On the Suitability of MPI as a PGAS Runtime

DOE Office of Scientific and Technical Information (OSTI.GOV)

Daily, Jeffrey A.; Vishnu, Abhinav; Palmer, Bruce J.

2014-12-18

Partitioned Global Address Space (PGAS) models are emerging as a popular alternative to MPI models for designing scalable applications. At the same time, MPI remains a ubiquitous communication subsystem due to its standardization, high performance, and availability on leading platforms. In this paper, we explore the suitability of using MPI as a scalable PGAS communication subsystem. We focus on the Remote Memory Access (RMA) communication in PGAS models which typically includes {\\em get, put,} and {\\em atomic memory operations}. We perform an in-depth exploration of design alternatives based on MPI. These alternatives include using a semantically-matching interface such as MPI-RMA,more » as well as not-so-intuitive interfaces such as MPI two-sided with a combination of multi-threading and dynamic process management. With an in-depth exploration of these alternatives and their shortcomings, we propose a novel design which is facilitated by the data-centric view in PGAS models. This design leverages a combination of highly tuned MPI two-sided semantics and an automatic, user-transparent split of MPI communicators to provide asynchronous progress. We implement the asynchronous progress ranks approach and other approaches within the Communication Runtime for Exascale which is a communication subsystem for Global Arrays. Our performance evaluation spans pure communication benchmarks, graph community detection and sparse matrix-vector multiplication kernels, and a computational chemistry application. The utility of our proposed PR-based approach is demonstrated by a 2.17x speed-up on 1008 processors over the other MPI-based designs.« less

Magnetic Particle Imaging for Real-Time Perfusion Imaging in Acute Stroke.

PubMed

Ludewig, Peter; Gdaniec, Nadine; Sedlacik, Jan; Forkert, Nils D; Szwargulski, Patryk; Graeser, Matthias; Adam, Gerhard; Kaul, Michael G; Krishnan, Kannan M; Ferguson, R Matthew; Khandhar, Amit P; Walczak, Piotr; Fiehler, Jens; Thomalla, Götz; Gerloff, Christian; Knopp, Tobias; Magnus, Tim

2017-10-24

The fast and accurate assessment of cerebral perfusion is fundamental for the diagnosis and successful treatment of stroke patients. Magnetic particle imaging (MPI) is a new radiation-free tomographic imaging method with a superior temporal resolution, compared to other conventional imaging methods. In addition, MPI scanners can be built as prehospital mobile devices, which require less complex infrastructure than computed tomography (CT) and magnetic resonance imaging (MRI). With these advantages, MPI could accelerate the stroke diagnosis and treatment, thereby improving outcomes. Our objective was to investigate the capabilities of MPI to detect perfusion deficits in a murine model of ischemic stroke. Cerebral ischemia was induced by inserting of a microfilament in the internal carotid artery in C57BL/6 mice, thereby blocking the blood flow into the medial cerebral artery. After the injection of a contrast agent (superparamagnetic iron oxide nanoparticles) specifically tailored for MPI, cerebral perfusion and vascular anatomy were assessed by the MPI scanner within seconds. To validate and compare our MPI data, we performed perfusion imaging with a small animal MRI scanner. MPI detected the perfusion deficits in the ischemic brain, which were comparable to those with MRI but in real-time. For the first time, we showed that MPI could be used as a diagnostic tool for relevant diseases in vivo, such as an ischemic stroke. Due to its shorter image acquisition times and increased temporal resolution compared to that of MRI or CT, we expect that MPI offers the potential to improve stroke imaging and treatment.

Myocardial perfusion in patients with suspected coronary artery disease: comparison between 320-MDCT and rubidium-82 PET.

PubMed

Dantas, Roberto Nery; Assuncao, Antonildes Nascimento; Marques, Ismar Aguiar; Fahel, Mateus Guimaraes; Nomura, Cesar Higa; Avila, Luiz Francisco Rodrigues; Giorgi, Maria Clementina Pinto; Soares, Jose; Meneghetti, Jose Claudio; Parga, Jose Rodrigues

2018-06-01

Despite advances in non-invasive myocardial perfusion imaging (MPI) evaluation, computed tomography (CT) multiphase MPI protocols have not yet been compared with the highly accurate rubidium-82 positron emission tomography ( 82 RbPET) MPI. Thus, this study aimed to evaluate agreement between 82 RbPET and 320-detector row CT (320-CT) MPI using a multiphase protocol in suspected CAD patients. Forty-four patients referred for MPI evaluation were prospectively enrolled and underwent dipyridamole stress 82 RbPET and multiphase 320-CT MPI (five consecutive volumetric acquisitions during stress). Statistical analyses were performed using the R software. There was high agreement for recognizing summed stress scores ≥ 4 (kappa 0.77, 95% CI 0.55-0.98, p < 0.001) and moderate for detecting SDS ≥ 2 (kappa 0.51, 95% CI 0.23-0.80, p < 0.001). In a per segment analysis, agreement was high for the presence of perfusion defects during stress and rest (kappa 0.75 and 0.82, respectively) and was moderate for impairment severity (kappa 0.58 and 0.65, respectively). The 320-CT protocol was safe, with low radiation burden (9.3 ± 2.4 mSv). There was a significant agreement between dipyridamole stress 320-CT MPI and 82 RbPET MPI in the evaluation of suspected CAD patients of intermediate risk. The multiphase 320-CT MPI protocol was feasible, diagnostic and with relatively low radiation exposure. • Rubidium-82 PET and 320-MDCT can perform MPI studies for CAD investigation. • There is high agreement between rubidium-82 PET and 320-MDCT for MPI assessment. • Multiphase CT perfusion protocols are feasible and with low radiation. • Multiphase CT perfusion protocols can identify image artefacts.

Magnetic Particle / Magnetic Resonance Imaging: In-Vitro MPI-Guided Real Time Catheter Tracking and 4D Angioplasty Using a Road Map and Blood Pool Tracer Approach.

PubMed

Salamon, Johannes; Hofmann, Martin; Jung, Caroline; Kaul, Michael Gerhard; Werner, Franziska; Them, Kolja; Reimer, Rudolph; Nielsen, Peter; Vom Scheidt, Annika; Adam, Gerhard; Knopp, Tobias; Ittrich, Harald

2016-01-01

In-vitro evaluation of the feasibility of 4D real time tracking of endovascular devices and stenosis treatment with a magnetic particle imaging (MPI) / magnetic resonance imaging (MRI) road map approach and an MPI-guided approach using a blood pool tracer. A guide wire and angioplasty-catheter were labeled with a thin layer of magnetic lacquer. For real time MPI a custom made software framework was developed. A stenotic vessel phantom filled with saline or superparamagnetic iron oxide nanoparticles (MM4) was equipped with bimodal fiducial markers for co-registration in preclinical 7T MRI and MPI. In-vitro angioplasty was performed inflating the balloon with saline or MM4. MPI data were acquired using a field of view of 37.3×37.3×18.6 mm3 and a frame rate of 46 volumes/sec. Analysis of the magnetic lacquer-marks on the devices were performed with electron microscopy, atomic absorption spectrometry and micro-computed tomography. Magnetic marks allowed for MPI/MRI guidance of interventional devices. Bimodal fiducial markers enable MPI/MRI image fusion for MRI based roadmapping. MRI roadmapping and the blood pool tracer approach facilitate MPI real time monitoring of in-vitro angioplasty. Successful angioplasty was verified with MPI and MRI. Magnetic marks consist of micrometer sized ferromagnetic plates mainly composed of iron and iron oxide. 4D real time MP imaging, tracking and guiding of endovascular instruments and in-vitro angioplasty is feasible. In addition to an approach that requires a blood pool tracer, MRI based roadmapping might emerge as a promising tool for radiation free 4D MPI-guided interventions.

MPI as high temporal resolution imaging technique for in vivo bolus tracking of Ferucarbotran in mouse model

NASA Astrophysics Data System (ADS)

Jung, C.; Salamon, J.; Hofmann, M.; Kaul, M. G.; Adam, G.; Ittrich, H.; Knopp, T.

2016-03-01

Purpose: The goal of this study was to achieve a real time 3D visualisation of the murine cardiovascular system by intravenously injected superparamagnetic nanoparticles using Magnetic particle imaging (MPI). Material and Methods: MPI scans of FVB mice were performed using a 3D imaging sequence (1T/m gradient strength, 10mT drive-field strength). A dynamic scan with a temporal resolution of 21.5ms per 3D volume acquisition was performed. 50μl ferucarbotran (Resovist®, Bayer Healthcare AG) were injected into the tail vein after baseline MPI measurements. As MPI delivers no anatomic information, MRI scans at a 7T ClinScan (Bruker) were performed using a T2-weighted 2D TSE sequence. The reconstruction of the MPI data was performed on the MPI console (ParaVision 6.0/MPI, Bruker). Image fusion was done using additional image processing software (Imalytics, Philips). The dynamic information was extracted using custom software developed in the Julia programming environment. Results: The combined MRI-MPI measurements were carried out successfully. MPI data clearly demonstrated the passage of the SPIO tracer through the inferior vena cava, the heart and finally the liver. By co-registration with MRI the anatomical regions were identified. Due to the volume frame rate of about 46 volumes per second a signal modulation with the frequency of the heart beat was detectable and a heart beat of 520 beats per minute (bpm) has been assumed. Moreover, the blood flow velocity of approximately 5cm/s in the vena cava has been estimated. Conclusions: The high temporal resolution of MPI allows real-time imaging and bolus tracking of intravenous injected nanoparticles and offers a real time tool to assess blood flow velocity.

Optimizing Blocking and Nonblocking Reduction Operations for Multicore Systems: Hierarchical Design and Implementation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gorentla Venkata, Manjunath; Shamis, Pavel; Graham, Richard L

2013-01-01

Many scientific simulations, using the Message Passing Interface (MPI) programming model, are sensitive to the performance and scalability of reduction collective operations such as MPI Allreduce and MPI Reduce. These operations are the most widely used abstractions to perform mathematical operations over all processes that are part of the simulation. In this work, we propose a hierarchical design to implement the reduction operations on multicore systems. This design aims to improve the efficiency of reductions by 1) tailoring the algorithms and customizing the implementations for various communication mechanisms in the system 2) providing the ability to configure the depth ofmore » hierarchy to match the system architecture, and 3) providing the ability to independently progress each of this hierarchy. Using this design, we implement MPI Allreduce and MPI Reduce operations (and its nonblocking variants MPI Iallreduce and MPI Ireduce) for all message sizes, and evaluate on multiple architectures including InfiniBand and Cray XT5. We leverage and enhance our existing infrastructure, Cheetah, which is a framework for implementing hierarchical collective operations to implement these reductions. The experimental results show that the Cheetah reduction operations outperform the production-grade MPI implementations such as Open MPI default, Cray MPI, and MVAPICH2, demonstrating its efficiency, flexibility and portability. On Infini- Band systems, with a microbenchmark, a 512-process Cheetah nonblocking Allreduce and Reduce achieves a speedup of 23x and 10x, respectively, compared to the default Open MPI reductions. The blocking variants of the reduction operations also show similar performance benefits. A 512-process nonblocking Cheetah Allreduce achieves a speedup of 3x, compared to the default MVAPICH2 Allreduce implementation. On a Cray XT5 system, a 6144-process Cheetah Allreduce outperforms the Cray MPI by 145%. The evaluation with an application kernel, Conjugate Gradient solver, shows that the Cheetah reductions speeds up total time to solution by 195%, demonstrating the potential benefits for scientific simulations.« less

Google Test MPI Listener

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oxberry, Geoffrey

Google Test MPI Listener is a plugin for the Google Test c++ unit testing library that organizes test output of software that uses both the MPI parallel programming model and Google Test. Typically, such output is ordered arbitrarily and disorganized, making difficult the process of interpreting test output. This plug organizes output in MPI rank order, enabling easy interpretation of test results.

Final report: Compiled MPI. Cost-Effective Exascale Application Development

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gropp, William Douglas

2015-12-21

This is the final report on Compiled MPI: Cost-Effective Exascale Application Development, and summarizes the results under this project. The project investigated runtime enviroments that improve the performance of MPI (Message-Passing Interface) programs; work at Illinois in the last period of this project looked at optimizing data access optimizations expressed with MPI datatypes.

SBML-PET-MPI: a parallel parameter estimation tool for Systems Biology Markup Language based models.

PubMed

Zi, Zhike

2011-04-01

Parameter estimation is crucial for the modeling and dynamic analysis of biological systems. However, implementing parameter estimation is time consuming and computationally demanding. Here, we introduced a parallel parameter estimation tool for Systems Biology Markup Language (SBML)-based models (SBML-PET-MPI). SBML-PET-MPI allows the user to perform parameter estimation and parameter uncertainty analysis by collectively fitting multiple experimental datasets. The tool is developed and parallelized using the message passing interface (MPI) protocol, which provides good scalability with the number of processors. SBML-PET-MPI is freely available for non-commercial use at http://www.bioss.uni-freiburg.de/cms/sbml-pet-mpi.html or http://sites.google.com/site/sbmlpetmpi/.

Psychometric evaluation of the Spanish version of the MPI-SCI.

PubMed

Soler, M D; Cruz-Almeida, Y; Saurí, J; Widerström-Noga, E G

2013-07-01

Postal surveys. To confirm the factor structure of the Spanish version of the MPI-SCI (MPI-SCI-S, Multidimensional Pain Inventory in the SCI population) and to test its internal consistency and construct validity in a Spanish population. Guttmann Institute, Barcelona, Spain. The MPI-SCI-S along with Spanish measures of pain intensity (Numerical Rating Scale), pain interference (Brief Pain Inventory), functional independence (Functional Independence Measure), depression (Beck Depression Inventory), locus of control (Multidimensional health Locus of Control), support (Functional Social Support Questionnaire (Duke-UNC)), psychological well-being (Psychological Global Well-Being Index) and demographic/injury characteristics were assessed in persons with spinal cord injury (SCI) and chronic pain (n=126). Confirmatory factor analysis suggested an adequate factor structure for the MPI-SCI-S. The internal consistency of the MPI-SCI-S subscales ranged from acceptable (r=0.66, Life Control) to excellent (r=0.94, Life Interference). All MPI-SCI-S subscales showed adequate construct validity, with the exception of the Negative and Solicitous Responses subscales. The Spanish version of the MPI-SCI is adequate for evaluating chronic pain impact following SCI in a Spanish-speaking population. Future studies should include additional measures of pain-related support in the Spanish-speaking SCI population.

Relaxation in x-space magnetic particle imaging.

PubMed

Croft, Laura R; Goodwill, Patrick W; Conolly, Steven M

2012-12-01

Magnetic particle imaging (MPI) is a new imaging modality that noninvasively images the spatial distribution of superparamagnetic iron oxide nanoparticles (SPIOs). MPI has demonstrated high contrast and zero attenuation with depth, and MPI promises superior safety compared to current angiography methods, X-ray, computed tomography, and magnetic resonance imaging angiography. Nanoparticle relaxation can delay the SPIO magnetization, and in this work we investigate the open problem of the role relaxation plays in MPI scanning and its effect on the image. We begin by amending the x-space theory of MPI to include nanoparticle relaxation effects. We then validate the amended theory with experiments from a Berkeley x-space relaxometer and a Berkeley x-space projection MPI scanner. Our theory and experimental data indicate that relaxation reduces SNR and asymmetrically blurs the image in the scanning direction. While relaxation effects can have deleterious effects on the MPI scan, we show theoretically and experimentally that x-space reconstruction remains robust in the presence of relaxation. Furthermore, the role of relaxation in x-space theory provides guidance as we develop methods to minimize relaxation-induced blurring. This will be an important future area of research for the MPI community.

False-positive defects on exercise 99mTc-sestamibi SPECT imaging, but not on dipyridamole 99mTc-sestamibi SPECT imaging, in a patient with right bundle branch block (RBBB).

PubMed

Javadi, Hamid; Jallalat, Sara; Semnani, Shahriar; Mogharrabi, Mehdi; Nabipour, Iraj; Abbaszadeh, Moloud; Assadi, Majid

2013-01-01

False-positive findings with myocardial perfusion imaging (MPI) have frequently been identified in the presence of left bundle branch block (LBBB) and tend to lower the accuracy of MPI in individuals with normal coronary angiographs. Pharmacologic stress is recognized as the preferred method for MPI in patients with LBBB. In contrast, very few studies have evaluated the effect of right bundle branch block (RBBB) on MPI, and there is no consensus regarding the selection of pharmacologic versus exercise stress during MPI for the RBBB patient. In this study, we present a 45-year-old man with RBBB, who has a normal coronary artery angiography, but who showed abnormal myocardial perfusion with exercise MPI, and normal perfusion on dipyridamole MPI. The aim of the study is to stimulate awareness that the stress method selected for patients with RBBB can potentially interfere with the accuracy of the data.

Collective Framework and Performance Optimizations to Open MPI for Cray XT Platforms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ladd, Joshua S; Gorentla Venkata, Manjunath; Shamis, Pavel

2011-01-01

The performance and scalability of collective operations plays a key role in the performance and scalability of many scientific applications. Within the Open MPI code base we have developed a general purpose hierarchical collective operations framework called Cheetah, and applied it at large scale on the Oak Ridge Leadership Computing Facility's Jaguar (OLCF) platform, obtaining better performance and scalability than the native MPI implementation. This paper discuss Cheetah's design and implementation, and optimizations to the framework for Cray XT 5 platforms. Our results show that the Cheetah's Broadcast and Barrier perform better than the native MPI implementation. For medium data,more » the Cheetah's Broadcast outperforms the native MPI implementation by 93% for 49,152 processes problem size. For small and large data, it out performs the native MPI implementation by 10% and 9%, respectively, at 24,576 processes problem size. The Cheetah's Barrier performs 10% better than the native MPI implementation for 12,288 processes problem size.« less

MPI_XSTAR: MPI-based parallelization of XSTAR program

NASA Astrophysics Data System (ADS)

Danehkar, A.

2017-12-01

MPI_XSTAR parallelizes execution of multiple XSTAR runs using Message Passing Interface (MPI). XSTAR (ascl:9910.008), part of the HEASARC's HEAsoft (ascl:1408.004) package, calculates the physical conditions and emission spectra of ionized gases. MPI_XSTAR invokes XSTINITABLE from HEASoft to generate a job list of XSTAR commands for given physical parameters. The job list is used to make directories in ascending order, where each individual XSTAR is spawned on each processor and outputs are saved. HEASoft's XSTAR2TABLE program is invoked upon the contents of each directory in order to produce table model FITS files for spectroscopy analysis tools.

Mycobacterium tuberculosis Infection and Innate Responses in a New Model of Lung Alveolar Macrophages.

PubMed

Woo, Minjeong; Wood, Connor; Kwon, Doyoon; Park, Kyu-Ho Paul; Fejer, György; Delorme, Vincent

2018-01-01

Lung alveolar macrophages (AMs) are in the first line of immune defense against respiratory pathogens and play key roles in the pathogenesis of Mycobacterium tuberculosis ( Mtb ) in humans. Nevertheless, AMs are available only in limited amounts for in vitro studies, which hamper the detailed molecular understanding of host- Mtb interactions in these macrophages. The recent establishment of the self-renewing and primary Max Planck Institute (MPI) cells, functionally very close to lung AMs, opens unique opportunities for in vitro studies of host-pathogen interactions in respiratory diseases. Here, we investigated the suitability of MPI cells as a host cell system for Mtb infection. Bacterial, cellular, and innate immune features of MPI cells infected with Mtb were characterized. Live bacteria were readily internalized and efficiently replicated in MPI cells, similarly to primary murine macrophages and other cell lines. MPI cells were also suitable for the determination of anti-tuberculosis (TB) drug activity. The primary innate immune response of MPI cells to live Mtb showed significantly higher and earlier induction of the pro-inflammatory cytokines TNFα, interleukin 6 (IL-6), IL-1α, and IL-1β, as compared to stimulation with heat-killed (HK) bacteria. MPI cells previously showed a lack of induction of the anti-inflammatory cytokine IL-10 to a wide range of stimuli, including HK Mtb . By contrast, we show here that live Mtb is able to induce significant amounts of IL-10 in MPI cells. Autophagy experiments using light chain 3B immunostaining, as well as LysoTracker labeling of acidic vacuoles, demonstrated that MPI cells efficiently control killed Mtb by elimination through phagolysosomes. MPI cells were also able to accumulate lipid droplets in their cytoplasm following exposure to lipoproteins. Collectively, this study establishes the MPI cells as a relevant, versatile host cell model for TB research, allowing a deeper understanding of AMs functions in this pathology.

Mathematical analysis of the 1D model and reconstruction schemes for magnetic particle imaging

NASA Astrophysics Data System (ADS)

Erb, W.; Weinmann, A.; Ahlborg, M.; Brandt, C.; Bringout, G.; Buzug, T. M.; Frikel, J.; Kaethner, C.; Knopp, T.; März, T.; Möddel, M.; Storath, M.; Weber, A.

2018-05-01

Magnetic particle imaging (MPI) is a promising new in vivo medical imaging modality in which distributions of super-paramagnetic nanoparticles are tracked based on their response in an applied magnetic field. In this paper we provide a mathematical analysis of the modeled MPI operator in the univariate situation. We provide a Hilbert space setup, in which the MPI operator is decomposed into simple building blocks and in which these building blocks are analyzed with respect to their mathematical properties. In turn, we obtain an analysis of the MPI forward operator and, in particular, of its ill-posedness properties. We further get that the singular values of the MPI core operator decrease exponentially. We complement our analytic results by some numerical studies which, in particular, suggest a rapid decay of the singular values of the MPI operator.

Temperature dependence in magnetic particle imaging

NASA Astrophysics Data System (ADS)

Wells, James; Paysen, Hendrik; Kosch, Olaf; Trahms, Lutz; Wiekhorst, Frank

2018-05-01

Experimental results are presented demonstrating how temperature can influence the dynamics of magnetic nanoparticles (MNPs) in liquid suspension, when exposed to alternating magnetic fields in the kilohertz frequency range. The measurements used to probe the nanoparticle systems are directly linked to both the emerging biomedical technique of magnetic particle imaging (MPI), and to the recently proposed concept of remote nanoscale thermometry using MNPs under AC field excitation. Here, we report measurements on three common types of MNPs, two of which are currently leading candidates for use as tracers in MPI. Using highly-sensitive magnetic particle spectroscopy (MPS), we demonstrate significant and divergent thermal dependences in several key measures used in the evaluation of MNP dynamics for use in MPI and other applications. The temperature range studied was between 296 and 318 Kelvin, making our findings of particular importance for MPI and other biomedical technologies. Furthermore, we report the detection of the same temperature dependences in measurements conducted using the detection coils within an operational preclinical MPI scanner. This clearly shows the importance of considering temperature during MPI development, and the potential for temperature-resolved MPI using this system. We propose possible physical explanations for the differences in the behaviors observed between the different particle types, and discuss our results in terms of the opportunities and concerns they raise for MPI and other MNP based technologies.

Enhancing Application Performance Using Mini-Apps: Comparison of Hybrid Parallel Programming Paradigms

NASA Technical Reports Server (NTRS)

Lawson, Gary; Poteat, Michael; Sosonkina, Masha; Baurle, Robert; Hammond, Dana

2016-01-01

In this work, several mini-apps have been created to enhance a real-world application performance, namely the VULCAN code for complex flow analysis developed at the NASA Langley Research Center. These mini-apps explore hybrid parallel programming paradigms with Message Passing Interface (MPI) for distributed memory access and either Shared MPI (SMPI) or OpenMP for shared memory accesses. Performance testing shows that MPI+SMPI yields the best execution performance, while requiring the largest number of code changes. A maximum speedup of 23X was measured for MPI+SMPI, but only 10X was measured for MPI+OpenMP.

Effect of central hypothyroidism on Doppler-derived myocardial performance index.

PubMed

Doin, Fabio Luiz Casanova; Borges, Mariana da Rosa; Campos, Orlando; de Camargo Carvalho, Antonio Carlos; de Paola, Angelo Amato Vincenzo; Paiva, Marcelo Goulart; Abucham, Julio; Moises, Valdir Ambrosio

2004-06-01

Myocardial performance index (MPI) has been used to assess global ventricular function in different types of cardiac disease. Thyroid hormones influence cardiac performance directly and indirectly by changes in peripheral circulation. The aim of this study was to evaluate the possible effect of central hypothyroidism (CH) on MPI. The study included 28 control subjects and 7 patients with CH without cardiac disease. MPI was defined as the sum of isovolumetric contraction time (ICT) and isovolumetric relaxation time divided by ejection time. Patients were submitted to hormonal therapy with thyroxin and the study was repeated after 35 to 42 days. MPI was significantly higher in patients with CH (0.54 +/- 0.08) than in control subjects (0.40 +/- 0.05) (P =.002). The increase in MPI was caused by the prolongation of ICT without a significant variation of isovolumetric relaxation time and ejection time. After hormonal therapy there was a significant reduction of MPI (0.54 +/- 0.08 vs 0.42 +/- 0.07; P =.028) and ICT. MPI was increased in patients with untreated CH. The increase was related to prolongation of ICT and reverted by hormonal therapy.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sayan Ghosh, Jeff Hammond

OpenSHMEM is a community effort to unifyt and standardize the SHMEM programming model. MPI (Message Passing Interface) is a well-known community standard for parallel programming using distributed memory. The most recen t release of MPI, version 3.0, was designed in part to support programming models like SHMEM.OSHMPI is an implementation of the OpenSHMEM standard using MPI-3 for the Linux operating system. It is the first implementation of SHMEM over MPI one-sided communication and has the potential to be widely adopted due to the portability and widely availability of Linux and MPI-3. OSHMPI has been tested on a variety of systemsmore » and implementations of MPI-3, includingInfiniBand clusters using MVAPICH2 and SGI shared-memory supercomputers using MPICH. Current support is limited to Linux but may be extended to Apple OSX if there is sufficient interest. The code is opensource via https://github.com/jeffhammond/oshmpi« less

The Assessment and Potential Implications of the Myocardial Performance Index Post Exercise in an at Risk Population.

PubMed

Ruisi, Michael; Levine, Michael; Finkielstein, Dennis

2013-12-01

The myocardial performance index (MPI) first described by Chuwa Tei in 1995 is a relatively new echocardiographic variable used for assessment of overall cardiac function. Previous studies have demonstrated the MPI to be a sum representation of both left ventricular systolic and diastolic function with prognostic value in patients with coronary artery disease as well as symptomatic heart failure. Ninety patients with either established coronary artery disease (CAD) or CAD risk factors underwent routine treadmill exercise stress testing with two-dimensional Doppler echocardiography using the standard Bruce protocol. Both resting and stress MPI values were measured for all 90 of the patients. Using a normal MPI cut off of ≤ 0.47, the prevalence of an abnormal resting MPI in our 90 subjects was 72/90 or 80% and the prevalence of an abnormal stress MPI in our 90 subjects was 48/90 or 53.33%. The average MPI observed in the resting portion of the stress test for the cohort was: 0.636 with a standard deviation of 0.182. The average MPI in the stress portion of the stress test for the cohort was 0.530 with a standard deviation of 0.250. The P value with the use of a one-tailed dependent T test was calculated to be < 0.05. We postulate that these findings reflect that the MPI (Tei) index assessed during exercise may be a sensitive indicator of occult coronary disease in an at risk group independent of wall motion assessment.

Modified personal interviews: resurrecting reliable personal interviews for admissions?

PubMed

Hanson, Mark D; Kulasegaram, Kulamakan Mahan; Woods, Nicole N; Fechtig, Lindsey; Anderson, Geoff

2012-10-01

Traditional admissions personal interviews provide flexible faculty-student interactions but are plagued by low inter-interview reliability. Axelson and Kreiter (2009) retrospectively showed that multiple independent sampling (MIS) may improve reliability of personal interviews; thus, the authors incorporated MIS into the admissions process for medical students applying to the University of Toronto's Leadership Education and Development Program (LEAD). They examined the reliability and resource demands of this modified personal interview (MPI) format. In 2010-2011, LEAD candidates submitted written applications, which were used to screen for participation in the MPI process. Selected candidates completed four brief (10-12 minutes) independent MPIs each with a different interviewer. The authors blueprinted MPI questions to (i.e., aligned them with) leadership attributes, and interviewers assessed candidates' eligibility on a five-point Likert-type scale. The authors analyzed inter-interview reliability using the generalizability theory. Sixteen candidates submitted applications; 10 proceeded to the MPI stage. Reliability of the written application components was 0.75. The MPI process had overall inter-interview reliability of 0.79. Correlation between the written application and MPI scores was 0.49. A decision study showed acceptable reliability of 0.74 with only three MPIs scored using one global rating. Furthermore, a traditional admissions interview format would take 66% more time than the MPI format. The MPI format, used during the LEAD admissions process, achieved high reliability with minimal faculty resources. The MPI format's reliability and effective resource use were possible through MIS and employment of expert interviewers. MPIs may be useful for other admissions tasks.

Design analysis of an MPI human functional brain scanner

PubMed Central

Mason, Erica E.; Cooley, Clarissa Z.; Cauley, Stephen F.; Griswold, Mark A.; Conolly, Steven M.; Wald, Lawrence L.

2017-01-01

MPI’s high sensitivity makes it a promising modality for imaging brain function. Functional contrast is proposed based on blood SPION concentration changes due to Cerebral Blood Volume (CBV) increases during activation, a mechanism utilized in fMRI studies. MPI offers the potential for a direct and more sensitive measure of SPION concentration, and thus CBV, than fMRI. As such, fMPI could surpass fMRI in sensitivity, enhancing the scientific and clinical value of functional imaging. As human-sized MPI systems have not been attempted, we assess the technical challenges of scaling MPI from rodent to human brain. We use a full-system MPI simulator to test arbitrary hardware designs and encoding practices, and we examine tradeoffs imposed by constraints that arise when scaling to human size as well as safety constraints (PNS and central nervous system stimulation) not considered in animal scanners, thereby estimating spatial resolutions and sensitivities achievable with current technology. Using a projection FFL MPI system, we examine coil hardware options and their implications for sensitivity and spatial resolution. We estimate that an fMPI brain scanner is feasible, although with reduced sensitivity (20×) and spatial resolution (5×) compared to existing rodent systems. Nonetheless, it retains sufficient sensitivity and spatial resolution to make it an attractive future instrument for studying the human brain; additional technical innovations can result in further improvements. PMID:28752130

Feasibility of using auto Mod-MPI system, a novel technique for automated measurement of fetal modified myocardial performance index.

PubMed

Lee, M-Y; Won, H-S; Jeon, E-J; Yoon, H C; Choi, J Y; Hong, S J; Kim, M-J

2014-06-01

To evaluate the reproducibility of measurement of the fetal left modified myocardial performance index (Mod-MPI) determined using a novel automated system. This was a prospective study of 116 ultrasound examinations from 110 normal singleton pregnancies at 12 + 1 to 37 + 1 weeks' gestation. Two experienced operators each measured the left Mod-MPI twice manually and twice automatically using the Auto Mod-MPI system. Intra- and interoperator reproducibility were assessed using intraclass correlation coefficients (ICCs) and the manual and automated measurements obtained by the more experienced operator were compared using Bland-Altman plots and ICCs. Both operators successfully measured the left Mod-MPI in all cases using the Auto Mod-MPI system. For both operators, intraoperator reproducibility was higher when performing automated measurements (ICC = 0.967 and 0.962 for Operators 1 and 2, respectively) than when performing manual measurements (ICC = 0.857 and 0.856 for Operators 1 and 2, respectively). Interoperator agreement was also better for automated than for manual measurements (ICC = 0.930 vs 0.723, respectively). There was good agreement between the automated and manual values measured by the more experienced operator. The Auto Mod-MPI system is a reliable technique for measuring fetal left Mod-MPI and demonstrates excellent reproducibility. Copyright © 2013 ISUOG. Published by John Wiley & Sons Ltd.

Effect of caffeine on SPECT myocardial perfusion imaging during regadenoson pharmacologic stress: rationale and design of a prospective, randomized, multicenter study.

PubMed

Tejani, Furqan H; Thompson, Randall C; Iskandrian, Ami E; McNutt, Bruce E; Franks, Billy

2011-02-01

Caffeine attenuates the coronary hyperemic response to adenosine by competitive A₂(A) receptor blockade. This study aims to determine whether oral caffeine administration compromises diagnostic accuracy in patients undergoing vasodilator stress myocardial perfusion imaging (MPI) with regadenoson, a selective adenosine A(2A) agonist. This multicenter, randomized, double-blind, placebo-controlled, parallel-group study includes patients with suspected coronary artery disease who regularly consume caffeine. Each participant undergoes three SPECT MPI studies: a rest study on day 1 (MPI-1); a regadenoson stress study on day 3 (MPI-2), and a regadenoson stress study on day 5 with double-blind administration of oral caffeine 200 or 400 mg or placebo capsules (MPI-3; n = 90 per arm). Only participants with ≥ 1 reversible defect on the second MPI study undergo the subsequent stress MPI test. The primary endpoint is the difference in the number of reversible defects on the two stress tests using a 17-segment model. Pharmacokinetic/pharmacodynamic analyses will evaluate the effect of caffeine on the regadenoson exposure-response relationship. Safety will also be assessed. The results of this study will show whether the consumption of caffeine equivalent to 2-4 cups of coffee prior to an MPI study with regadenoson affects the diagnostic validity of stress testing (ClinicalTrials.gov number, NCT00826280).

Doppler-derived myocardial performance index in patients with impaired left ventricular relaxation and preserved systolic function.

PubMed

Fernandes, José Maria G; Rivera, Ivan Romero; de Oliveira Romão, Benício; Mendonça, Maria Alayde; Vasconcelos, Miriam Lira Castro; Carvalho, Antônio Carlos; Campos, Orlando; De Paola, Angelo Amato V; Moisés, Valdir A

2009-09-01

The Doppler-derived myocardial performance index (MPI) has been used in the evaluation of left ventricular (LV) function in several diseases. In patients with isolated diastolic dysfunction, the diagnostic utility of this index remains unclear. The aim of this study was to determine the diagnostic utility of MPI in patients with systemic hypertension, impaired LV relaxation, and normal ejection fraction. Thirty hypertensive patients with impaired LV relaxation were compared to 30 control subjects. MPI and its components, isovolumetric relaxation time (IRT), isovolumetric contraction time (ICT), and the ejection time (ET), were measured from LV outflow and mitral inflow Doppler velocity profiles. MPI was higher in patients than in control subjects (0.45 +/- 0.13 vs 0.37 +/- 0.07 P < 0.0029). The increase in MPI was due to the prolongation of IRT without significant change of ICT and ET. MPI cutoff value of > or =0.40 identified impaired LV relaxation with a sensitivity of 63% and specificity of 70% while an IRT >94 ms had a sensitivity of 67% and specificity of 80%. Multivariate analysis identified relative wall thickness, mitral early filling wave velocity (E), and systolic myocardial velocity (Sm) as independent predictors of MPI in patients with hypertension. MPI was increase in patients with hypertension, diastolic dysfunction, and normal ejection fraction but was not superior to IRT to detect impaired LV relaxation.

Adenosine triphosphate stress myocardial perfusion imaging for risk stratification of patients aged 70 years and older with suspected coronary artery disease.

PubMed

Yao, Zhiming; Zhu, Hui; Li, Wenchan; Chen, Congxia; Wang, Hua; Shi, Lei; Zhang, Wenjie

2017-04-01

We investigated the cardiac risk stratification value of adenosine triphosphate stress myocardial perfusion imaging (ATP-MPI) in patients aged 70 years and older with suspected coronary artery disease (CAD). We identified a series of 415 consecutive patients aged 70 years and older with suspected CAD, who had undergone ATP-MPI with 99m Tc-MIBI. The presence of a fixed and/or reversible perfusion defect was considered as an abnormal MPI. Follow-up was available in 399 patients (96.1%) over 3.45 ± 1.71 years after excluding 16 patients who underwent early coronary revascularization <60 days after MPI. The major adverse cardiac events (MACE), including cardiac death, nonfatal infarction, and late coronary revascularization, were recorded. One hundred twenty-five (31.3%) patients had abnormal MPI and the remaining had normal MPI. A multivariable analysis using Cox regression demonstrated that abnormal MPI was independently associated with MACE (hazard ratio 19.50 and 95% confidence interval 5.91-64.31, P value .000). The patients with SSS > 8 had significantly higher cumulative MACE rate than patients with SSS ≤ 8 had (37.8% vs 5.2%, respectively, P < .001). The Kaplan-Meier cumulative MACE-free survival in patients with abnormal MPI (57.0%) was significantly lower than that in patients with normal MPI (89.6%), P < .0001. Among patients with SSS > 8, the Kaplan-Meier cumulative MACE-free survival were 36.9% in patients ≥80 years old and 49.5% in patients 70-79 years old, respectively, P < .05. However, among patients with SSS ≤ 8, there was no difference between the Kaplan-Meier cumulative MACE-free survivals of these two age groups. ATP-MPI data are useful for the prediction of major adverse cardiac events in patients aged 70 years and older with suspected CAD.

Acceleration of Semiempirical QM/MM Methods through Message Passage Interface (MPI), Hybrid MPI/Open Multiprocessing, and Self-Consistent Field Accelerator Implementations.

PubMed

Ojeda-May, Pedro; Nam, Kwangho

2017-08-08

The strategy and implementation of scalable and efficient semiempirical (SE) QM/MM methods in CHARMM are described. The serial version of the code was first profiled to identify routines that required parallelization. Afterward, the code was parallelized and accelerated with three approaches. The first approach was the parallelization of the entire QM/MM routines, including the Fock matrix diagonalization routines, using the CHARMM message passage interface (MPI) machinery. In the second approach, two different self-consistent field (SCF) energy convergence accelerators were implemented using density and Fock matrices as targets for their extrapolations in the SCF procedure. In the third approach, the entire QM/MM and MM energy routines were accelerated by implementing the hybrid MPI/open multiprocessing (OpenMP) model in which both the task- and loop-level parallelization strategies were adopted to balance loads between different OpenMP threads. The present implementation was tested on two solvated enzyme systems (including <100 QM atoms) and an S N 2 symmetric reaction in water. The MPI version exceeded existing SE QM methods in CHARMM, which include the SCC-DFTB and SQUANTUM methods, by at least 4-fold. The use of SCF convergence accelerators further accelerated the code by ∼12-35% depending on the size of the QM region and the number of CPU cores used. Although the MPI version displayed good scalability, the performance was diminished for large numbers of MPI processes due to the overhead associated with MPI communications between nodes. This issue was partially overcome by the hybrid MPI/OpenMP approach which displayed a better scalability for a larger number of CPU cores (up to 64 CPUs in the tested systems).

Magnetic Particle Imaging (MPI) for NMR and MRI researchers

NASA Astrophysics Data System (ADS)

Saritas, Emine U.; Goodwill, Patrick W.; Croft, Laura R.; Konkle, Justin J.; Lu, Kuan; Zheng, Bo; Conolly, Steven M.

2013-04-01

Magnetic Particle Imaging (MPI) is a new tracer imaging modality that is gaining significant interest from NMR and MRI researchers. While the physics of MPI differ substantially from MRI, it employs hardware and imaging concepts that are familiar to MRI researchers, such as magnetic excitation and detection, pulse sequences, and relaxation effects. Furthermore, MPI employs the same superparamagnetic iron oxide (SPIO) contrast agents that are sometimes used for MR angiography and are often used for MRI cell tracking studies. These SPIOs are much safer for humans than iodine or gadolinium, especially for Chronic Kidney Disease (CKD) patients. The weak kidneys of CKD patients cannot safely excrete iodine or gadolinium, leading to increased morbidity and mortality after iodinated X-ray or CT angiograms, or after gadolinium-MRA studies. Iron oxides, on the other hand, are processed in the liver, and have been shown to be safe even for CKD patients. Unlike the “black blood” contrast generated by SPIOs in MRI due to increased T2∗ dephasing, SPIOs in MPI generate positive, “bright blood” contrast. With this ideal contrast, even prototype MPI scanners can already achieve fast, high-sensitivity, and high-contrast angiograms with millimeter-scale resolutions in phantoms and in animals. Moreover, MPI shows great potential for an exciting array of applications, including stem cell tracking in vivo, first-pass contrast studies to diagnose or stage cancer, and inflammation imaging in vivo. So far, only a handful of prototype small-animal MPI scanners have been constructed worldwide. Hence, MPI is open to great advances, especially in hardware, pulse sequence, and nanoparticle improvements, with the potential to revolutionize the biomedical imaging field.

Performance comparison analysis library communication cluster system using merge sort

NASA Astrophysics Data System (ADS)

Wulandari, D. A. R.; Ramadhan, M. E.

2018-04-01

Begins by using a single processor, to increase the speed of computing time, the use of multi-processor was introduced. The second paradigm is known as parallel computing, example cluster. The cluster must have the communication potocol for processing, one of it is message passing Interface (MPI). MPI have many library, both of them OPENMPI and MPICH2. Performance of the cluster machine depend on suitable between performance characters of library communication and characters of the problem so this study aims to analyze the comparative performances libraries in handling parallel computing process. The case study in this research are MPICH2 and OpenMPI. This case research execute sorting’s problem to know the performance of cluster system. The sorting problem use mergesort method. The research method is by implementing OpenMPI and MPICH2 on a Linux-based cluster by using five computer virtual then analyze the performance of the system by different scenario tests and three parameters for to know the performance of MPICH2 and OpenMPI. These performances are execution time, speedup and efficiency. The results of this study showed that the addition of each data size makes OpenMPI and MPICH2 have an average speed-up and efficiency tend to increase but at a large data size decreases. increased data size doesn’t necessarily increased speed up and efficiency but only execution time example in 100000 data size. OpenMPI has a execution time greater than MPICH2 example in 1000 data size average execution time with MPICH2 is 0,009721 and OpenMPI is 0,003895 OpenMPI can customize communication needs.

Cardiovascular mortality prediction in veterans with arm exercise vs pharmacologic myocardial perfusion imaging.

PubMed

Martin, Wade H; Xian, Hong; Chandiramani, Pooja; Bainter, Emily; Klein, Andrew J P

2015-08-01

No data exist comparing outcome prediction from arm exercise vs pharmacologic myocardial perfusion imaging (MPI) stress test variables in patients unable to perform treadmill exercise. In this retrospective study, 2,173 consecutive lower extremity disabled veterans aged 65.4 ± 11.0years (mean ± SD) underwent either pharmacologic MPI (1730 patients) or arm exercise stress tests (443 patients) with MPI (n = 253) or electrocardiography alone (n = 190) between 1997 and 2002. Cox multivariate regression models and reclassification analysis by integrated discrimination improvement (IDI) were used to characterize stress test and MPI predictors of cardiovascular mortality at ≥10-year follow-up after inclusion of significant demographic, clinical, and other variables. Cardiovascular death occurred in 561 pharmacologic MPI and 102 arm exercise participants. Multivariate-adjusted cardiovascular mortality was predicted by arm exercise resting metabolic equivalents (hazard ratio [HR] 0.52, 95% CI 0.39-0.69, P < .001), 1-minute heart rate recovery (HR 0.61, 95% CI 0.44-0.86, P < .001), and pharmacologic and arm exercise delta (peak-rest) heart rate (both P < .001). Only an abnormal arm exercise MPI prognosticated cardiovascular death by multivariate Cox analysis (HR 1.98, 95% CI 1.04-3.77, P < .05). Arm exercise MPI defect number, type, and size provided IDI over covariates for prediction of cardiovascular mortality (IDI = 0.074-0.097). Only pharmacologic defect size prognosticated cardiovascular mortality (IDI = 0.022). Arm exercise capacity, heart rate recovery, and pharmacologic and arm exercise heart rate responses are robust predictors of cardiovascular mortality. Arm exercise MPI results are equivalent and possibly superior to pharmacologic MPI for cardiovascular mortality prediction in patients unable to perform treadmill exercise. Published by Elsevier Inc.

Negative predictive value and potential cost savings of acute nuclear myocardial perfusion imaging in low risk patients with suspected acute coronary syndrome: A prospective single blinded study

PubMed Central

Forberg, Jakob L; Hilmersson, Catarina E; Carlsson, Marcus; Arheden, Håkan; Björk, Jonas; Hjalte, Krister; Ekelund, Ulf

2009-01-01

Background Previous studies from the USA have shown that acute nuclear myocardial perfusion imaging (MPI) in low risk emergency department (ED) patients with suspected acute coronary syndrome (ACS) can be of clinical value. The aim of this study was to evaluate the utility and hospital economics of acute MPI in Swedish ED patients with suspected ACS. Methods We included 40 patients (mean age 55 ± 2 years, 50% women) who were admitted from the ED at Lund University Hospital for chest pain suspicious of ACS, and who had a normal or non-ischemic ECG and no previous myocardial infarction. All patients underwent MPI from the ED, and the results were analyzed only after patient discharge. The current diagnostic practice of admitting the included patients for observation and further evaluation was compared to a theoretical "MPI strategy", where patients with a normal MPI test would have been discharged home from the ED. Results Twenty-seven patients had normal MPI results, and none of them had ACS. MPI thus had a negative predictive value for ACS of 100%. With the MPI strategy, 2/3 of the patients would thus have been discharged from the ED, resulting in a reduction of total hospital cost by some 270 EUR and of bed occupancy by 0.8 days per investigated patient. Conclusion Our findings in a Swedish ED support the results of larger American trials that acute MPI has the potential to safely reduce the number of admissions and decrease overall costs for low-risk ED patients with suspected ACS. PMID:19545365

Development and Initial Validation of the Multicultural Personality Inventory (MPI).

PubMed

Ponterotto, Joseph G; Fietzer, Alexander W; Fingerhut, Esther C; Woerner, Scott; Stack, Lauren; Magaldi-Dopman, Danielle; Rust, Jonathan; Nakao, Gen; Tsai, Yu-Ting; Black, Natasha; Alba, Renaldo; Desai, Miraj; Frazier, Chantel; LaRue, Alyse; Liao, Pei-Wen

2014-01-01

Two studies summarize the development and initial validation of the Multicultural Personality Inventory (MPI). In Study 1, the 115-item prototype MPI was administered to 415 university students where exploratory factor analysis resulted in a 70-item, 7-factor model. In Study 2, the 70-item MPI and theoretically related companion instruments were administered to a multisite sample of 576 university students. Confirmatory factory analysis found the 7-factor structure to be a relatively good fit to the data (Comparative Fit Index =.954; root mean square error of approximation =.057), and MPI factors predicted variance in criterion variables above and beyond the variance accounted for by broad personality traits (i.e., Big Five). Study limitations and directions for further validation research are specified.

CLOMP v1.5

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gyllenhaal, J.

CLOMP is the C version of the Livermore OpenMP benchmark developed to measure OpenMP overheads and other performance impacts due to threading. For simplicity, it does not use MPI by default but it is expected to be run on the resources a threaded MPI task would use (e.g., a portion of a shared memory compute node). Compiling with -DWITH_MPI allows packing one or more nodes with CLOMP tasks and having CLOMP report OpenMP performance for the slowest MPI task. On current systems, the strong scaling performance results for 4, 8, or 16 threads are of the most interest. Suggested weakmore » scaling inputs are provided for evaluating future systems. Since MPI is often used to place at least one MPI task per coherence or NUMA domain, it is recommended to focus OpenMP runtime measurements on a subset of node hardware where it is most possible to have low OpenMP overheads (e.g., within one coherence domain or NUMA domain).« less

How to use MPI communication in highly parallel climate simulations more easily and more efficiently.

NASA Astrophysics Data System (ADS)

Behrens, Jörg; Hanke, Moritz; Jahns, Thomas

2014-05-01

In this talk we present a way to facilitate efficient use of MPI communication for developers of climate models. Exploitation of the performance potential of today's highly parallel supercomputers with real world simulations is a complex task. This is partly caused by the low level nature of the MPI communication library which is the dominant communication tool at least for inter-node communication. In order to manage the complexity of the task, climate simulations with non-trivial communication patterns often use an internal abstraction layer above MPI without exploiting the benefits of communication aggregation or MPI-datatypes. The solution for the complexity and performance problem we propose is the communication library YAXT. This library is built on top of MPI and takes high level descriptions of arbitrary domain decompositions and automatically derives an efficient collective data exchange. Several exchanges can be aggregated in order to reduce latency costs. Examples are given which demonstrate the simplicity and the performance gains for selected climate applications.

Murine Polyomavirus Virus-Like Particles Carrying Full-Length Human PSA Protect BALB/c Mice from Outgrowth of a PSA Expressing Tumor

PubMed Central

Eriksson, Mathilda; Andreasson, Kalle; Weidmann, Joachim; Lundberg, Kajsa; Tegerstedt, Karin

2011-01-01

Virus-like particles (VLPs) consist of capsid proteins from viruses and have been shown to be usable as carriers of protein and peptide antigens for immune therapy. In this study, we have produced and assayed murine polyomavirus (MPyV) VLPs carrying the entire human Prostate Specific Antigen (PSA) (PSA-MPyVLPs) for their potential use for immune therapy in a mouse model system. BALB/c mice immunized with PSA-MPyVLPs were only marginally protected against outgrowth of a PSA-expressing tumor. To improve protection, PSA-MPyVLPs were co-injected with adjuvant CpG, either alone or loaded onto murine dendritic cells (DCs). Immunization with PSA-MPyVLPs loaded onto DCs in the presence of CpG was shown to efficiently protect mice from tumor outgrowth. In addition, cellular and humoral immune responses after immunization were examined. PSA-specific CD4+ and CD8+ cells were demonstrated, but no PSA-specific IgG antibodies. Vaccination with DCs loaded with PSA-MPyVLPs induced an eight-fold lower titre of anti-VLP antibodies than vaccination with PSA-MPyVLPs alone. In conclusion, immunization of BALB/c mice with PSA-MPyVLPs, loaded onto DCs and co-injected with CpG, induces an efficient PSA-specific tumor protective immune response, including both CD4+ and CD8+ cells with a low induction of anti-VLP antibodies. PMID:21858228

Usefulness of the comprehensive geriatric assessment in older patients with upper gastrointestinal bleeding: a two-year follow-up study.

PubMed

Pilotto, Alberto; Ferrucci, Luigi; Scarcelli, Carlo; Niro, Valeria; Di Mario, Francesco; Seripa, Davide; Andriulli, Angelo; Leandro, Gioacchino; Franceschi, Marilisa

2007-01-01

The potential usefulness of standardized comprehensive geriatric assessment (CGA) in evaluating treatment and follow-up of older patients with upper gastrointestinal bleeding is unknown. To evaluate the usefulness of the CGA as a 2-year mortality multidimensional prognostic index (MPI) in older patients hospitalized for upper gastrointestinal bleeding. Patients aged > or =65 years consecutively hospitalized for acute upper gastrointestinal bleeding were included. Diagnosis of bleeding was based on clinical and endoscopic features. All patients underwent a CGA that included six standardized scales, i.e., Activities of Daily Living (ADL), Instrumental Activities of Daily Living (IADL), Short Portable Mental Status Questionnaire (SPMSQ), Mini Nutritional Assessment (MNA), Exton-Smith Score (ESS) and Comorbity Index Rating Scale (CIRS), as well as information on medication history and cohabitation, for a total of 63 items. A MPI was calculated from the integrated total scores and expressed as MPI 1 = low risk, MPI 2 = moderate risk, and MPI 3 = severe risk. The predictive value of the MPI for mortality over a 24-month follow-up was calculated. 36 elderly patients (M 16/F 20, mean age 82.8 +/- 7.9 years, range 70-101 years) were included in the study. A significant difference in mean age was observed between males and females (M 80.1 +/- 4.8 vs. F 84.9 +/- 9.3 years; p < 0.05). The causes of upper gastrointestinal bleeding were duodenal ulcer in 38.8%, gastric ulcer in 22.2%, and erosive gastritis in 16.6% of the patients, while 16.6% had gastrointestinal bleeding from unknown origin. The overall 2-year mortality rate was 30.5%. 18 patients (50%) were classified as having a low-risk MPI (mean value 0.18 +/- 0.09), 12 (33.3%) as having a moderate-risk MPI (mean value 0.48 +/- 0.08) and 6 (16.6%) as having a severe-risk MPI (mean value 0.83 +/- 0.06). Higher MPI grades were significantly associated with higher mortality (grade 1 = 12.5%, grade 2 = 41.6%, grade 3 = 83.3%; p = 0.001). Adjusting for age and sex, the prognostic efficacy of MPI for mortality was confirmed and highly significant (odds ratio 10.47, 95% CI 2.04-53.6). CGA is a useful tool for calculating a MPI that significantly predicts the risk of 2-year mortality in older patients with upper gastrointestinal bleeding. Copyright 2007 S. Karger AG, Basel.

Singapore Students' Performance on Australian and Singapore Assessment Items

ERIC Educational Resources Information Center

Ho, Siew Yin; Lowrie, Tom

2012-01-01

This study describes Singapore students' (N = 607) performance on a recently developed Mathematics Processing Instrument (MPI). The MPI comprised tasks sourced from Australia's NAPLAN and Singapore's PSLE. In addition, the MPI had a corresponding question which encouraged students to describe how they solved the respective tasks. In particular,…

Magnetic particle imaging for radiation-free, sensitive and high-contrast vascular imaging and cell tracking.

PubMed

Zhou, Xinyi Y; Tay, Zhi Wei; Chandrasekharan, Prashant; Yu, Elaine Y; Hensley, Daniel W; Orendorff, Ryan; Jeffris, Kenneth E; Mai, David; Zheng, Bo; Goodwill, Patrick W; Conolly, Steven M

2018-05-10

Magnetic particle imaging (MPI) is an emerging ionizing radiation-free biomedical tracer imaging technique that directly images the intense magnetization of superparamagnetic iron oxide nanoparticles (SPIOs). MPI offers ideal image contrast because MPI shows zero signal from background tissues. Moreover, there is zero attenuation of the signal with depth in tissue, allowing for imaging deep inside the body quantitatively at any location. Recent work has demonstrated the potential of MPI for robust, sensitive vascular imaging and cell tracking with high contrast and dose-limited sensitivity comparable to nuclear medicine. To foster future applications in MPI, this new biomedical imaging field is welcoming researchers with expertise in imaging physics, magnetic nanoparticle synthesis and functionalization, nanoscale physics, and small animal imaging applications. Copyright © 2018 Elsevier Ltd. All rights reserved.

MPI_XSTAR: MPI-based Parallelization of the XSTAR Photoionization Program

NASA Astrophysics Data System (ADS)

Danehkar, Ashkbiz; Nowak, Michael A.; Lee, Julia C.; Smith, Randall K.

2018-02-01

We describe a program for the parallel implementation of multiple runs of XSTAR, a photoionization code that is used to predict the physical properties of an ionized gas from its emission and/or absorption lines. The parallelization program, called MPI_XSTAR, has been developed and implemented in the C++ language by using the Message Passing Interface (MPI) protocol, a conventional standard of parallel computing. We have benchmarked parallel multiprocessing executions of XSTAR, using MPI_XSTAR, against a serial execution of XSTAR, in terms of the parallelization speedup and the computing resource efficiency. Our experience indicates that the parallel execution runs significantly faster than the serial execution, however, the efficiency in terms of the computing resource usage decreases with increasing the number of processors used in the parallel computing.

OPAL: An Open-Source MPI-IO Library over Cray XT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yu, Weikuan; Vetter, Jeffrey S; Canon, Richard Shane

Parallel IO over Cray XT is supported by a vendor-supplied MPI-IO package. This package contains a proprietary ADIO implementation built on top of the sysio library. While it is reasonable to maintain a stable code base for application scientists' convenience, it is also very important to the system developers and researchers to analyze and assess the effectiveness of parallel IO software, and accordingly, tune and optimize the MPI-IO implementation. A proprietary parallel IO code base relinquishes such flexibilities. On the other hand, a generic UFS-based MPI-IO implementation is typically used on many Linux-based platforms. We have developed an open-source MPI-IOmore » package over Lustre, referred to as OPAL (OPportunistic and Adaptive MPI-IO Library over Lustre). OPAL provides a single source-code base for MPI-IO over Lustre on Cray XT and Linux platforms. Compared to Cray implementation, OPAL provides a number of good features, including arbitrary specification of striping patterns and Lustre-stripe aligned file domain partitioning. This paper presents the performance comparisons between OPAL and Cray's proprietary implementation. Our evaluation demonstrates that OPAL achieves the performance comparable to the Cray implementation. We also exemplify the benefits of an open source package in revealing the underpinning of the parallel IO performance.« less

Magnetic particle imaging: advancements and perspectives for real-time in vivo monitoring and image-guided therapy

NASA Astrophysics Data System (ADS)

Pablico-Lansigan, Michele H.; Situ, Shu F.; Samia, Anna Cristina S.

2013-05-01

Magnetic particle imaging (MPI) is an emerging biomedical imaging technology that allows the direct quantitative mapping of the spatial distribution of superparamagnetic iron oxide nanoparticles. MPI's increased sensitivity and short image acquisition times foster the creation of tomographic images with high temporal and spatial resolution. The contrast and sensitivity of MPI is envisioned to transcend those of other medical imaging modalities presently used, such as magnetic resonance imaging (MRI), X-ray scans, ultrasound, computed tomography (CT), positron emission tomography (PET) and single photon emission computed tomography (SPECT). In this review, we present an overview of the recent advances in the rapidly developing field of MPI. We begin with a basic introduction of the fundamentals of MPI, followed by some highlights over the past decade of the evolution of strategies and approaches used to improve this new imaging technique. We also examine the optimization of iron oxide nanoparticle tracers used for imaging, underscoring the importance of size homogeneity and surface engineering. Finally, we present some future research directions for MPI, emphasizing the novel and exciting opportunities that it offers as an important tool for real-time in vivo monitoring. All these opportunities and capabilities that MPI presents are now seen as potential breakthrough innovations in timely disease diagnosis, implant monitoring, and image-guided therapeutics.

Comparative accuracy of supine-only and combined supine-prone myocardial perfusion imaging in men.

PubMed

Taasan, Vicente; Wokhlu, Anita; Taasan, Michael V; Dusaj, Raman S; Mehta, Ajay; Kraft, Steven; Winchester, David; Wymer, David

2016-12-01

Combined supine-prone myocardial perfusion imaging (CSP MPI) has been shown to reduce attenuation artifact in comparison to supine-only (SU) MPI in mixed-gender populations with varying risk for coronary artery disease (CAD), often where patients served as their own controls. However, there is limited direct comparison of these imaging strategies in men. 934 male patients underwent CSP or SU MPI. Diagnostic certainty of interpretation was compared. Within the cohort, 116 were referred for left heart catheterization (LHC) to assess for CAD. Sensitivity, specificity, and area under the curve (AUC) were compared with additional analysis based on body mass index (BMI). 597 patients completed the SU protocol and 337 patients completed the CSP protocol. Equivocal studies were seen more frequently in the SU group (13%) than in the CSP group (4%, P < .001). At catheterization, the specificity for CSP MPI of 70% was higher than 40% for SU MPI (P = .032). The CSP AUC (0.80 ± 0.06) was significantly larger than SU AUC (0.57 ± 0.05, P = .004). CSP specificity was significantly higher in obese patients. CSP MPI increases diagnostic certainty and improves test accuracy for CAD detection in men with CAD risk factors, especially obese patients, compared to SU MPI.

Determination of the optimal atrioventricular interval in sick sinus syndrome during DDD pacing.

PubMed

Kato, Masaya; Dote, Keigo; Sasaki, Shota; Goto, Kenji; Takemoto, Hiroaki; Habara, Seiji; Hasegawa, Daiji; Matsuda, Osamu

2005-09-01

Although the AAI pacing mode has been shown to be electromechanically superior to the DDD pacing mode in sick sinus syndrome (SSS), there is evidence suggesting that during AAI pacing the presence of natural ventricular activation pattern is not enough for hemodynamic benefit to occur. Myocardial performance index (MPI) is a simply measurable Doppler-derived index of combined systolic and diastolic myocardial performance. The aim of this study was to investigate whether AAI pacing mode is electromechanically superior to the DDD mode in patients with SSS by using Doppler-derived MPI. Thirty-nine SSS patients with dual-chamber pacing devices were evaluated by using Doppler echocardiography in AAI mode and DDD mode. The optimal atrioventricular (AV) interval in DDD mode was determined and atrial stimulus-R interval was measured in AAI mode. The ratio of the atrial stimulus-R interval to the optimal AV interval was defined as relative AV interval (rAVI) and the ratio of MPI in AAI mode to that in DDD mode was defined as relative MPI (rMPI). The rMPI was significantly correlated with atrial stimulus-R interval and rAVI (r = 0.57, P = 0.0002, and r = 0.67, P < 0.0001, respectively). A cutoff point of 1.73 for rAVI provided optimum sensitivity and specificity for rMPI >1 based on the receiver operator curves. Even though the intrinsic AV conduction is moderately prolonged, some SSS patients with dual-chamber pacing devices benefit from the ventricular pacing with optimal AV interval. MPI is useful to determine the optimal pacing mode in acute experiment.

An MPI-CUDA approach for hypersonic flows with detailed state-to-state air kinetics using a GPU cluster

NASA Astrophysics Data System (ADS)

Bonelli, Francesco; Tuttafesta, Michele; Colonna, Gianpiero; Cutrone, Luigi; Pascazio, Giuseppe

2017-10-01

This paper describes the most advanced results obtained in the context of fluid dynamic simulations of high-enthalpy flows using detailed state-to-state air kinetics. Thermochemical non-equilibrium, typical of supersonic and hypersonic flows, was modeled by using both the accurate state-to-state approach and the multi-temperature model proposed by Park. The accuracy of the two thermochemical non-equilibrium models was assessed by comparing the results with experimental findings, showing better predictions provided by the state-to-state approach. To overcome the huge computational cost of the state-to-state model, a multiple-nodes GPU implementation, based on an MPI-CUDA approach, was employed and a comprehensive code performance analysis is presented. Both the pure MPI-CPU and the MPI-CUDA implementations exhibit excellent scalability performance. GPUs outperform CPUs computing especially when the state-to-state approach is employed, showing speed-ups, of the single GPU with respect to the single-core CPU, larger than 100 in both the case of one MPI process and multiple MPI process.

Iron Oxide Nanoparticle-Micelles (ION-Micelles) for Sensitive (Molecular) Magnetic Particle Imaging and Magnetic Resonance Imaging

PubMed Central

Starmans, Lucas W. E.; Burdinski, Dirk; Haex, Nicole P. M.; Moonen, Rik P. M.; Strijkers, Gustav J.; Nicolay, Klaas; Grüll, Holger

2013-01-01

Background Iron oxide nanoparticles (IONs) are a promising nanoplatform for contrast-enhanced MRI. Recently, magnetic particle imaging (MPI) was introduced as a new imaging modality, which is able to directly visualize magnetic particles and could serve as a more sensitive and quantitative alternative to MRI. However, MPI requires magnetic particles with specific magnetic properties for optimal use. Current commercially available iron oxide formulations perform suboptimal in MPI, which is triggering research into optimized synthesis strategies. Most synthesis procedures aim at size control of iron oxide nanoparticles rather than control over the magnetic properties. In this study, we report on the synthesis, characterization and application of a novel ION platform for sensitive MPI and MRI. Methods and Results IONs were synthesized using a thermal-decomposition method and subsequently phase-transferred by encapsulation into lipidic micelles (ION-Micelles). Next, the material and magnetic properties of the ION-Micelles were analyzed. Most notably, vibrating sample magnetometry measurements showed that the effective magnetic core size of the IONs is 16 nm. In addition, magnetic particle spectrometry (MPS) measurements were performed. MPS is essentially zero-dimensional MPI and therefore allows to probe the potential of iron oxide formulations for MPI. ION-Micelles induced up to 200 times higher signal in MPS measurements than commercially available iron oxide formulations (Endorem, Resovist and Sinerem) and thus likely allow for significantly more sensitive MPI. In addition, the potential of the ION-Micelle platform for molecular MPI and MRI was showcased by MPS and MRI measurements of fibrin-binding peptide functionalized ION-Micelles (FibPep-ION-Micelles) bound to blood clots. Conclusions The presented data underlines the potential of the ION-Micelle nanoplatform for sensitive (molecular) MPI and warrants further investigation of the FibPep-ION-Micelle platform for in vivo, non-invasive imaging of fibrin in preclinical disease models of thrombus-related pathologies and atherosclerosis. PMID:23437371

Iron oxide nanoparticle-micelles (ION-micelles) for sensitive (molecular) magnetic particle imaging and magnetic resonance imaging.

PubMed

Starmans, Lucas W E; Burdinski, Dirk; Haex, Nicole P M; Moonen, Rik P M; Strijkers, Gustav J; Nicolay, Klaas; Grüll, Holger

2013-01-01

Iron oxide nanoparticles (IONs) are a promising nanoplatform for contrast-enhanced MRI. Recently, magnetic particle imaging (MPI) was introduced as a new imaging modality, which is able to directly visualize magnetic particles and could serve as a more sensitive and quantitative alternative to MRI. However, MPI requires magnetic particles with specific magnetic properties for optimal use. Current commercially available iron oxide formulations perform suboptimal in MPI, which is triggering research into optimized synthesis strategies. Most synthesis procedures aim at size control of iron oxide nanoparticles rather than control over the magnetic properties. In this study, we report on the synthesis, characterization and application of a novel ION platform for sensitive MPI and MRI. IONs were synthesized using a thermal-decomposition method and subsequently phase-transferred by encapsulation into lipidic micelles (ION-Micelles). Next, the material and magnetic properties of the ION-Micelles were analyzed. Most notably, vibrating sample magnetometry measurements showed that the effective magnetic core size of the IONs is 16 nm. In addition, magnetic particle spectrometry (MPS) measurements were performed. MPS is essentially zero-dimensional MPI and therefore allows to probe the potential of iron oxide formulations for MPI. ION-Micelles induced up to 200 times higher signal in MPS measurements than commercially available iron oxide formulations (Endorem, Resovist and Sinerem) and thus likely allow for significantly more sensitive MPI. In addition, the potential of the ION-Micelle platform for molecular MPI and MRI was showcased by MPS and MRI measurements of fibrin-binding peptide functionalized ION-Micelles (FibPep-ION-Micelles) bound to blood clots. The presented data underlines the potential of the ION-Micelle nanoplatform for sensitive (molecular) MPI and warrants further investigation of the FibPep-ION-Micelle platform for in vivo, non-invasive imaging of fibrin in preclinical disease models of thrombus-related pathologies and atherosclerosis.

''Towards a High-Performance and Robust Implementation of MPI-IO on Top of GPFS''

DOE Office of Scientific and Technical Information (OSTI.GOV)

Prost, J.P.; Tremann, R.; Blackwore, R.

2000-01-11

MPI-IO/GPFS is a prototype implementation of the I/O chapter of the Message Passing Interface (MPI) 2 standard. It uses the IBM General Parallel File System (GPFS), with prototyped extensions, as the underlying file system. this paper describes the features of this prototype which support its high performance and robustness. The use of hints at the file system level and at the MPI-IO level allows tailoring the use of the file system to the application needs. Error handling in collective operations provides robust error reporting and deadlock prevention in case of returning errors.

A novel artificial neural network method for biomedical prediction based on matrix pseudo-inversion.

PubMed

Cai, Binghuang; Jiang, Xia

2014-04-01

Biomedical prediction based on clinical and genome-wide data has become increasingly important in disease diagnosis and classification. To solve the prediction problem in an effective manner for the improvement of clinical care, we develop a novel Artificial Neural Network (ANN) method based on Matrix Pseudo-Inversion (MPI) for use in biomedical applications. The MPI-ANN is constructed as a three-layer (i.e., input, hidden, and output layers) feed-forward neural network, and the weights connecting the hidden and output layers are directly determined based on MPI without a lengthy learning iteration. The LASSO (Least Absolute Shrinkage and Selection Operator) method is also presented for comparative purposes. Single Nucleotide Polymorphism (SNP) simulated data and real breast cancer data are employed to validate the performance of the MPI-ANN method via 5-fold cross validation. Experimental results demonstrate the efficacy of the developed MPI-ANN for disease classification and prediction, in view of the significantly superior accuracy (i.e., the rate of correct predictions), as compared with LASSO. The results based on the real breast cancer data also show that the MPI-ANN has better performance than other machine learning methods (including support vector machine (SVM), logistic regression (LR), and an iterative ANN). In addition, experiments demonstrate that our MPI-ANN could be used for bio-marker selection as well. Copyright © 2013 Elsevier Inc. All rights reserved.

Gender differences in the diagnostic accuracy of SPECT myocardial perfusion imaging: a bivariate meta-analysis.

PubMed

Iskandar, Aline; Limone, Brendan; Parker, Matthew W; Perugini, Andrew; Kim, Hyejin; Jones, Charles; Calamari, Brian; Coleman, Craig I; Heller, Gary V

2013-02-01

It remains controversial whether the diagnostic accuracy of single-photon emission computed tomography myocardial perfusion imaging (SPECT MPI) is different in men as compared to women. We performed a meta-analysis to investigate gender differences of SPECT MPI for the diagnosis of CAD (≥50% stenosis). Two investigators independently performed a systematic review of the MEDLINE and EMBASE databases from inception through January 2012 for English-language studies determining the diagnostic accuracy of SPECT MPI. We included prospective studies that compared SPECT MPI with conventional coronary angiography which provided sufficient data to calculate gender-specific true and false positives and negatives. Data from studies evaluating <20 patients of one gender were excluded. Bivariate meta-analysis was used to create summary receiver operating curves. Twenty-six studies met inclusion criteria, representing 1,148 women and 1,142 men. Bivariate meta-analysis yielded a mean sensitivity and specificity of 84.2% (95% confidence interval [CI] 78.7%-88.6%) and 78.7% (CI 70.0%-85.3%) for SPECT MPI in women and 89.1% (CI 84.0%-92.7%) and 71.2% (CI 60.8%-79.8%) for SPECT MPI in men. There was no significant difference in the sensitivity (P = .15) or specificity (P = .23) between male and female subjects. In a bivariate meta-analysis of the available literature, the diagnostic accuracy of SPECT MPI is similar for both men and women.

Direct comparison of rest and adenosine stress myocardial perfusion CT with rest and stress SPECT

PubMed Central

Okada, David R.; Ghoshhajra, Brian B.; Blankstein, Ron; Rocha-Filho, Jose A.; Shturman, Leonid D.; Rogers, Ian S.; Bezerra, Hiram G.; Sarwar, Ammar; Gewirtz, Henry; Hoffmann, Udo; Mamuya, Wilfred S.; Brady, Thomas J.; Cury, Ricardo C.

2010-01-01

Introduction We have recently described a technique for assessing myocardial perfusion using adenosine-mediated stress imaging (CTP) with dual source computed tomography. SPECT myocardial perfusion imaging (SPECT-MPI) is a widely utilized and extensively validated method for assessing myocardial perfusion. The aim of this study was to determine the level of agreement between CTP and SPECT-MPI at rest and under stress on a per-segment, per-vessel, and per-patient basis. Methods Forty-seven consecutive patients underwent CTP and SPECT-MPI. Perfusion images were interpreted using the 17 segment AHA model and were scored on a 0 (normal) to 3 (abnormal) scale. Summed rest and stress scores were calculated for each vascular territory and patient by adding corresponding segmental scores. Results On a per-segment basis (n = 799), CTP and SPECT-MPI demonstrated excellent correlation: Goodman-Kruskall γ = .59 (P < .0001) for stress and .75 (P < .0001) for rest. On a per-vessel basis (n = 141), CTP and SPECT-MPI summed scores demonstrated good correlation: Pearson r = .56 (P < .0001) for stress and .66 (P < .0001) for rest. On a per-patient basis (n = 47), CTP and SPECT-MPI demonstrated good correlation: Pearson r = .60 (P < .0001) for stress and .76 (P < .0001) for rest. Conclusions CTP compares favorably with SPECT-MPI for detection, extent, and severity of myocardial perfusion defects at rest and stress. PMID:19936863

Association of Antidementia Drugs and Mortality in Community-Dwelling Frail Older Patients With Dementia: The Role of Mortality Risk Assessment.

PubMed

Pilotto, Alberto; Polidori, Maria Cristina; Veronese, Nicola; Panza, Francesco; Arboretti Giancristofaro, Rosa; Pilotto, Andrea; Daragjati, Julia; Carrozzo, Eleonora; Prete, Camilla; Gallina, Pietro; Padovani, Alessandro; Maggi, Stefania

2018-02-01

To evaluate whether treatment with antidementia drugs is associated with reduced mortality in older patients with different mortality risk at baseline. Retrospective. Community-dwelling. A total of 6818 older people who underwent a Standardized Multidimensional Assessment Schedule for Adults and Aged Persons (SVaMA) evaluation to determine accessibility to homecare services or nursing home admission from 2005 to 2013 in the Padova Health District, Italy were included. Mortality risk at baseline was calculated by the Multidimensional Prognostic Index (MPI), based on information collected with the SVaMA. Participants were categorized to have mild (MPI-SVaMA-1), moderate (MPI-SVaMA-2), and high (MPI-SVaMA-3) mortality risk. Propensity score-adjusted hazard ratios (HR) of 2-year mortality were calculated according to antidementia drug treatment. Patients treated with antidementia drugs had a significant lower risk of death than untreated patients (HR 0.82; 95% confidence interval [CI] 0.73-0.92 and 0.56; 95% CI 0.49-0.65 for patients treated less than 2 years and more than 2 years treatment, respectively). After dividing patients according to their MPI-SVaMA grade, antidementia treatment was significantly associated with reduced mortality in the MPI-SVaMA-1 mild (HR 0.71; 95% CI 0.54-0.92) and MPI-SVaMA-2 moderate risk (HR 0.61; 95% CI 0.40-0.91, matched sample), but not in the MPI-SVaMA-3 high risk of death. This large community-dwelling patient study suggests that antidementia drugs might contribute to increased survival in older adults with dementia with lower mortality risk. Copyright © 2017 AMDA – The Society for Post-Acute and Long-Term Care Medicine. Published by Elsevier Inc. All rights reserved.

Cardiovascular outcomes after pharmacologic stress myocardial perfusion imaging.

PubMed

Lee, Douglas S; Husain, Mansoor; Wang, Xuesong; Austin, Peter C; Iwanochko, Robert M

2016-04-01

While pharmacologic stress single photon emission computed tomography myocardial perfusion imaging (SPECT-MPI) is used for noninvasive evaluation of patients who are unable to perform treadmill exercise, its impact on net reclassification improvement (NRI) of prognosis is unknown. We evaluated the prognostic value of pharmacologic stress MPI for prediction of cardiovascular death or non-fatal myocardial infarction (MI) within 1 year at a single-center, university-based laboratory. We examined continuous and categorical NRI of pharmacologic SPECT-MPI for prediction of outcomes beyond clinical factors alone. Six thousand two hundred forty patients (median age 66 years [IQR 56-74], 3466 men) were studied and followed for 5963 person-years. SPECT-MPI variables associated with increased risk of cardiovascular death or non-fatal MI included summed stress score, stress ST-shift, and post-stress resting left ventricular ejection fraction ≤50%. Compared to a clinical model which included age, sex, cardiovascular disease, risk factors, and medications, model χ(2) (210.5 vs. 281.9, P < .001) and c-statistic (0.74 vs. 0.78, P < .001) were significantly increased by addition of SPECT-MPI predictors (summed stress score, stress ST-shift and stress resting left ventricular ejection fraction). SPECT-MPI predictors increased continuous NRI by 49.4% (P < .001), reclassifying 66.5% of patients as lower risk and 32.8% as higher risk of cardiovascular death or non-fatal MI. Addition of MPI predictors to clinical factors using risk categories, defined as <1%, 1% to 3%, and >3% annualized risk of cardiovascular death or non-fatal MI, yielded a 15.0% improvement in NRI (95% CI 7.6%-27.6%, P < .001). Pharmacologic stress MPI substantially improved net reclassification of cardiovascular death or MI risk beyond that afforded by clinical factors. Copyright © 2016 Elsevier Inc. All rights reserved.

Relation of Coronary Flow Reserve to Other Findings on Positron Emission Tomography Myocardial Perfusion Imaging and Left Heart Catheterization in Patients With End-stage Renal Disease Being Evaluated for Kidney Transplant.

PubMed

Paz, Yehuda; Morgenstern, Rachelle; Weinberg, Richard; Chiles, Mariana; Bhatti, Navdeep; Ali, Ziad; Mohan, Sumit; Bokhari, Sabahat

2017-12-01

Cardiovascular disease is the leading cause of death in patients with end-stage renal disease (ESRD) and often goes undetected. Abnormal coronary flow reserve (CFR), which predicts increased risk of cardiac death, may be present in patients with ESRD without other evidence of coronary artery disease (CAD). We prospectively studied 131 patients who had rest and dipyridamole pharmacologic stress N 13 -ammonia positron emission tomography myocardial perfusion imaging (PET MPI) for kidney transplant evaluation. Thirty-four patients also had left heart catheterization. Abnormal PET MPI was defined as qualitative ischemia or infarct, stress electrocardiogram ischemia, or transient ischemic dilation. CFR was calculated as the ratio of stress to rest coronary blood flow. Global CFR < 2 was defined as abnormal. Of 131 patients who had PET MPI (66% male, 55.6 ± 12.1 years), 30% (39 of 131) had abnormal PET MPI and 59% (77 of 131) had abnormal CFR. In a subset of 34 patients who had left heart catheterization (66% male, 61.0 ± 12.1 years), 68% (23 of 34) had abnormal CFR on PET MPI, and 68% (23 of 34) had ≥70% obstruction on left heart catheterization. Abnormal CFR was not significantly associated with abnormal PET MPI (p = 0.13) or obstructive CAD on left heart catheterization (p = 0.26). In conclusion, in the first prospective study of PET MPI in patients with ESRD, abnormal CFR is highly prevalent and is independent of abnormal findings on PET MPI or obstructive CAD on left heart catheterization. Copyright © 2017 Elsevier Inc. All rights reserved.

Dobutamine stress myocardial perfusion imaging: 8-year outcomes in patients with diabetes mellitus.

PubMed

Boiten, Hendrik J; van Domburg, Ron T; Valkema, Roelf; Zijlstra, Felix; Schinkel, Arend F L

2016-08-01

Many studies have examined the prognostic value of myocardial perfusion imaging (MPI) using single-photon emission computed tomography (SPECT) for the prediction of short- to medium-term outcomes. However, the long-term prognostic value of MPI in patients with diabetes mellitus remains unclear. Therefore, this study assessed the long-term prognostic value of MPI in a high-risk cohort of patients with diabetes mellitus. A high-risk cohort of 207 patients with diabetes mellitus who were unable to undergo exercise testing underwent dobutamine stress MPI. Follow-up was successful in 206 patients; 12 patients were excluded due to early revascularization. The current data are based on the remaining 194 patients. Follow-up end points were all-cause mortality, cardiac mortality, and nonfatal myocardial infarction. The Kaplan-Meier survival curves were constructed, and univariable and multivariable analyses were performed to identify predictors of long-term outcome. During a mean follow-up of 8.1 ± 5.9 years, 134 (69%) patients died of which 68 (35%) died due to cardiac causes. Nonfatal myocardial infarction occurred in 24 patients (12%), and late (>60 days) coronary revascularization was performed in 61 (13%) patients. Survival analysis showed that MPI provided optimal risk stratification up to 4 years after testing. After that period, the outcome was comparable in patients with normal and abnormal MPI. Multivariable analyses showed that MPI provided incremental prognostic value up to 4 years after testing. In high-risk patients with diabetes mellitus, dobutamine MPI provides incremental prognostic information in addition to clinical data for a 4-year period after testing. Published on behalf of the European Society of Cardiology. All rights reserved. © The Author 2016. For permissions please email: journals.permissions@oup.com.

The Comprehensive Geriatric Assessment and the multidimensional approach. A new look at the older patient with gastroenterological disorders.

PubMed

Pilotto, Alberto; Addante, Filomena; D'Onofrio, Grazia; Sancarlo, Daniele; Ferrucci, Luigi

2009-01-01

The Comprehensive Geriatric Assessment (CGA) is a multidimensional, usually interdisciplinary, diagnostic process intended to determine an elderly person's medical, psychosocial, and functional capacity and problems with the objective of developing an overall plan for treatment and short- and long-term follow-up. The potential usefulness of the CGA in evaluating treatment and follow-up of older patients with gastroenterological disorders is unknown. In the paper we reported the efficacy of a Multidimensional-Prognostic Index (MPI), calculated from information collected by a standardized CGA, in predicting mortality risk in older patients hospitalized with upper gastrointestinal bleeding and liver cirrhosis. Patients underwent a CGA that included six standardized scales, i.e. Activities of Daily Living (ADL), Instrumental Activities of Daily Living (IADL), Short-Portable Mental Status Questionnaire (SPMSQ), Mini-Nutritional Assessment (MNA), Exton-Smith Score (ESS) and Comorbity Index Rating Scale (CIRS), as well as information on medication history and cohabitation, for a total of 63 items. The MPI was calculated from the integrated total scores and expressed as MPI 1=low risk, MPI 2=moderate risk and MPI 3=severe risk of mortality. Higher MPI values were significantly associated with higher short- and long-term mortality in older patients with both upper gastrointestinal bleeding and liver cirrhosis. A close agreement was found between the estimated mortality by MPI and the observed mortality. Moreover, MPI seems to have a greater discriminatory power than organ-specific prognostic indices such as Rockall and Blatchford scores (in upper gastrointestinal bleeding patients) and Child-Plugh score (in liver cirrhosis patients). All these findings support the concept that a multidimensional approach may be appropriate for the evaluation of older patients with gastroenterological disorders, like it has been reported for patients with other pathological conditions.

Myocardial perfusion imaging with PET

PubMed Central

Nakazato, Ryo; Berman, Daniel S; Alexanderson, Erick; Slomka, Piotr

2013-01-01

PET-myocardial perfusion imaging (MPI) allows accurate measurement of myocardial perfusion, absolute myocardial blood flow and function at stress and rest in a single study session performed in approximately 30 min. Various PET tracers are available for MPI, and rubidium-82 or nitrogen-13-ammonia is most commonly used. In addition, a new fluorine-18-based PET-MPI tracer is currently being evaluated. Relative quantification of PET perfusion images shows very high diagnostic accuracy for detection of obstructive coronary artery disease. Dynamic myocardial blood flow analysis has demonstrated additional prognostic value beyond relative perfusion imaging. Patient radiation dose can be reduced and image quality can be improved with latest advances in PET/CT equipment. Simultaneous assessment of both anatomy and perfusion by hybrid PET/CT can result in improved diagnostic accuracy. Compared with SPECT-MPI, PET-MPI provides higher diagnostic accuracy, using lower radiation doses during a shorter examination time period for the detection of coronary artery disease. PMID:23671459

How Formal Dynamic Verification Tools Facilitate Novel Concurrency Visualizations

NASA Astrophysics Data System (ADS)

Aananthakrishnan, Sriram; Delisi, Michael; Vakkalanka, Sarvani; Vo, Anh; Gopalakrishnan, Ganesh; Kirby, Robert M.; Thakur, Rajeev

With the exploding scale of concurrency, presenting valuable pieces of information collected by formal verification tools intuitively and graphically can greatly enhance concurrent system debugging. Traditional MPI program debuggers present trace views of MPI program executions. Such views are redundant, often containing equivalent traces that permute independent MPI calls. In our ISP formal dynamic verifier for MPI programs, we present a collection of alternate views made possible by the use of formal dynamic verification. Some of ISP’s views help pinpoint errors, some facilitate discerning errors by eliminating redundancy, while others help understand the program better by displaying concurrent even orderings that must be respected by all MPI implementations, in the form of completes-before graphs. In this paper, we describe ISP’s graphical user interface (GUI) capabilities in all these areas which are currently supported by a portable Java based GUI, a Microsoft Visual Studio GUI, and an Eclipse based GUI whose development is in progress.

Multiphoton imaging with high peak power VECSELs

NASA Astrophysics Data System (ADS)

Mirkhanov, Shamil; Quarterman, Adrian H.; Swift, Samuel; Praveen, Bavishna B.; Smyth, Conor J. C.; Wilcox, Keith G.

2016-03-01

Multiphoton imaging (MMPI) has become one of thee key non-invasive light microscopy techniques. This technique allows deep tissue imaging with high resolution and less photo-damage than conventional confocal microscopy. MPI is type of laser-scanning microscopy that employs localized nonlinear excitation, so that fluorescence is excited only with is scanned focal volume. For many years, Ti: sapphire femtosecond lasers have been the leading light sources for MPI applications. However, recent developments in laser sources and new types of fluorophores indicate that longer wavelength excitation could be a good alternative for these applications. Mode-locked VECSEELs have the potential to be low cost, compact light sources for MPI systems, with the additional advantage of broad wavelength coverage through use of different semiconductor material systems. Here, we use a femtosecond fibber laser to investigate the effect average power and repetition rate has on MPI image quality, to allow us to optimize our mode-locked VVECSELs for MPI.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Murase, Kenya, E-mail: murase@sahs.med.osaka-u.ac.jp; Song, Ruixiao; Hiratsuka, Samu

We investigated the feasibility of visualizing blood coagulation using a system for magnetic particle imaging (MPI). A magnetic field-free line is generated using two opposing neodymium magnets and transverse images are reconstructed from the third-harmonic signals received by a gradiometer coil, using the maximum likelihood-expectation maximization algorithm. Our MPI system was used to image the blood coagulation induced by adding CaCl{sub 2} to whole sheep blood mixed with magnetic nanoparticles (MNPs). The “MPI value” was defined as the pixel value of the transverse image reconstructed from the third-harmonic signals. MPI values were significantly smaller for coagulated blood samples than thosemore » without coagulation. We confirmed the rationale of these results by calculating the third-harmonic signals for the measured viscosities of samples, with an assumption that the magnetization and particle size distribution of MNPs obey the Langevin equation and log-normal distribution, respectively. We concluded that MPI can be useful for visualizing blood coagulation.« less

Memory Compression Techniques for Network Address Management in MPI

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guo, Yanfei; Archer, Charles J.; Blocksome, Michael

MPI allows applications to treat processes as a logical collection of integer ranks for each MPI communicator, while internally translating these logical ranks into actual network addresses. In current MPI implementations the management and lookup of such network addresses use memory sizes that are proportional to the number of processes in each communicator. In this paper, we propose a new mechanism, called AV-Rankmap, for managing such translation. AV-Rankmap takes advantage of logical patterns in rank-address mapping that most applications naturally tend to have, and it exploits the fact that some parts of network address structures are naturally more performance criticalmore » than others. It uses this information to compress the memory used for network address management. We demonstrate that AV-Rankmap can achieve performance similar to or better than that of other MPI implementations while using significantly less memory.« less

Facilitating Co-Design for Extreme-Scale Systems Through Lightweight Simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Engelmann, Christian; Lauer, Frank

This work focuses on tools for investigating algorithm performance at extreme scale with millions of concurrent threads and for evaluating the impact of future architecture choices to facilitate the co-design of high-performance computing (HPC) architectures and applications. The approach focuses on lightweight simulation of extreme-scale HPC systems with the needed amount of accuracy. The prototype presented in this paper is able to provide this capability using a parallel discrete event simulation (PDES), such that a Message Passing Interface (MPI) application can be executed at extreme scale, and its performance properties can be evaluated. The results of an initial prototype aremore » encouraging as a simple 'hello world' MPI program could be scaled up to 1,048,576 virtual MPI processes on a four-node cluster, and the performance properties of two MPI programs could be evaluated at up to 16,384 virtual MPI processes on the same system.« less

Evaluating and extending user-level fault tolerance in MPI applications

DOE PAGES

Laguna, Ignacio; Richards, David F.; Gamblin, Todd; ...

