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Investigating enzyme systems from deep-sea fungal secretomes for biological pre-treatment of cattle paunch contents and bioenergy production
No full textCattle paunch contents are the recalcitrant, lignocellulose-rich feed found in the rumen of cattle. To improve the microbial degradation of paunch solids during AD, pre-treatments can be effective. While physicochemical treatments can increase biomethane production from cattle paunch contents, biological pre-treatments e.g. enzymatic can require less energy, uncomplicated equipment and operating conditions, can be more targeted and controllable, recycling of chemicals after the treatment is unnecessary, downstream processing is low-cost, and there is very little, or no, inhibitor formation. Despite this, paunch contents have not been pre-treated biologically to-date outside of the rumen. Therefore, this thesis focused on developing a novel biological pre-treatment for cattle paunch contents, to improve their biodegradability during AD and thereby increase biomethane production. Lignocellulolytic fungal secretomes were characterised and applied in the saccharification of paunch contents, and were from strains of Emericellopsis maritima, Penicillium chrysogenum, P. antarcticum and Talaromyces stollii isolated from deep-sea sediments, an extreme environment, in the North Atlantic. Extremophiles can produce more robust proteins than those produced by their terrestrial counterparts, as a direct result of their inhospitable natural environment. The T. stollii SFI-F17 secretome demonstrated remarkable levels of exo-glycoside hydrolase activity, and was superior to the others in its ability to saccharify paunch contents. Therefore, the pre-treatment of three compositionally different lots of paunch contents was investigated using the T. stollii SFI-F17 secretome and/or rumen fluid, which is rich in lignocellulolytic microbes, to determine if they could improve the biomethane potential (BMP) of the paunch contents. A BMP test carried out over 50 days revealed that, when both rumen fluid and the T. stollii SFI-F17 secretome were used, the BMP increased by 104.68%, 104.84% and 83.24% compared to the controls. When pre-treated with just the T. stollii SFI-F17 secretome, the BMP increased by 44.58%, 74.47% and 101.35% compared to the controls. Finally, whole de novo shotgun sequencing of T. stollii SFI-F17 and characterisation of its Carbohydrate Active Enzyme (CAZy) repertoire showed that it encodes 605 CAZymes out of 11,458 genes, of which over 200 were predicted to be involved in lignocellulose degradation. These included 366 glycoside hydrolases (GHs), 115 glycosyl transferases (GTs), 28 carbohydrate esterases (CEs), 7 polysaccharide lyases (PLs), 78 auxiliary activities (AAs) and 84 carbohydrate-binding modules (CBMs)
Cerebral organoids with integrated endothelial networks emulate the neurovascular unit and mitigate core necrosis
No full textCerebral organoids (COs) are multicellular, self-organized, in vitro, 3D brain-like tissues used for developmental biology, disease modelling, and drug screening. However, their lack of vascularity renders them less physiologically accurate. Vascularization of COs remains challenging due to the different requirements between COs and vascular cells, limited vascular network penetration within the organoid, and the absence of luminal perfusion. Here, an encapsulation approach is devised in which human brain microvascular endothelial cells (HBMVECs) are delivered to developing COs from progressively degrading extracellular matrix (ECM)-based hydrogel droplets. By tuning this hydrogel concentration and media composition, an enhanced vascular-like network formation is observed, expanding within the organoid tissue. Using pathway inhibitors, a subset of the endothelial cells (ECs) is shown to originate from the CO itself, promoting network integration. Endothelial networks displayed blood-brain barrier (BBB) features, including astrocytic end-foot-like interactions, pericyte wrapping, and collagen-laminin basal lamina. Vascularized COs exhibited greater media internalization and up to three-fold lower apoptosis than non-vascularized COs. This comprehensive 3D neurovascular model is a promising platform for cerebrovascular research and drug testing applications.This work was supported by CÚRAM, Research Ireland Centre for Medical Devices, the School of Biological and Chemical Sciences, College of Science and Engineering, University of Galway, the Research Ireland 18/EPSRC-CDT/3583, Engineering and Physical Sciences Research Council EP/S02347X/1, European Union's Horizon Europe Excellent Science programme under the Marie Skłodowska-Curie Actions Grant Agreement (Grant Agreement No 101081457), Research Ireland and the European Regional Development Fund (ERDF) under grant number 13/RC/2073_P2, and Simons Initiative for the Developing Brain (grant number 529085).peer-reviewe
Lightweight, privacy-compliant motion detection system for constrained devices
