Jeremy Fox results 34
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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...
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...
The existence and strength of higher order interactions is sensitive to environmental contextNARA Subscribed
One strategy for understanding the dynamics of any complex system, such as a community of competing species, is to study the dynamics of parts of the system in isolation. Ecological communities can be decomposed into single species, and pairs of interacting species. This reductionist strategy assumes that whole‐community dynamics are predictable and explainable from knowledge of the dynamics of single species and pairs of spec...
Decline effects are rare in ecology: ReplyNARA Subscribed
Decline effects are rare in ecologyNARA Subscribed
The scientific evidence base on any given topic changes over time as more studies are published. Currently, there is widespread concern about nonrandom, directional changes over time in the scientific evidence base associated with many topics. In particular, if studies finding large effects (e.g., large differences between treatment and control means) tend to get published quickly, while small effects tend to get published slo...
Azole‐resistant Aspergillus fumigatus is highly prevalent in the environment of Vietnam, with marked variability by land use typeNARA Subscribed
Summary Azole‐resistant environmental Aspergillus fumigatus presents a threat to public health but the extent of this threat in Southeast Asia is poorly described. We conducted environmental surveillance in the Mekong Delta region of Vietnam, collecting air and ground samples across key land‐use types, and determined antifungal susceptibilities of Aspergillus section Fumigati (ASF) isolates and azole concentrations in soils. O...
Our ability to completely and repeatedly map natural environments at a global scale have increased significantly over the past decade. These advances are from delivery of a range of on-line global satellite image archives and global-scale processing capabilities, along with improved spatial and temporal resolution satellite imagery. The ability to accurately train and validate these global scale-mapping programs from what we w...
Species loss drives ecosystem function in experiments, but in nature the importance of species loss depends on dominanceNARA Subscribed
Aim Decades of experimental research have conclusively shown a positive relationship between species richness and ecosystem function. However, authoritative reviews find no consensus on how species loss affects function in natural communities. We analyse experimental and observational data in an identical way and test whether they produce similar results. Location North America and Europe (experimental communities); global (na...
Aim Why are so many species rare, yet persistent? Possibly, rare species experience strong negative frequency dependence (NFD, i.e. strong intraspecific competition relative to interspecific competition), which both makes them rare and buffers them against extinction. A second, not mutually exclusive, possibility is that rare species that experience weak NFD go extinct quickly due to demographic and environmental stochasticity...
Intraspecific variation can promote or inhibit species coexistence, both by increasing species’ competitive abilities, and by altering the relative strengths of intraspecific and interspecific competition. Effects of intraspecific variation on coexistence can occur via complementarity of different variants, and via a selection effect: initially‐variable populations are more likely to contain highly competitive variants that mi...
Moving forward in circles: challenges and opportunities in modelling population cyclesNARA Subscribed
Population cycling is a widespread phenomenon, observed across a multitude of taxa in both laboratory and natural conditions. Historically, the theory associated with population cycles was tightly linked to pairwise consumer–resource interactions and studied via deterministic models, but current empirical and theoretical research reveals a much richer basis for ecological cycles. Stochasticity and seasonality can modulate or c...
The relative importance of pollinator abundance and species richness for the temporal variance of pollination servicesNARA Subscribed
The relationship between biodiversity and the stability of ecosystem function is a fundamental question in community ecology, and hundreds of experiments have shown a positive relationship between species richness and the stability of ecosystem function. However, these experiments have rarely accounted for common ecological patterns, most notably skewed species abundance distributions and non‐random extinction risks, making it...
Abundance of common species, not species richness, drives delivery of a real‐world ecosystem serviceNARA Subscribed
Biodiversity‐ecosystem functioning experiments have established that species richness and composition are both important determinants of ecosystem function in an experimental context. Determining whether this result holds for real‐world ecosystem services has remained elusive, however, largely due to the lack of analytical methods appropriate for large‐scale, associational data. Here, we use a novel analytical approach, the Pr...
Landscape connectivity has been shown to alter community assembly and its consequences. Here we examine how strong, sudden changes in connectivity may affect community assembly by conducting experiments on the effects of “community mixing,” situations where previously isolated communities become completely connected with consequent community reorganization. Previous theory indicates that assembly history dictates the outcome o...
Biodiversity simultaneously enhances the production and stability of community biomass, but the effects are independentNARA Subscribed
To predict the ecological consequences of biodiversity loss, researchers have spent much time and effort quantifying how biological variation affects the magnitude and stability of ecological processes that underlie the functioning of ecosystems. Here we add to this work by looking at how biodiversity jointly impacts two aspects of ecosystem functioning at once: (1) the production of biomass at any single point in time (biomas...