2016-01-11

The user-level failure mitigation (ULFM) interface has been proposed to provide fault-tolerant semantics in the Message Passing Interface (MPI). Previous work presented performance evaluations of ULFM; yet questions related to its programability and applicability, especially to non-trivial, bulk synchronous applications, remain unanswered. In this article, we present our experiences on using ULFM in a case study with a large, highly scalable, bulk synchronous molecular dynamics application to shed light on the advantages and difficulties of this interface to program fault-tolerant MPI applications. We found that, although ULFM is suitable for master–worker applications, it provides few benefits for more common bulkmore » synchronous MPI applications. Furthermore, to address these limitations, we introduce a new, simpler fault-tolerant interface for complex, bulk synchronous MPI programs with better applicability and support than ULFM for application-level recovery mechanisms, such as global rollback.« less

Accelerating Climate Simulations Through Hybrid Computing

NASA Technical Reports Server (NTRS)

Zhou, Shujia; Sinno, Scott; Cruz, Carlos; Purcell, Mark

2009-01-01

Unconventional multi-core processors (e.g., IBM Cell B/E and NYIDIDA GPU) have emerged as accelerators in climate simulation. However, climate models typically run on parallel computers with conventional processors (e.g., Intel and AMD) using MPI. Connecting accelerators to this architecture efficiently and easily becomes a critical issue. When using MPI for connection, we identified two challenges: (1) identical MPI implementation is required in both systems, and; (2) existing MPI code must be modified to accommodate the accelerators. In response, we have extended and deployed IBM Dynamic Application Virtualization (DAV) in a hybrid computing prototype system (one blade with two Intel quad-core processors, two IBM QS22 Cell blades, connected with Infiniband), allowing for seamlessly offloading compute-intensive functions to remote, heterogeneous accelerators in a scalable, load-balanced manner. Currently, a climate solar radiation model running with multiple MPI processes has been offloaded to multiple Cell blades with approx.10% network overhead.

A Convex Formulation for Magnetic Particle Imaging X-Space Reconstruction.

PubMed

Konkle, Justin J; Goodwill, Patrick W; Hensley, Daniel W; Orendorff, Ryan D; Lustig, Michael; Conolly, Steven M

2015-01-01

Magnetic Particle Imaging (mpi) is an emerging imaging modality with exceptional promise for clinical applications in rapid angiography, cell therapy tracking, cancer imaging, and inflammation imaging. Recent publications have demonstrated quantitative mpi across rat sized fields of view with x-space reconstruction methods. Critical to any medical imaging technology is the reliability and accuracy of image reconstruction. Because the average value of the mpi signal is lost during direct-feedthrough signal filtering, mpi reconstruction algorithms must recover this zero-frequency value. Prior x-space mpi recovery techniques were limited to 1d approaches which could introduce artifacts when reconstructing a 3d image. In this paper, we formulate x-space reconstruction as a 3d convex optimization problem and apply robust a priori knowledge of image smoothness and non-negativity to reduce non-physical banding and haze artifacts. We conclude with a discussion of the powerful extensibility of the presented formulation for future applications.

Tracking short-term biodistribution and long-term clearance of SPIO tracers in magnetic particle imaging

NASA Astrophysics Data System (ADS)

Keselman, Paul; Yu, Elaine Y.; Zhou, Xinyi Y.; Goodwill, Patrick W.; Chandrasekharan, Prashant; Ferguson, R. Matthew; Khandhar, Amit P.; Kemp, Scott J.; Krishnan, Kannan M.; Zheng, Bo; Conolly, Steven M.

2017-05-01

Magnetic particle imaging (MPI) is an emerging tracer-based medical imaging modality that images non-radioactive, kidney-safe superparamagnetic iron oxide (SPIO) tracers. MPI offers quantitative, high-contrast and high-SNR images, so MPI has exceptional promise for applications such as cell tracking, angiography, brain perfusion, cancer detection, traumatic brain injury and pulmonary imaging. In assessing MPI’s utility for applications mentioned above, it is important to be able to assess tracer short-term biodistribution as well as long-term clearance from the body. Here, we describe the biodistribution and clearance for two commonly used tracers in MPI: Ferucarbotran (Meito Sangyo Co., Japan) and LS-oo8 (LodeSpin Labs, Seattle, WA). We successfully demonstrate that 3D MPI is able to quantitatively assess short-term biodistribution, as well as long-term tracking and clearance of these tracers in vivo.

Using Modules with MPICH-G2 (and "Loose Ends")

NASA Technical Reports Server (NTRS)

Chang, Johnny; Thigpen, William W. (Technical Monitor)

2002-01-01

A new approach to running complex, distributed MPI jobs using the MPICH-G2 library is described. This approach allows the user to switch between different versions of compilers, system libraries, MPI libraries, etc. via the "module" command. The key idea is a departure from the prescribed "(jobtype=mpi)" approach to running distributed MPI jobs. The new method requires the user to provide a script that will be run as the "executable" with the "(jobtype=single)" RSL attribute. The major advantage of the proposed method is to enable users to decide in their own script what modules, environment, etc. they would like to have in running their job.

A Log-Scaling Fault Tolerant Agreement Algorithm for a Fault Tolerant MPI

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hursey, Joshua J; Naughton, III, Thomas J; Vallee, Geoffroy R

The lack of fault tolerance is becoming a limiting factor for application scalability in HPC systems. The MPI does not provide standardized fault tolerance interfaces and semantics. The MPI Forum's Fault Tolerance Working Group is proposing a collective fault tolerant agreement algorithm for the next MPI standard. Such algorithms play a central role in many fault tolerant applications. This paper combines a log-scaling two-phase commit agreement algorithm with a reduction operation to provide the necessary functionality for the new collective without any additional messages. Error handling mechanisms are described that preserve the fault tolerance properties while maintaining overall scalability.

New Trends in Radionuclide Myocardial Perfusion Imaging

PubMed Central

Hung, Guang-Uei; Wang, Yuh-Feng; Su, Hung-Yi; Hsieh, Te-Chun; Ko, Chi-Lun; Yen, Ruoh-Fang

2016-01-01

Radionuclide myocardial perfusion imaging (MPI) with single photon emission computed tomography (SPECT) has been widely used clinically as one of the major functional imaging modalities for patients with coronary artery disease (CAD) for decades. Ample evidence has supported the use of MPI as a useful and important tool in the diagnosis, risk stratification and treatment planning for CAD. Although popular in the United States, MPI has become the most frequently used imaging modality among all nuclear medicine tests in Taiwan. However, it should be acknowledged that MPI SPECT does have its limitations. These include false-positive results due to certain artifacts, false-negative due to balanced ischemia, complexity and adverse reaction arising from current pharmacological stressors, time consuming nature of the imaging procedure, no blood flow quantitation and relatively high radiation exposure. The purpose of this article was to review the recent trends in nuclear cardiology, including the utilization of positron emission tomography (PET) for MPI, new stressor, new SPECT camera with higher resolution and higher sensitivity, dynamic SPECT protocol for blood flow quantitation, new software of phase analysis for evaluation of LV dyssynchrony, and measures utilized for reducing radiation exposure of MPI. PMID:27122946

Relaxation-based viscosity mapping for magnetic particle imaging.

PubMed

Utkur, M; Muslu, Y; Saritas, E U

2017-05-07

Magnetic particle imaging (MPI) has been shown to provide remarkable contrast for imaging applications such as angiography, stem cell tracking, and cancer imaging. Recently, there is growing interest in the functional imaging capabilities of MPI, where 'color MPI' techniques have explored separating different nanoparticles, which could potentially be used to distinguish nanoparticles in different states or environments. Viscosity mapping is a promising functional imaging application for MPI, as increased viscosity levels in vivo have been associated with numerous diseases such as hypertension, atherosclerosis, and cancer. In this work, we propose a viscosity mapping technique for MPI through the estimation of the relaxation time constant of the nanoparticles. Importantly, the proposed time constant estimation scheme does not require any prior information regarding the nanoparticles. We validate this method with extensive experiments in an in-house magnetic particle spectroscopy (MPS) setup at four different frequencies (between 250 Hz and 10.8 kHz) and at three different field strengths (between 5 mT and 15 mT) for viscosities ranging between 0.89 mPa · s-15.33 mPa · s. Our results demonstrate the viscosity mapping ability of MPI in the biologically relevant viscosity range.

Development of training modules for magnetic particle inspection

NASA Astrophysics Data System (ADS)

Kosaka, Daigo; Eisenmann, David J.; Enyart, Darrel; Nakagawa, Norio; Lo, Chester; Orman, David

2015-03-01

Magnetic particle inspection (MPI) is a nondestructive evaluation technique used with ferromagnetic materials. Although the application of this method may appear straightforward, MPI combines the complicated nature of electromagnetics, metallurgical material effects, fluid-particle motion dynamics, and physiological human factors into a single inspection. To fully appreciate industry specifications such as ASTM E-1444, users should develop a basic understanding of the many factors that are involved in MPI. We have developed a series of MPI training modules that are aimed at addressing this requirement. The modules not only offer qualitative explanations, but also show quantitative explanations in terms of measurement and numerical simulation data in many instances. There are five modules in all. Module ♯1 shows characteristics of waveforms and magnetizing methods. This allows MPI practitioners to make optimum choice of waveform and magnetizing method. Module ♯2 explains how material properties relate to the magnetic characteristics. Module ♯3 shows the strength of the excitation field or the flux leakage from a crack and how it compares to the detectability of a crack by MPI. Module ♯4 shows how specimen status may influence defect detection. Module ♯5 shows the effects of particle properties on defect detection.

Mannose phosphate isomerase regulates fibroblast growth factor receptor family signaling and glioma radiosensitivity.

PubMed

Cazet, Aurélie; Charest, Jonathan; Bennett, Daniel C; Sambrooks, Cecilia Lopez; Contessa, Joseph N

2014-01-01

Asparagine-linked glycosylation is an endoplasmic reticulum co- and post-translational modification that enables the transit and function of receptor tyrosine kinase (RTK) glycoproteins. To gain insight into the regulatory role of glycosylation enzymes on RTK function, we investigated shRNA and siRNA knockdown of mannose phosphate isomerase (MPI), an enzyme required for mature glycan precursor biosynthesis. Loss of MPI activity reduced phosphorylation of FGFR family receptors in U-251 and SKMG-3 malignant glioma cell lines and also resulted in significant decreases in FRS2, Akt, and MAPK signaling. However, MPI knockdown did not affect ligand-induced activation or signaling of EGFR or MET RTKs, suggesting that FGFRs are more susceptible to MPI inhibition. The reductions in FGFR signaling were not caused by loss of FGF ligands or receptors, but instead were caused by interference with receptor dimerization. Investigations into the cellular consequences of MPI knockdown showed that cellular programs driven by FGFR signaling, and integral to the clinical progression of malignant glioma, were impaired. In addition to a blockade of cellular migration, MPI knockdown also significantly reduced glioma cell clonogenic survival following ionizing radiation. Therefore our results suggest that targeted inhibition of enzymes required for cell surface receptor glycosylation can be manipulated to produce discrete and limited consequences for critical client glycoproteins expressed by tumor cells. Furthermore, this work identifies MPI as a potential enzymatic target for disrupting cell surface receptor-dependent survival signaling and as a novel approach for therapeutic radiosensitization.

Eddy current-shielded x-space relaxometer for sensitive magnetic nanoparticle characterization

PubMed Central

Bauer, L. M.; Hensley, D. W.; Zheng, B.; Tay, Z. W.; Goodwill, P. W.; Griswold, M. A.; Conolly, S. M.

2016-01-01

The development of magnetic particle imaging (MPI) has created a need for optimized magnetic nanoparticles. Magnetic particle relaxometry is an excellent tool for characterizing potential tracers for MPI. In this paper, we describe the design and construction of a high-throughput tabletop relaxometer that is able to make sensitive measurements of MPI tracers without the need for a dedicated shield room. PMID:27250472

Eddy current-shielded x-space relaxometer for sensitive magnetic nanoparticle characterization.

PubMed

Bauer, L M; Hensley, D W; Zheng, B; Tay, Z W; Goodwill, P W; Griswold, M A; Conolly, S M

2016-05-01

The development of magnetic particle imaging (MPI) has created a need for optimized magnetic nanoparticles. Magnetic particle relaxometry is an excellent tool for characterizing potential tracers for MPI. In this paper, we describe the design and construction of a high-throughput tabletop relaxometer that is able to make sensitive measurements of MPI tracers without the need for a dedicated shield room.

[Peritonitis in diverticulitis: the Bern concept].

PubMed

Seiler, C A; Brügger, L; Maurer, C A; Renzulli, P; Büchler, M W

1998-01-01

The colon is the most frequent origine for a diffuse peritonitis and diverticular perforation is again the most common source of a spontaneous secondary peritonitis. This paper first focuses on the treatment of peritonitis and secondly on the strategies of source control in peritonitis with special emphasis on the tactics (primary anastomosis vs. Hartmann procedure with colostomy) for surgical source control. Prospective analysis of 404 patients suffering from peritonitis (11/93-2/98), treated with an uniform treatment concept including early operation, source control and extensive intraoperative lavage (20 to 30 liters) as a standard procedure. Other treatment measures were added in special indications "on demand" only. Peritonitis was graded with the Mannheim Peritonitis Index (MPI). Tactics of source control in peritonitis due to diverticulitis were performed according to "general condition" respectively the MPI of the patient. The 404 patients averaged a MPI of 19 (0-35) in "local" peritonitis and a MPI of 26 (11-43) in "diffuse" peritonitis. The colon as a source of peritonitis resulted in MPI of 16 (0-33) in the case of "local" respectively 27 (11-43) in "diffuse" peritonitis. From 181 patients suffering from diverticulitis 144 needed an operation and in 78 (54%) peritonitis was present. Fourty-six percent (36) of the patients suffered from "local", 54% (42) from "diffuse" peritonitis. Resection with primary anastomosis was performed in 26% (20/78) whereas in 74% (58/78) of the patients a Hartmann procedure with colostomy was performed. The correlating MPI was 16 (0-28) vs. 23 (16-27) respectively. The analysis of complications and mortality based on the MPI showed a decent discrimination potential for primary anastomosis vs Hartmann procedure: morbidity 35% vs. 41%; reoperation 5% vs. 5%; mortality 0% vs. 14%. In case of peritonitis due to diverticulitis the treatment of peritonitis comes first. Thanks to advances in intensive care and improved anti-inflammatory care, a more conservative surgical concept nowadays is accepted. In the case of diverticulitis the MPI is helpful to choose between primary anastomosis vs. Hartmann procedure with colostomy as source control. The MPI includes the "general condition" of the patient into the tactical decision how to attain source control.

Improved field free line magnetic particle imaging using saddle coils.

PubMed

Erbe, Marlitt; Sattel, Timo F; Buzug, Thorsten M

2013-12-01

Magnetic particle imaging (MPI) is a novel tracer-based imaging method detecting the distribution of superparamagnetic iron oxide (SPIO) nanoparticles in vivo in three dimensions and in real time. Conventionally, MPI uses the signal emitted by SPIO tracer material located at a field free point (FFP). To increase the sensitivity of MPI, however, an alternative encoding scheme collecting the particle signal along a field free line (FFL) was proposed. To provide the magnetic fields needed for line imaging in MPI, a very efficient scanner setup regarding electrical power consumption is needed. At the same time, the scanner needs to provide a high magnetic field homogeneity along the FFL as well as parallel to its alignment to prevent the appearance of artifacts, using efficient radon-based reconstruction methods arising for a line encoding scheme. This work presents a dynamic FFL scanner setup for MPI that outperforms all previously presented setups in electrical power consumption as well as magnetic field quality.

MPI implementation of PHOENICS: A general purpose computational fluid dynamics code

NASA Astrophysics Data System (ADS)

Simunovic, S.; Zacharia, T.; Baltas, N.; Spalding, D. B.

1995-03-01

PHOENICS is a suite of computational analysis programs that are used for simulation of fluid flow, heat transfer, and dynamical reaction processes. The parallel version of the solver EARTH for the Computational Fluid Dynamics (CFD) program PHOENICS has been implemented using Message Passing Interface (MPI) standard. Implementation of MPI version of PHOENICS makes this computational tool portable to a wide range of parallel machines and enables the use of high performance computing for large scale computational simulations. MPI libraries are available on several parallel architectures making the program usable across different architectures as well as on heterogeneous computer networks. The Intel Paragon NX and MPI versions of the program have been developed and tested on massively parallel supercomputers Intel Paragon XP/S 5, XP/S 35, and Kendall Square Research, and on the multiprocessor SGI Onyx computer at Oak Ridge National Laboratory. The preliminary testing results of the developed program have shown scalable performance for reasonably sized computational domains.

MPI implementation of PHOENICS: A general purpose computational fluid dynamics code

DOE Office of Scientific and Technical Information (OSTI.GOV)

Simunovic, S.; Zacharia, T.; Baltas, N.

1995-04-01

PHOENICS is a suite of computational analysis programs that are used for simulation of fluid flow, heat transfer, and dynamical reaction processes. The parallel version of the solver EARTH for the Computational Fluid Dynamics (CFD) program PHOENICS has been implemented using Message Passing Interface (MPI) standard. Implementation of MPI version of PHOENICS makes this computational tool portable to a wide range of parallel machines and enables the use of high performance computing for large scale computational simulations. MPI libraries are available on several parallel architectures making the program usable across different architectures as well as on heterogeneous computer networks. Themore » Intel Paragon NX and MPI versions of the program have been developed and tested on massively parallel supercomputers Intel Paragon XP/S 5, XP/S 35, and Kendall Square Research, and on the multiprocessor SGI Onyx computer at Oak Ridge National Laboratory. The preliminary testing results of the developed program have shown scalable performance for reasonably sized computational domains.« less

Enhancing Application Performance Using Mini-Apps: Comparison of Hybrid Parallel Programming Paradigms

NASA Technical Reports Server (NTRS)

Lawson, Gary; Sosonkina, Masha; Baurle, Robert; Hammond, Dana

2017-01-01

In many fields, real-world applications for High Performance Computing have already been developed. For these applications to stay up-to-date, new parallel strategies must be explored to yield the best performance; however, restructuring or modifying a real-world application may be daunting depending on the size of the code. In this case, a mini-app may be employed to quickly explore such options without modifying the entire code. In this work, several mini-apps have been created to enhance a real-world application performance, namely the VULCAN code for complex flow analysis developed at the NASA Langley Research Center. These mini-apps explore hybrid parallel programming paradigms with Message Passing Interface (MPI) for distributed memory access and either Shared MPI (SMPI) or OpenMP for shared memory accesses. Performance testing shows that MPI+SMPI yields the best execution performance, while requiring the largest number of code changes. A maximum speedup of 23 was measured for MPI+SMPI, but only 11 was measured for MPI+OpenMP.

Performance of OVERFLOW-D Applications based on Hybrid and MPI Paradigms on IBM Power4 System

NASA Technical Reports Server (NTRS)

Djomehri, M. Jahed; Biegel, Bryan (Technical Monitor)

2002-01-01

This report briefly discusses our preliminary performance experiments with parallel versions of OVERFLOW-D applications. These applications are based on MPI and hybrid paradigms on the IBM Power4 system here at the NAS Division. This work is part of an effort to determine the suitability of the system and its parallel libraries (MPI/OpenMP) for specific scientific computing objectives.

: A Scalable and Transparent System for Simulating MPI Programs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Perumalla, Kalyan S

2010-01-01

is a scalable, transparent system for experimenting with the execution of parallel programs on simulated computing platforms. The level of simulated detail can be varied for application behavior as well as for machine characteristics. Unique features of are repeatability of execution, scalability to millions of simulated (virtual) MPI ranks, scalability to hundreds of thousands of host (real) MPI ranks, portability of the system to a variety of host supercomputing platforms, and the ability to experiment with scientific applications whose source-code is available. The set of source-code interfaces supported by is being expanded to support a wider set of applications, andmore » MPI-based scientific computing benchmarks are being ported. In proof-of-concept experiments, has been successfully exercised to spawn and sustain very large-scale executions of an MPI test program given in source code form. Low slowdowns are observed, due to its use of purely discrete event style of execution, and due to the scalability and efficiency of the underlying parallel discrete event simulation engine, sik. In the largest runs, has been executed on up to 216,000 cores of a Cray XT5 supercomputer, successfully simulating over 27 million virtual MPI ranks, each virtual rank containing its own thread context, and all ranks fully synchronized by virtual time.« less

Assessment of Fetal Myocardial Performance Index in Women with Placenta Previa.

PubMed

Zhang, Na; Sun, Lijuan; Zhang, Lina; Li, Zhen; Han, Jijing; Wu, Qingqing

2017-12-15

BACKGROUND This study investigated whether fetuses of placenta previa pregnancies have cardiac dysfunction by use of a modified myocardial performance index (Mod-MPI). MATERIAL AND METHODS A prospective cross-sectional study was conducted including 178 fetuses at 28-40 weeks of gestation. Eighty-nine fetuses of mothers with placenta previa and without pregnancy complications were recruited (placenta previa group) and matched with 89 fetuses of mothers with normal pregnancies (control group). Fetal cardiac function parameters and perinatal outcomes as well as the Mod-MPI were compared between the 2 groups. RESULTS The median Mod-MPI was significantly increased in fetuses of mothers with placenta previa compared with controls (0.47±0.05 vs. 0.45±0.05; P<0.01). Among fetuses of mothers with or without placenta previa, the Mod-MPI was significantly higher in the incomplete placenta previa group compared with the complete placenta previa group and control group (P<0.01). An increased Mod-MPI in placenta previa pregnancies was independently associated with fetal cord pH <7.2 (odds ratio, 4.8; 95% confidence interval, 0.98-23.54; P=0.003). CONCLUSIONS There is impairment of fetal cardiac function in pregnancies with placenta previa. An increased MPI was independently associated with adverse perinatal outcomes to some extent in the placenta previa pregnancies.

[Three-dimensional finite element modeling and biomechanical simulation for evaluating and improving postoperative internal instrumentation of neck-thoracic vertebral tumor en bloc resection].

PubMed

Qinghua, Zhao; Jipeng, Li; Yongxing, Zhang; He, Liang; Xuepeng, Wang; Peng, Yan; Xiaofeng, Wu

2015-04-07

To employ three-dimensional finite element modeling and biomechanical simulation for evaluating the stability and stress conduction of two postoperative internal fixed modeling-multilevel posterior instrumentation ( MPI) and MPI with anterior instrumentation (MPAI) with neck-thoracic vertebral tumor en bloc resection. Mimics software and computed tomography (CT) images were used to establish the three-dimensional (3D) model of vertebrae C5-T2 and simulated the C7 en bloc vertebral resection for MPI and MPAI modeling. Then the statistics and images were transmitted into the ANSYS finite element system and 20N distribution load (simulating body weight) and applied 1 N · m torque on neutral point for simulating vertebral displacement and stress conduction and distribution of motion mode, i. e. flexion, extension, bending and rotating. With a better stability, the displacement of two adjacent vertebral bodies of MPI and MPAI modeling was less than that of complete vertebral modeling. No significant differences existed between each other. But as for stress shielding effect reduction, MPI was slightly better than MPAI. From biomechanical point of view, two internal instrumentations with neck-thoracic tumor en bloc resection may achieve an excellent stability with no significant differences. But with better stress conduction, MPI is more advantageous in postoperative reconstruction.

Quantitative Magnetic Particle Imaging Monitors the Transplantation, Biodistribution, and Clearance of Stem Cells In Vivo

PubMed Central

Zheng, Bo; von See, Marc P.; Yu, Elaine; Gunel, Beliz; Lu, Kuan; Vazin, Tandis; Schaffer, David V.; Goodwill, Patrick W.; Conolly, Steven M.

2016-01-01

Stem cell therapies have enormous potential for treating many debilitating diseases, including heart failure, stroke and traumatic brain injury. For maximal efficacy, these therapies require targeted cell delivery to specific tissues followed by successful cell engraftment. However, targeted delivery remains an open challenge. As one example, it is common for intravenous deliveries of mesenchymal stem cells (MSCs) to become entrapped in lung microvasculature instead of the target tissue. Hence, a robust, quantitative imaging method would be essential for developing efficacious cell therapies. Here we show that Magnetic Particle Imaging (MPI), a novel technique that directly images iron-oxide nanoparticle-tagged cells, can longitudinally monitor and quantify MSC administration in vivo. MPI offers near-ideal image contrast, depth penetration, and robustness; these properties make MPI both ultra-sensitive and linearly quantitative. Here, we imaged, for the first time, the dynamic trafficking of intravenous MSC administrations using MPI. Our results indicate that labeled MSC injections are immediately entrapped in lung tissue and then clear to the liver within one day, whereas standard iron oxide particle (Resovist) injections are immediately taken up by liver and spleen. Longitudinal MPI-CT imaging also indicated a clearance half-life of MSC iron oxide labels in the liver at 4.6 days. Finally, our ex vivo MPI biodistribution measurements of iron in liver, spleen, heart, and lungs after injection showed excellent agreement (R2 = 0.943) with measurements from induction coupled plasma spectrometry. These results demonstrate that MPI offers strong utility for noninvasively imaging and quantifying the systemic distribution of cell therapies and other therapeutic agents. PMID:26909106

Costs and clinical outcomes for non-invasive versus invasive diagnostic approaches to patients with suspected in-stent restenosis.

PubMed

Min, James K; Hasegawa, James T; Machacz, Susanne F; O'Day, Ken

2016-02-01

This study compared costs and clinical outcomes of invasive versus non-invasive diagnostic evaluations for patients with suspected in-stent restenosis (ISR) after percutaneous coronary intervention. We developed a decision model to compare 2 year diagnosis-related costs for patients who presented with suspected ISR and were evaluated by: (1) invasive coronary angiography (ICA); (2) non-invasive stress testing strategy of myocardial perfusion imaging (MPI) with referral to ICA based on MPI; (3) coronary CT angiography-based testing strategy with referral to ICA based on CCTA. Costs were modeled from the payer's perspective using 2014 Medicare rates. 56 % of patients underwent follow-up diagnostic testing over 2 years. Compared to ICA, MPI (98.6 %) and CCTA (98.1 %) exhibited lower rates of correct diagnoses. Non-invasive strategies were associated with reduced referrals to ICA and costs compared to an ICA-based strategy, with diagnostic costs lower for CCTA than MPI. Overall 2-year costs were highest for ICA for both metallic as well as BVS stents ($1656 and $1656, respectively) when compared to MPI ($1444 and $1411) and CCTA. CCTA costs differed based upon stent size and type, and were highest for metallic stents >3.0 mm followed by metallic stents <3.0 mm, BVS < 3.0 mm and BVS > 3.0 mm ($1466 vs. $1242 vs. $855 vs. $490, respectively). MPI for suspected ISR results in lower costs and rates of complications than invasive strategies using ICA while maintaining high diagnostic performance. Depending upon stent size and type, CCTA results in lower costs than MPI.

Multiple Testing, Cumulative Radiation Dose, and Clinical Indications in Patients Undergoing Myocardial Perfusion Imaging

PubMed Central

Einstein, Andrew J.; Weiner, Shepard D.; Bernheim, Adam; Kulon, Michal; Bokhari, Sabahat; Johnson, Lynne L.; Moses, Jeffrey W.; Balter, Stephen

2013-01-01

Context Myocardial perfusion imaging (MPI) is the single medical test with the highest radiation burden to the US population. While many patients undergoing MPI receive repeat MPI testing, or additional procedures involving ionizing radiation, no data are available characterizing their total longitudinal radiation burden and relating radiation burden with reasons for testing. Objective To characterize procedure counts, cumulative estimated effective doses of radiation, and clinical indications, for patients undergoing MPI. Design, Setting, Patients Retrospective cohort study evaluating, for 1097 consecutive patients undergoing index MPI during the first 100 days of 2006 at Columbia University Medical Center, all preceding medical imaging procedures involving ionizing radiation undergone beginning October 1988, and all subsequent procedures through June 2008, at that center. Main Outcome Measures Cumulative estimated effective dose of radiation, number of procedures involving radiation, and indications for testing. Results Patients underwent a median (interquartile range, mean) of 15 (6–32, 23.9) procedures involving radiation exposure; 4 (2–8, 6.5) were high-dose (≥3 mSv, i.e. one year's background radiation), including 1 (1–2, 1.8) MPI studies per patient. 31% of patients received cumulative estimated effective dose from all medical sources >100mSv. Multiple MPIs were performed in 39% of patients, for whom cumulative estimated effective dose was 121 (81–189, 149) mSv. Men and whites had higher cumulative estimated effective doses, and there was a trend towards men being more likely to undergo multiple MPIs than women (40.8% vs. 36.6%, Odds ratio 1.29, 95% confidence interval 0.98–1.69). Over 80% of initial and 90% of repeat MPI exams were performed in patients with known cardiac disease or symptoms consistent with it. Conclusion In this institution, multiple testing with MPI was very common, and in many patients associated with very high cumulative estimated doses of radiation. PMID:21078807

The geochemistry of Seine River Basin particulate matter: Distribution of an integrated metal pollution index

USGS Publications Warehouse

Meybeck, Michel; Horowitz, A.J.; Grosbois, C.

2004-01-01

Spatial analysis (1994-2001) and temporal trends (1980-2000) for particulate-associated metals at key stations in the Seine River Basin have been determined using a new metal pollution index (MPI). The MPI is based on the concentrations of Cd, Cu, Hg, Pb and Zn, normalized to calculated background levels estimated for each particulate matter samples for four fractions (clays and other aluminosilicates, carbonates, organic matter, and quartz). Background levels ascribed to each fraction were determined from a specific set of samples collected from relatively pristine areas in the upper Seine basin and validated on prehistoric samples. The unitless MPI is designed to vary between 0 for pristine samples to 100 for the ones extremely impacted by human activities and to assess the trends of general metal contamination and its mapping. Throughout the Seine basin, MPI currently range from 1 to 40, but values exceeding 100 have been found in periurban streams and the Eure tributary. Based on the MPI spatial distribution, the Seine River Basin displays a wide range of anthropogenic impacts linked to variations in population density, stream order, wastewater discharges and industrial activities. Correlations between the MPI and other trace elements indicate that anthropogenic impacts also strongly affect the concentrations of Ag, Sb, and P, marginally affect the concentrations of Ba, Ni, and Cr, and appear to have little effect on the concentrations of Li, Be, V, Co, and the major elements. Temporal MPI trends can also be reconstituted from past regulatory surveys. In the early 1980s, MPI were 2-5 times higher than nowadays at most locations, particularly downstream of Greater Paris where it reached levels as high as 250 (now 40), a value characteristic of present Paris urban sewage. The exceptional contamination of the Seine basin is gradually improving over the last 20 years but remains very high. ?? 2004 Elsevier B.V. All rights reserved.

Predictors and Diagnostic Significance of the Adenosine Related Side Effects on Myocardial Perfusion SPECT/CT Imaging

PubMed Central

Yıldırım Poyraz, Nilüfer; Özdemir, Elif; Poyraz, Barış Mustafa; Kandemir, Zuhal; Keskin, Mutlay; Türkölmez, Şeyda

2014-01-01

Objective: The aim of this study was to investigate the relationship between patient characteristics and adenosine-related side-effects during stress myocard perfusion imaging (MPI). The effect of presence of adenosine-related side-effects on the diagnostic value of MPI with integrated SPECT/CT system for coronary artery disease (CAD), was also assessed in this study. Methods: Total of 281 patients (109 M, 172 F; mean age:62.6±10) who underwent standard adenosine stress protocol for MPI, were included in this study. All symptoms during adenosine infusion were scored according to the severity and duration. For the estimation of diagnostic value of adenosine MPI with integrated SPECT/CT system, coronary angiography (CAG) or clinical follow-up were used as gold standard. Results: Total of 173 patients (61.6%) experienced adenosine-related side-effects (group 1); flushing, dyspnea, and chest pain were the most common. Other 108 patients completed pharmacologic stress (PS) test without any side-effects (group 2). Test tolerability were similar in the patients with cardiovascular or airway disease to others, however dyspnea were observed significantly more common in patients with mild airway disease. Body mass index (BMI) ≥30 kg/m2 and age ≤45 years were independent predictors of side-effects. The diagnostic value of MPI was similar in both groups. Sensitivity of adenosine MPI SPECT/CT was calculated to be 86%, specificity was 94% and diagnostic accuracy was 92% for diagnosis of CAD. Conclusion: Adenosine MPI is a feasible and well tolerated method in patients who are not suitable for exercise stress test as well as patients with cardiopulmonary disease. However age ≤45 years and BMI ≥30 kg/m2 are the positive predictors of adenosine-related side-effects, the diagnostic value of adenosine MPI SPECT/CT is not affected by the presence of adenosine related side-effects. PMID:25541932

What Multilevel Parallel Programs do when you are not Watching: A Performance Analysis Case Study Comparing MPI/OpenMP, MLP, and Nested OpenMP

NASA Technical Reports Server (NTRS)

Jost, Gabriele; Labarta, Jesus; Gimenez, Judit

2004-01-01

With the current trend in parallel computer architectures towards clusters of shared memory symmetric multi-processors, parallel programming techniques have evolved that support parallelism beyond a single level. When comparing the performance of applications based on different programming paradigms, it is important to differentiate between the influence of the programming model itself and other factors, such as implementation specific behavior of the operating system (OS) or architectural issues. Rewriting-a large scientific application in order to employ a new programming paradigms is usually a time consuming and error prone task. Before embarking on such an endeavor it is important to determine that there is really a gain that would not be possible with the current implementation. A detailed performance analysis is crucial to clarify these issues. The multilevel programming paradigms considered in this study are hybrid MPI/OpenMP, MLP, and nested OpenMP. The hybrid MPI/OpenMP approach is based on using MPI [7] for the coarse grained parallelization and OpenMP [9] for fine grained loop level parallelism. The MPI programming paradigm assumes a private address space for each process. Data is transferred by explicitly exchanging messages via calls to the MPI library. This model was originally designed for distributed memory architectures but is also suitable for shared memory systems. The second paradigm under consideration is MLP which was developed by Taft. The approach is similar to MPi/OpenMP, using a mix of coarse grain process level parallelization and loop level OpenMP parallelization. As it is the case with MPI, a private address space is assumed for each process. The MLP approach was developed for ccNUMA architectures and explicitly takes advantage of the availability of shared memory. A shared memory arena which is accessible by all processes is required. Communication is done by reading from and writing to the shared memory.

An evaluation of MPI message rate on hybrid-core processors

DOE PAGES

Barrett, Brian W.; Brightwell, Ron; Grant, Ryan; ...

2014-11-01

Power and energy concerns are motivating chip manufacturers to consider future hybrid-core processor designs that may combine a small number of traditional cores optimized for single-thread performance with a large number of simpler cores optimized for throughput performance. This trend is likely to impact the way in which compute resources for network protocol processing functions are allocated and managed. In particular, the performance of MPI match processing is critical to achieving high message throughput. In this paper, we analyze the ability of simple and more complex cores to perform MPI matching operations for various scenarios in order to gain insightmore » into how MPI implementations for future hybrid-core processors should be designed.« less

MPI investigation for 40G NRZ link with low-RL cable assemblies

NASA Astrophysics Data System (ADS)

Satake, Toshiaki; Berdinskikh, Tatiana; Thongdaeng, Rutsuda; Faysanyo, Pitak; Gurreri, Michael

2017-01-01

Bit Error Ratio (BER) dependence on received power was studied for 40Gb/s NRZ short optical fiber transmission, including a series of four low return loss (RL 21dB) and low insertion loss (IL 0.1dB) connections. The calculated power penalty (PP) was 0.15dB for BER 10-11. Although the fiber length was within DFB laser's coherent length of 100m and the multi path interference (MPI) value was 34.3dB, no PP of BER was observed. There was no PP due to low MPI probably because the polarization of the signal pulses were not aligned for optical interference, indicating that NRZ systems have a high resistance to MPI.

Exploiting Efficient Transpacking for One-Sided Communication and MPI-IO

NASA Astrophysics Data System (ADS)

Mir, Faisal Ghias; Träff, Jesper Larsson

Based on a construction of socalled input-output datatypes that define a mapping between non-consecutive input and output buffers, we outline an efficient method for copying of structured data. We term this operation transpacking, and show how transpacking can be applied for the MPI implementation of one-sided communication and MPI-IO. For one-sided communication via shared-memory, we demonstrate the expected performance improvements by up to a factor of two. For individual MPI-IO, the time to read or write from file dominates the overall time, but even here efficient transpacking can in some scenarios reduce file I/O time considerably. The reported results have been achieved on a single NEC SX-8 vector node.

Compiled MPI: Cost-Effective Exascale Applications Development

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bronevetsky, G; Quinlan, D; Lumsdaine, A

2012-04-10

The complexity of petascale and exascale machines makes it increasingly difficult to develop applications that can take advantage of them. Future systems are expected to feature billion-way parallelism, complex heterogeneous compute nodes and poor availability of memory (Peter Kogge, 2008). This new challenge for application development is motivating a significant amount of research and development on new programming models and runtime systems designed to simplify large-scale application development. Unfortunately, DoE has significant multi-decadal investment in a large family of mission-critical scientific applications. Scaling these applications to exascale machines will require a significant investment that will dwarf the costs of hardwaremore » procurement. A key reason for the difficulty in transitioning today's applications to exascale hardware is their reliance on explicit programming techniques, such as the Message Passing Interface (MPI) programming model to enable parallelism. MPI provides a portable and high performance message-passing system that enables scalable performance on a wide variety of platforms. However, it also forces developers to lock the details of parallelization together with application logic, making it very difficult to adapt the application to significant changes in the underlying system. Further, MPI's explicit interface makes it difficult to separate the application's synchronization and communication structure, reducing the amount of support that can be provided by compiler and run-time tools. This is in contrast to the recent research on more implicit parallel programming models such as Chapel, OpenMP and OpenCL, which promise to provide significantly more flexibility at the cost of reimplementing significant portions of the application. We are developing CoMPI, a novel compiler-driven approach to enable existing MPI applications to scale to exascale systems with minimal modifications that can be made incrementally over the application's lifetime. It includes: (1) New set of source code annotations, inserted either manually or automatically, that will clarify the application's use of MPI to the compiler infrastructure, enabling greater accuracy where needed; (2) A compiler transformation framework that leverages these annotations to transform the original MPI source code to improve its performance and scalability; (3) Novel MPI runtime implementation techniques that will provide a rich set of functionality extensions to be used by applications that have been transformed by our compiler; and (4) A novel compiler analysis that leverages simple user annotations to automatically extract the application's communication structure and synthesize most complex code annotations.« less

Myocardial performance index in female rats with myocardial infarction: relationship with ventricular function parameters by Doppler echocardiography.

PubMed

Cury, Alexandre Ferreira; Bonilha, Andre; Saraiva, Roberto; Campos, Orlando; Carvalho, Antonio Carlos C; De Paola, Angelo Amato V; Fischer, Claudio; Tucci, Paulo Ferreira; Moises, Valdir Ambrosio

2005-05-01

The aim of the study was to analyze the myocardial performance index (MPI), its relationship with the standard variables of systolic and diastolic functions, and the influence of time intervals in an experimental model of female rats with myocardial infarction (MI). Forty-one Wistar female rats were submitted to surgery to induce MI. Six weeks later, Doppler echocardiography was performed to assess infarct size (IS,%), fractional area change (FAC,%), ejection fraction biplane Simpson (EF), E/A ratio of mitral inflow, MPI and its time intervals: isovolumetric contraction (IVCT, ms) and relaxation (IVRT, ms) times, and ejection time (ET, ms); MPI = IVCT + IVRT/ET. EF and FAC were progressively lower in rats with small, medium and large-size MI ( P < .001). E/A ratio was higher only in rats with large-size MI (6.25 +/- 2.69; P < .001). MPI was not different between control rats and small-size MI (0.37 +/- 0.03 vs 0.34 +/- 0.06, P = .87), but different between large and medium-size MI (0.69 +/- 0.08 vs 0.47 +/- 0.07; P < .001) and between these two compared to small-size MI. MPI correlated with IS (r = 0.85; P < .001), EF (r = -0.86; P < .001), FAC (r = -0.77; P < .001) and E/A ratio (r = 0.77; P < .001, non-linear). IVCT was longer in large size MI compared to medium-size MI (31.87 +/- 7.99 vs 15.92 +/- 5.88; P < .001) and correlated with IS (r = 0.85; P < .001) and MPI (r = 0.92; P < .001). ET was shorter only in large-size MI (81.07 +/- 7.23; P < .001), and correlated with IS (r = -0.70; P < .001) and MPI (r = -0.85; P < .001). IVRT was shorter only in large-size compared to medium-size MI (24.40 +/- 5.38 vs 29.69 +/- 5.92; P < .037), had borderline correlation with MPI (r = 0.34; P = .0534) and no correlation with IS (r = 0.26; p = 0.144). The MPI increased with IS, correlated inversely with systolic function parameters and had a non-linear relationship with diastolic function. These changes were due to the increase of IVCT and a decrease of ET, without significant influence of IVRT.

A Case for Application Oblivious Energy-Efficient MPI Runtime

DOE Office of Scientific and Technical Information (OSTI.GOV)

Venkatesh, Akshay; Vishnu, Abhinav; Hamidouche, Khaled

Power has become the major impediment in designing large scale high-end systems. Message Passing Interface (MPI) is the {\\em de facto} communication interface used as the back-end for designing applications, programming models and runtime for these systems. Slack --- the time spent by an MPI process in a single MPI call --- provides a potential for energy and power savings, if an appropriate power reduction technique such as core-idling/Dynamic Voltage and Frequency Scaling (DVFS) can be applied without perturbing application's execution time. Existing techniques that exploit slack for power savings assume that application behavior repeats across iterations/executions. However, an increasingmore » use of adaptive, data-dependent workloads combined with system factors (OS noise, congestion) makes this assumption invalid. This paper proposes and implements Energy Aware MPI (EAM) --- an application-oblivious energy-efficient MPI runtime. EAM uses a combination of communication models of common MPI primitives (point-to-point, collective, progress, blocking/non-blocking) and an online observation of slack for maximizing energy efficiency. Each power lever incurs time overhead, which must be amortized over slack to minimize degradation. When predicted communication time exceeds a lever overhead, the lever is used {\\em as soon as possible} --- to maximize energy efficiency. When mis-prediction occurs, the lever(s) are used automatically at specific intervals for amortization. We implement EAM using MVAPICH2 and evaluate it on ten applications using up to 4096 processes. Our performance evaluation on an InfiniBand cluster indicates that EAM can reduce energy consumption by 5--41\\% in comparison to the default approach, with negligible (less than 4\\% in all cases) performance loss.« less

Rapeseed and milk protein exhibit a similar overall nutritional value but marked difference in postprandial regional nitrogen utilization in rats

PubMed Central

2011-01-01

Background Rapeseed is an emerging and promising source of dietary protein for human nutrition and health. We previously found that rapeseed protein displayed atypical nutritional properties in humans, characterized by low bioavailability and a high postprandial biological value. The objective of the present study was to investigate the metabolic fate of rapeseed protein isolate (RPI) and its effect on protein fractional synthesis rates (FSR) in various tissues when compared to a milk protein isolate (MPI). Methods Rats (n = 48) were given a RPI or MPI meal, either for the first time or after 2-week adaptation to a MPI or RPI-based diet. They were divided in two groups for measuring the fed-state tissue FSR 2 h after the meal (using a flooding dose of 13C-valine) and the dietary N postprandial distribution at 5 h (using 15N-labeled meals). Results RPI and MPI led to similar FSR and dietary nitrogen (N) losses (ileal and deamination losses of 4% and 12% of the meal, respectively). By contrast, the dietary N incorporation was significantly higher in the intestinal mucosa and liver (+36% and +16%, respectively) and lower in skin (-24%) after RPI than MPI. Conclusions Although RPI and MPI led to the same overall level of postprandial dietary N retention in rats (in line with our findings in humans), this global response conceals marked qualitative differences at the tissue level regarding dietary N accretion. The fact that FSR did not however differed between groups suggest a differential modulation of proteolysis after RPI or MPI ingestion, or other mechanisms that warrant further study. PMID:21787407

Synthesis and characterization of methyl pyrazolone functionalized magnetic chitosan composite for visible light photocatalytic degradation of methylene blue.

PubMed

Abdelwahab, N A; Morsy, E M H

2018-03-01

TiO 2 /Fe 3 O 4 , TiO 2 /Fe 3 O 4 /chitosan and Methylpyrazolone functionalized TiO 2 /Fe 3 O 4 /chitosan (MPyTMChi) were successfully prepared. The chemical structure of the prepared materials was confirmed by FT-IR spectra, XRD, SEM and TEM. BET surface area increased from 2.4 to 3.1m 2 /g, E g decreased from 2.58 to 2.25eV and more quenching of PL emission spectra was observed upon functionalization of TMChi by MPy. Moreover, high Ti and oxygen percentages were detected by EDX. Magnetization value (M s ) reached 21 emu.g -1 for MPyTMChi. MPyTMChi showed enhanced photocatalytic degradation rate of methylene blue (MB) dye under visibe light irradiation (99.8% after 40min) as compared with that for TiO 2 /Fe 3 O 4 (96.7% after 100min) and TMChi (98.9% after 60min), respectively. It was regarded that the photocatalytic degradation of MB dye on MPyTMChi follows apparent pseudo-first-order according to the Langmuir-Hinshelwood (L-H) model and k app value was 0.089min -1 . Active species trapping experiment revealed that h + and O 2 - played the main role in the photodegradation of MB dye while OH quenching did not greatly affect photodegradation rate. Additionally, MPyTMChi can be efficiently reused for six repetitive cycles. MPyTMChi showed higher antimicrobial activity against gram-positive, gram- negative bacterial and fungal strains while large inhibition zone was observed for gram-positive bacteria. Copyright © 2017 Elsevier B.V. All rights reserved.

Myocardial Perfusion Pattern for Stratification of Ischemic Mitral Regurgitation Response to Percutaneous Coronary Intervention

PubMed Central

Goyal, Parag; Kim, Jiwon; Feher, Attila; Ma, Claudia L.; Gurevich, Sergey; Veal, David R.; Szulc, Massimiliano; Wong, Franklin J.; Ratcliffe, Mark B.; Levine, Robert A.; Devereux, Richard B.; Weinsaft, Jonathan W.

2015-01-01

Objective Ischemic mitral regurgitation (MR) is common, but its response to percutaneous coronary intervention (PCI) is poorly understood. This study tested utility of myocardial perfusion imaging (MPI) for stratification of MR response to PCI. Methods MPI and echo were performed among patients undergoing PCI. MPI was used to assess stress/rest myocardial perfusion. MR was assessed via echo (performed pre- and post-PCI). Results 317 patients with abnormal myocardial perfusion on MPI underwent echo 25±39 days prior to PCI. MR was present in 52%, among whom 24% had advanced (≥moderate) MR. MR was associated with LV chamber dilation on MPI and echo (both p<0.001). Magnitude of global LV perfusion deficits increased in relation to MR severity (p<0.01). Perfusion differences were greatest for global summed rest scores, which were 1.6-fold higher among patients with advanced MR vs. those with mild MR (p=0.004), and 2.4-fold higher vs. those without MR (p<0.001). In multivariate analysis, advanced MR was associated with fixed perfusion defect size on MPI (OR 1.16 per segment [CI 1.002–1.34], p=0.046) independent of LV volume (OR 1.10 per 10ml [CI 1.04–1.17], p=0.002). Follow-up via echo (1.0±0.6 years) demonstrated MR to decrease (≥1 grade) in 31% of patients, and increase in 12%. Patients with increased MR after PCI had more severe inferior perfusion defects on baseline MPI (p=0.028), whereas defects in other distributions and LV volumes were similar (p=NS). Conclusions Extent and distribution of SPECT-evidenced myocardial perfusion defects impacts MR response to revascularization. Increased magnitude of inferior fixed perfusion defects predicts post-PCI progression of MR. PMID:26049923

Cationic ionene as an n-dopant agent of poly(3,4-ethylenedioxythiophene).

PubMed

Saborío, Maricruz G; Bertran, Oscar; Lanzalaco, Sonia; Häring, Marleen; Díaz Díaz, David; Estrany, Francesc; Alemán, Carlos

2018-04-18

We report the reduction of poly(3,4-ethylenedioxythiophene) (PEDOT) films with a cationic 1,4-diazabicyclo[2.2.2]octane-based ionene bearing N,N'-(meta-phenylene)dibenzamide linkages (mPI). Our main goal is to obtain n-doped PEDOT using a polymeric dopant agent rather than small conventional tetramethylammonium (TMA), as is usual. This has been achieved using a three-step process, which has been individually optimized: (1) preparation of p-doped (oxidized) PEDOT at a constant potential of +1.40 V in acetonitrile with LiClO4 as the electrolyte; (2) dedoping of oxidized PEDOT using a fixed potential of -1.30 V in water; and (3) redoping of dedoped PEDOT applying a reduction potential of -1.10 V in water with mPI. The resulting films display the globular appearance typically observed for PEDOT, with mPI being structured in separated phases forming nanospheres or ultrathin sheets. This organization, which has been supported by atomistic molecular dynamics simulations, resembles the nanosegregated phase distribution observed for PEDOT p-doped with poly(styrenesulfonate). Furthermore, the doping level achieved using mPI as the doping agent is comparable to that achieved using TMA, even though ionene provides distinctive properties to the conducting polymer. For example, films redoped with mPI exhibit much more hydrophilicity than the oxidized ones, whereas films redoped with TMA are hydrophobic. Similarly, films redoped with mPI exhibit the highest thermal stability, while those redoped with TMA show thermal stability that is intermediate between those of the latter and the dedoped PEDOT. Overall, the incorporation of an mPI polycation as the n-dopant into PEDOT has important advantages for modulating the properties of this emblematic conducting polymer.

Relationship Between Coronary Contrast-Flow Quantitative Flow Ratio and Myocardial Ischemia Assessed by SPECT MPI.

PubMed

Smit, Jeff M; Koning, Gerhard; van Rosendael, Alexander R; Dibbets-Schneider, Petra; Mertens, Bart J; Jukema, J Wouter; Delgado, Victoria; Reiber, Johan H C; Bax, Jeroen J; Scholte, Arthur J

2017-10-01

A new method has been developed to calculate fractional flow reserve (FFR) from invasive coronary angiography, the so-called "contrast-flow quantitative flow ratio (cQFR)". Recently, cQFR was compared to invasive FFR in intermediate coronary lesions showing an overall diagnostic accuracy of 85%. The purpose of this study was to investigate the relationship between cQFR and myocardial ischemia assessed by single-photon emission computed tomography myocardial perfusion imaging (SPECT MPI). Patients who underwent SPECT MPI and coronary angiography within 3 months were included. The cQFR computation was performed offline, using dedicated software. The cQFR computation was based on 3-dimensional quantitative coronary angiography (QCA) and computational fluid dynamics. The standard 17-segment model was used to determine the vascular territories. Myocardial ischemia was defined as a summed difference score ≥2 in a vascular territory. A cQFR of ≤0.80 was considered abnormal. Two hundred and twenty-four coronary arteries were analysed in 85 patients. Overall accuracy of cQFR to detect ischemia on SPECT MPI was 90%. In multivariable analysis, cQFR was independently associated with ischemia on SPECT MPI (OR per 0.01 decrease of cQFR: 1.10; 95% CI 1.04-1.18, p = 0.002), whereas clinical and QCA parameters were not. Furthermore, cQFR showed incremental value for the detection of ischemia compared to clinical and QCA parameters (global chi square 48.7 to 62.6; p <0.001). A good relationship between cQFR and SPECT MPI was found. cQFR was independently associated with ischemia on SPECT MPI and showed incremental value to detect ischemia compared to clinical and QCA parameters.

Accelerating free breathing myocardial perfusion MRI using multi coil radial k - t SLR

NASA Astrophysics Data System (ADS)

Goud Lingala, Sajan; DiBella, Edward; Adluru, Ganesh; McGann, Christopher; Jacob, Mathews

2013-10-01

The clinical utility of myocardial perfusion MR imaging (MPI) is often restricted by the inability of current acquisition schemes to simultaneously achieve high spatio-temporal resolution, good volume coverage, and high signal to noise ratio. Moreover, many subjects often find it difficult to hold their breath for sufficiently long durations making it difficult to obtain reliable MPI data. Accelerated acquisition of free breathing MPI data can overcome some of these challenges. Recently, an algorithm termed as k - t SLR has been proposed to accelerate dynamic MRI by exploiting sparsity and low rank properties of dynamic MRI data. The main focus of this paper is to further improve k - t SLR and demonstrate its utility in considerably accelerating free breathing MPI. We extend its previous implementation to account for multi-coil radial MPI acquisitions. We perform k - t sampling experiments to compare different radial trajectories and determine the best sampling pattern. We also introduce a novel augmented Lagrangian framework to considerably improve the algorithm’s convergence rate. The proposed algorithm is validated using free breathing rest and stress radial perfusion data sets from two normal subjects and one patient with ischemia. k - t SLR was observed to provide faithful reconstructions at high acceleration levels with minimal artifacts compared to existing MPI acceleration schemes such as spatio-temporal constrained reconstruction and k - t SPARSE/SENSE.

Practical Formal Verification of MPI and Thread Programs

NASA Astrophysics Data System (ADS)

Gopalakrishnan, Ganesh; Kirby, Robert M.

Large-scale simulation codes in science and engineering are written using the Message Passing Interface (MPI). Shared memory threads are widely used directly, or to implement higher level programming abstractions. Traditional debugging methods for MPI or thread programs are incapable of providing useful formal guarantees about coverage. They get bogged down in the sheer number of interleavings (schedules), often missing shallow bugs. In this tutorial we will introduce two practical formal verification tools: ISP (for MPI C programs) and Inspect (for Pthread C programs). Unlike other formal verification tools, ISP and Inspect run directly on user source codes (much like a debugger). They pursue only the relevant set of process interleavings, using our own customized Dynamic Partial Order Reduction algorithms. For a given test harness, DPOR allows these tools to guarantee the absence of deadlocks, instrumented MPI object leaks and communication races (using ISP), and shared memory races (using Inspect). ISP and Inspect have been used to verify large pieces of code: in excess of 10,000 lines of MPI/C for ISP in under 5 seconds, and about 5,000 lines of Pthread/C code in a few hours (and much faster with the use of a cluster or by exploiting special cases such as symmetry) for Inspect. We will also demonstrate the Microsoft Visual Studio and Eclipse Parallel Tools Platform integrations of ISP (these will be available on the LiveCD).

Safety and efficacy of Regadenoson in myocardial perfusion imaging (MPI) stress tests: A review

NASA Astrophysics Data System (ADS)

Ahmed, Ambereen

2018-02-01

Myocardial perfusion imaging (MPI) tests are often used to help diagnose coronary heart disease (CAD). The tests usually involve applying stress, such as hard physical exercise together with administration of vasodilators, to the patients. To date, many of these tests use non-selective A2A adenosine receptor agonists which, however, can be associated with highly undesirable and life-threatening side effects such as chest pain, dyspnea, severe bronchoconstriction and atrioventricular conduction anomalies. Regadenoson is a relatively new, highly selective A2A adenosine receptor agonist, suitable for use in MPI tests which exhibits far fewer adverse side effects and, unlike others testing agents, can be used without the necessity of excessive concomitant exercise. Also, the dose of regadenoson required is not dependent upon patient weight or renal impairment, and it can be rapidly administered by i.v. Injection. Regadenoson use in MPI testing thus has the potential as a simplified, relatively safe, time-saving and cost-effective method for helping diagnose CAD. The present study was designed to review several articles on the safety, efficacy, and suitability of regadenoson in MPI testing for CAD. Overall, the combined studies demonstrated that use of regadenoson in conjunction with low-level exercise in MPI is a highly efficient and relatively safe test for CAD, especially for more severe health-compromised patients.

Geometry planning and image registration in magnetic particle imaging using bimodal fiducial markers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Werner, F., E-mail: f.werner@uke.de; Hofmann, M.; Them, K.

Purpose: Magnetic particle imaging (MPI) is a quantitative imaging modality that allows the distribution of superparamagnetic nanoparticles to be visualized. Compared to other imaging techniques like x-ray radiography, computed tomography (CT), and magnetic resonance imaging (MRI), MPI only provides a signal from the administered tracer, but no additional morphological information, which complicates geometry planning and the interpretation of MP images. The purpose of the authors’ study was to develop bimodal fiducial markers that can be visualized by MPI and MRI in order to create MP–MR fusion images. Methods: A certain arrangement of three bimodal fiducial markers was developed and usedmore » in a combined MRI/MPI phantom and also during in vivo experiments in order to investigate its suitability for geometry planning and image fusion. An algorithm for automated marker extraction in both MR and MP images and rigid registration was established. Results: The developed bimodal fiducial markers can be visualized by MRI and MPI and allow for geometry planning as well as automated registration and fusion of MR–MP images. Conclusions: To date, exact positioning of the object to be imaged within the field of view (FOV) and the assignment of reconstructed MPI signals to corresponding morphological regions has been difficult. The developed bimodal fiducial markers and the automated image registration algorithm help to overcome these difficulties.« less

Assessment of Fetal Myocardial Performance Index in Women with Placenta Previa

PubMed Central

Zhang, Na; Sun, Lijuan; Zhang, Lina; Li, Zhen; Han, Jijing; Wu, Qingqing

2017-01-01

Background This study investigated whether fetuses of placenta previa pregnancies have cardiac dysfunction by use of a modified myocardial performance index (Mod-MPI). Material/Methods A prospective cross-sectional study was conducted including 178 fetuses at 28–40 weeks of gestation. Eighty-nine fetuses of mothers with placenta previa and without pregnancy complications were recruited (placenta previa group) and matched with 89 fetuses of mothers with normal pregnancies (control group). Fetal cardiac function parameters and perinatal outcomes as well as the Mod-MPI were compared between the 2 groups. Results The median Mod-MPI was significantly increased in fetuses of mothers with placenta previa compared with controls (0.47±0.05 vs. 0.45±0.05; P<0.01). Among fetuses of mothers with or without placenta previa, the Mod-MPI was significantly higher in the incomplete placenta previa group compared with the complete placenta previa group and control group (P<0.01). An increased Mod-MPI in placenta previa pregnancies was independently associated with fetal cord pH <7.2 (odds ratio, 4.8; 95% confidence interval, 0.98–23.54; P=0.003). Conclusions There is impairment of fetal cardiac function in pregnancies with placenta previa. An increased MPI was independently associated with adverse perinatal outcomes to some extent in the placenta previa pregnancies. PMID:29242496

Accelerating free breathing myocardial perfusion MRI using multi coil radial k-t SLR

PubMed Central

Lingala, Sajan Goud; DiBella, Edward; Adluru, Ganesh; McGann, Christopher; Jacob, Mathews

2013-01-01

The clinical utility of myocardial perfusion MR imaging (MPI) is often restricted by the inability of current acquisition schemes to simultaneously achieve high spatio-temporal resolution, good volume coverage, and high signal to noise ratio. Moreover, many subjects often find it difficult to hold their breath for sufficiently long durations making it difficult to obtain reliable MPI data. Accelerated acquisition of free breathing MPI data can overcome some of these challenges. Recently, an algorithm termed as k − t SLR has been proposed to accelerate dynamic MRI by exploiting sparsity and low rank properties of dynamic MRI data. The main focus of this paper is to further improve k − t SLR and demonstrate its utility in considerably accelerating free breathing MPI. We extend its previous implementation to account for multi-coil radial MPI acquisitions. We perform k − t sampling experiments to compare different radial trajectories and determine the best sampling pattern. We also introduce a novel augmented Lagrangian framework to considerably improve the algorithm's convergence rate. The proposed algorithm is validated using free breathing rest and stress radial perfusion data sets from two normal subjects and one patient with ischemia. k − t SLR was observed to provide faithful reconstructions at high acceleration levels with minimal artifacts compared to existing MPI acceleration schemes such as spatio-temporal constrained reconstruction (STCR) and k − t SPARSE/SENSE. PMID:24077063

Substrate dependent structure of adsorbed aryl isocyanides studied by sum frequency generation (SFG) spectroscopy.

PubMed

Ito, Mikio; Noguchi, Hidenori; Ikeda, Katsuyoshi; Uosaki, Kohei

2010-04-07

Effects of metal substrate on the bonding nature of isocyanide group of two aryl isocyanides, 1,4-phenylene diisocyanide (PDI) and 4-methylphenyl isocyanide (MPI), and tilt angle of MPI were examined by measuring sum frequency generation (SFG) spectra of the self-assembled monolayers (SAMs) of these molecules on Au, Pt, Ag, and Pd surfaces. The SFG peaks due to "metal bonded" and "free"-NC groups were resolved by comparing the SFG spectra of PDI with IR spectra obtained by DFT calculations and previous results of vibrational spectroscopy. Based on the peak positions of the "metal bonded"-NC, it is clarified that while PDI and MPI were adsorbed at top sites on Au, Ag, and Pt surfaces, they adsorbed at bridge sites on the Pd surface. The tilt angles of MPI were determined from the intensity ratio between the SFG peaks of C-H symmetric and asymmetric stretching vibrational modes of the CH(3) group. The tilt angles of the MPI SAMs were in the order of Pt < Pd < Ag < Au, reflecting the bonding nature between the -NC group and the substrate atoms.

First in vivo magnetic particle imaging of lung perfusion in rats

NASA Astrophysics Data System (ADS)

Zhou, Xinyi Y.; Jeffris, Kenneth E.; Yu, Elaine Y.; Zheng, Bo; Goodwill, Patrick W.; Nahid, Payam; Conolly, Steven M.

2017-05-01

Pulmonary embolism (PE), along with the closely related condition of deep vein thrombosis, affect an estimated 600 000 patients in the US per year. Untreated, PE carries a mortality rate of 30%. Because many patients experience mild or non-specific symptoms, imaging studies are necessary for definitive diagnosis of PE. Iodinated CT pulmonary angiography is recommended for most patients, while nuclear medicine-based ventilation/perfusion (V/Q) scans are reserved for patients in whom the use of iodine is contraindicated. Magnetic particle imaging (MPI) is an emerging tracer imaging modality with high image contrast (no tissue background signal) and sensitivity to superparamagnetic iron oxide (SPIO) tracer. Importantly, unlike CT or nuclear medicine, MPI uses no ionizing radiation. Further, MPI is not derived from magnetic resonance imaging (MRI); MPI directly images SPIO tracers via their strong electronic magnetization, enabling deep imaging of anatomy including within the lungs, which is very challenging with MRI. Here, the first high-contrast in vivo MPI lung perfusion images of rats are shown using a novel lung perfusion agent, MAA-SPIOs.

Early detection of the growth of Mycobacterium tuberculosis using magnetophoretic immunoassay in liquid culture.

PubMed

Kim, Jeonghyo; Lee, Kil-Soo; Kim, Eun Bee; Paik, Seungwha; Chang, Chulhun L; Park, Tae Jung; Kim, Hwa-Jung; Lee, Jaebeom

2017-10-15

Tuberculosis (TB) is an often neglected, epidemic disease that remains to be controlled by contemporary techniques of medicine and biotechnology. In this study, a nanoscale sensing system, referred to as magnetophoretic immunoassay (MPI) was designed to capture culture filtrate protein (CFP)-10 antigens effectively using two different types of nanoparticles (NPs). Two specific monoclonal antibodies against CFP-10 antigen were used, including gold NPs for signaling and magnetic particles for separation. These results were carefully compared with those obtained using the commercial mycobacteria growth indicator tube (MGIT) test via 2 sequential clinical tests (with ca. 260 clinical samples). The sensing linearity of MPI was shown in the range of pico- to micromoles and the detection limit was 0.3pM. MPI using clinical samples shows robust and reliable sensing while monitoring Mycobacterium tuberculosis (MTB) growth with monitoring time 3-10 days) comparable to that with the MGIT test. Furthermore, MPI distinguished false-positive samples from MGIT-positive samples, probably containing non-tuberculous mycobacteria. Thus, MPI shows promise in early TB diagnosis. Copyright © 2017 Elsevier B.V. All rights reserved.

Model-based phase-shifting interferometer

NASA Astrophysics Data System (ADS)

Liu, Dong; Zhang, Lei; Shi, Tu; Yang, Yongying; Chong, Shiyao; Miao, Liang; Huang, Wei; Shen, Yibing; Bai, Jian

2015-10-01

A model-based phase-shifting interferometer (MPI) is developed, in which a novel calculation technique is proposed instead of the traditional complicated system structure, to achieve versatile, high precision and quantitative surface tests. In the MPI, the partial null lens (PNL) is employed to implement the non-null test. With some alternative PNLs, similar as the transmission spheres in ZYGO interferometers, the MPI provides a flexible test for general spherical and aspherical surfaces. Based on modern computer modeling technique, a reverse iterative optimizing construction (ROR) method is employed for the retrace error correction of non-null test, as well as figure error reconstruction. A self-compiled ray-tracing program is set up for the accurate system modeling and reverse ray tracing. The surface figure error then can be easily extracted from the wavefront data in forms of Zernike polynomials by the ROR method. Experiments of the spherical and aspherical tests are presented to validate the flexibility and accuracy. The test results are compared with those of Zygo interferometer (null tests), which demonstrates the high accuracy of the MPI. With such accuracy and flexibility, the MPI would possess large potential in modern optical shop testing.

Association of ST segment depression >5 min after exercise testing with severity of coronary artery disease.

PubMed

Shaikh, Ayaz Hussain; Hanif, Bashir; Siddiqui, Adeel M; Shahab, Hunaina; Qazi, Hammad Ali; Mujtaba, Iqbal

2010-04-01

To determine the association of prolonged ST segment depression after an exercise test with severity of coronary artery disease. A cross sectional study of 100 consecutive patients referred to the cardiology laboratory for stress myocardial perfusion imaging (MPI) conducted between April-August 2008. All selected patients were monitored until their ST segment depression was recovered to baseline. ST segment recovery time was categorized into less and more than 5 minutes. Subsequent gated SPECT-MPI was performed and stratified according to severity of perfusion defect. Association was determined between post exercise ST segment depression recovery time (<5 minutes and >5 minutes) and severity of perfusion defect on MPI. The mean age of the patients was 57.12 +/- 9.0 years. The results showed statistically insignificant association (p > 0.05) between ST segment recovery time of <5 minutes and >5 minutes with low, intermediate or high risk MPI. Our findings suggest that the commonly used cut-off levels used in literature for prolonged, post exercise ST segment depression (>5 minutes into recovery phase) does not correlate with severity of ischaemia based on MPI results.

PVM Wrapper

NASA Technical Reports Server (NTRS)

Katz, Daniel

2004-01-01

PVM Wrapper is a software library that makes it possible for code that utilizes the Parallel Virtual Machine (PVM) software library to run using the message-passing interface (MPI) software library, without needing to rewrite the entire code. PVM and MPI are the two most common software libraries used for applications that involve passing of messages among parallel computers. Since about 1996, MPI has been the de facto standard. Codes written when PVM was popular often feature patterns of {"initsend," "pack," "send"} and {"receive," "unpack"} calls. In many cases, these calls are not contiguous and one set of calls may even exist over multiple subroutines. These characteristics make it difficult to obtain equivalent functionality via a single MPI "send" call. Because PVM Wrapper is written to run with MPI- 1.2, some PVM functions are not permitted and must be replaced - a task that requires some programming expertise. The "pvm_spawn" and "pvm_parent" function calls are not replaced, but a programmer can use "mpirun" and knowledge of the ranks of parent and child tasks with supplied macroinstructions to enable execution of codes that use "pvm_spawn" and "pvm_parent."

Message Passing and Shared Address Space Parallelism on an SMP Cluster

NASA Technical Reports Server (NTRS)

Shan, Hongzhang; Singh, Jaswinder P.; Oliker, Leonid; Biswas, Rupak; Biegel, Bryan (Technical Monitor)

2002-01-01

Currently, message passing (MP) and shared address space (SAS) are the two leading parallel programming paradigms. MP has been standardized with MPI, and is the more common and mature approach; however, code development can be extremely difficult, especially for irregularly structured computations. SAS offers substantial ease of programming, but may suffer from performance limitations due to poor spatial locality and high protocol overhead. In this paper, we compare the performance of and the programming effort required for six applications under both programming models on a 32-processor PC-SMP cluster, a platform that is becoming increasingly attractive for high-end scientific computing. Our application suite consists of codes that typically do not exhibit scalable performance under shared-memory programming due to their high communication-to-computation ratios and/or complex communication patterns. Results indicate that SAS can achieve about half the parallel efficiency of MPI for most of our applications, while being competitive for the others. A hybrid MPI+SAS strategy shows only a small performance advantage over pure MPI in some cases. Finally, improved implementations of two MPI collective operations on PC-SMP clusters are presented.

A study of patients with spinal disease using Maudsley Personality Inventory.

PubMed

Kasai, Yuichi; Takegami, Kenji; Uchida, Atsumasa

2004-02-01

We administered the Maudsley Personality Inventory (MPI) preoperatively to 303 patients with spinal diseases about to undergo surgery. Patients younger than 20 years, patients previously treated in the Department of Psychiatry, and patients with poor postoperative results were excluded. Patients with N-scores (neuroticism scale) of 39 points or greater or L-scores (lie scale) of 26 points or greater were regarded as "abnormal." Based on clinical definitions we identified 24 "problem patients" during the course and categorized them as "Unsatisfied," "Indecisive," "Doctor shoppers," or "Distrustful." Preoperative MPI categorized 26 patients as abnormal; 22 patients categorized as abnormal became problem patients ( p<0.001). MPI sensitivity and specificity was 84.6% and 99.3%, respectively. Preoperative MPI to patients with spinal disease was found to be useful in detecting problem patients.

32 CFR 637.8 - Identification of MPI.

Code of Federal Regulations, 2010 CFR

2010-07-01

... CRIMINAL INVESTIGATIONS MILITARY POLICE INVESTIGATION Investigations § 637.8 Identification of MPI. (a... referring to themselves as “INVESTIGATOR.” When signing military police records the title “Military Police...

Specification of Fenix MPI Fault Tolerance library version 1.0.1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gamble, Marc; Van Der Wijngaart, Rob; Teranishi, Keita

This document provides a specification of Fenix, a software library compatible with the Message Passing Interface (MPI) to support fault recovery without application shutdown. The library consists of two modules. The first, termed process recovery , restores an application to a consistent state after it has suffered a loss of one or more MPI processes (ranks). The second specifies functions the user can invoke to store application data in Fenix managed redundant storage, and to retrieve it from that storage after process recovery.

Simultaneous monitoring technique for ASE and MPI noises in distributed Raman Amplified Systems.

PubMed

Choi, H Y; Jun, S B; Shin, S K; Chung, Y C

2007-07-09

We develop a new technique for simultaneously monitoring the amplified spontaneous emission (ASE) and multi-path interference (MPI) noises in distributed Raman amplified (DRA) systems. This technique utilizes the facts that the degree-of polarization (DOP) of the MPI noise is 1/9, while the ASE noise is unpolarized. The results show that the proposed technique can accurately monitor both of these noises regardless of the bit rates, modulation formats, and optical signal-to-noise ratio (OSNR) levels of the signals.

In vitro and in vivo comparison of a tailored magnetic particle imaging blood pool tracer with Resovist.

PubMed

Kaul, Michael Gerhard; Mummert, Tobias; Jung, Caroline; Salamon, Johannes; Khandhar, Amit P; Ferguson, R Matthew; Kemp, Scott J; Ittrich, Harald; Krishnan, Kannan M; Adam, Gerhard; Knopp, Tobias

2017-05-07

Optimizing tracers for individual imaging techniques is an active field of research. The purpose of this study was to perform in vitro and in vivo magnetic particle imaging (MPI) measurements using a new monodisperse and size-optimized tracer, LS-008, and to compare it with the performance of Resovist, the standard MPI tracer. Magnetic particle spectroscopy (MPS) and in vitro MPI measurements were performed in concerns of concentration and amount of tracer in a phantom. In vivo studies were carried out in healthy FVB mice. The first group (n  =  3) received 60 µl LS-008 (87 mM) and the second (n  =  3) diluted Resovist of the same concentration and volume. Tracer injections were performed with a syringe pump during a dynamic MPI scan. For anatomic referencing MRI was applied beforehand of the MPI measurements. Summing up MPS examinations and in vitro MPI experiments, LS-008 showed better sensitivity and spatial resolution than Resovist. In vivo both tracers can visualize the propagation of the bolus through the inferior vena cava. MPI with LS-008 did show less temporal fluctuation artifacts and the pulsation of blood due to respiratory and cardiac cycle was detectable. With LS-008 the aorta was distinguishable from the caval vein while with Resovist this failed. A liver vessel and a vessel structure leading cranially could only be observed with LS-008 and not with Resovist. Beside these structural advantages both tracers showed very different blood half-life. For LS-008 we found 88 min. Resovist did show a fast liver accumulation and a half-life of 13 min. Only with LS-008 the perfusion fraction in liver and kidney was measureable. MPI for angiography can be significantly improved by applying more effective tracers. LS-008 shows a clear improvement concerning the delineation while resolving a larger number of vessels in comparison to Resovist. Therefore, in aspects of quality and quantity LS-008 is clearly favorable for angiographic and perfusion studies.

Differences in pain, function and coping in Multidimensional Pain Inventory subgroups of chronic back pain: a one-group pretest-posttest study.

PubMed

Verra, Martin L; Angst, Felix; Staal, J Bart; Brioschi, Roberto; Lehmann, Susanne; Aeschlimann, André; de Bie, Rob A

2011-06-30

Patients with non-specific back pain are not a homogeneous group but heterogeneous with regard to their bio-psycho-social impairments. This study examined a sample of 173 highly disabled patients with chronic back pain to find out how the three subgroups based on the Multidimensional Pain Inventory (MPI) differed in their response to an inpatient pain management program. Subgroup classification was conducted by cluster analysis using MPI subscale scores at entry into the program. At program entry and at discharge after four weeks, participants completed the MPI, the MOS Short Form-36 (SF-36), the Hospital Anxiety and Depression Scale (HADS), and the Coping Strategies Questionnaire (CSQ). Pairwise analyses of the score changes of the mentioned outcomes of the three MPI subgroups were performed using the Mann-Whitney-U-test for significance. Cluster analysis identified three MPI subgroups in this highly disabled sample: a dysfunctional, interpersonally distressed and an adaptive copers subgroup. The dysfunctional subgroup (29% of the sample) showed the highest level of depression in SF-36 mental health (33.4 ± 13.9), the interpersonally distressed subgroup (35% of the sample) a modest level of depression (46.8 ± 20.4), and the adaptive copers subgroup (32% of the sample) the lowest level of depression (57.8 ± 19.1). Significant differences in pain reduction and improvement of mental health and coping were observed across the three MPI subgroups, i.e. the effect sizes for MPI pain reduction were: 0.84 (0.44-1.24) for the dysfunctional subgroup, 1.22 (0.86-1.58) for the adaptive copers subgroup, and 0.53 (0.24-0.81) for the interpersonally distressed subgroup (p = 0.006 for pairwise comparison). Significant score changes between subgroups concerning activities and physical functioning could not be identified. MPI subgroup classification showed significant differences in score changes for pain, mental health and coping. These findings underscore the importance of assessing individual differences to understand how patients adjust to chronic back pain.

An MPI + $X$ implementation of contact global search using Kokkos

DOE PAGES

Hansen, Glen A.; Xavier, Patrick G.; Mish, Sam P.; ...

2015-10-05

This paper describes an approach that seeks to parallelize the spatial search associated with computational contact mechanics. In contact mechanics, the purpose of the spatial search is to find “nearest neighbors,” which is the prelude to an imprinting search that resolves the interactions between the external surfaces of contacting bodies. In particular, we are interested in the contact global search portion of the spatial search associated with this operation on domain-decomposition-based meshes. Specifically, we describe an implementation that combines standard domain-decomposition-based MPI-parallel spatial search with thread-level parallelism (MPI-X) available on advanced computer architectures (those with GPU coprocessors). Our goal ismore » to demonstrate the efficacy of the MPI-X paradigm in the overall contact search. Standard MPI-parallel implementations typically use a domain decomposition of the external surfaces of bodies within the domain in an attempt to efficiently distribute computational work. This decomposition may or may not be the same as the volume decomposition associated with the host physics. The parallel contact global search phase is then employed to find and distribute surface entities (nodes and faces) that are needed to compute contact constraints between entities owned by different MPI ranks without further inter-rank communication. Key steps of the contact global search include computing bounding boxes, building surface entity (node and face) search trees and finding and distributing entities required to complete on-rank (local) spatial searches. To enable source-code portability and performance across a variety of different computer architectures, we implemented the algorithm using the Kokkos hardware abstraction library. While we targeted development towards machines with a GPU accelerator per MPI rank, we also report performance results for OpenMP with a conventional multi-core compute node per rank. Results here demonstrate a 47 % decrease in the time spent within the global search algorithm, comparing the reference ACME algorithm with the GPU implementation, on an 18M face problem using four MPI ranks. As a result, while further work remains to maximize performance on the GPU, this result illustrates the potential of the proposed implementation.« less

Coinfection with Enterohepatic Helicobacter Species Can Ameliorate or Promote Helicobacter pylori-Induced Gastric Pathology in C57BL/6 Mice ▿

PubMed Central

Ge, Zhongming; Feng, Yan; Muthupalani, Sureshkumar; Eurell, Laura Lemke; Taylor, Nancy S.; Whary, Mark T.; Fox, James G.

2011-01-01

To investigate how different enterohepatic Helicobacter species (EHS) influence Helicobacter pylori gastric pathology, C57BL/6 mice were infected with Helicobacter hepaticus or Helicobacter muridarum, followed by H. pylori infection 2 weeks later. Compared to H. pylori-infected mice, mice infected with H. muridarum and H. pylori (HmHp mice) developed significantly lower histopathologic activity index (HAI) scores (P < 0.0001) at 6 and 11 months postinoculation (MPI). However, mice infected with H. hepaticus and H. pylori (HhHp mice) developed more severe gastric pathology at 6 MPI (P = 0.01), with a HAI at 11 MPI (P = 0.8) similar to that of H. pylori-infected mice. H. muridarum-mediated attenuation of gastritis in coinfected mice was associated with significant downregulation of proinflammatory Th1 (interlukin-1beta [Il-1β], gamma interferon [Ifn-γ], and tumor necrosis factor-alpha [Tnf-α]) cytokines at both time points and Th17 (Il-17A) cytokine mRNA levels at 6 MPI in murine stomachs compared to those of H. pylori-infected mice (P < 0.01). Coinfection with H. hepaticus also suppressed H. pylori-induced elevation of gastric Th1 cytokines Ifn-γ and Tnf-α (P < 0.0001) but increased Th17 cytokine mRNA levels (P = 0.028) at 6 MPI. Furthermore, mRNA levels of Il-17A were positively correlated with the severity of helicobacter-induced gastric pathology (HhHp>H. pylori>HmHp) (at 6 MPI, r2 = 0.92, P < 0.0001; at 11 MPI, r2 = 0.82, P < 0.002). Despite disparate effects on gastritis, colonization levels of gastric H. pylori were increased in HhHp mice (at 6 MPI) and HmHp mice (at both time points) compared to those in mono-H. pylori-infected mice. These data suggest that despite consistent downregulation of Th1 responses, EHS coinfection either attenuated or promoted the severity of H. pylori-induced gastric pathology in C57BL/6 mice. This modulation was related to the variable effects of EHS on gastric interleukin 17 (IL-17) responses to H. pylori infection. PMID:21788386

In vitro and in vivo comparison of a tailored magnetic particle imaging blood pool tracer with Resovist

NASA Astrophysics Data System (ADS)

Kaul, Michael Gerhard; Mummert, Tobias; Jung, Caroline; Salamon, Johannes; Khandhar, Amit P.; Ferguson, R. Matthew; Kemp, Scott J.; Ittrich, Harald; Krishnan, Kannan M.; Adam, Gerhard; Knopp, Tobias

2017-05-01

Optimizing tracers for individual imaging techniques is an active field of research. The purpose of this study was to perform in vitro and in vivo magnetic particle imaging (MPI) measurements using a new monodisperse and size-optimized tracer, LS-008, and to compare it with the performance of Resovist, the standard MPI tracer. Magnetic particle spectroscopy (MPS) and in vitro MPI measurements were performed in concerns of concentration and amount of tracer in a phantom. In vivo studies were carried out in healthy FVB mice. The first group (n  =  3) received 60 µl LS-008 (87 mM) and the second (n  =  3) diluted Resovist of the same concentration and volume. Tracer injections were performed with a syringe pump during a dynamic MPI scan. For anatomic referencing MRI was applied beforehand of the MPI measurements. Summing up MPS examinations and in vitro MPI experiments, LS-008 showed better sensitivity and spatial resolution than Resovist. In vivo both tracers can visualize the propagation of the bolus through the inferior vena cava. MPI with LS-008 did show less temporal fluctuation artifacts and the pulsation of blood due to respiratory and cardiac cycle was detectable. With LS-008 the aorta was distinguishable from the caval vein while with Resovist this failed. A liver vessel and a vessel structure leading cranially could only be observed with LS-008 and not with Resovist. Beside these structural advantages both tracers showed very different blood half-life. For LS-008 we found 88 min. Resovist did show a fast liver accumulation and a half-life of 13 min. Only with LS-008 the perfusion fraction in liver and kidney was measureable. MPI for angiography can be significantly improved by applying more effective tracers. LS-008 shows a clear improvement concerning the delineation while resolving a larger number of vessels in comparison to Resovist. Therefore, in aspects of quality and quantity LS-008 is clearly favorable for angiographic and perfusion studies.

What does fault tolerant Deep Learning need from MPI?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Amatya, Vinay C.; Vishnu, Abhinav; Siegel, Charles M.

Deep Learning (DL) algorithms have become the {\\em de facto} Machine Learning (ML) algorithm for large scale data analysis. DL algorithms are computationally expensive -- even distributed DL implementations which use MPI require days of training (model learning) time on commonly studied datasets. Long running DL applications become susceptible to faults -- requiring development of a fault tolerant system infrastructure, in addition to fault tolerant DL algorithms. This raises an important question: {\\em What is needed from MPI for designing fault tolerant DL implementations?} In this paper, we address this problem for permanent faults. We motivate the need for amore » fault tolerant MPI specification by an in-depth consideration of recent innovations in DL algorithms and their properties, which drive the need for specific fault tolerance features. We present an in-depth discussion on the suitability of different parallelism types (model, data and hybrid); a need (or lack thereof) for check-pointing of any critical data structures; and most importantly, consideration for several fault tolerance proposals (user-level fault mitigation (ULFM), Reinit) in MPI and their applicability to fault tolerant DL implementations. We leverage a distributed memory implementation of Caffe, currently available under the Machine Learning Toolkit for Extreme Scale (MaTEx). We implement our approaches by extending MaTEx-Caffe for using ULFM-based implementation. Our evaluation using the ImageNet dataset and AlexNet neural network topology demonstrates the effectiveness of the proposed fault tolerant DL implementation using OpenMPI based ULFM.« less

Task-parallel message passing interface implementation of Autodock4 for docking of very large databases of compounds using high-performance super-computers.

PubMed

Collignon, Barbara; Schulz, Roland; Smith, Jeremy C; Baudry, Jerome

2011-04-30

A message passing interface (MPI)-based implementation (Autodock4.lga.MPI) of the grid-based docking program Autodock4 has been developed to allow simultaneous and independent docking of multiple compounds on up to thousands of central processing units (CPUs) using the Lamarkian genetic algorithm. The MPI version reads a single binary file containing precalculated grids that represent the protein-ligand interactions, i.e., van der Waals, electrostatic, and desolvation potentials, and needs only two input parameter files for the entire docking run. In comparison, the serial version of Autodock4 reads ASCII grid files and requires one parameter file per compound. The modifications performed result in significantly reduced input/output activity compared with the serial version. Autodock4.lga.MPI scales up to 8192 CPUs with a maximal overhead of 16.3%, of which two thirds is due to input/output operations and one third originates from MPI operations. The optimal docking strategy, which minimizes docking CPU time without lowering the quality of the database enrichments, comprises the docking of ligands preordered from the most to the least flexible and the assignment of the number of energy evaluations as a function of the number of rotatable bounds. In 24 h, on 8192 high-performance computing CPUs, the present MPI version would allow docking to a rigid protein of about 300K small flexible compounds or 11 million rigid compounds.

MSAProbs-MPI: parallel multiple sequence aligner for distributed-memory systems.

PubMed

González-Domínguez, Jorge; Liu, Yongchao; Touriño, Juan; Schmidt, Bertil

2016-12-15

MSAProbs is a state-of-the-art protein multiple sequence alignment tool based on hidden Markov models. It can achieve high alignment accuracy at the expense of relatively long runtimes for large-scale input datasets. In this work we present MSAProbs-MPI, a distributed-memory parallel version of the multithreaded MSAProbs tool that is able to reduce runtimes by exploiting the compute capabilities of common multicore CPU clusters. Our performance evaluation on a cluster with 32 nodes (each containing two Intel Haswell processors) shows reductions in execution time of over one order of magnitude for typical input datasets. Furthermore, MSAProbs-MPI using eight nodes is faster than the GPU-accelerated QuickProbs running on a Tesla K20. Another strong point is that MSAProbs-MPI can deal with large datasets for which MSAProbs and QuickProbs might fail due to time and memory constraints, respectively. Source code in C ++ and MPI running on Linux systems as well as a reference manual are available at http://msaprobs.sourceforge.net CONTACT: jgonzalezd@udc.esSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Myocardial Performance Index for Patients with Overt and Subclinical Hypothyroidism.

PubMed

Karabulut, Aziz; Doğan, Abdullah; Tuzcu, Alpaslan Kemal

2017-05-25

BACKGROUND Hypothyroid has several effects on the cardiovascular system. Global myocardial performance index (MPI) is used in assessment of both left ventricular (LV) systolic and diastolic function. We compared MPI in hypothyroidism patients vs. normal control subjects. MATERIAL AND METHODS Eighty-two hypothyroid patients were divided into 2 groups: a subclinical hypothyroid (SH) group (n=50), and an overt hypothyroid (OH) group (n=32). The healthy control group (CG) constituted of 37 patients. TSH, FT3, and FT4, anti-TPO, anti-TG, insulin, lipid values, and fasting glucose levels were studied. All patients underwent an echocardiographic examination. Myocardial performance indexes were assessed and standard echocardiographic examinations were investigated. RESULTS MPI averages in OH, SH, and control groups were 0.53±0.06, 0.51±0.05, and 0.44±0.75 mm, respectively. MPI was increased in the OH and SH groups in comparison to CG (p<0.001, p<0.001, respectively). CONCLUSIONS MPI value was significantly higher in hypothyroid patients in comparison to the control group, showing that regression in global left ventricular functions is an important echocardiographic finding. Future studies are required to determine the effects of this finding on long-term cardiovascular outcomes.

