title:
A Novel Combinatorial Method for Estimating Transcript Expression with
  RNA-Seq: Bounding the Number of Paths

abstract:
  RNA-Seq technology offers new high-throughput ways for transcript
identification and quantification based on short reads, and has recently
attracted great interest. The problem is usually modeled by a weighted splicing
graph whose nodes stand for exons and whose edges stand for split alignments to
the exons. The task consists of finding a number of paths, together with their
expression levels, which optimally explain the coverages of the graph under
various fitness functions, such least sum of squares. In (Tomescu et al.
RECOMB-seq 2013) we showed that under general fitness functions, if we allow a
polynomially bounded number of paths in an optimal solution, this problem can
be solved in polynomial time by a reduction to a min-cost flow program. In this
paper we further refine this problem by asking for a bounded number k of paths
that optimally explain the splicing graph. This problem becomes NP-hard in the
strong sense, but we give a fast combinatorial algorithm based on dynamic
programming for it. In order to obtain a practical tool, we implement three
optimizations and heuristics, which achieve better performance on real data,
and similar or better performance on simulated data, than state-of-the-art
tools Cufflinks, IsoLasso and SLIDE. Our tool, called Traph, is available at
http://www.cs.helsinki.fi/gsa/traph/


title:
The jet-disc connection: evidence for a reinterpretation in radio loud
  and radio quiet active galactic nuclei

abstract:
  To constrain models of the jet-disc connection, we explore Eddington ratios
reported in Foschini (2011) and interpret them in relation to the values in
Sikora et al. across the active galactic nuclei population from radio loud
quasars, their flat spectrum radio quasar subclass, the recently discovered
gamma-ray loud narrow-line type 1 Seyfert galaxies, Fanaroff-Riley type I (FRI)
radio galaxies and radio quiet quasars of the Palomar Green survey. While
appeal to disc truncation in radiatively inefficient flow appears to explain
the observed inverse relation between radio loudness and Eddington ratio in
radio loud and radio quiet quasars, FR I objects, scale invariance and recent
data on powerful jets in narrow-line Seyfert 1 galaxies offer compelling
arguments in favour of a reinterpretaion of the jet-disc connection.


title:
A polynomial delay algorithm for the enumeration of bubbles with length
  constraints in directed graphs and its application to the detection of
  alternative splicing in RNA-seq data

abstract:
  We present a new algorithm for enumerating bubbles with length constraints in
directed graphs. This problem arises in transcriptomics, where the question is
to identify all alternative splicing events present in a sample of mRNAs
sequenced by RNA-seq. This is the first polynomial-delay algorithm for this
problem and we show that in practice, it is faster than previous approaches.
This enables us to deal with larger instances and therefore to discover novel
alternative splicing events, especially long ones, that were previously
overseen using existing methods.


title:
Wireless Message Dissemination via Selective Relay over Bluetooth
  (MDSRoB)

abstract:
  This paper presents a wireless message dissemination method designed with no
need to trust other users. This method utilizes modern wireless adaptors
ability to broadcast device name and identification information. Using the
scanning features built into Bluetooth and Wifi, messages can be exchanged via
their device names. This paper outlines a method of interchanging multiple
messages to discoverable and nondiscoverable devices using a user defined
scanning interval method along with a response based system. By selectively
relaying messages each user is in control of their involvement in the ad-hoc
network.


title: Models of Non-Minimal Chaotic Inflation in Supergravity

abstract:
  We show how we can implement chaotic inflation in the context of supergravity
by conveniently selecting the functional form of a strong enough non-minimal
coupling between the inflaton and the Ricci scalar curvature. The procedure can
be applied when a gauge singlet or non-singlet inflaton is coupled to another
singlet superfield within linear-quadratic, trilinear or bilinear
superpotential terms. The tachyonic instability occurring along the direction
of the accompanying non-inflaton field can be cured by expanding the kinetic
part of the frame function up to the fourth order in powers of the various
fields. In the case of a gauge non-singlet inflaton, though, a conjugation
symmetry has to be imposed on these terms in order for the flatness of the
inflationary potential is maintained. On the other hand, some of these terms
assist us to precisely reconcile the resulting scalar spectral index with the
current PLANCK measurements while the other inflationary observables are in
agreement with data.


title: An odd categorification of quantum sl(2)

abstract:
  We define a 2-category that categorifies the covering Kac-Moody algebra for
sl(2) introduced by Clark and Wang. This categorification forms the structure
of a super-2-category as formulated by Kang, Kashiwara, and Oh. The
super-2-category structure introduces a (Z x Z_2)-grading giving its
Grothendieck group the structure of a free module over the group algebra of Z x
Z_2. By specializing the Z_2-action to +1 or to -1, the construction
specializes to an "odd" categorification of sl(2) and to a
supercategorification of osp(1|2), respectively.


title:
Distribution of graph-distances in Boltzmann ensembles of RNA secondary
  structures

abstract:
  Large RNA molecules often carry multiple functional domains whose spatial
arrangement is an important determinant of their function. Pre-mRNA splicing,
furthermore, relies on the spatial proximity of the splice junctions that can
be separated by very long introns. Similar effects appear in the processing of
RNA virus genomes. Albeit a crude measure, the distribution of spatial
distances in thermodynamic equilibrium therefore provides useful information on
the overall shape of the molecule can provide insights into the interplay of
its functional domains. Spatial distance can be approximated by the
graph-distance in RNA secondary structure. We show here that the equilibrium
distribution of graph-distances between arbitrary nucleotides can be computed
in polynomial time by means of dynamic programming. A naive implementation
would yield recursions with a very high time complexity of O(n^11). Although we
were able to reduce this to O(n^6) for many practical applications a further
reduction seems difficult. We conclude, therefore, that sampling approaches,
which are much easier to implement, are also theoretically favorable for most
real-life applications, in particular since these primarily concern long-range
interactions in very large RNA molecules.


title:
PAC study of the static and dynamic aspects of metal atom inside C60
  cage

abstract:
  30 keV 111mCd and 50 keV 199mHg beams from ISOLDE were used to implant on
preformed target of C60 with the thickness of 1 mg/cm2. Endofullerene
compounds, viz.,111mCd@C60 and 199mHg@C60 formed during implantation were
separated by filtration through micropore filter paper followed by solvent
extraction. Dried samples of the endofullerene compounds were counted for the
coincidence for the 151-245 keV cascade of 111mCd and 374-158 keV cascade for
199mHg for the TDPAC measurement on a six LaBr3 detector system coupled with
digital electronics. The results indicate a single site occupied by the Cd atom
in the fullerene cage with fast relaxation component which means that the Cd
atom does move inside the cage at room temperature. The quadrupole interaction
frequency and asymmetry parameter of the Cd atom occupying the site in C60 are
WQ=8.14(42) Mrad/s and eta= 0.42(9) respectively with a site population of 28%.
Fast relaxation constant is 0.003 ns-1 with a site contribution of 72%. On the
other hand, Hg atom has two static sites of quadrupole frequencies,
WQ1=281.60(16.9) Mrad/s and WQ2=202.30(22.7) Mrad/s. Respective asymmetry
parameters are eta1=0.1(1) and eta2=0.2(1). The static components have a
contribution of 40% with the rest 60% coming from the fast relaxing component.


title: Complex versus real orthogonal polynomials of two variables

abstract:
  Orthogonal polynomials of two real variables can often be represented in
complex variables. We explore the connection between the two types of
representations and study the structural relations of complex orthogonal
polynomials. The complex Hermite orthogonal polynomials and the disk
polynomials are used as illustrating examples.


title: Faster Algorithms for RNA-folding using the Four-Russians method

abstract:
  The secondary structure that maximizes the number of non-crossing matchings
between complimentary bases of an RNA sequence of length n can be computed in
O(n^3) time using Nussinov's dynamic programming algorithm. The Four-Russians
method is a technique that will reduce the running time for certain dynamic
programming algorithms by a multiplicative factor after a preprocessing step
where solutions to all smaller subproblems of a fixed size are exhaustively
enumerated and solved. Frid and Gusfield designed an O(\frac{n^3}{\log n})
algorithm for RNA folding using the Four-Russians technique. In their algorithm
the preprocessing is interleaved with the algorithm computation. (Algo. Mol.
Biol., 2010).
  We simplify the algorithm and the analysis by doing the preprocessing once
prior to the algorithm computation. We call this the two-vector method. We also
show variants where instead of exhaustive preprocessing, we only solve the
subproblems encountered in the main algorithm once and memoize the results. We
give a simple proof of correctness and explore the practical advantages over
the earlier method. The Nussinov algorithm admits an O(n^2) time parallel
algorithm. We show a parallel algorithm using the two-vector idea that improves
the time bound to O(\frac{n^2}{log n}).
  We discuss the organization of the data structures to exploit coalesced
memory access for fast running times. The ideas to organize the data structures
also help in improving the running time of the serial algorithms. For sequences
of length up to 6000 bases the parallel algorithm takes only about 2.5 seconds
and the two-vector serial method takes about 57 seconds on a desktop and 15
seconds on a server. Among the serial algorithms, the two-vector and memoized
versions are faster than the Frid-Gusfield algorithm by a factor of 3, and are
faster than Nussinov by up to a factor of 20.


title:
Algorithms for the Majority Rule (+) Consensus Tree and the Frequency
  Difference Consensus Tree

abstract:
  This paper presents two new deterministic algorithms for constructing
consensus trees. Given an input of k phylogenetic trees with identical leaf
label sets and n leaves each, the first algorithm constructs the majority rule
(+) consensus tree in O(kn) time, which is optimal since the input size is
Omega(kn), and the second one constructs the frequency difference consensus
tree in min(O(kn^2), O(kn (k+log^2 n))) time.


title:
Truthful Mechanisms for Secure Communication in Wireless Cooperative
  System

abstract:
  To ensure security in data transmission is one of the most important issues
for wireless relay networks, and physical layer security is an attractive
alternative solution to address this issue. In this paper, we consider a
cooperative network, consisting of one source node, one destination node, one
eavesdropper node, and a number of relay nodes. Specifically, the source may
select several relays to help forward the signal to the corresponding
destination to achieve the best security performance. However, the relays may
have the incentive not to report their true private channel information in
order to get more chances to be selected and gain more payoff from the source.
We propose a Vickey-Clark-Grove (VCG) based mechanism and an
Arrow-d'Aspremont-Gerard-Varet (AGV) based mechanism into the investigated
relay network to solve this cheating problem. In these two different
mechanisms, we design different "transfer payment" functions to the payoff of
each selected relay and prove that each relay gets its maximum (expected)
payoff when it truthfully reveals its private channel information to the
source. And then, an optimal secrecy rate of the network can be achieved. After
discussing and comparing the VCG and AGV mechanisms, we prove that the AGV
mechanism can achieve all of the basic qualifications (incentive compatibility,
individual rationality and budget balance) for our system. Moreover, we discuss
the optimal quantity of relays that the source node should select. Simulation
results verify efficiency and fairness of the VCG and AGV mechanisms, and
consolidate these conclusions.


