Massively parallel approximate Gaussian process regression

We explore how the big-three computing paradigms -- symmetric multi-processor (SMC), graphical processing units (GPUs), and cluster computing -- can together be brought to bare on large-data Gaussian processes (GP) regression problems via a careful implementation of a newly developed local approximation scheme. Our methodological contribution focuses primarily on GPU computation, as this requires the most care and also provides the largest performance boost. However, in our empirical work we study the relative merits of all three paradigms to determine how best to combine them. The paper concludes with two case studies. One is a real data fluid-dynamics computer experiment which benefits from the local nature of our approximation; the second is a synthetic data example designed to find the largest design for which (accurate) GP emulation can performed on a commensurate predictive set under an hour.Comment: 24 pages, 6 figures, 1 tabl

Complexity in dislocation dynamics: model

We propose a numerical model to study the viscoplastic deformation of ice single crystals. We consider long-range elastic interactions among dislocations, the possibility of mutual annihilation, and a multiplication mechanism representing the activation of Frank-Read sources due to dislocation pinning. The overdamped equations of motion for a collection of dislocations are integrated numerically using different externally applied stresses. Using this approach we analyze the avalanche-like rearrangements of dislocations during the dynamic evolution. We observe a power law distribution of avalanche sizes which we compare with acoustic emission experiments in ice single crystals under creep deformation. We emphasize the connections of our model with non-equilibrium phase transitions and critical phenomena

The Cell-Cycle Regulatory Protein p21CIP1/WAF1 Is Required for Cytolethal Distending Toxin (Cdt)-Induced Apoptosis.

The Aggregatibacter actinomycetemcomitans cytolethal distending toxin (Cdt) induces lymphocytes to undergo cell-cycle arrest and apoptosis; toxicity is dependent upon the active Cdt subunit, CdtB. We now demonstrate that p21CIP1/WAF1 is critical to Cdt-induced apoptosis. Cdt induces increases in the levels of p21CIP1/WAF1 in lymphoid cell lines, Jurkat and MyLa, and in primary human lymphocytes. These increases were dependent upon CdtB's ability to function as a phosphatidylinositol (PI) 3,4,5-triphosphate (PIP3) phosphatase. It is noteworthy that Cdt-induced increases in the levels of p21CIP1/WAF1 were accompanied by a significant decline in the levels of phosphorylated p21CIP1/WAF1. The significance of Cdt-induced p21CIP1/WAF1 increase was assessed by preventing these changes with a two-pronged approach; pre-incubation with the novel p21CIP1/WAF1 inhibitor, UC2288, and development of a p21CIP1/WAF1-deficient cell line (Jurkatp21-) using clustered regularly interspaced short palindromic repeats (CRISPR)/cas9 gene editing. UC2288 blocked toxin-induced increases in p21CIP1/WAF1, and JurkatWT cells treated with this inhibitor exhibited reduced susceptibility to Cdt-induced apoptosis. Likewise, Jurkatp21- cells failed to undergo toxin-induced apoptosis. The linkage between Cdt, p21CIP1/WAF1, and apoptosis was further established by demonstrating that Cdt-induced increases in levels of the pro-apoptotic proteins Bid, Bax, and Bak were dependent upon p21CIP1/WAF1 as these changes were not observed in Jurkatp21- cells. Finally, we determined that the p21CIP1/WAF1 increases were dependent upon toxin-induced increases in the level and activity of the chaperone heat shock protein (HSP) 90. We propose that p21CIP1/WAF1 plays a key pro-apoptotic role in mediating Cdt-induced toxicity

Wildfire as a natural stressor and its effect on female phenotype and ornament development

Controlled low-intensity fires are commonly used in ecosystem management for both habitat restoration and wildfire management. Animals in those ecosystems may respond to fire by shifting energy allocation away from reproduction and growth, and toward maintenance. Stress-induced shifts in energy allocation may affect the expression of condition-dependent sexual signals, which are sensitive to energetic and physiological trade-offs mediated by glucocorticoids. Here, we examine the effect of fire on ornament expression, corticosterone, and other phenotypic traits in a population of striped plateau lizards, Sceloporus virgatus, affected by the Horseshoe 2 Fire in the Chiricahua Mountains, Arizona, USA. The condition-dependent female ornament was significantly smaller the month following the fire than 2 years prior and was both smaller and less orange on the burned site relative to a nearby unburned site. These patterns are similar to those found in a previous experimental study examining the response of the ornament to corticosterone manipulations. Yet, in the current study, corticosterone levels were not different in lizards on the burned and unburned sites. Perhaps glucocorticoid levels already returned to baseline, or do not adequately track environmental change. Females tended to be smaller and lighter on the burned site than the unburned site; however, the year after the fire, body condition was higher for females on the burned site, indicating a rapid recovery and potential long-term benefits in response to low-intensity fires in this fire-adapted ecosystem. We found that the lizards adjusted energy allocation away from sexual signaling and growth in response to low-intensity fires. As fires and fire management are likely to increase in response to changing fire regimes across the globe, it will be important to consider behavioral and physiological responses of impacted species, as well as population-, community-, and ecosystem-level responses

