CORA
Cork Open Research Archive (CORA) is UCC’s Open Access institutional repository which enables UCC researchers to make their research outputs freely available and accessible.
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Mining of food metagenomes reveals an unexplored diversity of dsDNA bacteriophages
(Nature Research, 2026-03-27) Walsh, Liam H.; Soni, Viyal; Ancla, Joseph; Somerville, Vincent; Segata, Nicola; Joyce, Susan; Sinderen, Douwe van; Mahony, Jennifer; Shkoporov, Andrey N.; Kenny, John G.; Cotter, Paul D.; O’Sullivan, Orla; European Union’s Horizon 2020 research and innovation programme; European Union’s Horizon Europe research and innovation programme; Italian Ministry of Foreign Affairs and International Cooperation; European Research Council; European Union's Horizon 2020; Taighde Éireann - Research Ireland; Enterprise Ireland
Bacteriophages are key drivers of microbial ecology, co-existing and co-evolving with bacteria across diverse environments. Limitations in culturing, alongside advances in sequencing and bioinformatics, have driven the use of metagenomics to explore viral diversity. Viral-specific analysis of >3000 food metagenomes from cFMD produced the FVGC, comprising ~3400 metagenome-assembled viruses, most of which belong to novel Caudoviricetes lineages (n = 91), with only ~15% represented in IMG/VR v4. Together, these findings reveal extensive uncharacterized viral diversity in food systems. Beyond serving as a reference, the FVGC facilitates detailed investigation of virus–host interactions. Viral sequences were pervasive across microbial genomes, with several bacterial families exhibiting near-universal associations with viral elements. Bacterial antiviral defence systems were abundant and taxonomically diverse, dominated by restriction–modification systems, while CRISPR–Cas systems showed pronounced lineage-specific distributions; in contrast, viral anti-defence genes were detected at low frequency (<10% of MAVs). Host prediction linked MAVs to clinically relevant taxa, including expanded ESKAPE pathogens such as Klebsiella pneumoniae, Acinetobacter baumannii, Staphylococcus aureus, and Enterobacter spp., highlighting the ecological connectivity between food-associated viruses and clinically important bacteria. Antimicrobial resistance signals were scarce, suggesting minimal phage-mediated AMR dissemination in food environments. This new publicly available viral database represents a valuable resource for further exploration of viral diversity.
Spinon mediation of witness spin dynamics in herbertsmithite
(Nature Research, 2026-06-10) Takahashi, Hiroto; Murphy, Jack; Wood-Thanan, Mitikorn; Puphal, Pascal; Sánchez-Martínez, Miguel Ángel; Jerzembeck, Fabian; Hsu, Chun Chih; Ward, Jonathan; Isobe, Masahiko; Matsumoto, Yosuke; Takagi, Hidenori; Blundell, Stephen J.; Norman, Michael R.; Flicker, Felix; Davis, J. C.Séamus; UK Research and Innovation; European Research Council; Gordon and Betty Moore Foundation; Royal Society; Science Foundation Ireland(SFI)
The kagome lattice of spin-1/2 copper atoms in herbertsmithite is conjectured to sustain a quantum spin liquid state with spinon quasiparticles. Ideally, the kagome crystal planes are each separated by a plane of spinless zinc atoms. However, in real crystals, some spin-1/2 copper atoms substitute randomly onto these inter-kagome zinc sites. Here we reconceptualize such ‘impurity’ atoms as quantum witness spins whose dynamics is designed to probe the spin liquid state. We then introduce spin noise spectroscopy to measure the frequency and temperature dependence of witness spin dynamics, demonstrating that their phenomenology is consistent with extensive interactions between witness spins mediated by propagation of spinons through a quantum spin liquid. Ultimately, a sharp transition occurs at around 260 mK, below which the properties of both spin noise and magnetic susceptibility suggest that the witness spins form a spin glass phase. Among the theoretical models considered, we demonstrate that our observations are only consistent with spinon-mediated interactions between witness spins by either a Z2 or U(1) quantum spin liquid, with the former model more closely matching the data. Our work demonstrates that quantum mechanical witness spins may now conceivably be used as a widely applicable probe of quantum spin liquid physics.
