Simit: A Language for Physical Simulation

Using existing programming tools, writing high-performance simulation code is labor intensive and requires sacrificing readability and portability. The alternative is to prototype simulations in a high-level language like Matlab, thereby sacrificing performance. The Matlab programming model naturally describes the behavior of an entire physical system using the language of linear algebra. However, simulations also manipulate individual geometric elements, which are best represented using linked data structures like meshes. Translating between the linked data structures and linear algebra comes at significant cost, both to the programmer and the machine. High-performance implementations avoid the cost by rephrasing the computation in terms of linked or index data structures, leaving the code complicated and monolithic, often increasing its size by an order of magnitude. In this paper, we present Simit, a new language for physical simulations that lets the programmer view the system both as a linked data structure in the form of a hypergraph, and as a set of global vectors, matrices and tensors depending on what is convenient at any given time. Simit provides a novel assembly construct that makes it conceptually easy and computationally efficient to move between the two abstractions. Using the information provided by the assembly construct, the compiler generates efficient in-place computation on the graph. We demonstrate that Simit is easy to use: a Simit program is typically shorter than a Matlab program; that it is high-performance: a Simit program running sequentially on a CPU performs comparably to hand-optimized simulations; and that it is portable: Simit programs can be compiled for GPUs with no change to the program, delivering 5-25x speedups over our optimized CPU code

Procoagulant Microparticles in Dogs with Immune-Mediated Hemolytic Anemia

BACKGROUND: Studies of some human prothrombotic diseases suggest that phosphatidylserine-positive (PS+) and tissue factor-positive (TF+) microparticles (MPs) might play a role in the pathogenesis of thrombosis or serve as biomarkers of thrombotic risk. HYPOTHESIS/OBJECTIVES: To determine if circulating levels of PS+MP and procoagulant activity (PCA) associated with PS+MPs and TF+ MPs are increased in dogs with IMHA. ANIMALS: Fifteen dogs with primary or secondary IMHA and 17 clinically healthy dogs. METHODS: Prospective case-controlled observational study. Circulating PS+MPs were measured by flow cytometry. PCA associated with PS+MPs and TF+MPs was measured by thrombin and Factor Xa generating assays, respectively. RESULTS: Circulating numbers of PS+MPs were not significantly higher in dogs with IMHA [control median 251,000/μL (36,992-1,141,250/μL); IMHA median 361,990/μL (21,766-47,650,600/μL) P = .30]. However, PS+MP PCA [control median 2.2 (0.0-16.8) nM PS eq; IMHA median 8.596, (0-49.33 nM PS eq) P = .01] and TF+MP PCA [control median 0.0, (0.0-0.0 pg/mL); IMHA median 0.0; (0-22.34 pg/mL], P = .04) were increased. Intravascular hemolysis, which we showed might increase PS+ and TF+MP PCA, was evident in 3 of 5 dogs with PS+MP PCA and 2 of 4 dogs with TF+MP PCA higher than controls. Underlying disease in addition to IMHA was detected in 1 of 5 dogs with PS+PCA and 3 of 4 dogs with TF+MP PCA higher than controls. CONCLUSIONS AND CLINICAL IMPORTANCE: TF+ and PS+MP PCA is increased in some dogs with IMHA. Further studies that determine if measuring TF+ and PS+ MP PCA can help identify dogs at risk for thrombosis are warranted

Orally Administered DTPA Penta-Ethyl Ester for the Decorporation of Inhaled 241Am

Diethylenetriaminepentaacetic acid (DTPA) is an effective decorporation agent to facilitate the elimination of radionuclides from the body, but its permeability-limited oral bioavailability limits its utility in mass-casualty emergencies. To overcome this limitation, a prodrug strategy using the penta-ethyl ester form of DTPA is under investigation. Pharmacokinetic and biodistribution studies were conducted in rats by orally administering [14C]DTPA penta-ethyl ester, and this prodrug and its hydrolysis products were analyzed as a single entity. Compared to a previous reporting of intravenously administered DTPA, the oral administration of this prodrug resulted in a sustained plasma concentration profile with higher plasma exposure and lower clearance. An assessment of the urine composition revealed that the bioactivation was extensive but incomplete, with no detectable levels of the penta- or tetra-ester forms. Tissue distribution at 12 h was limited, with approximately 73% of the administered dose being associated with the gastrointestinal tract. In the efficacy study, rats were exposed to aerosols of 241Am nitrate before receiving a single oral treatment of the prodrug. The urinary excretion of 241Am was found to be 19% higher than with the control. Consistent with prior reports of DTPA, the prodrug was most effective when the treatment delays were minimized

Adult-onset Alexander disease with typical "tadpole" brainstem atrophy and unusual bilateral basal ganglia involvement: a case report and review of the literature

