TViz : a taxonomy visualization tool

The Semantic Web is an emerging science in the world of computer information processing. RACER, a robust semantic web engine, represents the core of a semantic web system. The engine offers various inference services that return information about a given ontology, for instance, to compute its associated taxonomy of concept names. The taxonomy is generated in a form called the "TBox subsumption hierarchy" although it is not necessarily a true hierarchy. Since humans are more comfortable reading a graphical structure than a textual one, RACER needs a visualization tool in order to visualize taxonomies after processing them. Also, a graph delivers statistical information in addition to its easy interaction capabilities. In this thesis, we present TViz, a tool capable of visualizing large numbers of nodes representing the TBox subsumption hierarchy, using the Cone Tree layout. TViz, customized for taxonomy visualizations, gets its input from a text file that is created after streaming the information from RACER. TViz consists of three components: (1) a parser that parses the information obtained from the RACER server using a specific grammar, (2) an engine that simplifies and changes the non-hierarchical structure into a hierarchical tree, and (3) a graphics engine that graphs the hierarchical tree using the Cone Tree layout. The graphics engine handles the graphics, the user interface, and tools and is written using OpenGL and GLUI multiplatform libraries. TViz implements useful tools for an easy exploration of a dense environment such as the Compass, the Local View and the Information Window and is implemented using standard C/C++ multiplatform librarie

A Knowledge-based Approach for Creating Detailed Landscape Representations by Fusing GIS Data Collections with Associated Uncertainty

Geographic Information Systems (GIS) data for a region is of different types and collected from different sources, such as aerial digitized color imagery, elevation data consisting of terrain height at different points in that region, and feature data consisting of geometric information and properties about entities above/below the ground in that region. Merging GIS data and understanding the real world information present explicitly or implicitly in that data is a challenging task. This is often done manually by domain experts because of their superior capability to efficiently recognize patterns, combine, reason, and relate information. When a detailed digital representation of the region is to be created, domain experts are required to make best-guess decisions about each object. For example, a human would create representations of entities by collectively looking at the data layers, noting even elements that are not visible, like a covered overpass or underwater tunnel of a certain width and length. Such detailed representations are needed for use by processes like visualization or 3D modeling in applications used by military, simulation, earth sciences and gaming communities. Many of these applications are increasingly using digitally synthesized visuals and require detailed digital 3D representations to be generated quickly after acquiring the necessary initial data. Our main thesis, and a significant research contribution of this work, is that this task of creating detailed representations can be automated to a very large extent using a methodology which first fuses all Geographic Information System (GIS) data sources available into knowledge base (KB) assertions (instances) representing real world objects using a subprocess called GIS2KB. Then using reasoning, implicit information is inferred to define detailed 3D entity representations using a geometry definition engine called KB2Scene. Semantic Web is used as the semantic inferencing system and is extended with a data extraction framework. This framework enables the extraction of implicit property information using data and image analysis techniques. The data extraction framework supports extraction of spatial relationship values and attribution of uncertainties to inferred details. Uncertainty is recorded per property and used under Zadeh fuzzy semantics to compute a resulting uncertainty for inferred assertional axioms. This is achieved by another major contribution of our research, a unique extension of the KB ABox Realization service using KB explanation services. Previous semantics based research in this domain has concentrated more on improving represented details through the addition of artifacts like lights, signage, crosswalks, etc. Previous attempts regarding uncertainty in assertions use a modified reasoner expressivity and calculus. Our work differs in that separating formal knowledge from data processing allows fusion of different heterogeneous data sources which share the same context. Imprecision is modeled through uncertainty on assertions without defining a new expressivity as long as KB explanation services are available for the used expressivity. We also believe that in our use case, this simplifies uncertainty calculations. The uncertainties are then available for user-decision at output. We show that the process of creating 3D visuals from GIS data sources can be more automated, modular, verifiable, and the knowledge base instances available for other applications to use as part of a common knowledge base. We define our method’s components, discuss advantages and limitations, and show sample results for the transportation domain

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 < 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

Low incidence of SARS-CoV-2, risk factors of mortality and the course of illness in the French national cohort of dialysis patients

International audienceThe aim of this study was to estimate the incidence of COVID-19 disease in the French national population of dialysis patients, their course of illness and to identify the risk factors associated with mortality. Our study included all patients on dialysis recorded in the French REIN Registry in April 2020. Clinical characteristics at last follow-up and the evolution of COVID-19 illness severity over time were recorded for diagnosed cases (either suspicious clinical symptoms, characteristic signs on the chest scan or a positive reverse transcription polymerase chain reaction) for SARS-CoV-2. A total of 1,621 infected patients were reported on the REIN registry from March 16th, 2020 to May 4th, 2020. Of these, 344 died. The prevalence of COVID-19 patients varied from less than 1% to 10% between regions. The probability of being a case was higher in males, patients with diabetes, those in need of assistance for transfer or treated at a self-care unit. Dialysis at home was associated with a lower probability of being infected as was being a smoker, a former smoker, having an active malignancy, or peripheral vascular disease. Mortality in diagnosed cases (21%) was associated with the same causes as in the general population. Higher age, hypoalbuminemia and the presence of an ischemic heart disease were statistically independently associated with a higher risk of death. Being treated at a selfcare unit was associated with a lower risk. Thus, our study showed a relatively low frequency of COVID-19 among dialysis patients contrary to what might have been assumed

Characteristics and outcomes of an international cohort of 600 000 hospitalized patients with COVID-19

Background: We describe demographic features, treatments and clinical outcomes in the International Severe Acute Respiratory and emerging Infection Consortium (ISARIC) COVID-19 cohort, one of the world's largest international, standardized data sets concerning hospitalized patients. Methods: The data set analysed includes COVID-19 patients hospitalized between January 2020 and January 2022 in 52 countries. We investigated how symptoms on admission, co-morbidities, risk factors and treatments varied by age, sex and other characteristics. We used Cox regression models to investigate associations between demographics, symptoms, co-morbidities and other factors with risk of death, admission to an intensive care unit (ICU) and invasive mechanical ventilation (IMV). Results: Data were available for 689 572 patients with laboratory-confirmed (91.1%) or clinically diagnosed (8.9%) SARS-CoV-2 infection from 52 countries. Age [adjusted hazard ratio per 10 years 1.49 (95% CI 1.48, 1.49)] and male sex [1.23 (1.21, 1.24)] were associated with a higher risk of death. Rates of admission to an ICU and use of IMV increased with age up to age 60 years then dropped. Symptoms, co-morbidities and treatments varied by age and had varied associations with clinical outcomes. The case-fatality ratio varied by country partly due to differences in the clinical characteristics of recruited patients and was on average 21.5%. Conclusions: Age was the strongest determinant of risk of death, with a ∼30-fold difference between the oldest and youngest groups; each of the co-morbidities included was associated with up to an almost 2-fold increase in risk. Smoking and obesity were also associated with a higher risk of death. The size of our international database and the standardized data collection method make this study a comprehensive international description of COVID-19 clinical features. Our findings may inform strategies that involve prioritization of patients hospitalized with COVID-19 who have a higher risk of death

The value of open-source clinical science in pandemic response: lessons from ISARIC

International audienc