Towards Efficient Execution of MPI Applications on the Grid: Porting and Optimization Issues

The message passing interface (MPI) is a standard used by many parallel scientific applications. It offers the advantage of a smoother migration path for porting applications from high performance computing systems to the Grid. In this paper Grid-enabled tools and libraries for developing MPI applications are presented. The first is MARMOT, a tool that checks the adherence of an application to the MPI standard. The second is PACX-MPI, an implementation of the MPI standard optimized for Grid environments. Besides the efficient development of the program, an optimal execution is of paramount importance for most scientific applications. We therefore discuss not only performance on the level of the MPI library, but also several application specific optimizations, e.g., for a sparse, parallel equation solver and an RNA folding code, like latency hiding, prefetching, caching and topology-aware algorithms.     

Quantum Computer Development with Single Ion Implantation

Spins of single donor atoms are attractive candidates for large scale quantum information processing in silicon. Formation of devices with a few qubits is crucial for validation of basic ideas and development of a scalable architecture. We describe our development of a single ion implantation technique for placement of single atoms into device structures. Collimated highly charged ion beams are aligned with a scanning probe microscope. Enhanced secondary electron emission due tohigh ion charge states (e.g., ³¹P¹³⁺, or ¹²⁶Te³³⁺)allows efficient detection of single ion impacts. Studies of electrical activation of low dose, low energy implants of ³¹P in silicon show a drastic effect of dopant segregation to the SiO₂/Si interface,while Si₃N₄/Si retards ³¹P segregation. We discuss resolution limiting factors in ion placement, and process challenges forintegration of single atom arrays with control gates and single electron transistors. PACS: 03.67.Lx, 34.50.Dy, 85.35.Gv, 73.23, 61.72, 86.40.py, 07.79.-v     

Opaganib Protects against Radiation Toxicity: Implications for Homeland Security and Antitumor Radiotherapy

Exposure to ionizing radiation (IR) is a lingering threat from accidental or terroristic nuclear events, but is also widely used in cancer therapy. In both cases, host inflammatory responses to IR damage normal tissue causing morbidity and possibly mortality to the victim/patient. Opaganib, a first-in-class inhibitor of sphingolipid metabolism, has broad anti-inflammatory and anticancer activity. Opaganib elevates ceramide and reduces sphingosine 1-phosphate (S1P) in cells, conditions that increase the antitumor efficacy of radiation while concomitantly suppressing inflammatory damage to normal tissue. Therefore, opaganib may suppress toxicity from unintended IR exposure and improve patient response to chemoradiation. To test these hypotheses, we first examined the effects of opaganib on the toxicity and antitumor activity of radiation in mice exposed to total body irradiation (TBI) or IR with partial bone marrow shielding. Oral treatment with opaganib 2 h before TBI shifted the LD₇₅ from 9.5 Gy to 11.5 Gy, and provided substantial protection against gastrointestinal damage associated with suppression of radiation-induced elevations of S1P and TNFα in the small intestines. In the partially shielded model, opaganib provided dose-dependent survival advantages when administered 4 h before or 24 h after radiation exposure, and was particularly effective when given both prior to and following radiation. Relevant to cancer radiotherapy, opaganib decreased the sensitivity of IEC6 (non-transformed mouse intestinal epithelial) cells to radiation, while sensitizing PAN02 cells to in vitro radiation. Next, the in vivo effects of opaganib in combination with radiation were examined in a syngeneic tumor model consisting of C57BL/6 mice bearing xenografts of PAN02 pancreatic cancer cells and a cross-species xenograft model consisting of nude mice bearing xenografts of human FaDu cells. Mice were treated with opaganib and/or IR (plus cisplatin in the case of FaDu tumors). In both tumor models, the optimal suppression of tumor growth was attained by the combination of opaganib with IR (± cisplatin). Overall, opaganib substantially protects normal tissue from radiation damage that may occur through unintended exposure or cancer radiotherapy.     

Noise peaks influence communication in the operating room. An observational study

Noise peaks are powerful distractors. This study focuses on the impact of noise peaks on surgical teams’ communication during 109 long abdominal surgeries. We related measured noise peaks during 5-min intervals to the amount of observed communication during the same interval. Results show that noise peaks are associated with less case-relevant communication; this effect is moderated by the level of surgical experience; case-relevant communications decrease under high noise peak conditions among junior, but not among senior surgeons. However, case-irrelevant communication did not decrease under high noise level conditions, rather there was a trend to more case-irrelevant communication under high noise peaks. The results support the hypothesis that noise peaks impair communication because they draw on attentional resources rather than impairing understanding of communication. As case-relevant communication is important for surgical performance, exposure to high noise peaks in the OR should be minimised especially for less experienced surgeons.

Practitioner Summary: This study investigated whether noise during surgeries influenced the communication within surgical teams. During abdominal surgeries, noise levels were measured and communication was observed. Results showed that high noise peaks reduced the frequency of patient-related communication, but did not reduce patient-irrelevant communication. Noise may negatively affect team coordination in surgeries.     

