pwc-archive/papers-with-abstracts huggingface dataset:
The asexual genome of Drosophila
Date: 2017-11-29 00:00:00

The rate of recombination affects the mode of molecular evolution. In
high-recombining sequence, the targets of selection are individual genetic
loci; under low recombination, selection collectively acts on large,
genetically linked genomic segments. Selection under linkage can induce clonal
interference, a specific mode of evolution by competition of genetic clades
within a population. This mode is well known in asexually evolving microbes,
but has not been traced systematically in an obligate sexual organism. Here we
show that the Drosophila genome is partitioned into two modes of evolution: a
local interference regime with limited effects of genetic linkage, and an
interference condensate with clonal competition. We map these modes by
differences in mutation frequency spectra, and we show that the transition
between them occurs at a threshold recombination rate that is predictable from
genomic summary statistics. We find the interference condensate in segments of
low-recombining sequence that are located primarily in chromosomal regions
flanking the centromeres and cover about 20% of the Drosophila genome.
Condensate regions have characteristics of asexual evolution that impact gene
function: the efficacy of selection and the speed of evolution are lower and
the genetic load is higher than in regions of local interference. Our results
suggest that multicellular eukaryotes can harbor heterogeneous modes and tempi
of evolution within one genome. We argue that this variation generates
selection on genome architecture.
Parametric Investigation Of Different Modulation Techniques On Free Space Optical Systems
Date: 2017-11-29 00:00:00

Free Space Optics systems (FSO) is one of the evolving wireless technologies.
FSO is the only technology with highest data rates in wireless mode of
operation but it suffers from bad weather conditions. In this work, analysis is
carried out on FSO system having certain parameters constant using different
modulation formats (i.e. RZ, NRZ, MDRZ, MODB and CSRZ). Impact of data rate,
link range, input power and attenuation factor has been computed. Weather
conditions are supposed to be nearly clear and suitable for FSO communication
while taking attenuation factor up to 10dB/Km. Q-factor, received signal power
and BER is calculated in all scenarios for obtaining an estimate of system
performance. Results have shown that NRZ & RZ formats are in the lead until now
with highest Q values.
Effect of Weather Conditions on FSO link based in Islamabad
Date: 2017-11-29 00:00:00

Free space optics (FSO) is a field of curiosity and importance for the
scientists because of its numerous applications and advantages like low cost
FSO systems, easy deployment, high data rate, secure FSO links and license free
bands. Very high bandwidth FSO link can be effectively established between the
skyscrapers of the Islamabad Pakistan for the purpose high capacity
applications in these skyscrapers. FSO links are badly affected by the weather
conditions especially rain and fog because of high attenuation factors.
optisystem is used to study the effect of rain and fog on the performance of
FSO links.
The Tropospheric Scintillation Prediction based on measured data for earth-to-satellite link for Bangladeshi climatic condition
Date: 2017-10-26 00:00:00

The performance of earth-to-satellite link largely depends on various
environmental factors like rain, fog, cloud, and atmospheric effects like
ionospheric and tropospheric scintillation. In this paper, the tropospheric
scintillation of Bangladesh, a subtropical country, is predicted based on
measured climatic parameters, like relative humidity, temperature. In this
prediction, ITU scintillation model are used. Four major cities, named Dhaka,
Chittagong, Rajshahi and Sylhet, of Bangladesh are selected for prediction of
scintillation. From the simulation result, Rajshahi is found to be the most
badly affected region by the scintillation fade depth (SFD), which is followed
by Chittagong and the SFD is minimum in Dhaka and Sylhet. The difference in
SFDs among the considered cities does not vary heavily. It is also found that
the SFD varies from 3 dB to 13 dB depending on the frequency in used. Moreover,
higher scintillation is found in rainy season of Bangladesh. During this
period, the scintillation becomes double of the average figure.
Early processing of consonance and dissonance in human auditory cortex
Date: 2017-11-30 00:00:00

