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Löwer, Martin ; Weydig, Christiane ; Metzler, Dirk ; Reuter, Andreas ; Starzinski-Powitz, Anna ; Weßler, Silja ; Schneider, Gisbert
Exported proteases of Helicobacter pylori (H. pylori) are potentially involved in pathogen-associated disorders leading to gastric inflammation and neoplasia. By comprehensive sequence screening of the H. pylori proteome for predicted secreted proteases, we retrieved several candidate genes. We detected caseinolytic activities of several such proteases, which are released independently from the H. pylori type IV secretion system encoded by the cag pathogenicity island (cagPAI). Among these, we found the predicted serine protease HtrA (Hp1019), which was previously identified in the bacterial secretome of H. pylori. Importantly, we further found that the H. pylori genes hp1018 and hp1019 represent a single gene likely coding for an exported protein. Here, we directly verified proteolytic activity of HtrA in vitro and identified the HtrA protease in zymograms by mass spectrometry. Overexpressed and purified HtrA exhibited pronounced proteolytic activity, which is inactivated after mutation of Ser205 to alanine in the predicted active center of HtrA. These data demonstrate that H. pylori secretes HtrA as an active protease, which might represent a novel candidate target for therapeutic intervention strategies.
We investigate unary regular languages and compare deterministic finite automata (DFA’s), nondeterministic finite automata (NFA’s) and probabilistic finite automata (PFA’s) with respect to their size. Given a unary PFA with n states and an e-isolated cutpoint, we show that the minimal equivalent DFA has at most n exp 1/2e states in its cycle. This result is almost optimal, since for any alpha < 1 a family of PFA’s can be constructed such that every equivalent DFA has at least n exp alpha/2e states. Thus we show that for the model of probabilistic automata with a constant error bound, there is only a polynomial blowup for cyclic languages. Given a unary NFA with n states, we show that efficiently approximating the size of a minimal equivalent NFA within the factor sqrt(n)/ln n is impossible unless P = NP. This result even holds under the promise that the accepted language is cyclic. On the other hand we show that we can approximate a minimal NFA within the factor ln n, if we are given a cyclic unary n-state DFA.
We present a biologically-inspired system for real-time, feed-forward object recognition in cluttered scenes. Our system utilizes a vocabulary of very sparse features that are shared between and within different object models. To detect objects in a novel scene, these features are located in the image, and each detected feature votes for all objects that are consistent with its presence. Due to the sharing of features between object models our approach is more scalable to large object databases than traditional methods. To demonstrate the utility of this approach, we train our system to recognize any of 50 objects in everyday cluttered scenes with substantial occlusion. Without further optimization we also demonstrate near-perfect recognition on a standard 3-D recognition problem. Our system has an interpretation as a sparsely connected feed-forward neural network, making it a viable model for fast, feed-forward object recognition in the primate visual system.
A new approach to optimize multilevel logic circuits is introduced. Given a multilevel circuit, the synthesis method optimizes its area while simultaneously enhancing its random pattern testability. The method is based on structural transformations at the gate level. New transformations involving EX-OR gates as well as Reed–Muller expansions have been introduced in the synthesis of multilevel circuits. This method is augmented with transformations that specifically enhance random-pattern testability while reducing the area. Testability enhancement is an integral part of our synthesis methodology. Experimental results show that the proposed methodology not only can achieve lower area than other similar tools, but that it achieves better testability compared to available testability enhancement tools such as tstfx. Specifically for ISCAS-85 benchmark circuits, it was observed that EX-OR gate-based transformations successfully contributed toward generating smaller circuits compared to other state-of-the-art logic optimization tools.
Channel routing is an NP-complete problem. Therefore, it is likely that there is no efficient algorithm solving this problem exactly.In this paper, we show that channel routing is a fixed-parameter tractable problem and that we can find a solution in linear time for a fixed channel width.We implemented our approach for the restricted layer model. The algorithm finds an optimal route for channels with up to 13 tracks within minutes or up to 11 tracks within seconds.Such narrow channels occur for example as a leaf problem of hierarchical routers or within standard cell generators.
We present a theoretical analysis of structural FSM traversal, which is the basis for the sequential equivalence checking algorithm Record & Play presented earlier. We compare the convergence behaviour of exact and approximative structural FSM traversal with that of standard BDD-based FSM traversal. We show that for most circuits encountered in practice exact structural FSM traversal reaches the fixed point as fast as symbolic FSM traversal, while approximation can significantly reduce in the number of iterations needed. Our experiments confirm these results.