title: BFKL equation with running QCD coupling and HERA data

abstract:
  In this paper we developed approach based on the BFKL evolution in $\ln\Lb
Q^2\Rb$. We show that the simplest diffusion approximation with running QCD
coupling is able to describe the HERA experimental data on the deep inelastic
structure function with good $\chi^2/d.o.f. \approx 1.3$. From our description
of the experimental data we learned several lessons; (i) the non-perturbative
physics at long distances started to show up at $Q^2 = 0.25\,GeV^2$; (ii) the
scattering amplitude at $Q^2 = 0.25\,GeV^2$ cannot be written as sum of soft
Pomeron and the secondary Reggeon but the Pomeron interactions should be taken
into account; (iii) the Pomeron interactions can be reduced to the enhanced
diagrams and, therefore, we do not see any needs for the shadowing corrections
at HERA energies; and (iv) we demonstrated that the shadowing correction could
be sizable at higher than HERA energies without any contradiction with our
initial conditions.


title: The generalized Robinson-Foulds metric

abstract:
  The Robinson-Foulds (RF) metric is arguably the most widely used measure of
phylogenetic tree similarity, despite its well-known shortcomings: For example,
moving a single taxon in a tree can result in a tree that has maximum distance
to the original one; but the two trees are identical if we remove the single
taxon. To this end, we propose a natural extension of the RF metric that does
not simply count identical clades but instead, also takes similar clades into
consideration. In contrast to previous approaches, our model requires the
matching between clades to respect the structure of the two trees, a property
that the classical RF metric exhibits, too. We show that computing this
generalized RF metric is, unfortunately, NP-hard. We then present a simple
Integer Linear Program for its computation, and evaluate it by an
all-against-all comparison of 100 trees from a benchmark data set. We find that
matchings that respect the tree structure differ significantly from those that
do not, underlining the importance of this natural condition.


title:
Computing the Skewness of the Phylogenetic Mean Pairwise Distance in
  Linear Time

abstract:
  The phylogenetic Mean Pairwise Distance (MPD) is one of the most popular
measures for computing the phylogenetic distance between a given group of
species. More specifically, for a phylogenetic tree T and for a set of species
R represented by a subset of the leaf nodes of T, the MPD of R is equal to the
average cost of all possible simple paths in T that connect pairs of nodes in
R.
  Among other phylogenetic measures, the MPD is used as a tool for deciding if
the species of a given group R are closely related. To do this, it is important
to compute not only the value of the MPD for this group but also the
expectation, the variance, and the skewness of this metric. Although efficient
algorithms have been developed for computing the expectation and the variance
the MPD, there has been no approach so far for computing the skewness of this
measure.
  In the present work we describe how to compute the skewness of the MPD on a
tree T optimally, in Theta(n) time; here n is the size of the tree T. So far
this is the first result that leads to an exact, let alone efficient,
computation of the skewness for any popular phylogenetic distance measure.
Moreover, we show how we can compute in Theta(n) time several interesting
quantities in T that can be possibly used as building blocks for computing
efficiently the skewness of other phylogenetic measures.


title:
Condensated fermion system in the model of four-quark interaction with
  large correlation length

abstract:
  Studying a model of four-quark interaction with large correlation length we
find out both the features peculiar an unitary fermi gas and the specific
anomalous properties of the fermi systems with a fermion condensate. It is
argued that a possibility of phase transition originated by interface between
the Fermi sphere and fermion condensate appears in such quark systems. The
results obtained could be instrumental for phenomenological applications in
view of our conclusion about approximately the same behavior of the dynamical
characteristics of quark ensembles with different four-quark interaction forms
in a practical interval of coupling constant.


title: Epoxy-based broadband anti-reflection coating for millimeter-wave optics

abstract:
  We have developed epoxy-based, broadband anti-reflection coatings for
millimeter-wave astrophysics experiments with cryogenic optics. By using
multiple-layer coatings where each layer steps in dielectric constant, we
achieved low reflection over a wide bandwidth. We suppressed the reflection
from an alumina disk to 10% over fractional bandwidths of 92% and 104% using
two-layer and three-layer coatings, respectively. The dielectric constants of
epoxies were tuned between 2.06 and 7.44 by mixing three types of epoxy and
doping with strontium titanate powder required for the high dielectric
mixtures. At 140 Kelvin, the band-integrated absorption loss in the coatings
was suppressed to less than 1% for the two-layer coating, and below 10% for the
three-layer coating.


title:
Characterizing Compatibility and Agreement of Unrooted Trees via Cuts in
  Graphs

abstract:
  Deciding whether there is a single tree -a supertree- that summarizes the
evolutionary information in a collection of unrooted trees is a fundamental
problem in phylogenetics. We consider two versions of this question: agreement
and compatibility. In the first, the supertree is required to reflect precisely
the relationships among the species exhibited by the input trees. In the
second, the supertree can be more refined than the input trees.
  Tree compatibility can be characterized in terms of the existence of a
specific kind of triangulation in a structure known as the display graph.
Alternatively, it can be characterized as a chordal graph sandwich problem in a
structure known as the edge label intersection graph. Here, we show that the
latter characterization yields a natural characterization of compatibility in
terms of minimal cuts in the display graph, which is closely related to
compatibility of splits. We then derive a characterization for agreement.


title: High Performance Information Reconciliation for QKD with CASCADE

abstract:
  It is widely accepted in the quantum cryptography community that interactive
information reconciliation protocols, such as cascade, are ineffcient due to
the communication overhead. Instead, non-interactive information reconciliation
protocols based on i.e. LDPC codes or, more recently, polar codes have been
proposed. In this work, we argue that interactive protocols should be taken
into consideration in modern quantum key distribution systems. In particular,
we demonstrate how to improve the performance of cascade by proper
implementation and use. Our implementation of cascade reaches a throughput
above 80 Mbps under realistic conditions. This is more than four times the
throughput previously demonstrated in any information reconciliation protocol.


title: Semiparametric Exponential Families for Heavy-Tailed Data

abstract:
  We propose a semiparametric method for fitting the tail of a heavy-tailed
population given a relatively small sample from that population and a larger
sample from a related background population. We model the tail of the small
sample as an exponential tilt of the better-observed large-sample tail, using a
robust sufficient statistic motivated by extreme value theory. In particular,
our method induces an estimator of the small-population mean, and we give
theoretical and empirical evidence that this estimator outperforms methods that
do not use the background sample. We demonstrate substantial efficiency gains
over competing methods in simulation and on data from a large controlled
experiment conducted by Facebook.


title: Unifying Parsimonious Tree Reconciliation

abstract:
  Evolution is a process that is influenced by various environmental factors,
e.g. the interactions between different species, genes, and biogeographical
properties. Hence, it is interesting to study the combined evolutionary history
of multiple species, their genes, and the environment they live in. A common
approach to address this research problem is to describe each individual
evolution as a phylogenetic tree and construct a tree reconciliation which is
parsimonious with respect to a given event model. Unfortunately, most of the
previous approaches are designed only either for host-parasite systems, for
gene tree/species tree reconciliation, or biogeography. Hence, a method is
desirable, which addresses the general problem of mapping phylogenetic trees
and covering all varieties of coevolving systems, including e.g., predator-prey
and symbiotic relationships. To overcome this gap, we introduce a generalized
cophylogenetic event model considering the combinatorial complete set of local
coevolutionary events. We give a dynamic programming based heuristic for
solving the maximum parsimony reconciliation problem in time O(n^2), for two
phylogenies each with at most n leaves. Furthermore, we present an exact
branch-and-bound algorithm which uses the results from the dynamic programming
heuristic for discarding partial reconciliations. The approach has been
implemented as a Java application which is freely available from
http://pacosy.informatik.uni-leipzig.de/coresym.


title:
Narrow absorption line variability in repeat quasar observations from
  the Sloan Digital Sky Survey

abstract:
  We present the results from a time domain study of absorption lines detected
in quasar spectra with repeat observations from the Sloan Digital Sky Survey
Data Release 7 (SDSS DR7). Beginning with over 4500 unique time separation
baselines of various absorption line species identified in the SDSS DR7 quasar
spectra, we create a catalogue of 2522 quasar absorption line systems with two
to eight repeat observations, representing the largest collection of unbiased
and homogeneous multi-epoch absorption systems ever published. To investigate
these systems for time variability of narrow absorption lines, we refine this
sample based on the reliability of the system detection, the proximity of
pixels with bright sky contamination to individual absorption lines, and the
quality of the continuum fit. Variability measurements of this sub-sample based
on the absorption line equivalent widths yield a total of 33 systems with
indications of significantly variable absorption strengths on time-scales
ranging from one day to several years in the rest frame of the absorption
system. Of these, at least 10 are from a class known as intervening absorption
systems caused by foreground galaxies along the line of sight to the background
quasar. This is the first evidence of possible absorption line variability
detected in intervening systems, and their short time-scale variations suggest
that small-scale structures (~10-100 au) are likely to exist in their host
foreground galaxies.


title:
RISM -- Reputation Based Intrusion Detection System for Mobile Ad hoc
  Networks

abstract:
  This paper proposes a combination of an Intrusion Detection System with a
routing protocol to strengthen the defense of a Mobile Ad hoc Network. Our
system is Socially Inspired, since we use the new paradigm of Reputation
inherited from human behavior. The proposed IDS also has a unique
characteristic of being Semi-distributed, since it neither distributes its
Observation results globally nor keeps them entirely locally; however, managing
to communicate this vital information without accretion of the network traffic.
This innovative approach also avoids void assumptions and complex calculations
for calculating and maintaining trust values used to estimate the reliability
of other nodes observations. A robust Path Manager and Monitor system and
Redemption and Fading concepts are other salient features of this design. The
design has shown to outperform normal DSR in terms of Packet Delivery Ratio and
Routing Overhead even when up to half of nodes in the network behave as
malicious.