Pitch is the perceptual correlate of sound's periodicity and a fundamental
property of the auditory sensation. The interaction of two or more pitches
gives rise to a sensation that can be characterized by its degree of consonance
or dissonance. In the current study, we investigated the neuromagnetic
representations of consonant and dissonant musical dyads using a new model of
cortical activity, in an effort to assess the possible involvement of
pitch-specific neural mechanisms in consonance processing at early cortical
stages.
  In the first step of the study, we developed a novel model of cortical pitch
processing designed to explain the morphology of the pitch onset response
(POR), a pitch-specific subcomponent of the auditory evoked N100 component in
the human auditory cortex. The model explains the neural mechanisms underlying
the generation of the POR and quantitatively accounts for the relation between
its peak latency and the perceived pitch.
  Next, we applied magnetoencephalography (MEG) to record the POR as elicited
by six consonant and dissonant dyads. The peak latency of the POR was strongly
modulated by the degree of consonance within the stimuli; specifically, the
most dissonant dyad exhibited a POR with a latency that was about 30ms longer
than that of the most consonant dyad, an effect that greatly exceeds the
expected latency difference induced by a single pitch sound.
  Our model was able to predict the POR latency pattern observed in the
neuromagnetic data, and to generalize this prediction to additional dyads.
These results indicate that the neural mechanisms responsible for pitch
processing exhibit an intrinsic differential response to concurrent consonant
and dissonant pitch combinations, suggesting that the perception of consonance
and dissonance might be an emergent property of the pitch processing system in
human auditory cortex.
Sequencing single-stranded libraries on the Illumina NextSeq 500 platform
Authors: Johanna L. A. Paijmans, Sina Baleka, Kirstin Henneberger, Ulrike H. Taron, Alexandra Trinks, Michael V. Westbury, Axel Barlow
Date: 2017-11-29 00:00:00

Single-stranded libraries generated from ancient DNA extracts have specific sequencing requirements. The short library molecules typically associated with ancient DNA templates are expected to behave differently during the annealing to the flow cell and subsequent cluster generation (bridge PCR), requiring optimisation of loading amounts to obtain optimal and consistent cluster densities. For the past 3 years, we have carried out sequencing of single-stranded libraries on the Illumina NextSeq 500 sequencing platform at the Institute for Biochemistry and Biology, University of Potsdam. We report our optimisations here. This document may be useful for other researchers wishing to sequence single-stranded libraries on the NextSeq 500 platform. It does not replace the excellent documentation provided by Illumina (links provided below), but rather serves as additional information specific to single-stranded libraries. The original papers describing the library protocol should also be studied in detail, and complement the information presented here.
Computational strategies for dissecting the high-dimensional complexity of adaptive immune repertoires
Date: 2017-11-29 00:00:00
Tasks: Diversity, Specificity

The adaptive immune system recognizes antigens via an immense array of
antigen-binding antibodies and T-cell receptors, the immune repertoire. The
interrogation of immune repertoires is of high relevance for understanding the
adaptive immune response in disease and infection (e.g., autoimmunity, cancer,
HIV). Adaptive immune receptor repertoire sequencing (AIRR-seq) has driven the
quantitative and molecular-level profiling of immune repertoires thereby
revealing the high-dimensional complexity of the immune receptor sequence
landscape. Several methods for the computational and statistical analysis of
large-scale AIRR-seq data have been developed to resolve immune repertoire
complexity in order to understand the dynamics of adaptive immunity. Here, we
review the current research on (i) diversity, (ii) clustering and network,
(iii) phylogenetic and (iv) machine learning methods applied to dissect,
quantify and compare the architecture, evolution, and specificity of immune
repertoires. We summarize outstanding questions in computational immunology and
propose future directions for systems immunology towards coupling AIRR-seq with
the computational discovery of immunotherapeutics, vaccines, and
immunodiagnostics.
Meeting of Mobile Nodes Based on RSS Measurements in Wireless Ad Hoc Networks
Date: 2017-11-29 00:00:00