Relaxation-based viscosity mapping for magnetic particle imaging

NASA Astrophysics Data System (ADS)

Utkur, M.; Muslu, Y.; Saritas, E. U.

2017-05-01

Magnetic particle imaging (MPI) has been shown to provide remarkable contrast for imaging applications such as angiography, stem cell tracking, and cancer imaging. Recently, there is growing interest in the functional imaging capabilities of MPI, where ‘color MPI’ techniques have explored separating different nanoparticles, which could potentially be used to distinguish nanoparticles in different states or environments. Viscosity mapping is a promising functional imaging application for MPI, as increased viscosity levels in vivo have been associated with numerous diseases such as hypertension, atherosclerosis, and cancer. In this work, we propose a viscosity mapping technique for MPI through the estimation of the relaxation time constant of the nanoparticles. Importantly, the proposed time constant estimation scheme does not require any prior information regarding the nanoparticles. We validate this method with extensive experiments in an in-house magnetic particle spectroscopy (MPS) setup at four different frequencies (between 250 Hz and 10.8 kHz) and at three different field strengths (between 5 mT and 15 mT) for viscosities ranging between 0.89 mPa · s-15.33 mPa · s. Our results demonstrate the viscosity mapping ability of MPI in the biologically relevant viscosity range.

32 CFR 637.2 - Use of MPI and DAC Detectives/Investigators.

Code of Federal Regulations, 2010 CFR

2010-07-01

.../investigators may be employed in joint MPI/USACIDC drug suppression teams; however, the conduct of such... and DAC detectives/investigators may also be utilized to make controlled buys of suspected controlled...

76 FR 18865 - Airworthiness Directives; Bell Helicopter Textron, Inc. Model 212 Helicopters

Federal Register 2010, 2011, 2012, 2013, 2014

2011-04-06

... also requires performing a magnetic particle inspection (MPI) on fittings with certain serial numbers... expanding the applicability to require performing a magnetic particle inspection (MPI) for a crack on the...

MPI-IO: A Parallel File I/O Interface for MPI Version 0.3

NASA Technical Reports Server (NTRS)

Corbett, Peter; Feitelson, Dror; Hsu, Yarsun; Prost, Jean-Pierre; Snir, Marc; Fineberg, Sam; Nitzberg, Bill; Traversat, Bernard; Wong, Parkson

1995-01-01

Thanks to MPI [9], writing portable message passing parallel programs is almost a reality. One of the remaining problems is file I/0. Although parallel file systems support similar interfaces, the lack of a standard makes developing a truly portable program impossible. Further, the closest thing to a standard, the UNIX file interface, is ill-suited to parallel computing. Working together, IBM Research and NASA Ames have drafted MPI-I0, a proposal to address the portable parallel I/0 problem. In a nutshell, this proposal is based on the idea that I/0 can be modeled as message passing: writing to a file is like sending a message, and reading from a file is like receiving a message. MPI-IO intends to leverage the relatively wide acceptance of the MPI interface in order to create a similar I/0 interface. The above approach can be materialized in different ways. The current proposal represents the result of extensive discussions (and arguments), but is by no means finished. Many changes can be expected as additional participants join the effort to define an interface for portable I/0. This document is organized as follows. The remainder of this section includes a discussion of some issues that have shaped the style of the interface. Section 2 presents an overview of MPI-IO as it is currently defined. It specifies what the interface currently supports and states what would need to be added to the current proposal to make the interface more complete and robust. The next seven sections contain the interface definition itself. Section 3 presents definitions and conventions. Section 4 contains functions for file control, most notably open. Section 5 includes functions for independent I/O, both blocking and nonblocking. Section 6 includes functions for collective I/O, both blocking and nonblocking. Section 7 presents functions to support system-maintained file pointers, and shared file pointers. Section 8 presents constructors that can be used to define useful filetypes (the role of filetypes is explained in Section 2 below). Section 9 presents how the error handling mechanism of MPI is supported by the MPI-IO interface. All this is followed by a set of appendices, which contain information about issues that have not been totally resolved yet, and about design considerations. The reader can find there the motivation behind some of our design choices. More information on this would definitely be welcome and will be included in a further release of this document. The first appendix contains a description of MPI-I0's 'hints' structure which is used when opening a file. Appendix B is a discussion of various issues in the support for file pointers. Appendix C explains what we mean in talking about atomic access. Appendix D provides detailed examples of filetype constructors, and Appendix E contains a collection of arguments for and against various design decisions.

Use of bio-informatics assessment schema (BIAS) to improve diagnosis and prognosis of myocardial perfusion data: results from the NHLBI-sponsored women's ischemia syndrome evaluation (WISE).

PubMed

Doyle, Mark; Pohost, Gerald M; Bairey Merz, C Noel; Shaw, Leslee J; Sopko, George; Rogers, William J; Sharaf, Barry L; Pepine, Carl J; Thompson, Diane V; Rayarao, Geetha; Tauxe, Lindsey; Kelsey, Sheryl F; Biederman, Robert W W

2016-10-01

We introduce an algorithmic approach to optimize diagnostic and prognostic value of gated cardiac single photon emission computed tomography (SPECT) and magnetic resonance (MR) myocardial perfusion imaging (MPI) modalities in women with suspected myocardial ischemia. The novel approach: bio-informatics assessment schema (BIAS) forms a mathematical model utilizing MPI data and cardiac metrics generated by one modality to predict the MPI status of another modality. The model identifies cardiac features that either enhance or mask the image-based evidence of ischemia. For each patient, the BIAS model value is used to set an appropriate threshold for the detection of ischemia. Women (n=130), with symptoms and signs of suspected myocardial ischemia, underwent MPI assessment for regional perfusion defects using two different modalities: gated SPECT and MR. To determine perfusion status, MR data were evaluated qualitatively (MRI QL ) and semi-quantitatively (MRI SQ ) while SPECT data were evaluated using conventional clinical criteria. Evaluators were masked to results of the alternate modality. These MPI status readings were designated "original". Two regression models designated "BIAS" models were generated to model MPI status obtained with one modality (e.g., MRI) compared with a second modality (e.g., SPECT), but importantly, the BIAS models did not include the primary Original MPI reading of the predicting modality. Instead, the BIAS models included auxiliary measurements like left ventricular chamber volumes and myocardial wall thickness. For each modality, the BIAS model was used to set a progressive threshold for interpretation of MPI status. Women were then followed for 38±14 months for the development of a first major adverse cardiovascular event [MACE: CV death, nonfatal myocardial infarction (MI) or hospitalization for heart failure]. Original and BIAS-augmented perfusion status were compared in their ability to detect coronary artery disease (CAD) and for prediction of MACE. Adverse events occurred in 14 (11%) women and CAD was present in 13 (10%). There was a positive correlation of maximum coronary artery stenosis and BIAS score for MRI and SPECT (P<0.001). Receiver operator characteristic (ROC) analysis was conducted and showed an increase in the area under the curve of the BIAS-augmented MPI interpretation of MACE vs . the original for MRI SQ (0.78 vs . 0.54), MRI QL (0.78 vs . 0.64), SPECT (0.82 vs . 0.63) and the average of the three readings (0.80±0.02 vs . 0.60±0.05, P<0.05). Increasing values of the BIAS score generated by both MRI and SPECT corresponded to the increasing prevalence of CAD and MACE. The BIAS-augmented detection of ischemia better predicted MACE compared with the Original reading for the MPI data for both MRI and SPECT.

Use of bio-informatics assessment schema (BIAS) to improve diagnosis and prognosis of myocardial perfusion data: results from the NHLBI-sponsored women’s ischemia syndrome evaluation (WISE)

PubMed Central

Pohost, Gerald M.; Bairey Merz, C. Noel; Shaw, Leslee J.; Sopko, George; Rogers, William J.; Sharaf, Barry L.; Pepine, Carl J.; Thompson, Diane V.; Rayarao, Geetha; Tauxe, Lindsey; Kelsey, Sheryl F.; Biederman, Robert W. W.

2016-01-01

Background We introduce an algorithmic approach to optimize diagnostic and prognostic value of gated cardiac single photon emission computed tomography (SPECT) and magnetic resonance (MR) myocardial perfusion imaging (MPI) modalities in women with suspected myocardial ischemia. The novel approach: bio-informatics assessment schema (BIAS) forms a mathematical model utilizing MPI data and cardiac metrics generated by one modality to predict the MPI status of another modality. The model identifies cardiac features that either enhance or mask the image-based evidence of ischemia. For each patient, the BIAS model value is used to set an appropriate threshold for the detection of ischemia. Methods Women (n=130), with symptoms and signs of suspected myocardial ischemia, underwent MPI assessment for regional perfusion defects using two different modalities: gated SPECT and MR. To determine perfusion status, MR data were evaluated qualitatively (MRIQL) and semi-quantitatively (MRISQ) while SPECT data were evaluated using conventional clinical criteria. Evaluators were masked to results of the alternate modality. These MPI status readings were designated “original”. Two regression models designated “BIAS” models were generated to model MPI status obtained with one modality (e.g., MRI) compared with a second modality (e.g., SPECT), but importantly, the BIAS models did not include the primary Original MPI reading of the predicting modality. Instead, the BIAS models included auxiliary measurements like left ventricular chamber volumes and myocardial wall thickness. For each modality, the BIAS model was used to set a progressive threshold for interpretation of MPI status. Women were then followed for 38±14 months for the development of a first major adverse cardiovascular event [MACE: CV death, nonfatal myocardial infarction (MI) or hospitalization for heart failure]. Original and BIAS-augmented perfusion status were compared in their ability to detect coronary artery disease (CAD) and for prediction of MACE. Results Adverse events occurred in 14 (11%) women and CAD was present in 13 (10%). There was a positive correlation of maximum coronary artery stenosis and BIAS score for MRI and SPECT (P<0.001). Receiver operator characteristic (ROC) analysis was conducted and showed an increase in the area under the curve of the BIAS-augmented MPI interpretation of MACE vs. the original for MRISQ (0.78 vs. 0.54), MRIQL (0.78 vs. 0.64), SPECT (0.82 vs. 0.63) and the average of the three readings (0.80±0.02 vs. 0.60±0.05, P<0.05). Conclusions Increasing values of the BIAS score generated by both MRI and SPECT corresponded to the increasing prevalence of CAD and MACE. The BIAS-augmented detection of ischemia better predicted MACE compared with the Original reading for the MPI data for both MRI and SPECT. PMID:27747165

Temporal Trends in the Prevalence, Severity, and Localization of Myocardial Ischemia and Necrosis at Myocardial Perfusion Imaging After Myocardial Infarction.

PubMed

Nudi, Francesco; Schillaci, Orazio; Di Belardino, Natale; Versaci, Francesco; Tomai, Fabrizio; Pinto, Annamaria; Neri, Giandomenico; Procaccini, Enrica; Nudi, Alessandro; Frati, Giacomo; Biondi-Zoccai, Giuseppe

2017-10-15

The definition, presentation, and management of myocardial infarction (MI) have changed substantially in the last decade. Whether these changes have impacted on the presence, severity, and localization of necrosis at myocardial perfusion imaging (MPI) has not been appraised to date. Subjects undergoing MPI and reporting a history of clinical MI were shortlisted. We focused on the presence, severity, and localization of necrosis at MPI with a retrospective single-center analysis. A total of 10,476 patients were included, distinguishing 5 groups according to the period in which myocardial perfusion scintigraphy had been performed (2004 to 2005, 2006 to 2007, 2008 to 2009, 2010 to 2011, 2012 to 2013). Trend analysis showed over time a significant worsening in baseline features (e.g., age, diabetes mellitus, and Q waves at electrocardiogram), whereas medical therapy and revascularization were offered with increasing frequency. Over the years, there was also a lower prevalence of normal MPI (from 16.8% to 13.6%) and ischemic MPI (from 35.6% to 32.8%), and a higher prevalence of ischemic and necrotic MPI (from 12.0% to 12.7%) or solely necrotic MPI (from 35.7% to 40.9%, p <0.001). Yet the prevalence of severe ischemia decreased over time from 11.4% to 2.0%, with a similar trend for moderate ischemia (from 15.9% to 11.8%, p <0.001). Similarly sobering results were wound for the prevalence of severe necrosis (from 19.8% to 8.2%) and moderate necrosis (from 8.5% to 7.8%, p = 0.028). These trends were largely confirmed at regional level and after propensity score matching. In conclusion, the outlook of stable patients with previous MI has substantially improved in the last decade, with a decrease in the severity of residual myocardial ischemia and necrosis, despite an apparent worsening in baseline features. Copyright © 2017 Elsevier Inc. All rights reserved.

In vivo liver visualizations with magnetic particle imaging based on the calibration measurement approach

NASA Astrophysics Data System (ADS)

Dieckhoff, J.; Kaul, M. G.; Mummert, T.; Jung, C.; Salamon, J.; Adam, G.; Knopp, T.; Ludwig, F.; Balceris, C.; Ittrich, H.

2017-05-01

Magnetic particle imaging (MPI) facilitates the rapid determination of 3D in vivo magnetic nanoparticle distributions. In this work, liver MPI following intravenous injections of ferucarbotran (Resovist®) was studied. The image reconstruction was based on a calibration measurement, the so called system function. The application of an enhanced system function sample reflecting the particle mobility and aggregation status of ferucarbotran resulted in significantly improved image reconstructions. The finding was supported by characterizations of different ferucarbotran compositions with the magnetorelaxometry and magnetic particle spectroscopy technique. For instance, similar results were obtained between ferucarbotran embedded in freeze-dried mannitol sugar and liver tissue harvested after a ferucarbotran injection. In addition, the combination of multiple shifted measurement patches for a joint reconstruction of the MPI data enlarged the field of view and increased the covering of liver MPI on magnetic resonance images noticeably.

In vivo liver visualizations with magnetic particle imaging based on the calibration measurement approach.

PubMed

Dieckhoff, J; Kaul, M G; Mummert, T; Jung, C; Salamon, J; Adam, G; Knopp, T; Ludwig, F; Balceris, C; Ittrich, H

2017-05-07

Magnetic particle imaging (MPI) facilitates the rapid determination of 3D in vivo magnetic nanoparticle distributions. In this work, liver MPI following intravenous injections of ferucarbotran (Resovist ® ) was studied. The image reconstruction was based on a calibration measurement, the so called system function. The application of an enhanced system function sample reflecting the particle mobility and aggregation status of ferucarbotran resulted in significantly improved image reconstructions. The finding was supported by characterizations of different ferucarbotran compositions with the magnetorelaxometry and magnetic particle spectroscopy technique. For instance, similar results were obtained between ferucarbotran embedded in freeze-dried mannitol sugar and liver tissue harvested after a ferucarbotran injection. In addition, the combination of multiple shifted measurement patches for a joint reconstruction of the MPI data enlarged the field of view and increased the covering of liver MPI on magnetic resonance images noticeably.

Toxoplasma gondii strain-dependent effects on mouse behaviour.

PubMed

Kannan, Geetha; Moldovan, Krisztina; Xiao, Jian-Chun; Yolken, Robert H; Jones-Brando, Lorraine; Pletnikov, Mikhail V

2010-06-01

Toxoplasma gondii reportedly manipulates rodent behaviour to increase transmission to its definitive feline host. We compared the effects of mouse infection by two Type II strains of T. gondii, Prugniaud (PRU) and ME49, on attraction to cat odour, locomotor activity, anxiety, sensorimotor gating, and spatial working and recognition memory 2 months post-infection (mpi). Attraction to cat odour was reassessed 7 mpi. At 2 mpi, mice infected with either strain exhibited significantly more attraction to cat odour than uninfected animals did, but only PRU-infected mice exhibited this behaviour 7 mpi. PRU-infected mice had significantly greater body weights and hyperactivity, while ME49-infected mice exhibited impaired spatial working memory. No differences in parasite antibody titres were seen between PRU- and ME49-infected mice. The present data suggest the effect of T. gondii infection on mouse behaviour is parasite strain-dependent.

Conflict Detection Algorithm to Minimize Locking for MPI-IO Atomicity

NASA Astrophysics Data System (ADS)

Sehrish, Saba; Wang, Jun; Thakur, Rajeev

Many scientific applications require high-performance concurrent I/O accesses to a file by multiple processes. Those applications rely indirectly on atomic I/O capabilities in order to perform updates to structured datasets, such as those stored in HDF5 format files. Current support for atomicity in MPI-IO is provided by locking around the operations, imposing lock overhead in all situations, even though in many cases these operations are non-overlapping in the file. We propose to isolate non-overlapping accesses from overlapping ones in independent I/O cases, allowing the non-overlapping ones to proceed without imposing lock overhead. To enable this, we have implemented an efficient conflict detection algorithm in MPI-IO using MPI file views and datatypes. We show that our conflict detection scheme incurs minimal overhead on I/O operations, making it an effective mechanism for avoiding locks when they are not needed.

Architecture and method for a burst buffer using flash technology

DOEpatents

Tzelnic, Percy; Faibish, Sorin; Gupta, Uday K.; Bent, John; Grider, Gary Alan; Chen, Hsing-bung

2016-03-15

A parallel supercomputing cluster includes compute nodes interconnected in a mesh of data links for executing an MPI job, and solid-state storage nodes each linked to a respective group of the compute nodes for receiving checkpoint data from the respective compute nodes, and magnetic disk storage linked to each of the solid-state storage nodes for asynchronous migration of the checkpoint data from the solid-state storage nodes to the magnetic disk storage. Each solid-state storage node presents a file system interface to the MPI job, and multiple MPI processes of the MPI job write the checkpoint data to a shared file in the solid-state storage in a strided fashion, and the solid-state storage node asynchronously migrates the checkpoint data from the shared file in the solid-state storage to the magnetic disk storage and writes the checkpoint data to the magnetic disk storage in a sequential fashion.

Additive value of 3T cardiovascular magnetic resonance coronary angiography for detecting coronary artery disease.

PubMed

Zhang, Lijun; Song, Xiantao; Dong, Li; Li, Jianan; Dou, Ruiyu; Fan, Zhanming; An, Jing; Li, Debiao

2018-04-30

The purpose of the work was to evaluate the incremental diagnostic value of free-breathing, contrast-enhanced, whole-heart, 3 T cardiovascular magnetic resonance coronary angiography (CE-MRCA) to stress/rest myocardial perfusion imaging (MPI) and late gadolinium enhancement (LGE) imaging for detecting coronary artery disease (CAD). Fifty-one patients with suspected CAD underwent a comprehensive cardiovascular magnetic resonance (CMR) examination (CE-MRCA, MPI, and LGE). The additive diagnostic value of MRCA to MPI and LGE was evaluated using invasive x-ray coronary angiography (XA) as the standard for defining functionally significant CAD (≥ 50% stenosis in vessels > 2 mm in diameter). 90.2% (46/51) patients (54.0 ± 11.5 years; 71.7% men) completed CE-MRCA successfully. On per-patient basis, compared to MPI/LGE alone or MPI alone, the addition of MRCA resulted in higher sensitivity (100% vs. 76.5%, p < 0.01), no change in specificity (58.3% vs. 66.7%, p = 0.6), and higher accuracy (89.1% vs 73.9%, p < 0.01) for CAD detection (prevalence = 73.9%). Compared to LGE alone, the addition of CE-MRCA resulted in higher sensitivity (97.1% vs. 41.2%, p < 0.01), inferior specificity (83.3% vs. 91.7%, p = 0.02), and higher diagnostic accuracy (93.5% vs. 54.3%, p < 0.01). The inclusion of successful free-breathing, whole-heart, 3 T CE-MRCA significantly improved the sensitivity and diagnostic accuracy as compared to MPI and LGE alone for CAD detection.

77 FR 44677 - RG Steel Sparrows Point LLC, Formerly Known as Severstal Sparrows Point LLC, a Subsidiary of RG...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-30

... Leased Workers From Echelon Service Company, Sun Associated Industries, Inc., MPI Consultants LLC...-site leased workers from Echelon Service Company, Sun Associated Industries, Inc., MPI Consultants LLC...

Comparison of Gated SPECT Myocardial Perfusion Imaging with Echocardiography for the Measurement of Left Ventricular Volumes and Ejection Fraction in Patients With Severe Heart Failure

PubMed Central

Shojaeifard, Maryam; Ghaedian, Tahereh; Yaghoobi, Nahid; Malek, Hadi; Firoozabadi, Hasan; Bitarafan-Rajabi, Ahmad; Haghjoo, Majid; Amin, Ahmad; Azizian, Nasrin; Rastgou, Feridoon

2015-01-01

Background: Gated single-photon emission computed tomography (SPECT) myocardial perfusion imaging (MPI) is known as a feasible tool for the measurement of left ventricular ejection fraction (EF) and volumes, which are of great importance in the management and follow-up of patients with coronary artery diseases. However, considering the technical shortcomings of SPECT in the presence of perfusion defect, the accuracy of this method in heart failure patients is still controversial. Objectives: The aim of the present study was to compare the results from gated SPECT MPI with those from echocardiography in heart failure patients to compare echocardiographically-derived left ventricular dimension and function data to those from gated SPECT MPI in heart failure patients. Patients and Methods: Forty-one patients with severely reduced left ventricular systolic function (EF ≤ 35%) who were referred for gated SPECT MPI were prospectively enrolled. Quantification of EF, end-diastolic volume (EDV), and end-systolic volume (ESV) was performed by using quantitative gated spect (QGS) (QGS, version 0.4, May 2009) and emory cardiac toolbox (ECTb) (ECTb, revision 1.0, copyright 2007) software packages. EF, EDV, and ESV were also measured with two-dimensional echocardiography within 3 days after MPI. Results: A good correlation was found between echocardiographically-derived EF, EDV, and ESV and the values derived using QGS (r = 0.67, r = 0.78, and r = 0.80 for EF, EDV, and ESV, respectively; P < 0.001) and ECTb (r = 0.68, 0.79, and r = 0.80 for EF, EDV, and ESV, respectively; P < 0.001). However, Bland-Altman plots indicated significantly different mean values for EF, 11.4 and 20.9 using QGS and ECTb, respectively, as compared with echocardiography. ECTb-derived EDV was also significantly higher than the EDV measured with echocardiography and QGS. The highest correlation between echocardiography and gated SPECT MPI was found for mean values of ESV different. Conclusions: Gated SPECT MPI has a good correlation with echocardiography for the measurement of left ventricular EF, EDV, and ESV in patients with severe heart failure. However, the absolute values of these functional parameters from echocardiography and gated SPECT MPI measured with different software packages should not be used interchangeably. PMID:26889455

Application of the Low-dose One-stop-shop Cardiac CT Protocol with Third-generation Dual-source CT.

PubMed

Lin, Lu; Wang, Yining; Yi, Yan; Cao, Jian; Kong, Lingyan; Qian, Hao; Zhang, Hongzhi; Wu, Wei; Wang, Yun; Jin, Zhengyu

2017-02-20

Objective To evaluate the feasibility of a low-dose one-stop-shop cardiac CT imaging protocol with third-generation dual-source CT (DSCT). Methods Totally 23 coronary artery disease (CAD) patients were prospectively enrolled between March to September in 2016. All patients underwent an ATP stress dynamic myocardial perfusion imaging (MPI) (data acquired prospectively ECG-triggered during end systole by table shuttle mode in 32 seconds) at 70 kV combined with prospectively ECG-triggered high-pitch coronary artery angiography (CCTA) on a third-generation DSCT system. Myocardial blood flow (MBF) was quantified and compared between perfusion normal and abnormal myocardial segments based on AHA-17-segment model. CCTA images were evaluated qualitatively based on SCCT-18-segment model and the effective dose(ED) was calculated. In patients with subsequent catheter coronary angiography (CCA) as reference,the diagnosis performance of MPI (for per-vessel ≥50% and ≥70% stenosis) and CCTA (for≥50% stenosis) were assessed. Results Of 23 patients who had completed the examination of ATP stress MPI plus CCTA,12 patients received follow-up CCA. At ATP stress MPI,77 segments (19.7%) in 13 patients (56.5%) had perfusion abnormalities. The MBF values of hypo-perfused myocardial segments decreased significantly compared with normal segments [(93±22)ml/(100 ml·min) vs. (147±27)ml/(100 ml·min);t=15.978,P=0.000]. At CCTA,93.9% (308/328) of the coronary segments had diagnostic image quality. With CCA as the reference standard,the per-vessel and per-segment sensitivity,specificity,and accuracy of CCTA for stenosis≥50% were 94.1%,93.5%,and 93.7% and 90.9%,97.8%,and 96.8%,and the per-vessel sensitivity,specificity and accuracy of ATP stress MPI for stenosis≥50% and ≥70% were 68.7%,100%,and 89.5% and 91.7%,100%,and 97.9%. The total ED of MPI and CCTA was (3.9±1.3) mSv [MPI:(3.5±1.2) mSv,CCTA:(0.3±0.1) mSv]. Conclusion The third-generation DSCT stress dynamic MPI at 70 kV combined with prospectively ECG-triggered high-pitch CCTA is a feasible and reliable tool for clinical diagnosis,with remarkably reduced radiation dose.

Performance Evaluation of Supercomputers using HPCC and IMB Benchmarks

NASA Technical Reports Server (NTRS)

Saini, Subhash; Ciotti, Robert; Gunney, Brian T. N.; Spelce, Thomas E.; Koniges, Alice; Dossa, Don; Adamidis, Panagiotis; Rabenseifner, Rolf; Tiyyagura, Sunil R.; Mueller, Matthias;

High-Performance Design Patterns for Modern Fortran

DOE PAGES

Haveraaen, Magne; Morris, Karla; Rouson, Damian; ...

2015-01-01

This paper presents ideas for using coordinate-free numerics in modern Fortran to achieve code flexibility in the partial differential equation (PDE) domain. We also show how Fortran, over the last few decades, has changed to become a language well-suited for state-of-the-art software development. Fortran’s new coarray distributed data structure, the language’s class mechanism, and its side-effect-free, pure procedure capability provide the scaffolding on which we implement HPC software. These features empower compilers to organize parallel computations with efficient communication. We present some programming patterns that support asynchronous evaluation of expressions comprised of parallel operations on distributed data. We implemented thesemore » patterns using coarrays and the message passing interface (MPI). We compared the codes’ complexity and performance. The MPI code is much more complex and depends on external libraries. The MPI code on Cray hardware using the Cray compiler is 1.5–2 times faster than the coarray code on the same hardware. The Intel compiler implements coarrays atop Intel’s MPI library with the result apparently being 2–2.5 times slower than manually coded MPI despite exhibiting nearly linear scaling efficiency. As compilers mature and further improvements to coarrays comes in Fortran 2015, we expect this performance gap to narrow.« less

Accelerating k-NN Algorithm with Hybrid MPI and OpenSHMEM

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lin, Jian; Hamidouche, Khaled; Zheng, Jie

2015-08-05

Machine Learning algorithms are benefiting from the continuous improvement of programming models, including MPI, MapReduce and PGAS. k-Nearest Neighbors (k-NN) algorithm is a widely used machine learning algorithm, applied to supervised learning tasks such as classification. Several parallel implementations of k-NN have been proposed in the literature and practice. However, on high-performance computing systems with high-speed interconnects, it is important to further accelerate existing designs of the k-NN algorithm through taking advantage of scalable programming models. To improve the performance of k-NN on large-scale environment with InfiniBand network, this paper proposes several alternative hybrid MPI+OpenSHMEM designs and performs a systemicmore » evaluation and analysis on typical workloads. The hybrid designs leverage the one-sided memory access to better overlap communication with computation than the existing pure MPI design, and propose better schemes for efficient buffer management. The implementation based on k-NN program from MaTEx with MVAPICH2-X (Unified MPI+PGAS Communication Runtime over InfiniBand) shows up to 9.0% time reduction for training KDD Cup 2010 workload over 512 cores, and 27.6% time reduction for small workload with balanced communication and computation. Experiments of running with varied number of cores show that our design can maintain good scalability.« less

Normal Databases for the Relative Quantification of Myocardial Perfusion

PubMed Central

Rubeaux, Mathieu; Xu, Yuan; Germano, Guido; Berman, Daniel S.; Slomka, Piotr J.

2016-01-01

Purpose of review Myocardial perfusion imaging (MPI) with SPECT is performed clinically worldwide to detect and monitor coronary artery disease (CAD). MPI allows an objective quantification of myocardial perfusion at stress and rest. This established technique relies on normal databases to compare patient scans against reference normal limits. In this review, we aim to introduce the process of MPI quantification with normal databases and describe the associated perfusion quantitative measures that are used. Recent findings New equipment and new software reconstruction algorithms have been introduced which require the development of new normal limits. The appearance and regional count variations of normal MPI scan may differ between these new scanners and standard Anger cameras. Therefore, these new systems may require the determination of new normal limits to achieve optimal accuracy in relative myocardial perfusion quantification. Accurate diagnostic and prognostic results rivaling those obtained by expert readers can be obtained by this widely used technique. Summary Throughout this review, we emphasize the importance of the different normal databases and the need for specific databases relative to distinct imaging procedures. use of appropriate normal limits allows optimal quantification of MPI by taking into account subtle image differences due to the hardware and software used, and the population studied. PMID:28138354

Effects of variation in chain length on ternary polymer electrolyte - Ionic liquid mixture - A molecular dynamics simulation study

NASA Astrophysics Data System (ADS)

Raju, S. G.; Hariharan, Krishnan S.; Park, Da-Hye; Kang, HyoRang; Kolake, Subramanya Mayya

2015-10-01

Molecular dynamics (MD) simulations of ternary polymer electrolyte - ionic liquid mixtures are conducted using an all-atom model. N-alkyl-N-methylpyrrolidinium bis(trifluoromethylsulfonyl)imide ([CnMPy][TFSI], n = 1, 3, 6, 9) and polyethylene oxide (PEO) are used. Microscopic structure, energetics and dynamics of ionic liquid (IL) in these ternary mixtures are studied. Properties of these four pure IL are also calculated and compared to that in ternary mixtures. Interaction between pyrrolidinium cation and TFSI is stronger and there is larger propensity of ion-pair formation in ternary mixtures. Unlike the case in imidazolium IL, near neighbor structural correlation between TFSI reduces with increase in chain length on cation in both pure IL and ternary mixtures. Using spatial density maps, regions where PEO and TFSI interact with pyrrolidinium cation are identified. Oxygens of PEO are above and below the pyrrolidinium ring and away from the bulky alkyl groups whereas TFSI is present close to nitrogen atom of CnMPy. In pure IL, diffusion coefficient (D) of C3MPy is larger than of TFSI but D of C9MPy and C6MPy are larger than that of TFSI. The reasons for alkyl chain dependent phenomena are explored.

OpenGeoSys-GEMS: Hybrid parallelization of a reactive transport code with MPI and threads

NASA Astrophysics Data System (ADS)

Kosakowski, G.; Kulik, D. A.; Shao, H.

2012-04-01

OpenGeoSys-GEMS is a generic purpose reactive transport code based on the operator splitting approach. The code couples the Finite-Element groundwater flow and multi-species transport modules of the OpenGeoSys (OGS) project (http://www.ufz.de/index.php?en=18345) with the GEM-Selektor research package to model thermodynamic equilibrium of aquatic (geo)chemical systems utilizing the Gibbs Energy Minimization approach (http://gems.web.psi.ch/). The combination of OGS and the GEM-Selektor kernel (GEMS3K) is highly flexible due to the object-oriented modular code structures and the well defined (memory based) data exchange modules. Like other reactive transport codes, the practical applicability of OGS-GEMS is often hampered by the long calculation time and large memory requirements. • For realistic geochemical systems which might include dozens of mineral phases and several (non-ideal) solid solutions the time needed to solve the chemical system with GEMS3K may increase exceptionally. • The codes are coupled in a sequential non-iterative loop. In order to keep the accuracy, the time step size is restricted. In combination with a fine spatial discretization the time step size may become very small which increases calculation times drastically even for small 1D problems. • The current version of OGS is not optimized for memory use and the MPI version of OGS does not distribute data between nodes. Even for moderately small 2D problems the number of MPI processes that fit into memory of up-to-date workstations or HPC hardware is limited. One strategy to overcome the above mentioned restrictions of OGS-GEMS is to parallelize the coupled code. For OGS a parallelized version already exists. It is based on a domain decomposition method implemented with MPI and provides a parallel solver for fluid and mass transport processes. In the coupled code, after solving fluid flow and solute transport, geochemical calculations are done in form of a central loop over all finite element nodes with calls to GEMS3K and consecutive calculations of changed material parameters. In a first step the existing MPI implementation was utilized to parallelize this loop. Calculations were split between the MPI processes and afterwards data was synchronized by using MPI communication routines. Furthermore, multi-threaded calculation of the loop was implemented with help of the boost thread library (http://www.boost.org). This implementation provides a flexible environment to distribute calculations between several threads. For each MPI process at least one and up to several dozens of worker threads are spawned. These threads do not replicate the complete OGS-GEM data structure and use only a limited amount of memory. Calculation of the central geochemical loop is shared between all threads. Synchronization between the threads is done by barrier commands. The overall number of local threads times MPI processes should match the number of available computing nodes. The combination of multi-threading and MPI provides an effective and flexible environment to speed up OGS-GEMS calculations while limiting the required memory use. Test calculations on different hardware show that for certain types of applications tremendous speedups are possible.

Fenix, A Fault Tolerant Programming Framework for MPI Applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gamel, Marc; Teranihi, Keita; Valenzuela, Eric

2016-10-05

Fenix provides APIs to allow the users to add fault tolerance capability to MPI-based parallel programs in a transparent manner. Fenix-enabled programs can run through process failures during program execution using a pool of spare processes accommodated by Fenix.

Impact of age on the selection of nuclear cardiology stress protocols: The INCAPS (IAEA nuclear cardiology protocols) study.

PubMed

Al-Mallah, Mouaz H; Pascual, Thomas N B; Mercuri, Mathew; Vitola, João V; Karthikeyan, Ganesan; Better, Nathan; Dondi, Maurizio; Paez, Diana; Einstein, Andrew J

2018-05-15

There is growing concern about radiation exposure from nuclear myocardial perfusion imaging (MPI), particularly among younger patients who are more prone to develop untoward effects of ionizing radiation, and hence US and European professional society guidelines recommend age as a consideration in weighing radiation risk from MPI. We aimed to determine how patient radiation doses from MPI vary across age groups in a large contemporary international cohort. Data were collected as part of a global cross-sectional study of centers performing MPI coordinated by the International Atomic Energy Agency (IAEA). Sites provided information on each MPI study completed during a single week in March-April 2013. We compared across age groups laboratory adherence to pre-specified radiation-related best practices, radiation effective dose (ED; a whole-body measure reflecting the amount of radiation to each organ and its relative sensitivity to radiation's deleterious effects), and the proportion of patients with ED ≤ 9 mSv, a target level specified in guidelines. Among 7911 patients undergoing MPI in 308 laboratories in 65 countries, mean ED was 10.0 ± 4.5 mSv with slightly higher exposure among younger age groups (trend p value < 0.001). There was no difference in the proportion of patients with ED ≤ 9 mSv across age groups, or in adherence to best practices based on the median age of patients in a laboratory. In contemporary nuclear cardiology practice, the age of the patient appears not to impact protocol selection and radiation dose, contrary to professional society guidelines. Copyright © 2018. Published by Elsevier B.V.

Calibration free beam hardening correction for cardiac CT perfusion imaging

NASA Astrophysics Data System (ADS)

Levi, Jacob; Fahmi, Rachid; Eck, Brendan L.; Fares, Anas; Wu, Hao; Vembar, Mani; Dhanantwari, Amar; Bezerra, Hiram G.; Wilson, David L.

2016-03-01

Myocardial perfusion imaging using CT (MPI-CT) and coronary CTA have the potential to make CT an ideal noninvasive gate-keeper for invasive coronary angiography. However, beam hardening artifacts (BHA) prevent accurate blood flow calculation in MPI-CT. BH Correction (BHC) methods require either energy-sensitive CT, not widely available, or typically a calibration-based method. We developed a calibration-free, automatic BHC (ABHC) method suitable for MPI-CT. The algorithm works with any BHC method and iteratively determines model parameters using proposed BHA-specific cost function. In this work, we use the polynomial BHC extended to three materials. The image is segmented into soft tissue, bone, and iodine images, based on mean HU and temporal enhancement. Forward projections of bone and iodine images are obtained, and in each iteration polynomial correction is applied. Corrections are then back projected and combined to obtain the current iteration's BHC image. This process is iterated until cost is minimized. We evaluate the algorithm on simulated and physical phantom images and on preclinical MPI-CT data. The scans were obtained on a prototype spectral detector CT (SDCT) scanner (Philips Healthcare). Mono-energetic reconstructed images were used as the reference. In the simulated phantom, BH streak artifacts were reduced from 12+/-2HU to 1+/-1HU and cupping was reduced by 81%. Similarly, in physical phantom, BH streak artifacts were reduced from 48+/-6HU to 1+/-5HU and cupping was reduced by 86%. In preclinical MPI-CT images, BHA was reduced from 28+/-6 HU to less than 4+/-4HU at peak enhancement. Results suggest that the algorithm can be used to reduce BHA in conventional CT and improve MPI-CT accuracy.

Does Classification of Chronic Musculoskeletal Disorder Patients Into Psychosocial Subgroups Predict Differential Treatment Responsiveness and 1-Year Outcomes After a Functional Restoration Program?

PubMed

Asih, Sali; Mayer, Tom G; Williams, Mark; Choi, Yun Hee; Gatchel, Robert J

2015-12-01

The objectives of this study: (1) to assess whether Multidimensional Pain Inventory (MPI) profiles predicted differential responses to a functional restoration program (FRP) in chronic disabling occupational musculoskeletal disorder (CDOMD) patients; (2) to examine whether coping style improves following FRP; and (3) to determine whether discharge MPI profiles predict discharge psychosocial and 1-year socioeconomic outcomes. Consecutive CDOMD patients (N=716) were classified into Adaptive Coper (AC, n=209), Interpersonally Distressed (ID, n=154), Dysfunctional (DYS, n=310), and Anomalous (n=43) using the MPI, and reclassified at discharge. Profiles were compared on psychosocial measures and 1-year socioeconomic outcomes. An intent-to-treat sample analyzed the effect of drop-outs on treatment responsiveness. The MPI classification significantly predicted program completion (P=0.001), although the intent-to-treat analyses found no significant effects of drop-out on treatment responsiveness. There was a significant increase in the number of patients who became AC or Anomalous at FRP discharge and a decrease in those who were ID or DYS. Patients who changed or remained as DYS at FRP discharge reported the highest levels of pain, disability, and depression. No significant interaction effect was found between MPI group and time for pain intensity or disability. All groups improved on psychosocial measures at discharge. DYS patients had decreased work retention and a greater health care utilization at 1 year. An FRP was clinically effective for CDOMD patients regardless of initial MPI profiles. The FRP modified profiles, with patients changing from negative to positive profiles. Discharge DYS were more likely to have poor 1-year outcomes. Those classified as Anomalous had a good prognosis for functional recovery similar to ACs.

The effect of patient anxiety and depression on motion during myocardial perfusion SPECT imaging.

PubMed

Lyra, Vassiliki; Kallergi, Maria; Rizos, Emmanouil; Lamprakopoulos, Georgios; Chatziioannou, Sofia N

2016-08-22

Patient motion during myocardial perfusion SPECT imaging (MPI) may be triggered by a patient's physical and/or psychological discomfort. The aim of this study was to investigate the impact of state anxiety (patient's reaction to exam-related stress), trait anxiety (patient's personality characteristic) and depression on patient motion during MPI. All patients that underwent MPI in our department in a six-month period were prospectively enrolled. One hundred eighty-three patients (45 females; 138 males) filled in the State-Trait Anxiety Inventory (STAI) and the Beck Depression Inventory (BDI), along with a short questionnaire regarding their age, height and weight, level of education in years, occupation, and marital status. Cardiovascular and other co-morbidity factors were also evaluated. Through inspection of raw data on cinematic display, the presence or absence of patient motion was registered and classified into mild, moderate and severe, for both phases involved in image acquisition. The correlation of patient motion in the stress and delay phases of MPI and each of the other variables was investigated and the corresponding Pearson's coefficients of association were calculated. The anxiety-motion (r = 0.43, P < 0.0001) and depression-motion (r = 0.32, P < 0.0001) correlation results were moderately strong and statistically significant for the female but not the male patients. All the other variables did not demonstrate any association with motion in MPI, except a weak correlation between age and motion in females (r = 0.23, P < 0.001). The relationship between anxiety-motion and depression-motion identified in female patients represents the first supporting evidence of psychological discomfort as predisposing factor for patient motion during MPI.

Theoretical predictions for spatially-focused heating of magnetic nanoparticles guided by magnetic particle imaging field gradients

NASA Astrophysics Data System (ADS)

Dhavalikar, Rohan; Rinaldi, Carlos

2016-12-01

Magnetic nanoparticles in alternating magnetic fields (AMFs) transfer some of the field's energy to their surroundings in the form of heat, a property that has attracted significant attention for use in cancer treatment through hyperthermia and in developing magnetic drug carriers that can be actuated to release their cargo externally using magnetic fields. To date, most work in this field has focused on the use of AMFs that actuate heat release by nanoparticles over large regions, without the ability to select specific nanoparticle-loaded regions for heating while leaving other nanoparticle-loaded regions unaffected. In parallel, magnetic particle imaging (MPI) has emerged as a promising approach to image the distribution of magnetic nanoparticle tracers in vivo, with sub-millimeter spatial resolution. The underlying principle in MPI is the application of a selection magnetic field gradient, which defines a small region of low bias field, superimposed with an AMF (of lower frequency and amplitude than those normally used to actuate heating by the nanoparticles) to obtain a signal which is proportional to the concentration of particles in the region of low bias field. Here we extend previous models for estimating the energy dissipation rates of magnetic nanoparticles in uniform AMFs to provide theoretical predictions of how the selection magnetic field gradient used in MPI can be used to selectively actuate heating by magnetic nanoparticles in the low bias field region of the selection magnetic field gradient. Theoretical predictions are given for the spatial decay in energy dissipation rate under magnetic field gradients representative of those that can be achieved with current MPI technology. These results underscore the potential of combining MPI and higher amplitude/frequency actuation AMFs to achieve selective magnetic fluid hyperthermia (MFH) guided by MPI.

Usefulness of myocardial parametric imaging to evaluate myocardial viability in experimental and in clinical studies.

PubMed

Korosoglou, G; Hansen, A; Bekeredjian, R; Filusch, A; Hardt, S; Wolf, D; Schellberg, D; Katus, H A; Kuecherer, H

2006-03-01

To evaluate whether myocardial parametric imaging (MPI) is superior to visual assessment for the evaluation of myocardial viability. Myocardial contrast echocardiography (MCE) was assessed in 11 pigs before, during, and after left anterior descending coronary artery occlusion and in 32 patients with ischaemic heart disease by using intravenous SonoVue administration. In experimental studies perfusion defect area assessment by MPI was compared with visually guided perfusion defect planimetry. Histological assessment of necrotic tissue was the standard reference. In clinical studies viability was assessed on a segmental level by (1) visual analysis of myocardial opacification; (2) quantitative estimation of myocardial blood flow in regions of interest; and (3) MPI. Functional recovery between three and six months after revascularisation was the standard reference. In experimental studies, compared with visually guided perfusion defect planimetry, planimetric assessment of infarct size by MPI correlated more significantly with histology (r2 = 0.92 versus r2 = 0.56) and had a lower intraobserver variability (4% v 15%, p < 0.05). In clinical studies, MPI had higher specificity (66% v 43%, p < 0.05) than visual MCE and good accuracy (81%) for viability detection. It was less time consuming (3.4 (1.6) v 9.2 (2.4) minutes per image, p < 0.05) than quantitative blood flow estimation by regions of interest and increased the agreement between observers interpreting myocardial perfusion (kappa = 0.87 v kappa = 0.75, p < 0.05). MPI is useful for the evaluation of myocardial viability both in animals and in patients. It is less time consuming than quantification analysis by regions of interest and less observer dependent than visual analysis. Thus, strategies incorporating this technique may be valuable for the evaluation of myocardial viability in clinical routine.

Stress-induced ST-segment deviation in relation to the presence and severity of coronary artery disease in patients with normal myocardial perfusion imaging.

PubMed

Weinsaft, Jonathan W; Manoushagian, Shant J; Patel, Taral; Shakoor, Aqsa; Kim, Robert J; Mirchandani, Sunil; Lin, Fay; Wong, Franklin J; Szulc, Massimiliano; Okin, Peter M; Kligfield, Paul D; Min, James K

2009-01-01

To assess the utility of stress electrocardiography (ECG) for identifying the presence and severity of obstructive coronary artery disease (CAD) defined by coronary computed tomographic angiography (CCTA) among patients with normal nuclear myocardial perfusion imaging (MPI). The study population comprised 119 consecutive patients with normal MPI who also underwent CCTA (interval 3.5+/-3.8 months). Stress ECG was performed at the time of MPI. CCTA and MPI were interpreted using established scoring systems, and CCTA was used to define the presence and extent of CAD, which was quantified by a coronary artery jeopardy score. Within this population, 28 patients (24%) had obstructive CAD identified by CCTA. The most common CAD pattern was single-vessel CAD (61%), although proximal vessel involvement was present in 46% of patients. Patients with CAD were nearly three times more likely to have positive standard test responses (1 mm ST-segment deviation) than patients with patent coronary arteries (36 vs. 13%, P=0.007). In multivariate analysis, a positive ST-segment test response was an independent marker for CAD (odds ratio: 2.02, confidence interval: 1.09-3.78, P=0.03) even after adjustment for a composite of clinical cardiac risk factors (odds ratio: 1.85, confidence interval: 1.05-3.23, P=0.03). Despite uniformly normal MPI, mean coronary jeopardy score was three-fold higher among patients with positive compared to those with negative ST-segment response to exercise or dobutamine stress (1.9+/-2.7 vs. 0.5+/-1.4, P=0.03). Stress-induced ST-segment deviation is an independent marker for obstructive CAD among patients with normal MPI. A positive stress ECG identifies patients with a greater anatomic extent of CAD as quantified by coronary jeopardy score.

Effects of medially posted insoles on foot and lower limb mechanics across walking and running in overpronating men.

PubMed

Kosonen, Jukka; Kulmala, Juha-Pekka; Müller, Erich; Avela, Janne

2017-03-21

Anti-pronation orthoses, like medially posted insoles (MPI), have traditionally been used to treat various of lower limb problems. Yet, we know surprisingly little about their effects on overall foot motion and lower limb mechanics across walking and running, which represent highly different loading conditions. To address this issue, multi-segment foot and lower limb mechanics was examined among 11 overpronating men with normal (NORM) and MPI insoles during walking (self-selected speed 1.70±0.19m/s vs 1.72±0.20m/s, respectively) and running (4.04±0.17m/s vs 4.10±0.13m/s, respectively). The kinematic results showed that MPI reduced the peak forefoot eversion movement in respect to both hindfoot and tibia across walking and running when compared to NORM (p<0.05-0.01). No differences were found in hindfoot eversion between conditions. The kinetic results showed no insole effects in walking, but during running MPI shifted center of pressure medially under the foot (p<0.01) leading to an increase in frontal plane moments at the hip (p<0.05) and knee (p<0.05) joints and a reduction at the ankle joint (p<0.05). These findings indicate that MPI primarily controlled the forefoot motion across walking and running. While kinetic response to MPI was more pronounced in running than walking, kinematic effects were essentially similar across both modes. This suggests that despite higher loads placed upon lower limb during running, there is no need to have a stiffer insoles to achieve similar reduction in the forefoot motion than in walking. Copyright © 2017 Elsevier Ltd. All rights reserved.

Magnetic particle imaging for in vivo blood flow velocity measurements in mice

NASA Astrophysics Data System (ADS)

Kaul, Michael G.; Salamon, Johannes; Knopp, Tobias; Ittrich, Harald; Adam, Gerhard; Weller, Horst; Jung, Caroline

2018-03-01

Magnetic particle imaging (MPI) is a new imaging technology. It is a potential candidate to be used for angiographic purposes, to study perfusion and cell migration. The aim of this work was to measure velocities of the flowing blood in the inferior vena cava of mice, using MPI, and to evaluate it in comparison with magnetic resonance imaging (MRI). A phantom mimicking the flow within the inferior vena cava with velocities of up to 21 cm s‑1 was used for the evaluation of the applied analysis techniques. Time–density and distance–density analyses for bolus tracking were performed to calculate flow velocities. These findings were compared with the calibrated velocities set by a flow pump, and it can be concluded that velocities of up to 21 cm s‑1 can be measured by MPI. A time–density analysis using an arrival time estimation algorithm showed the best agreement with the preset velocities. In vivo measurements were performed in healthy FVB mice (n  =  10). MRI experiments were performed using phase contrast (PC) for velocity mapping. For MPI measurements, a standardized injection of a superparamagnetic iron oxide tracer was applied. In vivo MPI data were evaluated by a time–density analysis and compared to PC MRI. A Bland–Altman analysis revealed good agreement between the in vivo velocities acquired by MRI of 4.0  ±  1.5 cm s‑1 and those measured by MPI of 4.8  ±  1.1 cm s‑1. Magnetic particle imaging is a new tool with which to measure and quantify flow velocities. It is fast, radiation-free, and produces 3D images. It therefore offers the potential for vascular imaging.

Development of Modeling and Simulation for Magnetic Particle Inspection Using Finite Elements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Jun-Youl

2003-01-01

Magnetic particle inspection (MPI) is a widely used nondestructive inspection method for aerospace applications essentially limited to experiment-based approaches. The analysis of MPI characteristics that affect sensitivity and reliability contributes not only reductions in inspection design cost and time but also improvement of analysis of experimental data. Magnetic particles are easily attracted toward a high magnetic field gradient. Selection of a magnetic field source, which produces a magnetic field gradient large enough to detect a defect in a test sample or component, is an important factor in magnetic particle inspection. In this work a finite element method (FEM) has beenmore » employed for numerical calculation of the MPI simulation technique. The FEM method is known to be suitable for complicated geometries such as defects in samples. This thesis describes the research that is aimed at providing a quantitative scientific basis for magnetic particle inspection. A new FEM solver for MPI simulation has been developed in this research for not only nonlinear reversible permeability materials but also irreversible hysteresis materials that are described by the Jiles-Atherton model. The material is assumed to have isotropic ferromagnetic properties in this research (i.e., the magnetic properties of the material are identical in all directions in a single crystal). In the research, with a direct current field mode, an MPI situation has been simulated to measure the estimated volume of magnetic particles around defect sites before and after removing any external current fields. Currently, this new MPI simulation package is limited to solving problems with the single current source from either a solenoid or an axial directional current rod.« less

Resource-Efficient, Hierarchical Auto-Tuning of a Hybrid Lattice Boltzmann Computation on the Cray XT4

DOE Office of Scientific and Technical Information (OSTI.GOV)

Computational Research Division, Lawrence Berkeley National Laboratory; NERSC, Lawrence Berkeley National Laboratory; Computer Science Department, University of California, Berkeley

2009-05-04

We apply auto-tuning to a hybrid MPI-pthreads lattice Boltzmann computation running on the Cray XT4 at National Energy Research Scientific Computing Center (NERSC). Previous work showed that multicore-specific auto-tuning can improve the performance of lattice Boltzmann magnetohydrodynamics (LBMHD) by a factor of 4x when running on dual- and quad-core Opteron dual-socket SMPs. We extend these studies to the distributed memory arena via a hybrid MPI/pthreads implementation. In addition to conventional auto-tuning at the local SMP node, we tune at the message-passing level to determine the optimal aspect ratio as well as the correct balance between MPI tasks and threads permore » MPI task. Our study presents a detailed performance analysis when moving along an isocurve of constant hardware usage: fixed total memory, total cores, and total nodes. Overall, our work points to approaches for improving intra- and inter-node efficiency on large-scale multicore systems for demanding scientific applications.« less

Accelerating list management for MPI.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hemmert, K. Scott; Rodrigues, Arun F.; Underwood, Keith Douglas

2005-07-01

The latency and throughput of MPI messages are critically important to a range of parallel scientific applications. In many modern networks, both of these performance characteristics are largely driven by the performance of a processor on the network interface. Because of the semantics of MPI, this embedded processor is forced to traverse a linked list of posted receives each time a message is received. As this list grows long, the latency of message reception grows and the throughput of MPI messages decreases. This paper presents a novel hardware feature to handle list management functions on a network interface. By movingmore » functions such as list insertion, list traversal, and list deletion to the hardware unit, latencies are decreased by up to 20% in the zero length queue case with dramatic improvements in the presence of long queues. Similarly, the throughput is increased by up to 10% in the zero length queue case and by nearly 100% in the presence queues of 30 messages.« less

Parallel Fortran-MPI software for numerical inversion of the Laplace transform and its application to oscillatory water levels in groundwater environments

USGS Publications Warehouse

Zhan, X.

2005-01-01

A parallel Fortran-MPI (Message Passing Interface) software for numerical inversion of the Laplace transform based on a Fourier series method is developed to meet the need of solving intensive computational problems involving oscillatory water level's response to hydraulic tests in a groundwater environment. The software is a parallel version of ACM (The Association for Computing Machinery) Transactions on Mathematical Software (TOMS) Algorithm 796. Running 38 test examples indicated that implementation of MPI techniques with distributed memory architecture speedups the processing and improves the efficiency. Applications to oscillatory water levels in a well during aquifer tests are presented to illustrate how this package can be applied to solve complicated environmental problems involved in differential and integral equations. The package is free and is easy to use for people with little or no previous experience in using MPI but who wish to get off to a quick start in parallel computing. ?? 2004 Elsevier Ltd. All rights reserved.

Porting the AVS/Express scientific visualization software to Cray XT4.

PubMed

Leaver, George W; Turner, Martin J; Perrin, James S; Mummery, Paul M; Withers, Philip J

2011-08-28

Remote scientific visualization, where rendering services are provided by larger scale systems than are available on the desktop, is becoming increasingly important as dataset sizes increase beyond the capabilities of desktop workstations. Uptake of such services relies on access to suitable visualization applications and the ability to view the resulting visualization in a convenient form. We consider five rules from the e-Science community to meet these goals with the porting of a commercial visualization package to a large-scale system. The application uses message-passing interface (MPI) to distribute data among data processing and rendering processes. The use of MPI in such an interactive application is not compatible with restrictions imposed by the Cray system being considered. We present details, and performance analysis, of a new MPI proxy method that allows the application to run within the Cray environment yet still support MPI communication required by the application. Example use cases from materials science are considered.

An examination of the psychometric structure of the Multidimensional Pain Inventory in temporomandibular disorder patients: a confirmatory factor analysis

PubMed Central

Andreu, Yolanda; Galdon, Maria J; Durá, Estrella; Ferrando, Maite; Pascual, Juan; Turk, Dennis C; Jiménez, Yolanda; Poveda, Rafael

2006-01-01

Background This paper seeks to analyse the psychometric and structural properties of the Multidimensional Pain Inventory (MPI) in a sample of temporomandibular disorder patients. Methods The internal consistency of the scales was obtained. Confirmatory Factor Analysis was carried out to test the MPI structure section by section in a sample of 114 temporomandibular disorder patients. Results Nearly all scales obtained good reliability indexes. The original structure could not be totally confirmed. However, with a few adjustments we obtained a satisfactory structural model of the MPI which was slightly different from the original: certain items and the Self control scale were eliminated; in two cases, two original scales were grouped in one factor, Solicitous and Distracting responses on the one hand, and Social activities and Away from home activities, on the other. Conclusion The MPI has been demonstrated to be a reliable tool for the assessment of pain in temporomandibular disorder patients. Some divergences to be taken into account have been clarified. PMID:17169143

Projection x-space magnetic particle imaging.

PubMed

Goodwill, Patrick W; Konkle, Justin J; Zheng, Bo; Saritas, Emine U; Conolly, Steven M

2012-05-01

Projection magnetic particle imaging (MPI) can improve imaging speed by over 100-fold over traditional 3-D MPI. In this work, we derive the 2-D x-space signal equation, 2-D image equation, and introduce the concept of signal fading and resolution loss for a projection MPI imager. We then describe the design and construction of an x-space projection MPI scanner with a field gradient of 2.35 T/m across a 10 cm magnet free bore. The system has an expected resolution of 3.5 × 8.0 mm using Resovist tracer, and an experimental resolution of 3.8 × 8.4 mm resolution. The system images 2.5 cm × 5.0 cm partial field-of views (FOVs) at 10 frames/s, and acquires a full field-of-view of 10 cm × 5.0 cm in 4 s. We conclude by imaging a resolution phantom, a complex "Cal" phantom, mice injected with Resovist tracer, and experimentally confirm the theoretically predicted x-space spatial resolution.

Finite magnetic relaxation in x-space magnetic particle imaging: Comparison of measurements and ferrohydrodynamic models.

PubMed

Dhavalikar, R; Hensley, D; Maldonado-Camargo, L; Croft, L R; Ceron, S; Goodwill, P W; Conolly, S M; Rinaldi, C

2016-08-03

Magnetic Particle Imaging (MPI) is an emerging tomographic imaging technology that detects magnetic nanoparticle tracers by exploiting their non-linear magnetization properties. In order to predict the behavior of nanoparticles in an imager, it is possible to use a non-imaging MPI relaxometer or spectrometer to characterize the behavior of nanoparticles in a controlled setting. In this paper we explore the use of ferrohydrodynamic magnetization equations for predicting the response of particles in an MPI relaxometer. These include a magnetization equation developed by Shliomis (Sh) which has a constant relaxation time and a magnetization equation which uses a field-dependent relaxation time developed by Martsenyuk, Raikher and Shliomis (MRSh). We compare the predictions from these models with measurements and with the predictions based on the Langevin function that assumes instantaneous magnetization response of the nanoparticles. The results show good qualitative and quantitative agreement between the ferrohydrodynamic models and the measurements without the use of fitting parameters and provide further evidence of the potential of ferrohydrodynamic modeling in MPI.

The clinical implications of myocardial perfusion abnormalities in patients with esophageal or lung cancer after chemoradiation therapy.

PubMed

Gayed, Isis; Gohar, Salman; Liao, Zhongxing; McAleer, Mary; Bassett, Roland; Yusuf, Syed Wamique

2009-06-01

This study aims to identify the clinical implications of myocardial perfusion defects after chemoradiation therapy (CRT) in patients with esophageal and lung cancer. We retrospectively compared myocardial perfusion imaging (MPI) results before and after CRT in 16 patients with esophageal cancer and 24 patients with lung cancer. New MPI defects in the radiation therapy (RT) fields were considered related to RT. Follow-up to evaluate for cardiac complications and their relation with the results of MPI was performed. Statistical analysis identified predictors of cardiac morbidities. Eleven females and twenty nine males at a mean age of 66.7 years were included. Five patients (31%) with esophageal cancer and seven patients (29%) with lung cancer developed myocardial ischemia in the RT field at mean intervals of 7.0 and 8.4 months after RT. The patients were followed-up for mean intervals of 15 and 23 months in the esophageal and lung cancer groups, respectively. Seven patients in each of the esophageal (44%) and lung (29%) cancer patients (P = 0.5) developed cardiac complications of which one patient with esophageal cancer died of complete heart block. Six out of the fourteen patients (43%) with cardiac complication had new ischemia on MPI after CRT of which only one developed angina. The remaining eight patients with cardiac complications had normal MPI results. MPI result was not a statistically significant predictor of future cardiac complications after CRT. A history of congestive heart failure (CHF) (P = 0.003) or arrhythmia (P = 0.003) is a significant predictor of cardiac morbidity after CRT in univariate analysis but marginal predictors when multivariate analysis was performed (P = 0.06 and 0.06 for CHF and arrhythmia, respectively). Cardiac complications after CRT are more common in esophageal than lung cancer patients but the difference is not statistically significant. MPI abnormalities are frequently seen after CRT but are not predictive of future cardiac complications. A history of arrhythmia or CHF is significantly associated with cardiac complications after CRT.

Multiple Parton Interactions in p$$bar{p}$$ Collisions in D0 Experiment at the Tevatron Collider (in Russian)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Golovanov, Georgy

The thesis is devoted to the study of processes with multiple parton interactions (MPI) in a ppbar collision collected by D0 detector at the Fermilab Tevatron collider at sqrt(s) = 1.96 TeV. The study includes measurements of MPI event fraction and effective cross section, a process-independent parameter related to the effective interaction region inside the nucleon. The measurements are done using events with a photon and three hadronic jets in the final state. The measured effective cross section is used to estimate background from MPI for WH production at the Tevatron energy

A Generator-Produced Gallium-68 Radiopharmaceutical for PET Imaging of Myocardial Perfusion

PubMed Central

Sharma, Vijay; Sivapackiam, Jothilingam; Harpstrite, Scott E.; Prior, Julie L.; Gu, Hannah; Rath, Nigam P.; Piwnica-Worms, David

2014-01-01

Lipophilic cationic technetium-99m-complexes are widely used for myocardial perfusion imaging (MPI). However, inherent uncertainties in the supply chain of molybdenum-99, the parent isotope required for manufacturing 99Mo/99mTc generators, intensifies the need for discovery of novel MPI agents incorporating alternative radionuclides. Recently, germanium/gallium (Ge/Ga) generators capable of producing high quality 68Ga, an isotope with excellent emission characteristics for clinical PET imaging, have emerged. Herein, we report a novel 68Ga-complex identified through mechanism-based cell screening that holds promise as a generator-produced radiopharmaceutical for PET MPI. PMID:25353349

Cardiovascular outcomes of a positive nuclear stress test but negative coronary angiography in a multiethnic male predominant cohort.

PubMed

Addison, Daniel; Singh, Vinita; Okyere-Asante, K; Okafor, Henry

2014-01-01

Patients presenting with chest pain and evidence of functional ischemia by myocardial perfusion imaging (MPI), but lacking commensurate angiographic disease pose a diagnostic and therapeutic dilemma. They are often dismissed as having 'false-positive MPI'. Moreover, a majority of the available long-term outcome data for it has been derived from homogenous female populations. In this study, we sought to evaluate the long-term outcomes of this presentation in a multiethnic male-predominant cohort. We retrospectively identified 47 patients who presented to our institution between 2002 and 2005 with chest pain and evidence of ischemia on MPI, but with no significant angiographic disease on subsequent cardiac catheterization (cases). The occurrence of adverse cardiovascular outcomes (chest pain, congestive heart failure, acute myocardial infarction and stroke) post-index coronary angiogram was tracked. Similar data was collected for 37 patients who also presented with chest pain, but normal MPI over the same period (controls). Overall average follow-up was over 22 months. Fifty-three percent (26/47) of the cases had one or more of the adverse outcomes as compared with 22% (8/37) of controls (P < 0.01). Of these, 13 (50.0%) and 3 (37.5%) were males, respectively. Ischemia on MPI is predictive of long-term adverse cardiovascular outcomes despite normal ('false-negative') coronary angiography. This appears to be gender-neutral.

Multilevel Parallelization of AutoDock 4.2.

PubMed

Norgan, Andrew P; Coffman, Paul K; Kocher, Jean-Pierre A; Katzmann, David J; Sosa, Carlos P

2011-04-28

Virtual (computational) screening is an increasingly important tool for drug discovery. AutoDock is a popular open-source application for performing molecular docking, the prediction of ligand-receptor interactions. AutoDock is a serial application, though several previous efforts have parallelized various aspects of the program. In this paper, we report on a multi-level parallelization of AutoDock 4.2 (mpAD4). Using MPI and OpenMP, AutoDock 4.2 was parallelized for use on MPI-enabled systems and to multithread the execution of individual docking jobs. In addition, code was implemented to reduce input/output (I/O) traffic by reusing grid maps at each node from docking to docking. Performance of mpAD4 was examined on two multiprocessor computers. Using MPI with OpenMP multithreading, mpAD4 scales with near linearity on the multiprocessor systems tested. In situations where I/O is limiting, reuse of grid maps reduces both system I/O and overall screening time. Multithreading of AutoDock's Lamarkian Genetic Algorithm with OpenMP increases the speed of execution of individual docking jobs, and when combined with MPI parallelization can significantly reduce the execution time of virtual screens. This work is significant in that mpAD4 speeds the execution of certain molecular docking workloads and allows the user to optimize the degree of system-level (MPI) and node-level (OpenMP) parallelization to best fit both workloads and computational resources.

Hybrid cloud and cluster computing paradigms for life science applications

PubMed Central

2010-01-01

Background Clouds and MapReduce have shown themselves to be a broadly useful approach to scientific computing especially for parallel data intensive applications. However they have limited applicability to some areas such as data mining because MapReduce has poor performance on problems with an iterative structure present in the linear algebra that underlies much data analysis. Such problems can be run efficiently on clusters using MPI leading to a hybrid cloud and cluster environment. This motivates the design and implementation of an open source Iterative MapReduce system Twister. Results Comparisons of Amazon, Azure, and traditional Linux and Windows environments on common applications have shown encouraging performance and usability comparisons in several important non iterative cases. These are linked to MPI applications for final stages of the data analysis. Further we have released the open source Twister Iterative MapReduce and benchmarked it against basic MapReduce (Hadoop) and MPI in information retrieval and life sciences applications. Conclusions The hybrid cloud (MapReduce) and cluster (MPI) approach offers an attractive production environment while Twister promises a uniform programming environment for many Life Sciences applications. Methods We used commercial clouds Amazon and Azure and the NSF resource FutureGrid to perform detailed comparisons and evaluations of different approaches to data intensive computing. Several applications were developed in MPI, MapReduce and Twister in these different environments. PMID:21210982

Hybrid cloud and cluster computing paradigms for life science applications.

PubMed

Qiu, Judy; Ekanayake, Jaliya; Gunarathne, Thilina; Choi, Jong Youl; Bae, Seung-Hee; Li, Hui; Zhang, Bingjing; Wu, Tak-Lon; Ruan, Yang; Ekanayake, Saliya; Hughes, Adam; Fox, Geoffrey

2010-12-21

Clouds and MapReduce have shown themselves to be a broadly useful approach to scientific computing especially for parallel data intensive applications. However they have limited applicability to some areas such as data mining because MapReduce has poor performance on problems with an iterative structure present in the linear algebra that underlies much data analysis. Such problems can be run efficiently on clusters using MPI leading to a hybrid cloud and cluster environment. This motivates the design and implementation of an open source Iterative MapReduce system Twister. Comparisons of Amazon, Azure, and traditional Linux and Windows environments on common applications have shown encouraging performance and usability comparisons in several important non iterative cases. These are linked to MPI applications for final stages of the data analysis. Further we have released the open source Twister Iterative MapReduce and benchmarked it against basic MapReduce (Hadoop) and MPI in information retrieval and life sciences applications. The hybrid cloud (MapReduce) and cluster (MPI) approach offers an attractive production environment while Twister promises a uniform programming environment for many Life Sciences applications. We used commercial clouds Amazon and Azure and the NSF resource FutureGrid to perform detailed comparisons and evaluations of different approaches to data intensive computing. Several applications were developed in MPI, MapReduce and Twister in these different environments.

Advances in PET myocardial perfusion imaging: F-18 labeled tracers.

PubMed

Rischpler, Christoph; Park, Min-Jae; Fung, George S K; Javadi, Mehrbod; Tsui, Benjamin M W; Higuchi, Takahiro

2012-01-01

Coronary artery disease and its related cardiac disorders represent the most common cause of death in the USA and Western world. Despite advancements in treatment and accompanying improvements in outcome with current diagnostic and therapeutic modalities, it is the correct assignment of these diagnostic techniques and treatment options which are crucial. From a diagnostic standpoint, SPECT myocardial perfusion imaging (MPI) using traditional radiotracers like thallium-201 chloride, Tc-99m sestamibi or Tc-99m tetrofosmin is the most utilized imaging technique. However, PET MPI using N-13 ammonia, rubidium-82 chloride or O-15 water is increasing in availability and usage as a result of the growing number of medical centers with new-generation PET/CT systems taking advantage of the superior imaging properties of PET over SPECT. The routine clinical use of PET MPI is still limited, in part because of the short half-life of conventional PET MPI tracers. The disadvantages of these conventional PET tracers include expensive onsite production and inconvenient on-scanner tracer administration making them unsuitable for physical exercise stress imaging. Recently, two F-18 labeled radiotracers with longer radioactive half-lives than conventional PET imaging agents have been introduced. These are flurpiridaz F 18 (formerly known as F-18 BMS747158-02) and F-18 fluorobenzyltriphenylphosphonium. These longer half-life F-18 labeled perfusion tracers can overcome the production and protocol limitations of currently used radiotracers for PET MPI.

Cloning, expression, purification, crystallization and preliminary X-ray crystallographic analysis of the mannose 6-phosphate isomerase from Salmonella typhimurium

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gowda, Giri; Sagurthi, Someswar Rao; Savithri, H. S.

2008-02-01

The cloning, expression, purification, crystallization and preliminary X-ray crystallographic studies of mannose 6-phosphate isomerase from S. typhimurium are reported. Mannose 6-phosphate isomerase (MPI; EC 5.3.1.8) catalyzes the reversible isomerization of d-mannose 6-phosphate (M6P) and d-fructose 6-phosphate (F6P). In the eukaryotes and prokaryotes investigated to date, the enzyme has been reported to play a crucial role in d-mannose metabolism and supply of the activated mannose donor guanosine diphosphate d-mannose (GDP-d-mannose). In the present study, MPI was cloned from Salmonella typhimurium, overexpressed in Escherichia coli and purified using Ni–NTA affinity column chromatography. Purified MPI crystallized in space group P2{sub 1}2{sub 1}2{sub 1},more » with unit-cell parameters a = 36.03, b = 92.2, c = 111.01 Å. A data set extending to 1.66 Å resolution was collected with 98.8% completeness using an image-plate detector system mounted on a rotating-anode X-ray generator. The asymmetric unit of the crystal cell was compatible with the presence of a monomer of MPI. A preliminary structure solution of the enzyme has been obtained by molecular replacement using Candida albicans MPI as the phasing model and the program Phaser. Further refinement and model building are in progress.« less

Feasibility of SPECT myocardial perfusion imaging in the super-obese using a multi-head semiconductor camera with attenuation correction.

PubMed

DeCicco, Anthony E; Sokil, Alexis B; Marhefka, Gregary D; Reist, Kirk; Hansen, Christopher L

2015-04-01

Obesity is not only associated with an increased risk of coronary artery disease, but also decreases the accuracy of many diagnostic modalities pertinent to this disease. Advances in myocardial perfusion imaging (MPI) have mitigated somewhat the effects of obesity, although the feasibility of MPI in the super-obese (defined as a BMI > 50) is currently untested. We undertook this study to assess the practicality of MPI in the super-obese using a multi-headed solid-state gamma camera with attenuation correction. We retrospectively identified consecutive super-obese patients referred for MPI at our institution. The images were interpreted by 3 blinded, experienced readers and graded for quality and diagnosis, and subjectively evaluated the contribution of attenuation correction. Clinical follow-up was obtained from review of medical records. 72 consecutive super-obese patients were included. Their BMI ranged from 50 to 67 (55.7 ± 5.1). Stress image quality was considered good or excellent in 45 (63%), satisfactory in 24 (33%), poor in 3 (4%), and uninterpretable in 0 patients. Rest images were considered good or excellent in 34 (49%), satisfactory in 23 (33%), poor in 13 (19%), and uninterpretable in 0 patients. Attenuation correction changed the interpretation in 34 (47%) of studies. MPI is feasible and provides acceptable image quality for super-obese patients, although it may be camera and protocol dependent.

Dietary mung bean protein reduces high-fat diet-induced weight gain by modulating host bile acid metabolism in a gut microbiota-dependent manner.

PubMed

Nakatani, Akiho; Li, Xuan; Miyamoto, Junki; Igarashi, Miki; Watanabe, Hitoshi; Sutou, Asuka; Watanabe, Keita; Motoyama, Takayasu; Tachibana, Nobuhiko; Kohno, Mitsutaka; Inoue, Hiroshi; Kimura, Ikuo

2018-07-02

The 8-globulin-rich mung bean protein (MPI) suppresses hepatic lipogenesis in rodent models and reduces fasting plasma glucose and insulin levels in obese adults. However, its effects on mitigating high fat diet (HFD)-induced obesity and the mechanism underlying these effects remain to be elucidated. Herein, we examined the metabolic phenotype, intestinal bile acid (BA) pool, and gut microbiota of conventionally raised (CONV-R) male C57BL/6 mice and germ-free (GF) mice that were randomized to receive either regular HFD or HFD containing mung bean protein isolate (MPI) instead of the dairy protein present in regular HFD. MPI intake significantly reduced HFD-induced weight gain and adipose tissue accumulation, and attenuated hepatic steatosis. Enhancement in the secretion of intestinal glucagon-like peptide-1 (GLP-1) and an enlarged cecal and fecal BA pool of dramatically elevated secondary/primary BA ratio were observed in mice that had consumed MPI. These effects were abolished in GF mice, indicating that the effects were dependent upon the presence of the microbiota. As revealed by 16S rRNA gene sequence analysis, MPI intake also elicited dramatic changes in the gut microbiome, such as an expansion of taxa belonging to the phylum Bacteroidetes along with a reduced abundance of the Firmicutes. Copyright © 2018 Elsevier Inc. All rights reserved.

Differential Changes in Myocardial Performance Index and Its Time Intervals in Donors and Recipients of Twin-to-Twin Transfusion Syndrome before and after Laser Therapy.

PubMed

Ortiz, Javier U; Torres, Ximena; Eixarch, Elisenda; Bennasar, Mar; Cruz-Lemini, Monica; Gómez, Olga; Lobmaier, Silvia M; Martínez, Josep M; Gratacós, Eduard; Crispi, Fatima

2018-01-19

To evaluate left myocardial performance index (MPI) and time intervals in fetuses with twin-to-twin transfusion syndrome (TTTS) before and after laser surgery. Fifty-one fetal pairs with TTTS and 47 uncomplicated monochorionic twin pairs were included. Left ventricular isovolumetric contraction time (ICT), ejection time (ET), and isovolumetric relaxation time (IRT) were measured using conventional Doppler. Recipients showed prolonged ICT (46 ± 12 vs. 31 ± 8 vs. 30 ± 5 ms; p < 0.001) and IRT (51 ± 9 vs. 43 ± 8 vs. 43 ± 5 ms; p < 0.001) and higher MPI (0.57 ± 0.12 vs. 0.47 ± 0.09 vs. 0.44 ± 0.05; p < 0.001) than donors and controls. Donors showed shorter ET than recipients and controls (157 ± 12 vs. 169 ± 10 vs. 168 ± 10 ms; p < 0.001) and higher MPI than controls (0.47 ± 0.09 vs. 0.44 ± 0.05; p = 0.006). Preoperative MPI changes were observed in all TTTS stages. Time intervals partially improved after surgery. Donor and recipient twins had higher MPI due to different changes in the time intervals, possibly reflecting the state of hypovolemia in the donor and hypervolemia and pressure overload in the recipient. © 2018 S. Karger AG, Basel.

Climate Projections over Mediterranean Basin under RCP8.5 and RCP4.5 emission scenarios

NASA Astrophysics Data System (ADS)

Ilhan, Asli; Ünal, Yurdanur S.

2017-04-01

Climate Projections over Mediterranean Basin under RCP8.5 and RCP4.5 emission scenarios A. ILHAN ve Y. S. UNAL Istanbul Technical University, Department of Meteorology In the study, 50 km resolution downscaled results of two different Earth System Models (ESM) HadGEM2-ES and MPI-ESM with regional climate model of RegCM are used to estimate present and future climate conditions over Mediterranean Basin. The purpose of this study is to compare the projections of two ESMs under Representative Concentration Pathways 4.5 (RCP4.5) and 8.5 (RCP8.5) over the region of interest seasonally and annually with 50 km resolution. Temperature and precipitation parameters for reference period (1971-2000) and future (2015-2100) are analyzed. The average temperature and total precipitation distributions of each downscaled ESM simulations were compared with observation data (Climate Research Unit-CRU data) to explore the capability of each model for the representation of the current climate. According to reference period values of CRU, HadGEM2-ES and MPI-ESM, it is seen that both models are warmer and wetter than observations and have positive temperature biases only around Caspian Sea and positive precipitation biases over Eastern and Central Europe. The future projections (from 2015 to 2100) of HadGEM2-ES and MPI-ESM-MR simulations under RCP4.5 and RCP8.5 emission scenarios are compared with reference period (from 1971 to 2000) and analyzed for temperature and precipitation parameters. The downscaled HadGEM2-ES forced by RCP8.5 scenario produces higher temperatures than the MPI-ESM-MR. The reasons of this warming can be sensitivity of HadGEM2-ES to greenhouse gases and high radiative forcing (+8.5 W/m2). On the other hand, MPI-ESM produce more precipitation than HadGEM2-ES. In order to analyze regional responses of the climate model chains, five main regions are selected which are Turkey, Central Europe, Western Europe, Eastern Europe and North Africa. The average biases of the HadGEM2-ES+RegCM and MPI-ESM-MR+RegCM model chains are also calculated for temperature and precipitation variables, and future expectations in each region are discussed under RCP4.5 and RCP8.5 scenarios. According to the regional analysis, North Africa is the warmest region for HadGEM2-ES and MPI-ESM-MR, and Central Europe warms up similar to North Africa in MPI-ESM-MR coupled simulations under both RCPs. In addition, Eastern Europe is expected to be the wettest region in both models and in both emission scenarios. On the other hand, the driest conditions are expected over Western Europe for MPI-ESM-MR and over Turkey for HadGEM2-ES under RCPs.

78 FR 9793 - Airworthiness Directives; Bell Helicopter Textron Helicopters

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-12

...-numbered main rotor hub inboard strap fittings (fittings). This AD requires magnetic particle inspecting..., data, or views. We also invite comments relating to the economic, environmental, energy, or federalism..., perform a magnetic particle inspection (MPI) of each fitting for a crack. If an MPI was already performed...

Students' Performance on a Symmetry Task

ERIC Educational Resources Information Center

Ho, Siew Yin; Logan, Tracy

2013-01-01

This paper describes Singapore and Australian Grade 6 students' (n=1,187) performance on a symmetry task in a recently developed Mathematics Processing Instrument (MPI). The MPI comprised tasks sourced from Australia and Singapore's national assessments, NAPLAN and PSLE. Only half of the cohort solved the item successfully. It is possible that…

WinHPC System Programming | High-Performance Computing | NREL

Science.gov Websites

Programming WinHPC System Programming Learn how to build and run an MPI (message passing interface (mpi.h) and library (msmpi.lib) are. To build from the command line, run... Start > Intel Software Development Tools > Intel C++ Compiler Professional... > C++ Build Environment for applications running

77 FR 41806 - RG Steel Sparrows Point LLC, Formerly Known as Severstal Sparrows Point LLC, a Subsidiary of RG...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-16

... Leased Workers From Echelon Service Company, Sun Associated Industries, INC., MPI Consultants LLC... International, including on-site leased workers from Echelon Service Company, Sun Associated Industries, Inc... Company, Sun Associated Industries, Inc., MPI Consultants LLC, Alliance Engineering, Inc., Washington...

Performance Evaluation of Remote Memory Access (RMA) Programming on Shared Memory Parallel Computers

NASA Technical Reports Server (NTRS)

Jin, Hao-Qiang; Jost, Gabriele; Biegel, Bryan A. (Technical Monitor)

2002-01-01

The purpose of this study is to evaluate the feasibility of remote memory access (RMA) programming on shared memory parallel computers. We discuss different RMA based implementations of selected CFD application benchmark kernels and compare them to corresponding message passing based codes. For the message-passing implementation we use MPI point-to-point and global communication routines. For the RMA based approach we consider two different libraries supporting this programming model. One is a shared memory parallelization library (SMPlib) developed at NASA Ames, the other is the MPI-2 extensions to the MPI Standard. We give timing comparisons for the different implementation strategies and discuss the performance.

Development of mpi_EPIC model for global agroecosystem modeling

DOE PAGES

Kang, Shujiang; Wang, Dali; Jeff A. Nichols; ...

2014-12-31

Models that address policy-maker concerns about multi-scale effects of food and bioenergy production systems are computationally demanding. We integrated the message passing interface algorithm into the process-based EPIC model to accelerate computation of ecosystem effects. Simulation performance was further enhanced by applying the Vampir framework. When this enhanced mpi_EPIC model was tested, total execution time for a global 30-year simulation of a switchgrass cropping system was shortened to less than 0.5 hours on a supercomputer. The results illustrate that mpi_EPIC using parallel design can balance simulation workloads and facilitate large-scale, high-resolution analysis of agricultural production systems, management alternatives and environmentalmore » effects.« less

Applying Bayesian Item Selection Approaches to Adaptive Tests Using Polytomous Items

ERIC Educational Resources Information Center

Penfield, Randall D.

2006-01-01

This study applied the maximum expected information (MEI) and the maximum posterior-weighted information (MPI) approaches of computer adaptive testing item selection to the case of a test using polytomous items following the partial credit model. The MEI and MPI approaches are described. A simulation study compared the efficiency of ability…

Optimising the Parallelisation of OpenFOAM Simulations

DTIC Science & Technology

2014-06-01

UNCLASSIFIED UNCLASSIFIED Optimising the Parallelisation of OpenFOAM Simulations Shannon Keough Maritime Division Defence...Science and Technology Organisation DSTO-TR-2987 ABSTRACT The OpenFOAM computational fluid dynamics toolbox allows parallel computation of...performance of a given high performance computing cluster with several OpenFOAM cases, running using a combination of MPI libraries and corresponding MPI

32 CFR 637.2 - Use of MPI and DAC Detectives/Investigators.

Code of Federal Regulations, 2011 CFR

2011-07-01

... employed in the following investigations: (a) Offenses for which the maximum punishment listed in the Table of Maximum Punishment, Manual for Courts-Martial, United States, 2002 is confinement for 1 year or... MPI. The same punishment criteria apply. (b) Property-related offenses when the value is less than $1...

32 CFR 637.2 - Use of MPI and DAC Detectives/Investigators.

Code of Federal Regulations, 2014 CFR

2014-07-01

... employed in the following investigations: (a) Offenses for which the maximum punishment listed in the Table of Maximum Punishment, Manual for Courts-Martial, United States, 2002 is confinement for 1 year or... MPI. The same punishment criteria apply. (b) Property-related offenses when the value is less than $1...

32 CFR 637.2 - Use of MPI and DAC Detectives/Investigators.

Code of Federal Regulations, 2013 CFR

2013-07-01

... employed in the following investigations: (a) Offenses for which the maximum punishment listed in the Table of Maximum Punishment, Manual for Courts-Martial, United States, 2002 is confinement for 1 year or... MPI. The same punishment criteria apply. (b) Property-related offenses when the value is less than $1...

32 CFR 637.2 - Use of MPI and DAC Detectives/Investigators.

Code of Federal Regulations, 2012 CFR

2012-07-01

... employed in the following investigations: (a) Offenses for which the maximum punishment listed in the Table of Maximum Punishment, Manual for Courts-Martial, United States, 2002 is confinement for 1 year or... MPI. The same punishment criteria apply. (b) Property-related offenses when the value is less than $1...

Cheetah: A Framework for Scalable Hierarchical Collective Operations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Graham, Richard L; Gorentla Venkata, Manjunath; Ladd, Joshua S

2011-01-01

Collective communication operations, used by many scientific applications, tend to limit overall parallel application performance and scalability. Computer systems are becoming more heterogeneous with increasing node and core-per-node counts. Also, a growing number of data-access mechanisms, of varying characteristics, are supported within a single computer system. We describe a new hierarchical collective communication framework that takes advantage of hardware-specific data-access mechanisms. It is flexible, with run-time hierarchy specification, and sharing of collective communication primitives between collective algorithms. Data buffers are shared between levels in the hierarchy reducing collective communication management overhead. We have implemented several versions of the Message Passingmore » Interface (MPI) collective operations, MPI Barrier() and MPI Bcast(), and run experiments using up to 49, 152 processes on a Cray XT5, and a small InfiniBand based cluster. At 49, 152 processes our barrier implementation outperforms the optimized native implementation by 75%. 32 Byte and one Mega-Byte broadcasts outperform it by 62% and 11%, respectively, with better scalability characteristics. Improvements relative to the default Open MPI implementation are much larger.« less

Characterization of the cellular and antitumor effects of MPI-0479605, a small-molecule inhibitor of the mitotic kinase Mps1.

PubMed

Tardif, Keith D; Rogers, Aaron; Cassiano, Jared; Roth, Bruce L; Cimbora, Daniel M; McKinnon, Rena; Peterson, Ashley; Douce, Thomas B; Robinson, Rosann; Dorweiler, Irene; Davis, Thaylon; Hess, Mark A; Ostanin, Kirill; Papac, Damon I; Baichwal, Vijay; McAlexander, Ian; Willardsen, J Adam; Saunders, Michael; Christophe, Hoarau; Kumar, D Vijay; Wettstein, Daniel A; Carlson, Robert O; Williams, Brandi L

2011-12-01

Mps1 is a dual specificity protein kinase that is essential for the bipolar attachment of chromosomes to the mitotic spindle and for maintaining the spindle assembly checkpoint until all chromosomes are properly attached. Mps1 is expressed at high levels during mitosis and is abundantly expressed in cancer cells. Disruption of Mps1 function induces aneuploidy and cell death. We report the identification of MPI-0479605, a potent and selective ATP competitive inhibitor of Mps1. Cells treated with MPI-0479605 undergo aberrant mitosis, resulting in aneuploidy and formation of micronuclei. In cells with wild-type p53, this promotes the induction of a postmitotic checkpoint characterized by the ATM- and RAD3-related-dependent activation of the p53-p21 pathway. In both wild-type and p53 mutant cells lines, there is a growth arrest and inhibition of DNA synthesis. Subsequently, cells undergo mitotic catastrophe and/or an apoptotic response. In xenograft models, MPI-0479605 inhibits tumor growth, suggesting that drugs targeting Mps1 may have utility as novel cancer therapeutics.

