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

Study Protocol: A Randomized Controlled Trial of Patient Navigation-Activation to Reduce Cancer Health Disparities

Abstract Background Cancer health disparities affecting low-income and minority patients are well documented. Root-causes are multifactorial, including diagnostic and treatment delays, social and financial barriers, and poor communication. Patient navigation and communication coaching (activation) are potential interventions to address disparities in cancer treatment. The purpose of this clinical trial is to test the effectiveness of an intervention combining patient navigation and activation to improve cancer treatment. Methods/Design The Rochester Patient Navigation Research Program (PNRP) is a National Cancer Institute-sponsored, patient-level randomized trial (RCT) of patient navigation and activation, targeting newly-diagnosed breast and colorectal cancer patients in Rochester, NY. The goal of the program is to decrease cancer health disparities by addressing barriers to receipt of cancer care and promoting patient self-efficacy. The intervention uses trained, paraprofessional patient navigators recruited from the target community, and a detailed training and supervisory program. Recruited patients are randomly assigned to receive either usual care (except for baseline and follow-up questionnaires and interviews) or intervention. The intervention patients receive tailored assistance from their patient navigators, including phone calls, in-person meetings, and behind-the-scenes coordination of care. A total of 344 patients have been recruited. Outcomes measured at three month intervals include timeliness of care, patient adherence, patient satisfaction, quality of life, self-efficacy, health literacy, and cancer knowledge. Discussion This unique intervention combining patient navigation and patient activation is designed to address the multifactorial problem of cancer health disparities. If successful, this study will affect the design and implementation of patient navigation programs. Trials Registration clinicaltrials.gov identifier NCT00496678http://deepblue.lib.umich.edu/bitstream/2027.42/78254/1/1471-2407-10-551.xmlhttp://deepblue.lib.umich.edu/bitstream/2027.42/78254/2/1471-2407-10-551.pdfPeer Reviewe

Recycling of Pretreated Polyolefin-Based Ocean-Bound Plastic Waste by Incorporating Clay and Rubber

Plastic waste found in oceans has become a major concern because of its impact on marine organisms and human health. There is significant global interest in recycling these materials, but their reclamation, sorting, cleaning, and reprocessing, along with the degradation that occurs in the natural environment, all make it difficult to achieve high quality recycled resins from ocean plastic waste. To mitigate these limitations, various additives including clay and rubber were explored. In this study, we compounded different types of ocean-bound (o-HDPE and o-PP) and virgin polymers (v-LDPE and v-PS) with various additives including a functionalized clay, styrene-multi-block-copolymer (SMB), and ethylene-propylene-based rubber (EPR). Physical observation showed that all blends containing PS were brittle due to the weak interfaces between the polyolefin regions and the PS domains within the polymer blend matrix. Blends containing clay showed rough surfaces and brittleness because of the non-uniform distribution of clay particles in the polymer matrix. To evaluate the properties and compatibility of the blends, characterizations using differential scanning calorimetry (DSC), scanning electron microscopy (SEM), and small-amplitude oscillatory shear (SAOS) rheology were carried out. The polymer blend (v-LDPE, o-HDPE, o-PP) containing EPR showed improved elasticity. Incorporating additives such as rubber could improve the mechanical properties of polymer blends for recycling purposes

Design and fabrication of plasmonic cavities for magneto-optical sensing (article)

This is the author accepted manuscript. The final version is available from AIP Publishing via the DOI in this record.The dataset associated with this article is located in ORE at: http://hdl.handle.net/10871/32604The design and fabrication of a novel plasmonic cavity, intended to allow far-field recovery of signals arising from near field magneto-optical interactions, is presented. Finite element modeling is used to describe the interaction between a gold film, containing cross-shaped cavities, with a nearby magnetic under-layer. The modeling revealed strong electric field confinement near the center of the cross structure for certain optical wavelengths, which may be tuned by varying the length of the cross through a range that is compatible with available fabrication techniques. Furthermore, the magneto optical Kerr effect (MOKE) response of the composite structure can be enhanced with respect to that of the bare magnetic film. To confirm these findings, cavities were milled within gold films deposited upon a soluble film, allowing relocation to a ferromagnetic film using a float transfer technique. Cross cavity arrays were fabricated and characterized by optical transmission spectroscopy prior to floating, revealing resonances at optical wavelengths in good agreement with the finite element modeling. Following transfer to the magnetic film, circular test apertures within the gold film yielded clear magneto-optical signals even for diameters within the sub-wavelength regime. However, no magneto-optical signal was observed for the cross cavity arrays, since the FIB milling process was found to produce nanotube structures within the soluble under-layer that adhered to the gold. Further optimization of the fabrication process should allow recovery of magneto-optical signal from cross cavity structures.Financial support from the UK Engineering and Physical Science Research Council (EPSRC) grants EP/1038470/I and EP/1038411/1 is gratefully acknowledged. We also acknowledge the support of Seagate Technology (Ireland) under SOW 00077300.0. RMB contribution to project was supported by the Royal Academy of Engineering under the Research Chairs and Senior Research Fellowships Scheme

