3D visualisation of oil reservoirs

This research introduces a novel approach to storing compressed 3D grid information by applying octree compression techniques. This new data structure stores the octree in a pruned flattened fashion where only header and active leaf nodes are stored in a linear array. This generates high levels of lossless compression when applied to 3D geometry where clusters of homogeneous information exist. This data structure yields fast, log(n) look-up times and initial results show that when coupled with bespoke scanning methods searching times can surpass that of direct access. Hierarchical pyramid visualisations techniques are also presented using the information stored at each level in the tree structure. Integrating with this are face culling algorithms developed in this research, which eliminate hidden face and inner leaf node cells which eases the burden placed on the CPU and GPU. By integrating these pyramid scaling and face culling algorithms, grid models can be shown at various levels of resolution incorporating sub-regions, "regions of interest" displayed at full resolution. This further lightens the load on the GPU generating quicker loading times and higher refresh rates. This can potentially allow larger models to be visualised than would otherwise have been possible. This research was sponsored by Sciencesoft an oil reservoir visualisation company and the algorithms developed in this research have been applied to compressing oil reservoir information. Oil companies require accurate 3D computer-generated models of oil reservoirs in order to make oil and gas extraction as cost effective as possible. Advances in computing power has meant that it is now possible to run multi-million cell oil reservoir grid models, increasing the level of accuracy and precision available to engineers. This thesis applies 3D octree compression techniques to these computer models and compares these with industry standard storage and cell searching algorithms as industry benchmarks. This thesis suggests that octree compression techniques may prove to be a more efficient data structure for storing and searching active cell information within oil reservoirs than existing procedures

Competition or facilitation: Examination of interactions between endangered Sida hermaphrodita and invasive Phragmites australis

Virginia Mallow (Sida hermaphrodita) is a perennial herb of the Malvaceae family that is native to riparian habitats in northeastern North America. Throughout most of its geographical distribution however, it is considered threatened and only two populations are known from Canada. The biology and ecology of S. hermaphrodita are still poorly understood and although few studies have been performed to determine the factors that contribute to the species rarity, it is considered threatened potentially due to the loss of habitat caused by exotic European Common reed (Phragmites australis subsp. australis) invasion. Allelopathic and phytotoxic conditioning of soils to inhibit native species are mechanisms that have been proposed to explain the invasion success of P. australis. To quantify the interaction between the two species and assess the capacity for P. australis to inhibit S. hermaphrodita performance through belowground soil modifications, a series of field vegetation surveys were conducted at the Taquanyah Conservation Area during the growing seasons of 2016, 2017, and 2018. Field performance findings suggested that proximity to P. australis had no significant effect on S. hermaphrodita seedling mortality or seedling root arbuscular mycorrhizal colonization. A supplementary greenhouse study was also conducted to examine plant performance and mycorrhizal colonization of both species in soils that correspond to different soil-vegetation levels ranging between pure stands of S. hermaphrodita to pure stands of P. australis in order to determine the potential for P. australis to allelopathically modify soils making them inhospitable for native species. The results provided no evidence to support previous soil conditioning reports since performance and arbuscular mycorrhizal colonization of both species were inversely promoted in their competitor’s soil. Soil nutrient analysis coupled with the plant performance findings suggested that P. australis may not be as strictly competitive as previously believed since evidence of a belowground facilitative interaction between S. hermaphrodita and P. australis has been observed. Based on the results concluding that belowground conditions did not exclude native species, we believe aboveground competition for light is not only the main factor contributing to S. hermaphrodita’s limited distribution where it occurs with P. australis, but also key to the invasion success of P. australis. Future research and management treatments focussed on disrupting P. australis’ competitive exclusion of light would be beneficial to the recovery of endangered species like S. hermaphrodita

