James Scott-Brown
A5021538869- COVID-19 Clinical Research Studies
- Long-Term Effects of COVID-19
- SARS-CoV-2 and COVID-19 Research
- Gene Regulatory Network Analysis
- COVID-19 and healthcare impacts
- Data Visualization and Analytics
- RNA and protein synthesis mechanisms
- Sepsis Diagnosis and Treatment
- Microbial Metabolic Engineering and Bioproduction
- Respiratory Support and Mechanisms
- Bioinformatics and Genomic Networks
- Genetics, Bioinformatics, and Biomedical Research
- COVID-19 and Mental Health
- Intensive Care Unit Cognitive Disorders
- Complex Network Analysis Techniques
- Genomics and Phylogenetic Studies
- Scientific Computing and Data Management
- Antibiotic Use and Resistance
- Nosocomial Infections in ICU
- Respiratory viral infections research
- Cell Image Analysis Techniques
- Mental Health Research Topics
- SARS-CoV-2 detection and testing
- Frailty in Older Adults
- interferon and immune responses
University of Edinburgh
2020-2024
University of Alberta
2024
International Severe Acute Respiratory and Emerging Infection Consortium
2023
St Mary's Hospital
2023
All India Institute of Medical Sciences Raipur
2023
All India Institute of Medical Sciences Rishikesh
2023
University of Bristol
2023
Ninewells Hospital
2022
University of Dundee
2022
Centre for Inflammation Research
2022
Studies of patients admitted to hospital with COVID-19 have found varying mortality outcomes associated underlying respiratory conditions and inhaled corticosteroid use. Using data from a national, multicentre, prospective cohort, we aimed characterise people disease, assess the level care received, measure in-hospital mortality, examine effect use.We analysed International Severe Acute Respiratory emerging Infection Consortium (ISARIC) WHO Clinical Characterisation Protocol UK (CCP-UK)...
Abstract Synthetic biology builds upon genetics, molecular biology, and metabolic engineering by applying principles to the design of biological systems. When designing a synthetic system, biologists need exchange information about multiple types molecules, intended behavior actual experimental measurements. The Biology Open Language (SBOL) has been developed as standard support specification in following an open community process involving both bench scientists scientific modelers software...
Acute kidney injury (AKI) is common in coronavirus disease 2019 (COVID-19). This study investigated adults hospitalized with COVID-19 and hypothesized that risk factors for AKI would include comorbidities non-White race.
The Synthetic Biology Open Language (SBOL) is a community-developed data standard that allows knowledge about biological designs to be captured using machine-tractable, ontology-backed representation built Semantic Web technologies. While early versions of SBOL focused only on the description DNA-based components and their sub-components, can now used represent across multiple scales throughout entire synthetic biology workflow, from specification single molecule or DNA fragment through...
Biological engineers often find it useful to communicate using diagrams. These diagrams can include information both about the structure of nucleic acid sequences they are engineering and functional relationships between features these and/or other molecular species. A number conventions practices have begun emerge within synthetic biology for creating such diagrams, Synthetic Biology Open Language Visual (SBOL Visual) has been developed as a standard organize, systematize, extend in order...
Abstract Synthetic biology builds upon the techniques and successes of genetics, molecular biology, metabolic engineering by applying principles to design biological systems. The field still faces substantial challenges, including long development times, high rates failure, poor reproducibility. One method ameliorate these problems is improve exchange information about designed systems between laboratories. synthetic open language (SBOL) has been developed as a standard support specification...
Abstract Background Predicting bed occupancy for hospitalised patients with COVID-19 requires understanding of length stay (LoS) in particular types. LoS can vary depending on the patient’s “bed pathway” - sequence transfers individual between types during a hospital stay. In this study, we characterise these pathways, and their impact predicted occupancy. Methods We obtained data from University College Hospital (UCH) ISARIC4C Clinical Information Network (CO-CIN) who required care general...
Abstract Admission procalcitonin measurements and microbiology results were available for 1040 hospitalized adults with coronavirus disease 2019 (from 48 902 included in the International Severe Acute Respiratory Emerging Infections Consortium World Health Organization Clinical Characterisation Protocol UK study). Although was higher bacterial coinfection, this neither clinically significant (median [IQR], 0.33 [0.11–1.70] ng/mL vs 0.24 [0.10–0.90] ng/mL) nor diagnostically useful (area...
