Nigel Dyer
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View article: EnteroBase in 2025: exploring the genomic epidemiology of bacterial pathogens
EnteroBase in 2025: exploring the genomic epidemiology of bacterial pathogens Open
This paper presents an update on the content, accessibility and analytical tools of the EnteroBase platform for web-based pathogen genome analysis. EnteroBase provides manually curated databases of genome sequence data and associated metad…
View article: Epigenetic priming of immune/inflammatory pathways activation and abnormal activity of cell cycle pathway in a perinatal model of white matter injury
Epigenetic priming of immune/inflammatory pathways activation and abnormal activity of cell cycle pathway in a perinatal model of white matter injury Open
Prenatal inflammatory insults accompany prematurity and provoke diffuse white matter injury (DWMI), which is associated with increased risk of neurodevelopmental pathologies, including autism spectrum disorders. DWMI results from maturatio…
View article: Investigation of the effect of sustainable magnetic treatment on the microbiological communities in drinking water
Investigation of the effect of sustainable magnetic treatment on the microbiological communities in drinking water Open
The drinking water scarcity is posing a threat to mankind, hence better water quality management methods are required. Magnetic water treatment, which has been reported to improve aesthetic water quality and reduce scaling problems, can be…
View article: Effect of Cobalt–Chromium–Molybdenum Implant Surface Modifications on Biofilm Development of S. aureus and S. epidermidis
Effect of Cobalt–Chromium–Molybdenum Implant Surface Modifications on Biofilm Development of S. aureus and S. epidermidis Open
Periprosthetic infections are an eminent factor in patient care and also having significant economic implications. The number of biofilm-infection related replacement surgeries is increasing and will continue to do so in the following deca…
View article: TiAl6V4 Alloy Surface Modifications and Their Impact on Biofilm Development of S. aureus and S. epidermidis
TiAl6V4 Alloy Surface Modifications and Their Impact on Biofilm Development of S. aureus and S. epidermidis Open
One of the most serious complications following joint replacement surgeries are periprosthetic infections (PIs) arising from the adhesion of bacteria to the artificial joint. Various types of titanium–aluminum–vanadium (TiAl6V4) alloy surf…
View article: Hyperinflammation evokes different antiviral TMPRSS2 and ADAM17 expression responses in human gut xenograft versus host mouse gut although overall genomic responses are similar
Hyperinflammation evokes different antiviral TMPRSS2 and ADAM17 expression responses in human gut xenograft versus host mouse gut although overall genomic responses are similar Open
The global spread of the newly emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to the pandemic outbreak of coronavirus disease 2019 (COVID-19), an inflammatory disease that is primarily affecting the respirator…
View article: Consequences of the Integration of a Hyperbolic Funnel into a Showerhead for Droplets, Jet Break-Up Lengths, and Physical-Chemical Parameters
Consequences of the Integration of a Hyperbolic Funnel into a Showerhead for Droplets, Jet Break-Up Lengths, and Physical-Chemical Parameters Open
Introducing a hyperbolic vortex into a showerhead is a possibility to achieve higher spray velocities for a given discharge without reducing the nozzle diameter. Due to the introduction of air bubbles into the water by the vortex, the spra…
View article: Solar Eclipses and the Surface Properties of Water
Solar Eclipses and the Surface Properties of Water Open
During four solar eclipse events (two annular, one total and one partial) a correlation was observed between a change in water surface tension and the magnitude of the optical coverage. During one eclipse, evaporation experiments were carr…
View article: Peer Review #2 of "LiBiNorm: an htseq-count analogue with improved normalisation of Smart-seq2 data and library preparation diagnostics (v0.1)"
Peer Review #2 of "LiBiNorm: an htseq-count analogue with improved normalisation of Smart-seq2 data and library preparation diagnostics (v0.1)" Open
Protocols for preparing RNA-seq libraries, most prominently 'Smart-seq' variations, introduce global biases that can have a significant impact on the quantification of gene expression levels.This global bias can lead to drastic over-or und…
View article: LiBiNorm: an htseq-count analogue with improved normalisation of Smart-seq2 data and library preparation diagnostics
LiBiNorm: an htseq-count analogue with improved normalisation of Smart-seq2 data and library preparation diagnostics Open
Protocols for preparing RNA sequencing (RNA-seq) libraries, most prominently “Smart-seq” variations, introduce global biases that can have a significant impact on the quantification of gene expression levels. This global bias can lead to d…
View article: Peer Review #2 of "LiBiNorm: an htseq-count analogue with improved normalisation of Smart-seq2 data and library preparation diagnostics (v0.2)"
Peer Review #2 of "LiBiNorm: an htseq-count analogue with improved normalisation of Smart-seq2 data and library preparation diagnostics (v0.2)" Open
Protocols for preparing RNA-seq libraries, most prominently 'Smart-seq' variations, introduce global biases that can have a significant impact on the quantification of gene expression levels.This global bias can lead to drastic over-or und…
View article: Epigenome priming dictates transcription response and white matter fate upon perinatal inflammation
Epigenome priming dictates transcription response and white matter fate upon perinatal inflammation Open
Summary Inflammatory insults accompanying prematurity provokes diffuse white matter injury (DWMI) which is associated with increased risk of neurodevelopmental disorders: pre-term infants have a 10 to 18-fold increased risk of developing a…
View article: Circadian control of abscisic acid biosynthesis and signalling pathways revealed by genome‐wide analysis of <scp>LHY</scp> binding targets
Circadian control of abscisic acid biosynthesis and signalling pathways revealed by genome‐wide analysis of <span>LHY</span> binding targets Open
Summary The LATE ELONGATED HYPOCOTYL ( LHY ) transcription factor functions as part of the oscillatory mechanism of the Arabidopsis circadian clock. This paper reports the genome‐wide analysis of its binding targets and reveals a role in t…
View article: Analysis of chromatin accessibility in decidualizing human endometrial stromal cells
Analysis of chromatin accessibility in decidualizing human endometrial stromal cells Open
Spontaneous decidualization of the endometrium in response to progesterone signaling is confined to menstruating species, including humans and other higher primates. During this process, endometrial stromal cells (EnSCs) differentiate into…
View article: Integration of Kinase and Calcium Signaling at the Level of Chromatin Underlies Inducible Gene Activation in T Cells
Integration of Kinase and Calcium Signaling at the Level of Chromatin Underlies Inducible Gene Activation in T Cells Open
TCR signaling pathways cooperate to activate the inducible transcription factors NF-κB, NFAT, and AP-1. In this study, using the calcium ionophore ionomycin and/or PMA on Jurkat T cells, we show that the gene expression program associated …
View article: Success after failure: the role of endometrial stem cells in recurrent miscarriage
Success after failure: the role of endometrial stem cells in recurrent miscarriage Open
Endometrial stem-like cells, including mesenchymal stem cells (MSCs) and epithelial progenitor cells, are essential for cyclic regeneration of the endometrium following menstrual shedding. Emerging evidence indicates that endometrial MSCs …
View article: Molecular testing for familial hypercholesterolaemia-associated mutations in a UK-based cohort: development of an NGS-based method and comparison with multiplex polymerase chain reaction and oligonucleotide arrays
Molecular testing for familial hypercholesterolaemia-associated mutations in a UK-based cohort: development of an NGS-based method and comparison with multiplex polymerase chain reaction and oligonucleotide arrays Open
Background Detection of disease-associated mutations in patients with familial hypercholesterolaemia is crucial for early interventions to reduce risk of cardiovascular disease. Screening for these mutations represents a methodological cha…