Binding and lysing of blood clots using MRX-408

RATIONALE AND OBJECTIVES: A thrombus-specific ultrasound contrast agent, MRX-408, has been developed recently. This agent consists of phospholipid-coated microbubbles with a ligand capable of targeting the GPIIb/IIIa receptor, thereby allowing the microbubbles to bind with thrombi rich in activated platelets. In vitro and in vivo animal experiments have been conducted to examine imaging enhancement and sonothrombolysis using this agent compared with a nontargeted agent. METHODS: For clot binding, blood-smeared slides were incubated with microbubbles and examined under a light microscope. Change in backscatter signals from the blood clots after binding was examined by both an ultrasound scanner and two single-element transducers arranged in a transmitter-receiver pair. For clot lysis, either 1-MHz or 20-KHz ultrasound was used to enhance the lysing effects of MRX-408 with or without urokinase. RESULTS: Evidence of binding was demonstrated under a microscope. In vitro experiments showed that the "acoustic signature", or properties, of blood clots changed after binding. Clots became more echogenic and nonlinear. In vivo fundamental ultrasound imaging confirmed that as a result of binding, blood clots were more visible, the area of detection was improved, and shadowing behind clots was more noticeable. Under 1-MHz ultrasound and 30 minutes of treatment, lysis efficiency reached 34% with MRX-408, whereas there was no visible clot lysis with saline. CONCLUSION: The results of these preliminary studies show that as a contrast agent, MRX-408 enhanced clots under ultrasound imaging and facilitated sonothrombolysis with or without thrombolytic drugs.     

Monte Carlo simulations of systems with complex energy landscapes

Non-traditional Monte Carlo simulations are a powerful approach to the study of systems with complex energy landscapes. After reviewing several of these specialized algorithms we shall describe the behavior of typical systems including spin glasses, lattice proteins, and models for “real” proteins. In the Edwards-Anderson spin glass it is now possible to produce probability distributions in the canonical ensemble and thermodynamic results of high numerical quality. In the hydrophobic-polar (HP) lattice protein model Wang-Landau sampling with an improved move set (pull-moves) produces results of very high quality. These can be compared with the results of other methods of statistical physics. A more realistic membrane protein model for Glycophorin A is also examined. Wang-Landau sampling allows the study of the dimerization process including an elucidation of the nature of the process.     

Monte Carlo simulations of the HP model (the "Ising model" of protein folding)

Using Wang–Landau sampling with suitable Monte Carlo trial moves (pull moves and bond-rebridging moves combined) we have determined the density of states and thermodynamic properties for a short sequence of the HP protein model. For free chains these proteins are known to first undergo a collapse “transition” to a globule state followed by a second “transition” into a native state. When placed in the proximity of an attractive surface, there is a competition between surface adsorption and folding that leads to an intriguing sequence of “transitions”. These transitions depend upon the relative interaction strengths and are largely inaccessible to “standard” Monte Carlo methods.     

Anion modulation of taste responses in sodium-sensitive neurons of the hamster chorda tympani nerve

Beidler's work in the 1950s showed that anions can strongly influence gustatory responses to sodium salts. We have demonstrated "anion inhibition" in the hamster by showing that the chorda tympani nerve responds more strongly to NaCl than to Na acetate over a wide range of concentrations. Iontophoretic presentation of Cl- and acetate to the anterior tongue elicited no response in the chorda tympani, suggesting that these anions are not directly stimulatory. Drugs (0.01, 1.0, and 100 microM anthracene-9-carboxylate, diphenylamine-2-carboxylate, 4-acetamido-4'-isothiocyanatostilbene-2,2'-disulfonate, and furosemide) that interfere with movements of Cl- across epithelial cells were ineffective in altering chorda tympani responses to 0.03 M of either NaCl or Na acetate. Anion inhibition related to movements of anions across epithelial membranes therefore seems unlikely. The chorda tympani contains a population of nerve fibers highly selective for Na+ (N fibers) and another population sensitive to Na+ as well as other salts and acids (H fibers). We found that N fibers respond similarly to NaCl and Na acetate, with spiking activity increasing with increasing stimulus concentration (0.01-1.0 M). H fibers, however, respond more strongly to NaCl than to Na acetate. Furthermore, H fibers increase spiking with increases in NaCl concentration, but generally decrease their responses to increasing concentrations of Na acetate. It appears that anion inhibition applies to taste cells innervated by H fibers but not by N fibers. Taste cells innervated by N fibers use an apical Na+ channel, whereas those innervated by H fibers may use a paracellularly mediated, basolateral site of excitation.     

