pwc-archive/papers-with-abstracts huggingface dataset:
Stochastic Model of Tumor-induced Angiogenesis: Ensemble Averages and Deterministic Equations
Date: 2016-02-22 00:00:00

A recent conceptual model of tumor-driven angiogenesis including branching,
elongation, and anastomosis of blood vessels captures some of the intrinsic
multiscale structures of this complex system, yet allowing to extract a
deterministic integro-partial differential description of the vessel tip
density [Phys. Rev. E 90, 062716 (2014)]. Here we solve the stochastic model,
show that ensemble averages over many realizations correspond to the
deterministic equations, and fit the anastomosis rate coefficient so that the
total number of vessel tips evolves similarly in the deterministic and ensemble
averaged stochastic descriptions.
Bunching of numbers in a non-ideal roulette: the key to winning strategies
Date: 2016-01-19 00:00:00

Chances of a gambler are always lower than chances of a casino in the case of
an ideal, mathematically perfect roulette, if the capital of the gambler is
limited and the minimum and maximum allowed bets are limited by the casino.
However, a realistic roulette is not ideal: the probabilities of realisation of
different numbers slightly deviate. Describing this deviation by a statistical
distribution with a width {\delta} we find a critical {\delta} that equalizes
chances of gambler and casino in the case of a simple strategy of the game: the
gambler always puts equal bets to the last N numbers. For up-critical {\delta}
the expected return of the roulette becomes positive. We show that the dramatic
increase of gambler's chances is a manifestation of bunching of numbers in a
non-ideal roulette. We also estimate the critical starting capital needed to
ensure the low risk game for an indefinite time.
Limit Order Book and its modelling in terms of Gibbs Grand-Canonical Ensemble
Date: 2016-02-27 00:00:00

In the domain of the so called Econophysics some attempts already have been
made for applying the theory of Thermodynamics and Statistical Mechanics to
economics and financial markets. In this paper a similar approach is made from
a different perspective, trying to model the limit order book and price
formation process of a given stock by the Grand-Canonical Gibbs Ensemble for
the bid and ask processes. As a consequence we can define in a meaningful way
expressions for the temperatures of the ensembles of bid orders and of ask
orders, which are a function of maximum bid, minimum ask and closure prices of
the stock as well as of the exchanged volume of shares. It is demonstrated that
the difference between the ask and bid orders temperatures can be related to
the VAO (Volume Accumulation Oscillator) indicator, empirically defined in
Technical Analysis of stock markets. Furthermore the distributions for bid and
ask orders derived by the theory can be subject to well defined validations
against real data, giving a falsifiable character to the model.
Mathematical control theory, the immune system, and cancer
Date: 2016-07-11 00:00:00

Simple ideas, endowed from the mathematical theory of control, are used in
order to analyze in general grounds the human immune system. The general
principles are minimization of the pathogen load and economy of resources. They
should constrain the parameters describing the immune system. In the simplest
linear model, for example, where the response is proportional to the load, the
annihilation rate of pathogens in any tissue should be greater than the
pathogen's average rate of growth. When nonlinearities are added, a reference
value for the number of pathogens is set, and a stability condition emerges,
which relates strength of regular threats, barrier height and annihilation
rate. The stability condition allows a qualitative comparison between tissues.
On the other hand, in cancer immunity, the linear model leads to an expression
for the lifetime risk, which accounts for both the effects of carcinogens
(endogenous or external) and the immune response.
Optimal consumption and investment with liquid and illiquid assets
Date: 2019-01-29 00:00:00

