Bioassay techniques

Research in plant-herbivore interactions relies heavily on bioassays as analytical tools. Successful bioassay experiments are difficult to design because of the need to reconcile the exacting requirements of hypothesis testing with the dynamic nature of the plant and insect test organisms. Several research protocols are discussed that utilize ecologically flawed techniques to answer ecologically important questions.     

Detailed theoretical investigation of the input power dynamic rangefor gain-clamped semiconductor optical amplifier gates at 10 Gb/s

A detailed theoretical investigation of the input power dynamic range for gain-clamped semiconductor optical amplifier (GC-SOA) gates at 10 Gb/s is presented. We show that although the gain is clamped, the dynamic changes of the carrier distribution in the GC-SOA causes pattern effects on a time scale given by the relaxation frequency of the GC-SOA. Combined with a higher noise figure compared to a conventional SOA, this results in a dynamic range only ~0.5 dB better than for an optimized SOA gate     

3-D curve matching using splines

A machine vision algorithm to find the longest common subcurve of two 3-D curves is presented. The curves are represented by splines fitted through sequences of sample points extracted from dense range data. The approximated 3-D curves are transformed into 1-D numerical strings of rotation and translation invariant shape signatures, based on a multiresolution representation of the curvature and torsion values of the space curves. The shape signature strings are matched using an efficient hashing technique that finds longest matching substrings. The results of the string matching stage are later verified by a robust, least-squares, 3-D curve matching technique, which also recovers the Euclidean transformation between the curves being matched. This algorithm is of average complexity O(n) where n is the number of the sample points on the two curves. The algorithm has applications in assembly and object recognition tasks. Results of assembly experiments are included.     

A numerical solution to the generalized mapmaker's problem:flattening nonconvex polyhedral surfaces

Methods are described to unfold and flatten the curved, convoluted surfaces of the brain in order to study the functional architectures and neural maps embedded in them. In order to do this, it is necessary to solve the general mapmaker's problem for representing curved surfaces by planar models. This algorithm has applications in areas other than computer-aided neuroanatomy, such as robotics motion planning and geophysics. The algorithm maximizes the goodness of fit distances in these surfaces to distances in a planar configuration of points. It is illustrated with a flattening of monkey visual cortex, which is an extremely complex folded surface. Distance errors in the range of several percent are found, with isolated regions of larger error, for the class of cortical surfaces studied so far     

A 3D sequence-independent representation of the protein data bank

Here we address the following questions. How many structurally different entries are there in the Protein Data Bank (PDB)? How do the proteins populate the structural universe? To investigate these questions a structurally non-redundant set of representative entries was selected from the PDB. Construction of such a dataset is not trivial: (i) the considerable size of the PDB requires a large number of comparisons (there were more than 3250 structures of protein chains available in May 1994); (ii) the PDB is highly redundant, containing many structurally similar entries, not necessarily with significant sequence homology, and (iii) there is no clear-cut definition of structural similarity. The latter depend on the criteria and methods used. Here, we analyze structural similarity ignoring protein topology. To date, representative sets have been selected either by hand, by sequence comparison techniques which ignore the three-dimensional (3D) structures of the proteins or by using sequence comparisons followed by linear structural comparison (i.e. the topology, or the sequential order of the chains, is enforced in the structural comparison). Here we describe a 3D sequence-independent automated and efficient method to obtain a representative set of protein molecules from the PDB which contains all unique structures and which is structurally non-redundant. The method has two novel features. The first is the use of strictly structural criteria in the selection process without taking into account the sequence information. To this end we employ a fast structural comparison algorithm which requires on average approximately 2 s per pairwise comparison on a workstation. The second novel feature is the iterative application of a heuristic clustering algorithm that greatly reduces the number of comparisons required. We obtain a representative set of 220 chains with resolution better than 3.0 A, or 268 chains including lower resolution entries, NMR entries and models. The resulting set can serve as a basis for extensive structural classification and studies of 3D recurring motifs and of sequence-structure relationships. The clustering algorithm succeeds in classifying into the same structural family chains with no significant sequence homology, e.g. all the globins in one single group, all the trypsin-like serine proteases in another or all the immunoglobulin-like folds into a third. In addition, unexpected structural similarities of interest have been automatically detected between pairs of chains. A cluster analysis of the representative structures demonstrates the way the "structural universe' is populated.     

