A Shift Selection Strategy for Parallel Shift-invert Spectrum Slicing in Symmetric Self-consistent Eigenvalue Computation

© 2020 ACM. The central importance of large-scale eigenvalue problems in scientific computation necessitates the development of massively parallel algorithms for their solution. Recent advances in dense numerical linear algebra have enabled the routine treatment of eigenvalue problems with dimensions on the order of hundreds of thousands on the world's largest supercomputers. In cases where dense treatments are not feasible, Krylov subspace methods offer an attractive alternative due to the fact that they do not require storage of the problem matrices. However, demonstration of scalability of either of these classes of eigenvalue algorithms on computing architectures capable of expressing massive parallelism is non-trivial due to communication requirements and serial bottlenecks, respectively. In this work, we introduce the SISLICE method: a parallel shift-invert algorithm for the solution of the symmetric self-consistent field (SCF) eigenvalue problem. The SISLICE method drastically reduces the communication requirement of current parallel shift-invert eigenvalue algorithms through various shift selection and migration techniques based on density of states estimation and k-means clustering, respectively. This work demonstrates the robustness and parallel performance of the SISLICE method on a representative set of SCF eigenvalue problems and outlines research directions that will be explored in future work

Tone perception in Mandarin-speaking school age children with otitis media with effusion

published_or_final_versio

A laser-induced mouse model with long-term intraocular pressure elevation

Purpose: To develop and characterize a mouse model with intraocular pressure (IOP) elevation after laser photocoagulation on the trabecular meshwork (TM), which may serve as a model to investigate the potential of stem cell-based therapies for glaucoma. Methods: IOP was measured in 281 adult C57BL/6 mice to determine normal IOP range. IOP elevation was induced unilaterally in 50 adult mice, by targeting the TM through the limbus with a 532-nm diode laser. IOP was measured up to 24 weeks post-treatment. The optic nerve damage was detected by electroretinography and assessed by semiautomatic counting of optic nerve axons. Effects of laser treatment on the TM were evaluated by histology, immunofluorescence staining, optical coherence tomography (OCT) and transmission electron microscopy (TEM). Results: The average IOP of C57BL/6 mice was 14.5±2.6 mmHg (Mean ±SD). After laser treatment, IOP averaged above 20 mmHg throughout the follow-up period of 24 weeks. At 24 weeks, 57% of treated eyes had elevated IOP with the mean IOP of 22.5±2.5 mmHg (Mean ±SED). The difference of average axon count (59.0%) between laser treated and untreated eyes was statistically significant. Photopic negative response (PhNR) by electroretinography was significantly decreased. CD45+ inflammatory cells invaded the TM within 1 week. The expression of SPARC was increased in the TM from 1 to 12 weeks. Histology showed the anterior chamber angle open after laser treatment. OCT indicated that most of the eyes with laser treatment had no synechia in the anterior chamber angles. TEM demonstrated disorganized and compacted extracellular matrix in the TM. Conclusions: An experimental murine ocular hypertension model with an open angle and optic nerve axon loss was produced with laser photocoagulation, which could be used to investigate stem cell-based therapies for restoration of the outflow pathway integrity for ocular hypertension or glaucoma. Copyright

Nonequilibrium Forces Between Neutral Atoms Mediated by a Quantum Field

We study all known and as yet unknown forces between two neutral atoms, modeled as three dimensional harmonic oscillators, arising from mutual influences mediated by an electromagnetic field but not from their direct interactions. We allow as dynamical variables the center of mass motion of the atom, its internal degrees of freedom and the quantum field treated relativistically. We adopt the method of nonequilibrium quantum field theory which can provide a first principle, systematic and unified description including the intrinsic field fluctuations and induced dipole fluctuations. The inclusion of self-consistent back-actions makes possible a fully dynamical description of these forces valid for general atom motion. In thermal equilibrium we recover the known forces -- London, van der Waals and Casimir-Polder forces -- between neutral atoms in the long-time limit but also discover the existence of two new types of interatomic forces. The first, a `nonequilibrium force', arises when the field and atoms are not in thermal equilibrium, and the second, which we call an `entanglement force', originates from the correlations of the internal degrees of freedom of entangled atoms.Comment: 16 pages, 2 figure

Developing and applying heterogeneous phylogenetic models with XRate

Modeling sequence evolution on phylogenetic trees is a useful technique in computational biology. Especially powerful are models which take account of the heterogeneous nature of sequence evolution according to the "grammar" of the encoded gene features. However, beyond a modest level of model complexity, manual coding of models becomes prohibitively labor-intensive. We demonstrate, via a set of case studies, the new built-in model-prototyping capabilities of XRate (macros and Scheme extensions). These features allow rapid implementation of phylogenetic models which would have previously been far more labor-intensive. XRate's new capabilities for lineage-specific models, ancestral sequence reconstruction, and improved annotation output are also discussed. XRate's flexible model-specification capabilities and computational efficiency make it well-suited to developing and prototyping phylogenetic grammar models. XRate is available as part of the DART software package: http://biowiki.org/DART .Comment: 34 pages, 3 figures, glossary of XRate model terminolog

