regression (OLR) model for differential item functioning (DIF) analysis in psychometric research. Methods. A hypothetical ten-item quality of life scale with three, four, and five response categories was simulated. The power and type I error rates of OLR model for detecting uniform DIF were investigated under different combinations of ability distribution (θ), sample size, sample size ratio, and the magnitude of uniform DIF across reference and focal groups. Results. When θ was distributed identically in the reference and focal groups, increasing the number of response categories from 3 to 5 resulted in an increase of approximately 8% in power of OLR model for detecting uniform DIF. The power of OLR was less than 0.36 when ability distribution in the reference and focal groups was highly skewed to the left and right, respectively. Conclusions. The clearest conclusion from this research is that the minimum number of response categories for DIF analysis using OLR is five. However, the impact of the number of response categories in detecting DIF was lower than might be expected

Knowledge management national policies for moving towards knowledge-based development: A comparison between micro and macro level

Knowledge management is a business model that embraces knowledge as an organizational asset to drive sustainable business advantage. Nowadays the leaders know that they are moving towards knowledge era very fast and they should align all activities in a way that knowledge management facilitates the competition in a better way.Developed countries also try to apply knowledge policies all over their governance to deploy knowledge management in a national level. Existing studies have derived their findings from single perspective, organizational level, or country level, or in a better way, micro or macro level and have not considered a mutual perspective to cover all requirements in a systematic way and compare the micro and macro level for knowledge management establishment.This paper is aimed to bridge this gap through a framework resulted from the analysis of the research data