SARS-CoV-2 3D database: Understanding the Coronavirus Proteome and Evaluating Possible Drug Targets.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a rapidly growing infectious disease, widely spread with high mortality rates. Since the release of the SARS-CoV-2 genome sequence in March 2020, there has been an international focus on developing target-based drug discovery, which also requires knowledge of the 3D structure of the proteome. Where there are no experimentally solved structures, our group has created 3D models with coverage of 97.5% and characterised them using state-of-the-art computational approaches. Models of protomers and oligomers, together with predictions of substrate and allosteric binding sites, protein- ligand docking, SARS-CoV-2 protein interactions with human proteins, impacts of mutations, and mapped solved experimental structures are freely available for download. These are imple- mented in SARS CoV-2 3D, a comprehensive and user-friendly database, available at https://sars3d.com/. This provides essential information for drug discovery, both to evaluate targets and design new potential therapeutics.This work is supported and funded by King Abdullah scholarship (Saudi Arabia research coun- cil), and American Leprosy Missions grants (G88726), SET is funded by the Cystic Fibrosis Trust (RG 70975) and Fondation Botnar (RG91317). A.R.J is funded by the Biotechnology and Biological Sciences Research Council (BBSRC) DTP studentship (BB/M011194/1). B.B. is funded by the Cystic Fibrosis Trust and L.C. on a studentship from Ipsen. T.L.B. is funded by a the Wellcome Trust Investigator Award, PHZJ/489 RG83114 (2016-2021

Doctor of Philosophy

dissertationPublic health surveillance systems are crucial for the timely detection and response to public health threats. Since the terrorist attacks of September 11, 2001, and the release of anthrax in the following month, there has been a heightened interest in public health surveillance. The years immediately following these attacks were met with increased awareness and funding from the federal government which has significantly strengthened the United States surveillance capabilities; however, despite these improvements, there are substantial challenges faced by today's public health surveillance systems. Problems with the current surveillance systems include: a) lack of leveraging unstructured public health data for surveillance purposes; and b) lack of information integration and the ability to leverage resources, applications or other surveillance efforts due to systems being built on a centralized model. This research addresses these problems by focusing on the development and evaluation of new informatics methods to improve the public health surveillance. To address the problems above, we first identified a current public surveillance workflow which is affected by the problems described and has the opportunity for enhancement through current informatics techniques. The 122 Mortality Surveillance for Pneumonia and Influenza was chosen as the primary use case for this dissertation work. The second step involved demonstrating the feasibility of using unstructured public health data, in this case death certificates. For this we created and evaluated a pipeline iv composed of a detection rule and natural language processor, for the coding of death certificates and the identification of pneumonia and influenza cases. The second problem was addressed by presenting the rationale of creating a federated model by leveraging grid technology concepts and tools for the sharing and epidemiological analyses of public health data. As a case study of this approach, a secured virtual organization was created where users are able to access two grid data services, using death certificates from the Utah Department of Health, and two analytical grid services, MetaMap and R. A scientific workflow was created using the published services to replicate the mortality surveillance workflow. To validate these approaches, and provide proofs-of-concepts, a series of real-world scenarios were conducted

A web portal for Portuguese brain imaging network

Mestrado em Engenharia de Computadores e TelemáticaA Imagiologia Cerebral (IC) está na fronteira entre a neurologia, engenharia e física. écnicas de imagens médicas multimodais, tais como a Ressonância Magnética (MRI e fMRI) e Espectroscopia (MRS), Tomografia Computadorizada por Emissão de Fotões/Positrões (SPECT/PET), entre outros, são emergentes ferramentas de pesquisa médica que pode fornecer informações valiosas para o diagnóstico de doenças do cérebro. Eletroencefalograma de alta resolução (HR-EEG), técnicas para sincronizar e fundir seus resultados de análise e várias técnicas de imagem são também parte de IC. Em Portugal, dado o facto que a maioria das áreas relacionadas com IC (por exemplo, medicina, engenharia ou física) são assuntos de investigação em muitos grupos de P&D, um consórcio de universidades de Aveiro, Coimbra, Minho e Porto criou a Rede Nacional de Imagiologia Funcional Cerebral (RNIFC). A RNIFC é uma associação sem fins lucrativos que foi formalizada e assinada em fevereiro de 2009. Actualmente, com o suporte de sistemas digitais para armazenar imagens médicas, é possível partilhar dados entre essas instituições para melhorar o diagnóstico, e permitir investigações entre a comunidade médica de diferentes instituições. O principal objectivo desta dissertação é descrever a implementação dos serviços de sistemas de informação essenciais para a Brain Imaging Network (BIN) que suportam actualmente o RNIFC acessível através do Portal BIN, o principal ponto de entrada para a BING. O Portal BIN permite aos pesquisadores na comunidade BING espalhadas pelo país e no estrangeiro, quer para solicitar o acesso a instrumentos científicos ou para recuperar os seus casos e executar as suas análises. ABSTRACT: Brain Imaging is in the frontier between neurology, engineering and physics. Multimodal medical imaging techniques, such as Magnetic Resonance Imaging (MRI and fMRI) and Spectroscopy (MRS), Single Photon/Positron Emitting Tomography (SPECT/PET) among others, are emergent medical research tools that can provide valuable information for diagnosis of brain diseases. High-resolution electroencephalogram (HR-EEG), techniques for synchronizing and fuse its analysis results and several imaging techniques are also part of BI. In Portugal, given fact that most of the BI related areas (e.g. medical, engineering or physics) are subjects of research in many R&D groups, a consortium of the universities of Aveiro, Coimbra, Minho and Porto created the National Functional Brain Imaging Network (RNIFC). The RNIFC is a non-profitable association that was formalized and signed in February 2009. Currently, with the support of digital systems to store medical images, it is possible to share data among these institutions to improve diagnosis, and allow investigations by the medical community among different institutions. The main objective of this thesis is to describe the implementation of the essential Brain Imaging Network (BIN) information systems services that currently support the RNIFC accessible through the BIN Portal, the main entry point for the BING. BIN Portal enables researchers in the BING community scattered along the country and abroad either to apply for access to the scientific instruments or to retrieve their cases and run their analysis

