Three-dimensional modelling and inversion of controlled source electromagnetic data

The marine Controlled Source Electromagnetic (CSEM) method is an important and almost self-contained discipline in the toolkit of methods used by geophysicists for probing the earth. It has increasingly attracted attention from industry during the past decade due to its potential in detecting valuable natural resources such as oil and gas. A method for three-dimensional CSEM modelling in the frequency domain is presented. The electric field is decomposed in primary and secondary components, as this leads to a more stable solution near the source position. The primary field is computed using a resistivity model for which a closed form of solution exists, for example a homogeneous or layered resistivity model. The secondary electric field is computed by discretizing a second order partial differential equation for the electric field, also referred in the literature as the vector Helmholtz equation, using the edge finite element method. A range of methods for the solution of the linear system derived from the edge finite element discretization are investigated. The magnetic field is computed subsequently, from the solution for the electric field, using a local finite difference approximation of Faraday’s law and an interpolation method. Tests, that compare the solution obtained using the presented method with the solution computed using alternative codes for 1D and 3D synthetic models, show that the implemented approach is suitable for CSEM forward modelling and is an alternative to existing codes. An algorithm for 3D inversion of CSEM data in the frequency domain was developed and implemented. The inverse problem is solved using the L-BFGS method and is regularized with a smoothing constraint. The inversion algorithm uses the presented forward modelling scheme for the computation of the field responses and the adjoint field for the computation of the gradient of the misfit function. The presented algorithm was tested for a synthetic example, showing that it is capable of reconstructing a resistivity model which fits the synthetic data and is close to the original resistivity model in the least-squares sense. Inversion of CSEM data is known to lead to images with low spatial resolution. It is well known that integration with complementary data sets mitigates this problem. It is presented an algorithm for the integration of an acoustic velocity model, which is known a priori, in the inversion scheme. The algorithm was tested in a synthetic example and the results demonstrate that the presented methodology is promising for the improvement of resistivity models obtained from CSEM data

SARS-CoV-2 introductions and early dynamics of the epidemic in Portugal

Genomic surveillance of SARS-CoV-2 in Portugal was rapidly implemented by the National Institute of Health in the early stages of the COVID-19 epidemic, in collaboration with more than 50 laboratories distributed nationwide. Methods By applying recent phylodynamic models that allow integration of individual-based travel history, we reconstructed and characterized the spatio-temporal dynamics of SARSCoV-2 introductions and early dissemination in Portugal. Results We detected at least 277 independent SARS-CoV-2 introductions, mostly from European countries (namely the United Kingdom, Spain, France, Italy, and Switzerland), which were consistent with the countries with the highest connectivity with Portugal. Although most introductions were estimated to have occurred during early March 2020, it is likely that SARS-CoV-2 was silently circulating in Portugal throughout February, before the first cases were confirmed. Conclusions Here we conclude that the earlier implementation of measures could have minimized the number of introductions and subsequent virus expansion in Portugal. This study lays the foundation for genomic epidemiology of SARS-CoV-2 in Portugal, and highlights the need for systematic and geographically-representative genomic surveillance.We gratefully acknowledge to Sara Hill and Nuno Faria (University of Oxford) and Joshua Quick and Nick Loman (University of Birmingham) for kindly providing us with the initial sets of Artic Network primers for NGS; Rafael Mamede (MRamirez team, IMM, Lisbon) for developing and sharing a bioinformatics script for sequence curation (https://github.com/rfm-targa/BioinfUtils); Philippe Lemey (KU Leuven) for providing guidance on the implementation of the phylodynamic models; Joshua L. Cherry (National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health) for providing guidance with the subsampling strategies; and all authors, originating and submitting laboratories who have contributed genome data on GISAID (https://www.gisaid.org/) on which part of this research is based. The opinions expressed in this article are those of the authors and do not reflect the view of the National Institutes of Health, the Department of Health and Human Services, or the United States government. This study is co-funded by Fundação para a Ciência e Tecnologia and Agência de Investigação Clínica e Inovação Biomédica (234_596874175) on behalf of the Research 4 COVID-19 call. Some infrastructural resources used in this study come from the GenomePT project (POCI-01-0145-FEDER-022184), supported by COMPETE 2020 - Operational Programme for Competitiveness and Internationalisation (POCI), Lisboa Portugal Regional Operational Programme (Lisboa2020), Algarve Portugal Regional Operational Programme (CRESC Algarve2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF), and by Fundação para a Ciência e a Tecnologia (FCT).info:eu-repo/semantics/publishedVersio

