179566 research outputs found
Sort by
Estimating haplotype values and mutation effects in the context of a local DNA tree
No full textSingle nucleotide polymorphism (SNP) arrays provide genome-wide coverage of polymorphic sites across populations, but most quantitative genetics models assume that the effects of these mutations remain constant across generations and populations. This assumption overlooks population dynamics and genetic architecture that are central to trait expression, particularly when inferences are made across populations. Whole-genome sequence (WGS) data captures all variants and should, in principle, overcome these limitations, but its use has delivered only modest gains in prediction accuracy at considerable computational cost. Ancestral recombination graphs (ARGs) offer a representation of genome variations that describes how genetic variation is shaped by haplotype inheritance between generations (represented as local DNA trees) and associated mutations. This study investigates how a generative model on a local DNA tree can improve the estimation of mutation and haplotype effects, especially for rare or population-specific variants. We developed a TBLUP approach that uses local DNA tree information to estimate haplotype and mutation effects. In each local DNA tree, branches connecting ancestral and descendant haplotypes represent DNA inheritance, and the trait associated with a branch corresponds to the mutation(s) it carries. Summing these branch-specific mutation effects from the tree root to each haplotype defines the haplotype values. This recursive structure yields a sparse and computationally efficient approach for estimating haplotype and mutation effects from the local DNA tree and phenotypes. We show how the TBLUP approach is similar and different to the SNP-BLUP and GBLUP approaches and demonstrate it with cattle mitochondrial DNA, a non-recombining genomic region, using both simulated and real data. The TBLUP approach was computationally more efficient than SNP-BLUP/GBLUP approaches and produced more accurate estimates of haplotype values and mutation effects, which can vary between haplotypes. The accuracy increased when phenotypes were available for haplotypes across the local DNA tree rather than only for the recent haplotypes. Incorporating local DNA tree information enhances the use of genomic data in quantitative genetics. Extending the TBLUP approach to full ARGs will enable analysis across multiple local DNA trees (accounting and leveraging recombination), which will further improve quantitative genetic modelling and practical applications
Self-assessed digital competence of nurse educators—A cross-sectional study in four countries
No full textObjectiveThis study examines the self-assessed level of nurse educators’ digital competence in four European countries and explores variables associated with it.DesignA cross-sectional study was conducted.MethodNurse educators (n = 290) from 36 nursing education organizations in Finland, Malta, Slovakia, and Spain participated in the study. Data were collected from May 2021 to February 2022 through an online survey. The Educators and Educator Candidates’ Competence in Digital Pedagogy instrument contained 20 items in three categories. Descriptive statistics, the Kruskal–Wallis test, one-way analysis of variance (ANOVA), and multiple regression analysis were used in the analysis.ResultsNurse educators reported an overall moderate level of digital competence; the lowest level was in the safe and responsible use of technology. Slovak educators assessed their competence as higher than those from Finland, Malta, and Spain. Having a master's or doctoral degree and completing pedagogical studies were related to a higher level of digital competence.ConclusionNurse educators have successfully adopted the use of evolving teaching, learning, and assessment methods to ensure appropriate and practice-preparing healthcare education. The findings can be used in nursing education and healthcare practice organizations to focus nurse educators’ education on the safe and responsible use of digital pedagogical practices, such as the ethical utilization of electronic documents. Furthermore, in-depth examination of the relationship between educators’ education and digital competence is needed
COSIS’ quest for climate justice:A brief history of the ITLOS advisory opinion
No full textThis article provides a brief history of the origins of the Commission of Small Island States on Climate Change and International Law (COSIS) and its request for an ITLOS advisory opinion. In doing so, it will position COSIS’ journey and the unanimous 2024 ITLOS Advisory Opinion in a broader context of climate justice. Against a backdrop of long-standing frustrations with the failings of the UNFCCC and Paris Agreement COP process to abate dangerous climate change and keep global warming below 1.5 °C, small island States are aware that existing obligations under international law already support their fundamental demands. They have thus taken the reins in a turn to international courts and tribunals in an attempt to level the playing field against major emitters. This brief history and case analysis will reflect on this historic move, discussing the relationship between the parallel proceedings before ITLOS and the ICJ, as well as the procedural and substantive significance of the 2024 ITLOS Advisory Opinion
