SLIDER: Mining correlated motifs in protein-protein interaction networks

Abstract—Correlated motif mining (CMM) is the problem to find overrepresented pairs of patterns, called motif pairs, in interacting protein sequences. Algorithmic solutions for CMM thereby provide a computational method for predicting binding sites for protein interaction. In this paper, we adopt a motif-driven approach where the support of candidate motif pairs is evaluated in the network. We experimentally establish the superiority of the Chi-square-based support measure over other support measures. Furthermore, we obtain that CMM is an NP-hard problem for a large class of support measures (including Chi-square) and reformulate the search for correlated motifs as a combinatorial optimization problem. We then present the method SLIDER which uses local search with a neighborhood function based on sliding motifs and employs the Chi-square-based support measure. We show that SLIDER outperforms existing motif-driven CMM methods and scales to large protein-protein interaction networks

On Pebble Automata for Data Languages with Decidable Emptiness Problem

In this paper we study a subclass of pebble automata (PA) for data languages for which the emptiness problem is decidable. Namely, we introduce the so-called top view weak PA. Roughly speaking, top view weak PA are weak PA where the equality test is performed only between the data values seen by the two most recently placed pebbles. The emptiness problem for this model is decidable. We also show that it is robust: alternating, nondeterministic and deterministic top view weak PA have the same recognition power. Moreover, this model is strong enough to accept all data languages expressible in Linear Temporal Logic with the future-time operators, augmented with one register freeze quantifier.Comment: An extended abstract of this work has been published in the proceedings of the 34th International Symposium on Mathematical Foundations of Computer Science (MFCS) 2009}, Springer, Lecture Notes in Computer Science 5734, pages 712-72

Novi podaci o podzemnim gljivama Turske

In this study, three species of hypogeous fungi are reported in different regions of Anatolian. Of these, Hydnocystis piligera is presented as the first record of this genus for Turkish mycobiota, while Melanogaster variegatus and Octaviania asterosperma are given as new locality records for Turkey. Macroscopic and microscopic photographs along with description of the newly recorded taxa are presented.Provedenim istraživanjem zabilježene su tri vrste podzemnih gljiva u različitim regijama poluotoka Anatolija. Nalaz vrste Hydnocystis piligera predstavlja prvi nalaz ovoga roda za mikobiotu Turske, dok su vrste Melanogaster variegatus i Octaviania asterosperma zabilježene na novim lokalitetima u Turskoj. U radu se prikazuju makroskopske i mikroskopske fotografije zajedno s tekstualnim podacima o zabilježenim vrstama

Streaming Tree Transducers

Theory of tree transducers provides a foundation for understanding expressiveness and complexity of analysis problems for specification languages for transforming hierarchically structured data such as XML documents. We introduce streaming tree transducers as an analyzable, executable, and expressive model for transforming unranked ordered trees in a single pass. Given a linear encoding of the input tree, the transducer makes a single left-to-right pass through the input, and computes the output in linear time using a finite-state control, a visibly pushdown stack, and a finite number of variables that store output chunks that can be combined using the operations of string-concatenation and tree-insertion. We prove that the expressiveness of the model coincides with transductions definable using monadic second-order logic (MSO). Existing models of tree transducers either cannot implement all MSO-definable transformations, or require regular look ahead that prohibits single-pass implementation. We show a variety of analysis problems such as type-checking and checking functional equivalence are solvable for our model.Comment: 40 page

Logics for Unranked Trees: An Overview

Labeled unranked trees are used as a model of XML documents, and logical languages for them have been studied actively over the past several years. Such logics have different purposes: some are better suited for extracting data, some for expressing navigational properties, and some make it easy to relate complex properties of trees to the existence of tree automata for those properties. Furthermore, logics differ significantly in their model-checking properties, their automata models, and their behavior on ordered and unordered trees. In this paper we present a survey of logics for unranked trees

An automaton over data words that captures EMSO logic

We develop a general framework for the specification and implementation of systems whose executions are words, or partial orders, over an infinite alphabet. As a model of an implementation, we introduce class register automata, a one-way automata model over words with multiple data values. Our model combines register automata and class memory automata. It has natural interpretations. In particular, it captures communicating automata with an unbounded number of processes, whose semantics can be described as a set of (dynamic) message sequence charts. On the specification side, we provide a local existential monadic second-order logic that does not impose any restriction on the number of variables. We study the realizability problem and show that every formula from that logic can be effectively, and in elementary time, translated into an equivalent class register automaton

On the Nature of the X-ray Emission from the Ultraluminous X-ray Source, M33 X-8: New Constraints from NuSTAR and XMM-Newton

We present nearly simultaneous NuSTAR and XMM-Newton observations of the nearby (832 kpc) ultraluminous X-ray source (ULX) M33 X-8. M33 X-8 has a 0.3-10 keV luminosity of LX ~ 1.4 x 10^39 erg/s, near the boundary of the "ultraluminous" classification, making it an important source for understanding the link between typical Galactic X-ray binaries and ULXs. Past studies have shown that the 0.3-10 keV spectrum of X-8 can be characterized using an advection-dominated accretion disk model. We find that when fitting to our NuSTAR and XMM-Newton observations, an additional high-energy (>10 keV) Comptonization component is required, which allows us to rule out single advection-dominated disk and classical sub-Eddington models. With our new constraints, we analyze XMM-Newton data taken over the last 17 years to show that small (~30%) variations in the 0.3-10 keV flux of M33 X-8 result in spectral changes similar to those observed for other ULXs. The two most likely phenomenological scenarios suggested by the data are degenerate in terms of constraining the nature of the accreting compact object (i.e., black hole versus neutron star). We further present a search for pulsations using our suite of data; however, no clear pulsations are detected. Future observations designed to observe M33 X-8 at different flux levels across the full 0.3-30 keV range would significantly improve our constraints on the nature of this important source.Comment: Accepted for publication in ApJ (15 pages, 4 tables, 6 figures

Pseudo-Schwarzschild Spherical Accretion as a Classical Black Hole Analogue

We demonstrate that a spherical accretion onto astrophysical black holes, under the influence of Newtonian or various post-Newtonian pseudo-Schwarzschild gravitational potentials, may constitute a concrete example of classical analogue gravity naturally found in the Universe. We analytically calculate the corresponding analogue Hawking temperature as a function of the minimum number of physical parameters governing the accretion flow. We study both the polytropic and the isothermal accretion. We show that unlike in a general relativistic spherical accretion, analogue white hole solutions can never be obtained in such post-Newtonian systems. We also show that an isothermal spherical accretion is a remarkably simple example in which the only one information--the temperature of the fluid, is sufficient to completely describe an analogue gravity system. For both types of accretion, the analogue Hawking temperature may become higher than the usual Hawking temperature. However, the analogue Hawking temperature for accreting astrophysical black holes is considerably lower compared with the temperature of the accreting fluid.Comment: Final Version to appear in the journal General Relativity & Gravitation, Volume 27, Issue 11, 2005. 17 pages, Two colour and one black and white figures. Typos corrected. Recent reference on analogue effect in relativistic accretion disc adde