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Article
Open AccessCharacterisation and reproducibility of the HumanMethylationEPIC v2.0 BeadChip for DNA methylation profiling
The Illumina family of Infinium Methylation BeadChip microarrays has been widely used over the last 15 years for genome-wide DNA methylation profiling, including large-scale and population-based studies, due t...
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Article
Open AccessAntigen-driven EGR2 expression is required for exhausted CD8+ T cell stability and maintenance
Chronic stimulation of CD8+ T cells triggers exhaustion, a distinct differentiation state with diminished effector function. Exhausted cells exist in multiple differentiation states, from stem-like progenitors th...
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Article
Open AccessA multiomics approach to identify host-microbe alterations associated with infection severity in diabetic foot infections: a pilot study
Diabetic foot infections (DFIs) are a major cause of hospitalization and can lead to lower extremity amputation. In this pilot study, we used a multiomics approach to explore the host–microbe complex within DF...
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Article
Open AccessTemporal ordering of omics and multiomic events inferred from time-series data
Temporal changes in omics events can now be routinely measured; however, current analysis methods are often inadequate, especially for multiomics experiments. We report a novel analysis method that can infer e...
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Article
Open AccessConstitutively bound CTCF sites maintain 3D chromatin architecture and long-range epigenetically regulated domains
The architectural protein CTCF is a mediator of chromatin conformation, but how CTCF binding to DNA is orchestrated to maintain long-range gene expression is poorly understood. Here we perform RNAi knockdown t...
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Article
Open AccessMethylome and transcriptome maps of human visceral and subcutaneous adipocytes reveal key epigenetic differences at developmental genes
Adipocytes support key metabolic and endocrine functions of adipose tissue. Lipid is stored in two major classes of depots, namely visceral adipose (VA) and subcutaneous adipose (SA) depots. Increased visceral...
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Article
Open AccessMonozygotic twins and triplets discordant for amyotrophic lateral sclerosis display differential methylation and gene expression
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterised by the loss of upper and lower motor neurons. ALS exhibits high phenotypic variability including age and site of onset, an...
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Article
Open AccessWidespread promoter methylation of synaptic plasticity genes in long-term potentiation in the adult brain in vivo
DNA methylation is a key modulator of gene expression in mammalian development and cellular differentiation, including neurons. To date, the role of DNA modifications in long-term potentiation (LTP) has not be...
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Article
Open AccessEffect of prenatal DHA supplementation on the infant epigenome: results from a randomized controlled trial
Evidence is accumulating that nutritional exposures in utero can influence health outcomes in later life. Animal studies and human epidemiological studies have implicated epigenetic modifications as playing a ...
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Article
Open AccessCritical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling
In recent years the Illumina HumanMethylation450 (HM450) BeadChip has provided a user-friendly platform to profile DNA methylation in human samples. However, HM450 lacked coverage of distal regulatory elements...
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Article
Open AccessDe novo identification of differentially methylated regions in the human genome
The identification and characterisation of differentially methylated regions (DMRs) between phenotypes in the human genome is of prime interest in epigenetics. We present a novel method, DMRcate, that fits replic...
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Article
Open AccessRandomised controlled trial of a brief alcohol intervention in a general hospital setting
The evidence suggests that brief alcohol-focused interventions, directed at hazardous and harmful drinkers in non-specialist settings such as primary care are effective in reducing alcohol consumption. However...
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Article
Effect of areca nut on salivary copper concentration in chronic chewers
The chewing of areca nut is associated with the development of oral submucous fibrosis (OSF), a condition predominantly encountered in Asians indulging in the habit. The pathogenesis of this condition is howev...
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Article
Iron and cadmium uptake by duodenum of hypotransferrinaemic mice
Absorption from food is an important route for entry of the toxic metal, cadmium, into the body. Both cadmium and iron are believed to be taken up by duodenal enterocytes via the iron regulated, proton-coupled...
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Article
The importance of alcohol-induced muscle disease
Alcohol-induced muscle disease (AIMD) is a composite term to describe any muscle pathology (molecular, biochemical, structural or physiological) resulting from either acute or chronic alcohol ingestion or a co...
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Article
CASE REPORT: Celiac Disease in Patients with Variegate Porphyria
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Article
Acute effect of ethanol on 7-hydroperoxycholesterol in muscle and liver
We tested the hypotheses that ethanol sensitivities of muscle and liver can be discerned in the initial periods of ethanol exposure, especially when acetaldehyde levels are markedly raised with cyanamide, an a...
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Article
Structural and functional changes in skeletal muscle in anorexia nervosa
Protein-energy malnutrition in anorexia nervosa is an under-recognised cause of muscle dysfunction. To characterise the skeletal myopathy that occurs in patients with severe anorexia nervosa, muscle function ...
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Alcohol and acetaldehyde dehydrogenase gene polymorphism and alcoholism
Inherited variations in alcohol and aldehyde dehydrogenases, the principal enzymes of ethanol metabolism, have been implicated in determining susceptibility to alcoholism and alcohol-related organ damage. An a...
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Article
Diverse polymorphism within a short coding region of the human aldehyde dehydrogenase-5 (ALDH5) gene
Human aldehyde dehydrogenase-5 gene (originally named as ALDHX) is expressed in liver and testis. The ALDH5 does not contain introns in the coding sequence for 517 amino acid residues. Within a short nucleotide r...
