Detection of non-topological motifs in protein structures

We present an efficient technique for the comparison of proteinstructures. The algorithm uses a vector representation of thesecondary structure elements and searches for spatial configurationsof secondary structure elements in proteins. In such recurringprotein folds, the order of the secondary structure elementsin the protein chains is disregarded. The method is based onthe geometric hashing paradigm and implements approaches originatingin computer vision. It represents and matches the secondarystructure element vectors in a 3-D translation and rotationinvariant manner. The matching of a pair of proteins takes onaverage under 3 s on a Silicon Graphics Indigo2 workstation,allowing extensive all-against-all comparisons of the data setof non-redundant protein structures. Here we have carried outsuch a comparison for a data set of over 500 protein molecules.The detection of recurring topological and non-topological,secondary structure element order-independent protein foldsmay provide further insight into evolution. Moreover, as theserecurring folding units are likely to be conformationalHy favourable,the availability of a data set of such topological motifs canserve as a rich input for threading routines. Below, we describethis rapid technique and the results it has obtained. Whilesome of the obtained matches conserve the order of the secondarystructure elements, others are entirely order independent. Asan example, we focus on the results obtained for Che Y, a signaltransduction protein, and on the profilin-ß-actincomplex. The Che Y molecule is composed of a five-stranded,parallel ß-sheet flanked by five helices. Here weshow its similarity with the Escherichia coli elongation factor,with L-arabinose binding protein, with haloalkane dehalogenaseand with adenylate kinase. The profilin–ß-actincontains an antiparallel ß-pleated sheet with -helicaltermini. Its similarities to lipase, fructose disphosphataseand ß-lactamase are displayed.     

Operative creation of left to right cardiac shunts: pulmonary functional sequelae

The tuberomammillary nucleus, a cluster of cells in the posterior hypothalamus, is the only known source of brain histamine. Although this nucleus is well described in terms of anatomy and neurochemistry, only little is known about its function. In the present study, the effect of a lesion in the region of this nucleus on intracranial self-stimulation was examined. Rats were implanted bilaterally with stimulating electrodes in the lateral hypothalamus and unilaterally with one lesion electrode in the region of this nucleus. After three days of baseline testing, half of the animals were given an electrolytic lesion. The animals were retested for six consecutive days, and thereafter weekly for another seven weeks. From the second day postlesion on, we unexpectedly found a gradual increase in response rate, which peaked on day 13 in the ipsilateral hemisphere only. Although there was no further increase over subsequent days, response rates remained elevated during the following seven weekly tests. The observed increase in lateral hypothalamic self-stimulation after an electrolytic lesion of the tuberomammillary nucleus is discussed in terms of an inhibitory system, possibly located in the region of this nucleus which, when removed by the lesion, increased reinforcing effects of the electrical brain stimulation. The fact that the effects on self-stimulation were lateralized to one hemisphere rules out an interpretation in terms of unspecific "performance" variables that could influence rate of lever pressing.     

Relationships among alcohol availability, drinking location, alcohol consumption, and drinking problems in adolescents

We examined relationships among perceived alcohol availability, drinking location, alcohol consumption, and drinking problems. Subjects were 3,372 adolescent drinkers, ages 16-18, who participated in the Communities Mobilizing for Change on Alcohol Project baseline survey. Mixed-model regression was employed to identify predictors of alcohol consumption and drinking consequences. Perceived alcohol availability was significantly associated with higher levels of alcohol consumption for males. Drinking in a public location with higher levels of alcohol consumption for females. Results underscore the importance of youth alcohol assessibility.     

Comparison of the homoepitaxial growth of AlN crystals on Al and N surfaces

A special experimental technique capable of excluding the influence of differences between sources, substrate crystals, and growth process parameters has been employed to correctly compare the quality of homoepitaxial AlN layers grown by sublimation on Al and N surfaces of the substrate crystal with 〈0001〉 orientation. It has been found that, in most cases, the quality of layers grown on the N surface is somewhat higher; however, no differences have been observed in separate cases. Hence the conclusion follows that the range of growth process parameters is substantially wider for the N side compared with the Al side.     