We present the FPGA implementation of an algorithm [4] that computes implications between signal values in a boolean network. The research was performed as a masterrsquos thesis [5] at the University of Frankfurt. The recursive algorithm is rather complex for a hardware realization and therefore the FPGA implementation is an interesting example for the potential of reconfigurable computing beyond systolic algorithms. A circuit generator was written that transforms a boolean network into a network of small processing elements and a global control logic which together implement the algorithm. The resulting circuit performs the computation two orders of magnitudes faster than a software implementation run by a conventional workstation.
One of the most severe short-comings of currently available equivalence checkers is their inability to verify integer multipliers. In this paper, we present a bit level reverse-engineering technique that can be integrated into standard equivalence checking flows. We propose a Boolean mapping algorithm that extracts a network of half adders from the gate netlist of an addition circuit. Once the arithmetic bit level representation of the circuit is obtained, equivalence checking can be performed using simple arithmetic operations. Experimental results show the promise of our approach.
Considered are the classes QL (quasilinear) and NQL (nondet quasllmear) of all those problems that can be solved by deterministic (nondetermlnlsttc, respectively) Turmg machines in time O(n(log n) ~) for some k Effloent algorithms have time bounds of th~s type, it is argued. Many of the "exhausUve search" type problems such as satlsflablhty and colorabdlty are complete in NQL with respect to reductions that take O(n(log n) k) steps This lmphes that QL = NQL iff satisfiabdlty is m QL CR CATEGORIES: 5.25
In this paper we present a non-deterministic call-by-need (untyped) lambda calculus lambda nd with a constant choice and a let-syntax that models sharing. Our main result is that lambda nd has the nice operational properties of the standard lambda calculus: confluence on sets of expressions, and normal order reduction is sufficient to reach head normal form. Using a strong contextual equivalence we show correctness of several program transformations. In particular of lambdalifting using deterministic maximal free expressions. These results show that lambda nd is a new and also natural combination of non-determinism and lambda-calculus, which has a lot of opportunities for parallel evaluation. An intended application of lambda nd is as a foundation for compiling lazy functional programming languages with I/O based on direct calls. The set of correct program transformations can be rigorously distinguished from non-correct ones. All program transformations are permitted with the slight exception that for transformations like common subexpression elimination and lambda-lifting with maximal free expressions the involved subexpressions have to be deterministic ones.
Assessing enhanced knowledge discovery systems (eKDSs) constitutes an intricate issue that is understood merely to a certain extent by now. Based upon an analysis of why it is difficult to formally evaluate eKDSs, it is argued for a change of perspective: eKDSs should be understood as intelligent tools for qualitative analysis that support, rather than substitute, the user in the exploration of the data; a qualitative gap will be identified as the main reason why the evaluation of enhanced knowledge discovery systems is difficult. In order to deal with this problem, the construction of a best practice model for eKDSs is advocated. Based on a brief recapitulation of similar work on spoken language dialogue systems, first steps towards achieving this goal are performed, and directions of future research are outlined.
Syntactic coindexing restrictions are by now known to be of central importance to practical anaphor resolution approaches. Since, in particular due to structural ambiguity, the assumption of the availability of a unique syntactic reading proves to be unrealistic, robust anaphor resolution relies on techniques to overcome this deficiency.
This paper describes the ROSANA approach, which generalizes the verification of coindexing restrictions in order to make it applicable to the deficient syntactic descriptions that are provided by a robust state-of-the-art parser. By a formal evaluation on two corpora that differ with respect to text genre and domain, it is shown that ROSANA achieves high-quality robust coreference resolution. Moreover, by an in-depth analysis, it is proven that the robust implementation of syntactic disjoint reference is nearly optimal. The study reveals that, compared with approaches that rely on shallow preprocessing, the largely nonheuristic disjoint reference algorithmization opens up the possibility/or a slight improvement. Furthermore, it is shown that more significant gains are to be expected elsewhere, particularly from a text-genre-specific choice of preference strategies.
The performance study of the ROSANA system crucially rests on an enhanced evaluation methodology for coreference resolution systems, the development of which constitutes the second major contribution o/the paper. As a supplement to the model-theoretic scoring scheme that was developed for the Message Understanding Conference (MUC) evaluations, additional evaluation measures are defined that, on one hand, support the developer of anaphor resolution systems, and, on the other hand, shed light on application aspects of pronoun interpretation.
