pwc-archive/papers-with-abstracts huggingface dataset:
Noncontextuality with Marginal Selectivity in Reconstructing Mental Architectures
Date: 2015-06-19 00:00:00

We present a general theory of series-parallel mental architectures with
selectively influenced stochastically non-independent components. A mental
architecture is a hypothetical network of processes aimed at performing a task,
of which we only observe the overall time it takes under variable parameters of
the task. It is usually assumed that the network contains several processes
selectively influenced by different experimental factors, and then the question
is asked as to how these processes are arranged within the network, e.g.,
whether they are concurrent or sequential. One way of doing this is to consider
the distribution functions for the overall processing time and compute certain
linear combinations thereof (interaction contrasts). The theory of selective
influences in psychology can be viewed as a special application of the
interdisciplinary theory of (non)contextuality having its origins and main
applications in quantum theory. In particular, lack of contextuality is
equivalent to the existence of a "hidden" random entity of which all the random
variables in play are functions. Consequently, for any given value of this
common random entity, the processing times and their compositions (minima,
maxima, or sums) become deterministic quantities. These quantities, in turn,
can be treated as random variables with (shifted) Heaviside distribution
functions, for which one can easily compute various linear combinations across
different treatments, including interaction contrasts. This mathematical fact
leads to a simple method, more general than the previously used ones, to
investigate and characterize the interaction contrast for different types of
series-parallel architectures.
Scalable high-dimensional indexing and searching with Hadoop
Authors: Shestakov Denis, Moise Diana
Date: 2015-01-30 00:00:00
Tasks: Vocal Bursts Intensity Prediction

While high-dimensional search-by-similarity techniques reached their maturity
and in overall provide good performance, most of them are unable to cope with
very large multimedia collections. The 'big data' challenge however has to be
addressed as multimedia collections have been explosively growing and will grow
even faster than ever within the next few years. Luckily, computational
processing power has become more available to researchers due to easier access
to distributed grid infrastructures. In this paper, we show how
high-dimensional indexing and searching methods can be used on scientific grid
environments and present a scalable workflow for indexing and searching over 30
billion SIFT descriptors using a cluster running Hadoop. Besides its
scalability, the proposed scheme not only provides good search quality, but
also achieves a stable throughput of around 210ms per image when searching a
100M image collection. Our findings could help other researchers and
practitioners to cope with huge multimedia collections.
Electronic health record phenotyping improves detection and screening of type 2 diabetes in the general United States population: A cross-sectional, unselected, retrospective study
Date: 2015-01-10 00:00:00
Tasks: Vocal Bursts Type Prediction

Objectives: In the United States, 25% of people with type 2 diabetes are
undiagnosed. Conventional screening models use limited demographic information
to assess risk. We evaluated whether electronic health record (EHR) phenotyping
could improve diabetes screening, even when records are incomplete and data are
not recorded systematically across patients and practice locations. Methods: In
this cross-sectional, retrospective study, data from 9,948 US patients between
2009 and 2012 were used to develop a pre-screening tool to predict current type
2 diabetes, using multivariate logistic regression. We compared (1) a full EHR
model containing prescribed medications, diagnoses, and traditional predictive
information, (2) a restricted EHR model where medication information was
removed, and (3) a conventional model containing only traditional predictive
information (BMI, age, gender, hypertensive and smoking status). We
additionally used a random-forests classification model to judge whether
including additional EHR information could increase the ability to detect
patients with Type 2 diabetes on new patient samples. Results: Using a
patient's full or restricted EHR to detect diabetes was superior to using basic
covariates alone (p<0.001). The random forests model replicated on out-of-bag
data. Migraines and cardiac dysrhythmias were negatively associated with type 2
diabetes, while acute bronchitis and herpes zoster were positively associated,
among other factors. Conclusions: EHR phenotyping resulted in markedly superior
detection of type 2 diabetes in a general US population, could increase the
efficiency and accuracy of disease screening, and are capable of picking up
signals in real-world records.
Surface modified sulfur nanoparticles can escape the glutathione reductase mediated detoxification system in fungi
Date: 2015-01-11 00:00:00