A method for isolating adult and neonatal airway smooth muscle cells and measuring shortening velocity

Methods are described for isolating smooth muscle cells from the tracheae of adult and neonatal sheep and measuring the single-cell shortening velocity. Isolated cells were elongated, Ca2+ tolerant, and contracted rapidly and substantially when exposed to cholinergic agonists, KCl, serotonin, or caffeine. Adult cells were longer and wider than preterm cells. Mean cell length in 1.6 mM CaCl2 was 194 +/- 57 (SD) microm (n = 66) for adult cells and 93 +/- 32 microm (n = 20) for preterm cells (P < 0.05). Mean cell width at the widest point of the adult cells was 8.2 +/- 1.8 microm (n = 66) and 5.2 +/- 1.5 microm (n = 20) for preterm cells (P < 0.05). Cells were loaded into a perfusion dish maintained at 35 degreesC and exposed to agonists, and contractions were videotaped. Cell lengths were measured from 30 video frames and plotted as a function of time. Nonlinear fitting of cell length to an exponential model gave shortening velocities faster than most of those reported for airway smooth muscle tissues. For a sample of 10 adult and 10 preterm cells stimulated with 100 microM carbachol, mean (+/- SD) shortening velocity of the preterm cells was not different from that of the adult cells (0.64 +/- 0.30 vs. 0.54 +/- 0.27 s-1, respectively), but preterm cells shortened more than adult cells (68 +/- 12 vs. 55 +/- 11% of starting length, respectively; P < 0.05). The preparative and analytic methods described here are widely applicable to other smooth muscles and will allow contraction to be studied quantitatively at the single-cell level.     

Context-free attentional operators: The generalized symmetry transform

Active vision systems, and especially foveated vision systems, depend on efficient attentional mechanisms. We propose that machine visual attention should consist of both high-level, context-dependent components, and low-level, context free components. As a basis for the context-free component, we present an attention operator based on the intuitive notion of symmetry, which generalized many of the existing methods of detecting regions of interest. It is a low-level operator that can be applied successfully without a priori knowledge of the world. The resultingsymmetry edge map can be applied in various low, intermediate-and high- level tasks, such as extraction of interest points, grouping, and object recognition. In particular, we have implemented an algorithm that locates interest points in real time, and can be incorporated in active and purposive vision systems. The results agree with some psychophysical findings concerning symmetry as well as evidence concerning selection of fixation points. We demonstrate the performance of the transform on natural, cluttered images.     

PARULEL: Parallel rule processing using meta-rules for redaction

Although the problem of increasing the speed of rule-based programs has been studied for a long while, so far the level of parallelism achieved under various parallel processing schemes fails to meet expectations of high performance gains. Most of the work has focused on manipulating existing rule programs to accommodate parallel architectures. However, without changing the inherently sequential algorithms encoded in rule form and without using intrinsic parallel rule languages to exploit parallelism, speedup is severely limited. In this paper we demonstrate that to maximize parallelism, manipulations must take place at the algorithmic level in addition to the program level. However, traditional rule languages are not equipped to easily express parallel algorithms. Thus, an inherently parallel rule language must be devised to enable maximum parallelism. We present our initial specification of such a language, named PARULEL. Preliminary performance results are detailed for one test case program. PARULEL is one part of a larger research effort that considers four key approaches to parallel rule processing: inherently parallel execution semantics; the use of redaction meta-rules to allow programmer control of the set of parallel instantiations; an incremental evaluation algorithm that incorporates, in an efficient manner, updates to the initial set of assumptions; and an algorithm that maps a program to a parallel architecture.     

Parallel processing of graph reachability in databases

In this paper we consider parallel processing of a graph represented by a database relation, and we achieved two objectives. First, we propose a methodology for analyzing the speedup of a parallel processing strategy with the purpose of selecting at runtime one of several candidate strategies, depending on the hardware architecture and the input graph. Second, we study the single-source reachability problem, namely the problem of computing the set of nodes reachable from a given node in a directed graph. We propose several parallel strategies for solving this problem, and we analyze their performance using our new methodology. The analysis is confirmed experimentally in a UNIX-Ethernet environment. We also extend the results to the transitive closure problem.A preliminary shortened version of this paper has appeared inPDIS. See Ref. 1.This author's work was supported in part by NSF Grant 90-03341.This author's work was supported in part by the Natural Sciences and Engineering Research Council of Canada.This author's work was supported in part by NSF Grant 90-03341.     

A note about preferred orientations at the first and second stages of complex (second-order) texture channels

Complex (second-order) channels have been useful in explaining many of the phenomena of perceived texture segregation. These channels contain two stages of linear filtering with an intermediate pointwise nonlinearity. One unanswered question about these hypothetical channels is that of the relationship between the preferred orientations of the two stages of filtering. Is a particular orientation at the second stage equally likely to occur with all orientations at the first stage, or is there a bias in the "mapping" between the two stages' preferred orientations? In this study we consider two possible mappings: that where the orientations at the two stages are identical (called "consistent" here) and that where the orientations at the two stages are perpendicular ("inconsistent"). We explore these mappings using a texture-segregation task with textures composed of arrangements of grating-patch elements. The results imply that, to explain perceived texture segregation, complex channels with a consistent orientation mapping must be either somewhat more prevalent or more effective than those with an inconsistent mapping.