179566 research outputs found
Sort by
Dysbiosis of bacterial and fungal microbiomes affects the disease process and treatment outcome in fungal keratitis
No full textFungal keratitis (FK) is a severe eye infection mainly caused by Aspergillus flavus and Fusarium solani. We examined the changes in bacterial and fungal microbiome profiles over a week of disease progression, treatment, and clinical status using targeted next-generation sequencing (NGS). Samples were collected from infected and healthy contralateral eyes of 25 FK patients and one eye of 10 healthy, non-infected cataract controls. QIIME (Quantitative Insights into Microbial Ecology) and MicrobiomeAnalyst were utilised for the data analysis. There was a reduction in beneficial bacteria like Prevotella, Lactobacillus, and Leuconostoc in FK patients compared to the control samples. On the other hand, opportunistic bacteria including Clostridium, Bifidobacterium, and Pseudomonas increased in FK patients. Aspergillus, Colletotrichum, and Basidiobolus were more abundant in keratitis patients, whereas Malassezia and Trichoderma were less abundant. This dysbiosis was also evident in the uninfected contralateral eyes of FK patients. Treatment resulted in significant changes in bacterial genera like Dolosigranulum, Sutterella, and Akkermansia, and fungal genera such as Myrothecium, Corynespora, and Penicillium. Further, treatment returned them to the control group levels, except for Akkermansia and Corynespora. Among the treated patients, a large subset remains nonresponsive to treatment. This treatment outcome, responder versus non-responder, was reflected in the abundance of bacterial genera such as Tannerella, Sutterella, Odoribacter, and fungal genera such as Coprinellus and Volutella. This study highlights the clinical relevance of microbiome signatures in FK, demonstrating bilateral dysbiosis, integrated bacterial–fungal profiling, and correlations with treatment outcomes. These findings suggest potential for microbiome-informed diagnostics, prognostic biomarkers, and risk stratification
From impact to extinction to recovery: Discoveries of IODP-ICDP Expedition 364 to the Chicxulub impact structure
Full text linkIn 2016, International Ocean Discovery Program Expedition 364, with support from the International Continental Scientific Drilling Program, drilled into the peak ring of the Chicxulub impact structure, famous for its causal link to the mass extinction at the end of the Cretaceous. In this summary paper, we discuss key findings from Site M0077 on the cratering processes, marine ecosystem recovery after the mass extinction, and the post-impact hydrothermal system and habitability of the impact structure. Important results include (1) the confirmation of the dynamic collapse model of peak ring formation, (2) insights into impactite emplacement processes on Earth, where water is a key component, (3) discovery of the iridium anomaly within the impact basin, unequivocally linking the Chicxulub impact basin to the global Cretaceous-Paleogene (K-Pg) boundary layer, (4) evidence for key atmospheric inputs of dust, sulfate aerosols, and soot, all likely contributing to global cooling and reduction of photosynthesis as drivers for extinction, (5) rapid recovery of life within the ocean overlying the crater, including a primary succession driven by in part by picoplankton before a transition over 100 s kyr to diversifying planktic communities, and (6) the presence of a long-lived hydrothermal system with extant thermophilic life in the buried peak ring 66 Myr later. The Chicxulub crater represents exceptional scientific opportunity in that it bridges planetary science, impact dynamics, and astrobiology; the integration of such findings continue to reveal the transformative power of asteroid impacts as a major geologic and biologic process
Virus-inclusive single nucleus RNA-sequencing reveals two distinct endothelial response patterns in infectious salmon anaemia
No full textViral replication in endothelial cells is a hallmark of many viral diseases, underscoring the importance of understanding mechanisms that restrict viral replication and the associated consequences for vascular health. Pathogenic infectious salmon anaemia virus (ISAV, Isavirus salaris) targets endothelial cells of Atlantic salmon (Salmo salar L.), causing severe disease and economic losses in aquaculture. Using single nucleus RNA-sequencing at pre-clinical (12 days post infection, dpi) and clinical (16 dpi) stages of infection, we characterized the endothelial transcriptional response to ISAV at unprecedented resolution. ISAV RNA was predominantly detected in endothelial cells, which, along with mononuclear