title: Prospects for collider searches for dark matter with heavy quarks

abstract:
  We present projections for future collider searches for dark matter produced
in association with bottom or top quarks. Such production channels give rise to
final states with missing transverse energy and one or more b-jets. Limits are
given assuming an effective scalar operator coupling dark matter to quarks,
where the dedicated analysis discussed here improves significantly over a
generic monojet analysis. We give updated results for an anticipated
high-luminosity LHC run at 14 TeV and for a 33 TeV hadron collider.


title: Landau's statistical mechanics for quasiparticle models

abstract:
  Landau's formalism of statistical mechanics \cite{la.1} is applied to the
quasiparticle model of quark gluon plasma. It is a general formalism and
consistent with our earlier studies \cite{ba.1} based on Pathria's formalism
\cite{pa.1}. Both the formalism are consistent with thermodynamics and
statistical mechanics. Under certain conditions, which are wrongly called
thermodynamic consistent relation, we recover other formalism of quasiparticle
system \cite{go.1}, widely studied in quark gluon plasma.


title:
A nearly optimal algorithm for deciding connectivity queries in smooth
  and bounded real algebraic sets

abstract:
  A roadmap for a semi-algebraic set $S$ is a curve which has a non-empty and
connected intersection with all connected components of $S$. Hence, this kind
of object, introduced by Canny, can be used to answer connectivity queries
(with applications, for instance, to motion planning) but has also become of
central importance in effective real algebraic geometry, since it is used in
higher-level algorithms. In this paper, we provide a probabilistic algorithm
which computes roadmaps for smooth and bounded real algebraic sets. Its output
size and running time are polynomial in $(nD)^{n\log(d)}$, where $D$ is the
maximum of the degrees of the input polynomials, $d$ is the dimension of the
set under consideration and $n$ is the number of variables. More precisely, the
running time of the algorithm is essentially subquadratic in the output size.
Even under our assumptions, it is the first roadmap algorithm with output size
and running time polynomial in $(nD)^{n\log(d)}$.


title: Asymptotics of solutions to the Navier-Stokes system in exterior domains

abstract:
  We consider the incompressible Navier-Stokes equations with the Dirichlet
boundary condition in an exterior domain of $\mathbb{R}^n$ with $n\geq2$. We
compare the long-time behaviour of solutions to this initial-boundary value
problem with the long-time behaviour of solutions of the analogous Cauchy
problem in the whole space $\mathbb{R}^n$. We find that the long-time
asymptotics of solutions to both problems coincide either in the case of small
initial data in the weak $L^{n}$-space or for a certain class of large initial
data.


title:
Asymmetric-valued Spectrum Auction and Competition in Wireless Broadband
  Services

abstract:
  We study bidding and pricing competition between two spiteful mobile network
operators (MNOs) with considering their existing spectrum holdings. Given
asymmetric-valued spectrum blocks are auctioned off to them via a first-price
sealed-bid auction, we investigate the interactions between two spiteful MNOs
and users as a three-stage dynamic game and characterize the dynamic game's
equilibria. We show an asymmetric pricing structure and different market share
between two spiteful MNOs. Perhaps counter-intuitively, our results show that
the MNO who acquires the less-valued spectrum block always lowers his service
price despite providing double-speed LTE service to users. We also show that
the MNO who acquires the high-valued spectrum block, despite charing a higher
price, still achieves more market share than the other MNO. We further show
that the competition between two MNOs leads to some loss of their revenues. By
investigating a cross-over point at which the MNOs' profits are switched, it
serves as the benchmark of practical auction designs.


title: A Non-Abelian Vortex Lattice in Strongly Coupled Systems

abstract:
  The AdS/CFT correspondence predicts that background non-abelian magnetic
fields induce instabilities in strongly-coupled systems with non-abelian global
symmetries. These instabilities lead to the formation of vortex lattices in
which the non-abelian currents "antiscreen" the applied magnetic field. From
the bulk perspective, this behaviour can be traced to a well-known instability
of Yang-Mills theory. We analyse the phase structure of the instability and
comment on aspects of the vortex lattice.


title: On the Matrix Median Problem

abstract:
  The Genome Median Problem is an important problem in phylogenetic
reconstruction under rearrangement models. It can be stated as follows: given
three genomes, find a fourth that minimizes the sum of the pairwise
rearrangement distances between it and the three input genomes. Recently,
Feijao and Meidanis extended the algebraic theory for genome rearrangement to
allow for linear chromosomes, thus yielding a new rearrangement model (the
algebraic model), very close to the celebrated DCJ model. In this paper, we
study the genome median problem under the algebraic model, whose complexity is
currently open, proposing a more general form of the problem, the matrix median
problem. It is known that, for any metric distance, at least one of the corners
is a 4/3-approximation of the median. Our results allow us to compute up to
three additional matrix median candidates, all of them with approximation
ratios at least as good as the best corner, when the input matrices come from
genomes. From the application point of view, it is usually more interesting to
locate medians farther from the corners. We also show a fourth median candidate
that gives better results in cases we tried. However, we do not have proven
bounds for this fourth candidate yet.


title: A nominal association matrix with feature selection for categorical data

abstract:
  We introduce an informative probabilistic association matrix to measure a
proportional local-to-global association of categories of one variable with
another categorical variable. Towards a probability based proportional
prediction, the association matrix gives rise to the expected predictive
distribution of the first and second types of errors for a multinomial response
variable. In addition, the normalization of the diagonal of the matrix gives
rise to an association vector, which provides the expected category accuracy
lift rate distribution. A general scheme of global-to-global association
measures with flexible weight vectors is further developed from the matrix. A
hierarchy of equivalence relations defined by the association matrix and vector
is shown. Applications to financial and survey data together with simulations
results are presented.


title:
A Fixed-Parameter Algorithm for Minimum Common String Partition with Few
  Duplications

abstract:
  Motivated by the study of genome rearrangements, the NP-hard Minimum Common
String Partition problems asks, given two strings, to split both strings into
an identical set of blocks. We consider an extension of this problem to
unbalanced strings, so that some elements may not be covered by any block. We
present an efficient fixed-parameter algorithm for the parameters number k of
blocks and maximum occurrence d of a letter in either string. We then evaluate
this algorithm on bacteria genomes and synthetic data.


title:
Effect of exchange interaction on the spin fluctuations of localized
  electrons

abstract:
  In this paper a microscopic theory of spin fluctuations in an ensemble of
electrons localized on donors in a bulk semiconductor has been developed. Both
the hyperfine interaction of the electron spin with spins of lattice nuclei and
the exchange interaction between the electrons have been taken into account. We
propose a model of clusters to calculate spin noise spectra of the ensemble of
localized charge carriers. It has been shown that the electron-electron
exchange interaction leads to an effective averaging of random nuclear fields
and a shift of the peak in the spin-fluctuation spectrum towards lower
frequencies.


title: MSARC: Multiple Sequence Alignment by Residue Clustering

abstract:
  Progressive methods offer efficient and reasonably good solutions to the
multiple sequence alignment problem. However, resulting alignments are biased
by guide-trees, especially for relatively distant sequences.
  We propose MSARC, a new graph-clustering based algorithm that aligns sequence
sets without guide-trees. Experiments on the BAliBASE dataset show that MSARC
achieves alignment quality similar to best progressive methods and
substantially higher than the quality of other non-progressive algorithms.
Furthermore, MSARC outperforms all other methods on sequence sets with the
similarity structure hardly represented by a phylogenetic tree. Furthermore,
MSARC outperforms all other methods on sequence sets whose evolutionary
distances are hardly representable by a phylogenetic tree. These datasets are
most exposed to the guide-tree bias of alignments.
  MSARC is available at http://bioputer.mimuw.edu.pl/msarc


title:
Superconductivity in an electron band just above the Fermi level:
  possible route to BCS-BEC superconductivity

abstract:
  Conventional superconductivity follows Bardeen-Cooper-Schrieffer(BCS) theory
of electrons-pairing in momentum-space, while superfluidity is the
Bose-Einstein condensation(BEC) of atoms paired in real-space. These properties
of solid metals and ultra-cold gases, respectively, are connected by the
BCS-BEC crossover. Here we investigate the band dispersions in
FeTe$_{0.6}$Se$_{0.4}$($T_c$ = 14.5 K $\sim$ 1.2 meV) in an accessible range
below and above the Fermi level($E_F$) using ultra-high resolution laser
angle-resolved photoemission spectroscopy. We uncover an electron band lying
just 0.7 meV ($\sim$ 8 K) above $E_F$ at the $\Gamma$-point, which shows a
sharp superconducting coherence peak with gap formation below $T_c$. The
estimated superconducting gap $\Delta$ and Fermi energy $\epsilon_F$ indicate
composite superconductivity in an iron-based superconductor, consisting of
strong-coupling BEC in the electron band and weak-coupling BCS-like
superconductivity in the hole band. The study identifies the possible route to
BCS-BEC superconductivity.


title: Belief-Propagation Guided Monte-Carlo Sampling

abstract:
  A Monte-Carlo algorithm for discrete statistical models that combines the
full power of the Belief Propagation algorithm with the advantages of a
detailed-balanced heat bath approach is presented. A sub-tree inside the factor
graph is first extracted randomly; Belief Propagation is then used as a perfect
sampler to generate a configuration on the tree given the boundary conditions
and the procedure is iterated. This appoach is best adapted for locally tree
like graphs, it is therefore tested on the hard cases of spin-glass models for
random graphs demonstrating its state-of-the art status in those cases.


title:
Mutual Enrichment in Ranked Lists and the Statistical Assessment of
  Position Weight Matrix Motifs

abstract:
  Statistics in ranked lists is important in analyzing molecular biology
measurement data, such as ChIP-seq, which yields ranked lists of genomic
sequences. State of the art methods study fixed motifs in ranked lists. More
flexible models such as position weight matrix (PWM) motifs are not addressed
in this context. To assess the enrichment of a PWM motif in a ranked list we
use a PWM induced second ranking on the same set of elements. Possible orders
of one ranked list relative to the other are modeled by permutations. Due to
sample space complexity, it is difficult to characterize tail distributions in
the group of permutations. In this paper we develop tight upper bounds on tail
distributions of the size of the intersection of the top of two uniformly and
independently drawn permutations and demonstrate advantages of this approach
using our software implementation, mmHG-Finder, to study PWMs in several
datasets.


