Accurate and efficient spin integration for particle accelerators

Accurate spin tracking is a valuable tool for understanding spin dynamics in particle accelerators and can help improve the performance of an accelerator. In this paper, we present a detailed discussion of the integrators in the spin tracking code gpuSpinTrack. We have implemented orbital integrators based on drift-kick, bend-kick, and matrix-kick splits. On top of the orbital integrators, we have implemented various integrators for the spin motion. These integrators use quaternions and Romberg quadratures to accelerate both the computation and the convergence of spin rotations. We evaluate their performance and accuracy in quantitative detail for individual elements as well as for the entire RHIC lattice. We exploit the inherently data-parallel nature of spin tracking to accelerate our algorithms on graphics processing units.Comment: 43 pages, 17 figure

Optic neuropathy associated with systemic sarcoidosis

Objective: To identify and follow a series of 52 patients with optic neuropathy related to sarcoidosis. Methods: Prospective observational cohort study. Results: The disorder was more common in women and affected a wide age range. It was proportionately more common in African and Caribbean ethnic groups. Two clinical subtypes were identified: the more common was a subacute optic neuropathy resembling optic neuritis; a more slowly progressive optic neuropathy arose in the remaining 17%. Sixteen (31%) were bilateral. Concurrent intraocular inflammation was seen in 36%. Pain arose in only 27% of cases. An optic perineuritis was seen in 2 cases, and predominate involvement of the chiasm in one. MRI findings showed optic nerve involvement in 75% of cases, with adjacent and more widespread inflammation in 31%. Treatment with corticosteroids was helpful in those with an inflammatory optic neuropathy, but not those with mass lesions. Relapse of visual signs arose in 25% of cases, necessitating an increase or escalation of treatment, but relapse was not a poor prognostic factor. Conclusions: This is a large prospective study of the clinical characteristics and outcome of treatment in optic neuropathy associated with sarcoidosis. Patients who experience an inflammatory optic neuropathy respond to treatment but may relapse. Those with infiltrative or progressive optic neuropathies improve less well even though the inflammatory disorder responds to therapy

100 years of chemistry at Rhodes University

The history of Grahamstown is well documented and two books deal with the history of Rhodes University.1,2 Although the Chemistry Department was one of the founding departments, coverage in the official histories is minimal and sometimes inaccurate or misleading. The Rhodes University Centenary is an appropriate time to look back on some of the achievements of the department and some of its graduates over the past 100 years

Organic-Silica Interactions in Saline:Elucidating the Structural Influence of Calcium in Low-Salinity Enhanced Oil Recovery

Abstract Enhanced oil recovery using low-salinity solutions to sweep sandstone reservoirs is a widely-practiced strategy. The mechanisms governing this remain unresolved. Here, we elucidate the role of Ca2+ by combining chemical force microscopy (CFM) and molecular dynamics (MD) simulations. We probe the influence of electrolyte composition and concentration on the adsorption of a representative molecule, positively-charged alkylammonium, at the aqueous electrolyte/silica interface, for four electrolytes: NaCl, KCl, MgCl2, and CaCl2. CFM reveals stronger adhesion on silica in CaCl2 compared with the other electrolytes, and shows a concentration-dependent adhesion not observed for the other electrolytes. Using MD simulations, we model the electrolytes at a negatively-charged amorphous silica substrate and predict the adsorption of methylammonium. Our simulations reveal four classes of surface adsorption site, where the prevalence of these sites depends only on CaCl2 concentration. The sites relevant to strong adhesion feature the O− silica site and Ca2+ in the presence of associated Cl−, which gain prevalence at higher CaCl2 concentration. Our simulations also predict the adhesion force profile to be distinct for CaCl2 compared with the other electrolytes. Together, these analyses explain our experimental data. Our findings indicate in general how silica wettability may be manipulated by electrolyte concentration

Neuroimaging evidence implicating cerebellum in support of sensory/cognitive processes associated with thirst.

Recent studies implicate the cerebellum, long considered strictly a motor control structure, in cognitive, sensory, and affective phenomenon. The cerebellum, a phylogenetically ancient structure, has reciprocal ancient connections to the hypothalamus, a structure important in vegetative functions. The present study investigated whether the cerebellum was involved in vegetative functions and the primal emotions engendered by them. Using positron emission tomography, we examined the effects on the cerebellum of the rise of plasma sodium concentration and the emergence of thirst in 10 healthy adults. The correlation of regional cerebral blood flow with subjects' ratings of thirst showed major activation in the vermal central lobule. During the development of thirst, the anterior and posterior quadrangular lobule, lingula, and the vermis were activated. At maximum thirst and then during irrigation of the mouth with water to alleviate dryness, the cerebellum was less activated. However, 3 min after drinking to satiation, the anterior quadrangular lobule and posterior cerebellum were highly activated. The increased cerebellar activity was not related to motor behavior as this did not occur. Instead, responses in ancient cerebellar regions (vermis, fastigal nucleus, archicerebellum) may be more directly related to vegetative and affective aspects of thirst experiences, whereas activity in neocerebellar (posterior) regions may be related to sensory and cognitive aspects. Moreover, the cerebellum is apparently not involved in the computation of thirst per se but rather is activated during changes in thirst/satiation state when the brain is "vigilant" and is monitoring its sensory systems. Some neocerebellar activity may also reflect an intentionality for gratification by drinking inherent in the consciousness of thirst

