Comparing Patient-Centered Medical Home Implementation in Urban and Rural VHA Clinics: Results from the Patient Aligned Care Team (PACT) Initiative

Thesis (Master's)--University of Washington, 2016-06

CLARITY and PACT-based imaging of adult zebrafish and mouse for whole-animal analysis of infections.

Visualization of infection and the associated host response has been challenging in adult vertebrates. Owing to their transparency, zebrafish larvae have been used to directly observe infection in vivo; however, such larvae have not yet developed a functional adaptive immune system. Cells involved in adaptive immunity mature later and have therefore been difficult to access optically in intact animals. Thus, the study of many aspects of vertebrate infection requires dissection of adult organs or ex vivo isolation of immune cells. Recently, CLARITY and PACT (passive clarity technique) methodologies have enabled clearing and direct visualization of dissected organs. Here, we show that these techniques can be applied to image host-pathogen interactions directly in whole animals. CLARITY and PACT-based clearing of whole adult zebrafish and Mycobacterium tuberculosis-infected mouse lungs enables imaging of mycobacterial granulomas deep within tissue to a depth of more than 1 mm. Using established transgenic lines, we were able to image normal and pathogenic structures and their surrounding host context at high resolution. We identified the three-dimensional organization of granuloma-associated angiogenesis, an important feature of mycobacterial infection, and characterized the induction of the cytokine tumor necrosis factor (TNF) within the granuloma using an established fluorescent reporter line. We observed heterogeneity in TNF induction within granuloma macrophages, consistent with an evolving view of the tuberculous granuloma as a non-uniform, heterogeneous structure. Broad application of this technique will enable new understanding of host-pathogen interactions in situ.

Dealing with the devil: a critical and creative look at the diabolical pact

This thesis is comprised of three parts: a critical dissertation, a creative work of fiction and a bridge piece that connects the two. The critical work is an examination of the Devil as a satirist in Faustian bargains. Through the usage of the Devil as a literary figure, his character has become a more secular being: a trickster rather than evil incarnate—a facilitator of sin rather than its originator. In the tragicomedy of pacts with the Devil, he acts as a mirror, reflecting mankind’s foibles and vanity, while elevating the reader in the process. The thesis considers the language, tone, purpose and conceits of several versions of the story. While the focus is primarily on American Literature, the influence of English, Scottish, French and German folklore and fiction are recognized as an essential component of the theme’s evolution. In the bridge piece, the pact with the Devil is literalized in a modern context; a corporate business of reaping souls is theorized in which techniques of persuasion are streamlined into an effective formula. Whether immersive or expository in approach, the portrayal of the supernatural depends on the literary principles of science fiction and fantasy in order to manipulate the reader and allow irrational concepts to obey rational laws. Such theories are cited to support how the Devil functions as a believable character. The novel, Could Be Much Worse, relates the story of an egocentric boss and his dependable employee, a scout who disguises himself as a taxi driver and seeks candidates who may succumb to temptation. Passengers’ monologues of desperation and pathos are interspersed throughout the protagonist’s day-to-day narrative. At times, the work is experimental, utilizing irregular storytelling techniques, alternative forms and conceits. Light-hearted, but nonetheless poignant, the story serves as a cautionary tale, illustrating the tedium of a bureaucratic job in a transmundane existence.

The promise of Iceland

Memoir, 288 pages. An account of journeys made by the author from Australia to Iceland as a way of interrogating notions of cultural belonging, family, and homecoming. "In 1990, Kári Gíslason travelled to Iceland to meet his father for the first time. What he finds is not what he expected. Born from a secret liaison between a British mother and an Icelandic father, Kári Gíslason was the subject of a promise – a promise elicited from his father to not reveal his identity. The Icelandic city of Reykjavík, where Kári was born, was also home to his father and his father’s wife and five children – none of whom knew of Kári’s existence. Moving regularly between Iceland and Australia, he grew up aware of his father’s identity, but understanding that it was the subject of a secret pact between his parents. At the age of 27, he makes a decision to break the pact and contacts his father’s other family. What follows, and what leads him there, makes for a riveting journey over landscapes, time and memory. Kári travels from the freezing cold winters of Iceland to the shark net at Sydney’s Balmoral, an unsettled life in the English countryside and the harsh yellow summer of Brisbane, and back again. He traces the steps of his mother who answered an ad in The Times for an English-speaking secretary in 1970 and found herself in Iceland among the ‘Army of Foreign Secretaries’, and in the arms of a secret lover. Iceland becomes the substitute for the father Kári never really knew as he discovers the meaning of ‘home’ and closes the circle of his own fatherless life."-- publisher website

