Fat vs. thin threading approach on GPUs: application to stochastic simulation of chemical reactions

We explore two different threading approaches on a graphics processing unit (GPU) exploiting two different characteristics of the current GPU architecture. The fat thread approach tries to minimise data access time by relying on shared memory and registers potentially sacrificing parallelism. The thin thread approach maximises parallelism and tries to hide access latencies. We apply these two approaches to the parallel stochastic simulation of chemical reaction systems using the stochastic simulation algorithm (SSA) by Gillespie (J. Phys. Chem, Vol. 81, p. 2340-2361, 1977). In these cases, the proposed thin thread approach shows comparable performance while eliminating the limitation of the reaction system’s size

STOCHSIMGPU Parallel stochastic simulation for the Systems\ud Biology Toolbox 2 for MATLAB

Motivation: The importance of stochasticity in biological systems is becoming increasingly recognised and the computational cost of biologically realistic stochastic simulations urgently requires development of efficient software. We present a new software tool STOCHSIMGPU which exploits graphics processing units (GPUs)for parallel stochastic simulations of biological/chemical reaction systems and show that significant gains in efficiency can be made. It is integrated into MATLAB and works with the Systems Biology Toolbox 2 (SBTOOLBOX2) for MATLAB.\ud \ud Results: The GPU-based parallel implementation of the Gillespie stochastic simulation algorithm (SSA), the logarithmic direct method (LDM), and the next reaction method (NRM) is approximately 85 times faster than the sequential implementation of the NRM on a central processing unit (CPU). Using our software does not require any changes to the user’s models, since it acts as a direct replacement of the stochastic simulation software of the SBTOOLBOX2

Christmas Island rock phosphate in poultry feeding trials

In Western Australia, increasing quantities of ground rock phosphate from Christmas Island are being incorporated in stock foods to increase the calcium and phosphorus content. In a previous article (Snook 1958) experiments are reported which indicate that this particular rock phosphate can be incorporated in the rations of laying hens without any apparent effect on the health or productivity of the birds

Field Theory On The World Sheet: Improvements And Generalizations

This article is the continuation of a project of investigating planar phi^3 model in various dimensions. The idea is to reformulate them on the world sheet, and then to apply the classical (meanfield) approximation, with two goals: To show that the ground state of the model is a solitonic configuration on the world sheet, and the quantum fluctuations around the soliton lead to the formation of a transverse string. After a review of some of the earlier work, we introduce and discuss several generalizations and new results. In 1+2 dimensions, a rigorous upper bound on the solitonic energy is established. A phi^4 interaction is added to stabilize the original phi^3 model. In 1+3 and 1+5 dimensions, an improved treatment of the ultraviolet divergences is given. And significantly, we show that our approximation scheme can be imbedded into a systematic strong coupling expansion. Finally, the spectrum of quantum fluctuations around the soliton confirms earlier results: In 1+2 and 1+3 dimensions, a transverse string is formed on the world sheet.Comment: 29 pages, 5 figures, several typos and eqs.(74) and (75) are corrected, a comment added to section

Fundamental studies of gas phase ionic reactions by ion mobility spectrometry

Ion mobility spectrometry (IMS) provides a promising approach to the study of gas phase ionic reactions in buffer gases at unusually high pressures. This point is illustrated here by studies of the Sn2 nucleophilic displacement reaction, Cl(-) + CH3Br yields Br + CH3Br, using IMS at atmospheric pressure. The equilibrium clustering reaction, Cl(-)(CHCI3)(n - 1) + CHCI3 yields Cl(-)(CHCI3)(n), where n = 1 and 2, and the effect of clustering on the Sn2 reaction with CH3Br have also been characterized by this IMS-based kinetic method. Present problems and anticipated improvements in the application of ion mobility spectrometry to studies of other gas phase ionic processes are discussed

Non-contrast renal magnetic resonance imaging to assess perfusion and corticomedullary differentiation in health and chronic kidney disease

