Fitting the Reproduction number from UK coronavirus case data, and why it is close to 1

We present a method for rapid calculation of coronavirus growth rates and R-numbers tailored to the publicly available data in the UK. The R-number is derived from time-series of case data, using bespoke data processing to remove systematic and errors and stochastic fluctuations. In principle, growth rate can be obtained by differentiating the reported case numbers, but in fact daily stochastic fluctuations disqualify this method. We therefore assume that the case data comprises a smooth, underlying trend which is differentiable and a noise term. The approach produces, up-to-date estimates of the R-number throughout the period of data availability. Our method is validated against published consensus R-numbers from the UK government, and shown to produce comparable results. A significant advantage of our method is that it is stable up to the most recent data, this enables us to make R-number estimates available over two weeks ahead of the published consensus. The short-lived peaks observed in the R-number and case data cannot be explained by a well-mixed model and are suggestive of spread on a localised network. Such a localised spread model tends to give an Rt number close to 1, regardless of how large R0. The case-driven approach is combined with Weight-Shift-Scale (WSS) methods to monitor trends in the epidemic and for medium term predictions. Using case-fatality ratios, we create a narrative for trends in the UK epidemic increased infectiousness of the alpha and delta variants, and the effectiveness of vaccination in reducing severity of infection.

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Estimating the effective sample size in association studies of quantitative traits

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkab057 ◽

2021 ◽

Author(s):

Andrey Ziyatdinov ◽

Jihye Kim ◽

Dmitry Prokopenko ◽

Florian Privé ◽

Fabien Laporte ◽

...

Keyword(s):

Statistical Power ◽

Quantitative Traits ◽

Mixed Model ◽

Association Studies ◽

Effective Sample Size ◽

Environment Interaction ◽

Uk Biobank ◽

Gene Environment Interaction ◽

Gene Environment ◽

The Uk

Abstract The effective sample size (ESS) is a metric used to summarize in a single term the amount of correlation in a sample. It is of particular interest when predicting the statistical power of genome-wide association studies (GWAS) based on linear mixed models. Here, we introduce an analytical form of the ESS for mixed-model GWAS of quantitative traits and relate it to empirical estimators recently proposed. Using our framework, we derived approximations of the ESS for analyses of related and unrelated samples and for both marginal genetic and gene-environment interaction tests. We conducted simulations to validate our approximations and to provide a quantitative perspective on the statistical power of various scenarios, including power loss due to family relatedness and power gains due to conditioning on the polygenic signal. Our analyses also demonstrate that the power of gene-environment interaction GWAS in related individuals strongly depends on the family structure and exposure distribution. Finally, we performed a series of mixed-model GWAS on data from the UK Biobank and confirmed the simulation results. We notably found that the expected power drop due to family relatedness in the UK Biobank is negligible.

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The UK and EMU: Choosing the Regime

National Institute Economic Review ◽

10.1177/002795010218000108 ◽

2002 ◽

Vol 180 ◽

pp. 54-71 ◽

Cited By ~ 9

Author(s):

Ray Barrell

Keyword(s):

Euro Area ◽

Policy Framework ◽

Medium Term ◽

Fiscal Regimes ◽

The Stability ◽

The Uk

The UK has to make a decision on membership of EMU in the next two years. The monetary and fiscal regimes in the Euro Area and in the UK do not differ greatly. However, we argue that membership of EMU will increase the stability of the economy and the credibility of the policy framework, and hence will enhance the prospects for growth and higher incomes and employment. There appear to be no major problems associated with joining EMU at around 1.50 euros to the pound, although there are risks to the UK if the euro appreciates against the dollar after we have entered. However, the costs associated with this risk have to be offset against the probability of the significant output gains that could come from EMU membership in the medium term.

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Assessing the Progression of Alzheimer’s Disease in Real-World Settings in Three European Countries

Journal of Alzheimer s Disease ◽

10.3233/jad-201172 ◽

2021 ◽

Vol 80 (2) ◽

pp. 749-759

Author(s):

Albert Lladó ◽

Lutz Froelich ◽

Rezaul K. Khandker ◽

Montserrat Roset ◽

Christopher M. Black ◽

...

