NERD-seq: a novel approach of Nanopore direct RNA sequencing that expands representation of non-coding RNAs.

Non-coding RNAs (ncRNAs) are frequently documented RNA modification substrates. Nanopore Technologies enables the direct sequencing of RNAs and the detection of modified nucleobases. Ordinarily, direct RNA sequencing uses polyadenylation selection, studying primarily mRNA gene expression.

Increased Alu RNA processing in Alzheimer brains is linked to gene expression changes.

Despite significant steps in our understanding of Alzheimer's disease (AD), many of the molecular processes underlying its pathogenesis remain largely unknown. Here, we focus on the role of non-coding RNAs produced by small interspersed nuclear elements (SINEs). RNAs from SINE B2 repeats in mouse and SINE Alu repeats in humans, long regarded as "junk" DNA, control gene expression by binding RNA polymerase II and suppressing transcription.

Increased processing of SINE B2 ncRNAs unveils a novel type of transcriptome deregulation in amyloid beta neuropathology.

The functional importance of many non-coding RNAs (ncRNAs) generated by repetitive elements and their connection with pathologic processes remains elusive. B2 RNAs, a class of ncRNAs of the B2 family of SINE repeats, mediate through their processing the transcriptional activation of various genes in response to stress. Here, we show that this response is dysfunctional during amyloid beta toxicity and pathology in the mouse hippocampus due to increased levels of B2 RNA processing, leading to constitutively elevated B2 RNA target gene expression and high levels.

Pollutants from primary sources dominate the oxidative potential of water-soluble PM in Hong Kong in terms of dithiothreitol (DTT) consumption and hydroxyl radical production.

Increasing scientific findings show that the adverse health effects of PM are related not only to its mass but also PM sources and chemical compositions. Here, we conducted a comprehensive characterization and source apportionment of oxidative potential (OP) of water-soluble PM collected in Hong Kong for one year. Two OP indicators, namely dithiothreitol (DTT) consumption and ∙OH formation, were quantified.

Correction to: Speciation of carboxylic components in humic-like substances (HULIS) and source apportionment of HULIS in ambient fine aerosols (PM) collected in Hong Kong.

The correct name of the 3 Author is presented in this paper.

Speciation of carboxylic components in humic-like substances (HULIS) and source apportionment of HULIS in ambient fine aerosols (PM) collected in Hong Kong.

Humic-like substances (HULIS) are an important mixture of organic compounds, which account for a great part of water-soluble organic compounds in ambient aerosols. In this study, individual carboxylic and hydroxylic species in HULIS extracts of PM samples collected in Hong Kong during summer were measured by gas chromatography mass spectrometry with prior chemical derivatization. Significantly higher levels of HULIS were observed on days mainly impacted by regional pollution (regional days, 4.

Optical properties, source apportionment and redox activity of humic-like substances (HULIS) in airborne fine particulates in Hong Kong.

Humic-like substances (HULIS) account for a considerable fraction of water-soluble organic matter (WSOM) in ambient fine particulates (PM) over the world. However, systemic studies regarding the chemical characteristics, sources and redox activity of HULIS are still limited. In this study, the mass concentration, optical properties, and reactive oxygen species (ROS)-generation potential of HULIS were investigated in PM samples collected in Hong Kong during 2011-2012, and they all showed higher levels on days under regional pollution than on days under long range transport (LRT) pollution and local emissions.

A quantitative assessment of source contributions to fine particulate matter (PM)-bound polycyclic aromatic hydrocarbons (PAHs) and their nitrated and hydroxylated derivatives in Hong Kong.

Atmospheric polycyclic aromatic hydrocarbons (PAHs) and their derivatives are of great concern due to their adverse health effects. However, source identification and apportionment of these compounds, particularly their nitrated and hydroxylated derivatives (i.e.

SCNVSim: somatic copy number variation and structure variation simulator.

Background: Somatically acquired structure variations (SVs) and copy number variations (CNVs) can induce genetic changes that are directly related to tumor genesis. Somatic SV/CNV detection using next-generation sequencing (NGS) data still faces major challenges introduced by tumor sample characteristics, such as ploidy, heterogeneity, and purity. A simulated cancer genome with known SVs and CNVs can serve as a benchmark for evaluating the performance of existing somatic SV/CNV detection tools and developing new methods.