title:
An Integrated System for 3D Gaze Recovery and Semantic Analysis of Human
  Attention

abstract:
  This work describes a computer vision system that enables pervasive mapping
and monitoring of human attention. The key contribution is that our methodology
enables full 3D recovery of the gaze pointer, human view frustum and associated
human centered measurements directly into an automatically computed 3D model in
real-time. We apply RGB-D SLAM and descriptor matching methodologies for the 3D
modeling, localization and fully automated annotation of ROIs (regions of
interest) within the acquired 3D model. This innovative methodology will open
new avenues for attention studies in real world environments, bringing new
potential into automated processing for human factors technologies.


title: Proceedings Sixth Workshop on Intersection Types and Related Systems

abstract:
  This volume contains the proceedings of the Sixth Workshop on Intersection
Types and Related Systems (ITRS 2012). The workshop was held in Dubrovnik
(Croatia) on June 29th, 2012, affiliated to Twenty-Seventh Annual ACM/IEEE
Symposium on Logic in Computer Science (LICS 2012). The ITRS workshop aims to
bring together researchers working on both the theory and practical
applications of systems based on intersection types and related approaches
(e.g., union types, refinement types, behavioural types, recursive types, and
so on).


title:
High-temperature superconductivity and normal state in the Holstein-t-J
  model

abstract:
  A possible origin of the high-temprature superconductivity in cuprates has
been suggested. It is supposed that electron-phonon interaction determines the
strong correlation narrowing of the electron band. It provides the conditions
for the formation of a singlet electron pair coupled by exchange interaction.
For the pure t-J model it has been proved that these electron pairs are
destroyed by a strong effective kinematic field. The detailed analysis of an
influence of the Holstein polaron excitations upon normal and superconducting
properties of the strongly correlated electrons was made. A calculated critical
temperature of the superconductivity and gap function are in good agreement
with experimental data for cuprates.


title: Hybrid Affinity Propagation

abstract:
  In this paper, we address a problem of managing tagged images with hybrid
summarization. We formulate this problem as finding a few image exemplars to
represent the image set semantically and visually, and solve it in a hybrid way
by exploiting both visual and textual information associated with images. We
propose a novel approach, called homogeneous and heterogeneous message
propagation ($\text{H}^\text{2}\text{MP}$). Similar to the affinity propagation
(AP) approach, $\text{H}^\text{2}\text{MP}$ reduce the conventional
\emph{vector} message propagation to \emph{scalar} message propagation to make
the algorithm more efficient. Beyond AP that can only handle homogeneous data,
$\text{H}^\text{2}\text{MP}$ generalizes it to exploit extra heterogeneous
relations and the generalization is non-trivial as the reduction to scalar
messages from vector messages is more challenging. The main advantages of our
approach lie in 1) that $\text{H}^\text{2}\text{MP}$ exploits visual similarity
and in addition the useful information from the associated tags, including the
associations relation between images and tags and the relations within tags,
and 2) that the summary is both visually and semantically satisfactory. In
addition, our approach can also present a textual summary to a tagged image
collection, which can be used to automatically generate a textual description.
The experimental results demonstrate the effectiveness and efficiency of the
roposed approach.


title: Scalable $k$-NN graph construction

abstract:
  The $k$-NN graph has played a central role in increasingly popular
data-driven techniques for various learning and vision tasks; yet, finding an
efficient and effective way to construct $k$-NN graphs remains a challenge,
especially for large-scale high-dimensional data. In this paper, we propose a
new approach to construct approximate $k$-NN graphs with emphasis in:
efficiency and accuracy. We hierarchically and randomly divide the data points
into subsets and build an exact neighborhood graph over each subset, achieving
a base approximate neighborhood graph; we then repeat this process for several
times to generate multiple neighborhood graphs, which are combined to yield a
more accurate approximate neighborhood graph. Furthermore, we propose a
neighborhood propagation scheme to further enhance the accuracy. We show both
theoretical and empirical accuracy and efficiency of our approach to $k$-NN
graph construction and demonstrate significant speed-up in dealing with large
scale visual data.


title: Bi-spectral beam extraction in combination with a focusing feeder

abstract:
  Bi-spectral beam extraction combines neutrons from two different kind of
moderators into one beamline, expanding the spectral range and thereby the
utilization of an instrument. This idea can be realized by a mirror that
reflects long wavelength neutrons from an off-axis colder moderator into a
neutron guide aligned with another moderator emitting neutrons with shorter
wavelengths which will be transmitted through the mirror. The mirror used in
such systems is typically several meters long, which is a severe disadvantage
because it reduces the possible length of a focusing device in design concepts
requiring a narrow beam at a short distance from the source, as used in many
instruments under development for the planned European Spallation Source (ESS).
We propose a shortened extraction system consisting of several mirrors, and
show that such an extraction system is better suited for combination with a
feeder in an eye of the needle design, illustrated here in the context of a
possible ESS imaging beamline.


title:
Generalized Lagrangian mean curvature flows in almost Calabi-Yau
  manifolds

abstract:
  In this paper, we study the generalized Lagrangian mean curvature flow in
almost Einstein manifold proposed by T. Behrndt. We show that the singularity
of this flow is characterized by the second fundamental form. We also show that
the rescaled flow at a singularity converges to a finite union of Special
Lagrangian cones for generalized Lagrangian mean curvature flow with
zero-Maslov class in almost Calabi-Yau manifold. As a corollary, there is no
finite time Type-I singularity for such a flow.


title: On possible origins of power-law distributions

abstract:
  Selected examples of possible origins of power-law distributions are
presented.


title:
Micron-Scale Mapping of Megagauss Magnetic Fields in Petawatt
  Laser-Solid Interactions

abstract:
  We report spatially and temporally resolved measurements of magnetic fields
generated by petawatt laser-solid interactions with high spatial resolution,
using optical polarimetry. The polarimetric measurements map the megagauss
magnetic field profiles generated by the fast electron currents at the target
rear. The magnetic fields at the rear of a 50 $\mu$m thick aluminum target
exhibit distinct and unambiguous signatures of electron beam filamentation.
These results are corroborated by hybrid simulations.


title: Classification of Finite Potent Endomorphisms

abstract:
  The aim of this work is to offer a family of invariants that allows us to
classify finite potent endomorphisms on arbitrary vector spaces, generalizing
the classification of endomorphisms on finite-dimensional vector spaces. As a
particular case we classify nilpotent endomorphisms on infinite-dimensional
vector spaces.


title:
The chromatic class and the chromatic number of the planar conjugated
  triangulation

abstract:
  This material is dedicated to the estimation of the chromatic number and
chromatic class of the conjugated triangulation (first conversion) and also of
the second conversion of the planar triangulation. Also this paper introduces
some new hypotheses, which are equivalent to Four Color Problem.


title: Interacting varying Ghost Dark energy models in General Relativity

abstract:
  Motivated by recent developments in Cosmology we would like to consider an
extension of the Ghost DE which we will call as varying Ghost DE. Ghost DE like
other models was introduced recently as a possible way to explain accelerated
expansion of the Universe. For the phenomenological origin of the varying Ghost
dark energy in our Universe we can suggest an existence of some unknown
dynamics between the Ghost Dark energy and a fluid which evaporated completely
making sense of the proposed effect. Moreover, we assume that this was in the
epochs and scales which are unreachable by nowadays experiments, like in very
early Universe. In this study we will investigate the model for cosmological
validity. We will apply observational and causality constraints to illuminate
physically correct behavior of the model from the phenomenological one. We saw
that an interaction between the varying Ghost DE and cold DM~(CDM) also
provides a solution to the cosmological coincidence problem. And we found that
the Ghost DE behaves as a matter like fluid in early Universe.


title:
Comparing Model Selection and Regularization Approaches to Variable
  Selection in Model-Based Clustering

abstract:
  We compare two major approaches to variable selection in clustering: model
selection and regularization. Based on previous results, we select the method
of Maugis et al. (2009b), which modified the method of Raftery and Dean (2006),
as a current state of the art model selection method. We select the method of
Witten and Tibshirani (2010) as a current state of the art regularization
method. We compared the methods by simulation in terms of their accuracy in
both classification and variable selection. In the first simulation experiment
all the variables were conditionally independent given cluster membership. We
found that variable selection (of either kind) yielded substantial gains in
classification accuracy when the clusters were well separated, but few gains
when the clusters were close together. We found that the two variable selection
methods had comparable classification accuracy, but that the model selection
approach had substantially better accuracy in selecting variables. In our
second simulation experiment, there were correlations among the variables given
the cluster memberships. We found that the model selection approach was
substantially more accurate in terms of both classification and variable
selection than the regularization approach, and that both gave more accurate
classifications than $K$-means without variable selection.


title: Probabilistic Approaches to Alignment with Tandem Repeats

abstract:
  We propose a simple tractable pair hidden Markov model for pairwise sequence
alignment that accounts for the presence of short tandem repeats. Using the
framework of gain functions, we design several optimization criteria for
decoding this model and describe the resulting decoding algorithms, ranging
from the traditional Viterbi and posterior decoding to block-based decoding
algorithms specialized for our model. We compare the accuracy of individual
decoding algorithms on simulated data and find our approach superior to the
classical three-state pair HMM in simulations.


title: Multiscale Identification of Topological Domains in Chromatin

abstract:
  Recent chromosome conformation capture experiments have led to the discovery
of dense, contiguous, megabase-sized topological domains that are similar
across cell types and conserved across species. These domains are strongly
correlated with a number of chromatin markers and have since been included in a
number of analyses. However, functionally-relevant domains may exist at
multiple length scales. We introduce a new and efficient algorithm that is able
to capture persistent domains across various resolutions by adjusting a single
scale parameter. The identified novel domains are substantially different from
domains reported previously and are highly enriched for insulating factor CTCF
binding and histone modfications at the boundaries.


title: Strengthened Grunsky and Milin inequalities

abstract:
  The method of Grunsky inequalities has many applications and has been
extended in many directions, even to bordered Riemann surfaces. However, unlike
the case of functions univalent in the disk, a quasiconformal variant of this
theory has not been developed so far. In this paper, we essentially improve the
basic facts concerning the classical Grunsky inequalities for univalent
functions on the disk and extend these results to arbitrary quasiconformal
disks. Several applications are given.


title: Curvaton with nonminimal derivative coupling to gravity

abstract:
  We show a curvaton model, in which the curvaton has a nonminimal derivative
coupling to gravity. Thanks to such a coupling, we find that the
scale-invariance of the perturbations can be achieved for arbitrary values of
the equation-of-state of background, provided that it is nearly a constant. We
also discussed about tensor perturbations, the local non-Gaussianities
generated by the nonminimal derivative coupling curvaton model, as well as the
adiabatic perturbations which are transferred from the field perturbations
during the curvaton decay.