Incremental database rule processing in PARADISER

Rule-based systems have been used extensively by the AI community in implementing knowledge-based expert systems. A current trend in the database community is to use rules for the purpose of providing inferential capabilities for large database applications. However, in the database context, performance of rule-program processing has proved to be a major stumbling block particularly in data-intensive and real-time applications. Similar work in the AI community has demonstrated the same problems mainly due to the predominantly sequential semantics of the underlying rule languages. In a previous paper, we presented an incremental evaluation algorithm forDatalog ^* programs. We show the general applicability of the incremental evaluation algorithm to a broad class ofDatalog-style rule languages with varying operational semantics, denoted byDatalog** to emphasize this generality. We present the proof of correctness of the algorithm within the Datalog^** frame work, and its extension for the PARULEL rule language, a principle component of the PARADISER (PARAllel and DIStributed Environment for Rules) rule processing environment for databases. We discuss the meta-rule formalism of PARULEL and argue that it provides a means for programmable operational semantics which separates control from the base logic of a rule program. This allows the realization of a wide range of operational semantics including those of Datalog and OPS5.     

Rigid-body modelling of shaken baby syndrome

Recent reassessment of the literature on the shaken baby syndrome (SBS) has revealed a lack of scientific evidence and understanding of all aspects of the syndrome. In particular, studies have been unable to clarify the mechanisms of injury, indicating that impact, rather than shaking alone, is necessary to cause the type of brain damage observed. Rigid-body modelling (RBM) was used to investigate the effect of neck stiffness on head motion and head-torso impacts as a possible mechanism of injury. Realistic shaking data obtained from an anthropometric test dummy (ATD) was used to simulate shaking. In each study injury levels for concussion were exceeded, though impact-type characteristics were required to do so in the neck stiffness study. Levels for the type of injury associated with the syndrome were not exceeded. It is unlikely that further gross biomechanical investigation of the syndrome will be able to significantly contribute to the understanding of SBS. Current injury criteria are based on high-energy, single-impact studies. Since this is not the type of loading in SBS it is suggested that their application here is inappropriate and that future studies should focus on injury mechanisms in low-energy cyclic loading.     

The effects of measles virus persistent infection on AP-1 transcription factor binding in neuroblastoma cells

"Aerobiologia 2.0" is a simple computer program created to handle the pollen data collected every 2 hrs and daily by aerobiological monitoring stations equipped with Hirst-type spore traps. "Aerobiologia 2.0" runs on Windows 3.1 and is compatible with other programs that run on this operating system. The program was developed to store and process pollen data through a few straightforward operations. An unlimited calendar automatically calculates the day of the week. The pollen dictionary, which can hold up to 1216 different pollen types, may be modified or changed completely. Concentrations for every pollen type (in pollen grains/m3) are automatically recorded daily and every 2 hrs. 10-day and monthly sums are also calculated. The percentage of selected types, groups, or families of pollen collected each day, every 10 days, and monthly is quickly available. Pollen calendars and spectra in 24-hr, 10-day, monthly, tri-monthly, half-year, and yearly periods are readily produced. As soon as it is entered, the pollen data are saved on hard disk. A year's worth of data can be saved on a single 1.44 M byte floppy disk. Aerobiologia 2.0 is being used successfully to process the aeropollen data collected at the two monitoring stations managed by our Palynological Laboratory.     

Some disturbing aspects of the drug scene

Three problems in the drug abuse field merit particular emphasis. These are:

(1) The dearth of adequate epidemiologic data on the prevalence of drug abuse. This encourages use of informal and often imprecise data. There is equal imprecision in the data on the effectiveness of various therapeutic programs; this could be obviated by having extramural standardized evaluation for all programs.

(2) The fact that many of the illicit drugs are adulterated with or replaced by a variety of substances. As a result the user often has no idea what he is ingesting or injecting. This not only poses threats to the users but also makes treatment more difficult for the physician.

(3) The failure to carefully consider alternative diagnoses in persons undergoing heroin withdrawal and having atypical manifestations. Tetanus, appendicitis, and pelvic inflammatory disease have all been at least temporarily overlooked.

The treatment of the opiate overdose is ordinarily not difficult; treatment of the barbiturate addict or the individual dependent on both opiates and barbiturates is far more treacherous.