Impact of COVID-19 on cardiovascular testing in the United States versus the rest of the world

Objectives: This study sought to quantify and compare the decline in volumes of cardiovascular procedures between the United States and non-US institutions during the early phase of the coronavirus disease-2019 (COVID-19) pandemic. Background: The COVID-19 pandemic has disrupted the care of many non-COVID-19 illnesses. Reductions in diagnostic cardiovascular testing around the world have led to concerns over the implications of reduced testing for cardiovascular disease (CVD) morbidity and mortality. Methods: Data were submitted to the INCAPS-COVID (International Atomic Energy Agency Non-Invasive Cardiology Protocols Study of COVID-19), a multinational registry comprising 909 institutions in 108 countries (including 155 facilities in 40 U.S. states), assessing the impact of the COVID-19 pandemic on volumes of diagnostic cardiovascular procedures. Data were obtained for April 2020 and compared with volumes of baseline procedures from March 2019. We compared laboratory characteristics, practices, and procedure volumes between U.S. and non-U.S. facilities and between U.S. geographic regions and identified factors associated with volume reduction in the United States. Results: Reductions in the volumes of procedures in the United States were similar to those in non-U.S. facilities (68% vs. 63%, respectively; p = 0.237), although U.S. facilities reported greater reductions in invasive coronary angiography (69% vs. 53%, respectively; p < 0.001). Significantly more U.S. facilities reported increased use of telehealth and patient screening measures than non-U.S. facilities, such as temperature checks, symptom screenings, and COVID-19 testing. Reductions in volumes of procedures differed between U.S. regions, with larger declines observed in the Northeast (76%) and Midwest (74%) than in the South (62%) and West (44%). Prevalence of COVID-19, staff redeployments, outpatient centers, and urban centers were associated with greater reductions in volume in U.S. facilities in a multivariable analysis. Conclusions: We observed marked reductions in U.S. cardiovascular testing in the early phase of the pandemic and significant variability between U.S. regions. The association between reductions of volumes and COVID-19 prevalence in the United States highlighted the need for proactive efforts to maintain access to cardiovascular testing in areas most affected by outbreaks of COVID-19 infection

COVID-19 symptoms at hospital admission vary with age and sex: results from the ISARIC prospective multinational observational study

Background: The ISARIC prospective multinational observational study is the largest cohort of hospitalized patients with COVID-19. We present relationships of age, sex, and nationality to presenting symptoms. Methods: International, prospective observational study of 60 109 hospitalized symptomatic patients with laboratory-confirmed COVID-19 recruited from 43 countries between 30 January and 3 August 2020. Logistic regression was performed to evaluate relationships of age and sex to published COVID-19 case definitions and the most commonly reported symptoms. Results: ‘Typical’ symptoms of fever (69%), cough (68%) and shortness of breath (66%) were the most commonly reported. 92% of patients experienced at least one of these. Prevalence of typical symptoms was greatest in 30- to 60-year-olds (respectively 80, 79, 69%; at least one 95%). They were reported less frequently in children (≤ 18 years: 69, 48, 23; 85%), older adults (≥ 70 years: 61, 62, 65; 90%), and women (66, 66, 64; 90%; vs. men 71, 70, 67; 93%, each P &lt; 0.001). The most common atypical presentations under 60 years of age were nausea and vomiting and abdominal pain, and over 60 years was confusion. Regression models showed significant differences in symptoms with sex, age and country. Interpretation: This international collaboration has allowed us to report reliable symptom data from the largest cohort of patients admitted to hospital with COVID-19. Adults over 60 and children admitted to hospital with COVID-19 are less likely to present with typical symptoms. Nausea and vomiting are common atypical presentations under 30 years. Confusion is a frequent atypical presentation of COVID-19 in adults over 60 years. Women are less likely to experience typical symptoms than men

Three-dimensional modelling and inversion of controlled source electromagnetic data

