284 Works

Chemical composition of different sources of diesel fuel

Nic Daeid & Mat-Desa
Diesel samples were collected directly from eight different public fuelling stations in Glasgow, Scotland. Samples of 10, 25, 50, 75, 90, and 95% evaporated product were prepared, resulting in 56 samples in total which were analyzed using gas chromatography–mass spectrometry.

Distinct Roles of Tumor Associated Mutations in Collective Cell Migration

Rachel Lee & Stuart Martin
Recent evidence suggests that groups of cells are more likely to form clinically dangerous metastatic tumors, emphasizing the importance of understanding mechanisms underlying collective behavior. The emergent collective behavior of migrating cell sheets in vitro has been shown to be disrupted in tumorigenic cells but the connection between this behavior and in vivo tumorigenicity remains unclear. We use particle image velocimetry to measure a multidimensional migration phenotype for genetically defined human breast epithelial cell lines...

Audience and Expert Perspectives on Second Screens

Gorkovenko & Taylor
This dataset contains transcripts of co-design workshops and expert interviews carried out as part of a research project exploring how second screens (i.e. devices used while watching television) could be used to support engagement with televised political debates. We conducted four two-hour workshops with 18 participants in total, where they discussed the issues with political discourse online at large and the opportunities for second screens. The discussions were structured around four open-ended topics: (1) content,...

In situ genome sequencing resolves DNA sequence and structure in intact biological samples

Edward S. Boyden, Jason Buenrostro & Fei Chen
Understanding genome organization requires integration of DNA sequence and 3D spatial context, however, existing genome-wide methods lack either base-pair sequence resolution or direct spatial localization. Here, we describe in situ genome sequencing (IGS), a method for simultaneously sequencing and imaging genomes within intact biological samples. We applied IGS to human fibroblasts and early mouse embryos, spatially localizing thousands of genomic loci in individual nuclei. Using these data, we characterized parent-specific changes in genome structure across...

In situ genome sequencing resolves DNA sequence and structure in intact biological samples

Edward S. Boyden, Jason Buenrostro & Fei Chen
Understanding genome organization requires integration of DNA sequence and 3D spatial context, however, existing genome-wide methods lack either base-pair sequence resolution or direct spatial localization. Here, we describe in situ genome sequencing (IGS), a method for simultaneously sequencing and imaging genomes within intact biological samples. We applied IGS to human fibroblasts and early mouse embryos, spatially localizing thousands of genomic loci in individual nuclei. Using these data, we characterized parent-specific changes in genome structure across...

Simultaneous visualization of DNA loci in single cells by combinatorial multi-color iFISH

Magda Bienko
We describe a dataset obtained by applying our recently developed iFISH pipeline to simultaneously visualize 16 small (size range: 62–73 kilobases, kb) evenly spaced DNA loci on chromosome 2 in human cells, in a single round of hybridization. We show how, using combinatorial color coding, multiple loci can be precisely 3D localized in single cells, and how inter-loci distances scale inversely with chromosome contact frequencies determined by Hi-C, as expected. We provide raw images and...

Quantification of within patient Staphylococcus aureus phenotypic heterogeneity as a proxy for presence of persisters across clinical presentations

Julian Baer
Staphylococcus aureus was isolated from patients suffering cardiovascular, prosthetic joint or other infections and plated on Columbia sheep blood agar. Macroscopic time-lapse imaging was performed to quantify colony appearance-time and growth-rate. As a baseline reference, the same time-lapse imaging protocol was used after subculturing clinical isolates in tryptic soy broth until bacteria reached exponential growth phase.

Quantification of within patient Staphylococcus aureus phenotypic heterogeneity as a proxy for presence of persisters across clinical presentations

Julian Baer
Staphylococcus aureus was isolated from patients suffering cardiovascular, prosthetic joint or other infections and plated on Columbia sheep blood agar. Macroscopic time-lapse imaging was performed to quantify colony appearance-time and growth-rate. As a baseline reference, the same time-lapse imaging protocol was used after subculturing clinical isolates in tryptic soy broth until bacteria reached exponential growth phase.

Quantification of Bone Marrow Compartments in Histological Sections

Josefine Tratwal & Olaia Naveiras
MarrowQuant, a digital and quantitative pathology tool was used to quantify the different compartments within the bone marrow at different conditions, mainly aplasia and aging conditions. By using our tool, we can compare the skeletal map induced by lethal irradiation(aplasia), with longitudinal quantification of the “red-to-yellow-to-red” transition over 2 months (aging) in C57BL/6 mouse femurs and tibiae.

Parallel compound screen for infection modulators identifies re-purposing candidates against common viral infections.

Fanny Georgi
Viral infectious diseases span a myriad of maladies, including immunosuppression, cancer, organ failure and, if lacking effective treatment, even death. While numerous targeted antiviral therapies have been developed over the past century, many viral diseases still lack effective antivirals to date. Revisiting compounds approved for other applications offers accelerated development, and automated screening and data processing boost the feasibility of the re-purposing approach. Here, we extended our high-content image-based platform on three human viruses differing...

Structural characterisation of a novel E3 ligase module and activity-based probe development for UBL E3 ligases

Lu Barnsby-Greer
E3 ligase enzymes are key regulators of many aspects of eukaryotic biology via the promotion of the ubiquitylation and subsequent degradation of proteins. There have been over 700 E3s identified within the ubiquitin system with diverse mechanisms of E3 ligase activity, however, significantly less have been identified for ubiquitin-like proteins. Recently developed activity-based probes allowed for the identification of novel E3 ligase proteins involved in the ubiquitin system that carry out unconventional ubiquitylation. The development...