Impact of COVID-19 on the Health of the General and More Vulnerable Population and Its Determinants: Health Care and Social Survey–ESSOC, Study Protocol

This manuscript describes the rationale and protocol of a real-world data (RWD) study entitled Health Care and Social Survey (ESSOC, Encuesta Sanitaria y Social). The study’s objective is to determine the magnitude, characteristics, and evolution of the COVID-19 impact on overall health as well as the socioeconomic, psychosocial, behavioural, occupational, environmental, and clinical determinants of both the general and more vulnerable population. The study integrates observational data collected through a survey using a probabilistic, overlapping panel design, and data from clinical, epidemiological, demographic, and environmental registries. The data will be analysed using advanced statistical, sampling, and machine learning techniques. The study is based on several measurements obtained from three random samples of the Andalusian (Spain) population: general population aged 16 years and over, residents in disadvantaged areas, and people over the age of 55. Given the current characteristics of this pandemic and its future repercussions, this project will generate relevant information on a regular basis, commencing from the beginning of the State of Alarm. It will also establish institutional alliances of great social value, explore and apply powerful and novel methodologies, and produce large, integrated, high-quality and open-access databases. The information described here will be vital for health systems in order to design tailor-made interventions aimed at improving the health care, health, and quality of life of the populations most affected by the COVID-19 pandemic.Andalusian Institute of Statistics and Cartography (IECA)Andalusian School of Public Health (EASP)SUPERA COVID-19 Fund of Santander Universities (SAUN)Conference of Spanish University Rectors (CRUE, Conferencia de Rectores de Universidades EspañolasSpanish National Research Council (CSIC, Consejo Superior de Investigaciones Científicas)COVID-19 Competitive Grant Program from Pfizer Global Medical GrantsIMAG–Maria de Maeztu grantMinisterio de Ciencia e Innovación, Spai

A geographical information system model to define COVID-19 problem areas with an analysis in the socio-economic context at the regional scale in the North of Spain

ABSTRACT: The work presented concerns the spatial behaviour of coronavirus disease 2019 (COVID-19) at the regional scale and the socio-economic context of problem areas over the 2020-2021 period. We propose a replicable geographical information systems (GIS) methodology based on geocodification and analysis of COVID-19 microdata registered by health authorities of the Government of Cantabria, Spain from the beginning of the pandemic register (29th February 2020) to 2nd December 2021. The spatial behaviour of the virus was studied using ArcGIS Pro and a 1x1 km vector grid as the homogeneous reference layer. The GIS analysis of 45,392 geocoded cases revealed a clear process of spatial contraction of the virus after the spread in 2020 with 432 km2 of problem areas reduced to 126.72 km2 in 2021. The socio-economic framework showed complex relationships between COVID-19 cases and the explanatory variables related to household characteristics, socio-economic conditions and demographic structure. Local bivariate analysis showed fuzzier results in persistent hotspots in urban and peri-urban areas. Questions about ?where, when and how? contribute to learning from experience as we must draw inspiration from, and explore connections to, those confronting the issues related to the current pandemic

Evidence-Based and Community Engaged Pandemic Responses for Calgary

Pandemics unduly burden those who are already economically and socially disadvantaged by poverty, disability, marginalization, and other vulnerabilities. Global pandemics increase disparities experienced by society’s most vulnerable, as inadequacies in systems-level protections make services challenging to access during emergencies. Families are specifically at risk, especially if they experience economic and social disparity concurrently with the pandemic. This study focuses on examining the way COVID-19 has exacerbated challenges to evidence based practice (EBP) implementation for community organizations in Calgary. Here we describe circumstances that make families vulnerable, the community organizations that support these families during the pandemic, and challenges with implementing EBP. To better understand policy barriers and facilitators as they relate to EBP access throughout the pandemic in Calgary, we conducted focus groups using the Nominal Group Technique (NGT) with diverse individuals representing local community organizations. Participants articulated the structural disparities that impede access to community-based EBP during the pandemic, and recognized potential solutions. The major themes uncovered in the research, as they apply to barriers to evidence-based service provision, included reduced revenue streams, access to technology, and lack of collaborative communication within and between ministries, as well as sectors. Proposed solutions to these barriers included person-centred policy and program approaches and reciprocal partnerships

