pwc-archive/papers-with-abstracts huggingface dataset:
In vivo evaluation of wearable head impact sensors
Date: 2015-08-20 00:00:00

Inertial sensors are commonly used to measure human head motion. Some sensors
have been validated with dummy or cadaver experiments, but methods to evaluate
sensors in vivo are lacking. Here we present an in vivo method using high speed
video to evaluate teeth-mounted (mouthguard), soft tissue-mounted (skin patch),
and headgear-mounted (skull cap) sensors during 6-13g sagittal soccer head
impacts. Sensor coupling to the skull is quantified by displacement from an
ear-canal reference. Mouthguard displacements were within video measurement
error (<1mm), while the skin patch and skull cap displaced up to 4mm and 13mm
from the ear-canal reference, respectively. We used the mouthguard, which had
the least displacement from skull, as the reference to assess
6-degree-of-freedom skin patch and skull cap measurements. Linear and
rotational acceleration magnitudes were over-predicted by both the skin patch
(with 120% NRMS error for a_mag, 290% for alpha_mag) and the skull cap (320%
NRMS error for a_mag, 500% for alpha_mag). Such over-predictions were largely
due to out-of-plane motion. To model sensor error, we found that in-plane
acceleration peaks from the skin patch in the anterior-posterior direction
could be modeled by an underdamped viscoelastic system. In summary, the
mouthguard showed tighter skull coupling in vivo than the other sensors.
Furthermore, the in vivo methods presented are valuable for investigating skull
acceleration sensor technologies.
Implementation of an efficient Fuzzy Logic based Information Retrieval System
Authors: Singh Prabhjot, Dhawan Sumit, Agarwal Shubham, Thakur Narina
Date: 2015-03-13 00:00:00
Tasks: Information Retrieval, Retrieval

This paper exemplifies the implementation of an efficient Information
Retrieval (IR) System to compute the similarity between a dataset and a query
using Fuzzy Logic. TREC dataset has been used for the same purpose. The dataset
is parsed to generate keywords index which is used for the similarity
comparison with the user query. Each query is assigned a score value based on
its fuzzy similarity with the index keywords. The relevant documents are
retrieved based on the score value. The performance and accuracy of the
proposed fuzzy similarity model is compared with Cosine similarity model using
Precision-Recall curves. The results prove the dominance of Fuzzy Similarity
based IR system.
Knowledge-based Query Expansion in Real-Time Microblog Search
Authors: Qiang Runwei, Fan Feifan, Lv Chao, Yang Jianwu
Date: 2015-03-13 00:00:00
Tasks: Information Retrieval, Language Modeling, Language Modelling, Retrieval

Since the length of microblog texts, such as tweets, is strictly limited to
140 characters, traditional Information Retrieval techniques suffer from the
vocabulary mismatch problem severely and cannot yield good performance in the
context of microblogosphere. To address this critical challenge, in this paper,
we propose a new language modeling approach for microblog retrieval by
inferring various types of context information. In particular, we expand the
query using knowledge terms derived from Freebase so that the expanded one can
better reflect users' search intent. Besides, in order to further satisfy
users' real-time information need, we incorporate temporal evidences into the
expansion method, which can boost recent tweets in the retrieval results with
respect to a given topic. Experimental results on two official TREC Twitter
corpora demonstrate the significant superiority of our approach over baseline
methods.
Measuring switching processes in financial markets with the Mean-Variance spin glass approach
Date: 2015-03-13 00:00:00

In this article we use the Mean-Variance Model in order to measure the
current market state. In our study we take the approach of detecting the
overall alignment of portfolios in the spin picture. The projection to the
ground-states enables us to use physical observables in order to describe the
current state of the explored market. The defined magnetization of portfolios
shows cursor effects, which we use to detect turmoils.
Developmental time windows for axon growth influence neuronal network topology
Date: 2015-03-13 00:00:00

