Scoring schemes of palindrome clusters for more sensitive prediction of replication origins in herpesviruses

Many empirical studies show that there are unusual clusters of palindromes, closely spaced direct and inverted repeats around the replication origins of herpesviruses. In this paper, we introduce two new scoring schemes to quantify the spatial abundance of palindromes in a genomic sequence. Based on these scoring schemes, a computational method to predict the locations of replication origins is developed. When our predictions are compared with 39 known or annotated replication origins in 19 herpesviruses, close to 80% of the replication origins are located within 2% of the genome length. A list of predicted locations of replication origins in all the known herpesviruses with complete genome sequences is reported

Long-range interactions and non-extensivity in ferromagnetic spin models

The Ising model with ferromagnetic interactions that decay as $1/r^\alpha$ is analyzed in the non-extensive regime $0\leq\alpha\leq d$, where the thermodynamic limit is not defined. In order to study the asymptotic properties of the model in the $N\rightarrow\infty$ limit ($N$ being the number of spins) we propose a generalization of the Curie-Weiss model, for which the $N\rightarrow\infty$ limit is well defined for all $\alpha\geq 0$. We conjecture that mean field theory is {\it exact} in the last model for all $0\leq\alpha\leq d$. This conjecture is supported by Monte Carlo heat bath simulations in the $d=1$ case. Moreover, we confirm a recently conjectured scaling (Tsallis\cite{Tsallis}) which allows for a unification of extensive ($\alpha>d$) and non-extensive ($0\leq\alpha\leq d$) regimes.Comment: RevTex, 12 pages, 1 eps figur

Perturbation and Variational Methods in Nonextensive Tsallis Statistics

A unified presentation of the perturbation and variational methods for the generalized statistical mechanics based on Tsallis entropy is given here. In the case of the variational method, the Bogoliubov inequality is generalized in a very natural way following the Feynman proof for the usual statistical mechanics. The inequality turns out to be form-invariant with respect to the entropic index $q$. The method is illustrated with a simple example in classical mechanics. The formalisms developed here are expected to be useful in the discussion of nonextensive systems.Comment: revte

The field theoretic derivation of the contact value theorem in planar geometries and its modification by the Casimir effect

The contact value theorem for Coulomb gases in planar or film-like geometries is derived using a Hamiltonian field theoretic representation of the system. The case where the film is enclosed by a material of different dielectric constant to that of the film is shown to contain an additional Casimir-like term which is generated by fluctuations of the electric potential about its mean-field value.Comment: Link between Sine-Gordon and Coulomb gas pressures via subtraction of self interaction terms included. Discussion of results within Debye-Huckel approximation included. Added reference

Average Entropy of a Subsystem from its Average Tsallis Entropy

In the nonextensive Tsallis scenario, Page's conjecture for the average entropy of a subsystem[Phys. Rev. Lett. {\bf 71}, 1291(1993)] as well as its demonstration are generalized, i.e., when a pure quantum system, whose Hilbert space dimension is $mn$, is considered, the average Tsallis entropy of an $m$-dimensional subsystem is obtained. This demonstration is expected to be useful to study systems where the usual entropy does not give satisfactory results.Comment: Revtex, 6 pages, 2 figures. To appear in Phys. Rev.

Data Mining and Machine Learning in Astronomy

We review the current state of data mining and machine learning in astronomy. 'Data Mining' can have a somewhat mixed connotation from the point of view of a researcher in this field. If used correctly, it can be a powerful approach, holding the potential to fully exploit the exponentially increasing amount of available data, promising great scientific advance. However, if misused, it can be little more than the black-box application of complex computing algorithms that may give little physical insight, and provide questionable results. Here, we give an overview of the entire data mining process, from data collection through to the interpretation of results. We cover common machine learning algorithms, such as artificial neural networks and support vector machines, applications from a broad range of astronomy, emphasizing those where data mining techniques directly resulted in improved science, and important current and future directions, including probability density functions, parallel algorithms, petascale computing, and the time domain. We conclude that, so long as one carefully selects an appropriate algorithm, and is guided by the astronomical problem at hand, data mining can be very much the powerful tool, and not the questionable black box.Comment: Published in IJMPD. 61 pages, uses ws-ijmpd.cls. Several extra figures, some minor additions to the tex

