pwc-archive/papers-with-abstracts huggingface dataset:
The challenges of purely mechanistic models in biology and the minimum need for a 'mechanism-plus-X' framework
Authors: Sepehr Ehsani
Date: 2019-05-27 00:00:00

Ever since the advent of molecular biology in the 1970s, mechanical models have become the dogma in the field, where a "true" understanding of any subject is equated to a mechanistic description. This has been to the detriment of the biomedical sciences, where, barring some exceptions, notable new feats of understanding have arguably not been achieved in normal and disease biology, including neurodegenerative disease and cancer pathobiology. I argue for a "mechanism-plus-X" paradigm, where mainstay elements of mechanistic models such as hierarchy and correlation are combined with nomological principles such as general operative rules and generative principles. Depending on the question at hand and the nature of the inquiry, X could range from proven physical laws to speculative biological generalizations, such as the notional principle of cellular synchrony. I argue that the "mechanism-plus-X" approach should ultimately aim to move biological inquiries out of the deadlock of oft-encountered mechanistic pitfalls and reposition biology to its former capacity of illuminating fundamental truths about the world.
Investigation of HIV-1 Gag binding with RNAs and Lipids using Atomic Force Microscopy
Date: 2019-05-27 00:00:00

Atomic Force Microscopy was utilized to study the morphology of Gag,
{\Psi}RNA, and their binding complexes with lipids in a solution environment
with 0.1{\AA} vertical and 1nm lateral resolution. TARpolyA RNA was used as a
RNA control. The lipid used was phospha-tidylinositol-(4,5)-bisphosphate
(PI(4,5)P2). The morphology of specific complexes Gag-{\Psi}RNA, Gag-TARpolyA
RNA, Gag-PI(4,5)P2 and PI(4,5)P2-{\Psi}RNA-Gag were studied. They were imaged
on either positively or negatively charged mica substrates depending on the net
charges carried. Gag and its complexes consist of monomers, dimers and
tetramers, which was confirmed by gel electrophoresis. The addition of specific
{\Psi}RNA to Gag is found to increase Gag multimerization. Non-specific
TARpolyA RNA was found not to lead to an increase in Gag multimerization. The
addition PI(4,5)P2 to Gag increases Gag multimerization, but to a lesser extent
than {\Psi}RNA. When both {\Psi}RNA and PI(4,5)P2 are present Gag undergoes
comformational changes and an even higher degree of multimerization.
Ranking power spectra: a proof of concept
Date: 2019-05-27 00:00:00
Tasks: Seizure Detection

Objective: To characterize the irregularity of the spectrum of a signal,
spectral entropy is a widely adopted measure. However, such a metric is
invariant under any permutation of the estimations of the powers of individual
frequency components on a predefined grid. This erases the order structure
inherent in the spectrum which is also an important aspect of irregularity of
the signal. To disentangle the order structure and extract meaningful
information from raw digital signal, novel analysis method is necessary.
Approach: A novel method to depict the order structure by simply ranking power
estimations on frequency grid of a evenly spaced signal is proposed. Two
descriptors mapping real- and vector-valued power spectrum estimation of a
signal into scalar value are defined in a heuristic manner. By definition, the
proposed descriptor is capable of distinguishing signals with identical
spectrum entropies. Main Results: The proposed descriptor showed its potential
in diverse problems. Significant (p<0.001) differences were observed from brain
signals and surface electromyography of different pathological/physiological
states. Drastic change accompanied by the alteration of the underlying process
of signals enables it as candidate feature for seizure detection and endpoint
detection in speech signal. Significance: This letter explores the previously
ignored order structure in the spectrum of physiological signal. We take one
step forward along this direction by proposing two computationally efficient
descriptors with guaranteed information gain. As far as the authors are
concerned, this is the first work revealing the effectiveness of the order
structure in the spectrum in physiological signal processing.
Contest Architecture with Public Disclosures
Date: 2019-05-28 00:00:00