Reframing cityLabs: Worldbuilding as situated pedagogy for public design learning
(Design Research Society, 2026-06-08) Yantaç, Asim Evren; Mulry, Cathal; Linehan, Denis
Urban design education increasingly calls for methods that prepare designers to act within complex public systems. This paper reframes the Malmö CityLab, an experimental module within a master’s program on post-industrial cities, as a situated pedagogy for public design learning. Combining worldbuilding, design fiction, and persona storytelling, the CityLab enabled students and stakeholders to collectively speculate on Malmö’s futures across themes of regeneration, migration, and climate transition. Drawing on student artifacts and expert interviews, the study explores how speculative storytelling cultivates political sensitivity, collaborative reflexes, and systemic awareness, key capabilities for acting as public designers. Findings show that worldbuilding supports reflective, plural, and civic learning, positioning CityLabs as infrastructures for collaborative knowledge production and inclusive urban imagination. The paper contributes to emerging discussions on speculative pedagogies and their role in shaping the competencies, sensitivities, and methods required for public design education.
Clinical practice guideline on the pharmacological management of antipsychotic-related dyslipidemia
(Oxford University Press (OUP), 2026-08-03) Carolan, Aoife; Hynes-Ryan, Caroline; Bourke, Rita; Columb, David; Cullen, Walter; deFerranti, Sarah; Harrington, Sophie Mae; Kelleher, Ian; Kennedy, Cormac; Khoury, Michael; Lally, John; Lyne, John; Norton, Michael; O’Connor, Karen; O’Connor, Patricia; O’Shea, Donal; Perry, Benjamin; Prendeville, Terence; Ryan, Cristin; Sadowska, Ewa; Shiers, David; Siskind, Dan; Strawbridge, Judith; Tae, Haeun; Keating, Dolores; O’Donoghue, Brian; Health Research Board
Background: People taking antipsychotic medicines and those with severe mental illness experience elevated cardiovascular risk compared to the general population which is not adequately addressed by existing guidelines. Increases in lipid levels can occur soon after starting antipsychotics but often go untreated. Cumulative exposure to dyslipidemia from childhood, through young adulthood, facilitates atherogenesis. Regression of early lesions is possible; however, plaque progression can be irreversible, leading to sustained long-term cardiovascular risk. Although lipid-lowering therapies are effective at lowering cardiovascular risk, they are underutilized in this population. We have thus developed a clinical practice guideline for the pharmacological management of antipsychotic-related dyslipidemia. Study Design: Using GRADE-ADOLOPMENT methodology, an international, multidisciplinary panel including experts-by-experience, developed a guideline for the pharmacological management of antipsychotic-related dyslipidemia. Literature was reviewed to answer key health questions. Patient important outcomes were identified. An evidence-to-decision framework informed the strength of recommendations and external reviews evaluated the rigor of the methods. Study Results: Seven recommendations were developed on how and when to initiate lipid-lowering therapy based on specific criteria including established cardiovascular disease/high-risk conditions, cardiovascular risk assessment, or lipid parameter thresholds. A guideline algorithm illustrates the recommendations alongside supporting prescribing information. Conclusions: This is the first clinical practice guideline for the management of antipsychotic-related dyslipidemia. The inclusion of recommendations for individuals aged 10 years and over represents a significant development. Implementation will be supported by shared decision-making resources including information videos and decision-aids.
Spatial distribution of glucose and amino acids within all-aqueous emulsions directs the Maillard reaction and oxidation pathways
(Springer Nature, 2026-03-21) Chen, Kangni; Madadlou, Ashkan; De Pascale, Sabrina; Scaloni, Andrea; Fogliano, Vincenzo; Troise, Antonio Dario; Wageningen University & Research; China Scholarship Council
All-aqueous emulsions represent a versatile platform for studying and controlling chemical reactions in foods and biological systems. Through the compartmentalization and segregation of reactants, distinct molecularly crowded microenvironments enable the generation of unique reaction products. We explored how spatial organization within all-aqueous emulsions composed of polyethylene glycol (PEG) and sodium sulfate (Na2SO4) modulates the Maillard reaction and oxidation reactions between glucose and amino acids. Using untargeted metabolomics and molecular networking, we characterized the chemical diversity of reaction products formed when the reactants were either co-encapsulated within the droplet phase or distributed (segregated) between the two phases of the emulsions. Over 500 compounds were annotated across both systems, revealing distinct molecular profiles driven by reactant localization and phase partitioning. When the precursors were segregated (tryptophan and glucose), oxidation products as aminobenzoyl-, hydroxy- and hydroperoxy-derivatives accumulated preferentially in the PEG phase. Conversely, when the reactants were co-encapsulated (asparagine and glucose) within Na2SO4 droplets, enhanced formation of the Amadori products and dipeptides was observed, guided by phase-specific microenvironment. Our results demonstrate that the reactant location, in addition to time and temperature, plays a critical role in modulating food-relevant reactions, with a new framework for controlling the formation of glycation compounds via emulsion-based microreactors. (Figure presented.)