Top Partner Discovery in the T→tZT\to tZ channel at the LHC

In this paper we study the discovery potential of the LHC run II for heavy vector-like top quarks in the decay channel to a top and a $Z$ boson. Despite the usually smaller branching ratio compared to charged-current decays, this channel is rather clean and allows for a complete mass reconstruction of the heavy top. The latter is achieved in the leptonic decay channel of the $Z$ boson and in the fully hadronic top channel using boosted jet and jet substructure techniques. To be as model-independent as possible, a simplified model approach with only two free parameters has been applied. The results are presented in terms of parameter space regions for $3\sigma$ evidence or $5\sigma$ discovery for such new states in that channel.Comment: 24 pages, 8 figures, version 2 updated to JHEP 01 (2015) 08

An Electronic Mach-Zehnder Interferometer

Double-slit electron interferometers, fabricated in high mobility two-dimensional electron gas (2DEG), proved to be very powerful tools in studying coherent wave-like phenomena in mesoscopic systems. However, they suffer from small fringe visibility due to the many channels in each slit and poor sensitivity to small currents due to their open geometry. Moreover, the interferometers do not function in a high magnetic field, namely, in the quantum Hall effect (QHE) regime, since it destroys the symmetry between left and right slits. Here, we report on the fabrication and operation of a novel, single channel, two-path electron interferometer that functions in a high magnetic field. It is the first electronic analog of the well-known optical Mach-Zehnder (MZ) interferometer. Based on single edge state and closed geometry transport in the QHE regime the interferometer is highly sensitive and exhibits very high visibility (62%). However, the interference pattern decays precipitously with increasing electron temperature or energy. While we do not understand the reason for the dephasing we show, via shot noise measurement, that it is not a decoherence process that results from inelastic scattering events.Comment: to appear in Natur

Site-specific incorporation of phosphotyrosine using an expanded genetic code.

Access to phosphoproteins with stoichiometric and site-specific phosphorylation status is key to understanding the role of protein phosphorylation. Here we report an efficient method to generate pure, active phosphotyrosine-containing proteins by genetically encoding a stable phosphotyrosine analog that is convertible to native phosphotyrosine. We demonstrate its general compatibility with proteins of various sizes, phosphotyrosine sites and functions, and reveal a possible role of tyrosine phosphorylation in negative regulation of ubiquitination

Fatigue evaluation in maintenance and assembly operations by digital human simulation

Virtual human techniques have been used a lot in industrial design in order to consider human factors and ergonomics as early as possible. The physical status (the physical capacity of virtual human) has been mostly treated as invariable in the current available human simulation tools, while indeed the physical capacity varies along time in an operation and the change of the physical capacity depends on the history of the work as well. Virtual Human Status is proposed in this paper in order to assess the difficulty of manual handling operations, especially from the physical perspective. The decrease of the physical capacity before and after an operation is used as an index to indicate the work difficulty. The reduction of physical strength is simulated in a theoretical approach on the basis of a fatigue model in which fatigue resistances of different muscle groups were regressed from 24 existing maximum endurance time (MET) models. A framework based on digital human modeling technique is established to realize the comparison of physical status. An assembly case in airplane assembly is simulated and analyzed under the framework. The endurance time and the decrease of the joint moment strengths are simulated. The experimental result in simulated operations under laboratory conditions confirms the feasibility of the theoretical approach

TGF-beta(2)- and H2O2-Induced Biological Changes in Optic Nerve Head Astrocytes Are Reduced by the Antioxidant Alpha-Lipoic Acid

Background/Aims: The goal of the present study was to determine whether transforming growth factor-beta(2) (TGF-beta(2))- and oxidative stress-induced cellular changes in cultured human optic nerve head (ONH) astrocytes could be reduced by pretreatment with the antioxidant alpha-lipoic acid (LA). Methods: Cultured ONH astrocytes were treated with 1.0 ng/ml TGF-beta(2) for 24 h or 200 mu M hydrogen peroxide (H2O2) for 1 h. Lipid peroxidation was measured by a decrease in cis-pari-naric acid fluorescence. Additionally, cells were pretreated with different concentrations of LA before TGF-beta 2 or H2O2 exposure. Expressions of the heat shock protein (Hsp) alpha B-crystallin and Hsp27, the extracellular matrix (ECM) component fibronectin and the ECM-modulating protein connective tissue growth factor (CTGF) were examined with immunohistochemistry and real-time PCR analysis. Results: Both TGF-beta(2) and H2O2 increased lipid peroxidation. Treatment of astrocytes with TGF-beta(2) and H2O2 upregulated the expression of alpha B-crystallin, Hsp27, fibronectin and CTGF. Pretreatment with different concentrations of LA reduced the TGF-beta(2)- and H2O2-stimulated gene expressions. Conclusion: We showed that TGF-beta(2)- and H2O2-stimulated gene expressions could be prevented by pretreatment with the antioxidant LA in cultured human ONH astrocytes. Therefore, it is tempting to speculate that the use of antioxidants could have protective effects in glaucomatous optic neuropathy. Copyright (C) 2012 S. Karger AG, Base