Filter matrix estimation in automated DNA sequencing

In four-color fluorescence-based automated DNA sequencing, a 4×4 filter matrix parameterizes the relationship between the dye-intensity signals of interest and the data collected by an optical imaging system. The filter matrix is important because the estimated DNA sequence is based on the dye intensities that can only be recovered via inversion of the matrix. Here, the authors present a calibration method for the estimation of the columns of this matrix, using data generated through a special experiment in which DNA samples are labeled with only one fluorescent dye at a time. Simulations and applications of the method to real data are provided, with promising results     

Use of cell ELISA for the screening of neurotrophic activities on minor cell populations in retinal monolayer cultures

BACKGROUND: Whereas the secretion of the male vesicular gland in most mammals is amorphous, that of the tree shrew, Tupaia glis, was observed to be stored as globules. METHODS: Vesicular and prostate glands from Tupaia, fixed in glutaraldehyde and osmium, were studied in the light and electron microscopes. Other materials considered included the Tupaia ejaculate produced by electroejaculation and, for comparative purposes, sections of the vesicular gland from a dermopteran, the flying lemur. RESULTS: The vesicular gland epithelium in Tupaia secretes small granular aggregates and occasionally a denser aggregate that is associated with cells having obvious apical Golgi lamellae. In the alveolar lumen, these aggregates unite with others to form, respectively, granular and some dense globules of up to approximately 15 mu in diameter, which appear as such in semen produced by electroejaculation. In contrast to the prostate, however, precursor secretion vesicles were rare in the vesicular epithelium. Although poorly fixed, the vesicular gland secretion from a flying lemur also appeared to form globules. CONCLUSIONS: Although it is unlike the homogeneous secretion elaborated in most mammals, including primates and insectivores, the globular product of the Tupaia vesicular gland seems comparable to that in a variety of mega- and microbats, among representative species of which it appears to provide the bulk material for the vaginal copulation plug. Because a museum specimen examined here also indicates its occurrence in a flying lemur, the globular vesicular gland secretion common to Tupaiidae, to at least some Mega- and Microchiroptera, and apparently to Dermoptera may provide a soft tissue feature of some value in the cladistic approach to phylogenetic reconstruction within the Archonta. Anat.     

Crystallinity and lateral crystallite size of different UHMW PE materials

Nascent high-molecular-weight (UHMW) polyethylene (PE) samples of different origins show a rather high crystallinity of about 70–75% and contain both a major portion of orthorhombic extended chain crystallites and a minor portion of triclinic crystallites. The triclinic content is greater the higher the molecular weight of the sample and the higher the activity of the used catalyser. A melting / recooling treatment results in a reduction of crystallinity by about 15–25% and disappearance of the triclinic phase. Further, an irreversible conversion of nascent orthorhombic extended chain crystallites to orthorhombic folded chain crystallites of increased lateral dimensions and crystalline perfections takes place during the melting / recooling treatment. The results are compared to those obtained for lower-molecular-weight PE samples and for high-strength / modulus PE fibers of different origins.     

Generalizing MUSIC and MVDR for multiple noncoherent arrays

We examine the problem of source localization and spatial spectrum estimation using sensor arrays that are noncoherent collections of small, coherent subarrays. The covariance of the signal snapshots at each of the coherent subarrays are functions of, among other things, the signal source locations (or the spatial spectrum). Our approach is to derive functions of the subarray covariance matrices that are close approximations of the signal source locations (or the spatial spectrum). We also show how these functions may be considered generalizations of the multiple signal classification (MUSIC) algorithm and the minimum variance distortionless response (MVDR) criterion, respectively. We demonstrate via simulation that, using this approach and array architecture, it is possible to resolve directional ambiguities.     

“Studierstube”: An environment for collaboration in augmented reality

We propose an architecture for multi-user augmented reality with applications in visualisation, presentation and education, which we call Studierstube. Our system presents three-dimensional stereoscopic graphics simultaneously to a group of users wearing light weight see-through head mounted displays. The displays do not affect natural communication and interaction, making working together very effective. Users see the same spatially aligned model, but can independently control their viewpoint and different layers of the data to be displayed. The setup serves computer supported cooperative work and enhances cooperation of visualisation experts. This paper presents the client-server software architecture underlying this system and details that must be addressed to create a high-quality augmented reality setup.     

Towards inverse modeling of turbidity currents: The inverse lock-exchange problem

A new approach is introduced for turbidite modeling, leveraging the potential of computational fluid dynamics methods to simulate the flow processes that led to turbidite formation. The practical use of numerical flow simulation for the purpose of turbidite modeling so far is hindered by the need to specify parameters and initial flow conditions that are a priori unknown. The present study proposes a method to determine optimal simulation parameters via an automated optimization process. An iterative procedure matches deposit predictions from successive flow simulations against available localized reference data, as in practice may be obtained from well logs, and aims at convergence towards the best-fit scenario. The final result is a prediction of the entire deposit thickness and local grain size distribution. The optimization strategy is based on a derivative-free, surrogate-based technique. Direct numerical simulations are performed to compute the flow dynamics. A proof of concept is successfully conducted for the simple test case of a two-dimensional lock-exchange turbidity current. The optimization approach is demonstrated to accurately retrieve the initial conditions used in a reference calculation.     

Implications of Weak Link Effects on Thermal Characteristics of Transition-Edge Sensors

Weak link behavior in transition-edge sensor (TES) microcalorimeters creates the need for a more careful characterization of a device’s thermal characteristics through its transition. This is particularly true for small TESs where a small change in the bias current results in large changes in effective transition temperature. To correctly interpret measurements, especially complex impedance, it is crucial to know the temperature-dependent thermal conductance, G(T), and heat capacity, C(T), at each point through the transition. We present data illustrating these effects and discuss how we overcome the challenges that are present in accurately determining G and T from I–V curves. We also show how these weak link effects vary with TES size. Additionally, we use this improved understanding of G(T) to determine that, for these TES microcalorimeters, Kaptiza boundary resistance dominates the G of devices with absorbers while the electron-phonon coupling also needs to be considered when determining G for devices without absorbers