Showing papers by "Mark D. Johnson published in 2005"

Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data

Abstract: Motivation: Array Comparative Genomic Hybridization (CGH) can reveal chromosomal aberrations in the genomic DNA. These amplifications and deletions at the DNA level are important in the pathogenesis of cancer and other diseases. While a large number of approaches have been proposed for analyzing the large array CGH datasets, the relative merits of these methods in practice are not clear. Results: We compare 11 different algorithms for analyzing array CGH data. These include both segment detection methods and smoothing methods, based on diverse techniques such as mixture models, Hidden Markov Models, maximum likelihood, regression, wavelets and genetic algorithms. We compute the Receiver Operating Characteristic (ROC) curves using simulated data to quantify sensitivity and specificity for various levels of signal-to-noise ratio and different sizes of abnormalities. We also characterize their performance on chromosomal regions of interest in a real dataset obtained from patients with Glioblastoma Multiforme. While comparisons of this type are difficult due to possibly sub-optimal choice of parameters in the methods, they nevertheless reveal general characteristics that are helpful to the biological investigator. Contact: peter_park@harvard.edu

Preliminary investigations into a new method of functional assessment of the fetal heart using a novel application of 'real-time' cardiac magnetic resonance imaging.

Abstract: Objectives: Because of quantitative echocardiographic limitations of fetal ventricular volumes as well as poor windows, we sought to determine if real-time magnetic resonance imaging (MRI) could be used. Methods: Real-time, functional, true fast imaging with steady-state precession, cardiac MRI was performed on 2 fetuses (one with hypoplastic left heart syndrome and one with ductal constriction). Fetal echocardiography was performed and cardiac index by Doppler was used to validate volume measures by MRI. Results: This technique was able to visualize the beating heart and assess ventricular volumes. Cardiac index and assessment of right ventricular hypertrophy and dilation by echocardiography were consistent with the ventricular volumes and right ventricular hypertrophy obtained by cardiac MRI. Conclusion: Real-time, functional fetal cardiac MRI is possible and can be used to quantitatively assess ventricular volumes and cardiac index in utero.

Temperature-Induced Density Anomaly in Te-Rich Liquid Germanium Tellurides: p versus sp 3 Bonding?

Abstract: The density anomaly of liquid ${\mathrm{Ge}}_{0.15}{\mathrm{Te}}_{0.85}$ measured between 633 and 733 K is investigated with ab initio molecular dynamics calculations at four temperatures and at the corresponding experimental densities. For box sizes ranging from 56 to 112 atoms, an 8 $k$-points sampling of the Brillouin zone is necessary to obtain reliable results. Contrary to other Ge chalcogenides, no $s{p}^{3}$ hybridization of the Ge bonding is observed. As a consequence, the negative thermal expansion of the liquid is not related to a tetrahedral bonding as in the case of water or silica. We show that it results from the symmetry recovery of the local environment of Ge atoms that is distorted at low temperature by a Peierls-like mechanism acting in the liquid state in the same way as in the parent solid phases.

The proteomics of neurodegeneration.

Abstract: The continuing improvement and refinement of proteomic and bioinformatic tools has made it possible to obtain increasing amounts of structural and functional information about proteins on a global scale. The emerging field of neuroproteomics promises to provide powerful strategies for further characterizing neuronal dysfunction and cell loss associated with neurodegenerative diseases. Neuroproteomic studies have thus far revealed relatively comprehensive quantitative changes and post-translational modifications (mostly oxidative damage) of high abundance proteins, confirming deficits in energy production, protein degradation, antioxidant protein function, and cytoskeletal regulation associated with neurodegenerative diseases such as Alzheimer and Parkinson disease. The identification of changes in low-abundance proteins and characterization of their functions based on protein-protein interactions still await further development of proteomic methodologies and more dedicated application of these technologies by neuroscientists. Once accomplished, however, the resulting information will certainly provide a truly comprehensive view of neurodegeneration-associated changes in protein expression, facilitating the identification of novel biomarkers for the early detection of neurodegenerative diseases and new targets for therapeutic intervention.

Recording head metrology at sub-100 nm device dimensions

Abstract: A patterned InAs Hall cross was used to quantitatively image the magnetic field produced by magnetic recording write head as a function of current, obtaining field-current transfer functions for both poles. Using the same instrument, the magnetic field of current-carrying wires as small as 95 nm was measured using a magnetic recording read head in near-contact with the wire surface. The measured magnetic fields from the wire agree closely with the Biot–Savart law predictions for the field from a rectangular current carrying wire over a range of sub-500 nm wire widths. However, for narrow wires, a broadening of the wire field is observed. This broadening is likely due to the finite magnetic response width of the read head. These measurements demonstrate the potential of near-contact recording metrology for magnetic recording heads targeting 1Tbit∕in2 areal-density information storage.