pwc-archive/papers-with-abstracts huggingface dataset:
Open Access and Discovery Tools: How do Primo Libraries Manage Green Open Access Collections?
Authors: Renaville François
Date: 2016-02-28 00:00:00
Tasks: Articles

Scholarly Open Access repositories contain lots of treasures including rare
or otherwise unpublished materials and articles that scholars self-archive,
often as part of their institution's mandate. But it can be hard to discover
this material unless users know exactly where to look. Since the very
beginning, libraries have played a major role in supporting the OA movement.
Next to all services they can provide to support the deposit of research output
in the repositories, they can make Open Access materials widely discoverable by
their patrons through general search engines (Google, Bing...), specialized
search engines (like Google Scholar) and library discovery tools, thus
expanding their collection to include materials that they would not necessarily
pay for. In this paper, we intend to focus on two aspects regarding Open Access
and Primo discovery tool. In early 2013, Ex Libris Group started to add
institutional repositories to Primo Central Index (PCI), their mega-aggregation
of hundreds of millions of scholarly e-resources. After 2 years, it may be
interesting to take stock of the current situation of PCI regarding Open Access
institutional repositories. On basis of a survey to carry out among the Primo
community, the paper also shows how libraries using Primo discovery tool
integrate Green Open Access contents in their catalog. Two major ways are
possible for them: Firstly, they can directly harvest, index and manage any
repository in their Primo and display those free contents next to the more
traditional library collections; Secondly, if they are PCI subscribers, they
can quickly and easily activate any, if not all, of the Open Access
repositories contained PCI, making thus the contents of those directly
discoverable to their end users.
Ranking Entities in the Age of Two Webs, an Application to Semantic Snippets
Authors: Alsarem Mazen  LIRIS, Portier Pierre-Edouard  LIRIS, Calabretto Sylvie  LIRIS, Kosch Harald  FMI
Date: 2015-09-15 00:00:00
Tasks: Dimensionality Reduction

The advances of the Linked Open Data (LOD) initiative are giving rise to a
more structured Web of data. Indeed, a few datasets act as hubs (e.g., DBpedia)
connecting many other datasets. They also made possible new Web services for
entity detection inside plain text (e.g., DBpedia Spotlight), thus allowing for
new applications that can benefit from a combination of the Web of documents
and the Web of data. To ease the emergence of these new applications, we
propose a query-biased algorithm (LDRANK) for the ranking of web of data
resources with associated textual data. Our algorithm combines link analysis
with dimensionality reduction. We use crowdsourcing for building a publicly
available and reusable dataset for the evaluation of query-biased ranking of
Web of data resources detected in Web pages. We show that, on this dataset,
LDRANK outperforms the state of the art. Finally, we use this algorithm for the
construction of semantic snippets of which we evaluate the usefulness with a
crowdsourcing-based approach.
The role of demographic stochasticity in a speciation model with sexual reproduction
Date: 2016-03-21 00:00:00

Recent theoretical studies have shown that demographic stochasticity can
greatly increase the tendency of asexually reproducing phenotypically diverse
organisms to spontaneously evolve into localised clusters, suggesting a simple
mechanism for sympatric speciation. Here we study the role of demographic
stochasticity in a model of competing organisms subject to assortative mating.
We find that in models with sexual reproduction, noise can also lead to the
formation of phenotypic clusters in parameter ranges where deterministic models
would lead to a homogeneous distribution. In some cases, noise can have a
sizeable effect, rendering the deterministic modelling insufficient to
understand the phenotypic distribution.
Regional and temporal characteristics of bovine tuberculosis of cattle in Great Britain
Date: 2015-09-15 00:00:00
Tasks: Time Series Analysis