The antifungal effects of orthorhombic (~10 nm; spherical) and monoclinic
(~50 nm; tetrapod) sulfur nanoparticles (SNPs) were studied against the
NADPH-dependent glutathione reductase (GR) mediated xenobiotic detoxification
system (GSH-GSSG) in filamentous fungi (Aspergillus niger as a model organism).
Both the SNPs induced significant reduction in fungal growth and spore
formation, and also introduced marked deformities on the surface of
conidiophores at their sub-inhibitory concentrations. A genome wide
transcriptome profile then revealed manifold reduction in the expression of
GSH-GSSG transcripts among SNPs treated fungal isolates, which is unusual for
the micron sized elemental sulfur but probably effective in terms of antifungal
efficacy.
Stochastic simulation framework for the Limit Order Book using liquidity motivated agents
Date: 2015-01-18 00:00:00

In this paper we develop a new form of agent-based model for limit order
books based on heterogeneous trading agents, whose motivations are liquidity
driven. These agents are abstractions of real market participants, expressed in
a stochastic model framework. We develop an efficient way to perform
statistical calibration of the model parameters on Level 2 limit order book
data from Chi-X, based on a combination of indirect inference and
multi-objective optimisation. We then demonstrate how such an agent-based
modelling framework can be of use in testing exchange regulations, as well as
informing brokerage decisions and other trading based scenarios.
Functional optoacoustic neuro-tomography (FONT) for whole-brain monitoring of calcium indicators
Date: 2015-01-11 00:00:00

Non-invasive observation of spatiotemporal neural activity of large neural
populations distributed over entire brains is a longstanding goal of
neuroscience. We developed a real-time volumetric and multispectral
optoacoustic tomography platform for imaging of neural activation deep in
scattering brains. The system can record 100 volumetric frames per second
across a 200mm3 field of view and spatial resolutions below 70um. Experiments
performed in immobilized and freely swimming larvae and in adult zebrafish
brains demonstrate, for the first time, the fundamental ability to
optoacoustically track neural calcium dynamics in animals labeled with
genetically encoded calcium indicator GCaMP5G, while overcoming the
longstanding penetration barrier of optical imaging in scattering brains. The
newly developed platform offers unprecedented capabilities for functional
whole-brain observations of fast calcium dynamics; in combination with
optoacoustics' well-established capacity in resolving vascular hemodynamics, it
could open new vistas in the study of neural activity and neurovascular
coupling in health and disease.
The enzyme cost of given metabolic flux distributions, as a function of logarithmic metabolite levels, is convex
Date: 2015-01-11 00:00:00

Enzyme costs play a major role in the choice of metabolic routes, both in
evolution and bioengineering. Given desired fluxes, necessary enzyme levels can
be estimated based on known rate laws and on a principle of minimal enzyme
cost. With logarithmic metabolite levels as free variables, enzyme cost
functions and constraints in optimality and sampling problems can be handled
easily. The set of feasible metabolite profiles forms a polytope in
log-concentration space, whose points represent all possible steady states of a
kinetic model. We show that enzyme cost is a convex function on this polytope.
This makes enzyme cost minimization - finding optimal enzyme profiles and
corresponding metabolite profiles that realize a desired flux at a minimal cost
- a convex optimization problem.
Bibliometric-enhanced Information Retrieval: 2nd International BIR Workshop
Authors: Mayr Philipp, Frommholz Ingo, Scharnhorst Andrea, Mutschke Peter
Date: 2015-01-12 00:00:00
Tasks: Information Retrieval, Retrieval, Transfer Learning

