Biostatistics Series Module 3: Comparing Groups: Numerical Variables

Numerical data that are normally distributed can be analyzed with parametric tests, that is, tests which are based on the parameters that define a normal distribution curve. If the distribution is uncertain, the data can be plotted as a normal probability plot and visually inspected, or tested for normality using one of a number of goodness of fit tests, such as the Kolmogorov–Smirnov test. The widely used Student''s t-test has three variants. The one-sample t-test is used to assess if a sample mean (as an estimate of the population mean) differs significantly from a given population mean. The means of two independent samples may be compared for a statistically significant difference by the unpaired or independent samples t-test. If the data sets are related in some way, their means may be compared by the paired or dependent samples t-test. The t-test should not be used to compare the means of more than two groups. Although it is possible to compare groups in pairs, when there are more than two groups, this will increase the probability of a Type I error. The one-way analysis of variance (ANOVA) is employed to compare the means of three or more independent data sets that are normally distributed. Multiple measurements from the same set of subjects cannot be treated as separate, unrelated data sets. Comparison of means in such a situation requires repeated measures ANOVA. It is to be noted that while a multiple group comparison test such as ANOVA can point to a significant difference, it does not identify exactly between which two groups the difference lies. To do this, multiple group comparison needs to be followed up by an appropriate post hoc test. An example is the Tukey''s honestly significant difference test following ANOVA. If the assumptions for parametric tests are not met, there are nonparametric alternatives for comparing data sets. These include Mann–Whitney U-test as the nonparametric counterpart of the unpaired Student''s t-test, Wilcoxon signed-rank test as the counterpart of the paired Student''s t-test, Kruskal–Wallis test as the nonparametric equivalent of ANOVA and the Friedman''s test as the counterpart of repeated measures ANOVA.     

A randomized cross-over trial to define neurophysiological correlates of AV-101 N-methyl-d-aspartate receptor blockade in healthy veterans

The kynurenine pathway (KP) is a strategic metabolic system that combines regulation of neuronal excitability via glutamate receptor function and neuroinflammation via other KP metabolites. This pathway has great promise in treatment of depression and suicidality. The KP modulator AV-101 (4-chlorokynurenine, 4-Cl-KYN), an oral prodrug of 7-chlorokynurenic acid (7-Cl-KYNA), an N-methyl-d-aspartate receptor (NMDAR) glycine site antagonist, and of 4-chloro-3-hydroxyanthranilic acid (4-Cl-3-HAA), a suppressor of NMDAR agonist quinolinic acid (QUIN), is a promising potential antidepressant that targets glutamate functioning via the KP. However, a recent placebo-controlled clinical trial of AV-101 in depression found negative results. This raises the question of whether AV-101 can penetrate the brain and engage the NMDAR and KP effectively. To address this problem, ten healthy US military veterans (mean age = 32.6 years ± 6.11; 1 female) completed a phase-1 randomized, double-blind, placebo-controlled, crossover study to examine dose-related effects of AV-101 (720 and 1440 mg) on NMDAR engagement measured by γ-frequency band auditory steady-state response (40 Hz ASSR) and resting EEG. Linear mixed models revealed that 1440 mg AV-101, but not 720 mg, increased 40 Hz ASSR and 40 Hz ASSR γ-inter-trial phase coherence relative to placebo. AV-101 also increased 4-Cl-KYN, 7-Cl-KYNA, 4-Cl-3-HAA, 3-HAA, and KYNA in a dose-dependent manner, without affecting KYN and QUIN. AV-101 was safe and well tolerated. These results corroborate brain target engagement of 1440 mg AV-101 in humans, consistent with blockade of interneuronal NMDAR blockade. Future studies should test higher doses of AV-101 in depression. Suicidal behavior, which has been associated with high QUIN and low KYNA, is also a potential target for AV-101.Subject terms: Biomarkers, Neurophysiology, Neuroscience     

Development and Evaluation of Probioticated Cucumber Juice Using <Emphasis Type="Italic">Lactobacillus plantarum</Emphasis>

The aim of the present study was to develop a probioticated cucumber juice by optimizing the concentration of prebiotic (inulin), stevia (Stevia rebudiana) and inoculum (Lactobacillus plantarum) by varying one factor at a time. Cucumber juice with 2% prebiotic had a pH 3.76, acidity 0.239%, total sugars 198.2 μg/mL, reducing sugars 102.3 μg/mL and microbial viability of 1.36 × 10⁸ colony forming units (CFU)/mL, respectively. The juice with 3% stevia had a pH 3.59, acidity 0.388%, total sugars 214 μg/mL, reducing sugars 156.7 μg/mL and microbial viability of 6.7 × 10⁷ CFU/mL, respectively. The juice with 3% inoculum size had a pH 3.82, acidity 0.39%, total sugars 128.3 μg/mL, reducing sugars 198.6 μg/mL and microbial viability of 3.5 × 10⁸ CFU/mL, respectively. Maximum growth of the probiotic (L. plantarum) in the cucumber juice was obtained at the end of 48 h of fermentation for 2% prebiotic, 3% stevia and 3% inoculum size without much changes in nutritional and organoleptic properties. The probiotic strain namely L. plantarum proved its ability and suitability to ferment cucumber juice. The growth of the probiotic in the cucumber juice was found maximum with 2% prebiotic, 3% stevia and 3% inoculum size at the end of 48 h of fermentation with minimal changes in nutritional value and organoleptic characteristics with a good shelf life at 4 °C in polyethylene terephthalate bottles.     

