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Electroactive taxa stabilise a metal overdosed syntrophic propionate oxidising methanogenic consortia
No full textPropionate oxidation is a critical yet rate-limiting step in anaerobic digestion (AD), vulnerable to disruption by metal toxicity. Electroactive bacteria facilitating extracellular electron transfer (EET) may mitigate such toxicities; yet mechanisms remain unclear. This study hypothesized that ethanol feed electroactive taxa mitigate continuous metal overdosing stress by augmenting propionate oxidation and methanogenesis. Duplicate expanded granular sludge bed (EGSB) reactors were operated under two regimes (i) propionate enrichment (PE) or, (ii) with propionate plus ethanol enrichment (EE). A continuous supply of low concentration iron (Fe), nickel (Ni), cobalt (Co), molybdenum (Mo), tungsten (W), manganese (Mn), and selenium (Se) simulated metal stress. Key indicators - carbon removal, methane production, and microbial community dynamics were systematically monitored. EE reactors exhibited adaptive responses to metal-induced stress, demonstrated by higher propionate removal (58 % vs 27 %) and CO2-reducing methanogenesis by Day 65. The EE biomass retained significantly more W (290 vs 45.7 mg W kg−1) (p < 0.01) than PE, indicating a stronger capacity for metal accumulation. These outcomes were associated with (i) enrichment of Uncultured Geobacteraceae, (ii) increased mcrA gene expression (iii) putative cytochrome-based respiration and (iv) potential heme and co-factor biosynthesis modules. Collectively, these findings suggest that ethanol-fed Geobacteraceae plays a role in promoting W retention, stabilizing Co levels and sustaining propionate oxidation/methanogenesis under severe continuous metal exposure. Strengthening such microbial interactions is essential for enhancing AD systems to metal toxicity. These insights help explore the role of electroactive taxa in anaerobic environments and their potential to improve the stability of environmental treatment systems.This research was supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No. 861088.peer-reviewe
Action design research to develop an interactive dashboard to visualise and compare patient data from Irish general practice (CARA)
No full textOBJECTIVE: A dashboard was developed with and for Irish general practitioners (GPs) to improve their understanding of practice data. The aim of this study was to design and develop interactive CARA dashboards to enable Irish GPs to visualise patient data and compare their data with other practices.
DESIGN: An interpretivist qualitative approach was taken to create a deeper understanding of how GPs view and engage with data. It included four stages: (a) problem formulation, (b) building, intervention and evaluation, (c) reflection and learning and (d) formalisation of learning. The process included interviews to explore what type of information GPs need, as well as iterative testing of the CARA dashboard prototype.
SETTING: General practice.
PARTICIPANTS: GPs, design experts and domain experts (antibiotic prescribing and stewardship).
RESULTS: Key challenges identified from the interviews (context, sense-making, audits, relevance, action, engagement and ease of use) formed the basis for developing the CARA dashboard prototype. The first exemplar dashboard focused on antibiotic prescribing to develop and showcase the proposed platform, including automated audit reports, filters (within-practice) and between-practice comparisons, as well as a visual overview of practice demographics. The design thinking approach helped to capture and build an understanding of the GPs' perspectives and identify unmet needs. This approach benefits the quality improvement methodology commonly adopted across healthcare, which aims to understand the process, not the users.