This workshop brings together experts of communities which often have been
perceived as different once: bibliometrics / scientometrics / informetrics on
the one side and information retrieval on the other. Our motivation as
organizers of the workshop started from the observation that main discourses in
both fields are different, that communities are only partly overlapping and
from the belief that a knowledge transfer would be profitable for both sides.
Bibliometric techniques are not yet widely used to enhance retrieval processes
in digital libraries, although they offer value-added effects for users. On the
other side, more and more information professionals, working in libraries and
archives are confronted with applying bibliometric techniques in their
services. This way knowledge exchange becomes more urgent. The first workshop
set the research agenda, by introducing in each other methods, reporting about
current research problems and brainstorming about common interests. This
follow-up workshop continues the overall communication, but also puts one
problem into the focus. In particular, we will explore how statistical
modelling of scholarship can improve retrieval services for specific
communities, as well as for large, cross-domain collections like Mendeley or
ResearchGate. This second BIR workshop continues to raise awareness of the
missing link between Information Retrieval (IR) and bibliometrics and
contributes to create a common ground for the incorporation of
bibliometric-enhanced services into retrieval at the scholarly search engine
interface.
Effects of ligand binding upon flexibility of proteins
Date: 2015-01-12 00:00:00

Binding of a ligand on a protein changes the flexibility of certain parts of
the protein, which directly affects its function. These changes are not the
same at each point, some parts become more flexible and some others become
stiffer. Here, an equation is derived that gives the stiffness map for
proteins. The model is based on correlations of fluctuations of pairs of points
that need to be evaluated by molecular dynamics simulations. The model is also
cast in terms of the Gaussian Network Model and changes of stiffness upon
dimerization of AKT1 are evaluated as an example.
Modulation of N- to C-terminal interactions enhances protein stability
Date: 2015-01-12 00:00:00

Although, several factors have been attributed to thermostability, the
stabilization strategies used by proteins are still enigmatic. Studies on
recombinant xylanase which has the ubiquitous (\b{eta}/{\alpha})8 TIM
(Triosephosphate isomerase) barrel fold showed that, just a single extreme
N-terminus mutation (V1L) markedly enhanced the thermostability by 5 {\deg}C
without loss of catalytic activity whereas another mutation, V1A at the same
position decreased the stability by 2 {\deg}C. Based on computational analysis
of their crystal structures including residue interaction network, we
established a link between N- to C-terminal contacts and protein stability. We
demonstrate that augmenting of N- to C-terminal non-covalent interactions is
associated with the enhancement of protein stability. We propose that the
strategy of mutations at the termini could be exploited with a view to modulate
stability without compromising on enzymatic activity, or in general, protein
function, in diverse folds where N- and C-termini are in close proximity.
Finally, we discuss the implications of our results for the development of
therapeutics involving proteins and for designing effective protein engineering
strategies.
Self-Financing Trading and the Ito-Doeblin Lemma
Date: 2015-01-12 00:00:00
Tasks: LEMMA

The objective of the note is to remind readers on how self-financing works in
Quantitative Finance. The authors have observed continuing uncertainty on this
issue which may be because it lies exactly at the intersection of stochastic
calculus and finance. The concept of a self-financing trading strategy was
originally, and carefully, introduced in (Harrison and Kreps 1979) and expanded
very generally in (Harrison and Pliska 1981).
Signal focusing through active transport
Date: 2015-01-13 00:00:00
Tasks: Diagnostic

In biological cells and novel diagnostic devices biochemical receptors need
to be sensitive to extremely small concentration changes of signaling
molecules. The accuracy of such molecular signaling is ultimately limited by
the counting noise imposed by the thermal diffusion of molecules. Many
macromolecules and organelles transiently bind to molecular motors and are then
actively transported. We here show that a random albeit directed delivery of
signaling molecules to within a typical diffusion distance to the receptor
reduces the correlation time of the counting noise, effecting an improved
sensing precision. The conditions for this active focusing are indeed
compatible with observations in living cells. Our results are relevant for a
better understanding of molecular cellular signaling and the design of novel
diagnostic devices.
Non-concave utility maximisation on the positive real axis in discrete time
Date: 2015-04-22 00:00:00

