pwc-archive/papers-with-abstracts huggingface dataset:
Stability Analysis of Population Dynamics Model in Microbial Biofilms with Non-participating Strains
Date: 2016-09-20 00:00:00

The existence of phenotypic heterogeneity in single-species bacterial
biofilms is well-established in the published literature. However, the modeling
of population dynamics in biofilms from the viewpoint of social interactions,
i.e. interplay between heterotypic strains, and the analysis of this kind using
control theory are not addressed significantly. Therefore, in this paper, we
theoretically analyze the population dynamics model in microbial biofilms with
non-participating strains (coexisting with public goods producers and
non-producers) in the context of evolutionary game theory and nonlinear
dynamics. Our analysis of the replicator dynamics model is twofold: first
without the inclusion of spatial pattern, and second with the consideration of
degree of assortment. In the first case, Lyapunov stability analysis of the
stable equilibrium point of the proposed replicator system determines (1,0)
('full dominance of cooperators') as a global asymptotic stable equilibrium
whenever the return exceeds the metabolic cost of cooperation. Hence, the
global asymptotic stable nature of (1,0) in the context of non-consideration of
spatial pattern helps to justify mathematically the adversity in the
eradication of "cooperative enterprise" that is an infectious biofilm. In the
second case, we found non-existence of global asymptotic stability in the
system, and it unveils two additional phenomena - bistability and coexistence.
In this context, two inequality conditions are derived for the 'full dominance
of cooperators' and coexistence. Therefore, the inclusion of spatial pattern in
biofilms with non-competing strains intends conditional dominance of pathogenic
(with respect to the hosts) public goods producers which can be an effective
strategy towards the control of an infectious biofilm with the drug-dependent
regulation of degree of segregation.
OCR++: A Robust Framework For Information Extraction from Scholarly Articles
Authors: Singh Mayank, Barua Barnopriyo, Palod Priyank, Garg Manvi, Satapathy Sidhartha, Bushi Samuel, Ayush Kumar, Rohith Krishna Sai, Gamidi Tulasi, Goyal Pawan, Mukherjee Animesh
Date: 2016-09-23 00:00:00
Proceeding: COLING 2016 12
Tasks: Articles, Optical Character Recognition (OCR)

This paper proposes OCR++, an open-source framework designed for a variety of
information extraction tasks from scholarly articles including metadata (title,
author names, affiliation and e-mail), structure (section headings and body
text, table and figure headings, URLs and footnotes) and bibliography (citation
instances and references). We analyze a diverse set of scientific articles
written in English language to understand generic writing patterns and
formulate rules to develop this hybrid framework. Extensive evaluations show
that the proposed framework outperforms the existing state-of-the-art tools
with huge margin in structural information extraction along with improved
performance in metadata and bibliography extraction tasks, both in terms of
accuracy (around 50% improvement) and processing time (around 52% improvement).
A user experience study conducted with the help of 30 researchers reveals that
the researchers found this system to be very helpful. As an additional
objective, we discuss two novel use cases including automatically extracting
links to public datasets from the proceedings, which would further accelerate
the advancement in digital libraries. The result of the framework can be
exported as a whole into structured TEI-encoded documents. Our framework is
accessible online at http://cnergres.iitkgp.ac.in/OCR++/home/.
Do Japanese and Italian women live longer than women in Scandinavia?
Date: 2016-09-21 00:00:00

Life expectancies at birth are routinely computed from period life tables.
Such period life expectancies may be distorted by selection when comparing
countries where the living conditions improved earlier (like Norway and Sweden)
with countries where they improved later (like Italy and Japan). One way to get
a fair comparison between the countries, is to use cohort data and consider the
expected number of years lost before a given age a. Contrary to the results
based on period data, one then finds that Italian women may expect to lose more
years than women in Norway and Sweden, while there are no indications that
Japanese women will lose fewer years than Scandinavian women.
Differential equations of electrodiffusion: constant field solutions, uniqueness, and new formulas of Goldman-Hodgkin-Katz type
Date: 2016-09-21 00:00:00

The equations governing one-dimensional, steady-state electrodiffusion are
considered when there are arbitrarily many mobile ionic species present, in any
number of valence classes, possibly also with a uniform distribution of fixed
charges. Exact constant field solutions and new formulas of
Goldman-Hodgkin-Katz type are found. All of these formulas are exact, unlike
the usual approximate ones. Corresponding boundary conditions on the ionic
concentrations are identified. The question of uniqueness of constant field
solutions with such boundary conditions is considered, and is re-posed in terms
of an autonomous ordinary differential equation of order $n+1$ for the electric
field, where $n$ is the number of valence classes. When there are no fixed
charges, the equation can be integrated once to give the non-autonomous
equation of order $n$ considered previously in the literature including, in the
case $n=2$, the form of Painlev\'e's second equation considered first in the
context of electrodiffusion by one of us. When $n=1$, the new equation is a
form of Li\'enard's equation. Uniqueness of the constant field solution is
established in this case.
Drifting states and synchronization induced chaos in autonomous networks of excitable neurons
Date: 2016-09-21 00:00:00
Tasks: Time Series Analysis