A Stimulatory Role for Cytokinin in the Arbuscular Mycorrhizal Symbiosis of Pea

The arbuscular mycorrhizal (AM) symbiosis between terrestrial plants and AM fungi is regulated by plant hormones. For most of these, a role has been clearly assigned in this mutualistic interaction; however, there are still contradictory reports for cytokinin (CK). Here, pea plants, the wild type (WT) cv. Sparkle and its mutant E151 (Pssym15), were inoculated with the AM fungus Rhizophagus irregularis. E151 has previously been characterized as possessing high CK levels in non-mycorrhizal (myc-) roots and exhibiting high number of fungal structures in mycorrhizal (myc+) roots. Myc- and myc+ plants were treated 7, 9, and 11 days after inoculation (DAI) with synthetic compounds known to alter CK status. WT plants were treated with a synthetic CK [6-benzylaminopurine (BAP)] or the CK degradation inhibitor INCYDE, whereas E151 plants were treated with the CK receptor antagonist PI-55. At 13 DAI, plant CK content was analyzed by mass spectrometry. The effects of the synthetic compounds on AM colonization were assessed at 28 (WT) or 35 (E151) DAI via a modified magnified intersections method. The only noticeable difference seen between myc- and myc+ plants in terms of CK content was in the levels of nucleotides (NTs). Whereas WT plants responded to fungi by lowering their NT levels, E151 plants did not. Since NTs are thought to be converted into active CK forms, this result suggests that active CKs were synthesized more effectively in WT than in E151. In general, myc+ and myc- WT plants responded similarly to INCYDE by lowering significantly their NT levels and increasing slightly their active CK levels; these responses were less obvious in BAP-treated WT plants. In contrast, the response of E151 plants to PI-55 depended on the plant mycorrhizal status. Whereas treated myc- plants exhibited high NT and low active CK levels, treated myc+ plants displayed low levels of both NTs and active CKs. Moreover, treated WT plants were more colonized than treated E151 plants. We concluded that CKs have a stimulatory role in AM colonization because increased active CK levels were paralleled with increased AM colonization while decreased CK levels corresponded to reduced AM colonization

Crusted scabies in remote Australia, a new way forward: Lessons and outcomes from the east arnhem scabies control program

Crusted scabies is a highly infectious, debilitating and disfi guring disease, and remote Aboriginal communities of northern Australia have the highest reported rates of the condition in the world. We draw on monitoring data of the East Arnhem Scabies Control Program to discuss outcomes and lessons learnt through managing the condition in remote communities. Using active case fi nding, we identifi ed seven patients with crusted scabies in three communities and found most had not presented to health services despite active disease. We compared presentations and hospitalisations for a cumulative total of 99 months during a novel preventive program with 99 months immediately before the program for the seven cases and seven sentinel household contacts. Our preventive long-term case management approach was associated with a signifi cant 44% reduction in episodes of recurrent crusted scabies (from 36 to 20; P = 0.025) in the seven cases, and a non-signifi cant 80% reduction in days spent in hospital (from 173 to 35; P = 0.09). It was also associated with a signifi cant 75% reduction in scabies-related presentations (from 28 to 7; P = 0.017) for the seven sentinel household contacts. We recommend active surveillance and wider adoption of this preventive case management approach, with ongoing evaluation to refi ne protocols and improve effi ciency. Contacts of children presenting with recurrent scabies should be examined to exclude crusted scabies. In households where crusted scabies is present, a diagnosis of parental neglect due to recurrent scabies and weight loss in children should be made with extreme caution. Improved coordination of care by health services, and research and development of new therapies including immunotherapies for crusted scabies, must be a priority

Drug screening of biopsy-derived multicellular spheroids using microfluidic technology

Performing drug screening, of physiologically relevant three-dimensional (3D) tumor models, for personalized treatment remains challenging, due to the small amount of tissue available from most biopsies. New microfluidic technologies, enabling greater control over cell positioning and fluid behavior at the micro-scale, allow extensive testing of anticancer agents on human tumor tissue preparations in 3D and offer new solutions for the development of anticancer compounds and personalized medicine. We have developed a microfluidic platform for extensive drug screening of tumor biopsies in a cost-effective manner and validated the system with tumor prostate patient samples. As a typical drug screening assay, up to 22 drug concentration-response curves could be generated from a single biopsy, within a time frame of up to 4 weeks. Biopsy tissue, grown as a heterogeneous co-culture from the primary sample, was prepared as cancer-cell enriched multicellular spheroids, cultured for 3 to 5 days prior to the application of a panel of standard-of-care drugs for prostate cancer. Readouts were obtained via bright-field and epifluorescence microscopy. The microfluidic platform was designed to be operated entirely without the need of external fluid actuation, with the microfluidic network capable of generating long-lasting, stable and repeatable drug concentration gradients across arrays of 240 spheroids. Outcomes were generated as 8-point drug concentration response curves per device, with each drug concentration tested on at least 24 spheroids. In-house developed software was used to analyze bright-field and fluorescent images to provide readouts of spheroid growth and viability, as well as information on drug penetration and drug efficacy over time. Following platform and assay validation using cancer cell lines, proof-of-concept screening was performed on prostate biopsies from 2 different patients. Results showed that biopsy-derived spheroids were more resistant to treatment than LNCaP spheroids, a prostate cancer cell line. For one biopsy, spheroids were sensitive to docetaxel, but resistant to enzalutamide, despite the presence of intact androgen receptors. This preliminary data outlines how this technology could become a useful tool to investigate patient-specific drug resistance and to test novel anticancer agents in a cost-effective manner, based on maximized screening of human tumor tissue in a 3D format

Impact on emergency and elective hospital-based care in Scotland over the first 12 months of the pandemic: interrupted time-series analysis of national lockdowns