The Grizzly, November 5, 1982

Clinic Offered for Ski-Bums • Outstanding Choral Students Chosen • U.C. Poses for Posterity • Letters to the Editor: Greeks Piqued • USGA Notes • President\u27s Corner • Ropes and Chains or Can You Eat Plasterboard? • Protheatre Presents Comedy at its Best • The Messiah is Coming! • The World\u27s Largest Picture at Ursinus: Get Yours Now! • Take That, West Chester! • Soccer Season Ends With Win Over Widener • Bear Pack Waltzes to Victory • Bears Battle But Lose War • Lady Bears Dominatehttps://digitalcommons.ursinus.edu/grizzlynews/1087/thumbnail.jp

Building, scaling, and sustaining a learning health system for surgical quality improvement: A toolkit

This article describes how to start, replicate, scale, and sustain a learning health system for quality improvement, based on the experience of the Michigan Surgical Quality Collaborative (MSQC). The key components to operationalize a successful collaborative improvement infrastructure and the features of a learning health system are explained. This information is designed to guide others who desire to implement quality improvement interventions across a regional network of hospitals using a collaborative approach. A toolkit is provided (under Supporting Information) with practical information for implementation.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/156156/3/lrh210215.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/156156/2/lrh210215-sup-0001-supinfo.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/156156/1/lrh210215_am.pd

"The non-ischemic repair" as a safe alternative method for repair of anterior post-infarction VSD

Patient's myocardium with post-infarction ventricular septum defect (VSD) is characterized by severe dysfunction. The "additive ischemia" caused by the operating process of cross-clamp ischemia and reperfusion injury, has a significant aggravation to the myocardium and overall negative impact to patient's outcome. We present a useful, safe and advantageous methodology in order to abolish "the toxic phase" of ischemia-reperfusion which is adopted by most as the "classic repair method" of myocardial protection. This abolition is in our opinion, particularly beneficial in order to reverse postoperatively the Low Cardiac Output Syndrome (LOS) and achieve better short and long term results. By using this method we avoid the aortic occlusion, the use of systematic hypothermia and any cardioplegic arrest. Furthermore, the total cardio-pulmonary bypass (CPB) time is significantly reduced, tissue debridement and stitching is much easier and safer. We think the method is applicable for every anterior and apical case of post-infarction septum rupture. After application of method in 3 patients with anterior post-myocardial infarction VSD, we are convinced that the patient will have a better postoperative haemodynamic condition and therefore a better outcome

Intruder to the Sanctorum: Sub-Nuclear Localization and Interaction of Cytolethal Distending Toxins in Host Cells

Bacterial toxins constitute a broad class of enzymes with the capability of targeting hosts to its advantage. Exploring the relationship between pathogen and host has led to the understanding of many mechanistic aspects that bacterial effectors exploit to manipulate the host cellular machinery. A unique class of bacterial exotoxins called Cytolethal Distending Toxins (CDT), target the host genome resulting in DNA damage. CDT is secreted by many bacteria such as Escherichia coli, Campylobacter jejuni, Salmonella typhi, and Haemophilus ducreyi that persist with high frequency amongst mucocutaneous niches. Uptake of CTDs are dependent on its structural components as a hetero-tripartite toxin with a CdtA and CdtC subunit necessary for binding and delivery of the catalytic CdtB subunit into the host cell. To elicit physiological effects, CDT traffics to the host nucleus upon uptake and causes DNA damage. However, little is known about CDTs nuclear actions that allow it to incur a host response. It is likely that CDT associates with a host factor within the nucleus to induce DNA damage. Our aim is to identify an interaction between CDT and a host factor necessary to invoke DNA damage. Thus far, we have demonstrated that CDT colocalizes to interchromatin granule clusters. To further analyze this interaction, we will conduct immunoblot analysis and subnuclear fractionation techniques. Understanding the localization and mechanism of CDT necessary for inducing a host cellular response will not only help us to better understand genotoxins, but also allow us to explore the interactions of host factors within minimally characterized nuclear compartments.NIH – AI059095, GM098756Ope

Faecal and Urinary Incontinence after Multimodality Treatment of Rectal Cancer

Marilyne Lange and Cornelis van de Velde discuss the differential diagnosis and management of incontinence after rectal cancer treatment