SUMMARY: Although translation initiation has been well studied, many questions remain in elucidating its mechanisms. An ongoing challenge is to understand how ribosomes choose a translation initiation site (TIS). To gain new insights, we analyzed large sets of TISs with the aim of identifying common characteristics that are potentially of functional importance. Nucleotide sequence context has previously been demonstrated to play an important role in the ribosome's selection of a TIS, and mRNA secondary structure is also emerging as a contributing factor. Here, we analyze mRNA secondary structure using the folding predictions of the RNAfold algorithm. We present a method for analyzing these results using a rank-ordering approach to assess the overall degree of predicted secondary structure in a given region of mRNA. In addition, we used a modified version of the algorithm that makes use of only a subset of the standard version's output to incorporate base-pairing polarity constraints suggested by the ribosome scanning process. These methods were employed to study the TISs of 1735 genes in Saccharomyces cerevisiae. Trends in base composition and base-pairing probabilities suggest that efficient translation initiation and high protein expression are aided by reduced secondary structure upstream and downstream of the TIS. However, the downstream reduction is not observed for sets of TISs with nucleotide sequence contexts unfavorable for translation initiation, consistent with previous suggestions that secondary structure downstream of the ribosome can facilitate TIS recognition.

This paper presents several basic results about the non-existence of reflexive objects in cartesian closed topological categories of Hausdorff spaces. In particular, we prove that there are no non-trivial countably compact reflexive objects in the category of Hausdorff k-spaces and, more generally, that any non-trivial reflexive Tychonoff space in this category contains a closed discrete subspace corresponding to a numeral system in the sense of Wadsworth. In addition, we establish that a reflexive Tychonoff space in a cartesian-closed topological category cannot contain a non-trivial continuous image of the unit interval. Therefore, if there exists a non-trivial reflexive Tychonoff space, it does not have a nice geometric structure.

Presents an adaptive error control technique based on the use of type-I hybrid-ARQ protocols. The communication channel is assumed to be slowly varying and is modeled using a finite state Markov chain. The system counts the number of retransmission requests during an observation interval called a frame and, together with knowledge of the error control strategy in use and a set of thresholds, estimates the state of the channel. The coding strategy which maximizes throughput while maintaining a minimum required level of reliability is chosen for use in the next frame. Examples are provided showing system design and performance using families of Reed-Solomon codes.>

Improved performance of error control techniques over slowly varying channels can be realized by a system which adapts itself to changes in the channel conditions. Such action requires a method for monitoring the channel state and detecting a change in it. The frequency of retransmission requests in ARQ and type-I hybrid-ARQ error control strategies provides a natural source of channel state information. The proposed scheme incorporates the retransmission requests into the scoring of a statistical sequential inspection scheme proposed by E. Page in 1954. Each transmitted packet is scored based on the outcome of the decoding process (i.e., whether it is accepted or rejected). When the cumulative score crosses a decision boundary, the coding strategy is altered and the sequential inspection scheme is restarted using the same scoring routine with different weighting and boundary constants. In this way the channel encoder/decoder is able to alter its strategy and adapt itself to changes in the channel. The analysis of this system is based on the average run length of the tests in the various channel states. These values indicate the delay the system experiences in reacting to a change in the channel and the tendency the test has to terminate prematurely. These factors are a function of the test constants which are determined algorithmatically by maximizing the system throughput using the system reliability as a constraint. Results show that the performance of this system is close to that of the ideal system with perfect channel state information.>

A model is proposed that formalizes the design of hierarchical module structures. The model is specified by a collection of Z schema type definitions that is invariant across all applications. A particular application is described by specifying the values of generic parameters and adding application-specific declarations and constraints to the schema definitions. As applications, the definitions in the model are used to describe the Conic configuration language and the STILE graphical design and development environment.>

Reliability information provided by sets of orthogonal check sums in a majority logic decoder for block codes is used in a type-I hybrid automatic-repeat-request (ARQ) error control scheme. The reliability information is obtained through a simple modification of the majority logic decoding rule. It is shown that the reliability performance of Reed-Muller and other majority logic decodable codes can be substantially improved at the expense of a very small reduction in throughput. The simplicity of the decoding circuit permits implementation in systems with very high data rates.>