The author(s) disclosed receipt of the following financial support for the research, authorship, and/or publication of this article: This analysis is part of the Early Pandemic Evaluation and Enhanced Surveillance of COVID-19 (EAVE II) study. EAVE II is funded by the Medical Research Council (MR/R008345/1) with the support of BREATHE – The Health Data Research Hub for Respiratory Health (MC_PC_19004), which is funded through the UK Research and Innovation Industrial Strategy Challenge Fund and delivered through Health Data Research UK. Additional support has been provided through the Scottish Government DG Health and Social Care. SAS and AS are also supported by the COVID-19 Longitudinal Health and Wellbeing National Core Study, funded by the Medical Research Council (MC_PC_20030). SVK acknowledges funding from a NRS Senior Clinical Fellowship (SCAF/15/02), the Medical Research Council (MC_UU_00022/2) and the Scottish Government Chief Scientist Office (SPHSU17). JM is partly funded by the National Institute for Health Research Applied Research Collaboration West (NIHR ARC West).Objectives COVID-19 has resulted in the greatest disruption to National Health Service (NHS) care in its over 70-year history. Building on our previous work, we assessed the ongoing impact of pandemic-related disruption on provision of emergency and elective hospital-based care across Scotland over the first year of the pandemic. Design We undertook interrupted time-series analyses to evaluate the impact of ongoing pandemic-related disruption on hospital NHS care provision at national level and across demographics and clinical specialties spanning the period 29 March 2020?28 March 2021. Setting Scotland, UK. Participants Patients receiving hospital care from NHS Scotland. Main outcome measures We used the percentage change of accident and emergency attendances, and emergency and planned hospital admissions during the pandemic compared to the average admission rate for equivalent weeks in 2018-2019. Results As restrictions were gradually lifted in Scotland after the first lockdown, hospital-based admissions increased approaching pre-pandemic levels. Subsequent tightening of restrictions in September 2020 were associated with a change in slope of relative weekly admissions rate: -1.98% (-2.38, -1.58) in accident and emergency attendance, -1.36% (-1.68, -1.04) in emergency admissions and -2.31% (-2.95, -1.66) in planned admissions. A similar pattern was seen across sex, socioeconomic status and most age groups, except children (0-14 years) where accident and emergency attendance, and emergency admissions were persistently low over the study period. Conclusions We found substantial disruption to urgent and planned inpatient healthcare provision in hospitals across NHS Scotland. There is the need for urgent policy responses to address continuing unmet health needs and to ensure resilience in the context of future pandemics.Publisher PDFPeer reviewe

A Stimulatory Role for Cytokinin in the Arbuscular Mycorrhizal Symbiosis of Pea

The arbuscular mycorrhizal (AM) symbiosis between terrestrial plants and AM fungi is regulated by plant hormones. For most of these, a role has been clearly assigned in this mutualistic interaction; however, there are still contradictory reports for cytokinin (CK). Here, pea plants, the wild type (WT) cv. Sparkle and its mutant E151 (Pssym15), were inoculated with the AM fungus Rhizophagus irregularis. E151 has previously been characterized as possessing high CK levels in non-mycorrhizal (myc-) roots and exhibiting high number of fungal structures in mycorrhizal (myc+) roots. Myc- and myc+ plants were treated 7, 9, and 11 days after inoculation (DAI) with synthetic compounds known to alter CK status. WT plants were treated with a synthetic CK [6-benzylaminopurine (BAP)] or the CK degradation inhibitor INCYDE, whereas E151 plants were treated with the CK receptor antagonist PI-55. At 13 DAI, plant CK content was analyzed by mass spectrometry. The effects of the synthetic compounds on AM colonization were assessed at 28 (WT) or 35 (E151) DAI via a modified magnified intersections method. The only noticeable difference seen between myc- and myc+ plants in terms of CK content was in the levels of nucleotides (NTs). Whereas WT plants responded to fungi by lowering their NT levels, E151 plants did not. Since NTs are thought to be converted into active CK forms, this result suggests that active CKs were synthesized more effectively in WT than in E151. In general, myc+ and myc- WT plants responded similarly to INCYDE by lowering significantly their NT levels and increasing slightly their active CK levels; these responses were less obvious in BAP-treated WT plants. In contrast, the response of E151 plants to PI-55 depended on the plant mycorrhizal status. Whereas treated myc- plants exhibited high NT and low active CK levels, treated myc+ plants displayed low levels of both NTs and active CKs. Moreover, treated WT plants were more colonized than treated E151 plants. We concluded that CKs have a stimulatory role in AM colonization because increased active CK levels were paralleled with increased AM colonization while decreased CK levels corresponded to reduced AM colonization

The UK clinical eye research strategy: refreshing research priorities for clinical eye research in the UK