title:
Supramolecular interaction of singlewall carbon nanotubes with a
  functional TTF-based mediator probed by field-effect transistor devices

abstract:
  The supramolecular interaction between individual singlewall carbon nanotubes
and a functional organic material based on tetrathiafulvalene (TTF) is
investigated by means of electric transport measurements in field effect
transistor configuration as well as by NIR absorption spectroscopy. The results
clearly point to a charge transfer interaction in which the adsorbed molecule
serves as electron acceptor for the nanotubes through its pyrene units.
Exposure to iodine vapors enhances this effect. The comparison with pristine
carbon nanotube field effect transistor devices demonstrates the possibility to
exploit charge transfer interactions taking place in supramolecular assemblies
in which a mediator unit is used to transduce and enhance an external signal.


title: Hierarchical masses and universal mixing in quark-lepton mass matrices

abstract:
  The universality hypothesis for quark and lepton mixing matrices (CKM and
MNS) is further developed. This hypothesis explains why the CKM is almost
diagonal whereas the MNS is almost maximally mixed. If this hypothesis is true,
the Dirac CP violating phase of the MNS mixing matrix is bounded around $\pi$
or 0. Quark-lepton mass matrices which realizes this hypothesis are
constructed, showing simple power law relations among mass matrices for
up-type, down-type quarks and neutrinos.


title: A space-time parallel solver for the three-dimensional heat equation

abstract:
  The paper presents a combination of the time-parallel "parallel full
approximation scheme in space and time" (PFASST) with a parallel multigrid
method (PMG) in space, resulting in a mesh-based solver for the
three-dimensional heat equation with a uniquely high degree of efficient
concurrency. Parallel scaling tests are reported on the Cray XE6 machine "Monte
Rosa" on up to 16,384 cores and on the IBM Blue Gene/Q system "JUQUEEN" on up
to 65,536 cores. The efficacy of the combined spatial- and temporal
parallelization is shown by demonstrating that using PFASST in addition to PMG
significantly extends the strong-scaling limit. Implications of using spatial
coarsening strategies in PFASST's multi-level hierarchy in large-scale parallel
simulations are discussed.


title:
The thermoballistic approach to charge carrier transport in
  semiconductors

abstract:
  A comprehensive survey is given of the thermoballistic approach to charge
carrier transport in semiconductors. This semiclassical approach bridges the
gap between the drift-diffusion and ballistic ("thermionic") models of carrier
transport, whose validity is limited to the range of very small and very large
values, respectively, of the carrier mean free path. The physical concept
underlying the thermoballistic approach, while incorporating basic features of
the drift-diffusion and ballistic descriptions, constitutes a novel, unifying
scheme. It is based on the introduction of "ballistic configurations" defined
by a random partitioning of the length of a semiconducting sample into
ballistic transport intervals, which are linked by points of local
thermodynamic equilibrium at which carriers are emitted or absorbed. By
averaging the carrier currents in the ballistic intervals over all ballistic
configurations, a position-dependent thermoballistic current is derived for
arbitrary magnitude of the carrier mean free path. This current is the key
element of the thermoballistic concept and forms the point of departure of the
calculation of various transport quantities. The present article starts out
with an account of the standard drift-diffusion and ballistic transport models,
and of a prototype model which paves the way for the fully developed form of
that concept. In the main body of the article, a coherent exposition of the
thermoballistic approach is given within a general formulation that takes into
account arbitrarily shaped, spin-split potential energy profiles and spin
relaxation during the carrier motion across ballistic intervals. The
calculational procedures devised for implementing the thermoballistic concept
are described. Specific examples relevant to present-day semiconductor and
spintronics research are considered.


title: Thermal Instability behind a Shock Wave in HI and Molecular Clouds

abstract:
  We performed one-dimensional hydrodynamic simulations with detailed cooling,
heating and chemical processes to examine the thermal stability of shocked gas
in cold neutral medium (CNM) and molecular clouds. We find that both CNM and
molecular clouds can be thermally unstable in the cooling layer behind the
shock wave. The characteristic wavelength of the thermal instability ranges
from 10^-5 pc to 0.1 pc in the CNM, and from 10^-7 pc to 0.1 pc in the
molecular clouds. This coincides with the size of observed tiny scale
structures in the CNM and molecular clouds, indicating that the thermal
instability in the shocked gas could be a formation mechanism of these tiny
structures in the interstellar medium. We have also calculated the e-folding
number of the thermal instability to estimate the amplification of the density
fluctuation in the shocked gas. Density perturbations in the CNM grow by a
factor of exp(5)~150, whereas the perturbations in the molecular clouds grow
only by a factor of a few behind a high Mach number shock. The amplification
factor is larger at lower densities and higher velocities. Formation of very
small-scale structures by thermal instability in shocked gas is more effective
in lower densities.


title:
New and updated stellar parameters for 71 evolved planet hosts. On the
  metallicity - giant planet connection

abstract:
  It is still being debated whether the well-known metallicity - giant planet
correlation for dwarf stars is also valid for giant stars. For this reason,
having precise metallicities is very important. Different methods can provide
different results that lead to discrepancies in the analysis of planet hosts.
To study the impact of different analyses on the metallicity scale for evolved
stars, we compare different iron line lists to use in the atmospheric parameter
derivation of evolved stars. Therefore, we use a sample of 71 evolved stars
with planets. With these new homogeneous parameters, we revisit the metallicity
- giant planet connection for evolved stars. A spectroscopic analysis based on
Kurucz models in local thermodynamic equilibrium (LTE) was performed through
the MOOG code to derive the atmospheric parameters. Two different iron line
list sets were used, one built for cool FGK stars in general, and the other for
giant FGK stars. Masses were calculated through isochrone fitting, using the
Padova models. Kolmogorov-Smirnov tests (K-S tests) were then performed on the
metallicity distributions of various different samples of evolved stars and red
giants. All parameters compare well using a line list set, designed
specifically for cool and solar-like stars to provide more accurate
temperatures. All parameters derived with this line list set are preferred and
are thus adopted for future analysis. We find that evolved planet hosts are
more metal-poor than dwarf stars with giant planets. However, a bias in giant
stellar samples that are searched for planets is present. Because of a colour
cut-off, metal-rich low-gravity stars are left out of the samples, making it
hard to compare dwarf stars with giant stars. Furthermore, no metallicity
enhancement is found for red giants with planets ($\log g < 3.0$\,dex) with
respect to red giants without planets.


title:
Characterization of Fe-N nano crystals and nitrogen-containing
  inclusions in (Ga,Fe)N thin films using transmission electron microscopy

abstract:
  Nanometric inclusions filled with nitrogen, located adjacent to FenN (n = 3
or 4) nanocrystals within (Ga,Fe)N layers, are identified and characterized
using scanning transmission electron microscopy (STEM) and electron energy-loss
spectroscopy (EELS). High-resolution STEM images reveal a truncation of the
Fe-N nanocrystals at their boundaries with the nitrogen-containing inclusion. A
controlled electron beam hole drilling experiment is used to release nitrogen
gas from an inclusion in situ in the electron microscope. The density of
nitrogen in an individual inclusion is measured to be 1.4 +- 0.3 g/cm3. These
observations provide an explanation for the location of surplus nitrogen in the
(Ga,Fe)N layers, which is liberated by the nucleation of FenN (n> 1)
nanocrystals during growth.


title: Generating functionals for guided self-organization

abstract:
  Time evolution equations for dynamical systems can often be derived from
generating functionals. Examples are Newton's equations of motion in classical
dynamics which can be generated within the Lagrange or the Hamiltonian
formalism. We propose that generating functionals for self-organizing complex
systems offer several advantages. Generating functionals allow to formulate
complex dynamical systems systematically and the results obtained are typically
valid for classes of complex systems, as defined by the type of their
respective generating functionals. The generated dynamical systems tend, in
addition, to be minimal, containing only few free and undetermined parameters.
We point out that two or more generating functionals may be used to define a
complex system and that multiple generating function may not, and should not,
be combined into a single overall objective function. We provide and discuss
examples in terms of adapting neural networks.


title:
Theory of quasiparticle scattering interference on the surface of
  topological superconductors

abstract:
  Topological superconductors, such as noncentrosymmetric superconductors with
strong spin-orbit coupling, exhibit protected zero-energy surface states, which
possess an intricate helical spin structure. We show that this nontrival spin
character of the surface states can be tested experimentally from the absence
of certain backscattering processes in Fourier-transform scanning tunneling
measurements. A detailed theoretical analysis is given of the quasiparticle
scattering interference on the surface of both nodal and fully gapped
topological superconductors with different crystal point-group symmetries. We
determine the universal features in the interference patterns resulting from
magnetic and nonmagnetic scattering processes of the surface quasiparticles. It
is shown that Fourier-transform scanning tunneling spectroscopy allows us to
uniquely distinguish among different types of topological surface states, such
as zero-energy flat bands, arc surface states, and helical Majorana modes,
which in turn provides valuable information on the spin and orbital pairing
symmetry of the bulk superconducting state.


title: Dual Lukacs regressions of negative orders for non-commutative variables

abstract:
  In the paper we study characterizations of probability measures in free
probability. By constancy of regressions for random variable $\V(\I-\U)\V$
given by $\V\U\V$, where $\U$ and $\V$ are free, we characterize free Poisson
and free binomial distributions. Our paper is analog in free probability of
results known in classical probability \cite{BobWes2002Dual}, where gamma and
beta distributions are characterized by constancy of $\E((V(1-U))^{i}|UV)$, for
$i \in \{-2,-1,1,2\}$. This paper together with previous results
\cite{SzpojanWesol} exhaust all cases of characterizations from
\cite{BobWes2002Dual}.


title: Determination of Charm Quark Mass and $\alpha_s(M_Z)$ from HERA data

abstract:
  Charm production data from HERA can be used to determine the charm quark mass
and jet production data from HERA can be used to detrmine $\alpha_s(M_Z)$.
recent results are summarised.