Internet usage trends in medical informatics

Technological growth in the 21st century is exponential. Simultaneously, development of the associated risk, uncertainty and user acceptance are scattered. This required appropriate study to establish people accepting controversial technology (PACT). The Internet and services around it, such as World Wide Web, e-mail, instant messaging and social networking are increasingly becoming important in many aspects of our lives. Information related to medical and personal health sharing using the Internet is controversial and demand validity, usability and acceptance. Whilst literature suggest, Internet enhances patients and physicians’ positive interactions some studies establish opposite of such interaction in particular the associated risk. In recent years Internet has attracted considerable attention as a means to improve health and health care delivery. However, it is not clear how widespread the use of Internet for health care really is or what impact it has on health care utilisation. Estimated impact of Internet usage varies widely from the locations locally and globally. As a result, an estimate (or predication) of Internet use and their effects in Medical Informatics related decision-making is impractical. This open up research issues on validating and accepting Internet usage when designing and developing appropriate policy and processes activities for Medical Informatics, Health Informatics and/or e-Health related protocols. Access and/or availability of data on Internet usage for Medical Informatics related activities are unfeasible. This paper presents a trend analysis of the growth of Internet usage in medical informatics related activities. In order to perform the analysis, data was extracted from ERA (Excellence Research in Australia) ranked “A” and “A*” Journal publications and reports from the authenticated public domain. The study is limited to the analyses of Internet usage trends in United States, Italy, France and Japan. Projected trends and their influence to the field of medical informatics is reviewed and discussed. The study clearly indicates a trend of patients becoming active consumers of health information rather than passive recipients.

Trick or treaty?: The Australian debate over the Anti-Counterfeiting Trade Agreement