CONCLUSIONS: The development of a dashboard is based on two key elements: users' requirements and their continued involvement in the development of content and overall design decisions. The next step will be an incremental inclusion of GPs using the dashboard and an exploratory study on dashboard engagement. Additional dashboards, such as for chronic disease, will be developed.This work was funded by grant number RL-20200-03 from the Research Leader Awards (RL) 2020, Health Research Board, Ireland. NG-O was supported by this grant and is a SPHeRE scholar
Insight and involuntary care
No full textImpaired insight is a regularly documented clinical observation in patients undergoing involuntary care, but is easily misunderstood since it refers to different phenomena depending on the context. Within the context of psychotic illness, which comprises the majority of involuntary care, it is more accurately portrayed as unawareness of illness which intersects with the element of capacity related to the ability to appreciate information and weigh it up to make a judgement. Psychotic disorders associated with persistent unawareness of illness are negatively associated with illness outcome and attitudes towards clinical services. There is some evidence that metacognitive therapy can improve insight, but compassionate care which seeks to enhance therapeutic alliance more commonly engages such patients in successful recovery. When insight is substantially impaired, the apparent will and the stated preferences of patients often diverge, in which case involuntary care should not be considered “against the will,” but more accurately “without the consent” of the patient
Sox9 and Sox10: Comparative role in neural crest and placode development
No full textNeural crest (NC) cells and cranial placodes play essential roles in the development and evolution of the vertebrate head. NC cells contribute to the cranial skeleton, cranial sensory ganglia and multiple other structures. Placodes form the olfactory, otic, lateral line organs and many sensory neurons. The SoxE proteins Sox9 and Sox10 are transcription factors acting as neural crest specifiers. They are also expressed in the otic placode, which gives rise to the inner ear. However, little is known about their different functions during NC and placode development. This study identified their candidate direct target genes in each tissue during two developmental stages in Xenopus laevis: neurula and organogenesis. After overexpression of hormone inducible forms of Sox9 and Sox10, NC or placodes were explanted from GFP labelled embryos or were grafted orthotopically from GFP-labelled donor embryos into unlabelled hosts and nuclear translocation of Sox9 or Sox10 was induced. Cells were then FACS-sorted, followed by bulk RNA sequencing to identify candidate target genes in these two tissues. To confirm the direct binding sites of Sox9/10, CUT&RUN sequencing was then performed using NC and placodal explants overexpressing Sox9 and Sox10. The data obtained show that during neurula stages, Sox9 activates NC specifier genes specifically in the NC, whilst repressing them in the placodal region. Only a handful of placode-specific genes were activated by Sox9 or Sox10 in the placodal region. However, both Sox9 and Sox10 repressed certain NC specifiers and neural plate border genes in the placodal region, while activating genes that promote non-neural ectodermal (NNE) competence. During organogenesis stages, Sox9 suppresses numerous NC, neural plate (NP) and placodal genes in the NC while activating certain placodal genes in the otic placode. In contrast, Sox10 suppresses some but activates other neural ectodermal (NE) and NP genes in the NC, while activating NNE genes in the otic placode. In addition, Sox9 and, to some extent, Sox10 also activate transcription factors, which promote neurogenesis in the NC at the neurula stage and in the otic placode at the organogenesis stage. Overall, the data presented in this thesis demonstrate that during neurulation, Sox9 acts as a transcriptional activator of NC genes in the NC, and it represses the same in placodes. In contrast, Sox10 functions primarily by suppressing non-neural, placodal, and neural plate-specific genes in the NC while activating PPR genes in the placode. This has important implications for our understanding of syndromic neurocristopathies with deficits in tissues derived from both NC and otic placode
DGA structures on minimal free resolutions of binomial edge ideals
No full textWe provide a characterisation of all graphs whose parity binomial edge ideals have pure resolutions. Specifically, we show that the minimal free resolution of a parity binomial edge ideal is pure if and only if the corresponding graph is a complete bipartite graph, or a disjoint union of paths and odd cycles. We then prove the existence of a differential graded algebra (DGA) structure on the minimal free resolution of the initial ideal of the binomial edge ideal of a complete graph using algebraic Morse theory, and provide code to compute the products explicitly. Finally, we prove the non-existence of a DGA structure on the minimal free resolution of the binomial edge ideal of a complete graph with 5 or more vertices, in cases where the coefficient field of the ground ring has characteristic 2 or 3