Finite magnetic relaxation in x-space magnetic particle imaging: Comparison of measurements and ferrohydrodynamic models

PubMed Central

Dhavalikar, R; Hensley, D; Maldonado-Camargo, L; Croft, L R; Ceron, S; Goodwill, P W; Conolly, S M

2016-01-01

Magnetic Particle Imaging (MPI) is an emerging tomographic imaging technology that detects magnetic nanoparticle tracers by exploiting their non-linear magnetization properties. In order to predict the behavior of nanoparticles in an imager, it is possible to use a non-imaging MPI relaxometer or spectrometer to characterize the behavior of nanoparticles in a controlled setting. In this paper we explore the use of ferrohydrodynamic magnetization equations for predicting the response of particles in an MPI relaxometer. These include a magnetization equation developed by Shliomis (Sh) which has a constant relaxation time and a magnetization equation which uses a field-dependent relaxation time developed by Martsenyuk, Raikher and Shliomis (MRSh). We compare the predictions from these models with measurements and with the predictions based on the Langevin function that assumes instantaneous magnetization response of the nanoparticles. The results show good qualitative and quantitative agreement between the ferrohydrodynamic models and the measurements without the use of fitting parameters and provide further evidence of the potential of ferrohydrodynamic modeling in MPI. PMID:27867219

Optimizing NEURON Simulation Environment Using Remote Memory Access with Recursive Doubling on Distributed Memory Systems.

PubMed

Shehzad, Danish; Bozkuş, Zeki

2016-01-01

Increase in complexity of neuronal network models escalated the efforts to make NEURON simulation environment efficient. The computational neuroscientists divided the equations into subnets amongst multiple processors for achieving better hardware performance. On parallel machines for neuronal networks, interprocessor spikes exchange consumes large section of overall simulation time. In NEURON for communication between processors Message Passing Interface (MPI) is used. MPI_Allgather collective is exercised for spikes exchange after each interval across distributed memory systems. The increase in number of processors though results in achieving concurrency and better performance but it inversely affects MPI_Allgather which increases communication time between processors. This necessitates improving communication methodology to decrease the spikes exchange time over distributed memory systems. This work has improved MPI_Allgather method using Remote Memory Access (RMA) by moving two-sided communication to one-sided communication, and use of recursive doubling mechanism facilitates achieving efficient communication between the processors in precise steps. This approach enhanced communication concurrency and has improved overall runtime making NEURON more efficient for simulation of large neuronal network models.

Optimizing NEURON Simulation Environment Using Remote Memory Access with Recursive Doubling on Distributed Memory Systems

PubMed Central

Bozkuş, Zeki

2016-01-01

Increase in complexity of neuronal network models escalated the efforts to make NEURON simulation environment efficient. The computational neuroscientists divided the equations into subnets amongst multiple processors for achieving better hardware performance. On parallel machines for neuronal networks, interprocessor spikes exchange consumes large section of overall simulation time. In NEURON for communication between processors Message Passing Interface (MPI) is used. MPI_Allgather collective is exercised for spikes exchange after each interval across distributed memory systems. The increase in number of processors though results in achieving concurrency and better performance but it inversely affects MPI_Allgather which increases communication time between processors. This necessitates improving communication methodology to decrease the spikes exchange time over distributed memory systems. This work has improved MPI_Allgather method using Remote Memory Access (RMA) by moving two-sided communication to one-sided communication, and use of recursive doubling mechanism facilitates achieving efficient communication between the processors in precise steps. This approach enhanced communication concurrency and has improved overall runtime making NEURON more efficient for simulation of large neuronal network models. PMID:27413363

Multipath interference test method for distributed amplifiers

NASA Astrophysics Data System (ADS)

Okada, Takahiro; Aida, Kazuo

2005-12-01

A method for testing distributed amplifiers is presented; the multipath interference (MPI) is detected as a beat spectrum between the multipath signal and the direct signal using a binary frequency shifted keying (FSK) test signal. The lightwave source is composed of a DFB-LD that is directly modulated by a pulse stream passing through an equalizer, and emits the FSK signal of the frequency deviation of about 430MHz at repetition rate of 80-100 kHz. The receiver consists of a photo-diode and an electrical spectrum analyzer (ESA). The base-band power spectrum peak appeared at the frequency of the FSK frequency deviation can be converted to amount of MPI using a calibration chart. The test method has improved the minimum detectable MPI as low as -70 dB, compared to that of -50 dB of the conventional test method. The detailed design and performance of the proposed method are discussed, including the MPI simulator for calibration procedure, computer simulations for evaluating the error caused by the FSK repetition rate and the fiber length under test and experiments on singlemode fibers and distributed Raman amplifier.

Glauber gluons and multiple parton interactions

NASA Astrophysics Data System (ADS)

Gaunt, Jonathan R.

2014-07-01

We show that for hadronic transverse energy E T in hadron-hadron collisions, the classic Collins-Soper-Sterman (CSS) argument for the cancellation of Glauber gluons breaks down at the level of two Glauber gluons exchanged between the spectators. Through an argument that relates the diagrams with these Glauber gluons to events containing additional soft scatterings, we suggest that this failure of the CSS cancellation actually corresponds to a failure of the `standard' factorisation formula with hard, soft and collinear functions to describe E T at leading power. This is because the observable receives a leading power contribution from multiple parton interaction (or spectator-spectator Glauber) processes. We also suggest that the same argument can be used to show that a whole class of observables, which we refer to as MPI sensitive observables, do not obey the standard factorisation at leading power. MPI sensitive observables are observables whose distributions in hadron-hadron collisions are disrupted strongly by the presence of multiple parton interactions (MPI) in the event. Examples of further MPI sensitive observables include the beam thrust B {/a, b +} and transverse thrust.

Reproducibility of a silicone-based test food to masticatory performance evaluation by different sieve methods.

PubMed

Sánchez-Ayala, Alfonso; Vilanova, Larissa Soares Reis; Costa, Marina Abrantes; Farias-Neto, Arcelino

2014-01-01

The aim of this study was to evaluate the reproducibility of the condensation silicone Optosil Comfort® as an artificial test food for masticatory performance evaluation. Twenty dentate subjects with mean age of 23.3±0.7 years were selected. Masticatory performance was evaluated using the simple (MPI), the double (IME) and the multiple sieve methods. Trials were carried out five times by three examiners: three times by the first, and once by the second and third examiners. Friedman's test was used to find the differences among time trials. Reproducibility was determined by the intra-class correlation (ICC) test (α=0.05). No differences among time trials were found, except for MPI-4 mm (p=0.022) from the first examiner results. The intra-examiner reproducibility (ICC) of almost all data was high (ICC≥0.92, p<0.001), being moderate only for MPI-0.50 mm (ICC=0.89, p<0.001). The inter-examiner reproducibility was high (ICC>0.93, p<0.001) for all results. For the multiple sieve method, the average mean of absolute difference from repeated measurements were lower than 1 mm. This trend was observed only from MPI-0.50 to MPI-1.4 for the single sieve method, and from IME-0.71/0.50 to IME-1.40/1.00 for the double sieve method. The results suggest that regardless of the method used, the reproducibility of Optosil Comfort® is high.

LV dyssynchrony as assessed by phase analysis of gated SPECT myocardial perfusion imaging in patients with Wolff-Parkinson-White syndrome.

PubMed

Chen, Chun; Li, Dianfu; Miao, Changqing; Feng, Jianlin; Zhou, Yanli; Cao, Kejiang; Lloyd, Michael S; Chen, Ji

2012-07-01

The purpose of this study was to evaluate left ventricular (LV) mechanical dyssynchrony in patients with Wolff-Parkinson-White (WPW) syndrome pre- and post-radiofrequency catheter ablation (RFA) using phase analysis of gated single photon emission computed tomography (SPECT) myocardial perfusion imaging (MPI). Forty-five WPW patients were enrolled and had gated SPECT MPI pre- and 2-3 days post-RFA. Electrophysiological study (EPS) was used to locate accessory pathways (APs) and categorize the patients according to the AP locations (septal, left and right free wall). Electrocardiography (ECG) was performed pre- and post-RFA to confirm successful elimination of the APs. Phase analysis of gated SPECT MPI was used to assess LV dyssynchrony pre- and post-RFA. Among the 45 patients, 3 had gating errors, and thus 42 had SPECT phase analysis. Twenty-two patients (52.4%) had baseline LV dyssynchrony. Baseline LV dyssynchrony was more prominent in the patients with septal APs than in the patients with left or right APs (p < 0.05). RFA improved LV synchrony in the entire cohort and in the patients with septal APs (p < 0.01). Phase analysis of gated SPECT MPI demonstrated that LV mechanical dyssynchrony can be present in patients with WPW syndrome. Septal APs result in the greatest degree of LV mechanical dyssynchrony and afford the most benefit after RFA. This study supports further investigation in the relationship between electrical and mechanical activation using EPS and phase analysis of gated SPECT MPI.

Usefulness of myocardial parametric imaging to evaluate myocardial viability in experimental and in clinical studies

PubMed Central

Korosoglou, G; Hansen, A; Bekeredjian, R; Filusch, A; Hardt, S; Wolf, D; Schellberg, D; Katus, H A; Kuecherer, H

2006-01-01

Objective To evaluate whether myocardial parametric imaging (MPI) is superior to visual assessment for the evaluation of myocardial viability. Methods and results Myocardial contrast echocardiography (MCE) was assessed in 11 pigs before, during, and after left anterior descending coronary artery occlusion and in 32 patients with ischaemic heart disease by using intravenous SonoVue administration. In experimental studies perfusion defect area assessment by MPI was compared with visually guided perfusion defect planimetry. Histological assessment of necrotic tissue was the standard reference. In clinical studies viability was assessed on a segmental level by (1) visual analysis of myocardial opacification; (2) quantitative estimation of myocardial blood flow in regions of interest; and (3) MPI. Functional recovery between three and six months after revascularisation was the standard reference. In experimental studies, compared with visually guided perfusion defect planimetry, planimetric assessment of infarct size by MPI correlated more significantly with histology (r2  =  0.92 versus r2  =  0.56) and had a lower intraobserver variability (4% v 15%, p < 0.05). In clinical studies, MPI had higher specificity (66% v 43%, p < 0.05) than visual MCE and good accuracy (81%) for viability detection. It was less time consuming (3.4 (1.6) v 9.2 (2.4) minutes per image, p < 0.05) than quantitative blood flow estimation by regions of interest and increased the agreement between observers interpreting myocardial perfusion (κ  =  0.87 v κ  =  0.75, p < 0.05). Conclusion MPI is useful for the evaluation of myocardial viability both in animals and in patients. It is less time consuming than quantification analysis by regions of interest and less observer dependent than visual analysis. Thus, strategies incorporating this technique may be valuable for the evaluation of myocardial viability in clinical routine. PMID:15939722

Improving results of surgery for fecal peritonitis due to perforated colorectal disease: A single center experience.

PubMed

Mineccia, Michela; Zimmitti, Giuseppe; Ribero, Dario; Giraldi, Francesco; Bertolino, Franco; Brambilla, Romeo; Ferrero, Alessandro

2016-01-01

fecal peritonitis due to colorectal perforation is a dramatic event characterized by high mortality. Our study aims at determining how results of sigmoid resection (eventually extended to upper rectum) for colorectal perforation with fecal peritonitis changed in recent years and which factors affected eventual changes. Seventy-four patients were operated on at our institution (2005-2014) for colorectal perforation with fecal peritonitis and were divided into two numerically equal groups (operated on before (ERA1-group) and after (ERA2-group) May 2010). Mannheim Peritonitis Index (MPI) was calculated for each patient. Characteristics of two groups were compared. Predictors of postoperative outcomes were identified. Postoperative overall complications, major complications, and mortality occurred in 59%, 28%, and 18% of cases, respectively, and were less frequent in ERA2-group (51%, 16%, and 8%, respectively), compared to ERA1-group (68%, 41%, and 27%, respectively; p = .155, .02, and .032, respectively). Such results paralleled lower MPI values in ERA2-group, compared to ERA1-group (23(16-39) vs. 28(21-43), p = .006). Using receiver operating characteristic analysis, the best cut-off value for MPI for predicting postoperative complications and mortality was 28.5. MPI>28 was the only independent predictor of postoperative overall (p = .009, OR = 4.491) and major complications (p < .001, OR = 23.182) and was independently associated with a higher risk of mortality (p = .016, OR = 13.444), as well as duration of preoperative peritonitis longer than 24 h (p = .045, OR = 17.099). results of surgery for colorectal perforation with fecal peritonitis have improved over time, matching a concurrent decrease of MPI values and a better preoperative patient management. MPI value may help in selecting patients benefitting from surgical treatment. Copyright © 2015 IJS Publishing Group Limited. Published by Elsevier Ltd. All rights reserved.

Simultaneous dual-radionuclide myocardial perfusion imaging with a solid-state dedicated cardiac camera.

PubMed

Ben-Haim, Simona; Kacperski, Krzysztof; Hain, Sharon; Van Gramberg, Dean; Hutton, Brian F; Erlandsson, Kjell; Sharir, Tali; Roth, Nathaniel; Waddington, Wendy A; Berman, Daniel S; Ell, Peter J

2010-08-01

We compared simultaneous dual-radionuclide (DR) stress and rest myocardial perfusion imaging (MPI) with a novel solid-state cardiac camera and a conventional SPECT camera with separate stress and rest acquisitions. Of 27 consecutive patients recruited, 24 (64.5+/-11.8 years of age, 16 men) were injected with 74 MBq of (201)Tl (rest) and 250 MBq (99m)Tc-MIBI (stress). Conventional MPI acquisition times for stress and rest are 21 min and 16 min, respectively. Rest (201)Tl for 6 min and simultaneous DR 15-min list mode gated scans were performed on a D-SPECT cardiac scanner. In 11 patients DR D-SPECT was performed first and in 13 patients conventional stress (99m)Tc-MIBI SPECT imaging was performed followed by DR D-SPECT. The DR D-SPECT data were processed using a spill-over and scatter correction method. DR D-SPECT images were compared with rest (201)Tl D-SPECT and with conventional SPECT images by visual analysis employing the 17-segment model and a five-point scale (0 normal, 4 absent) to calculate the summed stress and rest scores. Image quality was assessed on a four-point scale (1 poor, 4 very good) and gut activity was assessed on a four-point scale (0 none, 3 high). Conventional MPI studies were abnormal at stress in 17 patients and at rest in 9 patients. In the 17 abnormal stress studies DR D-SPECT MPI showed 113 abnormal segments and conventional MPI showed 93 abnormal segments. In the nine abnormal rest studies DR D-SPECT showed 45 abnormal segments and conventional MPI showed 48 abnormal segments. The summed stress and rest scores on conventional SPECT and DR D-SPECT were highly correlated (r=0.9790 and 0.9694, respectively). The summed scores of rest (201)Tl D-SPECT and DR-DSPECT were also highly correlated (r=0.9968, p<0.0001 for all). In six patients stress perfusion defects were significantly larger on stress DR D-SPECT images, and five of these patients were imaged earlier by D-SPECT than by conventional SPECT. Fast and high-quality simultaneous DR MPI is feasible with D-SPECT in a single imaging session with comparable diagnostic performance and image quality to conventional SPECT and to a separate rest (201)Tl D-SPECT acquisition.

Randomized, single-blind, factorial design study of the interaction of food and time on intestinal activity in 99mTc-tetrofosmin stress myocardial perfusion scintigraphy.

PubMed

Lyngholm, Ann Marie; Pedersen, Begitte H; Petersen, Lars J

2008-09-01

Intestinal activity at the inferior myocardial wall represents an issue for assessment of myocardial perfusion imaging (MPI) with 99mTc-labelled tracers. The aim of this study was to investigate the effect of time and food on upper abdominal activity in 99mTc-tetrofosmin MPI. The study population consisted of 152 consecutive patients referred for routine MPI. All patients underwent 2-day stress-rest 99mTc-tetrofosmin single-photon emission computed tomography MPI. Before stress testing, patients were randomized in a factorial design to four different regimens. Group A: early scan (image acquisition initiated within 15 min after injection of the tracer) and no food; group B: early scan and food (two pieces of white bread with butter and a minimum of 450 ml of water); group C: late scan (image acquisition 30-60 min after injection of the tracer) and no food; and group D: late and scan with food. Patients underwent standard bicycle exercise or pharmacological stress test. The degree of upper abdominal activity was evaluated by trained observers blinded to the randomization code. The primary endpoint was the proportion of accepted scans in the intention-to-treat population in stress MPI. The results showed statistical significant impact on both time and food on upper abdominal activity. The primary endpoint showed that the acceptance rate improved from 55% in group A to 100% success rate in group D. An early scan reduced the acceptance rate by 30% versus a late scan [hazard ratio 0.70, 95% confidence interval 0.58-0.84; P<0.0001], whereas the addition of food improved the success rate versus no food by 27% (hazard ratio 1.27, 95% confidence interval 1.07-1.51; P=0.006). No significant interaction between food and time was observed. An analysis of accepted scans according to the actual scan time and food consumption confirmed the findings of the intention-to-treat analysis. In addition, similar findings were seen in 116 of 152 patients with a rest MPI (success rate of 53% in group A vs. 96% in group D). A combination of solid food and water administered after injection of the tracer and delayed image acquisition led to significant and clinically relevant decrease of interfering upper abdominal activity in 99mTc-tetrofosmin MPI.

The influence of hunger on meal to pellet intervals in barred owls

USGS Publications Warehouse

Duke, G.E.; Fuller, M.R.; Huberty, B.J.

1980-01-01

1. Barred owls fed at a sub-maintenance (SM) level had significantly (P < 0.01) longer meal to pellet intervals (MPI)/g eaten/kg body weight (BW) than those fed at an above maintenance (AM) level; MPI/g per kg for owls fed at a maintenance (M) level was intermediate but significantly (P < 0.01) different from both SM and AM.2. During SM feeding, MPI/g per kg gradually increased.3. The proportion of a meal occurring in a pellet was less in “hungry” owls whether losing weight (SM) or gaining (AM) as compared to owls maintaining their normal body weight (M).4. SM fed owls appear to be able to increase digestion time as well as thoroughness of digestion.

Contaminant studies in the Sierra Nevadas

USGS Publications Warehouse

Sparling, Don; Fellers, Gary M.

2002-01-01

1. 1. Barred owls fed at a sub-maintenance (SM) level had significantly (P < 0.01) longer meal to pellet intervals (MPI)/g eaten/kg body weight (BW) than those fed at an above maintenance (AM) level; MPI/g per kg for owls fed at a maintenance (M) level was intermediate but significantly (P < 0.01) different from both SM and AM. 2. 2. During SM feeding, MPI/g per kg gradually increased. 3. 3. The proportion of a meal occurring in a pellet was less in ?hungry? owls whether losing weight (SM) or gaining (AM) as compared to owls maintaining their normal body weight (M). 4. 4. SM fed owls appear to be able to increase digestion time as well as thoroughness of digestion.

Parallel PAB3D: Experiences with a Prototype in MPI

NASA Technical Reports Server (NTRS)

Guerinoni, Fabio; Abdol-Hamid, Khaled S.; Pao, S. Paul

1998-01-01

PAB3D is a three-dimensional Navier Stokes solver that has gained acceptance in the research and industrial communities. It takes as computational domain, a set disjoint blocks covering the physical domain. This is the first report on the implementation of PAB3D using the Message Passing Interface (MPI), a standard for parallel processing. We discuss briefly the characteristics of tile code and define a prototype for testing. The principal data structure used for communication is derived from preprocessing "patching". We describe a simple interface (COMMSYS) for MPI communication, and some general techniques likely to be encountered when working on problems of this nature. Last, we identify levels of improvement from the current version and outline future work.

A Posteriori Error Bounds for the Empirical Interpolation Method

DTIC Science & Technology

2010-03-18

paramètres (x̄1, x̄2) ≡ µ ∈ DII ≡ [0.4, 0.6]2 et α = 0.1 fixé, les résultats sont similaires au cas d’un seul paramètre (Fig. 2). 1. Introduction...and denote the set of all distinct multi-indices β of dimension P of length I by MPI . The cardinality of MPI is given by card (MPI ) = ( P+I−1 I...operations, and we compute the interpolation errors ‖F (β)(·; τ) − F (β)M (·; τ)‖L∞(Ω), 0 < |β| < p − 1, for all τ ∈ Φ, in O(nΦMN ) ∑p−1 j=0 card (MPj

An MPI-based MoSST core dynamics model

NASA Astrophysics Data System (ADS)

Jiang, Weiyuan; Kuang, Weijia

2008-09-01

Distributed systems are among the main cost-effective and expandable platforms for high-end scientific computing. Therefore scalable numerical models are important for effective use of such systems. In this paper, we present an MPI-based numerical core dynamics model for simulation of geodynamo and planetary dynamos, and for simulation of core-mantle interactions. The model is developed based on MPI libraries. Two algorithms are used for node-node communication: a "master-slave" architecture and a "divide-and-conquer" architecture. The former is easy to implement but not scalable in communication. The latter is scalable in both computation and communication. The model scalability is tested on Linux PC clusters with up to 128 nodes. This model is also benchmarked with a published numerical dynamo model solution.

Experimental and simulation studies on the behavior of signal harmonics in magnetic particle imaging.

PubMed

Murase, Kenya; Konishi, Takashi; Takeuchi, Yuki; Takata, Hiroshige; Saito, Shigeyoshi

2013-07-01

Our purpose in this study was to investigate the behavior of signal harmonics in magnetic particle imaging (MPI) by experimental and simulation studies. In the experimental studies, we made an apparatus for MPI in which both a drive magnetic field (DMF) and a selection magnetic field (SMF) were generated with a Maxwell coil pair. The MPI signals from magnetic nanoparticles (MNPs) were detected with a solenoid coil. The odd- and even-numbered harmonics were calculated by Fourier transformation with or without background subtraction. The particle size of the MNPs was measured by transmission electron microscopy (TEM), dynamic light-scattering, and X-ray diffraction methods. In the simulation studies, the magnetization and particle size distribution of MNPs were assumed to obey the Langevin theory of paramagnetism and a log-normal distribution, respectively. The odd- and even-numbered harmonics were calculated by Fourier transformation under various conditions of DMF and SMF and for three different particle sizes. The behavior of the harmonics largely depended on the size of the MNPs. When we used the particle size obtained from the TEM image, the simulation results were most similar to the experimental results. The similarity between the experimental and simulation results for the even-numbered harmonics was better than that for the odd-numbered harmonics. This was considered to be due to the fact that the odd-numbered harmonics were more sensitive to background subtraction than were the even-numbered harmonics. This study will be useful for a better understanding, optimization, and development of MPI and for designing MNPs appropriate for MPI.

Downstream resource utilization following hybrid cardiac imaging with an integrated cadmium-zinc-telluride/64-slice CT device.

PubMed

Fiechter, Michael; Ghadri, Jelena R; Wolfrum, Mathias; Kuest, Silke M; Pazhenkottil, Aju P; Nkoulou, Rene N; Herzog, Bernhard A; Gebhard, Cathérine; Fuchs, Tobias A; Gaemperli, Oliver; Kaufmann, Philipp A

2012-03-01

Low yield of invasive coronary angiography and unnecessary coronary interventions have been identified as key cost drivers in cardiology for evaluation of coronary artery disease (CAD). This has fuelled the search for noninvasive techniques providing comprehensive functional and anatomical information on coronary lesions. We have evaluated the impact of implementation of a novel hybrid cadmium-zinc-telluride (CZT)/64-slice CT camera into the daily clinical routine on downstream resource utilization. Sixty-two patients with known or suspected CAD were referred for same-day single-session hybrid evaluation with CZT myocardial perfusion imaging (MPI) and coronary CT angiography (CCTA). Hybrid MPI/CCTA images from the integrated CZT/CT camera served for decision-making towards conservative versus invasive management. Based on the hybrid images patients were classified into those with and those without matched findings. Matched findings were defined as the combination of MPI defect with a stenosis by CCTA in the coronary artery subtending the respective territory. All patients with normal MPI and CCTA as well as those with isolated MPI or CCTA finding or combined but unmatched findings were categorized as "no match". All 23 patients with a matched finding underwent invasive coronary angiography and 21 (91%) were revascularized. Of the 39 patients with no match, 5 (13%, p < 0.001 vs matched) underwent catheterization and 3 (8%, p < 0.001 vs matched) were revascularized. Cardiac hybrid imaging in CAD evaluation has a profound impact on patient management and may contribute to optimal downstream resource utilization.

Vibrational and electronic investigations, NLO, FMO analysis on a hetarylazoindole disperse dye by density functional theory

NASA Astrophysics Data System (ADS)

Çatıkkaş, Berna; Aktan, Ebru; Yalçın, Ergin

2016-08-01

This work deals with the optimized molecular structure, vibrational spectra, nonlinear optic (NLO) and frontier molecule orbital (FMO) properties of 1-Methyl-2-phenyl-3-(1,3,4-thiadiazol-2-yldiazenyl)-1H-indole (MPI) by quantum chemical calculations. The Fourier transform infrared (FT-MIR and FT-FIR) and Raman spectra of 1-Methyl-2-phenyl-3-(1,3,4-thiadiazol-2-yldiazenyl)-1H-indole (MPI) were recorded in the region (4000-400 cm-1 and 400-30 cm-1) and (3200-92 cm-1), respectively. The analysis and complete vibrational assignments of the fundamental modes of the MPI molecule were carried out by using the observed FT-IR and FT-Raman data and calculated Total Energy Distribution (TED) according to Scaled Quantum Mechanics procedure. The calculated geometrical parameters of the MPI molecule are in agreement with the obtained values from XRD studies. On the other hand, the difference between the scaled and observed wavenumber values of the most of the fundamentals are very small. 1H NMR and 13C NMR chemical shift values, and energy gap between LUMO-HOMO and molecular electrostatic potential (MEP) were investigated by using density functional theory (B3LYP) methods. UV/Visible spectra and λ maximum absorption values, the oscillator strengths in the chloroform, methanol and DMSO solvation in combination with different basis sets were calculated by using the time-dependent density functional theory (TD-DFT). Additionally, the predicted nonlinear optical (NLO) properties of the MPI are quite greater than that of urea at the B3LYP/6-31++G(d,p) level.

Psychometric Properties of the Multidimensional Pain Inventory Applied to Brazilian Patients with Orofacial Pain.

PubMed

Zucoloto, Miriane Lucindo; Maroco, João; Duarte Bonini Campos, Juliana Alvares

2015-01-01

To evaluate the psychometric properties of the Multidimensional Pain Inventory (MPI) in a Brazilian sample of patients with orofacial pain. A total of 1,925 adult patients, who sought dental care in the School of Dentistry of São Paulo State University's Araraquara campus, were invited to participate; 62.5% (n=1,203) agreed to participate. Of these, 436 presented with orofacial pain and were included. The mean age was 39.9 (SD=13.6) years and 74.5% were female. Confirmatory factor analysis was conducted using χ²/df, comparative fit index, goodness of fit index, and root mean square error of approximation as indices of goodness of fit. Convergent validity was estimated by the average variance extracted and composite reliability, and internal consistency by Cronbach's alpha standardized coefficient (α). The stability of the models was tested in independent samples (test and validation; dental pain and orofacial pain). The factorial invariance was estimated by multigroup analysis (Δχ²). Factorial, convergent validity, and internal consistency were adequate in all three parts of the MPI. To achieve this adequate fit for Part 1, item 15 needed to be deleted (λ=0.13). Discriminant validity was compromised between the factors "activities outside the home" and "social activities" of Part 3 of the MPI in the total sample, validation sample, and in patients with dental pain and with orofacial pain. A strong invariance between different subsamples from the three parts of the MPI was detected. The MPI produced valid, reliable, and stable data for pain assessment among Brazilian patients with orofacial pain.

An automatic alignment tool to improve repeatability of left ventricular function and dyssynchrony parameters in serial gated myocardial perfusion SPECT studies

PubMed Central

Zhou, Yanli; Faber, Tracy L.; Patel, Zenic; Folks, Russell D.; Cheung, Alice A.; Garcia, Ernest V.; Soman, Prem; Li, Dianfu; Cao, Kejiang; Chen, Ji

2013-01-01

Objective Left ventricular (LV) function and dyssynchrony parameters measured from serial gated single-photon emission computed tomography (SPECT) myocardial perfusion imaging (MPI) using blinded processing had a poorer repeatability than when manual side-by-side processing was used. The objective of this study was to validate whether an automatic alignment tool can reduce the variability of LV function and dyssynchrony parameters in serial gated SPECT MPI. Methods Thirty patients who had undergone serial gated SPECT MPI were prospectively enrolled in this study. Thirty minutes after the first acquisition, each patient was repositioned and a gated SPECT MPI image was reacquired. The two data sets were first processed blinded from each other by the same technologist in different weeks. These processed data were then realigned by the automatic tool, and manual side-by-side processing was carried out. All processing methods used standard iterative reconstruction and Butterworth filtering. The Emory Cardiac Toolbox was used to measure the LV function and dyssynchrony parameters. Results The automatic tool failed in one patient, who had a large, severe scar in the inferobasal wall. In the remaining 29 patients, the repeatability of the LV function and dyssynchrony parameters after automatic alignment was significantly improved from blinded processing and was comparable to manual side-by-side processing. Conclusion The automatic alignment tool can be an alternative method to manual side-by-side processing to improve the repeatability of LV function and dyssynchrony measurements by serial gated SPECT MPI. PMID:23211996

The predictive value of chronic kidney disease for assessing cardiovascular events under consideration of pretest probability for coronary artery disease in patients who underwent stress myocardial perfusion imaging.

PubMed

Furuhashi, Tatsuhiko; Moroi, Masao; Joki, Nobuhiko; Hase, Hiroki; Masai, Hirofumi; Kunimasa, Taeko; Fukuda, Hiroshi; Sugi, Kaoru

2013-02-01

Pretest probability of coronary artery disease (CAD) facilitates diagnosis and risk stratification of CAD. Stress myocardial perfusion imaging (MPI) and chronic kidney disease (CKD) are established major predictors of cardiovascular events. However, the role of CKD to assess pretest probability of CAD has been unclear. This study evaluates the role of CKD to assess the predictive value of cardiovascular events under consideration of pretest probability in patients who underwent stress MPI. Patients with no history of CAD underwent stress MPI (n = 310; male = 166; age = 70; CKD = 111; low/intermediate/high pretest probability = 17/194/99) and were followed for 24 months. Cardiovascular events included cardiac death and nonfatal acute coronary syndrome. Cardiovascular events occurred in 15 of the 310 patients (4.8 %), but not in those with low pretest probability which included 2 CKD patients. In patients with intermediate to high pretest probability (n = 293), multivariate Cox regression analysis identified only CKD [hazard ratio (HR) = 4.88; P = 0.022) and summed stress score of stress MPI (HR = 1.50; P < 0.001) as independent and significant predictors of cardiovascular events. Cardiovascular events were not observed in patients with low pretest probability. In patients with intermediate to high pretest probability, CKD and stress MPI are independent predictors of cardiovascular events considering the pretest probability of CAD in patients with no history of CAD. In assessing pretest probability of CAD, CKD might be an important factor for assessing future cardiovascular prognosis.

Hybrid MPI-OpenMP Parallelism in the ONETEP Linear-Scaling Electronic Structure Code: Application to the Delamination of Cellulose Nanofibrils.

PubMed

Wilkinson, Karl A; Hine, Nicholas D M; Skylaris, Chris-Kriton

2014-11-11

We present a hybrid MPI-OpenMP implementation of Linear-Scaling Density Functional Theory within the ONETEP code. We illustrate its performance on a range of high performance computing (HPC) platforms comprising shared-memory nodes with fast interconnect. Our work has focused on applying OpenMP parallelism to the routines which dominate the computational load, attempting where possible to parallelize different loops from those already parallelized within MPI. This includes 3D FFT box operations, sparse matrix algebra operations, calculation of integrals, and Ewald summation. While the underlying numerical methods are unchanged, these developments represent significant changes to the algorithms used within ONETEP to distribute the workload across CPU cores. The new hybrid code exhibits much-improved strong scaling relative to the MPI-only code and permits calculations with a much higher ratio of cores to atoms. These developments result in a significantly shorter time to solution than was possible using MPI alone and facilitate the application of the ONETEP code to systems larger than previously feasible. We illustrate this with benchmark calculations from an amyloid fibril trimer containing 41,907 atoms. We use the code to study the mechanism of delamination of cellulose nanofibrils when undergoing sonification, a process which is controlled by a large number of interactions that collectively determine the structural properties of the fibrils. Many energy evaluations were needed for these simulations, and as these systems comprise up to 21,276 atoms this would not have been feasible without the developments described here.

Nuclear Cardiology Practice in Asia: Analysis of Radiation Exposure and Best Practice for Myocardial Perfusion Imaging　- Results From the IAEA Nuclear Cardiology Protocols Cross-Sectional Study (INCAPS).

PubMed

Pascual, Thomas N B; Mercuri, Mathew; El-Haj, Noura; Bom, Henry Hee-Sung; Lele, Vikram; Al-Mallah, Mouaz H; Luxenburg, Osnat; Karthikeyan, Ganesan; Vitola, Joao; Mahmarian, John J; Better, Nathan; Shaw, Leslee J; Rehani, Madan M; Kashyap, Ravi; Paez, Diana; Dondi, Maurizio; Einstein, Andrew J

2017-03-24

This paper examines the current status of radiation exposure to patients in myocardial perfusion imaging (MPI) in Asia.Methods and Results:Laboratories voluntarily provided information on MPI performed over a 1-week period. Eight best practice criteria regarding MPI were predefined by an expert panel. Implementation of ≥6 best practices (quality index [QI] ≥6) was pre-specified as a desirable goal for keeping radiation exposure at a low level. Radiation effective dose (ED) in 1,469 patients and QI of 69 laboratories in Asia were compared against data from 239 laboratories in the rest of the world (RoW). Mean ED was significantly higher in Asia (11.4 vs. 9.6 mSv; P<0.0001), with significantly lower doses in South-East vs. East Asia (9.7 vs. 12.7 mSv; P<0.0001). QI in Asia was lower than in RoW. In comparison with RoW, Asian laboratories used thallium more frequently, used weight-based technetium dosing less frequently, and trended towards a lower rate of stress-only imaging. MPI radiation dose in Asia is higher than that in the RoW and linked to less consistent use of laboratory best practices such as avoidance of thallium, weight-based dosing, and use of stress-only imaging. Given that MPI is performed in Asia within a diverse array of medical contexts, laboratory-specific adoption of best practices offers numerous opportunities to improve quality of care.

SurF: an innovative framework in biosecurity and animal health surveillance evaluation.

PubMed

Muellner, Petra; Watts, Jonathan; Bingham, Paul; Bullians, Mark; Gould, Brendan; Pande, Anjali; Riding, Tim; Stevens, Paul; Vink, Daan; Stärk, Katharina Dc

2018-05-16

Surveillance for biosecurity hazards is being conducted by the New Zealand Competent Authority, the Ministry for Primary Industries (MPI) to support New Zealand's biosecurity system. Surveillance evaluation should be an integral part of the surveillance life cycle, as it provides a means to identify and correct problems and to sustain and enhance the existing strengths of a surveillance system. The surveillance evaluation Framework (SurF) presented here was developed to provide a generic framework within which the MPI biosecurity surveillance portfolio, and all of its components, can be consistently assessed. SurF is an innovative, cross-sectoral effort that aims to provide a common umbrella for surveillance evaluation in the animal, plant, environment and aquatic sectors. It supports the conduct of the following four distinct components of an evaluation project: (i) motivation for the evaluation, (ii) scope of the evaluation, (iii) evaluation design and implementation and (iv) reporting and communication of evaluation outputs. Case studies, prepared by MPI subject matter experts, are included in the framework to guide users in their assessment. Three case studies were used in the development of SurF in order to assure practical utility and to confirm usability of SurF across all included sectors. It is anticipated that the structured approach and information provided by SurF will not only be of benefit to MPI but also to other New Zealand stakeholders. Although SurF was developed for internal use by MPI, it could be applied to any surveillance system in New Zealand or elsewhere. © 2018 2018 The Authors. Transboundary and Emerging Diseases Published by Blackwell Verlag GmbH.

LV dyssynchrony as assessed by phase analysis of gated SPECT myocardial perfusion imaging in patients with Wolff-Parkinson-White syndrome

PubMed Central

Chen, Chun; Miao, Changqing; Feng, Jianlin; Zhou, Yanli; Cao, Kejiang; Lloyd, Michael S.; Chen, Ji

2013-01-01

Purpose The purpose of this study was to evaluate left ventricular (LV) mechanical dyssynchrony in patients with Wolff-Parkinson-White (WPW) syndrome pre- and post-radiofrequency catheter ablation (RFA) using phase analysis of gated single photon emission computed tomography (SPECT) myocardial perfusion imaging (MPI). Methods Forty-five WPW patients were enrolled and had gated SPECT MPI pre- and 2–3 days post-RFA. Electrophysiological study (EPS) was used to locate accessory pathways (APs) and categorize the patients according to the AP locations (septal, left and right free wall). Electrocardiography (ECG) was performed pre- and post-RFA to confirm successful elimination of the APs. Phase analysis of gated SPECT MPI was used to assess LV dyssynchrony pre- and post-RFA. Results Among the 45 patients, 3 had gating errors, and thus 42 had SPECT phase analysis. Twenty-two patients (52.4 %) had baseline LV dyssynchrony. Baseline LV dyssynchrony was more prominent in the patients with septal APs than in the patients with left or right APs (p<0.05). RFA improved LV synchrony in the entire cohort and in the patients with septal APs (p<0.01). Conclusion Phase analysis of gated SPECT MPI demonstrated that LV mechanical dyssynchrony can be present in patients with WPW syndrome. Septal APs result in the greatest degree of LV mechanical dyssynchrony and afford the most benefit after RFA. This study supports further investigation in the relationship between electrical and mechanical activation using EPS and phase analysis of gated SPECT MPI. PMID:22532253

A Naval Marksmanship Training Transfer Study: The Use of Indoor Simulated Marksmanship Trainers to Train for Live Fire

DTIC Science & Technology

2012-03-01

on the standard Navy Handgun Qualification Course. Results partially supported the hypotheses. The simulation group showed greater improvement in MPI...standard Navy Handgun Qualification Course. Results partially supported the hypotheses. The simulation group showed greater improvement in MPI than the...14 3. Navy Handgun Qualification Course Firing Sequence ..................15 F. PROCEDURES

Performance Comparison of HPF and MPI Based NAS Parallel Benchmarks

NASA Technical Reports Server (NTRS)

Saini, Subhash

1997-01-01

Compilers supporting High Performance Form (HPF) features first appeared in late 1994 and early 1995 from Applied Parallel Research (APR), Digital Equipment Corporation, and The Portland Group (PGI). IBM introduced an HPF compiler for the IBM RS/6000 SP2 in April of 1996. Over the past two years, these implementations have shown steady improvement in terms of both features and performance. The performance of various hardware/ programming model (HPF and MPI) combinations will be compared, based on latest NAS Parallel Benchmark results, thus providing a cross-machine and cross-model comparison. Specifically, HPF based NPB results will be compared with MPI based NPB results to provide perspective on performance currently obtainable using HPF versus MPI or versus hand-tuned implementations such as those supplied by the hardware vendors. In addition, we would also present NPB, (Version 1.0) performance results for the following systems: DEC Alpha Server 8400 5/440, Fujitsu CAPP Series (VX, VPP300, and VPP700), HP/Convex Exemplar SPP2000, IBM RS/6000 SP P2SC node (120 MHz), NEC SX-4/32, SGI/CRAY T3E, and SGI Origin2000. We would also present sustained performance per dollar for Class B LU, SP and BT benchmarks.

Performance of hybrid programming models for multiscale cardiac simulations: preparing for petascale computation.

PubMed

Pope, Bernard J; Fitch, Blake G; Pitman, Michael C; Rice, John J; Reumann, Matthias

2011-10-01

Future multiscale and multiphysics models that support research into human disease, translational medical science, and treatment can utilize the power of high-performance computing (HPC) systems. We anticipate that computationally efficient multiscale models will require the use of sophisticated hybrid programming models, mixing distributed message-passing processes [e.g., the message-passing interface (MPI)] with multithreading (e.g., OpenMP, Pthreads). The objective of this study is to compare the performance of such hybrid programming models when applied to the simulation of a realistic physiological multiscale model of the heart. Our results show that the hybrid models perform favorably when compared to an implementation using only the MPI and, furthermore, that OpenMP in combination with the MPI provides a satisfactory compromise between performance and code complexity. Having the ability to use threads within MPI processes enables the sophisticated use of all processor cores for both computation and communication phases. Considering that HPC systems in 2012 will have two orders of magnitude more cores than what was used in this study, we believe that faster than real-time multiscale cardiac simulations can be achieved on these systems.

PyPele Rewritten To Use MPI

NASA Technical Reports Server (NTRS)

Hockney, George; Lee, Seungwon

2008-01-01

A computer program known as PyPele, originally written as a Pythonlanguage extension module of a C++ language program, has been rewritten in pure Python language. The original version of PyPele dispatches and coordinates parallel-processing tasks on cluster computers and provides a conceptual framework for spacecraft-mission- design and -analysis software tools to run in an embarrassingly parallel mode. The original version of PyPele uses SSH (Secure Shell a set of standards and an associated network protocol for establishing a secure channel between a local and a remote computer) to coordinate parallel processing. Instead of SSH, the present Python version of PyPele uses Message Passing Interface (MPI) [an unofficial de-facto standard language-independent application programming interface for message- passing on a parallel computer] while keeping the same user interface. The use of MPI instead of SSH and the preservation of the original PyPele user interface make it possible for parallel application programs written previously for the original version of PyPele to run on MPI-based cluster computers. As a result, engineers using the previously written application programs can take advantage of embarrassing parallelism without need to rewrite those programs.

Diagnostic yield and accuracy of coronary CT angiography after abnormal nuclear myocardial perfusion imaging.

PubMed

Meinel, Felix G; Schoepf, U Joseph; Townsend, Jacob C; Flowers, Brian A; Geyer, Lucas L; Ebersberger, Ullrich; Krazinski, Aleksander W; Kunz, Wolfgang G; Thierfelder, Kolja M; Baker, Deborah W; Khan, Ashan M; Fernandes, Valerian L; O'Brien, Terrence X

2018-06-15

We aimed to determine the diagnostic yield and accuracy of coronary CT angiography (CCTA) in patients referred for invasive coronary angiography (ICA) based on clinical concern for coronary artery disease (CAD) and an abnormal nuclear stress myocardial perfusion imaging (MPI) study. We enrolled 100 patients (84 male, mean age 59.6 ± 8.9 years) with an abnormal MPI study and subsequent referral for ICA. Each patient underwent CCTA prior to ICA. We analyzed the prevalence of potentially obstructive CAD (≥50% stenosis) on CCTA and calculated the diagnostic accuracy of ≥50% stenosis on CCTA for the detection of clinically significant CAD on ICA (defined as any ≥70% stenosis or ≥50% left main stenosis). On CCTA, 54 patients had at least one ≥50% stenosis. With ICA, 45 patients demonstrated clinically significant CAD. A positive CCTA had 100% sensitivity and 84% specificity with a 100% negative predictive value and 83% positive predictive value for clinically significant CAD on a per patient basis in MPI positive symptomatic patients. In conclusion, almost half (48%) of patients with suspected CAD and an abnormal MPI study demonstrate no obstructive CAD on CCTA.

Message Passing vs. Shared Address Space on a Cluster of SMPs

NASA Technical Reports Server (NTRS)

Shan, Hongzhang; Singh, Jaswinder Pal; Oliker, Leonid; Biswas, Rupak

2000-01-01

The convergence of scalable computer architectures using clusters of PCs (or PC-SMPs) with commodity networking has become an attractive platform for high end scientific computing. Currently, message-passing and shared address space (SAS) are the two leading programming paradigms for these systems. Message-passing has been standardized with MPI, and is the most common and mature programming approach. However message-passing code development can be extremely difficult, especially for irregular structured computations. SAS offers substantial ease of programming, but may suffer from performance limitations due to poor spatial locality, and high protocol overhead. In this paper, we compare the performance of and programming effort, required for six applications under both programming models on a 32 CPU PC-SMP cluster. Our application suite consists of codes that typically do not exhibit high efficiency under shared memory programming. due to their high communication to computation ratios and complex communication patterns. Results indicate that SAS can achieve about half the parallel efficiency of MPI for most of our applications: however, on certain classes of problems SAS performance is competitive with MPI. We also present new algorithms for improving the PC cluster performance of MPI collective operations.

Novel magnetic multicore nanoparticles designed for MPI and other biomedical applications: From synthesis to first in vivo studies

PubMed Central

Taupitz, Matthias; Ariza de Schellenberger, Angela; Kosch, Olaf; Eberbeck, Dietmar; Wagner, Susanne; Trahms, Lutz; Hamm, Bernd; Schnorr, Jörg

2018-01-01

Synthesis of novel magnetic multicore particles (MCP) in the nano range, involves alkaline precipitation of iron(II) chloride in the presence of atmospheric oxygen. This step yields green rust, which is oxidized to obtain magnetic nanoparticles, which probably consist of a magnetite/maghemite mixed-phase. Final growth and annealing at 90°C in the presence of a large excess of carboxymethyl dextran gives MCP very promising magnetic properties for magnetic particle imaging (MPI), an emerging medical imaging modality, and magnetic resonance imaging (MRI). The magnetic nanoparticles are biocompatible and thus potential candidates for future biomedical applications such as cardiovascular imaging, sentinel lymph node mapping in cancer patients, and stem cell tracking. The new MCP that we introduce here have three times higher magnetic particle spectroscopy performance at lower and middle harmonics and five times higher MPS signal strength at higher harmonics compared with Resovist®. In addition, the new MCP have also an improved in vivo MPI performance compared to Resovist®, and we here report the first in vivo MPI investigation of this new generation of magnetic nanoparticles. PMID:29300729

Implementing the PM Programming Language using MPI and OpenMP - a New Tool for Programming Geophysical Models on Parallel Systems

NASA Astrophysics Data System (ADS)

Bellerby, Tim

2015-04-01

PM (Parallel Models) is a new parallel programming language specifically designed for writing environmental and geophysical models. The language is intended to enable implementers to concentrate on the science behind the model rather than the details of running on parallel hardware. At the same time PM leaves the programmer in control - all parallelisation is explicit and the parallel structure of any given program may be deduced directly from the code. This paper describes a PM implementation based on the Message Passing Interface (MPI) and Open Multi-Processing (OpenMP) standards, looking at issues involved with translating the PM parallelisation model to MPI/OpenMP protocols and considering performance in terms of the competing factors of finer-grained parallelisation and increased communication overhead. In order to maximise portability, the implementation stays within the MPI 1.3 standard as much as possible, with MPI-2 MPI-IO file handling the only significant exception. Moreover, it does not assume a thread-safe implementation of MPI. PM adopts a two-tier abstract representation of parallel hardware. A PM processor is a conceptual unit capable of efficiently executing a set of language tasks, with a complete parallel system consisting of an abstract N-dimensional array of such processors. PM processors may map to single cores executing tasks using cooperative multi-tasking, to multiple cores or even to separate processing nodes, efficiently sharing tasks using algorithms such as work stealing. While tasks may move between hardware elements within a PM processor, they may not move between processors without specific programmer intervention. Tasks are assigned to processors using a nested parallelism approach, building on ideas from Reyes et al. (2009). The main program owns all available processors. When the program enters a parallel statement then either processors are divided out among the newly generated tasks (number of new tasks < number of processors) or tasks are divided out among the available processors (number of tasks > number of processors). Nested parallel statements may further subdivide the processor set owned by a given task. Tasks or processors are distributed evenly by default, but uneven distributions are possible under programmer control. It is also possible to explicitly enable child tasks to migrate within the processor set owned by their parent task, reducing load unbalancing at the potential cost of increased inter-processor message traffic. PM incorporates some programming structures from the earlier MIST language presented at a previous EGU General Assembly, while adopting a significantly different underlying parallelisation model and type system. PM code is available at www.pm-lang.org under an unrestrictive MIT license. Reference Ruymán Reyes, Antonio J. Dorta, Francisco Almeida, Francisco de Sande, 2009. Automatic Hybrid MPI+OpenMP Code Generation with llc, Recent Advances in Parallel Virtual Machine and Message Passing Interface, Lecture Notes in Computer Science Volume 5759, 185-195

Impact of motion and partial volume effects correction on PET myocardial perfusion imaging using simultaneous PET-MR

NASA Astrophysics Data System (ADS)

Petibon, Yoann; Guehl, Nicolas J.; Reese, Timothy G.; Ebrahimi, Behzad; Normandin, Marc D.; Shoup, Timothy M.; Alpert, Nathaniel M.; El Fakhri, Georges; Ouyang, Jinsong

2017-01-01

PET is an established modality for myocardial perfusion imaging (MPI) which enables quantification of absolute myocardial blood flow (MBF) using dynamic imaging and kinetic modeling. However, heart motion and partial volume effects (PVE) significantly limit the spatial resolution and quantitative accuracy of PET MPI. Simultaneous PET-MR offers a solution to the motion problem in PET by enabling MR-based motion correction of PET data. The aim of this study was to develop a motion and PVE correction methodology for PET MPI using simultaneous PET-MR, and to assess its impact on both static and dynamic PET MPI using 18F-Flurpiridaz, a novel 18F-labeled perfusion tracer. Two dynamic 18F-Flurpiridaz MPI scans were performed on healthy pigs using a PET-MR scanner. Cardiac motion was tracked using a dedicated tagged-MRI (tMR) sequence. Motion fields were estimated using non-rigid registration of tMR images and used to calculate motion-dependent attenuation maps. Motion correction of PET data was achieved by incorporating tMR-based motion fields and motion-dependent attenuation coefficients into image reconstruction. Dynamic and static PET datasets were created for each scan. Each dataset was reconstructed as (i) Ungated, (ii) Gated (end-diastolic phase), and (iii) Motion-Corrected (MoCo), each without and with point spread function (PSF) modeling for PVE correction. Myocardium-to-blood concentration ratios (MBR) and apparent wall thickness were calculated to assess image quality for static MPI. For dynamic MPI, segment- and voxel-wise MBF values were estimated by non-linear fitting of a 2-tissue compartment model to tissue time-activity-curves. MoCo and Gating respectively decreased mean apparent wall thickness by 15.1% and 14.4% and increased MBR by 20.3% and 13.6% compared to Ungated images (P  <  0.01). Combined motion and PSF correction (MoCo-PSF) yielded 30.9% (15.7%) lower wall thickness and 82.2% (20.5%) higher MBR compared to Ungated data reconstructed without (with) PSF modeling (P  <  0.01). For dynamic PET, mean MBF across all segments were comparable for MoCo (0.72  ±  0.21 ml/min/ml) and Gating (0.69  ±  0.18 ml/min/ml). Ungated data yielded significantly lower mean MBF (0.59  ±  0.16 ml/min/ml). Mean MBF for MoCo-PSF was 0.80  ±  0.22 ml/min/ml, which was 37.9% (25.0%) higher than that obtained from Ungated data without (with) PSF correction (P  <  0.01). The developed methodology holds promise to improve the image quality and sensitivity of PET MPI studies performed using PET-MR.

High-Performance Data Analysis Tools for Sun-Earth Connection Missions

NASA Technical Reports Server (NTRS)

Messmer, Peter

2011-01-01

The data analysis tool of choice for many Sun-Earth Connection missions is the Interactive Data Language (IDL) by ITT VIS. The increasing amount of data produced by these missions and the increasing complexity of image processing algorithms requires access to higher computing power. Parallel computing is a cost-effective way to increase the speed of computation, but algorithms oftentimes have to be modified to take advantage of parallel systems. Enhancing IDL to work on clusters gives scientists access to increased performance in a familiar programming environment. The goal of this project was to enable IDL applications to benefit from both computing clusters as well as graphics processing units (GPUs) for accelerating data analysis tasks. The tool suite developed in this project enables scientists now to solve demanding data analysis problems in IDL that previously required specialized software, and it allows them to be solved orders of magnitude faster than on conventional PCs. The tool suite consists of three components: (1) TaskDL, a software tool that simplifies the creation and management of task farms, collections of tasks that can be processed independently and require only small amounts of data communication; (2) mpiDL, a tool that allows IDL developers to use the Message Passing Interface (MPI) inside IDL for problems that require large amounts of data to be exchanged among multiple processors; and (3) GPULib, a tool that simplifies the use of GPUs as mathematical coprocessors from within IDL. mpiDL is unique in its support for the full MPI standard and its support of a broad range of MPI implementations. GPULib is unique in enabling users to take advantage of an inexpensive piece of hardware, possibly already installed in their computer, and achieve orders of magnitude faster execution time for numerically complex algorithms. TaskDL enables the simple setup and management of task farms on compute clusters. The products developed in this project have the potential to interact, so one can build a cluster of PCs, each equipped with a GPU, and use mpiDL to communicate between the nodes and GPULib to accelerate the computations on each node.

Myocardial perfusion imaging in patients with a recent, normal exercise test.

PubMed

Bovin, Ann; Klausen, Ib C; Petersen, Lars J

2013-03-26

To investigate the added value of myocardial perfusion scintigraphy imaging (MPI) in consecutive patients with suspected coronary artery disease (CAD) and a recent, normal exercise electrocardiography (ECG). This study was a retrospective analysis of consecutive patients referred for MPI during a 2-year period from 2006-2007 at one clinic. All eligible patients were suspected of suffering from CAD, and had performed a satisfactory bicycle exercise test (i.e., peak heart rate > 85% of the expected, age-predicted maximum) within 6 mo of referral, their exercise ECG was had no signs of ischemia, there was no exercise-limiting angina, and no cardiac events occurred between the exercise test and referral. The patients subsequently underwent a standard 2-d, stress-rest exercise MPI. Ischemia was defined based on visual scoring supported by quantitative segmental analysis (i.e., sum of stress score > 3). The results of cardiac catheterization were analyzed, and clinical follow up was performed by review of electronic medical files. A total of 56 patients fulfilled the eligibility criteria. Most patients had a low or intermediate ATPIII pre-test risk of CAD (6 patients had a high pre-test risk). The referral exercise test showed a mean Duke score of 5 (range: 2 to 11), which translated to a low post-exercise risk in 66% and intermediate risk in 34%. A total of seven patients were reported with ischemia by MPI. Three of these patients had high ATPIII pre-test risk scores. Six of these seven patients underwent cardiac catheterization, which showed significant stenosis in one patient with a high pre-test risk of CAD, and indeterminate lesions in three patients (two of whom had high pre-test risk scores). With MPI as a gate keeper for catheterization, no significant, epicardial stenosis was observed in any of the 50 patients (0%, 95% confidence interval 0.0 to 7.1) with low to intermediate pre-test risk of CAD and a negative exercise test. No cardiac events occurred in any patients within a median follow up period of > 1200 d. The added diagnostic value of MPI in patients with low or intermediate risk of CAD and a recent, normal exercise test is marginal.

Distribution of N2O in the atmosphere under global warming - a simulation study with the MPI Earth System Model

NASA Astrophysics Data System (ADS)

Kracher, Daniela; Manzini, Elisa; Reick, Christian H.; Schultz, Martin; Stein, Olaf

2014-05-01

Climate change is driven by an increasing release of anthropogenic greenhouse gases (GHGs) such as carbon dioxide and nitrous oxide (N2O). Besides fossil fuel burning, also land use change and land management are anthropogenic sources of GHGs. Especially inputs of reactive nitrogen via fertilizer and deposition lead to enhanced emissions of N2O. One effect of a drastic future increase in surface temperature is a modification of atmospheric circulation, e.g. an accelerated Brewer Dobson circulation affecting the exchange between troposphere and stratosphere. N2O is inert in the troposphere and decayed only in the stratosphere. Thus, changes in atmospheric circulation, especially changes in the exchange between troposphere and stratosphere, will affect the atmospheric transport, decay, and distribution of N2O. In our study we assess the impact of global warming on atmospheric circulation and implied effects on the distribution and lifetime of atmospheric N2O. As terrestrial N2O emissions are highly determined by inputs of reactive nitrogen - the location of which being determined by human choice - we examine in particular the importance of latitudinal source regions of N2O for its global distribution. For this purpose we apply the Max Planck Institute Earth System Model, MPI-ESM. MPI-ESM consists of the atmospheric general circulation model ECHAM, the land surface model JSBACH, and MPIOM/HAMOCC representing ocean circulation and ocean biogeochemistry. Prognostic atmospheric N2O concentrations in MPI-ESM are determined by land N2O emissions, ocean N2O exchange and atmospheric tracer transport. As stratospheric chemistry is not explicitly represented in MPI-ESM, stratospheric decay rates of N2O are prescribed from a MACC MOZART simulation.

Response properties of the refractory auditory nerve fiber.

PubMed

Miller, C A; Abbas, P J; Robinson, B K

2001-09-01

The refractory characteristics of auditory nerve fibers limit their ability to accurately encode temporal information. Therefore, they are relevant to the design of cochlear prostheses. It is also possible that the refractory property could be exploited by prosthetic devices to improve information transfer, as refractoriness may enhance the nerve's stochastic properties. Furthermore, refractory data are needed for the development of accurate computational models of auditory nerve fibers. We applied a two-pulse forward-masking paradigm to a feline model of the human auditory nerve to assess refractory properties of single fibers. Each fiber was driven to refractoriness by a single (masker) current pulse delivered intracochlearly. Properties of firing efficiency, latency, jitter, spike amplitude, and relative spread (a measure of dynamic range and stochasticity) were examined by exciting fibers with a second (probe) pulse and systematically varying the masker-probe interval (MPI). Responses to monophasic cathodic current pulses were analyzed. We estimated the mean absolute refractory period to be about 330 micros and the mean recovery time constant to be about 410 micros. A significant proportion of fibers (13 of 34) responded to the probe pulse with MPIs as short as 500 micros. Spike amplitude decreased with decreasing MPI, a finding relevant to the development of computational nerve-fiber models, interpretation of gross evoked potentials, and models of more central neural processing. A small mean decrement in spike jitter was noted at small MPI values. Some trends (such as spike latency-vs-MPI) varied across fibers, suggesting that sites of excitation varied across fibers. Relative spread was found to increase with decreasing MPI values, providing direct evidence that stochastic properties of fibers are altered under conditions of refractoriness.

Effect of balloon mitral valvotomy on left ventricular function in rheumatic mitral stenosis.

PubMed

Rajesh, Gopalan Nair; Sreekumar, Pradeep; Haridasan, Vellani; Sajeev, C G; Bastian, Cicy; Vinayakumar, D; Kadermuneer, P; Mathew, Dolly; George, Biju; Krishnan, M N

Mitral stenosis (MS) is found to produce left ventricular (LV) dysfunction in some studies. We sought to study the left ventricular function in patients with rheumatic MS undergoing balloon mitral valvotomy (BMV). Ours is the first study to analyze effect of BMV on mitral annular plane systolic excursion (MAPSE), and to quantify prevalence of longitudinal left ventricular dysfunction in rheumatic MS. In this prospective cohort study, we included 43 patients with severe rheumatic mitral stenosis undergoing BMV. They were compared to twenty controls whose distribution of age and gender were similar to that of patients. The parameters compared were LV ejection fraction (EF) by modified Simpson's method, mitral annular systolic velocity (MASV), MAPSE, mitral annular early diastolic velocity (E'), and myocardial performance index (MPI). These parameters were reassessed immediately following BMV and after 3 months of procedure. MASV, MAPSE, E', and EF were significantly lower and MPI was higher in mitral stenosis group compared to controls. Impaired longitudinal LV function was present in 77% of study group. MAPSE and EF did not show significant change after BMV while MPI, MASV, and E' improved significantly. MASV and E' showed improvement immediately after BMV, while MPI decreased only at 3 months follow-up. There were significantly lower mitral annular motion parameters including MAPSE in patients with rheumatic mitral stenosis. Those with atrial fibrillation had higher MPI. Immediately after BMV, there was improvement in LV long axis function with a gradual improvement in global LV function. There was no significant change of MAPSE after BMV. Copyright © 2015 Cardiological Society of India. Published by Elsevier B.V. All rights reserved.

Improvement of the myocardial performance index in atrial fibrilation patients treated with amiodarone after cardioversion.

PubMed

Besli, Feyzullah; Basar, Cengiz; Kecebas, Mesut; Turker, Yasin

2015-03-01

This study evaluated the response to electrical cardioversion (EC) and the effect on the myocardial performance index (MPI) in patients with persistent and long-standing persistent atrial fibrillation (AF). We enrolled 103 patients (mean age 69.6 ± 8.9 years, 40.7% males) with a diagnosis of persistent and long-standing persistent AF. EC was applied to all patients after one g of amiodarone administration. Echocardiographic findings before EC were compared in patients with successful versus unsuccessful cardioversions and in patients with maintained sinus rhythm (SR) versus those with AF recurrence at the end of the first month. We also compared echocardiographic data before EC versus at the end of the first month in the same patients with maintained SR. SR was achieved in 72.8% of patients and was continued at the end of the first month in 69.3% of the patients. The MPI value of all patients was found to be 0.73 ± 0.21. The size of the left atrium was determined to be an independent predictor of the maintenance of SR at 1 month. In subgroup analyses, when we compared echocardiographic findings before EC and at the end of the first month in patients with maintained SR, the MPI (0.66 ± 0.14 vs 0.56 ± 0.09, p < 0.001) values were significantly decreased. Our study is the first to show impairment of the MPI, which is an indicator of systolic and diastolic function, in patients with persistent and long-standing persistent AF and improvement of the MPI after successful EC.

Nuclear cardiology practices and radiation exposure in Africa: results from the IAEA Nuclear Cardiology Protocols Study (INCAPS).

PubMed

Bouyoucef, Salah E; Mercuri, Mathew; Pascual, Thomas N; Allam, Adel H; Vangu, Mboyo; Vitola, João V; Better, Nathan; Karthikeyan, Ganesan; Mahmarian, John J; Rehani, Madan M; Kashyap, Ravi; Dondi, Maurizio; Paez, Diana; Einstein, Andrew J

While nuclear myocardial perfusion imaging (MPI) offers many benefits to patients with known or suspected cardiovascular disease, concerns exist regarding radiation-associated health effects. Little is known regarding MPI practice in Africa. We sought to characterise radiation doses and the use of MPI best practices that could minimise radiation in African nuclear cardiology laboratories, and compare these to practice worldwide. Demographics and clinical characteristics were collected for a consecutive sample of 348 patients from 12 laboratories in six African countries over a one-week period from March to April 2013. Radiation effective dose (ED) was estimated for each patient. A quality index (QI) enumerating adherence to eight best practices, identified a priori by an IAEA expert panel, was calculated for each laboratory. We compared these metrics with those from 7 563 patients from 296 laboratories outside Africa. Median (interquartile range) patient ED in Africa was similar to that of the rest of the world [9.1 (5.1-15.6) vs 10.3 mSv (6.8-12.6), p = 0.14], although a larger proportion of African patients received a low ED, ≤ 9 mSv targeted in societal recommendations (49.7 vs 38.2%, p < 0.001). Bestpractice adherence was higher among African laboratories (QI score: 6.3 ± 1.2 vs 5.4 ± 1.3, p = 0.013). However, median ED varied significantly among African laboratories (range: 2.0-16.3 mSv; p < 0.0001) and QI range was 4-8. Patient radiation dose from MPI in Africa was similar to that in the rest of the world, and adherence to best practices was relatively high in African laboratories. Nevertheless there remain opportunities to further reduce radiation exposure to African patients from MPI.

Current worldwide nuclear cardiology practices and radiation exposure: results from the 65 country IAEA Nuclear Cardiology Protocols Cross-Sectional Study (INCAPS).

PubMed

Einstein, Andrew J; Pascual, Thomas N B; Mercuri, Mathew; Karthikeyan, Ganesan; Vitola, João V; Mahmarian, John J; Better, Nathan; Bouyoucef, Salah E; Hee-Seung Bom, Henry; Lele, Vikram; Magboo, V Peter C; Alexánderson, Erick; Allam, Adel H; Al-Mallah, Mouaz H; Flotats, Albert; Jerome, Scott; Kaufmann, Philipp A; Luxenburg, Osnat; Shaw, Leslee J; Underwood, S Richard; Rehani, Madan M; Kashyap, Ravi; Paez, Diana; Dondi, Maurizio

2015-07-07

To characterize patient radiation doses from nuclear myocardial perfusion imaging (MPI) and the use of radiation-optimizing 'best practices' worldwide, and to evaluate the relationship between laboratory use of best practices and patient radiation dose. We conducted an observational cross-sectional study of protocols used for all 7911 MPI studies performed in 308 nuclear cardiology laboratories in 65 countries for a single week in March-April 2013. Eight 'best practices' relating to radiation exposure were identified a priori by an expert committee, and a radiation-related quality index (QI) devised indicating the number of best practices used by a laboratory. Patient radiation effective dose (ED) ranged between 0.8 and 35.6 mSv (median 10.0 mSv). Average laboratory ED ranged from 2.2 to 24.4 mSv (median 10.4 mSv); only 91 (30%) laboratories achieved the median ED ≤ 9 mSv recommended by guidelines. Laboratory QIs ranged from 2 to 8 (median 5). Both ED and QI differed significantly between laboratories, countries, and world regions. The lowest median ED (8.0 mSv), in Europe, coincided with high best-practice adherence (mean laboratory QI 6.2). The highest doses (median 12.1 mSv) and low QI (4.9) occurred in Latin America. In hierarchical regression modelling, patients undergoing MPI at laboratories following more 'best practices' had lower EDs. Marked worldwide variation exists in radiation safety practices pertaining to MPI, with targeted EDs currently achieved in a minority of laboratories. The significant relationship between best-practice implementation and lower doses indicates numerous opportunities to reduce radiation exposure from MPI globally. © The Author 2015. Published by Oxford University Press on behalf of the European Society of Cardiology.

Current worldwide nuclear cardiology practices and radiation exposure: results from the 65 country IAEA Nuclear Cardiology Protocols Cross-Sectional Study (INCAPS)

PubMed Central

Einstein, Andrew J.; Pascual, Thomas N. B.; Mercuri, Mathew; Karthikeyan, Ganesan; Vitola, João V.; Mahmarian, John J.; Better, Nathan; Bouyoucef, Salah E.; Hee-Seung Bom, Henry; Lele, Vikram; Magboo, V. Peter C.; Alexánderson, Erick; Allam, Adel H.; Al-Mallah, Mouaz H.; Flotats, Albert; Jerome, Scott; Kaufmann, Philipp A.; Luxenburg, Osnat; Shaw, Leslee J.; Underwood, S. Richard; Rehani, Madan M.; Kashyap, Ravi; Paez, Diana; Dondi, Maurizio

2015-01-01

Aims To characterize patient radiation doses from nuclear myocardial perfusion imaging (MPI) and the use of radiation-optimizing ‘best practices’ worldwide, and to evaluate the relationship between laboratory use of best practices and patient radiation dose. Methods and results We conducted an observational cross-sectional study of protocols used for all 7911 MPI studies performed in 308 nuclear cardiology laboratories in 65 countries for a single week in March–April 2013. Eight ‘best practices’ relating to radiation exposure were identified a priori by an expert committee, and a radiation-related quality index (QI) devised indicating the number of best practices used by a laboratory. Patient radiation effective dose (ED) ranged between 0.8 and 35.6 mSv (median 10.0 mSv). Average laboratory ED ranged from 2.2 to 24.4 mSv (median 10.4 mSv); only 91 (30%) laboratories achieved the median ED ≤ 9 mSv recommended by guidelines. Laboratory QIs ranged from 2 to 8 (median 5). Both ED and QI differed significantly between laboratories, countries, and world regions. The lowest median ED (8.0 mSv), in Europe, coincided with high best-practice adherence (mean laboratory QI 6.2). The highest doses (median 12.1 mSv) and low QI (4.9) occurred in Latin America. In hierarchical regression modelling, patients undergoing MPI at laboratories following more ‘best practices’ had lower EDs. Conclusion Marked worldwide variation exists in radiation safety practices pertaining to MPI, with targeted EDs currently achieved in a minority of laboratories. The significant relationship between best-practice implementation and lower doses indicates numerous opportunities to reduce radiation exposure from MPI globally. PMID:25898845

Impact of insurance carrier, prior authorization, and socioeconomic status on appropriate use of SPECT myocardial perfusion imaging in private community-based office practice.

PubMed

Doukky, Rami; Hayes, Kathleen; Frogge, Nathan; Nazir, Noreen T; Collado, Fareed M; Williams, Kim A

2015-05-01

The impact of health insurance carrier and socioeconomic status (SES) on the adherence to appropriate use criteria (AUC) for radionuclide myocardial perfusion imaging (MPI) is unknown. Health insurance carrier's prior authorization and patient's SES impact adherence to AUC for MPI in a fee-for-service setting. We conducted a prospective cohort study of 1511 consecutive patients who underwent outpatient MPI in a multi-site, office-based, fee-for-service setting. The patients were stratified according to the 2009 AUC into appropriate/uncertain appropriateness and inappropriate use groups. Insurance status was categorized as Medicare (does not require prior authorization) vs commercial (requires prior authorization). Socioeconomic status was determined by the median household income in the ZIP code of residence. The proportion of patients with Medicare was 33% vs 67% with commercial insurance. The rate of inappropriate use was higher among patients with commercial insurance vs Medicare (55% vs 24%; P < 0.001); this difference was not significant after adjusting for confounders known to impact AUC determination (odds ratio: 1.06, 95% confidence interval: 0.62-1.82, P = 0.82). The mean annual household income in the residential areas of patients with inappropriate use as compared to those with appropriate/uncertain use was $72 000 ± 21 000 vs $68 000 ± 20 000, respectively (P < 0.001). After adjusting for covariates known to impact AUC determination, SES (top vs bottom quartile income area) was not independently predictive of inappropriate MPI use (odds ratio: 0.9, 95% confidence interval: 0.53-1.52, P = 0.69). Insurance carriers prior authorization and SES do not seem to play a significant role in determining physicians adherence to AUC for MPI. © 2015 Wiley Periodicals, Inc.

Early myocardial damage assessment in dystrophinopathies using (99)Tc(m)-MIBI gated myocardial perfusion imaging.

PubMed

Zhang, Li; Liu, Zhe; Hu, Ke-You; Tian, Qing-Bao; Wei, Ling-Ge; Zhao, Zhe; Shen, Hong-Rui; Hu, Jing

2015-01-01

Early detection of muscular dystrophy (MD)-associated cardiomyopathy is important because early medical treatment may slow cardiac remodeling and attenuate symptoms of cardiac dysfunction; however, no sensitive and standard diagnostic method for MD at an earlier stage has been well-recognized. Thus, the aim of this study was to test the early diagnostic value of technetium 99m-methoxyisobutylisonitrile ((99)Tc(m)-MIBI) gated myocardial perfusion imaging (G-MPI) for MD. Ninety-one patients underwent (99)Tc(m)-MIBI G-MPI examinations when they were diagnosed with Duchenne muscular dystrophy (DMD) (n=77) or Becker muscular dystrophy (BMD; n=14). (99)Tc(m)-MIBI G-MPI examinations were repeated in 43 DMD patients who received steroid treatments for 2 years as a follow-up examination. Myocardial defects were observed in nearly every segment of the left ventricular wall in both DMD and BMD patients compared with controls, especially in the inferior walls and the apices by using (99)Tc(m)-MIBI G-MPI. Cardiac wall movement impairment significantly correlated with age in the DMD and BMD groups (r s=0.534 [P<0.05] and r s=0.784 [P<0.05], respectively). Intermittent intravenous doses of glucocorticoids and continuation with oral steroid treatments significantly improved myocardial function in DMD patients (P<0.05), but not in BMD patients. (99)Tc(m)-MIBI G-MPI is a sensitive and safe approach for early evaluation of cardiomyopathy in patients with DMD or BMD, and can serve as a candidate method for the evaluation of progression, prognosis, and assessment of the effect of glucocorticoid treatment in these patients.

Nuclear cardiology practices and radiation exposure in Africa: results from the IAEA Nuclear Cardiology Protocols Study (INCAPS)

PubMed Central

Bouyoucef, Salah E; Mercuri, Mathew; Einstein, Andrew J; Pascual, Thomas NB; Kashyap, Ravi; Dondi, Maurizio; Paez, Diana; Allam, Adel H; Vangu, Mboyo; Vitola, João V; Better, Nathan; Karthikeyan, Ganesan; Mahmarian, John J; Rehani, Madan M; Einstein, Andrew J

2017-01-01

Summary Objective: While nuclear myocardial perfusion imaging (MPI) offers many benefits to patients with known or suspected cardiovascular disease, concerns exist regarding radiationassociated health effects. Little is known regarding MPI practice in Africa. We sought to characterise radiation doses and the use of MPI best practices that could minimise radiation in African nuclear cardiology laboratories, and compare these to practice worldwide. Methods: Demographics and clinical characteristics were collected for a consecutive sample of 348 patients from 12 laboratories in six African countries over a one-week period from March to April 2013. Radiation effective dose (ED) was estimated for each patient. A quality index (QI) enumerating adherence to eight best practices, identified a priori by an IAEA expert panel, was calculated for each laboratory. We compared these metrics with those from 7 563 patients from 296 laboratories outside Africa. Results: to that of the rest of the world [9.1 (5.1–15.6) vs 10.3 mSv (6.8–12.6), p = 0.14], although a larger proportion of African patients received a low ED, ≤ 9 mSv targeted in societal recommendations (49.7 vs 38.2%, p < 0.001). Bestpractice adherence was higher among African laboratories (QI score: 6.3 ± 1.2 vs 5.4 ± 1.3, p = 0.013). However, median ED varied significantly among African laboratories (range: 2.0–16.3 mSv; p < 0.0001) and QI range was 4–8. Conclusion: Patient radiation dose from MPI in Africa was similar to that in the rest of the world, and adherence to best practices was relatively high in African laboratories. Nevertheless there remain opportunities to further reduce radiation exposure to African patients from MPI. PMID:28906538

Assessment of left ventricular mechanical dyssynchrony by phase analysis of gated-SPECT myocardial perfusion imaging and tissue Doppler imaging: comparison between QGS and ECTb software packages.

PubMed

Rastgou, Fereydoon; Shojaeifard, Maryam; Amin, Ahmad; Ghaedian, Tahereh; Firoozabadi, Hasan; Malek, Hadi; Yaghoobi, Nahid; Bitarafan-Rajabi, Ahmad; Haghjoo, Majid; Amouzadeh, Hedieh; Barati, Hossein

2014-12-01

Recently, the phase analysis of gated single-photon emission computed tomography (SPECT) myocardial perfusion imaging (MPI) has become feasible via several software packages for the evaluation of left ventricular mechanical dyssynchrony. We compared two quantitative software packages, quantitative gated SPECT (QGS) and Emory cardiac toolbox (ECTb), with tissue Doppler imaging (TDI) as the conventional method for the evaluation of left ventricular mechanical dyssynchrony. Thirty-one patients with severe heart failure (ejection fraction ≤35%) and regular heart rhythm, who referred for gated-SPECT MPI, were enrolled. TDI was performed within 3 days after MPI. Dyssynchrony parameters derived from gated-SPECT MPI were analyzed by QGS and ECTb and were compared with the Yu index and septal-lateral wall delay measured by TDI. QGS and ECTb showed a good correlation for assessment of phase histogram bandwidth (PHB) and phase standard deviation (PSD) (r = 0.664 and r = 0.731, P < .001, respectively). However, the mean value of PHB and PSD by ECTb was significantly higher than that of QGS. No significant correlation was found between ECTb and QGS and the Yu index. Nevertheless, PHB, PSD, and entropy derived from QGS revealed a significant (r = 0.424, r = 0.478, r = 0.543, respectively; P < .02) correlation with septal-lateral wall delay. Despite a good correlation between QGS and ECTb software packages, different normal cut-off values of PSD and PHB should be defined for each software package. There was only a modest correlation between phase analysis of gated-SPECT MPI and TDI data, especially in the population of heart failure patients with both narrow and wide QRS complex.

Constraining a land-surface model with multiple observations by application of the MPI-Carbon Cycle Data Assimilation System V1.0

NASA Astrophysics Data System (ADS)

Schürmann, Gregor J.; Kaminski, Thomas; Köstler, Christoph; Carvalhais, Nuno; Voßbeck, Michael; Kattge, Jens; Giering, Ralf; Rödenbeck, Christian; Heimann, Martin; Zaehle, Sönke

2016-09-01

We describe the Max Planck Institute Carbon Cycle Data Assimilation System (MPI-CCDAS) built around the tangent-linear version of the JSBACH land-surface scheme, which is part of the MPI-Earth System Model v1. The simulated phenology and net land carbon balance were constrained by globally distributed observations of the fraction of absorbed photosynthetically active radiation (FAPAR, using the TIP-FAPAR product) and atmospheric CO2 at a global set of monitoring stations for the years 2005 to 2009. When constrained by FAPAR observations alone, the system successfully, and computationally efficiently, improved simulated growing-season average FAPAR, as well as its seasonality in the northern extra-tropics. When constrained by atmospheric CO2 observations alone, global net and gross carbon fluxes were improved, despite a tendency of the system to underestimate tropical productivity. Assimilating both data streams jointly allowed the MPI-CCDAS to match both observations (TIP-FAPAR and atmospheric CO2) equally well as the single data stream assimilation cases, thereby increasing the overall appropriateness of the simulated biosphere dynamics and underlying parameter values. Our study thus demonstrates the value of multiple-data-stream assimilation for the simulation of terrestrial biosphere dynamics. It further highlights the potential role of remote sensing data, here the TIP-FAPAR product, in stabilising the strongly underdetermined atmospheric inversion problem posed by atmospheric transport and CO2 observations alone. Notwithstanding these advances, the constraint of the observations on regional gross and net CO2 flux patterns on the MPI-CCDAS is limited through the coarse-scale parametrisation of the biosphere model. We expect improvement through a refined initialisation strategy and inclusion of further biosphere observations as constraints.

Does classification of persons with fibromyalgia into Multidimensional Pain Inventory subgroups detect differences in outcome after a standard chronic pain management program?

PubMed Central

Verra, Martin L; Angst, Felix; Brioschi, Roberto; Lehmann, Susanne; Keefe, Francis J; Staal, J Bart; de Bie, Rob A; Aeschlimann, André

2009-01-01

INTRODUCTION: The present study aimed to replicate and validate the empirically derived subgroup classification based on the Multidimensional Pain Inventory (MPI) in a sample of highly disabled fibromyalgia (FM) patients. Second, it examined how the identified subgroups differed in their response to an intensive, interdisciplinary inpatient pain management program. METHODS: Participants were 118 persons with FM who experienced persistent pain and were disabled. Subgroup classification was conducted by cluster analysis using MPI subscale scores at entry to the program. At program entry and discharge, participants completed the MPI, Medical Outcomes Study Short Form-36, Hospital Anxiety and Depression Scale and Coping Strategies Questionnaire. RESULTS: Cluster analysis identified three subgroups in the highly disabled sample that were similar to those described by other studies using less disabled samples of FM. The dysfunctional subgroup (DYS; 36% of the sample) showed the highest level of depression, the interpersonally distressed subgroup (ID; 24%) showed a modest level of depression and the adaptive copers subgroup (AC; 38%) showed the lowest depression scores in the MPI (negative mood), Medical Outcomes Study Short Form-36 (mental health), Hospital Anxiety and Depression Scale (depression) and Coping Strategies Questionnaire (catastrophizing). Significant differences in treatment outcome were observed among the three subgroups in terms of reduction of pain severity (as assessed using the MPI). The effect sizes were 1.42 for DYS, 1.32 for AC and 0.62 for ID (P=0.004 for pairwise comparison of ID-AC and P=0.018 for ID-DYS). DISCUSSION: These findings underscore the importance of assessing individuals’ differences in how they adjust to FM. PMID:20011715

Future cardiac events in patients with ischemic ECG changes during adenosine infusion as a myocardial stress agent and normal cardiac scan.

PubMed

Amer, Hamid; Niaz, Khalid; Hatazawa, Jun; Gasmelseed, Ahmed; Samiri, Hussain Al; Al Othman, Maram; Hammad, Mai Al

2017-11-01

We sought to determine the prognostic importance of adenosine-induced ischemic ECG changes in patients with normal single-photon emission computed tomography myocardial perfusion images (MPI). We carried out a retrospective analysis of 765 patients undergoing adenosine MPI between January 2013 and January 2015. Patients with baseline ECG abnormalities and/or abnormal scan were excluded. Overall, 67 (8.7%) patients had ischemic ECG changes during adenosine infusion in the form of ST depression of 1 mm or more. Of these, 29 [43% (3.8% of all patients)] had normal MPI (positive ECG group). An age-matched and sex-matched group of 108 patients with normal MPI without ECG changes served as control participants (negative ECG group). During a mean follow-up duration of 33.3±6.1 months, patients in the positive ECG group did not have significantly more adverse cardiac events than those in the negative ECG group. One (0.9%) patient in the negative ECG group had a nonfatal myocardial infarction (0.7% annual event rate after a negative MPI). Also in this group, two (1.8%) patients admitted with a diagnosis of CAD where they have been ruled out by angiography. A fourth case in this, in the negative ECG group, was admitted because of heart failure that proved to be secondary to a pulmonary cause and not CAD. A case only in the positive ECG group was admitted as a CAD that was ruled out by coronary angiography. Patients with normal myocardial perfusion scintigraphy in whom ST-segment depression develops during adenosine stress test appear to have no increased risk for future cardiac events compared with similar patients without ECG evidence of ischemia.

Magnetic particle imaging: from proof of principle to preclinical applications

NASA Astrophysics Data System (ADS)

Knopp, T.; Gdaniec, N.; Möddel, M.

2017-07-01

Tomographic imaging has become a mandatory tool for the diagnosis of a majority of diseases in clinical routine. Since each method has its pros and cons, a variety of them is regularly used in clinics to satisfy all application needs. Magnetic particle imaging (MPI) is a relatively new tomographic imaging technique that images magnetic nanoparticles with a high spatiotemporal resolution in a quantitative way, and in turn is highly suited for vascular and targeted imaging. MPI was introduced in 2005 and now enters the preclinical research phase, where medical researchers get access to this new technology and exploit its potential under physiological conditions. Within this paper, we review the development of MPI since its introduction in 2005. Besides an in-depth description of the basic principles, we provide detailed discussions on imaging sequences, reconstruction algorithms, scanner instrumentation and potential medical applications.

Military Interoperable Digital Hospital Testbed

DTIC Science & Technology

2012-07-01

Subject outcome measures include blood pressure, waist circumference, weight, body mass index (BMI), body fat, HDL cholesterol, triglycerides , glucose ...master patient index (MPI), 625 duplicate chest x-rays and CT scans of the head between sending and receiving institution (taken within 0-7 days) were... Index (MPI) software. The report included chest x-rays (CPT 71010 and 71020) and CT scans of the head (CPT 70450) for the stated time periods. The

GSD-1G and MPI-DING Reference Glasses for In Situ and Bulk Isotopic Determination

USGS Publications Warehouse

Jochum, K.P.; Wilson, S.A.; Abouchami, W.; Amini, M.; Chmeleff, J.; Eisenhauer, A.; Hegner, E.; Iaccheri, L.M.; Kieffer, B.; Krause, J.; McDonough, W.F.; Mertz-Kraus, R.; Raczek, I.; Rudnick, R.L.; Scholz, Donna K.; Steinhoefel, G.; Stoll, B.; Stracke, A.; Tonarini, S.; Weis, D.; Weis, U.; Woodhead, J.D.

2011-01-01

This paper contains the results of an extensive isotopic study of United States Geological Survey GSD-1G and MPI-DING reference glasses. Thirteen different laboratories were involved using high-precision bulk (TIMS, MC-ICP-MS) and microanalytical (LA-MC-ICP-MS, LA-ICP-MS) techniques. Detailed studies were performed to demonstrate the large-scale and small-scale homogeneity of the reference glasses. Together with previously published isotopic data from ten other laboratories, preliminary reference and information values as well as their uncertainties at the 95% confidence level were determined for H, O, Li, B, Si, Ca, Sr, Nd, Hf, Pb, Th and U isotopes using the recommendations of the International Association of Geoanalysts for certification of reference materials. Our results indicate that GSD-1G and the MPI-DING glasses are suitable reference materials for microanalytical and bulk analytical purposes. Ce document contient les r??sultats d'une importante ??tude isotopique des verres de r??f??rence USGS GSD-1G et MPI-DING. Treize laboratoires diff??rents ont particip?? au travers de techniques analytiques de haute pr??cision travaillant soit sur ??chantillon total (TIMS, MC-ICP-MS) soit par microanalyse ??in situ?? (LA-MC-ICP-MS, LA-ICP-MS). ?? 2010 The Authors. Geostandards and Geoanalytical Research ?? 2010 International Association of Geoanalysts.

Lactoferrin conjugated iron oxide nanoparticles for targeting brain glioma cells in magnetic particle imaging

NASA Astrophysics Data System (ADS)

Tomitaka, Asahi; Arami, Hamed; Gandhi, Sonu; Krishnan, Kannan M.

2015-10-01

Magnetic Particle Imaging (MPI) is a new real-time imaging modality, which promises high tracer mass sensitivity and spatial resolution directly generated from iron oxide nanoparticles. In this study, monodisperse iron oxide nanoparticles with median core diameters ranging from 14 to 26 nm were synthesized and their surface was conjugated with lactoferrin to convert them into brain glioma targeting agents. The conjugation was confirmed with the increase of the hydrodynamic diameters, change of zeta potential, and Bradford assay. Magnetic particle spectrometry (MPS), performed to evaluate the MPI performance of these nanoparticles, showed no change in signal after lactoferrin conjugation to nanoparticles for all core diameters, suggesting that the MPI signal is dominated by Néel relaxation and thus independent of hydrodynamic size difference or presence of coating molecules before and after conjugations. For this range of core sizes (14-26 nm), both MPS signal intensity and spatial resolution improved with increasing core diameter of nanoparticles. The lactoferrin conjugated iron oxide nanoparticles (Lf-IONPs) showed specific cellular internalization into C6 cells with a 5-fold increase in MPS signal compared to IONPs without lactoferrin, both after 24 h incubation. These results suggest that Lf-IONPs can be used as tracers for targeted brain glioma imaging using MPI.

Nanoparticle encapsulation in red blood cells enables blood-pool magnetic particle imaging hours after injection

NASA Astrophysics Data System (ADS)

Rahmer, J.; Antonelli, A.; Sfara, C.; Tiemann, B.; Gleich, B.; Magnani, M.; Weizenecker, J.; Borgert, J.

2013-06-01

Magnetic particle imaging (MPI) is a new medical imaging approach that is based on the nonlinear magnetization response of super-paramagnetic iron oxide nanoparticles (SPIOs) injected into the blood stream. To date, real-time MPI of the bolus passage of an approved MRI SPIO contrast agent injected into the tail vein of living mice has been demonstrated. However, nanoparticles are rapidly removed from the blood stream by the mononuclear phagocyte system. Therefore, imaging applications for long-term monitoring require the repeated administration of bolus injections, which complicates quantitative comparisons due to the temporal variations in concentration. Encapsulation of SPIOs into red blood cells (RBCs) has been suggested to increase the blood circulation time of nanoparticles. This work presents first evidence that SPIO-loaded RBCs can be imaged in the blood pool of mice several hours after injection using MPI. This finding is supported by magnetic particle spectroscopy performed to quantify the iron concentration in blood samples extracted from the mice 3 and 24 h after injection of SPIO-loaded RBCs. Based on these results, new MPI applications can be envisioned, such as permanent 3D real-time visualization of the vessel tree during interventional procedures, bleeding monitoring after stroke, or long-term monitoring and treatment control of cardiovascular diseases.

