On sample size calculation in drug interaction trials.

Drug-drug interaction (DDI) trials are an important part of drug development as they provide evidence on the benefits and risks when two or more drugs are taken concomitantly. Sample size calculation is typically recommended to be based on the existence of clinically justified no-effect boundaries but these are challenging to define in practice, while the default no-effect boundaries of 0.8-1.25 are known to be overly conservative requiring a large sample size. In addition, no-effect boundaries are of little use when there is prior pharmacological evidence that a mild or moderate interaction between two drugs may be present, in which case effect boundaries would be more useful. We introduce precision-based sample size calculation that accounts for both the stochastic nature of the pharmacokinetic parameters and the anticipated width of (no-)effect boundaries, should these exist. The methodology is straightforward, requires considerably less sample size and has favorable operating characteristics. A case study on statins is presented to illustrate the ideas.

A 24-Week, Phase IIa, Randomized, Double-Blind, Placebo-Controlled Study of Ziritaxestat in Early Diffuse Cutaneous Systemic Sclerosis.

OBJECTIVE: We undertook this study to explore the efficacy, safety, and tolerability of ziritaxestat, a selective autotaxin inhibitor, in patients with early diffuse cutaneous systemic sclerosis (dcSSc). METHODS: NOVESA was a 24-week, multicenter, phase IIa, double-blind, placebo-controlled study. Adults with dcSSc were randomized to oral ziritaxestat 600 mg once daily or matching placebo. The primary efficacy end point was change from baseline in modified Rodnan skin score (MRSS) at week 24. Secondary end points assessed safety and tolerability; other end points included assessment of skin and blood biomarkers. Patients in NOVESA could enter a 104-week open-label extension (OLE). RESULTS: Patients were randomized to ziritaxestat (n = 21) or placebo (n = 12). Reduction in MRSS was significantly greater in the ziritaxestat group versus the placebo group (-8.9 versus -6.0 units, respectively; P = 0.0411). Placebo patients switching to ziritaxestat in the OLE showed similar reductions in MRSS to those observed for ziritaxestat patients in the parent study. Ziritaxestat was well tolerated; the most frequent treatment-related treatment-emergent adverse events were headache and diarrhea. Circulating lysophosphatidic acid (LPA) C18:2 was significantly reduced, demonstrating ziritaxestat target engagement, and levels of fibrosis biomarkers were reduced in the blood. No differentially expressed genes were identified in skin biopsies. Significant changes in 109 genes were identified in blood samples. CONCLUSION: Ziritaxestat resulted in significantly greater reduction in MRSS at week 24 than placebo; no new safety signals emerged. Biomarker analysis suggests ziritaxestat may reduce fibrosis. Modulation of the autotaxin/LPA pathway could improve skin involvement in patients with dcSSc. A plain language summary is provided in the Supplementary Material, available on the Arthritis & Rheumatology website at https://onlinelibrary.wiley.com/doi/10.1002/art.42477.

Pathway testing for longitudinal metabolomics.

We propose a top-down approach for pathway analysis of longitudinal metabolite data. We apply a score test based on a shared latent process mixed model which can identify pathways with differentially progressing metabolites. The strength of our approach is that it can handle unbalanced designs, deals with potential missing values in the longitudinal markers, and gives valid results even with small sample sizes. Contrary to bottom-up approaches, correlations between metabolites are explicitly modeled leveraging power gains. For large pathway sizes, a computationally efficient solution is proposed based on pseudo-likelihood methodology. We demonstrate the advantages of the proposed method in identification of differentially expressed pathways through simulation studies. Finally, longitudinal metabolite data from a mice experiment is analyzed to demonstrate our methodology.

Peripheral blood transcriptome profiling enables monitoring disease progression in dystrophic mice and patients.

DMD is a rare disorder characterized by progressive muscle degeneration and premature death. Therapy development is delayed by difficulties to monitor efficacy non-invasively in clinical trials. In this study, we used RNA-sequencing to describe the pathophysiological changes in skeletal muscle of 3 dystrophic mouse models. We show how dystrophic changes in muscle are reflected in blood by analyzing paired muscle and blood samples. Analysis of repeated blood measurements followed the dystrophic signature at five equally spaced time points over a period of seven months. Treatment with two antisense drugs harboring different levels of dystrophin recovery identified genes associated with safety and efficacy. Evaluation of the blood gene expression in a cohort of DMD patients enabled the comparison between preclinical models and patients, and the identification of genes associated with physical performance, treatment with corticosteroids and body measures. The presented results provide evidence that blood RNA-sequencing can serve as a tool to evaluate disease progression in dystrophic mice and patients, as well as to monitor response to (dystrophin-restoring) therapies in preclinical drug development and in clinical trials.

