Proteomic analysis of laser capture microdissected human prostate cancer and in vitro prostate cell lines

Specific populations of normal and malignant epithelium from three radical prostatectomy tissue specimens were procured by laser capture microdissection (LCM) and analyzed by two-dimensional polyacrylamide gel electrophoresis (2-D PAGE). Six proteins that were only seen in malignant cells and two proteins that were only seen in benign epithelium were reproducibly observed in two of two cases examined. Furthermore, these proteins were not observed in the 2-D PAGE profiles from the patient-matched microdissected stromal cell populations, but were seen in the protein profiles from the undissected whole cryostat sections. One of these proteins was determined to be prostate-specific antigen (PSA) by Western blot analysis, and intriguingly the remaining protein candidates were found to be at least as abundant as the PSA protein. Comparison of 2-D PAGE profiles of microdissected cell with matched in vitro cell lines from the same patient, and metastatic prostate cancer cell lines (LnCaP and PC3) showed striking differences between prostate cells in vivo and in vitro with less than 20% shared proteins. The data demonstrate that 2-D PAGE analysis of LCM-derived cells can reliably detect alterations in protein expression associated with prostate cancer, and that these differentially expressed proteins are produced in high enough levels which could allow for their clinical utility as new targets for therapeutic intervention, serum markers, and/or imaging markers.     

Differences in the Low-Energy Collision-Activated Dissociation of Car☐ylate Anions from Structurally Similar Prostaglandins: E2, F2α, D2 and DHKF2α

Some intriguing discoveries were made concerning the collision-activated dissociation behavior of the derivatized car☐ylate anions of PGE₂ and PGF_2α. The car☐ylate anion [M-PFB]⁻ formed from electron-capture negative chemical ionization of the pentafluorobenzyl ester-trimethylsilyl derivative of PGF_2α showed little fragmentation under typical collision gas pressures and energies (<2.0 mtorr N₂ and <20 eV). In contrast, the daughter spectra of the car☐ylate anion of the methoxime-pentafluorobenzyl ester-trimethylsilyl derivative of PGE₂ produced many intense fragments under the same conditions.     

Combined effect of pore radius and protein dielectric coefficient on the selectivity of a calcium channel

Calcium-selective ion channels often contain a selectivity filter made of similar amino acids, rich in carboxlylates, although the Ca2+ affinities of these channels range from micromolar to millimolar. To understand the physical mechanism for this range of affinities, we use grand canonical Monte Carlo simulations to study the competition of Na+ and Ca2+ in the selectivity filter of a reduced model of a Ca channel. We show that Ca2+ affinity is increased dramatically when both the volume and dielectric coefficient of the protein are reduced.     

On the homotopy category of AC-injective complexes

Let R be any ring. We motivate the study of a class of chain complexes of injective R-modules that we call AC-injective complexes, showing that K(AC-Inj), the chain homotopy category of all AC-injective complexes, is always a compactly generated triangulated category. In general, all DGinjective complexes are AC-injective and in fact there is a recollement linking K(AC-Inj) to the usual derived category D(R). This is based on the author’s recent work inspired by work of Krause and Stovicek. Our focus here is on giving straightforward proofs that our categories are compactly generated.     

Flexure analysis of unsymmetric orthotropic beams with an interlayer

This paper presents a layer-wise stress and deformation analysis of a three-layer beam configuration consisting of two dissimilar orthotropic adherends of different thicknesses that are joined together by a deformable interlayer of finite thickness. Analytical solutions for the case of three-point flexure loading are presented for both compressible and incompressible interlayers. Parametric analysis reveals the influences of asymmetry of moduli and adherend thicknesses, interlayer thickness, and overhang of the beams on the beam compliance. Analytical predictions of beam compliance show very good agreement with finite element results. Experimental measurements of compliance of various unsymmetric beams consisting of aluminum adherends separated by a rubber interlayer were performed in order to validate the analysis. Excellent agreement between measured and predicted compliance values was observed.     

Autonomous atmospheric compensation (AAC) of high resolution hyperspectral thermal infrared remote-sensing imagery

Atmospheric emission and absorption significantly modify the thermal infrared (TIR) radiation spectra from Earth's land surface. A new algorithm, autonomous atmospheric compensation (AAC), was developed to estimate and compensate for the atmospheric effects. The algorithm estimates from hyperspectral TIR measurements two atmospheric index parameters, the transmittance ratio, and the path radiance difference between strong and weak absorption channels near the 11.73 /spl mu/m water band. These two parameters depend on the atmospheric water and temperature distribution profiles, and thus, from them, the complete atmospheric transmittance and path radiance spectra can be predicted. The AAC algorithm is self-contained and needs no supplementary data. Its accuracy depends largely on instrument characteristics, particularly spectral and spatial resolution. Atmospheric conditions, especially humidity and temperature, and other meteorological parameters, also have some secondary impacts. The AAC algorithm was successfully applied to a hyperspectral TIR data set, and the results suggest its accuracy is comparable to that based on the in situ radiosonde measurements.     

Investigating the transient response of a shear thickening fluid using the split Hopkinson pressure bar technique

The split Hopkinson pressure bar (SHPB) technique is implemented to evaluate the transient response of a colloidal suspension exhibiting shear thickening at strain rates and timescales never before explored in a laboratory instrument. These suspensions are shown to exhibit a discontinuous transition from fluid-like (shear thinning) to solid-like (shear thickening) behavior when evaluated using rotational rheometry. The effect of loading rate on this transition time is studied for a particle volume fraction of 0.54 using the SHPB technique. It is shown that the time required for transition to occur decreases logarithmically with loading rate. From these results, we conclude that transition is not triggered by a characteristic shear rate, but rather a critical shear strain is required. Results from SHPB experiments performed up to Peclet numbers of order 10⁷ are presented and discussed for 0.50, 0.52, and 0.54 particle volume fraction suspensions.     

Optimizing time-frequency kernels for classification

In many pattern recognition applications, features are traditionally extracted from standard time-frequency representations (TFRs). This assumes that the implicit smoothing of, say, a spectrogram is appropriate for the classification task. Making such assumptions may degrade classification performance. In general, ana time-frequency classification technique that uses a singular quadratic TFR (e.g., the spectrogram) as a source of features will never surpass the performance of the same technique using a regular quadratic TFR (e,g., Rihaczek or Wigner-Ville). Any TFR that is not regular is said to be singular. Use of a singular quadratic TFR implicitly discards information without explicitly determining if it is germane to the classification task. We propose smoothing regular quadratic TFRs to retain only that information that is essential for classification. We call the resulting quadratic TFRs class-dependent TFRs. This approach makes no a priori assumptions about the amount and type of time-frequency smoothing required for classification. The performance of our approach is demonstrated on simulated and real data. The simulated study indicates that the performance can approach the Bayes optimal classifier. The real-world pilot studies involved helicopter fault diagnosis and radar transmitter identification