Blazar jets imaged with Very Long Baseline Interferometry (VLBI) - Kinematics of helical trajectories in 3C273 and 3C345

In this work a large collection of VLBI (Very Long Baseline Interferometry) maps are presented based upon data from the VLBA (Very Long Baseline Array) for 29 sources. The maps are the result of three epochs of imaging. A kinematic study was undertaken with a view to understanding some interesting structure seen in the quasars 3C273 and 3C345. Fortunately, these two sources present a large number of components and it was possible to perform model fitting to pinpoint their positions. In addition, model fitting was performed upon all of the sources that were successfully imaged. The aim of this was to eventually derive component velocities for as many blazars studied as possible. The outcomes of the work are presented in tables in the main thesis. In order to further understand the 3C273 and 3C345 jet structures seen a physical model was developed with A. Papageorgiou. With this kinematic model it was possible to trace out a variety of helical jet structures. The free parameters are the injection velocity for new components, the period of jet precession, the viewing angle and the jet half angle. Using the Levenberg- Marquardt algorithm (references given below) it was possible to fit jet trajectories to my model fitted component data. The algorithm produced quantitative output for some of the free parameters in my physical model. Therefore I report average jet half angles for 3C273 and 3C345 of 2.968 0.153 degrees and 2.519 0.573 degrees respectively. In ad dition, I find the precessional periods of 3C273 and 3C345 to be 71.161 19.066 years and 48.478 3.385 years respectively.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Blazar jets imaged with Very Long Baseline Interferometry (VLBI) - kinematics of helical trajectories in 3C273 and 3C345

In this work a large collection of VLBI (Very Long Baseline Interferometry) maps are presented based upon data from the VLBA (Very Long Baseline Array) for 29 sources. The maps are the result of three epochs of imaging. A kinematic study was undertaken with a view to understanding some interesting structure seen in the quasars 3C273 and 3C345. Fortunately, these two sources present a large number of components and it was possible to perform model fitting to pinpoint their positions. In addition, model fitting was performed upon all of the sources that were successfully imaged. The aim of this was to eventually derive component velocities for as many blazars studied as possible. The outcomes of the work are presented in tables in the main thesis. In order to further understand the 3C273 and 3C345 jet structures seen a physical model was developed with A. Papageorgiou. With this kinematic model it was possible to trace out a variety of helical jet structures. The free parameters are the injection velocity for new components, the period of jet precession, the viewing angle and the jet half angle. Using the Levenberg- Marquardt algorithm (references given below) it was possible to fit jet trajectories to my model fitted component data. The algorithm produced quantitative output for some of the free parameters in my physical model. Therefore I report average jet half angles for 3C273 and 3C345 of 2.968 0.153 degrees and 2.519 0.573 degrees respectively. In ad dition, I find the precessional periods of 3C273 and 3C345 to be 71.161 19.066 years and 48.478 3.385 years respectively

Meyouandus: Interactive in-venue displays. Research and Development Report

Arts practice MeYouAndUs will produce TILO, a hybrid display system for cultural venues. It uses digital screens situated in the public spaces of a venue, combined with live feeds and sensors to display engaging, interactive and personalised content. TILO aims to create a dialogue between the arts organisation, the building and its visitors, and will allow artists to carry out their own interventions. The system will be piloted at FACT, the popular cross-arts venue in Liverpool

Added value of second biopsy target in screen-detected widespread suspicious breast calcifications

Introduction: There is controversy on the optimal work‐up of screen‐detected widespread breast calcifications: whether to biopsy a single target or multiple targets. This study evaluates agreement between multiple biopsy targets within the same screen‐detected widespread (≥25 mm) breast calcification to determine if the second biopsy adds value. Methods: Retrospective observational study of women screened in a statewide general population risk breast cancer mammographic screening program from 2009 to 2016. Screening episodes recalled for widespread calcifications where further views indicated biopsy, and two or more separate target areas were sampled within the same lesion were included. Percentage agreement and Cohen\u27s Kappa were calculated. Results: A total of 293317 women were screened during 761124 separate episodes with recalls for widespread calcifications in 2355 episodes. In 171 women, a second target was biopsied within the same lesion. In 149 (86%) cases, the second target biopsy result agreed with the first biopsy (κ = 0.6768). Agreement increased with increasing mammography score (85%, 86% and 92% for score 3, 4 and 5 lesions). Same day multiple biopsied lesions were three times more likely to yield concordant results compared to post‐hoc second target biopsy cases. Conclusion: While a single target biopsy is sufficient to discriminate a benign vs. malignant diagnosis in most cases, in 14% there is added value in performing a second target biopsy. Biopsies performed prospectively are more likely to yield concordant results compared to post‐hoc second target biopsy cases, suggesting a single prospective biopsy may be sufficient when results are radiological‐pathological concordant; discordance still requires repeat sampling