In this work, we address a completely novel case which is the meeting problem
of mobile nodes (players) in a wireless ad hoc network. We assume that the only
information players have is the received signal strength (RSS) measurements of
other players and there is no centralized communication. Each node has a
different frequency band and they try to meet with each other in a
decentralized manner. We consider the case where players are allowed to move in
four orthogonal directions in a grid. Then, we use multi-armed bandit approach
to give rewards in the end of every move that players do using RSS
measurements. Taking into account that we have an adversarial setting, we
propose different algorithms to solve the meeting problem. We start with
considering two players and then extend the work to multiplayer by considering
multiplayer problem as multiple two player problems. Throughout the paper, we
construct mathematical bounds on meeting times and related concepts and
evaluate the simulation results in the end.
Analysis of Seismocardiographic Signals Using Polynomial Chirplet Transform and Smoothed Pseudo Wigner-Ville Distribution
Date: 2017-11-29 00:00:00

Seismocardiographic (SCG) signals are chest surface vibrations induced by
cardiac activity. These signals may offer a method for diagnosing and
monitoring heart function. Successful classification of SCG signals in health
and disease depends on accurate signal characterization and feature extraction.
One approach of determining signal features is to estimate its time-frequency
characteristics. In this regard, four different time-frequency distribution
(TFD) approaches were used including short-time Fourier transform (STFT),
polynomial chirplet transform (PCT), Wigner-Ville distribution (WVD), and
smoothed pseudo Wigner-Ville distribution (SPWVD). Synthetic SCG signals with
known time-frequency properties were generated and used to evaluate the
accuracy of the different TFDs in extracting SCG spectral characteristics.
Using different TFDs, the instantaneous frequency (IF) of each synthetic signal
was determined and the error (NRMSE) in estimating IF was calculated. STFT had
lower NRMSE than WVD for synthetic signals considered. PCT and SPWVD were,
however, more accurate IF estimators especially for the signal with
time-varying frequencies. PCT and SPWVD also provided better discrimination
between signal frequency components. Therefore, the results of this study
suggest that PCT and SPWVD would be more reliable methods for estimating IF of
SCG signals. Analysis of actual SCG signals showed that these signals had
multiple spectral components with slightly time-varying frequencies. More
studies are needed to investigate SCG spectral properties for healthy subjects
as well as patients with different cardiac conditions.
Grouping Similar Seismocardiographic Signals Using Respiratory Information
Date: 2017-11-29 00:00:00

Seismocardiography (SCG) offers a potential non-invasive method for cardiac
monitoring. Quantification of the effects of different physiological conditions
on SCG can lead to enhanced understanding of SCG genesis, and may explain how
some cardiac pathologies may affect SCG morphology. In this study, the effect
of the respiration on the SCG signal morphology is investigated. SCG, ECG, and
respiratory flow rate signals were measured simultaneously in 7 healthy
subjects. Results showed that SCG events tended to have two slightly different
morphologies. The respiratory flow rate and lung volume information were used
to group the SCG events into inspiratory/expiratory groups or low/high
lung-volume groups, respectively. Although respiratory flow information could
separate similar SCG events into two different groups, the lung volume
information provided better grouping of similar SCGs. This suggests that
variations in SCG morphology may be due, at least in part, to changes in the
intrathoracic pressure or heart location since those parameters correlates more
with lung volume than respiratory flow. Categorizing SCG events into different
groups containing similar events allows more accurate estimation of SCG
features, and better signal characterization, and classification.
Can Complex Collective Behaviour Be Generated Through Randomness, Memory and a Pinch of Luck?
Authors: Pedro M. F. Pereira
Date: 2017-11-29 00:00:00
Tasks: reinforcement-learning, Reinforcement Learning (RL)

