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Analysis of mitogenomes from the family Keratoisididae reveals mitonuclear discordance and the presence of unknown open reading frames
No full textHistorically, evolutionary studies have not been able to resolve relationships within Octocorallia but recent advances in genomic techniques have allowed large numbers of Ultra Conserved Elements and exons, collectively referred to as conserved elements, to be extracted from the nuclear genome. Few studies have compared evolutionary histories generated with these conserved elements and with those inferred from complete mitogenomes. We examined the characteristics of 26 complete mitogenomes and constructed both mitochondrial and nuclear (1418 conserved elements) phylogenies of the family Keratoisididae, a prolific group of exclusively deep-sea corals. Relationships among most keratoisidid groups were well supported by the conserved element phylogeny while many were unresolved from mitogenomic inferences. In addition, some incongruences were observed. The position of keratoisidid groups F1 and I4, and the observed polyphyly of D2 in the nuclear inference phylogeny, provide evidence for mitonuclear discordance within the group. Multiple novel Open Reading Frames (ORFs) of unknown function were found in the mitogenome between cob and nad6. These ORFs ranged in size from 84 to 537 bp and were present in all examined mitogenomes except those assigned to keratoisidid group A1 which only has a 10 bp gap between coding regions. Further investigation is required to determine whether these ORFs are expressed and, if so, what function they have. The presence of mitonuclear discordance within the family indicates that phylogenies constructed with concatenated mitochondrial and nuclear markers may be inappropriate.Open Access funding provided by the IReL Consortium. Declan Morrissey was funded by an Irish Research Council Postgraduate Scholarship (GOIPG/2019/3682), a Kenneth Jay Boss Fellowship in the Department of Invertebrate Zoology from The Smithsonian Institute National Museum of Natural History, and by an Irish Naturalist’s Journal Grant 2021. Newly collected corals were gathered using ROV Holland I aboard RV Celtic Explorer research expedition CE21010 which was funded by the Irish National Ship Time Programme awarded to A.L. Allcock or were acquired as part of the EMFF Offshore Reef Project SeaRover, coordinated and led by Ireland’s Marine Institute and INFOMAR (Integrated Mapping for the Sustainable Development of Ireland’s Marine Resource) and funded by the European Maritime and Fisheries Fund (EMFF) Marine Biodiversity Scheme, and the National Parks and Wildlife Service (NPWS).peer-reviewe
A clinical investigation of hip implant migration and wear
No full textThe prediction of survival rate probability for hip implants, based on clinical data acquired before and after surgery, incorporating patient-specific parameters, represents a pivotal advancement in enabling more precise risk assessment for potential complications, such as aseptic loosening and implant wear-related inflammation, on an individualized basis. This critical step marks a substantial progression toward the realization of digitized and personalized medicine. The objective of this study was to establish prediction aiding correlations between implant wear and migration data, derived from X-ray imaging of 149 patients diagnosed with hip arthritis, and the performance of hip implants. The patients underwent cementless hip replacement surgery, receiving implants consisting of ultra-high-molecular-weight polyethylene (UHMWPE) paired with titanium-aluminum-vanadium (Ti6Al4V) wedges. Over the course of a median follow-up period of 4 years, X-ray assessments were conducted to monitor the migration of the femoral head and acetabular components using Ein Bild Röntgen Analyse (EBRA). Clinical findings revealed a linear relationship between average migration and wear. Notably, it was observed that increased cup migration corresponded proportionally to greater wear values. Furthermore, in-depth analysis revealed significant distinctions based on gender and age. Specifically, the established relationship can confidently serve as a reliable predictive model for the behavior of hip implants in female subjects and individuals aged 50–60 years.peer-reviewe
Evaluation of staff training methodologies to increase implementation of behaviour support plans for individuals with intellectual disabilities
No full textAim: Positive Behaviour Support (PBS) is legislated within the Republic of Ireland as best practice to support individuals with intellectual disabilities who engage in behaviours that challenge and reside in residential services or attend day service settings. Within schools and organisations PBS offers a three-tiered model of interventions and supports, ranging from organisation wide supports (Tier 1), to highly individualised supports (Tier 3). The application of PBS within the Republic of Ireland is primarily Tier 3 through highly individualised behaviour support plans. On a daily basis, it is the responsibility of front-line support staff in services to put behaviour supports into practice. Consistent implementation of behaviour supports with fidelity is essential in supporting individuals to learn new skills, become less reliant on behaviours that challenge, and to improve quality of life (QOL). Therefore, it is essential that effective staff training strategies are identified and the context of BSP implementation is understood, which is the aim of the current thesis.