We consider an optimal consumption/investment problem to maximize expected
utility from consumption. In this market model, the investor is allowed to
choose a portfolio which consists of one bond, one liquid risky asset (no
transaction costs) and one illiquid risky asset (proportional transaction
costs). We fully characterize the optimal consumption and trading strategies in
terms of the solution of the free boundary ODE with an integral constraint. We
find an explicit characterization of model parameters for the well-posedness of
the problem, and show that the problem is well-posed if and only if there
exists a shadow price process. Finally, we describe how the investor's optimal
strategy is affected by the additional opportunity of trading the liquid risky
asset, compared to the simpler model with one bond and one illiquid risky
asset.
Genetic redundancies enhance information transfer in noisy regulatory circuits
Date: 2016-02-23 00:00:00
Tasks: Decision Making

Cellular decision making is based on regulatory circuits that associate
signal thresholds to specific physiological actions. This transmission of
information is subjected to molecular noise what can decrease its fidelity.
Here, we show instead how such intrinsic noise enhances information transfer in
the presence of multiple circuit copies. The result is due to the contribution
of noise to the generation of autonomous responses by each copy, which are
altogether associated with a common decision. Moreover, factors that correlate
the responses of the redundant units (extrinsic noise or regulatory cross-talk)
contribute to reduce fidelity, while those that further uncouple them
(heterogeneity within the copies) can lead to stronger information gain.
Overall, our study emphasizes how the interplay of signal thresholding,
redundancy, and noise influences the accuracy of cellular decision making.
Understanding this interplay provides a basis to explain collective cell
signaling mechanisms, and to engineer robust decisions with noisy genetic
circuits.
Connectopic mapping with resting-state fMRI
Date: 2017-07-17 00:00:00
Tasks: Functional Connectivity

Brain regions are often topographically connected: nearby locations within
one brain area connect with nearby locations in another area. Mapping these
connection topographies, or 'connectopies' in short, is crucial for
understanding how information is processed in the brain. Here, we propose
principled, fully data-driven methods for mapping connectopies using functional
magnetic resonance imaging (fMRI) data acquired at rest by combining spectral
embedding of voxel-wise connectivity 'fingerprints' with a novel approach to
spatial statistical inference. We applied the approach in human primary motor
and visual cortex, and show that it can trace biologically plausible,
overlapping connectopies in individual subjects that follow these regions'
somatotopic and retinotopic maps. As a generic mechanism to perform inference
over connectopies, the new spatial statistics approach enables rigorous
statistical testing of hypotheses regarding the fine-grained spatial profile of
functional connectivity and whether that profile is different between subjects
or between experimental conditions. The combined framework offers a fundamental
alternative to existing approaches to investigating functional connectivity in
the brain, from voxel- or seed-pair wise characterizations of functional
association, towards a full, multivariate characterization of spatial
topography.
Visualizing Gene Ontology annotations
Date: 2016-02-23 00:00:00

Contemporary techniques in biology produce readouts for large numbers of
genes simultaneously, the typical example being differential gene expression
measurements. Moreover, those genes are often richly annotated using GO terms
that describe gene function and that can be used to summarize the results of
the genome-scale experiments. However, making sense of such GO enrichment
analyses may be challenging. For instance, overrepresented GO functions in a
set of differentially expressed genes are typically output as a flat list, a
format not adequate to capture the complexities of the hierarchical structure
of the GO annotation labels.
  In this chapter, we survey the various methods to visualize large,
difficult-to-interpret lists of GO terms. We catalogue their availability
(web-based or standalone), the main principles they employ in summarizing large
lists of GO terms, and the visualization styles they support. These brief
commentaries on each software are intended as a helpful inventory, rather than
comprehensive descriptions of the underlying algorithms. Instead, we show
examples of their use and suggest that the choice of an appropriate
visualization tool may be crucial to the utility of GO in biological discovery.
Variabilitatea structurala a padurii naturale. Studiu de caz: Calimani
Date: 2016-02-24 00:00:00
Tasks: Management