Bell-state preparation for electron spins in a semiconductor double quantum dot

A robust scheme for state preparation and state trapping for the spins of two electrons in a semiconductor double quantum dot is presented. The system is modeled by two spins coupled to two independent bosonic reservoirs. Decoherence effects due to this environment are minimized by application of optimized control fields which make the target state to the ground state of the isolated driven spin system. We show that stable spin entanglement with respect to pure dephasing is possible. Specifically, we demonstrate state trapping in a maximally entangled state (Bell state) in the presence of decoherence.Comment: 9 pages, 4 figure

Loeb Extension and Loeb Equivalence

In Keisler and Sun (2004), the authors raise several open problems on Loeb equivalences between various internal probability spaces. We provide counter-examples for the first two open problems. Moreover, we reduce the third open problem to the following question: Is the internal algebra generated by the union of two Loeb equivalent internal algebras a subset of the Loeb extension of any one of the internal algebra?Comment: 10 page

Accurate preoperative diagnosis of pericardial constriction using cine computed tomography

AbstractObjectives. The purpose of this study was to determine the accuracy of cine computed tomography in the diagnosis of constrictive pericarditis.Background. Constrictive pericarditis is characterized by abnormalities of both cardiac structure and function. Accurate diagnosis requires detection of both a thickened pericardium and abnormal ventricular diastolic filling. At present, no one diagnostic technique has demonstrated sufficient accuracy in this setting. Cine computed tomography is a relatively new cardiac imaging mode with very high time and spatial resolution that has the potential to accurately diagnose constrictive pericarditis.Methods. Twelve consecutive patients were retrospectively identified who had catheterization findings suggestive of constrictive physiology, had undergone a cine computed tomographic examination and had pathologic data that delineated the status of the pericardium. Group 1 (with constrictive pericarditis; n = 5) had surgical confirmation of thickened pericardium and improved clinically after pericardiectomy. Group 2 (no constrictive pericarditis; n = 7) had cardiomyopathy with normal pericardium. Seven normal volunteers (Group 3) were also studied. Cine computed tomograms were obtained for the entire heart (8-mm slices, 17 frames/s, nonionic contrast medium). Pericardial thickness was measured at 10 ° intervals at three ventricular levels in each subject. The rapidity of diastolic filling was assessed by calculating the percent filling fraction in early diastole.Results. Pericardial thickness was 10 ± 2 mm (mean ± SD) in Group 1, 2 ± 1 mm in Group 2 and 1 ± 1 mm in Group 3 (p < 0.05, constrictive pericarditis vs. no constrictive pericarditis). Left ventricular filling fraction was 83 ± 6% in Group 1, 62 ± 9% in Group 2 and 44 ± 5% in Group 3. Right ventricular filling fraction was 93 ± 5% in Group 1, 62 ± 14% in Group 2 and 35 ± 6% in Group 3 (p < 0.05, Group 1 vs. Groups 2 and 3). Both indexes provided a clear-cut distinction between patients with and without constriction.Conclusions. Cine computed tomography simultaneously provides both anatomic and physiologic data that allow accurate preoperative diagnosis of pericardial constriction

Exact solution of a model of qubit dephasing due to telegraph noise

We present a general and exact formalism for finding the evolution of a quantum system subject to external telegraph noise. The various qubit decoherence rates are determined by the eigenvalues of a transfer matrix. The formalism can be applied to a qubit subject to an arbitrary combination of dephasing and relaxational telegraph noise, in contrast to existing non-perturbative methods that treat only one or the other of these limits. We present 3 applications: 1) We obtain the full qubit dynamics on time scales short compared with the enviromental correlation times. In the strong coupling cases this reveals unexpected oscillations and induced magnetization components; 2) We find in strong coupling case strong violations of the widely used relation 1/T$_2$ = 1/2T$_1$ + 1/T$_{\phi}$, which is a result of perturbation theory; 3) We discuss the effects of bang-bang and spin-echo controls of the qubit dynamics in general settings of the telegraph noises. %The result shows that these methods are not very effective in %reducing decoherence arising from a single telegraph noise. Finally, we discuss the extension of the method to the cases of many telegraph noise sources and multiple qubits. The method still works when white noise is also present.Comment: 7 pages, 6 figures, revised and extende