Bovine tuberculosis (TB) is a chronic disease in cattle that causes a serious
food security challenge to the agricultural industry in terms of dairy and meat
production. In GB, Scotland has had a risk based surveillance testing policy
under which high risk herds are tested frequently, and in Sept 2009 was
officially declared as TB free. Wales have had an annual or more frequent
testing policy for all cattle herds since Jan 2010, while in England several
herds are still tested every 4 years except some high TB prevalence areas where
annual testing is applied. Time series analysis using publicly available data
for total tests on herds, total cattle slaughtered, new herd incidents, and
herds not TB free, were analysed globally for GB and locally for the
constituent regions of Wales, Scotland, West, North, and East England. After
detecting trends over time, underlying regional differences were compared with
the testing policies in the region. Total cattle slaughtered are decreasing in
Wales, Scotland and West England, but increasing in the North and East English
regions. New herd incidents, i.e., disease incidence, are decreasing in Wales,
Scotland, West English region, but increasing in North and East English
regions. Herds not TB free, are increasing in West, North, and East English
regions, while they are decreasing in Wales and Scotland. Total cattle
slaughtered were positively correlated with total tests in the West, North, and
East English regions, with high slopes of regression. There was no correlation
between total cattle slaughtered and total tests on herds in Wales indicating
that herds are tested frequent enough in order to detect all likely cases and
so control TB. The main conclusion of the analysis conducted here is that more
frequent testing is leading to lower TB infections in cattle both in terms of
TB prevalence as well as TB incidence.
Optimal Insurance with Rank-Dependent Utility and Increasing Indemnities
Date: 2015-09-16 00:00:00

Bernard et al. (2015) study an optimal insurance design problem where an
individual's preference is of the rank-dependent utility (RDU) type, and show
that in general an optimal contract covers both large and small losses.
However, their contracts suffer from a problem of moral hazard for paying more
compensation for a smaller loss. This paper addresses this setback by
exogenously imposing the constraint that both the indemnity function and the
insured's retention function be increasing with respect to the loss. We
characterize the optimal solutions via calculus of variations, and then apply
the result to obtain explicitly expressed contracts for problems with Yaari's
dual criterion and general RDU. Finally, we use a numerical example to compare
the results between ours and that of Bernard et al. (2015).
Life without dUTPase
Date: 2015-09-16 00:00:00

Fine-tuned regulation of the cellular nucleotide pools is indispensable for
faithful replication of DNA. The genetic information is also safeguarded by DNA
damage recognition and repair processes. Uracil is one of the most frequently
occurring erroneous base in DNA; it can arise from cytosine deamination or
thymine-replacing incorporation. Two enzyme families are primarily involved in
keeping DNA uracil-free: dUTPases that prevent thymine-replacing incorporation
and uracil-DNA glycosylases that excise uracil from DNA and initiate
uracil-excision repair. Both dUTPase and the most efficient uracil-DNA
glycosylase UNG is thought to be ubiquitous in free-living organisms. In the
present work, we have systematically investigated the genotype of deposited
fully sequenced bacterial and Archaeal genomes. Surprisingly, we have found
that in contrast to the generally held opinion, a wide number of bacterial and
Archaeal species lack the dUTPase gene(s). The dut- genotype is present in
diverse bacterial phyla indicating that loss of this (or these) gene(s) has
occurred multiple times during evolution. We have identified several survival
strategies in lack of dUTPases: i) simultaneous lack or inhibition of UNG, ii)
acquisition of a less dUTP-specific sanitizing nucleotide pyrophosphatase, and
iii) supply of dUTPase from bacteriophages. Our data indicate that several
unicellular microorganisms may efficiently cope with a dut- genotype
potentially leading to an unusual uracil-enrichment in their genomic DNA.
Estimating Tipping Points in Feedback-Driven Financial Networks
Date: 2015-09-16 00:00:00