Keyword(s):

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Mixed Model ◽

Primary Objective ◽

Community Dwelling ◽

Behavioral Changes ◽

The Uk ◽

State Examination ◽

Study Inclusion

Background: There exists considerable variation in disease progression rates among patients with Alzheimer’s disease (AD). Objective: The primary objective of this observational study is to assess the progression of AD by characterizing cognitive, functional, and behavioral changes during the follow-up period between 6 and 24 months. Methods: A longitudinal prospective study with community-dwelling patients with an established clinical diagnosis of AD of mild to moderate severity was conducted in Germany, Spain and the UK. A sample of 616 patients from 69 sites was included. Results: Patients had a mean of 1.9 years (SD = 1.9) since AD diagnosis at study inclusion. Cognitive symptoms were reported to have first occurred a mean of 1.1 years (SD = 1.7) prior to AD diagnosis and 1.4 (SD = 1.8) years prior to AD treatment. Patients initially diagnosed with mild and moderate AD spent a median (95%CI) of 3.7 (2.8; 4.4) and 11.1 (6.1, ‘not reached’) years until progression to moderate and severe AD, respectively, according to the Mini-Mental State Examination (MMSE) scores. A mixed model developed for cognitive, functional, and neuropsychiatric scores, obtained from study patients at baseline and during follow-up period, showed progressive deterioration of AD patients over time. Conclusion: The study showed a deterioration of cognitive, functional, and neuropsychiatric functions during the follow-up period. Cognitive deterioration was slightly faster in patients with moderate AD compared to mild AD. The duration of moderate AD can be overestimated due to the use of retrospective data, lack of availability of MMSE scores in clinical charts and exclusion of patients at time of institutionalization.

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Evolution of case fatality rates in the second wave of coronavirus in England: effects of false positives, a Variant of Concern and vaccination.

10.1101/2021.04.14.21255385 ◽

2021 ◽

Author(s):

James A Ackland ◽

Graeme J Ackland ◽

David J Wallace

Keyword(s):

False Positive ◽

Age Groups ◽

Case Fatality ◽

Potential Effect ◽

Time To Death ◽

New Variant ◽

Government Data ◽

The Uk ◽

Second Wave ◽

Over Time

Objective: To track the statistical case fatality rate (CFR) in the second wave of the UK coronavirus outbreak, and to understand its variations over time. Design: Publicly available UK government data and clinical evidence on the time between first positive PCR test and death are used to determine the relationships between reported cases and deaths, according to age groups and across regions in England. Main Outcome Measures: Estimates of case fatality rates and their variations over time. Results: Throughout October and November 2020, deaths in England can be broadly understood in terms of CFRs which are approximately constant over time. The same CFRs prove a poor predictor of deaths when applied back to September, when prevalence of the virus was comparatively low, suggesting that the potential effect of false positive tests needs to be taken into account. Similarly, increasing CFRs are needed to match cases to deaths when projecting the model forwards into December. The growth of the S gene dropout VOC in December occurs too late to explain this increase in CFR alone, but at 33% increased mortality, it can explain the peak in deaths in January. On our analysis, if there were other factors responsible for the higher CFRs in December and January, 33% would be an upper bound for the higher mortality of the VOC. From the second half of January, the CFRs for older age groups show a marked decline. Since the fraction of the VOC has not decreased, this decline is likely to be the result of the rollout of vaccination. However, due to the rapidly decreasing nature of the raw cases data (likely due to a combination of vaccination and lockdown), any imprecisions in the time-to-death distribution are greatly exacerbated in this time period, rendering estimates of vaccination effect imprecise. Conclusions: The relationship between cases and deaths, even when controlling for age, is not static through the second wave of coronavirus in England. An apparently anomalous low case-fatality ratio in September can be accounted for by a modest 0.4% false-positive fraction. The large jump in CFR in December can be understood in terms of a more deadly new variant B1.1.7, while a decline in January correlates with vaccine roll-out, suggesting that vaccine reduce the severity of infection, as well as the risk.

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The acute and medium-term effects of treatment with electroconvulsive therapy on memory in patients with major depressive disorder

Psychological Medicine ◽

10.1017/s0033291715002287 ◽

2015 ◽

Vol 46 (4) ◽

pp. 797-806 ◽

Cited By ~ 13

Author(s):

N. P. Maric ◽

Z. Stojanovic ◽

S. Andric ◽

I. Soldatovic ◽

M. Dolic ◽

...