Ecological status assessment in Irish coastal and estuarine sedimentary habitats using the Water Framework Directive Ecological Quality Ratio Infaunal Quality Index
No full textThe Infaunal Quality Index (IQI) is an Ecological Quality Ratio (EQR) developed for the purposes of monitoring coastal and polyhaline (estuarine) waterbodies to meet the requirements of the European directive Water Framework Directive WFD. In Ireland, from 2010 to 2023, IQI was calculated from benthic macrofaunal and sediment data using a custom Microsoft Excel software tool with embedded Visual Basic macros to determine suitable reference conditions for each station sampled. This involved the analysis of 4374 stations in 354 surveys of coastal and estuarine Assessment Groups (AG). The macrofaunal data was processed using a taxa library with a fixed taxonomy. An updated software tool, IQI V2 was released in 2024 including a substantially revised taxa library. Intercalibration between the IQI tools in coastal and estuarine surveys (Assessment Groups; AG) revealed that using all of the survey data, the agreement between the IQI was largely classified as “Very Good”. This is less than the required classification of “Almost Perfect” required for intercalibration between different EQR under the requirements of the WFD. This was true of sample stations, AG and also in the classifications of the probabilities that the true mean EQR value for AG was above the critical Good/Moderate boundary in WFD ecological status assessment. The difference in output between the tools appears to be caused by differences in how the surveyed fauna taxonomy is entered into the tools, what taxonomic groups are included in calculating the EQR, and how taxa abundances are processed. When the stations dataset was reanalysed with the removal of 2033 stations where IQI V2 did not include >10% of the fauna in the EQR calculation, the agreement between the tools was greatly improved. The interpretation of IQI monitoring data from AG surveyed following the introduction of the IQI V2 tool should involve the recalculation of IQI from that waterbody in previous years to place subsequent findings in context. The use of IQI in monitoring salmon aquaculture impacts in coastal waters was assessed using five years of survey data collected at three aquaculture sites on the west coast of Ireland (total 14 surveys). IQI was modelled as a function of distance from the sea pens, sediment organic content and the depth of the sediment apparent redox potential discontinuity (aRPD), including a random effect of aquaculture site. IQI decreased in response to increasing organic enrichment at the aquaculture sites (measured as increasing sediment organic content and decreasing aRPD). IQI was effective in mapping aquaculture impacts on coastal benthic communities. Adoption of IQI in aquaculture monitoring would facilitate improved management of coastal waterbodies by providing a common framework for aquaculture and other potential stressors to be assessed and managed in a cohesive network
Incorporating the gender dimension into infectious disease research: how is Parasitology progressing?
No full textBoth sex (biological) and gender (socio-cultural) are increasingly recognized as important factors in disease risks and outcomes, including parasitic infections and especially those of the genital tract. Many funding agencies now require these dimensions be incorporated into research proposals, though little guidance is given regarding how, leading to confusion among those who do not specialize in this area. In this commentary, I review instances of the use of the word ‘gender’ in the archives of Parasitology (174 articles) to assess how parasitologists are progressing in the incorporation of this dimension and identify what can be done to improve efforts. Use of the term has increased since 1990, reflecting an enthusiasm among parasitologists for including this dimension to their work. Examination of articles which use this term reveals that correct and thorough incorporation of the gender dimension has also increased, but that these articles only account for 8.0% of all articles using the term, demonstrating widespread persistent confusion around terminology regarding sex and gender and how to best account for gender in parasitological research. Parasitologists studying animals should only refer to sex and should incorporate sex into their research design and report whether there are differences in baseline or response between sexes. Parasitologists studying humans should incorporate sex, but then also consider whether any observed differences are due to biological factors like sex hormones and immunity or gendered social variables like behavioural norms and healthcare access. These considerations will further our understanding of host–parasite interactions and improve health outcomes
The role of the domestic and international law in enabling and constraining internment: A case study of Northern Ireland during ‘the Troubles’ and Guantánamo Bay during the ‘War on Terror’