Early brain connectivity development consists of multiple stages: birth of
neurons, their migration and the subsequent growth of axons and dendrites. Each
stage occurs within a certain period of time depending on types of neurons and
cortical layers. Forming synapses between neurons either by growing axons
starting at similar times for all neurons (much-overlapped time windows) or at
different time points (less-overlapped) may affect the topological and spatial
properties of neuronal networks. Here, we explore the extreme cases of axon
formation especially concerning short-distance connectivity during early
development, either starting at the same time for all neurons (parallel, i.e.
maximally-overlapped time windows) or occurring for each neuron separately one
neuron after another (serial, i.e. no overlaps in time windows). For both
cases, the number of potential and established synapses remained comparable.
Topological and spatial properties, however, differed: neurons that started
axon growth early on in serial growth achieved higher out-degrees, higher local
efficiency, and longer axon lengths while neurons demonstrated more homogeneous
connectivity patterns for parallel growth. Second, connection probability
decreased more rapidly with distance between neurons for parallel growth than
for serial growth. Third, bidirectional connections were more numerous for
parallel growth. Finally, we tested our predictions with C. elegans data.
Together, this indicates that time windows for axon growth influence the
topological and spatial properties of neuronal networks opening the possibility
to a posteriori estimate developmental mechanisms based on network properties
of a developed network.
A scale-free method for testing the proportionality of branch lengths between two phylogenetic trees
Date: 2015-03-13 00:00:00

We introduce a scale-free method for testing the proportionality of branch
lengths between two phylogenetic trees that have the same topology and contain
the same set of taxa. This method scales both trees to a total length of 1 and
sums up the differences for each branch. Compared to previous methods, ours
yields a fully symmetrical score that measures proportionality without being
affected by scale. We call this score the normalized tree distance (NTD). Based
on real data, we demonstrate that NTD scores are distributed unimodally, in a
manner similar to a lognormal distribution. The NTD score can be used to, for
example, detect co-evolutionary processes and measure the accuracy of branch
length estimates.
Consistency of VDJ rearrangement and substitution parameters enables accurate B cell receptor sequence annotation
Date: 2015-05-28 00:00:00

VDJ rearrangement and somatic hypermutation work together to produce
antibody-coding B cell receptor (BCR) sequences for a remarkable diversity of
antigens. It is now possible to sequence these BCRs in high throughput;
analysis of these sequences is bringing new insight into how antibodies
develop, in particular for broadly-neutralizing antibodies against HIV and
influenza. A fundamental step in such sequence analysis is to annotate each
base as coming from a specific one of the V, D, or J genes, or from an
N-addition (a.k.a. non-templated insertion). Previous work has used simple
parametric distributions to model transitions from state to state in a hidden
Markov model (HMM) of VDJ recombination, and assumed that mutations occur via
the same process across sites. However, codon frame and other effects have been
observed to violate these parametric assumptions for such coding sequences,
suggesting that a non-parametric approach to modeling the recombination process
could be useful. In our paper, we find that indeed large modern data sets
suggest a model using parameter-rich per-allele categorical distributions for
HMM transition probabilities and per-allele-per-position mutation
probabilities, and that using such a model for inference leads to significantly
improved results. We present an accurate and efficient BCR sequence annotation
software package using a novel HMM "factorization" strategy. This package,
called partis (https://github.com/psathyrella/partis/), is built on a new
general-purpose HMM compiler that can perform efficient inference given a
simple text description of an HMM.
Bridging Social Media via Distant Supervision
Authors: Magdy Walid, Sajjad Hassan, El-Ganainy Tarek, Sebastiani Fabrizio
Date: 2015-03-15 00:00:00
Tasks: Classification, General Classification, Multi-class Classification