I study optimal disclosure policies in sequential contests. A contest
designer chooses at which periods to publicly disclose the efforts of previous
contestants. I provide results for a wide range of possible objectives for the
contest designer. While different objectives involve different trade-offs, I
show that under many circumstances the optimal contest is one of the three
basic contest structures widely studied in the literature: simultaneous,
first-mover, or sequential contest.
Performance Comparison of a proposed Vector Tracking architecture versus the Scalar configuration for a L1/E1 GPS/Galileo receiver
Date: 2019-05-27 00:00:00
Tasks: Position

In urban environments, standalone GNSS receivers can be strongly affected to
the point of not being able to provide a position accuracy suitable for use in
vehicular applications. In this paper, a vector delay/frequency-locked loop
(VDFLL) architecture for a dual constellation L1/E1 GPS/Galileo receiver is
proposed. In this implementation, the individual DLLs and FLLs of each tracked
satellite are replaced with an Extended Kalman filter (EKF), responsible for
both estimating the user's position, velocity and clock bias and closing the
code/carrier updates for each GPS L1 and Galileo E1 tracking channels. In this
work, a detailed performance comparison between the scalar tracking and VDFLL
configuration is assessed under signal outages and significant power drops
conditions that are simulated in different satellite channels. Contrary to the
conventional tracking, the L1/E1 VDFLL loop is able to recover the frequency
and code-delay estimation at the end of the simulated outages without the
requirement of signal reacquisition process.
Cooperativity transitions driven by higher-order oligomer formations in ligand-induced receptor dimerization
Authors: Masaki Watabe, Satya N. V. Arjunan, Wei Xiang Chew, Kazunari Kaizu, Koichi Takahashi
Date: 2019-05-27 00:00:00

While cooperativity in ligand-induced receptor dimerization has been linked with receptor-receptor couplings via minimal representations of physical observables, effects arising from higher-order oligomer (e.g., trimer and tetramer) formations of unobserved receptors have received less attention. Here, we propose a dimerization model of ligand-induced receptors in multivalent form representing physical observables under basis vectors of various aggregated receptor-states. Our simulations of multivalent models not only reject Wofsy-Goldstein parameter conditions for cooperativity, but show higher-order oligomer formations can shift cooperativity from positive to negative.
3D Trajectory Optimization for Secure UAV Communication with CoMP Reception
Date: 2019-05-27 00:00:00

This paper studies a secrecy unmanned aerial vehicle (UAV) communication
system with coordinated multi-point (CoMP) reception, in which one UAV sends
confidential messages to a set of distributed ground nodes (GNs) that can
cooperate in signal detection, in the presence of several colluding suspicious
eavesdroppers. Different from prior works considering the two-dimensional (2D)
horizontal trajectory design in the non-CoMP scenario, this paper additionally
exploits the UAV's vertical trajectory (or altitude) control for further
improving the secrecy communication performance with CoMP. In particular, we
jointly optimize the three dimensional (3D) trajectory and transmit power
allocation of the UAV to maximize the average secrecy rate at GNs over a
particular flight period, subject to the UAV's maximum flight speed and maximum
transmit power constraints. To solve the non-convex optimization problem, we
propose an alternating-optimization-based approach, which optimizes the
transmit power allocation and trajectory design in an alternating manner, by
convex optimization and successive convex approximation (SCA), respectively.
Numerical results show that in the scenario with CoMP reception, our proposed
3D trajectory optimization significantly outperforms the conventional 2D
horizontal trajectory design, by exploiting the additional degree of freedom in
vertical trajectory.
Local Asymptotic Equivalence of the Bai and Ng (2004) and Moon and Perron (2004) Frameworks for Panel Unit Root Testing
Date: 2019-05-27 00:00:00