Implementing Multidisciplinary and Multi-Zonal Applications Using MPI

NASA Technical Reports Server (NTRS)

Fineberg, Samuel A.

1995-01-01

Multidisciplinary and multi-zonal applications are an important class of applications in the area of Computational Aerosciences. In these codes, two or more distinct parallel programs or copies of a single program are utilized to model a single problem. To support such applications, it is common to use a programming model where a program is divided into several single program multiple data stream (SPMD) applications, each of which solves the equations for a single physical discipline or grid zone. These SPMD applications are then bound together to form a single multidisciplinary or multi-zonal program in which the constituent parts communicate via point-to-point message passing routines. Unfortunately, simple message passing models, like Intel's NX library, only allow point-to-point and global communication within a single system-defined partition. This makes implementation of these applications quite difficult, if not impossible. In this report it is shown that the new Message Passing Interface (MPI) standard is a viable portable library for implementing the message passing portion of multidisciplinary applications. Further, with the extension of a portable loader, fully portable multidisciplinary application programs can be developed. Finally, the performance of MPI is compared to that of some native message passing libraries. This comparison shows that MPI can be implemented to deliver performance commensurate with native message libraries.

Determining post-test risk in a national sample of stress nuclear myocardial perfusion imaging reports: Implications for natural language processing tools.

PubMed

Levy, Andrew E; Shah, Nishant R; Matheny, Michael E; Reeves, Ruth M; Gobbel, Glenn T; Bradley, Steven M

2018-04-25

Reporting standards promote clarity and consistency of stress myocardial perfusion imaging (MPI) reports, but do not require an assessment of post-test risk. Natural Language Processing (NLP) tools could potentially help estimate this risk, yet it is unknown whether reports contain adequate descriptive data to use NLP. Among VA patients who underwent stress MPI and coronary angiography between January 1, 2009 and December 31, 2011, 99 stress test reports were randomly selected for analysis. Two reviewers independently categorized each report for the presence of critical data elements essential to describing post-test ischemic risk. Few stress MPI reports provided a formal assessment of post-test risk within the impression section (3%) or the entire document (4%). In most cases, risk was determinable by combining critical data elements (74% impression, 98% whole). If ischemic risk was not determinable (25% impression, 2% whole), inadequate description of systolic function (9% impression, 1% whole) and inadequate description of ischemia (5% impression, 1% whole) were most commonly implicated. Post-test ischemic risk was determinable but rarely reported in this sample of stress MPI reports. This supports the potential use of NLP to help clarify risk. Further study of NLP in this context is needed.

Recent developments in bend-insensitive and ultra-bend-insensitive fibers

NASA Astrophysics Data System (ADS)

Boivin, David; de Montmorillon, Louis-Anne; Provost, Lionel; Montaigne, Nelly; Gooijer, Frans; Aldea, Eugen; Jensma, Jaap; Sillard, Pierre

2010-02-01

Designed to overcome the limitations in case of extreme bending conditions, Bend- and Ultra-Bend-Insensitive Fibers (BIFs and UBIFs) appear as ideal solutions for use in FTTH networks and in components, pigtails or patch-cords for ever demanding applications such as military or sensing. Recently, however, questions have been raised concerning the Multi-Path-Interference (MPI) levels in these fibers. Indeed, they are potentially subject to interferences between the fundamental mode and the higher-order mode that is also bend resistant. This MPI is generated because of discrete discontinuities such as staples, bends and splices/connections that occur on distance scales that become comparable to the laser coherent length. In this paper, we will demonstrate the high MPI tolerance of all-solid single-trench-assisted BIFs and UBIFs. We will present the first comprehensive study combining theoretical and experimental points of view to quantify the impact of fusion splices on coherent MPI. To be complete, results for mechanical splices will also be reported. Finally, we will show how the single-trench- assisted concept combined with the versatile PCVD process allows to tightly control the distributions of fibers characteristics. Such controls are needed to massively produce BIFs and to meet the more stringent specifications of the UBIFs.

Toward Abstracting the Communication Intent in Applications to Improve Portability and Productivity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mintz, Tiffany M; Hernandez, Oscar R; Kartsaklis, Christos

Programming with communication libraries such as the Message Passing Interface (MPI) obscures the high-level intent of the communication in an application and makes static communication analysis difficult to do. Compilers are unaware of communication libraries specifics, leading to the exclusion of communication patterns from any automated analysis and optimizations. To overcome this, communication patterns can be expressed at higher-levels of abstraction and incrementally added to existing MPI applications. In this paper, we propose the use of directives to clearly express the communication intent of an application in a way that is not specific to a given communication library. Our communicationmore » directives allow programmers to express communication among processes in a portable way, giving hints to the compiler on regions of computations that can be overlapped with communication and relaxing communication constraints on the ordering, completion and synchronization of the communication imposed by specific libraries such as MPI. The directives can then be translated by the compiler into message passing calls that efficiently implement the intended pattern and be targeted to multiple communication libraries. Thus far, we have used the directives to express point-to-point communication patterns in C, C++ and Fortran applications, and have translated them to MPI and SHMEM.« less

Atmospheric corrosion performance of different steels in early exposure in the coastal area region West Java, Indonesia

NASA Astrophysics Data System (ADS)

Nuraini, Lutviasari; Prifiharni, Siska; Priyotomo, Gadang; Sundjono, Gunawan, Hadi; Purawiardi, Ibrahim

2018-05-01

The performance of carbon steel, galvanized steel and aluminium after one month exposed in the atmospheric coastal area, which is in Limbangan and Karangsong Beach, West Java, Indonesia was evaluated. The corrosion rate was determined by weight loss method and the morphology of the steel after exposed was observed by Scanning Electron Microscopy(SEM)/Energy Dispersive X-Ray Analysis(EDX). The site was monitored to determine the chloride content in the marine atmosphere. Then, the corrosion products formed at carbon steel were characterized by X-Ray diffraction (XRD). The result showed the aggressively corrosion in Karangsong beach, indicated from the corrosion rate of carbon steel, galvanized steel and aluminium were 38.514 mpy; 4.7860 mpy and 0.5181 mpy, respectively. While in Limbangan Beach the corrosion rate of specimen carbon steel, galvanized steel and aluminium were 3.339; 0.219 and 0.166 mpy, respectively. The chloride content was found to be the main factor that influences in the atmospheric corrosion process in this area. Chloride content accumulated in Karangsong and Limbangan was 497 mg/m2.day and 117 mg/m2.day, respectively. The XRD Analysis on each carbon steel led to the characterization of a complex mixture of iron oxides phases.

High frequency QRS ECG predicts ischemic defects during myocardial perfusion imaging

NASA Technical Reports Server (NTRS)

2004-01-01

Changes in high frequency QRS components of the electrocardiogram (HF QRS ECG) (150-250 Hz) are more sensitive than changes in conventional ST segments for detecting myocardial ischemia. We investigated the accuracy of 12-lead HF QRS ECG in detecting ischemia during adenosine tetrofosmin myocardial perfusion imaging (MPI). 12-lead HF QRS ECG recordings were obtained from 45 patients before and during adenosine technetium-99 tetrofosmin MPI tests. Before the adenosine infusions, recordings of HF QRS were analyzed according to a morphological score that incorporated the number, type and location of reduced amplitude zones (RAZs) present in the 12 leads. During the adenosine infusions, recordings of HF QRS were analyzed according to the maximum percentage changes (in both the positive and negative directions) that occurred in root mean square (RMS) voltage amplitudes within the 12 leads. The best set of prospective HF QRS criteria had a sensitivity of 94% and a specificity of 83% for correctly identifying the MPI result. The sensitivity of simultaneous ST segment changes (18%) was significantly lower than that of any individual HF QRS criterion (P less than 0.00l). Analysis of 12-lead HF QRS ECG is highly sensitive and specific for detecting ischemic perfusion defects during adenosine MPI stress tests and significantly more sensitive than analysis of conventional ST segments.

High frequency QRS ECG predicts ischemic defects during myocardial perfusion imaging

NASA Technical Reports Server (NTRS)

Rahman, Atiar

2006-01-01

Background: Changes in high frequency QRS components of the electrocardiogram (HF QRS ECG) (150-250 Hz) are more sensitive than changes in conventional ST segments for detecting myocardial ischemia. We investigated the accuracy of 12-lead HF QRS ECG in detecting ischemia during adenosine tetrofosmin myocardial perfusion imaging (MPI). Methods and Results: 12-lead HF QRS ECG recordings were obtained from 45 patients before and during adenosine technetium-99 tetrofosmin MPI tests. Before the adenosine infusions, recordings of HF QRS were analyzed according to a morphological score that incorporated the number, type and location of reduced amplitude zones (RAZs) present in the 12 leads. During the adenosine infusions, recordings of HF QRS were analyzed according to the maximum percentage changes (in both the positive and negative directions) that occurred in root mean square (RMS) voltage amplitudes within the 12 leads. The best set of prospective HF QRS criteria had a sensitivity of 94% and a specificity of 83% for correctly identifying the MPI result. The sensitivity of simultaneous ST segment changes (18%) was significantly lower than that of any individual HF QRS criterion (P<0.001). Conclusions: Analysis of 12-lead HF QRS ECG is highly sensitive and specific for detecting ischemic perfusion defects during adenosine MPI stress tests and significantly more sensitive than analysis of conventional ST segments.

Fortran code for SU(3) lattice gauge theory with and without MPI checkerboard parallelization

NASA Astrophysics Data System (ADS)

Berg, Bernd A.; Wu, Hao

2012-10-01

We document plain Fortran and Fortran MPI checkerboard code for Markov chain Monte Carlo simulations of pure SU(3) lattice gauge theory with the Wilson action in D dimensions. The Fortran code uses periodic boundary conditions and is suitable for pedagogical purposes and small scale simulations. For the Fortran MPI code two geometries are covered: the usual torus with periodic boundary conditions and the double-layered torus as defined in the paper. Parallel computing is performed on checkerboards of sublattices, which partition the full lattice in one, two, and so on, up to D directions (depending on the parameters set). For updating, the Cabibbo-Marinari heatbath algorithm is used. We present validations and test runs of the code. Performance is reported for a number of currently used Fortran compilers and, when applicable, MPI versions. For the parallelized code, performance is studied as a function of the number of processors. Program summary Program title: STMC2LSU3MPI Catalogue identifier: AEMJ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEMJ_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 26666 No. of bytes in distributed program, including test data, etc.: 233126 Distribution format: tar.gz Programming language: Fortran 77 compatible with the use of Fortran 90/95 compilers, in part with MPI extensions. Computer: Any capable of compiling and executing Fortran 77 or Fortran 90/95, when needed with MPI extensions. Operating system: Red Hat Enterprise Linux Server 6.1 with OpenMPI + pgf77 11.8-0, Centos 5.3 with OpenMPI + gfortran 4.1.2, Cray XT4 with MPICH2 + pgf90 11.2-0. Has the code been vectorised or parallelized?: Yes, parallelized using MPI extensions. Number of processors used: 2 to 11664 RAM: 200 Mega bytes per process. Classification: 11.5. Nature of problem: Physics of pure SU(3) Quantum Field Theory (QFT). This is relevant for our understanding of Quantum Chromodynamics (QCD). It includes the glueball spectrum, topological properties and the deconfining phase transition of pure SU(3) QFT. For instance, Relativistic Heavy Ion Collision (RHIC) experiments at the Brookhaven National Laboratory provide evidence that quarks confined in hadrons undergo at high enough temperature and pressure a transition into a Quark-Gluon Plasma (QGP). Investigations of its thermodynamics in pure SU(3) QFT are of interest. Solution method: Markov Chain Monte Carlo (MCMC) simulations of SU(3) Lattice Gauge Theory (LGT) with the Wilson action. This is a regularization of pure SU(3) QFT on a hypercubic lattice, which allows approaching the continuum SU(3) QFT by means of Finite Size Scaling (FSS) studies. Specifically, we provide updating routines for the Cabibbo-Marinari heatbath with and without checkerboard parallelization. While the first is suitable for pedagogical purposes and small scale projects, the latter allows for efficient parallel processing. Targetting the geometry of RHIC experiments, we have implemented a Double-Layered Torus (DLT) lattice geometry, which has previously not been used in LGT MCMC simulations and enables inside and outside layers at distinct temperatures, the lower-temperature layer acting as the outside boundary for the higher-temperature layer, where the deconfinement transition goes on. Restrictions: The checkerboard partition of the lattice makes the development of measurement programs more tedious than is the case for an unpartitioned lattice. Presently, only one measurement routine for Polyakov loops is provided. Unusual features: We provide three different versions for the send/receive function of the MPI library, which work for different operating system +compiler +MPI combinations. This involves activating the correct row in the last three rows of our latmpi.par parameter file. The underlying reason is distinct buffer conventions. Running time: For a typical run using an Intel i7 processor, it takes (1.8-6) E-06 seconds to update one link of the lattice, depending on the compiler used. For example, if we do a simulation on a small (4 * 83) DLT lattice with a statistics of 221 sweeps (i.e., update the two lattice layers of 4 * (4 * 83) links each 221 times), the total CPU time needed can be 2 * 4 * (4 * 83) * 221 * 3 E-06 seconds = 1.7 minutes, where 2 — two layers of lattice 4 — four dimensions 83 * 4 — lattice size 221 — sweeps of updating 6 E-06 s mdash; average time to update one link variable. If we divide the job into 8 parallel processes, then the real time is (for negligible communication overhead) 1.7 mins / 8 = 0.2 mins.

Enhancing nurses' roles to improve quality and efficiency of non-medical cardiac stress tests.

PubMed

Bernhardt, Lizelle; Ross, Lisa; Greaves, Claire

Myocardial perfusion imaging (MPI) is a test that aids the diagnosis of coronary heart disease, of which pharmacological stress is a key component. An increase in demand had resulted in a 42 week waiting time for MPI in Leicester. This article looks at how implementing non-medically led stress tests reduced this waiting list. It discusses the obstacles involved and the measures needed to make the service a success.

Hybrid MPI+OpenMP Programming of an Overset CFD Solver and Performance Investigations

NASA Technical Reports Server (NTRS)

Djomehri, M. Jahed; Jin, Haoqiang H.; Biegel, Bryan (Technical Monitor)

2002-01-01

This report describes a two level parallelization of a Computational Fluid Dynamic (CFD) solver with multi-zone overset structured grids. The approach is based on a hybrid MPI+OpenMP programming model suitable for shared memory and clusters of shared memory machines. The performance investigations of the hybrid application on an SGI Origin2000 (O2K) machine is reported using medium and large scale test problems.

Indirect spectrophotometric determination of trace cyanide with cationic porphyrins.

PubMed

Ishii, H; Kohata, K

1991-05-01

Three highly sensitive methods for the determination of cyanide have been developed, based on the fact that the complexation of silver ions with three cationic porphyrins, 5,10,15,20-tetrakis-(1-methyl-2-pyridinio)porphine [T(2-MPy)P], 5,10,15,20-tetrakis(1-methyl-3-pyridinio)porphine [T(3-MPy)P] and 5,10,15,20-tetrakis(1-methyl-4-pyridinio)porphine [T(4-MPy)P], in alkaline media is inhibited by cyanide and the decrease in absorbance of the silver(II) complex is proportional to the cyanide concentration. Sensitivities of the procedures developed are 0.133, 0.126 and 0.234 ng/cm(2), respectively for an absorbance of 0.001. Cadmium(II), copper(II), mercury(II), zinc(II), iodide and sulfide interfere with the cyanide determination. One of the proposed methods was applied to the determination of cyanide in waste-water samples, with satisfactory results.

Potential Application of a Graphical Processing Unit to Parallel Computations in the NUBEAM Code

NASA Astrophysics Data System (ADS)

Payne, J.; McCune, D.; Prater, R.

2010-11-01

NUBEAM is a comprehensive computational Monte Carlo based model for neutral beam injection (NBI) in tokamaks. NUBEAM computes NBI-relevant profiles in tokamak plasmas by tracking the deposition and the slowing of fast ions. At the core of NUBEAM are vector calculations used to track fast ions. These calculations have recently been parallelized to run on MPI clusters. However, cost and interlink bandwidth limit the ability to fully parallelize NUBEAM on an MPI cluster. Recent implementation of double precision capabilities for Graphical Processing Units (GPUs) presents a cost effective and high performance alternative or complement to MPI computation. Commercially available graphics cards can achieve up to 672 GFLOPS double precision and can handle hundreds of thousands of threads. The ability to execute at least one thread per particle simultaneously could significantly reduce the execution time and the statistical noise of NUBEAM. Progress on implementation on a GPU will be presented.

Comparison of the oral and rectal mucosal and colonic serosal microcirculations of healthy, anesthetized horses.

PubMed

Kieffer, Philip J; Williams, Jarred M; Shepard, Molly K; Giguère, Steeve; Epstein, Kira L

2018-01-01

The objectives of the study were to: i) determine baseline microvascular perfusion indices (MPI) and assess their repeatability in healthy horses under general anesthesia, and ii) compare the MPIs of 3 microvascular beds (oral mucosa, colonic serosa, and rectal mucosa). Healthy adult horses were anesthetized and sidestream dark field microscopy was used to collect video loops of the oral mucosa, rectal mucosa, and colonic serosa under normotensive conditions without cardiovascular support drugs; videos were later analyzed to produce MPIs. Baseline MPI values were determined for each site, which included the total vessel density (TVD), perfused vessel density (PVD), portion perfused vessels (PPV), and microcirculatory flow index (MFI). Differences in MPIs between microvascular beds were not statistically significant. Repeatability of the measurements varied for each MPI. In particular, the site of sampling had a profound effect on the repeatability of the PPV measurements and should be considered in future studies.

Comparison of the oral and rectal mucosal and colonic serosal microcirculations of healthy, anesthetized horses

PubMed Central

Kieffer, Philip J.; Williams, Jarred M.; Shepard, Molly K.; Giguère, Steeve; Epstein, Kira L.

2018-01-01

The objectives of the study were to: i) determine baseline microvascular perfusion indices (MPI) and assess their repeatability in healthy horses under general anesthesia, and ii) compare the MPIs of 3 microvascular beds (oral mucosa, colonic serosa, and rectal mucosa). Healthy adult horses were anesthetized and sidestream dark field microscopy was used to collect video loops of the oral mucosa, rectal mucosa, and colonic serosa under normotensive conditions without cardiovascular support drugs; videos were later analyzed to produce MPIs. Baseline MPI values were determined for each site, which included the total vessel density (TVD), perfused vessel density (PVD), portion perfused vessels (PPV), and microcirculatory flow index (MFI). Differences in MPIs between microvascular beds were not statistically significant. Repeatability of the measurements varied for each MPI. In particular, the site of sampling had a profound effect on the repeatability of the PPV measurements and should be considered in future studies. PMID:29382969

Review of progress in magnetic particle inspection

NASA Astrophysics Data System (ADS)

Eisenmann, David J.; Enyart, Darrel; Lo, Chester; Brasche, Lisa

2014-02-01

Magnetic particle inspection (MPI) has been widely utilized for decades, and sees considerable use in the aerospace industry with a majority of the steel parts being inspected with MPI at some point in the lifecycle. Typical aircraft locations inspected are landing gear, engine components, attachment hardware, and doors. In spite of its numerous applications the method remains poorly understood, and there are many aspects of that method which would benefit from in-depth study. This shortcoming is due to the fact that MPI combines the complicated nature of electromagnetics, metallurgical material effects, fluid-particle motion dynamics, and physiological human factors into a single inspection. To promote understanding of the intricate method issues that affect sensitivity, or to assist with the revision of industry specifications and standards, research studies will be prioritized through the guidance of a panel of industry experts, using an approach which has worked successfully in the past to guide fluorescent penetrant inspection (FPI) research efforts.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Katti, Amogh; Di Fatta, Giuseppe; Naughton III, Thomas J

Future extreme-scale high-performance computing systems will be required to work under frequent component failures. The MPI Forum's User Level Failure Mitigation proposal has introduced an operation, MPI_Comm_shrink, to synchronize the alive processes on the list of failed processes, so that applications can continue to execute even in the presence of failures by adopting algorithm-based fault tolerance techniques. This MPI_Comm_shrink operation requires a fault tolerant failure detection and consensus algorithm. This paper presents and compares two novel failure detection and consensus algorithms. The proposed algorithms are based on Gossip protocols and are inherently fault-tolerant and scalable. The proposed algorithms were implementedmore » and tested using the Extreme-scale Simulator. The results show that in both algorithms the number of Gossip cycles to achieve global consensus scales logarithmically with system size. The second algorithm also shows better scalability in terms of memory and network bandwidth usage and a perfect synchronization in achieving global consensus.« less

NDL-v2.0: A new version of the numerical differentiation library for parallel architectures

NASA Astrophysics Data System (ADS)

Hadjidoukas, P. E.; Angelikopoulos, P.; Voglis, C.; Papageorgiou, D. G.; Lagaris, I. E.

2014-07-01

We present a new version of the numerical differentiation library (NDL) used for the numerical estimation of first and second order partial derivatives of a function by finite differencing. In this version we have restructured the serial implementation of the code so as to achieve optimal task-based parallelization. The pure shared-memory parallelization of the library has been based on the lightweight OpenMP tasking model allowing for the full extraction of the available parallelism and efficient scheduling of multiple concurrent library calls. On multicore clusters, parallelism is exploited by means of TORC, an MPI-based multi-threaded tasking library. The new MPI implementation of NDL provides optimal performance in terms of function calls and, furthermore, supports asynchronous execution of multiple library calls within legacy MPI programs. In addition, a Python interface has been implemented for all cases, exporting the functionality of our library to sequential Python codes. Catalog identifier: AEDG_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEDG_v2_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 63036 No. of bytes in distributed program, including test data, etc.: 801872 Distribution format: tar.gz Programming language: ANSI Fortran-77, ANSI C, Python. Computer: Distributed systems (clusters), shared memory systems. Operating system: Linux, Unix. Has the code been vectorized or parallelized?: Yes. RAM: The library uses O(N) internal storage, N being the dimension of the problem. It can use up to O(N2) internal storage for Hessian calculations, if a task throttling factor has not been set by the user. Classification: 4.9, 4.14, 6.5. Catalog identifier of previous version: AEDG_v1_0 Journal reference of previous version: Comput. Phys. Comm. 180(2009)1404 Does the new version supersede the previous version?: Yes Nature of problem: The numerical estimation of derivatives at several accuracy levels is a common requirement in many computational tasks, such as optimization, solution of nonlinear systems, and sensitivity analysis. For a large number of scientific and engineering applications, the underlying functions correspond to simulation codes for which analytical estimation of derivatives is difficult or almost impossible. A parallel implementation that exploits systems with multiple CPUs is very important for large scale and computationally expensive problems. Solution method: Finite differencing is used with a carefully chosen step that minimizes the sum of the truncation and round-off errors. The parallel versions employ both OpenMP and MPI libraries. Reasons for new version: The updated version was motivated by our endeavors to extend a parallel Bayesian uncertainty quantification framework [1], by incorporating higher order derivative information as in most state-of-the-art stochastic simulation methods such as Stochastic Newton MCMC [2] and Riemannian Manifold Hamiltonian MC [3]. The function evaluations are simulations with significant time-to-solution, which also varies with the input parameters such as in [1, 4]. The runtime of the N-body-type of problem changes considerably with the introduction of a longer cut-off between the bodies. In the first version of the library, the OpenMP-parallel subroutines spawn a new team of threads and distribute the function evaluations with a PARALLEL DO directive. This limits the functionality of the library as multiple concurrent calls require nested parallelism support from the OpenMP environment. Therefore, either their function evaluations will be serialized or processor oversubscription is likely to occur due to the increased number of OpenMP threads. In addition, the Hessian calculations include two explicit parallel regions that compute first the diagonal and then the off-diagonal elements of the array. Due to the barrier between the two regions, the parallelism of the calculations is not fully exploited. These issues have been addressed in the new version by first restructuring the serial code and then running the function evaluations in parallel using OpenMP tasks. Although the MPI-parallel implementation of the first version is capable of fully exploiting the task parallelism of the PNDL routines, it does not utilize the caching mechanism of the serial code and, therefore, performs some redundant function evaluations in the Hessian and Jacobian calculations. This can lead to: (a) higher execution times if the number of available processors is lower than the total number of tasks, and (b) significant energy consumption due to wasted processor cycles. Overcoming these drawbacks, which become critical as the time of a single function evaluation increases, was the primary goal of this new version. Due to the code restructure, the MPI-parallel implementation (and the OpenMP-parallel in accordance) avoids redundant calls, providing optimal performance in terms of the number of function evaluations. Another limitation of the library was that the library subroutines were collective and synchronous calls. In the new version, each MPI process can issue any number of subroutines for asynchronous execution. We introduce two library calls that provide global and local task synchronizations, similarly to the BARRIER and TASKWAIT directives of OpenMP. The new MPI-implementation is based on TORC, a new tasking library for multicore clusters [5-7]. TORC improves the portability of the software, as it relies exclusively on the POSIX-Threads and MPI programming interfaces. It allows MPI processes to utilize multiple worker threads, offering a hybrid programming and execution environment similar to MPI+OpenMP, in a completely transparent way. Finally, to further improve the usability of our software, a Python interface has been implemented on top of both the OpenMP and MPI versions of the library. This allows sequential Python codes to exploit shared and distributed memory systems. Summary of revisions: The revised code improves the performance of both parallel (OpenMP and MPI) implementations. The functionality and the user-interface of the MPI-parallel version have been extended to support the asynchronous execution of multiple PNDL calls, issued by one or multiple MPI processes. A new underlying tasking library increases portability and allows MPI processes to have multiple worker threads. For both implementations, an interface to the Python programming language has been added. Restrictions: The library uses only double precision arithmetic. The MPI implementation assumes the homogeneity of the execution environment provided by the operating system. Specifically, the processes of a single MPI application must have identical address space and a user function resides at the same virtual address. In addition, address space layout randomization should not be used for the application. Unusual features: The software takes into account bound constraints, in the sense that only feasible points are used to evaluate the derivatives, and given the level of the desired accuracy, the proper formula is automatically employed. Running time: Running time depends on the function's complexity. The test run took 23 ms for the serial distribution, 25 ms for the OpenMP with 2 threads, 53 ms and 1.01 s for the MPI parallel distribution using 2 threads and 2 processes respectively and yield-time for idle workers equal to 10 ms. References: [1] P. Angelikopoulos, C. Paradimitriou, P. Koumoutsakos, Bayesian uncertainty quantification and propagation in molecular dynamics simulations: a high performance computing framework, J. Chem. Phys 137 (14). [2] H.P. Flath, L.C. Wilcox, V. Akcelik, J. Hill, B. van Bloemen Waanders, O. Ghattas, Fast algorithms for Bayesian uncertainty quantification in large-scale linear inverse problems based on low-rank partial Hessian approximations, SIAM J. Sci. Comput. 33 (1) (2011) 407-432. [3] M. Girolami, B. Calderhead, Riemann manifold Langevin and Hamiltonian Monte Carlo methods, J. R. Stat. Soc. Ser. B (Stat. Methodol.) 73 (2) (2011) 123-214. [4] P. Angelikopoulos, C. Paradimitriou, P. Koumoutsakos, Data driven, predictive molecular dynamics for nanoscale flow simulations under uncertainty, J. Phys. Chem. B 117 (47) (2013) 14808-14816. [5] P.E. Hadjidoukas, E. Lappas, V.V. Dimakopoulos, A runtime library for platform-independent task parallelism, in: PDP, IEEE, 2012, pp. 229-236. [6] C. Voglis, P.E. Hadjidoukas, D.G. Papageorgiou, I. Lagaris, A parallel hybrid optimization algorithm for fitting interatomic potentials, Appl. Soft Comput. 13 (12) (2013) 4481-4492. [7] P.E. Hadjidoukas, C. Voglis, V.V. Dimakopoulos, I. Lagaris, D.G. Papageorgiou, Supporting adaptive and irregular parallelism for non-linear numerical optimization, Appl. Math. Comput. 231 (2014) 544-559.

On the reduced lifetime of nitrous oxide due to climate change induced acceleration of the Brewer-Dobson circulation as simulated by the MPI Earth System Model

NASA Astrophysics Data System (ADS)

Kracher, D.; Manzini, E.; Reick, C. H.; Schultz, M. G.; Stein, O.

2014-12-01

Greenhouse gas induced climate change will modify the physical conditions of the atmosphere. One of the projected changes is an acceleration of the Brewer-Dobson circulation in the stratosphere, as it has been shown in many model studies. This change in the stratospheric circulation consequently bears an effect on the transport and distribution of atmospheric components such as N2O. Since N2O is involved in ozone destruction, a modified distribution of N2O can be of importance for ozone chemistry. N2O is inert in the troposphere and decays only in the stratosphere. Thus, changes in the exchange between troposphere and stratosphere can also affect the stratospheric sink of N2O, and consequently its atmospheric lifetime. N2O is a potent greenhouse gas with a global warming potential of currently approximately 300 CO2-equivalents in a 100-year perspective. A faster decay in atmospheric N2O mixing ratios, i.e. a decreased atmospheric lifetime of N2O, will also reduce its global warming potential. In order to assess the impact of climate change on atmospheric circulation and implied effects on the distribution and lifetime of atmospheric N2O, we apply the Max Planck Institute Earth System Model, MPI-ESM. MPI-ESM consists of the atmospheric general circulation model ECHAM, the land surface model JSBACH, and MPIOM/HAMOCC representing ocean circulation and ocean biogeochemistry. Prognostic atmospheric N2O concentrations in MPI-ESM are determined by land N2O emissions, ocean-atmosphere N2O exchange and atmospheric tracer transport. As stratospheric chemistry is not explicitly represented in MPI-ESM, stratospheric decay rates of N2O are prescribed from a MACC MOZART simulation. Increasing surface temperatures and CO2 concentrations in the stratosphere impact atmospheric circulation differently. Thus, we conduct a series of transient runs with the atmospheric model of MPI-ESM to isolate different factors governing a shift in atmospheric circulation. From those transient simulations we diagnose decreasing tropospheric N2O concentrations, increased transport of N2O from the troposphere to the stratosphere, and increasing stratospheric decay of N2O leading to a reduction in atmospheric lifetime of N2O, in dependency to climate change evolution.

The influence of an atmospheric Two-Way coupled model system on the predictability of extratropical cyclones

NASA Astrophysics Data System (ADS)

Schuster, Mareike; Thürkow, Markus; Weiher, Stefan; Kirchner, Ingo; Ulbrich, Uwe; Will, Andreas

2016-04-01

A general bias of global atmosphere ocean models, and also of the MPI-ESM, is an under-representation of the high latitude cyclone activity and an overestimation of the mid latitude cyclone activity in the North Atlantic, thus representing the extra-tropical storm track too zonal. We will show, that this effect can be antagonized by applying an atmospheric Two-Way Coupling (TWC). In this study we present a newly developed Two-Way Coupled model system, which is based on the MPI-ESM, and show that it is able to capture the mean storm track location more accurate. It also influences the sub-decadal deterministic predictability of extra-tropical cyclones and shows significantly enhanced skill compared to the "uncoupled" MPI-ESM standalone system. This study evaluates a set of hindcast experiments performed with said Two-Way Coupled model system. The regional model COSMO CLM is Two-Way Coupled to the atmosphere of the global Max-Plack-Institute Earth System Model (MPI-ESM) and therefore integrates and exchanges the state of the atmosphere every 10 minutes (MPI-TWC-ESM). In the coupled source region (North Atlantic), mesoscale processes which are relevant for the formation and early-stage development of cyclones are expected to be better represented, and therefore influence the large scale dynamics of the target region (Europe). The database covers 102 "uncoupled" years and 102 Two-Way Coupled years of the recent climate (1960-2010). Results are validated against the ERA-Interim reanalysis. Besides the climatological point of view, the design of this single model ensemble allows for an analysis of the predictability of the first and second leadyears of the hindcasts. As a first step to understand the improved predictability of cyclones, we will show a detailed analysis of climatologies for specific cyclone categories, sorted by season and region. Especially for cyclones affecting Europe, the TWC is capable to counteract the AOGCM's biases in the North Atlantic. Also, cyclones which are generated in the northern North Atlantic and the Labrador Sea are to an extraordinary extent underestimated in the "uncoupled" MPI-ESM - for the latter region the TWC can balance this shortcoming. In the Northern Hemisphere annual mean statistics the TWC does not change the distribution of the strength of cyclones, but it changes the distribution of the lifetime of cyclones.

Using WEED to simulate the global wetland distribution in a ESM

NASA Astrophysics Data System (ADS)

Stacke, Tobias; Hagemann, Stefan

2016-04-01

Lakes and wetlands are an important land surface feature. In terms of hydrology, they regulate river discharge, mitigate flood events and constitute a significant surface water storage. Considering physical processes, they link the surface water and energy balances by altering the separation of incoming energy into sensible and latent heat fluxes. Finally, they impact biogeochemical processes and may act as carbon sinks or sources. Most global hydrology and climate models regard wetland extent and properties as constant in time. However, to study interactions between wetlands and different states of climate, it is necessary to implement surface water bodies (thereafter referred to as wetlands) with dynamical behavior into these models. Besides an improved representation of geophysical feedbacks between wetlands, land surface and atmosphere, a dynamical wetland scheme could also provide estimates of soil wetness as input for biogeochemical models, which are used to compute methane production in wetlands. Recently, a model for the representation of wetland extent dynamics (WEED) was developed as part of the hydrology model (MPI-HM) of the Max-Planck-Institute for Meteorology (MPI-M). The WEED scheme computes wetland extent in agreement with the range of observations for the high northern latitudes. It simulates a realistic seasonal cycle which shows sensitivity to northern snow-melt as well as rainy seasons in the tropics. Furthermore, flood peaks in river discharge are mitigated. However, the WEED scheme overestimates wetland extent in the Tropics which might be related to the MPI-HM's simplified potential evapotranspiration computation. In order to overcome this limitation, the WEED scheme is implemented into the MPI-M's land surface model JSBACH. Thus, not only its effect on water fluxes can be investigated but also its impact on the energy cycle, which is not included in the MPI-HM. Furthermore, it will be possible to analyze the physical effects of wetlands in a coupled land-atmosphere simulation. First simulations with JSBACH-WEED show results similar to the MPI-HM simulations. As the next step, the scheme is modified to account for energy cycle relevant issues such as the dynamical alteration of surface albedo as well as the allocation of appropriate thermal properties to the wetlands. In our presentation, we will give an overview on the functionality of the WEED scheme and the effect of wetlands in coupled land-atmosphere simulations.

Advances in Parallel Computing and Databases for Digital Pathology in Cancer Research

DTIC Science & Technology

2016-11-13

these technologies and how we have used them in the past. We are interested in learning more about the needs of clinical pathologists as we continue to...such as image processing and correlation. Further, High Performance Computing (HPC) paradigms such as the Message Passing Interface (MPI) have been...Defense for Research and Engineering. such as pMatlab [4], or bcMPI [5] can significantly reduce the need for deep knowledge of parallel computing. In

A comprehensive study of MPI parallelism in three-dimensional discrete element method (DEM) simulation of complex-shaped granular particles

NASA Astrophysics Data System (ADS)

Yan, Beichuan; Regueiro, Richard A.

2018-02-01

A three-dimensional (3D) DEM code for simulating complex-shaped granular particles is parallelized using message-passing interface (MPI). The concepts of link-block, ghost/border layer, and migration layer are put forward for design of the parallel algorithm, and theoretical scalability function of 3-D DEM scalability and memory usage is derived. Many performance-critical implementation details are managed optimally to achieve high performance and scalability, such as: minimizing communication overhead, maintaining dynamic load balance, handling particle migrations across block borders, transmitting C++ dynamic objects of particles between MPI processes efficiently, eliminating redundant contact information between adjacent MPI processes. The code executes on multiple US Department of Defense (DoD) supercomputers and tests up to 2048 compute nodes for simulating 10 million three-axis ellipsoidal particles. Performance analyses of the code including speedup, efficiency, scalability, and granularity across five orders of magnitude of simulation scale (number of particles) are provided, and they demonstrate high speedup and excellent scalability. It is also discovered that communication time is a decreasing function of the number of compute nodes in strong scaling measurements. The code's capability of simulating a large number of complex-shaped particles on modern supercomputers will be of value in both laboratory studies on micromechanical properties of granular materials and many realistic engineering applications involving granular materials.

DISP: Optimizations towards Scalable MPI Startup

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fu, Huansong; Pophale, Swaroop S; Gorentla Venkata, Manjunath

2016-01-01

Despite the popularity of MPI for high performance computing, the startup of MPI programs faces a scalability challenge as both the execution time and memory consumption increase drastically at scale. We have examined this problem using the collective modules of Cheetah and Tuned in Open MPI as representative implementations. Previous improvements for collectives have focused on algorithmic advances and hardware off-load. In this paper, we examine the startup cost of the collective module within a communicator and explore various techniques to improve its efficiency and scalability. Accordingly, we have developed a new scalable startup scheme with three internal techniques, namelymore » Delayed Initialization, Module Sharing and Prediction-based Topology Setup (DISP). Our DISP scheme greatly benefits the collective initialization of the Cheetah module. At the same time, it helps boost the performance of non-collective initialization in the Tuned module. We evaluate the performance of our implementation on Titan supercomputer at ORNL with up to 4096 processes. The results show that our delayed initialization can speed up the startup of Tuned and Cheetah by an average of 32.0% and 29.2%, respectively, our module sharing can reduce the memory consumption of Tuned and Cheetah by up to 24.1% and 83.5%, respectively, and our prediction-based topology setup can speed up the startup of Cheetah by up to 80%.« less

MPIRUN: A Portable Loader for Multidisciplinary and Multi-Zonal Applications

NASA Technical Reports Server (NTRS)

Fineberg, Samuel A.; Woodrow, Thomas S. (Technical Monitor)

1994-01-01

Multidisciplinary and multi-zonal applications are an important class of applications in the area of Computational Aerosciences. In these codes, two or more distinct parallel programs or copies of a single program are utilized to model a single problem. To support such applications, it is common to use a programming model where a program is divided into several single program multiple data stream (SPMD) applications, each of which solves the equations for a single physical discipline or grid zone. These SPMD applications are then bound together to form a single multidisciplinary or multi-zonal program in which the constituent parts communicate via point-to-point message passing routines. One method for implementing the message passing portion of these codes is with the new Message Passing Interface (MPI) standard. Unfortunately, this standard only specifies the message passing portion of an application, but does not specify any portable mechanisms for loading an application. MPIRUN was developed to provide a portable means for loading MPI programs, and was specifically targeted at multidisciplinary and multi-zonal applications. Programs using MPIRUN for loading and MPI for message passing are then portable between all machines supported by MPIRUN. MPIRUN is currently implemented for the Intel iPSC/860, TMC CM5, IBM SP-1 and SP-2, Intel Paragon, and workstation clusters. Further, MPIRUN is designed to be simple enough to port easily to any system supporting MPI.

Comparison of conventional and cadmium-zinc-telluride single-photon emission computed tomography for analysis of thallium-201 myocardial perfusion imaging: an exploratory study in normal databases for different ethnicities.

PubMed

Ishihara, Masaru; Onoguchi, Masahisa; Taniguchi, Yasuyo; Shibutani, Takayuki

2017-12-01

The aim of this study was to clarify the differences in thallium-201-chloride (thallium-201) myocardial perfusion imaging (MPI) scans evaluated by conventional anger-type single-photon emission computed tomography (conventional SPECT) versus cadmium-zinc-telluride SPECT (CZT SPECT) imaging in normal databases for different ethnic groups. MPI scans from 81 consecutive Japanese patients were examined using conventional SPECT and CZT SPECT and analyzed with the pre-installed quantitative perfusion SPECT (QPS) software. We compared the summed stress score (SSS), summed rest score (SRS), and summed difference score (SDS) for the two SPECT devices. For a normal MPI reference, we usually use Japanese databases for MPI created by the Japanese Society of Nuclear Medicine, which can be used with conventional SPECT but not with CZT SPECT. In this study, we used new Japanese normal databases constructed in our institution to compare conventional and CZT SPECT. Compared with conventional SPECT, CZT SPECT showed lower SSS (p < 0.001), SRS (p = 0.001), and SDS (p = 0.189) using the pre-installed SPECT database. In contrast, CZT SPECT showed no significant difference from conventional SPECT in QPS analysis using the normal databases from our institution. Myocardial perfusion analyses by CZT SPECT should be evaluated using normal databases based on the ethnic group being evaluated.

Dynamic CT perfusion imaging of the myocardium: a technical note on improvement of image quality.

PubMed

Muenzel, Daniela; Kabus, Sven; Gramer, Bettina; Leber, Vivian; Vembar, Mani; Schmitt, Holger; Wildgruber, Moritz; Fingerle, Alexander A; Rummeny, Ernst J; Huber, Armin; Noël, Peter B

2013-01-01

To improve image and diagnostic quality in dynamic CT myocardial perfusion imaging (MPI) by using motion compensation and a spatio-temporal filter. Dynamic CT MPI was performed using a 256-slice multidetector computed tomography scanner (MDCT). Data from two different patients-with and without myocardial perfusion defects-were evaluated to illustrate potential improvements for MPI (institutional review board approved). Three datasets for each patient were generated: (i) original data (ii) motion compensated data and (iii) motion compensated data with spatio-temporal filtering performed. In addition to the visual assessment of the tomographic slices, noise and contrast-to-noise-ratio (CNR) were measured for all data. Perfusion analysis was performed using time-density curves with regions-of-interest (ROI) placed in normal and hypoperfused myocardium. Precision in definition of normal and hypoperfused areas was determined in corresponding coloured perfusion maps. The use of motion compensation followed by spatio-temporal filtering resulted in better alignment of the cardiac volumes over time leading to a more consistent perfusion quantification and improved detection of the extend of perfusion defects. Additionally image noise was reduced by 78.5%, with CNR improvements by a factor of 4.7. The average effective radiation dose estimate was 7.1±1.1 mSv. The use of motion compensation and spatio-temporal smoothing will result in improved quantification of dynamic CT MPI using a latest generation CT scanner.

A comparison of echocardiographic variables of right ventricular function with exercise capacity after bosentan treatment in patients with pulmonary arterial hypertension: Results from a multicenter, prospective, cohort study.

PubMed

Kim, Hyungseop; Bae Lee, Jin; Park, Jae-Hyeong; Yoo, Byung-Su; Son, Jang-Won; Yang, Dong Heon; Lee, Bong-Ryeol

2017-01-01

Bosentan reduces pulmonary arterial pressure and improves exercise capacity in patients with pulmonary arterial hypertension (PAH). However, there are limited data regarding the extent to which the changes in echocardiographic variables reflect improvements in exercise capacity. We aimed to assess the improvement of echocardiographic variables and exercise capacity after 6 months of bosentan treatment for PAH. We performed a prospective study from June 2012 to June 2015 in seven participating medical centers. Echocardiography, including tissue Doppler imaging (TDI) and the 6-minute walk test distance (6MWD), was performed at baseline and after 6 months of bosentan treatment. We analyzed 19 patients with PAH: seven with congenital shunt, six with collagen vascular disease, and six with idiopathic PAH. After bosentan treatment, mean 6MWD increased by 50 meters. Right ventricle (RV) systolic pressure, tricuspid annular plane systolic excursion, myocardial performance index (MPI) derived from TDI (MPI-TDI) of RV and left ventricle (LV), RV fractional area change, and RV ejection fraction were significantly improved. In particular, the magnitude of RV and LV MPI-TDI showed good correlation with changes in the 6MWD. The magnitude of RV and LV MPI-TDI was strongly associated with improvements in exercise capacity. © 2016 Wiley Periodicals, Inc. J Clin Ultrasound 45:28-34, 2017. © 2016 Wiley Periodicals, Inc.

Experience of low-dose aminophylline use to relieve minor adverse effects of dipyridamole in patients undergoing stress myocardial perfusion imaging.

PubMed

Lin, Li-Fan; Cheng, Cheng-Yi; Hou, Cheng-Han; Ku, Chih-Hung; Tseng, Neng-Chuan; Shen, Daniel H Y

2014-06-01

Intravenous administration of aminophylline is widely adopted to reverse dipyridamole-related adverse effects (AEs) during stress myocardial perfusion imaging (MPI). The study aimed to investigate the efficacy of lower-dose aminophylline to relieve minor AEs. 2,250 consecutive patients undergoing dipyridamole-stressed MPI were enrolled. Information concerning AE occurrence and dosages of aminophylline was collected to evaluate the efficacy of lower-dose aminophylline. A logistic regression was used to determine independent predictors of dipyridamole-related AE occurrence. No severe AE was noted. Overall mild AE incidence was 37.0% (833/2,250 patients). Initial low-dose (25 mg) aminophylline relieved symptoms in 98.8% of patients with mild AEs (823/833 patients). An extra 25 mg aminophylline sufficed to reverse all such AEs. Mean body mass index (BMI) differed significantly between patients with and without any AE [25.6 vs 25.1 (P = .009)]. There was no significant difference between two subgroups in mean age, male gender prevalence, body height and weight, dipyridamole dose/BMI, or prevalence of significant perfusion defect(s) on MPI. Multivariable logistic regression demonstrated BMI remained the independent predictor of dipyridamole-related AE occurrence (odds ratio 1.028, 95% confidence interval 1.007-1.049, P = .01). Low-dose (≦50 mg, and usually 25 mg) aminophylline seems sufficient to relieve mild dipyridamole-related AEs during stress MPI.

Corrosion Inhibition of Cold-rolled Low Carbon Steel with Pulse Fiber Laser Ablation in Water

NASA Astrophysics Data System (ADS)

Chan, Sze Ney; Wong, Wai Yin; Walvekar, Rashmi; Kadhum, Abdul Amir H.; Khalid, Mohammad; Lim, Kean Long

2018-04-01

This study aims at the use of a fiber laser for modifying the surface properties of cold-rolled low carbon steel via a pulse laser ablation technique in water. The effect on the corrosion behavior of the fiber laser-treated metal surface was investigated in NaCl and HCl environments. Electrochemical tests showed significant improvement in the corrosion resistance of the laser-treated sample in NaCl, with an increase in open-circuit potential (OCP) from - 0.65 to - 0.60 V and an inhibition efficiency of 89.22% as obtained from the impedance study. Such improvement was less significant in an acidic environment. Lower corrosion rates of 20.9 mpy and 5.819 × 103 mpy were obtained for the laser-treated samples in neutral and acidic electrolytes, respectively, than the corrosion rates obtained for the as-received samples (33.2 mpy and 11.98 × 103 mpy). Morphological analysis indicated a passive film built by spherical grains of regular size on the metal surface after laser treatment. The corrosion inhibition effects in NaCl were evident by the nonexistence of the common corrosion products of lepidocrocite and crystalline structures that were seen on as-received samples; only polyhedral crystals with micrograins grown on them were seen covering the laser-treated surface. Therefore, the laser treatment using a fiber laser source improved the corrosion resistance of cold-rolled low carbon steel.

Biomedical imaging and therapy with physically and physiologically tailored magnetic nanoparticles

NASA Astrophysics Data System (ADS)

Khandhar, Amit Praful

Magnetic particle imaging (MPI) and magnetic fluid hyperthermia (MFH) are emerging imaging and therapy approaches that have the potential to improve diagnostic safety and disease management of heart disease and cancer - the number 1 and 2 leading causes of deaths in the United States. MPI promises real-time, tomographic and quantitative imaging of superparamagnetic iron oxide nanoparticle (SPION) tracers distributed in vivo, and is targeted to offer a safer angiography alternative for its first clinical application. MFH uses ac-fields to dissipate heat from SPIONs that can be delivered locally to promote hyperthermia therapy (~42°C) in cancer cells. Both technologies use safe radiofrequency magnetic fields to exploit the fundamental magnetic relaxation properties of superparamagnetic iron oxide nanoparticles (SPIONs), which must be tailored for optimal imaging in the case of MPI, and maximum hyperthermia potency in the case of MFH. Furthermore, the magnetic core and shell of SPIONs are both central to the optimization process; the shell, in particular, bridges the translational gap between the optimized core and its safe and effective use in the physiological environment. Unfortunately, existing SPIONs that were originally designed as MRI contrast agents lack the basic physical properties that enable the clinical translation of MPI and MFH. In this work, the core and shell of monodisperse SPIONs were optimized in concert to accomplish two equally important objectives: (1) biocompatibility, and (2) MPI and MFH efficacy of SPIONs in physiological environments. Critically, it was found that the physical and physiological responses of SPIONs are coupled, and impacting one can have consequences on the other. It was shown that the poly(ethylene glycol) (PEG)-based shell when properly optimized reduced protein adsorption to SPION surface and phagocytic uptake in macrophages - both prerequisites for designing long-circulating SPIONs. In MPI, tailoring the surface coating reduced protein adsorption and improved colloidal stability, which were critical in retaining the magnetization relaxation properties of the SPIONs. The improvements in surface coatings enabled the use of larger SPION cores (> 20 nm core diameter), which were used to demonstrate benchmark-imaging performance in some of the world's first MPI scanners at Philips Medical Imaging and University of California, Berkeley. In MFH, it was shown for the first time that optimization of heat loss from SPIONs (W/g) is possible by tailoring the core size and size distribution for the given ac-field conditions. Biodistribution and blood circulation studies in mice showed that SPIONs accumulated primarily in the liver and spleen with minimal renal involvement, and demonstrated gradual clearance. Circulation time was evaluated using the MPI signal detected over time in blood, which offered insight on the relevant circulation time for angiography applications. In comparison with carboxy-dextran coated ResovistRTM SPIONs, the PEG-coated SPIONs developed in this work circulated substantially longer; furthermore, reducing the hydrodynamic diameter showed a 4.5x improvement in blood half-life. The work presented in this thesis demonstrates that the combined effort in optimizing the core and shell properties of SPIONs enhances biocompatibility and efficacy, with the in vivo studies providing critical feedback on the success (or failure) of the optimization process. Future work will entail designing functionalized SPIONs for targeting specific disease sites, which will further enable the molecular level diagnosis and therapy of diseases.

Deep Learning for Prediction of Obstructive Disease From Fast Myocardial Perfusion SPECT: A Multicenter Study.

PubMed

Betancur, Julian; Commandeur, Frederic; Motlagh, Mahsaw; Sharir, Tali; Einstein, Andrew J; Bokhari, Sabahat; Fish, Mathews B; Ruddy, Terrence D; Kaufmann, Philipp; Sinusas, Albert J; Miller, Edward J; Bateman, Timothy M; Dorbala, Sharmila; Di Carli, Marcelo; Germano, Guido; Otaki, Yuka; Tamarappoo, Balaji K; Dey, Damini; Berman, Daniel S; Slomka, Piotr J

2018-03-12

The study evaluated the automatic prediction of obstructive disease from myocardial perfusion imaging (MPI) by deep learning as compared with total perfusion deficit (TPD). Deep convolutional neural networks trained with a large multicenter population may provide improved prediction of per-patient and per-vessel coronary artery disease from single-photon emission computed tomography MPI. A total of 1,638 patients (67% men) without known coronary artery disease, undergoing stress 99m Tc-sestamibi or tetrofosmin MPI with new generation solid-state scanners in 9 different sites, with invasive coronary angiography performed within 6 months of MPI, were studied. Obstructive disease was defined as ≥70% narrowing of coronary arteries (≥50% for left main artery). Left ventricular myocardium was segmented using clinical nuclear cardiology software and verified by an expert reader. Stress TPD was computed using sex- and camera-specific normal limits. Deep learning was trained using raw and quantitative polar maps and evaluated for prediction of obstructive stenosis in a stratified 10-fold cross-validation procedure. A total of 1,018 (62%) patients and 1,797 of 4,914 (37%) arteries had obstructive disease. Area under the receiver-operating characteristic curve for disease prediction by deep learning was higher than for TPD (per patient: 0.80 vs. 0.78; per vessel: 0.76 vs. 0.73: p < 0.01). With deep learning threshold set to the same specificity as TPD, per-patient sensitivity improved from 79.8% (TPD) to 82.3% (deep learning) (p < 0.05), and per-vessel sensitivity improved from 64.4% (TPD) to 69.8% (deep learning) (p < 0.01). Deep learning has the potential to improve automatic interpretation of MPI as compared with current clinical methods. Copyright © 2018 American College of Cardiology Foundation. Published by Elsevier Inc. All rights reserved.

Usefulness for Predicting Cardiac Events After Orthotopic Liver Transplantation of Myocardial Perfusion Imaging and Dobutamine Stress Echocardiography Preoperatively.

PubMed

Snipelisky, David; Ray, Jordan; Vallabhajosyula, Saraschandra; Matcha, Gautam; Squier, Samuel; Lewis, Jacob; Holliday, Rex; Aggarwal, Niti; Askew, J Wells; Shapiro, Brian; Anavekar, Nandan

2017-04-01

Patients undergoing orthotopic liver transplantation have high rates of cardiac morbidity and mortality. Although guidelines recommend noninvasive stress testing as part of the preoperative evaluation, little data have evaluated clinical outcomes following orthotopic liver transplantation. A retrospective study at 2 high-volume liver transplantation centers was performed. All patients undergoing noninvasive stress testing (myocardial perfusion imaging [MPI] or dobutamine stress echocardiography [DSE]) over a 5-year period were included. Descriptive analyses, including clinical outcomes and perioperative and postoperative ischemic events, were performed. Comparisons were made between subsets of patients within each stress modality based on abnormal versus normal results. A total of 506 patients were included, of which 343 underwent DSE and 163 MPI. Few patients had abnormal results, with 19 (5.5%) in the DSE group and 13 (8%) in the MPI group. Perioperative and postoperative cardiac complications were low (n = 20, 5.8% and n = 3, 0.9% in DSE group and n = 15, 9.2% and n = 3, 1.8% in MPI group). Comparisons between abnormal versus normal findings showed a trend toward periprocedural cardiac complications in the abnormal DSE group (n = 3, 15.8% vs n = 17, 5.25%; p = 0.09) with no difference in 6-month postprocedural complications (n = 0 vs n = 3, 0.9%; p = 1.0). In the MPI group, a trend toward periprocedural ischemic complications (n = 3, 23.1% vs n = 12, 8%; p = 0.1) was noted with no difference in 6-month postprocedural complications (n = 0 vs n = 3, 2%; p = 1.0). In conclusion, our study found a significantly lower than reported cardiac event rate. In addition, it demonstrated that ischemic cardiac events are uncommon in patients with normal stress testing. Copyright © 2017 Elsevier Inc. All rights reserved.

The Effect of Higher Than Recommended Protein Feedings Post-Exercise on Recovery Following Downhill Running in Masters Triathletes.

PubMed

Doering, Thomas M; Reaburn, Peter R; Borges, Nattai R; Cox, Gregory R; Jenkins, David G

2017-02-01

Following exercise-induced muscle damage (EIMD), masters athletes take longer to recover than younger athletes. The purpose of this study was to determine the effect of higher than recommended postexercise protein feedings on the recovery of knee extensor peak isometric torque (PIT), perceptions of recovery, and cycling time trial (TT) performance following EIMD in masters triathletes. Eight masters triathletes (52 ± 2 y, V̇O 2max , 51.8 ± 4.2 ml•kg -1 •min -1 ) completed two trials separated by seven days in a randomized, doubleblind, crossover study. Trials consisted of morning PIT testing and a 30-min downhill run followed by an eight-hour recovery. During recovery, a moderate (MPI; 0.3 g•kg -1 •bolus -1 ) or high (0.6 g•kg -1 •bolus -1 ) protein intake (HPI) was consumed in three bolus feedings at two hour intervals commencing immediately postexercise. PIT testing and a 7 kJ•kg -1 cycling TT were completed postintervention. Perceptions of recovery were assessed pre- and postexercise. The HPI did not significantly improve recovery compared with MPI (p > .05). However, comparison of within-treatment change shows the HPI provided a moderate beneficial effect (d = 0.66), attenuating the loss of afternoon PIT (-3.6%, d = 0.09) compared with the MPI (-8.6%, d = 0.24). The HPI provided a large beneficial effect (d = 0.83), reducing perceived fatigue over the eight-hour recovery (d = 1.25) compared with the MPI (d = 0.22). Despite these effects, cycling performance was unchanged (HPI = 2395 ± 297 s vs. MPI = 2369 ± 278 s; d = 0.09). In conclusion, doubling the recommended postexercise protein intake did not significantly improve recovery in masters athletes; however, HPI provided moderate to large beneficial effects on recovery that may be meaningful following EIMD.

WImpiBLAST: web interface for mpiBLAST to help biologists perform large-scale annotation using high performance computing.

PubMed

Sharma, Parichit; Mantri, Shrikant S

2014-01-01

The function of a newly sequenced gene can be discovered by determining its sequence homology with known proteins. BLAST is the most extensively used sequence analysis program for sequence similarity search in large databases of sequences. With the advent of next generation sequencing technologies it has now become possible to study genes and their expression at a genome-wide scale through RNA-seq and metagenome sequencing experiments. Functional annotation of all the genes is done by sequence similarity search against multiple protein databases. This annotation task is computationally very intensive and can take days to obtain complete results. The program mpiBLAST, an open-source parallelization of BLAST that achieves superlinear speedup, can be used to accelerate large-scale annotation by using supercomputers and high performance computing (HPC) clusters. Although many parallel bioinformatics applications using the Message Passing Interface (MPI) are available in the public domain, researchers are reluctant to use them due to lack of expertise in the Linux command line and relevant programming experience. With these limitations, it becomes difficult for biologists to use mpiBLAST for accelerating annotation. No web interface is available in the open-source domain for mpiBLAST. We have developed WImpiBLAST, a user-friendly open-source web interface for parallel BLAST searches. It is implemented in Struts 1.3 using a Java backbone and runs atop the open-source Apache Tomcat Server. WImpiBLAST supports script creation and job submission features and also provides a robust job management interface for system administrators. It combines script creation and modification features with job monitoring and management through the Torque resource manager on a Linux-based HPC cluster. Use case information highlights the acceleration of annotation analysis achieved by using WImpiBLAST. Here, we describe the WImpiBLAST web interface features and architecture, explain design decisions, describe workflows and provide a detailed analysis.

Prognostic value of stress myocardial perfusion positron emission tomography: results from a multicenter observational registry.

PubMed

Dorbala, Sharmila; Di Carli, Marcelo F; Beanlands, Rob S; Merhige, Michael E; Williams, Brent A; Veledar, Emir; Chow, Benjamin J W; Min, James K; Pencina, Michael J; Berman, Daniel S; Shaw, Leslee J

2013-01-15

The primary objective of this multicenter registry was to study the prognostic value of positron emission tomography (PET) myocardial perfusion imaging (MPI) and the improved classification of risk in a large cohort of patients with suspected or known coronary artery disease (CAD). Limited prognostic data are available for MPI with PET. A total of 7,061 patients from 4 centers underwent a clinically indicated rest/stress rubidium-82 PET MPI, with a median follow-up of 2.2 years. The primary outcome of this study was cardiac death (n = 169), and the secondary outcome was all-cause death (n = 570). Net reclassification improvement (NRI) and integrated discrimination analyses were performed. Risk-adjusted hazard of cardiac death increased with each 10% myocardium abnormal with mildly, moderately, or severely abnormal stress PET (hazard ratio [HR]: 2.3 [95% CI: 1.4 to 3.8; p = 0.001], HR: 4.2 [95% CI: 2.3 to 7.5; p < 0.001], and HR: 4.9 [95% CI: 2.5 to 9.6; p < 0.0001], respectively [normal MPI: referent]). Addition of percent myocardium ischemic and percent myocardium scarred to clinical information (age, female sex, body mass index, history of hypertension, diabetes, dyslipidemia, smoking, angina, beta-blocker use, prior revascularization, and resting heart rate) improved the model performance (C-statistic 0.805 [95% CI: 0.772 to 0.838] to 0.839 [95% CI: 0.809 to 0.869]) and risk reclassification for cardiac death (NRI 0.116 [95% CI: 0.021 to 0.210]), with smaller improvements in risk assessment for all-cause death. In patients with known or suspected CAD, the extent and severity of ischemia and scar on PET MPI provided powerful and incremental risk estimates of cardiac death and all-cause death compared with traditional coronary risk factors. Copyright © 2013 American College of Cardiology Foundation. Published by Elsevier Inc. All rights reserved.

Literature-based compound profiling: application to toxicogenomics.

PubMed

Frijters, Raoul; Verhoeven, Stefan; Alkema, Wynand; van Schaik, René; Polman, Jan

2007-11-01

To reduce continuously increasing costs in drug development, adverse effects of drugs need to be detected as early as possible in the process. In recent years, compound-induced gene expression profiling methodologies have been developed to assess compound toxicity, including Gene Ontology term and pathway over-representation analyses. The objective of this study was to introduce an additional approach, in which literature information is used for compound profiling to evaluate compound toxicity and mode of toxicity. Gene annotations were built by text mining in Medline abstracts for retrieval of co-publications between genes, pathology terms, biological processes and pathways. This literature information was used to generate compound-specific keyword fingerprints, representing over-represented keywords calculated in a set of regulated genes after compound administration. To see whether keyword fingerprints can be used for assessment of compound toxicity, we analyzed microarray data sets of rat liver treated with 11 hepatotoxicants. Analysis of keyword fingerprints of two genotoxic carcinogens, two nongenotoxic carcinogens, two peroxisome proliferators and two randomly generated gene sets, showed that each compound produced a specific keyword fingerprint that correlated with the experimentally observed histopathological events induced by the individual compounds. By contrast, the random sets produced a flat aspecific keyword profile, indicating that the fingerprints induced by the compounds reflect biological events rather than random noise. A more detailed analysis of the keyword profiles of diethylhexylphthalate, dimethylnitrosamine and methapyrilene (MPy) showed that the differences in the keyword fingerprints of these three compounds are based upon known distinct modes of action. Visualization of MPy-linked keywords and MPy-induced genes in a literature network enabled us to construct a mode of toxicity proposal for MPy, which is in agreement with known effects of MPy in literature. Compound keyword fingerprinting based on information retrieved from literature is a powerful approach for compound profiling, allowing evaluation of compound toxicity and analysis of the mode of action.

WImpiBLAST: Web Interface for mpiBLAST to Help Biologists Perform Large-Scale Annotation Using High Performance Computing

PubMed Central

Sharma, Parichit; Mantri, Shrikant S.

2014-01-01

The function of a newly sequenced gene can be discovered by determining its sequence homology with known proteins. BLAST is the most extensively used sequence analysis program for sequence similarity search in large databases of sequences. With the advent of next generation sequencing technologies it has now become possible to study genes and their expression at a genome-wide scale through RNA-seq and metagenome sequencing experiments. Functional annotation of all the genes is done by sequence similarity search against multiple protein databases. This annotation task is computationally very intensive and can take days to obtain complete results. The program mpiBLAST, an open-source parallelization of BLAST that achieves superlinear speedup, can be used to accelerate large-scale annotation by using supercomputers and high performance computing (HPC) clusters. Although many parallel bioinformatics applications using the Message Passing Interface (MPI) are available in the public domain, researchers are reluctant to use them due to lack of expertise in the Linux command line and relevant programming experience. With these limitations, it becomes difficult for biologists to use mpiBLAST for accelerating annotation. No web interface is available in the open-source domain for mpiBLAST. We have developed WImpiBLAST, a user-friendly open-source web interface for parallel BLAST searches. It is implemented in Struts 1.3 using a Java backbone and runs atop the open-source Apache Tomcat Server. WImpiBLAST supports script creation and job submission features and also provides a robust job management interface for system administrators. It combines script creation and modification features with job monitoring and management through the Torque resource manager on a Linux-based HPC cluster. Use case information highlights the acceleration of annotation analysis achieved by using WImpiBLAST. Here, we describe the WImpiBLAST web interface features and architecture, explain design decisions, describe workflows and provide a detailed analysis. PMID:24979410

Machine-learning model observer for detection and localization tasks in clinical SPECT-MPI

NASA Astrophysics Data System (ADS)

Parages, Felipe M.; O'Connor, J. Michael; Pretorius, P. Hendrik; Brankov, Jovan G.

2016-03-01

In this work we propose a machine-learning MO based on Naive-Bayes classification (NB-MO) for the diagnostic tasks of detection, localization and assessment of perfusion defects in clinical SPECT Myocardial Perfusion Imaging (MPI), with the goal of evaluating several image reconstruction methods used in clinical practice. NB-MO uses image features extracted from polar-maps in order to predict lesion detection, localization and severity scores given by human readers in a series of 3D SPECT-MPI. The population used to tune (i.e. train) the NB-MO consisted of simulated SPECT-MPI cases - divided into normals or with lesions in variable sizes and locations - reconstructed using filtered backprojection (FBP) method. An ensemble of five human specialists (physicians) read a subset of simulated reconstructed images, and assigned a perfusion score for each region of the left-ventricle (LV). Polar-maps generated from the simulated volumes along with their corresponding human scores were used to train five NB-MOs (one per human reader), which are subsequently applied (i.e. tested) on three sets of clinical SPECT-MPI polar maps, in order to predict human detection and localization scores. The clinical "testing" population comprises healthy individuals and patients suffering from coronary artery disease (CAD) in three possible regions, namely: LAD, LcX and RCA. Each clinical case was reconstructed using three reconstruction strategies, namely: FBP with no SC (i.e. scatter compensation), OSEM with Triple Energy Window (TEW) SC method, and OSEM with Effective Source Scatter Estimation (ESSE) SC. Alternative Free-Response (AFROC) analysis of perfusion scores shows that NB-MO predicts a higher human performance for scatter-compensated reconstructions, in agreement with what has been reported in published literature. These results suggest that NB-MO has good potential to generalize well to reconstruction methods not used during training, even for reasonably dissimilar datasets (i.e. simulated vs. clinical).

NAS Parallel Benchmarks. 2.4

NASA Technical Reports Server (NTRS)

VanderWijngaart, Rob; Biegel, Bryan A. (Technical Monitor)

2002-01-01

We describe a new problem size, called Class D, for the NAS Parallel Benchmarks (NPB), whose MPI source code implementation is being released as NPB 2.4. A brief rationale is given for how the new class is derived. We also describe the modifications made to the MPI (Message Passing Interface) implementation to allow the new class to be run on systems with 32-bit integers, and with moderate amounts of memory. Finally, we give the verification values for the new problem size.

Automatic translation of MPI source into a latency-tolerant, data-driven form

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nguyen, Tan; Cicotti, Pietro; Bylaska, Eric

Hiding communication behind useful computation is an important performance programming technique but remains an inscrutable programming exercise even for the expert. We present Bamboo, a code transformation framework that can realize communication overlap in applications written in MPI without the need to intrusively modify the source code. We reformulate MPI source into a task dependency graph representation, which partially orders the tasks, enabling the program to execute in a data-driven fashion under the control of an external runtime system. Experimental results demonstrate that Bamboo significantly reduces communication delays while requiring only modest amounts of programmer annotation for a variety ofmore » applications and platforms, including those employing co-processors and accelerators. Moreover, Bamboo’s performance meets or exceeds that of labor-intensive hand coding. As a result, the translator is more than a means of hiding communication costs automatically; it demonstrates the utility of semantic level optimization against a well-known library.« less

Automatic translation of MPI source into a latency-tolerant, data-driven form

DOE PAGES

Nguyen, Tan; Cicotti, Pietro; Bylaska, Eric; ...

2017-03-06

Hiding communication behind useful computation is an important performance programming technique but remains an inscrutable programming exercise even for the expert. We present Bamboo, a code transformation framework that can realize communication overlap in applications written in MPI without the need to intrusively modify the source code. We reformulate MPI source into a task dependency graph representation, which partially orders the tasks, enabling the program to execute in a data-driven fashion under the control of an external runtime system. Experimental results demonstrate that Bamboo significantly reduces communication delays while requiring only modest amounts of programmer annotation for a variety ofmore » applications and platforms, including those employing co-processors and accelerators. Moreover, Bamboo’s performance meets or exceeds that of labor-intensive hand coding. As a result, the translator is more than a means of hiding communication costs automatically; it demonstrates the utility of semantic level optimization against a well-known library.« less

Establishment and Characterization of Immortalized Minipig Neural Stem Cell Line

PubMed Central

Choi, Sung S.; Yoon, Seung-Bin; Lee, Sang-Rae; Kim, Sun-Uk; Cha, Young Joo; Lee, Daniel; Kim, Seung U.; Chang, Kyu-Tae; Lee, Hong J.

2017-01-01

Despite the increasing importance of minipigs in biomedical research, there has been relatively little research concerning minipig-derived adult stem cells as a promising research tool that could be used to develop stem cell-based therapies. We first generated immortalized neural stem cells (iNSCs) from primary minipig olfactory bulb cells (pmpOBCs) and defined the characteristics of the cell line. Primary neural cells were prepared from minipig neonate olfactory bulbs and immortalized by infection with retrovirus carrying the v-myc gene. The minipig iNSCs (mpiNSCs) had normal karyotypes and expressed NSC-specific markers, including nestin, vimentin, Musashi1, and SOX2, suggesting a similarity to human NSCs. On the basis of the global gene expression profiles from the microarray analysis, neurogenesis-associated transcript levels were predominantly altered in mpiNSCs compared with pmpOBCs. These findings increase our understanding of minipig stem cells and contribute to the utility of mpiNSCs as resources for immortalized stem cell experiments. PMID:27524466

Performance Analysis of Ivshmem for High-Performance Computing in Virtual Machines

NASA Astrophysics Data System (ADS)

Ivanovic, Pavle; Richter, Harald

2018-01-01

High-Performance computing (HPC) is rarely accomplished via virtual machines (VMs). In this paper, we present a remake of ivshmem which can change this. Ivshmem was a shared memory (SHM) between virtual machines on the same server, with SHM-access synchronization included, until about 5 years ago when newer versions of Linux and its virtualization library libvirt evolved. We restored that SHM-access synchronization feature because it is indispensable for HPC and made ivshmem runnable with contemporary versions of Linux, libvirt, KVM, QEMU and especially MPICH, which is an implementation of MPI - the standard HPC communication library. Additionally, MPICH was transparently modified by us to get ivshmem included, resulting in a three to ten times performance improvement compared to TCP/IP. Furthermore, we have transparently replaced MPI_PUT, a single-side MPICH communication mechanism, by an own MPI_PUT wrapper. As a result, our ivshmem even surpasses non-virtualized SHM data transfers for block lengths greater than 512 KBytes, showing the benefits of virtualization. All improvements were possible without using SR-IOV.

Automatic translation of MPI source into a latency-tolerant, data-driven form

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nguyen, Tan; Cicotti, Pietro; Bylaska, Eric

Hiding communication behind useful computation is an important performance programming technique but remains an inscrutable programming exercise even for the expert. We present Bamboo, a code transformation framework that can realize communication overlap in applications written in MPI without the need to intrusively modify the source code. Bamboo reformulates MPI source into the form of a task dependency graph that expresses a partial ordering among tasks, enabling the program to execute in a data-driven fashion under the control of an external runtime system. Experimental results demonstrate that Bamboo significantly reduces communication delays while requiring only modest amounts of programmer annotationmore » for a variety of applications and platforms, including those employing co-processors and accelerators. Moreover, Bamboo's performance meets or exceeds that of labor-intensive hand coding. The translator is more than a means of hiding communication costs automatically; it demonstrates the utility of semantic level optimization against a wellknown library.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Katti, Amogh; Di Fatta, Giuseppe; Naughton, Thomas

Future extreme-scale high-performance computing systems will be required to work under frequent component failures. The MPI Forum s User Level Failure Mitigation proposal has introduced an operation, MPI Comm shrink, to synchronize the alive processes on the list of failed processes, so that applications can continue to execute even in the presence of failures by adopting algorithm-based fault tolerance techniques. This MPI Comm shrink operation requires a failure detection and consensus algorithm. This paper presents three novel failure detection and consensus algorithms using Gossiping. The proposed algorithms were implemented and tested using the Extreme-scale Simulator. The results show that inmore » all algorithms the number of Gossip cycles to achieve global consensus scales logarithmically with system size. The second algorithm also shows better scalability in terms of memory and network bandwidth usage and a perfect synchronization in achieving global consensus. The third approach is a three-phase distributed failure detection and consensus algorithm and provides consistency guarantees even in very large and extreme-scale systems while at the same time being memory and bandwidth efficient.« less

Establishment and Characterization of Immortalized Minipig Neural Stem Cell Line.

PubMed

Choi, Sung S; Yoon, Seung-Bin; Lee, Sang-Rae; Kim, Sun-Uk; Cha, Young Joo; Lee, Daniel; Kim, Seung U; Chang, Kyu-Tae; Lee, Hong J

2017-02-16

Despite the increasing importance of minipigs in biomedical research, there has been relatively little research concerning minipig-derived adult stem cells as a promising research tool that could be used to develop stem cell-based therapies. We first generated immortalized neural stem cells (iNSCs) from primary minipig olfactory bulb cells (pmpOBCs) and defined the characteristics of the cell line. Primary neural cells were prepared from minipig neonate olfactory bulbs and immortalized by infection with retrovirus carrying the v-myc gene. The minipig iNSCs (mpiNSCs) had normal karyotypes and expressed NSC-specific markers, including nestin, vimentin, Musashi1, and SOX2, suggesting a similarity to human NSCs. On the basis of the global gene expression profiles from the microarray analysis, neurogenesis-associated transcript levels were predominantly altered in mpiNSCs compared with pmpOBCs. These findings increase our understanding of minipig stem cells and contribute to the utility of mpiNSCs as resources for immortalized stem cell experiments.

High-frequency Electrocardiogram Analysis in the Ability to Predict Reversible Perfusion Defects during Adenosine Myocardial Perfusion Imaging

NASA Technical Reports Server (NTRS)

Tragardh, Elin; Schlegel, Todd T.; Carlsson, Marcus; Pettersson, Jonas; Nilsson, Klas; Pahlm, Olle

2007-01-01

Background: A previous study has shown that analysis of high-frequency QRS components (HF-QRS) is highly sensitive and reasonably specific for detecting reversible perfusion defects on myocardial perfusion imaging (MPI) scans during adenosine. The purpose of the present study was to try to reproduce those findings. Methods: 12-lead high-resolution electrocardiogram recordings were obtained from 100 patients before (baseline) and during adenosine Tc-99m-tetrofosmin MPI tests. HF-QRS were analyzed regarding morphology and changes in root mean square (RMS) voltages from before the adenosine infusion to peak infusion. Results: The best area under the curve (AUC) was found in supine patients (AUC=0.736) in a combination of morphology and RMS changes. None of the measurements, however, were statistically better than tossing a coin (AUC=0.5). Conclusion: Analysis of HF-QRS was not significantly better than tossing a coin for determining reversible perfusion defects on MPI scans.

The MPI-Mainz UV/VIS Spectral Atlas of Gaseous Molecules of Atmospheric Interest

NASA Astrophysics Data System (ADS)

Keller-Rudek, H.; Moortgat, G. K.; Sander, R.; Sörensen, R.

2013-12-01

We present the MPI-Mainz UV/VIS Spectral Atlas of Gaseous Molecules, which is a large collection of absorption cross sections and quantum yields in the ultraviolet and visible (UV/VIS) wavelength region for gaseous molecules and radicals primarily of atmospheric interest. The data files contain results of individual measurements, covering research of almost a whole century. To compare and visualize the data sets, multicoloured graphical representations have been created. The MPI-Mainz UV/VIS Spectral Atlas is available on the Internet at http://www.uv-vis-spectral-atlas-mainz.org. It now appears with improved browse and search options, based on new database software. In addition to the Web pages, which are continuously updated, a frozen version of the data is available under the doi:10.5281/zenodo.6951.

Cardiovascular outcomes of a positive nuclear stress test but negative coronary angiography in a multiethnic male predominant cohort

PubMed Central

Addison, Daniel; Singh, Vinita; Okyere-Asante, K; Okafor, Henry

2014-01-01

Background: Patients presenting with chest pain and evidence of functional ischemia by myocardial perfusion imaging (MPI), but lacking commensurate angiographic disease pose a diagnostic and therapeutic dilemma. They are often dismissed as having ‘false-positive MPI’. Moreover, a majority of the available long-term outcome data for it has been derived from homogenous female populations. In this study, we sought to evaluate the long-term outcomes of this presentation in a multiethnic male-predominant cohort. Materials and Methods: We retrospectively identified 47 patients who presented to our institution between 2002 and 2005 with chest pain and evidence of ischemia on MPI, but with no significant angiographic disease on subsequent cardiac catheterization (cases). The occurrence of adverse cardiovascular outcomes (chest pain, congestive heart failure, acute myocardial infarction and stroke) post-index coronary angiogram was tracked. Similar data was collected for 37 patients who also presented with chest pain, but normal MPI over the same period (controls). Overall average follow-up was over 22 months. Results: Fifty-three percent (26/47) of the cases had one or more of the adverse outcomes as compared with 22% (8/37) of controls (P < 0.01). Of these, 13 (50.0%) and 3 (37.5%) were males, respectively. Conclusions: Ischemia on MPI is predictive of long-term adverse cardiovascular outcomes despite normal (‘false-negative’) coronary angiography. This appears to be gender-neutral. PMID:24970963

Slew-rate dependence of tracer magnetization response in magnetic particle imaging.

PubMed

Shah, Saqlain A; Ferguson, R M; Krishnan, K M

2014-10-28

Magnetic Particle Imaging (MPI) is a new biomedical imaging technique that produces real-time, high-resolution tomographic images of superparamagnetic iron oxide nanoparticle tracers. Currently, 25 kHz and 20 mT/μ 0 excitation fields are common in MPI, but lower field amplitudes may be necessary for patient safety in future designs. Here, we address fundamental questions about MPI tracer magnetization dynamics and predict tracer performance in future scanners that employ new combinations of excitation field amplitude ( H o ) and frequency ( ω ). Using an optimized, monodisperse MPI tracer, we studied how several combinations of drive field frequencies and amplitudes affect the tracer's response, using Magnetic Particle Spectrometry and AC hysteresis, for drive field conditions at 15.5, 26, and 40.2 kHz, with field amplitudes ranging from 7 to 52 mT/μ 0 . For both fluid and immobilized nanoparticle samples, we determined that magnetic response was dominated by Néel reversal. Furthermore, we observed that the peak slew-rate ( ωH o ) determined the tracer magnetic response. Smaller amplitudes provided correspondingly smaller field of view, sometimes resulting in excitation of minor hysteresis loops. Changing the drive field conditions but keeping the peak slew-rate constant kept the tracer response almost the same. Higher peak slew-rates led to reduced maximum signal intensity and greater coercivity in the tracer response. Our experimental results were in reasonable agreement with Stoner-Wohlfarth model based theories.

Slew-rate dependence of tracer magnetization response in magnetic particle imaging

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shah, Saqlain A.; Krishnan, K. M., E-mail: kannanmk@uw.edu; Ferguson, R. M.

2014-10-28

Magnetic Particle Imaging (MPI) is a new biomedical imaging technique that produces real-time, high-resolution tomographic images of superparamagnetic iron oxide nanoparticle tracers. Currently, 25 kHz and 20 mT/μ{sub 0} excitation fields are common in MPI, but lower field amplitudes may be necessary for patient safety in future designs. Here, we address fundamental questions about MPI tracer magnetization dynamics and predict tracer performance in future scanners that employ new combinations of excitation field amplitude (H{sub o}) and frequency (ω). Using an optimized, monodisperse MPI tracer, we studied how several combinations of drive field frequencies and amplitudes affect the tracer's response, using Magnetic Particlemore » Spectrometry and AC hysteresis, for drive field conditions at 15.5, 26, and 40.2 kHz, with field amplitudes ranging from 7 to 52 mT/μ{sub 0}. For both fluid and immobilized nanoparticle samples, we determined that magnetic response was dominated by Néel reversal. Furthermore, we observed that the peak slew-rate (ωH{sub o}) determined the tracer magnetic response. Smaller amplitudes provided correspondingly smaller field of view, sometimes resulting in excitation of minor hysteresis loops. Changing the drive field conditions but keeping the peak slew-rate constant kept the tracer response almost the same. Higher peak slew-rates led to reduced maximum signal intensity and greater coercivity in the tracer response. Our experimental results were in reasonable agreement with Stoner-Wohlfarth model based theories.« less

Analysis of pain behavior profiles and functional disability in outpatient physical therapy clinics.

PubMed

Hankin, H A; Spencer, T; Kegerreis, S; Worrell, T; Rice, J M

2001-02-01

Descriptive, ex post facto. To determine the proportion of physical therapy outpatients with pain who exhibit various pain behavior profiles, and to determine whether there are differences in functional disability across the profiles. Physical therapists treat many patients who have chronic pain. Research suggests that early identification and multidisciplinary treatment are effective and economical for these patients. The Multidimensional Pain Inventory (MPI) and the Pain Disability Index (PDI) are potential screening tools that could be used in physical therapy clinics to determine which patients should be referred for multidisciplinary treatment. MPI and PDI data were gathered on 57 physical therapy outpatients (mean age 44.3 +/- 14.5 years, 22 men and 35 women) with pain of 3 or more months duration. ANOVA was used to analyze differences in mean PDI scores across the MPI profiles. Of all patients, 42.1% fit the Adaptive Coper profile, 29.8% fit the Interpersonally Distressed profile, and 28.1% fit the Dysfunctional profile. There were significant differences in PDI scores among profile groups. Post hoc analysis showed that the PDI scores of the Adaptive Coper and Interpersonally Distressed groups were different from the Dysfunctional group, but that there was no difference between the Adaptive Coper and Interpersonally Distressed groups. Many patients in outpatient physical therapy settings exhibit behavioral, affective, and cognitive characteristics associated with chronic pain. Thirty-three patients (57.9%) had MPI profiles (interpersonally distressed and dysfunctional) that suggest they might benefit from multidisciplinary treatment.

Minimizing rubidium-82 tracer activity for relative PET myocardial perfusion imaging.

PubMed

Huizing, Eline D; van Dijk, Joris D; van Dalen, Jorn A; Timmer, Jorik R; Arkies, Hester; Slump, Cees H; Jager, Pieter L

2017-08-01

Recommended rubidium-82 activities for relative myocardial perfusion imaging (MPI) using present-generation PET scanners may be unnecessarily high. Our aim was to derive the minimum activity for a reliable relative PET MPI assessment. We analyzed 140 scans from 28 consecutive patients who underwent rest-stress MPI-PET (Ingenuity TF). Scans of 852, 682, 511, and 341 MBq were simulated from list-mode data and compared with a reference scan using 1023 MBq. Differences in the summed rest score, total perfusion deficit, and image quality were obtained between the reference and each of the simulated rest scans. Combined stress-rest scans obtained at a selected activity of 682 MBq were diagnostically interpreted by experts and outcome was compared with the reference scan interpretation. Differences in summed rest score more than or equal to 3 were found using 682, 511, and 341 MBq in two (7%), four (14%), and five (18%) patients, respectively. Differences in total perfusion deficit more than 7% were only found at 341 MBq in one patient. Image quality deteriorated significantly only for the 341 MBq scans (P<0.001). Interpretation of stress-rest scans did not differ between 682 and 1023 MBq scans. A significant reduction in administered Rb-82 activity is feasible in relative MPI. An activity of 682 MBq resulted in reliable diagnostic outcomes and image quality, and can therefore be considered for clinical adoption.

On the retrieval of significant wave heights from spaceborne Synthetic Aperture Radar using the Max-Planck Institut algorithm.

PubMed

Violante-Carvalho, Nelson

2005-12-01

Synthetic Aperture Radar (SAR) onboard satellites is the only source of directional wave spectra with continuous and global coverage. Millions of SAR Wave Mode (SWM) imagettes have been acquired since the launch in the early 1990's of the first European Remote Sensing Satellite ERS-1 and its successors ERS-2 and ENVISAT, which has opened up many possibilities specially for wave data assimilation purposes. The main aim of data assimilation is to improve the forecasting introducing available observations into the modeling procedures in order to minimize the differences between model estimates and measurements. However there are limitations in the retrieval of the directional spectrum from SAR images due to nonlinearities in the mapping mechanism. The Max-Planck Institut (MPI) scheme, the first proposed and most widely used algorithm to retrieve directional wave spectra from SAR images, is employed to compare significant wave heights retrieved from ERS-1 SAR against buoy measurements and against the WAM wave model. It is shown that for periods shorter than 12 seconds the WAM model performs better than the MPI, despite the fact that the model is used as first guess to the MPI method, that is the retrieval is deteriorating the first guess. For periods longer than 12 seconds, the part of the spectrum that is directly measured by SAR, the performance of the MPI scheme is at least as good as the WAM model.

Safety of regadenoson in patients with severe chronic obstructive pulmonary disease.

PubMed

Salgado-Garcia, C; Jimenez-Heffernan, A; Ramos-Font, C; Lopez-Martin, J; Sanchez-de-Mora, E; Aroui, T; Lopez-Aguilar, R; Rivera-de-Los-Santos, F; Ruiz-Frutos, C

2016-01-01

To assess the safety of regadenoson, a selective agonist of A2A adenosine receptors, combined with low-level exercise in subjects with severe chronic obstructive pulmonary disease (COPD), referred for myocardial perfusion imaging (MPI). We studied prospectively 12 male patients with severe COPD. Stress was 4min of low-level exercise with bolus injection of regadenoson (0.4mg) at 1.5min, followed by (99m)Tc-MPI agent injection. Demographics, medical history, lung medications, adverse events, oxygen saturation (SatO2), MPI findings for coronary artery disease (CAD), and changes in systolic blood pressure (SBP), and heart rate (HR) were registered. The observed adverse event profile of regadenoson was similar to that of patients with mild-moderate COPD. There was no clinical exacerbation of COPD. Adverse events were self-limiting: dyspnea (33.3%), fatigue (25.0%), chest pain, headache (16.7%, respectively), and gastrointestinal discomfort, dry mouth, flushing, feeling hot and dizziness (8.3%, respectively). 25.0% of patients did not report any symptoms. We observed significant increases in SBP and HR from baseline (142.6mmHg±22.3 vs 152.5mmHg±18.5, and 80 b.p.m.±18 vs 105 b.p.m.±22, respectively; p<0.05). Regadenoson combined with low-level exercise is safe and well tolerated in stable patients with severe COPD undergoing MPI. Copyright © 2016 Elsevier España, S.L.U. y SEMNIM. All rights reserved.

Hybrid x-space: a new approach for MPI reconstruction.