The secretive 2011 Anti-Counterfeiting Trade Agreement – known in short by the catchy acronym ACTA – is a controversial trade pact designed to provide for stronger enforcement of intellectual property rights. The preamble to the treaty reads like pulp fiction – it raises moral panics about piracy, counterfeiting, organised crime, and border security. The agreement contains provisions on civil remedies and criminal offences; copyright law and trademark law; the regulation of the digital environment; and border measures. Memorably, Susan Sell called the international treaty a TRIPS Double-Plus Agreement, because its obligations far exceed those of the World Trade Organization's TRIPS Agreement 1994, and TRIPS-Plus Agreements, such as the Australia-United States Free Trade Agreement 2004. ACTA lacks the language of other international intellectual property agreements, which emphasise the need to balance the protection of intellectual property owners with the wider public interest in access to medicines, human development, and transfer of knowledge and technology. In Australia, there was much controversy both about the form and the substance of ACTA. While the Department of Foreign Affairs and Trade was a partisan supporter of the agreement, a wide range of stakeholders were openly critical. After holding hearings and taking note of the position of the European Parliament and the controversy in the United States, the Joint Standing Committee on Treaties in the Australian Parliament recommended the deferral of ratification of ACTA. This was striking as representatives of all the main parties agreed on the recommendation. The committee was concerned about the lack of transparency, due process, public participation, and substantive analysis of the treaty. There were also reservations about the ambiguity of the treaty text, and its potential implications for the digital economy, innovation and competition, plain packaging of tobacco products, and access to essential medicines. The treaty has provoked much soul-searching as to whether the Trick or Treaty reforms on the international treaty-making process in Australia have been compromised or undermined. Although ACTA stalled in the Australian Parliament, the debate over it is yet to conclude. There have been concerns in Australia and elsewhere that ACTA will be revived as a ‘zombie agreement’. Indeed, in March 2013, the Canadian government introduced a bill to ensure compliance with ACTA. Will it be also resurrected in Australia? Has it already been revived? There are three possibilities. First, the Australian government passed enhanced remedies with respect to piracy, counterfeiting and border measures in a separate piece of legislation – the Intellectual Property Laws Amendment (Raising the Bar) Act 2012 (Cth). Second, the Department of Foreign Affairs and Trade remains supportive of ACTA. It is possible, after further analysis, that the next Australian Parliament – to be elected in September 2013 – will ratify the treaty. Third, Australia is involved in the Trans-Pacific Partnership negotiations. The government has argued that ACTA should be a template for the Intellectual Property Chapter in the Trans-Pacific Partnership. The United States Trade Representative would prefer a regime even stronger than ACTA. This chapter provides a portrait of the Australian debate over ACTA. It is the account of an interested participant in the policy proceedings. This chapter will first consider the deliberations and recommendations of the Joint Standing Committee on Treaties on ACTA. Second, there was a concern that ACTA had failed to provide appropriate safeguards with respect to civil liberties, human rights, consumer protection and privacy laws. Third, there was a concern about the lack of balance in the treaty’s copyright measures; the definition of piracy is overbroad; the suite of civil remedies, criminal offences and border measures is excessive; and there is a lack of suitable protection for copyright exceptions, limitations and remedies. Fourth, there was a worry that the provisions on trademark law, intermediary liability and counterfeiting could have an adverse impact upon consumer interests, competition policy and innovation in the digital economy. Fifth, there was significant debate about the impact of ACTA on pharmaceutical drugs, access to essential medicines and health-care. Sixth, there was concern over the lobbying by tobacco industries for ACTA – particularly given Australia’s leadership on tobacco control and the plain packaging of tobacco products. Seventh, there were concerns about the operation of border measures in ACTA. Eighth, the Joint Standing Committee on Treaties was concerned about the jurisdiction of the ACTA Committee, and the treaty’s protean nature. Finally, the chapter raises fundamental issues about the relationship between the executive and the Australian Parliament with respect to treaty-making. There is a need to reconsider the efficacy of the Trick or Treaty reforms passed by the Australian Parliament in the 1990s.

Essays on macroeconomic effects of fiscal policy rules

Economic and Monetary Union can be characterised as a complicated set of legislation and institutions governing monetary and fiscal responsibilities. The measures of fiscal responsibility are to be guided by the Stability and Growth Pact, which sets rules for fiscal policy and makes a discretionary fiscal policy virtually impossible. To analyse the effects of the fiscal and monetary policy mix, we modified the New Keynesian framework to allow for supply effects of fiscal policy. We show that defining a supply-side channel for fiscal policy using an endogenous output gap changes the stabilising properties of monetary policy rules. The stability conditions are affected by fiscal policy, so that the dichotomy between active (passive) monetary policy and passive (active) fiscal policy as stabilising regimes does not hold, and it is possible to have an active monetary - active fiscal policy regime consistent with dynamical stability of the economy. We show that, if we take supply-side effects into ac-count, we get more persistent inflation and output reactions. We also show that the dichotomy does not hold for a variety of different fiscal policy rules based on government debt and budget deficit, using the tax smoothing hypothesis and formulating the tax rules as difference equations. The debt rule with active monetary policy results in indeterminacy, while the deficit rule produces a determinate solution with active monetary policy, even with active fiscal policy. The combination of fiscal requirements in a rule results in cyclical responses to shocks. The amplitude of the cycle is larger with more weight on debt than on deficit. Combining optimised monetary policy with fiscal policy rules means that, under a discretionary monetary policy, the fiscal policy regime affects the size of the inflation bias. We also show that commitment to an optimal monetary policy not only corrects the inflation bias but also increases the persistence of output reactions. With fiscal policy rules based on the deficit we can retain the tax smoothing hypothesis also in a sticky price model.