Abstract Synthetic biology builds upon genetics, molecular biology, and metabolic engineering by applying principles to the design of biological systems. When designing a synthetic system, biologists need exchange information about multiple types molecules, intended behavior actual experimental measurements. The Biology Open Language (SBOL) has been developed as standard support specification in following an open community process involving both wet bench scientists dry scientific modelers...
Abstract People who engineer biological organisms often find it useful to draw diagrams in order communicate both the structure of nucleic acid sequences that they are engineering and functional relationships between sequence features other molecular species. Some typical practices conventions have begun emerge for such diagrams. SBOL Visual aims organize systematize produce a coherent language expressing function genetic designs. This document details version 3.0 Visual, new major revision...
This article reports on an in-depth study that investigates barriers to network exploration with visualizations. Network visualization tools are becoming increasingly popular, but little is known about how analysts plan and engage in the visual of data—which strategies they employ, prepare their data, define questions, decide mappings. Our involved a series workshops, interaction logging, observations from 6-week course. findings shed light stages analysts' approaches experienced by some...
Abstract Prognostic models to predict the risk of clinical deterioration in acute COVID-19 are required inform management decisions. Among 75,016 consecutive adults across England, Scotland and Wales prospectively recruited ISARIC Coronavirus Clinical Characterisation Consortium (ISARIC4C) study, we developed validated a multivariable logistic regression model for in-hospital (defined as any requirement ventilatory support or critical care, death) using 11 routinely measured variables. We...
This paper introduces semi-automatic data tours to aid the exploration of complex networks. Exploring networks requires significant effort and expertise can be time-consuming challenging. Distinct from guidance recommender systems for visual analytics, we provide a set goal-oriented network overview, ego-network analysis, community exploration, other tasks. Based on interviews with five analysts, developed user interface (NetworkNarratives) 10 example tours. The allows analysts navigate an...
Abstract People who are engineering biological organisms often find it useful to communicate in diagrams, both about the structure of nucleic acid sequences that they and functional relationships between sequence features other molecular species. Some typical practices conventions have begun emerge for such diagrams. The Synthetic Biology Open Language Visual (SBOL Visual) has been developed as a standard organizing systematizing order produce coherent language expressing function genetic...
People who are engineering biological organisms often find it useful to communicate in diagrams, both about the structure of nucleic acid sequences that they and functional relationships between sequence features other molecular species. Some typical practices conventions have begun emerge for such diagrams. The Synthetic Biology Open Language Visual (SBOL Visual) has been developed as a standard organizing systematizing order produce coherent language expressing function genetic designs....
Abstract Choosing optimal outcome measures maximizes statistical power, accelerates discovery and improves reliability in early-phase trials. We devised evaluated a modification to pragmatic measure of oxygenation function, the $$S/F$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mi>S</mml:mi> <mml:mo>/</mml:mo> <mml:mi>F</mml:mi> </mml:math> ratio. Because ceiling effect oxyhaemoglobin saturation, ratio ceases reflect pulmonary function at high $${S}_{p}{O}_{2}$$...
We present sbml-diff, a tool that is able to read model of biochemical reaction network in SBML format and produce range diagrams showing different levels detail. Each diagram type can be used visualize single or visually compare two more models. The default view depicts species as ellipses, reactions rectangles, rules parallelograms, events diamonds. A cartoon replaces the symbols for on basis associated Systems Biology Ontology terms. An abstract represents ellipses draws edges between...
VisBOL is a web-based visualization tool used to depict genetic circuit designs. This depicts simple DNA circuits adequately, but it has become increasingly outdated as new versions of SBOL Visual were released. paper introduces VisBOL2, heavily redesigned version that makes number improvements the original VisBOL, including proper functional interaction rendering, dynamic viewing, more maintainable code base, and modularity facilitates compatibility with other software tools. demonstrated...
This paper introduces NetPanorama, a domain-specific language and declarative grammar for interactive network visualizations. Exploring complex networks with multivariate, geographical, or temporal information often require bespoke visualization designs, such as adjacency matrices, arc-diagrams, small multiples, timelines, geographic map However, creating these requires implementing data loading, transformations, visualization, interactivity, which is time-consuming slows down the iterative...
Abstract Diagrams constructed from standardized glyphs are central to communicating complex design information in many engineering fields. For example, circuit diagrams commonplace electronics and allow for a suitable abstraction of the physical system that helps support process. With development Synthetic Biology Open Language Visual (SBOLv), bioengineers now positioned better describe share their biological designs visually. However, computational tools creation these is currently hampered...