Blue carbon audit of Orkney waters

This study provides an audit of the potential blue carbon resources present in the coastal waters around Orkney, bounded by the 12 nautical mile limit and including the Loch of Stenness brackish water lagoon. This report builds on previous work in which blue carbon stocks in Marine Protected Areas in Scottish waters were estimated from i) contributions of biological material to the fixation of carbon, also referred to as production, and ii) contributions of sediments to blue carbon storage. The methodology has been further developed here to allow regional-scale estimation of habitat extent and provides estimates of blue carbon associated with habitats and surface sediments.Publisher PD

ChIP on SNP-chip for genome-wide analysis of human histone H4 hyperacetylation

<p>Abstract</p> <p>Background</p> <p>SNP microarrays are designed to genotype Single Nucleotide Polymorphisms (SNPs). These microarrays report hybridization of DNA fragments and therefore can be used for the purpose of detecting genomic fragments.</p> <p>Results</p> <p>Here, we demonstrate that a SNP microarray can be effectively used in this way to perform chromatin immunoprecipitation (ChIP) on chip as an alternative to tiling microarrays. We illustrate this novel application by mapping whole genome histone H4 hyperacetylation in human myoblasts and myotubes. We detect clusters of hyperacetylated histone H4, often spanning across up to 300 kilobases of genomic sequence. Using complementary genome-wide analyses of gene expression by DNA microarray we demonstrate that these clusters of hyperacetylated histone H4 tend to be associated with expressed genes.</p> <p>Conclusion</p> <p>The use of a SNP array for a ChIP-on-chip application (ChIP on SNP-chip) will be of great value to laboratories whose interest is the determination of general rules regarding the relationship of specific chromatin modifications to transcriptional status throughout the genome and to examine the asymmetric modification of chromatin at heterozygous loci.</p

Recent developments in StemBase: a tool to study gene expression in human and murine stem cells

<p>Abstract</p> <p>Background</p> <p>Currently one of the largest online repositories for human and mouse stem cell gene expression data, StemBase was first designed as a simple web-interface to DNA microarray data generated by the Canadian Stem Cell Network to facilitate the discovery of gene functions relevant to stem cell control and differentiation.</p> <p>Findings</p> <p>Since its creation, StemBase has grown in both size and scope into a system with analysis tools that examine either the whole database at once, or slices of data, based on tissue type, cell type or gene of interest. As of September 1, 2008, StemBase contains gene expression data (microarray and Serial Analysis of Gene Expression) from 210 stem cell samples in 60 different experiments.</p> <p>Conclusion</p> <p>StemBase can be used to study gene expression in human and murine stem cells and is available at <url>http://www.stembase.ca</url>.</p

Gene function in early mouse embryonic stem cell differentiation

BACKGROUND: Little is known about the genes that drive embryonic stem cell differentiation. However, such knowledge is necessary if we are to exploit the therapeutic potential of stem cells. To uncover the genetic determinants of mouse embryonic stem cell (mESC) differentiation, we have generated and analyzed 11-point time-series of DNA microarray data for three biologically equivalent but genetically distinct mESC lines (R1, J1, and V6.5) undergoing undirected differentiation into embryoid bodies (EBs) over a period of two weeks. RESULTS: We identified the initial 12 hour period as reflecting the early stages of mESC differentiation and studied probe sets showing consistent changes of gene expression in that period. Gene function analysis indicated significant up-regulation of genes related to regulation of transcription and mRNA splicing, and down-regulation of genes related to intracellular signaling. Phylogenetic analysis indicated that the genes showing the largest expression changes were more likely to have originated in metazoans. The probe sets with the most consistent gene changes in the three cell lines represented 24 down-regulated and 12 up-regulated genes, all with closely related human homologues. Whereas some of these genes are known to be involved in embryonic developmental processes (e.g. Klf4, Otx2, Smn1, Socs3, Tagln, Tdgf1), our analysis points to others (such as transcription factor Phf21a, extracellular matrix related Lama1 and Cyr61, or endoplasmic reticulum related Sc4mol and Scd2) that have not been previously related to mESC function. The majority of identified functions were related to transcriptional regulation, intracellular signaling, and cytoskeleton. Genes involved in other cellular functions important in ESC differentiation such as chromatin remodeling and transmembrane receptors were not observed in this set. CONCLUSION: Our analysis profiles for the first time gene expression at a very early stage of mESC differentiation, and identifies a functional and phylogenetic signature for the genes involved. The data generated constitute a valuable resource for further studies. All DNA microarray data used in this study are available in the StemBase database of stem cell gene expression data [1] and in the NCBI's GEO database

