A domain-specific language for the hybridization and static condensation of finite element methods

In this paper, we introduce a domain-specific language (DSL) for concisely expressing localized linear algebra on finite element tensors and its integration within a code-generation framework. This DSL is general enough to facilitate the automatic generation of element-based dense linear algebra kernels necessary for the implementation of static condensation methods and local solvers for a variety of problems. We demonstrate its use for the static condensation of continuous Galerkin problems, and systems arising from hybridizing finite element discretizations. We also describe how this DSL can be used to execute local post-processing procedures to construct superconvergent approximations to mixed problems. This work also features high-level implementations of static condensation and hybrid-mixed methods as preconditioners conforming to PETSc's interface for solving linear systems. These preconditioning interfaces provide reduced operators, which are obtained from locally assembled expressions, with the necessary context to specify full solver configurations on the resulting linear systems. We validate our implementations within the context of model second-order elliptic problems. Finally, we conclude with a performance comparison highlighting the use of a hybrid-mixed method as an efficient preconditioner in a semi-implicit method for the nonlinear rotating shallow water equations

Spud 1.0: generalising and automating the user interfaces of scientific computer models

The interfaces by which users specify the scenarios to be simulated by scientific computer models are frequently primitive, under-documented and ad-hoc text files which make using the model in question difficult and error-prone and significantly increase the development cost of the model. In this paper, we present a model-independent system, Spud, which formalises the specification of model input formats in terms of formal grammars. This is combined with an automated graphical user interface which guides users to create valid model inputs based on the grammar provided, and a generic options reading module, libspud, which minimises the development cost of adding model options. <br><br> Together, this provides a user friendly, well documented, self validating user interface which is applicable to a wide range of scientific models and which minimises the developer input required to maintain and extend the model interface

Trim17, novel E3 ubiquitin-ligase, initiates neuronal apoptosis

Accumulating data indicate that the ubiquitin-proteasome system controls apoptosis by regulating the level and the function of key regulatory proteins. In this study, we identified Trim17, a member of the TRIM/RBCC protein family, as one of the critical E3 ubiquitin ligases involved in the control of neuronal apoptosis upstream of mitochondria. We show that expression of Trim17 is increased both at the mRNA and protein level in several in vitro models of transcription-dependent neuronal apoptosis. Expression of Trim17 is controlled by the PI3K/Akt/GSK3 pathway in cerebellar granule neurons (CGN). Moreover, the Trim17 protein is expressed in vivo, in apoptotic neurons that naturally die during post-natal cerebellar development. Overexpression of active Trim17 in primary CGN was sufficient to induce the intrinsic pathway of apoptosis in survival conditions. This pro-apoptotic effect was abolished in Bax(-/-) neurons and depended on the E3 activity of Trim17 conferred by its RING domain. Furthermore, knock-down of endogenous Trim17 and overexpression of dominant-negative mutants of Trim17 blocked trophic factor withdrawal-induced apoptosis both in CGN and in sympathetic neurons. Collectively, our data are the first to assign a cellular function to Trim17 by showing that its E3 activity is both necessary and sufficient for the initiation of neuronal apoptosis. Cell Death and Differentiation (2010) 17, 1928-1941; doi: 10.1038/cdd.2010.73; published online 18 June 201

Density-dependence of functional development in spiking cortical networks grown in vitro

During development, the mammalian brain differentiates into specialized regions with distinct functional abilities. While many factors contribute to functional specialization, we explore the effect of neuronal density on the development of neuronal interactions in vitro. Two types of cortical networks, dense and sparse, with 50,000 and 12,000 total cells respectively, are studied. Activation graphs that represent pairwise neuronal interactions are constructed using a competitive first response model. These graphs reveal that, during development in vitro, dense networks form activation connections earlier than sparse networks. Link entropy analysis of dense net- work activation graphs suggests that the majority of connections between electrodes are reciprocal in nature. Information theoretic measures reveal that early functional information interactions (among 3 cells) are synergetic in both dense and sparse networks. However, during later stages of development, previously synergetic relationships become primarily redundant in dense, but not in sparse networks. Large link entropy values in the activation graph are related to the domination of redundant ensembles in late stages of development in dense networks. Results demonstrate differences between dense and sparse networks in terms of informational groups, pairwise relationships, and activation graphs. These differences suggest that variations in cell density may result in different functional specialization of nervous system tissue in vivo.Comment: 10 pages, 7 figure

Prime-Boost Vaccine Regimen for SjTPl and SjC23 Schistosome Vaccines, Increases Efficacy in Water Buffalo in a Field Trial in China