This paper considers unit-root tests in large n and large T heterogeneous
panels with cross-sectional dependence generated by unobserved factors. We
reconsider the two prevalent approaches in the literature, that of Moon and
Perron (2004) and the PANIC setup proposed in Bai and Ng (2004). While these
have been considered as completely different setups, we show that, in case of
Gaussian innovations, the frameworks are asymptotically equivalent in the sense
that both experiments are locally asymptotically normal (LAN) with the same
central sequence. Using Le Cam's theory of statistical experiments we determine
the local asymptotic power envelope and derive an optimal test jointly in both
setups. We show that the popular Moon and Perron (2004) and Bai and Ng (2010)
tests only attain the power envelope in case there is no heterogeneity in the
long-run variance of the idiosyncratic components. The new test is
asymptotically uniformly most powerful irrespective of possible heterogeneity.
Moreover, it turns out that for any test, satisfying a mild regularity
condition, the size and local asymptotic power are the same under both data
generating processes. Thus, applied researchers do not need to decide on one of
the two frameworks to conduct unit root tests. Monte-Carlo simulations
corroborate our asymptotic results and document significant gains in
finite-sample power if the variances of the idiosyncratic shocks differ
substantially among the cross sectional units.
Simulation Environment for Link Energy Estimation in Networks-on-Chip with Virtual Channels
Date: 2019-05-23 00:00:00

Network-on-chip (NoC) is the most promising design paradigm for the
interconnect architecture of a multiprocessor system-on-chip (MPSoC). On the
downside, a NoC has a significant impact on the overall energy consumption of
the system. NoC simulators are highly relevant for design space exploration
even at an early stage. Since links in NoC consume up to 50% of the energy, a
realistic energy consumption of links in NoC simulators is important. This work
presents a simulation environment which implements a technique to precisely
estimate the data dependent link energy consumption in NoCs with virtual
channels for the first time. Our model works at a high level of abstraction,
making it feasible to estimate the energy requirements at an early design
stage. Additionally, it enables the fast evaluation and early exploration of
low-power coding techniques. The presented model is applicable for 2D and 3D
NoCs. A case study for an image processing application shows that the current
link model leads to an underestimate of the link energy consumption by up to a
factor of four. In contrast, the technique presented in this paper estimates
the energy quantities precisely with an error below 1% compared to results
obtained by precise, but computational extensive, bit-level simulation.
Delay lines test method for the Blade Template
Date: 2019-05-23 00:00:00

This paper proposes a method for testing the delay lines of Blade
asynchronous timing resilience template. It consists of an offline test method,
with low area overhead, for measuring the internal propagation delay of the
delay lines with external testers.
Tractable Approach to MmWaves Cellular Analysis with FSO Backhauling under Feedback Delay and Hardware Limitations
Date: 2019-05-23 00:00:00
Tasks: Denoising

In this work, we investigate the performance of a millimeter waves (mmWaves)
cellular system with free space optical (FSO) backhauling. MmWave channels are
subject to Nakagami-m fading while the optical links experience the Double
Generalized Gamma including atmospheric turbulence, path loss and the
misalignment between the transmitter and the receiver aperture (also known as
the pointing errors). The FSO model also takes into account the receiver
detection technique which could be either heterodyne or intensity modulation
and direct detection (IM/DD). Each user equipment (UE) has to be associated to
one serving base station (BS) based on the received signal strength (RSS) or
Channel State Information (CSI). We assume partial relay selection (PRS) with
CSI based on mmWaves channels to select the BS associated with the highest
received CSI. Each serving BS decodes the received signal for denoising,
converts it into modulated FSO signal, and then forwards it to the data center.
Thereby, each BS can be viewed as a decode-and-forward (DF) relay. In practice,
the relay hardware suffers from nonlinear high power amplification (HPA)
impairments which, substantially degrade the system performance. In this work,
we will discuss the impacts of three common HPA impairments named respectively,
soft envelope limiter (SEL), traveling wave tube amplifier (TWTA), and solid
state power amplifier (SSPA). Novel closed-forms and tight upper bounds of the
outage probability, the probability of error, and the achievable rate are
derived. Capitalizing on these performance, we derive the high SNR asymptotes
to get engineering insights into the system gain such as the diversity order.
UWB-NTIS Speaker Diarization System for the DIHARD II 2019 Challenge
Date: 2019-05-27 00:00:00
Tasks: Clustering, speaker-diarization, Speaker Diarization

