Modelling capture efficiency of single-cell RNA-sequencing data improves inference of transcriptome-wide burst kinetics

MOTIVATION: Gene expression is characterised by stochastic bursts of transcription that occur at brief and random periods of promoter activity. The kinetics of gene expression burstiness differs across the genome and is dependent on the promoter sequence, among other factors. Single-cell RNA sequencing (scRNA-seq) has made it possible to quantify the cell-to-cell variability in transcription at a global genome-wide level. However, scRNA-seq data is prone to technical variability, including low and variable capture efficiency of transcripts from individual cells. RESULTS: Here, we propose a novel mathematical theory for the observed variability in scRNA-seq data. Our method captures burst kinetics and variability in both the cell size and capture efficiency, which allows us to propose several likelihood-based and simulation-based methods for the inference of burst kinetics from scRNA-seq data. Using both synthetic and real data, we show that the simulation-based methods provide an accurate, robust and flexible tool for inferring burst kinetics from scRNA-seq data. In particular, in a supervised manner, a simulation-based inference method based on neural networks proves to be accurate and useful when applied to both allele and non-allele-specific scRNA-seq data. AVAILABILITY: The code for Neural Network and Approximate Bayesian Computation inference is available at https://github.com/WT215/nnRNA and https://github.com/WT215/Julia_ABC respectively. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online

LAYSI: A layered approach for SLA-violation propagation in self-manageable cloud infrastructures

Cloud computing represents a promising comput ing paradigm where computing resources have to be allocated to software for their execution. Self-manageable Cloud in frastructures are required to achieve that level of flexibility on one hand, and to comply to users' requirements speci fied by means of Service Level Agreements (SLAs) on the other. Such infrastructures should automatically respond to changing component, workload, and environmental conditions minimizing user interactions with the system and preventing violations of agreed SLAs. However, identification of sources responsible for the possible SLA violation and the decision about the reactive actions necessary to prevent SLA violation is far from trivial. First, in this paper we present a novel approach for mapping low-level resource metrics to SLA parameters necessary for the identification of failure sources. Second, we devise a layered Cloud architecture for the bottom-up propagation of failures to the layer, which can react to sensed SLA violation threats. Moreover, we present a communication model for the propagation of SLA violation threats to the appropriate layer of the Cloud infrastructure, which includes negotiators, brokers, and automatic service deployer. © 2010 IEEE

香港977位慢性鼻炎患者的過敏原皮膚點刺測試結果

OBJECTIVES: To evaluate the prevalence of aetiological allergens identifiable by skin prick test alone in patients suffering from chronic rhinitis in Hong Kong, and also compare the clinical history and symptoms of skin prick test-positive versus skin prick test-negative patients. DESIGN: Prospective study. SETTING: Otorhinolaryngology clinic in Queen Mary Hospital of Hong Kong. PATIENTS: A total of 977 patients suffering from chronic rhinitis were recruited into the study. Skin prick test was performed with a panel of allergens including house dust mites, cockroach, cat, dog, moulds, and pollens. MAIN OUTCOME MEASURES: Skin prick test results and their correlation with symptoms. RESULTS: Of the 977 patients, 651 (67%) had positive skin prick test reactions. The commonest allergen was house dust mite which was positive in 63% of the 977 patients and 95% of those 651 skin prick test-positive patients. The other allergens were in order of cockroach (23%), cat (14%), dog (5%), pollen (4%), and mould (3%). Compared with skin prick test-negative patients, skin prick test-positive patients were more likely to have earlier age of onset of the chronic rhinitis, association with asthma, more severe symptom in the morning, more severe symptoms of itchy nose, sneezing, nasal discharge, itchy eye, and watery eye. CONCLUSIONS: Identifiable aeroallergens could be detected in 67% chronic rhinitis patients by skin prick test alone. House dust mites were the most prevalent causative allergen. There were significant differences of patterns of clinical history and symptoms severity between skin prick test-positive and skin prick test-negative patients.published_or_final_versio

Regional innovation and spillover effects of foreign direct investment in China: a threshold approach

Using a data set on twenty-nine Chinese provinces for the period 1985–2008, this paper establishes a threshold model to analyse the relationship between spillover effects of foreign direct investment (FDI) and regional innovation in China. There is clear evidence of double-threshold effects of regional innovation on productivity spillovers from FDI. Specifically, only when the level of regional innovation reaches the minimum innovation threshold will FDI in the region begin to produce positive productivity spillovers. Furthermore, positive productivity spillovers from FDI will be substantial only when the level of regional innovation attains a higher threshold. The double threshold divides Chinese provinces into three super-regions in terms of innovation, with most provinces positioned within the middle-level innovation super-region. Policy implications are discussed

Using workplace population statistics to understand retail store performance

We explore the value of recently released workplace geographies and accompanying census-based workplace zone statistics (WZS) and an associated classification of workplace zones (COWZ). We consider how these data could support retailers in their operational and strategic decision making, including the evaluation of retail demand and retail store performance in localities where trade is driven by non-residential demand. In collaboration with major UK grocery retailer ‘The Co-operative Group’ we explore the relationship between workplace population composition and store trading characteristics using a series of case study stores within Inner London. We use empirical store trading data to identify store and product category level temporal sales fluctuations attributable to workplace populations. We also use census-derived flow data to identify the spatial origins of workplace population inflow. We identify that store performance exhibits characteristics attributable to demand driven by these populations. We conclude that workplace population geographies, WZS and the COWZ afford considerable potential for understanding drivers of store performance, observed store trading patterns and evaluation of retail store performance. We suggest that the next step is to build these populations and their micro geography spatial and temporal characteristics into predictive models and evaluate their potential for store performance evaluation and location-based store and network decision making within this sector

Bio-economic modelling of arable farming system, comparison of conventional and organic farming systems in the Netherlands

Met behulp van twee statische lineaire programmeringsmodellen zijn de technische, economische en milieu resultaten van een gespecialiseerd gangbaar en een gespecialiseerd biologisch landbouwbedrijf vergeleken. Deze modellen zullen als basis dienen voor een dynamisch model waarbij de bottlenecks tijdens de overgang van gangbare naar biologische landbouw kan worden bestudeer

The regional economic impact of more graduates in the labour market: a “micro-to-macro” analysis for Scotland

This paper explores the system-wide impact of graduates on the regional economy. Graduates enjoy a significant wage premium, often interpreted as reflecting their greater productivity relative to non-graduates. If this is so there is a clear and direct supply-side impact of HEI activities on regional economies. We use an HEI-disaggregated computable general equilibrium model of Scotland to estimate the impact of the growing proportion of graduates in the Scottish labour force that is implied by the current participation rate and demographic change, taking the graduate wage premium in Scotland as an indicator of productivity enhancement. While the detailed results vary with alternative assumptions about the extent to which wage premia reflect productivity, they do suggest that the long-term supply-side impacts of HEIs provide a significant boost to regional GDP. Furthermore, the results suggest that the supply-side impacts of HEIs are likely to be more important than the expenditure impacts that are the focus of most HEI impact studies

Business experience and start-up size: buying more lottery tickets next time around?

This paper explores the determinants of start-up size by focusing on a cohort of 6247 businesses that started trading in 2004, using a unique dataset on customer records at Barclays Bank. Quantile regressions show that prior business experience is significantly related with start-up size, as are a number of other variables such as age, education and bank account activity. Quantile treatment effects (QTE) estimates show similar results, with the effect of business experience on (log) start-up size being roughly constant across the quantiles. Prior personal business experience leads to an increase in expected start-up size of about 50%. Instrumental variable QTE estimates are even higher, although there are concerns about the validity of the instrument