Linking Simulation Model Specification and Parallel Execution through UNITY

Chandy and Misra's UNITY is a computation model and proof system suitable for development of parallel (and distributed) programs through step-wise refinement of specifications. UNITY supports the development of correct programs and the efficient implementation of those programs on parallel computer architectures. This paper assesses the potential of UNITY for simulation model specification and implementation by developing a UNITY specification of the machine interference problem with a patrolling repairman service discipline. The conclusions reached are that the UNITY proof system can assist formal verification of simulation models and the UNITY mappings of programs to various computer architectures offer some potential for assisting the automatic implementation of simulation models on parallel architectures. The paper gives some insights into the relationship of time flow mechanisms, parallel simulation protocols, and target parallel computer architectures

Model Generation Issues in a Simulation Support Environment

No longer available as a technical report. Contact authors re reprints of published article

Precision Electron-Beam Polarimetry using Compton Scattering at 1 GeV

We report on the highest precision yet achieved in the measurement of the polarization of a low energy, $\mathcal{O}$(1 GeV), electron beam, accomplished using a new polarimeter based on electron-photon scattering, in Hall~C at Jefferson Lab. A number of technical innovations were necessary, including a novel method for precise control of the laser polarization in a cavity and a novel diamond micro-strip detector which was able to capture most of the spectrum of scattered electrons. The data analysis technique exploited track finding, the high granularity of the detector and its large acceptance. The polarization of the $180~\mu$A, $1.16$~GeV electron beam was measured with a statistical precision of $<$~1\% per hour and a systematic uncertainty of 0.59\%. This exceeds the level of precision required by the \qweak experiment, a measurement of the vector weak charge of the proton. Proposed future low-energy experiments require polarization uncertainty $<$~0.4\%, and this result represents an important demonstration of that possibility. This measurement is also the first use of diamond detectors for particle tracking in an experiment.Comment: 9 pages, 7 figures, published in PR

Kenneth Lewis Roberts Correspondence

Entries include brief biographical information, a typed biography, typed and handwritten correspondence on personal stationery from Kennebunk Beach, Maine, including a humorous letter in 1933 concerning the Society for Helping Maine Literature, his belief that the author collection was in need of Arnoldiana such as a donated pike head handmade by Arnold\u27s blacksmiths for the attack on Quebec, the manuscript of Arundel sent to be opened after publication and loaned to Leonard for Doubleday Doran and Company and a surprising Western Union telegram requesting permanent loan of the manuscript for MIT, handwritten and typed correspondence from Roberts in Italy including a handwritten artistic postcard from his wife, numerous biographical newspaper review clippings with photographic images, book synopses, and a poem for Theodore Roosevelt who could remember neither the author nor title of the book he was reading, a research question concerning Maine people on cookery, notes through the years concerning his friends, the staff at Doubleday, historians, libraries, and librarians as well as transition at the Maine Development Commission, correspondence with Mary A. Benjamin on Walter R. Benjamin, Autographs, stationery and a postcard concerning the possible sale of a copy of a Maine land grant document, a gift instead from Roberts of his vellum copy of the Trelawny-Goodyear grant of 1631, and the reply of Stubbs from the Maine State Library on receipt of this copy of the Casco Bay land grant

Patients' experiences of living with and receiving treatment for fibromyalgia syndrome: a qualitative study

<p>Abstract</p> <p>Background</p> <p>Fibromyalgia syndrome (FMS) presents a challenge for patients and health care staff across many medical specialities. The aetiology is multi-dimensional, involving somatic, psychological and social factors. Patients' views were obtained to understand their experience of living with this long-term condition, using qualitative interviews.</p> <p>Methods</p> <p>12 patients were recruited and stratified by age, gender and ethnicity from one rheumatology outpatient clinic, and a departmental held database of patients diagnosed with FMS.</p> <p>Results</p> <p>Patients' accounts of their experience of FMS resonated well with two central concepts: social identity and illness intrusiveness. These suggested three themes for the analytical framework: life before and after diagnosis (e.g. lack of information about FMS, invisibility of FMS); change in health identity (e.g. mental distress, impact on social life) and perceived quality of care (e.g. lack of contact with nurses, attitudes of specialists). The information provided from one male participant did not differ from the female patients, but black and ethnic community patients expressed a degree of suspicion towards the medication prescribed, and the attitudes displayed by some doctors, a finding that has not been previously reported amongst this patient group. Patients expected more consultation time and effective treatment than they received. Subjective experiences and objective physical and emotional changes were non-overlapping. Patients' accounts revealed that their physical, mental and social health was compromised, at times overwhelming and affected their identity.</p> <p>Conclusion</p> <p>FMS is a condition that intrudes upon many aspects of patients' lives and is little understood. At the same time, it is a syndrome that evokes uneasiness in health care staff (as current diagnostic criteria are not well supported by objective markers of physiological or biochemical nature, and indeed because of doubt about the existence of the condition) and places great demands on resources in clinical practice. Greater attention needs to be paid to the links between the explanatory models of patients and staff, and most important, to the interrelationship between the complex physical, psychological and social needs of patients with FMS. Taking a less medical but more holistic approach when drawing up new diagnostic criteria for FMS might match better individuals' somatic and psycho-social symptom profile and may result in more effective treatment.</p

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Formally Reasoning About and Automatically Generating Sequential and Parallel Simulations

This paper proposes a methodology to automate the construction of simulation programs within the context of a simulation support environment. The methodology starts with a simulation model specification in the form of a set of coupled state transition systems. The paper provides a mechanical method of mapping the transition systems first into a set of formal assertions, permitting formal verification of the transition systems, and second into an executable program. UNITY, a computational model and proof system suitable for development of parallel and distributed programs through step-wise refinement of specifications, is used as the specification and program notation. The methodology provides a means to independently verify the correctness of the transition systems: one can specify properties formally that the model should obey and prove them as theorems using the formal specification

Simulation Model Specifications: On the Role of Representation in theModel-Centered Sciences

The old adage that "a problem correctly formulated is half solved" is rarely challenged. Model-centered problem solving relies critically on a correct model. Complete, clearly stated assumptions, a precise statement of objectives, and an adequate representation of the model of the system under study are readily accepted as responsibilities of the modeler. But just how important are both the process and product of model representation? The modeler's responsibilities in producing a correct model can be either significantly aided or drastically inhibited by the representational mechanism - the language - being used. The comprehensibility of the model, subsequent extension, adaptation, or maintenance of the model, are highly dependent on the representational language. Language for model representation is therefore an indispensible tool. The pivotal role of this tool is described through its relationship to modeling methodology, model development environments, and automated model diagnosis. The need for an emphasis on the capabilities for conceptual expressiveness, in contrast with execution efficiency is discussed. While software engineering research clearly advocates this redefinition of emphasis, we observe that much of the research in the rising disciplines within parallel computation appears to ignore the lessons of this history

Parallel Discrete Event Simulation: A Modeling MethodologicalPerspective

The field of parallel discrete event simulation is entering a period of self-assessment. Fifteen years of investigation has seen great strides in techniques for efficiently executing discrete event simulations on parallel and distributed machines. Still, the discrete event simulation community at large has failed to recognize much of these results. One reason for this is perhaps a disagreement in the focus and purpose of the parallel discrete event simulation research community (primarily computer scientists) and the discrete event simulation community (a widely diverse group including operations researchers, statisticians, as well as computer scientists). An examination of the parallel discrete event simulation problem from a modeling methodological perspective illustrates some of these differences and reveals potentials for their resolution