Schistosomiasis remains a serious zoonotic disease in China and the Philippines. Water buffalo and cattle account for the majority of transmission. Vaccination of water buffalo is considered a key strategy to reduce disease prevalence. Previously, we showed that vaccination of water buffalo with SjC23 or SjCTPI plasmid DNA vaccines, induced 50% efficacy to challenge infection. Here, we evaluated several parameters to determine if we can develop a two dose vaccine that maintains the efficacy of the three dose vaccine. We performed four trials evaluating: (1) lab produced vs. GLP grade vaccines, (2) varying the time between prime and boost, (3) the influence of an IL-12 adjuvant, and (4) a two dose heterologous (DNA-protein) prime-boost. We found the source of the DNA vaccines did not matter, nor did increasing the interval between prime and boost. Elimination of the IL-12 plasmid lowered homologous DNA-DNA vaccine efficacy. A major finding was that the heterologous prime boost improved vaccine efficacy, with the prime-boost regimen incorporating both antigens providing a 55% reduction in adult worms and 53% reduction in liver eggs. Vaccinated buffalo produced vaccine-specific antibody responses. These trials suggest that highly effective vaccination against schistosomes can be achieved using a two dose regimen. No adjuvants were used with the protein boost, and the potential that addition of adjuvant to the protein boost to further increase efficacy should be evaluated. These results suggest that use of these two schistosome vaccines can be part of an integrated control strategy to reduce transmission of schistosomiasis in Asia

Effect of stress relieving heat treatment on surface topography and dimensional accuracy of incrementally formed grade 1 titanium sheet parts

The forming of parts with an optimized surface roughness and high dimensional accuracy is important in many applications of incremental sheet forming (ISF). To realize this, the effect of stress relieving heat treatment of grade-1 Ti parts performed before and after forming on the surface finish and dimensional accuracy was studied. It was found that heat treatment at a temperature of 540 °C for 2 h improves the surface finish of formed parts resulting in a surface with little or no visible tool marks. Additionally, it improves the dimensional accuracy of parts after unclamping from the rig used for forming, in particular, that of parts with shallow wall angles (typically <25°). It was also noted that post-forming heat treatment improves the surface finish of parts. The surface topography of formed parts was studied using interferometry to yield areal surface roughness parameters and subsequently using secondary electron imaging. Back-scatter electron microscopy imaging results coupled with energy-dispersive X-ray (EDX) analysis showed that heat treatment prior to forming leads to tool wear as indicated by the presence of Fe in samples. Furthermore, post-forming heat treatment prevents curling up of formed parts due to compressive stresses if the formed part is trimmed

Chronic non-specific abdominal complaints in general practice: a prospective study on management, patient health status and course of complaints

BACKGROUND: While in general practice chronic non-specific abdominal complaints are common, there is insufficient data on the clinical course and the management of these complaints. Aim of this study was to present a primary care based profile of these chronic complaints including health care involvement, health status and clinical course. METHODS: Thirty general practitioners (GPs) and patients from their practices participated in a prospective follow-up study. All patients and GPs were asked to complete questionnaires at baseline and at 6, 12 and 18 months of follow-up. The GPs provided information on diagnostic and therapeutic management and on referral concerning 619 patients with chronic non-specific abdominal complaints, while 291 patients provided information about health status and clinical course of the complaints. RESULTS: When asked after 18 months of follow-up, 51,7% of the patients reported an equal or worsened severity of complaints. General health perception was impaired and patients had high scores on SCL-anxiety and SCL-depression scales. Diagnostic tests other than physical examination and laboratory tests were not frequently used. Medication was the most frequent type of treatment. The persistence of chronic non-specific abdominal complaints was quite stable. CONCLUSION: Once non-specific chronic abdominal complaints have become labelled as chronic by the attending physician, little improvement can be expected. The impact on patients' physiological and psychological well-being is large. GPs use a variety of diagnostic and therapeutic strategies. Research into the evidence base of currently applied management strategies is recommended

Higgs production in CP-violating supersymmetric cascade decays: probing the `open hole' at the Large Hadron Collider

A benchmark CP-violating supersymmetric scenario (known as 'CPX-scenario' in the literature) is studied in the context of the Large Hadron Collider (LHC). It is shown that the LHC, with low to moderate accumulated luminosity, will be able to probe the existing `hole' in the $m_{h_1}$-$\tan\beta$ plane, which cannot be ruled out by the LEP data. We explore the parameter space with cascade decay of third generation squarks and gluino with CP-violating decay branching fractions. We propose a multi-channel analysis to probe this parameter space some of which are background free at an integrated luminosity of 5-10 fb$^{-1}$. Specially, multi-lepton final states (3\l,\, 4\l and like sign di-lepton) are almost background free and have $5\sigma$ reach for the corresponding signals with very early data of LHC for both 14 TeV and 7 TeV center of mass energy.Comment: 24 pages, 9 figures, references added as in the journal versio