The study of balanced networks of excitatory and inhibitory neurons has led
to several open questions. On the one hand it is yet unclear whether the
asynchronous state observed in the brain is autonomously generated, or if it
results from the interplay between external drivings and internal dynamics. It
is also not known, which kind of network variabilities will lead to irregular
spiking and which to synchronous firing states. Here we show how isolated
networks of purely excitatory neurons generically show asynchronous firing
whenever a minimal level of structural variability is present together with a
refractory period. Our autonomous networks are composed of excitable units, in
the form of leaky integrators spiking only in response to driving inputs. For a
non-uniform network, composed exclusively of excitatory neurons, we find a rich
repertoire of self-induced dynamical states, including asynchronous drifting
states, fully synchronized, or mixed, containing both drifting and synchronized
components. The individual neurons considered are excitable and hence do not
dispose of intrinsic natural firing frequencies. An effective network-wide
distribution of natural frequencies is however generated autonomously through
self-consistent feedback loops. We find two types of asynchronous activity,
with the individual neurons spiking regularly in the pure drifting state,
albeit with a continuous distribution of firing frequencies. The activity of
the drifting component, however, becomes irregular in the mixed state, due to
the periodic driving of the synchronized component. We propose a new tool for
the study of chaos in spiking neural networks, which consists of an analysis of
the time series of pairs of consecutive interspike intervals. In this space, we
show that a strange attractor with a fractal dimension is formed.
On the Mathematical Relationship between Expected n-call@k and the Relevance vs. Diversity Trade-off
Authors: Lim Kar Wai, Sanner Scott, Guo Shengbo
Date: 2016-09-21 00:00:00
Tasks: Combinatorial Optimization, Diversity

It has been previously noted that optimization of the n-call@k relevance
objective (i.e., a set-based objective that is 1 if at least n documents in a
set of k are relevant, otherwise 0) encourages more result set diversification
for smaller n, but this statement has never been formally quantified. In this
work, we explicitly derive the mathematical relationship between expected
n-call@k and the relevance vs. diversity trade-off --- through fortuitous
cancellations in the resulting combinatorial optimization, we show the
trade-off is a simple and intuitive function of n (notably independent of the
result set size k e n), where diversification increases as n approaches 1.
Effects of population growth on the success of invading mutants
Date: 2017-03-28 00:00:00

Understanding if and how mutants reach fixation in populations is an
important question in evolutionary biology. We study the impact of population
growth has on the success of mutants. To systematically understand the effects
of growth we decouple competition from reproduction; competition follows a
birth--death process and is governed by an evolutionary game, while growth is
determined by an externally controlled branching rate. In stochastic
simulations we find non-monotonic behaviour of the fixation probability of
mutants as the speed of growth is varied; the right amount of growth can lead
to a higher success rate. These results are observed in both coordination and
coexistence game scenarios, and we find that the 'one-third law' for
coordination games can break down in the presence of growth. We also propose a
simplified description in terms of stochastic differential equations to
approximate the individual-based model.
Protein-protein docking by generalized Fourier transforms on 5D rotational manifolds
Date: 2016-09-21 00:00:00

Energy evaluation using fast Fourier transforms enables sampling billions of
putative complex structures and hence revolutionized rigid protein-protein
docking. However, in current methods efficient acceleration is achieved only in
either the translational or the rotational subspace. Developing an efficient
and accurate docking method that expands FFT based sampling to 5 rotational
coordinates is an extensively studied but still unsolved problem. The algorithm
presented here retains the accuracy of earlier methods but yields at least
tenfold speedup. The improvement is due to two innovations. First, the search
space is treated as the product manifold $\mathbf{SO(3)x(SO(3)\setminus S^1)}$,
where $\mathbf{SO(3)}$ is the rotation group representing the space of the
rotating ligand, and $\mathbf{(SO(3)\setminus S^1)}$ is the space spanned by
the two Euler angles that define the orientation of the vector from the center
of the fixed receptor toward the center of the ligand. This representation
enables the use of efficient FFT methods developed for $\mathbf{SO(3)}$.
Second, we select the centers of highly populated clusters of docked
structures, rather than the lowest energy conformations, as predictions of the
complex, and hence there is no need for very high accuracy in energy
evaluation. Therefore it is sufficient to use a limited number of spherical
basis functions in the Fourier space, which increases the efficiency of
sampling while retaining the accuracy of docking results. A major advantage of
the method is that, in contrast to classical approaches, increasing the number
of correlation function terms is computationally inexpensive, which enables
using complex energy functions for scoring.
Predicting evolutionary rescue via evolving plasticity in stochastic environments
Date: 2016-09-21 00:00:00

