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Interpretable deep learning reveals spatiotemporal MRI features of brain aging that align with neurodegenerationNARA Subscribed
Cortical thinning and atrophy are hallmarks of brain aging that have been characterized using magnetic resonance imaging (MRI). Brain aging involves many neuroanatomic features whose effects on brain structure remain unexplored. To address this challenge, we trained interpretable deep neural networks (DNNs) to estimate brain age (BA) from T 1 -weighted ( T 1 w) MRI. By identifying MRI features unapparent to humans, DNNs can fi...
Alzheimer’s disease (AD) disproportionately affects women and carriers of the apolipoprotein E ε4 allele (APOE4), yet little is known about how sex and APOE interact to influence white matter (WM) integrity during disease progression. We integrated diffusion MRI and matched blood transcriptomic data to investigate these interactions and their underlying biological mechanisms. WM microstructure was quantified using diffusion te...
River regulation has reduced natural flow peaks in rivers globally, and in some cases has also reduced the occurrence of low-flows that expose the riverbed. Minimum low-flows are commonly mandated for temperate managed waterways in summer to maintain water quality and aquatic habitat for flora and fauna, at levels which prevent riverbed exposure. Very low flows that allow partial riverbed exposure may have many important roles...
Predicting the progression of MCI and Alzheimer’s disease on structural brain integrity and other features with machine learningNARA Subscribed
Machine learning (ML) on structural MRI data shows high potential for classifying Alzheimer’s disease (AD) progression, but the specific contribution of brain regions, demographics, and proteinopathy remains unclear. Using Alzheimer’s Disease Neuroimaging Initiative (ADNI) data, we applied an extreme gradient-boosting algorithm and SHAP (SHapley Additive exPlanations) values to classify cognitively normal (CN) older adults, th...
Identification of Regulatory Elements in Primary Sensory Neurons Involved in Trauma-Induced Neuropathic PainNARA Subscribed
Chronic pain is a significant public health issue that is often refractory to existing therapies. Here we use a multiomic approach to identify cis-regulatory elements that show differential chromatin accessibility and reveal transcription factor (TF) binding motifs with functional regulation in the rat dorsal root ganglion (DRG), which contain cell bodies of primary sensory neurons, after nerve injury. We integrated RNA-seq to...
Introduction There is an emerging need for the offshore renewable industry to have their own bespoke design guidelines because the associated projects and offshore facilities differ in fundamental ways to oil and gas facilities. Offshore renewable energy (ORE) facilities have already surpassed the numbers of installed facilities in the oil and gas industry by an order of magnitude and demand is forecast to continue growing exp...
The health and well-being effects of drought: assessing multi-stakeholder perspectives through narratives from the UKNARA Subscribed
The global literature on drought and health highlights a variety of health effects for people in developing countries where certain prevailing social, economic and environmental conditions increase their vulnerability especially with climate change. Despite increased focus on climate change, relatively less is known about the health-drought impacts in the developed country context. In the UK, where climate change–related risk...
TRY plant trait database – enhanced coverage and open accessNARA Subscribed
Plant traits—the morphological, anatomical, physiological, biochemical and phenological characteristics of plants—determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodivers...
Ruminococcal cellulosome systems from rumen to humanNARA Subscribed
Summary A cellulolytic fiber‐degrading bacterium, R uminococcus champanellensis , was isolated from human faecal samples, and its genome was recently sequenced. Bioinformatic analysis of the R . champanellensis genome revealed numerous cohesin and dockerin modules, the basic elements of the cellulosome, and manual sequencing of partially sequenced genomic segments revealed two large tandem scaffoldin‐coding genes that form par...
Gut microbiome composition and metabolomic profiles of wild western lowland gorillas ( Gorilla gorilla gorilla ) reflect host ecologyNARA Subscribed
The metabolic activities of gut microbes significantly influence host physiology; thus, characterizing the forces that modulate this micro‐ecosystem is key to understanding mammalian biology and fitness. To investigate the gut microbiome of wild primates and determine how these microbial communities respond to the host's external environment, we characterized faecal bacterial communities and, for the first time, gut metabolome...
Phage–bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiomeNARA Subscribed
Summary Viruses are the most abundant biological entities on the planet and play an important role in balancing microbes within an ecosystem and facilitating horizontal gene transfer. Although bacteriophages are abundant in rumen environments, little is known about the types of viruses present or their interaction with the rumen microbiome. We undertook random pyrosequencing of virus‐enriched metagenomes (viromes) isolated fro...
A speciation process is ongoing in the primary vector of malaria in Africa, Anopheles gambiae . Assortatively mating incipient species known as the M and S forms differentially exploit larval breeding sites associated with different ecological settings. However, some ongoing gene flow between M and S limits significant genomic differentiation mainly to small centromere‐proximal regions on chromosomes X and 2L, termed ‘speciati...
Suppressive subtractive hybridization as a tool for identifying genetic diversity in an environmental metagenome: the rumen as a modelNARA Subscribed
Summary Molecular techniques previously used for genome comparisons of closely related bacterial species could prove extremely valuable for comparisons of complex microbial communities, or metagenomes. Our study aimed to determine the breadth and value of suppressive subtractive hybridization (SSH) in a pilot‐scale analysis of metagenomic DNA from communities of microorganisms in the rumen. Suppressive subtractive hybridizatio...
Summary Two closely related strains of the Gram‐positive, cellulolytic ruminal bacterium Ruminococcus flavefaciens were compared at the genomic level by suppressive subtractive hybridization. The two strains investigated in this study differ by 1.94% in their respective 16S rDNA genes. Three hundred and eighty‐four PCR‐amplified products were cloned and then screened for their strain identity by dot blot hybridization. Based o...
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