1,122 research outputs found
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
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