Measurement of the LCG2 and glite file catalogue's performance

When the Large Hadron Collider (LHC) begins operation at CERN in 2007 it will produce data in volumes never before seen. Physicists around the world will manage, distribute and analyse petabytes of this data using the middleware provided by the LHC Computing Grid. One of the critical factors in the smooth running of this system is the performance of the file catalogues which allow users to access their files with a logical filename without knowing their physical location. This paper presents a detailed study comparing the performance and respective merits and shortcomings of two of the main catalogues: the LCG File Catalogue and the gLite FiReMan catalogue

The role of HER1-HER4 and EGFRvIII in hormone-refractory prostate cancer

<b>Purpose</b>: The role of the type I receptor tyrosine kinase (HER) family in progression of prostate cancer is controversial. Breast cancer studies show that these receptors should be investigated as a family. The current study investigates expression of HER1-HER4 and EGFRvIII in matched hormone-sensitive and hormone-refractory prostate tumors. <b>Experimental Design</b>: Immunohistochemical analysis was used to investigate protein expression of HER1-HER4, EGFRvIII, and phosphorylated Akt (pAkt) in matched hormone-sensitive and hormone-refractory prostate tumors. <b>Results</b>: Surprisingly, high HER2 membrane expression in hormone-sensitive tumors was associated with an increased time to biochemical relapse (<i>P</i> = 0.0003), and this translated into longer overall survival (<i>P</i> = 0.0021). Consistent with other studies, HER4 membrane expression in hormone-sensitive tumors was associated with longer time to biochemical relapse (<i>P</i> = 0.042), and EGFRvIII membrane expression was associated with shorter time to biochemical relapse (<i>P</i> = 0.015). An increase in pAkt expression was associated with reduced survival (<i>P</i> = 0.0098). Multivariate analysis showed that HER2 was an independent positive predictive marker of time to relapse in hormone-sensitive prostate tumors (<i>P</i> = 0.014). In contrast, high HER2 expression in hormone-refractory tumors was associated with decreased time to death from biochemical relapse (<i>P</i> = 0.039), and EGFRvIII nuclear expression was associated with decreased time to death from biochemical relapse and decreased overall survival (<i>P</i> = 0.02 and <i>P</i> = 0.005). <b>Conclusion</b>: These results suggest that the HER family may have multiple roles in prostate cancer, and that expression of the proteins alone is insufficient to predict the biological response that they may elicit

Van der Waals Frictional Drag induced by Liquid Flow in Low- Dimensional Systems

We study the van der Waals frictional drag force induced by liquid flow in low-dimensional systems (2D and 1D electron systems, and 2D and 1D channels with liquid). We find that for both 1D and 2D systems, the frictional drag force induced by liquid flow may be several orders of magnitude larger than the frictional drag induced by electronic current.Comment: 10 pages, 4 figure

Selection from read-only memory with limited workspace

Given an unordered array of $N$ elements drawn from a totally ordered set and an integer $k$ in the range from $1$ to $N$, in the classic selection problem the task is to find the $k$-th smallest element in the array. We study the complexity of this problem in the space-restricted random-access model: The input array is stored on read-only memory, and the algorithm has access to a limited amount of workspace. We prove that the linear-time prune-and-search algorithm---presented in most textbooks on algorithms---can be modified to use $\Theta(N)$ bits instead of $\Theta(N)$ words of extra space. Prior to our work, the best known algorithm by Frederickson could perform the task with $\Theta(N)$ bits of extra space in $O(N \lg^{*} N)$ time. Our result separates the space-restricted random-access model and the multi-pass streaming model, since we can surpass the $\Omega(N \lg^{*} N)$ lower bound known for the latter model. We also generalize our algorithm for the case when the size of the workspace is $\Theta(S)$ bits, where $\lg^3{N} \leq S \leq N$. The running time of our generalized algorithm is $O(N \lg^{*}(N/S) + N (\lg N) / \lg{} S)$, slightly improving over the $O(N \lg^{*}(N (\lg N)/S) + N (\lg N) / \lg{} S)$ bound of Frederickson's algorithm. To obtain the improvements mentioned above, we developed a new data structure, called the wavelet stack, that we use for repeated pruning. We expect the wavelet stack to be a useful tool in other applications as well.Comment: 16 pages, 1 figure, Preliminary version appeared in COCOON-201

Absolute quantification of the host-to-parasite DNA ratio in Theileria parva-infected lymphocyte cell lines