Much research has been conducted arguing that tipping points at which complex
systems experience phase transitions are difficult to identify. To test the
existence of tipping points in financial markets, based on the alternating
offer strategic model we propose a network of bargaining agents who mutually
either cooperate or where the feedback mechanism between trading and price
dynamics is driven by an external "hidden" variable R that quantifies the
degree of market overpricing. Due to the feedback mechanism, R fluctuates and
oscillates over time, and thus periods when the market is underpriced and
overpriced occur repeatedly. As the market becomes overpriced, bubbles are
created that ultimately burst in a market crash. The probability that the index
will drop in the next year exhibits a strong hysteresis behavior from which we
calculate the tipping point. The probability distribution function of R has a
bimodal shape characteristic of small systems near the tipping point. By
examining the S&P500 index we illustrate the applicability of the model and
demonstate that the financial data exhibits a hysteresis and a tipping point
that agree with the model predictions. We report a cointegration between the
returns of the S&P 500 index and its intrinsic value.
Melodic Contour and Mid-Level Global Features Applied to the Analysis of Flamenco Cantes
Authors: Gómez Francisco, Mora Joaquín, Gómez Emilia, Díaz-Báñez José Miguel
Date: 2015-09-16 00:00:00

This work focuses on the topic of melodic characterization and similarity in
a specific musical repertoire: a cappella flamenco singing, more specifically
in debla and martinete styles. We propose the combination of manual and
automatic description. First, we use a state-of-the-art automatic transcription
method to account for general melodic similarity from music recordings. Second,
we define a specific set of representative mid-level melodic features, which
are manually labeled by flamenco experts. Both approaches are then contrasted
and combined into a global similarity measure. This similarity measure is
assessed by inspecting the clusters obtained through phylogenetic algorithms
algorithms and by relating similarity to categorization in terms of style.
Finally, we discuss the advantage of combining automatic and expert annotations
as well as the need to include repertoire-specific descriptions for meaningful
melodic characterization in traditional music collections.
The impact of microfibril orientations on the biomechanics of plant cell walls and tissues: modelling and simulations
Date: 2015-09-15 00:00:00

It is known that the orientation of cellulose microfibrils within plant cell
walls has an important impact on the morphogenesis of plant cells and tissues.
Viewing the shape of a plant cell as a square prism or cylinder with the axis
aligning with the primary direction of expansion and growth, the orientation of
the microfibrils within the cell wall on the sides of the cell is known.
However, not much is known about their orientation at the ends of the cell.
Here we investigate the impact of the orientation of cellulose microfibrils
within a plant cell wall at the ends of the cell by solving the equations of
linear elasticity numerically. Three different scenarios for the orientation of
the microfibrils are considered. The macroscopic elastic properties of the cell
wall are obtained using homogenization theory from the microscopic description
of the elastic properties of the cell wall microfibrils and wall matrix. It is
found that the orientation of the microfibrils in the upper and lower parts of
cell walls do not affect the expansion of the cell in the direction of its axis
but do affect its expansion in the lateral directions. The arrangement of the
microfibrils in the upper and lower parts of cell walls is especially important
in the case of directed forces acting on plant cell walls and tissues.
Modeling Concordances of Company's Investment Directions With Its Market Attraction
Date: 2015-09-13 00:00:00
Tasks: regression

This work models the interconnection of company's investment managers'
representations and the market attraction of its shares. The models that
reflect the connection of the company's market effectiveness indices and
parameters of its economic activity are created on the basis of the
Mean-Variance Analysis and Regression Analysis. On another side, expert
evaluation methods also clarified the same influence parameters, but it was
made according to the opinion of company managers. These two evaluation rows
are used when making managerial decisions.
Detecting Community Structures in Hi-C Genomic Data
Date: 2015-09-17 00:00:00
Tasks: Community Detection

Community detection (CD) algorithms are applied to Hi-C data to discover new
communities of loci in the 3D conformation of human and mouse DNA. We find that
CD has some distinct advantages over pre-existing methods: (1) it is capable of
finding a variable number of communities, (2) it can detect communities of DNA
loci either adjacent or distant in the 1D sequence, and (3) it allows us to
obtain a principled value of k, the number of communities present. Forcing k =
2, our method recovers earlier findings of Lieberman-Aiden, et al. (2009), but
letting k be a parameter, our method obtains as optimal value k = 6,
discovering new candidate communities. In addition to discovering large
communities that partition entire chromosomes, we also show that CD can detect
small-scale topologically associating domains (TADs) such as those found in
Dixon, et al. (2012). CD thus provides a natural and flexible statistical
framework for understanding the folding structure of DNA at multiple scales in
Hi-C data.
Numerical study of variable lung ventilation strategies
Date: 2015-09-17 00:00:00

