Opportunities for machine learning and artificial intelligence in national mapping agencies:enhancing ordnance survey workflow

National Mapping agencies (NMA) are frequently tasked with providing highly accurate geospatial data for a range of customers. Traditionally, this challenge has been met by combining the collection of remote sensing data with extensive field work, and the manual interpretation and processing of the combined data. Consequently, this task is a significant logistical undertaking which benefits the production of high quality output, but which is extremely expensive to deliver. Therefore, novel approaches that can automate feature extraction and classification from remotely sensed data, are of great potential interest to NMAs across the entire sector. Using research undertaken at Great Britain’s NMA; Ordnance Survey (OS) as an example, this paper provides an overview of the recent advances at an NMA in the use of artificial intelligence (AI), including machine learning (ML) and deep learning (DL) based applications. Examples of these approaches are in automating the process of feature extraction and classification from remotely sensed aerial imagery. In addition, recent OS research in applying deep (convolutional) neural network architectures to image classification are also described. This overview is intended to be useful to other NMAs who may be considering the adoption of similar approaches within their workflows

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission

AbstractUnderstanding SARS-CoV-2 transmission in higher education settings is important to limit spread between students, and into at-risk populations. In this study, we sequenced 482 SARS-CoV-2 isolates from the University of Cambridge from 5 October to 6 December 2020. We perform a detailed phylogenetic comparison with 972 isolates from the surrounding community, complemented with epidemiological and contact tracing data, to determine transmission dynamics. We observe limited viral introductions into the university; the majority of student cases were linked to a single genetic cluster, likely following social gatherings at a venue outside the university. We identify considerable onward transmission associated with student accommodation and courses; this was effectively contained using local infection control measures and following a national lockdown. Transmission clusters were largely segregated within the university or the community. Our study highlights key determinants of SARS-CoV-2 transmission and effective interventions in a higher education setting that will inform public health policy during pandemics.</jats:p

Multiorgan MRI findings after hospitalisation with COVID-19 in the UK (C-MORE): a prospective, multicentre, observational cohort study

Introduction: The multiorgan impact of moderate to severe coronavirus infections in the post-acute phase is still poorly understood. We aimed to evaluate the excess burden of multiorgan abnormalities after hospitalisation with COVID-19, evaluate their determinants, and explore associations with patient-related outcome measures. Methods: In a prospective, UK-wide, multicentre MRI follow-up study (C-MORE), adults (aged ≥18 years) discharged from hospital following COVID-19 who were included in Tier 2 of the Post-hospitalisation COVID-19 study (PHOSP-COVID) and contemporary controls with no evidence of previous COVID-19 (SARS-CoV-2 nucleocapsid antibody negative) underwent multiorgan MRI (lungs, heart, brain, liver, and kidneys) with quantitative and qualitative assessment of images and clinical adjudication when relevant. Individuals with end-stage renal failure or contraindications to MRI were excluded. Participants also underwent detailed recording of symptoms, and physiological and biochemical tests. The primary outcome was the excess burden of multiorgan abnormalities (two or more organs) relative to controls, with further adjustments for potential confounders. The C-MORE study is ongoing and is registered with ClinicalTrials.gov, NCT04510025. Findings: Of 2710 participants in Tier 2 of PHOSP-COVID, 531 were recruited across 13 UK-wide C-MORE sites. After exclusions, 259 C-MORE patients (mean age 57 years [SD 12]; 158 [61%] male and 101 [39%] female) who were discharged from hospital with PCR-confirmed or clinically diagnosed COVID-19 between March 1, 2020, and Nov 1, 2021, and 52 non-COVID-19 controls from the community (mean age 49 years [SD 14]; 30 [58%] male and 22 [42%] female) were included in the analysis. Patients were assessed at a median of 5·0 months (IQR 4·2–6·3) after hospital discharge. Compared with non-COVID-19 controls, patients were older, living with more obesity, and had more comorbidities. Multiorgan abnormalities on MRI were more frequent in patients than in controls (157 [61%] of 259 vs 14 [27%] of 52; p&lt;0·0001) and independently associated with COVID-19 status (odds ratio [OR] 2·9 [95% CI 1·5–5·8]; padjusted=0·0023) after adjusting for relevant confounders. Compared with controls, patients were more likely to have MRI evidence of lung abnormalities (p=0·0001; parenchymal abnormalities), brain abnormalities (p&lt;0·0001; more white matter hyperintensities and regional brain volume reduction), and kidney abnormalities (p=0·014; lower medullary T1 and loss of corticomedullary differentiation), whereas cardiac and liver MRI abnormalities were similar between patients and controls. Patients with multiorgan abnormalities were older (difference in mean age 7 years [95% CI 4–10]; mean age of 59·8 years [SD 11·7] with multiorgan abnormalities vs mean age of 52·8 years [11·9] without multiorgan abnormalities; p&lt;0·0001), more likely to have three or more comorbidities (OR 2·47 [1·32–4·82]; padjusted=0·0059), and more likely to have a more severe acute infection (acute CRP &gt;5mg/L, OR 3·55 [1·23–11·88]; padjusted=0·025) than those without multiorgan abnormalities. Presence of lung MRI abnormalities was associated with a two-fold higher risk of chest tightness, and multiorgan MRI abnormalities were associated with severe and very severe persistent physical and mental health impairment (PHOSP-COVID symptom clusters) after hospitalisation. Interpretation: After hospitalisation for COVID-19, people are at risk of multiorgan abnormalities in the medium term. Our findings emphasise the need for proactive multidisciplinary care pathways, with the potential for imaging to guide surveillance frequency and therapeutic stratification

Pre-hospital lowest recorded oxygen saturation independently predicts death in patients with COVID-19

&lt;sec id="s1"&gt;Background: The coronavirus disease 2019 (COVID-19) results in hypoxia in around a fifth of adult patients. Severe hypoxia in the absence of visible respiratory distress (‘silent hypoxia’) is increasingly recognised in these patients. There are no published data evaluating lowest recorded pre-hospital oxygen saturation or pre-hospital National Early Warning Score 2 (NEWS2) as a predictor of outcome in patients with COVID-19. &lt;/sec&gt; &lt;sec id="s2"&gt;Methods: In this retrospective service evaluation, we included adult inpatients with laboratory confirmed COVID-19 who were discharged from hospital or who died in hospital between 12 March and 28 April 2020 (n = 143). Pre-hospital and in-hospital data were extracted and analysed to explore risk factors associated with in-hospital mortality to inform local triage and emergency management. &lt;/sec&gt; &lt;sec id="s3"&gt;Results: The lowest recorded pre-hospital oxygen saturation was an independent predictor of mortality when controlling for age, gender and history of COPD. A 1% reduction in pre-hospital oxygen saturation increased the odds of death by 13% (OR 1.13, p &lt; 0.001). Lower pre-hospital oxygen saturation predicted mortality after adjusting for the pre-hospital NEWS2 (OR for a 1% reduction in pre-hospital oxygen saturation 1.09, p = 0.02). The pre-hospital NEWS2 was higher in those who died (Median 9; IQR 7-10; n = 24) than in those who survived to discharge (Median 6; IQR 5-8; n = 63). &lt;/sec&gt; &lt;sec id="s4"&gt;Conclusion: This service evaluation suggests that the lowest recorded pre-hospital oxygen saturation may be an independent predictor of mortality in COVID-19 patients. Lowest pre-hospital oxygen saturation should be recorded and used in the assessment of patients with suspected COVID-19 in pre-hospital and emergency department triage settings. &lt;/sec&gt;</jats:p