No full textWhen States are confronted with a terrorist attack that threatens the life of the nation, they typically react by adopting emergency legislation to enable the use of counter-terrorism tactics. While there is extensive literature on this topic, little has been written about the precise role that domestic law and international human rights law play in both enabling and constraining such tactics. This thesis investigates how the law and courts (including quasi-judicial bodies) have at once enabled and constrained counter-terrorism tactics, using a comparison of internment in Northern Ireland during ‘The Trouble’ (a period in time when international human rights law was a newly emerging body of law) and Guantánamo Bay in the context of the present day Global War on Terror (with international human rights law now a well-established area of law with a broad range of treaties and case law). These two case studies were selected due to the similarities between them in terms of the counter-terrorism tactics and used the alleged human rights violations, despite the differences in terms of temporal scope, geographic location, and the state of development of international human rights law. Ultimately, this thesis shows that despite the considerable enabling function of the law, in the form of deference to the executive by courts and legislatures, as well as sovereignty deference mechanisms built into the very fabric of human rights law, the law also constrains the nature and extent of counter-terrorism tactics. This study not only adds to the literature on States’ obligations to protect the general public and national security in response to a terrorist threat but develops the idea of a civil liberties and human rights duty to protect suspected terrorists. Finally, it explores the role and limits of the law in finding a durable solution to the vexed problem of terrorism
Value in the cloud: A study of the factors affecting value appropriation by enterprises consuming cloud services
No full textEnterprise consumption of cloud based services has mushroomed in recent years, with an estimated 73% or enterprises having at least a portion of their computing infrastructure hosted in the cloud. Additionally, Traditional software vendors are launching hosted alternatives to traditional perpetual on premises licencing models, while Cloud Native Vendors with cloud only offerings have surfaced in the market and in many instances have overtaken their more traditional competitors as they build, test, iterate and release and product in/to the cloud consistently, hosting their platforms for the most part on hyper scalars such as AWS (Amazon Web Services) , Microsoft Azure and GCP (Google Cloud Platform). This current picture is in stark contrast to the landscape which existed less than fifteen years ago, where cloud as a concept was very much a space where earlier adopters played, learned and iterated. However cloud is now very much a prime time offering and it provides enterprises with cost effective, scalable, customisable, stable solutions. That said, while cloud offerings have matured significantly during the intervening period, not all enterprises are at the point where they consume cloud based platforms/services end to end across their entire Infrastructure, Network, Database, Platform and Application stack. For that reason this dissertation looks to focus on the demand side of the cloud based equation to ascertain the factors which affect the consumption/adoption of cloud based services and additionally to determine what value is captured/appropriated by enterprises who consume. Cloud based services. The study will focus on reviewing the foundational literature focused on both Value Creation and Cloud and the factors enterprises associate with adoption/consumption. A filed based study will be undertaken to capture ‘real world’ data which can then be analysed and compared against the literature The findings provide various insights highlighting some discrepancies between the literature and the real world while also calling out some focus areas for future research in this space
N terminal protein binding and disorder-to-order transition by a synthetic receptor
No full textWe describe the capture and structuring of disordered N-terminal regions by the macrocycle sulfonato-calix[4]arene (sclx4). Using the trimeric β-propeller Ralstonia solanacearum lectin (RSL) as a scaffold, we generated a series of mutants with extended and dynamic N-termini. Three of the mutants feature an N-terminal methionine-lysine motif. The fourth mutant contains the disordered 8-residue N-terminus of Histone 3, a component of the nucleosome. X-ray crystallography and NMR spectroscopy provide evidence for sclx4 binding to the flexible N-terminal regions. Three crystal structures reveal that the calixarene recognizes the N-terminal Met-Lys motif, capturing either residue. We provide crystallographic proof for sclx4 encapsulation of N-terminal methionine. Calixarene capture of intrinsically disordered regions may have applications in regulating protein secondary (and tertiary) structure.We thank University of Galway, the Irish Research Council and Science Foundation Ireland for funding.peer-reviewe