RabbitQC: high-speed scalable quality control for sequencing data.

MOTIVATION: Modern sequencing technologies continue to revolutionize many areas of biology and medicine. Since the generated datasets are error-prone, downstream applications usually require quality control methods to pre-process FASTQ files. However, existing tools for this task are currently not able to fully exploit the capabilities of computing platforms leading to slow runtimes. RESULTS: We present RabbitQC, an extremely fast integrated quality control tool for FASTQ files, which can take full advantage of modern hardware. It includes a variety of operations and supports different sequencing technologies (Illumina, Oxford Nanopore and PacBio). RabbitQC achieves speedups between one and two orders-of-magnitude compared to other state-of-the-art tools. AVAILABILITY AND IMPLEMENTATION: C++ sources and binaries are available at https://github.com/ZekunYin/RabbitQC. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Development of triphenylamine functional dye for selective photoelectrochemical sensing of cysteine.

A novel triphenylamine-based organic dye, TTA, with an acrylic group is designed to graft TiO2 nanoparticles for sensitive and selective photoelectrochemical sensing. The synthesized TTA possesses a high molar absorption coefficient, leading to an enhanced photoelectron emission ability of the electron donor. The carboxyl group of TTA acts as not only an electron acceptor but also a linker to connect TTA to TiO2 nanoparticles. Under irradiation, TTA shows fast intramolecular charge transfer from triphenylamine to carboxyl group via the π-bridge of thiophene moiety, thus producing a sensitive photocurrent response. Meanwhile, the acrylic moiety provides an active site for the Michael addition reaction, which would destroy the π-bridge and decrease the photocurrent response. Thus, a selective photoelectrochemical sensing strategy is proposed for detection of small biomolecules. Using cysteine as a model analyte, this sensing strategy shows a detectable range from 1 to 200 µM, without the interference from natural amino acids and various biological reducing reagents. This work offers a new photoelectrochemical route to highly selective and sensitive detection of biologically important small molecules.

RabbitFX: Efficient Framework for FASTA/Q File Parsing on Modern Multi-Core Platforms.

The continuous growth of generated sequencing data leads to the development of a variety of associated bioinformatics tools. However, many of them are not able to fully exploit the resources of modern multi-core systems since they are bottlenecked by parsing files leading to slow execution times. This motivates the design of an efficient method for parsing sequencing data that can exploit the power of modern hardware, especially for modern CPUs with fast storage devices. We have developed RabbitFX, a fast, efficient, and easy-to-use framework for processing biological sequencing data on modern multi-core platforms. It can efficiently read FASTA and FASTQ files by combining a lightweight parsing method by means of an optimized formatting implementation. Furthermore, we provide user-friendly and modularized C++ APIs that can be easily integrated into applications in order to increase their file parsing speed. As proof-of-concept, we have integrated RabbitFX into three I/O-intensive applications: fastp, Ktrim, and Mash. Our evaluation shows that the inclusion of RabbitFX leads to speedups of at least 11.6 (6.6), 2.4 (2.4), and 3.7 (3.2) compared to the original versions on plain (gzip-compressed) files, respectively. These case studies demonstrate that RabbitFX can be easily integrated into a variety of NGS analysis tools to significantly reduce associated runtimes. It is open source software available at https://github.com/RabbitBio/RabbitFX.

Turn-on electrochemiluminescence sensing of Cd(2+) based on CdTe quantum dots.

A simple and sensitive method for the detection of cadmium ion was proposed based on the electrochemiluminescence (ECL) of thioglycolic acid capped-CdTe quantum dots (CdTe QDs). The ECL of CdTe QDs was firstly quenched by introduction of S(2)(-) and was restored due to following addition of Cd(2+), on the basis of which, a "turn-on" ECL method for the detection of Cd(2+) was demonstrated. The ECL of CdTe QDs exhibited linear response toward Cd(2+) concentration in the range from 6.3nM to 3.4µM (R=0.999) with a detection limit of 2.1nM. The proposed assay was simple, sensitive, selective, and practicable in real water samples.

Risk of hepatitis B virus (HBV) reactivation in non-Hodgkin lymphoma patients receiving rituximab-chemotherapy: a meta-analysis.

BACKGROUND: The addition of Rituximab to standard chemotherapy (C) has been reported to improve the end of treatment outcome in non-Hodgkin lymphoma (NHL) patients. Nevertheless, rituximab has been associated with hepatitis B virus reactivation (HBV-R). OBJECTIVES: The aim of this systematic review and meta-analysis is to research the relationship between rituximab and HBV-R. STUDY DESIGN: We searched the commonly used databases both in English and Chinese from November 1997 to June 30, 2012. Meta-analysis was performed in fixed/random-effects models using Review Manager 5.1 and STATA 10.0. Publication bias was examined through Egger's test and Begg's funnel plot. RESULTS: Nine eligible articles were selected in this review (8 studies in English and 1 studies in Chinese), which included 971 adult patients and met all inclusion and exclusion criteria. Of rituximab-associated HBV-R cases reported through case series (n=387), 304 were HBcAb (+)/HBsAg (-) and 83 HBsAg (+). The pooled effect of rituximab-based therapy on HBV-R significantly increased under fixed-effects model [Relative risk (RR) 2.14, 95%CI 1.42-3.22, P=0.0003]. In subgroup analysis, rituximab-associated HBV-R in isolated HBcAb (+) patients remained high, and the RR was 5.52 (95%CI 2.05-14.85, P=0.0007). The RR of HBV-R in NHL patients with HBsAg (+) treated with R-based therapy when compared with the control population was 1.63 by the random-effects model. CONCLUSIONS: Rituximab therapy may increase the risk of developing HBV-R in NHL patients with HBcAb(+).