Region Based Structure Layout Optimization by Selective Data Copying

As the gap between processor and memory continues to grow Memory performance becomes a key performance bottleneck for many applications. Compilers therefore increasingly seek to modify an application’s data layout to improve cache locality and cache reuse. Whole program Structure Layout [WPSL] transformations can significantly increase the spatial locality of data and reduce the runtime of programs that use link-based data structures, by increasing the cache line utilization. However, in production compilers WPSL transformations do not realize the entire performance potential possible due to a number of factors. Structure layout decisions made on the basis of whole program aggregated affinity/hotness of structure fields, can be sub optimal for local code regions. WPSL is also restricted in applicability in production compilers for type unsafe languages like C/C++ due to the extensive legality checks and field sensitive pointer analysis required over the entire application. In order to overcome the issues associated with WPSL, we propose Region Based Structure Layout (RBSL) optimization framework, using selective data copying. We describe our RBSL framework, implemented in the production compiler for C/C++ on HP-UX IA-64. We show that acting in complement to the existing and mature WPSL transformation framework in our compiler, RBSL improves application performance in pointer intensive SPEC benchmarks ranging from 3% to 28% over WPSL

Two-level Mapping Based Cache Index Selection for Packet Forwarding Engines

Packet forwarding is a memory-intensive application requiring multiple accesses through a trie structure. The efficiency of a cache for this application critically depends on the placement function to reduce conflict misses. Traditional placement functions use a one-level mapping that naively partitions trie-nodes into cache sets. However, as a significant percentage of trie nodes are not useful, these schemes suffer from a non-uniform distribution of useful nodes to sets. This in turn results in increased conflict misses. Newer organizations such as variable associativity caches achieve flexibility in placement at the expense of increased hit-latency. This makes them unsuitable for L1 caches.We propose a novel two-level mapping framework that retains the hit-latency of one-level mapping yet incurs fewer conflict misses. This is achieved by introducing a secondlevel mapping which reorganizes the nodes in the naive initial partitions into refined partitions with near-uniform distribution of nodes. Further as this remapping is accomplished by simply adapting the index bits to a given routing table the hit-latency is not affected. We propose three new schemes which result in up to 16% reduction in the number of misses and 13% speedup in memory access time. In comparison, an XOR-based placement scheme known to perform extremely well for general purpose architectures, can obtain up to 2% speedup in memory access time.

Making STMs Cache Friendly with Compiler Transformations

Software transactional memory (STM) is a promising programming paradigm for shared memory multithreaded programs. In order for STMs to be adopted widely for performance critical software, understanding and improving the cache performance of applications running on STM becomes increasingly crucial, as the performance gap between processor and memory continues to grow. In this paper, we present the most detailed experimental evaluation to date, of the cache behavior of STM applications and quantify the impact of the different STM factors on the cache misses experienced by the applications. We find that STMs are not cache friendly, with the data cache stall cycles contributing to more than 50% of the execution cycles in a majority of the benchmarks. We find that on an average, misses occurring inside the STM account for 62% of total data cache miss latency cycles experienced by the applications and the cache performance is impacted adversely due to certain inherent characteristics of the STM itself. The above observations motivate us to propose a set of specific compiler transformations targeted at making the STMs cache friendly. We find that STM's fine grained and application unaware locking is a major contributor to its poor cache behavior. Hence we propose selective Lock Data co-location (LDC) and Redundant Lock Access Removal (RLAR) to address the lock access misses. We find that even transactions that are completely disjoint access parallel, suffer from costly coherence misses caused by the centralized global time stamp updates and hence we propose the Selective Per-Partition Time Stamp (SPTS) transformation to address this. We show that our transformations are effective in improving the cache behavior of STM applications by reducing the data cache miss latency by 20.15% to 37.14% and improving execution time by 18.32% to 33.12% in five of the 8 STAMP applications.

