Exploring the value of hybrid capture-based next-generation sequencing technology in the suspected diagnosis of bloodstream infections.

Background: Determining the source of infection is significant for the treatment of bloodstream infections (BSI). The gold standard of blood infection detection, blood cultures, have low positive rates to meet clinical needs. In this study, we investigated the ability of hybrid capture-based next generation sequencing technology to detect pathogens in peripheral blood samples collected from patients with suspected BSI.

Etiological diagnostic performance of probe capture-based targeted next-generation sequencing in bloodstream infection.

Background: A rapid and precise etiological diagnosis is crucial for the effective treatment of bloodstream infection (BSI). In this study, the performance of probe capture-based targeted next-generation sequencing (tNGS) was compared to that of blood culture and metagenomic next-generation sequencing (mNGS) in detecting potential pathogens in patients with BSI.

Methods: A total of 80 patients with suspected BSI were prospectively enrolled from 24 November 2023 to 30 December 2023 at Zhongshan Hospital, Shanghai, China.

A novel synthetic nucleic acid mixture for quantification of microbes by mNGS.

Metagenomic next-generation sequencing (mNGS) provides considerable advantages in identifying emerging and re-emerging, difficult-to-detect and co-infected pathogens; however, the clinical application of mNGS remains limited primarily due to the lack of quantitative capabilities. This study introduces a novel approach, KingCreate-Quantification (KCQ) system, for quantitative analysis of microbes in clinical specimens by mNGS, which co-sequence the target DNA extracted from the specimens along with a set of synthetic dsDNA molecules used as Internal-Standard (IS). The assay facilitates the conversion of microbial reads into their copy numbers based on IS reads utilizing a mathematical model proposed in this study.

Efficacy and safety of oral Chinese patent medicines in the treatment of coronary heart disease combined with hyperlipidemia: a systematic review and network meta-analysis of 78 trials.

Aim Of The Study: To evaluate the clinical efficacy and safety of commonly used oral Chinese patent medicines for the treatment of coronary heart disease combined with hyperlipidemia in clinical practice through a network meta-analysis.

Materials And Methods: PubMed, Embase, Cochrane Library, Web of Science, Wanfang, VIP, SinoMed, and CNKI databases were searched for all published randomized controlled trials (RCTs) on the treatment of coronary heart disease combined with hyperlipidemia using Chinese patent medicines. NoteExpress software was used to screen the literature obtained from the databases according to the inclusion and exclusion criteria.

Dynamic obstacle detection method based on U-V disparity and residual optical flow for autonomous driving.

As a core step of obstacle avoidance and path planning, dynamic obstacle detection is critical for autonomous driving. This study aimed to propose a dynamic obstacle detection method based on U-V disparity and residual optical flow for autonomous driving. First, a drivable area of an unmanned vehicle was detected using U-V disparity images.

A miniature U-net for -space-based parallel magnetic resonance imaging reconstruction with a mixed loss function.

Background: Deep learning-based magnetic resonance imaging (MRI) methods require in most cases a separate dataset with thousands of images for each anatomical site to train the network model. This paper proposes a miniature U-net method for -space-based parallel MRI where the network model is trained individually for each scan using scan-specific autocalibrating signal data.

Methods: The original U-net was tailored with fewer layers and channels, and the network was trained using the autocalibrating signal data with a mixing loss function involving magnitude loss and phase loss.

Endothelial GABBR2 Regulates Post-ischemic Angiogenesis by Inhibiting the Glycolysis Pathway.

Angiogenesis post-ischemia plays an essential role in preventing ischemic damage to tissue by improving the blood recovery. Determining the regulatory mechanism of ischemic angiogenesis, therefore, could provide effective therapeutics for ischemic injury. The RNA sequencing (RNA-seq) database was used to predict the association of gamma-aminobutyric acid type B receptor subunit 2 (GABBR2) with endothelial-specific expression.

Evaluation of superinfection, antimicrobial usage, and airway microbiome with metagenomic sequencing in COVID-19 patients: A cohort study in Shanghai.

Background: In COVID-19 patients, information regarding superinfection, antimicrobial assessment, and the value of metagenomic sequencing (MS) could help develop antimicrobial stewardship.

Method: This retrospective study analyzed 323 laboratory-confirmed COVID-19 patients for co-infection rate and antimicrobial usage in the Shanghai Public Health Clinical Center (SPHCC) from January 23rd to March 14th 2020. The microbiota composition was also investigated in patients with critically severe COVID-19.

Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding.

Background: In late December, 2019, patients presenting with viral pneumonia due to an unidentified microbial agent were reported in Wuhan, China. A novel coronavirus was subsequently identified as the causative pathogen, provisionally named 2019 novel coronavirus (2019-nCoV). As of Jan 26, 2020, more than 2000 cases of 2019-nCoV infection have been confirmed, most of which involved people living in or visiting Wuhan, and human-to-human transmission has been confirmed.

Genome Sequencing Explores Complexity of Chromosomal Abnormalities in Recurrent Miscarriage.