Inflated false discovery rate due to volcano plots: problem and solutions.

MOTIVATION: Volcano plots are used to select the most interesting discoveries when too many discoveries remain after application of Benjamini-Hochberg's procedure (BH). The volcano plot suggests a double filtering procedure that selects features with both small adjusted $P$-value and large estimated effect size. Despite its popularity, this type of selection overlooks the fact that BH does not guarantee error control over filtered subsets of discoveries. Therefore the selected subset of features may include an inflated number of false discoveries. RESULTS: In this paper, we illustrate the substantially inflated type I error rate of volcano plot selection with simulation experiments and RNA-seq data. In particular, we show that the feature with the largest estimated effect is a very likely false positive result. Next, we investigate two alternative approaches for multiple testing with double filtering that do not inflate the false discovery rate. Our procedure is implemented in an interactive web application and is publicly available.

Simultaneous Enrichment Analysis of all Possible Gene-sets: Unifying Self-Contained and Competitive Methods.

Studying sets of genomic features is increasingly popular in genomics, proteomics and metabolomics since analyzing at set level not only creates a natural connection to biological knowledge but also offers more statistical power. Currently, there are two gene-set testing approaches, self-contained and competitive, both of which have their advantages and disadvantages, but neither offers the final solution. We introduce simultaneous enrichment analysis (SEA), a new approach for analysis of feature sets in genomics and other omics based on a new unified null hypothesis, which includes the self-contained and competitive null hypotheses as special cases. We employ closed testing using Simes tests to test this new hypothesis. For every feature set, the proportion of active features is estimated, and a confidence bound is provided. Also, for every unified null hypotheses, a $P$-value is calculated, which is adjusted for family-wise error rate. SEA does not need to assume that the features are independent. Moreover, users are allowed to choose the feature set(s) of interest after observing the data. We develop a novel pipeline and apply it on RNA-seq data of dystrophin-deficient mdx mice, showcasing the flexibility of the method. Finally, the power properties of the method are evaluated through simulation studies.

Transcranial DC stimulation modifies functional connectivity of large-scale brain networks in abstinent methamphetamine users.

Background: Transcranial direct current stimulation (tDCS) is a noninvasive brain stimulation tool suited to alter cortical excitability and activity via the application of weak direct electrical currents. An increasing number of studies in the addiction literature suggests that tDCS modulates subjective self-reported craving through stimulation of dorsolateral prefrontal cortex (DLPFC). The major goal of this study was to explore effects of bilateral DLPFC stimulation on resting state networks (RSNs) in association with drug craving modulation. We targeted three large-scale RSNs; the default mode network (DMN), the executive control network (ECN), and the salience network (SN). Methods: Fifteen males were recruited after signing written informed consent. We conducted a double-blinded sham-controlled crossover study. Twenty-minute "real" and "sham" tDCS (2 mA) were applied over the DLPFC on two separate days in random order. Each subject received both stimulation conditions with a 1-week washout period. The anode and cathode electrodes were located over the right and left DLPFC, respectively. Resting state fMRI was acquired before and after real and sham stimulation. Subjective craving was assessed before and after each fMRI scan. The RSNs were identified using seed-based analysis and were compared using a generalized linear model. Results: Subjective craving decreased significantly after real tDCS compared to sham stimulation (p = .03). Moreover, the analysis shows significant modulation of DMN, ECN, and SN after real tDCS compared to sham stimulation. Additionally, alteration of subjective craving score was correlated with modified activation of the three networks. Discussion: Given the observed alteration of the targeted functional brain networks in methamphetamine users, new potentials are highlighted for tDCS as a network intervention strategy and rsfMRI as a suitable monitoring method for these interventions.

Not single brain areas but a network is involved in language: Applications in presurgical planning.

OBJECTIVES: Language is an important human function, and is a determinant of the quality of life. In conditions such as brain lesions, disruption of the language function may occur, and lesion resection is a solution for that. Presurgical planning to determine the language-related brain areas would enhance the chances of language preservation after the operation; however, availability of a normative language template is essential. PATIENTS AND METHODS: In this study, using data from 60 young individuals who were meticulously checked for mental and physical health, and using fMRI and robust imaging and data analysis methods, functional brain maps for the language production, perception and semantic were produced. RESULTS: The obtained templates showed that the language function should be considered as the product of the collaboration of a network of brain regions, instead of considering only few brain areas to be involved in that. CONCLUSION: This study has important clinical applications, and extends our knowledge on the neuroanatomy of the language function.