Theileria parva is a tick-transmitted intracellular apicomplexan pathogen of cattle in sub-Saharan Africa that causes East Coast fever (ECF). ECF is an acute fatal disease that kills over one million cattle annually, imposing a tremendous burden on African small-holder cattle farmers. The pathology and level of T. parva infections in its wildlife host, African buffalo (Syncerus caffer), and in cattle are distinct. We have developed an absolute quantification method based on quantitative PCR (qPCR) in which recombinant plasmids containing single copy genes specific to the parasite (apical membrane antigen 1 gene, ama1) or the host (hypoxanthine phosphoribosyltransferase 1, hprt1) are used as the quantification reference standards. Our study shows that T. parva and bovine cells are present in similar numbers in T. parva-infected lymphocyte cell lines and that consequently, due to its much smaller genome size, T. parva DNA comprises between 0.9% and 3% of the total DNA samples extracted from these lines. This absolute quantification assay of parasite and host genome copy number in a sample provides a simple and reliable method of assessing T. parva load in infected bovine lymphocytes, and is accurate over a wide range of host-to-parasite DNA ratios. Knowledge of the proportion of target DNA in a sample, as enabled by this method, is essential for efficient high-throughput genome sequencing applications for a variety of intracellular pathogens. This assay will also be very useful in future studies of interactions of distinct host-T. parva stocks and to fully characterize the dynamics of ECF infection in the field

Spectral Effects of Strong Chi-2 Non-Linearity for Quantum Processing

Optical $\chi^{(2)}$ non-linearity can be used for parametric amplification and producing down-converted entangled photon pairs that have broad applications. It is known that weak non-linear media exhibit dispersion and produce a frequency response. It is therefore of interest to know how spectral effects of a strong $\chi^{(2)}$ crystal affect the performance. Here we model the spectral effects of the dispersion of a strong $\chi^{(2)}$ crystal and illustrate how this affects its ability to perform Bell measurements and influence the performance of a quantum gates that employ such a Bell measurement. We show that a Dyson series expansion of the unitary operator is necessary in general, leading to unwanted spectral entanglement. We identify a limiting situation employing periodic poling, in which a Taylor series expansion is a good approximation and this entanglement can be removed.Comment: Will be submitted to PR

Optimal States for Bell inequality Violations using Quadrature Phase Homodyne Measurements

We identify what ideal correlated photon number states are to required to maximize the discrepancy between local realism and quantum mechanics when a quadrature homodyne phase measurement is used. Various Bell inequality tests are considered.Comment: 6 pages, 5 Figure

Sediment resuspension and erosion by vortex rings

Particle resuspension and erosion induced by a vortex ringinteracting with a sediment layer was investigated experimentally using flow visualization (particle image velocimetry), high-speed video, and a recently developed light attenuation method for measuring displacements in bed level. Near-spherical sediment particles were used throughout with relative densities of 1.2–7 and diameters (d)(d) ranging between 90 and 1600 μm1600 μm. Attention was focused on initially smooth, horizontal bedforms with the vortex ring aligned to approach the bed vertically. Interaction characteristics were investigated in terms of the dimensionless Shields parameter, defined using the vortex-ring propagation speed. The critical conditions for resuspension (whereby particles are only just resuspended) were determined as a function of particle Reynolds number (based on the particle settling velocity and dd). The effects of viscous damping were found to be significant for d/δ<15d/δ<15, where δδ denotes the viscous sublayer thickness. Measurements of bed deformation were obtained during the interaction period, for a range of impact conditions. The (azimuthal) mean crater profile is shown to be generally self-similar during the interaction period, except for the most energetic impacts and larger sediment types. Loss of similarity occurs when the local bed slope approaches the repose limit, leading to collapse. Erosion, deposition, and resuspension volumes are analyzed as a function interaction time, impact condition, and sediment size

Biofilm formation is a risk factor for mortality in patients with Candida albicans bloodstream infection-Scotland, 2012-2013

Acknowledgements This work was supported by the Wellcome Trust Strategic Award for Medical Mycology and Fungal Immunology 097377/Z/11/Z. Data collection was supported by a grant from Pfizer. G. Ramage was also supported by a research fellowship grant from Gilead Sciences. We are grateful to microbiology colleagues throughout Scotland for submitting isolates.Peer reviewedPublisher PD

Secure self-calibrating quantum random bit generator

Random bit generators (RBGs) are key components of a variety of information processing applications ranging from simulations to cryptography. In particular, cryptographic systems require "strong" RBGs that produce high-entropy bit sequences, but traditional software pseudo-RBGs have very low entropy content and therefore are relatively weak for cryptography. Hardware RBGs yield entropy from chaotic or quantum physical systems and therefore are expected to exhibit high entropy, but in current implementations their exact entropy content is unknown. Here we report a quantum random bit generator (QRBG) that harvests entropy by measuring single-photon and entangled two-photon polarization states. We introduce and implement a quantum tomographic method to measure a lower bound on the "min-entropy" of the system, and we employ this value to distill a truly random bit sequence. This approach is secure: even if an attacker takes control of the source of optical states, a secure random sequence can be distilled.Comment: 5 pages, 2 figure