No full textThis research is conducted under the research project funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Action (MSCA) grant agreement No 101109961In a rapidly evolving digital landscape, embedded vision systems are becoming increasingly prominent in applications such as home security, surveillance, and autonomous monitoring. However, existing solutions often lack computational efficiency for embedded hardware or fail to meet key ethical and regulatory requirements. This paper presents a lightweight, privacy-compliant motion detection system with integrated facial recognition deployed on the Qualcomm RB5 platform. The system enforces data minimisation by recording video only when motion is detected, reducing unnecessary data collection. To protect privacy, facial anonymisation is applied using Gaussian blurring, and Role-Based Access Control (RBAC) restricts access to sensitive data. Experimental evaluations demonstrate an approximate 80% reduction in storage requirements compared to continuous recording while maintaining acceptable CPU and memory usage. The system also achieves reliable detection accuracy while aligning with data protection principles, making it suitable for privacy-sensitive, resource-constrained devices.This research is conducted under the research project funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Action (MSCA) grant agreement No 101109961peer-reviewe
Approaches to assessment of community level health literacy: a scoping review
No full textAddressing health literacy at the community level can provide the potential for improving health knowledge, skills, and behaviours that can ultimately lead to better health outcomes. While many tools exist for measuring individual and disease-specific health literacy, community and critical health literacy have received less attention. The review focuses on geographic communities and includes the concepts of ‘health literacy’, ‘critical health literacy’, and ‘assessment’. Key information sources for the review were Scopus, EMBASE, MEDLINE, CINAHL, ERIC, and PsycINFO, along with Google Scholar for grey literature. Hand searches of reference lists from included studies were also conducted. The search was limited to articles published between 1 January 2010, and 1 June 2023, with no restrictions on data collection methods or study design. Data were charted following guidelines from the Joanna Briggs Institute and PRISMA ScR. Initially, 14 216 citations were retrieved, with 8612 remaining after removing duplicates. Double-blind screening of titles and abstracts resulted in 33 articles, which underwent double-blind full-text screening. Three articles were included, and a hand search identified one more, totalling four articles. The small number of eligible articles and the heterogeneity of content reflect the nascent stage of development of community level health literacy and its assessment. The review findings highlight the need to develop tools to assess community level health literacy to support interventions in empowering communities in maintaining and promoting their own health.J.M. was supported by a School of Medicine, University of Galway, Summer Scholarship
Generation of equine induced pluripotent stem cells from cells of embryonic, perinatal and adult tissues
No full textBackground
Regenerative therapies are quickly expanding to application in equine patients because of their importance as sporting and companion animals. Furthermore, aligning with a One Health concept, veterinary medicine offers a unique platform for preclinical studies. While mesenchymal stem/stromal cells (MSCs) therapies are already used in treating horses, strategies involving induced pluripotent stem cells (iPSCs) are poorly developed. iPSCs present great potential for therapy and disease modelling, but their consistent generation in horses requires further investigation into the source of somatic cells and the reprogramming method and conditions.
Methods
The reprogramming potential of equine cells from tissues of three developmental origins was compared: prenatal (embryo-derived MSCs, eMSCs), perinatal (cord blood-derived MSCs, CB-MSCs) and adult (articular chondrocytes, ACs). Two reprogramming methods (retroviral, lentiviral) and different culture conditions (serum/serum-free, feeder cells/feeder-free, with/without small molecules) were tested. Pluripotent gene expression was analyzed at different time-points to reveal transcriptomic changes associated with reprogramming. The generated equine iPSCs (eqiPSCs) were characterized by alkaline phosphatase (AP) staining, expression of pluripotent genes and proteins, three-germ layer differentiation (embryoid body) and karyotype.
Results
Using a lentiviral vector with serum-free media and feeder cells resulted in the most favorable conditions for eqiPSCs reprogramming, but adding small molecules had a negative effect. Equine CB-MSCs and ACs were only partially reprogrammed and could not be efficiently expanded in culture. Only eMSCs generated putative eqiPSCs that met the cellular, molecular and functional criteria of pluripotent cells. Equine eMSCs showed higher proliferation and basal expression of pluripotent genes compared to CB-MSCs and ACs, and showed the highest upregulation of pluripotent genes along reprogramming.