OBJECTIVES: To validate and update the 2013 James Lind Alliance (JLA) Sight Loss and Vision Priority Setting Partnership (PSP)'s research priorities for Ophthalmology, as part of the UK Clinical Eye Research Strategy. METHODS: Twelve ophthalmology research themes were identified from the JLA report. They were allocated to five Clinical Study Groups of diverse stakeholders who reviewed the top 10 research priorities for each theme. Using an online survey (April 2021-February 2023), respondents were invited to complete one or more of nine subspecialty surveys. Respondents indicated which of the research questions they considered important and subsequently ranked them. RESULTS: In total, 2240 people responded to the survey (mean age, 59.3 years), from across the UK. 68.1% were female. 68.2% were patients, 22.3% healthcare professionals or vision researchers, 7.1% carers, and 2.1% were charity support workers. Highest ranked questions by subspecialty: Cataract (prevention), Cornea (improving microbial keratitis treatment), Optometric (impact of integration of ophthalmic primary and secondary care via community optometric care pathways), Refractive (factors influencing development and/or progression of refractive error), Childhood onset (improving early detection of visual disorders), Glaucoma (effective and improved treatments), Neuro-ophthalmology (improvements in prevention, diagnosis and treatment of neurodegeneration affecting vision), Retina (improving prevention, diagnosis and treatment of dry age-related macular degeneration), Uveitis (effective treatments for ocular and orbital inflammatory diseases). CONCLUSIONS: A decade after the initial PSP, the results refocus the most important research questions for each subspecialty, and prime targeted research proposals within Ophthalmology, a chronically underfunded specialty given the substantial burden of disability caused by eye disease

Implementation of corticosteroids in treating COVID-19 in the ISARIC WHO Clinical Characterisation Protocol UK:prospective observational cohort study

BACKGROUND: Dexamethasone was the first intervention proven to reduce mortality in patients with COVID-19 being treated in hospital. We aimed to evaluate the adoption of corticosteroids in the treatment of COVID-19 in the UK after the RECOVERY trial publication on June 16, 2020, and to identify discrepancies in care. METHODS: We did an audit of clinical implementation of corticosteroids in a prospective, observational, cohort study in 237 UK acute care hospitals between March 16, 2020, and April 14, 2021, restricted to patients aged 18 years or older with proven or high likelihood of COVID-19, who received supplementary oxygen. The primary outcome was administration of dexamethasone, prednisolone, hydrocortisone, or methylprednisolone. This study is registered with ISRCTN, ISRCTN66726260. FINDINGS: Between June 17, 2020, and April 14, 2021, 47 795 (75·2%) of 63 525 of patients on supplementary oxygen received corticosteroids, higher among patients requiring critical care than in those who received ward care (11 185 [86·6%] of 12 909 vs 36 415 [72·4%] of 50 278). Patients 50 years or older were significantly less likely to receive corticosteroids than those younger than 50 years (adjusted odds ratio 0·79 [95% CI 0·70–0·89], p=0·0001, for 70–79 years; 0·52 [0·46–0·58], p80 years), independent of patient demographics and illness severity. 84 (54·2%) of 155 pregnant women received corticosteroids. Rates of corticosteroid administration increased from 27·5% in the week before June 16, 2020, to 75–80% in January, 2021. INTERPRETATION: Implementation of corticosteroids into clinical practice in the UK for patients with COVID-19 has been successful, but not universal. Patients older than 70 years, independent of illness severity, chronic neurological disease, and dementia, were less likely to receive corticosteroids than those who were younger, as were pregnant women. This could reflect appropriate clinical decision making, but the possibility of inequitable access to life-saving care should be considered. FUNDING: UK National Institute for Health Research and UK Medical Research Council

Search for heavy resonances decaying to two Higgs bosons in final states containing four b quarks

A search is presented for narrow heavy resonances X decaying into pairs of Higgs bosons (H) in proton-proton collisions collected by the CMS experiment at the LHC at root s = 8 TeV. The data correspond to an integrated luminosity of 19.7 fb(-1). The search considers HH resonances with masses between 1 and 3 TeV, having final states of two b quark pairs. Each Higgs boson is produced with large momentum, and the hadronization products of the pair of b quarks can usually be reconstructed as single large jets. The background from multijet and t (t) over bar events is significantly reduced by applying requirements related to the flavor of the jet, its mass, and its substructure. The signal would be identified as a peak on top of the dijet invariant mass spectrum of the remaining background events. No evidence is observed for such a signal. Upper limits obtained at 95 confidence level for the product of the production cross section and branching fraction sigma(gg -> X) B(X -> HH -> b (b) over barb (b) over bar) range from 10 to 1.5 fb for the mass of X from 1.15 to 2.0 TeV, significantly extending previous searches. For a warped extra dimension theory with amass scale Lambda(R) = 1 TeV, the data exclude radion scalar masses between 1.15 and 1.55 TeV