A Study of Care Leavers Lived Experiences of Social Orphanhood in Latvia

Zoe Kessler
This study set out to investigate social orphanhood through narratives of young people with experiences of growing up in care in Latvia. The study uses the life histories of participants to explore the phenomenon of social orphans. To date, narratives about the lived experiences of social orphans in Latvia have been told in the third person as most studies have used methodologies that kept participants passive rather than active. In this study the research process...

New approaches to studying the GPI biosynthesis pathway in T. brucei: uncovering the missing links

Zhe Ji
Trypanosoma brucei is a protozoan that causes Human African Trypanosomiasis and nagana in cattle. The bloodstream form (BSF) of T. brucei has a dense surface-coat of variant surface glycoprotein (VSG) that acts as the first line of defence against the host immune system while the main cell surface glycoproteins of the procyclic form (PCF) are the procyclins. VSGs and procyclins are attached to the cell membrane through glycosylphosphatidylinositol (GPI) anchors. Despite its importance, the GPI...

The Development and Characterisation of a Novel and Modular Virus-like Particle Platform

Aleksandra Moleda

A study of teacher wellbeing in post-primary schools in the West of Ireland

Teresa Crawford
This thesis explores teacher wellbeing in two post-primary schools in the West of Ireland. The research was conducted using a qualitative case study methodology, through semi-structured interviews with twenty-six newly qualified and experienced teachers in two urban schools, one located in a disadvantaged area and the other in a middle-class area. Research on wellbeing suggests that it is a multi-dimensional concept and difficult to define despite a steep increase in scholarly research across a myriad...

Investigating the Effect of Cytokines on the Proliferation and Metabolism of Intraepithelial Lymphocytes

Nicole Salgado Fernandez
The gut is exposed constantly to invading bacterial populations and dietary antigens. To protect it from harm, a complex and diverse network of patrolling immune cells can be found spread throughout the gut and in specialized lymphoid structures. One immune cells type playing a key role in the protection and homeostasis of the gut, are the intraepithelial T-lymphocytes (IELs). This population of T cells, reside within the epithelial layer of the gut and are primarily...

Evaluation of the Clinical Efficacy of Cine CMR Texture Analysis in Myocardial Quantification

Ping Tie
Recently, researchers have reported the potential value of CMR texture, especially for evaluation of ischemic and non-ischemic cardiomyopathy. However, these studies were mostly based on more advanced CMR sequences, and focused on myocardial disease at a later stage. Just one paper reports the application of TA using conventional CINE CMR sequences, and only one paper mentions healthy population myocardial TA with a small cohort. There are three main aims of this thesis. Firstly, to explore...

Work related stress and wellbeing in critical care nurses and their relationship with patient safety

Carol Louise McCallum
Background: In the United Kingdom 2,460 per 100,000 nurses reported high work stress (Health & Safety Executive, 2020). The prevalence of work stress in critical care nurses (CCNs) is unknown. Despite a large literature base, the causes, and consequences of CCN work stress cannot be determined. Little is known of the effects of CCN work stress on patient outcomes. Methods: Phase I explored the work-related stress literature and identified measures to capture work-related stress and...

A Ground Truth Data Set of Gas Chromatography mass spectrometry (GCMS) Analysed Synthesised Methylenedioxymethylamphetamine (MDMA)

Jonathan Miller, Niamh NicDaeid & Roberto Puch-Solis
An open source format data set of Methylenedioxymethylamphetamine. This data set was derived from a PhD project which involved the repetitive chemical synthesis of a series of methylenedioxymethylamphetamine (MDMA) samples following a series of known synthetic chemical routes. Controlled drug samples are normally chemically analysed to determine their identity and in some cases, their purity. There are also circumstances where a more broad chemical characterisation of drug samples may also be required. This involves investigating...

The Construction of the \"Mad\" Female Criminal in Medical Discourse and Legal Practice at London's Old Bailey, 1863-1913

Fiona Aisling MacHugh
This thesis looks at the practical application of medical discourse to women found insane at London’s Old Bailey between 1863 and1913. Through in-depth analysis of all cases of women found insane at the Old Bailey, 1863-1913, this PhD thesis analyses the various discourses, medical, legal and cultural which appear to have been applied to these women in order to achieve a successful insanity plea. Using trial transcripts, newspaper reports, and published medical discourse the thesis...

Investigation of the biofilm contributing eps gene operon of Bacillus subtilis

Jonathan William Archibald Blackburn

An exploration of technologies for targeted protein modification

Luke Martin Simpson
Targeted protein degradation (TPD) is a promising strategy for both therapeutics and research, providing new opportunities to overcome some of the current limitations associated with traditional small-molecule therapeutics, RNA interference (RNAi) and genome editing approaches. Proteolysis-targeting chimeras (PROTACs) are typically heterobifunctional molecules which bring a protein of interest (POI) into spatial proximity of an E3 ubiquitin ligase, triggering POI ubiquitylation and proteasomal degradation. The Sapkota lab previously developed an affinity-directed protein missile (AdPROM) system for...

Investor and Assuror perspectives on materiality for sustainability reporting: An exploratory case study of Nigeria's oil and gas industry

Osai Simeon Nnodim
This thesis utilises the materiality concept of accounting to investigate institutional investor and assuror practitioner perspectives on sustainability reporting in the Nigerian oil and gas sector. The outcome of this investigation is expected to provide some insight into the prospects of success for the Nigerian financial sector’s drive to normalise sustainability reporting. For this purpose, a qualitative case study research was undertaken, which involved interviews of investors in decision making roles and auditors with social...

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