Conclusions
The developmental stage of the starting cell strongly influences their reprogramming potential in equine species. This has been suggested for human and other animal species, but direct comparison of equine cells from prenatal, perinatal and adult sources has not been reported before. Novel preliminary insight into the transcriptomic changes of different equine cell types during reprogramming, and on the effect of different culture conditions, can contribute improving the generation of eqiPSCs. While transgene-free methods are the goal, putative eqiPSCs are critical to enlarge our knowledge on animal iPSC biology.This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement no. 101026825, and from the Ministerio de Ciencia e Innovación (Spain) under grant number PID2020-116352GB-I00
Composite material selection and testing for tidal turbines
No full textThe objective of the DeepCData Project is to generate test data on novel composite materials that are used in tidal turbine blades. The test data will be used to (i) characterize the performance of the selected composite materials after accelerated water aging, (ii) identify the mechanical properties of novel, sustainable materials for tidal turbine applications, and (iii) create a comprehensive fatigue testing dataset for use in blade design and structural analyses. This paper describes the selection of four viable composite material systems and their associated manufacturing methods, using the hydrofoils of ORPC’s RivGen 2.1 as the basis for selection. The selection process involves the iterative assessment of materials, product shape, equipment, tooling, consumables and processing factors leading to the identification of candidate materials for testing. The paper also describes the test matrix defined to characterise the materials and to investigate key processing parameters for the materials. The paper outlines the water immersion process used to age the composite test samples and concludes with preliminary testing results from the campaign.The authors would like to acknowledge the financial support through the TIDAL-GES project of the University of Galway Global Challenges Programme, the MaREI Research Ireland Centre for Energy, Climate and Marine (Grant no. 12/RC/2302_2), the DeepCData project funded by the Sustainable Energy Authority of Ireland (Grant no. 23/RDD/1021) and Construct Innovate, which is funded by Enterprise Ireland
Attitudes towards LLM use among software engineering researchers: Results from a two-phase survey study
No full textThis two-phase survey study investigates Software Engineering (SE) researchers' attitudes toward incorporating AI tools, particularly large language models (LLMs), in their workflows. Conducted at a large, independent European research institute, the study provides insights into the emerging norms and attitudes regarding AI integration within empirical SE practices, crucial insights for ensuring responsible AI use and maintaining scientific integrity in the SE field. Our findings reveal that SE researchers prefer LLM contributions when applied on small, narrowly scoped, and verifiable tasks rather than open-ended tasks, and used as a as supplementary tool to traditional methods. In contrast, it is viewed as inappropriate for evaluating others' work. Finally, we observed conflicting views regarding high-stakes tasks traditionally reflecting genuine human effort and emotional commitment.This publication has emanated from research jointly funded by Taighde Éireann – Research Ireland under Grant number 13/RC/2094_2, and co-funded by the European Union. Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Executive Agency. Neither the European Union nor the granting authority can be held responsible for them. The study was co-funded by the Research Council of Norway
High-sensitivity nanometamaterial near-infrared biosensor for label-free early cancer detection via exosomal biomarkers
No full textThis study presents a novel, to the best of our knowledge, ultra-wideband nanobiosensor based on a doublenegative (DNG) metamaterial perfect absorber for early cancer detection through exosomal biomarker analysis. Ourbiosensor operates across a broad frequency range from 70 THz to 3 PHz, exhibiting near-unity absorption, i.e., exceeding 99%, and angular and polarization insensitivity, i.e., providing polarization-independent absorption across the full spectrum of polarization angles (0 to 90), ensuring stable performance under both transverse electric (TE) and transverse magnetic (TM) polarized waves. Of particular interest is its performance in the nearinfrared (NIR) region (70–400 THz), where the sensor’s DNG characteristics manifest through simultaneously negative permittivity and permeability, enhancing field confinement and sensitivity. This spectral window is especially conducive to label-free, non-invasive detection of circulating exosomes, critical indicators of early stage oncogenesis. The sensor is constructed using a tri-layer metal–insulator–metal (MIM) architecture comprising nickel (Ni) layers and a silicon dioxide (SiO2) dielectric spacer. The design leverages the plasmonic and thermal stability properties of Ni and the low optical attenuation of SiO2 to achieve optimal absorption and structural robustness. Electromagnetic simulations demonstrate strong electric and magnetic resonances, producing significant near-field enhancements. These improve the detection of subtle dielectric changes associated with exosomal binding events. The sensor maintains high absorption efficiency across oblique incidence angles and various polarization states, making it suitable for real-world biomedical diagnostic applications. By focusing on the NIR regime where tissue transparency and molecular vibrational modes intersect, the proposed biosensor enables the discrimination between cancer-derived exosomes and their normal counterparts, as confirmed through spectral and field distribution analyses. The demonstrated performance highlights the sensor’s promise for next-generation photonic platforms targeting early cancer diagnostics, with potential extension to environmental monitoring and energy harvesting technologies.Taighde Éireann–Research Ireland (13/RC/2094_2); European Union’s Marie Sklodowska-Curie Actions (101126578); University of Galway; University of Doha for Science and Technology (KK-2024005); Icelandic Research Fund (2410297); Narodowe Centrum Nauki (2022/47/B/ST7/00072); Irish Research eLibrary
Identification and characterisation of biomarkers that determine the quality of life in cancer survivors
No full textMicroRNAs (miRNAs) have been well-documented in cancer- and cancer treatment-induced complications, and exercise physiology. Oestrogen has been demonstrated to play an important role in response to exercise. However, whether miRNAs altered by cancer and cancer treatment can be used to monitor exercise progress in rehabilitation programmes and whether oestrogen levels can be a potential biomarker of exercise intensity remain unclear. This study aimed to identify potential miRNAs that could be used to monitor exercise progress in cancer survivors and explore the correlations between oestrogen levels and physiological parameters.