Quorum sensing in Escherichia coli, Salmonella typhimurium, and Vibrio harveyi: a new family of genes responsible for autoinducer production

In bacteria, the regulation of gene expression in response to changes in cell density is called quorum sensing. Quorum-sensing bacteria produce, release, and respond to hormone-like molecules (autoinducers) that accumulate in the external environment as the cell population grows. In the marine bacterium Vibrio harveyi two parallel quorum-sensing systems exist, and each is composed of a sensor-autoinducer pair. V. harveyi reporter strains capable of detecting only autoinducer 1 (AI-1) or autoinducer 2 (AI-2) have been constructed and used to show that many species of bacteria, including Escherichia coli MG1655, E. coli O157:H7, Salmonella typhimurium 14028, and S. typhimurium LT2 produce autoinducers similar or identical to the V. harveyi system 2 autoinducer AI-2. However, the domesticated laboratory strain E. coli DH5alpha does not produce this signal molecule. Here we report the identification and analysis of the gene responsible for AI-2 production in V. harveyi, S. typhimurium, and E. coli. The genes, which we have named luxSV.h., luxSS.t., and luxSE.c. respectively, are highly homologous to one another but not to any other identified gene. E. coli DH5alpha can be complemented to AI-2 production by the introduction of the luxS gene from V. harveyi or E. coli O157:H7. Analysis of the E. coli DH5alpha luxSE.c. gene shows that it contains a frameshift mutation resulting in premature truncation of the LuxSE.c. protein. Our results indicate that the luxS genes define a new family of autoinducer-production genes.     

Supplemental methionine and time of supplementation effects on ruminal fermentation, digesta kinetics, and in situ dry matter and neutral detergent fiber disappearance in cattle

Two experiments were conducted to study the effects of methionine supplementation on ruminal fermentation and digesta kinetics. In Exp. 1, nine ruminally cannulated beef heifers (average initial BW = 527 kg) in a crossover design were fed low-quality grass hay and cottonseed meal with or without 11.4 g of supplemental methionine (polysaccharide-coated). Particulate and fluid kinetics, rate of DM and NDF disappearance, ruminal VFA and NH3 N concentrations, and pH were not altered (P > .10) by supplemental methionine; however, ruminal purine concentration was greater (P < .05) in methionine-supplemented heifers than in unsupplemented heifers. In Exp. 2, 12 ruminally cannulated Holstein steers (average initial BW = 622 kg) grazing a fescue pasture were allotted to one of three groups: no supplemental methionine (CON) or 11.4 g of supplemental methionine fed at 0700 (AM) or at 1200 (PM). Forage intake, particulate kinetics, ruminal fluid kinetics, pH, VFA, and NH3 N concentrations were not altered (P > .10) by supplemental methionine or supplementation time. In situ rate of DM and NDF disappearance was greater (P < .05) in supplemented steers than in CON steers; AM steers exhibited faster (P < .05) rates than PM steers. Overall, methionine supplementation of low-quality forage increased ruminal purine concentration but did not alter in situ fermentation or digesta passage, whereas supplementation at 0700, but not at 1200, of steers grazing fescue forage increased rate of NDF fermentation.     

A proposed criteria to identify wind turbine drivetrain bearing loads that induce roller slip based white-Etching cracks

Forschung im Ingenieurwesen - In this article, the type of roller slip behavior that may result in the formation of white-etching cracks (WECs) in wind turbine gearbox bearings is identified....     

A preferred approach to the linearization of turbulent boundary-layer equations

An efficient procedure for solving the fully linearized form of the boundary-layer equations is described for turbulent flows. The procedure makes use of the so-called bordering algorithm and is applicable to problems in which the structure of the linearized system of equations deviates from the block triagonal matrix form which may be caused by boundary conditions.     

Apple quality,storage, and washing treatments affect patulin levels in apple cider

Patulin is a mycotoxin produced primarily by Penicillium expansum, a mold responsible for rot in apples and other fruits. The growth of this fungus and the production of patulin are common in fruit that has been damaged. However, patulin can be detected in visibly sound fruit. The purpose of this project was to determine how apple quality, storage, and washing treatments affect patulin levels in apple cider. Patulin was not detected in cider pressed from fresh tree-picked apples (seven cultivars) but was found at levels of 40.2 to 374 microg/liter in cider pressed from four cultivars of fresh ground-harvested (dropped) apples. Patulin was not detected in cider pressed from culled tree-picked apples stored for 4 to 6 weeks at 0 to 2 degrees C but was found at levels of 0.97 to 64.0 microg/liter in cider pressed from unculled fruit stored under the same conditions. Cider from controlled-atmosphere-stored apples that were culled before pressing contained 0 to 15.1 microg of patulin per liter, while cider made from unculled fruit contained 59.9 to 120.5 microg of patulin per liter. The washing of ground-harvested apples before pressing reduced patulin levels in cider by 10 to 100%, depending on the initial patulin levels and the type of wash solution used. These results indicate that patulin is a good indicator of the quality of the apples used to manufacture cider. The avoidance of ground-harvested apples and the careful culling of apples before pressing are good methods for reducing patulin levels in cider.