Memory Access Optimizations for High-Performance Computing

This paper discusses the importance of memory access optimizations which are shown to be highly effective on the MasPar architecture. The study is based on two MasPar machines, a 16K-processor MP-1 and a 4K-processor MP-2. A software pipelining technique overlaps memory accesses with computation and/or communication. Another optimization, called the register window technique reduces the number of loads in a loop. These techniques are evaluated using three parallel matrix multiplication algorithms on both the MasPar machines. The matrix multiplication study shows that for a highly computation intensive problem, reducing the interprocessor communication can become a secondary issue compared to memory access optimization. Also, it is shown that memory access optimizations can play a more important role than the choice of a superior parallel algorithm. Keywords: load/store architecture, memory accesses, matrix multiplication, parallel programming

Chronic alcohol ingestion exacerbates skeletal muscle myopathy in HIV-1 transgenic rats

<p>Abstract</p> <p>Background</p> <p>Separately, chronic alcohol ingestion and HIV-1 infection are associated with severe skeletal muscle derangements, including atrophy and wasting, weakness, and fatigue. One prospective cohort study reported that 41% of HIV-infected patients met the criteria for alcoholism, however; few reports exist on the co-morbid effects of these two disease processes on skeletal muscle homeostasis. Thus, we analyzed the atrophic effects of chronic alcohol ingestion in HIV-1 transgenic rats and identified alterations to several catabolic and anabolic factors.</p> <p>Findings</p> <p>Relative plantaris mass, total protein content, and fiber cross-sectional area were reduced in each experimental group compared to healthy, control-fed rats. Alcohol abuse further reduced plantaris fiber area in HIV-1 transgenic rats. Consistent with previous reports, gene levels of myostatin and its receptor activin IIB were not increased in HIV-1 transgenic rat muscle. However, myostatin and activin IIB were induced in healthy and HIV-1 transgenic rats fed alcohol for 12 weeks. Catabolic signaling factors such as TGFβ₁, TNFα, and phospho-p38/total-p38 were increased in all groups compared to controls. There was no effect on IL-6, leukemia inhibitory factor (LIF), cardiotrophin-1 (CT-1), or ciliary neurotrophic factor (CNTF) in control-fed, transgenic rats. However, the co-morbidity of chronic alcohol abuse and HIV-1-related protein expression decreased expression of the two anabolic factors, CT-1 and CNTF.</p> <p>Conclusions</p> <p>Consistent with previous reports, alcohol abuse accentuated skeletal muscle atrophy in an animal model of HIV/AIDS. While some catabolic pathways known to drive alcoholic or HIV-1-associated myopathies were also elevated in this co-morbid model (e.g., TGFβ₁), consistent expression patterns were not apparent. Thus, specific alterations to signaling mechanisms such as the induction of the myostatin/activin IIB system or reductions in growth factor signaling via CT-1- and CNTF-dependent mechanisms may play larger roles in the regulation of muscle mass in alcoholic, HIV-1 models.</p

Predicting youth participation in urban agriculture in Malaysia: insights from the theory of planned behavior and the functional approach to volunteer motivation

This study examines factors associated with the decision of Malaysian youth to participate in a voluntary urban agriculture program. Urban agriculture has generated significant interest in developing countries to address concerns over food security, growing urbanization and employment. While an abundance of data shows attracting the participation of young people in traditional agriculture has become a challenge for many countries, few empirical studies have been conducted on youth motivation to participate in urban agriculture programs, particularly in non-Western settings. Drawing on the theories of planned behavior and the functional approach to volunteer motivation, we surveyed 890 students from a public university in Malaysia about their intention to join a new urban agriculture program. Hierarchical regression findings indicated that the strongest predictor of participation was students’ attitude toward urban agriculture, followed by subjective norms, career motives and perceived barriers to participation. The findings from this study may provide useful information to the university program planners in Malaysia in identifying mechanisms for future students’ involvement in the program

Comparison of Proteomic Assessment Methods in Multiple Cohort Studies

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/155922/1/pmic13292_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/155922/2/pmic13292.pd

Melanoma Patients with Positive Sentinel Nodes Who Did Not Undergo Completion Lymphadenectomy: A Multi-Institutional Study