Mechanical ventilation is used for patients with a variety of lung diseases.
Traditionally, ventilators have been designed to monotonously deliver equal
sized breaths. While it may seem intuitive that lungs may benefit from
unvarying and stable ventilation pressure strategy, recently it has been
reported that variable lung ventilation is advantageous. In this study, we
analyze the mean tidal volume in response to different `variable ventilation
pressure' strategies. We found that uniformly distributed variability in
pressure gives the best tidal volume as compared to that of normal, scale-
free, log normal and linear distributions.
A pharmacokinetic -- viral kinetic model describes the effect of alisporivir monotherapy or in combination with peg-IFN on 2 hepatitis C virologic response
Date: 2015-09-17 00:00:00

Alisporivir is a cyclophilin inhibitor with demonstrated in vitro and in vivo
activity against hepatitis C 11 virus (HCV). We estimated antiviral
effectiveness of alisporivir alone or in combination with 12
pegylated-Inteferon (peg-IFN) in 88 patients infected with different HCV
genotypes treated for four 13 weeks. The pharmacokinetics of both drugs were
modeled and used as driving functions for the viral 14 kinetic model. Genotype
was found to significantly affect pegylated-Inteferon effectiveness
($\epsilon$= 86.3% 15 and 99.1% in genotype-1/4 and genotype-2/3, respectively,
p\textless{}10 -7) and infected cells loss rate ($\delta$= 16 0.22 vs 0.39 day
-1 in genotype-1/4 and genotype-2/3, respectively, p\textless{}10 -6).
Alisporivir effectiveness 17 was not significantly different across genotype
and was high for doses $\ge$600 mg QD. We simulated 18 virologic responses with
other alisporivir dosing regimens in HCV genotype-2/3 patients using the 19
model. Our predictions consistently matched the observed responses,
demonstrating that this model 20 could be a useful tool for anticipating
virologic response and optimize alisporivir-based therapies.
The Bulk and The Tail of Minimal Absent Words in Genome Sequences
Date: 2015-09-17 00:00:00

Minimal absent words (MAW) of a genomic sequence are subsequences that are
absent themselves but the subwords of which are all present in the sequence.
The characteristic distribution of genomic MAWs as a function of their length
has been observed to be qualitatively similar for all living organisms, the
bulk being rather short, and only relatively few being long. It has been an
open issue whether the reason behind this phenomenon is statistical or reflects
a biological mechanism, and what biological information is contained in absent
words. In this work we demonstrate that the bulk can be described by a
probabilistic model of sampling words from random sequences, while the tail of
long MAWs is of biological origin. We introduce the novel concept of a core of
a minimal absent word, which are sequences present in the genome and closest to
a given MAW. We show that in bacteria and yeast the cores of the longest MAWs,
which exist in two or more copies, are located in highly conserved regions the
most prominent example being ribosomal RNAs (rRNAs). We also show that while
the distribution of the cores of long MAWs is roughly uniform over these
genomes on a coarse-grained level, on a more detailed level it is strongly
enhanced in 3' untranslated regions (UTRs) and, to a lesser extent, also in 5'
UTRs. This indicates that MAWs and associated MAW cores correspond to
fine-tuned evolutionary relationships, and suggest that they can be more widely
used as markers for genomic complexity.
Assessment of the potential impacts of plant traits across environments by combining global sensitivity analysis and dynamic modeling in wheat
Date: 2015-09-17 00:00:00
Tasks: Management, Sensitivity

