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## Mathematics : Publications since January 2017

List all publications in the database.    :chronological  alphabetical  by author listing:
%%
@article{fds333565,
Author = {Liu, J-G and Xu, X},
Title = {Partial regularity of weak solutions to a PDE system with
cubic nonlinearity},
Journal = {Journal of Differential Equations},
Volume = {264},
Number = {8},
Pages = {5489-5526},
Year = {2018},
Month = {April},
url = {http://dx.doi.org/10.1016/j.jde.2018.01.0010022},
Doi = {10.1016/j.jde.2018.01.0010022},
Key = {fds333565}
}

@article{fds332810,
Author = {van den Boom, W and Schroeder, RA and Manning, MW and Setji, TL and Fiestan, G-O and Dunson, DB},
Title = {Effect of A1C and Glucose on Postoperative Mortality in
Noncardiac and Cardiac Surgeries.},
Journal = {Diabetes Care},
Volume = {41},
Number = {4},
Pages = {782-788},
Year = {2018},
Month = {April},
url = {http://dx.doi.org/10.2337/dc17-2232},
Abstract = {Hemoglobin A1c (A1C) is used in assessment of patients for
elective surgeries because hyperglycemia increases risk of
adverse events. However, the interplay of A1C, glucose, and
surgical outcomes remains unclarified, with often only two
of these three factors considered simultaneously. We
assessed the association of preoperative A1C with
perioperative glucose control and their relationship with
30-day mortality.Retrospective analysis on 431,480 surgeries
within the Duke University Health System determined the
association of preoperative A1C with perioperative glucose
(averaged over the first 3 postoperative days) and 30-day
mortality among 6,684 noncardiac and 6,393 cardiac surgeries
with A1C and glucose measurements. A generalized additive
model was used, enabling nonlinear relationships.A1C and
glucose were strongly associated. Glucose and mortality were
positively associated for noncardiac cases: 1.0% mortality
at mean glucose of 100 mg/dL and 1.6% at mean glucose of 200
mg/dL. For cardiac procedures, there was a striking U-shaped
relationship between glucose and mortality, ranging from
4.5% at 100 mg/dL to a nadir of 1.5% at 140 mg/dL and rising
again to 6.9% at 200 mg/dL. A1C and 30-day mortality were
not associated when controlling for glucose in noncardiac or
cardiac procedures.Although A1C is positively associated
with perioperative glucose, it is not associated with
increased 30-day mortality after controlling for glucose.
Perioperative glucose predicts 30-day mortality, linearly in
noncardiac and nonlinearly in cardiac procedures. This
confirms that perioperative glucose control is related to
surgical outcomes but that A1C, reflecting antecedent
glycemia, is a less useful predictor.},
Doi = {10.2337/dc17-2232},
Key = {fds332810}
}

@article{fds329931,
Author = {Gao, T and Yapuncich, GS and Daubechies, I and Mukherjee, S and Boyer,
DM},
Title = {Development and Assessment of Fully Automated and Globally
Transitive Geometric Morphometric Methods, With Application
to a Biological Comparative Dataset With High Interspecific
Variation.},
Journal = {The Anatomical Record : Advances in Integrative Anatomy and
Evolutionary Biology},
Volume = {301},
Number = {4},
Pages = {636-658},
Year = {2018},
Month = {April},
url = {http://dx.doi.org/10.1002/ar.23700},
Abstract = {Automated geometric morphometric methods are promising tools
for shape analysis in comparative biology, improving
researchers' abilities to quantify variation extensively (by
permitting more specimens to be analyzed) and intensively
(by characterizing shapes with greater fidelity). Although
use of these methods has increased, published automated
methods have some notable limitations: pairwise
correspondences are frequently inaccurate and pairwise
mappings are not globally consistent (i.e., they lack
transitivity across the full sample). Here, we reassess the
accuracy of published automated methods-cPDist (Boyer et al.
Proc Nat Acad Sci 108 () 18221-18226) and auto3Dgm (Boyer et
al.: Anat Rec 298 () 249-276)-and evaluate several
modifications to these methods. We show that a substantial
percentage of alignments and pairwise maps between specimens
of dissimilar geometries were inaccurate in the study of
Boyer et al. (Proc Nat Acad Sci 108 () 18221-18226), despite
a taxonomically partitioned variance structure of continuous
Procrustes distances. We show these inaccuracies are
remedied using a globally informed methodology within a
collection of shapes, rather than relying on pairwise
comparisons (c.f. Boyer et al.: Anat Rec 298 () 249-276).
Unfortunately, while global information generally enhances
maps between dissimilar objects, it can degrade the quality
of correspondences between similar objects due to the
accumulation of numerical error. We explore a number of
approaches to mitigate this degradation, quantify their
performance, and compare the generated pairwise maps (and
the shape space characterized by these maps) to a "ground
truth" obtained from landmarks manually collected by
geometric morphometricians. Novel methods both improve the
quality of the pairwise correspondences relative to cPDist
and achieve a taxonomic distinctiveness comparable to
auto3Dgm. Anat Rec, 301:636-658, 2018. © 2017 Wiley
Periodicals, Inc.},
Doi = {10.1002/ar.23700},
Key = {fds329931}
}

@article{fds333668,
Author = {Duncan, W and Best, J and Golubitsky, M and Nijhout, HF and Reed,
M},
Title = {Homeostasis despite instability.},
Journal = {Mathematical Biosciences},
Volume = {300},
Pages = {130-137},
Year = {2018},
Month = {March},
url = {http://dx.doi.org/10.1016/j.mbs.2018.03.025},
Abstract = {We have shown previously that different homeostatic
mechanisms in biochemistry create input-output curves with a
"chair" shape. At equilibrium, for intermediate values of a
parameter (often an input), a variable, Z, changes very
little (the homeostatic plateau), but for low and high
values of the parameter, Z changes rapidly (escape from
homeostasis). In all cases previously studied, the steady
state was stable for each value of the input parameter. Here
we show that, for the feedback inhibition motif, stability
may be lost through a Hopf bifurcation on the homeostatic
plateau and then regained by another Hopf bifurcation. If
the limit cycle oscillations are relatively small in the
unstable interval, then the variable Z maintains homeostasis
despite the instability. We show that the existence of an
input interval in which there are oscillations, the length
of the interval, and the size of the oscillations depend in
interesting and complicated ways on the properties of the
inhibition function, f, the length of the chain, and the
size of a leakage parameter.},
Doi = {10.1016/j.mbs.2018.03.025},
Key = {fds333668}
}

@article{fds330929,
Author = {Tralie, CJ and Smith, A and Borggren, N and Hineman, J and Bendich, P and Zulch, P and Harer, J},
Title = {Geometric Cross-Modal Comparison of Heterogeneous Sensor
Data},
Journal = {Proceedings of the 39th IEEE Aerospace Conference},
Year = {2018},
Month = {March},
Abstract = {In this work, we address the problem of cross-modal
comparison of aerial data streams. A variety of simulated
automobile trajectories are sensed using two different
modalities: full-motion video, and radio-frequency (RF)
signals received by detectors at various locations. The
information represented by the two modalities is compared
using self-similarity matrices (SSMs) corresponding to
time-ordered point clouds in feature spaces of each of these
data sources; we note that these feature spaces can be of
entirely different scale and dimensionality. Several metrics
for comparing SSMs are explored, including a cutting-edge
time-warping technique that can simultaneously handle local
time warping and partial matches, while also controlling for
the change in geometry between feature spaces of the two
modalities. We note that this technique is quite general,
and does not depend on the choice of modalities. In this
particular setting, we demonstrate that the cross-modal
distance between SSMs corresponding to the same trajectory
type is smaller than the cross-modal distance between SSMs
corresponding to distinct trajectory types, and we formalize
this observation via precision-recall metrics in
experiments. Finally, we comment on promising implications
of these ideas for future integration into
multiple-hypothesis tracking systems.},
Key = {fds330929}
}

@article{fds330205,
Author = {Tralie, CJ and Smith, A and Borggren, N and Hineman, J and Bendich, P and Zulch, P and Harer, J},
Title = {Geometric Cross-Modal Comparison of Heterogeneous Sensor
Data},
Journal = {Proceedings of the 39th IEEE Aerospace Conference},
Year = {2018},
Month = {March},
Abstract = {In this work, we address the problem of cross-modal
comparison of aerial data streams. A variety of simulated
automobile trajectories are sensed using two different
modalities: full-motion video, and radio-frequency (RF)
signals received by detectors at various locations. The
information represented by the two modalities is compared
using self-similarity matrices (SSMs) corresponding to
time-ordered point clouds in feature spaces of each of these
data sources; we note that these feature spaces can be of
entirely different scale and dimensionality. Several metrics
for comparing SSMs are explored, including a cutting-edge
time-warping technique that can simultaneously handle local
time warping and partial matches, while also controlling for
the change in geometry between feature spaces of the two
modalities. We note that this technique is quite general,
and does not depend on the choice of modalities. In this
particular setting, we demonstrate that the cross-modal
distance between SSMs corresponding to the same trajectory
type is smaller than the cross-modal distance between SSMs
corresponding to distinct trajectory types, and we formalize
this observation via precision-recall metrics in
experiments. Finally, we comment on promising implications
of these ideas for future integration into
multiple-hypothesis tracking systems.},
Key = {fds330205}
}

@article{fds332750,
Author = {Shen, C and Frasch, MG and Wu, HT and Herry, CL and Cao, M and Desrochers,
A and Fecteau, G and Burns, P},
Title = {Non-invasive acquisition of fetal ECG from the maternal
xyphoid process: a feasibility study in pregnant sheep and a
call for open data sets.},
Journal = {Physiological Measurement},
Volume = {39},
Number = {3},
Pages = {035005},
Year = {2018},
Month = {March},
url = {http://dx.doi.org/10.1088/1361-6579/aaaaa4},
Abstract = {The utility of fetal heart rate (FHR) monitoring can only be
achieved with an acquisition sampling rate that preserves
the underlying physiological information on the millisecond
time scale (1000 Hz rather than 4 Hz). For such acquisition,
fetal ECG (fECG) is required, rather than the ultrasound to
derive FHR. We tested one recently developed algorithm,
SAVER, and two widely applied algorithms to extract fECG
from a single-channel maternal ECG signal recorded over the
xyphoid process rather than the routine abdominal signal.At
126dG, ECG was attached to near-term ewe and fetal
shoulders, manubrium and xyphoid processes
(n  =  12). fECG served as the ground-truth to which
the fetal ECG signal extracted from the simultaneously-acquired
maternal ECG was compared. All fetuses were in good health
during surgery (pH 7.29  ±  0.03, pO2
33.2  ±  8.4, pCO2 56.0  ±  7.8, O2Sat
78.3  ±  7.6, lactate 2.8  ±  0.6,
BE  -0.3  ±  2.4).In all animals, single lead
fECG extraction algorithm could not extract fECG from the
maternal ECG signal over the xyphoid process with the F1
less than 50%.The applied fECG extraction algorithms might
be unsuitable for the maternal ECG signal over the xyphoid
process, or the latter does not contain strong enough fECG
signal, although the lead is near the mother's abdomen.
Fetal sheep model is widely used to mimic various fetal
conditions, yet ECG recordings in a public data set form are
not available to test the predictive ability of fECG and
FHR. We are making this data set openly available to other
researchers to foster non-invasive fECG acquisition in this
animal model.},
Doi = {10.1088/1361-6579/aaaaa4},
Key = {fds332750}
}

@article{fds332374,
Author = {Tralie, CJ and Smith, A and Borggren, N and Hineman, J and Bendich, P and Zulch, P and Harer, J},
Title = {Geometric Cross-Modal Comparison of Heterogeneous Sensor
Data},
Journal = {Proceedings of the 39th IEEE Aerospace Conference},
Year = {2018},
Month = {March},
Abstract = {In this work, we address the problem of cross-modal
comparison of aerial data streams. A variety of simulated
automobile trajectories are sensed using two different
modalities: full-motion video, and radio-frequency (RF)
signals received by detectors at various locations. The
information represented by the two modalities is compared
using self-similarity matrices (SSMs) corresponding to
time-ordered point clouds in feature spaces of each of these
data sources; we note that these feature spaces can be of
entirely different scale and dimensionality. Several metrics
for comparing SSMs are explored, including a cutting-edge
time-warping technique that can simultaneously handle local
time warping and partial matches, while also controlling for
the change in geometry between feature spaces of the two
modalities. We note that this technique is quite general,
and does not depend on the choice of modalities. In this
particular setting, we demonstrate that the cross-modal
distance between SSMs corresponding to the same trajectory
type is smaller than the cross-modal distance between SSMs
corresponding to distinct trajectory types, and we formalize
this observation via precision-recall metrics in
experiments. Finally, we comment on promising implications
of these ideas for future integration into
multiple-hypothesis tracking systems.},
Key = {fds332374}
}

@article{fds330520,
Author = {Ekholm, T and Ng, L and Shende, V},
Title = {A complete knot invariant from contact homology},
Journal = {Inventiones mathematicae},
Volume = {211},
Number = {3},
Pages = {1149-1200},
Year = {2018},
Month = {March},
url = {http://dx.doi.org/10.1007/s00222-017-0761-1},
Abstract = {© 2017, Springer-Verlag GmbH Germany. We construct an
enhanced version of knot contact homology, and show that we
can deduce from it the group ring of the knot group together
with the peripheral subgroup. In particular, it completely
determines a knot up to smooth isotopy. The enhancement
consists of the (fully noncommutative) Legendrian contact
homology associated to the union of the conormal torus of
the knot and a disjoint cotangent fiber sphere, along with a
product on a filtered part of this homology. As a corollary,
we obtain a new, holomorphic-curve proof of a result of the
third author that the Legendrian isotopy class of the
conormal torus is a complete knot invariant.},
Doi = {10.1007/s00222-017-0761-1},
Key = {fds330520}
}

@article{fds332859,
Author = {Huang, Y and Lu, J and Ming, P},
Title = {A Concurrent Global–Local Numerical Method for Multiscale
PDEs},
Journal = {Journal of Scientific Computing},
Pages = {1-28},
Year = {2018},
Month = {February},
url = {http://dx.doi.org/10.1007/s10915-018-0662-5},
Springer Nature We present a new hybrid numerical method for
multiscale partial differential equations, which
simultaneously captures the global macroscopic information
and resolves the local microscopic events over regions of
relatively small size. The method couples concurrently the
microscopic coefficients in the region of interest with the
homogenized coefficients elsewhere. The cost of the method
is comparable to the heterogeneous multiscale method, while
being able to recover microscopic information of the
solution. The convergence of the method is proved for
problems with bounded and measurable coefficients, while the
rate of convergence is established for problems with rapidly
oscillating periodic or almost-periodic coefficients.
Numerical results are reported to show the efficiency and
accuracy of the proposed method.},
Doi = {10.1007/s10915-018-0662-5},
Key = {fds332859}
}

@article{fds330278,
Author = {Kiselev, A and Tan, C},
Title = {Finite time blow up in the hyperbolic Boussinesq
system},
Volume = {325},
Pages = {34-55},
Year = {2018},
Month = {February},
url = {http://dx.doi.org/10.1016/j.aim.2017.11.019},
Abstract = {© 2017 Elsevier Inc. In recent work of Luo and Hou [10], a
new scenario for finite time blow up in solutions of 3D
Euler equation has been proposed. The scenario involves a
ring of hyperbolic points of the flow located at the
boundary of a cylinder. In this paper, we propose a two
dimensional model that we call “hyperbolic Boussinesq
system”. This model is designed to provide insight into
the hyperbolic point blow up scenario. The model features an
incompressible velocity vector field, a simplified
Biot–Savart law, and a simplified term modeling buoyancy.
We prove that finite time blow up happens for a natural
class of initial data.},
Doi = {10.1016/j.aim.2017.11.019},
Key = {fds330278}
}

@article{fds330841,
Author = {Bray, H and Roesch, H},
Title = {Proof of a Null Geometry Penrose Conjecture},
Journal = {Notices of the American Mathematical Society.},
Volume = {65},
Publisher = {American Mathematical Society},
Year = {2018},
Month = {February},
Key = {fds330841}
}

@article{fds332805,
Author = {Vu, M-AT and Adalı, T and Ba, D and Buzsáki, G and Carlson, D and Heller,
K and Liston, C and Rudin, C and Sohal, VS and Widge, AS and Mayberg, HS and Sapiro, G and Dzirasa, K},
Title = {A Shared Vision for Machine Learning in Neuroscience.},
Journal = {The Journal of neuroscience : the official journal of the
Society for Neuroscience},
Volume = {38},
Number = {7},
Pages = {1601-1607},
Year = {2018},
Month = {February},
url = {http://dx.doi.org/10.1523/jneurosci.0508-17.2018},
Abstract = {With ever-increasing advancements in technology,
neuroscientists are able to collect data in greater volumes
and with finer resolution. The bottleneck in understanding
how the brain works is consequently shifting away from the
amount and type of data we can collect and toward what we
actually do with the data. There has been a growing interest
in leveraging this vast volume of data across levels of
analysis, measurement techniques, and experimental paradigms
to gain more insight into brain function. Such efforts are
visible at an international scale, with the emergence of big
data neuroscience initiatives, such as the BRAIN initiative
(Bargmann et al., 2014), the Human Brain Project, the Human
Connectome Project, and the National Institute of Mental
Health's Research Domain Criteria initiative. With these
large-scale projects, much thought has been given to
data-sharing across groups (Poldrack and Gorgolewski, 2014;
Sejnowski et al., 2014); however, even with such
data-sharing initiatives, funding mechanisms, and
infrastructure, there still exists the challenge of how to
cohesively integrate all the data. At multiple stages and
levels of neuroscience investigation, machine learning holds
great promise as an addition to the arsenal of analysis
tools for discovering how the brain works.},
Doi = {10.1523/jneurosci.0508-17.2018},
Key = {fds332805}
}

@article{fds327666,
Author = {Pisharady, PK and Sotiropoulos, SN and Duarte-Carvajalino, JM and Sapiro, G and Lenglet, C},
Title = {Estimation of white matter fiber parameters from compressed
multiresolution diffusion MRI using sparse Bayesian
learning.},
Journal = {NeuroImage},
Volume = {167},
Pages = {488-503},
Year = {2018},
Month = {February},
url = {http://dx.doi.org/10.1016/j.neuroimage.2017.06.052},
Abstract = {We present a sparse Bayesian unmixing algorithm BusineX:
Bayesian Unmixing for Sparse Inference-based Estimation of
Fiber Crossings (X), for estimation of white matter fiber
parameters from compressed (under-sampled) diffusion MRI
(dMRI) data. BusineX combines compressive sensing with
linear unmixing and introduces sparsity to the previously
proposed multiresolution data fusion algorithm RubiX,
resulting in a method for improved reconstruction,
especially from data with lower number of diffusion
gradients. We formulate the estimation of fiber parameters
as a sparse signal recovery problem and propose a linear
unmixing framework with sparse Bayesian learning for the
recovery of sparse signals, the fiber orientations and
volume fractions. The data is modeled using a parametric
spherical deconvolution approach and represented using a
dictionary created with the exponential decay components
along different possible diffusion directions. Volume
fractions of fibers along these directions define the
dictionary weights. The proposed sparse inference, which is
based on the dictionary representation, considers the
sparsity of fiber populations and exploits the spatial
redundancy in data representation, thereby facilitating
inference from under-sampled q-space. The algorithm improves
parameter estimation from dMRI through data-dependent local
learning of hyperparameters, at each voxel and for each
possible fiber orientation, that moderate the strength of
priors governing the parameter variances. Experimental
results on synthetic and in-vivo data show improved accuracy
with a lower uncertainty in fiber parameter estimates.
BusineX resolves a higher number of second and third fiber
crossings. For under-sampled data, the algorithm is also
shown to produce more reliable estimates.},
Doi = {10.1016/j.neuroimage.2017.06.052},
Key = {fds327666}
}

@article{fds332860,
Author = {Lu, J and Zhou, Z},
Title = {Accelerated sampling by infinite swapping of path integral
molecular dynamics with surface hopping.},
Journal = {Journal of Chemical Physics},
Volume = {148},
Number = {6},
Pages = {064110},
Year = {2018},
Month = {February},
url = {http://dx.doi.org/10.1063/1.5005024},
Abstract = {To accelerate the thermal equilibrium sampling of
multi-level quantum systems, the infinite swapping limit of
a recently proposed multi-level ring polymer representation
is investigated. In the infinite swapping limit, the ring
polymer evolves according to an averaged Hamiltonian with
respect to all possible surface index configurations of the
ring polymer and thus connects the surface hopping approach
to the mean-field path-integral molecular dynamics. A
multiscale integrator for the infinite swapping limit is
also proposed to enable efficient sampling based on the
limiting dynamics. Numerical results demonstrate the huge
improvement of sampling efficiency of the infinite swapping
compared with the direct simulation of path-integral
molecular dynamics with surface hopping.},
Doi = {10.1063/1.5005024},
Key = {fds332860}
}

@article{fds332384,
Author = {Vu, M-AT and Adalı, T and Ba, D and Buzsáki, G and Carlson, D and Heller,
K and Liston, C and Rudin, C and Sohal, VS and Widge, AS and Mayberg, HS and Sapiro, G and Dzirasa, K},
Title = {A Shared Vision for Machine Learning in Neuroscience.},
Journal = {The Journal of neuroscience : the official journal of the
Society for Neuroscience},
Volume = {38},
Number = {7},
Pages = {1601-1607},
Year = {2018},
Month = {February},
url = {http://dx.doi.org/10.1523/jneurosci.0508-17.2018},
Abstract = {With ever-increasing advancements in technology,
neuroscientists are able to collect data in greater volumes
and with finer resolution. The bottleneck in understanding
how the brain works is consequently shifting away from the
amount and type of data we can collect and toward what we
actually do with the data. There has been a growing interest
in leveraging this vast volume of data across levels of
analysis, measurement techniques, and experimental paradigms
to gain more insight into brain function. Such efforts are
visible at an international scale, with the emergence of big
data neuroscience initiatives, such as the BRAIN initiative
(Bargmann et al., 2014), the Human Brain Project, the Human
Connectome Project, and the National Institute of Mental
Health's Research Domain Criteria initiative. With these
large-scale projects, much thought has been given to
data-sharing across groups (Poldrack and Gorgolewski, 2014;
Sejnowski et al., 2014); however, even with such
data-sharing initiatives, funding mechanisms, and
infrastructure, there still exists the challenge of how to
cohesively integrate all the data. At multiple stages and
levels of neuroscience investigation, machine learning holds
great promise as an addition to the arsenal of analysis
tools for discovering how the brain works.},
Doi = {10.1523/jneurosci.0508-17.2018},
Key = {fds332384}
}

@article{fds332862,
Author = {Ji, H and Witelski, TP},
Title = {Instability and dynamics of volatile thin
films},
Volume = {3},
Number = {2},
Year = {2018},
Month = {February},
url = {http://dx.doi.org/10.1103/PhysRevFluids.3.024001},
Abstract = {© 2018 American Physical Society. Volatile viscous fluids
on partially wetting solid substrates can exhibit
interesting interfacial instabilities and pattern formation.
We study the dynamics of vapor condensation and fluid
evaporation governed by a one-sided model in a
low-Reynolds-number lubrication approximation incorporating
surface tension, intermolecular effects, and evaporative
fluxes. Parameter ranges for evaporation-dominated and
condensation-dominated regimes and a critical case are
identified. Interfacial instabilities driven by the
competition between the disjoining pressure and evaporative
effects are studied via linear stability analysis. Transient
pattern formation in nearly flat evolving films in the
critical case is investigated. In the weak evaporation limit
unstable modes of finite-amplitude nonuniform steady states
lead to rich droplet dynamics, including flattening,
symmetry breaking, and droplet merging. Numerical
simulations show that long-time behaviors leading to
evaporation or condensation are sensitive to transitions
between filmwise and dropwise dynamics.},
Doi = {10.1103/PhysRevFluids.3.024001},
Key = {fds332862}
}