The paper presents the importance of research which characterizes the natural
forest structure for the forest management. The lessons learned in these
particular forest ecosystems can be integrated by the forest management
objectives, in order to increase the sustainability of this type of resources.
The project NATFORMAN was focused on the structure of the natural forest, thus
research methodologies and modern technology (such as Field-Map) investigation
and determination were used in order to record information on forest structural
parameters. The results obtained refer to these structural parameters and to
the possibility of transferring such information in practice, in order to
achieve forest sustainable management.
Dissortativity and duplications in Oral cancer
Date: 2016-02-23 00:00:00

More than 300,000 new cases worldwide are being diagnosed with oral cancer
annually. Complexity of oral cancer renders designing drug targets very
difficult. We analyse protein-protein interaction network for the normal and
oral cancer tissue and detect crucial changes in the structural properties of
the networks in terms of the interactions of the hub proteins and the
degree-degree correlations. Further analysis of the spectra of both the
networks, while exhibiting universal statistical behavior, manifest distinction
in terms of the zero degeneracy, providing insight to the complexity of the
underlying system.
3D-Printing for Analytical Ultracentrifugation
Date: 2016-02-23 00:00:00
Tasks: Experimental Design

Analytical ultracentrifugation (AUC) is a classical technique of physical
biochemistry providing information on size, shape, and interactions of
macromolecules from the analysis of their migration in centrifugal fields while
free in solution. A key mechanical element in AUC is the centerpiece, a
component of the sample cell assembly that is mounted between the optical
windows to allow imaging and to seal the sample solution column against high
vacuum while exposed to gravitational forces in excess of 300,000 g. For
sedimentation velocity it needs to be precisely sector-shaped to allow
unimpeded radial macromolecular migration. During the history of AUC a great
variety of centerpiece designs have been developed for different types of
experiments. Here, we report that centerpieces can now be readily fabricated by
3D printing at low cost, from a variety of materials, and with customized
designs. The new centerpieces can exhibit sufficient mechanical stability to
withstand the gravitational forces at the highest rotor speeds and be
sufficiently precise for sedimentation equilibrium and sedimentation velocity
experiments. Sedimentation velocity experiments with bovine serum albumin as a
reference molecule in 3D printed centerpieces with standard double-sector
design result in sedimentation boundaries virtually indistinguishable from
those in commercial double-sector epoxy centerpieces, with sedimentation
coefficients well within the range of published values. The statistical error
of the measurement is slightly above that obtained with commercial epoxy, but
still below 1%. Facilitated by modern open-source design and fabrication
paradigms, we believe 3D printed centerpieces and AUC accessories can spawn a
variety of improvements in AUC experimental design, efficiency and resource
allocation.
Re-refinement of 4xan: hen egg white lysozyme with carboplatin in sodium bromide solution including details of solute, solvent, ion and split occupancy amino acid electron density evidence
Date: 2016-02-23 00:00:00

A re-refinement of 4xan, hen egg white lysozyme (HEWL) with carboplatin
crystallised in NaBr solution, has been made (Tanley et al 2016). This follows
our Response article (Tanley et al 2015) to the Critique article of Shabalin et
al 2015, suggesting the need for corrections to some solute molecule
interpretations of electron density in 4xan and removal of an organic moiety as
a ligand to the platinum ion coordinated to His15. We note Shabalin et al
(2015) model of a chlorine in that density and a close by bromine at partial
occupancy to explain the shape. However, as the bromide concentration is in
huge excess over chloride (by 20 fold), we think that the 4yem Shabalin et al
2015 interpretation highly unlikely, but nevertheless we still cannot offer an
explanation for that shape, confirming our earlier analysis described in Tanley
et al (2014). Following Shabalin et al (2015) reprocessing of the raw
diffraction data for 4g4a, we also redid the diffraction data processing for
4xan to a higher resolution using EVAL (Schreurs et al 2010) concluding in
favour of 1.3 Angstrom as the resolution limit and which is the basis for our
revised PDB file for 4xan (5HMJ). It is very interesting that there is extra
X-ray diffraction data from 1.47 to 1.30 Angstrom resolution e.g. with
<I/sigma(I)> =0.39 and CC1/2 = 0.181 in the final shell (1.30 to 1.322
Angstrom). In this arXiv article we document in detail our different solvent
and split occupancy side chain electron density interpretations as evidence for
our statement of approach in our Response article (Tanley et al 2015). Our
critical re-examination includes comparisons based on the 4xan diffraction data
images reprocessing with three different software packages so as to evaluate
the possibility of variations in electron density interpretations due to that.
Overall our finalised model (PDB code 5HMJ) is now improved over 4xan.
Systematic reviews in paediatric multiple sclerosis and Creutzfeldt-Jakob disease exemplify shortcomings in methods used to evaluate therapies in rare conditions
Date: 2016-02-21 00:00:00

