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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Distal course and variability of the spinal accessory nerve: a cadaveric study with surgical implications
(Springer-Verlag Italia s.r.l., 2026-09-11) Stasiewicz, Martyna; O’Flynn, Carrie; Hand, Collette K.; Toulouse, André
Purpose: The spinal accessory nerve (SAN) is most vulnerable to injury along its distal extracranial course in the posterior cervical triangle. While proximal anatomy is well described, distal branching patterns and cervical plexus contributions to trapezius innervation remain poorly defined. This study aimed to characterise distal extracranial SAN branching and cervical plexus contributions and to assess whether proximal configurations predict distal trapezial innervation. Methods: Ten sides from five adult cadavers were dissected from the emergence of the SAN at the posterior border of the sternocleidomastoid muscle (SCM) to its intramuscular termination in the trapezius. Emergence level, SCM branching pattern (Shiozaki classification), cervical plexus communications, loop formations, and distal branching were recorded. Linear morphometric measurements were obtained where feasible. Results: The SAN entered the posterior cervical triangle at variable levels (4.5–8.5 cm from the mastoid). Only Shiozaki Type A and B SCM patterns were identified. Cervical plexus contributions were present in all specimens. An independent cervical branch to the superior trapezius occurred in 6/10 sides, and SAN-cervical loop formation in 2/10 sides. Distal intramuscular branching ranged from two to five terminal branches, with no clear relationship to proximal configuration or measurements. Conclusion: Distal SAN anatomy is highly variable and cannot be predicted from proximal patterns or surface landmarks alone, underscoring the need for meticulous identification of both the SAN and cervical contributions during posterior cervical triangle and trapezius-based surgery.
VIRE: a metagenome-derived, planetary-scale virome resource with environmental context
(Oxford University Press, 2026-01-06) Nishijima, Suguru; Fullam, Anthony; Schmidt, Thomas S B; Kuhn, Michael; Bork, Peer; Takeda Science Foundation; Uehara Memorial Foundation; Taighde Éireann - Research Ireland, 12/RC/2273-P2
Viruses are the most abundant biological entities on Earth, yet their global diversity remains largely unexplored. Here, we present VIRE, a comprehensive resource comprising over 1.7 million high- and medium-quality viral genomes recovered from >100 000 publicly available metagenomes derived from samples that cover diverse ecosystems, including host-associated, aquatic, terrestrial, and anthropogenic environments. Using a unified and scalable pipeline, we systematically assembled viral genomes and provided detailed information on genome completeness, taxonomic classification, predicted lifestyle, and host assignment based on CRISPR spacer matches. VIRE contains >89 million predicted viral open reading frames, as well as detailed functional annotations derived from multiple databases. Importantly, VIRE is seamlessly integrated with related microbiome resources such as SPIRE (https://spire.embl.de) and Metalog (https://metalog.embl.de), enabling users to jointly explore viral genomes, metagenome-assembled genomes, and associated environmental or clinical metadata. Accessible at https://vire.embl.de, VIRE provides an open-access, scalable platform for investigating viral diversity, evolution, and ecology on a planetary scale.
Establishing an Australian Nurse Practitioner research agenda: a national consensus study
(John Wiley and Sons Inc, 2025-10-15) Jennings, Natasha; Dunningham, Corinne; McKenna, Lisa; Lee, Geraldine; Tori, Kathleen; National Health and Medical Research Council, NHMRC; Australian College of Nurse Practitioners, ACNP; Australian College of Nursing, ACN
Aim: To establish research priorities for Australian Nurse Practitioners and develop a robust research agenda. Design: A descriptive, exploratory approach was used and conducted in two stages. Methods: Data were collected over two stages. Data for Stage 1 were collected from 14 December 2023 to 16 February 2024. For the Delphi rounds (Stage 2), data were collected from 11 March to 24 March 2024 for Delphi Round 1 and from 12 June to 26 June 2024 for Delphi Round 2. An exploratory survey was used in Stage 1 to identify clinical challenges and research themes perceived as important for Australian Nurse Practitioners. In Stage 2, a two-phased modified Delphi survey was conducted to prioritise the research themes identified in Stage 1. Results: A total of 315 participants responded to the exploratory survey, with a majority being female (77%), aged between 30 and 75 years. Participants were primarily employed in the public healthcare sector (60%), the private sector (23%), while 17% practised across both sectors. A total of 1335 challenges facing Australian Nurse Practitioners were identified. Sixty-nine participants completed the first Delphi round, and 33 the second, giving response rates of 21% (69/315) and 48% (33/69), respectively. The first Delphi round yielded 11 research themes. Seven of these yielded Content Validity Indices of < 0.90. Four research priority areas remained and were ranked in order of importance. Conclusion: The identified Australian Nurse Practitioner research priorities will play a pivotal role in shaping policies, fostering the efficient integration of Nurse Practitioners into the healthcare system and advancing research capacity. Impact: Nurse Practitioners are established providers of high-quality care internationally; however, they face persistent integration challenges in Australia. This study delivers a nationally relevant, consensus-based research agenda that identifies key priorities across clinical, educational and leadership domains. Patient or Public Contribution: No patient or public contribution.