Translation and commentary:Meret Oppenheim, ‘Kaspar Hauser or the Golden Freedom’
No full textMeret Oppenheim, born to a Swiss family in Berlin in 1913, was a key figure in Parisian Surrealism in the 1930s. While criticism has focused on controversial object-works like Déjeuner en fourrure (1936), her transmedial art (painting, sculpture, writing) offers complex engagements with European history. Kaspar Hauser, oder die goldene Freiheit, an unrealized screenplay written in Switzerland during the dark, wartime years of 1942–1943, displays the artist’s concern with Germanic cultural traditions and with metaphors of transformation and self-redefinition. Oppenheim died in Basel in 1985
Ecological momentary assessment for adolescents with anorexia nervosa and their parents/caregivers in family-based treatment
Get PDFIntroduction: Studies have shown that early weight gain in family-based treatment (FBT) predicts treatment response in adolescents with anorexia nervosa (AN); however, research examining factors associated with early weight gain in FBT is limited. This study tested the feasibility and acceptability of ecological momentary assessment (EMA) in early FBT, particularly to capture momentary data on family climate during mealtimes. Methods: Using multiple methods, quantitative (EMA) and qualitative (interviews) data were collected in the first 4 weeks of FBT. Participants (11 families; 9 adolescents, 19 parents/caregivers) completed EMA assessments daily on the emotional climate during meals, parental strategies and confidence/agreement in renourishment. Qualitative interviews obtained technological and procedural data using EMA. Completion rates and markers of change were explored using repeated measures ANOVA. Interviews were analyzed using reflexive thematic analysis. Results: The EMA completion rate for all family members was 78%: 84% for adolescents, 83% for mothers, 64% for fathers. Results demonstrated changes in caregivers' use of renourishment strategies and in the emotional climate (decreased anger) at mealtimes. No changes were observed in caregiver confidence/agreement in renourishment. Qualitative analyses revealed factors interfering with and facilitating the use of EMA. Discussion: EMA is an acceptable and feasible tool for use with adolescents and their families in early FBT, particularly to capture momentary data on family climate during mealtimes. Future research is needed with larger sample sizes to examine the mechanisms of change in early FBT, and the utility of EMA as a clinical tool in FBT.</p
The association of the rumen virome with methane emissions in dairy cattle
Get PDFEnteric methane production in ruminants is a major environmental concern, yet its association with the ruminal virome remains largely unexplored. Here, we conduct a bioinformatic analysis on previously published ruminal metagenomes from 448 Holstein cows to investigate the virome and its association with methane production. We identify 8933 viral operational taxonomic units (vOTUs), including bacteriophages, archaeophages, megaviruses, and virophages. Differences between high- and low-emitting cows are observed. Low emitters show greater abundance (mean log-FC = 0.72, Padj ≤ 0.049) of some vOTUs infecting bacteria like Prevotella, whereas greater abundance (mean log-FC = 0.70, Padj ≤ 0.047) of archaeophages and megaviruses infecting Methanobrevibacter, ciliates, and fungi, all microorganisms linked to methane production, are observed in high emitters. Associations between viruses and microorganisms might suggest viruses influence methane emissions by modulating key microbial populations. Although mechanisms remain unclear, rumen viruses could serve as biomarkers for selecting low-emission animals or developing microbial interventions.</p
Characterisation of post-translational and transcriptional reprogramming of the immune response to ISAV and IPNV infections in salmon head kidney cells
Get PDFViral diseases remain a major barrier to the sustainable production of farmed fish, primarily attributable to the absence of effective prevention and treatment options. Understanding host-pathogen interactions can guide the development of vaccines, antiviral therapies, or gene editing strategies. Ubiquitination is a post-translational modification capable of regulating protein activation, structure, and degradation. As such, it is known to regulate many aspects of immune functions in model species, but is currently understudied in fish. This study leverages ubiquitin-enriched mass spectroscopy complemented with RNA sequencing to characterise the role of ubiquitination in response to infection. A challenge experiment was conducted by infecting Atlantic salmon head kidney (SHK-1) cells with Infectious salmon anaemia virus (ISAV) and Infectious pancreatic necrosis virus (IPNV). At 24 and 48 hours post-infection, dramatic