Chronic Brucella Pyelonephritis with Calcification: Short Review of the Literature and Report of a Case

A CAJM article on Chronic Brucella Pyelonephritis.The localisation of brucellosis in the urinary tract is an infrequently reported condition. The paucity of recorded cases may be due to the rarity of the condition or to the fact that the profession as a whole is not sufficiently aware of the possibility of urinary tract involvement in brucellosis. Having recently investigated a patient who is suffering from pyelonephritis and cystitis occurring as a complication of brucellosis, we were prompted to publish his case record with the aim of calling the attention of the profession to the various aspects of this disease and emphasising its localisation in the genitourinary system

Durham extremely large telescope adaptive optics simulation platform

Adaptive optics systems are essential on all large telescopes for which image quality is important. These are complex systems with many design parameters requiring optimization before good performance can be achieved. The simulation of adaptive optics systems is therefore necessary to categorize the expected performance. We describe an adaptive optics simulation platform, developed at Durham University, which can be used to simulate adaptive optics systems on the largest proposed future extremely large telescopes as well as on current systems. This platform is modular, object oriented, and has the benefit of hardware application acceleration that can be used to improve the simulation performance, essential for ensuring that the run time of a given simulation is acceptable. The simulation platform described here can be highly parallelized using parallelization techniques suited for adaptive optics simulation, while still offering the user complete control while the simulation is running. The results from the simulation of a ground layer adaptive optics system are provided as an example to demonstrate the flexibility of this simulation platform

Cerulean: A hybrid assembly using high throughput short and long reads

Genome assembly using high throughput data with short reads, arguably, remains an unresolvable task in repetitive genomes, since when the length of a repeat exceeds the read length, it becomes difficult to unambiguously connect the flanking regions. The emergence of third generation sequencing (Pacific Biosciences) with long reads enables the opportunity to resolve complicated repeats that could not be resolved by the short read data. However, these long reads have high error rate and it is an uphill task to assemble the genome without using additional high quality short reads. Recently, Koren et al. 2012 proposed an approach to use high quality short reads data to correct these long reads and, thus, make the assembly from long reads possible. However, due to the large size of both dataset (short and long reads), error-correction of these long reads requires excessively high computational resources, even on small bacterial genomes. In this work, instead of error correction of long reads, we first assemble the short reads and later map these long reads on the assembly graph to resolve repeats. Contribution: We present a hybrid assembly approach that is both computationally effective and produces high quality assemblies. Our algorithm first operates with a simplified version of the assembly graph consisting only of long contigs and gradually improves the assembly by adding smaller contigs in each iteration. In contrast to the state-of-the-art long reads error correction technique, which requires high computational resources and long running time on a supercomputer even for bacterial genome datasets, our software can produce comparable assembly using only a standard desktop in a short running time.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

A Shack-Hartmann wavefront sensor projected on to the sky with reduced focal anisoplanatism

A method for producing a laser guide star wavefront sensor for adaptive optics with reduced focal anisoplanatism is presented. A theoretical analysis and numerical simulations have been carried out and the results are presented. The technique, named Sky-Projected Laser Array Shack–Hartmann (SPLASH), is shown to suffer considerably less from focal anisoplanatism than a conventional laser guide star system. The method is potentially suitable for large telescope apertures (8 m), and possibly for extremely large telescopes

Results from the adaptive optics coronagraph at the William Herschel Telescope

Described here is the design and commissioning of a coronagraph facility for the 4.2-m William Herschel Telescope (WHT) and its Nasmyth Adaptive Optics for Multi-purpose Instrumentation (NAOMI). The use of the NAOMI system gives an improved image resolution of 0.15 arcsec at a wavelength of 2.2 μm. This enables the Optimised Stellar Coronagraph for Adaptive optics (OSCA) to suppress stellar light using smaller occulting masks and thus allows regions closer to bright astronomical objects to be imaged. OSCA provides a selection of 10 different occulting masks with sizes of 0.25–2.0 arcsec in diameter, including two with full grey-scale Gaussian profiles. There is also a choice of different sized and shaped Lyot stops (pupil plane masks). Computer simulations of the different coronagraphic options with the NAOMI segmented mirror have relevance for the next generation of highly segmented extremely large telescopes

