An article published in BMCBiology presents RNAlysis: a user-friendly graphical user interface, allowing researchers to analyze data without writing code.
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Identification of cell barcodes from long-read single-cell RNA-seq with BLAZE - Genome BiologyLong-read single-cell RNA sequencing (scRNA-seq) enables the quantification of RNA isoforms in individual cells. However, long-read scRNA-seq using the Oxford Nanopore platform has largely relied upon matched short-read data to identify cell barcodes. We introduce BLAZE, which accurately and efficiently identifies 10x cell barcodes using only nanopore long-read scRNA-seq data. BLAZE outperforms the existing tools and provides an accurate representation of the cells present in long-read scRNA-seq when compared to matched short reads. BLAZE simplifies long-read scRNA-seq while improving the results, is compatible with downstream tools accepting a cell barcode file, and is available at https://github.com/shimlab/BLAZE .
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Increased iron deposition in nucleus accumbens associated with disease progression and chronicity in migraine - BMC MedicineBackground Migraine is one of the world’s most prevalent and disabling diseases. Despite huge advances in neuroimaging research, more valuable neuroimaging markers are still urgently needed to provide important insights into the brain mechanisms that underlie migraine symptoms. We therefore aim to investigate the regional iron deposition in subcortical nuclei of migraineurs as compared to controls and its association with migraine-related pathophysiological assessments. Methods A total of 200 migraineurs (56 chronic migraine [CM], 144 episodic migraine [EM]) and 41 matched controls were recruited. All subjects underwent MRI and clinical variables including frequency/duration of migraine, intensity of migraine, 6-item Headache Impact Test (HIT-6), Migraine Disability Assessment (MIDAS), and Pittsburgh Sleep Quality Index (PSQI) were recorded. Quantitative susceptibility mapping was employed to quantify the regional iron content in subcortical regions. Associations between clinical variables and regional iron deposition were studied as well. Results Increased iron deposition in the putamen, caudate, and nucleus accumbens (NAC) was observed in migraineurs more than controls. Meanwhile, patients with CM had a significantly higher volume of iron deposits compared to EM in multiple subcortical nuclei, especially in NAC. Volume of iron in NAC can be used to distinguish patients with CM from EM with a sensitivity of 85.45% and specificity of 71.53%. As the most valuable neuroimaging markers in all of the subcortical nuclei, higher iron deposition in NAC was significantly associated with disease progression, and higher HIT-6, MIDAS, and PSQI. Conclusions These findings provide evidence that iron deposition in NAC may be a biomarker for migraine chronicity and migraine-related dysfunctions, thus may help to understand the underlying vascular and neural mechanisms of migraine. Trial registration ClinicalTrials.gov, number NCT04939922.
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The Human Genome Project transformed biologyGenomics will increasingly inform doctors’ decisions. Starting later this year, 100,000 babies in England will have their genomes sequenced and screened for around 200 conditions
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transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation - BMC BioinformaticsBackground RNA-seq followed by de novo transcriptome assembly has been a transformative technique in biological research of non-model organisms, but the computational processing of RNA-seq data entails many different software tools. The complexity of these de novo transcriptomics workflows therefore presents a major barrier for researchers to adopt best-practice methods and up-to-date versions of software. Results Here we present a streamlined and universal de novo transcriptome assembly and annotation pipeline, transXpress, implemented in Snakemake. transXpress supports two popular assembly programs, Trinity and rnaSPAdes, and allows parallel execution on heterogeneous cluster computing hardware. Conclusions transXpress simplifies the use of best-practice methods and up-to-date software for de novo transcriptome assembly, and produces standardized output files that can be mined using SequenceServer to facilitate rapid discovery of new genes and proteins in non-model organisms.
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Scoping review of the association between bacterial vaginosis and emotional, sexual and social health - BMC Women's HealthBackground Bacterial vaginosis (BV) is a condition that, if symptomatic, is characterized by discharge and odor, with high recurrence rates even when treated. This study aims to review what literature exists on the association between BV and the emotional, sexual, and social health of women. Methods MEDLINE, Embase and Web of Science databases were searched from inception until November 2020. Studies reporting an association between women’s emotional, sexual and/or social health and symptomatic BV in a qualitative and/or quantitative manner were included. Selected studies were divided in three categories, i.e. reporting on the emotional, sexual and/or social association. All studies were critically evaluated and discussed. Results Sixteen studies were included. Concerning emotional health, we found eight studies that calculated the association between stress and BV, in four this was statistically significant. Four qualitative studies on emotional health showed that the severity of the symptoms influenced the impact on women’s lives. All studies on sexual health reported that many women experienced an impact on their relationship and sexual intimacy. Results for social life ranged from no association found to most of the study population showing avoidance behavior. Conclusion This review shows that symptomatic BV can be associated with diminished emotional, sexual, and social health, but there is too little evidence to state the extent of this association.
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Post-COVID-19 condition and persisting symptoms in English schoolchildren: repeated surveys to March 2022 - BMC Infectious DiseasesBackground Both post-COVID-19 condition (long COVID) and the presence of persisting symptoms that do not meet formal definitions of post-COVID-19-condition may adversely affect quality of life and function. However, their prevalence among children and young people in England is unclear. Methods We used data from repeated surveys in a large cohort of English schoolchildren from the COVID-19 Schools Infection Survey (SIS) for the school year 2021/22 to describe the weighted prevalence of post-COVID-19-condition and compare persisting symptoms between individuals with a positive SARS-CoV-2 test and those with neither a positive test history nor suspected infection. Results Among 7797 children from 173 schools, 1.8% of primary school pupils (aged 4 to 11 years), 4.5% of secondary school pupils in years 7–11 (aged 11 to 16 years) and 6.9% of those in years 12–13 (aged 16 to 18 years) met a definition of post-COVID-19 condition in March 2022. Specific persisting symptoms such as anxiety or difficulty concentrating were frequently reported regardless of prior infection status and increased with age: 48.0% of primary school pupils, 52.9% of secondary school pupils in years 7–11 and 79.5% in years 12–13 reporting at least one symptom lasting more than 12 weeks. Persisting loss of smell and taste, cardiovascular and some systemic symptoms were more frequently reported by those with a previous positive test. Conclusions We showed that ongoing symptoms were frequently reported by English schoolchildren regardless of SARS-CoV-2 test results and some specific symptoms such as loss of smell and taste were more prevalent in those with a positive test history. Our study emphasises the wide-ranging impacts of the COVID-19 pandemic on the health and wellbeing of children and young people.
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