changes were observed in the global ubiquitination state of host proteins. Many post-translational modifying proteins increased in abundance upon ISAV infection, whilst IPNV infection resulted in a reduction in abundance of many of these proteins. Transcriptomics showed a delay in the activation of the antiviral response to ISAV infection, with major upregulation of genes associated with immune pathways only at 48h. On the contrary, IPNV infection resulted in upregulation of classic innate immune response genes at both timepoints. Clear activation of Rig-like receptor pathways is demonstrated in both infections, in addition to upregulation of both conserved and novel antiviral TRIM E3 ubiquitin ligase genes. Network analysis identified clusters of immune genes and putatively regulatory proteins showing differential ubiquitination upon viral infection. This study highlights the capacity of post-translational control of the host innate immune response to viruses in Atlantic salmon. Clear differences in ubiquitination between the two viruses indicate either virus-specific post-translational regulation or viral antagonism of the immune response. Additionally, the ubiquitination of various proteins was linked to the regulation of innate immune pathways, suggesting a direct role of ubiquitination in the regulation of antiviral responses.</p
Distinct spatiotemporal patterns of white matter hyperintensity progression
Get PDFWhite matter hyperintensity, a key imaging biomarker for brain health, has prognostic implications for stroke. Using a multicenter MRI dataset of 9179 stroke patients plus the UK Biobank (n = 36,210 low/high risk controls), we employ Subtype and Stage Inference modeling and identify three distinct white matter hyperintensity progression subtypes: fronto-parietal, radial, and temporo-occipital. Longitudinal validation confirms classification stability. The fronto-parietal subtype shows delayed onset and more hypertension, while the temporo-occipital subtype has more atrial fibrillation and coronary heart disease. The fronto-parietal and radial subtypes are linked to small vessel stroke, while the temporo-occipital subtype is linked to cardioembolism. The fronto-parietal subtype has higher 1-year ischemic stroke recurrence, while the temporo-occipital subtype shows a higher incidence of early neurological deterioration by symptomatic hemorrhagic transformation and worse 3-month outcomes. Beyond capturing progression, demographics, and vascular risks, and improving post-stroke outcome prediction, this subtyping-staging model also holds potential for stroke prediction.</p
Laymen and Church reform around the year 1000:A reflection
Get PDFThis article reflects on an article published in the Journal of Medieval History in 1979 by Constance Brittain Bouchard, ‘Laymen and Church Reform Around the Year 1000: the Case of Otto-William, Count of Burgundy’, as part of the celebrations for the journal’s fiftieth year. I examine the intervention Bouchard’s article made and its subsequent reception, as well as considering how the themes it emphasised have developed in recent historiography. The article concludes with reflections on where the field might be going next
Peer and sibling bullying victimization in childhood:Prevalence in a national Australian cohort aged 16 years and older
Get PDFTo examine the population prevalence of bullying victimization by peers and siblings reported in a nationally-representative sample of Australian adults. Australians 16 years and older participated in a computer-assisted telephone interview survey (N = 8503) and answered questions about childhood bullying victimization perpetrated by peers and siblings. For peer bullying victimization, they were also asked about the duration of their experiences, and experiences of bias-based bullying victimization (i.e., bullying targeting identity characteristics). Overall, 28.7% (27.5–29.9) of Australian adults reported being bullied by peers and 11.5% (10.6–12.4) by siblings during childhood. Prevalence of peer bullying and sibling bullying victimization was significantly higher for gender diverse individuals and women (as compared with men) and for sexuality diverse individuals (as compared with heterosexual individuals). The most common experience was for peer bullying victimization to have endured for more than 3 years (56.9% [54.5–59.4] of those bullied by peers). Around 67.1% (64.7–69.3) of those who reported being bullied by peers experienced at least one type of bias-based bullying. Being bullied about weight or height (12.8% [11.9–13.7]) was more prevalent than other forms of bias-based bullying (race or ethnicity: 6.1% [5.5–6.8]; disability or impairment: 4.9% [4.3–5.5]; sexuality or gender identity: 3.8% [3.4–4.4]). Peer and sibling bullying victimization are common experiences of childhood in Australia. The prevention of bullying victimization remains a priority for creating safer environments for children
Access Repository Dashboard
Do you manage Edinburgh Research Explorer? Access insider analytics, issue reports and manage access to outputs from your repository in the CORE Repository Dashboard!