Reconstruction of cellular biological structures from optical microscopy data

Developments in optical microscopy imaging have generated large high-resolution data sets that have spurred medical researchers to conduct investigations into mechanisms of disease, including cancer at cellular and subcellular levels. The work reported here demonstrates that a suitable methodology can be conceived that isolates modality-dependent effects from the larger segmentation task and that 3D reconstructions can be cognizant of shapes as evident in the available 2D planar images. In the current realization, a method based on active geodesic contours is first deployed to counter the ambiguity that exists in separating overlapping cells on the image plane. Later, another segmentation effort based on a variant of Voronoi tessellations improves the delineation of the cell boundaries using a Bayesian formulation. In the next stage, the cells are interpolated across the third dimension thereby mitigating the poor structural correlation that exists in that dimension. We deploy our methods on three separate data sets obtained from light, confocal, and phase-contrast microscopy and validate the results appropriately.     

Computer program for automated sleep depth estimation

In this article, we present a new implementation of an amplitude-independent method for continuous-scale sleep depth estimation. Having been implemented as an add-on analysis module under commercially available biosignal recording and analysis software, it can be easily applied in clinical routine. The software gives the user full freedom to change all the analysis parameters inside theoretical limits. Computational sleep depth profiles produced by the presented software compare favourably with visual classifications. Future work will concentrate on systematic optimization of analysis parameters, further evaluation of the method with disturbed sleep and application of the method for automated adaptive sleep analysis.     

A theory of mode of action of azolylalkylquinolines as DNA binding agents using automated flexible ligand docking

Azolylalkylquinolines (AAQs) are a family of quinolines with varying degrees of cytotoxic activity (comparable or moderately superior to adriamycin in some cases) developed in the past decade in our group where their exact mode of action is still unclear. In this study the most probable DNA binding mode of AAQs was investigated employing a novel flexible ligand docking approach by using AutoDock 3.0. Forty-nine AAQs with known experimental inhibitory activity were docked onto d(CGCAAATTTGCG)(2), d(CGATCG)(2) and d(CGCG)(2) oligonucleotides retrieved from the Protein Data Bank (PDB IDs: 102D, 1D12 and 1D32, respectively) as the representatives of the three plausible models of interactions between chemotherapeutic agents and DNA (groove binding, groove binding plus intercalation and bisintercalation, respectively). Good correlation (r(2)=0.64) between calculated binding energies and experimental inhibitory activities was obtained using groove binding plus intercalation model for phenyl-azolylalkylquinoline (PAAQ) series. Our findings show that the most probable mode of action of PAAQs as DNA binding agents is via intercalation of quinolinic moiety between CG base pairs with linker chain and azole moiety binding to the minor groove.     

Building the IBM 4758 secure coprocessor

Meeting the challenge of building a user-configurable secure coprocessor provided several lessons in hardware and software development and continues to spur further research. In developing the 4758, we met our major research security goals and provided the following features: (1) a lifetime-secure tamper-responding device, rather than one that is secure only between resets that deployment-specific security officers perform; (2) a secure booting process in which each layer progressively validates the next less-trusted layer, with hardware restricting access to its secrets before passing control to that layer; (3) an actual manufacturable product - a nontrivial accomplishment considering that we designed the device so that it does not have a personality until configured in the field; (4) the first FIPS 140-1 Level 4 validation, arguably the only general-purpose computational platform validated at this level so far; and (5) a multipurpose programmable device based on a 99-MHz 486 CPU internal environment, with a real operating system, a C language development environment and relatively high-speed cryptography     

Fluorescence in situ hybridization of three oncogenes on a leiomyoma

Using fluorescence in situ hybridization technique, expression of three oncogenes, C-myc, RARa, and cyclin-D was tested on a uterine leiomyoma. C-myc and RARa were amplified in approximately 30% and 90% of the cells, respectively. Numerous small signals of C-myc were indicative of the presence of double minutes. Amplification of RARa is being reported for the first time in a leiomyoma. Cyclin-D was normal in diploid cells while it was highly amplified in polyploid cells. Low levels of amplified C-myc and cyclin-D cells seem to be the reason for this tumor to be benign, while RARa could not be effective without the association of some other gene such as PML. Information presented here are significant toward developing new curative strategies such as gene-specific drugs and molecular manipulation to stop the activity of cancer gene. Further study may elucidate that how fibroids grow and maintain their rare benign nature.     

Macsyma: A personal history

The Macsyma system arose out of research on mathematical software in the AI group at MIT in the 1960s. Algorithm development in symbolic integration and simplification arose out of the interest of people, such as the author, who were also mathematics students. The later development of algorithms for the GCD of sparse polynomials, for example, arose out of the needs of our user community. During various times in the 1970s the computer on which Macsyma ran was one of the most popular nodes on the ARPANET. We discuss the attempts in the late 70s and the 80s to develop Macsyma systems that ran on popular computer architectures. Finally, we discuss the impact of the fundamental ideas in Macsyma on the author’s current research on large scale engineering and socio-technical systems.     

Nondestructive NMR determination of oil composition in transformed canola seeds

Magic-angle spinning (MAS) ¹³C nuclear magnetic resonance (NMR) spectroscopy is a convenient method for nondestructive, quantitative characterization of seed oil composition. We describe results for intact hybrid and transformed canola seeds. The MAS ¹³C NMR technique complements and agrees with gas chromatography results. The spectral resolution approaches that of neat, liquid oils. MAS ¹³C NMR data allow quantitative analysis of major oil components, including saturates and oleic, linoleic, and linolenic acyl chains. ¹³C NMR directly and quantitatively elucidates, triglyceride regiochemistry and acyl chain cis-trans isomers that cannot be quickly detected by other methods. MAS ¹³C NMR can serve as the primary method for development of near-infrared seed oil calibrations. These NMR methods are nondestructive and attractive for plant-breeding programs or other studies (e.g., functional genomics) where loss of seed viability is inconvenient.     

Characteristics of Metal Droplets in Slag Tapped from the Blast Furnace

Slag samples, hot‐metal samples and hot‐metal temperatures were obtained during tapping of two blast furnaces. Sampling was carried out at different time points during tapping of three separate heats. The size distribution and composition of metal droplets found in the slag were determined using scanning electron microscopy. Only metal droplets above 0.75 μm could be counted and analysed. All droplets were below 8 μm in diameter and the great majority of these droplets were found to be between 0.75 and 2 μm. The size distribution did not differ significantly for different slag samples. Iron was the main droplet component. Electron probe microanalysis showed that the droplets contained small amounts of carbon. The percentage of the area in a studied cross‐section that was covered with metal droplets varied between 0.01 and 0.07%. Calculations based on Stoke's law showed that the distance droplets travel in the slag is in the micron range. Slag samples taken in the beginning of slag tapping contained more droplets than those taken in the middle of slag tapping, an indication that most droplets can be found in the area near the furnace wall. Some droplets were determined to have magnesium enrichment at the external surface.