@article{fds332774,
Author = {Zhang, Z and Jiang, W and Dolbow, JE and Spencer,
BW},
Title = {A modified moment-fitted integration scheme for X-FEM
applications with history-dependent material
data},
Journal = {Computational Mechanics},
Pages = {1-20},
Year = {2018},
Month = {January},
url = {http://dx.doi.org/10.1007/s00466-018-1544-2},
Abstract = {© 2018 Springer-Verlag GmbH Germany, part of Springer
Nature We present a strategy for the numerical integration
of partial elements with the eXtended finite element method
(X-FEM). The new strategy is specifically designed for
problems with propagating cracks through a bulk material
that exhibits inelasticity. Following a standard approach
with the X-FEM, as the crack propagates new partial elements
are created. We examine quadrature rules that have
sufficient accuracy to calculate stiffness matrices
regardless of the orientation of the crack with respect to
the element. This permits the number of integration points
within elements to remain constant as a crack propagates,
and for state data to be easily transferred between
successive discretizations. In order to maintain weights
that are strictly positive, we propose an approach that
blends moment-fitted weights with volume-fraction based
weights. To demonstrate the efficacy of this simple
approach, we present results from numerical tests and
examples with both elastic and plastic material
response.},
Doi = {10.1007/s00466-018-1544-2},
Key = {fds332774}
}

@article{fds333512,
Author = {Zhang, Z and Descoteaux, M and Zhang, J and Girard, G and Chamberland,
M and Dunson, D and Srivastava, A and Zhu, H},
Title = {Mapping population-based structural connectomes.},
Journal = {NeuroImage},
Volume = {172},
Pages = {130-145},
Year = {2018},
Month = {January},
url = {http://dx.doi.org/10.1016/j.neuroimage.2017.12.064},
Abstract = {Advances in understanding the structural connectomes of
human brain require improved approaches for the
construction, comparison and integration of high-dimensional
whole-brain tractography data from a large number of
structural connectome (PSC) mapping framework to address
these challenges. PSC simultaneously characterizes a large
number of white matter bundles within and across different
subjects by registering different subjects' brains based on
coarse cortical parcellations, compressing the bundles of
each connection, and extracting novel connection weights. A
robust tractography algorithm and streamline post-processing
techniques, including dilation of gray matter regions,
streamline cutting, and outlier streamline removal are
applied to improve the robustness of the extracted
structural connectomes. The developed PSC framework can be
used to reproducibly extract binary networks, weighted
networks and streamline-based brain connectomes. We apply
the PSC to Human Connectome Project data to illustrate its
application in characterizing normal variations and
heritability of structural connectomes in healthy
subjects.},
Doi = {10.1016/j.neuroimage.2017.12.064},
Key = {fds333512}
}

@article{fds332366,
Author = {Giryes, R and Eldar, YC and Bronstein, A and Sapiro,
G},
Title = {Tradeoffs between Convergence Speed and Reconstruction
Accuracy in Inverse Problems},
Journal = {IEEE Transactions on Signal Processing},
Year = {2018},
Month = {January},
url = {http://dx.doi.org/10.1109/TSP.2018.2791945},
Abstract = {IEEE Solving inverse problems with iterative algorithms is
popular, especially for large data. Due to time constraints,
the number of possible iterations is usually limited,
potentially limiting the achievable accuracy. Given an error
one is willing to tolerate, an important question is whether
it is possible to modify the original iterations to obtain
faster convergence to a minimizer achieving the allowed
error without increasing the computational cost of each
iteration considerably. Relying on recent recovery
techniques developed for settings in which the desired
signal belongs to some low-dimensional set, we show that
using a coarse estimate of this set may lead to a faster
convergence at the cost of an additional error in the
reconstruction related to the accuracy of the set
approximation. Our theory ties to recent advances in sparse
recovery, compressed sensing, and deep learning.
Particularly, it may provide a possible explanation to the
successful approximation of the l_1-minimization solution by
neural networks with layers representing iterations, as
practiced in the learned iterative shrinkage-thresholding
algorithm (LISTA).},
Doi = {10.1109/TSP.2018.2791945},
Key = {fds332366}
}

@article{fds330134,
Author = {Arlotto, A and Wei, Y and Xie, X},
Title = {An adaptive O(log n)-optimal policy for the online selection
of a monotone subsequence from a random sample},
Journal = {Random Structures and Algorithms},
Volume = {52},
Number = {1},
Pages = {41-53},
Publisher = {Wiley},
Year = {2018},
Month = {January},
url = {http://dx.doi.org/10.1002/rsa.20728},
Abstract = {© 2017 Wiley Periodicals, Inc. Given a sequence of n
independent random variables with common continuous
distribution, we propose a simple adaptive online policy
that selects a monotone increasing subsequence. We show that
the expected number of monotone increasing selections made
by such a policy is within (Figure presented.) of optimal.
Our construction provides a direct and natural way for
proving the (Figure presented.) -optimality gap. An earlier
proof of the same result made crucial use of a key
inequality of Bruss and Delbaen [5] and of
de-Poissonization.},
Doi = {10.1002/rsa.20728},
Key = {fds330134}
}

@article{fds333543,
Author = {Rafat, M and Stone, HA and Auguste, DT and Dabagh, M and Randles, A and Heller, M and Rabinov, JD},
Title = {Impact of diversity of morphological characteristics and
Reynolds number on local hemodynamics in basilar
aneurysms},
Journal = {Aiche Journal},
Year = {2018},
Month = {January},
url = {http://dx.doi.org/10.1002/aic.16091},
Abstract = {© 2018 American Institute of Chemical Engineers.
Morphological and hemodynamic parameters have been suggested
to affect the rupture of cerebral aneurysms, but detailed
mechanisms of rupture are poorly understood. The purpose of
our study is to determine criteria for predicting the risk
of aneurysm rupture, which is critical for improved patient
management. Existing aneurysm hemodynamics studies generally
evaluate limited geometries or Reynolds numbers (Re), which
are difficult to apply to a wide range of patient-specific
cases. Association between hemodynamic characteristics and
morphology is focused. Several two-dimensional (2D) and
three-dimensional (3D) idealized and physiological
geometries is assessed to characterize the hemodynamic
landscape between flow patterns. The impact of morphology on
velocity and wall shear stress (WSS) profiles were
evaluated. Slight changes in aneurysm geometry is found or
Re result in significant changes in the hemodynamic and WSS
profiles. Our systematic mapping and nondimensional analysis
qualitatively identify hemodynamic conditions that may
predispose aneurysms to rupture.},
Doi = {10.1002/aic.16091},
Key = {fds333543}
}

@article{fds330816,
Author = {Conrey, JB and Turnage-Butterbaugh, CL},
Title = {On r-gaps between zeros of the Riemann zeta-function},
Journal = {Bulletin of the London Mathematical Society},
Year = {2018},
Month = {January},
url = {http://dx.doi.org/10.1112/blms.12142},
Abstract = {© 2018 London Mathematical Society. Under the Riemann
Hypothesis, we prove for any natural number r there exist
infinitely many natural numbers n such that
(γn+r-γn)/(2πr/logγn) > 1+Θ/r and (γn+r-γn)/(2πr/logγn)
< 1-θ/r for explicit absolute positive constants Θ and θ,
where γ denotes an ordinate of a zero of the Riemann
zeta-function on the critical line. Selberg published
announcements of this result several times without
proof.},
Doi = {10.1112/blms.12142},
Key = {fds330816}
}

@article{fds333225,
Author = {Dunson, DB},
Title = {Statistics in the big data era: Failures of the
machine},
Journal = {Statistics & Probability Letters},
Year = {2018},
Month = {January},
url = {http://dx.doi.org/10.1016/j.spl.2018.02.028},
Abstract = {© 2018. There is vast interest in automated methods for
complex data analysis. However, there is a lack of
consideration of (1) interpretability, (2) uncertainty
quantification, (3) applications with limited training data,
and (4) selection bias. Statistical methods can achieve
(1)-(4) with a change in focus.},
Doi = {10.1016/j.spl.2018.02.028},
Key = {fds333225}
}

@article{fds333710,
Author = {Talmon, R and Wu, H-T},
Title = {Latent common manifold learning with alternating diffusion:
Analysis and applications},
Journal = {Applied and Computational Harmonic Analysis},
Year = {2018},
Month = {January},
url = {http://dx.doi.org/10.1016/j.acha.2017.12.006},
Doi = {10.1016/j.acha.2017.12.006},
Key = {fds333710}
}

@article{fds328822,
Author = {Kowalski, M and Meynard, A and Wu, H-T},
Title = {Convex Optimization approach to signals with fast varying
instantaneous frequency},
Journal = {Applied and Computational Harmonic Analysis},
Volume = {44},
Number = {1},
Pages = {89-122},
Year = {2018},
Month = {January},
url = {http://dx.doi.org/10.1016/j.acha.2016.03.008},
Doi = {10.1016/j.acha.2016.03.008},
Key = {fds328822}
}

@article{fds333315,
Author = {Xu, J and Yang, H and Daubechies, I},
Title = {Recursive diffeomorphism-based regression for shape
functions},
Journal = {SIAM Journal on Mathematical Analysis},
Volume = {50},
Number = {1},
Pages = {5-32},
Year = {2018},
Month = {January},
url = {http://dx.doi.org/10.1137/16M1097535},
Abstract = {© 2018 Society for Industrial and Applied Mathematics. This
paper proposes a recursive diffeomorphism-based regression
method for the one-dimensional generalized mode
decomposition problem that aims at extracting generalized
modes α k (t)s k (2πN k φ k (t)) from their superposition
K k =1 α k (t)s k (2πN k φ k (t)). We assume that the
instantaneous information, e.g., α k (t) and N k φ k (t),
is determined by, e.g., a one-dimensional synchrosqueezed
transform or some other methods. Our main contribution is to
propose a novel approach based on diffeomorphisms and
nonparametric regression to estimate wave shape functions s
k (t). This leads to a framework for the generalized mode
decomposition problem under a weak well-separation
condition. Numerical examples of synthetic and real data are
provided to demonstrate the successful application of our
approach.},
Doi = {10.1137/16M1097535},
Key = {fds333315}
}

@article{fds320413,
Author = {Getz, JR},
Title = {Nonabelian fourier transforms for spherical
representations},
Journal = {Pacific Journal of Mathematics},
Volume = {294},
Number = {2},
Pages = {351-373},
Publisher = {Mathematical Sciences Publishers},
Year = {2018},
Month = {January},
url = {arXiv:1506.09128},
Abstract = {© 2018 Mathematical Sciences Publishers. Braverman and
Kazhdan have introduced an influential conjecture on local
functional equations for general Langlands L-functions. It
is related to L. Lafforgue's equally influential conjectural
construction of kernels for functorial transfers. We
formulate and prove a version of Braverman and Kazhdan's
conjecture for spherical representations over an archimedean
field that is suitable for application to the trace formula.
We then give a global application related to Langlands'
beyond endoscopy proposal. It is motivated by Ngô's
suggestion that one combine nonabelian Fourier transforms
with the trace formula in order to prove the functional
equations of Langlands L-functions in general.},
Doi = {10.2140/pjm.2018.294.351},
Key = {fds320413}
}

@article{fds332861,
Author = {Dai, S and Li, B and Lu, J},
Title = {Convergence of Phase-Field Free Energy and Boundary Force
for Molecular Solvation},
Journal = {Archive for Rational Mechanics and Analysis},
Volume = {227},
Number = {1},
Pages = {105-147},
Year = {2018},
Month = {January},
url = {http://dx.doi.org/10.1007/s00205-017-1158-4},
Doi = {10.1007/s00205-017-1158-4},
Key = {fds332861}
}

@article{fds333566,
Author = {Li, L and Liu, JG},
Title = {p-Euler equations and p-Navier-Stokes equations},
Journal = {Journal of Differential Equations},
Year = {2018},
Month = {January},
url = {http://dx.doi.org/10.1016/j.jde.2017.12.023},
Abstract = {© 2017 Elsevier Inc. We propose in this work new systems of
equations which we call p-Euler equations and
p-Navier-Stokes equations. p-Euler equations are derived as
the Euler-Lagrange equations for the action represented by
the Benamou-Brenier characterization of Wasserstein-p
distances, with incompressibility constraint. p-Euler
equations have similar structures with the usual Euler
equations but the 'momentum' is the signed (p-1)-th power of
the velocity. In the 2D case, the p-Euler equations have
streamfunction-vorticity formulation, where the vorticity is
given by the p-Laplacian of the streamfunction. By adding
diffusion presented by γ-Laplacian of the velocity, we
obtain what we call p-Navier-Stokes equations. If γ=p, the
a priori energy estimates for the velocity and momentum have
dual symmetries. Using these energy estimates and a
time-shift estimate, we show the global existence of weak
solutions for the p-Navier-Stokes equations in Rd for γ=p
and p≥d≥2 through a compactness criterion.},
Doi = {10.1016/j.jde.2017.12.023},
Key = {fds333566}
}

@article{fds333280,
Author = {Agarwal, PK and Fox, K and Nath, A},
Title = {Maintaining reeb graphs of triangulated 2-manifolds},
Journal = {LIPIcs},
Volume = {93},
Year = {2018},
Month = {January},
ISBN = {9783959770552},
url = {http://dx.doi.org/10.4230/LIPIcs.FSTTCS.2017.8},
Abstract = {© Pankaj K. Agarwal, Kyle Fox and Abhinandan Nath. Let M be
a triangulated, orientable 2-manifold of genus g without
boundary, and let h be a height function over M that is
linear within each triangle. We present a kinetic data
structure (KDS) for maintaining the Reeb graph R of h as the
heights of M’s vertices vary continuously with time.
Assuming the heights of two vertices of M become equal only
O(1) times, the KDS processes O((? + g)n polylog n) events;
n is the number of vertices in M, and ? is the number of
external events which change the combinatorial structure of
R. Each event is processed in O(log 2 n) time, and the total
size of our KDS is O(gn). The KDS can be extended to
maintain an augmented Reeb graph as well.},
Doi = {10.4230/LIPIcs.FSTTCS.2017.8},
Key = {fds333280}
}

@article{fds330135,
Author = {Arlotto, A and Frazelle, AE and Wei, Y},
Title = {Strategic open routing in service networks},
Journal = {Management Science},
Publisher = {INFORMS},
Year = {2018},
Key = {fds330135}
}

@article{fds330136,
Author = {Arlotto, A and Steele, JM},
Title = {A central limit theorem for costs in Bulinskaya’s
inventory management problem when deliveries face
delays},
Journal = {Methodology and Computing in Applied Probability},
Year = {2018},
url = {http://dx.doi.org/10.1007/s11009-016-9522-7},
Doi = {10.1007/s11009-016-9522-7},
Key = {fds330136}
}

@article{fds331376,
Author = {Pierce, LB and Yung, PL},
Title = {A polynomial Carleson operator along the
paraboloid},
Journal = {Revista Matematica Iberoamericana},
Publisher = {European Mathematical Society},
Year = {2018},
Key = {fds331376}
}

@article{fds320773,
Author = {Saper, L},
Title = {ℒ-modules and micro-support},
Journal = {to appear in Annals of Mathematics},
Year = {2018},
Key = {fds320773}
}

@article{fds330525,
Author = {Perez-Arancibia, C and Shipman, S and Turc, C and Venakides,
S},
Title = {DDM solutions of quasiperiodic transmission problems in
layered media via robust boundary integral equations at all
frequencies},
Year = {2017},
Month = {December},
Key = {fds330525}
}

@article{fds333703,
Author = {Suppiramaniam, V and Bloemer, J and Reed, M and Bhattacharya,
S},
Title = {Neurotransmitter Receptors},
Volume = {6-15},
Pages = {174-201},
Booktitle = {Comprehensive Toxicology: Third Edition},
Year = {2017},
Month = {December},
ISBN = {9780081006122},
url = {http://dx.doi.org/10.1016/B978-0-12-801238-3.65382-5},
receptors play a vital role in the normal functioning of the
nervous system. Controlled modulation of neurotransmitter
receptors is critical for proper signaling between nerve
cells and effector organs. Factors that disrupt normal
neurotransmitter signaling can alter the homeostasis of the
neurotransmitters at the presynaptic neuron and the
subsequent activation of postsynaptic receptors lead to
stimulation or inhibition of neuronal transmission. The
excitatory neurotransmission involves depolarization of the
postsynaptic neuron or cell due to a decrease in the
polarity of the cells by the influx of cations such as
sodium ions. The excitatory neurotransmission is mainly
carried out by glutamate receptors in the mammalian nervous
system. The inhibitory neurotransmission is due to
hyperpolarization of the cells by either influx of anions
such as chloride ions or efflux of cations such as potassium
ions. The GABA and glycine receptors serve as major
inhibitory neurotransmitter receptors. Toxins and toxicants
can interfere with neuronal transmission by directly binding
receptors and modulating their function or by altering
transmitter synthesis, release, and reuptake mechanisms.
Therefore, neurotoxins can impair neuronal transmission at
the synapse by either presynaptic modulation or postsynaptic
modifications. Due to the intricate network of the nervous
system, impairment of the receptor functions in the synapse
can lead to regional network dysfunction, eventually
resulting in adverse cellular effects and behavioral
deficits. Therefore, a thorough knowledge of
neurotransmitter receptor modulation by toxins and toxicants
is essential for future development of therapies against
adverse effects of these neurotoxic substances.},
Doi = {10.1016/B978-0-12-801238-3.65382-5},
Key = {fds333703}
}

@article{fds331377,
Author = {Best, J and Nijhout, HF and Samaranayake, S and Hashemi, P and Reed,
M},
Title = {A mathematical model for histamine synthesis, release, and
control in varicosities.},
Journal = {Theoretical Biology and Medical Modelling},
Volume = {14},
Number = {1},
Pages = {24},
Year = {2017},
Month = {December},
url = {http://dx.doi.org/10.1186/s12976-017-0070-9},
Abstract = {Histamine (HA), a small molecule that is synthesized from
the amino acid histidine, plays an important role in the
immune system where it is associated with allergies,
inflammation, and T-cell regulation. In the brain, histamine
is stored in mast cells and other non-neuronal cells and
also acts as a neurotransmitter. The histamine neuron cell
bodies are in the tuberomammillary (TM) nucleus of the
hypothalamus and these neurons send projections throughout
the central nervous system (CNS), in particular to the
cerebral cortex, amygdala, basal ganglia, hippocampus,
thalamus, retina, and spinal cord. HA neurons make few
synapses, but release HA from the cell bodies and from
varicosities when the neurons fire. Thus the HA neural
system seems to modulate and control the HA concentration in
projection regions. It is known that high HA levels in the
extracellular space inhibit serotonin release, so HA may
play a role in the etiology of depression.We compare model
predictions to classical physiological experiments on HA
half-life, the concentration of brain HA after histidine
increased or decreased in the diet. The model predictions
are also consistent with in vivo experiments in which
extracellular HA is measured, using Fast Scan Cyclic
Voltammetry, in the premammillary nucleus (PM) after a 2 s
antidromic stimulation of the TM, both without and in the
presence of the H 3 autoreceptor antagonist thioperamide. We
show that the model predicts well the temporal behavior of
HA in the extracellular space over 30 s in both
experiments.Our ability to measure in vivo histamine
dynamics in the extracellular space after stimulation
presents a real opportunity to understand brain function and
control. The observed extracellular dynamics depends on
synthesis, storage, neuronal firing, release, reuptake,
glial cells, and control by autoreceptors, as well as the
behavioral state of the animal (for example, depression) or
the presence of neuroinflammation. In this complicated
situation, the mathematical model will be useful for
interpreting data and conducting in silico experiments to
understand causal mechanisms. And, better understanding can
suggest new therapeutic drug targets.},
Doi = {10.1186/s12976-017-0070-9},
Key = {fds331377}
}

@article{fds332378,
Author = {Minsker, S and Srivastava, S and Lin, L and Dunson,
DB},
Title = {Robust and scalable bayes via a median of subset posterior
measures},
Journal = {Journal of machine learning research : JMLR},
Volume = {18},
Pages = {1-40},
Year = {2017},
Month = {December},
Abstract = {© 2017 Stanislav Minsker, Sanvesh Srivastava, Lizhen Lin
and David B. Dunson. We propose a novel approach to Bayesian
analysis that is provably robust to outliers in the data and
often has computational advantages over standard methods.
Our technique is based on splitting the data into
non-overlapping subgroups, evaluating the posterior
distribution given each independent subgroup, and then
combining the resulting measures. The main novelty of our
approach is the proposed aggregation step, which is based on
the evaluation of a median in the space of probability
measures equipped with a suitable collection of distances
that can be quickly and efficiently evaluated in practice.
We present both theoretical and numerical evidence
illustrating the improvements achieved by our
method.},
Key = {fds332378}
}

@article{fds332363,
Author = {Wheeler, MW and Dunson, DB and Herring, AH},
Title = {Bayesian Local Extremum Splines.},
Journal = {Biometrika},
Volume = {104},
Number = {4},
Pages = {939-952},
Publisher = {Oxford University Press (OUP)},
Year = {2017},
Month = {December},
Abstract = {We consider shape restricted nonparametric regression on a
closed set [Formula: see text], where it is reasonable to
assume the function has no more than H local extrema
interior to [Formula: see text]. Following a Bayesian
approach we develop a nonparametric prior over a novel class
of local extremum splines. This approach is shown to be
consistent when modeling any continuously differentiable
function within the class considered, and is used to develop
methods for testing hypotheses on the shape of the curve.
Sampling algorithms are developed, and the method is applied
in simulation studies and data examples where the shape of
the curve is of interest.},
Key = {fds332363}
}

@article{fds332886,
Author = {Shang, Y and Dunson, D and Song, J-S},
Title = {Exploiting Big Data in Logistics Risk Assessment via
Bayesian Nonparametrics},
Journal = {Operations Research},
Volume = {65},
Number = {6},
Pages = {1574-1588},
Year = {2017},
Month = {December},
url = {http://dx.doi.org/10.1287/opre.2017.1612},
Doi = {10.1287/opre.2017.1612},
Key = {fds332886}
}

@article{fds329941,
Author = {Wu, H-K and Ko, Y-S and Lin, Y-S and Wu, H-T and Tsai, T-H and Chang,
H-H},
Title = {Corrigendum to "The correlation between pulse diagnosis and
constitution identification in traditional Chinese medicine"
[Complementary Ther. Med. 30 (2017) 107-112].},
Journal = {Complementary Therapies in Medicine},
Volume = {35},
Pages = {145},
Year = {2017},
Month = {December},
url = {http://dx.doi.org/10.1016/j.ctim.2017.09.004},
Doi = {10.1016/j.ctim.2017.09.004},
Key = {fds329941}
}

@article{fds332858,
Author = {Alaifari, R and Daubechies, I and Grohs, P and Thakur,
G},
Title = {Reconstructing Real-Valued Functions from Unsigned
Coefficients with Respect to Wavelet and Other
Frames},
Journal = {Journal of Fourier Analysis and Applications},
Volume = {23},
Number = {6},
Pages = {1480-1494},
Year = {2017},
Month = {December},
url = {http://dx.doi.org/10.1007/s00041-016-9513-7},
Doi = {10.1007/s00041-016-9513-7},
Key = {fds332858}
}

@article{fds329343,
Author = {Lu, J and Thicke, K},
Title = {Cubic scaling algorithms for RPA correlation using
interpolative separable density fitting},
Journal = {Journal of Computational Physics},
Volume = {351},
Pages = {187-202},
Year = {2017},
Month = {December},
url = {http://dx.doi.org/10.1016/j.jcp.2017.09.012},
Doi = {10.1016/j.jcp.2017.09.012},
Key = {fds329343}
}