phagocytes, showed the highest number of differentially regulated genes at both time points. To retain statistical power, timepoint-specific analyses were performed on all endothelial subsets combined. Differentially expressed genes at 12 dpi were enriched for pathways related to NOD-like receptor signaling, antiviral responses, and regulation of apoptosis, but by 16 dpi shifted toward pathways associated with cellular senescence, apelin signaling, and insulin signaling. At both time points, we identified two distinct infection-related states: (1) a virus-permissive state, characterized by differential expression of genes involved in the regulation of small GTPase signalling and downstream processes including intracellular trafficking, cytoskeletal remodelling, and control of cell growth and death; and (2) a bystander phenotype, marked by activation of cytokine and chemokine signalling and degradation of viral products. This study is the first to capture cell type-specific responses to ISAV infection, and to characterize the in vivo endothelial response to active viral replication at single-cell resolution in any species.</p
Nov2016 ImageXpress backup
No full text## Access ## This dataset is held in the Edinburgh DataVault, directly accessible only to authorised University of Edinburgh users.The ImageXpress MicroXl platform is a high content instrument from Molecular Devices. Incorporation of a large sensor scientific CMOS camera together with LED solid light source provides enhanced optical sensitivity and image quality over standard high content systems. New MetaXpressTM software solutions such as a “Digital Confocal Option” and “Custom Module Editor” provides increased capability and flexibility to customize image analysis routines for quantification of defined phenotypes. The AcuityXpressTM software facilitates quality control assessment across multiple plates and tissue slides and incorporates multivariate statistical and similarity profiling tools to exploit multiparametric phenotypic data. The ImageXpress platform represents a fully equipped high content solution integrated with plate handling robotics (PAA Scara 4 robot), barcode reader and an extensive image-informatics suite (MetaXpressTM and AcuityXpressTM software) that stream-lines; complex high-content analysis routines; data analysis; image storage and review
Preterm birth, socioeconomic status, and white matter development across childhood
Full text linkBACKGROUND: Preterm birth and socioeconomic status (SES) are associated with brain development in early life, but the contribution of each over time is uncertain. We examined the effects of gestational age (GA) and SES on white matter microstructure in the neonatal period and at five years.METHODS: Participants included preterm and term children. Diffusion MRI was collected at term-equivalent age (n=153 preterm, n=90 term [127/243 female]) and from a subset at five years (n=26 preterm, n=32 term [22/58 female]). We assessed linear associations of GA, SES (Scottish Index of Multiple Deprivation [SIMD] and maternal education), and GA×SES interactions on fractional anisotropy (FA) using tract-based spatial statistics. We compared the proportion of voxels with significant associations between timepoints.RESULTS: In preterm neonates, higher GA and higher maternal education, but not SIMD, were associated with higher FA (p corrected for family-wise error rate, p FWER <0.05). GA-FA associations depended on maternal education and SIMD (β=|0.001-0.005|, p<0.001). At five years, the strength and direction of GA-FA associations depended on SIMD (β=|0.013-0.028|, p<0.001), but not maternal education. In term infants, lower SES was associated with higher FA at the neonatal timepoint only (p FWER <0.05).CONCLUSIONS: Preterm birth and SES both shape brain development at birth and continue to do so at five years. The SES measure most strongly associated with FA in preterm infants switches from a family-level (i.e. maternal education) to neighborhood-level (i.e. SIMD) measure between birth and five years, which suggests strategies to mitigate adverse effects of social inequalities on development may require adaptation as children grow.</p
Chemical tuning of a double-double perovskite oxide
No full textData are for the publication 'Chemical tuning of a double-double perovskite oxide' by Azizah Almadhi, Sean D. Injac, Kunlang Ji, Clemens Ritter, and J. Paul Attfield. Abstract: The feasibility of chemical doping of a double double perovskite (DDPv) is demonstrated by LaxCa1-xMnMnReO6 solid solutions in which cation-site ordering is preserved to x ≥ 0.5 while La3+/Ca2+ substitution at one site tunes magnetic properties. Each of the ~20 DDPv’s discovered by high pressure synthesis in recent years is thus a starting point for chemical tuning to discover and tune electronic and magnetic properties