Self-gravitating Brownian particles in two dimensions: the case of N=2 particles

We study the motion of N=2 overdamped Brownian particles in gravitational interaction in a space of dimension d=2. This is equivalent to the simplified motion of two biological entities interacting via chemotaxis when time delay and degradation of the chemical are ignored. This problem also bears some similarities with the stochastic motion of two point vortices in viscous hydrodynamics [Agullo & Verga, Phys. Rev. E, 63, 056304 (2001)]. We analytically obtain the density probability of finding the particles at a distance r from each other at time t. We also determine the probability that the particles have coalesced and formed a Dirac peak at time t (i.e. the probability that the reduced particle has reached r=0 at time t). Finally, we investigate the variance of the distribution and discuss the proper form of the virial theorem for this system. The reduced particle has a normal diffusion behaviour for small times with a gravity-modified diffusion coefficient =r_0^2+(4k_B/\xi\mu)(T-T_*)t, where k_BT_{*}=Gm_1m_2/2 is a critical temperature, and an anomalous diffusion for large times ~t^(1-T_*/T). As a by-product, our solution also describes the growth of the Dirac peak (condensate) that forms in the post-collapse regime of the Smoluchowski-Poisson system (or Keller-Segel model) for T<T_c=GMm/(4k_B). We find that the saturation of the mass of the condensate to the total mass is algebraic in an infinite domain and exponential in a bounded domain.Comment: Revised version (20/5/2010) accepted for publication in EPJ

HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot

The growth in the number of completely sequenced microbial genomes (bacterial and archaeal) has generated a need for a procedure that provides UniProtKB/Swiss-Prot-quality annotation to as many protein sequences as possible. We have devised a semi-automated system, HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes), that uses manually built annotation templates for protein families to propagate annotation to all members of manually defined protein families, using very strict criteria. The HAMAP system is composed of two databases, the proteome database and the family database, and of an automatic annotation pipeline. The proteome database comprises biological and sequence information for each completely sequenced microbial proteome, and it offers several tools for CDS searches, BLAST options and retrieval of specific sets of proteins. The family database currently comprises more than 1500 manually curated protein families and their annotation templates that are used to annotate proteins that belong to one of the HAMAP families. On the HAMAP website, individual sequences as well as whole genomes can be scanned against all HAMAP families. The system provides warnings for the absence of conserved amino acid residues, unusual sequence length, etc. Thanks to the implementation of HAMAP, more than 200 000 microbial proteins have been fully annotated in UniProtKB/Swiss-Prot (HAMAP website: http://www.expasy.org/sprot/hamap)

Ventrolateral Origin of Each Cycle of Rhythmic Activity Generated by the Spinal Cord of the Chick Embryo

BACKGROUND: The mechanisms responsible for generating rhythmic motor activity in the developing spinal cord of the chick embryo are poorly understood. Here we investigate whether the activity of motoneurons occurs before other neuronal populations at the beginning of each cycle of rhythmic discharge. METHODOLOGY/PRINCIPAL FINDINGS: The spatiotemporal organization of neural activity in transverse slices of the lumbosacral cord of the chick embryo (E8-E11) was investigated using intrinsic and voltage-sensitive dye (VSD) imaging. VSD signals accompanying episodes of activity comprised a rhythmic decrease in light transmission that corresponded to each cycle of electrical activity recorded from the ipsilateral ventral root. The rhythmic signals were widely synchronized across the cord face, and the largest signal amplitude was in the ventrolateral region where motoneurons are located. In unstained slices we recorded two classes of intrinsic signal. In the first, an episode of rhythmic activity was accompanied by a slow decrease in light transmission that peaked in the dorsal horn and decayed dorsoventrally. Superimposed on this signal was a much smaller rhythmic increase in transmission that was coincident with each cycle of discharge and whose amplitude and spatial distribution was similar to that of the VSD signals. At the onset of a spontaneously occurring episode and each subsequent cycle, both the intrinsic and VSD signals originated within the lateral motor column and spread medially and then dorsally. By contrast, following a dorsal root stimulus, the optical signals originated within the dorsal horn and traveled ventrally to reach the lateral motor column. CONCLUSIONS/SIGNIFICANCE: These findings suggest that motoneuron activity contributes to the initiation of each cycle of rhythmic activity, and that motoneuron and/or R-interneuron synapses are a plausible site for the activity-dependent synaptic depression that modeling studies have identified as a critical mechanism for cycling within an episode