@article{fds332172,
Author = {Cao, Y and Lu, J},
Title = {Lindblad equation and its semiclassical limit of the
Anderson-Holstein model},
Journal = {Journal of Mathematical Physics},
Volume = {58},
Number = {12},
Year = {2017},
Month = {December},
url = {http://dx.doi.org/10.1063/1.4993431},
Abstract = {© 2017 Author(s). For multi-level open quantum systems, the
interaction between different levels could pose a challenge
to understand the quantum system both analytically and
numerically. In this work, we study the approximation of the
dynamics of the Anderson-Holstein model, as a model of the
multi-level open quantum system, by Redfield and Lindblad
equations. Both equations have a desirable property that if
the density operators for different levels are diagonal
initially, they remain to be diagonal for any time. Thanks
to this nice property, the semiclassical limit of both
Redfield and Lindblad equations could be derived explicitly;
the resulting classical master equations share similar
structures of transport and hopping terms. The Redfield and
Lindblad equations are also compared from the angle of time
dependent perturbation theory.},
Doi = {10.1063/1.4993431},
Key = {fds332172}
}

@article{fds329932,
Author = {Gleeson, JP and Durrett, R},
Title = {Temporal profiles of avalanches on networks},
Journal = {Nature Communications},
Volume = {8},
Number = {1},
Year = {2017},
Month = {December},
url = {http://dx.doi.org/10.1038/s41467-017-01212-0},
Doi = {10.1038/s41467-017-01212-0},
Key = {fds329932}
}

@article{fds331943,
Author = {Struck, AF and Ustun, B and Ruiz, AR and Lee, JW and LaRoche, SM and Hirsch, LJ and Gilmore, EJ and Vlachy, J and Haider, HA and Rudin, C and Westover, MB},
Title = {Association of an Electroencephalography-Based Risk Score
With Seizure Probability in Hospitalized
Patients.},
Journal = {JAMA Neurology},
Volume = {74},
Number = {12},
Pages = {1419-1424},
Year = {2017},
Month = {December},
url = {http://dx.doi.org/10.1001/jamaneurol.2017.2459},
Abstract = {Continuous electroencephalography (EEG) use in critically
ill patients is expanding. There is no validated method to
combine risk factors and guide clinicians in assessing
seizure risk.To use seizure risk factors from EEG and
clinical history to create a simple scoring system
associated with the probability of seizures in patients with
acute illness.We used a prospective multicenter (Emory
University Hospital, Brigham and Women's Hospital, and Yale
University Hospital) database containing clinical and
electrographic variables on 5427 continuous EEG sessions
from eligible patients if they had continuous EEG for
clinical indications, excluding epilepsy monitoring unit
admissions. We created a scoring system model to estimate
seizure risk in acutely ill patients undergoing continuous
EEG. The model was built using a new machine learning method
(RiskSLIM) that is designed to produce accurate,
risk-calibrated scoring systems with a limited number of
variables and small integer weights. We validated the
accuracy and risk calibration of our model using
cross-validation and compared its performance with models
built with state-of-the-art logistic regression methods. The
database was developed by the Critical Care EEG Research
Consortium and used data collected over 3 years. The EEG
variables were interpreted using standardized terminology by
certified reviewers.All patients had more than 6 hours of
uninterrupted EEG recordings.The main outcome was the
average risk calibration error.There were 5427 continuous
EEGs performed on 4772 participants (2868 men, 49.9%; median
age, 61 years) performed at 3 institutions, without further
demographic stratification. Our final model, 2HELPS2B, had
an area under the curve of 0.819 and average calibration
error of 2.7% (95% CI, 2.0%-3.6%). It included 6 variables
with the following point assignments: (1) brief (ictal)
rhythmic discharges (B[I]RDs) (2 points); (2) presence of
lateralized periodic discharges, lateralized rhythmic delta
activity, or bilateral independent periodic discharges (1
point); (3) prior seizure (1 point); (4) sporadic
epileptiform discharges (1 point); (5) frequency greater
than 2.0 Hz for any periodic or rhythmic pattern (1 point);
and (6) presence of "plus" features (superimposed, rhythmic,
sharp, or fast activity) (1 point). The probable seizure
risk of each score was 5% for a score of 0, 12% for a score
of 1, 27% for a score of 2, 50% for a score of 3, 73% for a
score of 4, 88% for a score of 5, and greater than 95% for a
score of 6 or 7.The 2HELPS2B model is a quick accurate tool
to aid clinical judgment of the risk of seizures in
critically ill patients.},
Doi = {10.1001/jamaneurol.2017.2459},
Key = {fds331943}
}

@article{fds330900,
Author = {Singleton, KR and Crawford, L and Tsui, E and Manchester, HE and Maertens, O and Liu, X and Liberti, MV and Magpusao, AN and Stein, EM and Tingley, JP and Frederick, DT and Boland, GM and Flaherty, KT and McCall, SJ and Krepler, C and Sproesser, K and Herlyn, M and Adams, DJ and Locasale, JW and Cichowski, K and Mukherjee, S and Wood,
KC},
Title = {Melanoma Therapeutic Strategies that Select against
Resistance by Exploiting MYC-Driven Evolutionary
Convergence.},
Journal = {Cell Reports},
Volume = {21},
Number = {10},
Pages = {2796-2812},
Year = {2017},
Month = {December},
url = {http://dx.doi.org/10.1016/j.celrep.2017.11.022},
Abstract = {Diverse pathways drive resistance to BRAF/MEK inhibitors in
BRAF-mutant melanoma, suggesting that durable control of
resistance will be a challenge. By combining statistical
modeling of genomic data from matched pre-treatment and
post-relapse patient tumors with functional interrogation of
>20 in vitro and in vivo resistance models, we discovered
that major pathways of resistance converge to activate the
transcription factor, c-MYC (MYC). MYC expression and
pathway gene signatures were suppressed following drug
treatment, and then rebounded during progression.
Critically, MYC activation was necessary and sufficient for
resistance, and suppression of MYC activity using genetic
approaches or BET bromodomain inhibition was sufficient to
resensitize cells and delay BRAFi resistance. Finally,
MYC-driven, BRAFi-resistant cells are hypersensitive to the
inhibition of MYC synthetic lethal partners, including SRC
family and c-KIT tyrosine kinases, as well as glucose,
glutamine, and serine metabolic pathways. These insights
enable the design of combination therapies that select
against resistance evolution.},
Doi = {10.1016/j.celrep.2017.11.022},
Key = {fds330900}
}

@article{fds329936,
Author = {Li, Y and Ying, L},
Title = {Distributed-memory hierarchical interpolative
factorization},
Journal = {Research in the Mathematical Sciences},
Volume = {4},
Number = {1},
Year = {2017},
Month = {December},
url = {http://dx.doi.org/10.1186/s40687-017-0100-6},
Doi = {10.1186/s40687-017-0100-6},
Key = {fds329936}
}

@article{fds330931,
Author = {Lopatkin, AJ and Meredith, HR and Srimani, JK and Pfeiffer, C and Durrett, R and You, L},
Title = {Persistence and reversal of plasmid-mediated antibiotic
resistance.},
Journal = {Nature Communications},
Volume = {8},
Number = {1},
Pages = {1689},
Year = {2017},
Month = {November},
url = {http://dx.doi.org/10.1038/s41467-017-01532-1},
Abstract = {In the absence of antibiotic-mediated selection, sensitive
bacteria are expected to displace their resistant
counterparts if resistance genes are costly. However, many
resistance genes persist for long periods in the absence of
antibiotics. Horizontal gene transfer (primarily
conjugation) could explain this persistence, but it has been
suggested that very high conjugation rates would be
required. Here, we show that common conjugal plasmids, even
when costly, are indeed transferred at sufficiently high
rates to be maintained in the absence of antibiotics in
Escherichia coli. The notion is applicable to nine plasmids
from six major incompatibility groups and mixed populations
carrying multiple plasmids. These results suggest that
reducing antibiotic use alone is likely insufficient for
reversing resistance. Therefore, combining conjugation
inhibition and promoting plasmid loss would be an effective
strategy to limit conjugation-assisted persistence of
antibiotic resistance.},
Doi = {10.1038/s41467-017-01532-1},
Key = {fds330931}
}

@article{fds330395,
Author = {Tralie, CJ},
Title = {Self-Similarity Based Time Warping},
Year = {2017},
Month = {November},
Abstract = {In this work, we explore the problem of aligning two
time-ordered point clouds which are spatially transformed
and re-parameterized versions of each other. This has a
diverse array of applications such as cross modal time
series synchronization (e.g. MOCAP to video) and alignment
of discretized curves in images. Most other works that
address this problem attempt to jointly uncover a spatial
alignment and correspondences between the two point clouds,
or to derive local invariants to spatial transformations
such as curvature before computing correspondences. By
contrast, we sidestep spatial alignment completely by using
self-similarity matrices (SSMs) as a proxy to the
time-ordered point clouds, since self-similarity matrices
are blind to isometries and respect global geometry. Our
algorithm, dubbed "Isometry Blind Dynamic Time Warping"
(IBDTW), is simple and general, and we show that its
associated dissimilarity measure lower bounds the L1
Gromov-Hausdorff distance between the two point sets when
restricted to warping paths. We also present a local,
partial alignment extension of IBDTW based on the Smith
Waterman algorithm. This eliminates the need for tedious
manual cropping of time series, which is ordinarily
necessary for global alignment algorithms to function
properly.},
Key = {fds330395}
}

@article{fds329938,
Author = {Motta, FC},
Title = {Topological Data Analysis: Developments and
Applications},
Pages = {369-391},
Booktitle = {Advances in Nonlinear Geosciences},
Publisher = {SPRINGER},
Editor = {Tsonis, A},
Year = {2017},
Month = {November},
ISBN = {3319588958},
Abstract = {Topological Data Analysis (TDA) and its mainstay
computational device, persistent homology (PH), has
established a strong track record of providing researchers
across the data-driven sciences with new insights and
methodologies by characterizing low-dimensional geometric
structures in high-dimensional data. When combined with
machine learning (ML) methods, PH is valued as a
discriminating-feature extraction tool. This work highlights
many of the recent successes at the intersection of TDA and
ML, introduces some of the foundational mathematics
underpinning TDA, and summarizes the efforts to strengthen
the bridge between TDA and ML. Thus, this document is a
launching point for experimentalists and theoreticians to
consider what can be learned from the shape of their
data.},
Key = {fds329938}
}

@article{fds332953,
Author = {Rav, M and Lowe, A and Agarwal, PK},
Title = {Flood Risk Analysis on Terrains},
Journal = {GIS: Proceedings of the ACM International Symposium on
Volume = {2017-November},
Year = {2017},
Month = {November},
ISBN = {9781450354905},
url = {http://dx.doi.org/10.1145/3139958.3139985},
problem in terrain analysis is modeling how water flows
across a terrain and creates floods by filling up
depressions. In this paper we study the flooding query
problem: Given a rain region R and a query point q on the
terrain, quickly determine how much rain has to fall in R so
that q is flooded. Available terrain data is often subject
to uncertainty which must be incorporated into the terrain
analysis. For instance, the digital elevation models of
terrains have to be refined to incorporate underground
pipes, tunnels, and waterways under bridges, but there is
often uncertainty in their existence. By representing the
uncertainty in the terrain data explicitly, we can develop
methods for flood risk analysis that properly incorporate
terrain uncertainty when reporting what areas are at risk of
flooding. We present two results. First, we present a linear
size data structure that given a terrain (with no data
uncertainty) can answer the flooding query in O(m log 2 n)
time, where m is the number of minima of the terrain at
which rain is falling and n is the number of vertices of the
terrain. Next, we extend this data structure to handle
“uncertain” terrains, using a standard Monte Carlo
method. Given a probability distribution on terrains, our
data structure solves the problem of determining the
probability that if a specified amount of rain falls on a
given region a query point is flooded. We implement our data
structures and show that they work very well in
practice.},
Doi = {10.1145/3139958.3139985},
Key = {fds332953}
}

@article{fds329189,
Author = {Edwards, A and Layton, AT},
Title = {Cell Volume Regulation in the Proximal Tubule of Rat Kidney
: Proximal Tubule Cell Volume Regulation.},
Journal = {Bulletin of Mathematical Biology},
Volume = {79},
Number = {11},
Pages = {2512-2533},
Year = {2017},
Month = {November},
url = {http://dx.doi.org/10.1007/s11538-017-0338-6},
Abstract = {We developed a dynamic model of a rat proximal convoluted
tubule cell in order to investigate cell volume regulation
mechanisms in this nephron segment. We examined whether
regulatory volume decrease (RVD), which follows exposure to
a hyposmotic peritubular solution, can be achieved solely
via stimulation of basolateral K[Formula: see text] and
[Formula: see text] channels and [Formula: see
text]-[Formula: see text] cotransporters. We also determined
whether regulatory volume increase (RVI), which follows
exposure to a hyperosmotic peritubular solution under
certain conditions, may be accomplished by activating
basolateral [Formula: see text]/H[Formula: see text]
exchangers. Model predictions were in good agreement with
experimental observations in mouse proximal tubule cells
assuming that a 10% increase in cell volume induces a
fourfold increase in the expression of basolateral
K[Formula: see text] and [Formula: see text] channels and
[Formula: see text]-[Formula: see text] cotransporters. Our
results also suggest that in response to a hyposmotic
challenge and subsequent cell swelling, [Formula: see
text]-[Formula: see text] cotransporters are more efficient
than basolateral K[Formula: see text] and [Formula: see
text] channels at lowering intracellular osmolality and
reducing cell volume. Moreover, both RVD and RVI are
predicted to stabilize net transcellular [Formula: see text]
reabsorption, that is, to limit the net [Formula: see text]
flux decrease during a hyposmotic challenge or the net
[Formula: see text] flux increase during a hyperosmotic
challenge.},
Doi = {10.1007/s11538-017-0338-6},
Key = {fds329189}
}

@article{fds330279,
Author = {Choi, K and Hou, TY and Kiselev, A and Luo, G and Sverak, V and Yao,
Y},
Title = {On the Finite-Time Blowup of a One-Dimensional Model for the
Three-Dimensional Axisymmetric Euler Equations},
Journal = {Communications on Pure & Applied Mathematics},
Volume = {70},
Number = {11},
Pages = {2218-2243},
Year = {2017},
Month = {November},
url = {http://dx.doi.org/10.1002/cpa.21697},
Doi = {10.1002/cpa.21697},
Key = {fds330279}
}

@article{fds329286,
Author = {Randles, A and Frakes, DH and Leopold, JA},
Title = {Computational Fluid Dynamics and Additive Manufacturing to
Diagnose and Treat Cardiovascular Disease.},
Journal = {Trends in Biotechnology},
Volume = {35},
Number = {11},
Pages = {1049-1061},
Year = {2017},
Month = {November},
url = {http://dx.doi.org/10.1016/j.tibtech.2017.08.008},
Abstract = {Noninvasive engineering models are now being used for
diagnosing and planning the treatment of cardiovascular
disease. Techniques in computational modeling and additive
manufacturing have matured concurrently, and results from
simulations can inform and enable the design and
optimization of therapeutic devices and treatment
strategies. The emerging synergy between large-scale
simulations and 3D printing is having a two-fold benefit:
first, 3D printing can be used to validate the complex
simulations, and second, the flow models can be used to
improve treatment planning for cardiovascular disease. In
this review, we summarize and discuss recent methods and
manufacturing and patient-specific computational modeling,
with an emphasis on new directions in these fields and
remaining open questions.},
Doi = {10.1016/j.tibtech.2017.08.008},
Key = {fds329286}
}

@article{fds330396,
Author = {Tralie, C},
Title = {Moebius Beats: The Twisted Spaces of Sliding Window Audio
Novelty Functions with Rhythmic Subdivisions},
Year = {2017},
Month = {November},
Abstract = {In this work, we show that the sliding window embeddings of
certain audio novelty functions (ANFs) representing songs
with rhythmic subdivisions concentrate on the boundary of
non-orientable surfaces such as the Moebius strip. This
insight provides a radically different topological approach
to classifying types of rhythm hierarchies. In particular,
we use tools from topological data analysis (TDA) to detect
subdivisions, and we use thresholds derived from TDA to
build graphs at different scales. The Laplacian eigenvectors
of these graphs contain information which can be used to
estimate tempos of the subdivisions. We show a proof of
concept example on an audio snippet from the MIREX tempo
training dataset, and we hope in future work to find a place
for this in other MIR pipelines.},
Key = {fds330396}
}

@article{fds330268,
Author = {Cao, Y and Feng, Y and Ryser, MD and Zhu, K and Herschlag, G and Cao, C and Marusak, K and Zauscher, S and You, L},
Title = {Programmable assembly of pressure sensors using
pattern-forming bacteria.},
Journal = {Nature Biotechnology},
Volume = {35},
Number = {11},
Pages = {1087-1093},
Year = {2017},
Month = {November},
url = {http://dx.doi.org/10.1038/nbt.3978},
Abstract = {Biological systems can generate microstructured materials
that combine organic and inorganic components and possess
diverse physical and chemical properties. However, these
natural processes in materials fabrication are not readily
programmable. Here, we use a synthetic-biology approach to
assemble patterned materials. We demonstrate programmable
fabrication of three-dimensional (3D) materials by printing
engineered self-patterning bacteria on permeable membranes
that serve as a structural scaffold. Application of gold
nanoparticles to the colonies creates hybrid
organic-inorganic dome structures. The dynamics of the dome
structures' response to pressure is determined by their
geometry (colony size, dome height, and pattern), which is
easily modified by varying the properties of the membrane
(e.g., pore size and hydrophobicity). We generate resettable
pressure sensors that process signals in response to varying
pressure intensity and duration.},
Doi = {10.1038/nbt.3978},
Key = {fds330268}
}

@article{fds320928,
Author = {Little, AV and Maggioni, M and Rosasco, L},
Title = {Multiscale geometric methods for data sets I: Multiscale
SVD, noise and curvature},
Journal = {Applied and Computational Harmonic Analysis},
Volume = {43},
Number = {3},
Pages = {504-567},
Year = {2017},
Month = {November},
url = {http://dx.doi.org/10.1016/j.acha.2015.09.009},
Doi = {10.1016/j.acha.2015.09.009},
Key = {fds320928}
}

@article{fds328917,
Author = {Carneiro, E and Madrid, J and Pierce, LB},
Title = {Endpoint Sobolev and BV continuity for maximal
operators},
Journal = {Journal of Functional Analysis},
Volume = {273},
Number = {10},
Pages = {3262-3294},
Year = {2017},
Month = {November},
url = {http://dx.doi.org/10.1016/j.jfa.2017.08.012},
Doi = {10.1016/j.jfa.2017.08.012},
Key = {fds328917}
}

@article{fds328811,
Author = {Heath-Brown, DR and Pierce, LB},
Title = {Averages and moments associated to class numbers of
Journal = {Compositio Mathematica},
Volume = {153},
Number = {11},
Pages = {2287-2309},
Year = {2017},
Month = {November},
url = {http://dx.doi.org/10.1112/S0010437X1700728X},
Doi = {10.1112/S0010437X1700728X},
Key = {fds328811}
}

@article{fds329014,
Author = {Reed, M and Best, J and Golubitsky, M and Stewart, I and Nijhout,
HF},
Title = {Analysis of Homeostatic Mechanisms in Biochemical
Networks.},
Journal = {Bulletin of Mathematical Biology},
Volume = {79},
Number = {11},
Pages = {2534-2557},
Year = {2017},
Month = {November},
url = {http://dx.doi.org/10.1007/s11538-017-0340-z},
Abstract = {Cell metabolism is an extremely complicated dynamical system
that maintains important cellular functions despite large
changes in inputs. This "homeostasis" does not mean that the
dynamical system is rigid and fixed. Typically, large
changes in external variables cause large changes in some
internal variables so that, through various regulatory
mechanisms, certain other internal variables (concentrations
or velocities) remain approximately constant over a finite
range of inputs. Outside that range, the mechanisms cease to
function and concentrations change rapidly with changes in
inputs. In this paper we analyze four different common
biochemical homeostatic mechanisms: feedforward excitation,
feedback inhibition, kinetic homeostasis, and parallel
inhibition. We show that all four mechanisms can occur in a
single biological network, using folate and methionine
metabolism as an example. Golubitsky and Stewart have
proposed a method to find homeostatic nodes in networks. We
show that their method works for two of these mechanisms but
not the other two. We discuss the many interesting
mathematical and biological questions that emerge from this
analysis, and we explain why understanding homeostatic
control is crucial for precision medicine.},
Doi = {10.1007/s11538-017-0340-z},
Key = {fds329014}
}

@article{fds332761,
Author = {Darnell, G and Georgiev, S and Mukherjee, S and Engelhardt,
BE},
Title = {Adaptive randomized dimension reduction on massive
data},
Journal = {Journal of machine learning research : JMLR},
Volume = {18},
Year = {2017},
Month = {November},
Abstract = {© 2017 Gregory Darnell, Stoyan Georgiev, Sayan Mukherjee,
Barbara E Engelhardt. The scalability of statistical
estimators is of increasing importance in modern
applications. One approach to implementing scalable
algorithms is to compress data into a low dimensional latent
space using dimension reduction methods. In this paper, we
develop an approach for dimension reduction that exploits
the assumption of low rank structure in high dimensional
data to gain both computational and statistical advantages.
We adapt recent randomized low-rank approximation algorithms
to provide an efficient solution to principal component
analysis (PCA), and we use this efficient solver to improve
estimation in large-scale linear mixed models (LMM) for
association mapping in statistical genomics. A key
observation in this paper is that randomization serves a
dual role, improving both computational and statistical
performance by implicitly regularizing the covariance matrix
estimate of the random effect in an LMM. These statistical
and computational advantages are highlighted in our
experiments on simulated data and large-scale genomic
studies.},
Key = {fds332761}
}

@article{fds330399,
Author = {Bruno, OP and Shipman, SP and Turc, C and Venakides,
S},
Title = {Three-dimensional quasi-periodic shifted Green function
throughout the spectrum, including Wood anomalies},
Journal = {Proceedings of the Royal Society of London: Mathematical,
Physical and Engineering Sciences},
Volume = {473},
Number = {2207},
Year = {2017},
Month = {November},
url = {http://dx.doi.org/10.1098/rspa.2017.0242},
rights reserved. This work, part II in a series, presents an
efficient method for evaluation of wave scattering by doubly
periodic diffraction gratings at or near what are commonly
called ‘Wood anomaly frequencies’. At these frequencies,
there is a grazing Rayleigh wave, and the quasi-periodic
Green function ceases to exist. We present a modification of
the Green function by adding two types of terms to its
lattice sum. The first type are transversely shifted Green
functions with coefficients that annihilate the growth in
the original lattice sum and yield algebraic convergence.
The second type are quasi-periodic plane wave solutions of
the Helmholtz equation which reinstate certain necessary
grazing modes without leading to blowup at Wood anomalies.
Using the new quasi-periodic Green function, we establish,
for the first time, that the Dirichlet problem of scattering
by a smooth doubly periodic scattering surface at a Wood
frequency is uniquely solvable. We also present an efficient
high-order numerical method based on this new Green function
for scattering by doubly periodic surfaces at and around
Wood frequencies. We believe this is the first solver able
to handle Wood frequencies for doubly periodic scattering
problems in three dimensions.We demonstrate the method by
applying it to acoustic scattering.},
Doi = {10.1098/rspa.2017.0242},
Key = {fds330399}
}

@article{fds330800,
Author = {Lu, J and Lu, Y and Wang, X and Li, X and Linderman, GC and Wu, C and Cheng,
X and Mu, L and Zhang, H and Liu, J and Su, M and Zhao, H and Spatz, ES and Spertus, JA and Masoudi, FA and Krumholz, HM and Jiang,
L},
Title = {Prevalence, awareness, treatment, and control of
hypertension in China: data from 1·7 million adults in a
population-based screening study (China PEACE Million
Persons Project)},
Journal = {The Lancet},
Year = {2017},
Month = {November},
url = {http://dx.doi.org/10.1016/S0140-6736(17)32478-9},
Doi = {10.1016/S0140-6736(17)32478-9},
Key = {fds330800}
}

