Comparative survey of the relative impact of mRNA features on local ribosome profiling read density

Ribosome profiling (Ribo-seq), a promising technology for exploring ribosome decoding rates, is characterized by the presence of infrequent high peaks in ribosome footprint density and by long alignment gaps. Here, to reduce the impact of data heterogeneity we introduce a simple normalization method, Ribo-seq Unit Step Transformation (RUST). RUST is robust and outperforms other normalization techniques in the presence of heterogeneous noise. We illustrate how RUST can be used for identifying mRNA sequence features that affect ribosome footprint densities globally. We show that a few parameters extracted with RUST are sufficient for predicting experimental densities with high accuracy. Importantly the application of RUST to 30 publicly available Ribo-seq data sets revealed a substantial variation in sequence determinants of ribosome footprint frequencies, questioning the reliability of Ribo-seq as an accurate representation of local ribosome densities without prior quality control. This emphasizes our incomplete understanding of how protocol parameters affect ribosome footprint densities.

Machine-to-machine communications with in-network data aggregation, processing, and actuation for large-scale cyber-physical systems

Machine-to-Machine (M2M) paradigm enables machines (sensors, actuators, robots, and smart meter readers) to communicate with each other with little or no human intervention. M2M is a key enabling technology for the cyber-physical systems (CPSs). This paper explores CPS beyond M2M concept and looks at futuristic applications. Our vision is CPS with distributed actuation and in-network processing. We describe few particular use cases that motivate the development of the M2M communication primitives tailored to large-scale CPS. M2M communications in literature were considered in limited extent so far. The existing work is based on small-scale M2M models and centralized solutions. Different sources discuss different primitives. Few existing decentralized solutions do not scale well. There is a need to design M2M communication primitives that will scale to thousands and trillions of M2M devices, without sacrificing solution quality. The main paradigm shift is to design localized algorithms, where CPS nodes make decisions based on local knowledge. Localized coordination and communication in networked robotics, for matching events and robots, were studied to illustrate new directions.

Correcting for bias when estimating the cost of hospital-acquired infection : an analysis of lower respiratory tract infections in non-surgical patients

Hospital acquired infections (HAI) are costly but many are avoidable. Evaluating prevention programmes requires data on their costs and benefits. Estimating the actual costs of HAI (a measure of the cost savings due to prevention) is difficult as HAI changes cost by extending patient length of stay, yet, length of stay is a major risk factor for HAI. This endogeneity bias can confound attempts to measure accurately the cost of HAI. We propose a two-stage instrumental variables estimation strategy that explicitly controls for the endogeneity between risk of HAI and length of stay. We find that a 10% reduction in ex ante risk of HAI results in an expected savings of £693 ($US 984).