Computational Design of Artificial RNA Molecules For Gene Regulation

This volume provides an overview of RNA bioinformatics methodologies, including basic strategies to predict secondary and tertiary structures, and novel algorithms based on massive RNA sequencing. Interest in RNA bioinformatics has rapidly increased thanks to the recent high-throughput sequencing technologies allowing scientists to investigate complete transcriptomes at single nucleotide resolution. Adopting advanced computational technics, scientists are now able to conduct more in-depth studies and present them to you in this book. Written in the highly successful Methods of Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and equipment, step-by-step, readily reproducible bioinformatics protocols, and key tips to avoid known pitfalls.Authoritative and practical, RNA Bioinformatics seeks to aid scientists in the further study of bioinformatics and computational biology of RNA

Membrane domains and polarized trafficking of sphingolipids

The plasma membrane of polarized cells consists of distinct domains, the apical and basolateral membrane that are characterized by a distinct lipid and protein content. Apical protein transport is largely mediated by (glyco)sphingolipid-cholesterol enriched membrane microdomains, so called rafts. In addition changes in the direction of polarized sphingolipid transport appear instrumental in cell polarity development. Knowledge is therefore required of the mechanisms that mediate sphingolipid sorting and the complexity of the trafficking pathways that are involved in polarized transport of both sphingolipids and Proteins. Here rue summarize specific biophysical properties that underly mechanisms relevant to sphingolipid sorting, cargo recruitment and polarized trafficking, and discuss the central role of a subapical compartment, SAC or common endosome (CE), as a major intracellular site involved In polarized sorting of sphingolipids, and in development and maintenance of membrane polarity

Membrane dynamics and cell polarity: the role of sphingolipids

In recent years, glycosphingolipids (GSLs) have attracted widespread attention due to the appreciation that this class of lipids has a major impact on biological life. Inhibition of the synthesis of glucosylceramide, which serves as a precursor for the generation of complex glycosphinglipids, is embryonic lethal. GSLs play a major role in growth and development. Metabolites of sphingolipids, such as ceramide, sphinganine, and sphingosine, may function as second messengers or regulators of signal transduction that affect events ranging from apoptosis to the (co)regulation of the cell cycle. In addition, GSLs can provide a molecular platform for clustering of signal transducers. The ability of sphingolipids, with or without cholesterol, to form microdomains or rafts is critical in sorting and membrane transport that underlies the biogenesis of polarized membrane domains. Here, a brief summary is presented of some recent developments in this field, with a particular emphasis on raft assembly and membrane transport in the establishment of membrane polarity

Efficacy and Safety of Ceritinib 450 mg/day with Food and 750 mg/day in Fasted State in Treatment-Naïve Patients with ALK+ Non-Small Cell Lung Cancer: Results from the ASCEND-8 Asian Subgroup Analysis

PURPOSE: Previous report from the ASCEND-8 trial showed consistent efficacy with less gastrointestinal (GI) toxicity in patients with anaplastic lymphoma kinase-rearranged (ALK+) advanced/metastatic non-small cell lung cancer (NSCLC) treated with ceritinib 450-mg with food compared with 750-mg fasted. In this subgroup analysis, we report outcomes in Asian patients of the ASCEND-8 trial. MATERIALS AND METHODS: Key efficacy endpoints were blinded independent review committee (BIRC)-assessed overall response rate (ORR) and duration of response (DOR) evaluated per Response Evaluation Criteria in Solid Tumors v1.1. Other efficacy endpoints were investigator-assessed ORR and DOR; BIRC- and investigator-assessed progression-free survival (PFS) and disease control rate; overall survival (OS). Safety was evaluated by frequency and severity of adverse events. RESULTS: At final data cutoff (6 March 2020), 198 treatment-naïve patients were included in efficacy analysis, of which 74 (37%) comprised the Asian subset; 450-mg fed (n=29), 600-mg fed (n=19), and 750-mg fasted (n=26). Baseline characteristics were mostly comparable across study arms. At baseline, more patients in 450-mg fed arm (44.8%) had brain metastases than in 750-mg fasted arm (26.9%). Per BIRC, patients in the 450-mg fed arm had a numerically higher ORR, 24-month DOR rate and 24-month PFS rate than the 750-mg fasted arm. The 36-month OS rate was 93.1% in 450-mg fed arm and 70.9% in 750-mg fasted arm. Any-grade GI toxicity occurred in 82.8% and 96.2% of patients in the 450-mg fed and 750-mg fasted arms, respectively. CONCLUSION: Asian patients with ALK+ advanced/metastatic NSCLC treated with ceritinib 450-mg fed showed numerically higher efficacy and lower GI toxicity than 750-mg fasted patients.Y

Feature Extraction of Hidden Oscillation in ECG Data Via Multiple-FOD Method

Fourier transform (FT) is a non-parametric method which can be used to convert the time domain data into the frequency domain and can be used to find the periodicity of oscillations in time series datasets. In order to detect periodic-like outliers in time series data, a novel and promising method, named as the outlier detection via Fourier transform (FOD), has been developed. From our previous studies, it has been shown that FOD outperforms most of the commonly used approaches for the detection of outliers when the outliers have periodicity with low fold changes or high sample sizes. Recently, the multiple oscillation and hidden periodic-like pattern cases for time series data have been investigated and found that the multiple application of FOD, shortly multiple-FOD, can also be a successful method in the detection of such patterns. These empirical results are based on real electrocardiogram (ECG) data where the discrimination of disorders can be helpful for the diagnosis of certain heart diseases in advance. Hereby, in this study, we evaluate the performance of multiple-FOD in different types of simulated datasets which have distinct sample sizes, percentage of outliers and distinct hidden patterns