@article{fds330137,
Author = {Arlotto, A and Gurvich, I},
Title = {Uniformly bounded regret in the multi-secretary
problem},
Year = {2017},
Month = {October},
Abstract = {In the secretary problem of Cayley (1875) and Moser (1956),
$n$ non-negative, independent, random variables with common
distribution are sequentially presented to a decision maker
who decides when to stop and collect the most recent
realization. The goal is to maximize the expected value of
the collected element. In the $k$-choice variant, the
decision maker is allowed to make $k \leq n$ selections to
maximize the expected total value of the selected elements.
Assuming that the values are drawn from a known distribution
with finite support, we prove that the best regret---the
expected gap between the optimal online policy and its
offline counterpart in which all $n$ values are made visible
at time $0$---is uniformly bounded in the the number of
candidates $n$ and the budget $k$. Our proof is
constructive: we develop an adaptive Budget-Ratio policy
that achieves this performance. The policy selects or skips
values depending on where the ratio of the residual budget
to the remaining time stands relative to multiple thresholds
that correspond to middle points of the distribution. We
also prove that being adaptive is crucial: in general, the
minimal regret among non-adaptive policies grows like the
square root of $n$. The difference is the value of
Key = {fds330137}
}

@article{fds331595,
Author = {Wang, YG and Maggioni, M and Chen, G},
Title = {Enhanced detection of chemical plumes in hyperspectral
images and movies throughimproved backgroundmodeling},
Journal = {Proceedings of Hyperspectral Image and Signal Processing:
Evolution in Remote Sensing},
Volume = {2015-June},
Year = {2017},
Month = {October},
ISBN = {9781467390156},
url = {http://dx.doi.org/10.1109/WHISPERS.2015.8075369},
Abstract = {© 2015 IEEE. We extend recent work that models the
background in hyperspectral images by a single distribution
(Gaussian or subspace) to use a mixture of such
distributions. This seems to better capture the complexity
of the background, which often consists of heterogeneous
regions (e.g., sky, mountain and ground). We derive mixture
versions of the previous estimators and apply them to
benchmark data sets for detecting chemical plumes of known
chemicals in hyperspectral images and movies. Our
experiments show that the mixture background models
consistently outperform their counterparts with a single
distribution.},
Doi = {10.1109/WHISPERS.2015.8075369},
Key = {fds331595}
}

@article{fds330010,
Author = {Gao, T and Yapuncich, GS and Daubechies, I and Mukherjee, S and Boyer,
DM},
Title = {Development and Assessment of Fully Automated and Globally
Transitive Geometric Morphometric Methods, With Application
to a Biological Comparative Dataset With High Interspecific
Variation.},
Journal = {The Anatomical Record : Advances in Integrative Anatomy and
Evolutionary Biology},
Year = {2017},
Month = {October},
url = {http://dx.doi.org/10.1002/ar.23700},
Abstract = {Automated geometric morphometric methods are promising tools
for shape analysis in comparative biology, improving
researchers' abilities to quantify variation extensively (by
permitting more specimens to be analyzed) and intensively
(by characterizing shapes with greater fidelity). Although
use of these methods has increased, published automated
methods have some notable limitations: pairwise
correspondences are frequently inaccurate and pairwise
mappings are not globally consistent (i.e., they lack
transitivity across the full sample). Here, we reassess the
accuracy of published automated methods-cPDist (Boyer et al.
Proc Nat Acad Sci 108 (2011) 18221-18226) and auto3Dgm
(Boyer et al.: Anat Rec 298 (2015a) 249-276)-and evaluate
several modifications to these methods. We show that a
substantial percentage of alignments and pairwise maps
between specimens of dissimilar geometries were inaccurate
in the study of Boyer et al. (Proc Nat Acad Sci 108 (2011)
18221-18226), despite a taxonomically partitioned variance
structure of continuous Procrustes distances. We show these
inaccuracies are remedied using a globally informed
methodology within a collection of shapes, rather than
relying on pairwise comparisons (c.f. Boyer et al.: Anat Rec
298 (2015a) 249-276). Unfortunately, while global
information generally enhances maps between dissimilar
objects, it can degrade the quality of correspondences
between similar objects due to the accumulation of numerical
error. We explore a number of approaches to mitigate this
degradation, quantify their performance, and compare the
generated pairwise maps (and the shape space characterized
by these maps) to a "ground truth" obtained from landmarks
manually collected by geometric morphometricians. Novel
methods both improve the quality of the pairwise
correspondences relative to cPDist and achieve a taxonomic
distinctiveness comparable to auto3Dgm. Anat Rec, 2017. ©
2017 Wiley Periodicals, Inc.},
Doi = {10.1002/ar.23700},
Key = {fds330010}
}

@article{fds332379,
Author = {Durante, D and Dunson, DB and Vogelstein, JT},
Title = {Rejoinder: Nonparametric Bayes Modeling of Populations of
Networks},
Journal = {Journal of the American Statistical Association},
Volume = {112},
Number = {520},
Pages = {1547-1552},
Year = {2017},
Month = {October},
url = {http://dx.doi.org/10.1080/01621459.2017.1395643},
Doi = {10.1080/01621459.2017.1395643},
Key = {fds332379}
}

@article{fds330206,
Author = {Tralie, CJ},
Title = {Early MFCC And HPCP Fusion for Robust Cover Song
Identification},
Journal = {18th International Society for Music Information Retrieval
(ISMIR)},
Year = {2017},
Month = {October},
Abstract = {While most schemes for automatic cover song identification
have focused on note-based features such as HPCP and chord
profiles, a few recent papers surprisingly showed that local
self-similarities of MFCC-based features also have
classification power for this task. Since MFCC and HPCP
capture complementary information, we design an unsupervised
algorithm that combines normalized, beat-synchronous blocks
of these features using cross-similarity fusion before
attempting to locally align a pair of songs. As an added
bonus, our scheme naturally incorporates structural
information in each song to fill in alignment gaps where
both feature sets fail. We show a striking jump in
performance over MFCC and HPCP alone, achieving a state of
the art mean reciprocal rank of 0.87 on the Covers80
dataset. We also introduce a new medium-sized hand designed
benchmark dataset called "Covers 1000," which consists of
395 cliques of cover songs for a total of 1000 songs, and we
show that our algorithm achieves an MRR of 0.9 on this
dataset for the first correctly identified song in a clique.
We provide the precomputed HPCP and MFCC features, as well
as beat intervals, for all songs in the Covers 1000 dataset
for use in further research.},
Key = {fds330206}
}

@article{fds329352,
Author = {Reddy, A and Zhang, J and Davis, NS and Moffitt, AB and Love, CL and Waldrop, A and Leppa, S and Pasanen, A and Meriranta, L and Karjalainen-Lindsberg, M-L and Nørgaard, P and Pedersen, M and Gang,
AO and Høgdall, E and Heavican, TB and Lone, W and Iqbal, J and Qin, Q and Li, G and Kim, SY and Healy, J and Richards, KL and Fedoriw, Y and Bernal-Mizrachi, L and Koff, JL and Staton, AD and Flowers, CR and Paltiel, O and Goldschmidt, N and Calaminici, M and Clear, A and Gribben, J and Nguyen, E and Czader, MB and Ondrejka, SL and Collie, A and Hsi, ED and Tse, E and Au-Yeung, RKH and Kwong, Y-L and Srivastava, G et
al.},
Title = {Genetic and Functional Drivers of Diffuse Large B Cell
Lymphoma.},
Journal = {Cell},
Volume = {171},
Number = {2},
Pages = {481-494.e15},
Year = {2017},
Month = {October},
url = {http://dx.doi.org/10.1016/j.cell.2017.09.027},
Abstract = {Diffuse large B cell lymphoma (DLBCL) is the most common
form of blood cancer and is characterized by a striking
degree of genetic and clinical heterogeneity. This
heterogeneity poses a major barrier to understanding the
genetic basis of the disease and its response to therapy.
Here, we performed an integrative analysis of whole-exome
sequencing and transcriptome sequencing in a cohort of 1,001
DLBCL patients to comprehensively define the landscape of
150 genetic drivers of the disease. We characterized the
functional impact of these genes using an unbiased CRISPR
screen of DLBCL cell lines to define oncogenes that promote
cell growth. A prognostic model comprising these genetic
alterations outperformed current established methods: cell
of origin, the International Prognostic Index comprising
clinical variables, and dual MYC and BCL2 expression. These
results comprehensively define the genetic drivers and their
functional roles in DLBCL to identify new therapeutic
opportunities in the disease.},
Doi = {10.1016/j.cell.2017.09.027},
Key = {fds329352}
}

@article{fds328894,
Author = {Li, L and Liu, J-G and Lu, J},
Title = {Fractional Stochastic Differential Equations Satisfying
Fluctuation-Dissipation Theorem},
Journal = {Journal of Statistical Physics},
Volume = {169},
Number = {2},
Pages = {316-339},
Year = {2017},
Month = {October},
url = {http://dx.doi.org/10.1007/s10955-017-1866-z},
this work a fractional stochastic differential equation
(FSDE) model consistent with the over-damped limit of the
generalized Langevin equation model. As a result of the
‘fluctuation-dissipation theorem’, the differential
equations driven by fractional Brownian noise to model
memory effects should be paired with Caputo derivatives, and
this FSDE model should be understood in an integral form. We
establish the existence of strong solutions for such
equations and discuss the ergodicity and convergence to
Gibbs measure. In the linear forcing regime, we show
rigorously the algebraic convergence to Gibbs measure when
the ‘fluctuation-dissipation theorem’ is satisfied, and
this verifies that satisfying ‘fluctuation-dissipation
theorem’ indeed leads to the correct physical behavior. We
further discuss possible approaches to analyze the
ergodicity and convergence to Gibbs measure in the nonlinear
forcing regime, while leave the rigorous analysis for future
works. The FSDE model proposed is suitable for systems in
contact with heat bath with power-law kernel and
subdiffusion behaviors.},
Doi = {10.1007/s10955-017-1866-z},
Key = {fds328894}
}

@article{fds329519,
Author = {Li, L and Liu, J-G and Lu, J},
Title = {Fractional Stochastic Differential Equations Satisfying
Fluctuation-Dissipation Theorem},
Journal = {Journal of Statistical Physics},
Volume = {169},
Number = {2},
Pages = {316-339},
Year = {2017},
Month = {October},
url = {http://dx.doi.org/10.1007/s10955-017-1866-z},
Doi = {10.1007/s10955-017-1866-z},
Key = {fds329519}
}

@article{fds330518,
Author = {Hughes, ME and Abruzzi, KC and Allada, R and Anafi, R and Arpat, AB and Asher, G and Baldi, P and de Bekker, C and Bell-Pedersen, D and Blau, J and Brown, S and Ceriani, MF and Chen, Z and Chiu, JC and Cox, J and Crowell,
AM and DeBruyne, JP and Dijk, D-J and DiTacchio, L and Doyle, FJ and Duffield, GE and Dunlap, JC and Eckel-Mahan, K and Esser, KA and FitzGerald, GA and Forger, DB and Francey, LJ and Fu, Y-H and Gachon, F and Gatfield, D and de Goede, P and Golden, SS and Green, C and Harer, J and Harmer, S and Haspel, J and Hastings, MH and Herzel, H and Herzog, ED and Hoffmann, C and Hong, C and Hughey, JJ et al.},
Title = {Guidelines for Genome-Scale Analysis of Biological
Rhythms.},
Journal = {Journal of Biological Rhythms},
Volume = {32},
Number = {5},
Pages = {380-393},
Year = {2017},
Month = {October},
url = {http://dx.doi.org/10.1177/0748730417728663},
Abstract = {Genome biology approaches have made enormous contributions
to our understanding of biological rhythms, particularly in
identifying outputs of the clock, including RNAs, proteins,
and metabolites, whose abundance oscillates throughout the
day. These methods hold significant promise for future
discovery, particularly when combined with computational
modeling. However, genome-scale experiments are costly and
laborious, yielding "big data" that are conceptually and
statistically difficult to analyze. There is no obvious
consensus regarding design or analysis. Here we discuss the
relevant technical considerations to generate reproducible,
statistically sound, and broadly useful genome-scale data.
Rather than suggest a set of rigid rules, we aim to codify
principles by which investigators, reviewers, and readers of
the primary literature can evaluate the suitability of
different experimental designs for measuring different
aspects of biological rhythms. We introduce CircaInSilico, a
web-based application for generating synthetic genome
biology data to benchmark statistical methods for studying
biological rhythms. Finally, we discuss several unmet
analytical needs, including applications to clinical
medicine, and suggest productive avenues to address
them.},
Doi = {10.1177/0748730417728663},
Key = {fds330518}
}

@article{fds329321,
Author = {Li, L and Liu, J-G and Lu, J},
Title = {Fractional Stochastic Differential Equations Satisfying
Fluctuation-Dissipation Theorem},
Journal = {Journal of Statistical Physics},
Volume = {169},
Number = {2},
Pages = {316-339},
Year = {2017},
Month = {October},
url = {http://dx.doi.org/10.1007/s10955-017-1866-z},
Doi = {10.1007/s10955-017-1866-z},
Key = {fds329321}
}

@article{fds329101,
Author = {Cho, C-Y and Motta, FC and Kelliher, CM and Deckard, A and Haase,
SB},
Title = {Reconciling conflicting models for global control of
cell-cycle transcription.},
Journal = {Cell Cycle},
Volume = {16},
Number = {20},
Pages = {1965-1978},
Year = {2017},
Month = {October},
url = {http://dx.doi.org/10.1080/15384101.2017.1367073},
Abstract = {Models for the control of global cell-cycle transcription
have advanced from a CDK-APC/C oscillator, a transcription
factor (TF) network, to coupled CDK-APC/C and TF networks.
Nonetheless, current models were challenged by a recent
study that concluded that the cell-cycle transcriptional
program is primarily controlled by a CDK-APC/C oscillator in
budding yeast. Here we report an analysis of the
transcriptome dynamics in cyclin mutant cells that were not
queried in the previous study. We find that B-cyclin
oscillation is not essential for control of phase-specific
transcription. Using a mathematical model, we demonstrate
that the function of network TFs can be retained in the face
of significant reductions in transcript levels. Finally, we
show that cells arrested at mitotic exit with
non-oscillating levels of B-cyclins continue to cycle
transcriptionally. Taken together, these findings support a
critical role of a TF network and a requirement for CDK
activities that need not be periodic.},
Doi = {10.1080/15384101.2017.1367073},
Key = {fds329101}
}

@article{fds328588,
Author = {Agarwal, PK and Har-Peled, S and Suri, S and Yıldız, H and Zhang,
W},
Title = {Convex Hulls Under Uncertainty},
Journal = {Algorithmica},
Volume = {79},
Number = {2},
Pages = {340-367},
Year = {2017},
Month = {October},
url = {http://dx.doi.org/10.1007/s00453-016-0195-y},
Doi = {10.1007/s00453-016-0195-y},
Key = {fds328588}
}

@article{fds329310,
Author = {Kiehart, DP and Crawford, JM and Aristotelous, A and Venakides, S and Edwards, GS},
Title = {Cell Sheet Morphogenesis: Dorsal Closure in Drosophila
melanogaster as a Model System.},
Journal = {Annual Review of Cell and Developmental Biology},
Volume = {33},
Pages = {169-202},
Year = {2017},
Month = {October},
url = {http://dx.doi.org/10.1146/annurev-cellbio-111315-125357},
Abstract = {Dorsal closure is a key process during Drosophila
morphogenesis that models cell sheet movements in chordates,
including neural tube closure, palate formation, and wound
healing. Closure occurs midway through embryogenesis and
entails circumferential elongation of lateral epidermal cell
sheets that close a dorsal hole filled with amnioserosa
cells. Signaling pathways regulate the function of cellular
structures and processes, including Actomyosin and
complexes, and endocytosis/vesicle trafficking. These
orchestrate complex shape changes and movements that entail
interactions between five distinct cell types. Genetic and
laser perturbation studies establish that closure is robust,
resilient, and the consequence of redundancy that
contributes to four distinct biophysical processes:
contraction of the amnioserosa, contraction of supracellular
Actomyosin cables, elongation (stretching?) of the lateral
epidermis, and zipping together of two converging cell
sheets. What triggers closure and what the emergent
properties are that give rise to its extraordinary
resilience and fidelity remain key, extant
questions.},
Doi = {10.1146/annurev-cellbio-111315-125357},
Key = {fds329310}
}

@article{fds330801,
Author = {Cheng, X and Mishne, G and Steinerberger, S},
Title = {The geometry of nodal sets and outlier detection},
Journal = {Journal of Number Theory},
Year = {2017},
Month = {October},
url = {http://dx.doi.org/10.1016/j.jnt.2017.09.021},
Doi = {10.1016/j.jnt.2017.09.021},
Key = {fds330801}
}

@article{fds328986,
Author = {Charbonneau, P and Li, YC and Pfister, HD and Yaida,
S},
Title = {Cycle-expansion method for the Lyapunov exponent,
susceptibility, and higher moments.},
Journal = {Physical review. E},
Volume = {96},
Number = {3-1},
Pages = {032129},
Year = {2017},
Month = {September},
url = {http://dx.doi.org/10.1103/physreve.96.032129},
Abstract = {Lyapunov exponents characterize the chaotic nature of
dynamical systems by quantifying the growth rate of
uncertainty associated with the imperfect measurement of
initial conditions. Finite-time estimates of the exponent,
however, experience fluctuations due to both the initial
condition and the stochastic nature of the dynamical path.
The scale of these fluctuations is governed by the Lyapunov
susceptibility, the finiteness of which typically provides a
sufficient condition for the law of large numbers to apply.
Here, we obtain a formally exact expression for this
susceptibility in terms of the Ruelle dynamical ζ function
for one-dimensional systems. We further show that, for
systems governed by sequences of random matrices, the cycle
expansion of the ζ function enables systematic computations
of the Lyapunov susceptibility and of its higher-moment
generalizations. The method is here applied to a class of
dynamical models that maps to static disordered spin chains
with interactions stretching over a varying distance and is
tested against Monte Carlo simulations.},
Doi = {10.1103/physreve.96.032129},
Key = {fds328986}
}

@article{fds328918,
Author = {Robles, C},
Title = {Characterization of Calabi–Yau variations of Hodge
structure over tube domains by characteristic
forms},
Journal = {Mathematische Annalen},
Pages = {1-25},
Year = {2017},
Month = {September},
url = {http://dx.doi.org/10.1007/s00208-017-1594-3},
Abstract = {© 2017 Springer-Verlag GmbH Deutschland Sheng and Zuo’s
characteristic forms are invariants of a variation of Hodge
structure. We show that they characterize Gross’s
canonical variations of Hodge structure of Calabi–Yau type
over (Hermitian symmetric) tube domains.},
Doi = {10.1007/s00208-017-1594-3},
Key = {fds328918}
}

@article{fds329937,
Author = {Zhang, L and Sun, L and Guan, Z and Lee, S and Li, Y and Deng, HD and Li, Y and Ahlborg, NL and Boloor, M and Melosh, NA and Chueh,
WC},
Title = {Quantifying and Elucidating Thermally Enhanced Minority
Carrier Diffusion Length Using Radius-Controlled Rutile
Nanowires},
Journal = {Nano Letters},
Volume = {17},
Number = {9},
Pages = {5264-5272},
Year = {2017},
Month = {September},
url = {http://dx.doi.org/10.1021/acs.nanolett.7b01504},
Doi = {10.1021/acs.nanolett.7b01504},
Key = {fds329937}
}

@article{fds329136,
Author = {Pisharady, PK and Sotiropoulos, SN and Sapiro, G and Lenglet,
C},
Title = {A Sparse Bayesian Learning Algorithm for White Matter
Parameter Estimation from Compressed Multi-shell Diffusion
MRI.},
Journal = {Medical image computing and computer-assisted intervention :
MICCAI ... International Conference on Medical Image
Computing and Computer-Assisted Intervention},
Volume = {10433},
Pages = {602-610},
Year = {2017},
Month = {September},
ISBN = {9783319661810},
url = {http://dx.doi.org/10.1007/978-3-319-66182-7_69},
Abstract = {We propose a sparse Bayesian learning algorithm for improved
estimation of white matter fiber parameters from compressed
(under-sampled q-space) multi-shell diffusion MRI data. The
multi-shell data is represented in a dictionary form using a
non-monoexponential decay model of diffusion, based on
continuous gamma distribution of diffusivities. The fiber
volume fractions with predefined orientations, which are the
unknown parameters, form the dictionary weights. These
unknown parameters are estimated with a linear un-mixing
framework, using a sparse Bayesian learning algorithm. A
localized learning of hyperparameters at each voxel and for
each possible fiber orientations improves the parameter
estimation. Our experiments using synthetic data from the
ISBI 2012 HARDI reconstruction challenge and in-vivo data
from the Human Connectome Project demonstrate the
improvements.},
Doi = {10.1007/978-3-319-66182-7_69},
Key = {fds329136}
}

@article{fds328807,
Author = {Herschlag, G and Ravier, R and Mattingly, JC},
Title = {Evaluating Partisan Gerrymandering in Wisconsin},
Year = {2017},
Month = {September},
Abstract = {We examine the extent of gerrymandering for the 2010 General
Assembly district map of Wisconsin. We find that there is
substantial variability in the election outcome depending on
what maps are used. We also found robust evidence that the
district maps are highly gerrymandered and that this
gerrymandering likely altered the partisan make up of the
Wisconsin General Assembly in some elections. Compared to
the distribution of possible redistricting plans for the
General Assembly, Wisconsin's chosen plan is an outlier in
that it yields results that are highly skewed to the
Republicans when the statewide proportion of Democratic
votes comprises more than 50-52% of the overall vote (with
the precise threshold depending on the election considered).
Wisconsin's plan acts to preserve the Republican majority by
providing extra Republican seats even when the Democratic
vote increases into the range when the balance of power
would shift for the vast majority of redistricting
plans.},
Key = {fds328807}
}

@article{fds328946,
Author = {Burt, T and Noveck, RJ and MacLeod, DB and Layton, AT and Rowland, M and Lappin, G},
Title = {Intra-Target Microdosing (ITM): A Novel Drug Development
Approach Aimed at Enabling Safer and Earlier Translation of
Biological Insights Into Human Testing.},
Journal = {Clinical and Translational Science},
Volume = {10},
Number = {5},
Pages = {337-350},
Year = {2017},
Month = {September},
url = {http://dx.doi.org/10.1111/cts.12464},
Doi = {10.1111/cts.12464},
Key = {fds328946}
}

@article{fds320879,
Author = {Sgouralis, I and Evans, RG and Layton, AT},
Title = {Renal medullary and urinary oxygen tension during
cardiopulmonary bypass in the rat.},
Journal = {Mathematical Medicine and Biology: A Journal of the
IMA},
Volume = {34},
Number = {3},
Pages = {313-333},
Year = {2017},
Month = {September},
url = {http://dx.doi.org/10.1093/imammb/dqw010},
Abstract = {Renal hypoxia could result from a mismatch in renal oxygen
supply and demand, particularly in the renal medulla.
Medullary hypoxic damage is believed to give rise to acute
kidney injury, which is a prevalent complication of cardiac
surgery performed on cardiopulmonary bypass (CPB). To
determine the mechanisms that could lead to medullary
hypoxia during CPB in the rat kidney, we developed a
mathematical model which incorporates (i) autoregulation of
renal blood flow and glomerular filtration rate, (ii)
detailed oxygen transport and utilization in the renal
medulla and (iii) oxygen transport along the ureter. Within
the outer medulla, the lowest interstitial tissue P$_{\rm O2}$, which is an indicator of renal hypoxia, is predicted
near the thick ascending limbs. Interstitial tissue P$_{\rm O2}$ exhibits a general decrease along the inner medullary
axis, but urine P$_{\rm O2}$ increases significantly along
the ureter. Thus, bladder urinary P$_{\rm O2}$ is predicted
to be substantially higher than medullary P$_{\rm O2}$. The
model is used to identify the phase of cardiac surgery
performed on CPB that is associated with the highest risk
for hypoxic kidney injury. Simulation results indicate that
the outer medulla's vulnerability to hypoxic injury depends,
in part, on the extent to which medullary blood flow is
autoregulated. With imperfect medullary blood flow
autoregulation, the model predicts that the rewarming phase
of CPB, in which medullary blood flow is low but medullary
oxygen consumption remains high, is the phase in which the
kidney is most likely to suffer hypoxic injury.},
Doi = {10.1093/imammb/dqw010},
Key = {fds320879}
}

