Research issues in genomic signal processing

Genomic signal processing (GSP) concerns the processing of genomic signals. It may be defined as the analysis, processing, and use of genomic signals to gain biological knowledge and the translation of that knowledge into systems-based applications. In this article, the authors discuss the key research issues for GSP. It is important to recognize that "genomic signal processing" is not a name for genomic bioinformatics nor for the application of signal processing methods in genomics. We note that the research issues pertaining to GSP fit within the overall challenges confronting research in the area of multimodal biomedical systems.     

Complete joint weight enumerators and self-dual codes

We define the complete joint weight enumerator in genus g for codes over /spl Zopf//sub 2k/ and use it to study self-dual codes and their shadows. These weight enumerators are related to the theta series of the associated lattices and Siegel and Jacobi forms are formed from these series.     

Codes Over the p-adic Integers

We study codes over the p-adic integers and correct errors in the existing literature. We show that MDS codes exist over the p-adics for all lengths, ranks and p. We show that self-dual codes exist over the 2-adics if and only if the length is a multiple of 8 and that self-dual codes exist over the p-adics with p odd if and only if the length is 0 (mod 4) for p ≡ 3 (mod 4) and 0 (mod 2) for p ≡ 1 (mod 4).     

Efficient derivation of the optimal mean-square binary morphological filter from the conditional expectation via a switching algorithm for discrete power-set lattice

Once designed, implementation of an optimal mean-square binary morphological filter is extremely fast, especially when the erosions are implemented on a suitable parallel processor. On the other hand, optimal filter design involes a computationally burdensome search procedure that can, in practice, be intractable. The present paper provides an algorithm for filter design that is based on the relationship between the optimal morphological filter and the conditional expectation. The algorithm proceeds by changing the conditional expectation into a morphological filter while at the same time increasing the mean-square error by a minimal amount. It does so by switching observations between the 1-set and the 0-set of the conditional expectation. The switching algorithm is extremely efficient in many noise environments, and therefore provides a filter design that can be useful for online structuring-element updating. Owing to the relationship between stack and morphological filters, the algorithm is at once useful for finding optimal binary stack filters.     

Correlation between Site ll-Specific Human Serum Albumin (HSA) Binding Affinity and Murine in vivo Photosensitizing Efficacy of Some Photofrin Components

Human serum albumin (HSA) is one of the key components in human blood that may influence drug distribution. As such, it is important to know the affinity of any drug for albumin. Previously, Photofrina mixture of monomeric, dimeric and oligomeric porphyrins, has been subjected to HSA binding studies. However, due to its complex nature, binding studies on Photofrin or other hematoporphyrin derivatives with HSA are inconclusive. In this report, the binding properties of some components (dimers and trimers) of Photofrin® and the relationship between murine photosensitizing efficacy and those binding properties were investigated. The interaction of these porphyrins with HSA was investigated by direct ultrafiltration and fluorescent titration techniques with fluorescent probes such as dansyl-L-proline (DP), which is known to interact selectively with site II on HSA. Porphyrins also were tested for antitumor activity in a mouse model following intravenous administration and exposure to laser light. Together, the results suggest that the photosensitizers that were preferentially bound to site II of HSA were most effective at controlling murine tumor regrowth     

SN2 reactions in the gas phase. Structure of the transition state

The alkylhalide-halide association ions, [RX₂]^? that are observed in the negative chemical ionization mass spectra of alkyl halides appear to be directly related to the corresponding S_N2 transition states in solution. ‘Frontside’ association of halide ions with bridgehead alkyl halides does not occur in our system. The Change in heats and entropies of association for the chloromethane series is consistent with delocalization in the [RX]₂^? ions.