Human hepatocyte assessment of imatinib drug–drug interactions – complexities in clinical translation

Aim

Inducers and inhibitors of CYP3A, such as ritonavir and efavirenz, may be used as part of the highly active antiretroviral therapy (HAART) to treat HIV patients. HIV patients with chronic myeloid leukemia or gastrointestinal stromal tumour may need imatinib, a CYP3A4 substrate with known exposure response–relationships. Administration of imatinib to patients on ritonavir or efavirenz may result in altered imatinib exposure leading to increased toxicity or failure of therapy, respectively. We used primary human hepatocyte cultures to evaluate the magnitude of interaction between imatinib and ritonavir/efavirenz.

Methods

Hepatocytes were pre-treated with vehicle, ritonavir, ketoconazole, efavirenz or rifampicin, and the metabolism of imatinib was characterized over time. Concentrations of imatinib and metabolite were quantitated in combined lysate and medium, using LC-MS.

Results

The predicted changes in imatinib CL_oral (95% CI) with ketoconazole, ritonavir, rifampicin and efavirenz were 4.0-fold (0, 9.2) lower, 2.8-fold (0.04, 5.5) lower, 2.9-fold (2.2, 3.5) higher and 2.0-fold (0.42, 3.5) higher, respectively. These predictions were in good agreement with clinical single dose drug–drug interaction studies, but not with reports of imatinib interactions at steady-state. Alterations in metabolism were similar after acute or chronic imatinib exposure.

Conclusions

In vitro human hepatocytes predicted increased clearance of imatinib with inducers and decreased clearance with inhibitors of CYP enzymes. The impact of HAART on imatinib may depend on whether it is being initiated or has already been dosed chronically in patients. Therapeutic drug monitoring may have a role in optimizing imatinib therapy in this patient population.     

Effectiveness of medical thoracoscopy and thoracoscopic talc poudrage in patients with exudative pleural effusion

INTRODUCTION

This study aimed to assess the effectiveness of medical thoracoscopy (MT) and thoracoscopic talc poudrage (TTP) in patients with exudative pleural effusion.

METHODS

We evaluated the diagnostic yields, complications and outcomes of MT and TTP in 41 consecutive patients with symptomatic pleural effusions who were planned to undergo both procedures from 1 December 2011 to 30 November 2012. Data was reviewed retrospectively and prospectively up to March 2013.

RESULTS

Among the 41 patients, 36 underwent MT with the intent of biopsy and talc pleurodesis, 2 underwent MT for pleurodesis only and 3 had failed MT. Aetiologies of pleural effusion included lung cancer (n = 14), tuberculosis (n = 9), breast cancer (n = 7), ovarian cancer (n = 2), malignant mesothelioma (n = 1), congestive cardiac failure (n = 1), peritoneal dialysis (n = 1) and hepatic hydrothorax (n = 1); pleural effusion was undiagnosed in five patients. The overall diagnostic yield of MT, and the yield in tubercular and malignant pleural effusions were 77.8%, 100.0% and 82.6%, respectively; it was inconclusive in 22.2%. Complications that occurred were self-limiting, with no procedure-related mortality. The 30-day mortality rate was 17.1%. A total of 15 patients underwent TTP. The 30-, 60- and 90-day success rates were 77.8%, 80.0% and 80.0%, respectively, with one patient having complications (i.e. empyema). The 30-day mortality was 40.0%.

CONCLUSION

MT is a safe procedure with high diagnostic yields in undiagnosed pleural effusions. TTP is an effective method to stop recurrence of pleural effusions.     

Clinical, histopathologic, and genetic features of pediatric primary myelofibrosis--an entity different from adults

Primary myelofibrosis is a chronic myeloproliferative neoplasm characterized by cytopenias, leukoerythroblastosis, extramedullary hematopoiesis, hepatosplenomegaly and bone marrow fibrosis. Primary myelofibrosis is a rare disorder in adults; children are even less commonly affected by this entity, with the largest pediatric case series reporting on three patients. Most literature suggests spontaneous resolution of myelofibrosis without long term complications in the majority of affected children. We describe the clinical, pathologic, and molecular characteristics and outcomes of nineteen children with primary myelofibrosis treated in our center from 1984 to 2011. Most patients had cytopenia significant enough to require supportive therapy. No child developed malignant transformation and only five of the 19 children (26%) had spontaneous resolution of disease. Sequence analyses for JAK2V617F and MPLW515L mutations were performed on bone marrow samples from 17 and six patients, respectively, and the results were negative. In conclusion, analysis of this large series of pediatric patients with primary myelofibrosis demonstrates distinct clinical, hematologic, bone marrow, and molecular features from adult patients.