Keyword(s):

Major Depressive Disorder ◽

Depressive Disorder ◽

Electroconvulsive Therapy ◽

Visual Memory ◽

Mixed Model ◽

Linear Mixed Model ◽

Neuropsychological Test ◽

Medium Term ◽

Major Depressive ◽

Visual Spatial

BackgroundCurrent literature provides insufficient information on the degree of cognitive impairment during and after electroconvulsive therapy (ECT), mostly due to the fact that applied tests lacked sensitivity and flexibility. Our goal was to evaluate cognitive functioning in adult depressed patients treated with bi-temporal ECT, using tests sensitive for detection of possible acute and medium-term memory changes.MethodThirty adult patients with major depressive disorder, treated with a course of bi-temporal ECT, underwent clinical and cognitive measurements three times: at baseline, immediately after a course of ECT, and 1 month later. For cognition assessment, we used learning and visual, spatial and figural memory tests from the Cambridge Neuropsychological Test Automated Battery (CANTAB).ResultsBi-temporal ECT has proven to be an effective treatment. The linear mixed model, used to analyze changes in depression severity and patients’ cognitive performances over time and to assess dynamic correlations between aforementioned features, did not show any significant memory impairment as a potential acute or medium-term ECT effect. However, it yielded significant improvement on visual memory and learning at the follow-up, which positively correlated with the improvement of depression.ConclusionGood progress is being made in the search for ECT-related acute and medium-term cognitive side-effects by using the tests sensitive to detect memory dysfunction with parallel forms of the tasks (to counter practice effects on repeat testing). Our results on learning and memory in relation to ECT during treatment of depression did not bring forth any prolonged and significant bi-temporal ECT-related memory deficit.

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Big Data and Natural Language Processing for Analysing Railway Safety

Innovative Applications of Big Data in the Railway Industry - Advances in Civil and Industrial Engineering ◽

10.4018/978-1-5225-3176-0.ch011 ◽

2018 ◽

pp. 240-267

Author(s):

Kanza Noor Syeda ◽

Syed Noorulhassan Shirazi ◽

Syed Asad Ali Naqvi ◽

Howard J Parkinson ◽

Gary Bamford

Keyword(s):

Big Data ◽

Natural Language Processing ◽

Natural Language ◽

Language Processing ◽

Machine Intelligence ◽

Data Availability ◽

Accident Data ◽

Data Driven Approach ◽

Advanced Analytics ◽

The Uk

Due to modern powerful computing and the explosion in data availability and advanced analytics, there should be opportunities to use a Big Data approach to proactively identify high risk scenarios on the railway. In this chapter, we comprehend the need for developing machine intelligence to identify heightened risk on the railway. In doing so, we have explained a potential for a new data driven approach in the railway, we then focus the rest of the chapter on Natural Language Processing (NLP) and its potential for analysing accident data. We review and analyse investigation reports of railway accidents in the UK, published by the Rail Accident Investigation Branch (RAIB), aiming to reveal the presence of entities which are informative of causes and failures such as human, technical and external. We give an overview of a framework based on NLP and machine learning to analyse the raw text from RAIB reports which would assist the risk and incident analysis experts to study causal relationship between causes and failures towards the overall safety in the rail industry.

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PROSPECTS FOR THE UK BALANCE OF PAYMENTS OVER THE MEDIUM TERM

Dynamic Modelling and Control of National Economies 1989 ◽

10.1016/b978-0-08-037538-0.50067-8 ◽

1990 ◽

pp. 423-429

Author(s):

D. Turner

Keyword(s):

Balance Of Payments ◽

Medium Term ◽

The Uk

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Road Traffic Collisions—Case Fatality Rate, Crash Injury Rate, and Number of Motor Vehicles: Time Trends between a Developed and Developing Country

The American Surgeon ◽

10.1177/000313481007600933 ◽

2010 ◽

Vol 76 (9) ◽

pp. 977-981 ◽

Cited By ~ 3

Author(s):

Sanchia S. Goonewardene ◽

Khalid Baloch ◽

Keith Porter ◽

Ian Sargeant ◽

Gamini Punchihewa

Keyword(s):