A memory checker for a data structure provides a method to check that the output of the data structure operations is consistent with the input even if the data is stored on some insecure medium. In [8] we present a general solution for all data structures that are based on insert(i,v) and delete(j) commands. In particular this includes stacks, queues, deques (double-ended queues) and lists. Here, we describe more time and space efficient solutions for stacks, queues and deques. Each algorithm takes only a single function evaluation of a pseudorandomlike function like DES or a collision-free hash function like MD5 or SHA for each push/pop resp. enqueue/dequeue command making our methods applicable to smart cards.
We analyse a continued fraction algorithm (abbreviated CFA) for arbitrary dimension n showing that it produces simultaneous diophantine approximations which are up to the factor 2^((n+2)/4) best possible. Given a real vector x=(x_1,...,x_{n-1},1) in R^n this CFA generates a sequence of vectors (p_1^(k),...,p_{n-1}^(k),q^(k)) in Z^n, k=1,2,... with increasing integers |q^{(k)}| satisfying for i=1,...,n-1 | x_i - p_i^(k)/q^(k) | <= 2^((n+2)/4) sqrt(1+x_i^2) |q^(k)|^(1+1/(n-1)) By a theorem of Dirichlet this bound is best possible in that the exponent 1+1/(n-1) can in general not be increased.
Parallel FFT-hashing
(1994)
We propose two families of scalable hash functions for collision resistant hashing that are highly parallel and based on the generalized fast Fourier transform (FFT). FFT hashing is based on multipermutations. This is a basic cryptographic primitive for perfect generation of diffusion and confusion which generalizes the boxes of the classic FFT. The slower FFT hash functions iterate a compression function. For the faster FFT hash functions all rounds are alike with the same number of message words entering each round.
Let b1, . . . , bm 2 IRn be an arbitrary basis of lattice L that is a block Korkin Zolotarev basis with block size ¯ and let ¸i(L) denote the successive minima of lattice L. We prove that for i = 1, . . . ,m 4 i + 3 ° 2 i 1 ¯ 1 ¯ · kbik2/¸i(L)2 · ° 2m i ¯ 1 ¯ i + 3 4 where °¯ is the Hermite constant. For ¯ = 3 we establish the optimal upper bound kb1k2/¸1(L)2 · µ3 2¶m 1 2 1 and we present block Korkin Zolotarev lattice bases for which this bound is tight. We improve the Nearest Plane Algorithm of Babai (1986) using block Korkin Zolotarev bases. Given a block Korkin Zolotarev basis b1, . . . , bm with block size ¯ and x 2 L(b1, . . . , bm) a lattice point v can be found in time ¯O(¯) satisfying kx vk2 · m° 2m ¯ 1 ¯ minu2L kx uk2.
Coster, Matthijs J. ; Joux, Antoine ; LaMacchia, Brian A. ; Odlyzko, Andrew M. ; Schnorr, Claus Peter ; Stern, Jacques
The general subset sum problem is NP-complete. However, there are two algorithms, one due to Brickell and the other to Lagarias and Odlyzko, which in polynomial time solve almost all subset sum problems of sufficiently low density. Both methods rely on basis reduction algorithms to find short nonzero vectors in special lattices. The Lagarias-Odlyzko algorithm would solve almost all subset sum problems of density < 0.6463 . . . in polynomial time if it could invoke a polynomial-time algorithm for finding the shortest non-zero vector in a lattice. This paper presents two modifications of that algorithm, either one of which would solve almost all problems of density < 0.9408 . . . if it could find shortest non-zero vectors in lattices. These modifications also yield dramatic improvements in practice when they are combined with known lattice basis reduction algorithms.
We present a novel parallel one-more signature forgery against blind Okamoto-Schnorr and blind Schnorr signatures in which an attacker interacts some times with a legitimate signer and produces from these interactions signatures. Security against the new attack requires that the following ROS-problem is intractable: find an overdetermined, solvable system of linear equations modulo with random inhomogenities (right sides). There is an inherent weakness in the security result of POINTCHEVAL AND STERN. Theorem 26 [PS00] does not cover attacks with 4 parallel interactions for elliptic curves of order 2200. That would require the intractability of the ROS-problem, a plausible but novel complexity assumption. Conversely, assuming the intractability of the ROS-problem, we show that Schnorr signatures are secure in the random oracle and generic group model against the one-more signature forgery.