UTV Tools:Matlab Templates for Rank-Revealing UTV Decompositions

published in Numerical Algorithms and the paper's text is reprinted here by kind permissio

UTV Tools:Matlab Templates for Rank-Revealing UTV Decompositions

We describe a Matlab 5.2 package for computing and modifying certain rank-revealing decompositions that have found widespread use in signal processing and other applications. The package focuses on algorithms for URV and ULV decompositions, collectively known as UTV decompositions. We include algorithms for the ULLV decomposition, which generalizes the ULV decomposition to a pair of matrices. For completeness a few algorithms for computation of the RRQR decomposition are also included. The software in this package can be used as is, or can be considered as templates for specialized implementations on signal processors and similar dedicated hardware platforms

Online detection and sorting of extracellularly recorded action potentials in human medial temporal lobe recordings, in vivo

Understanding the function of complex cortical circuits requires the simultaneous recording of action potentials from many neurons in awake and behaving animals. Practically, this can be achieved by extracellularly recording from multiple brain sites using single wire electrodes. However, in densely packed neural structures such as the human hippocampus, a single electrode can record the activity of multiple neurons. Thus, analytic techniques that differentiate action potentials of different neurons are required. Offline spike sorting approaches are currently used to detect and sort action potentials after finishing the experiment. Because the opportunities to record from the human brain are relatively rare, it is desirable to analyze large numbers of simultaneous recordings quickly using online sorting and detection algorithms. In this way, the experiment can be optimized for the particular response properties of the recorded neurons. Here we present and evaluate a method that is capable of detecting and sorting extracellular single-wire recordings in realtime. We demonstrate the utility of the method by applying it to an extensive data set we acquired from chronically-implanted depth electrodes in the hippocampus of human epilepsy patients. This dataset is particularly challenging because it was recorded in a noisy clinical environment. This method will allow the development of closed-loop experiments, which immediately adapt the experimental stimuli and/or tasks to the neural response observed.Comment: 9 figures, 2 tables. Journal of Neuroscience Methods 2006 (in press). Journal of Neuroscience Methods, 2006 (in press

Entropy and Exergy in Renewable Energy

Lovelock identified Newcomen’s atmospheric steam engine as the start of Anthropocene with these words: “…there have been two previous decisive events in the history of our planet. The first was … when photosynthetic bacteria first appeared [conversing sunlight to usable energy]. The second was in 1712 when Newcomen created an efficient machine that converted the sunlight locked in coal directly into work.” This book is about the necessity of energy transition toward renewables that convert sunlight diurnally, thus a sustainable Anthropocene. Such an energy transition is equally momentous as that of the kick start of the second Industrial Revolution in 1712. Such an energy transition requires “it takes a village” collective effort of mankind; the book is a small part of the collective endeavor

Developing high-speed scatterometry tools to detect early events during Nucleotide Excision Repair

Exposure of DNA to ultraviolet (UV) radiation results in the formation of numerous lesions which threaten genome integrity. The nucleotide excision DNA repair pathway detects and repairs a range of such UV-induced DNA lesions. In bacteria, initial damage detection and verification is carried out by two proteins: UvrA and UvrB. Despite decades of study, the process of how these proteins locate damage remains unclear. Here we first demonstrate implementations of novel versions of both conventional dark-field microscopy, and interference reflection microscopy (IRM) for the imaging of gold nanoparticle (AuNP) labelled proteins. We then develop these into an implementation of interferometric scattering (iSCAT) microscopy to allow for high-speed imaging of protein-DNA interactions, including a method that can be used to achieve accurate active stabilisation of an iSCAT microscope in 3-axes using a software-based 3D localisation routine to extract the X, Y, and Z positions of a particle. Combining iSCAT microscopy with a novel, highly customisable, surface-bound-DNA assay, we investigate early damage detection by UvrA. Through this method we have discovered that UvrA interacts with DNA in two phases; a slow phase (~1.3/s) that correlates with an ATP-consuming state previously identified, and a second, much faster search mode. These faster interactions persist for ~130 ms and using ATP analogues we determine this phase does not require ATP consumption. Additionally, by modelling the rate at which UvrA is able to search the E. coli genome, we demonstrate that these rapid interactions allow for basal levels of UvrA to explore 99% of the E. coli genome within a single division cycle. Altogether, this work uncovers the presence of a rapid, energy-efficient search mechanism, which allows UvrA alone to search the entirety of the E. coli genome within a single division cycle and highlights the exciting potential for use of iSCAT microscopy for the study of protein-DNA interactions

Sixth NASTRAN (R) Users' Colloquium

Papers are presented on NASTRAN programming, and substructuring methods, as well as on fluids and thermal applications. Specific applications and capabilities of NASTRAN were also delineated along with general auxiliary programs