Algebraic computing in general relativity and supergravity : space-time embeddings and higher dimensional theories

Imperial Users onl

A Fast Parallel Poisson Solver on Irregular Domains Applied to Beam Dynamic Simulations

We discuss the scalable parallel solution of the Poisson equation within a Particle-In-Cell (PIC) code for the simulation of electron beams in particle accelerators of irregular shape. The problem is discretized by Finite Differences. Depending on the treatment of the Dirichlet boundary the resulting system of equations is symmetric or `mildly' nonsymmetric positive definite. In all cases, the system is solved by the preconditioned conjugate gradient algorithm with smoothed aggregation (SA) based algebraic multigrid (AMG) preconditioning. We investigate variants of the implementation of SA-AMG that lead to considerable improvements in the execution times. We demonstrate good scalability of the solver on distributed memory parallel processor with up to 2048 processors. We also compare our SAAMG-PCG solver with an FFT-based solver that is more commonly used for applications in beam dynamics

Meristem Tip Culture for In Vitro Eradication of Grapevine Leaf Roll-associated Virus-1 (GLRaV-1) and Grapevine Fan Leaf Virus (GFLV) from Infected Flame Seedless Grapevine Plantlets

Grapevine (Vitis vinifera cv. Flame Seedless) was found infected with viral diseases; showing thicker leaves than normal, brittle, with margins rolled downwards and yellowish, which were identified as Grapevine Leaf roll-associated Virus-1 (GLRaV-1). Other symptoms were observed on leaves. The infected leaves showed malformation with abnormal gather primary veins, giving the leaf the appearance of an open fan, including yellowing and mosaic pattern on leaves, or bright yellow bands along major veins. Fan-shaped leaves were associated with mosaic or vein banding symptoms, these observations were identified as Grapevine Fan leaf Virus (GFLV). Both viruses were detected using Double Antibody Sandwich – Enzyme Linked Immuno Sorbent Assay (DAS-ELISA) and Reverse Transcription-Polymerase Chain Reaction (RT-PCR). The use of tissue culture was investigated as a mean to eliminate the two viruses. Virus-free plants were produced within six months using meristem tip culture. Woody plant (WP) medium supplied with benzyl amino purine BAP (4.44 µM) was used for shoot proliferation, and indole butyric acid IBA (0.2 µM) for plantlets rooting. Before acclimatization, the plantlets were submitted to DAS-ELISA and RT-PCR in order to evaluate virus eradication. GLRaV-1 and GFLV free plants (95 and 90 %, respectively) were obtained from the optimum size (0.5 mm) of meristem tips (as indexed by DAS-ELISA). Of these, 82.5 and 75 % plants were found negative for GLRaV-1 and GFLV, respectively, as diagnosed by RT-PCR. RT-PCR and meristem tip culture were found to be reliable methods for virus indexing and elimination of GLRaV-1 and GFLV

Factors Defining the Functional Oligomeric State of Escherichia coli DegP Protease

Escherichia coli DegP protein is a periplasmic protein that functions both as a protease and as a chaperone. In the absence of substrate, DegP oligomerizes as a hexameric cage but in its presence DegP reorganizes into 12 and 24-mer cages with large chambers that house the substrate for degradation or refolding. Here, we studied the factors that determine the oligomeric state adopted by DegP in the presence of substrate. Using size exclusion chromatography and electron microscopy, we found that the size of the substrate molecule is the main factor conditioning the oligomeric state adopted by the enzyme. Other factors such as temperature, a major regulatory factor of the activity of this enzyme, did not influence the oligomeric state adopted by DegP. In addition, we observed that substrate concentration exerted an effect only when large substrates (full-length proteins) were used. However, small substrate molecules (peptides) always triggered the same oligomeric state regardless of their concentration. These results clarify important aspects of the regulation of the oligomeric state of DegP

Venous thrombosis in immunocompetent patients with acute cytomegalovirus infection: a complication that may be underestimated

In the present study, we retrospectively studied clinical and laboratory findings associated with cytomegalovirus (CMV) infection in immunocompetent patients. We focused on severe CMV infection. Among 38 patients, five had a severe form of infection: one had meningitis, one had symptomatic thrombocytopenia and three had venous thromboses with pulmonary embolism, a rarely described complication. CMV-induced thrombosis has been reported in immunocompromised patients such as transplant recipients and patients with AIDS. Recent case reports have also described thrombotic phenomena in immunocompetent patients with CMV infection. Our study suggests that venous thrombosis during acute CMV infection is an underestimated complication

Time-varying time-frequency complexity measures for epileptic EEG data analysis

Objective: Our goal is to use existing and to propose new time-frequency entropy measures that objectively evaluate the improvement on epileptic patients after medication by studying their resting state EEG recordings. An increase in the complexity of the signals would confirm an improvement in the general state of the patient. Methods: We review the Rényi entropy based on time-frequency representations, along with its time-varying version. We also discuss the entropy based on singular value decomposition computed from a time-frequency representation, and introduce its corresponding time-dependant version. We test these quantities on synthetic data. Friedman tests are used to confirm the differences between signals (before and after proper medication). Principal component analysis is used for dimensional reduction prior to a simple threshold discrimination. Results: Experimental results show a consistent increase in complexity measures in the different regions of the brain. These findings suggest that extracted features can be used to monitor treatment. When combined, they are useful for classification purposes, with areas under ROC curves higher than 0.93 in some regions. Conclusion: Here we applied time-frequency complexity measures to resting state EEG signals from epileptic patients for the first time. We also introduced a new time-varying complexity measure. We showed that these features are able to evaluate the treatment of the patient, and to perform classification. Significance: The time-frequency complexities, and their time-varying versions, can be used to monitor the treatment of epileptic patients. They could be applied to a wider range of problems