<p>Abstract</p> <p>Background</p> <p>Alexander disease (ALX) is a rare neurological disorder characterized by white matter degeneration and cytoplasmic inclusions in astrocytes called Rosenthal fibers, labeled by antibodies against glial fibrillary acidic protein (GFAP). Three subtypes are distinguished according to age at onset: infantile (under age 2), juvenile (age 2 to 12) and adult (over age 12). Following the identification of heterozygous mutations in <it>GFAP </it>that cause this disease, cases of adult-onset ALX have been increasingly reported.</p> <p>Case Presentation</p> <p>We present a 60-year-old Japanese man with an unremarkable past and no family history of ALX. After head trauma in a traffic accident at the age of 46, his character changed, and dementia and dysarthria developed, but he remained independent. Spastic paresis and dysphagia were observed at age 57 and 59, respectively, and worsened progressively. Neurological examination at the age of 60 revealed dementia, pseudobulbar palsy, left-side predominant spastic tetraparesis, axial rigidity, bradykinesia and gaze-evoked nystagmus. Brain MRI showed tadpole-like atrophy of the brainstem, caused by marked atrophy of the medulla oblongata, cervical spinal cord and midbrain tegmentum, with an intact pontine base. Analysis of the <it>GFAP </it>gene revealed a heterozygous missense mutation, c.827G>T, p.R276L, which was already shown to be pathogenic in a case of pathologically proven hereditary adult-onset ALX.</p> <p>Conclusion</p> <p>The typical tadpole-like appearance of the brainstem is strongly suggestive of adult-onset ALX, and should lead to a genetic investigation of the <it>GFAP </it>gene. The unusual feature of this patient is the symmetrical involvement of the basal ganglia, which is rarely observed in the adult form of the disease. More patients must be examined to confirm, clinically and neuroradiologically, extrapyramidal involvement of the basal ganglia in adult-onset ALX.</p

Indirect monitoring shot-to-shot shock waves strength reproducibility during pump-probe experiments

We present an indirect method of estimating the strength of a shock wave, allowing on line monitoring of its reproducibility in each laser shot. This method is based on a shot-to-shot measurement of the X-ray emission from the ablated plasma by a high resolution, spatially resolved focusing spectrometer. An optical pump laser with energy of 1.0 J and pulse duration of ∼660 ps was used to irradiate solid targets or foils with various thicknesses containing Oxygen, Aluminum, Iron, and Tantalum. The high sensitivity and resolving power of the X-ray spectrometer allowed spectra to be obtained on each laser shot and to control fluctuations of the spectral intensity emitted by different plasmas with an accuracy of ∼2%, implying an accuracy in the derived electron plasma temperature of 5%-10% in pump-probe high energy density science experiments. At nano- and sub-nanosecond duration of laser pulse with relatively low laser intensities and ratio Z/A ∼ 0.5, the electron temperature follows Te ∼ Ilas2/3. Thus, measurements of the electron plasma temperature allow indirect estimation of the laser flux on the target and control its shot-to-shot fluctuation. Knowing the laser flux intensity and its fluctuation gives us the possibility of monitoring shot-to-shot reproducibility of shock wave strength generation with high accuracy.T. A. Pikuz, A. Ya. Faenov, N. Ozaki, N. J. Hartley, B. Albertazzi, T. Matsuoka, K. Takahashi, H. Habara, Y. Tange, S. Matsuyama, K. Yamauchi, R. Ochante, K. Sueda, O. Sakata, T. Sekine, T. Sato, Y. Umeda, Y. Inubushi, T. Yabuuchi, T. Togashi, T. Katayama, M. Yabashi, M. Harmand, G. Morard, M. Koenig, V. Zhakhovsky, N. Inogamov, A. S. Safronova, A. Stafford, I. Yu. Skobelev, S. A. Pikuz, T. Okuchi, Y. Seto, K. A. Tanaka, T. Ishikawa, and R. Kodama, "Indirect monitoring shot-to-shot shock waves strength reproducibility during pump–probe experiments", Journal of Applied Physics 120, 035901 (2016) https://doi.org/10.1063/1.4958796

Evidence for association between the HLA-DQA locus and abdominal aortic aneurysms in the Belgian population: a case control study

BACKGROUND: Chronic inflammation and autoimmunity likely contribute to the pathogenesis of abdominal aortic aneurysms (AAAs). The aim of this study was to investigate the role of autoimmunity in the etiology of AAAs using a genetic association study approach with HLA polymorphisms. METHODS: HLA-DQA1, -DQB1, -DRB1 and -DRB3-5 alleles were determined in 387 AAA cases (180 Belgian and 207 Canadian) and 426 controls (269 Belgian and 157 Canadian) by a PCR and single-strand oligonucleotide probe hybridization assay. RESULTS: We observed a potential association with the HLA-DQA1 locus among Belgian males (empirical p = 0.027, asymptotic p = 0.071). Specifically, there was a significant difference in the HLA-DQA1*0102 allele frequencies between AAA cases (67/322 alleles, 20.8%) and controls (44/356 alleles, 12.4%) in Belgian males (empirical p = 0.019, asymptotic p = 0.003). In haplotype analyses, marginally significant association was found between AAA and haplotype HLA-DQA1-DRB1 (p = 0.049 with global score statistics and p = 0.002 with haplotype-specific score statistics). CONCLUSION: This study showed potential evidence that the HLA-DQA1 locus harbors a genetic risk factor for AAAs suggesting that autoimmunity plays a role in the pathogenesis of AAAs