@article{fds329109,
Author = {Li, C and Srivastava, S and Dunson, DB},
Title = {Simple, scalable and accurate posterior interval
estimation},
Journal = {Biometrika},
Volume = {104},
Number = {3},
Pages = {665-680},
Year = {2017},
Month = {September},
url = {http://dx.doi.org/10.1093/biomet/asx033},
Abstract = {© 2017 Biometrika Trust. Standard posterior sampling
algorithms, such as Markov chain Monte Carlo procedures,
face major challenges in scaling up to massive datasets. We
propose a simple and general posterior interval estimation
algorithm to rapidly and accurately estimate quantiles of
the posterior distributions for one-dimensional functionals.
Our algorithm runs Markov chain Monte Carlo in parallel for
subsets of the data, and then averages quantiles estimated
from each subset. We provide strong theoretical guarantees
and show that the credible intervals from our algorithm
asymptotically approximate those from the full posterior in
the leading parametric order. Our algorithm has a better
balance of accuracy and efficiency than its competitors
across a variety of simulations and a real-data
example.},
Doi = {10.1093/biomet/asx033},
Key = {fds329109}
}

@article{fds323700,
Author = {Lock, EF and Dunson, DB},
Title = {Bayesian genome- and epigenome-wide association studies with
gene level dependence.},
Journal = {Biometrics},
Volume = {73},
Number = {3},
Pages = {1018-1028},
Year = {2017},
Month = {September},
url = {http://dx.doi.org/10.1111/biom.12649},
Abstract = {High-throughput genetic and epigenetic data are often
screened for associations with an observed phenotype. For
example, one may wish to test hundreds of thousands of
genetic variants, or DNA methylation sites, for an
association with disease status. These genomic variables can
naturally be grouped by the gene they encode, among other
criteria. However, standard practice in such applications is
independent screening with a universal correction for
multiplicity. We propose a Bayesian approach in which the
prior probability of an association for a given genomic
variable depends on its gene, and the gene-specific
probabilities are modeled nonparametrically. This
hierarchical model allows for appropriate gene and
genome-wide multiplicity adjustments, and can be
incorporated into a variety of Bayesian association
screening methodologies with negligible increase in
computational complexity. We describe an application to
screening for differences in DNA methylation between lower
grade glioma and glioblastoma multiforme tumor samples from
The Cancer Genome Atlas. Software is available via the
package BayesianScreening for R: github.com/lockEF/BayesianScreening.},
Doi = {10.1111/biom.12649},
Key = {fds323700}
}

@article{fds329110,
Author = {Srivastava, S and Engelhardt, BE and Dunson, DB},
Title = {Expandable factor analysis.},
Journal = {Biometrika},
Volume = {104},
Number = {3},
Pages = {649-663},
Year = {2017},
Month = {September},
url = {http://dx.doi.org/10.1093/biomet/asx030},
Abstract = {Bayesian sparse factor models have proven useful for
characterizing dependence in multivariate data, but scaling
computation to large numbers of samples and dimensions is
problematic. We propose expandable factor analysis for
scalable inference in factor models when the number of
factors is unknown. The method relies on a continuous
shrinkage prior for efficient maximum a posteriori
structure of the prior leads to an estimation algorithm that
accommodates uncertainty in the number of factors. We
propose an information criterion to select the
hyperparameters of the prior. Expandable factor analysis has
better false discovery rates and true positive rates than
its competitors across diverse simulation settings. We apply
the proposed approach to a gene expression study of ageing
in mice, demonstrating superior results relative to four
competing methods.},
Doi = {10.1093/biomet/asx030},
Key = {fds329110}
}

@article{fds329481,
Author = {Sokolić, J and Giryes, R and Sapiro, G and Rodrigues,
MRD},
Title = {Generalization error of deep neural networks: Role of
classification margin and data structure},
Journal = {2017 12th International Conference on Sampling Theory and
Applications, SampTA 2017},
Pages = {147-151},
Year = {2017},
Month = {September},
ISBN = {9781538615652},
url = {http://dx.doi.org/10.1109/SAMPTA.2017.8024476},
Abstract = {© 2017 IEEE. Understanding the generalization properties of
deep learning models is critical for their successful usage
in many applications, especially in the regimes where the
number of training samples is limited. We study the
generalization properties of deep neural networks (DNNs) via
the Jacobian matrix of the network. Our analysis is general
to arbitrary network structures, types of non-linearities
and pooling operations. We show that bounding the spectral
norm of the Jacobian matrix in the network reduces the
generalization error. In addition, we tie this error to the
invariance in the data and the network. Experiments on the
MNIST and ImageNet datasets support these findings. This
short paper summarizes our generalization error theorems for
DNNs and for general invariant classifiers [1], [2]
.},
Doi = {10.1109/SAMPTA.2017.8024476},
Key = {fds329481}
}

@article{fds329344,
Author = {Yu, VW-Z and Corsetti, F and García, A and Huhn, WP and Jacquelin, M and Jia, W and Lange, B and Lin, L and Lu, J and Mi, W and Seifitokaldani, A and Vázquez-Mayagoitia, Á and Yang, C and Yang, H and Blum,
V},
Title = {ELSI: A unified software interface for Kohn–Sham
electronic structure solvers},
Journal = {Computer Physics Communications},
Year = {2017},
Month = {September},
url = {http://dx.doi.org/10.1016/j.cpc.2017.09.007},
Doi = {10.1016/j.cpc.2017.09.007},
Key = {fds329344}
}

@article{fds333283,
Author = {Li, Q and Lu, J and Sun, W},
Title = {A convergent method for linear half-space kinetic
equations},
Journal = {ESAIM. Mathematical modelling and numerical analysis =
ESAIM. Modelisation mathematique et analyse numerique :
M=2AN},
Volume = {51},
Number = {5},
Pages = {1583-1615},
Year = {2017},
Month = {September},
url = {http://dx.doi.org/10.1051/m2an/2016076},
Doi = {10.1051/m2an/2016076},
Key = {fds333283}
}

@article{fds329137,
Author = {Peco, C and Chen, W and Liu, Y and Bandi, MM and Dolbow, JE and Fried,
E},
Title = {Influence of surface tension in the surfactant-driven
fracture of closely-packed particulate monolayers.},
Journal = {Soft Matter},
Volume = {13},
Number = {35},
Pages = {5832-5841},
Year = {2017},
Month = {September},
url = {http://dx.doi.org/10.1039/c7sm01245d},
Abstract = {A phase-field model is used to capture the surfactant-driven
formation of fracture patterns in particulate monolayers.
The model is intended for the regime of closely-packed
systems in which the mechanical response of the monolayer
can be approximated as that of a linearly elastic solid. The
model approximates the loss in tensile strength of the
monolayer with increasing surfactant concentration through
the evolution of a damage field. Initial-boundary value
problems are constructed and spatially discretized with
finite element approximations to the displacement and
surfactant damage fields. A comparison between model-based
simulations and existing experimental observations indicates
a qualitative match in both the fracture patterns and
temporal scaling of the fracture process. The importance of
surface tension differences is quantified by means of a
dimensionless parameter, revealing thresholds that separate
different regimes of fracture. These findings are supported
by newly performed experiments that validate the model and
demonstrate the strong sensitivity of the fracture pattern
to differences in surface tension.},
Doi = {10.1039/c7sm01245d},
Key = {fds329137}
}

@article{fds329100,
Author = {Hoffman, C and Johnson, T and Junge, M},
Title = {Recurrence and transience for the frog model on
trees},
Journal = {Annals of Probability},
Volume = {45},
Number = {5},
Pages = {2826-2854},
Year = {2017},
Month = {September},
url = {http://dx.doi.org/10.1214/16-AOP1125},
Doi = {10.1214/16-AOP1125},
Key = {fds329100}
}

@article{fds329363,
Author = {Agarwal, PK and Rubin, N and Sharir, M},
Title = {Approximate nearest neighbor search amid higher-dimensional
flats},
Journal = {LIPIcs},
Volume = {87},
Year = {2017},
Month = {September},
ISBN = {9783959770491},
url = {http://dx.doi.org/10.4230/LIPIcs.ESA.2017.4},
Abstract = {© Pankaj K. Agarwal, Natan Rubin, and Micha Sharir. We
consider the approximate nearest neighbor (ANN) problem
where the input set consists of n k-flats in the Euclidean
Rd, for any fixed parameters 0 ≤ k < d, and where, for
each query point q, we want to return an input flat whose
distance from q is at most (1 + ϵ) times the shortest such
distance, where ϵ > 0 is another prespecified parameter. We
present an algorithm that achieves this task with
nk+1(log(n)/ ϵ)O(1) storage and preprocessing (where the
constant of proportionality in the big-O notation depends on
d), and can answer a query in O(polylog(n)) time (where the
power of the logarithm depends on d and k). In particular,
amid a set of n lines in any fixed-dimensional Euclidean
space. As a by-product, our approach also yields an
algorithm, with similar performance bounds, for answering
exact nearest neighbor queries amid k-flats with respect to
any polyhedral distance function. Our results are more
general, in that they also provide a tradeoff between
storage and query time.},
Doi = {10.4230/LIPIcs.ESA.2017.4},
Key = {fds329363}
}

@article{fds328895,
Author = {Lu, J and Steinerberger, S},
Title = {A variation on the Donsker-Varadhan inequality for the
principal eigenvalue.},
Journal = {Proceedings of the Royal Society of London: Mathematical,
Physical and Engineering Sciences},
Volume = {473},
Number = {2204},
Pages = {20160877},
Year = {2017},
Month = {August},
url = {http://dx.doi.org/10.1098/rspa.2016.0877},
Abstract = {The purpose of this short paper is to give a variation on
the classical Donsker-Varadhan inequality, which bounds the
first eigenvalue of a second-order elliptic operator on a
bounded domain Ω by the largest mean first exit time of the
associated drift-diffusion process via [Formula: see
text]Instead of looking at the mean of the first exit time,
we study quantiles: let [Formula: see text] be the smallest
time t such that the likelihood of exiting within that time
is p, then [Formula: see text]Moreover, as [Formula: see
text], this lower bound converges to λ1.},
Doi = {10.1098/rspa.2016.0877},
Key = {fds328895}
}

@article{fds329940,
Author = {Chao, Y-S and Wu, H-T and Scutari, M and Chen, T-S and Wu, C-J and Durand,
M and Boivin, A},
Title = {A network perspective on patient experiences and health
status: the Medical Expenditure Panel Survey 2004 to
2011.},
Journal = {BMC Health Services Research},
Volume = {17},
Number = {1},
Pages = {579},
Year = {2017},
Month = {August},
url = {http://dx.doi.org/10.1186/s12913-017-2496-5},
Abstract = {There is a growing emphasis on the need to engage patients
in order to improve the quality of health care and improve
health outcomes. However, we are still lacking a
comprehensive understanding on how different measures of
patient experiences interact with one another or relate to
health status. This study takes a network perspective to 1)
study the associations between patient characteristics and
patient experience in health care and 2) identify factors
that could be prioritized to improve health status.This
study uses data from the two-year panels from the Medical
Expenditure Panel Survey (MEPS) initiated between 2004 and
2011 in the United States. The 88 variables regarding
patient health and experience with health care were
identified through the MEPS documentation. Sex, age,
race/ethnicity, and years of education were also included
for analysis. The bnlearn package within R (v3.20) was used
to 1) identify the structure of the network of variables, 2)
assess the model fit of candidate algorithms, 3)
cross-validate the network, and 4) fit conditional
probabilities with the given structure.There were 51,023
MEPS interviewees aged 18 to 85 years (mean = 44, 95%
CI = 43.9 to 44.2), with years of education ranging from 1
to 19 (mean = 7.4, 95% CI = 7.40 to 7.46). Among all,
55% and 74% were female and white, respectively. There were
nine networks identified and 17 variables not linked to
others, including death in the second years, sex, entry
years to the MEPS, and relations of proxies. The health
status in the second years was directly linked to that in
the first years. The health care ratings were associated
with how often professionals listened to them and whether
professionals' explanation was understandable.It is
feasible to construct Bayesian networks with information on
patient characteristics and experiences in health care.
Network models help to identify significant predictors of
health care quality ratings. With temporal relationships
established, the structure of the variables can be
meaningful for health policy researchers, who search for one
or a few key priorities to initiate interventions or health
care quality improvement programs.},
Doi = {10.1186/s12913-017-2496-5},
Key = {fds329940}
}

@article{fds328812,
Author = {Lin, T-Y and Fang, Y-F and Huang, S-H and Wang, T-Y and Kuo, C-H and Wu,
H-T and Kuo, H-P and Lo, Y-L},
Title = {Capnography monitoring the hypoventilation during the
induction of bronchoscopic sedation: A randomized controlled
trial.},
Journal = {Scientific Reports},
Volume = {7},
Number = {1},
Pages = {8685},
Year = {2017},
Month = {August},
url = {http://dx.doi.org/10.1038/s41598-017-09082-8},
Abstract = {We hypothesize that capnography could detect hypoventilation
during induction of bronchoscopic sedation and starting
bronchoscopy following hypoventilation, may decrease
hypoxemia. Patients were randomized to: starting
bronchoscopy when hypoventilation (hypopnea, two successive
breaths of at least 50% reduction of the peak wave compared
to baseline or apnea, no wave for 10 seconds) (Study
group, n = 55), or when the Observer Assessment of
Alertness and Sedation scale (OAAS) was less than 4 (Control
group, n = 59). Propofol infusion was titrated to
maintain stable vital signs and sedative levels. The
hypoventilation during induction in the control group and
the sedative outcome were recorded. The patient
characteristics and procedures performed were similar.
Hypoventilation was observed in 74.6% of the patients before
achieving OAAS < 4 in the control group. Apnea occurred
more than hypopnea (p < 0.0001). Hypoventilation
preceded OAAS < 4 by 96.5 ± 88.1 seconds. In the
study group, the induction time was shorter (p = 0.03)
and subjects with any two events of hypoxemia during
sedation, maintenance or recovery were less than the control
group (1.8 vs. 18.6%, p < 0.01). Patient tolerance,
wakefulness during sedation, and cooperation were similar in
both groups. Significant hypoventilation occurred during the
induction and start bronchoscopy following hypoventilation
may decrease hypoxemia without compromising patient
tolerance.},
Doi = {10.1038/s41598-017-09082-8},
Key = {fds328812}
}

@article{fds328865,
Author = {Sokolic, J and Giryes, R and Sapiro, G and Rodrigues,
MRD},
Title = {Robust Large Margin Deep Neural Networks},
Journal = {IEEE Transactions on Signal Processing},
Volume = {65},
Number = {16},
Pages = {4265-4280},
Year = {2017},
Month = {August},
url = {http://dx.doi.org/10.1109/TSP.2017.2708039},
Doi = {10.1109/TSP.2017.2708039},
Key = {fds328865}
}

@article{fds330620,
Author = {Ustun, B and Rudin, C},
Title = {Optimized risk scores},
Journal = {Proceedings of the ACM SIGKDD International Conference on
Knowledge Discovery and Data Mining},
Volume = {Part F129685},
Pages = {1125-1134},
Year = {2017},
Month = {August},
ISBN = {9781450348874},
url = {http://dx.doi.org/10.1145/3097983.3098161},
are simple classification models that let users quickly
assess risk by adding, subtracting, and multiplying a few
small numbers. Such models are widely used in healthcare and
criminal justice, but are often built ad hoc. In this paper,
we present a principled approach to learn risk scores that
are fully optimized for feature selection, integer
coefficients, and operational constraints. We formulate the
risk score problem as a mixed integer nonlinear program, and
present a new cutting plane algorithm to efficiently recover
its optimal solution. Our approach can fit optimized risk
scores in a way that scales linearly with the sample size of
a dataset, provides a proof of optimality, and obeys complex
constraints without parameter tuning. We illustrate these
benefits through an extensive set of numerical experiments,
and an application where we build a customized risk score
for ICU seizure prediction.},
Doi = {10.1145/3097983.3098161},
Key = {fds330620}
}

@article{fds330621,
Author = {Angelino, E and Larus-Stone, N and Alabi, D and Seltzer, M and Rudin,
C},
Title = {Learning certifiably optimal rule lists},
Journal = {Proceedings of the ACM SIGKDD International Conference on
Knowledge Discovery and Data Mining},
Volume = {Part F129685},
Pages = {35-44},
Year = {2017},
Month = {August},
ISBN = {9781450348874},
url = {http://dx.doi.org/10.1145/3097983.3098047},
the design and implementation of a custom discrete
optimization technique for building rule lists over a
categorical feature space. Our algorithm provides the
optimal solution, with a certificate of optimality. By
leveraging algorithmic bounds, efficient data structures,
and computational reuse, we achieve several orders of
magnitude speedup in time and a massive reduction of memory
consumption. We demonstrate that our approach produces
optimal rule lists on practical problems in seconds. This
framework is a novel alternative to CART and other decision
tree methods.},
Doi = {10.1145/3097983.3098047},
Key = {fds330621}
}

@article{fds329933,
Author = {Tomasetti, C and Durrett, R and Kimmel, M and Lambert, A and Parmigiani,
G and Zauber, A and Vogelstein, B},
Title = {Role of stem-cell divisions in cancer risk},
Journal = {Nature},
Volume = {548},
Number = {7666},
Pages = {E13-E14},
Year = {2017},
Month = {August},
url = {http://dx.doi.org/10.1038/nature23302},
Doi = {10.1038/nature23302},
Key = {fds329933}
}

@article{fds328036,
Author = {Chen, Y and Sullivan, JC and Edwards, A and Layton,
AT},
Title = {Sex-specific computational models of the spontaneously
hypertensive rat kidneys: factors affecting nitric oxide
bioavailability.},
Journal = {American Journal of Physiology: Renal Physiology},
Volume = {313},
Number = {2},
Pages = {F174-F183},
Year = {2017},
Month = {August},
url = {http://dx.doi.org/10.1152/ajprenal.00482.2016},
Abstract = {The goals of this study were to 1) develop a computational
model of solute transport and oxygenation in the kidney of
the female spontaneously hypertensive rat (SHR), and 2)
apply that model to investigate sex differences in nitric
oxide (NO) levels in SHR and their effects on medullary
oxygenation and oxidative stress. To accomplish these goals,
we first measured NO synthase (NOS) 1 and NOS3 protein
expression levels in total renal microvessels of male and
female SHR. We found that the expression of both NOS1 and
NOS3 is higher in the renal vasculature of females compared
with males. To predict the implications of that finding on
medullary oxygenation and oxidative stress levels, we
developed a detailed computational model of the female SHR
kidney. The model was based on a published male kidney model
and represents solute transport and the biochemical
reactions among O2, NO, and superoxide ([Formula: see text])
in the renal medulla. Model simulations conducted using both
male and female SHR kidney models predicted significant
and NO and [Formula: see text] concentration in the outer
medulla and upper inner medulla. The models also predicted
that increases in endothelial NO-generating capacity, even
when limited to specific vascular segments, may
substantially raise medullary NO and Po2 levels. Other
potential sex differences in SHR, including [Formula: see
text] production rate, are predicted to significantly impact
oxidative stress levels, but effects on NO concentration and
Po2 are limited.},
Doi = {10.1152/ajprenal.00482.2016},
Key = {fds328036}
}

@article{fds328608,
Author = {Layton, AT and Edwards, A and Vallon, V},
Title = {Adaptive changes in GFR, tubular morphology, and transport
in subtotal nephrectomized kidneys: modeling and
analysis.},
Journal = {American Journal of Physiology: Renal Physiology},
Volume = {313},
Number = {2},
Pages = {F199-F209},
Year = {2017},
Month = {August},
url = {http://dx.doi.org/10.1152/ajprenal.00018.2017},
Abstract = {Removal of renal mass stimulates anatomical and functional
adaptations in the surviving nephrons, including elevations
in single-nephron glomerular filtration rate (SNGFR) and
tubular hypertrophy. A goal of this study is to assess the
extent to which the concomitant increases in filtered load
and tubular transport capacity preserve homeostasis of water
and salt. To accomplish that goal, we developed
computational models to simulate solute transport and
metabolism along nephron populations in a uninephrectomized
(UNX) rat and a 5/6-nephrectomized (5/6-NX) rat. Model
simulations indicate that nephrectomy-induced SNGFR increase
and tubular hypertrophy go a long way to normalize
excretion, but alone are insufficient to fully maintain salt
balance. We then identified increases in the protein density
of Na+-K+-ATPase, Na+-K+-2Cl- cotransporter, Na+-Cl-
cotransporter, and epithelial Na+ channel, such that the UNX
and 5/6-NX models predict urine flow and urinary Na+ and K+
excretions that are similar to sham levels. The models
predict that, in the UNX and 5/6-NX kidneys, fractional
water and salt reabsorption is similar to sham along the
initial nephron segments (i.e., from the proximal tubule to
the distal convoluted tubule), with a need to further reduce
Na+ reabsorption and increase K+ secretion primarily along
the connecting tubules and collecting ducts to achieve
balance. Additionally, the models predict that, given the
substantially elevated filtered and thus transport load
among each of the surviving nephrons, oxygen consumption per
nephron segment in a UNX or 5/6-NX kidney increases
substantially. But due to the reduced nephron population,
whole animal renal oxygen consumption is lower. The
efficiency of tubular Na+ transport in the UNX and 5/6-NX
kidneys is predicted to be similar to sham.},
Doi = {10.1152/ajprenal.00018.2017},
Key = {fds328608}
}

@article{fds330512,
Author = {Cheng, C and Jiang, Y and Sun, Q},
Title = {Spatially distributed sampling and reconstruction},
Journal = {Applied and Computational Harmonic Analysis},
Year = {2017},
Month = {August},
url = {http://dx.doi.org/10.1016/j.acha.2017.07.007},
Doi = {10.1016/j.acha.2017.07.007},
Key = {fds330512}
}

@article{fds329353,
Author = {Guhaniyogi, R and Qamar, S and Dunson, DB},
Title = {Bayesian tensor regression},
Journal = {Journal of machine learning research : JMLR},
Volume = {18},
Pages = {1-31},
Year = {2017},
Month = {August},
Abstract = {©2017 Rajarshi Guhaniyogi and Shaan Qamar and David B.
Dunson. We propose a Bayesian approach to regression with a
scalar response on vector and tensor covariates.
Vectorization of the tensor prior to analysis fails to
exploit the structure, often leading to poor estimation and
predictive performance. We introduce a novel class of
multiway shrinkage priors for tensor coefficients in the
regression setting and present posterior consistency results
under mild conditions. A computationally efficient Markov
chain Monte Carlo algorithm is developed for posterior
computation. Simulation studies illustrate substantial gains
over existing tensor regression methods in terms of
estimation and parameter inference. Our approach is further
illustrated in a neuroimaging application.},
Key = {fds329353}
}

@article{fds328808,
Author = {Bakhtin, Y and Hurth, T and Lawley, SD and Mattingly,
JC},
Title = {Smooth invariant densities for random switching on the
torus},
Year = {2017},
Month = {August},
Abstract = {We consider a random dynamical system obtained by switching
between the flows generated by two smooth vector fields on
the 2d-torus, with the random switchings happening according
to a Poisson process. Assuming that the driving vector
fields are transversal to each other at all points of the
torus and that each of them allows for a smooth invariant
density and no periodic orbits, we prove that the switched
system also has a smooth invariant density, for every
switching rate. Our approach is based on an integration by
parts formula inspired by techniques from Malliavin
calculus.},
Key = {fds328808}
}

