Fast Solvers for Models of Fluid Flow with Spectral Elements

We introduce a preconditioning technique based on Domain Decomposition and the Fast Diagonalization Method that can be applied to tensor product based discretizations of the steady convection-diffusion and the linearized Navier-Stokes equations. The method is based on iterative substructuring where fast diagonalization is used to efficiently eliminate the interior degrees of freedom and subsidiary subdomain solves. We demonstrate the effectiveness of this preconditioner in numerical simulations using a spectral element discretization. This work extends the use of Fast Diagonalization to steady convection-diffusion systems. We also extend the "least-squares commutator" preconditioner, originally developed for the finite element method, to a matrix-free spectral element framework. We show that these two advances, when used together, allow for efficient computation of steady-state solutions the the incompressible Navier-Stokes equations using high-order spectral element discretizations

Simplifying gene trees for easier comprehension

BACKGROUND: In the genomic age, gene trees may contain large amounts of data making them hard to read and understand. Therefore, an automated simplification is important. RESULTS: We present a simplification tool for gene trees called TreeSimplifier. Based on species tree information and HUGO gene names, it summarizes "monophyla". These monophyla correspond to subtrees of the gene tree where the evolution of a gene follows species phylogeny, and they are simplified to single leaves in the gene tree. Such a simplification may fail, for example, due to genes in the gene tree that are misplaced. In this way, misplaced genes can be identified. Optionally, our tool glosses over a limited degree of "paraphyly" in a further simplification step. In both simplification steps, species can be summarized into groups and treated as equivalent. In the present study we used our tool to derive a simplified tree of 397 leaves from a tree of 1138 leaves. Comparing the simplified tree to a "cartoon tree" created manually, we note that both agree to a high degree. CONCLUSION: Our automatic simplification tool for gene trees is fast, accurate, and effective. It yields results of similar quality as manual simplification. It should be valuable in phylogenetic studies of large protein families. The software is available at

Poisson geometry and first integrals of geostrophic equations

We describe first integrals of geostrophic equations, which are similar to the enstrophy invariants of the Euler equation for an ideal incompressible fluid. We explain the geometry behind this similarity, give several equivalent definitions of the Poisson structure on the space of smooth densities on a symplectic manifold, and show how it can be obtained via the Hamiltonian reduction from a symplectic structure on the diffeomorphism group.Comment: 6 pages, to appear in Physica

The HABP2 G534E polymorphism does not increase nonmedullary thyroid cancer risk in Hispanics.

Familial nonmedullary thyroid cancer (NMTC) has not been clearly linked to causal germline variants, despite the large role that genetic factors play in risk. Recently, HABP2 G534E (rs7080536A) has been implicated as a causal variant in NMTC. We have previously shown that the HABP2 G534E variant is not associated with TC risk in patients from the British Isles. Hispanics are the largest and the youngest minority in the United States and NMTC is now the second most common malignancy in women from this population. In order to determine if the HABP2 G534E variant played a role in NMTC risk among Hispanic populations, we analyzed 281 cases and 1105 population-matched controls from a multicenter study in Colombia, evaluating the association through logistic regression. We found that the HABP2 G534E variant was not significantly associated with NMTC risk (P=0.843) in this Hispanic group. We also stratified available clinical data by multiple available clinicopathological variables and further analyzed the effect of HABP2 on NMTC presentation. However, we failed to detect associations between HABP2 G534E and NMTC risk, regardless of disease presentation (P≥0.273 for all cases). Therefore, without any significant associations between the HABP2 G534E variant and NMTC risk, we conclude that the variant is not causal of NMTC in this Hispanic population

Computer memories: the history of computer form

This paper looks at the computer as a truly global form. The similar beige boxes found in offices across the world are analysed from the perspective of design history rather than that of the history of science and technology. Through the exploration of an archive of computer manufacturer's catalogues and concurrent design texts, this paper examines the changes that have occurred in the production and consumption of the computer in the context of the workplace, from its inception as a room-sized mainframe operated through a console of flashing lights, to the personal computer as a 'universal' form, reproduced by many manufacturers. It shows how the computer in the past has been as diverse as any other product, and asks how and why it now appears as a standardised, sanitised object. In doing so our relationship with the office computer, past and present is explored, revealing a complex history of vicissitude.</p

Interaction of Serum- and Glucocorticoid Regulated Kinase 1 (SGK1) with the WW-Domains of Nedd4-2 Is Required for Epithelial Sodium Channel Regulation