Methods and results: Firstly, a systematic review of PBS training literature, focusing on training components, delivered to staff working in residential and day service settings in the intellectual disability sector was carried out (Chapter 2). The findings of Chapter 2 identified the need for a pilot feasibility study to lay the foundation to examine which training components used within current training practices are efficacious, necessary, efficient, feasible and cost-effective. It also highlighted the methodological research considerations necessary to identify evidenced based training practice. Secondly, insights from key stakeholders were gathered within focus groups and interviews, on their perceived barriers and facilitators to implementation (Chapter 3). The findings indicated that frontline staff primarily believe that organisational factors and social influences are necessary for the successful implementation of BSPs. The thesis aims to gain an understanding of the most commonly recommended behavioural interventions in practice, assessed through an online survey of practitioners working across the UK and Ireland (Chapter 4). The findings of Chapter 4 were cross-referenced with evidenced based practice (EBP) for behavioural interventions to support individual with intellectual disabilities, the combined information was used to identify training content for the pilot and feasibility study. Finally, a pilot and feasibility study was undertaken to evaluate the components of Behavioural Skills Training delivered in a group format (Chapter 5). The pilot and feasibility study found that it was not feasible to run a component analysis of current models of training, due to issues with follow up data collection. Recommended adaptations are provided which would enable a feasible group evaluation of current staff training models in this area.
Conclusion: The current thesis lays the foundation for identification of evidenced based training delivered in a group format to staff working within residential and day service settings in the intellectual disability sector. It also enriches and expands on the understanding of th
Antimicrobial resistant Enterobacterales of clinical importance in mute swans
No full textUrban water environments, including canals, harbours and estuaries are susceptible to contamination with antimicrobials and drug-resistant bacteria through domestic and industrial wastewater discharges and storm water overflows. There is potential for wildlife using these waters to acquire and transmit drug-resistant bacteria and antimicrobial resistance genes (ARGs) of clinical importance. This study aimed to assess clinically important drug-resistant bacteria in urban waterfowl, particularly mute swans. Faecal samples were collected from 17 mute swans in the Greater Dublin Area, Ireland during July, August, October, and November of 2022. Samples were swabbed directly onto agars to select for carbapenem resistant, Extended-spectrum Beta-lactamase (ESBL)-producing, ciprofloxacin resistant and colistin resistant bacteria. Isolates identified by MALDI-TOF as Enterobacterales were tested for susceptibility to a panel of 16 antimicrobials and real-time PCR was employed to detect cefotaximase and carbapenemase genes (CRGs). Drug-resistant isolates were characterised by Whole Genome Sequencing (WGS), including long read sequencing for carbapenemase and mobile colistin resistance (mcr) gene-producing Enterobacterales isolates.
