On the utility of RNA sample pooling to optimize cost and statistical power in RNA sequencing experiments

Background: In gene expression studies, RNA sample pooling is sometimes considered because of budget constraints or lack of sufficient input material. Using microarray technology, RNA sample pooling strategies have been reported to optimize both the cost of data generation as well as the statistical power for differential gene expression (DGE) analysis. For RNA sequencing, with its different quantitative output in terms of counts and tunable dynamic range, the adequacy and empirical validation of RNA sample pooling strategies have not yet been evaluated. In this study, we comprehensively assessed the utility of pooling strategies in RNA-seq experiments using empirical and simulated RNA-seq datasets. Result: The data generating model in pooled experiments is defined mathematically to evaluate the mean and variability of gene expression estimates. The model is further used to examine the trade-off between the statistical power of testing for DGE and the data generating costs. Empirical assessment of pooling strategies is done through analysis of RNA-seq datasets under various pooling and non-pooling experimental settings. Simulation study is also used to rank experimental scenarios with respect to the rate of false and true discoveries in DGE analysis. The results demonstrate that pooling strategies in RNA-seq studies can be both cost-effective and powerful when the number of pools, pool size and sequencing depth are optimally defined. Conclusion: For high within-group gene expression variability, small RNA sample pools are effective to reduce the variability and compensate for the loss of the number of replicates. Unlike the typical cost-saving strategies, such as reducing sequencing depth or number of RNA samples (replicates), an adequate pooling strategy is effective in maintaining the power of testing DGE for genes with low to medium abundance levels, along with a substantial reduction of the total cost of the experiment. In general, pooling RNA samples or pooling RNA samples in conjunction with moderate reduction of the sequencing depth can be good options to optimize the cost and maintain the power

Distributed Verification of Rare Properties using Importance Splitting Observers

Rare properties remain a challenge for statistical model checking (SMC) due to the quadratic scaling of variance with rarity. We address this with a variance reduction framework based on lightweight importance splitting observers. These expose the model-property automaton to allow the construction of score functions for high performance algorithms. The confidence intervals defined for importance splitting make it appealing for SMC, but optimising its performance in the standard way makes distribution inefficient. We show how it is possible to achieve equivalently good results in less time by distributing simpler algorithms. We first explore the challenges posed by importance splitting and present an algorithm optimised for distribution. We then define a specific bounded time logic that is compiled into memory-efficient observers to monitor executions. Finally, we demonstrate our framework on a number of challenging case studies

Methods and Tools for the Microsimulation and Forecasting of Household Expenditure

This paper reviews potential methods and tools for the microsimulation and forecasting of household expenditure. It begins with a discussion of a range of approaches to the forecasting of household populations via agent-based modelling tools. Then it evaluates approaches to the modelling of household expenditure. A prototype implementation is described and the paper concludes with an outline of an approach to be pursued in future work

CGIAR Excellence in Breeding Platform - Plan of Work and Budget 2020

At the end of 2019, all CGIAR centers had submitted improvement plans based on an EiB template and in close collaboration with EiB staff while – in a parallel process with breeding programs, funders and private sector representatives – a vision for breeding program modernization was developed and presented to CGIAR breeding leadership at the EiB Annual Meeting. This vision represents an evolution of EiB in the context of the Crops to End Hunger Initiative (CtEH) beyond the initial scope of providing tools, services and expert advice, and serves as a guide for Center leadership to drive changes with EiB support. In addition, EiB has taken the role of managing and disbursing funding, made available by Funders via CtEH to modernize breeding and enable CGIAR breeding programs to implement the vision provided by EiB

Stress concentration analysis of plate with circular hole : elasticity theory and finite element comparison

Stress concentration factor for a plate with circular free stress hole subjected to a uniform far field tension in single was investigated in this study. The stress concentration level along X and Y axis was determined by the elasticity theoritical method. Finite element analysis using LISA free source software was validate by the elasticity theoritical results. It was found that finite element analysis stress concentration factor results shows similar pattern as theoretical but higher near of the hole. Plain strain analysis with Quad 8 element type showed better results compared to plain stress with Quad 4 element type and plain strain with Quad 4 element type

The Seedling Sanctuary: Automated Cold Frame for Gardner Elementary

The purpose of this report is to provide the details of the Seedling Sanctuary, a mechanical engineering senior design project. The project in question is an automated cold frame designed specifically for Gardner Academy, a local elementary school in San Jose. A cold frame is a miniature greenhouse that opens like a chest and is made from clear plastic. Automated ventilation and watering systems create a microclimate within this greenhouse structure to create the ideal growing conditions for seeds. The main purposes of the cold frame are to lengthen the growing season, be maintenance free, and enhance garden education. From testing, the project goals were verified to have been achieved through several performance metrics. First, the system’s ability to lengthen the growing season is dependent on germinating seedlings that can be planted earlier in the season. The automated system maintained the seedlings at the proper soil moisture levels to grow. The system also implemented passive temperature control systems to maintain the plants in ideal conditions. With the ventilation and thermal mass, the system is able to be cooler at the hottest times of day and warmer at night than unprotected plants. The system has also successfully automated the care of the seedlings, achieving our goal of being maintenance free. Finally, the enhancement of garden education was incorporated through community engagement with the design and building of the cold frame, as well as the Bluetooth application which will be used in the school curriculum