S. Duffy

Biophysical Profiling of Red Blood Cells from Thin-film Blood Smears using Deep Learning

This paper develops a deep learning model to detect RBC deformability and storage-related changes in blood smears, showing high accuracy in categorizing deformability groups.

Geographic, ecological, and temporal patterns of seabird mortality during the 2022 HPAI H5N1 outbreak on the island of Newfoundland

Wild bird mass mortalities in eastern Canada associated with the Highly Pathogenic Avian Influenza A(H5N1) virus, 2022

The paper estimates 40,966 wild bird mortalities in eastern Canada due to H5N1 avian influenza in 2022, highlighting potential population-level impacts on Northern Gannets and American Common Eiders.

Phylogeographic analysis of Begomovirus coat and replication-associated proteins

The paper reevaluates begomovirus phylogeographic groupings using coat and replication-associated proteins, finding broad support for AAEO and Americas groupings but not fine-scaled divisions.

On-target, dual aminopeptidase inhibition provides cross-species antimalarial activity.

This paper identifies MMV1557817 as a dual aminopeptidase inhibitor effective against multiple Plasmodium species and highlights its potential as a multi-target antimalarial drug.

SARS-CoV-2 ORF7a mutation found in BF.5 and BF.7 sublineages impacts its functions

The paper evaluates the effect of the H47Y mutation in ORF7a of SARS-CoV-2 BF.5 and BF.7 sublineages on its three main functions, finding it impairs IFN-I antagonism and MHC-I downregulation but not anti-SERINC5 function.

Post-glacial recolonization and multiple scales of secondary contact contribute to contemporary Atlantic salmon (Salmo salar) genomic variation in North America.

This study uses genomic data from Atlantic salmon to show that post-glacial recolonization and secondary contact at multiple scales shaped contemporary genetic diversity in North America.

High pathogenicity avian influenza (H5N1) in Northern Gannets: Global spread, clinical signs, and demographic consequences

This study tracks the global spread of HPAI H5N1 in Northern Gannets, documenting high mortality rates and demographic impacts across multiple colonies.

A Transducing Bacteriophage Infecting Staphylococcus epidermidis Contributes to the Expansion of aNovel Siphovirus Genus and Implies Genus is Inappropriate for Phage Therapy

The paper reports a novel siphovirus phage infecting Staphylococcus epidermidis that can transduce antibiotic resistance, suggesting the genus is unsuitable for phage therapy.

Parallel genomic basis of age at maturity across spatial scales in Atlantic Salmon

This study investigates the genomic basis of age at maturity in North American Atlantic Salmon, finding both parallel and population-specific genetic patterns.

Rapid multilocus adaptation of clonal cabbage leaf curl virus populations to Arabidopsis thaliana

This study shows rapid adaptation of CabLCV populations in Arabidopsis thaliana through spontaneous mutations and convergent evolution, challenging the assumption of high adaptation.

Interspecies recombination has driven the macroevolution of cassava mosaic begomoviruses

This study shows that interspecies recombination drives speciation in cassava mosaic begomoviruses, contributing to their rapid evolution and genetic diversity.

Population diversity of cassava mosaic begomoviruses increases over the course of serial vegetative propagation

This study shows that vegetative propagation increases viral diversity in cassava mosaic begomoviruses over time, while temperature and satellite DNA have minimal impact.

An improved experimental pipeline for preparing circular ssDNA viruses for next-generation sequencing

The paper presents an optimized protocol for sequencing single-stranded DNA viruses using rolling circle amplification and size selection, achieving at least 50% read mapping to the viral reference genome.

Deeply sequenced infectious clones of key cassava begomovirus isolates from Cameroon

The paper deeply sequences and makes publicly available infectious clones of two cassava begomoviruses from Cameroon.

A comprehensive genealogy of the replication associated protein of CRESS DNA viruses reveals a single origin of intron-containing Rep

The paper constructs a genealogy of Rep proteins in CRESS DNA viruses using a custom amino acid substitution model, revealing a single origin of intron-containing Reps and challenging the monophyly of Geminiviridae.

Existing host range mutations constrain further emergence of RNA viruses

This paper shows that pre-existing host range mutations in RNA viruses restrict the genetic pathways available for further host range expansion, using bacteriophage phi6 as a model system.

Broad spectrum capture of clinical pathogens using engineered Fc-Mannose-Binding Lectin (FcMBL) enhanced by antibiotic treatment

This study demonstrates that FcMBL binds to 86% of pathogen isolates and 90% of pathogen species, including bacteria, fungi, viruses, and parasites, and antibiotic treatment enhances its binding efficiency.