Phenotypic plasticity and its evolution may help evolutionary rescue in a
novel and stressful environment, especially if environmental novelty reveals
cryptic genetic variation that enables the evolution of increased plasticity.
However, the environmental stochasticity ubiquitous in natural systems may
alter these predictions because high plasticity may amplify
phenotype-environment mismatches. Although previous studies have highlighted
this potential detrimental effect of plasticity in stochastic environments,
they have not investigated how it affects extinction risk in the context of
evolutionary rescue and with evolving plasticity. We investigate this question
here by integrating stochastic demography with quantitative genetic theory in a
model with simultaneous change in the mean and predictability (temporal
autocorrelation) of the environment. We develop an approximate prediction of
long-term persistence under the new pattern of environmental fluctuations, and
compare it with numerical simulations for short- and long-term extinction risk.
We find that reduced predictability increases extinction risk and reduces
persistence because it increases stochastic load during rescue. This
understanding of how stochastic demography, phenotypic plasticity, and
evolution interact when evolution acts on cryptic genetic variation revealed in
a novel environment can inform expectations for invasions, extinctions, or the
emergence of chemical resistance in pests.
Fluctuations in protein aggregation: Design of preclinical screening for early diagnosis of neurodegenerative disease
Date: 2016-09-22 00:00:00
Tasks: Diagnostic

Autocatalytic fibril nucleation has recently been proposed to be a
determining factor for the spread of neurodegenerative diseases, but the same
process could also be exploited to amplify minute quantities of protein
aggregates in a diagnostic context. Recent advances in microfluidic technology
allow analysis of protein aggregation in micron-scale samples potentially
enabling such diagnostic approaches, but the theoretical foundations for the
analysis and interpretation of such data are so far lacking. Here we study
computationally the onset of protein aggregation in small volumes and show that
the process is ruled by intrinsic fluctuations whose volume dependent
distribution we also estimate theoretically. Based on these results, we develop
a strategy to quantify in silico the statistical errors associated with the
detection of aggregate containing samples. Our work opens a new perspective on
the forecasting of protein aggregation in asymptomatic subjects.
Finite symmetries in agent-based epidemic models
Date: 2016-09-27 00:00:00

We present an algorithm which explores permutation symmetries to describe the
time evolution of agent-based epidemic models. The main idea to improve
computation times relies on restricting the stochastic process to one sector of
the vector space, labeled by a single permutation eigenvalue. In this scheme,
the transition matrix reduces to block diagonal form, enhancing computational
performance.
Stiffness of the C-terminal disordered linker affects the geometry of the active site in endoglucanase Cel8A
Date: 2016-09-22 00:00:00

Cellulosomes are complex multi-enzyme machineries which efficiently degrade
plant cell-wall polysaccharides. The multiple domains of the cellulosome
proteins are often tethered together by intrinsically disordered regions. The
properties and functions of these disordered linkers are not well understood.
In this work, we study endoglucanase Cel8A, which is a relevant enzymatic
component of the cellulosomes of Clostridium thermocellum. We use both all-atom
and coarse-grained simulations to investigate how the equilibrium conformations
of the catalytic domain of Cel8A are affected by the disordered linker at its C
terminus. We find that when the endoglucanase is bound to its substrate, the
effective stiffness of the linker can influence the distances between groups of
amino-acid residues throughout the entire enzymatic domain. In particular,
variations in the linker stiffness can lead to small changes in the geometry of
the active-site cleft. We suggest that such geometrical changes may, in turn,
have an effect on the catalytic activity of the enzyme.
Multivariate Garch with dynamic beta
Authors: Matthias Raddant, Friedrich Wagner
Date: 2016-09-22 00:00:00

We investigate a solution for the problems related to the application of multivariate GARCH models to markets with a large number of stocks by restricting the form of the conditional covariance matrix. The model is a factor model and uses only six free GARCH parameters. One factor can be interpreted as the market component, the remaining factors are equal. This allow the analytical calculation of the inverse covariance matrix. The time-dependence of the factors enables the determination of dynamical beta coefficients. We compare the results from our model with the results of other GARCH models for the daily returns from the S\&P500 market and find that they are competitive. As applications we use the daily values of beta coefficients to confirm a transition of the market in 2006. Furthermore we discuss the relationship of our model with the leverage effect.
Growth and proline content in NaCl stressed plants of annual medic species
Date: 2016-09-23 00:00:00