State dependent effect of transcranial direct current stimulation (tDCS) on methamphetamine craving.

Transcranial direct current stimulation (tDCS) has been shown to modulate subjective craving ratings in drug dependents by modification of cortical excitability in dorsolateral prefrontal cortex (DLPFC). Given the mechanism of craving in methamphetamine (meth) users, we aimed to test whether tDCS of DLPFC could also alter self-reported craving in abstinent meth users while being exposed to meth cues. In this double-blinded, crossover, sham-controlled study, thirty two right-handed abstinent male meth users were recruited. We applied 20 min 'anodal' tDCS (2 mA) or 'sham' tDCS over right DLPFC in a random sequence while subjects performed a computerized cue-induced craving task (CICT) starting after 10 min of stimulation. Immediate craving was assessed before the stimulation, after 10 min of tDCS, and after tDCS termination by visual analog scale (VAS) of 0 to 100. Anodal tDCS of rDLPFC altered craving ratings significantly. We found a significant reduction of craving at rest in real tDCS relative to the sham condition (p = 0.016) after 10 min of stimulation. On the other hand, cue-induced VAS craving was rated significantly higher in the real condition in comparison with sham stimulation (p = 0.012). Our findings showed a state dependent effect of tDCS: while active prefrontal tDCS acutely reduced craving at rest in the abstinent meth users, it increased craving during meth-related cue exposure. These findings reflect the important role of the prefrontal cortex in both cue saliency evaluation and urge to meth consumption.

Association between psychological stress and stimulation of inflammatory responses in periodontal disease.

OBJECTIVE: Based on the evidence regarding the relationship between inflammatory processes and stress responses, the present study investigated the association between psychological stress and elevation of inflammatory mediators related to periodontal disease in adult patients. MATERIALS AND METHODS: The study consisted of 50 patients including 25 patients with chronic periodontitis and 25 cases with aggressive periodontitis. Twenty-five healthy subjects without any evidence of periodontal disorder were also randomly selected as the control group. The clinical parameters including plaque index (PI), bleeding on probing (BOP), probing depth (PPD) and clinical attachment loss (CAL) were recorded and GCF samples were collected for analysis of GCF contents of IL-6 and IL-1ß levels. The Kettle stress questionnaire was also used to determine stress severity. RESULTS: IL-1ß was significantly higher, but IL-6 was only slightly higher(marginal p-value=0.058)The median score of stress was higher in aggressive periodontitis than the chronic disorder and also in the two periodontal disease groups than the healthy subjects. Among studied clinical parameters, CAL and PPD were positively correlated with the GCF IL-1ß level. No significant correlations were found between clinical parameters and GCF IL-6 level. There were strong positive relationships between stress severity and in both aggressive and chronic periodontitis; however stress did not influence GCF contents of IL-6. CONCLUSION: Psychological stress has a pivotal role in the stimulation of inflammatory processes via IL-1ß increase in aggressive and chronic periodontitis.

Prooxidant-antioxidant balance and malondialdehyde over time in adult rats after tubal sterilization and vasectomy.

OBJECTIVE: Sterilization (tubal sterilization and vasectomy) is a widely applied contraceptive method worldwide. Although most studies have described sterilization as a safe method, there are reports of tubal ligation (TL) and vasectomy complications. The aim of this study was to evaluate the effects of TL and vasectomy on the serum oxidative stress, specifically prooxidant-antioxidant balance (PAB) and malondialdehyde (MDA) levels, over time. METHODS: Male and female rats were classified into vasectomy, sham-vasectomy, TL, and sham-TL groups, respectively. The PAB and MDA levels were measured on days 15 and 45 and months 3 and 6 after the intervention. For female rats, blood sampling was performed during the diestrous phase and estradiol and progesterone were also measured. RESULTS: Serum PAB and MDA increased after TL (p<0.05). Vasectomy increased serum MDA remarkably after 45 days, 3 months, and 6 months (p<0.05). After vasectomy, serum PAB also increased although not significantly. Serum estradiol and progesterone decreased remarkably in the TL group compared to the sham group (p<0.05). CONCLUSION: Bilateral TL and vasectomy both increase the serum oxidative stress; however the imbalance after TL was very noticeable. As for the TL, the reduction of serum estrogen levels can be involved in this imbalance. Complications followed by TL or vasectomy could be due to increased levels of oxidants. Thus, prescribing antioxidants during and or after surgery may be a solution.