Applying an abstract data structure description approach to parallelizing scientific pointer programs

Even though impressive progress has been made in the area of parallelizing scientific programs with arrays, the application of similar techniques to programs with pointer data structures has remained difficult. Unlike arrays which have a small number of well-defined properties that can be utilized by a parallelizing compiler, pointer data structures are used to implement a wide variety of structures that exhibit a much more diverse set of properties. The complexity and diversity of such properties means that, in general, scientific programs with pointer data structures cannot be effectively analyzed by an optimizing and parallelizing compiler.In order to provide a system in which the compiler can fully utilize the properties of different types of pointer data structures, we have developed a mechanism for the Abstract Description of Data Structures (ADDS). With our approach, the programmer can explicitly describe important properties such as dimensionality of the pointer data structure, independence of dimensions, and direction of traversal. These abstract descriptions of pointer data structures are then used by the compiler to guide analysis, optimization, and parallelization.In this paper we summarize the ADDS approach through the use of numerous examples of data structures used in scientific computations, we illustrate how such declarations are natural and non-tedious to specify, and we show how the ADDS declarations can be used to improve compile-time analysis. In order to demonstrate the viability of our approach, we show how such techniques can be used to parallelize an important class of scientific codes which naturally use recursive pointer data structures. In particular, we use our approach to develop the parallelization of an N-body simulation that is based on a relatively complicated pointer data structure, and we report the speedup results for a Sequent multiprocessor

Bio-Inspired Materials for Electrochemical Sensors

Electrochemical biosensors are a rapidly growing research area that has greatly improved its specificity, accuracy, and precision in the detection of biomolecules in contemporary literature and industry alike. Typically, these systems exist in a three-electrode conformation with a working electrode functioning as the anode, a counter electrode functioning as the cathode, and a reference electrode allowing for the control of potential in the system. The method by which these sensors work is through the sharing of electrons via redox reactions with the target molecule and the working electrode or modifications on its surface. By exploiting the function of biomaterials that participate in natural substrate-binding redox phenomena, new opportunities for detecting critical molecules in complex situations can be created. In this dissertation, three distinct electrochemical biosensors were created by mimicking natural phenomena and implementing materials that directly or indirectly participate in the corresponding reactions. First, a dopamine sensor was created via a composite of lignin-derived graphene oxide and the marine algae-derived polysaccharide kappa carrageenan. Different ratios of GO, a known electrooxidizing catalyst of dopamine, with kappa carrageenan were used to create a binder-free film for dropcasting on the working electrode. It was designed on the principle of its interactions with the nervous system when injected in rats to induce analgesia, interfering with standard dopamine behavior. The system demonstrated a linear range of 1 - 250 μmol L-1 and a limit of detection of 0.14 μmol L-1 (s/n=3). In the second chapter, a sensor for the human and animal health hazard nitrite was constructed using the transition metal sulfide NiS. Transition metal sulfides are the catalytic center for nitrite oxidation to nitrate in nitrogen fixing bacteria found in the environment. This section utilized a novel electrodeposition method for creating a binderfree layer of NiS on the surface of the glassy carbon electrode. This system demonstrated a linear range of 0.04 – 1 μM, 1 – 5.3 μM and a detection limit of 0.01 μM. For the final chapter, a novel sensor was created for the cryoprotective sugar trehalose, an indicator of bacterial contamination in meat and produce without any electrochemical assay precedent. This system utilized the interactions found between alkali earth metal ions and trehalose in which the two molecules form complexes. Magnesium phthalocyanine, which is a commercially available dye, as well as synthesized magnesium tetraphenylporphyrin and calcium tetraphenylporphyrin were implemented as drop-casted coatings on the working electrode to electrodeposit trehalose on the surface and detect its oxidation via squarewave anodic stripping voltammetry in the complex media Luria-Bertani broth. The system was also used to gauge fluctuations in E. coli in broth by autoclaving the cultures and directly testing the media containing lysed bacteria. The system demonstrated a linear range of 0.25 mM – 100 mM, with magnesium mesotetraphenylporphyrin exhibiting the highest repeatability

