Epitope mapping using mRNA display and a unidirectional nested deletion library

In vitro selection targeting an anti-polyhistidine monoclonal antibody was performed using mRNA display with a random, unconstrained 27-mer peptide library. After six rounds of selection, epitope-like peptides were identified that contain two to five consecutive, internal histidines and are biased for arginine residues, without any other identifiable consensus. The epitope was further refined by constructing a high-complexity, unidirectional fragment library from the final selection pool. Selection by mRNA display minimized the dominant peptide from the original selection to a 15-residue functional sequence (peptide Cmin: RHDAGDHHHHHGVRQ; K-D = 38 nM). Other peptides recovered from the fragment library selection revealed a separate consensus motif (ARRXA) C-terminal to the histidine track. Kinetics measurements made by surface plasmon resonance, using purified Fab (antigen-binding fragment) to prevent avidity effects, demonstrate that the selected peptides bind with 10- to 75-fold higher affinities than a hexahistidine peptide. The highest affinity peptides (K-D approximate to 10 nM) encode both a short histidine track and the ARRXA motif, suggesting that the motif and other flanking residues make important contacts adjacent to the core polyhistidine-binding site and can contribute > 2.5 kcal/mol of binding free energy. The fragment library construction methodology described here is applicable to the development of high-complexity protein or cDNA expression libraries for the identification of protein-protein interaction domains

Predictions of the emergence of vaccine-resistant hepatitis B in The Gambia using a mathematical model

Vaccine escape variants of hepatitis B virus (HBV) have been identified world-wide. A mathematical model of HBV transmission is used to investigate the potential pattern of emergence of such variants. Attention is focused on The Gambia as a country with high quality epidemiological data, universal infant immunization and in which escape mutants after childhood infections have been observed. We predict that a variant cannot become dominant for at least 20 years from the start of vaccination, even when using a vaccine which affords no cross protection. The dominant factor responsible for this long time scale is the low rate of infectious contacts between infected and susceptible individuals (we estimate the basic reproduction number of hepatitis B in The Gambia to be 1·7). A variant strain that achieves high prevalence will also take many years to control, and it is questionable whether emergence will be identifiable by sero-surveillance until of high prevalence. The sensitivity of the model predictions to epidemiological and demographic factors is explored

Predictions of the emergence of vaccine-resistant hepatitis B in The Gambia using a mathematical model

Vaccine escape variants of hepatitis B virus (HBV) have been identified world-wide. A mathematical model of HBV transmission is used to investigate the potential pattern of emergence of such variants. Attention is focused on The Gambia as a country with high quality epidemiological data, universal infant immunization and in which escape mutants after childhood infections have been observed. We predict that a variant cannot become dominant for at least 20 years from the start of vaccination, even when using a vaccine which affords no cross protection. The dominant factor responsible for this long time scale is the low rate of infectious contacts between infected and susceptible individuals (we estimate the basic reproduction number of hepatitis B in The Gambia to be 1·7). A variant strain that achieves high prevalence will also take many years to control, and it is questionable whether emergence will be identifiable by sero-surveillance until of high prevalence. The sensitivity of the model predictions to epidemiological and demographic factors is explored

Automated System for Early Breast Cancer Detection in Mammograms

The increasing demand on mammographic screening for early breast cancer detection, and the subtlety of early breast cancer signs on mammograms, suggest an automated image processing system that can serve as a diagnostic aid in radiology clinics. We present a fully automated algorithm for detecting clusters of microcalcifications that are the most common signs of early, potentially curable breast cancer. By using the contour map of the mammogram, the algorithm circumvents some of the difficulties encountered with standard image processing methods. The clinical implementation of an automated instrument based on this algorithm is also discussed

Employing pre-stress to generate finite cloaks for antiplane elastic waves

It is shown that nonlinear elastic pre-stress of neo-Hookean hyperelastic materials can be used as a mechanism to generate finite cloaks and thus render objects near-invisible to incoming antiplane elastic waves. This approach appears to negate the requirement for special cloaking metamaterials with inhomogeneous and anisotropic material properties in this case. These properties are induced naturally by virtue of the pre-stress. This appears to provide a mechanism for broadband cloaking since dispersive effects due to metamaterial microstructure will not arise.Comment: 4 pages, 2 figure