title: Exceptional and regular spectra of a generalized Rabi model

abstract:
  We study the spectrum of the generalized Rabi model in which co- and
counter-rotating terms have different coupling strengths. It is also equivalent
to the model of a two-dimensional electron gas in a magnetic field with Rashba
and Dresselhaus spin-orbit couplings. Like in case of the Rabi model, the
spectrum of the generalized Rabi model consists of the regular and the
exceptional parts. The latter is represented by the energy levels which cross
at certain parameters' values which we determine explicitly. The wave functions
of these exceptional states are given by finite order polynomials in the
Bargmann representation. The roots of these polynomials satisfy a Bethe ansatz
equation of the Gaudin type. At the exceptional points the model is therefore
quasi-exactly solvable. An analytical approximation is derived for the regular
part of the spectrum in the weak- and strong-coupling limits. In particular, in
the strong-coupling limit the spectrum consists of two quasi-degenerate
equidistant ladders.

categories: quant-ph cond-mat.mes-hall math-ph math.MP


title: An Integral View of Balmer-dominated Shocks in Supernova Remnants

abstract:
  We present integral-field spectroscopic observations with the VIMOS-IFU at
the VLT of fast (2000-3000 km/s) Balmer-dominated shocks surrounding the
northwestern rim of the remnant of supernova 1006. The high spatial and
spectral resolution of the instrument enable us to show that the physical
characteristics of the shocks exhibit a strong spatial variation over few
atomic scale lengths across 133 sky locations. Our results point to the
presence of a population of non-thermal protons (10-100 keV) which might well
be the seed particles for generating high-energy cosmic rays. We also present
observations of Tycho's supernova remnant taken with the narrow-band tunable
filter imager OSIRIS at the GTC and the Fabry-Perot interferometer GHaFaS at
the WHT to resolve respectively the broad and narrow H\alpha\ lines across a
large part of the remnant.


title:
Kinematic distance study of the planetary nebulae-supernova remnant-HII
  region complex at G35.6-0.5

abstract:
  Two possible planetary nebulae (PN G035.5-00.4 and IRAS 18551+0159), one
newly re-identified supernova remnant (SNR G35.6-0.4), and one HII region
(G35.6-0.5) form a line-of-sight-overlapped complex known as G35.6-0.5. We
analyze 21 cm HI absorption spectra towards the complex to constrain their
kinematic distances. PN G035.5-00.4 has a distance from 3.8+/-0.4 kpc to
5.4+/-0.7 kpc. IRAS 18551+0159 is at 4.3+/-0.5 kpc. We discuss the distance for
SNR 35.6-0.4, for which the previous estimate was 10.5 kpc, and find plausible
for it to be 3.6+/-0.4 kpc. The new distance of SNR G35.6-0.4 and the derived
mass for the ~55 km/s CO molecular cloud can accommodate an association with
HESS J1858+020. We also conclude that SNR G35.6-0.4 is unlikely associated with
PSR J1857+0210 or PSR J1857+0212, which are projected into the SNR area.


title: Naturalness after LHC8

abstract:
  I review the status of naturalness of the weak scale after the results from
the LHC operating at an energy of 8 TeV. Talk delivered at the 2013 Europhysics
Conference on High Energy Physics (EPS), Stockholm, Sweden, 18-24 July 2013.


title:
On compactifications of character varieties of $n$-punctured projective
  line

abstract:
  In this paper, we construct compactifications of $SL_2(\mathbb{C})$-character
varieties of $n$-punctured projective line and study the boundary divisor of
the compactifications. This study is motivated by the conjecture for the
configuration of the boundary divisor, due to C. Simpson. We verify the
conjecture for a few examples.


title:
Modeling Dipolar Post-Shock Accretion Columns for Various Specific
  Accretion Rate Intermediate Polars

abstract:
  We model the post-shock accretion column (PSAC) for intermediate polars
(IPs), with parameterizing specific accretion rate between 0.0001 and 100 g
cm-2 s-1 and metal abundance between 0.1 and 2 times of solar abundance, and
taking into account the gravitational potential and non-equipartition between
ions, electrons and ionization degree. We assume the cylinder and dipole as
geometry of the PSAC. The PSAC becomes higher against the white dwarf (WD)
radius for lower specific accretion rate and more massive WD, and may be
comparable to the WD radius. The consideration of the dipolar geometry
significantly reduces the density and temperature over the whole PSAC comparing
with the cylindrical case when the specific accretion rate is lower than a
threshold which the PSAC height reachs 0.2 RWD with and is decreased by the
more massive white dwarf. We calculate the spectra of the cylindrical and
dipolar PSACs with the wide range of the specific accretion rate. Although the
spectra soften as the specific accretion rate decreases for the both
geometrical assumptions under the specific accretion rate threshold, the
softening is more speedy for the dipolar PSAC. The fact means that the both
geometrical assumptions lead the different WD masses for each other when their
spectra are applied to the IPs hosting the low accretion or a massive WD.
Although the ionization non-equilibrium are also involved for the spectral
calculation, the effects are trivial because the radiation from ionization
non-equilibrium plasma is a few percent of the whole at most.


title:
The genetic code, algebra of projection operators and problems of
  inherited biological ensembles

abstract:
  This article is devoted to applications of projection operators to simulate
phenomenological properties of the molecular-genetic code system. Oblique
projection operators are under consideration, which are connected with matrix
representations of the genetic coding system in forms of the Rademacher and
Hadamard matrices. Evidences are shown that sums of such projectors give
abilities for adequate simulations of ensembles of inherited biological
phenomena including ensembles of biological cycles, morphogenetic ensembles of
phyllotaxis patterns, mirror-symmetric patterns, etc. For such modeling, the
author proposes multidimensional vector spaces, whose subspaces are under a
selective control (or coding) by means of a set of matrix operators on base of
genetic projectors. Development of genetic biomechanics is discussed. The
author proposes and describes special systems of multidimensional numbers under
names united-hypercomplex numbers, which attracted his attention when he
studied genetic systems and genetic matrices. New rules of long nucleotide
sequences are described on the base of the proposed notion of tetra-groups of
equivalent oligonucleotides. Described results can be used for developing
algebraic biology, bio-technical applications and some other fields of science
and technology.


title: Mixing of gravitons with photons in primordial magnetic fields

abstract:
  Here I discuss the conversion of relic gravitons into photons in large scale
cosmological magnetic fields. It is shown that the conversion probability is
quite large at the post recombination epoch with a rather large density of
formed photons. The produced electromagnetic radiation could make a substantial
contribution to the cosmic extragalactic background light and even explain the
cosmic x ray background excess.


title:
Some existence results to the Dirichlet problem for the minimal
  hypersurface equation on non mean convex domains of a Riemannian manifold

abstract:
  We prove the existence of minimal hypersurfaces for the Dirichlet that
extends a similar result of Jenkins and Serrin in Euclidean Space to Riemannian
ambient manifolds


title:
A priori estimates and analytical construction of radially symmetric
  solutions in the gas dynamics

abstract:
  In this article we derive C^1-a priori estimates on the Riemann invariants of
the Euler compressible equations in the case of cylindrical or spherical
symmetry. These estimates allow then to construct shock waves with a time of
existence proportional to the distance to the origin at the initial time.


title: Domain wall fluctuations in ferroelectrics coupled to strain

abstract:
  Using a Ginzburg--Landau--Devonshire model that includes the coupling of
polarization to strain, we calculate the fluctuation spectra of ferroelectric
domain walls. The influence of the strain coupling differs between 180 degree
and 90 degree walls due to the different strain profiles of the two
configurations. The finite speed of acoustic phonons, $v_s$, retards the
response of the strain to polarization fluctuations, and the results depend on
$v_s$. For $v_s \to \infty$, the strain mediates an instantaneous
electrostrictive interaction, which is long-range in the 90 degree wall case.
For finite $v_s$, acoustic phonons damp the wall excitations, producing a
continuum in the spectral function. As $v_s\ to 0$, a gapped mode emerges,
which corresponds to the polarization oscillating in a fixed strain potential.


title:
Fast Algorithms for Refined Parameterized Telescoping in Difference
  Fields

abstract:
  Parameterized telescoping (including telescoping and creative telescoping)
and refined versions of it play a central role in the research area of symbolic
summation. Karr introduced 1981 $\Pi\Sigma$-fields, a general class of
difference fields, that enables one to consider this problem for indefinite
nested sums and products covering as special cases, e.g., the
($q$--)hypergeometric case and their mixed versions. This survey article
presents the available algorithms in the framework of $\Pi\Sigma$-extensions
and elaborates new results concerning efficiency.


title: Do Finite-Size Lyapunov Exponents Detect Coherent Structures?

abstract:
  Ridges of the Finite-Size Lyapunov Exponent (FSLE) field have been used as
indicators of hyperbolic Lagrangian Coherent Structures (LCSs). A rigorous
mathematical link between the FSLE and LCSs, however, has been missing. Here we
prove that an FSLE ridge satisfying certain conditions does signal a nearby
ridge of some Finite-Time Lyapunov Exponent (FTLE) field, which in turn
indicates a hyperbolic LCS under further conditions. Other FSLE ridges
violating our conditions, however, are seen to be false positives for LCSs. We
also find further limitations of the FSLE in Lagrangian coherence detection,
including ill-posedness, artificial jump-discontinuities, and sensitivity with
respect to the computational time step.

categories: math.DS nlin.CD physics.ao-ph physics.flu-dyn


title:
Selection and orientation of different particles in single particle
  imaging

abstract:
  The short pulses of X-ray free electron lasers can produce diffraction
patterns with structural information before radiation damage destroys the
particle. The particles are injected into the beam in random orientations and
they should be identical. However, in real experimental conditions it is not
always possible to have identical particles. In this paper we show that the
correlation maximization method, developed earlier, is able to select identical
particles from a mixture and find their orientations simultaneously.


title:
Remarks on decay of small solutions to systems of Klein-Gordon equations
  with dissipative nonlinearities

abstract:
  We consider the Cauchy problem for systems of cubic nonlinear Klein-Gordon
equations in one space dimension. Under a suitable structural condition on the
nonlinearity, we will show that the small amplitude solution gains an
additional logarithmic decay in comparison with the free evolution in the sense
of $L^p$, $2\le p \le \infty$.


title:
Symmetric Powers of Hyperbolic Forms and of Trace Forms on Symbol
  Algebras

abstract:
  Let $K$ be a field with characteristic different from 2 and let $S$ be a
symbol algebra over $K$. We compute the symmetric powers of hyperbolic
quadratic forms over $K$. Also, we compute the symmetric powers of the
quadratic trace form of $S$. In both cases we apply a generalised form of the
Vandermonde convolution in the course of the computations.