Wild populations of Medicago ciliaris and Medicago polymorpha were subjected
to four salt treatments 0, 50, 100 and 150 mM NaCl, plant growth and proline
concentration in leaves were assessed. The analyzed data revealed significant
variability in salt response within and between the two species, depending on
the salinity level. It was found that high NaCl concentrations affected all the
growth parameters. However, the reduction was more important at higher NaCl
concentrations and the highest reduction was obtained for the populations of
Medicago polymorpha where it reached around 90% in root length at 150 mM NaCl
for Pmar. The Tunisian population of Medicago ciliaris, prospected on soils
affected by salinity, was the best tolerant in all ecotypes studied in this
work. This population, exhibits a particular adaptability to salt environment
at both germination and seedling stage. Furthermore, the correlation among the
studied plants sensitivity and leaf proline concentration showed that high
proline contents were related to their reactivity to salt. Consequently, it
appeared that proline biosynthesis occurred presumably as a consequence of
disturbance in cell homoeostasis and reflected poor performance and greater
damage in response to salt stress. These findings indicated that this osmolytes
content may be used as another useful criterion to differentiate salt-tolerant
from salt sensitive plant in annual medics.
Cooperation in the two-population snowdrift game with punishment enforced through different mechanisms
Date: 2016-09-22 00:00:00

I study two mechanisms based on punishment to promote cooperation in the
two-population snowdrift game. The first mechanism follows the traditional
approach in the literature and is based on the inclusion of a third additional
strategy in the payoff matrix of the stage-game. The second mechanism consists
of letting cooperators to punish defectors with a given exogenous frequency.
While both mechanisms share the same result regarding the minimum required
level of punishment in order to eliminate defectors in both populations,
stability in the mechanism following the second approach is more robust in the
sense that extinction of defectors is a globally asymptotically stable state
for any interior initial conditions in the phase space. Results were obtained
analytically through non-linear differential equations and also using an
agent-based simulation. There was a good level of agreement between both
approaches with respect to the evolutionary pattern over time and the possible
steady-states.
The Evolving Definition of Sepsis
Date: 2016-09-23 00:00:00

Sepsis affects millions of people worldwide each year. It occurs when a
normal human immune response to a bacterial, viral or fungal infection becomes
dysfunctional and triggers widespread inflammation that results in severe
tissue damage that leads to organ failure, shock, and death. Sepsis, requires
immediate treatment and has a high readmission rate for survivors. It is also
one of the most expensive conditions to treat. In 2013, there were more than
1.6 million cases of sepsis in the United States with a financial cost of more
than $23 billion. Sepsis was first described in antiquity, and given its
current name, by the ancient Greek physician Hippocrates. Despite its long
medical history, severity, and financial burden, the causes of sepsis are not
well understood, and there is no standard approach to diagnosis and treatment.
The definition of sepsis, the characterization of its clinical stages, and
sepsis monitoring tools have changed three times in the past 25 years, most
recently in March 2016. The universal adoption of this latest definition,
sepsis-3, and a screening tool, qSOFA, are currently under debate in the
medical community. A means to rapidly identify and treat sepsis could reduce
the five million deaths due to sepsis each year worldwide. This paper reviews
the evolution of the definition of sepsis and the controversy surrounding the
sepsis-3 definition and the sepsis screening tool, qSOFA.
Nonlinear self-adapting wave patterns
Date: 2016-09-23 00:00:00

We propose a new type of traveling wave pattern, one that can adapt to the
size of physical system in which it is embedded. Such a system arises when the
initial state has an instability that extends down to zero wavevector,
connecting at that point to two symmetry modes of the underlying dynamical
system. The Min system of proteins in E. coli is such as system with the
symmetry emerging from the global conservation of two proteins, MinD and MinE.
For this and related systems, traveling waves can adiabatically deform as the
system is increased in size without the increase in node number that would be
expected for an oscillatory version of a Turing instability containing an
allowed wavenumber band with a finite minimum.
A spectral algorithm for fast de novo layout of uncorrected long nanopore reads
Date: 2017-07-17 00:00:00

Motivation: New long read sequencers promise to transform sequencing and
genome assembly by producing reads tens of kilobases long. However their high
error rate significantly complicates assembly and requires expensive correction
steps to layout the reads using standard assembly engines.
  Results: We present an original and efficient spectral algorithm to layout
the uncorrected nanopore reads, and its seamless integration into a
straightforward overlap/layout/consensus (OLC) assembly scheme. The method is
shown to assemble Oxford Nanopore reads from several bacterial genomes into
good quality (~99% identity to the reference) genome-sized contigs, while
yielding more fragmented assemblies from a Sacharomyces cerevisiae reference
strain.
  Availability and implementation: http://github.com/antrec/spectrassembler
  Contact: antoine.recanati@inria.fr