Completion lymph node dissection (CLND) is considered the standard of care in melanoma patients found to have sentinel lymph node (SLN) metastasis. However, the therapeutic utility of CLND is not known. The natural history of patients with positive SLNs who do not undergo CLND is undefined. This multi-institutional study was undertaken to characterize patterns of failure and survival rates in these patients and to compare results with those of positive-SLN patients who underwent CLND.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/45875/1/10434_2006_Article_10237.pd

Memory Access Optimizations for High-Performance Computing

This paper discusses the importance of memory access optimizations which are shown to be highly effective on the MasPar architecture. The study is based on two MasPar machines, a 16K-processor MP-1 and a 4K-processor MP-2. A software pipelining technique overlaps memory accesses with computation and/or communication. Another optimization, called the register window technique reduces the number of loads in a loop. These techniques are evaluated using three parallel matrix multiplication algorithms on both the MasPar machines. The matrix multiplication study shows that for a highly computation intensive problem, reducing the interprocessor communication can become a secondary issue compared to memory access optimization. Also, it is shown that memory access optimizations can play a more important role than the choice of a superior parallel algorithm. Keywords: load/store architecture, memory accesses, matrix multiplication, parallel programming.</p

Chronic alcohol ingestion delays skeletal muscle regeneration following injury

Background: Chronic alcohol ingestion may cause severe biochemical and pathophysiological derangements to skeletal muscle. Unfortunately, these alcohol-induced events may also prime skeletal muscle for worsened, delayed, or possibly incomplete repair following acute injury. As alcoholics may be at increased risk for skeletal muscle injury, our goals were to identify the effects of chronic alcohol ingestion on components of skeletal muscle regeneration. To accomplish this, age- and gender-matched C57Bl/6 mice were provided normal drinking water or water that contained 20% alcohol (v/v) for 18–20 wk. Subgroups of mice were injected with a 1.2% barium chloride (BaCl2) solution into the tibialis anterior (TA) muscle to initiate degeneration and regeneration processes. Body weights and voluntary wheel running distances were recorded during the course of recovery. Muscles were harvested at 2, 7 or 14 days post-injection and assessed for markers of inflammation and oxidant stress, fiber cross-sectional areas, levels of growth and fibrotic factors, and fibrosis. Results: Body weights of injured, alcohol-fed mice were reduced during the first week of recovery. These mice also ran significantly shorter distances over the two weeks following injury compared to uninjured, alcoholics. Injured TA muscles from alcohol-fed mice had increased TNFα and IL6 gene levels compared to controls 2 days after injury. Total protein oxidant stress and alterations to glutathione homeostasis were also evident at 7 and 14 days after injury. Ciliary neurotrophic factor (CNTF) induction was delayed in injured muscles from alcohol-fed mice which may explain, in part, why fiber cross-sectional area failed to normalize 14 days following injury. Gene levels of TGFβ1 were induced early following injury before normalizing in muscle from alcohol-fed mice compared to controls. However, TGFβ1 protein content was consistently elevated in injured muscle regardless of diet. Fibrosis was increased in injured, muscle from alcohol-fed mice at 7 and 14 days of recovery compared to injured controls. Conclusions: Chronic alcohol ingestion appears to delay the normal regenerative response following significant skeletal muscle injury. This is evidenced by reduced cross-sectional areas of regenerated fibers, increased fibrosis, and altered temporal expression of well-described growth and fibrotic factors

Parametric Micro-level Performance Models for Parallel Computing

Parametric micro-level (PM) performance models are introduced to address the important issue of how to realistically model parallel performance. These models can be used to predict execution times, identify performance bottlenecks, and compare machines. The accurate prediction and analysis of execution times is achieved by incorporating precise details of interprocessor communication, memory operations, auxiliary instructions, and effects of communication and computation schedules. Parameters are used for flexibility to study various algorithmic and architectural issues. The development and verification process, parameters and the scope of applicability of these models are discussed. A coherent view of performance is obtained from the execution profiles generated by PM models. The models are targeted at a large class numerical algorithms commonly implemented on both SIMD and MIMD machines. Specific models are presented for matrix multiplication, LU decomposition, and FFT on a 2-D proce..