Antibiotic resistance poses an increasing threat to public health. Horizontal gene transfer (HGT) promoted by antibiotics is recognized as a significant pathway disseminate antibiotic genes (ARGs). However, it unclear whether non-antibiotic, anti-microbial (NAAM) chemicals can directly promote HGT of ARGs in the environment.We aimed investigate triclosan (TCS), widely-used NAAM chemical personal care products, able stimulate conjugative multi-resistance carried plasmid within and across...

Sequencing by translocating DNA fragments through an array of nanopores is a rapidly maturing technology that offers faster and cheaper sequencing than other approaches. However, accurately deciphering the sequence from noisy complex electrical signal challenging. Here, we report Chiron, first deep learning model to achieve end-to-end basecalling directly translate raw without error-prone segmentation step. Trained with only small set 4,000 reads, show our provides state-of-the-art accuracy,...

A better understanding of the genomic changes that facilitate emergence and spread drug-resistant Mycobacterium tuberculosis strains is currently required. Here, we report use MinION nanopore sequencer (Oxford Nanopore Technologies) to sequence assemble an extensively (XDR) isolate, which part a modern Beijing sub-lineage strain, prevalent in Western Province, Papua New Guinea. Using 238-fold coverage obtained from single flow-cell, de novo assembly reads resulted into one contiguous with...

Detection of genomic inversions remains challenging. Many existing methods primarily target inzversions with a non repetitive breakpoint, leaving inverted repeat (IR) mediated non-allelic homologous recombination (NAHR) largely unexplored. We present npInv, novel tool specifically for detecting and genotyping NAHR inversion using long read sub-alignment sequencing data. benchmark npInv other tools in both simulation real use to generate whole-genome map NA12878 consisting 30 (of which 15 are...

Abstract Background Klebsiella pneumoniae frequently harbours multidrug resistance, and current diagnostics struggle to rapidly identify appropriate antibiotics treat these bacterial infections. The MinION device can sequence native DNA RNA in real time, providing an opportunity compare the utility of for prediction antibiotic susceptibility. However, effectiveness direct sequencing base-calling has not previously been investigated. This study interrogated genome transcriptome 4 extensively...

Background Breast cancer is the most common malignancy among women, with racial disparities in diagnosis, tumor characteristics and outcomes. Black women are disproportionately affected by aggressive subtypes advanced stage disease, influenced biological, socioeconomic, healthcare access factors. While these well-documented globally, their impact Portugal remains unknown. The Portuguese system ensures equal access, including for patients from African Portuguese-speaking countries (PALOPs),...

Este estudo teve como objetivo analisar os fatores associados ao Burnout em profissionais de saúde e identificar intervenções possíveis para mitigar seus impactos. A pesquisa foi realizada por meio uma revisão literatura nas bases SciELO LILACS, contemplando publicações dos últimos cinco anos (2019-2024). Utilizaram-se descritores "Burnout", "profissionais saúde" "intervenções", resultando 72 artigos, quais 10 atenderam aos critérios inclusão. Os consideraram estudos português, disponíveis...

Rapid diagnosis and appropriate treatment is imperative in bacterial sepsis due increasing risk of mortality with every hour without antibiotic therapy. Atypical infections fastidious organisms may take more than 4 days to diagnose leading calls for improved methods rapidly diagnosing sepsis. Capnocytophaga canimorsus a slow-growing, gram-negative bacillus which common commensal within the mouths dogs, but rarely cause humans. C. factors include immunosuppression, alcoholism elderly age....

<b><i>Purpose:</i></b> To explore phenotype-genotype correlations that may contribute to a better understanding of diabetic retinopathy (DR). <b><i>Procedures:</i></b> An exploratory association study was performed identify genetic variants associated with non-proliferative DR (NPDR) in 307 type 2 patients who were previously stratified into 3 different phenotypes NPDR progression. The genotyped for 174 single nucleotide polymorphisms 11...

ABSTRACT Sequencing by translocating DNA fragments through an array of nanopores is a rapidly maturing technology which offers faster and cheaper sequencing than other approaches. However, accurately deciphering the sequence from noisy complex electrical signal challenging. Here, we report Chiron, first deep learning model to achieve end-to-end basecalling: directly translating raw without error-prone segmentation step. Trained with only small set 4000 reads, show that our provides...

High throughput screening of phage display libraries for target binding molecules using electrohydrodynamic nanomixing and nanopore sequencing.