PubMed

Tateo, A; Iurino, A; Settanni, G; Andrisani, A; Stifanelli, P F; Larizza, P; Mazzia, F; Mininni, R M; Tangaro, S; Bellotti, R

2016-06-07

Magnetic particle imaging (MPI) is a new medical imaging technique capable of recovering the distribution of superparamagnetic particles from their measured induced signals. In literature there are two main MPI reconstruction techniques: measurement-based (MB) and x-space (XS). The MB method is expensive because it requires a long calibration procedure as well as a reconstruction phase that can be numerically costly. On the other side, the XS method is simpler than MB but the exact knowledge of the field free point (FFP) motion is essential for its implementation. Our simulation work focuses on the implementation of a new approach for MPI reconstruction: it is called hybrid x-space (HXS), representing a combination of the previous methods. Specifically, our approach is based on XS reconstruction because it requires the knowledge of the FFP position and velocity at each time instant. The difference with respect to the original XS formulation is how the FFP velocity is computed: we estimate it from the experimental measurements of the calibration scans, typical of the MB approach. Moreover, a compressive sensing technique is applied in order to reduce the calibration time, setting a fewer number of sampling positions. Simulations highlight that HXS and XS methods give similar results. Furthermore, an appropriate use of compressive sensing is crucial for obtaining a good balance between time reduction and reconstructed image quality. Our proposal is suitable for open geometry configurations of human size devices, where incidental factors could make the currents, the fields and the FFP trajectory irregular.

Parallelization of Rocket Engine Simulator Software (PRESS)

NASA Technical Reports Server (NTRS)

Cezzar, Ruknet

1998-01-01

We have outlined our work in the last half of the funding period. We have shown how a demo package for RESSAP using MPI can be done. However, we also mentioned the difficulties with the UNIX platform. We have reiterated some of the suggestions made during the presentation of the progress of the at Fourth Annual HBCU Conference. Although we have discussed, in some detail, how TURBDES/PUMPDES software can be run in parallel using MPI, at present, we are unable to experiment any further with either MPI or PVM. Due to X windows not being implemented, we are also not able to experiment further with XPVM, which it will be recalled, has a nice GUI interface. There are also some concerns, on our part, about MPI being an appropriate tool. The best thing about MPr is that it is public domain. Although and plenty of documentation exists for the intricacies of using MPI, little information is available on its actual implementations. Other than very typical, somewhat contrived examples, such as Jacobi algorithm for solving Laplace's equation, there are few examples which can readily be applied to real situations, such as in our case. In effect, the review of literature on both MPI and PVM, and there is a lot, indicate something similar to the enormous effort which was spent on LISP and LISP-like languages as tools for artificial intelligence research. During the development of a book on programming languages [12], when we searched the literature for very simple examples like taking averages, reading and writing records, multiplying matrices, etc., we could hardly find a any! Yet, so much was said and done on that topic in academic circles. It appears that we faced the same problem with MPI, where despite significant documentation, we could not find even a simple example which supports course-grain parallelism involving only a few processes. From the foregoing, it appears that a new direction may be required for more productive research during the extension period (10/19/98 - 10/18/99). At the least, the research would need to be done on Windows 95/Windows NT based platforms. Moreover, with the acquisition of Lahey Fortran package for PC platform, and the existing Borland C + + 5. 0, we can do work on C + + wrapper issues. We have carefully studied the blueprint for Space Transportation Propulsion Integrated Design Environment for the next 25 years [13] and found the inclusion of HBCUs in that effort encouraging. Especially in the long period for which a map is provided, there is no doubt that HBCUs will grow and become better equipped to do meaningful research. In the shorter period, as was suggested in our presentation at the HBCU conference, some key decisions regarding the aging Fortran based software for rocket propellants will need to be made. One important issue is whether or not object oriented languages such as C + + or Java should be used for distributed computing. Whether or not "distributed computing" is necessary for the existing software is yet another, larger, question to be tackled with.

Nuclear Cardiology Practices and Radiation Exposure in the Oceania Region: Results From the IAEA Nuclear Cardiology Protocols Study (INCAPS).

PubMed

Biswas, Sinjini; Better, Nathan; Pascual, Thomas N B; Mercuri, Mathew; Vitola, João V; Karthikeyan, Ganesan; Westcott, James; Alexánderson, Erick; Allam, Adel H; Al-Mallah, Mouaz H; Bom, Henry Hee-Seung; Bouyoucef, Salah E; Flotats, Albert; Jerome, Scott; Kaufman, Philip A; Lele, Vikram; Luxenburg, Osnat; Mahmarian, John J; Shaw, Leslee J; Underwood, S Richard; Rehani, Madan; Kashyap, Ravi; Dondi, Maurizio; Paez, Diana; Einstein, Andrew J

2017-01-01

There is concern about radiation exposure with radionuclide myocardial perfusion imaging (MPI). This sub-study of the International Atomic Energy Agency (IAEA) Nuclear Cardiology Protocols Study reports radiation doses from MPI, and use of dose-optimisation protocols in Australia and New Zealand (ANZ), and compares them with data from the rest of the world. Data were collected from 7911 MPI studies performed in 308 laboratories worldwide in one week in 2013, including 439 MPI studies from 34 ANZ laboratories. For each laboratory, effective radiation dose (ED) and a quality index (QI) score (out of 8) based on pre-specified "best practices" was determined. In ANZ patients, ED ranged from 0.9-17.9 milliSievert (mSv). Median ED was similar in ANZ compared with the rest of the world (10.0 (IQR: 6.5-11.7) vs. 10.0 (IQR 6.4-12.6, P=0.15), as were mean QI scores (5.5±0.7 vs. 5.4±1.3, P=0.84). Use of stress-only imaging (17.6% vs. 31.8% of labs, P=0.09) and weight-based dosing of technetium-99m (14.7% vs. 30.3%, P=0.07) was lower in ANZ compared with the rest of the world but this difference was not statistically significant. Median ED was significantly lower in metropolitan versus non-metropolitan laboratories (10.1 mSv vs. 11.6 mSv, P<0.01), although mean QI scores were similar (5.4±0.8 vs. 5.5±0.7, P=0.75). Across ANZ, there is variability in ED from MPI, and use of radiation safety practices, particularly between metropolitan and non-metropolitan laboratories. Overall, ANZ laboratories have a similar median ED to laboratories in the rest of the world. Copyright © 2016 Australian and New Zealand Society of Cardiac and Thoracic Surgeons (ANZSCTS) and the Cardiac Society of Australia and New Zealand (CSANZ). Published by Elsevier B.V. All rights reserved.

Use of carbonated water in reduction of adjacent gastric activity in 456 consecutive technetium-99m myocardial perfusion imaging studies.

PubMed

Thomas, Dustin M; Lee, Joshua S; Charmforoush, Anthony; Rubal, Bernard J; Rosenblatt, Stephen A; Butler, Joshua T; Clemenshaw, Michael; Cheezum, Michael K; Slim, Ahmad M

2015-12-01

Small, observational trials have suggested a reduction in adjacent gastric activity with ingestion of soda water in myocardial perfusion imaging (MPI). We report our findings prior to and after implementation of soda water in 467 consecutive MPI studies. Consecutive MPI studies performed at a high-volume facility referred for vasodilator (VD) or exercise treadmill testing (ETT) were retrospectively reviewed before and after implementation of the soda water protocol. Patients undergoing the soda water protocol received 100 ml of soda water administered 30 min prior to image acquisition and after stress. Studies were performed using a same day rest/stress protocol. Incidence of adjacent gastric activity, diaphragmatic attenuation, stress and rest perfusion defects, and major adverse cardiovascular events (MACE) outcomes defined as death, myocardial infarction, stroke, reevaluation for chest pain, and late revascularization (>90 days from MPI) were abstracted using International Classification of Diseases, Ninth Revision (ICD-9) search. Two hundred and eighteen studies were performed prior to implementation of the soda water protocol and 249 studies were performed with the use of soda water. Baseline demographic data were equal between the groups with the exception of more patients undergoing VD stress receiving soda water (p < 0.001). Soda water was not associated with a decreased incidence of adjacent gastric activity with stress (54.7% versus 61.9% with no soda water, p = 0.129) or rest (68.6% versus 69.5% with no soda water, p = 0.919) imaging. Less adjacent gastric activity was observed with patients undergoing ETT who received soda water (42.5% versus 56.9% with no soda water, p = 0.031), but no difference was observed between the groups with VD stress (69.0% versus 68.1% with no soda water, p = 1.000). The use of soda water prior to technetium-99m MPI was associated with lower rates of adjacent gastric activity only in patients undergoing ETT stress but not rest or VD stress. This differs from previously published data. © The Author(s), 2015.

Addressing the challenges of standalone multi-core simulations in molecular dynamics

NASA Astrophysics Data System (ADS)

Ocaya, R. O.; Terblans, J. J.

2017-07-01

Computational modelling in material science involves mathematical abstractions of force fields between particles with the aim to postulate, develop and understand materials by simulation. The aggregated pairwise interactions of the material's particles lead to a deduction of its macroscopic behaviours. For practically meaningful macroscopic scales, a large amount of data are generated, leading to vast execution times. Simulation times of hours, days or weeks for moderately sized problems are not uncommon. The reduction of simulation times, improved result accuracy and the associated software and hardware engineering challenges are the main motivations for many of the ongoing researches in the computational sciences. This contribution is concerned mainly with simulations that can be done on a "standalone" computer based on Message Passing Interfaces (MPI), parallel code running on hardware platforms with wide specifications, such as single/multi- processor, multi-core machines with minimal reconfiguration for upward scaling of computational power. The widely available, documented and standardized MPI library provides this functionality through the MPI_Comm_size (), MPI_Comm_rank () and MPI_Reduce () functions. A survey of the literature shows that relatively little is written with respect to the efficient extraction of the inherent computational power in a cluster. In this work, we discuss the main avenues available to tap into this extra power without compromising computational accuracy. We also present methods to overcome the high inertia encountered in single-node-based computational molecular dynamics. We begin by surveying the current state of the art and discuss what it takes to achieve parallelism, efficiency and enhanced computational accuracy through program threads and message passing interfaces. Several code illustrations are given. The pros and cons of writing raw code as opposed to using heuristic, third-party code are also discussed. The growing trend towards graphical processor units and virtual computing clouds for high-performance computing is also discussed. Finally, we present the comparative results of vacancy formation energy calculations using our own parallelized standalone code called Verlet-Stormer velocity (VSV) operating on 30,000 copper atoms. The code is based on the Sutton-Chen implementation of the Finnis-Sinclair pairwise embedded atom potential. A link to the code is also given.

Comparison of quantitative myocardial perfusion imaging CT to fluorescent microsphere-based flow from high-resolution cryo-images

NASA Astrophysics Data System (ADS)

Eck, Brendan L.; Fahmi, Rachid; Levi, Jacob; Fares, Anas; Wu, Hao; Li, Yuemeng; Vembar, Mani; Dhanantwari, Amar; Bezerra, Hiram G.; Wilson, David L.

2016-03-01

Myocardial perfusion imaging using CT (MPI-CT) has the potential to provide quantitative measures of myocardial blood flow (MBF) which can aid the diagnosis of coronary artery disease. We evaluated the quantitative accuracy of MPI-CT in a porcine model of balloon-induced LAD coronary artery ischemia guided by fractional flow reserve (FFR). We quantified MBF at baseline (FFR=1.0) and under moderate ischemia (FFR=0.7) using MPI-CT and compared to fluorescent microsphere-based MBF from high-resolution cryo-images. Dynamic, contrast-enhanced CT images were obtained using a spectral detector CT (Philips Healthcare). Projection-based mono-energetic images were reconstructed and processed to obtain MBF. Three MBF quantification approaches were evaluated: singular value decomposition (SVD) with fixed Tikhonov regularization (ThSVD), SVD with regularization determined by the L-Curve criterion (LSVD), and Johnson-Wilson parameter estimation (JW). The three approaches over-estimated MBF compared to cryo-images. JW produced the most accurate MBF, with average error 33.3+/-19.2mL/min/100g, whereas LSVD and ThSVD had greater over-estimation, 59.5+/-28.3mL/min/100g and 78.3+/-25.6 mL/min/100g, respectively. Relative blood flow as assessed by a flow ratio of LAD-to-remote myocardium was strongly correlated between JW and cryo-imaging, with R2=0.97, compared to R2=0.88 and 0.78 for LSVD and ThSVD, respectively. We assessed tissue impulse response functions (IRFs) from each approach for sources of error. While JW was constrained to physiologic solutions, both LSVD and ThSVD produced IRFs with non-physiologic properties due to noise. The L-curve provided noise-adaptive regularization but did not eliminate non-physiologic IRF properties or optimize for MBF accuracy. These findings suggest that model-based MPI-CT approaches may be more appropriate for quantitative MBF estimation and that cryo-imaging can support the development of MPI-CT by providing spatial distributions of MBF.

Development of a software framework for data assimilation and its applications for streamflow forecasting in Japan

NASA Astrophysics Data System (ADS)

Noh, S. J.; Tachikawa, Y.; Shiiba, M.; Yorozu, K.; Kim, S.

2012-04-01

Data assimilation methods have received increased attention to accomplish uncertainty assessment and enhancement of forecasting capability in various areas. Despite of their potentials, applicable software frameworks to probabilistic approaches and data assimilation are still limited because the most of hydrologic modeling software are based on a deterministic approach. In this study, we developed a hydrological modeling framework for sequential data assimilation, so called MPI-OHyMoS. MPI-OHyMoS allows user to develop his/her own element models and to easily build a total simulation system model for hydrological simulations. Unlike process-based modeling framework, this software framework benefits from its object-oriented feature to flexibly represent hydrological processes without any change of the main library. Sequential data assimilation based on the particle filters is available for any hydrologic models based on MPI-OHyMoS considering various sources of uncertainty originated from input forcing, parameters and observations. The particle filters are a Bayesian learning process in which the propagation of all uncertainties is carried out by a suitable selection of randomly generated particles without any assumptions about the nature of the distributions. In MPI-OHyMoS, ensemble simulations are parallelized, which can take advantage of high performance computing (HPC) system. We applied this software framework for short-term streamflow forecasting of several catchments in Japan using a distributed hydrologic model. Uncertainty of model parameters and remotely-sensed rainfall data such as X-band or C-band radar is estimated and mitigated in the sequential data assimilation.

Roles of thermophilic thiosulfate-reducing bacteria and methanogenic archaea in the biocorrosion of oil pipelines

PubMed Central

Liang, Renxing; Grizzle, Robert S.; Duncan, Kathleen E.; McInerney, Michael J.; Suflita, Joseph M.

2014-01-01

Thermophilic sulfide-producing microorganisms from an oil pipeline network were enumerated with different sulfur oxyanions as electron acceptors at 55°C. Most-probable number (MPN) analysis showed that thiosulfate-reducing bacteria were the most numerous sulfidogenic microorganisms in pipeline inspection gauge (PIG) scrapings. Thiosulfate-reducing and methanogenic enrichments were obtained from the MPN cultures that were able to use yeast extract as the electron donor. Molecular analysis revealed that both enrichments harbored the same dominant bacterium, which belonged to the genus Anaerobaculum. The dominant archaeon in the methanogenic enrichment was affiliated with the genus Methanothermobacter. With yeast extract as the electron donor, the general corrosion rate by the thiosulfate-reducing enrichment (8.43 ± 1.40 milli-inch per year, abbreviated as mpy) was about 5.5 times greater than the abiotic control (1.49 ± 0.15 mpy), while the comparable measures for the methanogenic culture were 2.03 ± 0.49 mpy and 0.62 ± 0.07 mpy, respectively. Total iron analysis in the cultures largely accounted for the mass loss of iron measured in the weight loss determinations. Profilometry analysis of polished steel coupons incubated in the presence of the thiosulfate-reducing enrichment revealed 59 pits over an area of 71.16 mm2, while only 6 pits were evident in the corresponding methanogenic incubations. The results show the importance of thiosulfate-utilizing, sulfide-producing fermentative bacteria such as Anaerobaculum sp. in the corrosion of carbon steel, but also suggest that Anaerobaculum sp. are of far less concern when growing syntrophically with methanogens. PMID:24639674

Roles of thermophilic thiosulfate-reducing bacteria and methanogenic archaea in the biocorrosion of oil pipelines.

PubMed

Liang, Renxing; Grizzle, Robert S; Duncan, Kathleen E; McInerney, Michael J; Suflita, Joseph M

2014-01-01

Thermophilic sulfide-producing microorganisms from an oil pipeline network were enumerated with different sulfur oxyanions as electron acceptors at 55°C. Most-probable number (MPN) analysis showed that thiosulfate-reducing bacteria were the most numerous sulfidogenic microorganisms in pipeline inspection gauge (PIG) scrapings. Thiosulfate-reducing and methanogenic enrichments were obtained from the MPN cultures that were able to use yeast extract as the electron donor. Molecular analysis revealed that both enrichments harbored the same dominant bacterium, which belonged to the genus Anaerobaculum. The dominant archaeon in the methanogenic enrichment was affiliated with the genus Methanothermobacter. With yeast extract as the electron donor, the general corrosion rate by the thiosulfate-reducing enrichment (8.43 ± 1.40 milli-inch per year, abbreviated as mpy) was about 5.5 times greater than the abiotic control (1.49 ± 0.15 mpy), while the comparable measures for the methanogenic culture were 2.03 ± 0.49 mpy and 0.62 ± 0.07 mpy, respectively. Total iron analysis in the cultures largely accounted for the mass loss of iron measured in the weight loss determinations. Profilometry analysis of polished steel coupons incubated in the presence of the thiosulfate-reducing enrichment revealed 59 pits over an area of 71.16 mm(2), while only 6 pits were evident in the corresponding methanogenic incubations. The results show the importance of thiosulfate-utilizing, sulfide-producing fermentative bacteria such as Anaerobaculum sp. in the corrosion of carbon steel, but also suggest that Anaerobaculum sp. are of far less concern when growing syntrophically with methanogens.

Hierarchical Parallelization of Gene Differential Association Analysis

PubMed Central

2011-01-01

Background Microarray gene differential expression analysis is a widely used technique that deals with high dimensional data and is computationally intensive for permutation-based procedures. Microarray gene differential association analysis is even more computationally demanding and must take advantage of multicore computing technology, which is the driving force behind increasing compute power in recent years. In this paper, we present a two-layer hierarchical parallel implementation of gene differential association analysis. It takes advantage of both fine- and coarse-grain (with granularity defined by the frequency of communication) parallelism in order to effectively leverage the non-uniform nature of parallel processing available in the cutting-edge systems of today. Results Our results show that this hierarchical strategy matches data sharing behavior to the properties of the underlying hardware, thereby reducing the memory and bandwidth needs of the application. The resulting improved efficiency reduces computation time and allows the gene differential association analysis code to scale its execution with the number of processors. The code and biological data used in this study are downloadable from http://www.urmc.rochester.edu/biostat/people/faculty/hu.cfm. Conclusions The performance sweet spot occurs when using a number of threads per MPI process that allows the working sets of the corresponding MPI processes running on the multicore to fit within the machine cache. Hence, we suggest that practitioners follow this principle in selecting the appropriate number of MPI processes and threads within each MPI process for their cluster configurations. We believe that the principles of this hierarchical approach to parallelization can be utilized in the parallelization of other computationally demanding kernels. PMID:21936916

Hierarchical parallelization of gene differential association analysis.

PubMed

Needham, Mark; Hu, Rui; Dwarkadas, Sandhya; Qiu, Xing

2011-09-21

Microarray gene differential expression analysis is a widely used technique that deals with high dimensional data and is computationally intensive for permutation-based procedures. Microarray gene differential association analysis is even more computationally demanding and must take advantage of multicore computing technology, which is the driving force behind increasing compute power in recent years. In this paper, we present a two-layer hierarchical parallel implementation of gene differential association analysis. It takes advantage of both fine- and coarse-grain (with granularity defined by the frequency of communication) parallelism in order to effectively leverage the non-uniform nature of parallel processing available in the cutting-edge systems of today. Our results show that this hierarchical strategy matches data sharing behavior to the properties of the underlying hardware, thereby reducing the memory and bandwidth needs of the application. The resulting improved efficiency reduces computation time and allows the gene differential association analysis code to scale its execution with the number of processors. The code and biological data used in this study are downloadable from http://www.urmc.rochester.edu/biostat/people/faculty/hu.cfm. The performance sweet spot occurs when using a number of threads per MPI process that allows the working sets of the corresponding MPI processes running on the multicore to fit within the machine cache. Hence, we suggest that practitioners follow this principle in selecting the appropriate number of MPI processes and threads within each MPI process for their cluster configurations. We believe that the principles of this hierarchical approach to parallelization can be utilized in the parallelization of other computationally demanding kernels.

Thread-Level Parallelization and Optimization of NWChem for the Intel MIC Architecture

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shan, Hongzhang; Williams, Samuel; Jong, Wibe de

In the multicore era it was possible to exploit the increase in on-chip parallelism by simply running multiple MPI processes per chip. Unfortunately, manycore processors' greatly increased thread- and data-level parallelism coupled with a reduced memory capacity demand an altogether different approach. In this paper we explore augmenting two NWChem modules, triples correction of the CCSD(T) and Fock matrix construction, with OpenMP in order that they might run efficiently on future manycore architectures. As the next NERSC machine will be a self-hosted Intel MIC (Xeon Phi) based supercomputer, we leverage an existing MIC testbed at NERSC to evaluate our experiments.more » In order to proxy the fact that future MIC machines will not have a host processor, we run all of our experiments in tt native mode. We found that while straightforward application of OpenMP to the deep loop nests associated with the tensor contractions of CCSD(T) was sufficient in attaining high performance, significant effort was required to safely and efficiently thread the TEXAS integral package when constructing the Fock matrix. Ultimately, our new MPI OpenMP hybrid implementations attain up to 65x better performance for the triples part of the CCSD(T) due in large part to the fact that the limited on-card memory limits the existing MPI implementation to a single process per card. Additionally, we obtain up to 1.6x better performance on Fock matrix constructions when compared with the best MPI implementations running multiple processes per card.« less

Thread-level parallelization and optimization of NWChem for the Intel MIC architecture

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shan, Hongzhang; Williams, Samuel; de Jong, Wibe

In the multicore era it was possible to exploit the increase in on-chip parallelism by simply running multiple MPI processes per chip. Unfortunately, manycore processors' greatly increased thread- and data-level parallelism coupled with a reduced memory capacity demand an altogether different approach. In this paper we explore augmenting two NWChem modules, triples correction of the CCSD(T) and Fock matrix construction, with OpenMP in order that they might run efficiently on future manycore architectures. As the next NERSC machine will be a self-hosted Intel MIC (Xeon Phi) based supercomputer, we leverage an existing MIC testbed at NERSC to evaluate our experiments.more » In order to proxy the fact that future MIC machines will not have a host processor, we run all of our experiments in native mode. We found that while straightforward application of OpenMP to the deep loop nests associated with the tensor contractions of CCSD(T) was sufficient in attaining high performance, significant e ort was required to safely and efeciently thread the TEXAS integral package when constructing the Fock matrix. Ultimately, our new MPI+OpenMP hybrid implementations attain up to 65× better performance for the triples part of the CCSD(T) due in large part to the fact that the limited on-card memory limits the existing MPI implementation to a single process per card. Additionally, we obtain up to 1.6× better performance on Fock matrix constructions when compared with the best MPI implementations running multiple processes per card.« less

Space-Spurred Metallized Materials

NASA Technical Reports Server (NTRS)

1990-01-01

Spurred R&D toward improved vacuum metallizing techniques led to an extensive line of commercial products, from insulated outdoor garments to packaging for foods, from wall coverings to window shades, from life rafts to candy wrappings, reflective blankets to photographic reflectors. Metallized Products, Inc. (MPI) was one of the companies that worked with NASA in development of the original space materials. MPI markets its own metallized products and supplies materials to other manufacturers. One of the most widely used MPI products is TXG laminate. An example is a reflective kite, the S.O.S. Signal Kite that can be flown as high as 200 feet to enhance radar and visual detectability. It offers a boon to campers, hikers, mountain climbers and boaters. It is produced by Solar Reflections, Inc. The company also markets a solar reflective hat. Another example is by Pro-Tektion, Inc. to provide protection for expensive musical equipment that have sensitive electronic components subject to damage from the heat of stage lights, dust, or rain at outdoor concerts. MP supplied the material and acceptance of the covers by the sound industry has been excellent.

An efficient MPI/OpenMP parallelization of the Hartree–Fock–Roothaan method for the first generation of Intel® Xeon Phi™ processor architecture

DOE PAGES

Mironov, Vladimir; Moskovsky, Alexander; D’Mello, Michael; ...

2017-10-04

The Hartree-Fock (HF) method in the quantum chemistry package GAMESS represents one of the most irregular algorithms in computation today. Major steps in the calculation are the irregular computation of electron repulsion integrals (ERIs) and the building of the Fock matrix. These are the central components of the main Self Consistent Field (SCF) loop, the key hotspot in Electronic Structure (ES) codes. By threading the MPI ranks in the official release of the GAMESS code, we not only speed up the main SCF loop (4x to 6x for large systems), but also achieve a significant (>2x) reduction in the overallmore » memory footprint. These improvements are a direct consequence of memory access optimizations within the MPI ranks. We benchmark our implementation against the official release of the GAMESS code on the Intel R Xeon PhiTM supercomputer. Here, scaling numbers are reported on up to 7,680 cores on Intel Xeon Phi coprocessors.« less

Performance Comparison of a Matrix Solver on a Heterogeneous Network Using Two Implementations of MPI: MPICH and LAM

NASA Technical Reports Server (NTRS)

Phillips, Jennifer K.

1995-01-01

Two of the current and most popular implementations of the Message-Passing Standard, Message Passing Interface (MPI), were contrasted: MPICH by Argonne National Laboratory, and LAM by the Ohio Supercomputer Center at Ohio State University. A parallel skyline matrix solver was adapted to be run in a heterogeneous environment using MPI. The Message-Passing Interface Forum was held in May 1994 which lead to a specification of library functions that implement the message-passing model of parallel communication. LAM, which creates it's own environment, is more robust in a highly heterogeneous network. MPICH uses the environment native to the machine architecture. While neither of these free-ware implementations provides the performance of native message-passing or vendor's implementations, MPICH begins to approach that performance on the SP-2. The machines used in this study were: IBM RS6000, 3 Sun4, SGI, and the IBM SP-2. Each machine is unique and a few machines required specific modifications during the installation. When installed correctly, both implementations worked well with only minor problems.

[A utopian episode - Carl Friedrich von Weizsäcker in the networks of the Max-Planck Society].

PubMed

Kant, Horst; Renn, Jürgen

2014-01-01

Carl Friedrich von Weizsäcker was a key figure in the history of the Max Planck Society (MPS). This essay contextualises his work with the development of the MPS, highlighting the institutional and personal networks upon which it was based. Some of the stations addressed in the following are his role in the German Uranium Project, in preparing the Mainau Declaration, the Göttingen Manifesto, and the Memorandum of Tübingen as well as his involvement in the foundation of the Max Planck Institute (MPI) for Human Development and his own MPI for the Research of Living Conditions in the Modern World located in Starnberg. The relationship between Weizsäcker and Hellmut Becker, long-time friend and founding director of the MPI for Human Development, will be of particular interest. Another issue broached here is the connection between natural science and the humanities in Weizsäcker's work, and subsequently the relation between these two science cultures in the MPS. Finally, we look at the challenges Weizsäcker's work could present to the MPS today.

Stress-induced alteration of left ventricular eccentricity: An additional marker of multivessel CAD.

PubMed

Gimelli, Alessia; Liga, Riccardo; Giorgetti, Assuero; Casagranda, Mirta; Marzullo, Paolo

2017-03-28

Abnormal left ventricular (LV) eccentricity index (EI) is a marker of adverse cardiac remodeling. However, the interaction between stress-induced alterations of EI and major cardiac parameters has not been explored. We sought to evaluate the relationship between LV EI and coronary artery disease (CAD) burden in patients submitted to myocardial perfusion imaging (MPI). Three-hundred and forty-three patients underwent MPI and coronary angiography. LV ejection fraction (EF) and EI were computed from gated stress images as measures of stress-induced functional impairment. One-hundred and thirty-six (40%), 122 (35%), and 85 (25%) patients had normal coronary arteries, single-vessel CAD, and multivessel CAD, respectively. Post-stress EI was lower in patients with multivessel CAD than in those with normal coronary arteries and single-vessel CAD (P = 0.001). This relationship was confirmed only in patients undergoing exercise stress test, where a lower post-stress EI predicted the presence of multivessel CAD (P = 0.039). Post-stress alterations of LV EI on MPI may unmask the presence of multivessel CAD.

Balancing Conflicting Requirements for Grid and Particle Decomposition in Continuum-Lagrangian Solvers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sitaraman, Hariswaran; Grout, Ray

2015-10-30

The load balancing strategies for hybrid solvers that involve grid based partial differential equation solution coupled with particle tracking are presented in this paper. A typical Message Passing Interface (MPI) based parallelization of grid based solves are done using a spatial domain decomposition while particle tracking is primarily done using either of the two techniques. One of the techniques is to distribute the particles to MPI ranks to whose grid they belong to while the other is to share the particles equally among all ranks, irrespective of their spatial location. The former technique provides spatial locality for field interpolation butmore » cannot assure load balance in terms of number of particles, which is achieved by the latter. The two techniques are compared for a case of particle tracking in a homogeneous isotropic turbulence box as well as a turbulent jet case. We performed a strong scaling study for more than 32,000 cores, which results in particle densities representative of anticipated exascale machines. The use of alternative implementations of MPI collectives and efficient load equalization strategies are studied to reduce data communication overheads.« less

MLP: A Parallel Programming Alternative to MPI for New Shared Memory Parallel Systems

NASA Technical Reports Server (NTRS)

Taft, James R.

1999-01-01

Recent developments at the NASA AMES Research Center's NAS Division have demonstrated that the new generation of NUMA based Symmetric Multi-Processing systems (SMPs), such as the Silicon Graphics Origin 2000, can successfully execute legacy vector oriented CFD production codes at sustained rates far exceeding processing rates possible on dedicated 16 CPU Cray C90 systems. This high level of performance is achieved via shared memory based Multi-Level Parallelism (MLP). This programming approach, developed at NAS and outlined below, is distinct from the message passing paradigm of MPI. It offers parallelism at both the fine and coarse grained level, with communication latencies that are approximately 50-100 times lower than typical MPI implementations on the same platform. Such latency reductions offer the promise of performance scaling to very large CPU counts. The method draws on, but is also distinct from, the newly defined OpenMP specification, which uses compiler directives to support a limited subset of multi-level parallel operations. The NAS MLP method is general, and applicable to a large class of NASA CFD codes.

Advances in Patch-Based Adaptive Mesh Refinement Scalability

DOE PAGES

Gunney, Brian T.N.; Anderson, Robert W.

2015-12-18

Patch-based structured adaptive mesh refinement (SAMR) is widely used for high-resolution simu- lations. Combined with modern supercomputers, it could provide simulations of unprecedented size and resolution. A persistent challenge for this com- bination has been managing dynamically adaptive meshes on more and more MPI tasks. The dis- tributed mesh management scheme in SAMRAI has made some progress SAMR scalability, but early al- gorithms still had trouble scaling past the regime of 105 MPI tasks. This work provides two critical SAMR regridding algorithms, which are integrated into that scheme to ensure efficiency of the whole. The clustering algorithm is an extensionmore » of the tile- clustering approach, making it more flexible and efficient in both clustering and parallelism. The partitioner is a new algorithm designed to prevent the network congestion experienced by its prede- cessor. We evaluated performance using weak- and strong-scaling benchmarks designed to be difficult for dynamic adaptivity. Results show good scaling on up to 1.5M cores and 2M MPI tasks. Detailed timing diagnostics suggest scaling would continue well past that.« less

Epidemic failure detection and consensus for extreme parallelism

DOE PAGES

Katti, Amogh; Di Fatta, Giuseppe; Naughton, Thomas; ...

2017-02-01

Future extreme-scale high-performance computing systems will be required to work under frequent component failures. The MPI Forum s User Level Failure Mitigation proposal has introduced an operation, MPI Comm shrink, to synchronize the alive processes on the list of failed processes, so that applications can continue to execute even in the presence of failures by adopting algorithm-based fault tolerance techniques. This MPI Comm shrink operation requires a failure detection and consensus algorithm. This paper presents three novel failure detection and consensus algorithms using Gossiping. The proposed algorithms were implemented and tested using the Extreme-scale Simulator. The results show that inmore » all algorithms the number of Gossip cycles to achieve global consensus scales logarithmically with system size. The second algorithm also shows better scalability in terms of memory and network bandwidth usage and a perfect synchronization in achieving global consensus. The third approach is a three-phase distributed failure detection and consensus algorithm and provides consistency guarantees even in very large and extreme-scale systems while at the same time being memory and bandwidth efficient.« less

Experiencing meditation - Evidence for differential effects of three contemplative mental practices in micro-phenomenological interviews.

PubMed

Przyrembel, Marisa; Singer, Tania

2018-07-01

Despite increasing interest in effects of meditation, systematic in-depth research on how it qualitatively feels to engage in different kinds of contemplative practices is still missing. To fill this gap, we explore the validity of Micro-phenomenological Interviews (MpI) to assess experiences during breathing meditation (BM), observing-thought meditation (OTM), and loving-kindness meditation (LKM). We performed psycholinguistic analyses, quantitative ratings and qualitative explorations of 104 MpI (N = 57). All results reveal differential affective, bodily and sensorial fingerprints: BM-transcripts contain the most body-related vocabulary, specifically sensations in nose and abdomen. OTM-transcripts contain the most cognition-related vocabulary. OTM is experienced in head and face. LKM-transcripts contain the most vocabulary related to socio-affective processes. LKM is associated to love, sensations around the heart, and warmth. The LKM-outcomes were replicated with another independent set of MpI. These findings verify the merit of MpI as a scientific tool to gain reliable first-person data beyond questionnaires or rating scales. Copyright © 2018 Elsevier Inc. All rights reserved.

Multidisciplinary perspective intervention with community involvement to decrease antibiotic sales in village groceries in Thailand.

PubMed

Arparsrithongsagul, Somsak; Kulsomboon, Vithaya; Zuckerman, Ilene H

2015-03-01

In Thailand, antibiotics are rampantly available in village groceries, despite the fact that it is illegal to sell antibiotics without a pharmacy license. This study implemented a multidisciplinary perspectives intervention with community involvement (MPI&CI), which was developed based on information obtained from focus groups that included multidisciplinary stakeholders. Community leaders in the intervention group were trained to implement MPI&CI in their villages. A quasi-experiment with a pretest-posttest design was conducted. Data were collected from 20 villages in Mahasarakham Province (intervention group) along with another 20 villages (comparison group). Using a generalized linear mixed model Poisson regression with repeated measures, groceries in the intervention group had 87% fewer antibiotics available at postintervention compared with preintervention (relative rate = 0.13; 95% confidence interval = 0.07-0.23), whereas the control group had only an 8% reduction in antibiotic availability (relative rate = 0.92; 95% confidence interval = 0.88-0.97) between the 2 time periods. Further study should be made to assess the sustainability and long-term effectiveness of MPI&CI. © 2013 APJPH.

Hybrid MPI/OpenMP Implementation of the ORAC Molecular Dynamics Program for Generalized Ensemble and Fast Switching Alchemical Simulations.

PubMed

Procacci, Piero

2016-06-27

We present a new release (6.0β) of the ORAC program [Marsili et al. J. Comput. Chem. 2010, 31, 1106-1116] with a hybrid OpenMP/MPI (open multiprocessing message passing interface) multilevel parallelism tailored for generalized ensemble (GE) and fast switching double annihilation (FS-DAM) nonequilibrium technology aimed at evaluating the binding free energy in drug-receptor system on high performance computing platforms. The production of the GE or FS-DAM trajectories is handled using a weak scaling parallel approach on the MPI level only, while a strong scaling force decomposition scheme is implemented for intranode computations with shared memory access at the OpenMP level. The efficiency, simplicity, and inherent parallel nature of the ORAC implementation of the FS-DAM algorithm, project the code as a possible effective tool for a second generation high throughput virtual screening in drug discovery and design. The code, along with documentation, testing, and ancillary tools, is distributed under the provisions of the General Public License and can be freely downloaded at www.chim.unifi.it/orac .

Message Passing on GPUs

NASA Astrophysics Data System (ADS)

Stuart, J. A.

2011-12-01

This paper explores the challenges in implementing a message passing interface usable on systems with data-parallel processors, and more specifically GPUs. As a case study, we design and implement the ``DCGN'' API on NVIDIA GPUs that is similar to MPI and allows full access to the underlying architecture. We introduce the notion of data-parallel thread-groups as a way to map resources to MPI ranks. We use a method that also allows the data-parallel processors to run autonomously from user-written CPU code. In order to facilitate communication, we use a sleep-based polling system to store and retrieve messages. Unlike previous systems, our method provides both performance and flexibility. By running a test suite of applications with different communication requirements, we find that a tolerable amount of overhead is incurred, somewhere between one and five percent depending on the application, and indicate the locations where this overhead accumulates. We conclude that with innovations in chipsets and drivers, this overhead will be mitigated and provide similar performance to typical CPU-based MPI implementations while providing fully-dynamic communication.

Advances in Patch-Based Adaptive Mesh Refinement Scalability

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gunney, Brian T.N.; Anderson, Robert W.

Patch-based structured adaptive mesh refinement (SAMR) is widely used for high-resolution simu- lations. Combined with modern supercomputers, it could provide simulations of unprecedented size and resolution. A persistent challenge for this com- bination has been managing dynamically adaptive meshes on more and more MPI tasks. The dis- tributed mesh management scheme in SAMRAI has made some progress SAMR scalability, but early al- gorithms still had trouble scaling past the regime of 105 MPI tasks. This work provides two critical SAMR regridding algorithms, which are integrated into that scheme to ensure efficiency of the whole. The clustering algorithm is an extensionmore » of the tile- clustering approach, making it more flexible and efficient in both clustering and parallelism. The partitioner is a new algorithm designed to prevent the network congestion experienced by its prede- cessor. We evaluated performance using weak- and strong-scaling benchmarks designed to be difficult for dynamic adaptivity. Results show good scaling on up to 1.5M cores and 2M MPI tasks. Detailed timing diagnostics suggest scaling would continue well past that.« less

Dust Dynamics in Protoplanetary Disks: Parallel Computing with PVM

NASA Astrophysics Data System (ADS)

de La Fuente Marcos, Carlos; Barge, Pierre; de La Fuente Marcos, Raúl

2002-03-01

We describe a parallel version of our high-order-accuracy particle-mesh code for the simulation of collisionless protoplanetary disks. We use this code to carry out a massively parallel, two-dimensional, time-dependent, numerical simulation, which includes dust particles, to study the potential role of large-scale, gaseous vortices in protoplanetary disks. This noncollisional problem is easy to parallelize on message-passing multicomputer architectures. We performed the simulations on a cache-coherent nonuniform memory access Origin 2000 machine, using both the parallel virtual machine (PVM) and message-passing interface (MPI) message-passing libraries. Our performance analysis suggests that, for our problem, PVM is about 25% faster than MPI. Using PVM and MPI made it possible to reduce CPU time and increase code performance. This allows for simulations with a large number of particles (N ~ 105-106) in reasonable CPU times. The performances of our implementation of the pa! rallel code on an Origin 2000 supercomputer are presented and discussed. They exhibit very good speedup behavior and low load unbalancing. Our results confirm that giant gaseous vortices can play a dominant role in giant planet formation.

Internal standards for use in the comprehensive analysis of polychlorinated aromatic hydrocarbons using gas chromatography combined with multiphoton ionization mass spectrometry.

PubMed

Li, Adan; Imasaka, Totaro

2016-10-28

To decrease health-risks to humans, non-toxic compounds were evaluated for use as internal standards for calibrating data obtained by gas chromatography/multiphoton ionization mass spectrometry (GC-MPI-MS) using an ultraviolet femtosecond laser as the ionization source. The retention time in the mass chromatogram was calibrated using a retention index, in which a series of n-alkanes was employed as internal standards for evaluating the retention times for polychlorinated dibenzo-p-dioxins (PCDDs), polychlorinated dibenzofurans (PCDFs), and polychlorinated biphenyls (PCBs). To compensate for changes in signal intensity in MPI-MS, the dependence of signal intensity on the laser pulse energy was investigated for the dioxin-like compounds, in addition to five non-toxic aromatic hydrocarbons, that were used as internal standards. Based on their similar behavior,the non-toxic PCDD/PCDF, its 13 C-isotope, and pentachlorobenzene behave similarly, we conclude that they can be used for calibrating the signal intensities in MPI-MS. Copyright © 2016 Elsevier B.V. All rights reserved.

SeMPI: a genome-based secondary metabolite prediction and identification web server.

PubMed

Zierep, Paul F; Padilla, Natàlia; Yonchev, Dimitar G; Telukunta, Kiran K; Klementz, Dennis; Günther, Stefan

2017-07-03

The secondary metabolism of bacteria, fungi and plants yields a vast number of bioactive substances. The constantly increasing amount of published genomic data provides the opportunity for an efficient identification of gene clusters by genome mining. Conversely, for many natural products with resolved structures, the encoding gene clusters have not been identified yet. Even though genome mining tools have become significantly more efficient in the identification of biosynthetic gene clusters, structural elucidation of the actual secondary metabolite is still challenging, especially due to as yet unpredictable post-modifications. Here, we introduce SeMPI, a web server providing a prediction and identification pipeline for natural products synthesized by polyketide synthases of type I modular. In order to limit the possible structures of PKS products and to include putative tailoring reactions, a structural comparison with annotated natural products was introduced. Furthermore, a benchmark was designed based on 40 gene clusters with annotated PKS products. The web server of the pipeline (SeMPI) is freely available at: http://www.pharmaceutical-bioinformatics.de/sempi. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

FLY MPI-2: a parallel tree code for LSS

NASA Astrophysics Data System (ADS)

Becciani, U.; Comparato, M.; Antonuccio-Delogu, V.

2006-04-01

New version program summaryProgram title: FLY 3.1 Catalogue identifier: ADSC_v2_0 Licensing provisions: yes Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADSC_v2_0 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland No. of lines in distributed program, including test data, etc.: 158 172 No. of bytes in distributed program, including test data, etc.: 4 719 953 Distribution format: tar.gz Programming language: Fortran 90, C Computer: Beowulf cluster, PC, MPP systems Operating system: Linux, Aix RAM: 100M words Catalogue identifier of previous version: ADSC_v1_0 Journal reference of previous version: Comput. Phys. Comm. 155 (2003) 159 Does the new version supersede the previous version?: yes Nature of problem: FLY is a parallel collisionless N-body code for the calculation of the gravitational force Solution method: FLY is based on the hierarchical oct-tree domain decomposition introduced by Barnes and Hut (1986) Reasons for the new version: The new version of FLY is implemented by using the MPI-2 standard: the distributed version 3.1 was developed by using the MPICH2 library on a PC Linux cluster. Today the FLY performance allows us to consider the FLY code among the most powerful parallel codes for tree N-body simulations. Another important new feature regards the availability of an interface with hydrodynamical Paramesh based codes. Simulations must follow a box large enough to accurately represent the power spectrum of fluctuations on very large scales so that we may hope to compare them meaningfully with real data. The number of particles then sets the mass resolution of the simulation, which we would like to make as fine as possible. The idea to build an interface between two codes, that have different and complementary cosmological tasks, allows us to execute complex cosmological simulations with FLY, specialized for DM evolution, and a code specialized for hydrodynamical components that uses a Paramesh block structure. Summary of revisions: The parallel communication schema was totally changed. The new version adopts the MPICH2 library. Now FLY can be executed on all Unix systems having an MPI-2 standard library. The main data structure, is declared in a module procedure of FLY (fly_h.F90 routine). FLY creates the MPI Window object for one-sided communication for all the shared arrays, with a call like the following: CALL MPI_WIN_CREATE(POS, SIZE, REAL8, MPI_INFO_NULL, MPI_COMM_WORLD, WIN_POS, IERR) the following main window objects are created: win_pos, win_vel, win_acc: particles positions velocities and accelerations, win_pos_cell, win_mass_cell, win_quad, win_subp, win_grouping: cells positions, masses, quadrupole momenta, tree structure and grouping cells. Other windows are created for dynamic load balance and global counters. Restrictions: The program uses the leapfrog integrator schema, but could be changed by the user. Unusual features: FLY uses the MPI-2 standard: the MPICH2 library on Linux systems was adopted. To run this version of FLY the working directory must be shared among all the processors that execute FLY. Additional comments: Full documentation for the program is included in the distribution in the form of a README file, a User Guide and a Reference manuscript. Running time: IBM Linux Cluster 1350, 512 nodes with 2 processors for each node and 2 GB RAM for each processor, at Cineca, was adopted to make performance tests. Processor type: Intel Xeon Pentium IV 3.0 GHz and 512 KB cache (128 nodes have Nocona processors). Internal Network: Myricom LAN Card "C" Version and "D" Version. Operating System: Linux SuSE SLES 8. The code was compiled using the mpif90 compiler version 8.1 and with basic optimization options in order to have performances that could be useful compared with other generic clusters Processors

The Research of the Parallel Computing Development from the Angle of Cloud Computing

NASA Astrophysics Data System (ADS)

Peng, Zhensheng; Gong, Qingge; Duan, Yanyu; Wang, Yun

2017-10-01

Cloud computing is the development of parallel computing, distributed computing and grid computing. The development of cloud computing makes parallel computing come into people’s lives. Firstly, this paper expounds the concept of cloud computing and introduces two several traditional parallel programming model. Secondly, it analyzes and studies the principles, advantages and disadvantages of OpenMP, MPI and Map Reduce respectively. Finally, it takes MPI, OpenMP models compared to Map Reduce from the angle of cloud computing. The results of this paper are intended to provide a reference for the development of parallel computing.

Right ventricular failure resulting from pressure overload: role of intra-aortic balloon counterpulsation and vasopressor therapy.

PubMed

Liakopoulos, Oliver J; Ho, Jonathan K; Yezbick, Aaron B; Sanchez, Elizabeth; Singh, Vivek; Mahajan, Aman

2010-11-01

Augmentation of coronary perfusion may improve right ventricular (RV) failure following acute increases of RV afterload. We investigated whether intra-aortic balloon counterpulsation (IABP) can improve cardiac function by enhancing myocardial perfusion and reversing compromised biventricular interactions using a model of acute pressure overload. In 10 anesthetized pigs, RV failure was induced by pulmonary artery constriction and systemic hypertension strategies with IABP, phenylephrine (PE), or the combination of both were tested. Systemic and ventricular hemodynamics [cardiac index(CI), ventricular pressures, coronary driving pressures (CDP)] were measured and echocardiography was used to assess tricuspid valve regurgitation, septal positioning (eccentricity index (ECI)), and changes in ventricular and septal dimensions and function [myocardial performance index (MPI), peak longitudinal strain]. Pulmonary artery constriction resulted in doubling of RV systolic pressure (54 ± 4mm Hg), RV distension, severe TR (4+) with decreased RV function (strain: -33%; MPI: +56%), septal flattening (Wt%: -35%) and leftward septal shift (ECI:1.36), resulting in global hemodynamic deterioration (CI: -51%; SvO(2): -26%), and impaired CDP (-30%; P<0.05). IABP support alone failed to improve RV function despite higher CDP (+33%; P<0.05). Systemic hypertension by PE improved CDP (+70%), RV function (strain: +22%; MPI: -21%), septal positioning (ECI:1.12) and minimized TR, but LV dysfunction (strain: -25%; MPI: +31%) occurred after LV afterloading (P<0.05). With IABP, less PE (-41%) was needed to maintain hypertension and CDP was further augmented (+25%). IABP resulted in LV unloading and restored LV function, and increased CI (+46%) and SvO(2) (+29%; P<0.05). IABP with minimal vasopressors augments myocardial perfusion pressure and optimizes RV function after pressure-induced failure. Copyright © 2010 Elsevier Inc. All rights reserved.

Implementation of a Message Passing Interface into a Cloud-Resolving Model for Massively Parallel Computing

NASA Technical Reports Server (NTRS)

Juang, Hann-Ming Henry; Tao, Wei-Kuo; Zeng, Xi-Ping; Shie, Chung-Lin; Simpson, Joanne; Lang, Steve

2004-01-01

The capability for massively parallel programming (MPP) using a message passing interface (MPI) has been implemented into a three-dimensional version of the Goddard Cumulus Ensemble (GCE) model. The design for the MPP with MPI uses the concept of maintaining similar code structure between the whole domain as well as the portions after decomposition. Hence the model follows the same integration for single and multiple tasks (CPUs). Also, it provides for minimal changes to the original code, so it is easily modified and/or managed by the model developers and users who have little knowledge of MPP. The entire model domain could be sliced into one- or two-dimensional decomposition with a halo regime, which is overlaid on partial domains. The halo regime requires that no data be fetched across tasks during the computational stage, but it must be updated before the next computational stage through data exchange via MPI. For reproducible purposes, transposing data among tasks is required for spectral transform (Fast Fourier Transform, FFT), which is used in the anelastic version of the model for solving the pressure equation. The performance of the MPI-implemented codes (i.e., the compressible and anelastic versions) was tested on three different computing platforms. The major results are: 1) both versions have speedups of about 99% up to 256 tasks but not for 512 tasks; 2) the anelastic version has better speedup and efficiency because it requires more computations than that of the compressible version; 3) equal or approximately-equal numbers of slices between the x- and y- directions provide the fastest integration due to fewer data exchanges; and 4) one-dimensional slices in the x-direction result in the slowest integration due to the need for more memory relocation for computation.

Parallel workflow manager for non-parallel bioinformatic applications to solve large-scale biological problems on a supercomputer.

PubMed

Suplatov, Dmitry; Popova, Nina; Zhumatiy, Sergey; Voevodin, Vladimir; Švedas, Vytas

2016-04-01

Rapid expansion of online resources providing access to genomic, structural, and functional information associated with biological macromolecules opens an opportunity to gain a deeper understanding of the mechanisms of biological processes due to systematic analysis of large datasets. This, however, requires novel strategies to optimally utilize computer processing power. Some methods in bioinformatics and molecular modeling require extensive computational resources. Other algorithms have fast implementations which take at most several hours to analyze a common input on a modern desktop station, however, due to multiple invocations for a large number of subtasks the full task requires a significant computing power. Therefore, an efficient computational solution to large-scale biological problems requires both a wise parallel implementation of resource-hungry methods as well as a smart workflow to manage multiple invocations of relatively fast algorithms. In this work, a new computer software mpiWrapper has been developed to accommodate non-parallel implementations of scientific algorithms within the parallel supercomputing environment. The Message Passing Interface has been implemented to exchange information between nodes. Two specialized threads - one for task management and communication, and another for subtask execution - are invoked on each processing unit to avoid deadlock while using blocking calls to MPI. The mpiWrapper can be used to launch all conventional Linux applications without the need to modify their original source codes and supports resubmission of subtasks on node failure. We show that this approach can be used to process huge amounts of biological data efficiently by running non-parallel programs in parallel mode on a supercomputer. The C++ source code and documentation are available from http://biokinet.belozersky.msu.ru/mpiWrapper .

Protecting effect of PrP codons M142 and K222 in goats orally challenged with bovine spongiform encephalopathy prions.

PubMed

Fast, C; Goldmann, W; Berthon, P; Tauscher, K; Andréoletti, O; Lantier, I; Rossignol, C; Bossers, A; Jacobs, J G; Hunter, N; Groschup, M H; Lantier, F; Langeveld, J P M

2017-09-19

Breeding towards genetic resistance to prion disease is effective in eliminating scrapie. In sheep, classical forms of scrapie have been eradicated almost completely in several countries by breeding programs using a prion protein (PrP) gene (PRNP) amino acid polymorphism. For goats, field and experimental studies have provided evidence for several amino acid polymorphisms that are associated with resistance to scrapie, but only limited data are available concerning the susceptibility of caprine PRNP genotypes to BSE. In this study, goat kids representing five PRNP genotypes based on three polymorphisms (M142, Q211 and K222 and the wild type I142, R211 and Q222) were orally challenged with bovine or goat BSE. Wild type goats were killed with clinical signs between 24-28 months post inoculation (mpi) to both challenges, and goats with genotype R/Q211 succumbed between 29-36 mpi. I/M142 goats developed clinical signs at 44-45 mpi and M/M142 goats remained healthy until euthanasia at 48 mpi. None of the Q/K222 goats showed definite clinical signs. Taken together the highest attack ratios were seen in wild type and R/Q211 goats, and the lowest in I/M142, M/M142 and Q/K222. In all genotype groups, one or more goats remained healthy within the incubation period in both challenges and without detectable PrP deposition in the tissues. Our data show that both the K222 and M142 polymorphisms lengthen the incubation period significantly compared to wild type animals, but only K222 was associated with a significant increase in resistance to BSE infection after oral exposure to both BSE sources.

Development of instrumentation for differential spectroscopic measurements at millimeter wavelengths

NASA Astrophysics Data System (ADS)

D'Alessandro, G.; de Bernardis, P.; Masi, S.; Schillaci, A.

2016-07-01

The study of the spectral-spatial anisotropy of the high-latitude mm-wave sky is a powerful tool of cosmology. It can be used to provide deep insight in the Sunyaev-Zeldovich (SZ) effect, the Cosmic Infrared Background, the anisotropy of the CMB, using the spectral dimension to provide substantially increased information with respect to what is achievable by means of standard multiband photometry. Here we focus on spectral measurements of the SZ effect. Large mm-wave telescopes are now routinely mapping photometrically the SZ effect in a number of clusters, estimating the comptonisation parameter and using them as cosmological probes. Low-resolution spectroscopic measurements of the SZ effect would be very effective in removing the degeneracy between parameters inevitable in photometric measurements. We describe a real-world implementation of this measurement strategy, based on an imaging, efficient, differential Fourier transform spectrometer (FTS). The instrument is based on a Martin-Puplett interferometer (MPI) configuration. We combined two MPIs working synchronously to use the entire input power. In our implementation the observed sky field is divided into two halves along the meridian. Each half-field corresponds to one of the two input ports of the MPI. Each detector in the FTS focal planes measures the difference in brightness between two sky pixels, symmetrically located with respect to the meridian. Exploiting the high common mode rejection of the MPI, tiny sky brightness gradients embedded in an overwhelming isotropic background might be measured. We investigate experimentally the common-mode rejection achievable in the MPI at mm wavelengths, and discuss the use of such an instrument to measure the spectrum of cosmic microwave background (CMB) anisotropy and the SZ effect.

Detecting Myocardial Ischemia With 99mTechnetium-Tetrofosmin Myocardial Perfusion Imaging in Ischemic Stroke.

PubMed

Giannopoulos, Sotirios; Markoula, Sofia; Sioka, Chrissa; Zouroudi, Sofia; Spiliotopoulou, Maria; Naka, Katerina K; Michalis, Lampros K; Fotopoulos, Andreas; Kyritsis, Athanassios P

2017-10-01

To assess the myocardial status in patients with stroke, employing myocardial perfusion imaging (MPI) with 99m Technetium-tetrofosmin ( 99m Tc-TF)-single-photon emission computed tomography (SPECT). Fifty-two patients with ischemic stroke were subjected to 99m Tc-TF-SPECT MPI within 1 month after stroke occurrence. None of the patients had any history or symptoms of coronary artery disease or other heart disease. Myocardial perfusion imaging was evaluated visually using a 17-segment polar map. Myocardial ischemia (MIS) was defined as present when the summed stress score (SSS) was >4; MIS was defined as mild when SSS was 4 to 8, and moderate/severe with SSS ≥9. Patients with SSS >4 were compared to patients with SSS <4. Parameters such as age, body mass index, waist perimeter, smoking habits, and medical history (diabetes mellitus, dyslipidemia, etc) were evaluated according to MPI results. Myocardial ischemia was present in 32 (62%) of 52 patients with stroke. Among them, 20 (62%) of 32 patients had mild abnormalities and 12 (38%) of 32 had moderate/severe. The age and waist perimeter showed a tendency to relate to severe MIS when patients with SSS >9 were compared to patients with SSS <4. In MPI-positive patients, an age was to be association with SSS, with the oldest age exhibiting the highest SSS ( P = .01). The association of age with SSS remained statistically significant in the multivariate analysis ( P = .04). The study suggested that more than half of patients with stroke without a history of cardiac disease have MIS. Although most of them have mild MIS, we suggest a thorough cardiological evaluation in this group of patients for future prevention of severe myocardial outcome.

Diagnostic value of thallium-201 myocardial perfusion IQ-SPECT without and with computed tomography-based attenuation correction to predict clinically significant and insignificant fractional flow reserve

PubMed Central

Tanaka, Haruki; Takahashi, Teruyuki; Ohashi, Norihiko; Tanaka, Koichi; Okada, Takenori; Kihara, Yasuki

2017-01-01

Abstract The aim of this study was to clarify the predictive value of fractional flow reserve (FFR) determined by myocardial perfusion imaging (MPI) using thallium (Tl)-201 IQ-SPECT without and with computed tomography-based attenuation correction (CT-AC) for patients with stable coronary artery disease (CAD). We assessed 212 angiographically identified diseased vessels using adenosine-stress Tl-201 MPI-IQ-SPECT/CT in 84 consecutive, prospectively identified patients with stable CAD. We compared the FFR in 136 of the 212 diseased vessels using visual semiquantitative interpretations of corresponding territories on MPI-IQ-SPECT images without and with CT-AC. FFR inversely correlated most accurately with regional summed difference scores (rSDS) in images without and with CT-AC (r = −0.584 and r = −0.568, respectively, both P < .001). Receiver-operating characteristics analyses using rSDS revealed an optimal FFR cut-off of <0.80 without and with CT-AC. Although the diagnostic accuracy of FFR <0.80 did not significantly differ, FFR ≥0.82 was significantly more accurate with, than without CT-AC. Regions with rSDS ≥2 without or with CT-AC predicted FFR <0.80, and those with rSDS ≤1 without and with CT-AC predicted FFR ≥0.81, with 73% and 83% sensitivity, 84% and 67% specificity, and 79% and 75% accuracy, respectively. Although limited by the sample size and the single-center design, these findings showed that the IQ-SPECT system can predict FFR at an optimal cut-off of <0.80, and we propose a novel application of CT-AC to MPI-IQ-SPECT for predicting clinically significant and insignificant FFR even in nonobese patients. PMID:29390486

High performance Python for direct numerical simulations of turbulent flows

NASA Astrophysics Data System (ADS)

Mortensen, Mikael; Langtangen, Hans Petter

2016-06-01

Direct Numerical Simulations (DNS) of the Navier Stokes equations is an invaluable research tool in fluid dynamics. Still, there are few publicly available research codes and, due to the heavy number crunching implied, available codes are usually written in low-level languages such as C/C++ or Fortran. In this paper we describe a pure scientific Python pseudo-spectral DNS code that nearly matches the performance of C++ for thousands of processors and billions of unknowns. We also describe a version optimized through Cython, that is found to match the speed of C++. The solvers are written from scratch in Python, both the mesh, the MPI domain decomposition, and the temporal integrators. The solvers have been verified and benchmarked on the Shaheen supercomputer at the KAUST supercomputing laboratory, and we are able to show very good scaling up to several thousand cores. A very important part of the implementation is the mesh decomposition (we implement both slab and pencil decompositions) and 3D parallel Fast Fourier Transforms (FFT). The mesh decomposition and FFT routines have been implemented in Python using serial FFT routines (either NumPy, pyFFTW or any other serial FFT module), NumPy array manipulations and with MPI communications handled by MPI for Python (mpi4py). We show how we are able to execute a 3D parallel FFT in Python for a slab mesh decomposition using 4 lines of compact Python code, for which the parallel performance on Shaheen is found to be slightly better than similar routines provided through the FFTW library. For a pencil mesh decomposition 7 lines of code is required to execute a transform.

Proactive Fault Tolerance for HPC with Xen Virtualization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nagarajan, Arun Babu; Mueller, Frank; Engelmann, Christian

2007-01-01

with thousands of processors. At such large counts of compute nodes, faults are becoming common place. Current techniques to tolerate faults focus on reactive schemes to recover from faults and generally rely on a checkpoint/restart mechanism. Yet, in today's systems, node failures can often be anticipated by detecting a deteriorating health status. Instead of a reactive scheme for fault tolerance (FT), we are promoting a proactive one where processes automatically migrate from “unhealthy” nodes to healthy ones. Our approach relies on operating system virtualization techniques exemplied by but not limited to Xen. This paper contributes an automatic and transparent mechanismmore » for proactive FT for arbitrary MPI applications. It leverages virtualization techniques combined with health monitoring and load-based migration. We exploit Xen's live migration mechanism for a guest operating system (OS) to migrate an MPI task from a health-deteriorating node to a healthy one without stopping the MPI task during most of the migration. Our proactive FT daemon orchestrates the tasks of health monitoring, load determination and initiation of guest OS migration. Experimental results demonstrate that live migration hides migration costs and limits the overhead to only a few seconds making it an attractive approach to realize FT in HPC systems. Overall, our enhancements make proactive FT a valuable asset for long-running MPI application that is complementary to reactive FT using full checkpoint/ restart schemes since checkpoint frequencies can be reduced as fewer unanticipated failures are encountered. In the context of OS virtualization, we believe that this is the rst comprehensive study of proactive fault tolerance where live migration is actually triggered by health monitoring.« less

Oxyanion Induced Variations in Domain Structure for Amorphous Cobalt Oxide Oxygen Evolving Catalysts, Resolved by X-ray Pair Distribution Function Analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kwon, Gihan; Kokhan, Oleksandr; Han, Ali

Amorphous thin film oxygen evolving catalysts, OECs, of first-row transition metals show promise to serve as self-assembling photoanode materials in solar-driven, photoelectrochemical `artificial leaf' devices. This report demonstrates the ability to use high-energy X-ray scattering and atomic pair distribution function analysis, PDF, to resolve structure in amorphous metal oxide catalyst films. The analysis is applied here to resolve domain structure differences induced by oxyanion substitution during the electrochemical assembly of amorphous cobalt oxide catalyst films, Co-OEC. PDF patterns for Co-OEC films formed using phosphate, Pi, methylphosphate, MPi, and borate, Bi, electrolyte buffers show that the resulting domains vary in sizemore » following the sequence Pi < MPi < Bi. The increases in domain size for CoMPi and CoBi were found to be correlated with increases in the contributions from bilayer and trilayer stacked domains having structures intermediate between those of the LiCoOO and CoO(OH) mineral forms. The lattice structures and offset stacking of adjacent layers in the partially stacked CoMPi and CoBi domains were best matched to those in the LiCoOO layered structure. The results demonstrate the ability of PDF analysis to elucidate features of domain size, structure, defect content and mesoscale organization for amorphous metal oxide catalysts that are not readily accessed by other X-ray techniques. Finally, PDF structure analysis is shown to provide a way to characterize domain structures in different forms of amorphous oxide catalysts, and hence provide an opportunity to investigate correlations between domain structure and catalytic activity.« less

Oxyanion Induced Variations in Domain Structure for Amorphous Cobalt Oxide Oxygen Evolving Catalysts, Resolved by X-ray Pair Distribution Function Analysis

DOE PAGES

Kwon, Gihan; Kokhan, Oleksandr; Han, Ali; ...

2015-12-01

Amorphous thin film oxygen evolving catalysts, OECs, of first-row transition metals show promise to serve as self-assembling photoanode materials in solar-driven, photoelectrochemical `artificial leaf' devices. This report demonstrates the ability to use high-energy X-ray scattering and atomic pair distribution function analysis, PDF, to resolve structure in amorphous metal oxide catalyst films. The analysis is applied here to resolve domain structure differences induced by oxyanion substitution during the electrochemical assembly of amorphous cobalt oxide catalyst films, Co-OEC. PDF patterns for Co-OEC films formed using phosphate, Pi, methylphosphate, MPi, and borate, Bi, electrolyte buffers show that the resulting domains vary in sizemore » following the sequence Pi < MPi < Bi. The increases in domain size for CoMPi and CoBi were found to be correlated with increases in the contributions from bilayer and trilayer stacked domains having structures intermediate between those of the LiCoOO and CoO(OH) mineral forms. The lattice structures and offset stacking of adjacent layers in the partially stacked CoMPi and CoBi domains were best matched to those in the LiCoOO layered structure. The results demonstrate the ability of PDF analysis to elucidate features of domain size, structure, defect content and mesoscale organization for amorphous metal oxide catalysts that are not readily accessed by other X-ray techniques. Finally, PDF structure analysis is shown to provide a way to characterize domain structures in different forms of amorphous oxide catalysts, and hence provide an opportunity to investigate correlations between domain structure and catalytic activity.« less

Revised Extended Grid Library

DOE Office of Scientific and Technical Information (OSTI.GOV)

Martz, Roger L.

The Revised Eolus Grid Library (REGL) is a mesh-tracking library that was developed for use with the MCNP6TM computer code so that (radiation) particles can track on an unstructured mesh. The unstructured mesh is a finite element representation of any geometric solid model created with a state-of-the-art CAE/CAD tool. The mesh-tracking library is written using modern Fortran and programming standards; the library is Fortran 2003 compliant. The library was created with a defined application programmer interface (API) so that it could easily integrate with other particle tracking/transport codes. The library does not handle parallel processing via the message passing interfacemore » (mpi), but has been used successfully where the host code handles the mpi calls. The library is thread-safe and supports the OpenMP paradigm. As a library, all features are available through the API and overall a tight coupling between it and the host code is required. Features of the library are summarized with the following list: Can accommodate first and second order 4, 5, and 6-sided polyhedra; any combination of element types may appear in a single geometry model; parts may not contain tetrahedra mixed with other element types; pentahedra and hexahedra can be together in the same part; robust handling of overlaps and gaps; tracks element-to-element to produce path length results at the element level; finds element numbers for a given mesh location; finds intersection points on element faces for the particle tracks; produce a data file for post processing results analysis; reads Abaqus .inp input (ASCII) files to obtain information for the global mesh-model; supports parallel input processing via mpi; and support parallel particle transport by both mpi and OpenMP.« less

Contribution of Secretory Antibodies to Intestinal Mucosal Immunity against Helicobacter pylori

PubMed Central

Wijburg, Odilia L. C.; Pedersen, John S.; Walduck, Anna K.; Kwok, Terry; Strugnell, Richard A.; Robins-Browne, Roy M.

2013-01-01

The natural immune response to Helicobacter pylori neither clears infection nor prevents reinfection. However, the ability of secretory antibodies to influence the course of H. pylori infection has not been determined. We compared the natural progression of H. pylori infection in wild-type C57BL/6 mice with that in mice lacking the polymeric immunoglobulin receptor (pIgR) that is essential for the secretion of polymeric antibody across mucosal surfaces. H. pylori SS1-infected wild-type and pIgR knockout (KO) mice were sampled longitudinally for gastrointestinal bacterial load, antibody response, and histological changes. The gastric bacterial loads of wild-type and pIgR KO mice remained constant and comparable at up to 3 months postinfection (mpi) despite SS1-reactive secretory IgA in the intestinal contents of wild-type mice at that time. Conversely, abundant duodenal colonization of pIgR KO animals contrasted with the near-total eradication of H. pylori from the intestine of wild-type animals by 3 mpi. H. pylori was cultured only from the duodenum of those animals in which colonization in the distal gastric antrum was of sufficient density for immunohistological detection. By 6 mpi, the gastric load of H. pylori in wild-type mice was significantly lower than in pIgR KO animals. While there was no corresponding difference between the two mouse strains in gastric pathology results at 6 mpi, reductions in gastric bacterial load correlated with increased gastric inflammation together with an intestinal secretory antibody response in wild-type mice. Together, these results suggest that naturally produced secretory antibodies can modulate the progress of H. pylori infection, particularly in the duodenum. PMID:23918779

Preterm infant gut microbiota affects intestinal epithelial development in a humanized microbiome gnotobiotic mouse model.

PubMed

Yu, Yueyue; Lu, Lei; Sun, Jun; Petrof, Elaine O; Claud, Erika C

2016-09-01

Development of the infant small intestine is influenced by bacterial colonization. To promote establishment of optimal microbial communities in preterm infants, knowledge of the beneficial functions of the early gut microbiota on intestinal development is needed. The purpose of this study was to investigate the impact of early preterm infant microbiota on host gut development using a gnotobiotic mouse model. Histological assessment of intestinal development was performed. The differentiation of four epithelial cell lineages (enterocytes, goblet cells, Paneth cells, enteroendocrine cells) and tight junction (TJ) formation was examined. Using weight gain as a surrogate marker for health, we found that early microbiota from a preterm infant with normal weight gain (MPI-H) induced increased villus height and crypt depth, increased cell proliferation, increased numbers of goblet cells and Paneth cells, and enhanced TJs compared with the changes induced by early microbiota from a poor weight gain preterm infant (MPI-L). Laser capture microdissection (LCM) plus qRT-PCR further revealed, in MPI-H mice, a higher expression of stem cell marker Lgr5 and Paneth cell markers Lyz1 and Cryptdin5 in crypt populations, along with higher expression of the goblet cell and mature enterocyte marker Muc3 in villus populations. In contrast, MPI-L microbiota failed to induce the aforementioned changes and presented intestinal characteristics comparable to a germ-free host. Our data demonstrate that microbial communities have differential effects on intestinal development. Future studies to identify pioneer settlers in neonatal microbial communities necessary to induce maturation may provide new insights for preterm infant microbial ecosystem therapeutics. Copyright © 2016 the American Physiological Society.

In situ and in-transit analysis of cosmological simulations

DOE PAGES

Friesen, Brian; Almgren, Ann; Lukic, Zarija; ...

2016-08-24

Modern cosmological simulations have reached the trillion-element scale, rendering data storage and subsequent analysis formidable tasks. To address this circumstance, we present a new MPI-parallel approach for analysis of simulation data while the simulation runs, as an alternative to the traditional workflow consisting of periodically saving large data sets to disk for subsequent ‘offline’ analysis. We demonstrate this approach in the compressible gasdynamics/N-body code Nyx, a hybrid MPI+OpenMP code based on the BoxLib framework, used for large-scale cosmological simulations. We have enabled on-the-fly workflows in two different ways: one is a straightforward approach consisting of all MPI processes periodically haltingmore » the main simulation and analyzing each component of data that they own (‘ in situ’). The other consists of partitioning processes into disjoint MPI groups, with one performing the simulation and periodically sending data to the other ‘sidecar’ group, which post-processes it while the simulation continues (‘in-transit’). The two groups execute their tasks asynchronously, stopping only to synchronize when a new set of simulation data needs to be analyzed. For both the in situ and in-transit approaches, we experiment with two different analysis suites with distinct performance behavior: one which finds dark matter halos in the simulation using merge trees to calculate the mass contained within iso-density contours, and another which calculates probability distribution functions and power spectra of various fields in the simulation. Both are common analysis tasks for cosmology, and both result in summary statistics significantly smaller than the original data set. We study the behavior of each type of analysis in each workflow in order to determine the optimal configuration for the different data analysis algorithms.« less

Intracellular performance of tailored nanoparticle tracers in magnetic particle imaging

NASA Astrophysics Data System (ADS)

Arami, Hamed; Krishnan, Kannan M.

2014-05-01

Magnetic Particle Imaging (MPI) is a quantitative mass-sensitive, tracer-based imaging technique, with potential applications in various cellular imaging applications. The spatial resolution of MPI, in the first approximation, improves by decreasing the full width at half maximum (FWHM) of the field-derivative of the magnetization, dm/dH of the nanoparticle (NP) tracers. The FWHM of dm/dH depends critically on NPs' size, size distribution, and their environment. However, there is limited information on the MPI performance of the NPs after their internalization into cells. In this work, 30 to 150 μg of the iron oxide NPs were incubated in a lysosome-like acidic buffer (0.2 ml, 20 mM citric acid, pH 4.7) and investigated by vibrating sample magnetometry, magnetic particle spectroscopy, transmission electron microscopy, and dynamic light scattering (DLS). The FWHM of the dm/dH curves of the NPs increased with incubation time and buffer to NPs ratio, consistent with a decrease in the median core size of the NPs from ˜20.1 ± 0.98 to ˜18.5 ± 3.15 nm. Further, these smaller degraded NPs formed aggregates that responded to the applied field by hysteretic reversal at higher field values and increased the FWHM. The rate of core size decrease and aggregation were inversely proportional to the concentration of the incubated NPs, due to their slower biodegradation kinetics. The results of this model experiment show that the MPI performance of the NPs in the acidic environments of the intracellular organelles (i.e., lysosomes and endosomes) can be highly dependent on their rate of internalization, residence time, and degradation.

Cardiac PET perfusion tracers: current status and future directions.

PubMed

Maddahi, Jamshid; Packard, René R S

2014-09-01

PET myocardial perfusion imaging (MPI) is increasingly being used for noninvasive detection and evaluation of coronary artery disease. However, the widespread use of PET MPI has been limited by the shortcomings of the current PET perfusion tracers. The availability of these tracers is limited by the need for an onsite ((15)O water and (13)N ammonia) or nearby ((13)N ammonia) cyclotron or commitment to costly generators ((82)Rb). Owing to the short half-lives, such as 76 seconds for (82)Rb, 2.06 minutes for (15)O water, and 9.96 minutes for (13)N ammonia, their use in conjunction with treadmill exercise stress testing is either not possible ((82)Rb and (15)O water) or not practical ((13)N ammonia). Furthermore, the long positron range of (82)Rb makes image resolution suboptimal and its low myocardial extraction limits its defect resolution. In recent years, development of an (18)F-labeled PET perfusion tracer has gathered considerable interest. The longer half-life of (18)F (109 minutes) would make the tracer available as a unit dose from regional cyclotrons and allow use in conjunction with treadmill exercise testing. Furthermore, the short positron range of (18)F would result in better image resolution. Flurpiridaz F 18 is by far the most thoroughly studied in animal models and is the only (18)F-based PET MPI radiotracer currently undergoing clinical evaluation. Preclinical and clinical experience with Flurpiridaz F 18 demonstrated a high myocardial extraction fraction, high image and defect resolution, high myocardial uptake, slow myocardial clearance, and high myocardial-to-background contrast that was stable over time-important properties of an ideal PET MPI radiotracer. Preclinical data from other (18)F-labeled myocardial perfusion tracers are encouraging. Copyright © 2014. Published by Elsevier Inc.

Five year experience in management of perforated peptic ulcer and validation of common mortality risk prediction models - are existing models sufficient? A retrospective cohort study.

PubMed

Anbalakan, K; Chua, D; Pandya, G J; Shelat, V G

2015-02-01

Emergency surgery for perforated peptic ulcer (PPU) is associated with significant morbidity and mortality. Accurate and early risk stratification is important. The primary aim of this study is to validate the various existing MRPMs and secondary aim is to audit our experience of managing PPU. 332 patients who underwent emergency surgery for PPU at a single intuition from January 2008 to December 2012 were studied. Clinical and operative details were collected. Four MRPMs: American Society of Anesthesiology (ASA) score, Boey's score, Mannheim peritonitis index (MPI) and Peptic ulcer perforation (PULP) score were validated. Median age was 54.7 years (range 17-109 years) with male predominance (82.5%). 61.7% presented within 24 h of onset of abdominal pain. Median length of stay was 7 days (range 2-137 days). Intra-abdominal collection, leakage, re-operation and 30-day mortality rates were 8.1%, 2.1%, 1.2% and 7.2% respectively. All the four MRPMs predicted intra-abdominal collection and mortality; however, only MPI predicted leak (p = 0.01) and re-operation (p = 0.02) rates. The area under curve for predicting mortality was 75%, 72%, 77.2% and 75% for ASA score, Boey's score, MPI and PULP score respectively. Emergency surgery for PPU has low morbidity and mortality in our experience. MPI is the only scoring system which predicts all - intra-abdominal collection, leak, reoperation and mortality. All four MRPMs had a similar and fair accuracy to predict mortality, however due to geographic and demographic diversity and inherent weaknesses of exiting MRPMs, quest for development of an ideal model should continue. Copyright © 2015 Surgical Associates Ltd. Published by Elsevier Ltd. All rights reserved.

An approach to computing discrete adjoints for MPI-parallelized models applied to Ice Sheet System Model 4.11

NASA Astrophysics Data System (ADS)

Larour, Eric; Utke, Jean; Bovin, Anton; Morlighem, Mathieu; Perez, Gilberto

2016-11-01

Within the framework of sea-level rise projections, there is a strong need for hindcast validation of the evolution of polar ice sheets in a way that tightly matches observational records (from radar, gravity, and altimetry observations mainly). However, the computational requirements for making hindcast reconstructions possible are severe and rely mainly on the evaluation of the adjoint state of transient ice-flow models. Here, we look at the computation of adjoints in the context of the NASA/JPL/UCI Ice Sheet System Model (ISSM), written in C++ and designed for parallel execution with MPI. We present the adaptations required in the way the software is designed and written, but also generic adaptations in the tools facilitating the adjoint computations. We concentrate on the use of operator overloading coupled with the AdjoinableMPI library to achieve the adjoint computation of the ISSM. We present a comprehensive approach to (1) carry out type changing through the ISSM, hence facilitating operator overloading, (2) bind to external solvers such as MUMPS and GSL-LU, and (3) handle MPI-based parallelism to scale the capability. We demonstrate the success of the approach by computing sensitivities of hindcast metrics such as the misfit to observed records of surface altimetry on the northeastern Greenland Ice Stream, or the misfit to observed records of surface velocities on Upernavik Glacier, central West Greenland. We also provide metrics for the scalability of the approach, and the expected performance. This approach has the potential to enable a new generation of hindcast-validated projections that make full use of the wealth of datasets currently being collected, or already collected, in Greenland and Antarctica.

An Approach to Computing Discrete Adjoints for MPI-Parallelized Models Applied to the Ice Sheet System Model}

NASA Astrophysics Data System (ADS)

Perez, G. L.; Larour, E. Y.; Morlighem, M.

2016-12-01

Within the framework of sea-level rise projections, there is a strong need for hindcast validation of the evolution of polar ice sheets in a way that tightly matches observational records (from radar and altimetry observations mainly). However, the computational requirements for making hindcast reconstructions possible are severe and rely mainly on the evaluation of the adjoint state of transient ice-flow models. Here, we look at the computation of adjoints in the context of the NASA/JPL/UCI Ice Sheet System Model, written in C++ and designed for parallel execution with MPI. We present the adaptations required in the way the software is designed and written but also generic adaptations in the tools facilitating the adjoint computations. We concentrate on the use of operator overloading coupled with the AdjoinableMPI library to achieve the adjoint computation of ISSM. We present a comprehensive approach to 1) carry out type changing through ISSM, hence facilitating operator overloading, 2) bind to external solvers such as MUMPS and GSL-LU and 3) handle MPI-based parallelism to scale the capability. We demonstrate the success of the approach by computing sensitivities of hindcast metrics such as the misfit to observed records of surface altimetry on the North-East Greenland Ice Stream, or the misfit to observed records of surface velocities on Upernavik Glacier, Central West Greenland. We also provide metrics for the scalability of the approach, and the expected performance. This approach has the potential of enabling a new generation of hindcast-validated projections that make full use of the wealth of datasets currently being collected, or alreay collected in Greenland and Antarctica, such as surface altimetry, surface velocities, and/or gravity measurements.

On the Performance of an Algebraic MultigridSolver on Multicore Clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baker, A H; Schulz, M; Yang, U M

2010-04-29

Algebraic multigrid (AMG) solvers have proven to be extremely efficient on distributed-memory architectures. However, when executed on modern multicore cluster architectures, we face new challenges that can significantly harm AMG's performance. We discuss our experiences on such an architecture and present a set of techniques that help users to overcome the associated problems, including thread and process pinning and correct memory associations. We have implemented most of the techniques in a MultiCore SUPport library (MCSup), which helps to map OpenMP applications to multicore machines. We present results using both an MPI-only and a hybrid MPI/OpenMP model.

Accelerating Virtual High-Throughput Ligand Docking: current technology and case study on a petascale supercomputer.

PubMed

Ellingson, Sally R; Dakshanamurthy, Sivanesan; Brown, Milton; Smith, Jeremy C; Baudry, Jerome

2014-04-25

In this paper we give the current state of high-throughput virtual screening. We describe a case study of using a task-parallel MPI (Message Passing Interface) version of Autodock4 [1], [2] to run a virtual high-throughput screen of one-million compounds on the Jaguar Cray XK6 Supercomputer at Oak Ridge National Laboratory. We include a description of scripts developed to increase the efficiency of the predocking file preparation and postdocking analysis. A detailed tutorial, scripts, and source code for this MPI version of Autodock4 are available online at http://www.bio.utk.edu/baudrylab/autodockmpi.htm.

Using OFI libfabric on Cori/Edison

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pritchard, Howard Porter; Choi, Sung-Eun

2016-08-22

These are slides from a presentation during an NERSC site visit to Los Alamos National Laboratory. The following topics are covered: building/installing libfabric, OpenMPI using libfabric, MPICH using libfabric, Open SHMEM (Sandia), other applications, and what is next. The next steps are: get a libfabric 1.4 out, it would be nice to have libfabric 1.4 installed in system space on Cori, add libfabric modules on Cori, might be a good idea to have a SLURM PMI module to simplify its use when building/using Open MPI and MPICH built to use libfabric, and upgrade Edison to CLE 5.2 UP04 or newer.

Adding Fault Tolerance to NPB Benchmarks Using ULFM

DOE Office of Scientific and Technical Information (OSTI.GOV)

Parchman, Zachary W; Vallee, Geoffroy R; Naughton III, Thomas J

2016-01-01

In the world of high-performance computing, fault tolerance and application resilience are becoming some of the primary concerns because of increasing hardware failures and memory corruptions. While the research community has been investigating various options, from system-level solutions to application-level solutions, standards such as the Message Passing Interface (MPI) are also starting to include such capabilities. The current proposal for MPI fault tolerant is centered around the User-Level Failure Mitigation (ULFM) concept, which provides means for fault detection and recovery of the MPI layer. This approach does not address application-level recovery, which is currently left to application developers. In thismore » work, we present a mod- ification of some of the benchmarks of the NAS parallel benchmark (NPB) to include support of the ULFM capabilities as well as application-level strategies and mechanisms for application-level failure recovery. As such, we present: (i) an application-level library to checkpoint and restore data, (ii) extensions of NPB benchmarks for fault tolerance based on different strategies, (iii) a fault injection tool, and (iv) some preliminary results that show the impact of such fault tolerant strategies on the application execution.« less

Decadal prediction of European soil moisture from 1961 to 2010 using a regional climate model

NASA Astrophysics Data System (ADS)

Mieruch-Schnuelle, S.; Schädler, G.; Feldmann, H.

2014-12-01

The German national research program on decadal climate prediction(MiKlip) aims at the development of an operational decadal predictionsystem. To explore the potential of decadal predictions a hindcastensemble from 1961 to 2010 has been generated by the MPI-ESM, the newEarth system model of the Max Planck Institute for Meteorology. Toimprove the decadal predictions on higher spatial resolutions wedownscaled the MPI-ESM simulations by the regional model COSMO-CLM(CCLM) for Europe. In this study we will characterize and validatethe predictability of extreme states of soil moisture in Europesimulated by the MPI-ESM and the value added by the CCLM. The wateramount stored in the soil is a crucial component of the climate systemand especially important for agriculture, and has an influence onevaporation, groundwater and runoff. Thus, skillful prediction of soilmoisture in the order of years up to a decade could be used tomitigate risk and benefit society. Since soil moisture observationsare rare and validation of model output is difficult, we will ratherinvestigate the effective drought index (EDI), which can be retrievedsolely from precipitation data. Therefore we show that the EDI is agood estimator of the soil water content.

Left ventricular functional parameters by gated SPECT myocardial perfusion imaging in a Latin American country.

PubMed

Kapitan, Miguel; Beltran, Alvaro; Beretta, Mario; Mut, Fernando

2018-04-01

There is paucity of data on left ventricular (LV) functional parameters using gated SPECT myocardial perfusion imaging (MPI) from the Latin American region. This study provides detailed information in low-risk patients both at rest and during exercise. We studied 90 patients (50 men) with a very low likelihood of coronary artery disease. Gated-SPECT MPI was performed with Tc-99m MIBI using a 2-day protocol, with 16 frames/R-R cycle. The LV ejection fraction and volumes were not different between the rest and post-stress images. LVEF was 68 ± 7% post-stress and 70 ± 7% at rest in women, and 62 ± 7% and 63 ± 7%, respectively, in men (P = .19, .26). LV volumes were larger in men than women (P < .01). There were no differences in most variables obtained at rest or post-stress. Transient ischemic dilatation was similar, with upper limits of 1.20 and 1.19 in women and men, respectively (P = NS). These data could prove helpful for the interpretation of gated SPECT MPI data in Latin America using identical protocol as used in this study.

Risk stratification for large artery or chronic coronary artery disease-related ischemic stroke in octogenarians undergoing exercise stress myocardial perfusion imaging: A cohort study.

PubMed

Katsikis, Athanasios; Theodorakos, Athanasios; Drosatos, Alexandros; Konstantinou, Konstantinos; Papaioannou, Spyridon; Koutelou, Maria

2017-04-01

To test, if in octogenarians, treadmill exercise with myocardial perfusion imaging (exercise-MPI) can risk stratify for large artery or chronic CAD-related ischemic stroke (LACCIS). Exercise-MPI-related data of 237 octogenarians (55% prior MI or revascularization) without previous stroke were registered and prospective follow-up was performed to document LACCIS. LACCIS was defined as acute onset of neurological symptoms with CT/MRI findings of non-lacunar-type infarcts in the absence of atrial fibrillation or intracardiac embolic sources. After 7.3 years, 10 LACCIS were documented. SSS [HR 1.08 (1.02-1.13 95% CIs), SDS [HR 1.1 (1.04-1.16 95% CIs)], and non-sustained VT or transient AV block during exercise [HR 3.9 (1.7-9.0 95% CIs)] were predictors of LACCIS (P < .01 for all). A SSS threshold of 16 had 81% specificity for identification of future LACCIS and risk groups formed according to this cut-off had significantly different LACCIS-free survival (P = .015). Exercise-MPI in octogenarians can provide risk stratification markers for LACCIS.

Nucleon axial charge in (2+1)-flavor dynamical-lattice QCD with domain-wall fermions.

PubMed

Yamazaki, T; Aoki, Y; Blum, T; Lin, H W; Lin, M F; Ohta, S; Sasaki, S; Tweedie, R J; Zanotti, J M

2008-05-02

We present results for the nucleon axial charge g{A} at a fixed lattice spacing of 1/a=1.73(3) GeV using 2+1 flavors of domain wall fermions on size 16;{3} x 32 and 24;{3} x 64 lattices (L=1.8 and 2.7 fm) with length 16 in the fifth dimension. The length of the Monte Carlo trajectory at the lightest m_{pi} is 7360 units, including 900 for thermalization. We find finite volume effects are larger than the pion mass dependence at m{pi}=330 MeV. We also find a scaling with the single variable m{pi}L which can also be seen in previous two-flavor domain wall and Wilson fermion calculations. Using this scaling to eliminate the finite-volume effect, we obtain g{A}=1.20(6)(4) at the physical pion mass, m_{pi}=135 MeV, where the first and second errors are statistical and systematic. The observed finite-volume scaling also appears in similar quenched simulations, but disappear when V>or=(2.4 fm);{3}. We argue this is a dynamical quark effect.

