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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‘Follow the money. Or jail time.’ Perspectives on the role of senior management in secure software development
(Association for Computing Machinery, 2026-08-14) Ryan, Ita; Roedig, Utz; Stol, Klaas-Jan; Taighde Éireann - Research Ireland, Research Ireland
The number of recorded vulnerabilities in software continues to rise, despite attempts to improve secure coding practice. Much software security research focuses on software developers' abilities, tools and motivations. However, software security budgets and priorities ultimately derive from an organisation's senior management. There is little research on senior management's understanding of software security. We interviewed 21 professional developers, managers and consultants to assess perceptions of how management priorities shape software security in organisations. We found that management priorities are important in providing the resources needed for secure software development. Software-security understanding can be lacking in senior management, which, along with budget pressures, can affect its prioritisation. Developers can be self-motivated to code securely despite lack of management support. Disturbingly, some senior managers will actively subvert software security. Acquisitions, divestitures, downsizing, and funding issues may affect an organisation's software security stance. We make a number of recommendations for policymakers, the C-suite and other stakeholders, and suggest directions for further research.
Basing Ireland’s carbon budgets on temperature neutrality would undermine obligations under the Paris Agreement
(Zenodo, 2025-09-01) Moriarty, Róisín; Daly, Hannah; Environmental Protection Agency
Ireland has committed, through the Climate Action and Low Carbon Development (Amendment) Act 2021 and by ratifying the Paris Agreement, to pursue climate action with the highest possible ambition. Ireland is also bound under ambitious and binding climate targets at the EU level: a 55% reduction by 2030, a 90% reduction by 2040 (under discussion), and net-zero greenhouse gases by 2050. Together, that means doing everything feasible to reduce greenhouse gas emissions and to make a fair contribution to the Paris Agreement temperature goal limiting warming to 1.5°C. We are now perilously close to breaking that limit. Achieving the Paris Agreement goals requires rapid and sustained emissions reductions across all greenhouse gases, including methane (CH4), which is responsible for around 0.5°C of warming to date as a result of human activities. Given Ireland’s position as among the world’s highest per-capita emitters of methane, its approach to this gas in particular will set a precedent. The Climate Change Advisory Council (the Council) has done important work and led an extensive process in preparing and proposing Ireland’s second cycle of carbon budgets, an approach which has been documented in detail. However, the Council’s choice to interpret ‘climate neutrality’ as temperature neutrality (or ‘no additional warming‘) and use this as the basis for its proposed carbon budgets, carries serious risks. This interpretation allows high ongoing methane emissions to be treated as climate neutral, even though they continue to cause high ongoing warming.
The development of a family-focused intervention for parents of adolescents with cystic fibrosis
(University College Cork, 2026-01-31) Mullins, Dee; McCusker, Christopher; Lally, Nicola
Cystic fibrosis (CF) is a lifelong genetic condition that requires intensive, family-centred management across childhood and adolescence. Parents play a central role in treatment adherence, emotional regulation, and the gradual transfer of responsibility as adolescents move towards greater autonomy. Although the introduction of CFTR modulator therapies has transformed physical health outcomes for many young people with CF, emerging evidence has suggested that psychosocial challenges for families have not been eliminated. Instead, adolescence in the modulator era is characterised by reconfigured uncertainty, shifting parental roles, and complex negotiations of autonomy, responsibility, and risk. Despite this, psychosocial research and intervention in CF has remained largely focused on early childhood, individual distress, or adherence behaviours, with limited attention to parents as ongoing recipients of structured psychological support during adolescence.
This thesis presents a programme of research examining family experiences of CF during adolescence in the modulator era and the development and preliminary evaluation of a family-focused psychological intervention for parents. The programme comprised two interlinked studies. First, a qualitative healthcare provider engagement study explored multidisciplinary perspectives on emerging family challenges in adolescent CF care and examined how these challenges might inform the development of a feasible, clinically relevant intervention. Second, a mixed-methods feasibility pilot evaluated the acceptability, practicality, and preliminary psychological impact of a newly developed one-day Family-Focused Intervention (FFI) for parents of adolescents with CF.
The provider engagement study identified heightened parental vigilance, emotional reactivity, uncertainty regarding treatment expectations, and difficulties negotiating adolescent autonomy as central challenges shaping family dynamics in the modulator era. These findings informed the design of the FFI, which integrated principles from Acceptance and Commitment Therapy, narrative approaches, and structured problem-solving within a brief, service-compatible format. The feasibility pilot examined uptake, retention, acceptability, and early psychological change using qualitative interviews and standardised self-report measures targeting emotional distress, psychological flexibility, and perceived family functioning.