Recurrent miscarriage (RM) affects millions of couples globally, and half of them have no demonstrated etiology. Genome sequencing (GS) is an enhanced and novel cytogenetic tool to define the contribution of chromosomal abnormalities in human diseases. In this study we evaluated its utility in RM-affected couples.

Diminishing microbiome richness and distinction in the lower respiratory tract of lung cancer patients: A multiple comparative study design with independent validation.

Objectives: Current evidence suggests that microorganisms are associated with neoplastic diseases; however, the role of the airway microbiome in lung cancer remains unknown. To investigate the taxonomic profiles of the lower respiratory tract (LRT) microbiome in patients with lung cancer.

Materials And Methods: BALF samples were collected in a discovery set comprising 150 individuals, including 91 patients with lung cancer, 29 patients with nonmalignant pulmonary diseases and 30 healthy subjects, and an independent validation set including 85 participants.

A Resolution-Free Parallel Algorithm for Image Edge Detection within the Framework of Enzymatic Numerical P Systems.

Image edge detection is a fundamental problem in image processing and computer vision, particularly in the area of feature extraction. However, the time complexity increases squarely with the increase of image resolution in conventional serial computing mode. This results in being unbearably time consuming when dealing with a large amount of image data.

Balanced Chromosomal Rearrangement Detection by Low-Pass Whole-Genome Sequencing.

Balanced chromosomal rearrangements (or balanced chromosome abnormalities, BCAs) are common chromosomal structural variants. Emerging studies have demonstrated the feasibility of using whole-genome sequencing (WGS) for detection of BCA-associated breakpoints, but the requirement for a priori knowledge of the rearranged regions from G-banded chromosome analysis limits its application. The protocols described here are based on low-pass WGS for detecting BCA events independent from chromosome analysis, and has been validated using genomic data from the 1000 Genomes Project.

Identification of balanced chromosomal rearrangements previously unknown among participants in the 1000 Genomes Project: implications for interpretation of structural variation in genomes and the future of clinical cytogenetics.

Purpose: Recent studies demonstrate that whole-genome sequencing enables detection of cryptic rearrangements in apparently balanced chromosomal rearrangements (also known as balanced chromosomal abnormalities, BCAs) previously identified by conventional cytogenetic methods. We aimed to assess our analytical tool for detecting BCAs in the 1000 Genomes Project without knowing which bands were affected.

Methods: The 1000 Genomes Project provides an unprecedented integrated map of structural variants in phenotypically normal subjects, but there is no information on potential inclusion of subjects with apparent BCAs akin to those traditionally detected in diagnostic cytogenetics laboratories.

BMPR1B mutation causes Pierre Robin sequence.

Background: We investigated a large family with Pierre Robin sequence (PRS).

Aim Of The Study: This study aims to determine the genetic cause of PRS.

Results: The reciprocal translocation t(4;6)(q22;p21) was identified to be segregated with PRS in a three-generation family.

Erratum: SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler.

[This corrects the article DOI: 10.1186/2047-217X-1-18.].

Reflective long-period fiber grating-based sensor with Sagnac fiber loop mirror for simultaneous measurement of refractive index and temperature.

In this paper, we propose a reflective long-period grating-based sensor with a Sagnac fiber loop mirror (SFLM) for simultaneous measurement of refractive index (RI) and temperature. By cascading the SFLM to the end of a long-period fiber grating (LPFG), the LPFG works as a reflection operation, which is convenient in some applications. Further, the SFLM and the LPFG have different sensitivities to RI and temperature.

A flexile and high precision calibration method for binocular structured light scanning system.

3D (three-dimensional) structured light scanning system is widely used in the field of reverse engineering, quality inspection, and so forth. Camera calibration is the key for scanning precision. Currently, 2D (two-dimensional) or 3D fine processed calibration reference object is usually applied for high calibration precision, which is difficult to operate and the cost is high.

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.

Background: The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence).

COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly.

Motivation: The boost of next-generation sequencing technologies provides us with an unprecedented opportunity for elucidating genetic mysteries, yet the short-read length hinders us from better assembling the genome from scratch. New protocols now exist that can generate overlapping pair-end reads. By joining the 3' ends of each read pair, one is able to construct longer reads for assembling.

Comparison of the two major classes of assembly algorithms: overlap-layout-consensus and de-bruijn-graph.

Since the completion of the cucumber and panda genome projects using Illumina sequencing in 2009, the global scientific community has had to pay much more attention to this new cost-effective approach to generate the draft sequence of large genomes. To allow new users to more easily understand the assembly algorithms and the optimum software packages for their projects, we make a detailed comparison of the two major classes of assembly algorithms: overlap-layout-consensus and de-bruijn-graph, from how they match the Lander-Waterman model, to the required sequencing depth and reads length. We also discuss the computational efficiency of each class of algorithm, the influence of repeats and heterozygosity and points of note in the subsequent scaffold linkage and gap closure steps.