56 research outputs found
A methodology for determining amino-acid substitution matrices from set covers
We introduce a new methodology for the determination of amino-acid
substitution matrices for use in the alignment of proteins. The new methodology
is based on a pre-existing set cover on the set of residues and on the
undirected graph that describes residue exchangeability given the set cover.
For fixed functional forms indicating how to obtain edge weights from the set
cover and, after that, substitution-matrix elements from weighted distances on
the graph, the resulting substitution matrix can be checked for performance
against some known set of reference alignments and for given gap costs. Finding
the appropriate functional forms and gap costs can then be formulated as an
optimization problem that seeks to maximize the performance of the substitution
matrix on the reference alignment set. We give computational results on the
BAliBASE suite using a genetic algorithm for optimization. Our results indicate
that it is possible to obtain substitution matrices whose performance is either
comparable to or surpasses that of several others, depending on the particular
scenario under consideration
Complement Split Product C5a Mediates the Lipopolysaccharide‐Induced Mobilization of Cfu‐S and Haemopoietic Progenitor Cells, But Not the Mobilization Induced By Proteolytic Enzymes
Abstract. Intravenous (i.v.) injection of mice with lipopolysaccharide (LPS), and the proteolytic enzymes trypsin and proteinase, mobilizes pluripotent haemopoietic stem cells (CFU‐s) as well as granulocyte‐macrophage progenitor cells (GM‐CFU) and the early progenitors of the erythroid lineage (E‐BFU) from the haemopoietic tissues into the peripheral blood. We investigated the involvement of the complement (C) system in this process. It appeared that the early mobilization induced by LPS and other activators of the alternative complement pathway, such as Listeria monocytogenes (Lm) and zymosan, but not that induced by the proteolytic enzymes, was absent in C5‐deficient mice. the mobilization by C activators in these mice could be restored by injection of C5‐sufficient serum, suggesting a critical role for C5. The manner in which C5 was involved in the C activation‐mediated stem cell mobilization was studied using a serum transfer system. C5‐sufficient serum, activated in vitro by incubation with Lm and subsequently liberated from the bacteria, caused mobilization in both C5‐sufficient and C5‐deficient mice. C5‐deficient serum was not able to do so. the resistance of the mobilizing principle to heat treatment (56°C, 30 min) strongly suggests that it is identical with the C5 split product C5a, or an in vivo derivative of C5a. This conclusion was reinforced by the observation that a single injection of purified rat C5a into C5‐deficient mice also induced mobilization of CFU‐s. Copyrigh
Toward Automatic Label-Free Whispering Gallery Modes Biodetection with a Quantum Dot-Coated Microsphere Population
We explore a new calibration-free approach to biodetection based on whispering gallery modes (WGMs) without a reference measure and relative shifts. Thus, the requirement to keep track of the sensor position is removed, and a freely moving population of fluorophore-doped polystyrene microspheres can now fulfill this role of sensing resonator. Breaking free from fixed surface-based biosensing promotes adhesion between the microsphere sensors and the analytes since both can now be thoroughly mixed. The 70-nm-wide spectrum of green fluorescent microbeads allows us to monitor over 20 WGMs simultaneously without needing evanescent light coupling into the microspheres, hence enabling remote sensing. Since the exact radius of each microsphere is unknown a priori, it requires algorithmic analyses to obtain a reliable result for the refractive index of a solution. We first test our approach with different solutions of alcohol in water obtaining 3 × 10−4 precision on the refractive index at lower concentrations. Then, the solutions of bacterial spores in water yield clear evidence of biodetection in the statistical analysis of WGMs from 50 microspheres. To extend the fluorescence spectral range of our WGM sensors, we present preliminary results on coating microspheres with CdSe/ZnS quantum dots
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Statistical mechanics of adsorption and wetting
The adsorption and wetting behavior of fluids on solid surfaces and at fluid-fluid interfaces are consequential in numerous natural processes and technological applications. Though the scientific study of the subject is old, going back to the early nineteenth century when Young and Laplace identified the laws of capillarity, the molecular theory of interfacial phenomena is still a developing subject. It has been given a rigorous statistical mechanical foundation through the now classic works of Kirkwood, Buff and coworkers, the recent progress in the density functional theory of inhomogeneous systems, and the renormalization group theory of critical phenomena. It is interesting that perhaps the most fruitful development in the theory of interfacial phenomena has been the revival of the mean field theory of van der Waals. While not rigorous, this theory is tractable, has provided the insight and motivation for many useful new theories, and captures most of the known qualitative patterns of interfacial behavior, except for details near a critical point where renormalization group theory is required. Because of its simplicity and qualitative successes, we have chosen to use van der Waals theory as the main vehicle for presentation of an overview of our current understanding of adsorption and wetting. 52 refs., 25 figs
The Search for Water in Lunar Soils Through Coordinated Analysis of Space Weathering Characteristics in an Apollo 17 Sample
Hollow nanophase iron particles were identified in a vesicle-rich region of the space weathered rim in a mature lunar mare grain. Coordinated analyses may shed light on the relationship between vesicles, water, and the hollow nanoparticles
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