Machine Learning techniques have been used to teach computer programs how to play games as complicated as Chess and Go. These were achieved using powerful tools such as Neural Networks and Parallel Computing on Supercomputers. In this paper, we define a model of populational growth and evolution based on the idea of Reinforcement Learning, but using only the 3 sources stated in the title processed on a low-tier laptop. The model correctly predicts the development of a population around food sources and their migration in search of a new one when the known ones become saturated. Additionally, we compared our model to a pure random one and the population number was fitted to a logistic function for two interesting evolutions of the system.
The Frequent Subgraphs of the Connectome of the Human Brain
Date: 2017-11-30 00:00:00

In mapping the human structural connectome, we are in a very fortunate
situation: one can compute and compare graphs, describing the cerebral
connections between the very same, anatomically identified small regions of the
gray matter among hundreds of human subjects. The comparison of these graphs
has led to numerous recent results, as the (i) discovery that women's
connectomes have deeper and richer connectivity-related graph parameters like
those of men, or (ii) the description of more and less conservatively connected
lobes and cerebral regions, and (iii) the discovery of the phenomenon of the
Consensus Connectome Dynamics.
  Today one of the greatest challenges of brain science is the description and
modeling of the circuitry of the human brain. For this goal, we need to
identify sub-circuits that are present in almost all human subjects and those,
which are much less frequent: the former sub-circuits most probably have
functions with general importance, the latter sub-circuits are probably related
to the individual variability of the brain structure and functions. The present
contribution describes the frequent connected subgraphs (instead of
sub-circuits) of at most 6 edges in the human brain. We analyze these frequent
graphs and also examine sex differences in these graphs: we demonstrate
numerous connected sub-graphs that are more frequent in female or the male
connectome. While our results describe subgraphs, instead of sub-circuits, we
need to note that all macroscopic sub-circuits correspond to an underlying
connected subgraph.
  Our data source is the public release of the Human Connectome Project, and we
are applying the data of 426 human subjects in this study.
Theory of time-averaged neutral dynamics with environmental stochasticity
Date: 2018-01-15 00:00:00

Competition is the main driver of population dynamics, which shapes the
genetic composition of populations and the assembly of ecological communities.
Neutral models assume that all the individuals are equivalent and that the
dynamics is governed by demographic (shot) noise, with a steady state species
abundance distribution (SAD) that reflects a mutation-extinction equilibrium.
Recently, many empirical and theoretical studies emphasized the importance of
environmental variations that affect coherently the relative fitness of entire
populations. Here we consider two generic time-averaged neutral models, in both
the relative fitness of each species fluctuates independently in time but its
mean is zero. The first (model A) describes a system with local competition and
linear fitness-dependence of the birth-death rates, while in the second (model
B) the competition is global and the fitness dependence is nonlinear. Due to
this nonlinearity, model B admits a noise-induced stabilization mechanism that
facilitates the invasion of new mutants. A self-consistent mean-field approach
is used to reduce the multi-species problem to two-species dynamics, and the
large-$N$ asymptotics of the emerging set of Fokker-Planck equations is
presented and solved. Our analytic expressions are shown to fit the SADs
obtained from extensive Monte-Carlo simulations and from numerical solutions of
the corresponding master equations.
Raga Identification using Repetitive Note Patterns from prescriptive notations of Carnatic Music
Date: 2017-11-30 00:00:00

Carnatic music, a form of Indian Art Music, has relied on an oral tradition
for transferring knowledge across several generations. Over the last two
hundred years, the use of prescriptive notations has been adopted for learning,
sight-playing and sight-singing. Prescriptive notations offer generic
guidelines for a raga rendition and do not include information about the
ornamentations or the gamakas, which are considered to be critical for
characterizing a raga. In this paper, we show that prescriptive notations
contain raga attributes and can reliably identify a raga of Carnatic music from
its octave-folded prescriptive notations. We restrict the notations to 7 notes
and suppress the finer note position information. A dictionary based approach
captures the statistics of repetitive note patterns within a raga notation. The
proposed stochastic models of repetitive note patterns (or SMRNP in short)
obtained from raga notations of known compositions, outperforms the state of
the art melody based raga identification technique on an equivalent melodic
data corresponding to the same compositions. This in turn shows that for
Carnatic music, the note transitions and movements have a greater role in
defining the raga structure than the exact note positions.
Mean-Square Performance Analysis of Noise-Robust Normalized Subband Adaptive Filter Algorithm
Date: 2019-08-21 00:00:00