@article{fds329467,
Author = {Gerber, S and Maggioni, M},
Title = {Multiscale strategies for computing optimal
transport},
Journal = {Journal of machine learning research : JMLR},
Volume = {18},
Pages = {1-32},
Year = {2017},
Month = {August},
Abstract = {©2017 Samuel Gerber and Mauro Maggioni. This paper presents
a multiscale approach to efficiently compute approximate
optimal transport plans between point sets. It is
particularly well-suited for point sets that are in
high-dimensions, but are close to being intrinsically
low-dimensional. The approach is based on an adaptive
multiscale decomposition of the point sets. The multiscale
decomposition yields a sequence of optimal transport
problems, that are solved in a top-to-bottom fashion from
the coarsest to the finest scale. We provide numerical
evidence that this multiscale approach scales approximately
linearly, in time and memory, in the number of nodes,
Empirically, the multiscale approach results in less than
one percent relative error in the objective function.
Furthermore, the multiscale plans constructed are of
interest by themselves as they may be used to introduce
novel features and notions of distances between point sets.
An analysis of sets of brain MRI based on optimal transport
distances illustrates the effectiveness of the proposed
method on a real world data set. The application
demonstrates that multiscale optimal transport distances
have the potential to improve on state-of-the-art metrics
currently used in computational anatomy.},
Key = {fds329467}
}

@article{fds328996,
Author = {Agarwal, PK and Kumar, N and Sintos, S and Suri, S},
Title = {Efficient algorithms for k-regret minimizing
sets},
Journal = {LIPIcs},
Volume = {75},
Year = {2017},
Month = {August},
ISBN = {9783959770361},
url = {http://dx.doi.org/10.4230/LIPIcs.SEA.2017.7},
Abstract = {© Pankaj K. Agarwal, Nirman Kumar, Stavros Sintos, and
Subhash Suri. A regret minimizing set Q is a small size
representation of a much larger database P so that user
queries executed on Q return answers whose scores are not
much worse than those on the full dataset. In particular, a
k-regret minimizing set has the property that the regret
ratio between the score of the top-1 item in Q and the score
of the top-k item in P is minimized, where the score of an
item is the inner product of the item's attributes with a
user's weight (preference) vector. The problem is
challenging because we want to find a single representative
set Q whose regret ratio is small with respect to all
possible user weight vectors. We show that k-regret
minimization is NP-Complete for all dimensions d ≥ 3,
settling an open problem from Chester et al. [VLDB 2014].
Our main algorithmic contributions are two approximation
algorithms, both with provable guarantees, one based on
coresets and another based on hitting sets. We perform
extensive experimental evaluation of our algorithms, using
both real-world and synthetic data, and compare their
performance against the solution proposed in [VLDB 14] . The
results show that our algorithms are significantly faster
and scalable to much larger sets than the greedy algorithm
of Chester et al. for comparable quality
Doi = {10.4230/LIPIcs.SEA.2017.7},
Key = {fds328996}
}

@article{fds330703,
Author = {Nijhout, HF and Sadre-Marandi, F and Best, J and Reed,
MC},
Title = {Systems Biology of Phenotypic Robustness and
Plasticity.},
Journal = {Integrative and Comparative Biology (BioOne)},
Volume = {57},
Number = {2},
Pages = {171-184},
Year = {2017},
Month = {August},
url = {http://dx.doi.org/10.1093/icb/icx076},
Abstract = {Gene regulatory networks, cellular biochemistry, tissue
function, and whole body physiology are imbued with myriad
overlapping and interacting homeostatic mechanisms that
ensure that many phenotypes are robust to genetic and
environmental variation. Animals also often have plastic
responses to environmental variables, which means that many
different phenotypes can correspond to a single genotype.
Since natural selection acts on phenotypes, this raises the
question of how selection can act on the genome if genotypes
are decoupled from phenotypes by robustness and plasticity
mechanisms. The answer can be found in the systems biology
of the homeostatic mechanisms themselves. First, all such
mechanisms operate over a limited range and outside that
range the controlled variable changes rapidly allowing
natural selection to act. Second, mutations and
environmental stressors can disrupt homeostatic mechanisms,
exposing cryptic genetic variation and allowing natural
selection to act. We illustrate these ideas by examining the
systems biology of four specific examples. We show how it is
possible to analyze and visualize the roles of specific
genes and specific polymorphisms in robustness in the
context of large and realistic nonlinear systems. We also
describe a new method, system population models, that allows
one to connect causal dynamics to the variable outcomes that
one sees in biological populations with large
variation.},
Doi = {10.1093/icb/icx076},
Key = {fds330703}
}

@article{fds330932,
Author = {Huo, R and Durrett, R},
Title = {Latent voter model on locally tree-like random
graphs},
Journal = {Stochastic Processes and their Applications},
Year = {2017},
Month = {August},
url = {http://dx.doi.org/10.1016/j.spa.2017.08.004},
Doi = {10.1016/j.spa.2017.08.004},
Key = {fds330932}
}

@article{fds330622,
Author = {Wang, T and Rudin, C and Doshi-Velez, F and Liu, Y and Klampfl, E and MacNeille, P},
Title = {A Bayesian framework for learning rule sets for
interpretable classification},
Journal = {Journal of machine learning research : JMLR},
Volume = {18},
Pages = {1-37},
Year = {2017},
Month = {August},
Abstract = {©2017 Tong Wang, Cynthia Rudin, Finale Doshi-Velez, Yimin
Liu, Erica Klampfl, and Perry MacNeille. We present a
machine learning algorithm for building classifiers that are
comprised of a small number of short rules. These are
restricted disjunctive normal form models. An example of a
classifier of this form is as follows: If X satisfies
(condition A AND condition B) OR (condition C) OR · · · ,
then Y = 1. Models of this form have the advantage of being
interpretable to human experts since they produce a set of
rules that concisely describe a specific class. We present
two probabilistic models with prior parameters that the user
can set to encourage the model to have a desired size and
shape, to conform with a domain-specific definition of
interpretability. We provide a scalable MAP inference
approach and develop theoretical bounds to reduce
computation by iteratively pruning the search space. We
apply our method (Bayesian Rule Sets – BRS) to
characterize and predict user behavior with respect to
in-vehicle context-aware personalized recommender systems.
Our method has a major advantage over classical associative
classification methods and decision trees in that it does
not greedily grow the model.},
Key = {fds330622}
}

@article{fds329007,
Author = {Orizaga, S and Riahi, DN},
Title = {Triad resonant wave interactions in electrically charged
jets},
Journal = {Applied Mathematics and Mechanics},
Volume = {38},
Number = {8},
Pages = {1127-1148},
Year = {2017},
Month = {August},
url = {http://dx.doi.org/10.1007/s10483-017-2229-9},
Doi = {10.1007/s10483-017-2229-9},
Key = {fds329007}
}

@article{fds328809,
Author = {Johndrow, JE and Mattingly, JC},
Title = {Coupling and Decoupling to bound an approximating Markov
Chain},
Year = {2017},
Month = {July},
Abstract = {This simple note lays out a few observations which are well
known in many ways but may not have been said in quite this
way before. The basic idea is that when comparing two
different Markov chains it is useful to couple them is such
a way that they agree as often as possible. We construct
such a coupling and analyze it by a simple dominating chain
which registers if the two processes agree or disagree. We
find that this imagery is useful when thinking about such
problems. We are particularly interested in comparing the
invariant measures and long time averages of the processes.
However, since the paths agree for long runs, it also
provides estimates on various stopping times such as hitting
or exit times. We also show that certain bounds are tight.
Finally, we provide a simple application to a Markov Chain
Monte Carlo algorithm and show numerically that the results
of the paper show a good level of approximation at
considerable speed up by using an approximating chain rather
than the original sampling chain.},
Key = {fds328809}
}

@article{fds329934,
Author = {Aigerman, N and Kovalsky, SZ and Lipman, Y},
Title = {Spherical orbifold tutte embeddings},
Journal = {ACM Transactions on Graphics},
Volume = {36},
Number = {4},
Pages = {1-13},
Year = {2017},
Month = {July},
url = {http://dx.doi.org/10.1145/3072959.3073615},
Doi = {10.1145/3072959.3073615},
Key = {fds329934}
}

@article{fds329935,
Author = {Shtengel, A and Poranne, R and Sorkine-Hornung, O and Kovalsky, SZ and Lipman, Y},
Title = {Geometric optimization via composite majorization},
Journal = {ACM Transactions on Graphics},
Volume = {36},
Number = {4},
Pages = {1-11},
Year = {2017},
Month = {July},
url = {http://dx.doi.org/10.1145/3072959.3073618},
Doi = {10.1145/3072959.3073618},
Key = {fds329935}
}

@article{fds330204,
Author = {Pierce, LB},
Title = {The Vinogradov Mean Value Theorem [after Wooley, and
Bourgain, Demeter and Guth]},
Journal = {Asterisque},
Publisher = {Centre National de la Recherche Scientifique},
Year = {2017},
Month = {July},
Abstract = {This is the expository essay that accompanies my Bourbaki
Seminar on 17 June 2017 on the landmark proof of the
Vinogradov Mean Value Theorem, and the two approaches
developed in the work of Wooley and of Bourgain, Demeter and
Guth.},
Key = {fds330204}
}

@article{fds330522,
Author = {Pollack, A},
Title = {The spin -function on for Siegel modular
forms},
Journal = {Compositio Mathematica},
Volume = {153},
Number = {07},
Pages = {1391-1432},
Year = {2017},
Month = {July},
url = {http://dx.doi.org/10.1112/S0010437X17007114},
Doi = {10.1112/S0010437X17007114},
Key = {fds330522}
}

@article{fds326523,
Author = {Chen, Y and Fry, BC and Layton, AT},
Title = {Modeling glucose metabolism and lactate production in the
kidney.},
Journal = {Mathematical Biosciences},
Volume = {289},
Pages = {116-129},
Year = {2017},
Month = {July},
url = {http://dx.doi.org/10.1016/j.mbs.2017.04.008},
Abstract = {The metabolism of glucose provides most of the ATP required
for energy-dependent transport processes. In the inner
medulla of the mammalian kidney, limited blood flow and O2
supply yield low oxygen tension; therefore, a substantial
fraction of the glucose metabolism in that region is
anaerobic. Lactate is considered to be a waste product of
anaerobic glycolysis, which yields two lactate molecules for
each glucose molecule consumed, thereby likely leading to
the production and accumulation of a significant amount of
lactate in the inner medulla. To gain insights into the
transport and metabolic processes in the kidney, we have
developed a detailed mathematical model of the renal medulla
of the rat kidney. The model represents the radial
organization of the renal tubules and vessels, which centers
around the vascular bundles in the outer medulla and around
clusters of collecting ducts in the inner medulla. Model
interstitial fluid oxygen tension and glucose and lactate
concentrations in the outer medulla and upper inner medulla.
In the deep inner medulla, interstitial fluid concentrations
become much more homogeneous, as the radial organization of
tubules and vessels is not distinguishable. Using this
model, we have identified parameters concerning glucose
transport and basal metabolism, as well as lactate
production via anaerobic glycolysis, that yield predicted
blood glucose and lactate concentrations consistent with
experimental measurements in the papillary tip. In addition,
simulations indicate that the radial organization of the rat
kidney may affect lactate buildup in the inner
medulla.},
Doi = {10.1016/j.mbs.2017.04.008},
Key = {fds326523}
}

@article{fds330280,
Author = {Kiselev, A and Yao, Y and Zlatoš, A},
Title = {Local Regularity for the Modified SQG Patch
Equation},
Journal = {Communications on Pure & Applied Mathematics},
Volume = {70},
Number = {7},
Pages = {1253-1315},
Year = {2017},
Month = {July},
url = {http://dx.doi.org/10.1002/cpa.21677},
Doi = {10.1002/cpa.21677},
Key = {fds330280}
}

@article{fds326604,
Author = {Kerr, M and Robles, C},
Title = {Variations of Hodge structure and orbits in flag
varieties},
Volume = {315},
Pages = {27-87},
Year = {2017},
Month = {July},
url = {http://dx.doi.org/10.1016/j.aim.2017.05.013},
Abstract = {© 2017 Elsevier Inc.Period domains, the classifying spaces
for (pure, polarized) Hodge structures, and more generally
Mumford–Tate domains, arise as open GR-orbits in flag
varieties G/P. We investigate Hodge-theoretic aspects of the
geometry and representation theory associated with these
flag varieties. In particular, we relate the
Griffiths–Yukawa coupling to the variety of lines on G/P
(under a minimal homogeneous embedding), construct a large
class of polarized GR-orbits in G/P, and compute the
associated Hodge-theoretic boundary components. An emphasis
is placed throughout on adjoint flag varieties and the
corresponding families of Hodge structures of levels two and
four.},
Doi = {10.1016/j.aim.2017.05.013},
Key = {fds326604}
}

@article{fds325968,
Author = {Lu, J and Yang, H},
Title = {A cubic scaling algorithm for excited states calculations in
particle–particle random phase approximation},
Journal = {Journal of Computational Physics},
Volume = {340},
Pages = {297-308},
Year = {2017},
Month = {July},
url = {http://dx.doi.org/10.1016/j.jcp.2017.03.055},
Doi = {10.1016/j.jcp.2017.03.055},
Key = {fds325968}
}

@article{fds326795,
Author = {Kudekar, S and Kumar, S and Mondelli, M and Pfister, HD and Sasoglu, E and Urbanke, RL},
Title = {Reed–Muller Codes Achieve Capacity on Erasure
Channels},
Journal = {IEEE Transactions on Information Theory},
Volume = {63},
Number = {7},
Pages = {4298-4316},
Year = {2017},
Month = {July},
url = {http://dx.doi.org/10.1109/TIT.2017.2673829},
Doi = {10.1109/TIT.2017.2673829},
Key = {fds326795}
}

@article{fds326794,
Author = {Hager, C and Pfister, HD and Graell i Amat and A and Brannstrom,
F},
Title = {Density Evolution for Deterministic Generalized Product
Codes on the Binary Erasure Channel at High
Rates},
Journal = {IEEE Transactions on Information Theory},
Year = {2017},
Month = {July},
url = {http://dx.doi.org/10.1109/TIT.2017.2689783},
Doi = {10.1109/TIT.2017.2689783},
Key = {fds326794}
}

@article{fds328814,
Author = {Georgiou, A and Bello-Rivas, J and Gear, C and Wu, H-T and Chiavazzo, E and Kevrekidis, I},
Title = {An Exploration Algorithm for Stochastic Simulators Driven by
Journal = {Entropy (Basel, Switzerland)},
Volume = {19},
Number = {7},
Pages = {294-294},
Year = {2017},
Month = {July},
url = {http://dx.doi.org/10.3390/e19070294},
Doi = {10.3390/e19070294},
Key = {fds328814}
}

@article{fds325888,
Author = {Lu, J and Yang, H},
Title = {A cubic scaling algorithm for excited states calculations in
particle–particle random phase approximation},
Journal = {Journal of Computational Physics},
Volume = {340},
Pages = {297-308},
Year = {2017},
Month = {July},
url = {http://dx.doi.org/10.1016/j.jcp.2017.03.055},
Doi = {10.1016/j.jcp.2017.03.055},
Key = {fds325888}
}

@article{fds329520,
Author = {Liu, J-G and Ma, Z and Zhou, Z},
Title = {Explicit and Implicit TVD Schemes for Conservation Laws with
Caputo Derivatives},
Journal = {Journal of Scientific Computing},
Volume = {72},
Number = {1},
Pages = {291-313},
Year = {2017},
Month = {July},
url = {http://dx.doi.org/10.1007/s10915-017-0356-4},
Doi = {10.1007/s10915-017-0356-4},
Key = {fds329520}
}

@article{fds329521,
Author = {Gao, Y and Ji, H and Liu, J-G and Witelski, TP},
Title = {Global existence of solutions to a tear film model with
locally elevated evaporation rates},
Journal = {Physica D: Nonlinear Phenomena},
Volume = {350},
Pages = {13-25},
Year = {2017},
Month = {July},
url = {http://dx.doi.org/10.1016/j.physd.2017.03.005},
Doi = {10.1016/j.physd.2017.03.005},
Key = {fds329521}
}

@article{fds329102,
Author = {Burris, CS and Motta, FC and Shipman, PD},
Title = {An Unoriented Variation on de Bruijn Sequences},
Journal = {Graphs and Combinatorics},
Volume = {33},
Number = {4},
Pages = {845-858},
Year = {2017},
Month = {July},
url = {http://dx.doi.org/10.1007/s00373-017-1793-4},
Doi = {10.1007/s00373-017-1793-4},
Key = {fds329102}
}

@article{fds325294,
Author = {Gao, Y and Ji, H and Liu, J-G and Witelski, TP},
Title = {Global existence of solutions to a tear film model with
locally elevated evaporation rates},
Journal = {Physica D: Nonlinear Phenomena},
Volume = {350},
Pages = {13-25},
Year = {2017},
Month = {July},
url = {http://dx.doi.org/10.1016/j.physd.2017.03.005},
Doi = {10.1016/j.physd.2017.03.005},
Key = {fds325294}
}

@article{fds323230,
Author = {Liu, J-G and Ma, Z and Zhou, Z},
Title = {Explicit and Implicit TVD Schemes for Conservation Laws with
Caputo Derivatives},
Journal = {Journal of Scientific Computing},
Volume = {72},
Number = {1},
Pages = {291-313},
Year = {2017},
Month = {July},
url = {http://dx.doi.org/10.1007/s10915-017-0356-4},
paper, we investigate numerical approximations of the scalar
conservation law with the Caputo derivative, which
introduces the memory effect. We construct the first order
and the second order explicit upwind schemes for such
equations, which are shown to be conditionally (Formula
presented.) contracting and TVD. However, the Caputo
derivative leads to the modified CFL-type stability
condition, (Formula presented.), where (Formula presented.)
is the fractional exponent in the derivative. When (Formula
presented.) is small, such strong constraint makes the
numerical implementation extremely impractical. We have then
proposed the implicit upwind scheme to overcome this issue,
which is proved to be unconditionally (Formula presented.)
contracting and TVD. Various numerical tests are presented
to validate the properties of the methods and provide more
numerical evidence in interpreting the memory effect in
conservation laws.},
Doi = {10.1007/s10915-017-0356-4},
Key = {fds323230}
}

@article{fds328810,
Author = {Glatt-Holtz, NE and Herzog, DP and Mattingly, JC},
Title = {Scaling and Saturation in Infinite-Dimensional Control
Problems with Applications to Stochastic Partial
Differential Equations},
Year = {2017},
Month = {June},
Abstract = {We establish the dual notions of scaling and saturation from
geometric control theory in an infinite-dimensional setting.
This generalization is applied to the low-mode control
problem in a number of concrete nonlinear partial
differential equations. We also develop applications
concerning associated classes of stochastic partial
differential equations (SPDEs). In particular, we study the
support properties of probability laws corresponding to
these SPDEs as well as provide applications concerning the
ergodic and mixing properties of invariant measures for
these stochastic systems.},
Key = {fds328810}
}

@article{fds328038,
Author = {Gounley, J and Vardhan, M and Randles, A},
Title = {A computational framework to assess the influence of changes
in vascular geometry on blood flow},
Journal = {PASC 2017 - Proceedings of the Platform for Advanced
Scientific Computing Conference},
Year = {2017},
Month = {June},
ISBN = {9781450350624},
url = {http://dx.doi.org/10.1145/3093172.3093227},
Abstract = {© 2017 Association for Computing Machinery. Many vascular
abnormalities, such as aneurysms or stenoses, develop
gradually over time. In the early stages of their
development, they require monitoring but do not pose
sufficient risk to the patient for a clinician to recommend
invasive treatment. With a better understanding of the
interplay between hemodynamic factors and changes in blood
vessel geometry, there is an opportunity to improve clinical
care by earlier identification of aneurysms or stenoses with
significant potential for further development. Computational
fluid dynamics has shown great promise for investigating
this interplay and identifying the associated underlying
mechanisms, by using patient-derived geometries and
modifying them to represent potential evolution of the
vascular disease. However, a general, extensible framework
for comparing simulation results from different vascular
geometries in a direct, quantitative manner does not
currently exist. As a first step toward the development of
such a framework, we present a method for quantifying the
relationship between changes in vascular geometry and
hemodynamic factors, such as wall shear stress. We apply
this framework to study the correlation between wall shear
stress and geometric changes in two opposite settings: When
flow properties are associated with consequent changes in
the vascular geometry, as in a thoracic aortic aneurysm, and
when geometric changes alter the flow, as in a worsening
aortic stenosis.},
Doi = {10.1145/3093172.3093227},
Key = {fds328038}
}

@article{fds328813,
Author = {Malik, J and Reed, N and Wang, C-L and Wu, H-T},
Title = {Single-lead f-wave extraction using diffusion
geometry.},
Journal = {Physiological Measurement},
Volume = {38},
Number = {7},
Pages = {1310-1334},
Year = {2017},
Month = {June},
url = {http://dx.doi.org/10.1088/1361-6579/aa707c},
Abstract = {A novel single-lead f-wave extraction algorithm based on the
modern diffusion geometry data analysis framework is
proposed.The algorithm is essentially an averaged beat
subtraction algorithm, where the ventricular activity
template is estimated by combining a newly designed metric,
the 'diffusion distance', and the non-local Euclidean median
based on the non-linear manifold setup. We coined the
algorithm [Formula: see text].Two simulation schemes are
considered, and the new algorithm [Formula: see text]
outperforms traditional algorithms, including the average
beat subtraction, principal component analysis, and adaptive
singular value cancellation, in different evaluation metrics
with statistical significance.The clinical potential is
shown in the real Holter signal, and we introduce a new
score to evaluate the performance of the
algorithm.},
Doi = {10.1088/1361-6579/aa707c},
Key = {fds328813}
}

@article{fds332945,
Author = {Cnaan-On, I and Harms, A and Krolik, JL and Calderbank,
AR},
Title = {Run-length limited codes for backscatter
communication},
Journal = {IEEE International Conference on Acoustics Speech and Signal
Processing},
Pages = {6110-6114},
Year = {2017},
Month = {June},
ISBN = {9781509041176},
url = {http://dx.doi.org/10.1109/ICASSP.2017.7953330},
Abstract = {© 2017 IEEE. In backscatter communications, ultra-low power
devices signal by modulating the reflection of radio
frequency signals emitted from an external source. Unlike
conventional one-way communication, the backscatter channel
experiences unique self-interference and spread Doppler
clutter. Run-length limited (RLL) codes provide a method for
spectrum shaping that requires no hardware changes to the
communicating devices. The proposed coding framework is
suitable for any arbitrarily-shaped pulse train or
continuous wave reader waveform. It exploits the unique
between interference rejection and data rate. Analysis shows
that code rates of 1 and 4/5 are achievable when dealing
with low spread Doppler channels, which is an improvement
over the current rate 1/2 with current mainstream
backscatter communication techniques. Simulation results
with realistic channel assumptions are analyzed and
discussed to confirm the theoretical analysis.},
Doi = {10.1109/ICASSP.2017.7953330},
Key = {fds332945}
}

@article{fds327001,
Author = {Nanda, M and Durrett, R},
Title = {Spatial evolutionary games with weak selection},
Journal = {Proceedings of the National Academy of Sciences of
USA},
Volume = {114},
Number = {23},
Pages = {6046-6051},
Year = {2017},
Month = {June},
url = {http://dx.doi.org/10.1073/pnas.1620852114},
Doi = {10.1073/pnas.1620852114},
Key = {fds327001}
}

@article{fds325462,
Author = {Bryant, R and Huang, L and Mo, X},
Title = {On Finsler surfaces of constant flag curvature with a
Killing field},
Journal = {Journal of Geometry and Physics},
Volume = {116},
Pages = {345-357},
Year = {2017},
Month = {June},
url = {http://dx.doi.org/10.1016/j.geomphys.2017.02.012},
Doi = {10.1016/j.geomphys.2017.02.012},
Key = {fds325462}
}