AIMS Arterial spin labelling (ASL) MRI measures perfusion without administration of contrast agent. While ASL has been validated in animals and healthy volunteers (HVs), application to chronic kidney disease (CKD) has been limited. We investigated the utility of ASL MRI in patients with CKD. METHODS We studied renal perfusion in 24 HVs and 17 patients with CKD (age 22-77 years, 40% male) using ASL MRI at 3.0T. Kidney function was determined using estimated glomerular filtration rate (eGFR). T1 relaxation time was measured using modified look-locker inversion and xFB02;ow-sensitive alternating inversion recovery true-fast imaging and steady precession was performed to measure cortical and whole kidney perfusion. RESULTS T1 was higher in CKD within cortex and whole kidney, and there was association between T1 time and eGFR. No association was seen between kidney size and volume and either T1, or ASL perfusion. Perfusion was lower in CKD in cortex (136 ± 37 vs. 279 ± 69 ml/min/100 g; p < 0.001) and whole kidney (146 ± 24 vs. 221 ± 38 ml/min/100 g; p < 0.001). There was significant, negative, association between T1 longitudinal relaxation time and ASL perfusion in both the cortex (r = -0.75, p < 0.001) and whole kidney (r = -0.50, p < 0.001). There was correlation between eGFR and both cortical (r = 0.73, p < 0.01) and whole kidney (r = 0.69, p < 0.01) perfusion. CONCLUSIONS Significant differences in renal structure and function were demonstrated using ASL MRI. T1 may be representative of structural changes associated with CKD; however, further investigation is required into the pathological correlates of reduced ASL perfusion and increased T1 time in CKD

More On The Connection Between Planar Field Theory And String Theory

We continue work on the connection between world sheet representation of the planar phi^3 theory and string formation. The present article, like the earlier work, is based on the existence of a solitonic solution on the world sheet, and on the zero mode fluctuations around this solution. The main advance made in this paper is the removal of the cutoff and the transition to the continuum limit on the world sheet. The result is an action for the modes whose energies remain finite in this limit (light modes). The expansion of this action about a dense background of graphs on the world sheet leads to the formation of a string.Comment: 27 pages, 3 figure

Ensemble Sales Forecasting Study in Semiconductor Industry

Sales forecasting plays a prominent role in business planning and business strategy. The value and importance of advance information is a cornerstone of planning activity, and a well-set forecast goal can guide sale-force more efficiently. In this paper CPU sales forecasting of Intel Corporation, a multinational semiconductor industry, was considered. Past sale, future booking, exchange rates, Gross domestic product (GDP) forecasting, seasonality and other indicators were innovatively incorporated into the quantitative modeling. Benefit from the recent advances in computation power and software development, millions of models built upon multiple regressions, time series analysis, random forest and boosting tree were executed in parallel. The models with smaller validation errors were selected to form the ensemble model. To better capture the distinct characteristics, forecasting models were implemented at lead time and lines of business level. The moving windows validation process automatically selected the models which closely represent current market condition. The weekly cadence forecasting schema allowed the model to response effectively to market fluctuation. Generic variable importance analysis was also developed to increase the model interpretability. Rather than assuming fixed distribution, this non-parametric permutation variable importance analysis provided a general framework across methods to evaluate the variable importance. This variable importance framework can further extend to classification problem by modifying the mean absolute percentage error(MAPE) into misclassify error. Please find the demo code at : https://github.com/qx0731/ensemble_forecast_methodsComment: 14 pages, Industrial Conference on Data Mining 2017 (ICDM 2017

Extreme alpha-clustering in the 18O nucleus

The structure of the 18O nucleus at excitation energies above the alpha decay threshold was studied using 14C+alpha resonance elastic scattering. A number of states with large alpha reduced widths have been observed, indicating that the alpha-cluster degree of freedom plays an important role in this N not equal Z nucleus. However, the alpha-cluster structure of this nucleus is very different from the relatively simple pattern of strong alpha-cluster quasi-rotational bands in the neighboring 16O and 20Ne nuclei. A 0+ state with an alpha reduced width exceeding the single particle limit was identified at an excitation energy of 9.9+/-0.3 MeV. We discuss evidence that states of this kind are common in light nuclei and give possible explanations of this feature.Comment: 4 pages, 2 figures, 1 table. Resubmission with minor changes for clarity, including removal of one figur