BACKGROUND: Randomized controlled trials (RCTs) are the gold standard design
of clinical research to assess interventions. However, RCTs cannot always be
applied for practical or ethical reasons. To investigate the current practices
in rare diseases, we review evaluations of therapeutic interventions in
paediatric multiple sclerosis (MS) and Creutzfeldt-Jakob disease (CJD). In
particular, we shed light on the endpoints used, the study designs implemented
and the statistical methodologies applied.
  METHODS: We conducted literature searches to identify relevant primary
studies. Data on study design, objectives, endpoints, patient characteristics,
randomization and masking, type of intervention, control, withdrawals and
statistical methodology were extracted from the selected studies. The risk of
bias and the quality of the studies were assessed.
  RESULTS: Twelve (seven) primary studies on paediatric MS (CJD) were included
in the qualitative synthesis. No double-blind, randomized placebo-controlled
trial for evaluating interventions in paediatric MS has been published yet.
Evidence from one open-label RCT is available. The observational studies are
before-after studies or controlled studies. Three of the seven selected studies
on CJD are RCTs, of which two received the maximum mark on the Oxford Quality
Scale. Four trials are controlled observational studies.
  CONCLUSIONS: Evidence from double-blind RCTs on the efficacy of treatments
appears to be variable between rare diseases. With regard to paediatric
conditions it remains to be seen what impact regulators will have through e.g.,
paediatric investigation plans. Overall, there is space for improvement by
using innovative trial designs and data analysis techniques.
Query Expansion via structural motifs in Wikipedia Graph
Authors: Guisado-Gámez Joan, Prat-Pérez Arnau, Larriba-Pey Josep Lluís
Date: 2016-05-12 00:00:00

The search for relevant information can be very frustrating for users who,
unintentionally, use too general or inappropriate keywords to express their
requests. To overcome this situation, query expansion techniques aim at
transforming the user request by adding new terms, referred as expansion
features, that better describe the real intent of the users. We propose a
method that relies exclusively on relevant structures (as opposed to the use of
semantics) found in knowledge bases (KBs) to extract the expansion features. We
call our method Structural Query Expansion (SQE). The structural analysis of
KBs takes us to propose a set of structural motifs that connect their strongly
related entries, which can be used to extract expansion features. In this paper
we use Wikipedia as our KB, which is probably one of the largest sources of
information. SQE is capable of achieving more than 150% improvement over non
expanded queries and is able to identify the expansion features in less than
0.2 seconds in the worst case scenario. Most significantly, we believe that we
are contributing to open new research directions in query expansion, proposing
a method that is orthogonal to many current systems. For example, SQE improves
pseudo-relevance feedback techniques up to 13%
Supra-operonic clusters of functionally related genes (SOCs) are a source of horizontal gene co-transfers
Date: 2016-11-15 00:00:00