Optimized Lattice-Structured Flexible EIT Sensor for Tactile Reconstruction and Classification
No full textThis dataset is for publication "Optimized Lattice-Structured Flexible EIT Sensor for Tactile Reconstruction and Classification". ABSTRACT: Flexible electrical impedance tomography (EIT) offers a promising alternative to traditional tactile sensing approaches, enabling low-cost, scalable, and deformable sensor designs. Here, we propose an optimized lattice-structured flexible EIT tactile sensor incorporating a hydrogel-based conductive layer, systematically designed through three-dimensional coupling field simulations to optimize structural parameters for enhanced sensitivity and robustness. By tuning the lattice channel width and conductive layer thickness, we achieve significant improvements in tactile reconstruction quality and classification performance. Experimental results demonstrate high-quality tactile reconstruction with correlation coefficients up to 0.9275, peak signal-to-noise ratios reaching 29.0303 dB, and structural similarity indexes up to 0.9660, while maintaining low relative errors down to 0.3798. Furthermore, the optimized sensor accurately classifies 12 distinct tactile stimuli with an accuracy reaching 99.6%. These results highlight the potential of simulation-guided structural optimization for advancing flexible EIT-based tactile sensors toward practical applications in wearable systems, robotics, and human-machine interfaces
Data for `Abnormal vasculature reduces overlap between drugs and oxygen in a tumour computational model: implications for therapeutic efficacy`
No full textThis dataset contains the results of the drug and oxygen transport simulations in tumour and tumour decompressed microvascular networks published in the work "Abnormal vasculature reduces overlap between drugs and oxygen in a tumour computational model: implications for therapeutic efficacy"
Particle Sizing in Milk by Combined Differential Dynamic Microscopy and Cryo-FIB-SEM Tomography
No full textMilk is a suspension with a multimodal size distribution of fat droplets and protein micelles, which most sizing methods do not distinguish. We demonstrate the use of differential dynamic microscopy and cryo-FIB-SEM tomography to simultaneously size fat globules and casein micelles in homogenised milk without the need for prior physical separation. The two techniques are complimentary, with Cryo FIB-SEM tomography providing an in-depth picture of the constituents, which then allows for confident interpretation of the high-throughput DDM data with its associated improved statistics
Moving through menopause:A mixed methods study of UK women’s experiences of being physically active during the menopause life stage
Full text linkObjective: There is growing evidence for the benefits of physical activity during the menopause life stage. However, limited research has explored physical activity behavior of UK women. Using a mixed-methods approach, two-phases of research were undertaken to: 1) assess physical activity levels and examine the relationship with menopausal symptoms, and 2) use the COM-B theoretical framework to understand the influence of Capability, Opportunity and Motivation on physical activity Behavior.MethodsIn Phase 1, participants completed an online survey (n=655; mean age= 49.9yrs). Descriptive analyzes were supplemented with Chi-Squared tests, with Bonferroni correction. In Phase 2, four online focus groups (n=24; mean age=52.7yrs) were undertaken and thematically analyzed.ResultsIn Phase 1, 75% reported achieving 150 minutes of moderate to vigorous physical activity/week, although 57% reported activity levels had decreased during the menopause life stage. Twelve out of 14 symptoms were experienced by >50%, with changes in mood and brain fog most common (>80%). There was no significant difference in the proportion meeting the moderate to vigorous physical activity guidelines between those women who did or did not experience individual symptoms, although for 10/14 symptoms, >50% indicated a negative impact on likelihood to engage in activity. In Phase 2, capability (e.g., menopausal symptoms), opportunity (e.g., social support) and motivation (e.g., low confidence) were all influential on behavior. Conclusion These findings enhance our understanding of UK women’s experiences of being physically active during the menopause, and provide insight into potential intervention strategies to support women to be active at that time.<br/
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!