We treat a discrete-time asset allocation problem in an arbitrage-free,
generically incomplete financial market, where the investor has a possibly
non-concave utility function and wealth is restricted to remain non-negative.
Under easily verifiable conditions, we establish the existence of optimal
portfolios.
Hazard function models to estimate mortality rates affecting fish populations with application to the sea mullet (Mugil cephalus) fishery on the Queensland coast (Australia)
Date: 2015-10-19 00:00:00
Tasks: Management, Survival Analysis

Fisheries management agencies around the world collect age data for the
purpose of assessing the status of natural resources in their jurisdiction.
Estimates of mortality rates represent a key information to assess the
sustainability of fish stocks exploitation. Contrary to medical research or
manufacturing where survival analysis is routinely applied to estimate failure
rates, survival analysis has seldom been applied in fisheries stock assessment
despite similar purposes between these fields of applied statistics. In this
paper, we developed hazard functions to model the dynamic of an exploited fish
population. These functions were used to estimate all parameters necessary for
stock assessment (including natural and fishing mortality rates as well as gear
selectivity) by maximum likelihood using age data from a sample of catch. This
novel application of survival analysis to fisheries stock assessment was tested
by Monte Carlo simulations to assert that it provided un-biased estimations of
relevant quantities. The method was applied to data from the Queensland
(Australia) sea mullet (Mugil cephalus) commercial fishery collected between
2007 and 2014. It provided, for the first time, an estimate of natural
mortality affecting this stock: 0.22 $\pm$ 0.08 year$^{-1}$.
A note on choice and detect probabilities in the presence of choice bias
Date: 2015-01-13 00:00:00
Tasks: Decision Making

Recently we have presented the analytical relationship between choice
probabilities, noise correlations and read-out weights in the classical
feedforward decision-making framework (Haefner et al. 2013). The derivation
assumed that behavioral reports are distributed evenly between the two possible
choices. This assumption is often violated in empirical data - especially when
computing so-called grand CPs combining data across stimulus conditions. Here,
we extend our analytical results to situations when subjects show clear biases
towards one choice over the other, e.g. in non-zero signal conditions.
Importantly, this also extends our results from discrimination tasks to
detection tasks and detect probabilities for which much empirical data is
available. We find that CPs and DPs depend monotonously on the fraction, p, of
choices assigned to the more likely option: CPs and DPs are smallest for p
equal to 0.5 and increase as p increases, i.e. as the data deviates from the
ideal, zero-signal, unbiased scenario. While this deviation is small, our
results suggest a) an empirical test for the feedforward framework and b) a way
in which to correct choice probability and detect probability measurements
before combining different stimulus conditions to increase signal/noise.
We Did See This Coming: Response to, We Should Have Seen This Coming, by D. Sam Schwarzkopf
Date: 2015-01-18 00:00:00

We appreciate the effort by Schwarzkopf to examine alternative explanations
for predictive anticipatory activity (PAA) or presentiment (for first response,
see: Schwarzkopf 2014a; for additional response, see: Schwarzkopf 2014b, for
original article, see: Mossbridge et al. 2014). These commentaries are a
laudable effort to promote collegial discussion of the controversial claim of
presentiment, whereby physiological measures preceding unpredictable emotional
events differ from physiological measures preceding calm or neutral events
(Mossbridge et al., 2012; Mossbridge et al., 2014). What is called truth at any
given time in science has achieved that status through a continuous process of
measurement and interpretation based on the current knowledge at hand. Here we
address six points in his original commentary (Schwarzkopf 2014a), though our
responses are informed by the points he made in his his supplementary
commentary (Schwarzkopf 2014b). We hope our responses will help Schwarzkopf and
others understand our interpretation of these data.
Yeast caspase 1 suppresses the burst of reactive oxygen species and maintains mitochondrial stability in Saccharomyces cerevisiae
Date: 2015-01-14 00:00:00