Findings indicate that the FFI was acceptable to participating parents and feasible within existing service constraints. Qualitative process data suggested shifts in parental awareness, emotional regulation, and meaning-making following the intervention, while quantitative outcomes provided preliminary evidence of change in psychological flexibility and emotional wellbeing. Short-term changes in perceived family functioning were interpreted within a systemic and process-oriented framework, highlighting the importance of examining early activation effects alongside outcome measures.
Taken together, this thesis contributes novel empirical insight into family life in adolescent CF during the modulator era and demonstrates the feasibility of a provider-informed, family-focused psychological intervention embedded within routine care. The findings underscore the value of integrating stakeholder perspectives, targeting parental psychological processes, and examining process alongside outcome in early-stage intervention development.
Responsible research metrics policy development and alignment: National Open Research Forum policy brief
(Digital Repository of Ireland, 2022-04-22) Dalton, Michelle; Collins, Shane; Schwamm, Hardy; Smith, Sally
Ireland’s national ambitions for open research have been outlined in the National Framework on the Transition to an Open Research Environment (2019). The National Framework consists of 28 objectives across five strategic areas: open access to research publications; enabling FAIR (Findable, Accessible, Interoperable, Reusable) research data; infrastructures for access to and preservation of research; skills and competencies; and incentives and rewards. This report summarises progress and challenges in each of these areas. As such, it aims to provide a snapshot of the current state of the support structures for open research in Ireland.
Taxonomy and diversity of Caudoviricetes viruses
(University College Cork, 2026-04-28) Smith, Linda; Shkoporov, Andrey; Hill, Colin; Research Ireland
Viruses of the class Caudoviricetes are the most abundant and diverse biological entities on Earth, infecting bacteria and archaea across all known ecosystems.
These tailed double-stranded DNA viruses exhibit extraordinary genetic and morphological diversity, occupy broad host ranges, and play central roles in shaping
microbial community structure, nutrient cycling, and ecosystem function in environments ranging from the human gut and oceans to terrestrial soils. Historically, viral diversity has been investigated largely within ecosystem-specific contexts, with independent research efforts focusing on dominant phage groups in particular environments, leaving the evolutionary relatedness between these lineages—and the true extent of global Caudoviricetes diversity—unresolved. Despite their ubiquity and ecological importance, the taxonomy of Caudoviricetes has remained difficult to establish due to extensive genome mosaicism, frequent horizontal gene transfer, and the rapid evolution of nucleotide and amino acid sequences, which together obscure evolutionary relationships and limit the resolution of sequence-based classification approaches. As a result, bacteriophage genomes are best viewed as networks of modular genetic elements whose evolutionary histories cannot be reliably captured by single-gene phylogenies, but instead require large-scale, genome-wide comparative analyses.
This thesis addresses these challenges by developing and applying a structure-informed, whole-proteome framework for viral classification. The work begins with an in-depth examination of Crassvirales, a highly prevalent yet taxonomically narrow order within the class of Caudoviricetes, using it as a case study to illustrate the biological complexity and depth that can arise from a single viral order within the class. This review highlights how even a relatively small lineage can motivate extensive computational and experimental investigation, while providing a reference for contextualising dominant viral groups within the broader dsDNA tailed virosphere. Building on these insights, we introduce a scalable taxonomic framework based on a comparative analysis of genome-wide structural protein content. By integrating large-scale protein structure prediction, structural clustering, and supervised machine learning, this approach learns patterns of structural protein content associated with distinct viral clades, enabling robust taxonomic classification as well as the detection of novel viral sequences.
Finally, these concepts are leveraged to enable viral discovery in Irish soil metagenomes, providing the first insights into the Irish soil virome. In line with observations from other environmental studies, Caudoviricetes emerged as the dominant viral group in Irish soil. Although many detected viruses were spatially restricted, a subset of viral lineages was consistently recovered across all samples, irrespective of site location or soil type, indicating the presence of widespread and ecologically persistent soil phages. Comparative analyses further positioned these viruses within globally connected viral lineages, demonstrating how large-scale approaches can link local viral diversity to the broader virosphere. To support this, Irish soil viruses were placed within a taxonomic framework and compared against global reference databases, including GSVA and VIRE, revealing homology with viruses recovered from geographically and ecologically diverse environments.
Whole-proteome structural analyses of isolated Irish soil viral contigs revealed low levels of shared protein structures, highlighting the extensive diversity of the soil virosphere. In addition, we characterised the ecology of Irish soil viruses, including their predicted hosts, persistence strategies, and auxiliary metabolic gene (AMG) repertoires, and investigated the influence of soil physicochemical variables on their abundance and distribution. Collectively, this thesis advances viral taxonomy by establishing a
structure-based, machine-learning–driven framework for classifying Caudoviricetes and provides the first high-resolution characterization of the Irish soil virome.