Pole placement with sensitivity function shaping using 2nd order digital notch filters

This technical note deals with the design of robust digital controllers using pole placement with sensitivity shaping by means of the use of digital notch (band-stop) filters. The use of this type of filters drastically simplifies the effective shaping of the sensitivity functions and the resulting procedure competes with the procedure based on the use of Q-parameterization combined with convex optimization (Automatica 35 (1999) 1111). The feasibility of the technique is illustrated by its application to the control of a very flexible arm.     

Scaled and permuted string matching

The goal of scaled permuted string matching is to find all occurrences of a pattern in a text, in all possible scales and permutations. Given a text of length n and a pattern of length m we present an O(n) algorithm.     

The Barley Chloroplast Mutator (cpm) Mutant: All Roads Lead to the Msh1 Gene

The barley chloroplast mutator (cpm) is a nuclear gene mutant that induces a wide spectrum of cytoplasmically inherited chlorophyll deficiencies. Plastome instability of cpm seedlings was determined by identification of a particular landscape of polymorphisms that suggests failures in a plastome mismatch repair (MMR) protein. In Arabidopsis, MSH genes encode proteins that are in charge of mismatch repair and have anti-recombination activity. In this work, barley homologs of these genes were identified, and their sequences were analyzed in control and cpm mutant seedlings. A substitution, leading to a premature stop codon and a truncated MSH1 protein, was identified in the Msh1 gene of cpm plants. The relationship between this mutation and the presence of chlorophyll deficiencies was established in progenies from crosses and backcrosses. These results strongly suggest that the mutation identified in the Msh1 gene of the cpm mutant is responsible for the observed plastome instabilities. Interestingly, comparison of mutant phenotypes and molecular changes induced by the barley cpm mutant with those of Arabidopsis MSH1 mutants revealed marked differences.     

Construction of Aho Corasick automaton in linear time for integer alphabets

We present a new simple algorithm that constructs an Aho Corasick automaton for a set of patterns, P, of total length n, in O(n) time and space for integer alphabets. Processing a text of size m over an alphabet Σ with the automaton costs O(mlog|Σ|+k), where there are k occurrences of patterns in the text.A new, efficient implementation of nodes in the Aho Corasick automaton is introduced, which works for suffix trees as well.     

Edit distance of run-length encoded strings

Let X and Y be two run-length encoded strings, of encoded lengths k and l, respectively. We present a simple O(|X|l+|Y|k) time algorithm that computes their edit distance.     

Cyclic-3',5'-nucleotide phosphodiesterase isozymes in cell biology and pathophysiology of the kidney

Investigations of recent years revealed that isozymes of cyclic-3', 5'-nucleotide phosphodiesterase (PDE) are a critically important component of the cyclic-3',5'-adenosine monophosphate (cAMP) protein kinase A (PKA) signaling pathway. The superfamily of cyclic-3', 5'-phosphodiesterase (PDE) isozymes consists of at least nine gene families (types): PDE1 to PDE9. Some PDE families are very diverse and consist of several subtypes and numerous PDE isoform-splice variants. PDE isozymes differ in molecular structure, catalytic properties, intracellular regulation and location, and sensitivity to selective inhibitors, as well as differential expression in various cell types. A number of type-specific "second-generation" PDE inhibitors have been developed. Current evidence indicates that PDE isozymes play a role in several pathobiologic processes in kidney cells. In rat mesangial cells, PDE3 and PDE4 compartmentalize cAMP signaling to the PDE3-linked cAMP-PKA pathway that modulates mitogenesis and PDE4-linked cAMP-PKA pathway that modulates generation of reactive oxygen species. Administration of selective PDE isozyme inhibitors in vivo suppresses proteinuria and pathologic changes in experimental anti-Thy-1.1 mesangial proliferative glomerulonephritis in rats. Increased activity of PDE5 (and perhaps also PDE9) in glomeruli and in cells of collecting ducts in sodium-retaining states, such as nephrotic syndrome, accounts for renal resistance to atriopeptin; diminished ability to excrete sodium can be corrected by administration of the selective PDE5 inhibitor zaprinast. Anomalously high PDE4 activity in collecting ducts is a basis of unresponsiveness to vasopressin in mice with hereditary nephrogenic diabetes insipidus. Apparently, PDE isozymes apparently also play an important role in the pathogenesis of acute renal failure of different origins. Administration of PDE isozyme-selective inhibitors suppresses some components of immune responses to allograft transplant and improves preservation and survival of transplanted organ. PDE isozymes are a target for action of numerous novel selective PDE inhibitors, which are key components in the design of novel "signal transduction" pharmacotherapies of kidney diseases.