Medical Device Preemption: A Reasonable Avenue of Tort Reform?

Should manufacturers of cutting-edge medical devices ever be able to avoid liability from common law tort claims? Recently, the Seventh Circuit held that tort claims against these manufacturers are preempted when the manufacturer has received pre-market approval from the Food and Drug Administration. This article discusses whether this position adequately balances the competing concerns of developing technologically advanced medical devices with protecting the consumers of such devices

Escherichia coli: Great Diversity around a Common Core

The 2011 Escherichia coli outbreak in Germany, which resulted in more than 4,000 cases, including 908 cases of hemolytic-uremic syndrome (HUS) and at least 50 deaths, highlighted the genome plasticity of E. coli and the potential for new virulent strains to emerge. The analysis of 170 E. coli genome sequences for the presence of nine previously identified protective extraintestinal pathogenic E. coli antigens suggested the feasibility of a combination vaccine as a universal intervention against all pathogenic E. coli strains

Accurate Profiling of Microbial Communities from Massively Parallel Sequencing using Convex Optimization

We describe the Microbial Community Reconstruction ({\bf MCR}) Problem, which is fundamental for microbiome analysis. In this problem, the goal is to reconstruct the identity and frequency of species comprising a microbial community, using short sequence reads from Massively Parallel Sequencing (MPS) data obtained for specified genomic regions. We formulate the problem mathematically as a convex optimization problem and provide sufficient conditions for identifiability, namely the ability to reconstruct species identity and frequency correctly when the data size (number of reads) grows to infinity. We discuss different metrics for assessing the quality of the reconstructed solution, including a novel phylogenetically-aware metric based on the Mahalanobis distance, and give upper-bounds on the reconstruction error for a finite number of reads under different metrics. We propose a scalable divide-and-conquer algorithm for the problem using convex optimization, which enables us to handle large problems (with $\sim10^6$ species). We show using numerical simulations that for realistic scenarios, where the microbial communities are sparse, our algorithm gives solutions with high accuracy, both in terms of obtaining accurate frequency, and in terms of species phylogenetic resolution.Comment: To appear in SPIRE 1

Modelling the emergent dynamics and major metabolites of the human colonic microbiota

Funded by Scottish Government's Rural and Environment Science and Analytical Services Division (RESAS) Acknowledgements We would like to thank Thanasis Vogogias, David Nutter and Alec Mann for their assistance in developing the software for this model. We also acknowledge the Scottish Government’s Rural and Environment Science and Analytical Services Division (RESAS) for their financial support. Furthermore,many thanks go to the two anonymous reviewers whose hard work has greatly improved this paper.Peer reviewedPublisher PD

How Bacterial Communities Expand Functional Repertoires

Probiotics, live microorganisms administered to improve health, interact in as yet poorly understood ways with the complex microbial communities that inhabit the human host

Rapid quantitative profiling of complex microbial populations

Diverse and complex microbial ecosystems are found in virtually every environment on earth, yet we know very little about their composition and ecology. Comprehensive identification and quantification of the constituents of these microbial communities—a ‘census’—is an essential foundation for understanding their biology. To address this problem, we developed, tested and optimized a DNA oligonucleotide microarray composed of 10 462 small subunit (SSU) ribosomal DNA (rDNA) probes (7167 unique sequences) selected to provide quantitative information on the taxonomic composition of diverse microbial populations. Using our optimized experimental approach, this microarray enabled detection and quantification of individual bacterial species present at fractional abundances of <0.1% in complex synthetic mixtures. The estimates of bacterial species abundance obtained using this microarray are similar to those obtained by phylogenetic analysis of SSU rDNA sequences from the same samples—the current ‘gold standard’ method for profiling microbial communities. Furthermore, probes designed to represent higher order taxonomic groups of bacterial species reliably detected microbes for which there were no species-specific probes. This simple, rapid microarray procedure can be used to explore and systematically characterize complex microbial communities, such as those found within the human body

Colonic fermentation – more than meets the nose

Fermentation of undigested foods in the colon by its resident bacteria affects not only colonic health (protection against inflammation and tumour formation) but also influences metabolic health. Studying fermentation directly is difficult for lack of access. We hypothesise that the anatomical structure of the colon is suited to act as a fermenting chamber with the gaseous molecules (VOCs) emitted having direct effects on the colonocytes as well as gut neural and metabolic effects. We refer to this complex system as the ‘fermentome’, and further hypothesise that alteration in the ‘fermentome’ through dietary modification will have a direct impact on colonic as well as metabolic health and disease. The VOCs emitted may play a role in bacterial chemical signalling within the colon but importantly could also function as a ‘gas’ biomarker. Measurement of such VOCs through non-invasive methods would have important application as a hypothesis-generating tool with subsequent clinical application

The human gastrointestinal microbiota and prostate cancer development and treatment

The human gastrointestinal microbiome contains commensal bacteria and other microbiota that have been gaining increasing attention in the context of cancer development and response to treatment. Microbiota play a role in the maintenance of host barrier surfaces that contribute to both local inflammation and other systemic metabolic functions. In the context of prostate cancer, the gastrointestinal microbiome may play a role through metabolism of estrogen, an increase of which has been linked to the induction of prostatic neoplasia. Specific microbiota such as Bacteroides, Streptococcus, Bacteroides massiliensis, Faecalibacterium prausnitzii, Eubacterium rectalie, and Mycoplasma genitalium have been associated with differing risks of prostate cancer development or extensiveness of prostate cancer disease. In this Review, we discuss gastrointestinal microbiota’s effects on prostate cancer development, the ability of the microbiome to regulate chemotherapy for prostate cancer treatment, and the importance of using Next Generation Sequencing to further discern the microbiome’s systemic influence on prostate cancer

Microspheres of mixed proteins

This paper describes the synthesis of mixed proteinaceous microspheres (MPMs) by the sonochemical method. The current fundamental research follows the research of Suslick and co-workers who have developed a method by which high-intensity ultrasound is used to make aqueous suspensions of proteinaceous microcapsules filled with water-insoluble liquids.1 By using high-intensity ultrasound, we have synthesized microspheres made of a few different proteins. The three proteins used in the current experiments are bovine serum albumin (BSA), green fluorescent protein (GFP), and cyan fluorescent protein–glucose binding protein–yellow fluorescent fused protein (CFP-GBP-YFP). The two synthesized microspheres made of mixed proteins are BSA-GFP and BSA-(CFP-GBP-YFP). This paper presents the characterization of the sonochemically produced microspheres of mixed proteins. It also provides an estimate of the efficiency of the sonochemical process in converting the native proteins to microspheres