Adaptation of bacteria occurs predominantly via horizontal gene transfer
(HGT). While it is widely recognized that horizontal acquisitions frequently
encompass multiple genes, it is unclear what the size distribution of
successfully transferred DNA segments looks like and what evolutionary forces
shape this distribution. Here, we identified 1790 gene family pairs that were
consistently co-gained on the same branches across a phylogeny of 53 E. coli
strains. We estimated a lower limit of their genomic distances at the time they
were transferred to their host genomes; this distribution shows a sharp upper
bound at 30 kb. The same gene-pairs can have larger distances (up to 70 kb) in
other genomes. These more distant pairs likely represent recent acquisitions
via transduction that involve the co-transfer of excised prophage genes, as
they are almost always associated with intervening phage-associated genes. The
observed distribution of genomic distances of co-transferred genes is much
broader than expected from a model based on the co-transfer of genes within
operons; instead, this distribution is highly consistent with the size
distribution of supra-operonic clusters (SOCs), groups of co-occurring and
co-functioning genes that extend beyond operons. Thus, we propose that SOCs
form a basic unit of horizontal gene transfer.
When does inequality freeze an economy?
Date: 2016-04-21 00:00:00
Tasks: Relation

Inequality and its consequences are the subject of intense recent debate.
Using a simplified model of the economy, we address the relation between
inequality and liquidity, the latter understood as the frequency of economic
exchanges. Assuming a Pareto distribution of wealth for the agents, that is
consistent with empirical findings, we find an inverse relation between wealth
inequality and overall liquidity. We show that an increase in the inequality of
wealth results in an even sharper concentration of the liquid financial
resources. This leads to a congestion of the flow of goods and the arrest of
the economy when the Pareto exponent reaches one.
Selective activation of resting state networks following focal stimulation in a connectome- based network model of the human brain
Date: 2016-02-23 00:00:00
Tasks: Functional Connectivity

Imaging studies suggest that the functional connectivity patterns of resting
state networks (RS-networks) reflect underlying structural connectivity (SC).
If the connectome constrains how brain areas are functionally connected, the
stimulation of specific brain areas should produce a characteristic wave of
activity ultimately resolving into RS-networks. To systematically test this
hypothesis, we use a connectome-based network model of the human brain with
detailed realistic SC. We systematically activate all possible thalamic and
cortical areas with focal stimulation patterns and confirm that the stimulation
of specific areas evokes network patterns that closely resemble RS-networks.
For some sites, one or no RS-network is engaged, whereas for other sites more
than one RS-network may evolve. Our results confirm that the brain is operating
at the edge of criticality, wherein stimulation produces a cascade of
functional network recruitments, collapsing onto a smaller subspace that is
constrained in part by the anatomical local and long-range SCs. We suggest that
information flow, and subsequent cognitive processing, follows specific routes
imposed by connectome features, and that these routes explain the emergence of
RS-networks. Since brain stimulation can be used to diagnose/treat neurological
disorders, we provide a look-up table showing which areas need to be stimulated
to activate specific RS-networks.
Contagion in the world's stock exchanges seen as a set of coupled oscillators
Date: 2016-02-24 00:00:00

We study how the phenomenon of contagion can take place in the network of the
world's stock exchanges due to the behavioral trait "blindeness to small
changes". On large scale individual, the delay in the collective response may
significantly change the dynamics of the overall system. We explicitely insert
a term describing the behavioral phenomenon in a system of equations that
describe the build and release of stress across the worldwide stock markets. In
the mathematical formulation of the model, each stock exchange acts as an
integrate-and-fire oscillator. Calibration on market data validate the model.
  One advantage of the integrate-and-fire dynamics is that it enables for a
direct identification of cause and effect of price movements, without the need
for statistical tests such as for example Granger causality tests often used in
the identification of causes of contagion. Our methodology can thereby identify
the most relevant nodes with respect to onset of contagion in the network of
stock exchanges, as well as identify potential periods of high vulnerability of
the network. The model is characterized by a separation of time scales created
by a slow build up of stresses, for example due to (say monthly/yearly)
macroeconomic factors, and then a fast (say hourly/daily) release of stresses
through "price-quakes" of price movements across the worlds network of stock
exchanges.