@article{fds327152,
Author = {Kerr, M and Robles, C},
Title = {Classification of smooth horizontal Schubert
varieties},
Journal = {European Journal of Mathematics},
Volume = {3},
Number = {2},
Pages = {289-310},
Year = {2017},
Month = {June},
url = {http://dx.doi.org/10.1007/s40879-017-0140-x},
Doi = {10.1007/s40879-017-0140-x},
Key = {fds327152}
}

@article{fds326919,
Author = {Schaich Borg and J and Srivastava, S and Lin, L and Heffner, J and Dunson,
D and Dzirasa, K and de Lecea, L},
Title = {Rat intersubjective decisions are encoded by
frequency-specific oscillatory contexts.},
Journal = {Brain and Behavior},
Volume = {7},
Number = {6},
Pages = {e00710},
Year = {2017},
Month = {June},
url = {http://dx.doi.org/10.1002/brb3.710},
Abstract = {It is unknown how the brain coordinates decisions to
withstand personal costs in order to prevent other
individuals' distress. Here we test whether local field
potential (LFP) oscillations between brain regions create
"neural contexts" that select specific brain functions and
encode the outcomes of these types of intersubjective
decisions.Rats participated in an "Intersubjective Avoidance
Test" (IAT) that tested rats' willingness to enter an
innately aversive chamber to prevent another rat from
getting shocked. c-Fos immunoreactivity was used to screen
for brain regions involved in IAT performance. Multi-site
local field potential (LFP) recordings were collected
simultaneously and bilaterally from five brain regions
implicated in the c-Fos studies while rats made decisions in
the IAT. Local field potential recordings were analyzed
using an elastic net penalized regression framework.Rats
voluntarily entered an innately aversive chamber to prevent
another rat from getting shocked, and c-Fos immunoreactivity
in brain regions known to be involved in human
empathy-including the anterior cingulate, insula, orbital
frontal cortex, and amygdala-correlated with the magnitude
of "intersubjective avoidance" each rat displayed. Local
field potential recordings revealed that optimal accounts of
rats' performance in the task require specific frequencies
of LFP oscillations between brain regions in addition to
specific frequencies of LFP oscillations within brain
regions. Alpha and low gamma coherence between spatially
distributed brain regions predicts more intersubjective
avoidance, while theta and high gamma coherence between a
separate subset of brain regions predicts less
intersubjective avoidance. Phase relationship analyses
indicated that choice-relevant coherence in the alpha range
reflects information passed from the amygdala to cortical
structures, while coherence in the theta range reflects
information passed in the reverse direction.These results
indicate that the frequency-specific "neural context"
surrounding brain regions involved in social cognition
encodes outcomes of decisions that affect others, above and
beyond signals from any set of brain regions in
isolation.},
Doi = {10.1002/brb3.710},
Key = {fds326919}
}

@article{fds327028,
Author = {Zhu, B and Dunson, DB},
Title = {Bayesian Functional Data Modeling for Heterogeneous
Volatility},
Journal = {Bayesian Analysis},
Volume = {12},
Number = {2},
Pages = {335-350},
Year = {2017},
Month = {June},
url = {http://dx.doi.org/10.1214/16-BA1004},
Doi = {10.1214/16-BA1004},
Key = {fds327028}
}

@article{fds327029,
Author = {Wang, L and Durante, D and Jung, RE and Dunson, DB},
Title = {Bayesian network-response regression.},
Journal = {Bioinformatics},
Volume = {33},
Number = {12},
Pages = {1859-1866},
Year = {2017},
Month = {June},
url = {http://dx.doi.org/10.1093/bioinformatics/btx050},
Abstract = {There is increasing interest in learning how human brain
networks vary as a function of a continuous trait, but
flexible and efficient procedures to accomplish this goal
are limited. We develop a Bayesian semiparametric model,
which combines low-rank factorizations and flexible Gaussian
process priors to learn changes in the conditional
expectation of a network-valued random variable across the
values of a continuous predictor, while including
subject-specific random effects.The formulation leads to a
general framework for inference on changes in brain network
structures across human traits, facilitating borrowing of
information and coherently characterizing uncertainty. We
provide an efficient Gibbs sampler for posterior computation
along with simple procedures for inference, prediction and
goodness-of-fit assessments. The model is applied to learn
how human brain networks vary across individuals with
different intelligence scores. Results provide interesting
insights on the association between intelligence and brain
connectivity, while demonstrating good predictive
performance.Source code implemented in R and data are
available at https://github.com/wangronglu/BNRR.rl.wang@duke.edu.Supplementary
data are available at Bioinformatics online.},
Doi = {10.1093/bioinformatics/btx050},
Key = {fds327029}
}

@article{fds328815,
Author = {Sheu, Y-L and Hsu, L-Y and Chou, P-T and Wu, H-T},
Title = {Entropy-based time-varying window width selection for
nonlinear-type time–frequency analysis},
Journal = {International Journal of Data Science and
Analytics},
Volume = {3},
Number = {4},
Pages = {231-245},
Year = {2017},
Month = {June},
url = {http://dx.doi.org/10.1007/s41060-017-0053-2},
Doi = {10.1007/s41060-017-0053-2},
Key = {fds328815}
}

@article{fds326080,
Author = {Gao, Y and Liu, J-G and Lu, J},
Title = {Continuum Limit of a Mesoscopic Model with Elasticity of
Step Motion on Vicinal Surfaces},
Journal = {Journal of Nonlinear Science},
Volume = {27},
Number = {3},
Pages = {873-926},
Year = {2017},
Month = {June},
url = {http://dx.doi.org/10.1007/s00332-016-9354-1},
Doi = {10.1007/s00332-016-9354-1},
Key = {fds326080}
}

@article{fds326484,
Author = {Li, C and Lu, J and Yang, W},
Title = {On extending Kohn-Sham density functionals to systems with
fractional number of electrons.},
Journal = {Journal of Chemical Physics},
Volume = {146},
Number = {21},
Pages = {214109},
Year = {2017},
Month = {June},
url = {http://dx.doi.org/10.1063/1.4982951},
Abstract = {We analyze four ways of formulating the Kohn-Sham (KS)
density functionals with a fractional number of electrons,
through extending the constrained search space from the
Kohn-Sham and the generalized Kohn-Sham (GKS)
non-interacting v-representable density domain for integer
systems to four different sets of densities for fractional
systems. In particular, these density sets are (I) ensemble
interacting N-representable densities, (II) ensemble
non-interacting N-representable densities, (III)
non-interacting densities by the Janak construction, and
(IV) non-interacting densities whose composing orbitals
satisfy the Aufbau occupation principle. By proving the
equivalence of the underlying first order reduced density
matrices associated with these densities, we show that sets
(I), (II), and (III) are equivalent, and all reduce to the
Janak construction. Moreover, for functionals with the
ensemble v-representable assumption at the minimizer, (III)
reduces to (IV) and thus justifies the previous use of the
Aufbau protocol within the (G)KS framework in the study of
the ground state of fractional electron systems, as defined
in the grand canonical ensemble at zero temperature. By
further analyzing the Aufbau solution for different density
functional approximations (DFAs) in the (G)KS scheme, we
rigorously prove that there can be one and only one
fractional occupation for the Hartree Fock functional, while
there can be multiple fractional occupations for general
DFAs in the presence of degeneracy. This has been confirmed
by numerical calculations using the local density
approximation as a representative of general DFAs. This work
thus clarifies important issues on density functional theory
calculations for fractional electron systems.},
Doi = {10.1063/1.4982951},
Key = {fds326484}
}

@article{fds329522,
Author = {Gao, Y and Liu, J-G and Lu, J},
Title = {Continuum Limit of a Mesoscopic Model with Elasticity of
Step Motion on Vicinal Surfaces},
Journal = {Journal of Nonlinear Science},
Volume = {27},
Number = {3},
Pages = {873-926},
Year = {2017},
Month = {June},
url = {http://dx.doi.org/10.1007/s00332-016-9354-1},
Doi = {10.1007/s00332-016-9354-1},
Key = {fds329522}
}

@article{fds329182,
Author = {Agarwal, PK and Fox, K and Panigrahi, D and Varadarajan, KR and Xiao,
A},
Title = {Faster algorithms for the geometric transportation
problem},
Journal = {LIPIcs},
Volume = {77},
Pages = {71-716},
Year = {2017},
Month = {June},
ISBN = {9783959770385},
url = {http://dx.doi.org/10.4230/LIPIcs.SoCG.2017.7},
Abstract = {© Pankaj K. Agarwal, Kyle Fox, Debmalya Panigrahi, Kasturi
R. Varadarajan, and Allen Xiao. Let R, B C R d for constant
d, be two point sets with |R| + |B| = n, and let λ: R∪B
→ ℕ such that Σ r∈R λ(r) = Σ b∈B λ (b) be demand
functions over R and B. Let d(·, ·) be a suitable distance
function such as the L p distance. The transportation
problem asks to find a map τ: R × B → ℕ such that Σ
b∈B τ(r, b) = λ(r), Σ r∈R τ(r, b) = λ(b), and σ
r∈Rb∈B τ(r, b)d(r, b) is minimized. We present three
new results for the transportation problem when d(·, ·) is
any L p metric: • For any constant ϵ > 0, an O(n 1+ϵ )
expected time randomized algorithm that returns a
transportation map with expected cost O(log 2 (1/ϵ)) times
the optimal cost. • For any ϵ > 0, a (1 +
ϵ)-approximation in O(n 3/2 ϵ -d polylog(U) polylog(n))
time, where U = max p∈Rcup;B λ (p). •An exact strongly
polynomial O(n 2 polylogn) time algorithm, for d =
2.},
Doi = {10.4230/LIPIcs.SoCG.2017.7},
Key = {fds329182}
}

@article{fds320389,
Author = {Heath-Brown, DR and Pierce, LB and Heath-Brown, DR and Pierce,
LB},
Title = {Simultaneous integer values of pairs of quadratic
formsSimultaneous integer values of pairs of quadratic
forms},
Journal = {Journal für die Reine und Angewandte Mathematik (Crelle's
Journal)},
Volume = {2017},
Number = {727},
Pages = {85-143},
Year = {2017},
Month = {June},
url = {http://dx.doi.org/10.1515/crelle-2014-0112},
Abstract = {We prove that a pair of integral quadratic forms in five or
more variables will simultaneously represent "almost all"
pairs of integers that satisfy the necessary local
conditions, provided that the forms satisfy a suitable
nonsingularity condition. In particular such forms
simultaneously attain prime values if the obvious local
conditions hold. The proof uses the circle method, and in
particular pioneers a two-dimensional version of a
Kloosterman refinement.},
Doi = {10.1515/crelle-2014-0112},
Key = {fds320389}
}

@article{fds326748,
Author = {Wang, L and Chen, M and Rodrigues, M and Wilcox, D and Calderbank, R and Carin, L},
Title = {Information-Theoretic Compressive Measurement
Design.},
Journal = {IEEE Transactions on Pattern Analysis and Machine
Intelligence},
Volume = {39},
Number = {6},
Pages = {1150-1164},
Year = {2017},
Month = {June},
url = {http://dx.doi.org/10.1109/tpami.2016.2568189},
Abstract = {An information-theoretic projection design framework is
proposed, of interest for feature design and compressive
measurements. Both Gaussian and Poisson measurement models
are considered. The gradient of a proposed
information-theoretic metric (ITM) is derived, and a
gradient-descent algorithm is applied in design; connections
are made to the information bottleneck. The fundamental
solution structure of such design is revealed in the case of
a Gaussian measurement model and arbitrary input statistics.
This new theoretical result reveals how ITM parameter
settings impact the number of needed projection
measurements, with this verified experimentally. The ITM
achieves promising results on real data, for both signal
recovery and classification.},
Doi = {10.1109/tpami.2016.2568189},
Key = {fds326748}
}

@article{fds323833,
Author = {Bessonov, M and Durrett, R},
Title = {Phase transitions for a planar quadratic contact
process},
Journal = {Advances in Applied Mathematics},
Volume = {87},
Pages = {82-107},
Year = {2017},
Month = {June},
url = {http://dx.doi.org/10.1016/j.aam.2017.01.002},
Doi = {10.1016/j.aam.2017.01.002},
Key = {fds323833}
}

@article{fds330623,
Author = {Letham, B and Letham, PA and Rudin, C and Browne,
EP},
Title = {Erratum: "Prediction uncertainty and optimal experimental
design for learning dynamical systems" [Chaos 26, 063110
(2016)].},
Journal = {Chaos},
Volume = {27},
Number = {6},
Pages = {069901},
Year = {2017},
Month = {June},
url = {http://dx.doi.org/10.1063/1.4986799},
Doi = {10.1063/1.4986799},
Key = {fds330623}
}

@article{fds330624,
Author = {Zeng, J and Ustun, B and Rudin, C},
Title = {Interpretable classification models for recidivism
prediction},
Journal = {Journal of the Royal Statistical Society: Series A
(Statistics in Society)},
Volume = {180},
Number = {3},
Pages = {689-722},
Year = {2017},
Month = {June},
Key = {fds330624}
}

@article{fds326881,
Author = {Hadani, R and Rakib, S and Tsatsanis, M and Monk, A and Goldsmith, AJ and Molisch, AF and Calderbank, R},
Title = {Orthogonal time frequency space modulation},
Journal = {IEEE Wireless Communications and Networking
Conference},
Year = {2017},
Month = {May},
ISBN = {9781509041831},
url = {http://dx.doi.org/10.1109/WCNC.2017.7925924},
Abstract = {© 2017 IEEE. A new two-dimensional modulation technique
called Orthogonal Time Frequency Space (OTFS) modulation
designed in the delay-Doppler domain is introduced. Through
this design, which exploits full diversity over time and
frequency, OTFS coupled with equalization converts the
fading, time-varying wireless channel experienced by
modulated signals such as OFDM into a time-independent
channel with a complex channel gain that is roughly constant
for all symbols. Thus, transmitter adaptation is not needed.
This extraction of the full channel diversity allows OTFS to
greatly simplify system operation and significantly improves
performance, particular in systems with high Doppler, short
packets, and large antenna arrays. Simulation results
indicate at least several dB of block error rate performance
improvement for OTFS over OFDM in all of these settings. In
addition these results show that even at very high Dopplers
(500 km/h), OTFS approaches channel capacity through linear
scaling of throughput with the MIMO order, whereas the
performance of OFDM under typical design parameters breaks
down completely.},
Doi = {10.1109/WCNC.2017.7925924},
Key = {fds326881}
}

@article{fds326715,
Author = {Dabagh, M and Jalali, P and Butler, PJ and Randles, A and Tarbell,
JM},
Title = {Mechanotransmission in endothelial cells subjected to
oscillatory and multi-directional shear flow.},
Journal = {Journal of the Royal Society Interface},
Volume = {14},
Number = {130},
Year = {2017},
Month = {May},
url = {http://dx.doi.org/10.1098/rsif.2017.0185},
Abstract = {Local haemodynamics are linked to the non-uniform
distribution of atherosclerosic lesions in arteries. Low and
oscillatory (reversing in the axial flow direction) wall
shear stress (WSS) induce inflammatory responses in
endothelial cells (ECs) mediating disease localization. The
objective of this study is to investigate computationally
how the flow direction (reflected in WSS variation on the EC
surface over time) influences the forces experienced by
structural components of ECs that are believed to play
important roles in mechanotransduction. A three-dimensional,
multi-scale, multi-component, viscoelastic model of focally
adhered ECs is developed, in which oscillatory WSS
(reversing or non-reversing) parallel to the principal flow
direction, or multi-directional oscillatory WSS with
reversing axial and transverse components are applied over
the EC surface. The computational model includes the
glycocalyx layer, actin cortical layer, nucleus,
cytoskeleton, focal adhesions (FAs), stress fibres and
atherogenic flow profiles (reversing unidirectional flow and
reversing multi-directional flow) on subcellular structures
relative to non-atherogenic flow (non-reversing flow).
Reversing flow lowers stresses and strains due to
viscoelastic effects, and multi-directional flow alters
stress on the ADJs perpendicular to the axial flow
direction. The simulations predict forces on integrins, ADJ
filaments and other substructures in the range that activate
mechanotransduction.},
Doi = {10.1098/rsif.2017.0185},
Key = {fds326715}
}

@article{fds329991,
Author = {Ovaskainen, O and Tikhonov, G and Norberg, A and Guillaume Blanchet,
F and Duan, L and Dunson, D and Roslin, T and Abrego,
N},
Title = {How to make more out of community data? A conceptual
framework and its implementation as models and
software.},
Journal = {Ecology Letters},
Volume = {20},
Number = {5},
Pages = {561-576},
Year = {2017},
Month = {May},
url = {http://dx.doi.org/10.1111/ele.12757},
Abstract = {Community ecology aims to understand what factors determine
the assembly and dynamics of species assemblages at
different spatiotemporal scales. To facilitate the
integration between conceptual and statistical approaches in
community ecology, we propose Hierarchical Modelling of
Species Communities (HMSC) as a general, flexible framework
for modern analysis of community data. While
non-manipulative data allow for only correlative and not
causal inference, this framework facilitates the formulation
of data-driven hypotheses regarding the processes that
structure communities. We model environmental filtering by
variation and covariation in the responses of individual
species to the characteristics of their environment, with
potential contingencies on species traits and phylogenetic
relationships. We capture biotic assembly rules by
species-to-species association matrices, which may be
estimated at multiple spatial or temporal scales. We
operationalise the HMSC framework as a hierarchical Bayesian
joint species distribution model, and implement it as R- and
Matlab-packages which enable computationally efficient
analyses of large data sets. Armed with this tool, community
ecologists can make sense of many types of data, including
spatially explicit data and time-series data. We illustrate
the use of this framework through a series of diverse
ecological examples.},
Doi = {10.1111/ele.12757},
Key = {fds329991}
}

@article{fds329990,
Author = {Ovaskainen, O and Tikhonov, G and Dunson, D and Grøtan, V and Engen, S and Sæther, B-E and Abrego, N},
Title = {How are species interactions structured in species-rich
communities? A new method for analysing time-series
data.},
Journal = {Proceedings of the Royal Society of London: Biological
Sciences},
Volume = {284},
Number = {1855},
Pages = {20170768-20170768},
Year = {2017},
Month = {May},
url = {http://dx.doi.org/10.1098/rspb.2017.0768},
Abstract = {Estimation of intra- and interspecific interactions from
time-series on species-rich communities is challenging due
to the high number of potentially interacting species pairs.
The previously proposed sparse interactions model overcomes
this challenge by assuming that most species pairs do not
interact. We propose an alternative model that does not
assume that any of the interactions are necessarily zero,
but summarizes the influences of individual species by a
small number of community-level drivers. The community-level
drivers are defined as linear combinations of species
abundances, and they may thus represent e.g. the total
abundance of all species or the relative proportions of
different functional groups. We show with simulated and real
data how our approach can be used to compare different
hypotheses on community structure. In an empirical example
using aquatic microorganisms, the community-level drivers
model clearly outperformed the sparse interactions model in
predicting independent validation data.},
Doi = {10.1098/rspb.2017.0768},
Key = {fds329990}
}

@article{fds327282,
Author = {Moffitt, AB and Ondrejka, SL and McKinney, M and Rempel, RE and Goodlad,
JR and Teh, CH and Leppa, S and Mannisto, S and Kovanen, PE and Tse, E and Au-Yeung, RKH and Kwong, Y-L and Srivastava, G and Iqbal, J and Yu, J and Naresh, K and Villa, D and Gascoyne, RD and Said, J and Czader, MB and Chadburn, A and Richards, KL and Rajagopalan, D and Davis, NS and Smith,
EC and Palus, BC and Tzeng, TJ and Healy, JA and Lugar, PL and Datta, J and Love, C and Levy, S and Dunson, DB and Zhuang, Y and Hsi, ED and Dave,
SS},
Title = {Enteropathy-associated T cell lymphoma subtypes are
characterized by loss of function of SETD2.},
Journal = {The Journal of Experimental Medicine},
Volume = {214},
Number = {5},
Pages = {1371-1386},
Year = {2017},
Month = {May},
url = {http://dx.doi.org/10.1084/jem.20160894},
Abstract = {Enteropathy-associated T cell lymphoma (EATL) is a lethal,
and the most common, neoplastic complication of celiac
disease. Here, we defined the genetic landscape of EATL
through whole-exome sequencing of 69 EATL tumors. SETD2 was
the most frequently silenced gene in EATL (32% of cases).
The JAK-STAT pathway was the most frequently mutated
pathway, with frequent mutations in STAT5B as well as JAK1,
JAK3, STAT3, and SOCS1 We also identified mutations in KRAS,
TP53, and TERT Type I EATL and type II EATL (monomorphic
epitheliotropic intestinal T cell lymphoma) had highly
overlapping genetic alterations indicating shared mechanisms
underlying their pathogenesis. We modeled the effects of
SETD2 loss in vivo by developing a T cell-specific knockout
mouse. These mice manifested an expansion of γδ T cells,
indicating novel roles for SETD2 in T cell development and
lymphomagenesis. Our data render the most comprehensive
genetic portrait yet of this uncommon but lethal disease and
may inform future classification schemes.},
Doi = {10.1084/jem.20160894},
Key = {fds327282}
}

@article{fds324707,
Author = {Lu, J and Thicke, K},
Title = {Orbital minimization method with ℓ 1 regularization},
Journal = {Journal of Computational Physics},
Volume = {336},
Pages = {87-103},
Year = {2017},
Month = {May},
url = {http://dx.doi.org/10.1016/j.jcp.2017.02.005},
Doi = {10.1016/j.jcp.2017.02.005},
Key = {fds324707}
}

@article{fds325965,
Author = {Bongini, M and Fornasier, M and Hansen, M and Maggioni,
M},
Title = {Inferring interaction rules from observations of evolutive
systems I: The variational approach},
Journal = {Mathematical Models & Methods in Applied
Sciences},
Volume = {27},
Number = {05},
Pages = {909-951},
Year = {2017},
Month = {May},
url = {http://dx.doi.org/10.1142/S0218202517500208},
Doi = {10.1142/S0218202517500208},
Key = {fds325965}
}

@article{fds330625,
Author = {Ustun, B and Adler, LA and Rudin, C and Faraone, SV and Spencer, TJ and Berglund, P and Gruber, MJ and Kessler, RC},
Title = {The World Health Organization Adult Attention-Deficit/Hyperactivity
Disorder Self-Report Screening Scale for
DSM-5.},
Journal = {JAMA Psychiatry},
Volume = {74},
Number = {5},
Pages = {520-526},
Year = {2017},
Month = {May},
url = {http://dx.doi.org/10.1001/jamapsychiatry.2017.0298},
Abstract = {Recognition that adult attention-deficit/hyperactivity
disorder (ADHD) is common, seriously impairing, and usually
screening scales for use in community, workplace, and
primary care settings. However, these scales are all
calibrated to DSM-IV criteria, which are narrower than the
recently developed DSM-5 criteria.To update for DSM-5
criteria and improve the operating characteristics of the
Scale (ASRS) for screening.Probability subsamples of
participants in 2 general population surveys (2001-2003
household survey [n = 119] and 2004-2005 managed care
subscriber survey [n = 218]) who completed the full
29-question self-report ASRS, with both subsamples
over-sampling ASRS-screened positives, were blindly
administered a semistructured research diagnostic interview
Supersparse Linear Integer Model, a novel machine-learning
algorithm designed to create screening scales with optimal
integer weights and limited numbers of screening questions,
was applied to the pooled data to create a DSM-5 version of
the ASRS screening scale. The accuracy of the new scale was
then confirmed in an independent 2011-2012 clinical sample
of patients seeking evaluation at the New York University
2015-2016 primary care controls (n = 300). Data analysis
was conducted from April 4, 2016, to September 22, 2016.The
sensitivity, specificity, area under the curve (AUC), and
positive predictive value (PPV) of the revised ASRS.Of the
total 637 participants, 44 (37.0%) household survey
respondents, 51 (23.4%) managed care respondents, and 173
(57.7%) NYU Langone respondents met DSM-5 criteria for adult
ADHD in the semistructured diagnostic interview. Of the
male (45.9%); mean (SD) age was 33.1 (11.4) years. A
6-question screening scale was found to be optimal in
distinguishing cases from noncases in the first 2 samples.
Operating characteristics were excellent at the diagnostic
Clinical Diagnostic Scale population prevalence) data
(sensitivity, 91.4%; specificity, 96.0%; AUC, 0.94; PPV,
67.3%). Operating characteristics were similar despite a
much higher prevalence (57.7%) when the scale was applied to
the NYU Langone clinical sample (sensitivity, 91.9%;
specificity, 74.0%; AUC, 0.83; PPV, 82.8%).The new ADHD
screening scale is short, easily scored, detects the vast
majority of general population cases at a threshold that
also has high specificity and PPV, and could be used as a
screening tool in specialty treatment settings.},
Doi = {10.1001/jamapsychiatry.2017.0298},
Key = {fds330625}
}