Fast Searching in Packed Strings

Given strings $P$ and $Q$ the (exact) string matching problem is to find all positions of substrings in $Q$ matching $P$. The classical Knuth-Morris-Pratt algorithm [SIAM J. Comput., 1977] solves the string matching problem in linear time which is optimal if we can only read one character at the time. However, most strings are stored in a computer in a packed representation with several characters in a single word, giving us the opportunity to read multiple characters simultaneously. In this paper we study the worst-case complexity of string matching on strings given in packed representation. Let $m \leq n$ be the lengths $P$ and $Q$, respectively, and let $\sigma$ denote the size of the alphabet. On a standard unit-cost word-RAM with logarithmic word size we present an algorithm using time O\left(\frac{n}{\log_\sigma n} + m + \occ\right). Here \occ is the number of occurrences of $P$ in $Q$. For $m = o(n)$ this improves the $O(n)$ bound of the Knuth-Morris-Pratt algorithm. Furthermore, if $m = O(n/\log_\sigma n)$ our algorithm is optimal since any algorithm must spend at least \Omega(\frac{(n+m)\log \sigma}{\log n} + \occ) = \Omega(\frac{n}{\log_\sigma n} + \occ) time to read the input and report all occurrences. The result is obtained by a novel automaton construction based on the Knuth-Morris-Pratt algorithm combined with a new compact representation of subautomata allowing an optimal tabulation-based simulation.Comment: To appear in Journal of Discrete Algorithms. Special Issue on CPM 200

Black Hole Area in Brans-Dicke Theory

We have shown that the dynamics of the scalar field $\phi (x)= ``G^{-1}(x)"$ in Brans-Dicke theories of gravity makes the surface area of the black hole horizon {\it oscillatory} during its dynamical evolution. It explicitly explains why the area theorem does not hold in Brans-Dicke theory. However, we show that there exists a certain non-decreasing quantity defined on the event horizon which is proportional to the black hole entropy for the case of stationary solutions in Brans-Dicke theory. Some numerical simulations have been demonstrated for Oppenheimer-Snyder collapse in Brans-Dicke theory.Comment: 12 pages, latex, 5 figures, epsfig.sty, some statements clarified and two references added, to appear in Phys. Rev.

Orbit spaces of free involutions on the product of two projective spaces

Let $X$ be a finitistic space having the mod 2 cohomology algebra of the product of two projective spaces. We study free involutions on $X$ and determine the possible mod 2 cohomology algebra of orbit space of any free involution, using the Leray spectral sequence associated to the Borel fibration $X \hookrightarrow X_{\mathbb{Z}_2} \longrightarrow B_{\mathbb{Z}_2}$. We also give an application of our result to show that if $X$ has the mod 2 cohomology algebra of the product of two real projective spaces (respectively complex projective spaces), then there does not exist any $\mathbb{Z}_2$-equivariant map from $\mathbb{S}^k \to X$ for $k \geq 2$ (respectively $k \geq 3$), where $\mathbb{S}^k$ is equipped with the antipodal involution.Comment: 14 pages, to appear in Results in Mathematic

Constraints on Gravitational Scaling Dimensions from Non-Local Effective Field Equations

Quantum corrections to the classical field equations, induced by a scale dependent gravitational constant, are analyzed in the case of the static isotropic metric. The requirement of general covariance for the resulting non-local effective field equations puts severe restrictions on the nature of the solutions that can be obtained. In general the existence of vacuum solutions to the effective field equations restricts the value of the gravitational scaling exponent $\nu^{-1}$ to be a positive integer greater than one. We give further arguments suggesting that in fact only for $\nu^{-1}=3$ consistent solutions seem to exist in four dimensions.Comment: 14 page

Chemical telemetry of OH observed to measure interstellar magnetic fields

We present models for the chemistry in gas moving towards the ionization front of an HII region. When it is far from the ionization front, the gas is highly depleted of elements more massive than helium. However, as it approaches the ionization front, ices are destroyed and species formed on the grain surfaces are injected into the gas phase. Photodissociation removes gas phase molecular species as the gas flows towards the ionization front. We identify models for which the OH column densities are comparable to those measured in observations undertaken to study the magnetic fields in star forming regions and give results for the column densities of other species that should be abundant if the observed OH arises through a combination of the liberation of H2O from surfaces and photodissociation. They include CH3OH, H2CO, and H2S. Observations of these other species may help establish the nature of the OH spatial distribution in the clouds, which is important for the interpretation of the magnetic field results.Comment: 11 pages, 2 figures, accepted by Astrophysics and Space Scienc