Microblog classification has received a lot of attention in recent years.
Different classification tasks have been investigated, most of them focusing on
classifying microblogs into a small number of classes (five or less) using a
training set of manually annotated tweets. Unfortunately, labelling data is
tedious and expensive, and finding tweets that cover all the classes of
interest is not always straightforward, especially when some of the classes do
not frequently arise in practice. In this paper we study an approach to tweet
classification based on distant supervision, whereby we automatically transfer
labels from one social medium to another for a single-label multi-class
classification task. In particular, we apply YouTube video classes to tweets
linking to these videos. This provides for free a virtually unlimited number of
labelled instances that can be used as training data. The classification
experiments we have run show that training a tweet classifier via these
automatically labelled data achieves substantially better performance than
training the same classifier with a limited amount of manually labelled data;
this is advantageous, given that the automatically labelled data come at no
cost. Further investigation of our approach shows its robustness when applied
with different numbers of classes and across different languages.
Optimal risk allocation in a market with non-convex preferences
Date: 2015-03-15 00:00:00

The aims of this study are twofold. First, we consider an optimal risk
allocation problem with non-convex preferences. By establishing an infimal
representation for distortion risk measures, we give some necessary and
sufficient conditions for the existence of optimal and asymptotic optimal
allocations. We will show that, similar to a market with convex preferences, in
a non-convex framework with distortion risk measures the boundedness of the
optimal risk allocation problem depends only on the preferences. Second, we
consider the same optimal allocation problem by adding a further assumption
that allocations are co-monotone. We characterize the co-monotone optimal risk
allocations within which we prove the "marginal risk allocations" take only the
values zero or one. Remarkably, we can separate the role of the market
preferences and the total risk in our representation.
The overshoot and phenotypic equilibrium in characterizing cancer dynamics of reversible phenotypic plasticity
Date: 2015-09-15 00:00:00

The paradigm of phenotypic plasticity indicates reversible relations of
different cancer cell phenotypes, which extends the cellular hierarchy proposed
by the classical cancer stem cell (CSC) theory. Since it is still question able
if the phenotypic plasticity is a crucial improvement to the hierarchical model
or just a minor extension to it, it is worthwhile to explore the dynamic
behavior characterizing the reversible phenotypic plasticity. In this study we
compare the hierarchical model and the reversible model in predicting the
cell-state dynamics observed in biological experiments. Our results show that
the hierarchical model shows significant disadvantages over the reversible
model in describing both long-term stability (phenotypic equilibrium) and
short-term transient dynamics (overshoot) of cancer cells. In a very specific
case in which the total growth of population due to each cell type is
identical, the hierarchical model predicts neither phenotypic equilibrium nor
overshoot, whereas thereversible model succeeds in predicting both of them.
Even though the performance of the hierarchical model can be improved by
relaxing the specific assumption, its prediction to the phenotypic equilibrium
strongly depends on a precondition that may be unrealistic in biological
experiments, and it also fails to capture the overshoot of CSCs. By comparison,
it is more likely for the reversible model to correctly describe the stability
of the phenotypic mixture and various types of overshoot behavior.
Extensive fitness and human cooperation
Date: 2015-09-10 00:00:00

Evolution depends on the fitness of organisms, the expected rate of
reproducing. Directly getting offspring is the most basic form of fitness, but
fitness can also be increased indirectly by helping genetically related
individuals (such as kin) to increase their fitness. The combined effect is
known as inclusive fitness. Here it is argued that a further elaboration of
fitness has evolved, particularly in humans. It is called extensive fitness and
it incorporates producing organisms that are merely similar in phenotype. The
evolvability of this mechanism is illustrated by computations on a simple model
combining heredity and behaviour. Phenotypes are driven into the direction of
high fitness through a mechanism that involves an internal estimate of fitness,
implicitly made within the organism itself. This mechanism has recently been
conjectured to be responsible for producing agency and goals. In the model,
inclusive and extensive fitness are both implemented by letting fitness
increase nonlinearly with the size of subpopulations of similar heredity (for
the indirect part of inclusive fitness) and of similar phenotype (for the
phenotypic part of extensive fitness). Populations implementing extensive
fitness outcompete populations implementing mere inclusive fitness. This occurs
because groups with similar phenotype tend to be larger than groups with
similar heredity, and fitness increases more when groups are larger. Extensive
fitness has two components, a direct component where individuals compete in
inducing others to become like them and an indirect component where individuals
cooperate and help others who are already similar to them.
Two symmetry breaking mechanisms for the development of orientation selectivity in a neural system
Date: 2015-03-16 00:00:00