Eleven of seventeen (65 %) swan samples were positive for the resistant organism(s) (n = 35), comprising Escherichia coli (n = 32; 82 %) and other Enterobacterales (n = 3). Twenty E. coli (63 %) produced ESBL, with 16/20 (80 %) identified as positive for blaCTX-M-group 1 enzymes, comprising CTX-M-15 (n = 13), CTX-M-55 (n = 2) and CTX-M-1 (n = 1) and 4/20 (20 %) positive for blaCTX-M-group 9 enzymes CTX-M-27 (n = 2) and CTX-M-9 (n = 2). Three E. coli isolates were phenotypically ertapenem resistant, one of which was an ST4450 isolate which carried plasmid encoded blaOXA-181 and blaCMY-141 with blaCTX-M-15 identified chromosomally. One colistin resistant E. coli bore the mcr-1 gene chromosomally. Bioinformatic analysis revealed high-risk pathogenic ESBL E. coli clones including ST38 (n = 3), ST69 (n = 3), and ST131 (n = 2). The study indicates mute swans are a reservoir for drug-resistant Enterobacterales and ARGs of clinical importance and may be a useful sentinel species for antimicrobial resistance (AMR) surveillance in wildlife.This work was funded by the European Union's Erasmus+ Programme (2021-1-CZ01-KA131-HED-000008157), and through the AREST project which received funding from the Environmental Protection Agency, under the EPA Research Programme 2014–2020, and by the Health Service Executive (Grant number 2017-HW-LS-1). Thanks to University Hospital Galway Microbiology Department for facilitating access to MALDI-TOF for species identification.peer-reviewe
Four pathways for energy citizenship initiatives to contribute to a more democratic European energy system
No full textThe European Green Deal aims to put citizens at the heart of the European energy transition. Yet, their participation often falls short in terms of political involvement and self-governance. In contrast, the imaginary of energy democracy envisions democratising the energy system by involving citizens as political actors and assigns a key role to collectively organised energy citizenship initiatives in achieving this goal. However, it remains elusive how such initiatives contribute to democratisation processes and under what conditions of polycentric governance they achieve to do so. A Qualitative Comparative Analysis (QCA) of 14 energy citizenship initiatives in seven European countries shows that these contributions are diverse and characterised by national contexts. They range from strengthening local capacities for action to ownership and co-determination of energy infrastructure and direct participation of citizens in political decision-making processes. Four pathways of specific polycentric governance configurations are identified along which such contributions were achieved.This work was undertaken within the H2020 EnergyPROSPECTS project supported by the European Commission [Grant Agreement No. 101022492, 2021–2024].peer-reviewe
Sarcasm detection in Tamil and Malayalam YouTube comments
No full textThe expression of sarcasm is a standard literary device where individuals deliberately convey the opposite of what is intended. Accurately identifying sarcasm in the text can aid in comprehending a speaker’s genuine intentions and facilitate other natural language processing activities, particularly sentiment analysis and offensive language identification tasks. We created a dataset for sarcasm from YouTube comments in Dravidian languages and manually annotated them for sarcasm in two Dravidian languages: Tamil (42,244 comments) and Malayalam (18,840 comments). Subsequently, we benchmarked the dataset by comparing it with different text classifiers. Among these approaches, pre-trained transformer models performed well, achieving an accuracy of 0.798 with TamBERT for Tamil and 0.852 with the MuRIL model for Malayalam. Furthermore, we employed SHAP values (explainable AI) to help understand how individual model inputs influence predictions. We also released the dataset on CodaLab and analyzed the participants’ systems. We have presented the results of shared task participants.Open Access funding provided by the IReL Consortium. This research has not been funded by any company or organization.peer-reviewe
The KP equation of plane elastodynamics
No full textThe propagation of nonlinear and dispersive waves in various materials can be described by the well-known Kadomtsev–Petviashvili (KP) equation, which is a (2 + 1)-dimensional partial differential equation. In this paper, we show that the KP equation can be used to describe the in-plane motion of compressible elastic solids with dispersion. Furthermore, a modified KP equation with cubic nonlinearity is obtained in the case of incompressible solids with dispersion. Then, several solutions of these partial differential equations are discussed and computed using a Fourier spectral method. In particular, both equations admit solitary wave solutions.The work of the first author was supported by the European Union’s Horizon 2020 research and innovation programme grant TBI-WAVES - H2020-MSCA-IF-2020 project 101023950. The work of the third author was partially supported by the PRIN research project ‘The mathematics and mechanics of nonlinear wave propagation in solids’ grant 2022P5–R22A and by GNFM of Istituto Nazionale di Alta Matematica (INDAM).peer-reviewe