The worldwide demand on bionematicides is in a growing trend, fueled by environmental concerns with potential negative impacts of synthetic products ecosystems and non-target organisms, as well the need to provide solutions organic farming management. As such, main goal present study was evaluate impact 1,4-naphthoquinone (NTQ), nematicidal compound found natural such walnut husk, soil microbial community (non-target organisms), determine ecotoxicological indicators order follow quantify...

The recent introduction of a barcoding protocol for Oxford Nanopore sequencing has increased the versatility technology. Several bioinformatics tools have been developed to demultiplex barcoded reads, but none them supports streaming analysis. This limits use multiplexed in real-time applications, which is one main advantages technology.We introduced npBarcode, an open source and cross-platform tool barcode demultiplexing fashion that can be used pipe data further analyses. also provides...

Tandem repeats comprise significant proportion of the human genome including coding and regulatory regions. They are highly prone to repeat number variation nucleotide mutation due their repetitive unstable nature, making them a major source genomic between individuals. Despite recent advances in high throughput sequencing, analysis tandem context complex diseases is still hindered by technical limitations. We report novel targeted sequencing approach, which allows simultaneous hundreds...

Background and objective The use of herbal medicines has been increasing among cancer patients, as a way to control treatment-related symptoms; however, many patients are reluctant disclose this their medical practitioners. fact that oncological treatments have narrow therapeutic margin, associated with the lack clinical evidence concerning these supplements, makes medication-herbal interactions reality. These could lead increased toxicity or decreased effectiveness treatment. In light this,...

Abstract Motivation The recently introduced barcoding protocol to Oxford Nanopore sequencing has increased the versatility of technology. Several bioinformatic tools have been developed demultiplex barcoded reads, but none them support streaming analysis. This limits use pooled in real-time applications, which is one main advantages Results We npBarcode, an open source and cross platform tool for barcode fashion. npBarcode can be seamlessly integrated into a analysis pipeline. also provides...

Abstract A better understanding of the genomic changes that facilitate emergence and spread drug resistant M. tuberculosis strains is required. Short-read sequencing methods have limited capacity to identify long, repetitive regions gene duplications. We sequenced an extensively (XDR) Beijing sub-lineage 2.2.1.1 “epidemic strain” from Western Province Papua New Guinea using long-read (Oxford Nanopore MinION®). With up 274 fold coverage a single flow-cell, we assembled 4404947bp circular...

<ns5:p><ns5:bold>Background:</ns5:bold>The chloroplast (cp) genome is an important resource for studying plant diversity and phylogeny. Assembly of the cp genomes from next-generation sequencing data complicated by presence two large inverted repeats contained in DNA.</ns5:p><ns5:p><ns5:bold>Methods:</ns5:bold>We constructed a complete circular assembly hexaploid sweetpotato using extremely low coverage (&lt;1×) Oxford Nanopore whole-genome (WGS) coupled with Illumina...

Pandoraea fibrosis is a newly identified Gram-negative bacterial species that was isolated from the respiratory tract of an Australian cystic patient. The complete assembled genome sequences two consecutive isolates (second isolate collected 11 months after antibiotic treatment) same individual are presented here.

ABSTRACT Detection of genomic inversions remains challenging. Many existing methods primarily target with a non repetitive breakpoint, leaving inverted repeat (IR) mediated non-allelic homologous recombination (NAHR) largely unexplored. We present npInv, novel tool specifically for detecting and genotyping NAHR inversion using long read sub-alignment sequencing data. use npInv to generate whole-genome map NA12878 consisting 30 (of which 15 are novel), including all previously known in...

ABSTRACT Background Tandem repeats comprise significant proportion of the human genome including coding and regulatory regions. They are highly prone to repeat number variation nucleotide mutation due their repetitive unstable nature, making them a major source genomic between individuals. Despite recent advances in high throughput sequencing, analysis tandem context complex diseases is still hindered by technical limitations. Methods We report novel targeted sequencing approach, which...

We present a case of Capnocytophaga canimorsus septic shock after dog bite in an immunocompetent individual, where real-time nanopore metagenomic sequencing characterized the microbial agent within 19 hours, with subsequent confirmation using droplet digital PCR. Oral swabs from demonstrated nearly-identical C. isolate by sequencing.

<ns5:p><ns5:bold>Background:</ns5:bold>The chloroplast (cp) genome is an important resource for studying plant diversity and phylogeny. Assembly of the cp genomes from next-generation sequencing data complicated by presence two large inverted repeats contained in DNA.</ns5:p><ns5:p><ns5:bold>Methods:</ns5:bold>We constructed a complete circular assembly hexaploid sweetpotato using extremely low coverage (&lt;1×) Oxford Nanopore whole-genome (WGS) coupled with Illumina...