This paper studies the statistical models of the noise-robust normalized
subband adaptive filter (NR-NSAF) algorithm in the mean and mean square
deviation senses involving transient-state and steady-state behavior by
resorting to the method of the vectorization operation and the Kronecker
product. The analysis method does not require the Gaussian input signal.
Moreover, the proposed analysis removes the paraunitary assumption imposed on
the analysis filter banks as in the existing analyses of subband adaptive
algorithms. Simulation results in various conditions demonstrate the
effectiveness of our theoretical analysis. For a special form of the algorithm,
the proposed steady-state expression is also better accurate than the previous
analysis.
Factor endowment -- commodity output relationships in a three-factor, two-good general equilibrium trade model
Date: 2017-11-28 00:00:00
Tasks: Position

We analyze the Rybczynski sign pattern, which expresses the factor endowment
- commodity output relationships in a three-factor, two-good general
equilibrium trade model. The relationship determines whether a strong
Rybczynski result holds. We search for a sufficient condition for each
Rybczynski sign pattern to hold in a systematic manner, which no other studies
have derived. We assume factor-intensity ranking is constant. We use the EWS
(economy-wide substitution)-ratio vector and the Hadamard product in our
analysis. We show that the position of the EWS-ratio vector determines the
Rybczynski sign pattern. This article provides a basis for further
applications.
Scenario-based Economic Dispatch with Uncertain Demand Response
Date: 2017-11-29 00:00:00

This paper introduces a new computational framework to account for
uncertainties in day-ahead electricity market clearing process in the presence
of demand response providers. A central challenge when dealing with many demand
response providers is the uncertainty of its realization. In this paper, a new
economic dispatch framework that is based on the recent theoretical development
of the scenario approach is introduced. By removing samples from a finite
uncertainty set, this approach improves dispatch performance while guaranteeing
a quantifiable risk level with respect to the probability of violating the
constraints. The theoretical bound on the level of risk is shown to be a
function of the number of scenarios removed. This is appealing to the system
operator for the following reasons: (1) the improvement of performance comes at
the cost of a quantifiable level of violation probability in the constraints;
(2) the violation upper bound does not depend on the probability distribution
assumption of the uncertainty in demand response. Numerical simulations on (1)
3-bus and (2) IEEE 14-bus system (3) IEEE 118-bus system suggest that this
approach could be a promising alternative in future electricity markets with
multiple demand response providers.
Spectrum Sensing under Spectrum Misuse Behaviors: A Multi-Hypothesis Test Perspective
Date: 2017-11-29 00:00:00

Spectrum misuse behaviors, brought either by illegitimate access or by rogue
power emission, endanger the legitimate communication and deteriorate the
spectrum usage environment. In this paper, our aim is to detect whether the
spectrum band is occupied, and if it is occupied, recognize whether the misuse
behavior exists. One vital challenge is that the legitimate spectrum
exploitation and misuse behaviors coexist and the illegitimate user may act in
an intermittent and fast-changing manner, which brings about much uncertainty
for spectrum sensing. To tackle it, we firstly formulate the spectrum sensing
problems under illegitimate access and rogue power emission as a uniform
ternary hypothesis test. Then, we develop a novel test criterion, named the
generalized multi-hypothesis N-P criterion. Following the criterion, we derive
two test rules based on the generalized likelihood ratio test and the R-test,
respectively, whose asymptotic performances are analyzed and an upper bound is
also given. Furthermore, a cooperative spectrum sensing scheme is designed
based on the global N-P criterion to further improve the detection
performances. In addition, extensive simulations are provided to verify the
proposed schemes' performance under various parameter configurations.