An empirical study of software design practices

Software engineers have developed a large body of software design theory and folklore, much of which was never validated. The results of an empirical study of software design practices in one specific environment are presented. The practices examined affect module size, module strength, data coupling, descendant span, unreferenced variables, and software reuse. Measures characteristic of these practices were extracted from 887 FORTRAN modules developed for five flight dynamics software projects monitored by the Software Engineering Laboratory (SEL). The relationship of these measures to cost and fault rate was analyzed using a contingency table procedure. The results show that some recommended design practices, despite their intuitive appeal, are ineffective in this environment, whereas others are very effective

Evaporites and the salinity of the ocean during the Phanerozoic: Implications for climate, ocean circulation and life

A compilation of data on volumes and masses of evaporite deposits is used as the basis for reconstruction of the salinity of the ocean in the past. Chloride is tracked as the only ion essentially restricted to the ocean, and past salinities are calculated from reconstructed chlorine content of the ocean. Models for ocean salinity through the Phanerozoic are developed using maximal and minimal estimates of the volumes of existing evaporite deposits, and using constant and declining volumes of ocean water through the Phanerozoic. We conclude that there have been significant changes in the mean salinity of the ocean accompanying a general decline throughout the Phanerozoic. The greatest changes are related to major extractions of salt into the young ocean basins which developed during the Mesozoic as Pangaea broke apart. Unfortunately, the sizes of these salt deposits are also the least well known. The last major extractions of salt from the ocean occurred during the Miocene, shortly after the large scale extraction of water from the ocean to form the ice cap of Antarctica. However, these two modifications of the masses of H2O and salt in the ocean followed in sequence and did not cancel each other out. Accordingly, salinities during the Early Miocene were between 37‰ and 39‰. The Mesozoic was a time of generally declining salinity associated with the deep sea salt extractions of the North Atlantic and Gulf of Mexico (Middle to Late Jurassic) and South Atlantic (Early Cretaceous). The earliest of the major extractions of the Phanerozoic occurred during the Permian. There were few large extractions of salt during the earlier Palaeozoic. The models suggest that this was a time of relatively stable but slowly increasing salinities ranging through the upper 40‰'s into the lower 50‰'s. Higher salinities for the world ocean have profound consequences for the thermohaline circulation of the ocean in the past. In the modern ocean, with an average salinity of about 34.7‰, the density of water is only very slightly affected by cooling as it approaches the freezing point. Consequently, salinization through sea-ice formation or evaporation is usually required to make water dense enough to sink into the ocean interior. At salinities above about 40‰ water continues to become more dense as it approaches the freezing point, and salinization is not required. The energy-consuming phase changes involved in sea-ice formation and evaporation would not be required for vertical circulation in the ocean. The hypothesized major declines in salinity correspond closely to the evolution of both planktonic foraminifera and calcareous nannoplankton. Both groups were restricted to shelf regions in the Jurassic and early Cretaceous, but spread into the open ocean in the mid-Cretaceous. Their availability to inhabit the open ocean may be directly related to the decline in salinity. The Permian extraction may have created stress for marine organisms and may have been a factor contributing to the end-Permian extinction. The modeling also suggests that there was a major salinity decline from the Late Precambrian to the Cambrian, and it is tempting to speculate that this may have been a factor in the Cambrian explosion of life

Quantum-defect theory of resonant charge exchange

We apply the quantum-defect theory for $-1/R^4$ potential to study the resonant charge exchange process. We show that by taking advantage of the partial-wave-insensitive nature of the formulation, resonant charge exchange of the type of $^1$S+$^2$S can be accurately described over a wide range of energies using only three parameters, such as the \textit{gerade} and the \textit{ungerade} $s$ wave scattering lengths, and the atomic polarizability, even at energies where many partial waves contribute to the cross sections. The parameters can be determined experimentally, without having to rely on accurate potential energy surfaces, of which few exist for ion-atom systems. The theory further relates ultracold interactions to interactions at much higher temperatures.Comment: 8 pages, 7 figure

Designing with Ada for satellite simulation: A case study

A FORTRAN-operated and an Ada-oriented design for the same system are compared to learn whether an essentially different design was produced using Ada. The designs were produced by an experiment that involves the parallel development of software for a spacecraft dynamics simulator. Design differences are identified in the use of abstractions, system structure, and simulator operations. Although the designs were significantly different, this result may be influenced by some special characteristics discussed