Preferred analysis methods for single genomic regions in RNA sequencing revealed by processing the shape of coverage

The informational content of RNA sequencing is currently far from being completely explored. Most of the analyses focus on processing tables of counts or finding isoform deconvolution via exon junctions. This article presents a comparison of several techniques that can be used to estimate differential expression of exons or small genomic regions of expression, based on their coverage function shapes. The problem is defined as finding the differentially expressed exons between two samples using local expression profile normalization and statistical measures to spot the differences between two profile shapes. Initial experiments have been done using synthetic data, and real data modified with synthetically created differential patterns. Then, 160 pipelines (5 types of generator × 4 normalizations × 8 difference measures) are compared. As a result, the best analysis pipelines are selected based on linearity of the differential expression estimation and the area under the ROC curve. These platform-independent techniques have been implemented in the Bioconductor package rnaSeqMap. They point out the exons with differential expression or internal splicing, even if the counts of reads may not show this. The areas of application include significant difference searches, splicing identification algorithms and finding suitable regions for QPCR primer

DNA-Liposome Hybrid Carriers for Triggered Cargo Release

The design of simple and versatile synthetic routes to accomplish triggered-release properties in carriers is of particular interest for drug delivery purposes. In this context, the programmability and adaptability of DNA nanoarchitectures in combination with liposomes have great potential to render biocompatible hybrid carriers for triggered cargo release. We present an approach to form a DNA mesh on large unilamellar liposomes incorporating a stimuli-responsive DNA building block. Upon incubation with a single-stranded DNA trigger sequence, a hairpin closes, and the DNA building block is allowed to self-contract. We demonstrate the actuation of this building block by single-molecule Förster resonance energy transfer (FRET), fluorescence recovery after photobleaching, and fluorescence quenching measurements. By triggering this process, we demonstrate the elevated release of the dye calcein from the DNA-liposome hybrid carriers. Interestingly, the incubation of the doxorubicin-laden active hybrid carrier with HEK293T cells suggests increased cytotoxicity relative to a control carrier without the triggered-release mechanism. In the future, the trigger could be provided by peritumoral nucleic acid sequences and lead to site-selective release of encapsulated chemotherapeutics. © 2022 American Chemical Society. All rights reserved

Preferred analysis methods for single genomic regions in RNA sequencing revealed by processing the shape of coverage

The informational content of RNA sequencing is currently far from being completely explored. Most of the analyses focus on processing tables of counts or finding isoform deconvolution via exon junctions. This article presents a comparison of several techniques that can be used to estimate differential expression of exons or small genomic regions of expression, based on their coverage function shapes. The problem is defined as finding the differentially expressed exons between two samples using local expression profile normalization and statistical measures to spot the differences between two profile shapes. Initial experiments have been done using synthetic data, and real data modified with synthetically created differential patterns. Then, 160 pipelines (5 types of generator × 4 normalizations × 8 difference measures) are compared. As a result, the best analysis pipelines are selected based on linearity of the differential expression estimation and the area under the ROC curve. These platform-independent techniques have been implemented in the Bioconductor package rnaSeqMap. They point out the exons with differential expression or internal splicing, even if the counts of reads may not show this. The areas of application include significant difference searches, splicing identification algorithms and finding suitable regions for QPCR primers

Research data supporting Comparison of the ionic conductivity properties of microporous and mesoporous MOFs infiltrated with a Na-ion containing IL mixture

This repository contains the raw data necessary to reproduce figures and results from the published manuscript. The zipped data represents all of the techniques reported in this publication, including: Electrochemical Impedance Spectroscopy, Elemental Analysis, Nitrogen Gas Sorption, Proton Nuclear Magnetic Resonance, Scanning Electron Microscopy, Thermogravimetric Analysis, Transmission Electron Microscopy and X-ray Diffraction. The folder_directory.txt included contains a detailed explanation of the filetypes and the contents of each folder and subfolder

Cover, etc.

ESEC/FSE'05 - Proceedings of the Joint 10th European Software Engineering Conference (ESEC) and 13th ACM SIGSOFT Symposium on the Foundations of Software Engineering (FSE-13)156-16

Using condensed representations for interactive association rule mining

Abstract. Association rule mining is a popular data mining task. It has an interactive and iterative nature, i.e., the user has to refine his mining queries until he is satisfied with the discovered patterns. To support such an interactive process, we propose to optimize sequences of queries by means of a cache that stores information from previous queries. Unlike related works, we use condensed representations like free and closed itemsets for both data mining and caching. This results in a much more efficient mining technique in highly correlated data and a much smaller cache than in previous approaches