Application of Mismatch Detection Methods in DNA Computing

In many implementations of DNA computing, reliable detection of hybridization is of prime importance. We have applied several well-established DNA mutation scanning methods to this problem. Since they have been developed for speed and accuracy, these technologies are very promising for DNA computing. We have benchmarked a heteroduplex migration assay and enzymatic detection of mismatches on a 4 variable instance of 3SAT, using a previously described blocking algorithm. The first method is promising, but yielded ambiguous results. On the other hand, we were able to distinguish all perfect from imperfect duplexes by means of a CEL I mismatch endonuclease assay.     

Digital boundary tracking

In many three-dimensional imaging applications, the three-dimensional space is represented by an array of cubical volume elements (voxels) and a subset of the voxels is specified by some property. Objects in the scene are then recognised by being components of the specified set and individual boundaries are recognised as sets of voxel faces separating objects from components in the complement of the specified set. This paper deals with the problem of algorithmic tracking of such a boundary specified by one of the voxel faces lying in it. The paper is expository in that all ideas are carefully motivated and introduced. Its original contribution is the investigation of the question of whether the use of a queue (of loose ends in the tracking process which are to be picked up again to complete the tracking) is necessary for an algorithmic tracker of boundaries in three-dimensional space. Such a queue is not needed for two-dimensional boundary tracking, but published three-dimensional boundary trackers all make use of such a thing. We prove that this is not accidental: under some mild assumptions, a boundary tracker without a queue will fail its task on some three-dimensional boundaries.     

Graph visualization and navigation in information visualization: Asurvey

This is a survey on graph visualization and navigation techniques, as used in information visualization. Graphs appear in numerous applications such as Web browsing, state-transition diagrams, and data structures. The ability to visualize and to navigate in these potentially large, abstract graphs is often a crucial part of an application. Information visualization has specific requirements, which means that this survey approaches the results of traditional graph drawing from a different perspective     

Jordan surfaces in simply connected digital spaces

Certain tasks in multidimensional digital image analysis, in particular surface detection and volume estimation, lead us to the study of surfaces in the digital environment. It is desirable that these surfaces should have a Jordan property analogous to that of simple closed curves in two dimensions-namely, that they should partition the underlying space into an inside and an outside which are disconnected from each other. A version of this property, called near-Jordanness, has been previously defined and has been shown to be useful within a general theory of surfaces in digital spaces. The definition of a near-Jordan surface is global: it demands that all paths from the interior to the exterior cross the surface. This makes it difficult in many practical applications to check whether surfaces are near-Jordan. The work reported in this paper is motivated by the desire for a local condition, such that if a surface satisfies this condition at each of its elements, then it is guaranteed to be near-Jordan. In the search for such a condition, we were led to a concept of simple connectedness of a digital space, which resembles simple connectedness in ordinary topological spaces. We were then able to formulate the desired local condition for simply connected digital spaces. Many digital spaces, in particular those based on the commonly-studied tessellations of n-dimensional Euclidean space, are shown to be simply connected and thus our theory yields general sufficient conditions for boundaries in binary pictures to be near-Jordan.     

FAO’s AVHRR-based Agricultural Stress Index System (ASIS) for global drought monitoring

Agricultural production is highly dependent on climate variability in many parts of the world. In particular, drought may severely reduce crop yields, potentially affecting food availability at local, regional, and global scales. The Food and Agriculture Organization of the United Nations (FAO) operates the Global Early Warning System (GIEWS), which monitors global food supply and demand. One of the key challenges is to obtain synoptic information on a recurrent and timely basis about drought-affected agricultural zones. This is needed to quickly identify areas requiring immediate attention. The Agricultural Stress Index System (ASIS), based on imagery from the Advanced Very High Resolution Radiometer (AVHRR) sensors on board the National Oceanic and Atmospheric Administration (NOAA) and Meteorological Operational Satellite (METOP) satellites, was specifically developed to meet this need. The system is based on a methodology developed by Rojas, Vrieling, and Rembold over the African continent. This approach has been modified and adapted to the global scale to produce an agricultural stress index (ASI) representing, per administrative unit, the percentage of cropland (or pasture) areas affected by drought over the growing season. The vegetation health index (VHI), based on normalized difference vegetation index (NDVI) and temperature anomalies, is used as a drought indicator. A fused time series of AVHRR data from METOP and NOAA was used to produce a consistent time series of VHI at 1 km resolution. Global phenology maps, indicating the number of growing seasons and their start and end dates, were derived from a multi-annual image set of SPOT-Vegetation (1999–2011). The VHI time series and phenology maps were then combined to produce the ASI for the years 1984 to the present. This allowed evaluation of the suitability of the ASIS to identify drought using historical reports and ancillary data. As a result of this analysis, ASIS was positively evaluated to support the FAO early warning system.     