Visual Impairment ◽

Case Fatality Rate ◽

Road Traffic ◽

Case Fatality ◽

Injury Rate ◽

Cross Sectional Study ◽

Motor Vehicles ◽

Fatality Rate ◽

Cross Sectional ◽

The Uk

Road traffic collisions (RTCs) are one of the most common preventable causes of death and disability worldwide. We investigated changes in numbers of motor vehicles, case fatality rate, and crash injury rate for the most present recorded year (2002) 5 and 10 years before that in the United Kingdom (UK) and Sri Lanka (SL). We also investigated environmental and individual factors impacting patients at South Birmingham Trauma Unit, UK and Colombo General Hospital, SL. We conducted a descriptive cross-sectional study (both quantitative and qualitative). Over the 10-year period, numbers of motor vehicles have risen in both countries; the crash injury remained stable in both countries. Case fatality rate (far higher) in SL has decreased, as in the UK. Three hundred and twenty-five patients took part in the survey in SL, with 83 in the UK. In the categories investigated, including patient demographics, RTC environment, visual impairment, pedestrian and driver factors, the majority of results were significantly different between the two countries. Target factors such as inadequate street lighting, visual impairment, speeding, and not wearing seatbelts at time of accident were identified, and recommendations developed as a result.

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Impact of economic sentiment and economic policy uncertainty on travel and leisure stock return

Journal of Hospitality and Tourism Insights ◽

10.1108/jhti-05-2020-0070 ◽

2020 ◽

Vol ahead-of-print (ahead-of-print) ◽

Cited By ~ 1

Author(s):

Abobaker Al.Al. Hadood ◽

Farid Irani

Keyword(s):

Economic Policy ◽

Stock Returns ◽

Stock Index ◽

Policy Uncertainty ◽

Medium Term ◽

Content Type ◽

Economic Policy Uncertainty ◽

European Economic ◽

The Uk ◽

Stock Index Returns

PurposeThis paper considers the role of economic sentiment and economic policy uncertainty (both domestic and European) in explaining the changes in the contemporaneous and future travel and leisure stock index returns in top European Union (EU) tourism destinations, namely, in France, Germany, Spain and the UK.Design/methodology/approachThe authors conducted the ordinary least square (OLS) regression estimations to investigate the impact of changes in economic sentiment and economic policy uncertainty on travel and leisure stock returns. Furthermore, the authors used predictive regressions to determine whether economic sentiment and economic policy uncertainty are useful predictors over the short- or medium-term for travel and leisure stock returns.FindingsEmpirical results revealed that, in France and Spain, the changes in regional economic sentiments predominantly and positively affected travel and leisure stock index returns. Also, results indicated that changes in European economic sentiment have a strong positive effect on the future travel and leisure stock returns in Spain and the UK over the short run, while in France, changes in European economic policy uncertainty have a weak negative effect on the future travel and leisure stock returns over the medium-term.Research limitations/implicationsThis paper provides valuable practical implications for investors who trade travel and leisure stocks. Traders can use economic sentiment and economic policy uncertainty to establish arbitrageur strategies.Originality/valueThis study is the first to examine the effects of economic sentiment and economic policy uncertainty (both domestic and European) on contemporaneous and future travel and leisure stock returns in a top European tourism destination.

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Appendix A: Key Forecast Assumptions

National Institute Economic Review ◽

10.1177/0027950110389768 ◽

2010 ◽

Vol 214 ◽

pp. F23-F27

Keyword(s):

Financial Markets ◽

Production Functions ◽

Medium Term ◽

Long Run ◽

The World ◽

Net Assets ◽

Trade Competitiveness ◽

The Uk ◽

Forecast Assumptions ◽

Factor Inputs

The forecasts for the world and the UK economy reported in this Review are produced using NIESR's model, NiGEM. The NiGEM model has been in use at the National Institute for forecasting and policy analysis since 1987, and is also used by a group of about fifty model subscribers, mainly in the policy community. Most countries in the OECD are modelled separately, and there are also separate models of China, India, Russia, Hong Kong, Taiwan, Brazil, South Africa, Estonia, Latvia, Lithuania, Slovenia, Romania and Bulgaria. The rest of the world is modelled through regional blocks so that the model is global in scope. All models contain the determinants of domestic demand, export and import volumes, prices, current accounts and net assets. Output is tied down in the long run by factor inputs and technical progress interacting through production functions, but is driven by demand in the short to medium term. Economies are linked through trade, competitiveness and financial markets and are fully simultaneous. Further details on the NiGEM model are available on http://nimodel.niesr.ac.uk/.

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