Orientation selectivity is a remarkable feature of the neurons located in the
primary visual cortex. Provided that the visual neurons acquire orientation
selectivity through activity-dependent Hebbian learning, the development
process could be understood as a kind of symmetry breaking phenomenon in the
view of physics. The key mechanisms of the development process are examined
here in a neural system. Found is that there are at least two different
mechanisms which lead to the development of orientation selectivity through
breaking the radial symmetry in receptive fields. The first, a simultaneous
symmetry breaking mechanism, bases on the competition between neighboring
neurons, and the second, a spontaneous one, bases on the nonlinearity in
interactions. It turns out that only the second mechanism leads to the
formation of a columnar pattern which characteristics accord with those
observed in an animal experiment.
Dynamics of p53 and Wnt cross talk
Date: 2015-03-16 00:00:00

We present the mechanism of interaction of Wnt network module, which is
responsible for periodic sometogenesis, with p53 regulatory network, which is
one of the main regulators of various cellular functions, and switching of
various oscillating states by investigating p53-Wnt model. The variation in
Nutlin concentration in p53 regulating network drives the Wnt network module to
different states, stabilized, damped and sustain oscillation states, and even
to cycle arrest. Similarly, the change in Axin concentration in Wnt could able
to modulate the p53 dynamics at these states. We then solve the set of coupled
ordinary differential equations of the model using quasi steady state
approximation. We, further, demonstrate the change of p53 and Gsk3 interaction
rate, due to hypothetical catalytic reaction or external stimuli, can able to
regulate the dynamics of the two network modules, and even can control their
dynamics to protect the system from cycle arrest (apoptosis).
Forest Fire Model as a Supercritical Dynamic Model in Financial Systems
Date: 2015-02-24 00:00:00
Tasks: model

Recently, large-scale cascading failures in complex systems have garnered
substantial attention. Such extreme events have been treated as an integral
part of the self-organized criticality (SOC). Recent empirical work has
suggested that some extreme events systematically deviate from the SOC
paradigm, requiring a different theoretical framework. We shed additional
theoretical light on this possibility by studying financial crisis. We build
our model of financial crisis on the well-known forest fire model in scale-free
networks. Our analysis shows a non-trivial scaling feature indicating
supercritical behavior, which is independent of system size. Extreme events in
the supercritical state result from bursting of a fat bubble, seeds of which
are sown by a protracted period of a benign financial environment with few
shocks. Our findings suggest that policymakers can control the magnitude of
financial meltdowns by keeping the economy operating within reasonable duration
of a benign environment.
No substitute for real data: phylogenies from birth-death polytomy resolvers should not be used for many downstream comparative analyses
Date: 2015-03-17 00:00:00

The statistical estimation of phylogenies is always associated with
uncertainty, and accommodating this uncertainty is an important component of
modern phylogenetic comparative analysis. The birth-death polytomy resolver is
a method of accounting for phylogenetic uncertainty that places missing
(unsampled) taxa onto phylogenetic trees, using taxonomic information alone.
Recent studies of birds and mammals have used this approach to generate
pseudo-posterior distributions of phylogenetic trees that are complete at the
species level, even in the absence of genetic data for many species. Many
researchers have used these distributions of phylogenies for downstream
evolutionary analyses that involve inferences on phenotypic evolution,
geography, and community assembly. I demonstrate that the use of phylogenies
constructed in this fashion is inappropriate for many questions involving
traits. Because species are placed on trees at random with respect to trait
values, the birth-death polytomy resolver breaks down natural patterns of trait
phylogenetic structure. Inferences based on these trees are predictably and
often drastically biased in a direction that depends on the underlying (true)
pattern of phylogenetic structure in traits. I illustrate the severity of the
phenomenon for both continuous and discrete traits using examples from a global
bird phylogeny.
Synthetic circuit designs for Earth terraformation
Date: 2015-03-17 00:00:00

