Emily Shaw results 26
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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...
SNAPSHOT USA 2024: Year 6 of the Coordinated National Camera Trap Survey of the United StatesNARA Subscribed
Motivation SNAPSHOT USA is an annual, multi‐contributor camera trap survey of mammals across the United States. The growing SNAPSHOT USA dataset is intended for tracking the spatial and temporal responses of mammal populations to changes in land use, land cover and climate. These data will be useful for exploring the drivers of spatial and temporal changes in relative abundance and distribution, as well as the impacts of speci...
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...
Biodiversity conservation in northern Australia is characterised by high endemism, data deficiency, and high Indigenous land tenure and population. The Northern Australia Conservation Genomics Forum brought together experts to explore current genetic research with particular emphasis on integration of genomics within conservation practices. We discuss the regional biodiversity of northern Australia, highlighting the unique bio...
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...
SNAPSHOT USA 2019–2023: The First Five Years of Data From a Coordinated Camera Trap Survey of the United StatesNARA Subscribed
Motivation SNAPSHOT USA is an annual, multicontributor camera trap survey of mammals across the United States. The growing SNAPSHOT USA dataset is intended for tracking the spatial and temporal responses of mammal populations to changes in land use, land cover and climate. These data will be useful for exploring the drivers of spatial and temporal changes in relative abundance and distribution, as well as the impacts of specie...
Genetic diversity is the foundation of biodiversity, and preserving it is therefore fundamental to conservation practice. However, global conservation efforts face significant challenges integrating genetic and genomic approaches into applied management and policy. As collaborative partnerships are increasingly recognized as key components of successful conservation efforts, we explore their role and relevance in the Australia...
Peat profile database from peatlands in CanadaNARA Subscribed
Peatlands cover approximately 12% of the Canadian landscape and play an important role in the carbon cycle through their centennial‐ to millennial‐scale storage of carbon under waterlogged and anoxic conditions. In recognizing the potential of these ecosystems as natural climate solutions and therefore the need to include them in national greenhouse gas inventories, the Canadian Model for Peatlands module (CaMP v. 2.0) was dev...
Climate‐driven, but dynamic and complex? A reconciliation of competing hypotheses for species’ distributionsNARA Subscribed
Estimates of the percentage of species “committed to extinction” by climate change range from 15% to 37%. The question is whether factors other than climate need to be included in models predicting species’ range change. We created demographic range models that include climate vs. climate‐plus‐competition, evaluating their influence on the geographic distribution of Pinus edulis , a pine endemic to the semiarid southwestern U....
Alternative tissue fixation for combined histopathological and molecular analysis in a clinically representative settingNARA Subscribed
Formalin is the principal tissue fixative used worldwide for clinical and research purposes. Despite optimal preservation of morphology, its preservation of DNA and RNA is poor. As clinical diagnostics increasingly incorporates molecular-based analysis, the requirement for maintaining nucleic acid quality is of increasing importance. Here we assess an alternative non-formalin-based tissue fixation method, PAXgene Tissue system...
Globally, collapse of ecosystems—potentially irreversible change to ecosystem structure, composition and function—imperils biodiversity, human health and well‐being. We examine the current state and recent trajectories of 19 ecosystems, spanning 58° of latitude across 7.7 M km 2 , from Australia's coral reefs to terrestrial Antarctica. Pressures from global climate change and regional human impacts, occurring as chronic ‘press...
Natural in situ relationships suggest coral reef calcium carbonate production will decline with ocean acidificationNARA Subscribed
There are few in situ studies showing how net community calcification ( G net ) of coral reefs is related to carbonate chemistry, and the studies to date have demonstrated different predicted rates of change. In this study, we measured net community production ( P net ), G net , and carbonate chemistry of a reef flat at One Tree Island, Great Barrier Reef. Diurnal p CO 2 variability of 289–724 μatm was driven primarily by phot...
Ocean acidification, via an anthropogenic increase in seawater carbon dioxide ( CO 2 ), is potentially a major threat to coral reefs and other marine ecosystems. However, our understanding of how natural short‐term diurnal CO 2 variability in coral reefs influences longer term anthropogenic ocean acidification remains unclear. Here, we combine observed natural carbonate chemistry variability with future carbonate chemistry pre...
Pacific Rim Forestry / Silviculture and Forest EcologyNARA Subscribed
Leucaena leucocephala (leucaena) is an important agroforestry tree of tropics and subtropics due to its protein rich foliages, ability to grow on poor soils, and high level of tolerance to various stresses including drought and diseases. We hypothesized that leucaena have a unique set of genes which confer tolerance to various abiotic and biotic stresses and these genes are either absent or not expressed in other legumes that...