Warming could cause significant soil organic carbon loss around the southern Baltic Sea
No full textSoil organic carbon (SOC) is linked to greenhouse gas emissions and climate change. Loss of SOC is one of the main threats to European and global soils. The impact of climate change, especially warming, on SOC varies by regions but remains poorly understood. To address this, we used Random Forest (RF) to model SOC in topsoil of Europe based on LUCAS data and applied SHapley Additive exPlanations (SHAP) values to interpret spatial patterns. Key findings show temperature is the predominant factor influencing SOC in northern Europe (north of 55°N). Under the RCP4.5 scenario, projected warming over the next 50 years could lead to significant SOC loss around the southern Baltic Sea (55°N-60°N), while regions north of 65°N could experience SOC gain. Regions between 60°N-65°N would have mixed SOC changes or remain stable. The southern Baltic Sea region, with annual mean temperature of 2.5–7.5 °C, is identified as highly sensitive to SOC loss due to warming. These findings have improved our understanding of the spatially varying SOC-temperature relationships and highlighted the need to consider regional SOC dynamics in future soil management and climate-related policies. In addition, agro-environmental actions at the regional scale should be adopted to enhance SOC conservation.peer-reviewe
Examining the role of voluntary reciprocal altruism and collectivism interventions in enhancing intentions to donate blood among young non-donors: an experimental study
No full textObjective
To evaluate (i) if an enhanced Voluntary Reciprocal Altruism (VRA) intervention increases intentions to donate blood and registration seeking, (ii) if a Collectivism intervention enhances intentions to donate blood and registration seeking, and (iii) to ascertain if there is an interaction effect between VRA and Collectivism interventions on registration seeking and donation intentions.
Methods and measures
A two-way-between-subjects randomised control design was implemented. The dependent variables were intentions to donate and registration seeking, while the independent variables were VRA (VRA and Control) and Collectivism (Collectivism and Individualism). A total of 211 young adult participants were included in the analysis. The participants were randomised into four conditions. A two-way ANOVA was conducted to evaluate differences in intentions to donate, while Chi-Square analysis was used to investigate registration seeking across each condition.
Results
There was a significant difference in once-off intentions to donate blood among participants receiving the VRA intervention compared to the control group (Cohen’s d = 0.54). However, the Collectivism intervention had no significant effect on donation intentions or registration seeking. No interaction effect was detected between VRA and Collectivism.
Conclusions
The VRA intervention significantly influenced once-off intentions to donate and may be a cost-effective strategy to recruit new blood donors.peer-reviewe
Whistleblowing as disclosure injustice: Testimonial and structural barriers to being heard
No full textAre all whistleblowers able to raise disclosures effectively and safely? Or do some workers encounter unfair disadvantage because of who they are? Thus far, the concepts we use in whistleblowing scholarship fail to capture whether and how a whistleblower's gender, race, class, or ethnicity might shape their experience of disclosure. We address this discrepancy by interrogating how a specific social category, gender, intersects with whistleblowing. Our analysis yields a new conceptual framing: disclosure injustice. Disclosure injustice comprises, first, the variability in how different whistleblowers are perceived as credible and thus their testimony is taken into account (whistleblower testimony justice) and second, how structural arrangements support or otherwise people of different social categories coming forward (whistleblower structural justice). Viewing whistleblowing as a scene of potential disclosure injustice challenges extant assumptions that whistleblowing is, more-or-less, a universal experience. Contributions for research include, first, disclosure injustice offering a dual approach, testimonial and structural, that shows how whistleblowing is unevenly accessible depending on one's social category. Second, collective shields are shown to provide salience to speakers who are otherwise vulnerable to reprisal. They work precisely because they hedge against the credibility and support deficits that accompany the experience of whistleblowing. At its core, workplace whistleblowing is the act of speaking “truth to power” to challenge an oppressive status quo. Workers of all description must have equal capacity to engage.peer-reviewe