Community Resilience Management : Reflections and Strategies from Corporate Sustainability

Creating community resilience is a daunting task, both in scope and application, therefore it is useful to examine related efforts to inform our strategy. Sustainability, specifically corporate sustainability, has developed through similar challenges and provides insight into the possible trajectory of community resilience management. We find that both concepts reflect similar origins, developmental paths and merging goals at a scale that can be systematically managed. Therefore, we describe four strategies from corporate sustainability management that can be applied to community resilience 1) consider the community context while implementing an increasingly broad view of responsibility; 2) integrate and engage across constructs; 3) employ strategic approaches including performance measurement and assessment of progress; 4) communicate with and engage stakeholders; In doing this, we can leverage our efforts, experience, and successes to transform scorecards into strategies, programs into processes, results into sustained performance and engagement into capable, robust and resilient communities

Tidally-Triggered Star Formation in Close Pairs of Galaxies

We analyze new optical spectra of a sample of 502 galaxies in close pairs and n-tuples, separated by <= 50/h kpc. We extracted the sample objectively from the CfA2 redshift survey, without regard to the surroundings of the tight systems. We probe the relationship between star formation and the dynamics of the systems of galaxies. The equivalent widths of H\alpha (EW(H\alpha) and other emission lines anti-correlate strongly with pair spatial separation (\Delta D) and velocity separation. We use the measured EW(H\alpha) and the starburst models of Leitherer et al. to estimate the time since the most recent burst of star for- mation began for each galaxy. In the absence of a large contribution from an old stellar population to the continuum around H\alpha, the observed \Delta D -- EW(H\alpha) correlation signifies that starbursts with larger separations on the sky are, on average, older. By matching the dynamical timescale to the burst timescale, we show that the data support a simple picture in which a close pass initiates a starburst; EW(H\alpha) decreases with time as the pair separation increases, accounting for the anti-correlation. This picture leads to a method for measuring the duration and the initial mass function of interaction-induced starbursts: our data are compatible with the starburst and orbit models in many respects, as long as the starburst lasts longer than \sim10^8 years and the delay between the close pass and the initiation of the starburst is less than a few \times 10^7 years. If there is no large contribution from an old stellar population to the continuum around H\alpha the Miller-Scalo and cutoff (M <= 30 M_\sun) Salpeter initial mass functions fit the data much better than a standard Salpeter IMF. (Abridged.)Comment: 43 pages, 22 figures, to appear in the ApJ; we correct an error which had minor effects on numerical values in the pape

B cell, CD8 + T cell and gamma delta T cell infiltration alters alveolar immune cell homeostasis in HIV-infected Malawian adults

HIV infection is associated with increased risk to lower respiratory tract infections (LRTI). However, the impact of HIV infection on immune cell populations in the lung is not well defined. We sought to comprehensively characterise the impact of HIV infection on immune cell populations in the lung. : Twenty HIV-uninfected controls and 17 HIV-1 infected ART-naïve adults were recruited from Queen Elizabeth Central Hospital, Malawi. Immunophenotyping of lymphocyte and myeloid cell populations was done on bronchoalveolar lavage fluid and peripheral blood cells. : We found that the numbers of CD8 T cells, B cells and gamma delta T cells were higher in BAL fluid of HIV-infected adults compared to HIV-uninfected controls (all p<0.05). In contrast, there was no difference in the numbers of alveolar CD4 T cells in HIV-infected adults compared to HIV-uninfected controls (p=0.7065). Intermediate monocytes were the predominant monocyte subset in BAL fluid (HIV-, 63%; HIV+ 81%), while the numbers of classical monocytes was lower in HIV-infected individuals compared to HIV-uninfected adults (p=0.0006). The proportions of alveolar macrophages and myeloid dendritic cells was lower in HIV-infected adults compared to HIV-uninfected controls (all p<0.05). : Chronic HIV infection is associated with broad alteration of immune cell populations in the lung, but does not lead to massive depletion of alveolar CD4 T cells. Disruption of alveolar immune cell homeostasis likely explains in part the susceptibility for LRTIs in HIV-infected adults