title: FACT: Towards Robotic Operation of an Imaging Air Cherenkov Telescope

abstract:
  The First G-APD Cherenkov Telescope (FACT) became operational at La Palma in
October 2011. Since summer 2012, due to very smooth and stable operation, it is
the first telescope of its kind that is routinely operated from remote, without
the need for a data-taking crew on site. In addition, many standard tasks of
operation are executed automatically without the need for manual interaction.
Based on the experience gained so far, some alterations to improve the safety
of the system are under development to allow robotic operation in the future.
We present the setup and precautions used to implement remote operations and
the experience gained so far, as well as the work towards robotic operation.


title:
A Detailed Dynamical Investigation of the Proposed QS Virginis Planetary
  System

abstract:
  In recent years, a number of planetary systems have been proposed to orbit
evolved binary star systems. The presence of planets is invoked to explain
observed variations in the timing of mutual eclipses between the primary and
secondary components of the binary star system. The planets recently proposed
orbiting the cataclysmic variable system QS Virginis are the latest in this
on-going series of "extreme planets".
  The two planets proposed to orbit QS Virginis would move on mutually crossing
orbits - a situation that is almost invariably unstable on very short
timescales. In this work, we present the results of a detailed dynamical study
of the orbital evolution of the two proposed planets, revealing that they are
dynamically unstable on timescales of less than one thousand years across the
entire range of orbital elements that provide a plausible fit to the
observational data, and regardless of their mutual orbital inclination. We
conclude that the proposed planets around the cataclysmic variable QS Virginis
simply cannot exist.


title:
Phase transition and critical end point driven by an external magnetic
  field in asymmetric quark matter

abstract:
  The location of the critical end point (CEP) in the QCD phase diagram is
determined under different scenarios. The effect of strangeness, isospin/charge
asymmetry and an external magnetic field is investigated. The discussion is
performed within the 2+1 flavor Nambu--Jona-Lasinio model with Polyakov loop.
It is shown that isospin asymmetry shifts the CEP to larger baryonic chemical
potentials and smaller temperatures. At large asymmetries the CEP disappears.
However, a strong enough magnetic field drives the system into a first order
phase transition.


title:
Wavelet Analysis of Dynamic Behaviors of the Large Interconnected Power
  System

abstract:
  In this paper, the simulation of the disturbance propagation through a large
power system is performed on the WSCC 127 bus test system. The signal frequency
analysis from several parts of the power system is performed by applying the
Wavelet Transform (WT). The results show that this approach provides the system
operators with some useful information regarding the identification of the
power system low-frequency electromechanical oscillations, the identification
of the coherent groups of generators and the insight into the speed retardation
of some parts of the power system. The ability to localize the disturbance is
based on the disturbance propagation through the power system and the
time-frequency analysis performed by using the WT is presented along with
detailed physical interpretation of the used approach.


title: Realization of \hat{sl}_2(C) at the Critical Level

abstract:
  An explicit realization of the affine Lie algebra \hat{sl}_2(C) at the
critical level is constructed using a mixture of bosons and parafermions.
Subsequently a representation of the associated Lepowsky-Wilson Z-algebra is
given on a space of the tensor product of bosonic fields and certain
semi-infinite wedge products.


title:
Energy Distribution of EEG Signals: EEG Signal Wavelet-Neural Network
  Classifier

abstract:
  In this paper, a wavelet-based neural network (WNN) classifier for
recognizing EEG signals is implemented and tested under three sets EEG signals
(healthy subjects, patients with epilepsy and patients with epileptic syndrome
during the seizure). First, the Discrete Wavelet Transform (DWT) with the
Multi-Resolution Analysis (MRA) is applied to decompose EEG signal at
resolution levels of the components of the EEG signal (delta, theta, alpha,
beta and gamma) and the Parsevals theorem are employed to extract the
percentage distribution of energy features of the EEG signal at different
resolution levels. Second, the neural network (NN) classifies these extracted
features to identify the EEGs type according to the percentage distribution of
energy features. The performance of the proposed algorithm has been evaluated
using in total 300 EEG signals. The results showed that the proposed classifier
has the ability of recognizing and classifying EEG signals efficiently.


title: Dynamics of topological light states in spiraling structures

abstract:
  We expose a mechanism for the dynamical generation and control of light
states with diverse topologies in spiraling guiding structures. Specifically,
we show that spiraling shallow refractive index landscapes induce coupling and
periodic energy exchange between states with different topological charges.
Such a resonant effect enables excitation of optical vortices by vortex-free
inputs and allows the output topological charge of the beam to be controlled.
The presence of nonlinearity results in a strong asymmetrization of the
resonant curves and a shift of the resonant frequencies. Resonant vortex
dynamic generation, including revivals, is shown to be possible not only in
waveguides mediated by total internal reflection but also in Bragg-guiding
hollow-core geometries.


title:
Harmonic oscillator with minimal length, minimal momentum, and maximal
  momentum uncertainties in SUSYQM framework

abstract:
  We consider a Generalized Uncertainty Principle (GUP) framework which
predicts a maximal uncertainty in momentum and minimal uncertainties both in
position and momentum. We apply supersymmetric quantum mechanics method and the
shape invariance condition to obtain the exact harmonic oscillator eigenvalues
in this GUP context. We find the supersymmetric partner Hamiltonians and show
that the harmonic oscillator belongs to a hierarchy of Hamiltonians with a
shift in momentum representation and different masses and frequencies. We also
study the effect of a uniform electric field on the harmonic oscillator energy
spectrum in this setup.


title: On the Schr\"{o}dinger equation for the free gravitational field

abstract:
  The Hamiltonian of the metric General Relativity derived in our earlier study
(Gravitation, {\bf 17}, 314 - 323 (2011)) is analyzed by the methods of Matrix
Quantum Mechanics. This Hamiltonian is a quadratic function of the momenta
$\pi^{mn}$ conjugate to the spatial components $g_{mn}$ of the metric tensor
$g_{\alpha\beta}$. The Hamiltonian is reduced to the new form which is more
convenient to derive the Schr\"{o}dinger equation for the free gravitational
field. In turn, this Schr\"{o}dinger equation is used to study possible motions
of the free gravitational field(s). In particular, it is shown that harmonic
oscillations of the free gravitational field, or harmonic gravitational waves,
cannot be observed as an actual motion of this field. We also investigate the
internal structure of the solitary gravitational wave.


title: Poisson stochastic integration in Banach spaces

abstract:
  We prove new upper and lower bounds for Banach space-valued stochastic
integrals with respect to a compensated Poisson random measure. Our estimates
apply to Banach spaces with non-trivial martingale (co)type and extend various
results in the literature. We also develop a Malliavin framework to interpret
Poisson stochastic integrals as vector-valued Skorohod integrals, and prove a
Clark-Ocone representation formula.


title:
Fermionic computation is non-local tomographic and violates monogamy of
  entanglement

abstract:
  We show that the computational model based on local Fermionic modes in place
of qubits does not satisfy local tomography and monogamy of entanglement, and
has mixed states with maximal entanglement of formation. These features
directly follow from the parity conservation corresponding to the parity
superselection rule. We generalize quantum superselection rules to general
probabilistic theories as sets of linear constraints on the convex set of
states. We then provide a link between the cardinality of the superselection
rule and the degree of holism of the resulting theory.


title:
Analytical solution of stochastic model of risk-spreading with global
  coupling

abstract:
  We study a stochastic matrix model to understand the mechanics of
risk-spreading (or bet-hedging) by dispersion. Such model has been mostly dealt
numerically except for well-mixed case, so far. Here, we present an analytical
result, which shows that optimal dispersion leads to Zipf's law. Moreover, we
found that the arithmetic ensemble average of the total growth rate converges
to the geometric one, because the sample size is finite.


title: When Are Popescu-Rohrlich Boxes and Random Access Codes Equivalent?

abstract:
  We study a problem of interconvertibility of two supra-quantum resources: one
is so called PR-box, which violates CHSH inequality up to maximal algebraic
bound, and second is so called random access code (RAC). The latter is a
functionality that enables Bob (receiver) to choose one of two bits of Alice.
It has been known, that PR-box supplemented with one bit of communication can
be used to simulate RAC. We ask the converse question: to what extent RAC can
simulate PR-box? To this end we introduce racbox: a box such that supplemented
with one bit of communication offers RAC. As said, PR-box can simulate racbox.
The question we raise, is whether any racbox can simulate PR-box. We show that
a non-signaling racbox indeed can simulate PR-box, hence those two resources
are equivalent. We also provide an example of signalling racbox which cannot
simulate PR-box. We give a resource inequality between racbox es and PR-boxes,
and show that it is saturated.


title:
A Population of Teraelectronvolt Pulsar Wind Nebulae in the H.E.S.S.
  Galactic Plane Survey

abstract:
  The most numerous source class that emerged from the H.E.S.S. Galactic Plane
Survey are Pulsar Wind Nebulae (PWNe). The 2013 reanalysis of this survey,
undertaken after almost 10 years of observations, provides us with the most
sensitive and most complete census of gamma-ray PWNe to date. In addition to a
uniform analysis of spectral and morphological parameters, for the first time
also flux upper limits for energetic young pulsars were extracted from the
data. We present a discussion of the correlation between energetic pulsars and
TeV objects, and their respective properties. We will put the results in
context with the current theoretical understanding of PWNe and evaluate the
plausibility of previously non-established PWN candidates.


title: Single-Spin Asymmetries in Elastic Electron-Hadron Scattering

abstract:
  This is a short review of the physics of single-spin asymmetries caused by
two-photon exchange in elastic scattering of electrons by nucleons and nuclei.


title: A Kac Model for Fermions

abstract:
  We introduce a stochastic $N$-particle system and show that, as $N\to
\infty$, an effective description ruled by the homogeneous fermionic
Uehling-Uhlenbeck equation is recovered. The particle model we consider is the
same as the Kac model for the homogeneous Boltzmann equation with an additional
exclusion constraint taking into account the Pauli Exclusion Principle.


title:
$\tau^-\to K^-\eta^{(\prime)}\nu_\tau$ decays in Chiral Perturbation
  Theory with Resonances

abstract:
  We have studied the $\tau^-\to K^-\eta^{(\prime)}\nu_\tau$ decays within
Chiral Perturbation Theory including resonances as explicit degrees of freedom.
We have considered three different form factors according to treatment of
final-state interactions. In increasing degree of soundness: Breit-Wigner,
exponential resummation and dispersive representation. We find that although
the first one fails in accounting for the data on the $K\eta$ mode, the other
two approaches provide good fits to them which are sensitive to the
$K^\star(1410)$ pole parameters, that are determined to be
$M_{K^{\star\prime}}\,=\,(1330^{+27}_{-41})$ MeV and
$\Gamma_{K^{\star\prime}}\,=\,(217^{+68}_{-122})$ MeV. These values are
competitive with the standard determination from $\tau^-\to(K\pi)^-\nu_\tau$
decays. The corresponding predictions for the $\tau^-\to
K^-\eta^{\prime}\nu_\tau$ channel respect the current upper bound and hint to
the discovery of this decay mode in the near future.