A crop can be viewed as a complex system with outputs (e.g. yield) that are
affected by inputs of genetic, physiology, pedo-climatic and management
information. Application of numerical methods for model exploration assist in
evaluating the major most influential inputs, providing the simulation model is
a credible description of the biological system. A sensitivity analysis was
used to assess the simulated impact on yield of a suite of traits involved in
major processes of crop growth and development, and to evaluate how the
simulated value of such traits varies across environments and in relation to
other traits (which can be interpreted as a virtual change in genetic
background). The study focused on wheat in Australia, with an emphasis on
adaptation to low rainfall conditions. A large set of traits (90) was evaluated
in a wide target population of environments (4 sites x 125 years), management
practices (3 sowing dates x 2 N fertilization) and $CO_2$ (2 levels). The
Morris sensitivity analysis method was used to sample the parameter space and
reduce computational requirements, while maintaining a realistic representation
of the targeted trait x environment x management landscape ($\sim$ 82 million
individual simulations in total). The patterns of parameter x environment x
management interactions were investigated for the most influential parameters,
considering a potential genetic range of +/- 20% compared to a reference. Main
(i.e. linear) and interaction (i.e. non-linear and interaction) sensitivity
indices calculated for most of APSIM-Wheat parameters allowed the identifcation
of 42 parameters substantially impacting yield in most target environments.
Among these, a subset of parameters related to phenology, resource acquisition,
resource use efficiency and biomass allocation were identified as potential
candidates for crop (and model) improvement.
Measuring multiscaling in financial time-series
Date: 2015-09-21 00:00:00
Tasks: Time Series, Time Series Analysis

We discuss the origin of multiscaling in financial time-series and
investigate how to best quantify it. Our methodology consists in separating the
different sources of measured multifractality by analysing the
multi/uni-scaling behaviour of synthetic time-series with known properties. We
use the results from the synthetic time-series to interpret the measure of
multifractality of real log-returns time-series. The main finding is that the
aggregation horizon of the returns can introduce a strong bias effect on the
measure of multifractality. This effect can become especially important when
returns distributions have power law tails with exponents in the range [2,5].
We discuss the right aggregation horizon to mitigate this bias.
A proposal of a methodological framework with experimental guidelines to investigate clustering stability on financial time series
Date: 2015-09-17 00:00:00
Tasks: Clustering, Time Series, Time Series Analysis

We present in this paper an empirical framework motivated by the practitioner
point of view on stability. The goal is to both assess clustering validity and
yield market insights by providing through the data perturbations we propose a
multi-view of the assets' clustering behaviour. The perturbation framework is
illustrated on an extensive credit default swap time series database available
online at www.datagrapple.com.
Function changing mutations in glucocorticoid receptor evolution correlate with their relevance to mode coupling
Date: 2015-09-18 00:00:00

Nonlinear effects in protein dynamics are expected to play role in function,
particularly of allosteric nature, by facilitating energy transfer between
vibrational modes. A recently proposed method focusing on the non-Gaussian
shape of the population near equilibrium projects this information onto real
space in order to identify the aminoacids relevant to function. We here apply
this method to three ancestral proteins in glucocorticoid receptor (GR) family
and show that the mutations that restrict functional activity during GR
evolution correlate significantly with locations that are highlighted by the
nonlinear contribution to the near-native configurational distribution. Our
findings demonstrate that nonlinear effects are not only indispensible for
understanding functionality in proteins, but they can also be harnessed into a
predictive tool for functional site determination.
Firing dynamics of an autaptic neuron
Date: 2015-09-18 00:00:00

Autapses are synapses that connect a neuron to itself in the nervous system.
Previously, both experimental and theoretical studies have demonstrated that
autaptic connections in the nervous system have a significant physiological
function. Autapses in nature provide self-delayed feedback, thus introducing an
additional time scale to neuronal activities and causing many dynamic behaviors
in neurons. Recently, theoretical studies have revealed that an autapse
provides a control option for adjusting the response of a neuron: e.g., an
autaptic connection can cause the electrical activities of the Hindmarsh-Rose
neuron to switch between quiescent, periodic, and chaotic firing patterns; an
autapse can enhance or suppress the mode-locking status of a neuron injected
with sinusoidal current; and the firing frequency and interspike interval
distributions of the response spike train can also be modified by the autapse.
In this paper, we review recent studies that showed how an autapse affects the
response of a single neuron.