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The plant cell wall is an important factor for determining cell shape, function and response to the environment. Secondary cell walls, such as those found in xylem, are composed of cellulose, hemicelluloses and lignin and account for the bulk of plant biomass. The coordination between transcriptional regulation of synthesis for each polymer is complex and(More)
We present a unique FPGA that uses a mix of digital and large-signal analog computation for the simulation of gene regulatory networks. The prototype IC consists of a 4x5 array of configurable logic blocks along with programmable interconnect. It can simulate a network of pathways involving up to 20 genes and their associated proteins. The circuit design(More)
Bacterial populations have a remarkable capacity to cope with extreme environmental fluctuations in their natural environments. In certain cases, adaptation to one stressful environment provides a fitness advantage when cells are exposed to a second stressor, a phenomenon that has been coined as cross-stress protection. A tantalizing question in bacterial(More)
OBJECTIVE To develop a decision support system to identify patients at high risk for hyperlactatemia based upon routinely measured vital signs and laboratory studies. MATERIALS AND METHODS Electronic health records of 741 adult patients at the University of California Davis Health System who met at least two systemic inflammatory response syndrome(More)
Sepsis is a severe medical condition caused by an inordinate immune response to an infection. Early detection of sepsis symptoms is important to prevent the progression into the more severe stages of the disease, which kills one in four it effects. Electronic medical records of 1492 patients containing 233 cases of sepsis were used in a clustering analysis(More)
BACKGROUND A tantalizing question in medical informatics is how to construct knowledge from heterogeneous datasets, and as an extension, inform clinical decisions. The emergence of large-scale data integration in electronic health records (EHR) presents tremendous opportunities. However, our ability to efficiently extract informed decision support is(More)
The application of functional genomic analysis of breast cancer metastasis has led to the identification of a growing number of organ-specific metastasis genes, which often function in concert to facilitate different steps of the metastatic cascade. However, the gene regulatory network that controls the expression of these metastasis genes remains largely(More)
Automatic design of synthetic gene circuits poses a significant challenge to synthetic biology, primarily due to the complexity of biological systems, and the lack of rigorous optimization methods that can cope with the combinatorial explosion as the number of biological parts increases. Current optimization methods for synthetic gene design rely on(More)
The development of a scalable framework for biodesign automation is a formidable challenge given the expected increase in part availability and the ever-growing complexity of synthetic circuits. To allow for (a) the use of previously constructed and characterized circuits or modules and (b) the implementation of designs that can scale up to hundreds of(More)
Bacteria are some of the most ubiquitous, simple and fastest evolving life forms in the planet, yet even in their case, evolution is painstakingly difficult to trace in a laboratory setting. However, evolution of microorganisms in controlled and/or accelerated settings is crucial to advance our understanding on how various behavioral patterns emerge, or to(More)