3D modelling the long-term ageing performance of a CERN tunnel
(Elsevier Inc., 2026-03-06) Xiao, Zhipeng; Wang, Chao; Peng, Chuanyang; Osborne, John Andrew; Li, Zili; Irish Research Council, 713279; European Union's Horizon 2020, 713279
Many operational tunnels worldwide experience progressive deformation due to hydraulic drainage failure, structural deterioration, ground rheological behaviour, and other factors. This study presents a three-dimensional finite element analysis of an ageing horseshoe-shaped tunnel at CERN (European Organization for Nuclear Research), excavated in molasse rock, to investigate the effects of tunnel lining hydraulic and mechanical deterioration, marl swelling, ground layering, and ground permeability anisotropy. Hydraulic deterioration, caused by drainage clogging, is modelled by reducing lining permeability, while mechanical deterioration is represented by decreasing the lining stiffness. Model validation is conducted by comparing simulated results with geodetic and distributed fibre optic sensing (DFOS) data at a representative tunnel section. Parametric studies are then performed to assess the effects of ground layering and permeability anisotropy. Results show that: (1) hydraulic deterioration leads to vertical elongation, mechanical deterioration to tunnel contraction, and their combination to more severe deformation; (2) marl swelling is the dominant mechanism, with deterioration effects being secondary; (3) inclined tunnel alignment through stratified ground induces varying deformation modes due to geological heterogeneity; and (4) permeability anisotropy accelerates groundwater pressure buildup, amplifying vertical elongation. These findings highlight the complex interplay of deterioration and geological factors in ageing tunnels and demonstrate the need for 3D hydromechanical modelling to support long-term performance assessment and maintenance.
Fatty liver index and atherogenic risk determined by lipoprotein particle subclasses: a cross-sectional study of middle- to older-aged adults
(Elsevier Ltd, 2026-09-17) Millar, Seán R.; Perry, Ivan J.; Phillips, Catherine M.; Health Research Board
BACKGROUND The fatty liver index (FLI) provides a cost-effective way to screen for metabolic dysfunction-associated steatotic liver disease (MASLD). MASLD is associated with preclinical atherosclerosis, with cardiovascular disease (CVD) mortality being the leading cause of death among MASLD patients. OBJECTIVE Lipoprotein particles can provide better CVD risk prediction than traditional lipid measures. Yet, FLI associations with intermediate disease markers remain under-researched. This study addressed this gap by investigating FLI relationships with lipoprotein particle subclass concentrations. METHODS This was a cross-sectional study of 1713 middle-aged to older-aged men and women randomly selected from a large primary care center. The FLI was calculated using triglyceride, body mass index, waist circumference, and gamma-glutamyl transferase levels. Lipoprotein particle subclass concentrations and size were determined using nuclear magnetic resonance spectroscopy. Linear regression analyses examined FLI associations with lipoprotein biomarkers. RESULTS In fully adjusted models, higher FLI scores were associated with larger very low-density lipoprotein (VLDL) and smaller low-density lipoprotein (LDL) and high-density lipoprotein (HDL) particle size, more large and medium VLDL, small LDL, and less large HDL particle concentrations, and greater lipoprotein-related insulin resistance (all P <.001). In models that examined these variable associations across FLI quintiles, significant dose-response relationships were observed (P trend <.001 for all). CONCLUSION These findings support the clinical utility of the FLI as a marker of atherogenic risk and as a tool for identifying at-risk individuals. Incorporating the FLI into CVD risk assessment may help improve risk prediction in individuals with liver disease and guide targeted interventions.