In this paper, we present our system developed by the team from the New
Technologies for the Information Society (NTIS) research center of the
University of West Bohemia in Pilsen, for the Second DIHARD Speech Diarization
Challenge. The base of our system follows the currently-standard approach of
segmentation, i/x-vector extraction, clustering, and resegmentation. The
hyperparameters for each of the subsystems were selected according to the
domain classifier trained on the development set of DIHARD II. We compared our
system with results from the Kaldi diarization (with i/x-vectors) and combined
these systems. At the time of writing of this abstract, our best submission
achieved a DER of 23.47% and a JER of 48.99% on the evaluation set (in Track 1
using reference SAD).
Real-time Cellular Impedance Monitoring and Imaging of Biological Barriers in a dual flow membrane bioreactor
Date: 2019-05-27 00:00:00
Tasks: Cultural Vocal Bursts Intensity Prediction

The generation of physiologically relevant in-vitro models of biological
barriers can play a key role in understanding human diseases and in the
development of more predictive methods for assessing toxicity and drug or
nutrient absorption. Here, we present an advanced cell culture system able to
mimic the dynamic environment of biological barriers while monitoring cell
behaviour through real-time impedance measurements and imaging. It consists of
a fluidic device with an apical and a basal flow compartment separated by a
semi-permeable membrane. The main features of the device are the integration of
a transepithelial electrical impedance (TEEI) meter and transparent windows for
optical monitoring within a dual flow system. Caco-2 cells were cultured in the
TEEI bioreactor under both flow and static conditions. Although no differences
in the expression of peripheral actin and occludin were visible, the cells in
dynamic conditions developed higher impedance values at low frequencies,
indicative of a higher paracellular electrical impedance and thus suggesting
accelerated barrier and tight junction formation with respect to the static
cultures. TEEI measurements at high frequency also enabled monitoring the
evolution of transcellular impedance during culture. The cells subject to flow
showed a typical RC behaviour, while the controls showed minimal capacitive
behaviour, again highlighting the differences between flow and static
conditions.
Dynamical stability analysis of tumor growth and invasion: A reaction-diffusion model
Date: 2019-05-10 00:00:00

The acid-mediated tumor invasion hypothesis proposes that altered glucose
metabolism exhibited by the vast majority of tumors leads to increased acid (H+
ion) production which subsequently facilitates tumor invasion [1-3]. The
reaction-diffusion model [2] that captures the key elements of the hypothesis
shows how the densities of normal cells, tumor cells, and excess H+ ions change
with time due to both chemical reactions between these three populations and
density-dependent diffusion by which they spread out in three-dimensional
space. Moreover, it proposes that each cell has an optimal pH for survival;
that is, if the local pH deviates from the optimal value in either an acidic or
alkaline direction, the cells begin to die, and that the death rate saturates
at some maximum value when the microenvironment is extremely acidic or
alkaline. We have previously studied in detail how the death-rate functions of
the normal and tumor populations depend upon the H+ ion density [4]. Here, we
extend previous work by investigating how the equilibrium densities (at which
the time rates of change of the cellular densities are equal to zero) reached
by the normal and tumor populations in three-dimensional space are affected by
the presence of the H+ ions, and we present detailed analytical and
computational techniques to analyze the dynamical stability of these
equilibrium densities. For a sample set of biological input parameters and
within the acid-mediation hypothesis, our model predicts the transformation to
a malignant behavior, as indicated by the presence of unstable sets of
equilibrium densities.
Meta Distribution of SIR in Dual-Hop Internet-of-Things (IoT) Networks
Date: 2019-05-30 00:00:00

This paper characterizes the meta distribution of the downlink
signal-to-interference ratio (SIR) attained at a typical Internet-of-Things
(IoT) device in a dual-hop IoT network. The IoT device associates with either a
serving macro base station (MBS) for direct transmissions or associates with a
decode and forward (DF) relay for dual-hop transmissions, depending on the
biased received signal power criterion. In contrast to the conventional success
probability, the meta distribution is the distribution of the conditional
success probability (CSP), which is conditioned on the locations of the
wireless transmitters. The meta distribution is a fine-grained performance
metric that captures important network performance metrics such as the coverage
probability and the mean local delay as its special cases. Specifically, we
derive the moments of the CSP in order to calculate analytic expressions for
the meta distribution. Further, we derive mathematical expressions for special
cases such as the mean local delay, variance of the CSP, and success
probability of a typical IoT device and typical relay with different offloading
biases. We take in consideration in our analysis the association probabilities
of IoT devices. Finally, we investigate the impact of increasing the relay
density on the mean local delay using numerical results.
Physical Layer Security for Visible Light Communication Systems: A Survey
Date: 2019-05-27 00:00:00
Tasks: Survey