Palliative radiotherapy after oesophageal cancer stenting (ROCS): a multicentre, open-label, phase 3 randomised controlled trial

Background: patients with advanced oesophageal cancer have a median survival of 3-6 months, and most require intervention for dysphagia. Self-expanding metal stent (SEMS) insertion is the most typical form of palliation in these patients, but dysphagia deterioration and re-intervention are common. This study examined the efficacy of adjuvant external beam radiotherapy (EBRT) compared with usual care alone in preventing dysphagia deterioration and reducing service use after SEMS insertion.Methods: this was a multicentre, open-label, phase 3 randomised controlled trial based at cancer centres and acute care hospitals in England, Scotland, and Wales. Patients (aged ≥16 years) with incurable oesophageal carcinoma receiving stent insertion for primary management of dysphagia were randomly assigned (1:1) to receive usual care alone or EBRT (20 Gy in five fractions or 30 Gy in ten fractions) plus usual care after stent insertion. Usual care was implemented according to need as identified by the local multidisciplinary team (MDT). Randomisation was via the method of minimisation stratified by treating centre, stage at diagnosis (I-III vs IV), histology (squamous or non-squamous), and MDT intent to give chemotherapy (yes vs no). The primary outcome was difference in proportions of participants with dysphagia deterioration (&gt;11 point decrease on patient-reported European Organisation for Research and Treatment of Cancer quality of life questionnaire-oesophagogastric module [QLQ-OG25], or a dysphagia-related event consistent with such a deterioration) or death by 12 weeks in a modified intention-to-treat (ITT) population, which excluded patients who did not have a stent inserted and those without a baseline QLQ-OG25 assessment. Secondary outcomes included survival, quality of life (QoL), morbidities (including time to first bleeding event or hospital admission for bleeding event and first dysphagia-related stent complications or re-intervention), and cost-effectiveness. Safety analysis was undertaken in the modified ITT population. The study is registered with the International Standard Randomised Controlled Trial registry, ISRCTN12376468, and ClinicalTrials.gov, NCT01915693, and is completed.Findings: 220 patients were randomly assigned between Dec 16, 2013, and Aug 24, 2018, from 23 UK centres. The modified ITT population (n=199) comprised 102 patients in the usual care group and 97 patients in the EBRT group. Radiotherapy did not reduce dysphagia deterioration, which was reported in 36 (49%) of 74 patients receiving usual care versus 34 (45%) of 75 receiving EBRT (adjusted odds ratio 0·82 [95% CI 0·40-1·68], p=0·59) in those with complete data for the primary endpoint. No significant difference was observed in overall survival: median overall survival was 19·7 weeks (95% CI 14·4-27·7) with usual care and 18·9 weeks (14·7-25·6) with EBRT (adjusted hazard ratio 1·06 [95% CI 0·78-1·45], p=0·70; n=199). Median time to first bleeding event or hospital admission for a bleeding event was 49·0 weeks (95% CI 33·3-not reached) with EBRT versus 65·9 weeks (52·7-not reached) with usual care (adjusted subhazard ratio 0·52 [95% CI 0·28-0·97], p=0·038; n=199). No time versus treatment interaction was observed for prespecified QoL outcomes. We found no evidence of differences between trial group in time to first stent complication or re-intervention event. The most common (grade 3-4) adverse event was fatigue, reported in 19 (19%) of 102 patients receiving usual care alone and 22 (23%) of 97 receiving EBRT. On cost-utility analysis, EBRT was more expensive and less efficacious than usual care.Interpretation: patients with advanced oesophageal cancer having SEMS insertion for the primary management of their dysphagia did not gain additional benefit from concurrent palliative radiotherapy and it should not be routinely offered. For a minority of patients clinically considered to be at high risk of tumour bleeding, concurrent palliative radiotherapy might reduce bleeding risk and the need for associated interventions.Funding: National Institute for Health Research Health Technology Assessment Programme.</p