title: On the Virasoro constraints for torus knots

abstract:
  We construct Virasoro algebra of differential operators for the Jones-Rosso
matrix model. These operators generate various relations between Wilson loops.
Then we discuss the con- structed operators and corresponding relations in the
stability limit. A series of examples is given.


title: Sobolev norm estimates for a class of bilinear multipliers

abstract:
  We consider bilinear multipliers that appeared as a distinguished particular
case in the classification of two-dimensional bilinear Hilbert transforms by
Demeter and Thiele [9]. In this note we investigate their boundedness on
Sobolev spaces. Furthermore, we study structurally similar operators with
symbols that also depend on the spatial variables. The new results build on the
existing L^p estimates for a paraproduct-like operator previously studied by
the authors in [5] and [10]. Our primary intention is to emphasize the
analogies with Coifman-Meyer multipliers and with bilinear pseudodifferential
operators of order 0.


title: Fourier Methods for Harmonic Scalar Waves in General Waveguides

abstract:
  A set of semi-analytical techniques based on Fourier analysis is used to
solve wave scattering problems in variously shaped waveguides with varying
normal admittance boundary conditions. Key components are newly developed
conformal mapping methods, wave splitting, Fourier series expansions in
eigen-functions to non-normal operators, the building block method or the
cascade technique, Dirichlet-to-Neumann operators, and reformulation in terms
of stable differential equations for reflection and transmission matrices. For
an example the results show good correspondence with a finite element method
solution to the same problem in the low and medium frequency domain. The
Fourier method complements finite element analysis as a waveguide simulation
tool. For inverse engineering involving tuning of straight waveguide parts
joining complicated waveguide elements, the Fourier method is an attractive
alternative including time aspects. The prime motivation for the Fourier method
is its added physical understanding primarily at low frequencies.


title:
Simultaneous maximum-likelihood reconstruction for x-ray grating based
  phase-contrast tomography avoiding intermediate phase retrieval

abstract:
  Phase-wrapping artifacts, statistical image noise and the need for a minimum
amount of phase steps per projection limit the practicability of x-ray grating
based phase-contrast tomography, when using filtered back projection
reconstruction. For conventional x-ray computed tomography, the use of
statistical iterative reconstruction algorithms has successfully reduced
artifacts and statistical issues. In this work, an iterative reconstruction
method for grating based phase-contrast tomography is presented. The method
avoids the intermediate retrieval of absorption, differential phase and dark
field projections. It directly reconstructs tomographic cross sections from
phase stepping projections by the use of a forward projecting imaging model and
an appropriate likelihood function. The likelihood function is then maximized
with an iterative algorithm. The presented method is tested with tomographic
data obtained through a wave field simulation of grating based phase-contrast
tomography. The reconstruction results are in agreement with the expectations
and proof the validity of the concept.


title: The description of $^{150}$Nd Nucleus by a new alternative scheme

abstract:
  A new scheme was recently proposed in which the usual SU(3)
quadrupole-quadrupole interaction was replaced by an O(6) cubic interaction in
the Interacting Boson Model, and also successfully applied to the description
of $^{152}$Sm for the N = 90 rare earth isotones with X(5) symmetry. By using
this new scheme, in the present work, we further explore the properties of
another candidate of $^{150}$Nd for the N=90 with X(5) symmetry. The low-lying
energy levels and E2 transition rates are calculated and compared with the
experimental data. The results show that the new scheme can also reasonably
describe the experimental low-lying spectrum and the intraband and the
interband E2 transitions for $^{150}$Nd. However, for the low-lying spectrum,
the O(6) cubic interaction seems better in describing the energy levels,
especially in higher excited states and $\gamma$ band, yet the $0^{+}_{2}$
level within the $\beta$ band is lower than the corresponding experimental
value and, the U(5)-SU(3) scheme seems better to describe the low-lying levels
of $\beta$ band; and for the B(E2) transition, for the intraband transitions
within the ground band and some interband transitions between the $\beta$ band
and the ground band, the results from O(6) cubic interaction are better than
those from SU(3) quadrupole-quadrupole interaction, yet of which seems better
to describe the intraband E2 transitions within $\beta$ band. The present work
is very meaningful in helping us to deeply understand the new characteristics
of symmetry by the higher order O(6) cubic interaction.


title:
Attractive asymmetric inclusions in elastic membranes under tension:
  cluster phases and membrane invaginations

abstract:
  Up-down asymmetric inclusions impose a local, spontaneous curvature to an
elastic membrane. When several of them are inserted in a same membrane, they
feel effective forces mediated by the membrane, both of elastic and entropic
nature. Following an approach initiated by Dommersnes and Fournier in the
vanishing tension case [Eur. Phys. J. B 12, 9 (1999)], and also using a
pseudo-analytical micellization theory, we derive the statistical mechanics of
asymmetric inclusion assemblies when they are also subject to an additional
short-range, attractive interaction. Our main conclusion is that generically,
when the membrane is under tension, these inclusions live in small clusters at
equilibrium, leading to local membrane invaginations. We also propose a novel
curvature-induced demixing mechanism: when inclusions imposing local curvatures
of opposite sign coexist, they tend to demix in distinct clusters under
realistic conditions. This work has potential implications in the context of
the thermodynamics of proteins embedded in biological lipid bilayers.


title:
Some Classes of third and Fourth-order iterative methods for solving
  nonlinear equations

abstract:
  The object of the present work is to present the new classes of third-order
and fourth-order iterative methods for solving nonlinear equations. Our
third-order method includes methods of Weerakoon \cite{Weerakoon}, Homeier
\cite{Homeier2}, Chun \cite{Chun} e.t.c. as particular cases. After that we
make this third-order method to fourth-order (optimal) by using a single weight
function rather than using two different weight functions in \cite{Soleymani}.
Finally some examples are given to illustrate the performance of the our method
by comparing with new existing third and fourth-order methods.


title:
Modeling Intratumor Gene Copy Number Heterogeneity using Fluorescence in
  Situ Hybridization data

abstract:
  Tumorigenesis is an evolutionary process which involves a significant number
of genomic rearrangements typically coupled with changes in the gene copy
number profiles of numerous cells. Fluorescence in situ hybridization (FISH) is
a cytogenetic technique which allows counting copy numbers of genes in single
cells. The study of cancer progression using FISH data has received
considerably less attention compared to other types of cancer datasets.
  In this work we focus on inferring likely tumor progression pathways using
publicly available FISH data. We model the evolutionary process as a Markov
chain in the positive integer cone Z_+^g where g is the number of genes
examined with FISH. Compared to existing work which oversimplifies reality by
assuming independence of copy number changes, our model is able to capture
dependencies. We model the probability distribution of a dataset with
hierarchical log-linear models, a popular probabilistic model of count data.
Our choice provides an attractive trade-off between parsimony and good data
fit. We prove a theorem of independent interest which provides necessary and
sufficient conditions for reconstructing oncogenetic trees. Using this theorem
we are able to capitalize on the wealth of inter-tumor phylogenetic methods. We
show how to produce tumor phylogenetic trees which capture the dynamics of
cancer progression. We validate our proposed method on a breast tumor dataset.


title:
Asymptotic behavior of a multi-type nearly critical Galton--Watson
  processes with immigration

abstract:
  Multi-type inhomogeneous Galton--Watson process with immigration is
investigated, where the offspring mean matrix slowly converges to a critical
mean matrix. Under general conditions we obtain limit distribution for the
process, where the coordinates of the limit vector are not necessarily
independent.


title: The Chelyabinsk superbolide: a fragment of asteroid 2011 EO40?

abstract:
  Bright fireballs or bolides are caused by meteoroids entering the Earth's
atmosphere at high speed. On 2013 February 15, a superbolide was observed in
the skies near Chelyabinsk, Russia. Such a meteor could be the result of the
decay of an asteroid and here we explore this possibility applying a multistep
approach. First, we use available data and Monte Carlo optimization (validated
using 2008 TC3 as template) to obtain a robust solution for the pre-impact
orbit of the Chelyabinsk impactor (semimajor axis = 1.62 au, eccentricity =
0.53, inclination = 3.82 deg, longitude of the ascending node = 326.41 deg and
argument of perihelion = 109.44 deg). Then, we use this most probable orbit and
numerical analysis to single out candidates for membership in, what we call,
the Chelyabinsk asteroid family. Finally, we perform N-body simulations to
either confirm or reject any dynamical connection between candidates and
impactor. We find reliable statistical evidence on the existence of the
Chelyabinsk cluster. It appears to include multiple small asteroids and two
relatively large members: 2007 BD7 and 2011 EO40. The most probable parent body
for the Chelyabinsk superbolide is 2011 EO40. The orbits of these objects are
quite perturbed as they experience close encounters not only with the
Earth-Moon system but also with Venus, Mars and Ceres. Under such conditions,
the cluster cannot be older than about 20-40 kyr.


title: Phylogenetic Analysis of Cell Types using Histone Modifications

abstract:
  In cell differentiation, a cell of a less specialized type becomes one of a
more specialized type, even though all cells have the same genome.
Transcription factors and epigenetic marks like histone modifications can play
a significant role in the differentiation process. In this paper, we present a
simple analysis of cell types and differentiation paths using phylogenetic
inference based on ChIP-Seq histone modification data. We propose new data
representation techniques and new distance measures for ChIP-Seq data and use
these together with standard phylogenetic inference methods to build
biologically meaningful trees that indicate how diverse types of cells are
related. We demonstrate our approach on H3K4me3 and H3K27me3 data for 37 and 13
types of cells respectively, using the dataset to explore various issues
surrounding replicate data, variability between cells of the same type, and
robustness. The promising results we obtain point the way to a new approach to
the study of cell differentiation.


title: Counterexamples for Frobenius primality test

abstract:
  At present one can not find a single counterexample to even a simplest
version of Frobenius primality test. The assessment of probability of the
mistake, presented in [I.B. Damgard and G.S.Frandsen, Journal of Cryptology,
2006] is strongly overestimated. In the present paper, the properties of simple
divisors of FPP-numbers are proved. The lower bound for FPP are given.