A new approach to sample entropy of multi-channel signals: application to EEG signals

In this paper, we propose a new algorithm to calculate sample entropy of multivariate data. Over the existing method, the one proposed here has the advantage of maintaining good results as the number of channels increases. The new and already-existing algorithms were applied on multivariate white Gaussian noise signals, pink noise signals, and mixtures of both. For high number of channels, the existing method failed to show that white noise is always the most irregular whereas the proposed method always had the entropy of white noise the highest. Application of both algorithms on MIX process signals also confirmed the ability of the proposed method to handle larger number of channels without risking erroneous results. We also applied the proposed algorithm on EEG data from epileptic patients before and after treatments. The results showed an increase in entropy values after treatment in the regions where the focus was localized. This goes in the same way as the medical point of view that indicated a better health state for these patients

Human neutrophil clearance of bacterial pathogens triggers anti-microbial gamma delta T cell responses in early infection

Human blood Vc9/Vd2 T cells, monocytes and neutrophils share a responsiveness toward inflammatory chemokines and are rapidly recruited to sites of infection. Studying their interaction in vitro and relating these findings to in vivo observations in patients may therefore provide crucial insight into inflammatory events. Our present data demonstrate that Vc9/Vd2 T cells provide potent survival signals resulting in neutrophil activation and the release of the neutrophil chemoattractant CXCL8 (IL-8). In turn, Vc9/Vd2 T cells readily respond to neutrophils harboring phagocytosed bacteria, as evidenced by expression of CD69, interferon (IFN)-c and tumor necrosis factor (TNF)-a. This response is dependent on the ability of these bacteria to produce the microbial metabolite (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate (HMB-PP), requires cell-cell contact of Vc9/Vd2 T cells with accessory monocytes through lymphocyte function-associated antigen-1 (LFA-1), and results in a TNF-a dependent proliferation of Vc9/Vd2 T cells. The antibiotic fosmidomycin, which targets the HMB-PP biosynthesis pathway, not only has a direct antibacterial effect on most HMB-PP producing bacteria but also possesses rapid anti-inflammatory properties by inhibiting cd T cell responses in vitro. Patients with acute peritoneal-dialysis (PD)-associated bacterial peritonitis – characterized by an excessive influx of neutrophils and monocytes into the peritoneal cavity – show a selective activation of local Vc9/Vd2 T cells by HMB-PP producing but not by HMB-PP deficient bacterial pathogens. The cd T celldriven perpetuation of inflammatory responses during acute peritonitis is associated with elevated peritoneal levels of cd T cells and TNF-a and detrimental clinical outcomes in infections caused by HMB-PP positive microorganisms. Taken together, our findings indicate a direct link between invading pathogens, neutrophils, monocytes and microbe-responsive cd T cells in early infection and suggest novel diagnostic and therapeutic approaches.Martin S. Davey, Chan-Yu Lin, Gareth W. Roberts, Sinéad Heuston, Amanda C. Brown, James A. Chess, Mark A. Toleman, Cormac G.M. Gahan, Colin Hill, Tanya Parish, John D. Williams, Simon J. Davies, David W. Johnson, Nicholas Topley, Bernhard Moser and Matthias Eber

Effects of deletion of the Streptococcus pneumoniae lipoprotein diacylglyceryl transferase gene lgt on ABC transporter function and on growth in vivo

Lipoproteins are an important class of surface associated proteins that have diverse roles and frequently are involved in the virulence of bacterial pathogens. As prolipoproteins are attached to the cell membrane by a single enzyme, prolipoprotein diacylglyceryl transferase (Lgt), deletion of the corresponding gene potentially allows the characterisation of the overall importance of lipoproteins for specific bacterial functions. We have used a Δlgt mutant strain of Streptococcus pneumoniae to investigate the effects of loss of lipoprotein attachment on cation acquisition, growth in media containing specific carbon sources, and virulence in different infection models. Immunoblots of triton X-114 extracts, flow cytometry and immuno-fluorescence microscopy confirmed the Δlgt mutant had markedly reduced lipoprotein expression on the cell surface. The Δlgt mutant had reduced growth in cation depleted medium, increased sensitivity to oxidative stress, reduced zinc uptake, and reduced intracellular levels of several cations. Doubling time of the Δlgt mutant was also increased slightly when grown in medium with glucose, raffinose and maltotriose as sole carbon sources. These multiple defects in cation and sugar ABC transporter function for the Δlgt mutant were associated with only slightly delayed growth in complete medium. However the Δlgt mutant had significantly reduced growth in blood or bronchoalveolar lavage fluid and a marked impairment in virulence in mouse models of nasopharyngeal colonisation, sepsis and pneumonia. These data suggest that for S. pneumoniae loss of surface localisation of lipoproteins has widespread effects on ABC transporter functions that collectively prevent the Δlgt mutant from establishing invasive infection