A novel role for the LisRK two-component regulatory system in listerial osmotolerance

ABSTRACTUnderstanding how pathogenic bacteria sense and respond to environmental signals, including those involved in triggering virulence gene expression, is a fundamental biological goal. It is now known that the two-component regulatory system LisRK has a novel role in osmosensing and osmoregulation in the intracellular foodborne pathogen Listeria monocytogenes. Furthermore, htrA, a gene linked to osmotolerance and virulence potential in L. monocytogenes, is now known to be under the transcriptional control of LisRK

Maximum st-flow in directed planar graphs via shortest paths

Minimum cuts have been closely related to shortest paths in planar graphs via planar duality - so long as the graphs are undirected. Even maximum flows are closely related to shortest paths for the same reason - so long as the source and the sink are on a common face. In this paper, we give a correspondence between maximum flows and shortest paths via duality in directed planar graphs with no constraints on the source and sink. We believe this a promising avenue for developing algorithms that are more practical than the current asymptotically best algorithms for maximum st-flow.Comment: 20 pages, 4 figures. Short version to be published in proceedings of IWOCA'1

The K-Server Dual and Loose Competitiveness for Paging

This paper has two results. The first is based on the surprising observation that the well-known ``least-recently-used'' paging algorithm and the ``balance'' algorithm for weighted caching are linear-programming primal-dual algorithms. This observation leads to a strategy (called ``Greedy-Dual'') that generalizes them both and has an optimal performance guarantee for weighted caching. For the second result, the paper presents empirical studies of paging algorithms, documenting that in practice, on ``typical'' cache sizes and sequences, the performance of paging strategies are much better than their worst-case analyses in the standard model suggest. The paper then presents theoretical results that support and explain this. For example: on any input sequence, with almost all cache sizes, either the performance guarantee of least-recently-used is O(log k) or the fault rate (in an absolute sense) is insignificant. Both of these results are strengthened and generalized in``On-line File Caching'' (1998).Comment: conference version: "On-Line Caching as Cache Size Varies", SODA (1991

Low Ply Drawings of Trees

We consider the recently introduced model of \emph{low ply graph drawing}, in which the ply-disks of the vertices do not have many common overlaps, which results in a good distribution of the vertices in the plane. The \emph{ply-disk} of a vertex in a straight-line drawing is the disk centered at it whose radius is half the length of its longest incident edge. The largest number of ply-disks having a common overlap is called the \emph{ply-number} of the drawing. We focus on trees. We first consider drawings of trees with constant ply-number, proving that they may require exponential area, even for stars, and that they may not even exist for bounded-degree trees. Then, we turn our attention to drawings with logarithmic ply-number and show that trees with maximum degree $6$ always admit such drawings in polynomial area.Comment: This is a complete access version of a paper that will appear in the proceedings of GD201

Adding Isolated Vertices Makes some Online Algorithms Optimal

An unexpected difference between online and offline algorithms is observed. The natural greedy algorithms are shown to be worst case online optimal for Online Independent Set and Online Vertex Cover on graphs with 'enough' isolated vertices, Freckle Graphs. For Online Dominating Set, the greedy algorithm is shown to be worst case online optimal on graphs with at least one isolated vertex. These algorithms are not online optimal in general. The online optimality results for these greedy algorithms imply optimality according to various worst case performance measures, such as the competitive ratio. It is also shown that, despite this worst case optimality, there are Freckle graphs where the greedy independent set algorithm is objectively less good than another algorithm. It is shown that it is NP-hard to determine any of the following for a given graph: the online independence number, the online vertex cover number, and the online domination number.Comment: A footnote in the .tex file didn't show up in the last version. This was fixe

A quantum-mechanical Maxwell's demon

A Maxwell's demon is a device that gets information and trades it in for thermodynamic advantage, in apparent (but not actual) contradiction to the second law of thermodynamics. Quantum-mechanical versions of Maxwell's demon exhibit features that classical versions do not: in particular, a device that gets information about a quantum system disturbs it in the process. In addition, the information produced by quantum measurement acts as an additional source of thermodynamic inefficiency. This paper investigates the properties of quantum-mechanical Maxwell's demons, and proposes experimentally realizable models of such devices.Comment: 13 pages, Te

Multi-valued Logic Gates for Quantum Computation

We develop a multi-valued logic for quantum computing for use in multi-level quantum systems, and discuss the practical advantages of this approach for scaling up a quantum computer. Generalizing the methods of binary quantum logic, we establish that arbitrary unitary operations on any number of d-level systems (d > 2) can be decomposed into logic gates that operate on only two systems at a time. We show that such multi-valued logic gates are experimentally feasible in the context of the linear ion trap scheme for quantum computing. By using d levels in each ion in this scheme, we reduce the number of ions needed for a computation by a factor of log d.Comment: Revised version; 8 pages, 3 figures; to appear in Physical Review

Streptococcus pneumoniae NanC. Structural insights into the specificity and mechanism of a sialidase that produces a sialidase inhibitor

This work was supported by the Biotechnology and Biological Sciences Research Council (UK) and the Medical Research Council (UK).Streptococcus pneumoniae is an important human pathogen that causes a range of disease states. Sialidases are important bacterial virulence factors. There are three pneumococcal sialidases: NanA, NanB, and NanC. NanC is an unusual sialidase in that its primary reaction product is 2-deoxy-2,3-didehydro-N-acetylneuraminic acid (Neu5Ac2en, also known as DANA), a nonspecific hydrolytic sialidase inhibitor. The production of Neu5Ac2en from α2-3-linked sialosides by the catalytic domain is confirmed within a crystal structure. A covalent complex with 3-fluoro-β-N-acetylneuraminic acid is also presented, suggesting a common mechanism with other sialidases up to the final step of product formation. A conformation change in an active site hydrophobic loop on ligand binding constricts the entrance to the active site. In addition, the distance between the catalytic acid/base (Asp-315) and the ligand anomeric carbon is unusually short. These features facilitate a novel sialidase reaction in which the final step of product formation is direct abstraction of the C3 proton by the active site aspartic acid, forming Neu5Ac2en. NanC also possesses a carbohydrate-binding module, which is shown to bind α2-3- and α2-6-linked sialosides, as well as N-acetylneuraminic acid, which is captured in the crystal structure following hydration of Neu5Ac2en by NanC. Overall, the pneumococcal sialidases show remarkable mechanistic diversity while maintaining a common structural scaffold.Publisher PDFPeer reviewe

Factoring in a Dissipative Quantum Computer

We describe an array of quantum gates implementing Shor's algorithm for prime factorization in a quantum computer. The array includes a circuit for modular exponentiation with several subcomponents (such as controlled multipliers, adders, etc) which are described in terms of elementary Toffoli gates. We present a simple analysis of the impact of losses and decoherence on the performance of this quantum factoring circuit. For that purpose, we simulate a quantum computer which is running the program to factor N = 15 while interacting with a dissipative environment. As a consequence of this interaction randomly selected qubits may spontaneously decay. Using the results of our numerical simulations we analyze the efficiency of some simple error correction techniques.Comment: plain tex, 18 pages, 8 postscript figure