Distributed memory parallel Markov random fields using graph partitioning

DOE Office of Scientific and Technical Information (OSTI.GOV)

Heinemann, C.; Perciano, T.; Ushizima, D.

Markov random fields (MRF) based algorithms have attracted a large amount of interest in image analysis due to their ability to exploit contextual information about data. Image data generated by experimental facilities, though, continues to grow larger and more complex, making it more difficult to analyze in a reasonable amount of time. Applying image processing algorithms to large datasets requires alternative approaches to circumvent performance problems. Aiming to provide scientists with a new tool to recover valuable information from such datasets, we developed a general purpose distributed memory parallel MRF-based image analysis framework (MPI-PMRF). MPI-PMRF overcomes performance and memory limitationsmore » by distributing data and computations across processors. The proposed approach was successfully tested with synthetic and experimental datasets. Additionally, the performance of the MPI-PMRF framework is analyzed through a detailed scalability study. We show that a performance increase is obtained while maintaining an accuracy of the segmentation results higher than 98%. The contributions of this paper are: (a) development of a distributed memory MRF framework; (b) measurement of the performance increase of the proposed approach; (c) verification of segmentation accuracy in both synthetic and experimental, real-world datasets« less

Application of Cavitation Promoting Surfaces in Management of Acute Ischemic Stroke

PubMed Central

Soltani, Azita

2012-01-01

High frequency, low intensity ultrasound has the potential to accelerate the clearance of thrombotic occlusion in the absence of cavitation. At high frequency ultrasound, high acoustic pressures, > 5.2 MPa, are required to generate cavitation in thrombus. The focus of this study was to reduce the cavitation threshold by applying materials with appropriate nucleation sites at the transducer-thrombus boundary to further augment sonothrombolysis. Heterogeneous and homogenous nucleation sites were generated on the outer surface of a polyimide tube (PI) using microfringed (MPI) and laser induced (LPI) microcavities. The cavitation threshold of these materials was determined using a passive cavitation detection system. Furthermore, the biological impact of both materials was investigated in vitro. The results revealed that both MPI and LPI have the potential to induce cavitation at acoustic pressure levels as low as 2.3 MPa. In the presence of cavitation, thrombolysis rate could be enhanced by up to 2 times without any evidence of hemolysis that is generally associated with cavitation activities in blood. A prototype ultrasonic catheter operating at 1.7MHz frequency and acoustic pressure of 2.3MPa with either of MPI or LPI could be considered as a viable option for treatment of acute ischemic stroke. PMID:23141666

Numerical Modeling of 3D Seismic Wave Propagation around Yogyakarta, the Southern Part of Central Java, Indonesia, Using Spectral-Element Method on MPI-GPU Cluster

NASA Astrophysics Data System (ADS)

Sudarmaji; Rudianto, Indra; Eka Nurcahya, Budi

2018-04-01

A strong tectonic earthquake with a magnitude of 5.9 Richter scale has been occurred in Yogyakarta and Central Java on May 26, 2006. The earthquake has caused severe damage in Yogyakarta and the southern part of Central Java, Indonesia. The understanding of seismic response of earthquake among ground shaking and the level of building damage is important. We present numerical modeling of 3D seismic wave propagation around Yogyakarta and the southern part of Central Java using spectral-element method on MPI-GPU (Graphics Processing Unit) computer cluster to observe its seismic response due to the earthquake. The homogeneous 3D realistic model is generated with detailed topography surface. The influences of free surface topography and layer discontinuity of the 3D model among the seismic response are observed. The seismic wave field is discretized using spectral-element method. The spectral-element method is solved on a mesh of hexahedral elements that is adapted to the free surface topography and the internal discontinuity of the model. To increase the data processing capabilities, the simulation is performed on a GPU cluster with implementation of MPI (Message Passing Interface).

Streaming data analytics via message passing with application to graph algorithms

DOE PAGES

Plimpton, Steven J.; Shead, Tim

2014-05-06

The need to process streaming data, which arrives continuously at high-volume in real-time, arises in a variety of contexts including data produced by experiments, collections of environmental or network sensors, and running simulations. Streaming data can also be formulated as queries or transactions which operate on a large dynamic data store, e.g. a distributed database. We describe a lightweight, portable framework named PHISH which enables a set of independent processes to compute on a stream of data in a distributed-memory parallel manner. Datums are routed between processes in patterns defined by the application. PHISH can run on top of eithermore » message-passing via MPI or sockets via ZMQ. The former means streaming computations can be run on any parallel machine which supports MPI; the latter allows them to run on a heterogeneous, geographically dispersed network of machines. We illustrate how PHISH can support streaming MapReduce operations, and describe streaming versions of three algorithms for large, sparse graph analytics: triangle enumeration, subgraph isomorphism matching, and connected component finding. Lastly, we also provide benchmark timings for MPI versus socket performance of several kernel operations useful in streaming algorithms.« less

How much do different global GPP products agree in distribution and magnitude of GPP extremes?

NASA Astrophysics Data System (ADS)

Kim, S.; Ryu, Y.; Jiang, C.

2016-12-01

To evaluate uncertainty of global Gross Primary Productivity (GPP) extremes, we compare three global GPP datasets derived from different data processing methods (e.g. MPI-BGC: machine-learning, MODIS GPP (MOD17): semi-empirical, Breathing Earth System Simulator (BESS): process based). We preprocess the datasets following the method from Zscheischler et al., (2012) to detect GPP extremes which occur in less than 1% of the number of whole pixels, and to identify 3D-connected spatiotemporal GPP extremes. We firstly analyze global patterns and the magnitude of GPP extremes with MPI-BGC, MOD17, and BESS over 2001-2011. For consistent analysis in the three products, spatial and temporal resolution were set at 50 km and a monthly scale, respectively. Our results indicated that the global patterns of GPP extremes derived from MPI-BGC and BESS agreed with each other by showing hotspots in Northeastern Brazil and Eastern Texas. However, the extreme events detected from MOD17 were concentrated in tropical forests (e.g. Southeast Asia and South America). The amount of GPP reduction caused by climate extremes considerably differed across the products. For example, Russian heatwave in 2010 led to 100 Tg C uncertainty (198.7 Tg C in MPI-BGC, 305.6 Tg C in MOD17, and 237.8 Tg C in BESS). Moreover, the duration of extreme events differ among the three GPP datasets for the Russian heatwave (MPI-BGC: May-Sep, MOD17: Jun-Aug, and BESS: May-Aug). To test whether Sun induced Fluorescence (SiF), a proxy of GPP, can capture GPP extremes, we investigate global distribution of GPP extreme events in BESS, MOD17 and GOME-2 SiF between 2008 and 2014 when SiF data is available. We found that extreme GPP events in GOME-2 SiF and MOD17 appear in tropical forests whereas those in BESS emerged in Northeastern Brazil and Eastern Texas. The GPP extremes by severe 2011 US drought were detected by BESS and MODIS, but not by SiF. Our findings highlight that different GPP datasets could result in varying duration and intensity of GPP extremes and distribution of hotspots, and this study could contribute to quantifying uncertainties in GPP extremes.

Performance and Application of Parallel OVERFLOW Codes on Distributed and Shared Memory Platforms

NASA Technical Reports Server (NTRS)

Djomehri, M. Jahed; Rizk, Yehia M.

1999-01-01

The presentation discusses recent studies on the performance of the two parallel versions of the aerodynamics CFD code, OVERFLOW_MPI and _MLP. Developed at NASA Ames, the serial version, OVERFLOW, is a multidimensional Navier-Stokes flow solver based on overset (Chimera) grid technology. The code has recently been parallelized in two ways. One is based on the explicit message-passing interface (MPI) across processors and uses the _MPI communication package. This approach is primarily suited for distributed memory systems and workstation clusters. The second, termed the multi-level parallel (MLP) method, is simple and uses shared memory for all communications. The _MLP code is suitable on distributed-shared memory systems. For both methods, the message passing takes place across the processors or processes at the advancement of each time step. This procedure is, in effect, the Chimera boundary conditions update, which is done in an explicit "Jacobi" style. In contrast, the update in the serial code is done in more of the "Gauss-Sidel" fashion. The programming efforts for the _MPI code is more complicated than for the _MLP code; the former requires modification of the outer and some inner shells of the serial code, whereas the latter focuses only on the outer shell of the code. The _MPI version offers a great deal of flexibility in distributing grid zones across a specified number of processors in order to achieve load balancing. The approach is capable of partitioning zones across multiple processors or sending each zone and/or cluster of several zones into a single processor. The message passing across the processors consists of Chimera boundary and/or an overlap of "halo" boundary points for each partitioned zone. The MLP version is a new coarse-grain parallel concept at the zonal and intra-zonal levels. A grouping strategy is used to distribute zones into several groups forming sub-processes which will run in parallel. The total volume of grid points in each group are approximately balanced. A proper number of threads are initially allocated to each group, and in subsequent iterations during the run-time, the number of threads are adjusted to achieve load balancing across the processes. Each process exploits the multitasking directives already established in Overflow.

Chemical speciation of heavy metals by surface-enhanced Raman scattering spectroscopy: identification and quantification of inorganic- and methyl-mercury in water

NASA Astrophysics Data System (ADS)

Guerrini, Luca; Rodriguez-Loureiro, Ignacio; Correa-Duarte, Miguel A.; Lee, Yih Hong; Ling, Xing Yi; García de Abajo, F. Javier; Alvarez-Puebla, Ramon A.

2014-06-01

Chemical speciation of heavy metals has become extremely important in environmental and analytical research because of the strong dependence that toxicity, environmental mobility, persistence and bioavailability of these pollutants have on their specific chemical forms. Novel nano-optical-based detection strategies, capable of overcoming the intrinsic limitations of well-established analytic methods for the quantification of total metal ion content, have been reported, but the speciation of different chemical forms has not yet been achieved. Here, we report the first example of a SERS-based sensor for chemical speciation of toxic metal ions in water at trace levels. Specifically, the inorganic Hg2+ and the more toxicologically relevant methylmercury (CH3Hg+) are selected as analytical targets. The sensing platform consists of a self-assembled monolayer of 4-mercaptopyridine (MPY) on highly SERS-active and robust hybrid plasmonic materials formed by a dense layer of interacting gold nanoparticles anchored onto polystyrene microbeads. The co-ordination of Hg2+ and CH3Hg+ to the nitrogen atom of the MPY ring yields characteristic changes in the vibrational SERS spectra of the organic chemoreceptor that can be qualitatively and quantitatively correlated to the presence of the two different mercury forms.Chemical speciation of heavy metals has become extremely important in environmental and analytical research because of the strong dependence that toxicity, environmental mobility, persistence and bioavailability of these pollutants have on their specific chemical forms. Novel nano-optical-based detection strategies, capable of overcoming the intrinsic limitations of well-established analytic methods for the quantification of total metal ion content, have been reported, but the speciation of different chemical forms has not yet been achieved. Here, we report the first example of a SERS-based sensor for chemical speciation of toxic metal ions in water at trace levels. Specifically, the inorganic Hg2+ and the more toxicologically relevant methylmercury (CH3Hg+) are selected as analytical targets. The sensing platform consists of a self-assembled monolayer of 4-mercaptopyridine (MPY) on highly SERS-active and robust hybrid plasmonic materials formed by a dense layer of interacting gold nanoparticles anchored onto polystyrene microbeads. The co-ordination of Hg2+ and CH3Hg+ to the nitrogen atom of the MPY ring yields characteristic changes in the vibrational SERS spectra of the organic chemoreceptor that can be qualitatively and quantitatively correlated to the presence of the two different mercury forms. Electronic supplementary information (ESI) available: Representative TEM and ESEM images of AuNPs and PS@Au particles. Optical extinction spectra of AuNPs and PS@Au suspensions. SERS spectra of unmodified PS@Au suspension before and after the addition of CH3Hg+. SERS spectra of PS@Au-MPY upon addition of several metal solutions. Detailed SERS study of the MPY response to high concentration of CH3Hg+. See DOI: 10.1039/c4nr01464b

System identification of the JPL micro-precision interferometer truss - Test-analysis reconciliation

NASA Technical Reports Server (NTRS)

Red-Horse, J. R.; Marek, E. L.; Levine-West, M.

1993-01-01

The JPL Micro-Precision Interferometer (MPI) is a testbed for studying the use of control-structure interaction technology in the design of space-based interferometers. A layered control architecture will be employed to regulate the interferometer optical system to tolerances in the nanometer range. An important aspect of designing and implementing the control schemes for such a system is the need for high fidelity, test-verified analytical structural models. This paper focuses on one aspect of the effort to produce such a model for the MPI structure, test-analysis model reconciliation. Pretest analysis, modal testing, and model refinement results are summarized for a series of tests at both the component and full system levels.

Time-Dependent Simulation of Incompressible Flow in a Turbopump Using Overset Grid Approach

NASA Technical Reports Server (NTRS)

Kiris, Cetin; Kwak, Dochan

2001-01-01

This paper reports the progress being made towards complete unsteady turbopump simulation capability by using overset grid systems. A computational model of a turbo-pump impeller is used as a test case for the performance evaluation of the MPI, hybrid MPI/Open-MP, and MLP versions of the INS3D code. Relative motion of the grid system for rotor-stator interaction was obtained by employing overset grid techniques. Unsteady computations for a turbo-pump, which contains 114 zones with 34.3 Million grid points, are performed on Origin 2000 systems at NASA Ames Research Center. The approach taken for these simulations, and the performance of the parallel versions of the code are presented.

Can the origin of some metals in the seagrass Posidonia oceanica be determined by the indexes of metals pollutions?

PubMed

Stanković, Slavka; Jović, Mihajlo; Tanaskovski, Bojan; Mihajlović, Marija L; Joksimović, Danijela; Pezo, Lato

2015-06-01

To assess metal pollution, Fe, Mn, Cu, Zn, Pb, Ni, Co, As, Cd, and Hg contents in samples of the seagrass Posidonia oceanica and surface sediment, collected at eight locations along the Montenegrin coast, were determined. The metal pollution index (MPI) and metal enrichment factor (EF) were then calculated. MPI and EF were lower in sediment than in P. oceanica at the same locations. This was very evident for EF values of Hg and Cd. Based on the Pearson's correlations and EF values, it was possible to conclude that the last two metals' content in the seagrass did not originate from the crustal sources or natural weathering processes.

Spectral-element simulation of two-dimensional elastic wave propagation in fully heterogeneous media on a GPU cluster

NASA Astrophysics Data System (ADS)

Rudianto, Indra; Sudarmaji

2018-04-01

We present an implementation of the spectral-element method for simulation of two-dimensional elastic wave propagation in fully heterogeneous media. We have incorporated most of realistic geological features in the model, including surface topography, curved layer interfaces, and 2-D wave-speed heterogeneity. To accommodate such complexity, we use an unstructured quadrilateral meshing technique. Simulation was performed on a GPU cluster, which consists of 24 core processors Intel Xeon CPU and 4 NVIDIA Quadro graphics cards using CUDA and MPI implementation. We speed up the computation by a factor of about 5 compared to MPI only, and by a factor of about 40 compared to Serial implementation.

Aminophylline and caffeine for reversal of adverse symptoms associated with regadenoson SPECT MPI.

PubMed

Doran, Jesse A; Sajjad, Waseem; Schneider, Marabel D; Gupta, Rohit; Mackin, Maria L; Schwartz, Ronald G

2017-06-01

Aminophylline shortages led us to compare intravenous (IV) aminophylline with IV and oral (PO) caffeine during routine pharmacologic stress testing with SPECT MPI. We measured presence, duration, and reversal of adverse symptoms and cardiac events following regadenoson administration in consecutive patients randomized to IV aminophylline (100 mg administered over 30-60 seconds), IV caffeine citrate (60 mg infused over 3-5 minutes), or PO caffeine as coffee or diet cola. Of 241 patients, 152 (63%) received regadenoson reversal intervention. Complete (CR), predominant (PRE), or partial (PR) reversal was observed in 99%. CR by IV aminophylline (87%), IV caffeine (87%), and PO caffeine (78%) were similar (P = NS). Time to CR (162 ± 12.6 seconds, mean ± SD) was similar in treatment arms. PO caffeine was inferior to IV aminophylline for CR + PRE. IV aminophylline and IV caffeine provide rapid, safe reversal of regadenoson-induced adverse effects during SPECT MPI. Oral caffeine appeared similarly effective for CR but not for the combined CR + PRE. Our results suggest PO caffeine may be an effective initial strategy for reversal of regadenoson, but IV aminophylline or IV caffeine should be available to optimize symptom reversal as needed.

Diagnostic and clinical benefit of combined coronary calcium and perfusion assessment in patients undergoing PET/CT myocardial perfusion stress imaging.

PubMed

Bybee, Kevin A; Lee, John; Markiewicz, Richard; Longmore, Ryan; McGhie, A Iain; O'Keefe, James H; Hsu, Bai-Ling; Kennedy, Kevin; Thompson, Randall C; Bateman, Timothy M

2010-04-01

A limitation of stress myocardial perfusion imaging (MPI) is the inability to detect non-obstructive coronary artery disease (CAD). One advantage of MPI with a hybrid CT device is the ability to obtain same-setting measurement of the coronary artery calcium score (CACS). Utilizing our single-center nuclear database, we identified 760 consecutive patients with: (1) no CAD history; (2) a normal clinically indicated Rb-82 PET/CT stress perfusion study; and (3) a same-setting CAC scan. 487 of 760 patients (64.1%) had subclinical CAD based on an abnormal CACS. Of those with CAC, the CACS was > or =100, > or =400, and > or =1000 in 47.0%, 22.4%, and 8.4% of patients, respectively. Less than half of the patients with CAC were receiving aspirin or statin medications prior to PET/CT imaging. Patients with CAC were more likely to be initiated or optimized on proven medical therapy for CAD immediately following PET/CT MPI compared to those without CAC. Subclinical CAD is common in patients without known CAD and normal myocardial perfusion assessed by hybrid PET/CT imaging. Identification of CAC influences subsequent physician prescribing patterns such that those with CAC are more likely to be treated with proven medical therapy for the treatment of CAD.

Influence of proton-pump inhibitors on stomach wall uptake of 99mTc-tetrofosmin in cadmium-zinc-telluride SPECT myocardial perfusion imaging.

PubMed

Mouden, Mohamed; Rijkee, Karlijn S; Schreuder, Nanno; Timmer, Jorik R; Jager, Pieter L

2015-02-01

Proton-pump inhibitors (PPIs) induce potentially interfering stomach wall activity in single-photon emission computed tomography myocardial perfusion imaging (SPECT-MPI) with technetium-99m ((99m)Tc)-sestamibi. However, no data are available for (99m)Tc-tetrofosmin. We assessed the influence of prolonged (>2 weeks) PPI use on the stomach wall uptake of (99m)Tc-tetrofosmin in patients referred for stress MPI with a cadmium-zinc-telluride-based SPECT camera and its relation with dyspepsia symptoms. Consecutive patients (n=127) underwent a 1-day adenosine stress-first SPECT-MPI with (99m)Tc-tetrofosmin, of whom 54 (43%) patients had been on PPIs for more than 2 weeks. Stomach wall activity was identified on stress SPECT using computed tomographic attenuation maps and was scored using a four-point grading scale into clinically relevant (scores 2 or 3) or nonrelevant (scores 0 or 1).Patients on PPIs had stomach wall uptake more frequently as compared with patients not using PPIs (22 vs. 7%, P=0.017). Dyspepsia was similar in both groups. Prolonged use of PPIs is associated with stomach wall uptake of (99m)Tc-tetrofosmin in stress cadmium-zinc-telluride-SPECT images. Gastric symptoms were not associated with stomach wall uptake.

Integrating MPI and deduplication engines: a software architecture roadmap.

PubMed

Baksi, Dibyendu

2009-03-01

The objective of this paper is to clarify the major concepts related to architecture and design of patient identity management software systems so that an implementor looking to solve a specific integration problem in the context of a Master Patient Index (MPI) and a deduplication engine can address the relevant issues. The ideas presented are illustrated in the context of a reference use case from Integrating the Health Enterprise Patient Identifier Cross-referencing (IHE PIX) profile. Sound software engineering principles using the latest design paradigm of model driven architecture (MDA) are applied to define different views of the architecture. The main contribution of the paper is a clear software architecture roadmap for implementors of patient identity management systems. Conceptual design in terms of static and dynamic views of the interfaces is provided as an example of platform independent model. This makes the roadmap applicable to any specific solutions of MPI, deduplication library or software platform. Stakeholders in need of integration of MPIs and deduplication engines can evaluate vendor specific solutions and software platform technologies in terms of fundamental concepts and can make informed decisions that preserve investment. This also allows freedom from vendor lock-in and the ability to kick-start integration efforts based on a solid architecture.

A new deadlock resolution protocol and message matching algorithm for the extreme-scale simulator

DOE PAGES

Engelmann, Christian; Naughton, III, Thomas J.

2016-03-22

Investigating the performance of parallel applications at scale on future high-performance computing (HPC) architectures and the performance impact of different HPC architecture choices is an important component of HPC hardware/software co-design. The Extreme-scale Simulator (xSim) is a simulation toolkit for investigating the performance of parallel applications at scale. xSim scales to millions of simulated Message Passing Interface (MPI) processes. The overhead introduced by a simulation tool is an important performance and productivity aspect. This paper documents two improvements to xSim: (1)~a new deadlock resolution protocol to reduce the parallel discrete event simulation overhead and (2)~a new simulated MPI message matchingmore » algorithm to reduce the oversubscription management overhead. The results clearly show a significant performance improvement. The simulation overhead for running the NAS Parallel Benchmark suite was reduced from 102% to 0% for the embarrassingly parallel (EP) benchmark and from 1,020% to 238% for the conjugate gradient (CG) benchmark. xSim offers a highly accurate simulation mode for better tracking of injected MPI process failures. Furthermore, with highly accurate simulation, the overhead was reduced from 3,332% to 204% for EP and from 37,511% to 13,808% for CG.« less

Quantifying the role of ocean initial conditions in decadal prediction

NASA Astrophysics Data System (ADS)

Matei, D.; Pohlmann, H.; Müller, W.; Haak, H.; Jungclaus, J.; Marotzke, J.

2009-04-01

The forecast skill of decadal climate predictions is investigated using two different initialization strategies. First we apply an assimilation of ocean synthesis data provided by the GECCO project (Köhl and Stammer 2008) as initial conditions for the coupled model ECHAM5/MPI-OM. The results show promising skill up to decadal time scales particularly over the North Atlantic (see also Pohlmann et al. 2009). However, mismatches between the ocean climates of GECCO and the MPI-OM model may lead to inconsistencies in the representation of water masses. Therefore, we pursue an alternative approach to the representation of the observed North Atlantic climate for the period 1948-2007. Using the same MPI-OM ocean model as in the coupled system, we perform an ensemble of four NCEP integrations. The ensemble mean temperature and salinity anomalies are then nudged into the coupled model, followed by hindcast/forecast experiments. The model gives dynamically consistent three-dimensional temperature and salinity fields, thereby avoiding the problems of model drift that were encountered when the assimilation experiment was only driven by reconstructed SSTs (Keenlyside et al. 2008, Pohlmann et al. 2009). Differences between the two assimilation approaches are discussed by comparing them with the observational data in key regions and processes, such as North Atlantic and Tropical Pacific climate, MOC variability, Subpolar Gyre variability.

Communication Characterization and Optimization of Applications Using Topology-Aware Task Mapping on Large Supercomputers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sreepathi, Sarat; D'Azevedo, Eduardo; Philip, Bobby

On large supercomputers, the job scheduling systems may assign a non-contiguous node allocation for user applications depending on available resources. With parallel applications using MPI (Message Passing Interface), the default process ordering does not take into account the actual physical node layout available to the application. This contributes to non-locality in terms of physical network topology and impacts communication performance of the application. In order to mitigate such performance penalties, this work describes techniques to identify suitable task mapping that takes the layout of the allocated nodes as well as the application's communication behavior into account. During the first phasemore » of this research, we instrumented and collected performance data to characterize communication behavior of critical US DOE (United States - Department of Energy) applications using an augmented version of the mpiP tool. Subsequently, we developed several reordering methods (spectral bisection, neighbor join tree etc.) to combine node layout and application communication data for optimized task placement. We developed a tool called mpiAproxy to facilitate detailed evaluation of the various reordering algorithms without requiring full application executions. This work presents a comprehensive performance evaluation (14,000 experiments) of the various task mapping techniques in lowering communication costs on Titan, the leadership class supercomputer at Oak Ridge National Laboratory.« less

Comparison of Origin 2000 and Origin 3000 Using NAS Parallel Benchmarks

NASA Technical Reports Server (NTRS)

Turney, Raymond D.

2001-01-01

This report describes results of benchmark tests on the Origin 3000 system currently being installed at the NASA Ames National Advanced Supercomputing facility. This machine will ultimately contain 1024 R14K processors. The first part of the system, installed in November, 2000 and named mendel, is an Origin 3000 with 128 R12K processors. For comparison purposes, the tests were also run on lomax, an Origin 2000 with R12K processors. The BT, LU, and SP application benchmarks in the NAS Parallel Benchmark Suite and the kernel benchmark FT were chosen to determine system performance and measure the impact of changes on the machine as it evolves. Having been written to measure performance on Computational Fluid Dynamics applications, these benchmarks are assumed appropriate to represent the NAS workload. Since the NAS runs both message passing (MPI) and shared-memory, compiler directive type codes, both MPI and OpenMP versions of the benchmarks were used. The MPI versions used were the latest official release of the NAS Parallel Benchmarks, version 2.3. The OpenMP versiqns used were PBN3b2, a beta version that is in the process of being released. NPB 2.3 and PBN 3b2 are technically different benchmarks, and NPB results are not directly comparable to PBN results.

New SPECT and PET Radiopharmaceuticals for Imaging Cardiovascular Disease

PubMed Central

Sogbein, Oyebola O.; Pelletier-Galarneau, Matthieu; Schindler, Thomas H.; Wei, Lihui; Wells, R. Glenn; Ruddy, Terrence D.

2014-01-01

Nuclear cardiology has experienced exponential growth within the past four decades with converging capacity to diagnose and influence management of a variety of cardiovascular diseases. Single photon emission computed tomography (SPECT) myocardial perfusion imaging (MPI) with technetium-99m radiotracers or thallium-201 has dominated the field; however new hardware and software designs that optimize image quality with reduced radiation exposure are fuelling a resurgence of interest at the preclinical and clinical levels to expand beyond MPI. Other imaging modalities including positron emission tomography (PET) and magnetic resonance imaging (MRI) continue to emerge as powerful players with an expanded capacity to diagnose a variety of cardiac conditions. At the forefront of this resurgence is the development of novel target vectors based on an enhanced understanding of the underlying pathophysiological process in the subcellular domain. Molecular imaging with novel radiopharmaceuticals engineered to target a specific subcellular process has the capacity to improve diagnostic accuracy and deliver enhanced prognostic information to alter management. This paper, while not comprehensive, will review the recent advancements in radiotracer development for SPECT and PET MPI, autonomic dysfunction, apoptosis, atherosclerotic plaques, metabolism, and viability. The relevant radiochemistry and preclinical and clinical development in addition to molecular imaging with emerging modalities such as cardiac MRI and PET-MR will be discussed. PMID:24901002

Temporal Trends in the Utilization of Noninvasive Diagnostic Tests for Coronary Artery Disease in Ontario Between 2008 and 2014: A Population-Based Study.

PubMed

Roifman, Idan; Wijeysundera, Harindra C; Austin, Peter C; Maclagan, Laura C; Rezai, Mohammad R; Wright, Graham A; Tu, Jack V

2017-02-01

The proliferation of cardiac diagnostic tests over the past few decades has received substantial attention from policymakers. However, contemporary population-based temporal trends of the utilization of noninvasive cardiac diagnostic tests for coronary artery disease are not known. Our objective was to examine the temporal trends in the utilization of coronary computed tomography angiography (CCTA), myocardial perfusion imaging (MPI), exercise stress testing (GXT), and stress echocardiography between 2008 and 2014. We performed a population-based repeated cross-sectional study of the adult population of Ontario between January 1, 2008 and December 31, 2014. Annual utilization rates of noninvasive cardiac diagnostic tests were computed. For each cardiac testing modality, a negative binomial regression model was used to assess temporal changes in test utilization. GXT and MPI collectively accounted for 88% of all cardiac noninvasive diagnostic tests throughout our study period. Age- and sex-standardized rates of GXT declined from 26.7/1000 adult population to 21.6/1000 adult population (mean annual reduction of 3.4%; P < 0.001). MPI rates declined from 21.1/1000 adult population to 19.5/1000 adult population (mean annual reduction of 1.3%; P < 0.001). Although utilization rates for both CCTA and stress echocardiography increased over time, the combined rate of all available tests decreased from 50.8/1000 adult population to 49.1/1000 adult population (mean annual reduction of 1.1%; P < 0.001). In conclusion, utilization rates for the most prevalent noninvasive cardiac diagnostic tests-GXT and MPI-declined over our study period. Furthermore, the overall test utilization rate also declined over time. We believe our findings are encouraging from a health policy perspective. Nonetheless, rising utilization rates for CCTA and stress echocardiography will need to be monitored in the future. Copyright © 2016 Canadian Cardiovascular Society. Published by Elsevier Inc. All rights reserved.

Low child survival index in a multi-dimensionally poor Amerindian population in Venezuela.

PubMed

Villalba, Julian A; Liu, Yushi; Alvarez, Mauyuri K; Calderon, Luisana; Canache, Merari; Cardenas, Gaudymar; Del Nogal, Berenice; Takiff, Howard E; De Waard, Jacobus H

2013-01-01

Warao Amerindians, who inhabit the Orinoco Delta, are the second largest indigenous group in Venezuela.  High Warao general mortality rates were mentioned in a limited study 21 years ago. However, there have been no comprehensive studies addressing child survival across the entire population. To determine the Child Survival-Index (CSI) (ratio: still-living children/total-live births) in the Warao population, the principal causes of childhood death and the socio-demographic factors associated with childhood deaths. We conducted a cross-sectional epidemiological survey of 688 women from 97 communities in 7 different subregions of the Orinoco Delta. Data collected included socio-demographic characteristics and the reproductive history of each woman surveyed. The multidimensional poverty index (MPI) was used to classify the households as deprived across the three dimensions of the Human Development Index. Multivariable linear regression and Generalized Linear Model Procedures were used to identify socioeconomic and environmental characteristics statistically associated with the CSI. The average CSI was 73.8% ±26. The two most common causes of death were gastroenteritis/diarrhea (63%) and acute respiratory tract Infection/pneumonia (18%).  Deaths in children under five years accounted for 97.3% of childhood deaths, with 54% occurring in the neonatal period or first year of life.  Most of the women (95.5%) were classified as multidimensionally poor.  The general MPI in the sample was 0.56.   CSI was negatively correlated with MPI, maternal age, residence in a traditional dwelling and profession of the head of household other than nurse or teacher. The Warao have a low CSI which is correlated with MPI and maternal age.  Infectious diseases are responsible for 85% of childhood deaths.  The low socioeconomic development, lack of infrastructure and geographic and cultural isolation suggest that an integrated approach is urgently needed to improve the child survival and overall health of the Warao Amerindians. 

A Job Pause Service under LAM/MPI+BLCR for Transparent Fault Tolerance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Chao; Mueller, Frank; Engelmann, Christian

2007-01-01

Checkpoint/restart (C/R) has become a requirement for long-running jobs in large-scale clusters due to a meantime- to-failure (MTTF) in the order of hours. After a failure, C/R mechanisms generally require a complete restart of an MPI job from the last checkpoint. A complete restart, however, is unnecessary since all but one node are typically still alive. Furthermore, a restart may result in lengthy job requeuing even though the original job had not exceeded its time quantum. In this paper, we overcome these shortcomings. Instead of job restart, we have developed a transparent mechanism for job pause within LAM/MPI+BLCR. This mechanismmore » allows live nodes to remain active and roll back to the last checkpoint while failed nodes are dynamically replaced by spares before resuming from the last checkpoint. Our methodology includes LAM/MPI enhancements in support of scalable group communicationwith fluctuating number of nodes, reuse of network connections, transparent coordinated checkpoint scheduling and a BLCR enhancement for job pause. Experiments in a cluster with the NAS Parallel Benchmark suite show that our overhead for job pause is comparable to that of a complete job restart. A minimal overhead of 5.6% is only incurred in case migration takes place while the regular checkpoint overhead remains unchanged. Yet, our approach alleviates the need to reboot the LAM run-time environment, which accounts for considerable overhead resulting in net savings of our scheme in the experiments. Our solution further provides full transparency and automation with the additional benefit of reusing existing resources. Executing continues after failures within the scheduled job, i.e., the application staging overhead is not incurred again in contrast to a restart. Our scheme offers additional potential for savings through incremental checkpointing and proactive diskless live migration, which we are currently working on.« less

Patient- and clinician-reported satisfaction with pharmacological stress agents for single photon emission computed tomography (SPECT) myocardial perfusion imaging (MPI).

PubMed

Hudgens, Stacie; Breeze, Janis; Spalding, James

2013-01-01

The objective of this study was to compare clinician and patient measures of satisfaction with two pharmacological stress agents (PSA), regadenoson and dipyridamole, used in Single Photon Emission Computed Tomography (SPECT) Myocardial Perfusion Imaging (MPI). This observational study included patients who had undergone SPECT MPI with regadenoson or dipyridamole, as well as the clinician/clinical technologist who performed the test. Mean scores for individual item and domain scores of the main outcome measures were computed as well as the effect sizes (ES) of the mean difference in scores between treatment groups. Statistical significance of the mean item and domain score differences were assessed via Mann-Whitney tests. Two self-report questionnaires which had beeb previously developed and validated: Patient Satisfaction/Preference Questionnaire (PSPQ) and Clinician Satisfaction/Preference Questionnaire (CSPQ). A total of 87 patients (68 received regadenoson, 19 received dipyridamole) and nine clinicians/clinical technologists took part in the study. Patients had a mean age of 66.8 ± 12.2 years, and 56.3% were male. Compared to dipyridamole, use of regadenoson was associated with greater clinician satisfaction on all items and domains of the CSPQ (p < 0.001 for all comparisons). Among patients, regadenoson was associated with less bother and greater satisfaction than dipyridamole for all items on the PSPQ. These patients reported less stinging at the injection site (ES = -0.66) and less nervousness during injection (ES = -0.60). The PSPQ found that regadenoson patients were more satisfied with their PSA than dipyridamole patients in all areas. This study utilized a relatively small sample size of dipyridamole patients and lacked an adenosine group. A broader sampling of professionals would also help demonstrate generalizability. Both patients and clinicians reported higher satisfaction with regadenoson compared to dipyridamole for SPECT-MPI. Clinicians were particularly satisfied with the preparation and administration aspects of the drug, while patients rated it highly on convenience and reduced incidence of side-effects.

Comparison of Toxic Metal Distribution Characteristics and Health Risk between Cultured and Wild Fish Captured from Honghu City, China.

PubMed

Zhang, Jingdong; Zhu, Liyun; Li, Fei; Liu, Chaoyang; Qiu, Zhenzhen; Xiao, Minsi; Cai, Ying

2018-02-14

Honghu Lake, which listed in the "Ramsar Convention", is the seventh largest freshwater lake in China and is regarded as one of the biggest freshwater product output areas in China. The toxic element distribution in cultured and wild fish and the corresponding health risks through fish consumption from Honghu area were investigated. The mean concentration in the muscle of cultured and wild fish ( Carassius auratus and Ctenopharyngodon idellus ) decreased in the order: Zn (18.94) > Cu (0.8489) > Cr (0.2840) > Pb (0.2052) and Zn (16.30) > Cr (1.947) > Cu (0.4166) > Pb (0.0525) > Cd (0.0060) (mean; mg/kg, wet weight). Scales (Multi factor pollution index (MPI) = 3.342) and the liver (MPI = 1.276) were regarded as the main accumulation tissues for cultured fish, and the bladder (MPI = 0.640) and intestine (MPI = 0.477) were regarded as the main accumulation tissues for wild fish. There were no obvious health risks associated with the consumption of cultured and wild fish based on the calculated results of the target hazard quotient (THQ), carcinogenic risk (CR), and estimated weekly intake (EWI). Pb and Cr were recognized as the major health risk contributors for inhabitants through wild and cultured fish consumption. Cultured fish had a greater health risk than wild fish based on the calculation results of THQ and CR. Muscle consumption resulted in more health risks than mixed edible tissues for cultured fish, but for wild fish, the conclusion was the opposite. Mixed fish (cultured:wild = 1:1) muscle consumption had relatively lower risks than the consumption of cultured or wild fish muscle separately. Consuming no more than 465 g/day (wet wt) of cultured fish muscle, 68 g/day (wet wt) of wild fish muscle, 452 g/day (wet wt) of mixed cultured fish edible tissues or 186 g/day (wet wt) of mixed wild fish edible tissues from the Honghu area can assure human health.

Loss of MyD88 alters neuroinflammatory response and attenuates early Purkinje cell loss in a spinocerebellar ataxia type 6 mouse model

PubMed Central

Aikawa, Tomonori; Mogushi, Kaoru; Iijima-Tsutsui, Kumiko; Ishikawa, Kinya; Sakurai, Miyano; Tanaka, Hiroshi; Mizusawa, Hidehiro; Watase, Kei

2015-01-01

Spinocerebellar ataxia type 6 (SCA6) is dominantly inherited neurodegenerative disease, caused by an expansion of CAG repeat encoding a polyglutamine (PolyQ) tract in the Cav2.1 voltage-gated calcium channel. Its key pathological features include selective degeneration of the cerebellar Purkinje cells (PCs), a common target for PolyQ-induced toxicity in various SCAs. Mutant Cav2.1 confers toxicity primarily through a toxic gain-of-function mechanism; however, its molecular basis remains elusive. Here, we studied the cerebellar gene expression patterns of young Sca6-MPI118Q/118Q knockin (KI) mice, which expressed mutant Cav2.1 from an endogenous locus and recapitulated many phenotypic features of human SCA6. Transcriptional signatures in the MPI118Q/118Q mice were distinct from those in the Sca1154Q/2Q mice, a faithful SCA1 KI mouse model. Temporal expression profiles of the candidate genes revealed that the up-regulation of genes associated with microglial activation was initiated before PC degeneration and was augmented as the disease progressed. Histological analysis of the MPI118Q/118Q cerebellum showed the predominance of M1-like pro-inflammatory microglia and it was concomitant with elevated expression levels of tumor necrosis factor, interleukin-6, Toll-like receptor (TLR) 2 and 7. Genetic ablation of MyD88, a major adaptor protein conveying TLR signaling, altered expression patterns of M1/M2 microglial phenotypic markers in the MPI118Q/118Q cerebellum. More importantly, it ameliorated PC loss and partially rescued motor impairments in the early disease phase. These results suggest that early neuroinflammatory response may play an important role in the pathogenesis of SCA6 and its modulation could pave the way for slowing the disease progression during the early stage of the disease. PMID:26034136

Temporal trends in compliance with appropriateness criteria for stress single-photon emission computed tomography sestamibi studies in an academic medical center.

PubMed

Gibbons, Raymond J; Askew, J Wells; Hodge, David; Miller, Todd D

2010-03-01

The purpose of this study was to apply published appropriateness criteria for single-photon emission computed tomography (SPECT) myocardial perfusion imaging (MPI) in a single academic medical center to determine if the percentage of inappropriate studies was changing over time. In a previous study, we applied the American College of Cardiology Foundation/American Society of Nuclear Cardiology (ASNC) appropriateness criteria for stress SPECT MPI and reported that 14% of stress SPECT studies were performed for inappropriate reasons. Using similar methodology, we retrospectively examined 284 patients who underwent stress SPECT MPI in October 2006 and compared the findings to the previous cohort of 284 patients who underwent stress SPECT MPI in May 2005. The indications for testing in the 2 cohorts were very similar. The overall level of agreement in characterizing categories of appropriateness between 2 experienced cardiovascular nurse abstractors was good (kappa = 0.68), which represented an improvement from our previous study (kappa = 0.56). There was a significant change between May 2005 and October 2006 in the overall classification of categories for appropriateness (P = .024 by chi(2) statistic). There were modest, but insignificant, increases in the number of patients who were unclassified (15% in the current study vs 11% previously), appropriate (66% vs 64%), and uncertain (12% vs 11%). Only 7% of the studies in the current study were inappropriate, which represented a significant (P = .004) decrease from the 14% reported in the 2005 cohort. In the absence of any specific intervention, there was a significant change in the overall classification of SPECT appropriateness in an academic medical center over 17 months. The only significant difference in individual categories was a decrease in inappropriate studies. Additional measurements over time will be required to determine if this trend is sustainable or generalizable.

The Relation of Arm Exercise Peak Heart Rate to Stress Test Results and Outcome.

PubMed

Xian, Hong; Liu, Weijian; Marshall, Cynthia; Chandiramani, Pooja; Bainter, Emily; Martin, Wade H

2016-09-01

Arm exercise is an alternative to pharmacologic stress testing for >50% of patients unable to perform treadmill exercise, but no data exist regarding the effect of attained peak arm exercise heart rate on test sensitivity. Thus, the purpose of this investigation was to characterize the relationship of peak arm exercise heart rate responses to abnormal stress test findings, coronary revascularization, and mortality in patients unable to perform leg exercise. From 1997 until 2002, arm cycle ergometer stress tests were performed in 443 consecutive veterans age 64.1 yr (11.0 yr) (mean (SD)), of whom 253 also underwent myocardial perfusion imaging (MPI). Patients were categorized by frequency distributions of quartiles of percentage age-predicted peak heart rate (APPHR), heart rate reserve (HRR), and peak heart rate-systolic blood pressure product (PRPP). Exercise-induced ST-segment depression, abnormal MPI findings, coronary revascularization, and 12.0-yr (1.3 yr) Kaplan-Meier all-cause and cardiovascular mortality plots were then characterized by quartiles of APPHR, HRR, and PRPP. A reduced frequency of abnormal arm exercise ECG results was associated only with the lowest quartile of APPHR (≤69%) and HRR (≤43%), whereas higher frequency of abnormal MPI findings exhibited an inverse relationship trend with lower APPHR (P = 0.10) and HRR (P = 0.12). There was a strong inverse association of APPHR, HRR, and PRPP with all-cause (all P ≤ 0.01) and cardiovascular (P < 0.05) mortality. The frequency of coronary revascularization was unrelated to APPHR or HRR. Arm exercise ECG stress test sensitivity is only reduced at ≤69% APPHR or ≤43% HRR, whereas arm exercise MPI sensitivity and referral for coronary revascularization after arm exercise stress testing are not adversely affected by even a severely blunted peak heart rate. However, both all-cause mortality and cardiovascular mortality are strongly and inversely related to APPHR and HRR.

Transcriptome reprogramming of resistant and susceptible peach genotypes during Xanthomonas arboricola pv. pruni early leaf infection

PubMed Central

Gervasi, Fabio; Ferrante, Patrizia; Dettori, Maria Teresa; Scortichini, Marco

2018-01-01

Bacterial spot caused by Xanthomonas arboricola pv. pruni (Xap) is a major threat to Prunus species worldwide. The molecular mechanisms of peach resistance to Xap during early leaf infection were investigated by RNA-Seq analysis of two Prunus persica cultivars, ‘Redkist’ (resistant), and ‘JH Hale’ (susceptible) at 30 minutes, 1 and 3 hours-post-infection (hpi). Both cultivars exhibited extensive modulation of gene expression at 30 mpi, which reduced significantly at 1 hpi, increasing again at 3 hpi. Overall, 714 differentially expressed genes (DEGs) were detected in ‘Redkist’ (12% at 30 mpi and 1 hpi and 88% at 3 hpi). In ‘JH Hale’, 821 DEGs were identified (47% at 30 mpi and 1 hpi and 53% at 3 hpi). Highly up-regulated genes (fold change > 100) at 3 hpi exhibited higher fold change values in ‘Redkist’ than in ‘JH Hale’. RNA-Seq bioinformatics analyses were validated by RT-qPCR. In both cultivars, DEGs included genes with putative roles in perception, signal transduction, secondary metabolism, and transcription regulation, and there were defense responses in both cultivars, with enrichment for the gene ontology terms, ‘immune system process’, ‘defense response’, and ‘cell death’. There were particular differences between the cultivars in the intensity and kinetics of modulation of expression of genes with putative roles in transcriptional activity, secondary metabolism, photosynthesis, and receptor and signaling processes. Analysis of differential exon usage (DEU) revealed that both cultivars initiated remodeling their transcriptomes at 30 mpi; however, ‘Redkist’ exhibited alternative exon usage for a greater number of genes at every time point compared with ‘JH Hale’. Candidate resistance genes (WRKY-like, CRK-like, Copper amine oxidase-like, and TIR-NBS-LRR-like) are of interest for further functional characterization with the aim of elucidating their role in Prunus spp. resistance to Xap. PMID:29698473

Transcriptome reprogramming of resistant and susceptible peach genotypes during Xanthomonas arboricola pv. pruni early leaf infection.

PubMed

Gervasi, Fabio; Ferrante, Patrizia; Dettori, Maria Teresa; Scortichini, Marco; Verde, Ignazio

2018-01-01

Bacterial spot caused by Xanthomonas arboricola pv. pruni (Xap) is a major threat to Prunus species worldwide. The molecular mechanisms of peach resistance to Xap during early leaf infection were investigated by RNA-Seq analysis of two Prunus persica cultivars, 'Redkist' (resistant), and 'JH Hale' (susceptible) at 30 minutes, 1 and 3 hours-post-infection (hpi). Both cultivars exhibited extensive modulation of gene expression at 30 mpi, which reduced significantly at 1 hpi, increasing again at 3 hpi. Overall, 714 differentially expressed genes (DEGs) were detected in 'Redkist' (12% at 30 mpi and 1 hpi and 88% at 3 hpi). In 'JH Hale', 821 DEGs were identified (47% at 30 mpi and 1 hpi and 53% at 3 hpi). Highly up-regulated genes (fold change > 100) at 3 hpi exhibited higher fold change values in 'Redkist' than in 'JH Hale'. RNA-Seq bioinformatics analyses were validated by RT-qPCR. In both cultivars, DEGs included genes with putative roles in perception, signal transduction, secondary metabolism, and transcription regulation, and there were defense responses in both cultivars, with enrichment for the gene ontology terms, 'immune system process', 'defense response', and 'cell death'. There were particular differences between the cultivars in the intensity and kinetics of modulation of expression of genes with putative roles in transcriptional activity, secondary metabolism, photosynthesis, and receptor and signaling processes. Analysis of differential exon usage (DEU) revealed that both cultivars initiated remodeling their transcriptomes at 30 mpi; however, 'Redkist' exhibited alternative exon usage for a greater number of genes at every time point compared with 'JH Hale'. Candidate resistance genes (WRKY-like, CRK-like, Copper amine oxidase-like, and TIR-NBS-LRR-like) are of interest for further functional characterization with the aim of elucidating their role in Prunus spp. resistance to Xap.

Short-term effects of air quality and thermal stress on non-accidental morbidity-a multivariate meta-analysis comparing indices to single measures.

PubMed

Lokys, Hanna Leona; Junk, Jürgen; Krein, Andreas

2018-01-01

Air quality and thermal stress lead to increased morbidity and mortality. Studies on morbidity and the combined impact of air pollution and thermal stress are still rare. To analyse the correlations between air quality, thermal stress and morbidity, we used a two-stage meta-analysis approach, consisting of a Poisson regression model combined with distributed lag non-linear models (DLNMs) and a meta-analysis investigating whether latitude or the number of inhabitants significantly influence the correlations. We used air pollution, meteorological and hospital admission data from 28 administrative districts along a north-south gradient in western Germany from 2001 to 2011. We compared the performance of the single measure particulate matter (PM10) and air temperature to air quality indices (MPI and CAQI) and the biometeorological index UTCI. Based on the Akaike information criterion (AIC), it can be shown that using air quality indices instead of single measures increases the model strength. However, using the UTCI in the model does not give additional information compared to mean air temperature. Interaction between the 3-day average of air quality (max PM10, max CAQI and max MPI) and meteorology (mean air temperature and mean UTCI) did not improve the models. Using the mean air temperature, we found immediate effects of heat stress (RR 1.0013, 95% CI: 0.9983-1.0043) and by 3 days delayed effects of cold stress (RR: 1.0184, 95% CI: 1.0117-1.0252). The results for air quality differ between both air quality indices and PM10. CAQI and MPI show a delayed impact on morbidity with a maximum RR after 2 days (MPI 1.0058, 95% CI: 1.0013-1.0102; CAQI 1.0068, 95% CI: 1.0030-1.0107). Latitude was identified as a significant meta-variable, whereas the number of inhabitants was not significant in the model.

Optimizing R with SparkR on a commodity cluster for biomedical research.

PubMed

Sedlmayr, Martin; Würfl, Tobias; Maier, Christian; Häberle, Lothar; Fasching, Peter; Prokosch, Hans-Ulrich; Christoph, Jan

2016-12-01

Medical researchers are challenged today by the enormous amount of data collected in healthcare. Analysis methods such as genome-wide association studies (GWAS) are often computationally intensive and thus require enormous resources to be performed in a reasonable amount of time. While dedicated clusters and public clouds may deliver the desired performance, their use requires upfront financial efforts or anonymous data, which is often not possible for preliminary or occasional tasks. We explored the possibilities to build a private, flexible cluster for processing scripts in R based on commodity, non-dedicated hardware of our department. For this, a GWAS-calculation in R on a single desktop computer, a Message Passing Interface (MPI)-cluster, and a SparkR-cluster were compared with regards to the performance, scalability, quality, and simplicity. The original script had a projected runtime of three years on a single desktop computer. Optimizing the script in R already yielded a significant reduction in computing time (2 weeks). By using R-MPI and SparkR, we were able to parallelize the computation and reduce the time to less than three hours (2.6 h) on already available, standard office computers. While MPI is a proven approach in high-performance clusters, it requires rather static, dedicated nodes. SparkR and its Hadoop siblings allow for a dynamic, elastic environment with automated failure handling. SparkR also scales better with the number of nodes in the cluster than MPI due to optimized data communication. R is a popular environment for clinical data analysis. The new SparkR solution offers elastic resources and allows supporting big data analysis using R even on non-dedicated resources with minimal change to the original code. To unleash the full potential, additional efforts should be invested to customize and improve the algorithms, especially with regards to data distribution. Copyright © 2016 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

Short-term effects of air quality and thermal stress on non-accidental morbidity—a multivariate meta-analysis comparing indices to single measures

NASA Astrophysics Data System (ADS)

Lokys, Hanna Leona; Junk, Jürgen; Krein, Andreas

2018-01-01

Air quality and thermal stress lead to increased morbidity and mortality. Studies on morbidity and the combined impact of air pollution and thermal stress are still rare. To analyse the correlations between air quality, thermal stress and morbidity, we used a two-stage meta-analysis approach, consisting of a Poisson regression model combined with distributed lag non-linear models (DLNMs) and a meta-analysis investigating whether latitude or the number of inhabitants significantly influence the correlations. We used air pollution, meteorological and hospital admission data from 28 administrative districts along a north-south gradient in western Germany from 2001 to 2011. We compared the performance of the single measure particulate matter (PM10) and air temperature to air quality indices (MPI and CAQI) and the biometeorological index UTCI. Based on the Akaike information criterion (AIC), it can be shown that using air quality indices instead of single measures increases the model strength. However, using the UTCI in the model does not give additional information compared to mean air temperature. Interaction between the 3-day average of air quality (max PM10, max CAQI and max MPI) and meteorology (mean air temperature and mean UTCI) did not improve the models. Using the mean air temperature, we found immediate effects of heat stress (RR 1.0013, 95% CI: 0.9983-1.0043) and by 3 days delayed effects of cold stress (RR: 1.0184, 95% CI: 1.0117-1.0252). The results for air quality differ between both air quality indices and PM10. CAQI and MPI show a delayed impact on morbidity with a maximum RR after 2 days (MPI 1.0058, 95% CI: 1.0013-1.0102; CAQI 1.0068, 95% CI: 1.0030-1.0107). Latitude was identified as a significant meta-variable, whereas the number of inhabitants was not significant in the model.

A template-based approach to semi-quantitative SPECT myocardial perfusion imaging: Independent of normal databases.

PubMed

Hughes, Tyler; Shcherbinin, Sergey; Celler, Anna

2011-07-01

Normal patient databases (NPDs) are used to distinguish between normal and abnormal perfusion in SPECT myocardial perfusion imaging (MPI) and have gained wide acceptance in the clinical environment, yet there are limitations to this approach. This study introduces a template-based method for semi-quantitative MPI, which attempts to overcome some of the NPD limitations. Our approach involves the construction of a 3D digital healthy heart template from the delineation of the patient's left ventricle in the SPECT image. This patient-specific template of the heart, filled with uniform activity, is then analytically projected and reconstructed using the same algorithm as the original image. Subsequent to generating bulls-eye maps for the patient image (PB) and the template image (TB), a ratio (PB/TB) is calculated, which produces a reconstruction-artifact corrected image (CB). Finally, a threshold is used to define defects within CB enabling measurements of the perfusion defect extent (EXT). The SPECT-based template (Ts) measurements were compared to those of a CT-based "ideal" template (TI). Twenty digital phantoms were simulated: male and female, each with one healthy heart and nine hearts with various defects. Four physical phantom studies were performed modeling a healthy heart and three hearts with different defects. The phantom represented a thorax with spine, lung, and left ventricle inserts. Images were acquired on General Electric's (GE) Infinia Hawkeye SPECT/CT camera using standard clinical MPI protocol. Finally, our method was applied to 14 patient MPI rest/stress studies acquired on the GE Infinia Hawkeye SPECT/CT camera and compared to the results obtained from Cedars-Sinai's QPS software. In the simulation studies, the true EXT correlated well with the TI (slope= 1.08; offset = -0.40%; r = 0.99) and Ts (slope = 0.90; offset = 0.27%; r = 0.99) methods with no significant differences between them. Similarly, strong correlations were measured for EXT obtained from QPS and the template method for patient studies (slope =0.91; offset = 0.45%; r = 0.98). Mean errors in extent for the Ts method using simulation, physical phantom, and patient data were 2.7% +/- 2.4%, 0.9% +/- 0.5%, 2.0% +/- 2.7%, respectively. The authors introduced a method for semi-quantitative SPECT MPI, which offers a patient-specific approach to define the perfusion defect regions within the heart, as opposed to the patient-averaged NPD methodology.

Comparison of LVEF assessed by 2D echocardiography, gated blood pool SPECT, 99mTc tetrofosmin gated SPECT, and 18F-FDG gated PET with ERNV in patients with CAD and severe LV dysfunction.

PubMed

Raja, Senthil; Mittal, Bhagwant R; Santhosh, Sampath; Bhattacharya, Anish; Rohit, Manoj K

2014-11-01

Left ventricular ejection fraction (LVEF) is the single most important predictor of prognosis in patients with coronary artery disease (CAD) and left ventricular (LV) dysfunction. Equilibrium radionuclide ventriculography (ERNV) is considered the most reliable technique for assessing LVEF. Most of these patients undergo two dimensional (2D) echocardiography and myocardial viability study using gated myocardial perfusion imaging (MPI) or gated F-fluorodeoxyglucose (F-FDG) PET. However, the accuracy of LVEF assessed by these methods is not clear. This study has been designed to assess the correlation and agreement between the LVEF measured by 2D echocardiography, gated blood pool single photon emission computed tomography (SPECT), Tc tetrofosmin gated SPECT, and F-FDG gated PET with ERNV in CAD patients with severe LV dysfunction. Patients with CAD and severe LV dysfunction [ejection fraction (EF) <35 assessed by 2D echocardiography] were prospectively included in the study. These patients underwent ERNV along with gated blood pool SPECT, Tc tetrofosmin gated SPECT, and F-FDG gated PET as per the standard protocol for myocardial viability assessment and LVEF calculation. Spearman's coefficient of correlation (r) was calculated for the different sets of values with significance level kept at a P-value less than 0.05. Bland-Altman plots were inspected to visually assess the between-agreement measurements from different methods. Forty-one patients were prospectively included. LVEF calculated by various radionuclide methods showed good correlation with ERNV as follows: gated blood pool SPECT, r=0.92; MPI gated SPECT, r=0.85; and F-FDG gated PET, r=0.76. However, the correlation between 2D echocardiography and ERNV was poor (r=0.520). The Bland-Altman plot for LVEF measured by all radionuclide methods showed good agreement with ERNV. However, agreement between 2D echocardiography and ERNV is poor, as most of the values in this plot gave a negative difference for low EF and a positive difference for high EF. The mean difference between various techniques [2D echocardiography (a), gated blood pool SPECT (b), MPI gated SPECT (c), F-FDG gated PET (d)] and ERNV (e) was as follows: (a)-(e), 3.3; (b)-(e), 5; (c)-(e), 1.1; and (d)-(e), 2.9. The best possible correlation and agreement was found between MPI gated SPECT and ERNV. This study showed good correlation and agreement between MPI gated SPECT and F-FDG gated PET with ERNV for LVEF calculation in CAD patients with severe LV dysfunction. Thus, subjecting patients who undergo viability assessment by MPI gated SPECT or F-FDG gated PET to a separate procedure like ERNV for LVEF assessment may not be warranted. As the gated blood pool SPECT also showed good correlation and agreement with ERNV for LVEF assessment in CAD patients with severe LV dysfunction, with better characteristics than ERNV, it can be routinely used whenever accurate LVEF assessment is needed.

Parallel hyperbolic PDE simulation on clusters: Cell versus GPU

NASA Astrophysics Data System (ADS)

Rostrup, Scott; De Sterck, Hans

2010-12-01

Increasingly, high-performance computing is looking towards data-parallel computational devices to enhance computational performance. Two technologies that have received significant attention are IBM's Cell Processor and NVIDIA's CUDA programming model for graphics processing unit (GPU) computing. In this paper we investigate the acceleration of parallel hyperbolic partial differential equation simulation on structured grids with explicit time integration on clusters with Cell and GPU backends. The message passing interface (MPI) is used for communication between nodes at the coarsest level of parallelism. Optimizations of the simulation code at the several finer levels of parallelism that the data-parallel devices provide are described in terms of data layout, data flow and data-parallel instructions. Optimized Cell and GPU performance are compared with reference code performance on a single x86 central processing unit (CPU) core in single and double precision. We further compare the CPU, Cell and GPU platforms on a chip-to-chip basis, and compare performance on single cluster nodes with two CPUs, two Cell processors or two GPUs in a shared memory configuration (without MPI). We finally compare performance on clusters with 32 CPUs, 32 Cell processors, and 32 GPUs using MPI. Our GPU cluster results use NVIDIA Tesla GPUs with GT200 architecture, but some preliminary results on recently introduced NVIDIA GPUs with the next-generation Fermi architecture are also included. This paper provides computational scientists and engineers who are considering porting their codes to accelerator environments with insight into how structured grid based explicit algorithms can be optimized for clusters with Cell and GPU accelerators. It also provides insight into the speed-up that may be gained on current and future accelerator architectures for this class of applications. Program summaryProgram title: SWsolver Catalogue identifier: AEGY_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGY_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GPL v3 No. of lines in distributed program, including test data, etc.: 59 168 No. of bytes in distributed program, including test data, etc.: 453 409 Distribution format: tar.gz Programming language: C, CUDA Computer: Parallel Computing Clusters. Individual compute nodes may consist of x86 CPU, Cell processor, or x86 CPU with attached NVIDIA GPU accelerator. Operating system: Linux Has the code been vectorised or parallelized?: Yes. Tested on 1-128 x86 CPU cores, 1-32 Cell Processors, and 1-32 NVIDIA GPUs. RAM: Tested on Problems requiring up to 4 GB per compute node. Classification: 12 External routines: MPI, CUDA, IBM Cell SDK Nature of problem: MPI-parallel simulation of Shallow Water equations using high-resolution 2D hyperbolic equation solver on regular Cartesian grids for x86 CPU, Cell Processor, and NVIDIA GPU using CUDA. Solution method: SWsolver provides 3 implementations of a high-resolution 2D Shallow Water equation solver on regular Cartesian grids, for CPU, Cell Processor, and NVIDIA GPU. Each implementation uses MPI to divide work across a parallel computing cluster. Additional comments: Sub-program numdiff is used for the test run.

Comittees

NASA Astrophysics Data System (ADS)

2004-10-01

Fritz Caspers (CERN, Switzerland), Michel Chanel (CERN, Switzerland), Håkan Danared (MSL, Sweden), Bernhard Franzke (GSI, Germany), Manfred Grieser (MPI für Kernphysik, Germany), Dieter Habs (LMU München, Germany), Jeffrey Hangst (University of Aarhus, Denmark), Takeshi Katayama (RIKEN/Univ. Tokyo, Japan), H.-Jürgen Kluge (GSI, Germany), Shyh-Yuan Lee (Indiana University, USA), Rudolf Maier (FZ Jülich, Germany), John Marriner (FNAL, USA), Igor Meshkov (JINR, Russia), Dieter Möhl (CERN, Switzerland), Vasily Parkhomchuk (BINP, Russia), Robert Pollock (Indiana University), Dieter Prasuhn (FZ Jülich, Germany), Dag Reistad (TSL, Sweden), John Schiffer (ANL, USA), Andrew Sessler (LBNL, USA), Alexander Skrinsky (BINP, Russia), Markus Steck (GSI, Germany), Jie Wei (BNL, USA), Andreas Wolf (MPI für Kernphysik, Germany), Hongwei Zhao (IMP, People's Rep. of China).

WOMBAT: A Scalable and High-performance Astrophysical Magnetohydrodynamics Code

NASA Astrophysics Data System (ADS)

Mendygral, P. J.; Radcliffe, N.; Kandalla, K.; Porter, D.; O'Neill, B. J.; Nolting, C.; Edmon, P.; Donnert, J. M. F.; Jones, T. W.

2017-02-01

We present a new code for astrophysical magnetohydrodynamics specifically designed and optimized for high performance and scaling on modern and future supercomputers. We describe a novel hybrid OpenMP/MPI programming model that emerged from a collaboration between Cray, Inc. and the University of Minnesota. This design utilizes MPI-RMA optimized for thread scaling, which allows the code to run extremely efficiently at very high thread counts ideal for the latest generation of multi-core and many-core architectures. Such performance characteristics are needed in the era of “exascale” computing. We describe and demonstrate our high-performance design in detail with the intent that it may be used as a model for other, future astrophysical codes intended for applications demanding exceptional performance.

Cognitive factors in the close visual and magnetic particle inspection of welds underwater.

PubMed

Leach, J; Morris, P E

1998-06-01

Underwater close visual inspection (CVI) and magnetic particle inspection (MPI) are major components of the commercial diver's job of nondestructive testing and the maintenance of subsea structures. We explored the accuracy of CVI in Experiment 1 and that of MPI in Experiment 2 and observed high error rates (47% and 24%, respectively). Performance was strongly correlated with embedded figures and visual search tests and was unrelated to length of professional diving experience, formal inspection qualification, or age. Cognitive tests of memory for designs, spatial relations, dotted outlines, and block design failed to correlate with performance. Actual or potential applications of this research include more reliable inspection reporting, increased effectiveness from current inspection techniques, and directions for the refinement of subsea inspection equipment.

Simple, efficient allocation of modelling runs on heterogeneous clusters with MPI

USGS Publications Warehouse

Donato, David I.

2017-01-01

In scientific modelling and computation, the choice of an appropriate method for allocating tasks for parallel processing depends on the computational setting and on the nature of the computation. The allocation of independent but similar computational tasks, such as modelling runs or Monte Carlo trials, among the nodes of a heterogeneous computational cluster is a special case that has not been specifically evaluated previously. A simulation study shows that a method of on-demand (that is, worker-initiated) pulling from a bag of tasks in this case leads to reliably short makespans for computational jobs despite heterogeneity both within and between cluster nodes. A simple reference implementation in the C programming language with the Message Passing Interface (MPI) is provided.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shamis, Pavel; Graham, Richard L; Gorentla Venkata, Manjunath

The scalability and performance of collective communication operations limit the scalability and performance of many scientific applications. This paper presents two new blocking and nonblocking Broadcast algorithms for communicators with arbitrary communication topology, and studies their performance. These algorithms benefit from increased concurrency and a reduced memory footprint, making them suitable for use on large-scale systems. Measuring small, medium, and large data Broadcasts on a Cray-XT5, using 24,576 MPI processes, the Cheetah algorithms outperform the native MPI on that system by 51%, 69%, and 9%, respectively, at the same process count. These results demonstrate an algorithmic approach to the implementationmore » of the important class of collective communications, which is high performing, scalable, and also uses resources in a scalable manner.« less

First in vivo traumatic brain injury imaging via magnetic particle imaging

NASA Astrophysics Data System (ADS)

Orendorff, Ryan; Peck, Austin J.; Zheng, Bo; Shirazi, Shawn N.; Ferguson, R. Matthew; Khandhar, Amit P.; Kemp, Scott J.; Goodwill, Patrick; Krishnan, Kannan M.; Brooks, George A.; Kaufer, Daniela; Conolly, Steven

2017-05-01

Emergency room visits due to traumatic brain injury (TBI) is common, but classifying the severity of the injury remains an open challenge. Some subjective methods such as the Glasgow Coma Scale attempt to classify traumatic brain injuries, as well as some imaging based modalities such as computed tomography and magnetic resonance imaging. However, to date it is still difficult to detect and monitor mild to moderate injuries. In this report, we demonstrate that the magnetic particle imaging (MPI) modality can be applied to imaging TBI events with excellent contrast. MPI can monitor injected iron nanoparticles over long time scales without signal loss, allowing researchers and clinicians to monitor the change in blood pools as the wound heals.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mubarak, Misbah; Ross, Robert B.

This technical report describes the experiments performed to validate the MPI performance measurements reported by the CODES dragonfly network simulation with the Theta Cray XC system at the Argonne Leadership Computing Facility (ALCF).

Nonlinear Stress Relaxation of ``Quasi-monodisperse'' Miscible Blends of cis-Polyisoprene and Poly(ptert-butylstyrene)

NASA Astrophysics Data System (ADS)

Watanabe, Hiroshi; Matsumiya, Yumi

Viscoelastic relaxation was examined for entangled miscible blends of cis-polyisoprene (PI) and poly(ptert-butylstyrene) (PtBS). The terminal relaxation times of PI and PtBS therein, τPI and τPtBS, changed with the composition wPI and the molecular weights MPI and MPtBS. This ratio became unity when the wPI, MPI, and MPtBS values were chosen adequately. For example, in a blend with wPI = 0.75, MPI = 321k, and MPtBS = 91k at T = 40ûC, τPI/τPtBS = 1 and M/Me = 55 and 8.3 for PI and PtBS. Under small strains, this blend exhibited sharp, single-step terminal relaxation as similar to monodisperse homopolymers, thereby behaving as a ``quasi-monodisperse'' material. Under large step strains, the blend exhibited moderate nonlinear damping known as the type-A damping for entangled monodisperse homopolymers. Nevertheless, PI had M/Me = 55 in that blend, and homopolymers having such a large M/Me ratio exhibit very strong type-C damping. Thus, as compared to homopolymers, the nonlinearity was suppressed in the PI/PtBS blend having the large M/Me ratio. This suppression is discussed in relation to the slow Rouse retraction of the coexisting PtBS chains (having M/Me = 8.3 in the blend).

MPI-FAUN: An MPI-Based Framework for Alternating-Updating Nonnegative Matrix Factorization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kannan, Ramakrishnan; Ballard, Grey; Park, Haesun

Non-negative matrix factorization (NMF) is the problem of determining two non-negative low rank factors W and H, for the given input matrix A, such that A≈WH. NMF is a useful tool for many applications in different domains such as topic modeling in text mining, background separation in video analysis, and community detection in social networks. Despite its popularity in the data mining community, there is a lack of efficient parallel algorithms to solve the problem for big data sets. The main contribution of this work is a new, high-performance parallel computational framework for a broad class of NMF algorithms thatmore » iteratively solves alternating non-negative least squares (NLS) subproblems for W and H. It maintains the data and factor matrices in memory (distributed across processors), uses MPI for interprocessor communication, and, in the dense case, provably minimizes communication costs (under mild assumptions). The framework is flexible and able to leverage a variety of NMF and NLS algorithms, including Multiplicative Update, Hierarchical Alternating Least Squares, and Block Principal Pivoting. Our implementation allows us to benchmark and compare different algorithms on massive dense and sparse data matrices of size that spans from few hundreds of millions to billions. We demonstrate the scalability of our algorithm and compare it with baseline implementations, showing significant performance improvements. The code and the datasets used for conducting the experiments are available online.« less

Users manual for the Chameleon parallel programming tools

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gropp, W.; Smith, B.

1993-06-01

Message passing is a common method for writing programs for distributed-memory parallel computers. Unfortunately, the lack of a standard for message passing has hampered the construction of portable and efficient parallel programs. In an attempt to remedy this problem, a number of groups have developed their own message-passing systems, each with its own strengths and weaknesses. Chameleon is a second-generation system of this type. Rather than replacing these existing systems, Chameleon is meant to supplement them by providing a uniform way to access many of these systems. Chameleon`s goals are to (a) be very lightweight (low over-head), (b) be highlymore » portable, and (c) help standardize program startup and the use of emerging message-passing operations such as collective operations on subsets of processors. Chameleon also provides a way to port programs written using PICL or Intel NX message passing to other systems, including collections of workstations. Chameleon is tracking the Message-Passing Interface (MPI) draft standard and will provide both an MPI implementation and an MPI transport layer. Chameleon provides support for heterogeneous computing by using p4 and PVM. Chameleon`s support for homogeneous computing includes the portable libraries p4, PICL, and PVM and vendor-specific implementation for Intel NX, IBM EUI (SP-1), and Thinking Machines CMMD (CM-5). Support for Ncube and PVM 3.x is also under development.« less

Spectroscopic investigation of light-induced intracellular reactions of hydrophilic meso-tetraphenylporphyrins

NASA Astrophysics Data System (ADS)

Rueck, Angelika C.; Strauss, Wolfgang S. L.; Schneckenburger, Herbert; Steiner, Rudolf W.

1992-06-01

Light-induced reactions of different hydrophilic meso-tetraphenyl porphyrins (TPPS4, TPPC4, T4MPyP) were investigated during PDT treatment. These measurements were carried out in vitro using micro-spectrofluorometry and were correlated with measurements in buffer solutions. In the case of the anionic TPPS4, before light exposure, a neutral free base and a protonated species could be detected simultaneously in the cells. During irradiation, the protonated species first disappeared. Due to the fact that a coexistence of a protonated and unprotonated species requires a pH value around 5, TPPS4 was at first located in the lysosomes (pH 5) and was released into the cytoplasm during irradiation as a result of lysosomal rupture. Further light exposure led to a drastic fluorescence formation in the nuclei, in particular the nucleoli of the cells, which was concomitant with a renewed observation of a fluorescence emission spectrum similar to that of the protonated species. In the case of the anionic TPPC4, a similar fluorescence increase was observed during irradiation. However, the formation of a protonated species played a less important role. The cationic T4MPyP again showed fluorescence increase during irradiation. Two Soret-bands separated by about 20 nm could be detected. The red-shifted band may be due to a special intercalation of T4MPyP in nucleic acids.

Measuring the excitations in a new S  =  1/2 quantum spin chain material with competing interactions

NASA Astrophysics Data System (ADS)

Rule, K. C.; Mole, R. A.; Zanardo, J.; Krause-Heuer, A.; Darwish, T.; Lerch, M.; Yu, D.

2018-05-01

Recently a new one-dimensional (1D) quantum spin chain system has been reported: catena-dichloro(2-Cl-3Mpy)copper(II), (where 2-Cl-3Mpy=2-chloro-3-methylpyridine). Preliminary calculations and bulk magnetic property measurements indicate that this system does not undergo magnetic ordering down to 1.8 K and is a prime candidate for investigating frustration in a J 1/J 2 system (where the nearest neighbour interactions, J 1, are ferromagnetic and the next nearest neighbour interactions, J 2, are antiferromagnetic). Calculations predicted three possible magnetic interaction strengths for J 1 below 6 meV depending on the orientation of the ligand. For one of the predicted J 1 values, the existence of a quantum critical point is implied. A deuterated sample of catena-dichloro(2-Cl-3Mpy)copper(II) was synthesised and the excitations measured using inelastic neutron scattering. Scattering indicated the most likely scenario involves spin-chains where each chain consists of only one of the three possible magnetic excitations in this material, rather than the completely random array of exchange interactions within each chain as predicted by Herringer et al (2014 Chem. Eur. J. 20 8355–62). This indicates the possibility of tuning the chemical structure to favour a system which may exhibit a quantum critical point.

Measuring the excitations in a new S  =  1/2 quantum spin chain material with competing interactions.

PubMed

Rule, K C; Mole, R A; Zanardo, J; Krause-Heuer, A; Darwish, T; Lerch, M; Yu, D

2018-05-31

Recently a new one-dimensional (1D) quantum spin chain system has been reported: catena-dichloro(2-Cl-3Mpy)copper(II), (where 2-Cl-3Mpy=2-chloro-3-methylpyridine). Preliminary calculations and bulk magnetic property measurements indicate that this system does not undergo magnetic ordering down to 1.8 K and is a prime candidate for investigating frustration in a J 1 /J 2 system (where the nearest neighbour interactions, J 1 , are ferromagnetic and the next nearest neighbour interactions, J 2 , are antiferromagnetic). Calculations predicted three possible magnetic interaction strengths for J 1 below 6 meV depending on the orientation of the ligand. For one of the predicted J 1 values, the existence of a quantum critical point is implied. A deuterated sample of catena-dichloro(2-Cl-3Mpy)copper(II) was synthesised and the excitations measured using inelastic neutron scattering. Scattering indicated the most likely scenario involves spin-chains where each chain consists of only one of the three possible magnetic excitations in this material, rather than the completely random array of exchange interactions within each chain as predicted by Herringer et al (2014 Chem. Eur. J. 20 8355-62). This indicates the possibility of tuning the chemical structure to favour a system which may exhibit a quantum critical point.

Oak Ridge Institutional Cluster Autotune Test Drive Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jibonananda, Sanyal; New, Joshua Ryan

2014-02-01

The Oak Ridge Institutional Cluster (OIC) provides general purpose computational resources for the ORNL staff to run computation heavy jobs that are larger than desktop applications but do not quite require the scale and power of the Oak Ridge Leadership Computing Facility (OLCF). This report details the efforts made and conclusions derived in performing a short test drive of the cluster resources on Phase 5 of the OIC. EnergyPlus was used in the analysis as a candidate user program and the overall software environment was evaluated against anticipated challenges experienced with resources such as the shared memory-Nautilus (JICS) and Titanmore » (OLCF). The OIC performed within reason and was found to be acceptable in the context of running EnergyPlus simulations. The number of cores per node and the availability of scratch space per node allow non-traditional desktop focused applications to leverage parallel ensemble execution. Although only individual runs of EnergyPlus were executed, the software environment on the OIC appeared suitable to run ensemble simulations with some modifications to the Autotune workflow. From a standpoint of general usability, the system supports common Linux libraries, compilers, standard job scheduling software (Torque/Moab), and the OpenMPI library (the only MPI library) for MPI communications. The file system is a Panasas file system which literature indicates to be an efficient file system.« less

Right ventricular systolic function in hypertensive heart failure.

PubMed

Oketona, O A; Balogun, M O; Akintomide, A O; Ajayi, O E; Adebayo, R A; Mene-Afejuku, T O; Oketona, O T; Bamikole, O J

2017-01-01

Heart failure (HF) is a major cause of cardiovascular admissions and hypertensive heart failure (HHF) is the most common cause of HF admissions in sub-Saharan Africa, Nigeria inclusive. Right ventricular (RV) dysfunction is being increasingly recognized in HF and found to be an independent predictor of adverse outcomes in HF. This study aimed to determine the prevalence of RV systolic dysfunction in HHF by several echocardiographic parameters. One hundred subjects with HHF were recruited consecutively into the study along with 50 age and sex-matched controls. All study participants gave written informed consent, and had a full physical examination, blood investigations, 12-lead electrocardiogram, and transthoracic echocardiography. RV systolic function was assessed in all subjects using different methods based on the American Society of Echocardiography guidelines for echocardiographic assessment of the right heart in adults. This included tricuspid annular plane systolic excursion (TAPSE), RV myocardial performance index (MPI), and RV systolic excursion velocity by tissue Doppler (S'). RV systolic dysfunction was found in 53% of subjects with HHF by TAPSE, 56% by RV MPI, and 48% by tissue Doppler systolic excursion S'. RV systolic dysfunction increased with reducing left ventricular ejection fraction (LVEF) in subjects with HHF. A high proportion of subjects with HHF were found to have RV systolic functional abnormalities using TAPSE, RV MPI, and RV S'. Prevalence of RV systolic dysfunction increased with reducing LVEF.

Cationic, anionic and neutral dyes: effects of photosensitizing properties and experimental conditions on the photodynamic inactivation of pathogenic bacteria.

PubMed

Sabbahi, Sonia; Ben Ayed, Layla; Boudabbous, Abdellatif

2013-12-01

The aim of this study was to evaluate the photobactericidal effect of four photosensitizers (PSs) with different structural and physico-photochemical properties, namely mesotetracationic porphyrin (T4MPyP), dianionic rose Bengal (RB), monocationic methylene blue (MB) and neutral red (NR). Their photokilling activity was tested in vitro on pathogenic bacteria such as Pseudomonas aeruginosa (P. aeruginosa) and Staphylococcus aureus (S. aureus) suspended in nutrient broth (NB) and in phosphate buffered saline (PBS) through following their influence on the PSs antimicrobial efficacy. Photodynamic inactivation (PDI) experiments were performed using visible light (L) and different PSs concentrations (20-70 μM). The ability of these PSs to mediate bacterial photodynamic inactivation was investigated as a function of type of PS and its concentrations, spectral and physico-chemical properties, bacterial strain, irradiation time and suspending medium. Indeed, they showed antibacterial effects against S. aureus and P. aeruginosa with significant difference in potency. Staphylococcus aureus suspended in NB showed 0.92 log units reduction in viable count in the presence of T4MPyP at 20 μM. Changing the suspending medium from NB to PBS, S. aureus was successfully photoinactivated by T4MPyP (20 μM) when suspended in PBS at least time exposure (10 and 30 min), followed by MB and RB.

Cpu/gpu Computing for AN Implicit Multi-Block Compressible Navier-Stokes Solver on Heterogeneous Platform

NASA Astrophysics Data System (ADS)

Deng, Liang; Bai, Hanli; Wang, Fang; Xu, Qingxin

2016-06-01

CPU/GPU computing allows scientists to tremendously accelerate their numerical codes. In this paper, we port and optimize a double precision alternating direction implicit (ADI) solver for three-dimensional compressible Navier-Stokes equations from our in-house Computational Fluid Dynamics (CFD) software on heterogeneous platform. First, we implement a full GPU version of the ADI solver to remove a lot of redundant data transfers between CPU and GPU, and then design two fine-grain schemes, namely “one-thread-one-point” and “one-thread-one-line”, to maximize the performance. Second, we present a dual-level parallelization scheme using the CPU/GPU collaborative model to exploit the computational resources of both multi-core CPUs and many-core GPUs within the heterogeneous platform. Finally, considering the fact that memory on a single node becomes inadequate when the simulation size grows, we present a tri-level hybrid programming pattern MPI-OpenMP-CUDA that merges fine-grain parallelism using OpenMP and CUDA threads with coarse-grain parallelism using MPI for inter-node communication. We also propose a strategy to overlap the computation with communication using the advanced features of CUDA and MPI programming. We obtain speedups of 6.0 for the ADI solver on one Tesla M2050 GPU in contrast to two Xeon X5670 CPUs. Scalability tests show that our implementation can offer significant performance improvement on heterogeneous platform.

Analysis of 2D Torus and Hub Topologies of 100Mb/s Ethernet for the Whitney Commodity Computing Testbed

NASA Technical Reports Server (NTRS)

Pedretti, Kevin T.; Fineberg, Samuel A.; Kutler, Paul (Technical Monitor)

1997-01-01

A variety of different network technologies and topologies are currently being evaluated as part of the Whitney Project. This paper reports on the implementation and performance of a Fast Ethernet network configured in a 4x4 2D torus topology in a testbed cluster of 'commodity' Pentium Pro PCs. Several benchmarks were used for performance evaluation: an MPI point to point message passing benchmark, an MPI collective communication benchmark, and the NAS Parallel Benchmarks version 2.2 (NPB2). Our results show that for point to point communication on an unloaded network, the hub and 1 hop routes on the torus have about the same bandwidth and latency. However, the bandwidth decreases and the latency increases on the torus for each additional route hop. Collective communication benchmarks show that the torus provides roughly four times more aggregate bandwidth and eight times faster MPI barrier synchronizations than a hub based network for 16 processor systems. Finally, the SOAPBOX benchmarks, which simulate real-world CFD applications, generally demonstrated substantially better performance on the torus than on the hub. In the few cases the hub was faster, the difference was negligible. In total, our experimental results lead to the conclusion that for Fast Ethernet networks, the torus topology has better performance and scales better than a hub based network.

The clinical role of stress myocardial perfusion imaging in women with suspected coronary artery disease.

PubMed

Mieres, Jennifer H; Rosman, David R; Shaw, Leslee J

2004-01-01

Cardiovascular disease remains the number one cause of mortality for women in the United States, with coronary artery disease (CAD) accounting for 54% of all cardiovascular deaths. CAD claims the lives of more than 250,000 women each year and is therefore the single largest killer of American women. For several decades, the under-representation of women in clinical trials led to both a lack of available sex-specific evidence and a generalized misconception that CAD was a "man's disease." In actuality, not only are women vulnerable to CAD, they typically develop it 10 to 15 years later than men. Furthermore, sex differences exist in the mortality rates of women and men with CAD, such that once CAD is present in women, they have worse outcomes than their male counterparts. Consequently, early and accurate diagnosis of CAD is crucial for reducing mortality rates in women. Stress myocardial perfusion imaging (MPI) using contemporary techniques has been shown to have significant value in the diagnosis and prognosis of CAD in women. In the risk assessment of women with an intermediate clinical pretest likelihood of CAD, using MPI with exercise or pharmacologic stress has been shown to add incremental value to clinical variables or exercise electrocardiogram stress testing alone. This review discusses the clinical role of stress MPI in the management of women with suspected CAD.

Multi-GPU hybrid programming accelerated three-dimensional phase-field model in binary alloy

NASA Astrophysics Data System (ADS)

Zhu, Changsheng; Liu, Jieqiong; Zhu, Mingfang; Feng, Li

2018-03-01

In the process of dendritic growth simulation, the computational efficiency and the problem scales have extremely important influence on simulation efficiency of three-dimensional phase-field model. Thus, seeking for high performance calculation method to improve the computational efficiency and to expand the problem scales has a great significance to the research of microstructure of the material. A high performance calculation method based on MPI+CUDA hybrid programming model is introduced. Multi-GPU is used to implement quantitative numerical simulations of three-dimensional phase-field model in binary alloy under the condition of multi-physical processes coupling. The acceleration effect of different GPU nodes on different calculation scales is explored. On the foundation of multi-GPU calculation model that has been introduced, two optimization schemes, Non-blocking communication optimization and overlap of MPI and GPU computing optimization, are proposed. The results of two optimization schemes and basic multi-GPU model are compared. The calculation results show that the use of multi-GPU calculation model can improve the computational efficiency of three-dimensional phase-field obviously, which is 13 times to single GPU, and the problem scales have been expanded to 8193. The feasibility of two optimization schemes is shown, and the overlap of MPI and GPU computing optimization has better performance, which is 1.7 times to basic multi-GPU model, when 21 GPUs are used.

The reality of disability: Multidimensional poverty of people with disability and their families in Latin America.

PubMed

Pinilla-Roncancio, Mónica

2017-12-30

Disability and poverty are interconnected and although this relationship has been recognised, there is a lack of empirical evidence to support any possible causal relationship in this topic, particularly in the context of Latin America (LA). This study tests the hypothesis "Disability increases the risk of multidimensional poverty of people living with disabilities and their families". Using national census data from Brazil, Chile, Colombia, Costa Rica and Mexico, the Global Multidimensional Poverty Index (Global MPI) was calculated with the aim of measuring and comparing the levels of multidimensional poverty of people living in households with and without disabled members in the five countries. We found that in the five countries people with disabilities and their families had higher incidence, intensity and levels of multidimensional poverty compared with people living in other households. Their levels of deprivation were also higher for all the indicators included in the Global MPI and the contribution of this group to the national MPI was higher than their share of the population, thus people with disabilities and their families are overrepresented in those living in multidimensional poverty. People with disabilities and their families are in worse conditions than poor households without disabled members and social policies should aim to reduce their high levels of multidimensional poverty and deprivation. Copyright © 2017 Elsevier Inc. All rights reserved.

Increasing feasibility of the field-programmable gate array implementation of an iterative image registration using a kernel-warping algorithm

NASA Astrophysics Data System (ADS)

Nguyen, An Hung; Guillemette, Thomas; Lambert, Andrew J.; Pickering, Mark R.; Garratt, Matthew A.

2017-09-01

Image registration is a fundamental image processing technique. It is used to spatially align two or more images that have been captured at different times, from different sensors, or from different viewpoints. There have been many algorithms proposed for this task. The most common of these being the well-known Lucas-Kanade (LK) and Horn-Schunck approaches. However, the main limitation of these approaches is the computational complexity required to implement the large number of iterations necessary for successful alignment of the images. Previously, a multi-pass image interpolation algorithm (MP-I2A) was developed to considerably reduce the number of iterations required for successful registration compared with the LK algorithm. This paper develops a kernel-warping algorithm (KWA), a modified version of the MP-I2A, which requires fewer iterations to successfully register two images and less memory space for the field-programmable gate array (FPGA) implementation than the MP-I2A. These reductions increase feasibility of the implementation of the proposed algorithm on FPGAs with very limited memory space and other hardware resources. A two-FPGA system rather than single FPGA system is successfully developed to implement the KWA in order to compensate insufficiency of hardware resources supported by one FPGA, and increase parallel processing ability and scalability of the system.

Rationale and design of the dual-energy computed tomography for ischemia determination compared to "gold standard" non-invasive and invasive techniques (DECIDE-Gold): A multicenter international efficacy diagnostic study of rest-stress dual-energy computed tomography angiography with perfusion.