The epithelial sodium channel (ENaC) is an integral component of the pathway for Na(+) absorption in epithelial cells. The ubiquitin ligases Nedd4 and Nedd4-2 bind to ENaC and decrease its activity. Conversely, Serum- and Glucocorticoid regulated Kinase-1 (SGK1), a downstream mediator of aldosterone, increases ENaC activity. This effect is at least partly mediated by direct interaction between SGK and Nedd4-2. SGK binds both Nedd4 and Nedd4-2, but it is only able to phosphorylate Nedd4-2. Phosphorylation of Nedd4-2 reduces its ability to bind to ENaC, due to the interaction of phosphorylated Nedd4-2 with 14-3-3 proteins, and hence increases ENaC activity. WW-domains in Nedd4-like proteins bind PY-motifs (PPXY) present in ENaC subunits, and SGK also has a PY-motif.Here we show that single or tandem WW-domains of Nedd4 and Nedd4-2 mediate binding to SGK and that different WW-domains of Nedd4 and Nedd4-2 are involved. Our data also show that WW-domains 2 and 3 of Nedd4-2 mediate the interaction with SGK in a cooperative manner, that activated SGK has increased affinity for the WW-domains of Nedd4-2 in vitro, and a greater stimulatory effect on ENaC Na(+) transport compared to wildtype SGK. Further, SGK lacking a PY motif failed to stimulate ENaC activity in the presence of Nedd4-2.Binding of Nedd4-2 WW-domains to SGK is necessary for SGK-induced ENaC activity

Generalized Ricci Curvature Bounds for Three Dimensional Contact Subriemannian manifolds

Measure contraction property is one of the possible generalizations of Ricci curvature bound to more general metric measure spaces. In this paper, we discover sufficient conditions for a three dimensional contact subriemannian manifold to satisfy this property.Comment: 49 page

Eye Care Providers' Attitudes Towards Tele-ophthalmology

Background: The rapid rise of e-health and remote care systems will likely change the practice patterns of ophthalmologists. Although telemedicine practices are thriving in many specialties of medicine, telemedicine for ophthalmology has been limited primarily to asynchronous care for diabetic retinopathy. The goal of this research was to evaluate perspectives on and familiarity with telemedicine among eye care providers at a large tertiary-care medical center via an anonymous, descriptive survey. Results: In total, 58 eye care physicians completed surveys (response rates of 86% for physicians-in-training and 49% for faculty physicians, respectively). Although a majority of both faculty and physicians-in-training were willing to participate in telemedicine services, trainees were more likely to be willing to interpret photographs than faculty (p=0.04). Most respondents (71%) indicated that they did not use telemedicine. Over half had received photographs (via phone or e-mail) for interpretation from referring physicians (54%) or patients (56%) within the past 3 months. A majority of providers (82%) would be willing to participate in telemedicine for consultations and for interpreting photographs, but a majority (59%) had low confidence in remote care for providing an opinion on patient care. Conclusions: Most eye care providers viewed telemedicine as part of the future of eye care but were concerned about the use of telemedicine. Although most providers did not practice telemedicine, over half of them were comfortable managing eye care consultations (including patients' photographs) via the Internet.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/140282/1/tmj.2014.0115.pd

A critical review of the Exit-Voice-Loyalty-Neglect literature: limitations, key challenges and directions for future research

The study of human behaviour holds a prominent role in organizational behavior literature. For almost 45 years, the exit, voice, loyalty and neglect typology has attracted scholars' interest and has been linked to employee responses towards dissatisfaction and problematic events in the workplace. This paper reviews the literature and identifies and addresses key theoretical and methodological deficiencies that the exit, voice, loyalty and neglect typology faces that have been either ignored or undeveloped. Moreover, by unpicking this typology as currently portrayed in the existing literature, it proposes key challenges that need to be addressed and provides directions for future research

Down Syndrome: Age-Dependence of PiB Binding in Postmortem Frontal Cortex Across the Lifespan

Beta-amyloid (Aβ) deposition in brain accumulates as a function of age in people with Down syndrome (DS) with subsequent development into Alzheimer disease neuropathology, typically by 40 years of age. In vivo imaging using the Pittsburgh Compound B (PiB) ligand has facilitated studies linking Aβ, cognition, and dementia in DS. However, there are no studies of PiB binding across the lifespan in DS. The current study describes in vitro 3H-PiB binding in the frontal cortex of autopsy cases with DS compared to non-DS controls. Tissue from 64 cases included controls (N=25) and DS (N=39). In DS, 3H-PiB binding was significantly associated with age. After age 40 years in DS, 3H-PiB binding rose dramatically along with increasing individual variability. 3H-PiB binding correlated with the amount of Aβ42. Using fixed frontal tissue and fluorescent 6-CN-PiB, neuritic and cored plaques along with extensive cerebral amyloid angiopathy (CAA) showed 6-CN-PiB binding. These results suggest that cortical PiB binding as shown by positron emission tomography imaging reflects plaques and CAA in DS brain