Mounting evidence indicates that our planet might experience runaway effects
associated to rising temperatures and ecosystem overexploitation, leading to
catastrophic shifts on short time scales. Remediation scenarios capable of
counterbalancing these effects involve geoengineering, sustainable practices
and carbon sequestration, among others. None of these scenarios seems powerful
enough to achieve the desired restoration of safe boundaries. We hypothesise
that synthetic organisms with the appropriate engineering design could be used
to safely prevent declines in some stressed ecosystems and help improving
carbon sequestration. Such schemes would include engineering mutualistic
dependencies preventing undesired evolutionary processes. We hypothesise that
some particular design principles introduce unescapable constraints to the
engineered organisms that act as effective firewalls. Testing this designed
organisms can be achieved by using controlled bioreactor models and accurate
computational models including different scales (from genetic constructs and
metabolic pathways to population dynamics). Our hypothesis heads towards a
future anthropogenic action that should effectively act as Terraforming agents.
It also implies a major challenge in the existing biosafety policies, since we
suggest release of modified organisms as potentially necessary strategy for
success.
Analysis of whole mitogenomes from ancient samples
Date: 2016-04-25 00:00:00

Ancient mitochondrial DNA has been used in a wide variety of palaeontological
and archaeological studies, ranging from population dynamics of extinct species
to patterns of domestication. Most of these studies have traditionally been
based on the analysis of short fragments from the mitochondrial control region,
analysed using PCR coupled with Sanger sequencing. With the introduction of
high-throughput sequencing, as well as new enrichment technologies, the
recovery of full mitochondrial genomes (mitogenomes) from ancient specimens has
become significantly less complicated. Here we present a protocol to build
ancient extracts into Illumina high-throughput sequencing libraries, and
subsequent Agilent array-based capture to enrich for the desired mitogenome.
Both are based on previously published protocols, with the introduction of
several improvements aimed to increase the recovery of short DNA fragments,
while keeping the cost and effort requirements low. This protocol was designed
for enrichment of mitochondrial DNA in ancient or degraded samples. However,
the protocols can be easily adapted for using for building libraries for
shotgun-sequencing of whole genomes, or enrichment of other genomic regions.
Nonlinear Mixed-Effect Models for Prostate-Specific Antigen Kinetics and Link with Survival in the Context of Metastatic Prostate Cancer: a Comparison by Simulation of Two-Stage and Joint Approaches
Date: 2015-03-17 00:00:00

In metastatic castration-resistant prostate cancer (mCRPC) clinical trials,
the assessment of treatment efficacy essentially relies on the time-to-death
and the kinetics of prostate-specific antigen (PSA). Joint modelling has been
increasingly used to characterize the relationship between a time-to-event and
a biomarker kinetics but numerical difficulties often limit this approach to
linear models. Here we evaluated by simulation the capability of a new feature
of the Stochastic Approximation Expectation-Maximization algorithm in Monolix
to estimate the parameters of a joint model where PSA kinetics was defined by a
mechanistic nonlinear mixed-effect model. The design of the study and the
parameter values were inspired from one arm of a clinical trial. Increasingly
high levels of association between PSA and survival were considered and results
were compared with those found using two simplified alternatives to joint
model, a two-stage and a joint sequential model. We found that joint model
allowed for a precise estimation of all longitudinal and survival parameters.
In particular the effect of PSA kinetics on survival could be precisely
estimated, regardless of the strength of the association. In contrast, both
simplified approaches led to bias on longitudinal parameters and two-stage
model systematically underestimated the effect of PSA kinetics on survival. In
summary we showed that joint model can be used to characterize the relationship
between a nonlinear kinetics and survival. This opens the way for the use of
more complex and physiological models to improve treatment evaluation and
prediction in oncology.