PubMed

Truong, Quynh A; Knaapen, Paul; Pontone, Gianluca; Andreini, Daniele; Leipsic, Jonathon; Carrascosa, Patricia; Lu, Bin; Branch, Kelley; Raman, Subha; Bloom, Stephen; Min, James K

2015-10-01

Dual-energy CT (DECT) has potential to improve myocardial perfusion for physiologic assessment of coronary artery disease (CAD). Diagnostic performance of rest-stress DECT perfusion (DECTP) is unknown. DECIDE-Gold is a prospective multicenter study to evaluate the accuracy of DECT to detect hemodynamic (HD) significant CAD, as compared to fractional flow reserve (FFR) as a reference standard. Eligible participants are subjects with symptoms of CAD referred for invasive coronary angiography (ICA). Participants will undergo DECTP, which will be performed by pharmacological stress, and participants will subsequently proceed to ICA and FFR. HD-significant CAD will be defined as FFR ≤ 0.80. In those undergoing myocardial stress imaging (MPI) by positron emission tomography (PET), single photon emission computed tomography (SPECT) or cardiac magnetic resonance (CMR) imaging, ischemia will be graded by % ischemic myocardium. Blinded core laboratory interpretation will be performed for CCTA, DECTP, MPI, ICA, and FFR. Primary endpoint is accuracy of DECTP to detect ≥1 HD-significant stenosis at the subject level when compared to FFR. Secondary and tertiary endpoints are accuracies of combinations of DECTP at the subject and vessel levels compared to FFR and MPI. DECIDE-Gold will determine the performance of DECTP for diagnosing ischemia.

Interaction of the Mouse Polyomavirus Capsid Proteins with Importins Is Required for Efficient Import of Viral DNA into the Cell Nucleus.

PubMed

Soldatova, Irina; Prilepskaja, Terezie; Abrahamyan, Levon; Forstová, Jitka; Huérfano, Sandra

2018-03-31

The mechanism used by mouse polyomavirus (MPyV) overcomes the crowded cytosol to reach the nucleus has not been fully elucidated. Here, we investigated the involvement of importin α/β1 mediated transport in the delivery of MPyV genomes into the nucleus. Interactions of the virus with importin β1 were studied by co-immunoprecipitation and proximity ligation assay. For infectivity and nucleus delivery assays, the virus and its capsid proteins mutated in the nuclear localization signals (NLSs) were prepared and produced. We found that at early times post infection, virions bound importin β1 in a time dependent manner with a peak of interactions at 6 h post infection. Mutation analysis revealed that only when the NLSs of both VP1 and VP2/3 were disrupted, virus did not bind efficiently to importin β1 and its infectivity remarkably decreased (by 80%). Nuclear targeting of capsid proteins was improved when VP1 and VP2 were co-expressed. VP1 and VP2 were effectively delivered into the nucleus, even when one of the NLS, either VP1 or VP2, was disrupted. Altogether, our results showed that MPyV virions can use VP1 and/or VP2/VP3 NLSs in concert or individually to bind importins to deliver their genomes into the cell nucleus.

MPI-FAUN: An MPI-Based Framework for Alternating-Updating Nonnegative Matrix Factorization

DOE PAGES

Kannan, Ramakrishnan; Ballard, Grey; Park, Haesun

2017-10-30

Non-negative matrix factorization (NMF) is the problem of determining two non-negative low rank factors W and H, for the given input matrix A, such that A≈WH. NMF is a useful tool for many applications in different domains such as topic modeling in text mining, background separation in video analysis, and community detection in social networks. Despite its popularity in the data mining community, there is a lack of efficient parallel algorithms to solve the problem for big data sets. The main contribution of this work is a new, high-performance parallel computational framework for a broad class of NMF algorithms thatmore » iteratively solves alternating non-negative least squares (NLS) subproblems for W and H. It maintains the data and factor matrices in memory (distributed across processors), uses MPI for interprocessor communication, and, in the dense case, provably minimizes communication costs (under mild assumptions). The framework is flexible and able to leverage a variety of NMF and NLS algorithms, including Multiplicative Update, Hierarchical Alternating Least Squares, and Block Principal Pivoting. Our implementation allows us to benchmark and compare different algorithms on massive dense and sparse data matrices of size that spans from few hundreds of millions to billions. We demonstrate the scalability of our algorithm and compare it with baseline implementations, showing significant performance improvements. The code and the datasets used for conducting the experiments are available online.« less

Augmentation in the treatment of restless legs syndrome with transdermal rotigotine.

PubMed

Beneš, Heike; García-Borreguero, Diego; Ferini-Strambi, Luigi; Schollmayer, Erwin; Fichtner, Andreas; Kohnen, Ralf

2012-06-01

To assess the risk of augmentation under treatment with the transdermally delivered dopamine agonist rotigotine for restless legs syndrome (RLS). Experts in RLS augmentation retrospectively reviewed data from two double-blind, placebo-controlled 6-month trials (745 rotigotine and 214 placebo subjects, NCT00136045 and NCT00135993) and from two open-label 1-year trials (620 rotigotine subjects, NCT00498108 and NCT00263068). All study visits were systematically evaluated applying the Max Planck Institute (MPI) criteria for the diagnosis of both augmentation and clinically relevant augmentation. MPI criteria for augmentation were met on at least one visit by 8.2% of all subjects in the double-blind trials with 12 subjects meeting the criteria for clinically relevant augmentation: 11 under rotigotine (1.5%) and one under placebo treatment. In the open-label trials, 9.7% of all subjects met the MPI criteria for augmentation and 2.9% met the criteria for clinically relevant augmentation. None of the patients treated with rotigotine for up to 1.5 years (double-blind plus open-label trial) discontinued prematurely owing to augmentation. Neither could dose-dependency or a time pattern for clinically relevant augmentation episodes be detected. Our analyses suggest that the risk for clinically relevant augmentation for the duration of up to 18 months of rotigotine treatment is low. Copyright © 2012 Elsevier B.V. All rights reserved.

Value of automatic patient motion detection and correction in myocardial perfusion imaging using a CZT-based SPECT camera.

PubMed

van Dijk, Joris D; van Dalen, Jorn A; Mouden, Mohamed; Ottervanger, Jan Paul; Knollema, Siert; Slump, Cornelis H; Jager, Pieter L

2018-04-01

Correction of motion has become feasible on cadmium-zinc-telluride (CZT)-based SPECT cameras during myocardial perfusion imaging (MPI). Our aim was to quantify the motion and to determine the value of automatic correction using commercially available software. We retrospectively included 83 consecutive patients who underwent stress-rest MPI CZT-SPECT and invasive fractional flow reserve (FFR) measurement. Eight-minute stress acquisitions were reformatted into 1.0- and 20-second bins to detect respiratory motion (RM) and patient motion (PM), respectively. RM and PM were quantified and scans were automatically corrected. Total perfusion deficit (TPD) and SPECT interpretation-normal, equivocal, or abnormal-were compared between the noncorrected and corrected scans. Scans with a changed SPECT interpretation were compared with FFR, the reference standard. Average RM was 2.5 ± 0.4 mm and maximal PM was 4.5 ± 1.3 mm. RM correction influenced the diagnostic outcomes in two patients based on TPD changes ≥7% and in nine patients based on changed visual interpretation. In only four of these patients, the changed SPECT interpretation corresponded with FFR measurements. Correction for PM did not influence the diagnostic outcomes. Respiratory motion and patient motion were small. Motion correction did not appear to improve the diagnostic outcome and, hence, the added value seems limited in MPI using CZT-based SPECT cameras.

FleCSI: Connection to Legion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bergen, Benjamin Karl

2016-08-03

These are slides which are part of the ASC L2 Milestone Review. The following topics are covered: Legion Backend, Distributed-Memory Partitioning, Sparse Data Representations, and MPI-Legion Interoperability.

On the effect of tilted roof reflectors in Martin-Puplett spectrometers

NASA Astrophysics Data System (ADS)

Schillaci, Alessandro; de Bernardis, Paolo

2012-01-01

In this paper we analyze theoretically and experimentally the effect of tilt of the roof mirrors in a double pendulum Martin-Puplett Polarizing Interferometer (MPI), focusing on the polarization of the interfering beams. In principle, the tilt affects the efficiency and polarimetric properties of the interferometer. The case of a moderate resolution spectrometer is analysed in detail. Using the Stokes formalism we recover the analytical expressions for the orientation angle and the ellipticity of the beam reflected from a metallic surface, and we compute these quantities for the roof-mirror of a MPI. We find that the polarization rotation and depolarization are small. Using the Jones formalism we propagate their effect on the measured interferogram and spectrum, and demonstrate that the performance degradation is small compared to other systematic effects.

WOMBAT: A Scalable and High-performance Astrophysical Magnetohydrodynamics Code

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mendygral, P. J.; Radcliffe, N.; Kandalla, K.

2017-02-01

We present a new code for astrophysical magnetohydrodynamics specifically designed and optimized for high performance and scaling on modern and future supercomputers. We describe a novel hybrid OpenMP/MPI programming model that emerged from a collaboration between Cray, Inc. and the University of Minnesota. This design utilizes MPI-RMA optimized for thread scaling, which allows the code to run extremely efficiently at very high thread counts ideal for the latest generation of multi-core and many-core architectures. Such performance characteristics are needed in the era of “exascale” computing. We describe and demonstrate our high-performance design in detail with the intent that it maymore » be used as a model for other, future astrophysical codes intended for applications demanding exceptional performance.« less

Noise spatial nonuniformity and the impact of statistical image reconstruction in CT myocardial perfusion imaging.

PubMed

Lauzier, Pascal Theriault; Tang, Jie; Speidel, Michael A; Chen, Guang-Hong

2012-07-01

To achieve high temporal resolution in CT myocardial perfusion imaging (MPI), images are often reconstructed using filtered backprojection (FBP) algorithms from data acquired within a short-scan angular range. However, the variation in the central angle from one time frame to the next in gated short scans has been shown to create detrimental partial scan artifacts when performing quantitative MPI measurements. This study has two main purposes. (1) To demonstrate the existence of a distinct detrimental effect in short-scan FBP, i.e., the introduction of a nonuniform spatial image noise distribution; this nonuniformity can lead to unexpectedly high image noise and streaking artifacts, which may affect CT MPI quantification. (2) To demonstrate that statistical image reconstruction (SIR) algorithms can be a potential solution to address the nonuniform spatial noise distribution problem and can also lead to radiation dose reduction in the context of CT MPI. Projection datasets from a numerically simulated perfusion phantom and an in vivo animal myocardial perfusion CT scan were used in this study. In the numerical phantom, multiple realizations of Poisson noise were added to projection data at each time frame to investigate the spatial distribution of noise. Images from all datasets were reconstructed using both FBP and SIR reconstruction algorithms. To quantify the spatial distribution of noise, the mean and standard deviation were measured in several regions of interest (ROIs) and analyzed across time frames. In the in vivo study, two low-dose scans at tube currents of 25 and 50 mA were reconstructed using FBP and SIR. Quantitative perfusion metrics, namely, the normalized upslope (NUS), myocardial blood volume (MBV), and first moment transit time (FMT), were measured for two ROIs and compared to reference values obtained from a high-dose scan performed at 500 mA. Images reconstructed using FBP showed a highly nonuniform spatial distribution of noise. This spatial nonuniformity led to large fluctuations in the temporal direction. In the numerical phantom study, the level of noise was shown to vary by as much as 87% within a given image, and as much as 110% between different time frames for a ROI far from isocenter. The spatially nonuniform noise pattern was shown to correlate with the source trajectory and the object structure. In contrast, images reconstructed using SIR showed a highly uniform spatial distribution of noise, leading to smaller unexpected noise fluctuations in the temporal direction when a short scan angular range was used. In the numerical phantom study, the noise varied by less than 37% within a given image, and by less than 20% between different time frames. Also, the noise standard deviation in SIR images was on average half of that of FBP images. In the in vivo studies, the deviation observed between quantitative perfusion metrics measured from low-dose scans and high-dose scans was mitigated when SIR was used instead of FBP to reconstruct images. (1) Images reconstructed using FBP suffered from nonuniform spatial noise levels. This nonuniformity is another manifestation of the detrimental effects caused by short-scan reconstruction in CT MPI. (2) Images reconstructed using SIR had a much lower and more uniform noise level and thus can be used as a potential solution to address the FBP nonuniformity. (3) Given the improvement in the accuracy of the perfusion metrics when using SIR, it may be desirable to use a statistical reconstruction framework to perform low-dose dynamic CT MPI.

Noise spatial nonuniformity and the impact of statistical image reconstruction in CT myocardial perfusion imaging

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lauzier, Pascal Theriault; Tang Jie; Speidel, Michael A.

Purpose: To achieve high temporal resolution in CT myocardial perfusion imaging (MPI), images are often reconstructed using filtered backprojection (FBP) algorithms from data acquired within a short-scan angular range. However, the variation in the central angle from one time frame to the next in gated short scans has been shown to create detrimental partial scan artifacts when performing quantitative MPI measurements. This study has two main purposes. (1) To demonstrate the existence of a distinct detrimental effect in short-scan FBP, i.e., the introduction of a nonuniform spatial image noise distribution; this nonuniformity can lead to unexpectedly high image noise andmore » streaking artifacts, which may affect CT MPI quantification. (2) To demonstrate that statistical image reconstruction (SIR) algorithms can be a potential solution to address the nonuniform spatial noise distribution problem and can also lead to radiation dose reduction in the context of CT MPI. Methods: Projection datasets from a numerically simulated perfusion phantom and an in vivo animal myocardial perfusion CT scan were used in this study. In the numerical phantom, multiple realizations of Poisson noise were added to projection data at each time frame to investigate the spatial distribution of noise. Images from all datasets were reconstructed using both FBP and SIR reconstruction algorithms. To quantify the spatial distribution of noise, the mean and standard deviation were measured in several regions of interest (ROIs) and analyzed across time frames. In the in vivo study, two low-dose scans at tube currents of 25 and 50 mA were reconstructed using FBP and SIR. Quantitative perfusion metrics, namely, the normalized upslope (NUS), myocardial blood volume (MBV), and first moment transit time (FMT), were measured for two ROIs and compared to reference values obtained from a high-dose scan performed at 500 mA. Results: Images reconstructed using FBP showed a highly nonuniform spatial distribution of noise. This spatial nonuniformity led to large fluctuations in the temporal direction. In the numerical phantom study, the level of noise was shown to vary by as much as 87% within a given image, and as much as 110% between different time frames for a ROI far from isocenter. The spatially nonuniform noise pattern was shown to correlate with the source trajectory and the object structure. In contrast, images reconstructed using SIR showed a highly uniform spatial distribution of noise, leading to smaller unexpected noise fluctuations in the temporal direction when a short scan angular range was used. In the numerical phantom study, the noise varied by less than 37% within a given image, and by less than 20% between different time frames. Also, the noise standard deviation in SIR images was on average half of that of FBP images. In the in vivo studies, the deviation observed between quantitative perfusion metrics measured from low-dose scans and high-dose scans was mitigated when SIR was used instead of FBP to reconstruct images. Conclusions: (1) Images reconstructed using FBP suffered from nonuniform spatial noise levels. This nonuniformity is another manifestation of the detrimental effects caused by short-scan reconstruction in CT MPI. (2) Images reconstructed using SIR had a much lower and more uniform noise level and thus can be used as a potential solution to address the FBP nonuniformity. (3) Given the improvement in the accuracy of the perfusion metrics when using SIR, it may be desirable to use a statistical reconstruction framework to perform low-dose dynamic CT MPI.« less

Noise spatial nonuniformity and the impact of statistical image reconstruction in CT myocardial perfusion imaging

PubMed Central

Lauzier, Pascal Thériault; Tang, Jie; Speidel, Michael A.; Chen, Guang-Hong

2012-01-01

Purpose: To achieve high temporal resolution in CT myocardial perfusion imaging (MPI), images are often reconstructed using filtered backprojection (FBP) algorithms from data acquired within a short-scan angular range. However, the variation in the central angle from one time frame to the next in gated short scans has been shown to create detrimental partial scan artifacts when performing quantitative MPI measurements. This study has two main purposes. (1) To demonstrate the existence of a distinct detrimental effect in short-scan FBP, i.e., the introduction of a nonuniform spatial image noise distribution; this nonuniformity can lead to unexpectedly high image noise and streaking artifacts, which may affect CT MPI quantification. (2) To demonstrate that statistical image reconstruction (SIR) algorithms can be a potential solution to address the nonuniform spatial noise distribution problem and can also lead to radiation dose reduction in the context of CT MPI. Methods: Projection datasets from a numerically simulated perfusion phantom and an in vivo animal myocardial perfusion CT scan were used in this study. In the numerical phantom, multiple realizations of Poisson noise were added to projection data at each time frame to investigate the spatial distribution of noise. Images from all datasets were reconstructed using both FBP and SIR reconstruction algorithms. To quantify the spatial distribution of noise, the mean and standard deviation were measured in several regions of interest (ROIs) and analyzed across time frames. In the in vivo study, two low-dose scans at tube currents of 25 and 50 mA were reconstructed using FBP and SIR. Quantitative perfusion metrics, namely, the normalized upslope (NUS), myocardial blood volume (MBV), and first moment transit time (FMT), were measured for two ROIs and compared to reference values obtained from a high-dose scan performed at 500 mA. Results: Images reconstructed using FBP showed a highly nonuniform spatial distribution of noise. This spatial nonuniformity led to large fluctuations in the temporal direction. In the numerical phantom study, the level of noise was shown to vary by as much as 87% within a given image, and as much as 110% between different time frames for a ROI far from isocenter. The spatially nonuniform noise pattern was shown to correlate with the source trajectory and the object structure. In contrast, images reconstructed using SIR showed a highly uniform spatial distribution of noise, leading to smaller unexpected noise fluctuations in the temporal direction when a short scan angular range was used. In the numerical phantom study, the noise varied by less than 37% within a given image, and by less than 20% between different time frames. Also, the noise standard deviation in SIR images was on average half of that of FBP images. In the in vivo studies, the deviation observed between quantitative perfusion metrics measured from low-dose scans and high-dose scans was mitigated when SIR was used instead of FBP to reconstruct images. Conclusions: (1) Images reconstructed using FBP suffered from nonuniform spatial noise levels. This nonuniformity is another manifestation of the detrimental effects caused by short-scan reconstruction in CT MPI. (2) Images reconstructed using SIR had a much lower and more uniform noise level and thus can be used as a potential solution to address the FBP nonuniformity. (3) Given the improvement in the accuracy of the perfusion metrics when using SIR, it may be desirable to use a statistical reconstruction framework to perform low-dose dynamic CT MPI. PMID:22830741

Detection and severity classification of extracardiac interference in {sup 82}Rb PET myocardial perfusion imaging

DOE Office of Scientific and Technical Information (OSTI.GOV)

Orton, Elizabeth J., E-mail: eorton@physics.carleton.ca; Kemp, Robert A. de; Glenn Wells, R.

2014-10-15

Purpose: Myocardial perfusion imaging (MPI) is used for diagnosis and prognosis of coronary artery disease. When MPI studies are performed with positron emission tomography (PET) and the radioactive tracer rubidium-82 chloride ({sup 82}Rb), a small but non-negligible fraction of studies (∼10%) suffer from extracardiac interference: high levels of tracer uptake in structures adjacent to the heart which mask the true cardiac tracer uptake. At present, there are no clinically available options for automated detection or correction of this problem. This work presents an algorithm that detects and classifies the severity of extracardiac interference in {sup 82}Rb PET MPI images andmore » reports the accuracy and failure rate of the method. Methods: A set of 200 {sup 82}Rb PET MPI images were reviewed by a trained nuclear cardiologist and interference severity reported on a four-class scale, from absent to severe. An automated algorithm was developed that compares uptake at the external border of the myocardium to three thresholds, separating the four interference severity classes. A minimum area of interference was required, and the search region was limited to that facing the stomach wall and spleen. Maximizing concordance (Cohen’s Kappa) and minimizing failure rate for the set of 200 clinician-read images were used to find the optimal population-based constants defining search limit and minimum area parameters and the thresholds for the algorithm. Tenfold stratified cross-validation was used to find optimal thresholds and report accuracy measures (sensitivity, specificity, and Kappa). Results: The algorithm was capable of detecting interference with a mean [95% confidence interval] sensitivity/specificity/Kappa of 0.97 [0.94, 1.00]/0.82 [0.66, 0.98]/0.79 [0.65, 0.92], and a failure rate of 1.0% ± 0.2%. The four-class overall Kappa was 0.72 [0.64, 0.81]. Separation of mild versus moderate-or-greater interference was performed with good accuracy (sensitivity/specificity/Kappa = 0.92 [0.86, 0.99]/0.86 [0.71, 1.00]/0.78 [0.64, 0.92]), while separation of moderate versus severe interference severity classes showed reduced sensitivity/Kappa but little change in specificity (sensitivity/specificity/Kappa = 0.83 [0.77, 0.88]/0.82 [0.77, 0.88]/0.65 [0.60, 0.70]). Specificity was greater than sensitivity for all interference classes. Algorithm execution time was <1 min. Conclusions: The algorithm produced here has a low failure rate and high accuracy for detection of extracardiac interference in {sup 82}Rb PET MPI scans. It provides a fast, reliable, automated method for assessing severity of extracardiac interference.« less

How to stir a revolution as a reluctant rebel: Rudolf Trümpy in the Alps

NASA Astrophysics Data System (ADS)

Şengör, A. M. Celâl; Bernoulli, Daniel

2011-07-01

Rudolf Trümpy (1921-2009) was one of the great Alpine geologists of the twentieth century and an influential figure in the international geological community. He played a dominant role in the change of opinion concerning the Alpine evolution by showing that normal faulting dominated the early development of the Alpine realm from the Triassic to the early Cretaceous. This provided a convenient model for later plate-tectonic interpretations of collisional mountain belts. His further recognition of strike-slip faulting during all stages of the Alpine evolution presaged the realisation that the Alps were not built by a simple open-and-shut mechanism. Trümpy was educated during an intellectual lull, a time when simplistic models of the earth behaviour inherited from the middle of the nineteenth century became prevalent under the influence of a close-minded, positivist approach to geological problems. This period, which we term the Dark Intermezzo, lasted from about 1925 to 1965. The grand syntheses of Suess and Argand which preceded this period were viewed from this narrow angle and consequently misunderstood. It was thought that earth history was punctuated by global orogenic events of short duration taking place within and among continents and oceans whose relative positions had remained fixed since the origin of the planet. These views, summarised under the term `fixism', were developed when the ocean floors were almost totally unknown. When data began coming in from the post World War II oceanographic surveys, the world geological community was slow to receive and digest them. Trümpy followed these developments closely, realising that his work was important in placing the geology of the mountain belts within the emerging, new theoretical framework. He adopted the position of a critic and emphasised where detailed knowledge of the Alps, unquestionably the best known mountain belt in the world, supported and where it contradicted the new ideas. His voice was listened to carefully and subsequent developments have shown his critique to have been prescient. It is regrettable that he did not publish some of the theoretical criticisms he communicated to his colleagues during scientific meetings and informal conversations. His hesitance in becoming involved in theoretical arguments in geology may have stemmed partly from his scientific upbringing during the Dark Intermezzo and partly because he genuinely believed that he was better off sticking to what he thought he knew for sure. He nevertheless stressed that it is important for geologists `to dream'. It is often said about teachers that one should do what they say, not what they do. In Trümpy's case, it was the opposite. Both scientifically and as a human being, he was a most admirable man.

Relation between aortic knob width and subclinical left ventricular dysfunction in hypertensive patients.

PubMed

Gürbak, İsmail; Yıldız, İbrahim; Panç, Cafer

2018-01-29

The assessment of left ventricular (LV) structure and function is important in the evaluation of hypertensive heart disease, as it provides information on the cardiovascular morbidity and mortality. Aortic knob width (AKW) is a measurement of radiographic structure formed by the foreshortened aortic arch and a portion of the descending aorta. The main aim of this study was to investigate the relation between AKW on the routine chest radiography and subclinical LV dysfunction in hypertensive patients. A total of 144 patients with hypertension admitted to the cardiology outpatients clinic were enrolled consecutively. The patients were divided into two groups according to tissue Doppler-derived myocardial performance index (MPI): subclinical LV dysfunction group (abnormal MPI ≥ 0.5, n = 85) and absence of subclinical LV dysfunction group (normal MPI< 0.5, n = 59). Patients with subclinical LV dysfunction were older (60 ± 8 vs. 54 ± 8, p = 0.001). Left ventricular mass index (LVMI) (96 ± 27 vs. 74 ± 24, p < 0.001) and prevalence of LV hypertrophy (28 vs. 8%, p = 0.011) were significantly different between two groups. Patients with subclinical LV dysfunction had higher AKW (42 ± 6 vs. 34 ± 5, p < 0.001) compared with patients without subclinical LV dysfunction. There was a significant correlation between MPI and AKW (r = 0.7, p < 0.001). Multiple logistic regression analysis showed that AKW (β = 0.617, p = 0.001) and posterior wall thickness (PWth) (β = 1.189, p = 0.021) were independently associated with subclinical LV dysfunction. Analysis using the Receiver Operating Characteristic (ROC) curve has demonstrated that aortic knob of 37 mm constitutes the cutoff value for the presence of subclinical LV dysfunction with 85.9% sensitivity and 86.4% specificity (The Area under the Curve ± Standard Error (AUC±SE) = 0.916 ± 0.024, p < 0.001). AKW may provide important predictive information on subclinical LV dysfunction in patients with hypertension.

NAS Parallel Benchmark. Results 11-96: Performance Comparison of HPF and MPI Based NAS Parallel Benchmarks. 1.0

NASA Technical Reports Server (NTRS)

Saini, Subash; Bailey, David; Chancellor, Marisa K. (Technical Monitor)

1997-01-01

High Performance Fortran (HPF), the high-level language for parallel Fortran programming, is based on Fortran 90. HALF was defined by an informal standards committee known as the High Performance Fortran Forum (HPFF) in 1993, and modeled on TMC's CM Fortran language. Several HPF features have since been incorporated into the draft ANSI/ISO Fortran 95, the next formal revision of the Fortran standard. HPF allows users to write a single parallel program that can execute on a serial machine, a shared-memory parallel machine, or a distributed-memory parallel machine. HPF eliminates the complex, error-prone task of explicitly specifying how, where, and when to pass messages between processors on distributed-memory machines, or when to synchronize processors on shared-memory machines. HPF is designed in a way that allows the programmer to code an application at a high level, and then selectively optimize portions of the code by dropping into message-passing or calling tuned library routines as 'extrinsics'. Compilers supporting High Performance Fortran features first appeared in late 1994 and early 1995 from Applied Parallel Research (APR) Digital Equipment Corporation, and The Portland Group (PGI). IBM introduced an HPF compiler for the IBM RS/6000 SP/2 in April of 1996. Over the past two years, these implementations have shown steady improvement in terms of both features and performance. The performance of various hardware/ programming model (HPF and MPI (message passing interface)) combinations will be compared, based on latest NAS (NASA Advanced Supercomputing) Parallel Benchmark (NPB) results, thus providing a cross-machine and cross-model comparison. Specifically, HPF based NPB results will be compared with MPI based NPB results to provide perspective on performance currently obtainable using HPF versus MPI or versus hand-tuned implementations such as those supplied by the hardware vendors. In addition we would also present NPB (Version 1.0) performance results for the following systems: DEC Alpha Server 8400 5/440, Fujitsu VPP Series (VX, VPP300, and VPP700), HP/Convex Exemplar SPP2000, IBM RS/6000 SP P2SC node (120 MHz) NEC SX-4/32, SGI/CRAY T3E, SGI Origin2000.

Monitoring intrahepatic cholestasis of pregnancy using the fetal myocardial performance index: a cohort study.

PubMed

Henry, A; Welsh, A W

2015-11-01

To investigate use of the fetal myocardial performance index (MPI) in assessing intrahepatic cholestasis of pregnancy (ICP). This was a cohort study including cross-sectional and longitudinal data from 31 women with ICP recruited from June 2012 to March 2014. Fetal left, right and delta MPI (LMPI, RMPI and DMPI), and routine measures of fetal growth and wellbeing, were obtained at each ultrasound examination. Results were evaluated with respect to gestational age (GA)-adjusted reference intervals, level of maternal serum bile acid (SBA) and fetal outcome. Lower SBA (≥ 7.5 and < 40 μmol/L) and high SBA (≥ 40 μmol/L) subgroups of cases were defined for the analysis. A total of 51 ultrasound examinations were performed in 33 fetuses. The mean LMPI, and means of its isovolumetric relaxation time (IRT) and isovolumetric contraction time (ICT) components were significantly higher in all subgroups of cases of ICP relative to the normal reference mean. Considering only the first examination in each case of ICP, IRT was significantly more prolonged in the high SBA group (n = 10) in comparison to the lower SBA group (n = 23) (52.7 ± 8.0 ms vs 47.3 ± 4.8 ms, P = 0.02), and both IRT (r = 0.538, P = 0.001) and LMPI (r = 0.367, P = 0.036) were significantly correlated with SBA concentration. The proportion of high SBA cases with LMPI, RMPI or DMPI > 2 SD above the GA-adjusted reference mean was not significantly greater than for the lower SBA group. On analysis of all data from those cases with more than one examination, no significant correlation was found between SBA concentration and any of the MPI variables. LMPI values increase above the population GA-adjusted mean in cases of ICP, particularly amongst women with higher SBA. A significant correlation between IRT and LMPI at initial examination and increasing SBA concentration was found. A future multicenter prospective study may clarify the prognostic utility of MPI in ICP. Copyright © 2014 ISUOG. Published by John Wiley & Sons Ltd.

Creating a Parallel Version of VisIt for Microsoft Windows

DOE Office of Scientific and Technical Information (OSTI.GOV)

Whitlock, B J; Biagas, K S; Rawson, P L

2011-12-07

VisIt is a popular, free interactive parallel visualization and analysis tool for scientific data. Users can quickly generate visualizations from their data, animate them through time, manipulate them, and save the resulting images or movies for presentations. VisIt was designed from the ground up to work on many scales of computers from modest desktops up to massively parallel clusters. VisIt is comprised of a set of cooperating programs. All programs can be run locally or in client/server mode in which some run locally and some run remotely on compute clusters. The VisIt program most able to harness today's computing powermore » is the VisIt compute engine. The compute engine is responsible for reading simulation data from disk, processing it, and sending results or images back to the VisIt viewer program. In a parallel environment, the compute engine runs several processes, coordinating using the Message Passing Interface (MPI) library. Each MPI process reads some subset of the scientific data and filters the data in various ways to create useful visualizations. By using MPI, VisIt has been able to scale well into the thousands of processors on large computers such as dawn and graph at LLNL. The advent of multicore CPU's has made parallelism the 'new' way to achieve increasing performance. With today's computers having at least 2 cores and in many cases up to 8 and beyond, it is more important than ever to deploy parallel software that can use that computing power not only on clusters but also on the desktop. We have created a parallel version of VisIt for Windows that uses Microsoft's MPI implementation (MSMPI) to process data in parallel on the Windows desktop as well as on a Windows HPC cluster running Microsoft Windows Server 2008. Initial desktop parallel support for Windows was deployed in VisIt 2.4.0. Windows HPC cluster support has been completed and will appear in the VisIt 2.5.0 release. We plan to continue supporting parallel VisIt on Windows so our users will be able to take full advantage of their multicore resources.« less

Comparison of neuronal spike exchange methods on a Blue Gene/P supercomputer.

PubMed

Hines, Michael; Kumar, Sameer; Schürmann, Felix

2011-01-01

For neural network simulations on parallel machines, interprocessor spike communication can be a significant portion of the total simulation time. The performance of several spike exchange methods using a Blue Gene/P (BG/P) supercomputer has been tested with 8-128 K cores using randomly connected networks of up to 32 M cells with 1 k connections per cell and 4 M cells with 10 k connections per cell, i.e., on the order of 4·10(10) connections (K is 1024, M is 1024(2), and k is 1000). The spike exchange methods used are the standard Message Passing Interface (MPI) collective, MPI_Allgather, and several variants of the non-blocking Multisend method either implemented via non-blocking MPI_Isend, or exploiting the possibility of very low overhead direct memory access (DMA) communication available on the BG/P. In all cases, the worst performing method was that using MPI_Isend due to the high overhead of initiating a spike communication. The two best performing methods-the persistent Multisend method using the Record-Replay feature of the Deep Computing Messaging Framework DCMF_Multicast; and a two-phase multisend in which a DCMF_Multicast is used to first send to a subset of phase one destination cores, which then pass it on to their subset of phase two destination cores-had similar performance with very low overhead for the initiation of spike communication. Departure from ideal scaling for the Multisend methods is almost completely due to load imbalance caused by the large variation in number of cells that fire on each processor in the interval between synchronization. Spike exchange time itself is negligible since transmission overlaps with computation and is handled by a DMA controller. We conclude that ideal performance scaling will be ultimately limited by imbalance between incoming processor spikes between synchronization intervals. Thus, counterintuitively, maximization of load balance requires that the distribution of cells on processors should not reflect neural net architecture but be randomly distributed so that sets of cells which are burst firing together should be on different processors with their targets on as large a set of processors as possible.

Low Child Survival Index in a Multi-Dimensionally Poor Amerindian Population in Venezuela

PubMed Central

Villalba, Julian A.; Liu, Yushi; Alvarez, Mauyuri K.; Calderon, Luisana; Canache, Merari; Cardenas, Gaudymar; Del Nogal, Berenice; Takiff, Howard E.; De Waard, Jacobus H.

2013-01-01

Background Warao Amerindians, who inhabit the Orinoco Delta, are the second largest indigenous group in Venezuela.  High Warao general mortality rates were mentioned in a limited study 21 years ago. However, there have been no comprehensive studies addressing child survival across the entire population. Objectives To determine the Child Survival-Index (CSI) (ratio: still-living children/total-live births) in the Warao population, the principal causes of childhood death and the socio-demographic factors associated with childhood deaths. Methods We conducted a cross-sectional epidemiological survey of 688 women from 97 communities in 7 different subregions of the Orinoco Delta. Data collected included socio-demographic characteristics and the reproductive history of each woman surveyed. The multidimensional poverty index (MPI) was used to classify the households as deprived across the three dimensions of the Human Development Index. Multivariable linear regression and Generalized Linear Model Procedures were used to identify socioeconomic and environmental characteristics statistically associated with the CSI. Findings The average CSI was 73.8% ±26. The two most common causes of death were gastroenteritis/diarrhea (63%) and acute respiratory tract Infection/pneumonia (18%).  Deaths in children under five years accounted for 97.3% of childhood deaths, with 54% occurring in the neonatal period or first year of life.  Most of the women (95.5%) were classified as multidimensionally poor.  The general MPI in the sample was 0.56.   CSI was negatively correlated with MPI, maternal age, residence in a traditional dwelling and profession of the head of household other than nurse or teacher. Conclusions The Warao have a low CSI which is correlated with MPI and maternal age.  Infectious diseases are responsible for 85% of childhood deaths.  The low socioeconomic development, lack of infrastructure and geographic and cultural isolation suggest that an integrated approach is urgently needed to improve the child survival and overall health of the Warao Amerindians.  PMID:24392022

[Study on the aggregation behavior of cationic porphyrins and their interaction with ctDNA].

PubMed

Ma, Hong-Min; Chen, Xin; Sun, Shu-Ting; Zhang, Li-Na; Wu, Dan; Zhu, Pei-Hua; Li, Yan; Du, Bin; Wei, Qin

2009-02-01

Interest in the interaction between cationic porphyrins, particularly derivatives of meso-tetra(N-methylpyridinium-4-yl) porphyrin(TMPyP), and DNA abounds because they are versatile DNA-binding agents that could find application in photodynamic therapy, cancer detection, artificial nucleases, virus inhibition and so on. The interaction of two water-soluble cationic porphyrins, meso-tetrakis(4-N, N, N-trimethylanilinium) porphyrin (TMAP) and 5-phenyl-10,15,20-tris[4-(N-methyl) pyridinium]porphyrin (TriMPyP), with calf thymus DNA (ctDNA) was studied by UV-Vis absorption spectroscopy, fluorescence spectroscopy and resonance light scattering technique. TriMPyP forms aggregate in water due to the molecular asymmetry while TMAP exists as monomers. At lower concentrations of ctDNA (R > 1, R = c(TMAP)/c(DNA) base pair), the interaction of TMAP with DNA leads to significant hypochromicity and bathochromic shift of absorption spectra. And the fluorescence of TMAP was quenched while it showed enhanced resonance light scattering signals. But the extent of enhancement of resonance light scattering signals is very small, so the aggregate of TMAP is not very high. These observations indicate the self-stacking of TMAP along the DNA surface. At higher concentrations of ctDNA (R < 1), TMAP association with DNA is via outside binding which is accompanied with hyperchromic effect and fluorescence enhancement while the resonance light scattering signals is reduced. DNA addition decreases the fluorescence intensity of TriMPyP and it shifts the peak to the higher wavelengths (red shift). The interaction with DNA promotes the aggregation of TriMPyP and no simple outside binding is observed even at higher concentrations of ctDNA. The steric effect of molecular distortion constrains the intercalation or further binding to DNA. The effect of ionic strength on the interaction was investigated at two DNA concentrations, 1.2 and 24.0 micromol x L(-1), for TMAP. The Interactions of both porphyrins with DNA show high sensitivity to ionic strength. By addition of NaCl, electrostatic attraction is decreased, resulting in the change of binding mode.

Comparison of surface freshwater fluxes from different climate forecasts produced through different ensemble generation schemes.

NASA Astrophysics Data System (ADS)

Romanova, Vanya; Hense, Andreas; Wahl, Sabrina; Brune, Sebastian; Baehr, Johanna

2016-04-01

The decadal variability and its predictability of the surface net freshwater fluxes is compared in a set of retrospective predictions, all using the same model setup, and only differing in the implemented ocean initialisation method and ensemble generation method. The basic aim is to deduce the differences between the initialization/ensemble generation methods in view of the uncertainty of the verifying observational data sets. The analysis will give an approximation of the uncertainties of the net freshwater fluxes, which up to now appear to be one of the most uncertain products in observational data and model outputs. All ensemble generation methods are implemented into the MPI-ESM earth system model in the framework of the ongoing MiKlip project (www.fona-miklip.de). Hindcast experiments are initialised annually between 2000-2004, and from each start year 10 ensemble members are initialized for 5 years each. Four different ensemble generation methods are compared: (i) a method based on the Anomaly Transform method (Romanova and Hense, 2015) in which the initial oceanic perturbations represent orthogonal and balanced anomaly structures in space and time and between the variables taken from a control run, (ii) one-day-lagged ocean states from the MPI-ESM-LR baseline system (iii) one-day-lagged of ocean and atmospheric states with preceding full-field nudging to re-analysis in both the atmospheric and the oceanic component of the system - the baseline one MPI-ESM-LR system, (iv) an Ensemble Kalman Filter (EnKF) implemented into oceanic part of MPI-ESM (Brune et al. 2015), assimilating monthly subsurface oceanic temperature and salinity (EN3) using the Parallel Data Assimilation Framework (PDAF). The hindcasts are evaluated probabilistically using fresh water flux data sets from four different reanalysis data sets: MERRA, NCEP-R1, GFDL ocean reanalysis and GECCO2. The assessments show no clear differences in the evaluations scores on regional scales. However, on the global scale the physically motivated methods (i) and (iv) provide probabilistic hindcasts with a consistently higher reliability than the lagged initialization methods (ii)/(iii) despite the large uncertainties in the verifying observations and in the simulations.

Sources of sedimentary PAHs in tropical Asian waters: differentiation between pyrogenic and petrogenic sources by alkyl homolog abundance.

PubMed

Saha, Mahua; Togo, Ayako; Mizukawa, Kaoruko; Murakami, Michio; Takada, Hideshige; Zakaria, Mohamad P; Chiem, Nguyen H; Tuyen, Bui Cach; Prudente, Maricar; Boonyatumanond, Ruchaya; Sarkar, Santosh Kumar; Bhattacharya, Badal; Mishra, Pravakar; Tana, Touch Seang

2009-02-01

We collected surface sediment samples from 174 locations in India, Indonesia, Malaysia, Thailand, Vietnam, Cambodia, Laos, and the Philippines and analyzed them for polycyclic aromatic hydrocarbons (PAHs) and hopanes. PAHs were widely distributed in the sediments, with comparatively higher concentrations in urban areas (Sigma PAHs: approximately 1000 to approximately 100,000 ng/g-dry) than in rural areas ( approximately 10 to approximately 100g-dry), indicating large sources of PAHs in urban areas. To distinguish petrogenic and pyrogenic sources of PAHs, we calculated the ratios of alkyl PAHs to parent PAHs: methylphenanthrenes to phenanthrene (MP/P), methylpyrenes+methylfluoranthenes to pyrene+fluoranthene (MPy/Py), and methylchrysenes+methylbenz[a]anthracenes to chrysene+benz[a]anthracene (MC/C). Analysis of source materials (crude oil, automobile exhaust, and coal and wood combustion products) gave thresholds of MP/P=0.4, MPy/Py=0.5, and MC/C=1.0 for exclusive combustion origin. All the combustion product samples had the ratios of alkyl PAHs to parent PAHs below these threshold values. Contributions of petrogenic and pyrogenic sources to the sedimentary PAHs were uneven among the homologs: the phenanthrene series had a greater petrogenic contribution, whereas the chrysene series had a greater pyrogenic contribution. All the Indian sediments showed a strong pyrogenic signature with MP/P approximately 0.5, MPy/Py approximately 0.1, and MC/C approximately 0.2, together with depletion of hopanes indicating intensive inputs of combustion products of coal and/or wood, probably due to the heavy dependence on these fuels as sources of energy. In contrast, sedimentary PAHs from all other tropical Asian cities were abundant in alkylated PAHs with MP/P approximately 1-4, MPy/Py approximately 0.3-1, and MC/C approximately 0.2-1.0, suggesting a ubiquitous input of petrogenic PAHs. Petrogenic contributions to PAH homologs varied among the countries: largest in Malaysia whereas inferior in Laos. The higher abundance of alkylated PAHs together with constant hopane profiles suggests widespread inputs of automobile-derived petrogenic PAHs to Asian waters.

Radionuclide Ventriculography or Radionuclide Angiography (MUGA Scan)

MedlinePlus

... Attack Heart Failure Myocardial Perfusion Imaging (MPI) Single Photon Emission Computed Tomography (SPECT) Positron Emission Tomography (PET) ... stroke. Popular Articles 1 Understanding Blood Pressure Readings 2 Sodium and Salt 3 Heart Attack Symptoms in ...

Enterogastroesophageal reflux detected on 99m-technetium sestamibi cardiac imaging as a cause of chest pain

PubMed Central

Erdoğan, Zeynep; Silov, Güler; Özdal, Ayşegül; Turhal, Özgül

2013-01-01

Myocardial perfusion imaging (MPI) with technetium-99m sestamibi (Tc-99m MIBI) is considered a diagnostic technique that is widely used for the investigation of suspected coronary artery disease. Incidental inspection of an extracardiac activity is indirect, but important marker, which can identify a potentially treatable non-coronary cause for chest pain that may mimic cardiac symptoms. Here, we present an illustrative case in which significant enterogastroesophageal reflux of Tc-99m MIBI occurred during the cardiac imaging following prompt hepatobiliary clearance. Because, there was normal myocardial perfusion on MPI, presence of gastroesophageal reflux (GER) on GER scintigraphy and detection of mild inflammation with pathologically confirmed hyperplastic polyp by endoscopy, in view of the above findings we concluded that the probable cause of chest pain was reflux. PMID:24019679

birgHPC: creating instant computing clusters for bioinformatics and molecular dynamics.

PubMed

Chew, Teong Han; Joyce-Tan, Kwee Hong; Akma, Farizuwana; Shamsir, Mohd Shahir

2011-05-01

birgHPC, a bootable Linux Live CD has been developed to create high-performance clusters for bioinformatics and molecular dynamics studies using any Local Area Network (LAN)-networked computers. birgHPC features automated hardware and slots detection as well as provides a simple job submission interface. The latest versions of GROMACS, NAMD, mpiBLAST and ClustalW-MPI can be run in parallel by simply booting the birgHPC CD or flash drive from the head node, which immediately positions the rest of the PCs on the network as computing nodes. Thus, a temporary, affordable, scalable and high-performance computing environment can be built by non-computing-based researchers using low-cost commodity hardware. The birgHPC Live CD and relevant user guide are available for free at http://birg1.fbb.utm.my/birghpc.

Parallel processing optimization strategy based on MapReduce model in cloud storage environment

NASA Astrophysics Data System (ADS)

Cui, Jianming; Liu, Jiayi; Li, Qiuyan

2017-05-01

Currently, a large number of documents in the cloud storage process employed the way of packaging after receiving all the packets. From the local transmitter this stored procedure to the server, packing and unpacking will consume a lot of time, and the transmission efficiency is low as well. A new parallel processing algorithm is proposed to optimize the transmission mode. According to the operation machine graphs model work, using MPI technology parallel execution Mapper and Reducer mechanism. It is good to use MPI technology to implement Mapper and Reducer parallel mechanism. After the simulation experiment of Hadoop cloud computing platform, this algorithm can not only accelerate the file transfer rate, but also shorten the waiting time of the Reducer mechanism. It will break through traditional sequential transmission constraints and reduce the storage coupling to improve the transmission efficiency.

pFUnit 3.0 Tutorial Advanced

NASA Technical Reports Server (NTRS)

Clune, Tom

2014-01-01

This tutorial will introduce Fortran developers to unit-testing and test-driven development (TDD) using pFUnit. As with other unit-testing frameworks, pFUnit, simplifies the process of writing, collecting, and executing tests while providing clear diagnostic messages for failing tests. pFUnit specifically targets the development of scientific-technical software written in Fortran and includes customized features such as: assertions for multi-dimensional arrays, distributed (MPI) and thread-based (OpenMP) parallellism, and flexible parameterized tests.These sessions will include numerous examples and hands-on exercises that gradually build in complexity. Attendees are expected to have working knowledge of F90, but familiarity with object-oriented syntax in F2003 and MPI will be of benefit for the more advanced examples. By the end of the tutorial the audience should feel comfortable in applying pFUnit within their own development environment.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gorentla Venkata, Manjunath; Graham, Richard L; Ladd, Joshua S

This paper describes the design and implementation of InfiniBand (IB) CORE-Direct based blocking and nonblocking broadcast operations within the Cheetah collective operation framework. It describes a novel approach that fully ofFLoads collective operations and employs only user-supplied buffers. For a 64 rank communicator, the latency of CORE-Direct based hierarchical algorithm is better than production-grade Message Passing Interface (MPI) implementations, 150% better than the default Open MPI algorithm and 115% better than the shared memory optimized MVAPICH implementation for a one kilobyte (KB) message, and for eight mega-bytes (MB) it is 48% and 64% better, respectively. Flat-topology broadcast achieves 99.9% overlapmore » in a polling based communication-computation test, and 95.1% overlap for a wait based test, compared with 92.4% and 17.0%, respectively, for a similar Central Processing Unit (CPU) based implementation.« less

Initialization shock in decadal hindcasts due to errors in wind stress over the tropical Pacific

NASA Astrophysics Data System (ADS)

Pohlmann, Holger; Kröger, Jürgen; Greatbatch, Richard J.; Müller, Wolfgang A.

2017-10-01

Low prediction skill in the tropical Pacific is a common problem in decadal prediction systems, especially for lead years 2-5 which, in many systems, is lower than in uninitialized experiments. On the other hand, the tropical Pacific is of almost worldwide climate relevance through its teleconnections with other tropical and extratropical regions and also of importance for global mean temperature. Understanding the causes of the reduced prediction skill is thus of major interest for decadal climate predictions. We look into the problem of reduced prediction skill by analyzing the Max Planck Institute Earth System Model (MPI-ESM) decadal hindcasts for the fifth phase of the Climate Model Intercomparison Project and performing a sensitivity experiment in which hindcasts are initialized from a model run forced only by surface wind stress. In both systems, sea surface temperature variability in the tropical Pacific is successfully initialized, but most skill is lost at lead years 2-5. Utilizing the sensitivity experiment enables us to pin down the reason for the reduced prediction skill in MPI-ESM to errors in wind stress used for the initialization. A spurious trend in the wind stress forcing displaces the equatorial thermocline in MPI-ESM unrealistically. When the climate model is then switched into its forecast mode, the recovery process triggers artificial El Niño and La Niña events at the surface. Our results demonstrate the importance of realistic wind stress products for the initialization of decadal predictions.

Functional Properties of a High Protein Beverage Stabilized with Oat-β-Glucan.

PubMed

Vasquez-Orejarena, Eva; Simons, Christopher T; Litchfield, John H; Alvarez, Valente B

2018-05-01

This study evaluated the effect of oat flour and milk protein on the functional properties and sensory acceptability of shelf stable high protein dairy beverages containing at least 0.75 g of oat-β-glucan per serving size. Formulations adjusted to levels of 1.50% to 2.30% oat flour and 2.50% to 4.00% milk protein isolate (MPI) were thermal processed in a rotary retort. The finished product exhibited good suspension stability (>80%). The increase of oat and MPI contents lead to nectar-like beverages (51 to 100 mPas). However, oat flour was the component showing the highest effect on the viscosity coefficient values of the beverages. Sensory evaluation indicated that formulations with less than 1.9% oat flour and 2.5% MPI (thin liquid, <50 mPas) were the most accepted. Mouthfeel (perceived thickness), sweetness and aftertaste had the most influence on overall liking of the beverages. Overall, this study comprises the development of a functional food product. Supplementation of beverages with fiber from oats is an innovative approach to stabilize high protein beverages. Ready to drink protein beverage formulations use gums to stabilize the product and provide a desirable mouthfeel. The levels of oat-β-glucan used in the beverage increased the thickness and meet the requirement of the FDA approved health claim for reduction of the cardiovascular disease risk (21 CFR 101.81). © 2018 Institute of Food Technologists®.

Early detection of right ventricular dysfunction using transthoracic echocardiography in ARDS: a more objective approach.

PubMed

Wadia, Subeer Kanwar; Shah, Trushil G; Hedstrom, Grady; Kovach, Julie A; Tandon, Rajive

2016-12-01

Right ventricular (RV) dysfunction is an independent predictor of morbidity and mortality in acute respiratory distress syndrome (ARDS). Our goal was to describe morphologic changes in the RV using objective measures on transthoracic echocardiography (TTE) that occur following ARDS. We retrospectively measured changes in the following RV parameters from a pre-ARDS TTE to an ARDS TTE: tricuspid annular plane systolic excursion (TAPSE), myocardial performance index (MPI), fractional area change (FAC), systolic pulmonary artery pressure (SPAP), peak tricuspid regurgitant (TR) velocity, and septal shift. Over 24 months, 14 patients met inclusion/exclusion criteria. Mean TAPSE decreased from 22.4 mm pre-ARDS to 16.3 mm during ARDS, P<.001. Mean MPI increased from 0.19 to 0.38, P=.001. Mean FAC decreased from 60.8% to 41.2%, P=.003. Peak TR velocity increased from 2.67 m/s pre-ARDS to 3.31 m/s during ARDS, P=.02. SPAP and septal shift demonstrated trends but not statistically different between pre-ARDS and ARDS states. TAPSE correlated with ARDS severity (PaO 2 /FiO 2 ratios), P=.004, and was lower among 30-day nonsurvivors compared with survivors, P=.002. Mild RV dysfunction is common after ARDS onset. RV morphologic changes coupled with dysfunction can be detected noninvasively through TTE changes with TAPSE, MPI, and FAC. Mild RV dysfunction by TAPSE is associated with ARDS severity and mortality. © 2016, Wiley Periodicals, Inc.

Corrosion behavior of 2205 duplex stainless steel.

PubMed

Platt, J A; Guzman, A; Zuccari, A; Thornburg, D W; Rhodes, B F; Oshida, Y; Moore, B K

1997-07-01

The corrosion of 2205 duplex stainless steel was compared with that of AISI type 316L stainless steel. The 2205 stainless steel is a potential orthodontic bracket material with low nickel content (4 to 6 wt%), whereas the 316L stainless steel (nickel content: 10 to 14 wt%) is a currently used bracket material. Both stainless steels were subjected to electrochemical and immersion (crevice) corrosion tests in 37 degrees C, 0.9 wt% sodium chloride solution. Electrochemical testing indicates that 2205 has a longer passivation range than 316L. The corrosion rate of 2205 was 0.416 MPY (milli-inch per year), whereas 316L exhibited 0.647 MPY. When 2205 was coupled to 316L with equal surface area ratio, the corrosion rate of 2205 reduced to 0.260 MPY, indicating that 316L stainless steel behaved like a sacrificial anode. When 316L is coupled with NiTi, TMA, or stainless steel arch wire and was subjected to the immersion corrosion test, it was found that 316L suffered from crevice corrosion. On the other hand, 2205 stainless steel did not show any localized crevice corrosion, although the surface of 2205 was covered with corrosion products, formed when coupled to NiTi and stainless steel wires. This study indicates that considering corrosion resistance, 2205 duplex stainless steel is an improved alternative to 316L for orthodontic bracket fabrication when used in conjunction with titanium, its alloys, or stainless steel arch wires.

Frequency Mixing Magnetic Detection Scanner for Imaging Magnetic Particles in Planar Samples.

PubMed

Hong, Hyobong; Lim, Eul-Gyoon; Jeong, Jae-Chan; Chang, Jiho; Shin, Sung-Woong; Krause, Hans-Joachim

2016-06-09

The setup of a planar Frequency Mixing Magnetic Detection (p-FMMD) scanner for performing Magnetic Particles Imaging (MPI) of flat samples is presented. It consists of two magnetic measurement heads on both sides of the sample mounted on the legs of a u-shaped support. The sample is locally exposed to a magnetic excitation field consisting of two distinct frequencies, a stronger component at about 77 kHz and a weaker field at 61 Hz. The nonlinear magnetization characteristics of superparamagnetic particles give rise to the generation of intermodulation products. A selected sum-frequency component of the high and low frequency magnetic field incident on the magnetically nonlinear particles is recorded by a demodulation electronics. In contrast to a conventional MPI scanner, p-FMMD does not require the application of a strong magnetic field to the whole sample because mixing of the two frequencies occurs locally. Thus, the lateral dimensions of the sample are just limited by the scanning range and the supports. However, the sample height determines the spatial resolution. In the current setup it is limited to 2 mm. As examples, we present two 20 mm × 25 mm p-FMMD images acquired from samples with 1 µm diameter maghemite particles in silanol matrix and with 50 nm magnetite particles in aminosilane matrix. The results show that the novel MPI scanner can be applied for analysis of thin biological samples and for medical diagnostic purposes.

Cooperative Data Sharing: Simple Support for Clusters of SMP Nodes

NASA Technical Reports Server (NTRS)

DiNucci, David C.; Balley, David H. (Technical Monitor)

1997-01-01

Libraries like PVM and MPI send typed messages to allow for heterogeneous cluster computing. Lower-level libraries, such as GAM, provide more efficient access to communication by removing the need to copy messages between the interface and user space in some cases. still lower-level interfaces, such as UNET, get right down to the hardware level to provide maximum performance. However, these are all still interfaces for passing messages from one process to another, and have limited utility in a shared-memory environment, due primarily to the fact that message passing is just another term for copying. This drawback is made more pertinent by today's hybrid architectures (e.g. clusters of SMPs), where it is difficult to know beforehand whether two communicating processes will share memory. As a result, even portable language tools (like HPF compilers) must either map all interprocess communication, into message passing with the accompanying performance degradation in shared memory environments, or they must check each communication at run-time and implement the shared-memory case separately for efficiency. Cooperative Data Sharing (CDS) is a single user-level API which abstracts all communication between processes into the sharing and access coordination of memory regions, in a model which might be described as "distributed shared messages" or "large-grain distributed shared memory". As a result, the user programs to a simple latency-tolerant abstract communication specification which can be mapped efficiently to either a shared-memory or message-passing based run-time system, depending upon the available architecture. Unlike some distributed shared memory interfaces, the user still has complete control over the assignment of data to processors, the forwarding of data to its next likely destination, and the queuing of data until it is needed, so even the relatively high latency present in clusters can be accomodated. CDS does not require special use of an MMU, which can add overhead to some DSM systems, and does not require an SPMD programming model. unlike some message-passing interfaces, CDS allows the user to implement efficient demand-driven applications where processes must "fight" over data, and does not perform copying if processes share memory and do not attempt concurrent writes. CDS also supports heterogeneous computing, dynamic process creation, handlers, and a very simple thread-arbitration mechanism. Additional support for array subsections is currently being considered. The CDS1 API, which forms the kernel of CDS, is built primarily upon only 2 communication primitives, one process initiation primitive, and some data translation (and marshalling) routines, memory allocation routines, and priority control routines. The entire current collection of 28 routines provides enough functionality to implement most (or all) of MPI 1 and 2, which has a much larger interface consisting of hundreds of routines. still, the API is small enough to consider integrating into standard os interfaces for handling inter-process communication in a network-independent way. This approach would also help to solve many of the problems plaguing other higher-level standards such as MPI and PVM which must, in some cases, "play OS" to adequately address progress and process control issues. The CDS2 API, a higher level of interface roughly equivalent in functionality to MPI and to be built entirely upon CDS1, is still being designed. It is intended to add support for the equivalent of communicators, reduction and other collective operations, process topologies, additional support for process creation, and some automatic memory management. CDS2 will not exactly match MPI, because the copy-free semantics of communication from CDS1 will be supported. CDS2 application programs will be free to carefully also use CDS1. CDS1 has been implemented on networks of workstations running unmodified Unix-based operating systems, using UDP/IP and vendor-supplied high- performance locks. Although its inter-node performance is currently unimpressive due to rudimentary implementation technique, it even now outperforms highly-optimized MPI implementation on intra-node communication due to its support for non-copy communication. The similarity of the CDS1 architecture to that of other projects such as UNET and TRAP suggests that the inter-node performance can be increased significantly to surpass MPI or PVM, and it may be possible to migrate some of its functionality to communication controllers.

Benefits of Model Updating: A Case Study Using the Micro-Precision Interferometer Testbed

NASA Technical Reports Server (NTRS)

Neat, Gregory W.; Kissil, Andrew; Joshi, Sanjay S.

1997-01-01

This paper presents a case study on the benefits of model updating using the Micro-Precision Interferometer (MPI) testbed, a full-scale model of a future spaceborne optical interferometer located at JPL.

The MPI-Mainz UV/VIS Spectral Atlas of Gaseous Molecules of Atmospheric Interest

NASA Astrophysics Data System (ADS)

Sander, Rolf; Keller-Rudek, Hannelore; Moortgat, Geert; Sörensen, Rüdiger

2014-05-01

Measurements from satellites can be used to obtain global concentration maps of atmospheric trace constituents. Critical parameters needed in the analysis of the satellite data are the absorption cross sections of the observed molecules. Here, we present the MPI-Mainz UV/VIS Spectral Atlas, which is a large collection of more than 5000 absorption cross section and quantum yield data files in the ultraviolet and visible (UV/VIS) wavelength region for gaseous molecules and radicals primarily of atmospheric interest. The data files contain results of individual measurements, covering research of almost a whole century. To compare and visualize the data sets, multicoloured graphical representations have been created. The Spectral Atlas is available on the internet at http://www.uv-vis-spectral-atlas-mainz.org. It has been completely overhauled and now appears with improved browse and search options, based on PostgreSQL, Django and Python database software. The web pages are continuously updated.

A Locality-Based Threading Algorithm for the Configuration-Interaction Method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shan, Hongzhang; Williams, Samuel; Johnson, Calvin

The Configuration Interaction (CI) method has been widely used to solve the non-relativistic many-body Schrodinger equation. One great challenge to implementing it efficiently on manycore architectures is its immense memory and data movement requirements. To address this issue, within each node, we exploit a hybrid MPI+OpenMP programming model in lieu of the traditional flat MPI programming model. Here in this paper, we develop optimizations that partition the workloads among OpenMP threads based on data locality,-which is essential in ensuring applications with complex data access patterns scale well on manycore architectures. The new algorithm scales to 256 threadson the 64-core Intelmore » Knights Landing (KNL) manycore processor and 24 threads on dual-socket Ivy Bridge (Xeon) nodes. Compared with the original implementation, the performance has been improved by up to 7× on theKnights Landing processor and 3× on the dual-socket Ivy Bridge node.« less

A Locality-Based Threading Algorithm for the Configuration-Interaction Method

DOE PAGES

Shan, Hongzhang; Williams, Samuel; Johnson, Calvin; ...

2017-07-03

The Configuration Interaction (CI) method has been widely used to solve the non-relativistic many-body Schrodinger equation. One great challenge to implementing it efficiently on manycore architectures is its immense memory and data movement requirements. To address this issue, within each node, we exploit a hybrid MPI+OpenMP programming model in lieu of the traditional flat MPI programming model. Here in this paper, we develop optimizations that partition the workloads among OpenMP threads based on data locality,-which is essential in ensuring applications with complex data access patterns scale well on manycore architectures. The new algorithm scales to 256 threadson the 64-core Intelmore » Knights Landing (KNL) manycore processor and 24 threads on dual-socket Ivy Bridge (Xeon) nodes. Compared with the original implementation, the performance has been improved by up to 7× on theKnights Landing processor and 3× on the dual-socket Ivy Bridge node.« less

Improved Seasonal Prediction of European Summer Temperatures With New Five-Layer Soil-Hydrology Scheme

NASA Astrophysics Data System (ADS)

Bunzel, Felix; Müller, Wolfgang A.; Dobrynin, Mikhail; Fröhlich, Kristina; Hagemann, Stefan; Pohlmann, Holger; Stacke, Tobias; Baehr, Johanna

2018-01-01

We evaluate the impact of a new five-layer soil-hydrology scheme on seasonal hindcast skill of 2 m temperatures over Europe obtained with the Max Planck Institute Earth System Model (MPI-ESM). Assimilation experiments from 1981 to 2010 and 10-member seasonal hindcasts initialized on 1 May each year are performed with MPI-ESM in two soil configurations, one using a bucket scheme and one a new five-layer soil-hydrology scheme. We find the seasonal hindcast skill for European summer temperatures to improve with the five-layer scheme compared to the bucket scheme and investigate possible causes for these improvements. First, improved indirect soil moisture assimilation allows for enhanced soil moisture-temperature feedbacks in the hindcasts. Additionally, this leads to improved prediction of anomalies in the 500 hPa geopotential height surface, reflecting more realistic atmospheric circulation patterns over Europe.

Characterization of UMT2013 Performance on Advanced Architectures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Howell, Louis

2014-12-31

This paper presents part of a larger effort to make detailed assessments of several proxy applications on various advanced architectures, with the eventual goal of extending these assessments to codes of programmatic interest running more realistic simulations. The focus here is on UMT2013, a proxy implementation of deterministic transport for unstructured meshes. I present weak and strong MPI scaling results and studies of OpenMP efficiency on the Sequoia BG/Q system at LLNL, with comparison against similar tests on an Intel Sandy Bridge TLCC2 system. The hardware counters on BG/Q provide detailed information on many aspects of on-node performance, while informationmore » from the mpiP tool gives insight into the reasons for the differing scaling behavior on these two different architectures. Preliminary tests that exploit NVRAM as extended memory on an Ivy Bridge machine designed for “Big Data” applications are also included.« less

Exploring Infiniband Hardware Virtualization in OpenNebula towards Efficient High-Performance Computing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pais Pitta de Lacerda Ruivo, Tiago; Bernabeu Altayo, Gerard; Garzoglio, Gabriele

2014-11-11

has been widely accepted that software virtualization has a big negative impact on high-performance computing (HPC) application performance. This work explores the potential use of Infiniband hardware virtualization in an OpenNebula cloud towards the efficient support of MPI-based workloads. We have implemented, deployed, and tested an Infiniband network on the FermiCloud private Infrastructure-as-a-Service (IaaS) cloud. To avoid software virtualization towards minimizing the virtualization overhead, we employed a technique called Single Root Input/Output Virtualization (SRIOV). Our solution spanned modifications to the Linux’s Hypervisor as well as the OpenNebula manager. We evaluated the performance of the hardware virtualization on up to 56more » virtual machines connected by up to 8 DDR Infiniband network links, with micro-benchmarks (latency and bandwidth) as well as w a MPI-intensive application (the HPL Linpack benchmark).« less

Ferrenberg Swendsen Analysis of LLNL and NYBlue BG/L p4rhms Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Soltz, R

2007-12-05

These results are from the continuing Lattice Quantum Chromodynamics runs on BG/L. These results are from the Ferrenberg-Swendsen analysis [?] of the combined data from LLNL and NYBlue BG/L runs for 32{sup 3} x 8 runs with the p4rhmc v2.0 QMP-MPI.X (semi-optimized p4 code using qmp over mpi). The jobs include beta values ranging from 3.525 to 3.535 with an alternate analysis extending to 3.540. The NYBlue data sets are from 9k trajectories from Oct 2007, and the LLNL data are from two independent streams of {approx}5k each, taking from the July 2007 runs. The following outputs are produced bymore » the fs-2+1-chiub.c program. All outputs have had checksums produced by addCks.pl and checked by the checkCks.pl perl script after scanning.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bolton, Daniel R.; Briceno, Raul A.; Wilson, David J.

Here, we present a determination of the isovector,more » $P$-wave $$\\pi\\pi$$ scattering phase shift obtained by extrapolating recent lattice QCD results from the Hadron Spectrum Collaboration using $$m_\\pi =236$$ MeV. The finite volume spectra are described using extensions of L\\"uscher's method to determine the infinite volume Unitarized Chiral Perturbation Theory scattering amplitude. We exploit the pion mass dependence of this effective theory to obtain the scattering amplitude at $$m_\\pi= 140$$ MeV. The scattering phase shift is found to be in good agreement with experiment up to center of mass energies of 1.2 GeV. The analytic continuation of the scattering amplitude to the complex plane yields a $$\\rho$$-resonance pole at $$E_\\rho= \\left[755(2)(1)(^{20}_{02})-\\frac{i}{2}\\,129(3)(1)(^{7}_{1})\\right]~{\\rm MeV}$$. The techniques presented illustrate a possible pathway towards connecting lattice QCD observables of few-body, strongly interacting systems to experimentally accessible quantities.« less

Parallel Unsteady Turbopump Simulations for Liquid Rocket Engines

NASA Technical Reports Server (NTRS)

Kiris, Cetin C.; Kwak, Dochan; Chan, William

2000-01-01

This paper reports the progress being made towards complete turbo-pump simulation capability for liquid rocket engines. Space Shuttle Main Engine (SSME) turbo-pump impeller is used as a test case for the performance evaluation of the MPI and hybrid MPI/Open-MP versions of the INS3D code. Then, a computational model of a turbo-pump has been developed for the shuttle upgrade program. Relative motion of the grid system for rotor-stator interaction was obtained by employing overset grid techniques. Time-accuracy of the scheme has been evaluated by using simple test cases. Unsteady computations for SSME turbo-pump, which contains 136 zones with 35 Million grid points, are currently underway on Origin 2000 systems at NASA Ames Research Center. Results from time-accurate simulations with moving boundary capability, and the performance of the parallel versions of the code will be presented in the final paper.

The Mpi-M Aerosol Climatology (MAC)

NASA Astrophysics Data System (ADS)

Kinne, S.

2014-12-01

Monthly gridded global data-sets for aerosol optical properties (AOD, SSA and g) and for aerosol microphysical properties (CCN and IN) offer a (less complex) alternate path to include aerosol radiative effects and aerosol impacts on cloud-microphysics in global simulations. Based on merging AERONET sun-/sky-photometer data onto background maps provided by AeroCom phase 1 modeling output and AERONET sun-/the MPI-M Aerosol Climatology (MAC) version 1 was developed and applied in IPCC simulations with ECHAM and as ancillary data-set in satellite-based global data-sets. An updated version 2 of this climatology will be presented now applying central values from the more recent AeroCom phase 2 modeling and utilizing the better global coverage of trusted sun-photometer data - including statistics from the Marine Aerosol network (MAN). Applications include spatial distributions of estimates for aerosol direct and aerosol indirect radiative effects.

Matrix Factorizations at Scale: a Comparison of Scientific Data Analytics in Spark and C+MPI Using Three Case Studies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gittens, Alex; Devarakonda, Aditya; Racah, Evan

We explore the trade-offs of performing linear algebra using Apache Spark, compared to traditional C and MPI implementations on HPC platforms. Spark is designed for data analytics on cluster computing platforms with access to local disks and is optimized for data-parallel tasks. We examine three widely-used and important matrix factorizations: NMF (for physical plausibility), PCA (for its ubiquity) and CX (for data interpretability). We apply these methods to 1.6TB particle physics, 2.2TB and 16TB climate modeling and 1.1TB bioimaging data. The data matrices are tall-and-skinny which enable the algorithms to map conveniently into Spark’s data parallel model. We perform scalingmore » experiments on up to 1600 Cray XC40 nodes, describe the sources of slowdowns, and provide tuning guidance to obtain high performance.« less

A Martin-Puplett cartridge FIR interferometer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smith, Roger J.; Penniman, Edwin E.; Jarboe, Thomas R.

2004-10-01

A compact prealigned Martin-Puplett interferometer (MPI) cartridge for plasma interferometry is described. The MPI cartridge groups all components of a MP interferometer, with the exception of the end mirror for the scene beam, on a stand-alone rigid platform. The interferometer system is completed by positioning a cartridge anywhere along and coaxial with the scene beam, considerably reducing the amount of effort in alignment over a discrete component layout. This allows the interferometer to be expanded to any number of interferometry chords consistent with optical access, limited only by the laser power. The cartridge interferometer has been successfully incorporated as amore » second chord on the Helicity Injected Torus II (HIT-II) far infrared interferometer system and a comparison with the discrete component system is presented. Given the utility and compactness of the cartridge, a possible design for a five-chord interferometer arrangement on the HIT-II device is described.« less

The MPI-Mainz UV/VIS Spectral Atlas of Gaseous Molecules of Atmospheric Interest

NASA Astrophysics Data System (ADS)

Keller-Rudek, H.; Moortgat, G. K.; Sander, R.; Sörensen, R.

2013-08-01

We present the MPI-Mainz UV/VIS Spectral Atlas, which is a large collection of absorption cross sections and quantum yields in the ultraviolet and visible (UV/VIS) wavelength region for gaseous molecules and radicals primarily of atmospheric interest. The data files contain results of individual measurements, covering research of almost a whole century. To compare and visualize the data sets, multicoloured graphical representations have been created. The Spectral Atlas is available on the internet at http://www.uv-vis-spectral-atlas-mainz.org. It now appears with improved browse and search options, based on new database software. In addition to the web pages, which are continuously updated, a frozen version of the data is available under the doi:10.5281/zenodo.6951.

Effects of future anthropogenic pollution emissions on global air quality

NASA Astrophysics Data System (ADS)

Pozzer, A.; Zimmermann, P.; Doering, U.; van Aardenne, J.; Dentener, F.; Lelieveld, J.

2012-04-01

The atmospheric chemistry general circulation model EMAC is used to estimate the impact of anthropogenic emission changes on global and regional air quality in recent and future years (2005, 2010, 2025 and 2050). The emission scenario assumes that population and economic growth largely determine energy consumption and consequent pollution sources ("business as usual"). By comparing with recent observations, it is shown that the model reproduces the main features of regional air pollution distributions though with some imprecision inherent to the coarse horizontal resolution (around 100 km). To identify possible future hot spots of poor air quality, a multi pollutant index (MPI) has been applied. It appears that East and South Asia and the Arabian Gulf regions represent such hotspots due to very high pollutant concentrations. In East Asia a range of pollutant gases and particulate matter (PM2.5) are projected to reach very high levels from 2005 onward, while in South Asia air pollution, including ozone, will grow rapidly towards the middle of the century. Around the Arabian Gulf, where natural PM2.5 concentrations are already high (desert dust), ozone levels will increase strongly. By extending the MPI definition, we calculated a Per Capita MPI (PCMPI) in which we combined population projections with those of pollution emissions. It thus appears that a rapidly increasing number of people worldwide will experience reduced air quality during the first half of the 21st century. It is projected that air quality for the global average citizen in 2050 will be comparable to the average in East Asia in the year 2005.

Added prognostic value of ischaemic threshold in radionuclide myocardial perfusion imaging: a common-sense integration of exercise tolerance and ischaemia severity.

PubMed

Marini, Cecilia; Acampa, Wanda; Bauckneht, Matteo; Daniele, Stefania; Capitanio, Selene; Cantoni, Valeria; Fiz, Francesco; Zampella, Emilia; Dib, Bassam; Assante, Roberta; Bruzzi, Paolo; Sambuceti, Gianmario; Cuocolo, Alberto

2015-04-01

Reversible ischaemia at radionuclide myocardial perfusion imaging (MPI) accurately predicts risk of cardiac death and nonfatal myocardial infarction (major adverse cardiac events, MACE). This prognostic penetrance might be empowered by accounting for exercise tolerance as an indirect index of ischaemia severity. The present study aimed to verify this hypothesis integrating imaging assessment of ischaemia severity with exercise maximal rate pressure product (RPP) in a large cohort of patients with suspected or known coronary artery disease (CAD). We analysed 1,502 consecutive patients (1,014 men aged 59 ± 10 years) submitted to exercise stress/rest MPI. To account for exercise tolerance, the summed difference score (SDS) was divided by RPP at tracer injection providing a clinical prognostic index (CPI). Reversible ischaemia was documented in 357 patients (24 %) and was classified by SDS as mild (SDS 2-4) in 180, moderate (SDS 5-7) in 118 and severe (SDS >7) in 59. CPI values of ischaemic patients were clustered into tertiles with lowest and highest values indicating low and high risk, respectively. CPI modified SDS risk prediction in 119/357 (33 %) patients. During a 60-month follow-up, MACE occurred in 68 patients. Kaplan-Meier analysis revealed that CPI significantly improved predictive power for MACE incidence with respect to SDS alone. Multivariate Cox analysis confirmed the additive independent value of CPI-derived information. Integration of ischaemic threshold and ischaemia extension and severity can improve accuracy of exercise MPI in predicting long-term outcome in a large cohort of patients with suspected or known CAD.

A hypertensive response to exercise is associated with transient ischemic dilation on myocardial perfusion SPECT imaging.

PubMed

Smelley, Matthew P; Virnich, Daniel E; Williams, Kim A; Ward, R Parker

2007-07-01

A hypertensive response to exercise (HRE) is associated with false-positive stress echocardiograms and myocardial perfusion single photon emission computed tomography (myocardial perfusion imaging [MPI]) defects even in the absence of coronary artery disease (CAD). Transient ischemic dilation (TID) of the left ventricle on stress MPI is a marker of severe CAD and future cardiac events. This study evaluated the association between an HRE and TID. Blinded quantitative TID assessment was performed in 125 patients who had an HRE and a summed stress score (SSS) of less than 4, as well as 125 control patients with an SSS of less than 4 and without an HRE matched for age, gender, and resting systolic blood pressure. Cardiac comorbidities, pretest Framingham risk, and exercise results were recorded. TID was defined as a stress-to-rest volume ratio of 1.22 or greater. An HRE was associated with a high prevalence of TID and significantly more TID than no HRE (25.6% vs 11.2%; odds ratio, 3.00 [95% confidence interval, 1.41-6.38]). TID was more prevalent even in subgroups with a low pretest probability CAD, including those without diabetes mellitus or angina. On conditional logistic regression analysis, an HRE was found to be independently associated with TID after consideration of other clinical and exercise MPI variables (odds ratio, 2.72 [95% confidence interval, 1.01-7.31]). An HRE is associated with a high prevalence of TID in patients without other significant perfusion defects, possibly as a result of global subendocardial ischemia induced by the HRE.

Synthesis, characterization, DFT calculations and antibacterial activity of palladium(II) cyanide complexes with thioamides

NASA Astrophysics Data System (ADS)

Ahmad, Saeed; Nadeem, Shafqat; Anwar, Aneela; Hameed, Abdul; Tirmizi, Syed Ahmed; Zierkiewicz, Wiktor; Abbas, Azhar; Isab, Anvarhusein A.; Alotaibi, Mshari A.

2017-08-01

Palladium(II) cyanide complexes of thioamides (or thiones) having the general formula PdL2(CN)2, where L = Thiourea (Tu), Methylthiourea (Metu), N,N‧-Dimethylthiourea (Dmtu), Tetramethylthiourea (Tmtu), 2-Mercaptopyridine (Mpy) and 2-Mercaptopyrimidine (Mpm) were prepared by reacting K2[PdCl4] with potassium cyanide and thioamides in the molar ratio of 1:2:2. The complexes were characterized by elemental analysis, thermal and spectroscopic methods (IR, 1H and 13C NMR). The structures of three of the complexes were predicted by DFT calculations. The appearance of a band around 2100 cm-1 in IR and resonances around 120-130 ppm in the 13C NMR spectra indicated the coordination of cyanide to palladium(II). More than one resonances were observed for CN- carbon atoms in 13C NMR indicating the existence of equilibrium between different species in solution. DFT calculations revealed that in the case of the palladium(II) complex of Tmtu, the ionic dinuclear [Pd(Tmtu)4][Pd(CN)4] form was more stable than the dimer of mononuclear complex [Pd(Tmtu)2(CN)2] by 0.91 kcal mol-1, while for the complexes of Tu or Mpy ligands, the nonionic [Pd(L)2(CN)2] forms were more stable than the corresponding [Pd(L)4][Pd(CN)4] complexes by 1.26 and 6.49 kcal mol-1 for L = Tu and Mpy, respectively. The complexes were screened for antibacterial effects and some of them showed significant activities against both gram positive as well as gram negative bacteria.

Diagnostic Performance of Artificial Neural Network for Detecting Ischemia in Myocardial Perfusion Imaging.

PubMed

Nakajima, Kenichi; Matsuo, Shinro; Wakabayashi, Hiroshi; Yokoyama, Kunihiko; Bunko, Hisashi; Okuda, Koichi; Kinuya, Seigo; Nyström, Karin; Edenbrandt, Lars

2015-01-01

The purpose of this study was to apply an artificial neural network (ANN) in patients with coronary artery disease (CAD) and to characterize its diagnostic ability compared with conventional visual and quantitative methods in myocardial perfusion imaging (MPI). A total of 106 patients with CAD were studied with MPI, including multiple vessel disease (49%), history of myocardial infarction (27%) and coronary intervention (30%). The ANN detected abnormal areas with a probability of stress defect and ischemia. The consensus diagnosis based on expert interpretation and coronary stenosis was used as the gold standard. The left ventricular ANN value was higher in the stress-defect group than in the no-defect group (0.92±0.11 vs. 0.25±0.32, P<0.0001) and higher in the ischemia group than in the no-ischemia group (0.70±0.40 vs. 0.004±0.032, P<0.0001). Receiver-operating characteristics curve analysis showed comparable diagnostic accuracy between ANN and the scoring methods (0.971 vs. 0.980 for stress defect, and 0.882 vs. 0.937 for ischemia, both P=NS). The relationship between the ANN and defect scores was non-linear, with the ANN rapidly increased in ranges of summed stress score of 2-7 and summed defect score of 2-4. Although the diagnostic ability of ANN was similar to that of conventional scoring methods, the ANN could provide a different viewpoint for judging abnormality, and thus is a promising method for evaluating abnormality in MPI.

A U-shaped Association between Body Mass Index and Psychological Distress on the Multiphasic Personality Inventory: Retrospective Cross-sectional Analysis of 19-year-old Men in Korea.

PubMed

Kim, Taehyun; Kim, Jung Jun; Kim, Mi Yeon; Kim, Shin Kyoung; Roh, Sungwon; Seo, Jeong Seok

2015-06-01

Objective personality tests, such as the Minnesota Multiphasic Personality Inventory (MMPI), might be more sensitive to reflect subclinical personality and be more state-dependent in an individual's lifetime, so they are good scales to predict the psychological distress regarding certain states. The aim of this study was to identify the specific pattern between body mass index (BMI) and psychological distress using the objective personality test. For this study, we investigated BMI and the Korean Military Multiphasic Personality Inventory (MPI). A retrospective cross-sectional study was conducted with 19-yr-old examinees who were admitted to the Military Manpower Administration in Korea from February 2007 to January 2010. Of 1,088,107 examinees, we enrolled 771,408 subjects who were psychologically apparent healthy possible-military-service groups. Afterwards, we reviewed and analyzed directly measured BMI and MPI results. In terms of the validity scales, the faking-good subscale showed an inverted U-shaped association, and faking-bad and infrequency subscales showed a U-shaped association with BMI groups. In terms of the neurosis scales, all clinical subscales (anxiety, depression, somatization, and personality disorder) also showed a U-shaped association with BMI groups. For the psychopath scales, the schizophrenia subscale showed a U-shaped association, and the paranoia subscale showed a near-positive correlation with BMI. In conclusion, a specific U-shaped pattern was observed between BMI and the MPI in 19-yr-old men in Korea. Underweight and obesity are related to psychological distress, so supportive advice and education are needed to them.

Helicobacter cinaedi Induced Typhlocolitis in Rag-2-Deficient Mice

PubMed Central

Shen, Zeli; Feng, Yan; Rickman, Barry; Fox, James G.

2015-01-01

Background Helicobacter cinaedi, an enterohepatic helicobacter species (EHS), is an important human pathogen and is associated with a wide range of diseases, especially in immunocompromised patients. It has been convincingly demonstrated that innate immune response to certain pathogenic enteric bacteria is sufficient to initiate colitis and colon carcinogenesis in recombinase-activating gene (Rag)-2-deficient mice model. To better understand the mechanisms of human IBD and its association with development of colon cancer, we investigated whether H. cinaedi could induce pathological changes noted with murine enterohepatic helicobacter infections in the Rag2−/− mouse model. Materials and Methods Sixty 129SvEv Rag2−/− mice mouse were experimentally or sham infected orally with H. cinaedi strain CCUG 18818. Gastrointestinal pathology and immune responses in infected and control mice were analyzed at 3, 6 and 9 months postinfection (MPI). H. cinaedi colonized the cecum, colon, and stomach in infected mice. Results H. cinaedi induced typhlocolitis in Rag2−/− mice by 3 MPI and intestinal lesions became more severe by 9 MPI. H. cinaedi was also associated with the elevation of proinflammatory cytokines, interferon-γ, tumor-necrosis factor-α, IL-1β, IL-10; iNOS mRNA levels were also upregulated in the cecum of infected mice. However, changes in IL-4, IL-6, Cox-2, and c-myc mRNA expressions were not detected. Conclusions Our results indicated that the Rag2−/− mouse model will be useful to continue investigating the pathogenicity of H. cinaedi, and to study the association of host immune responses in IBD caused by EHS. PMID:25381744

The PRISM project

NASA Astrophysics Data System (ADS)

Guilyardi, E.

2003-04-01

The European Union's PRISM infrastructure project (PRogram for Integrated earth System Modelling) aims at designing a flexible environment to easily assemble and run Earth System Models (http://prism.enes.org). Europe's widely distributed modelling expertise is both a strength and a challenge. Recognizing this, the PRISM project aims at developing an efficient shared modelling software infrastructure for climate scientists, providing them with an opportunity for greater focus on scientific issues, including the necessary scientific diversity (models and approaches). The proposed PRISM system includes 1) the use - or definition - and promotion of scientific and technical standards to increase component modularity, 2) an end-to-end software environment (coupler, user interface, diagnostics) to launch, monitor and analyze complex Earth System Models built around the existing and future community models, 3) testing and quality standards to ensure HPC performance on a variety of platforms and 4) community wide inputs and requirements capture in all stages of system specifications and design through user/developers meetings, workshops and thematic schools. This science driven project, led by 22 institutes* and started December 1st 2001, benefits from a unique gathering of scientific and technical expertise. More than 30 models (both global and regional) have expressed interest to be part of the PRISM system and 6 types of components have been identified: atmosphere, atmosphere chemistry, land surface, ocean, sea ice and ocean biochemistry. Progress and overall architecture design will be presented. * MPI-Met (Coordinator), KNMI (co-coordinator), MPI-M&D, Met Office, University of Reading, IPSL, Meteo-France, CERFACS, DMI, SMHI, NERSC, ETH Zurich, INGV, MPI-BGC, PIK, ECMWF, UCL-ASTR, NEC, FECIT, SGI, SUN, CCRLE

Application of autogenic training in patients with Ménière disease.

PubMed

Goto, Fumiyuki; Nakai, Kimiko; Ogawa, Kaoru

2011-10-01

Data are limited on the role of psychotherapy in the treatment of Ménière disease. We sought to document the effect of a psychotherapeutic technique known as autogenic training on clinical outcome in Ménière disease. Six patients with Ménière disease were studied. Retrospective chart review was conducted. All patients were refractory to conventional therapy and completed a course of autogenic training, which was offered as a complementary treatment. Autogenic training with initial psychological counseling was conducted by a clinical psychologist during 45-min sessions. Outcome measures assessed were the frequency of vertigo and functional levels 2 years after initiation of autogenic training. Functional levels were evaluated according to the 1995 guidelines of the American Academy of Otolaryngology-Head Neck Surgery (AAO-HNS). As a personality measure, we used the Maudsley Personality Inventory (MPI), devised by Eysenck, which measures neuroticism (N), extraversion (E), and propensity to lie (L). Five of six patients showed improved functional level after three to eight sessions of psychotherapy; hearing level did not change. The score of the N scale of the MPI was closely related to the number of psychotherapy sessions. Prognosis was evaluated based on the AAO-HNS reporting guidelines, as follows: A = 3, B = 1, C = 1, F = 1. The value of N in MPI was closely related to the number of psychological counseling sessions (R = 0.97, P < 0.05). In conclusion, autogenic training may enhance the mental well-being of patients with Ménière disease and improve clinical outcome.

Strict Selection Criteria During Surgical Training Ensures Good Outcomes in Laparoscopic Omental Patch Repair (LOPR) for Perforated Peptic Ulcer (PPU).

PubMed

Shelat, Vishal G; Ahmed, Saleem; Chia, Clement L K; Cheah, Yee Lee

2015-02-01

Application of minimal access surgery in acute care surgery is limited due to various reasons. Laparoscopic omental patch repair (LOPR) for perforated peptic ulcer (PPU) surgery is safe and feasible but not widely implemented. We report our early experience of LOPR with emphasis on strict selection criteria. This is a descriptive study of all patients operated on for PPU at academic university-affiliated institutes from December 2010 to February 2012. All the patients who were operated on for LOPR were included as the study population and their records were studied. Perioperative outcomes, Boey score, Mannheim Peritonitis Index (MPI), and physiologic and operative severity scores for enumeration of mortality and morbidity (POSSUM) scores were calculated. All the data were tabulated in a Microsoft Excel spreadsheet and analyzed using Stata Version 8.x. (StataCorp, College Station, TX, USA). Fourteen patients had LOPR out of a total of 45 patients operated for the PPU. Mean age was 46 years (range 22-87 years). Twelve patients (86%) had a Boey score of 0 and all patients had MPI < 21 (mean MPI = 14). The predicted POSSUM morbidity and mortality were 36% and 7%, respectively. Mean ulcer size was 5 mm (range 2-10 mm), mean operating time was 100 minutes (range 70-123 minutes) and mean length of hospital stay was 4 days (range 3-6 days). There was no morbidity or mortality pertaining to LOPR. LOPR should be offered by acute care surgical teams when local expertise is available. This can optimize patient outcomes when strict selection criteria are applied.