@article{fds330397,
Author = {Tralie, CJ and Perea, JA},
Title = {(Quasi)Periodicity Quantification in Video Data, Using
Topology},
Year = {2017},
Month = {April},
Abstract = {This work introduces a novel framework for quantifying the
presence and strength of recurrent dynamics in video data.
Specifically, we provide continuous measures of periodicity
(perfect repetition) and quasiperiodicity (superposition of
periodic modes with non-commensurate periods), in a way
which does not require segmentation, training, object
tracking or 1-dimensional surrogate signals. Our methodology
operates directly on video data. The approach combines ideas
from nonlinear time series analysis (delay embeddings) and
computational topology (persistent homology), by translating
the problem of finding recurrent dynamics in video data,
into the problem of determining the circularity or
toroidality of an associated geometric space. Through
extensive testing, we show the robustness of our scores with
respect to several noise models/levels; we show that our
periodicity score is superior to other methods when compared
to human-generated periodicity rankings; and furthermore, we
show that our quasiperiodicity score clearly indicates the
presence of biphonation in videos of vibrating vocal
folds.},
Key = {fds330397}
}

@article{fds326146,
Author = {Simhal, AK and Aguerrebere, C and Collman, F and Vogelstein, JT and Micheva, KD and Weinberg, RJ and Smith, SJ and Sapiro,
G},
Title = {Probabilistic fluorescence-based synapse
detection.},
Journal = {PLoS computational biology},
Volume = {13},
Number = {4},
Pages = {e1005493},
Year = {2017},
Month = {April},
url = {http://dx.doi.org/10.1371/journal.pcbi.1005493},
Abstract = {Deeper exploration of the brain's vast synaptic networks
will require new tools for high-throughput structural and
molecular profiling of the diverse populations of synapses
that compose those networks. Fluorescence microscopy (FM)
and electron microscopy (EM) offer complementary advantages
and disadvantages for single-synapse analysis. FM combines
exquisite molecular discrimination capacities with high
speed and low cost, but rigorous discrimination between
synaptic and non-synaptic fluorescence signals is
challenging. In contrast, EM remains the gold standard for
reliable identification of a synapse, but offers only
limited molecular discrimination and is slow and costly. To
develop and test single-synapse image analysis methods, we
have used datasets from conjugate array tomography (cAT),
which provides voxel-conjugate FM and EM (annotated) images
of the same individual synapses. We report a novel
unsupervised probabilistic method for detection of synapses
from multiplex FM (muxFM) image data, and evaluate this
method both by comparison to EM gold standard annotated data
and by examining its capacity to reproduce known important
features of cortical synapse distributions. The proposed
probabilistic model-based synapse detector accepts
molecular-morphological synapse models as user queries, and
delivers a volumetric map of the probability that each voxel
represents part of a synapse. Taking human annotation of cAT
EM data as ground truth, we show that our algorithm detects
synapses from muxFM data alone as successfully as human
annotators seeing only the muxFM data, and accurately
reproduces known architectural features of cortical synapse
distributions. This approach opens the door to data-driven
discovery of new synapse types and their density. We suggest
that our probabilistic synapse detector will also be useful
for analysis of standard confocal and super-resolution FM
images, where EM cross-validation is not
practical.},
Doi = {10.1371/journal.pcbi.1005493},
Key = {fds326146}
}

@article{fds325778,
Author = {Layton, AT},
Title = {A new microscope for the kidney: mathematics.},
Journal = {American Journal of Physiology: Renal Physiology},
Volume = {312},
Number = {4},
Pages = {F671-F672},
Year = {2017},
Month = {April},
url = {http://dx.doi.org/10.1152/ajprenal.00648.2016},
Doi = {10.1152/ajprenal.00648.2016},
Key = {fds325778}
}

@article{fds330513,
Author = {Li, L and Cheng, C and Han, D and Sun, Q and Shi, G},
Title = {Phase Retrieval From Multiple-Window Short-Time Fourier
Measurements},
Journal = {IEEE Signal Processing Letters},
Volume = {24},
Number = {4},
Pages = {372-376},
Year = {2017},
Month = {April},
url = {http://dx.doi.org/10.1109/LSP.2017.2663668},
Doi = {10.1109/LSP.2017.2663668},
Key = {fds330513}
}

@article{fds331902,
Author = {D. Ma},
Title = {Period polynomial relations of binomial coefficients and
binomial realization of formal double zeta
space},
Journal = {International Journal of Number Theory},
Volume = {13},
Number = {03},
Pages = {761-774},
Year = {2017},
Month = {April},
url = {http://dx.doi.org/10.1142/S1793042117500403},
Keywords = {Period polynomial formal double zeta space binomial
coefficient},
Abstract = {In this paper, we give a realization of the formal double
zeta space by using binomial coefficients. Along with the
results in [Period polynomial relations between formal
double zeta values of odd weight, Math. Ann. 365 (2016)
345–362], this gives us two families of period polynomial
relations among binomial coefficients. We also give another
family of period polynomial relations among binomial
coefficients which cannot be obtained from our binomial
realization. At the end, some higher depth observation is
provided.},
Doi = {10.1142/S1793042117500403},
Key = {fds331902}
}

@article{fds329111,
Author = {Durante, D and Paganin, S and Scarpa, B and Dunson,
DB},
Title = {Bayesian modelling of networks in complex business
intelligence problems},
Journal = {Journal of the Royal Statistical Society: Series C (Applied
Statistics)},
Volume = {66},
Number = {3},
Pages = {555-580},
Year = {2017},
Month = {April},
Key = {fds329111}
}

@article{fds326037,
Author = {McKinney, M and Moffitt, AB and Gaulard, P and Travert, M and De Leval,
L and Nicolae, A and Raffeld, M and Jaffe, ES and Pittaluga, S and Xi, L and Heavican, T and Iqbal, J and Belhadj, K and Delfau-Larue, MH and Fataccioli, V and Czader, MB and Lossos, IS and Chapman-Fredricks,
JR and Richards, KL and Fedoriw, Y and Ondrejka, SL and Hsi, ED and Low, L and Weisenburger, D and Chan, WC and Mehta-Shah, N and Horwitz, S and Bernal-Mizrachi, L and Flowers, CR and Beaven, AW and Parihar, M and Baseggio, L and Parrens, M and Moreau, A and Sujobert, P and Pilichowska, M and Evens, AM and Chadburn, A et
al.},
Title = {The Genetic Basis of Hepatosplenic T-cell
Lymphoma.},
Journal = {Cancer Discovery},
Volume = {7},
Number = {4},
Pages = {369-379},
Year = {2017},
Month = {April},
url = {http://dx.doi.org/10.1158/2159-8290.cd-16-0330},
Abstract = {Hepatosplenic T-cell lymphoma (HSTL) is a rare and lethal
lymphoma; the genetic drivers of this disease are unknown.
Through whole-exome sequencing of 68 HSTLs, we define
recurrently mutated driver genes and copy-number alterations
in the disease. Chromatin-modifying genes, including SETD2,
INO80, and ARID1B, were commonly mutated in HSTL, affecting
62% of cases. HSTLs manifest frequent mutations in STAT5B
(31%), STAT3 (9%), and PIK3CD (9%), for which there
currently exist potential targeted therapies. In addition,
we noted less frequent events in EZH2, KRAS, and TP53SETD2
was the most frequently silenced gene in HSTL. We
experimentally demonstrated that SETD2 acts as a tumor
suppressor gene. In addition, we found that mutations in
STAT5B and PIK3CD activate critical signaling pathways
important to cell survival in HSTL. Our work thus defines
the genetic landscape of HSTL and implicates gene mutations
linked to HSTL pathogenesis and potential treatment
targets.Significance: We report the first systematic
application of whole-exome sequencing to define the genetic
basis of HSTL, a rare but lethal disease. Our work defines
SETD2 as a tumor suppressor gene in HSTL and implicates
genes including INO80 and PIK3CD in the disease. Cancer
Discov; 7(4); 369-79. ©2017 AACR.See related commentary by
the In This Issue feature, p. 339.},
Doi = {10.1158/2159-8290.cd-16-0330},
Key = {fds326037}
}

@article{fds329992,
Author = {Tikhonov, G and Abrego, N and Dunson, D and Ovaskainen,
O},
Title = {Using joint species distribution models for evaluating how
species-to-species associations depend on the environmental
context},
Journal = {Methods in Ecology and Evolution},
Volume = {8},
Number = {4},
Pages = {443-452},
Editor = {Warton, D},
Year = {2017},
Month = {April},
url = {http://dx.doi.org/10.1111/2041-210X.12723},
Doi = {10.1111/2041-210X.12723},
Key = {fds329992}
}

@article{fds323834,
Author = {Oliveira, G},
Title = {Gerbes on G2 manifolds},
Journal = {Journal of Geometry and Physics},
Volume = {114},
Pages = {570-580},
Year = {2017},
Month = {April},
url = {http://dx.doi.org/10.1016/j.geomphys.2017.01.007},
Doi = {10.1016/j.geomphys.2017.01.007},
Key = {fds323834}
}

@article{fds323853,
Author = {Campbell, K and Carpenter, KLH and Espinosa, S and Hashemi, J and Qiu,
Q and Tepper, M and Calderbank, R and Sapiro, G and Egger, HL and Baker,
JP and Dawson, G},
Title = {Use of a Digital Modified Checklist for Autism in Toddlers -
Revised with Follow-up to Improve Quality of Screening for
Autism.},
Journal = {The Journal of Pediatrics},
Volume = {183},
Pages = {133-139.e1},
Year = {2017},
Month = {April},
url = {http://dx.doi.org/10.1016/j.jpeds.2017.01.021},
Abstract = {To assess changes in quality of care for children at risk
for autism spectrum disorders (ASD) due to process
improvement and implementation of a digital screening
form.The process of screening for ASD was studied in an
academic primary care pediatrics clinic before and after
implementation of a digital version of the Modified
Checklist for Autism in Toddlers - Revised with Follow-up
with automated risk assessment. Quality metrics included
accuracy of documentation of screening results and
appropriate action for positive screens (secondary screening
or referral). Participating physicians completed pre- and
postintervention surveys to measure changes in attitudes
toward feasibility and value of screening for ASD. Evidence
of change was evaluated with statistical process control
charts and χ2 tests.Accurate documentation in the
electronic health record of screening results increased from
54% to 92% (38% increase, 95% CI 14%-64%) and appropriate
action for children screening positive increased from 25% to
85% (60% increase, 95% CI 35%-85%). A total of 90% of
participating physicians agreed that the transition to a
digital screening form improved their clinical assessment of
autism risk.Implementation of a tablet-based digital version
of the Modified Checklist for Autism in Toddlers - Revised
with Follow-up led to improved quality of care for children
at risk for ASD and increased acceptability of screening for
ASD. Continued efforts towards improving the process of
screening for ASD could facilitate rapid, early diagnosis of
ASD and advance the accuracy of studies of the impact of
screening.},
Doi = {10.1016/j.jpeds.2017.01.021},
Key = {fds323853}
}

@article{fds311605,
Author = {Li, Y and Yang, H and Ying, L},
Title = {Multidimensional butterfly factorization},
Journal = {Applied and Computational Harmonic Analysis},
Publisher = {Elsevier},
Year = {2017},
Month = {April},
ISSN = {1096-603X},
url = {http://hdl.handle.net/10161/11651 Duke open
access},
Doi = {10.1016/j.acha.2017.04.002},
Key = {fds311605}
}

@article{fds326081,
Author = {Lu, J and Zhou, Z},
Title = {Path integral molecular dynamics with surface hopping for
systems.},
Journal = {Journal of Chemical Physics},
Volume = {146},
Number = {15},
Pages = {154110},
Year = {2017},
Month = {April},
url = {http://dx.doi.org/10.1063/1.4981021},
Abstract = {In this work, a novel ring polymer representation for a
multi-level quantum system is proposed for thermal average
calculations. The proposed representation keeps the
discreteness of the electronic states: besides position and
momentum, each bead in the ring polymer is also
characterized by a surface index indicating the electronic
energy surface. A path integral molecular dynamics with
surface hopping (PIMD-SH) dynamics is also developed to
sample the equilibrium distribution of the ring polymer
configurational space. The PIMD-SH sampling method is
validated theoretically and by numerical
examples.},
Doi = {10.1063/1.4981021},
Key = {fds326081}
}

@article{fds325700,
Author = {Degond, P and Liu, J-G and Pego, RL},
Title = {Coagulation–Fragmentation Model for Animal Group-Size
Statistics},
Journal = {Journal of Nonlinear Science},
Volume = {27},
Number = {2},
Pages = {379-424},
Year = {2017},
Month = {April},
url = {http://dx.doi.org/10.1007/s00332-016-9336-3},
Doi = {10.1007/s00332-016-9336-3},
Key = {fds325700}
}

@article{fds327370,
Author = {Li, L and Xu, X and Spagnolie, SE},
Title = {A Locally Gradient-Preserving Reinitialization for Level Set
Functions},
Journal = {Journal of Scientific Computing},
Volume = {71},
Number = {1},
Pages = {274-302},
Year = {2017},
Month = {April},
url = {http://dx.doi.org/10.1007/s10915-016-0299-1},
Doi = {10.1007/s10915-016-0299-1},
Key = {fds327370}
}

@article{fds316609,
Author = {Mourrat, J-C and Nolen, J},
Title = {Scaling limit of the corrector in stochastic
homogenization},
Journal = {The annals of applied probability : an official journal of
the Institute of Mathematical Statistics},
Volume = {27},
Number = {2},
Pages = {944-959},
Publisher = {Institute of Mathematical Statistics (IMS)},
Year = {2017},
Month = {April},
ISSN = {1050-5164},
url = {http://arxiv.org/abs/1502.07440},
Abstract = {© Institute of Mathematical Statistics, 2017.In the
homogenization of divergence-form equations with random
coefficients, a central role is played by the corrector.We
focus on a discrete space setting and on dimension 3 and
more. Under a minor smoothness assumption on the law of the
random coefficients, we identify the scaling limit of the
corrector, which is akin to a Gaussian free field. This
completes the argument started in [Ann. Probab. 44 (2016)
3207-3233].},
Doi = {10.1214/16-AAP1221},
Key = {fds316609}
}

@article{fds325481,
Author = {Jockers, H and Katz, S and Morrison, DR and Plesser,
MR},
Title = {SU(N) Transitions in M-Theory on Calabi–Yau Fourfolds and
Background Fluxes},
Journal = {Communications in Mathematical Physics},
Volume = {351},
Number = {2},
Pages = {837-871},
Year = {2017},
Month = {April},
url = {http://dx.doi.org/10.1007/s00220-016-2741-5},
Doi = {10.1007/s00220-016-2741-5},
Key = {fds325481}
}

@article{fds326749,
Author = {Campbell, K and Carpenter, KLH and Espinosa, S and Hashemi, J and Qiu,
Q and Tepper, M and Calderbank, R and Sapiro, G and Egger, HL and Baker,
JP and Dawson, G},
Title = {Use of a Digital Modified Checklist for Autism in Toddlers -
Revised with Follow-up to Improve Quality of Screening for
Autism.},
Journal = {The Journal of Pediatrics},
Volume = {183},
Pages = {133-139.e1},
Year = {2017},
Month = {April},
url = {http://dx.doi.org/10.1016/j.jpeds.2017.01.021},
Abstract = {To assess changes in quality of care for children at risk
for autism spectrum disorders (ASD) due to process
improvement and implementation of a digital screening
form.The process of screening for ASD was studied in an
academic primary care pediatrics clinic before and after
implementation of a digital version of the Modified
Checklist for Autism in Toddlers - Revised with Follow-up
with automated risk assessment. Quality metrics included
accuracy of documentation of screening results and
appropriate action for positive screens (secondary screening
or referral). Participating physicians completed pre- and
postintervention surveys to measure changes in attitudes
toward feasibility and value of screening for ASD. Evidence
of change was evaluated with statistical process control
charts and χ2 tests.Accurate documentation in the
electronic health record of screening results increased from
54% to 92% (38% increase, 95% CI 14%-64%) and appropriate
action for children screening positive increased from 25% to
85% (60% increase, 95% CI 35%-85%). A total of 90% of
participating physicians agreed that the transition to a
digital screening form improved their clinical assessment of
autism risk.Implementation of a tablet-based digital version
of the Modified Checklist for Autism in Toddlers - Revised
with Follow-up led to improved quality of care for children
at risk for ASD and increased acceptability of screening for
ASD. Continued efforts towards improving the process of
screening for ASD could facilitate rapid, early diagnosis of
ASD and advance the accuracy of studies of the impact of
screening.},
Doi = {10.1016/j.jpeds.2017.01.021},
Key = {fds326749}
}

@article{fds328965,
Author = {Li, Y and Yang, H and Ying, L},
Title = {Multidimensional butterfly factorization},
Journal = {Applied and Computational Harmonic Analysis},
Year = {2017},
Month = {April},
url = {http://dx.doi.org/10.1016/j.acha.2017.04.002},
Doi = {10.1016/j.acha.2017.04.002},
Key = {fds328965}
}

@article{fds326270,
Author = {Lu, J and Zhou, Z},
Title = {Path integral molecular dynamics with surface hopping for
systems.},
Journal = {Journal of Chemical Physics},
Volume = {146},
Number = {15},
Pages = {154110},
Year = {2017},
Month = {April},
url = {http://dx.doi.org/10.1063/1.4981021},
Abstract = {In this work, a novel ring polymer representation for a
multi-level quantum system is proposed for thermal average
calculations. The proposed representation keeps the
discreteness of the electronic states: besides position and
momentum, each bead in the ring polymer is also
characterized by a surface index indicating the electronic
energy surface. A path integral molecular dynamics with
surface hopping (PIMD-SH) dynamics is also developed to
sample the equilibrium distribution of the ring polymer
configurational space. The PIMD-SH sampling method is
validated theoretically and by numerical
examples.},
Doi = {10.1063/1.4981021},
Key = {fds326270}
}

@article{fds322100,
Author = {Zhang, Z and Dolbow, JE},
Title = {Remeshing strategies for large deformation problems with
frictional contact and nearly incompressible
materials},
Journal = {International Journal for Numerical Methods in
Engineering},
Volume = {109},
Number = {9},
Pages = {1289-1314},
Year = {2017},
Month = {March},
url = {http://dx.doi.org/10.1002/nme.5325},
Doi = {10.1002/nme.5325},
Key = {fds322100}
}

@article{fds324463,
Author = {Sabag, O and Permuter, HH and Pfister, HD},
Title = {A Single-Letter Upper Bound on the Feedback Capacity of
Unifilar Finite-State Channels},
Journal = {IEEE Transactions on Information Theory},
Volume = {63},
Number = {3},
Pages = {1392-1409},
Year = {2017},
Month = {March},
url = {http://dx.doi.org/10.1109/TIT.2016.2636851},
Abstract = {© 1963-2012 IEEE.An upper bound on the feedback capacity of
unifilar finite-state channels (FSCs) is derived. A new
technique, called the Q-context mapping, is based on a
construction of a directed graph that is used for a
sequential quantization of the receiver's output sequences
to a finite set of contexts. For any choice of Q-graph, the
feedback capacity is bounded by a single-letter expression,
Cfb ≤ sup I (X, S; Y|Q), where the supremum is over p(x|s,
q) and the distribution of (S, Q) is their stationary
distribution. It is shown that the bound is tight for all
unifilar FSCs, where feedback capacity is known: channels
where the state is a function of the outputs, the trapdoor
channel, Ising channels, the no-consecutive-ones
input-constrained erasure channel, and the memoryless
channel. Its efficiency is also demonstrated by deriving a
new capacity result for the dicode erasure channel; the
upper bound is obtained directly from the above-mentioned
expression and its tightness is concluded with a general
sufficient condition on the optimality of the upper bound.
This sufficient condition is based on a fixed point
principle of the BCJR equation and, indeed, formulated as a
simple lower bound on feedback capacity of unifilar FSCs for
arbitrary Q-graphs. This upper bound indicates that a
single-letter expression might exist for the capacity of
finite-state channels with or without feedback based on a
construction of auxiliary random variable with specified
structure, such as the Q-graph, and not with i.i.d
distribution. The upper bound also serves as a non-trivial
bound on the capacity of channels without feedback, a
problem that is still open.},
Doi = {10.1109/TIT.2016.2636851},
Key = {fds324463}
}

@article{fds323719,
Author = {Stershic, AJ and Dolbow, JE and Moës, N},
Title = {The Thick Level-Set model for dynamic fragmentation},
Journal = {Engineering Fracture Mechanics},
Volume = {172},
Pages = {39-60},
Year = {2017},
Month = {March},
url = {http://dx.doi.org/10.1016/j.engfracmech.2016.12.012},
Doi = {10.1016/j.engfracmech.2016.12.012},
Key = {fds323719}
}

@article{fds316662,
Author = {Nolen, J and Roquejoffre, J-M and Ryzhik, L},
Title = {Convergence to a single wave in the Fisher-KPP
equation},
Journal = {Chinese Annals of Mathematics - Series B},
Volume = {38},
Number = {2},
Pages = {629-646},
Year = {2017},
Month = {March},
url = {http://arxiv.org/abs/1604.02994},
Doi = {10.1007/s11401-017-1087-4},
Key = {fds316662}
}

@book{fds15387,
Author = {A. O. Petters and M. C. Werner},
Title = {Gravitational Lensing and Black Holes},
Publisher = {Springer, in preparation},
Year = {2017},
Month = {Spring},
Key = {fds15387}
}

@article{fds320453,
Author = {Ji, H and Witelski, TP},
Title = {Finite-time thin film rupture driven by modified evaporative
loss},
Journal = {Physica D: Nonlinear Phenomena},
Volume = {342},
Pages = {1-15},
Year = {2017},
Month = {March},
url = {http://dx.doi.org/10.1016/j.physd.2016.10.002},
Doi = {10.1016/j.physd.2016.10.002},
Key = {fds320453}
}

@article{fds327636,
Author = {Huang, H and Liu, J-G},
Title = {Error estimate of a random particle blob method for the
Keller-Segel equation},
Journal = {Mathematics of Computation},
Volume = {86},
Number = {308},
Pages = {2719-2744},
Year = {2017},
Month = {February},
url = {http://dx.doi.org/10.1090/mcom/3174},
Doi = {10.1090/mcom/3174},
Key = {fds327636}
}

@article{fds328057,
Author = {Baldwin, JA and Levine, AS and Sarkar, S},
Title = {Khovanov homology and knot Floer homology for pointed
Journal = {Journal of Knot Theory & Its Ramifications},
Volume = {26},
Number = {02},
Pages = {1740004-1740004},
Year = {2017},
Month = {February},
url = {http://dx.doi.org/10.1142/S0218216517400041},
Doi = {10.1142/S0218216517400041},
Key = {fds328057}
}

@article{fds331513,
Author = {Nagy, