pwc-archive/papers-with-abstracts huggingface dataset:
Detecting somatic mutations in genomic sequences by means of Kolmogorov-Arnold analysis
Date: 2015-06-12 00:00:00
Tasks: Diagnostic

The Kolmogorov-Arnold stochasticity parameter technique is applied for the
first time to the study of cancer genome sequencing, to reveal mutations. Using
data generated by next generation sequencing technologies, we have analyzed the
exome sequences of brain tumor patients with matched tumor and normal blood. We
show that mutations contained in sequencing data can be revealed using this
technique thus providing a new methodology for determining subsequences of
given length containing mutations i.e. its value differs from those of
subsequences without mutations. A potential application for this technique
involves simplifying the procedure of finding segments with mutations, speeding
up genomic research, and accelerating its implementation in clinical
diagnostic. Moreover, the prediction of a mutation associated to a family of
frequent mutations in numerous types of cancers based purely on the value of
the Kolmogorov function, indicates that this applied marker may recognize
genomic sequences that are in extremely low abundance and can be used in
revealing new types of mutations.
The WDAqua ITN: Answering Questions using Web Data
Authors: Lange Christoph, Shekarpour Saeedeh, Auer Soren
Date: 2015-06-10 00:00:00
Tasks: Question Answering

WDAqua is a Marie Curie Innovative Training Network (ITN) and is funded under
EU grant number 642795 and runs from January 2015 to December 2018. WDAqua aims
at advancing the state of the art by intertwining training, research and
innovation efforts, centered around one service: data-driven question
answering. Question answering is immediately useful to a wide audience of end
users, and we will demonstrate this in settings including e-commerce, public
sector information, publishing and smart cities. Question answering also covers
web science and data science broadly, leading to transferrable research results
and to transferrable skills of the researchers who have finished our training
programme. To ensure that our research improves question answering overall,
every individual research project connects at least two of these steps.
Intersectional secondments (within a consortium covering academia, research
institutes and industrial research as well as network-wide workshops, R and D
challenges and innovation projects further balance ground-breaking research and
the needs of society and industry. Training-wise these offers equip early stage
researchers with the expertise and transferable technical and non-technical
skills that will allow them to pursue a successful career as an academic,
decision maker, practitioner or entrepreneur.
A risk management approach to capital allocation
Date: 2015-06-12 00:00:00
Tasks: Management

The European insurance sector will soon be faced with the application of
Solvency 2 regulation norms. It will create a real change in risk management
practices. The ORSA approach of the second pillar makes the capital allocation
an important exercise for all insurers and specially for groups. Considering
multi-branches firms, capital allocation has to be based on a multivariate risk
modeling. Several allocation methods are present in the literature and insurers
practices. In this paper, we present a new risk allocation method, we study its
coherence using an axiomatic approach, and we try to define what the best
allocation choice for an insurance group is.
Student Teaching and Research Laboratory Focusing on Brain-computer Interface Paradigms - A Creative Environment for Computer Science Students -
Date: 2015-06-13 00:00:00
Tasks: Brain Computer Interface, Philosophy

This paper presents an applied concept of a brain-computer interface (BCI)
student research laboratory (BCI-LAB) at the Life Science Center of TARA,
University of Tsukuba, Japan. Several successful case studies of the student
projects are reviewed together with the BCI Research Award 2014 winner case.
The BCI-LAB design and project-based teaching philosophy is also explained.
Future teaching and research directions summarize the review.
Safety Third: Roy's Criterion and Higher Order Moments
Date: 2015-06-13 00:00:00

Roy's `Safety First' criterion for selecting one risky asset from many is
adapted to the case of non-normal returns, via Cornish Fisher expansion. The
resulting investment objective is consistent with first order stochastic
dominance, and is equal to the Sharpe ratio for the case of normal returns. An
investor selecting assets via this objective is not universally attracted to
positive skew, rather the preference for skew depends on term, the expected
return and the disastrous rate of return.
Predicting single-neuron activity in locally connected networks
Date: 2015-06-13 00:00:00

The characterization of coordinated activity in neuronal populations has
received renewed interest in the light of advancing experimental techniques
which allow recordings from multiple units simultaneously. Across both in vitro
and in vivo preparations, nearby neurons show coordinated responses when
spontaneously active, and when subject to external stimuli. Recent work
(Truccolo, Hochberg, & Donoghue, 2010) has connected these coordinated
responses to behavior, showing that small ensembles of neurons in arm related
areas of sensorimotor cortex can reliably predict single-neuron spikes in
behaving monkeys and humans. We investigate this phenomenon utilizing an
analogous point process model, showing that in the case of a computational
model of cortex responding to random background inputs, one is similarly able
to predict the future state of a single neuron by considering its own spiking
history, together with the spiking histories of randomly sampled ensembles of
nearby neurons. This model exhibits realistic cortical architecture and
displays bursting episodes in the two distinct connectivity schemes studied. We
conjecture that the baseline predictability we find in these instances is
characteristic of locally connected networks more broadly considered.
Head-related Impulse Response Cues for Spatial Auditory Brain-computer Interface
Date: 2015-06-14 00:00:00
Tasks: Brain Computer Interface, EEG, Electroencephalogram (EEG)

This study provides a comprehensive test of a head-related impulse response
(HRIR) cues for a spatial auditory brain-computer interface (saBCI) speller
paradigm. We present a comparison with the conventional virtual sound
headphone-based spatial auditory modality. We propose and optimize the three
types of sound spatialization settings using a variable elevation in order to
evaluate the HRIR efficacy for the saBCI. Three experienced and seven naive BCI
users participated in the three experimental setups based on ten presented
Japanese syllables. The obtained EEG auditory evoked potentials (AEP) resulted
with encouragingly good and stable P300 responses in online BCI experiments.
Our case study indicated that users could perceive elevation in the saBCI
experiments generated using the HRIR measured from a general head model. The
saBCI accuracy and information transfer rate (ITR) scores have been improved
comparing to the classical horizontal plane-based virtual spatial sound
reproduction modality, as far as the healthy users in the current pilot study
are concerned.
Asymmetrical inheritance of plasmids depends on dynamic cellular geometry and volume exclusion effects
Date: 2015-06-14 00:00:00

The asymmetrical inheritance of plasmid DNA, as well as other cellular
components, has been shown to be involved in replicative aging. In
Saccharomyces cerevisiae, there is an ongoing debate regarding the mechanisms
underlying this important asymmetry. Currently proposed models suggest it is
established via diffusion, but differ on whether a diffusion barrier is
necessary or not. However, no study so far incorporated key aspects to
segregation, such as dynamic morphology changes throughout anaphase or plasmids
size. Here, we determine the distinct effects and contributions of individual
cellular variability, plasmid volume and moving boundaries in the asymmetric
segregation of plasmids. We do this by measuring cellular nuclear geometries
and plasmid diffusion rates with confocal microscopy, subsequently
incorporating this data into a growing domain stochastic spatial simulator. Our
modelling and simulations confirms that plasmid asymmetrical inheritance does
not require an active barrier to diffusion, and provides a full analysis on
plasmid size effects.
Bessel Functions in Mass Action. Modeling of Memories and Remembrances
Date: 2015-06-14 00:00:00

Data from experimental observations of a class of neurological processes
(Freeman K-sets) present functional distribution reproducing Bessel function
behavior. We model such processes with couples of damped/amplified oscillators
which provide time dependent representation of Bessel equation. The root loci
of poles and zeros conform to solutions of K-sets. Some light is shed on the
problem of filling the gap between the cellular level dynamics and the brain
functional activity. Breakdown of time-reversal symmetry is related with the
cortex thermodynamic features. This provides a possible mechanism to deduce
lifetime of recorded memory.
mTORC1 regulates cytokinesis through activation of Rho-ROCK signaling
Date: 2015-06-14 00:00:00

Understanding the mechanisms by which cells coordinate their size with their
ability to divide has long attracted the interest of biologists. The Target of
Rapamycin (TOR) pathway is becoming increasingly recognized as a master
regulator of cell size, however less is known how TOR activity might be coupled
with the cell cycle. Here, we establish that mTOR complex 1 (mTORC1) promotes
cytokinesis through activation of a Rho GTPase-Rho Kinase (ROCK) signaling
cascade. Hyperactivation of mTORC1 signaling by depletion of any of its
negative regulators: TSC1, TSC2, PTEN, or DEPTOR, induces polyploidy in a
rapamycin-sensitive manner. mTORC1 hyperactivation-mediated polyploidization
occurs by a prolonged, but ultimately failed attempt at abcission followed by
re-fusion. Similar to the effects of ROCK2 overexpression, these mTORC1-driven
aberrant cytokinesis events are accompanied by increased Rho-GTP loading,
extensive plasma membrane blebbing, and increased actin-myosin contractility,
all of which can be rescued by either mTORC1 or ROCK inhibition. These results
provide evidence for the existence of a novel mTORC1-Rho-ROCK pathway during
cytokinesis and suggest that mTORC1 might play a critical role in setting the
size at which a mammalian cell divides.
Folding and unfolding phylogenetic trees and networks
Date: 2015-06-14 00:00:00

Phylogenetic networks are rooted, labelled directed acyclic graphs which are
commonly used to represent reticulate evolution. There is a close relationship
between phylogenetic networks and multi-labelled trees (MUL-trees). Indeed, any
phylogenetic network $N$ can be 'unfolded' to obtain a MUL-tree $U(N)$ and,
conversely, a MUL-tree $T$ can in certain circumstances be 'folded' to obtain a
phylogenetic network $F(T)$ that exhibits $T$. In this paper, we study
properties of the operations $U$ and $F$ in more detail. In particular, we
introduce the class of stable networks, phylogenetic networks $N$ for which
$F(U(N))$ is isomorphic to $N$, characterise such networks, and show that that
they are related to the well-known class of tree-sibling networks. We also
explore how the concept of displaying a tree in a network $N$ can be related to
displaying the tree in the MUL-tree $U(N)$. To do this, we develop a
phylogenetic analogue of graph fibrations. This allows us to view $U(N)$ as the
analogue of the universal cover of a digraph, and to establish a close
connection between displaying trees in $U(N)$ and reconciling phylogenetic
trees with networks.
Probabilistic Approach for Evaluating Metabolite Sample Integrity
Date: 2015-06-14 00:00:00
Tasks: feature selection

The success of metabolomics studies depends upon the "fitness" of each
biological sample used for analysis: it is critical that metabolite levels
reported for a biological sample represent an accurate snapshot of the studied
organism's metabolite profile at time of sample collection. Numerous factors
may compromise metabolite sample fitness, including chemical and biological
factors which intervene during sample collection, handling, storage, and
preparation for analysis. We propose a probabilistic model for the quantitative
assessment of metabolite sample fitness. Collection and processing of nuclear
magnetic resonance (NMR) and ultra-performance liquid chromatography (UPLC-MS)
metabolomics data is discussed. Feature selection methods utilized for
multivariate data analysis are briefly reviewed, including feature clustering
and computation of latent vectors using spectral methods. We propose that the
time-course of metabolite changes in samples stored at different temperatures
may be utilized to identify changing-metabolite-to-stable-metabolite ratios as
markers of sample fitness. Tolerance intervals may be computed to characterize
these ratios among fresh samples. In order to discover additional structure in
the data relevant to sample fitness, we propose using data labeled according to
these ratios to train a Dirichlet process mixture model (DPMM) for assessing
sample fitness. DPMMs are highly intuitive since they model the metabolite
levels in a sample as arising from a combination of processes including, e.g.,
normal biological processes and degradation- or contamination-inducing
processes. The outputs of a DPMM are probabilities that a sample is associated
with a given process, and these probabilities may be incorporated into a final
classifier for sample fitness.
Transitions between homophilic and heterophilic modes of cooperation
Date: 2015-11-20 00:00:00
Tasks: TAG

Cooperation is ubiquitous in biological and social systems. Previous studies
revealed that a preference toward similar appearance promotes cooperation, a
phenomenon called tag-mediated cooperation or communitarian cooperation. This
effect is enhanced when a spatial structure is incorporated, because space
allows agents sharing an identical tag to regroup to form locally cooperative
clusters. In spatially distributed settings, one can also consider migration of
organisms, which has a potential to further promote evolution of cooperation by
facilitating spatial clustering. However, it has not yet been considered in
spatial tag-mediated cooperation models. Here we show, using computer
simulations of a spatial model of evolutionary games with organismal migration,
that tag-based segregation and homophilic cooperation arise for a wide range of
parameters. In the meantime, our results also show another evolutionarily
stable outcome, where a high level of heterophilic cooperation is maintained in
spatially well-mixed patterns. We found that these two different forms of
tag-mediated cooperation appear alternately as the parameter for temptation to
defect is increased.
Inter-stimulus Interval Study for the Tactile Point-pressure Brain-computer Interface
Date: 2015-06-15 00:00:00
Tasks: Brain Computer Interface, Classification, ERP

The paper presents a study of an inter-stimulus interval (ISI) influence on a
tactile point-pressure stimulus-based brain-computer interface's (tpBCI)
classification accuracy. A novel tactile pressure generating tpBCI stimulator
is also discussed, which is based on a three-by-three pins' matrix prototype.
The six pin-linear patterns are presented to the user's palm during the online
tpBCI experiments in an oddball style paradigm allowing for "the aha-responses"
elucidation, within the event related potential (ERP). A subsequent
classification accuracies' comparison is discussed based on two ISI settings in
an online tpBCI application. A research hypothesis of classification
accuracies' non-significant differences with various ISIs is confirmed based on
the two settings of 120 ms and 300 ms, as well as with various numbers of ERP
response averaging scenarios.
Chromatic and High-frequency cVEP-based BCI Paradigm
Date: 2015-06-22 00:00:00
Tasks: Brain Computer Interface, Vocal Bursts Intensity Prediction

We present results of an approach to a code-modulated visual evoked potential
(cVEP) based brain-computer interface (BCI) paradigm using four high-frequency
flashing stimuli. To generate higher frequency stimulation compared to the
state-of-the-art cVEP-based BCIs, we propose to use the light-emitting diodes
(LEDs) driven from a small micro-controller board hardware generator designed
by our team. The high-frequency and green-blue chromatic flashing stimuli are
used in the study in order to minimize a danger of a photosensitive epilepsy
(PSE). We compare the the green-blue chromatic cVEP-based BCI accuracies with
the conventional white-black flicker based interface.
Emergence of self-reinforcing information bottlenecks in multilevel selection
Date: 2015-06-15 00:00:00

We explain how hierarchical organization of biological systems emerges
naturally during evolution, through a transition in the units of individuality.
We will show how these transitions are the result of competing selective forces
operating at different levels of organization, each level having different
units of individuality. Such a transition represents a singular point in the
evolutionary process, which we will show corresponds to a phase transition in
the way information is encoded, with the formation of self-reinforcing
information bottlenecks. We present an abstract model for characterizing these
transitions that is quite general, applicable to many different versions of
such transitions. As a concrete example, we consider the transition to
multicellularity. Specifically, we study a stochastic model where isolated
communities of interacting individuals (e.g. cells) undergo a transition to
higher-order individuality (e.g. multicellularity). This transition is
indicated by the marked decrease in the number of cells utilized to generate
new communities from pre-existing ones. In this sense, the community begins to
reproduce as a whole via a decreasing number of cells. We show that the fitness
barrier to this transition is strongly reduced by horizontal gene transfer.
These features capture two of the most prominent aspects of the transition to
multicellularity: the evolution of a developmental process and reproduction
through a unicellular bottleneck.
Dendritic Integration Regulation and Neuronal Arithmetic Implemented in a Proton-Coupled Neuron Transistor
Date: 2015-06-12 00:00:00

Neuron is the most important building block in our brain, and information
processing in individual neuron involves the transformation of input synaptic
spike trains into an appropriate output spike train. Hardware implementation of
neuron by individual ionic/electronic coupled device is of great importance for
enhancing our understanding of the brain and solving sensory processing and
complex recognition tasks. Here, we provide a proof-of-principle artificial
neuron with multiple presynaptic inputs and one modulatory terminal based on a
proton-coupled oxide-based electric-double-layer transistor. Regulation of
dendritic integration was realized by tuning the voltage applied on the
modulatory terminal. Additionally, neuronal gain control (arithmetic) in the
scheme of temporal-correlated coding and rate coding are also mimicked. Our
results provide a new-concept approach for building brain-inspired neuromorphic
systems.
The Network of Counterparty Risk: Analysing Correlations in OTC Derivatives
Date: 2015-09-15 00:00:00

Counterparty risk denotes the risk that a party defaults in a bilateral
contract. This risk not only depends on the two parties involved, but also on
the risk from various other contracts each of these parties holds. In rather
informal markets, such as the OTC (over-the-counter) derivative market,
institutions only report their aggregated quarterly risk exposure, but no
details about their counterparties. Hence, little is known about the
diversification of counterparty risk. In this paper, we reconstruct the
weighted and time-dependent network of counterparty risk in the OTC derivatives
market of the United States between 1998 and 2012. To proxy unknown bilateral
exposures, we first study the co-occurrence patterns of institutions based on
their quarterly activity and ranking in the official report. The network
obtained this way is further analysed by a weighted k-core decomposition, to
reveal a core-periphery structure. This allows us to compare the activity-based
ranking with a topology-based ranking, to identify the most important
institutions and their mutual dependencies. We also analyse correlations in
these activities, to show strong similarities in the behavior of the core
institutions. Our analysis clearly demonstrates the clustering of counterparty
risk in a small set of about a dozen US banks. This not only increases the
default risk of the central institutions, but also the default risk of
peripheral institutions which have contracts with the central ones. Hence, all
institutions indirectly have to bear (part of) the counterparty risk of all
others, which needs to be better reflected in the price of OTC derivatives.
Quick or Persistent? Strategic Investment Demanding Versatility
Date: 2015-06-15 00:00:00

In this paper we analyse a dynamic model of investment under uncertainty in a
duopoly, in which each firm has an option to switch from the present market to
a new market. We construct a subgame perfect equilibrium in mixed strategies
and show that both preemption and attrition can occur along typical equilibrium
paths. In order to determine the attrition region a two-dimensional constrained
optimal stopping problem needs to be solved, for which we characterize the
non-trivial stopping boundary in the state space. We explicitly determine
Markovian equilibrium stopping rates in the attrition region and show that
there is always a positive probability of eventual preemption, contrasting the
deterministic version of the model. A simulation-based numerical example
illustrates the model and shows the relative likelihoods of investment taking
place in attrition and preemption regions.
Bayesian total evidence dating reveals the recent crown radiation of penguins
Date: 2017-01-24 00:00:00
Tasks: MORPH

The total-evidence approach to divergence-time dating uses molecular and
morphological data from extant and fossil species to infer phylogenetic
relationships, species divergence times, and macroevolutionary parameters in a
single coherent framework. Current model-based implementations of this approach
lack an appropriate model for the tree describing the diversification and
fossilization process and can produce estimates that lead to erroneous
conclusions. We address this shortcoming by providing a total-evidence method
implemented in a Bayesian framework. This approach uses a mechanistic tree
prior to describe the underlying diversification process that generated the
tree of extant and fossil taxa. Previous attempts to apply the total-evidence
approach have used tree priors that do not account for the possibility that
fossil samples may be direct ancestors of other samples. The fossilized
birth-death (FBD) process explicitly models the diversification, fossilization,
and sampling processes and naturally allows for sampled ancestors. This model
was recently applied to estimate divergence times based on molecular data and
fossil occurrence dates. We incorporate the FBD model and a model of
morphological trait evolution into a Bayesian total-evidence approach to dating
species phylogenies. We apply this method to extant and fossil penguins and
show that the modern penguins radiated much more recently than has been
previously estimated, with the basal divergence in the crown clade occurring at
~12.7 Ma and most splits leading to extant species occurring in the last 2
million years. Our results demonstrate that including stem-fossil diversity can
greatly improve the estimates of the divergence times of crown taxa. The method
is available in BEAST2 (v. 2.4) www.beast2.org with packages SA (v. at least
1.1.4) and morph-models (v. at least 1.0.4).