Assessment of average,population and individual bioequivalence in two- and four-period crossover studies

The aim of bioequivalence studies is to assess the equivalence of two pharmaceutical formulations of the same active drug substance. Currently three types of bioequivalence are distinguished: average, population and individual bioequivalence. Average and population bioequivalence can be assessed in two-period (non-replicated) crossover studies, whereas individual bioequivalence requires three- or four-period replicated studies, with a preference for four-period studies. The PC-program BIOEQV80 is presented for the statistical analysis of average and population bioequivalence from two-period crossover studies. The program BIOEQ2X2 is presented for the statistical analysis of all three types of bioequivalence from four-period replicated crossover studies. The statistical aspects of population and individual bioequivalence are based on a recent Guidance issued by the US Food and Drug Administration.     

Prediction of human observer performance by numerical observers: an experimental study

Numerical observers are investigated for predicting the outcome of a free-response human observer study involving the detection of simulated pulmonary nodules in images reconstructed from low-dose computed tomography projection data by use of several reconstruction algorithms. A new way of calculating the figure of merit of a numerical observer is proposed wherein the detectability of signals in a particular image depends on the noise properties associated with that image and not the other images in the data set. The resulting variants of numerical observers are found to perform better than their traditional counterparts. In particular, the imagewise variant of the region-of-interest observer is found to predict best the rank ordering of algorithms by human observers for the free-response task.     

The design and implementation of K: a high-level knowledge-base programming language of OSAM*.KBMS

The OSAM*.KBMS is a knowledge-base management system, or the so-called next-generation database management system, for non-traditional data/knowledge-intensive applications. In order to define, query, and manipulate a knowledge base, as well as to write codes to implement any application system, we have developed an object-oriented knowledge-base programming language called K to serve as the high-level interface of OSAM*.KBMS. This paper presents the design of K, its implementation, and its supporting KBMS developed at the Database Systems Research and Development Center of the University of Florida. Edited by Dennis McLeod. Received July 1992 / Accepted August 1995     

Microstructural investigation of plasma-sprayed aluminum coatings

Although plasma-sprayed coatings have been used extensively in industry, limited studies have been carried out on the microstructural details. In this program scanning and transmission electron microscopy, combined with other techniques, were used to examine the grain morphology in plasma-flame-sprayed aluminum coatings.In plasma spraying, the initial particles which impinge onto the cold substrate solidify at rates comparable with those obtained by splat quenching. Since such particles are responsible for the bonding between the coating and the substrate, the first layer has received the central emphasis in this study. Because subsequent layers experience lower cooling rates, a non-uniform grain morphology is obtained which is substantially affected by the particle morphology.The topography of the surface on which the particles impinge is shown to play a decisive role with respect to the orientation of the grains within each particle. These morphological details are considered in the light of models proposed for splat quenching. Another important factor in grain morphology is the position of the particle within the coating. For aluminum, the layers adjacent to the substrate contain highly oriented elongated grains, with the longitudinal axis perpendicular to the substrate. However, because of heating by the flame itself, the particles located away from the substrate are composed of large, equiaxed and randomly oriented grains.Finally, the reaction of the molten droplets with the plasma effluent and the surrounding environment is considered. Oxidation and porosity result when aluminum is sprayed in air. The oxidation of the particles results in a thin layer of oxide which (i) hinders particle-particle interaction and thus results in the formation of interparticle pores and (ii) provides a path for crack propagation and failure, which can occur by delamination. The pore structure of the coating was investigated and correlated with fractography.     

Three proteins involved in Caenorhabditis elegans vulval invagination are similar to components of a glycosylation pathway

We have molecularly analyzed three genes, sqv-3, sqv-7, and sqv-8, that are required for wild-type vulval invagination in Caenorhabditis elegans. The predicted SQV-8 protein is similar in sequence to two mammalian beta(1,3)-glucuronyltransferases, one of which adds glucuronic acid to protein-linked galactose-beta(1, 4)-N-acetylglucosamine. SQV-3 is similar to a family of glycosyltransferases that includes vertebrate beta(1, 4)-galactosyltransferases, which create galactose-beta(1, 4)-N-acetylglucosamine linkages. One model is therefore that SQV-8 uses a SQV-3 product as a substrate. SQV-7 is similar to members of a family of nucleotide-sugar transporters. The sqv genes therefore are likely to encode components of a conserved glycosylation pathway that assembles a C. elegans carbohydrate moiety, the absence of which perturbs vulval invagination.