Nanoinformatics: a new area of research in nanomedicine

Over a decade ago, nanotechnologists began research on applications of nanomaterials for medicine. This research has revealed a wide range of different challenges, as well as many opportunities. Some of these challenges are strongly related to informatics issues, dealing, for instance, with the management and integration of heterogeneous information, defining nomenclatures, taxonomies and classifications for various types of nanomaterials, and research on new modeling and simulation techniques for nanoparticles. Nanoinformatics has recently emerged in the USA and Europe to address these issues. In this paper, we present a review of nanoinformatics, describing its origins, the problems it addresses, areas of interest, and examples of current research initiatives and informatics resources. We suggest that nanoinformatics could accelerate research and development in nanomedicine, as has occurred in the past in other fields. For instance, biomedical informatics served as a fundamental catalyst for the Human Genome Project, and other genomic and ?omics projects, as well as the translational efforts that link resulting molecular-level research to clinical problems and findings

Nanoinformatics: a new area of research in nanomedicine

pre-printAbstract: Over a decade ago, nanotechnologists began research on applications of nanomaterials for medicine. This research has revealed a wide range of different challenges, as well as many opportunities. Some of these challenges are strongly related to informatics issues, dealing, for instance, with the management and integration of heterogeneous information, defining nomenclatures, taxonomies and classifications for various types of nanomaterials, and research on new modeling and simulation techniques for nanoparticles. Nanoinformatics has recently emerged in the USA and Europe to address these issues. In this paper, we present a review of nanoinformatics, describing its origins, the problems it addresses, areas of interest, and examples of current research initiatives and informatics resources. We suggest that nanoinformatics could accelerate research and development in nanomedicine, as has occurred in the past in other fields. For instance, biomedical informatics served as a fundamental catalyst for the Human Genome Project, and other genomic and -omics projects, as well as the translational efforts that link resulting molecular-level research to clinical problems and findings

The Global Risks Report 2016, 11th Edition

Now in its 11th edition, The Global Risks Report 2016 draws attention to ways that global risks could evolve and interact in the next decade. The year 2016 marks a forceful departure from past findings, as the risks about which the Report has been warning over the past decade are starting to manifest themselves in new, sometimes unexpected ways and harm people, institutions and economies. Warming climate is likely to raise this year's temperature to 1° Celsius above the pre-industrial era, 60 million people, equivalent to the world's 24th largest country and largest number in recent history, are forcibly displaced, and crimes in cyberspace cost the global economy an estimated US$445 billion, higher than many economies' national incomes. In this context, the Reportcalls for action to build resilience – the "resilience imperative" – and identifies practical examples of how it could be done.The Report also steps back and explores how emerging global risks and major trends, such as climate change, the rise of cyber dependence and income and wealth disparity are impacting already-strained societies by highlighting three clusters of risks as Risks in Focus. As resilience building is helped by the ability to analyse global risks from the perspective of specific stakeholders, the Report also analyses the significance of global risks to the business community at a regional and country-level

European Language Grid

This open access book provides an in-depth description of the EU project European Language Grid (ELG). Its motivation lies in the fact that Europe is a multilingual society with 24 official European Union Member State languages and dozens of additional languages including regional and minority languages. The only meaningful way to enable multilingualism and to benefit from this rich linguistic heritage is through Language Technologies (LT) including Natural Language Processing (NLP), Natural Language Understanding (NLU), Speech Technologies and language-centric Artificial Intelligence (AI) applications. The European Language Grid provides a single umbrella platform for the European LT community, including research and industry, effectively functioning as a virtual home, marketplace, showroom, and deployment centre for all services, tools, resources, products and organisations active in the field. Today the ELG cloud platform already offers access to more than 13,000 language processing tools and language resources. It enables all stakeholders to deposit, upload and deploy their technologies and datasets. The platform also supports the long-term objective of establishing digital language equality in Europe by 2030 – to create a situation in which all European languages enjoy equal technological support. This is the very first book dedicated to Language Technology and NLP platforms. Cloud technology has only recently matured enough to make the development of a platform like ELG feasible on a larger scale. The book comprehensively describes the results of the ELG project. Following an introduction, the content is divided into four main parts: (I) ELG Cloud Platform; (II) ELG Inventory of Technologies and Resources; (III) ELG Community and Initiative; and (IV) ELG Open Calls and Pilot Projects