The marine Controlled Source Electromagnetic (CSEM) method is an important and almost self-contained discipline in the toolkit of methods used by geophysicists for probing the earth. It has increasingly attracted attention from industry during the past decade due to its potential in detecting valuable natural resources such as oil and gas. A method for three-dimensional CSEM modelling in the frequency domain is presented. The electric field is decomposed in primary and secondary components, as this leads to a more stable solution near the source position. The primary field is computed using a resistivity model for which a closed form of solution exists, for example a homogeneous or layered resistivity model. The secondary electric field is computed by discretizing a second order partial differential equation for the electric field, also referred in the literature as the vector Helmholtz equation, using the edge finite element method. A range of methods for the solution of the linear system derived from the edge finite element discretization are investigated. The magnetic field is computed subsequently, from the solution for the electric field, using a local finite difference approximation of Faraday’s law and an interpolation method. Tests, that compare the solution obtained using the presented method with the solution computed using alternative codes for 1D and 3D synthetic models, show that the implemented approach is suitable for CSEM forward modelling and is an alternative to existing codes. An algorithm for 3D inversion of CSEM data in the frequency domain was developed and implemented. The inverse problem is solved using the L-BFGS method and is regularized with a smoothing constraint. The inversion algorithm uses the presented forward modelling scheme for the computation of the field responses and the adjoint field for the computation of the gradient of the misfit function. The presented algorithm was tested for a synthetic example, showing that it is capable of reconstructing a resistivity model which fits the synthetic data and is close to the original resistivity model in the least-squares sense. Inversion of CSEM data is known to lead to images with low spatial resolution. It is well known that integration with complementary data sets mitigates this problem. It is presented an algorithm for the integration of an acoustic velocity model, which is known a priori, in the inversion scheme. The algorithm was tested in a synthetic example and the results demonstrate that the presented methodology is promising for the improvement of resistivity models obtained from CSEM data.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Teses de doutoramento

Resumos das teses de doutoramento defendidas na área da Educação no Instituto de Educação da Universidade Lusófona de Humanidades e Tecnologia

Teses de doutoramento

Resumos das teses de doutoramento defendidas na área da Educação no Instituto de Educação da Universidade Lusófona de Humanidades e Tecnologia

Light-entrained and brain-tuned circadian circuits regulate ILC3s and gut homeostasis

© The Author(s), under exclusive licence to Springer Nature Limited 2019Group 3 innate lymphoid cells (ILC3s) are major regulators of inflammation, infection, microbiota composition and metabolism1. ILC3s and neuronal cells have been shown to interact at discrete mucosal locations to steer mucosal defence2,3. Nevertheless, it is unclear whether neuroimmune circuits operate at an organismal level, integrating extrinsic environmental signals to orchestrate ILC3 responses. Here we show that light-entrained and brain-tuned circadian circuits regulate enteric ILC3s, intestinal homeostasis, gut defence and host lipid metabolism in mice. We found that enteric ILC3s display circadian expression of clock genes and ILC3-related transcription factors. ILC3-autonomous ablation of the circadian regulator Arntl led to disrupted gut ILC3 homeostasis, impaired epithelial reactivity, a deregulated microbiome, increased susceptibility to bowel infection and disrupted lipid metabolism. Loss of ILC3-intrinsic Arntl shaped the gut 'postcode receptors' of ILC3s. Strikingly, light-dark cycles, feeding rhythms and microbial cues differentially regulated ILC3 clocks, with light signals being the major entraining cues of ILC3s. Accordingly, surgically or genetically induced deregulation of brain rhythmicity led to disrupted circadian ILC3 oscillations, a deregulated microbiome and altered lipid metabolism. Our work reveals a circadian circuitry that translates environmental light cues into enteric ILC3s, shaping intestinal health, metabolism and organismal homeostasis.C.G.-S., R.G.D. and M.R. were supported by Fundação para a Ciência e Tecnologia (FCT), Portugal. N.L.B.-M. is supported by FCT, Portugal, and the European Molecular Biology Organisation (EMBO). H.V.-F. is supported by the ERC (647274), the EU, The Paul G. Allen Frontiers Group, US, and the FCT, Portugal.info:eu-repo/semantics/publishedVersio