Chapter 3 described the expression of a panel of muscle-related (miR-1, miR-133, miR-208, miR-486, miR-499) and inflammation-related (miR-21, miR-126, miR- 146, and miR-155) miRNAs selected by literature review. We found that Luminal A had a greater impact on muscle-related miRNAs, while Luminal B had a greater impact on inflammation-related miRNAs. Surgery, chemotherapy, and combined therapy had a prominent effect on miR-21 and miR-486 compared to endocrine therapy. The expression of miR-133 and miR-486 was significantly impacted by treatment duration and age.
Chapter 4 described the impact of a 12-week exercise programme on the quality of life and the expression of selected miRNAs in cancer survivors of the CANReact study. We found a 12-week exercise programme could significantly improve physical well-being, but did not improve participants' fatigue levels. Exercise significantly improved the 6-minute walk distance and muscle strength. MiR-126 significantly increased after 12 weeks of exercise, and ΔmiR-126 was positively correlated with Δmuscle mass% (r = 0.548, p=0.015). Inflammation- and musclerelated miRNAs were interrelated, and the higher the inflammation-related miRNAs, the higher the muscle-related miRNAs. The correlations between physiological parameters and the selected miRNAs were weak.
Chapter 5 described the expression of oestradiol levels and the role of oestradiol levels in the response of physiological parameters to exercise in 50 female participants in the CAN-React study. We showed that 44 participants had an oestradiol level below 30 pg/mL, and six (12%) had an oestradiol level of more than 30 pg/mL, with a mean oestradiol level in this cohort of 31.5 pg/mL. The sensitivity of oestradiol in predicting the responsiveness of forced expiratory volume in 1 second (FEV1) and forced vital capacity (FVC) to exercise was 70% and 71.4%, with a specificity of 85.7% and 70%, respectively. When oestradiol was 8.64 and 9.93, the area under curve (AUC) was 0.700 and 0.629 in left- and right-hand grip strength, with a sensitivity of 75% and 70%, and a specificity of 80% and 71.4%, respectively
Failure of split posterior tibial tendon transfer in cerebral palsy complex foot deformities: A review of failure definitions and risk factors for failure
No full textPurpose of Review
This review examines variability in failure and recurrence rates following split posterior tibial tendon transfer (SPOTT) for spastic equinovarus deformity (SED) in children with cerebral palsy (CP). It evaluates patient-specific and surgical risk factors contributing to poor outcomes and assesses the inconsistent definitions of failure across the literature.
Recent Findings
Across the seven included studies, failure was more common in patients under the age of 8, non-ambulatory individuals, and those with quadriplegic CP. Surgical contributors included poor tendon tensioning, residual spasticity, over- or under-correction, and untreated bony deformities. Although modified techniques demonstrated improved outcomes, the risk of recurrence was not completely eliminated. All studies consistently lacked standardized definitions of surgical failure and recurrence, limiting cross-study comparability. Postoperative management strategies—particularly structured bracing protocols and delaying surgery until after age 8—were associated with more favorable outcomes.
Summary
SPOTT remains a viable surgical option for dynamic SED in children with CP, but long-term success is highly dependent on careful patient selection, surgical expertise, and consistent postoperative care. Inconsistent definitions of recurrence and failure remain a major barrier to improving clinical outcomes and conducting meaningful comparative research. To enhance clinical decision-making and guide future studies, a standardized grading system should be urgently developed and adopted in the field.peer-reviewe