DSpace Basic Tutorial

PDF of powerpoint slides presented at DSUG 2007 Roma

Patient Retention in Antiretroviral Therapy Programs in Sub-Saharan Africa: A Systematic Review

Paper published in PLoS Medicine in 2007.

PROPAGATION OF SONIC BOOMS THROUGH A REAL, STRATIFIED ATMOSPHERE

Sonic boom propagation in a quiet) stratified) lossy atmosphere is the subject of this dissertation. Two questions are considered in detail: (1) Does waveform freezing occur? (2) Are sonic booms shocks in steady state? Both assumptions have been invoked in the past to predict sonic boom waveforms at the ground. A very general form of the Burgers equation is derived and used as the model for the problem. The derivation begins with the basic conservation equations. The effects of nonlinearity) attenuation and dispersion due to multiple relaxations) viscosity) and heat conduction) geometrical spreading) and stratification of the medium are included. When the absorption and dispersion terms are neglected) an analytical solution is available. The analytical solution is used to answer the first question. Geometrical spreading and stratification of the medium are found to slow down the nonlinear distortion of finite-amplitude waves. In certain cases the distortion reaches an absolute limit) a phenomenon called waveform freezing. Judging by the maturity of the distortion mechanism, sonic booms generated by aircraft at 18 km altitude are not frozen when they reach the ground. On the other hand, judging by the approach of the waveform to its asymptotic shape, N waves generated by aircraft at 18 km altitude are frozen when they reach the ground. To answer the second question we solve the full Burgers equation and for this purpose develop a new computer code, THOR. The code is based on an algorithm by Lee and Hamilton (J. Acoust. Soc. Am. 97, 906-917, 1995) and has the novel feature that all its calculations are done in the time domain, including absorption and dispersion. Results from the code compare very well with analytical solutions. In a NASA exercise to compare sonic boom computer programs, THOR gave results that agree well with those of other participants and ran faster. We show that sonic booms are not steady state waves because they travel through a varying medium, suffer spreading, and fail to approximate step shocks closely enough. Although developed to predict sonic boom propagation, THOR can solve other problems for which the extended Burgers equation is a good propagation model.

OS Support for Portable Bulk Synchronous Parallel Programs

Predictability -- the ability to foretell that an implementation will not violate a set of specified reliability and timeliness requirements -- is a crucial, highly desirable property of responsive embedded systems. This paper overviews a development methodology for responsive systems, which enhances predictability by eliminating potential hazards resulting from physically-unsound specifications. The backbone of our methodology is the Time-constrained Reactive Automaton (TRA) formalism, which adopts a fundamental notion of space and time that restricts expressiveness in a way that allows the specification of only reactive, spontaneous, and causal computation. Using the TRA model, unrealistic systems – possessing properties such as clairvoyance, caprice, infinite capacity, or perfect timing -- cannot even be specified. We argue that this "ounce of prevention" at the specification level is likely to spare a lot of time and energy in the development cycle of responsive systems -- not to mention the elimination of potential hazards that would have gone, otherwise, unnoticed. The TRA model is presented to system developers through the Cleopatra programming language. Cleopatra features a C-like imperative syntax for the description of computation, which makes it easier to incorporate in applications already using C. It is event-driven, and thus appropriate for embedded process control applications. It is object-oriented and compositional, thus advocating modularity and reusability. Cleopatra is semantically sound; its objects can be transformed, mechanically and unambiguously, into formal TRA automata for verification purposes, which can be pursued using model-checking or theorem proving techniques. Since 1989, an ancestor of Cleopatra has been in use as a specification and simulation language for embedded time-critical robotic processes.

Hidden Type Variables and Conditional Extension for More Expressive Generic Programs

Generic object-oriented programming languages combine parametric polymorphism and nominal subtype polymorphism, thereby providing better data abstraction, greater code reuse, and fewer run-time errors. However, most generic object-oriented languages provide a straightforward combination of the two kinds of polymorphism, which prevents the expression of advanced type relationships. Furthermore, most generic object-oriented languages have a type-erasure semantics: instantiations of type parameters are not available at run time, and thus may not be used by type-dependent operations. This dissertation shows that two features, which allow the expression of many advanced type relationships, can be added to a generic object-oriented programming language without type erasure: 1. type variables that are not parameters of the class that declares them, and 2. extension that is dependent on the satisfiability of one or more constraints. We refer to the first feature as hidden type variables and the second feature as conditional extension. Hidden type variables allow: covariance and contravariance without variance annotations or special type arguments such as wildcards; a single type to extend, and inherit methods from, infinitely many instantiations of another type; a limited capacity to augment the set of superclasses after that class is defined; and the omission of redundant type arguments. Conditional extension allows the properties of a collection type to be dependent on the properties of its element type. This dissertation describes the semantics and implementation of hidden type variables and conditional extension. A sound type system is presented. In addition, a sound and terminating type checking algorithm is presented. Although designed for the Fortress programming language, hidden type variables and conditional extension can be incorporated into other generic object-oriented languages. Many of the same problems would arise, and solutions analogous to those we present would apply.

A Type System For Safe SN Resource Allocation

snBench is a platform on which novice users compose and deploy distributed Sense and Respond programs for simultaneous execution on a shared, distributed infrastructure. It is a natural imperative that we have the ability to (1) verify the safety/correctness of newly submitted tasks and (2) derive the resource requirements for these tasks such that correct allocation may occur. To achieve these goals we have established a multi-dimensional sized type system for our functional-style Domain Specific Language (DSL) called Sensor Task Execution Plan (STEP). In such a type system data types are annotated with a vector of size attributes (e.g., upper and lower size bounds). Tracking multiple size aspects proves essential in a system in which Images are manipulated as a first class data type, as image manipulation functions may have specific minimum and/or maximum resolution restrictions on the input they can correctly process. Through static analysis of STEP instances we not only verify basic type safety and establish upper computational resource bounds (i.e., time and space), but we also derive and solve data and resource sizing constraints (e.g., Image resolution, camera capabilities) from the implicit constraints embedded in program instances. In fact, the static methods presented here have benefit beyond their application to Image data, and may be extended to other data types that require tracking multiple dimensions (e.g., image "quality", video frame-rate or aspect ratio, audio sampling rate). In this paper we present the syntax and semantics of our functional language, our type system that builds costs and resource/data constraints, and (through both formalism and specific details of our implementation) provide concrete examples of how the constraints and sizing information are used in practice.