Row-buffer reorganization: simultaneously improving performance and reducing energy in DRAMs

In this paper, based on the temporal and spatial locality characteristics of memory accesses in multicores, we propose a re-organization of the existing single large row buffer in a DRAM bank into multiple smaller row-buffers. The proposed configuration helps improve the row hit rates and also brings down the energy required for row-activations. The major contribution of this work is proposing such a reorganization without requiring any significant changes to the existing widely accepted DRAM specifications. Our proposed reorganization improves performance by 35.8%, 14.5% and 21.6% in quad, eight and sixteen core workloads along with a 42%, 28% and 31% reduction in DRAM energy. Additionally, we introduce a Need Based Allocation scheme for buffer management that shows additional performance improvement.

Fast and efficient automatic memory management for GPUs using compiler-assisted runtime coherence scheme

Exploiting the performance potential of GPUs requires managing the data transfers to and from them efficiently which is an error-prone and tedious task. In this paper, we develop a software coherence mechanism to fully automate all data transfers between the CPU and GPU without any assistance from the programmer. Our mechanism uses compiler analysis to identify potential stale accesses and uses a runtime to initiate transfers as necessary. This allows us to avoid redundant transfers that are exhibited by all other existing automatic memory management proposals. We integrate our automatic memory manager into the X10 compiler and runtime, and find that it not only results in smaller and simpler programs, but also eliminates redundant memory transfers. Tested on eight programs ported from the Rodinia benchmark suite it achieves (i) a 1.06x speedup over hand-tuned manual memory management, and (ii) a 1.29x speedup over another recently proposed compiler--runtime automatic memory management system. Compared to other existing runtime-only and compiler-only proposals, it also transfers 2.2x to 13.3x less data on average.

Generating Efficient Data Movement Code for Heterogeneous Architectures with Distributed-Memory

Programming for parallel architectures that do not have a shared address space is extremely difficult due to the need for explicit communication between memories of different compute devices. A heterogeneous system with CPUs and multiple GPUs, or a distributed-memory cluster are examples of such systems. Past works that try to automate data movement for distributed-memory architectures can lead to excessive redundant communication. In this paper, we propose an automatic data movement scheme that minimizes the volume of communication between compute devices in heterogeneous and distributed-memory systems. We show that by partitioning data dependences in a particular non-trivial way, one can generate data movement code that results in the minimum volume for a vast majority of cases. The techniques are applicable to any sequence of affine loop nests and works on top of any choice of loop transformations, parallelization, and computation placement. The data movement code generated minimizes the volume of communication for a particular configuration of these. We use a combination of powerful static analyses relying on the polyhedral compiler framework and lightweight runtime routines they generate, to build a source-to-source transformation tool that automatically generates communication code. We demonstrate that the tool is scalable and leads to substantial gains in efficiency. On a heterogeneous system, the communication volume is reduced by a factor of 11X to 83X over state-of-the-art, translating into a mean execution time speedup of 1.53X. On a distributed-memory cluster, our scheme reduces the communication volume by a factor of 1.4X to 63.5X over state-of-the-art, resulting in a mean speedup of 1.55X. In addition, our scheme yields a mean speedup of 2.19X over hand-optimized UPC codes.

Parallel Flow-Sensitive Pointer Analysis by Graph-Rewriting

Precise pointer analysis is a problem of interest to both the compiler and the program verification community. Flow-sensitivity is an important dimension of pointer analysis that affects the precision of the final result computed. Scaling flow-sensitive pointer analysis to millions of lines of code is a major challenge. Recently, staged flow-sensitive pointer analysis has been proposed, which exploits a sparse representation of program code created by staged analysis. In this paper we formulate the staged flow-sensitive pointer analysis as a graph-rewriting problem. Graph-rewriting has already been used for flow-insensitive analysis. However, formulating flow-sensitive pointer analysis as a graph-rewriting problem adds additional challenges due to the nature of flow-sensitivity. We implement our parallel algorithm using Intel Threading Building Blocks and demonstrate considerable scaling (upto 2.6x) for 8 threads on a set of 10 benchmarks. Compared to the sequential implementation of staged flow-sensitive analysis, a single threaded execution of our implementation performs better in 8 of the benchmarks.