Caspases are a family of cysteine proteases that play essential roles during
apoptosis, and we presume some of them may also protect the cell from oxidative
stress. We found that the absence of yeast caspase 1(Yca1)in Saccharomyces
cerevisiae leads to a more intense burst of mitochondrial reactive oxygen
species (ROS) In addition, compared to wild type yeast cells, the ability of
yca1 mutant cells to maintain mitochondrial activity is significantly reduced
after either oxidative stress treatment or aging. During mitochondrial ROS
burst, deletion of the yca1 gene delayed structural damage of a green
fluorescent protein (GFP) reporter bound in the inner mitochondrial membrane.
This work implies that yeast caspase 1 is closely connected to the oxidative
stress response. We speculate that Yca1 can discriminate proteins damaged by
oxidation and accelerate their hydrolysis to attenuate the ROS burst.
Stochastic kinetics of the circular gene hypothesis: feedback effects and protein fluctuations
Date: 2015-08-11 00:00:00

Stochastic kinetic models of genetic expression are able to describe protein
fluctuations. A comparative study of the canonical and a feedback model is
given here by using stochastic simulation methods. The feedback model is
skeleton model implementation of the circular gene hypothesis, which suggests
the interaction between the synthesis and degradation of mRNA. Qualitative and
quantitative changes in the shape and in the numerical characteristics of the
stationary distributions suggest that more combined experimental and
theoretical studies should be done to uncover the details of the kinetic
mechanism of gene expression.
Google matrix analysis of the multiproduct world trade network
Date: 2015-01-14 00:00:00

Using the United Nations COMTRADE database \cite{comtrade} we construct the
Google matrix $G$ of multiproduct world trade between the UN countries and
analyze the properties of trade flows on this network for years 1962 - 2010.
This construction, based on Markov chains, treats all countries on equal
democratic grounds independently of their richness and at the same time it
considers the contributions of trade products proportionally to their trade
volume. We consider the trade with 61 products for up to 227 countries. The
obtained results show that the trade contribution of products is asymmetric:
some of them are export oriented while others are import oriented even if the
ranking by their trade volume is symmetric in respect to export and import
after averaging over all world countries. The construction of the Google matrix
allows to investigate the sensitivity of trade balance in respect to price
variations of products, e.g. petroleum and gas, taking into account the world
connectivity of trade links. The trade balance based on PageRank and CheiRank
probabilities highlights the leading role of China and other BRICS countries in
the world trade in recent years. We also show that the eigenstates of $G$ with
large eigenvalues select specific trade communities.
Extracting folding landscape characteristics of biomolecules using mechanical forces
Date: 2015-01-14 00:00:00

In recent years single molecule force spectroscopy has opened a new avenue to
provide profiles of the complex energy landscape of biomolecules. In this
field, quantitative analyses of the data employing sound theoretical models,
have played a major role in interpreting data and anticipating outcomes of
experiments. Here, we explain how by using temperature as a variable in
mechanical unfolding of biomolecules in force spectroscopy, the roughness of
the energy landscape can be measured without making any assumptions about the
underlying reaction coordinate. Estimates of other aspects of the energy
landscape such as free energy barriers or the transition state (TS) locations
could depend on the precise model used to analyze the experimental data. We
illustrate the inherent difficulties in obtaining the transition state location
from loading rate or force-dependent unfolding rates. Because the transition
state moves as the force or the loading rate is varied, which is reminiscent of
the Hammond effect, it is in general difficult to invert the experimental data.
The independence of the TS location on force holds good only for brittle or
hard biomolecules whereas the TS location changes considerably if the molecule
is soft or plastic. Finally, we discuss the goodness of the end-to-end distance
(or pulling) coordinate of the molecule as a surrogate reaction coordinate in a
situation like force-induced ligand-unbinding from a gated molecular receptor
as well as force-quench refolding of an RNA hairpin.