Due to the dramatic increase in high data rate services and in order to meet
the demands of the fifth-generation (5G) networks, researchers from both
academia and industry are exploring advanced transmission techniques, new
network architectures and new frequency spectrum such as the visible light
spectra. Visible light communication (VLC) particularly is an emerging
technology that has been introduced as a promising solution for 5G and beyond.
Although VLC systems are more immune against interference and less susceptible
to security vulnerabilities since light does not penetrate through walls,
security issues arise naturally in VLC channels due to their open and
broadcasting nature, compared to fiber-optic systems. In addition, since VLC is
considered to be an enabling technology for 5G, and security is one of the 5G
fundamental requirements, security issues should be carefully addressed and
resolved in the VLC context. On the other hand, due to the success of physical
layer security (PLS) in improving the security of radio-frequency (RF) wireless
networks, extending such PLS techniques to VLC systems has been of great
interest. Only two survey papers on security in VLC have been published in the
literature. However, a comparative and unified survey on PLS for VLC from
information theoretic and signal processing point of views is still missing.
This paper covers almost all aspects of PLS for VLC, including different
channel models, input distributions, network configurations,
precoding/signaling strategies, and secrecy capacity and information rates.
Furthermore, we propose a number of timely and open research directions for
PLS-VLC systems, including the application of measurement-based indoor and
outdoor channel models, incorporating user mobility and device orientation into
the channel model, and combining VLC and RF systems to realize the potential of
such technologies.
Microtubule Motility Analysis based on Time-Lapse Fluorescence Microscopy
Authors: Samira Masoudi, Cameron H. G. Wright, Jesse C. Gatlin, John. S. Oakey
Date: 2019-05-27 00:00:00

This paper describes an investigation into part of the mechanical mechanisms underlying the formation of mitotic spindle, the cellular machinery responsible for chromosomal separation during cell division. In normal eukaryotic cells, spindles are composed of microtubule filaments that radiate outward from two centrosomes. In many transformed cells, however, centrosome number is misregulated resulting in cells with more than two centrosomes. Addressing the question of how these cells accommodate these additional structures by coalescing supernumerary centrosomes to form normal spindles will provide a powerful insight toward understanding the proliferation of cancer cells and developing new therapeutics. The process of centrosome coalescence is thought to involve motor proteins that function to slide microtubules relative to one another. Here we use in vitro motility assays combined with fluorescence microscopy to visualize, characterize and quantify microtubule-microtubule interactions. After segmenting the microtubules, their speed and direction of movement are the extracted features to cluster their interaction type. In order to evaluate the potential of our processing algorithm, we created a simulated dataset similar to the time-lapse series. Once our procedure has been optimized using the simulated data, we will apply it to the real data. Results of our analyses will provide a quantitative description of interaction among microtubules. This is a potentially important step toward more thorough understanding of cancer.
Design and Performance Analysis of an Index Time Frequency Modulation Scheme for Optical Communications
Date: 2019-05-27 00:00:00

In this article, we propose an index modulation system suitable for optical
communications, based on jointly driving the time and frequency of the signal:
an index-time frequency hopping (I-TFH) system. We analyze its performance from
the point of view of its efficiency in power and spectrum, and its behavior in
terms of error probability for the non-turbulent free-space optical (FSO)
channel. We compare I-TFH with already proposed index modulated systems of the
same nature, but where the amplitude or the number of transmitters are driven
instead of the signal frequency. We derive and compare approximations for the
average symbol and bit error probabilities of all these systems. The simulation
results show that said approximations are tight enough for a wide range of
signal-to-noise ratios and system parameters. Moreover, I-TFH shows to be
better performing in BER and/or power efficiency than the comparative
alternatives, and may offer interesting properties in a variety of contexts.