Biology subjects

Doyle, S.

Publications and source records attributed to Doyle, S..

4 recordsLinked to original sources

bioRxiv2018

Objective Evaluation of Multiple Sclerosis Lesion Segmentation using a Data Management and Processing Infrastructure

We present a study of multiple sclerosis segmentation algorithms conducted at the international MICCAI 2016 challenge. This challenge was operated using a new open-science computing infrastructure. This allowed for the automatic and independent evaluation of a large range of algorithms in a fair and completely automatic manner. This computing infrastructure was used to evaluate thirteen methods of MS lesions segmentation, exploring a broad range of state-of-the-art algorithms, against a high-quality database of 53 MS cases coming from four centers following a common definition of the acquisition protocol. Each case was annotated manually by an unprecedented number of seven different experts. Results of the challenge highlighted that automatic algorithms, including the recent machine learning methods (random forests, deep learning, ...), are still trailing human expertise on both detection and delineation criteria. In addition, we demonstrate that computing a statistically robust consensus of the algorithms performs closer to human expertise on one score (segmentation) although still trailing on detection scores.

neuroscience↗

bioRxiv2017

Genome expansion and lineage-specific genetic innovations in the world’s largest organisms (Armillaria)

Armillaria species are both devastating forest pathogens and some of the largest terrestrial organisms on Earth. They forage for hosts and achieve immense colony sizes using rhizomorphs, root-like multicellular structures of clonal dispersal. Here, we sequenced and analyzed genomes of four Armillaria species and performed RNA-Seq and quantitative proteomic analysis on seven invasive and reproductive developmental stages of A. ostoyae. Comparison with 22 related fungi revealed a significant genome expansion in Armillaria, affecting several pathogenicity-related genes, lignocellulose degrading enzymes and lineage-specific genes likely involved in rhizomorph development. Rhizomorphs express an evolutionarily young transcriptome that shares features with the transcriptomes of fruiting bodies and vegetative mycelia. Several genes show concomitant upregulation in rhizomorphs and fruiting bodies and shared cis-regulatory signatures in their promoters, providing genetic and regulatory insights into complex multicellularity in fungi. Our results suggest that the evolution of the unique dispersal and pathogenicity mechanisms of Armillaria might have drawn upon ancestral genetic toolkits for wood-decay, morphogenesis and complex multicellularity.

evolutionary biology↗

bioRxiv2016

The food web of Potter Cove (Antarctica): complexity, structure and function

Knowledge of the food web structure and complexity are central to better understand ecosystem functioning. A food-web approach includes both species and energy flows among them, providing a natural framework for characterizing species ecological roles and the mechanisms through which biodiversity influences ecosystem dynamics. Here we present for the first time a high-resolution food web for a marine ecosystem at Potter Cove (northern Antarctic Peninsula). Eleven food web properties were analyzed in order to document network complexity, structure and topology. We found a low linkage density (3.4), connectance (0.04) and omnivory percentage (45), as well as a short path length (1.8) and a low clustering coefficient (0.08). Furthermore, relating the structure of the food web to its dynamics, an exponential degree distribution (in- and out-links) was found. This suggests that the Potter Cove food web may be vulnerable if the most connected species became locally extinct. For two of the three more connected functional groups, competition overlap graphs imply high trophic interaction between demersal fish and niche specialization according to feeding strategies in amphipods. On the other hand, the prey overlap graph shows also that multiple energy pathways of carbon flux exist across benthic and pelagic habitats in the Potter Cove ecosystem. Although alternative food sources might add robustness to the web, network properties (low linkage density, connectance and omnivory) suggest fragility and potential trophic cascade effects.

ecology↗

bioRxiv2016

Critical transitions and the fragmenting of global forests

The replacement of forest areas with human-dominated landscapes usually leads to fragmentation, altering the structure and function of the forest. Here we studied the dynamics of forest patch sizes at a global level, examining signals of a critical transition from an unfragmented to a fragmented state, using the MODIS vegetation continuous field. We defined wide regions of connected forest across continents and big islands, and combined five criteria, including the distribution of patch sizes and the fluctuations of the largest patch over the last sixteen years, to evaluate the closeness of each region to a fragmentation threshold. Regions with the highest deforestation rates--South America, Southeast Asia, Africa--all met these criteria and may thus be near a critical fragmentation threshold. This implies that if current forest loss rates are maintained, wide continental areas could suddenly fragment, triggering extensive species loss and degradation of ecosystems services.

ecology↗