Simultaneous genotyping and species identification using hybridization pattern recognition analysis of generic Mycobacterium DNA arrays

High-density oligonucleotide arrays can be used to rapidly examine large amounts of DNA sequence in a high throughput manner. An array designed to determine the specific nucleotide sequence of 705 bp of the rpoB gene of Mycobacterium tuberculosis accurately detected rifampin resistance associated with mutations of 44 clinical isolates of M. tuberculosis. The nucleotide sequence diversity in 121 Mycobacterial isolates (comprised of 10 species) was examined by both conventional dideoxynucleotide sequencing of the rpoB and 165 genes and by analysis of the rpoB oligonucleotide array hybridization patterns. Species identification for each of the isolates was similar irrespective of whether 16S sequence, rpoB sequence, or the pattern of rpoB hybridization was used. However, for several species, the number of alleles in the 16S and rpoB gene sequences provided discordant estimates of the genetic diversity within a species. In addition to confirming the array's intended utility for sequencing the region of M. tuberculosis that confers rifampin resistance, this work demonstrates that this array can identify the species of nontuberculous Mycobacteria. This demonstrates the general point that DNA microarrays that sequence important genomic regions (such as drug resistance or pathogenicity islands) can simultaneously identify species and provide some insight into the organism's population structure

The Novel Probes Project -- Tests of Gravity on Astrophysical Scales

The Novel Probes Project, an initiative to advance the field of astrophysical tests of the dark sector by creating a forum that connects observers and theorists, is introduced. This review focuses on tests of gravity and is intended to be of use primarily to observers, as well as theorists with an interest in the development of experimental tests. It is twinned with a separate upcoming review on dark matter self-interactions. The review focuses on astrophysical tests of gravity in the weak-field regime, ranging from stars to quasilinear cosmological scales. This regime is complementary to both strong-field tests of gravity and background and linear probes in cosmology. In particular, the nonlinear screening mechanisms that are an integral part of viable modified-gravity models lead to characteristic signatures, specifically on astrophysical scales. The potential of these probes is not limited by cosmic variance but comes with the challenge of building robust theoretical models of the nonlinear dynamics of stars, galaxies, and large-scale structure. The groundwork is laid for a thorough exploration of the weak-field, nonlinear regime, with an eye to using the current and next generation of observations for tests of gravity. The scene is set by showing how gravitational theories beyond general relativity are expected to behave, focusing primarily on screening mechanisms. Analytic and numerical techniques for exploring the relevant astrophysical regime are described, as are the pertinent observational signals. With these in hand a range of astrophysical tests of gravity are presented, and prospects for future measurements and theoretical developments are discussed

Clubbing masculinities: Gender shifts in gay men's dance floor choreographies

This is an Author's Accepted Manuscript of an article published in Journal of Homosexuality, 58(5), 608-625, 2011 [copyright Taylor & Francis], available online at: http://www.tandfonline.com/10.1080/00918369.2011.563660This article adopts an interdisciplinary approach to understanding the intersections of gender, sexuality, and dance. It examines the expressions of sexuality among gay males through culturally popular forms of club dancing. Drawing on political and musical history, I outline an account of how gay men's gendered choreographies changed throughout the 1970s, 80s, and 90s. Through a notion of “technologies of the body,” I situate these developments in relation to cultural levels of homophobia, exploring how masculine expressions are entangled with and regulated by musical structures. My driving hypothesis is that as perceptions of cultural homophobia decrease, popular choreographies of gay men's dance have become more feminine in expression. Exploring this idea in the context of the first decade of the new millennium, I present a case study of TigerHeat, one of the largest weekly gay dance club events in the United States

Simultaneous non-negative matrix factorization for multiple large scale gene expression datasets in toxicology

Non-negative matrix factorization is a useful tool for reducing the dimension of large datasets. This work considers simultaneous non-negative matrix factorization of multiple sources of data. In particular, we perform the first study that involves more than two datasets. We discuss the algorithmic issues required to convert the approach into a practical computational tool and apply the technique to new gene expression data quantifying the molecular changes in four tissue types due to different dosages of an experimental panPPAR agonist in mouse. This study is of interest in toxicology because, whilst PPARs form potential therapeutic targets for diabetes, it is known that they can induce serious side-effects. Our results show that the practical simultaneous non-negative matrix factorization developed here can add value to the data analysis. In particular, we find that factorizing the data as a single object allows us to distinguish between the four tissue types, but does not correctly reproduce the known dosage level groups. Applying our new approach, which treats the four tissue types as providing distinct, but related, datasets, we find that the dosage level groups are respected. The new algorithm then provides separate gene list orderings that can be studied for each tissue type, and compared with the ordering arising from the single factorization. We find that many of our conclusions can be corroborated with known biological behaviour, and others offer new insights into the toxicological effects. Overall, the algorithm shows promise for early detection of toxicity in the drug discovery process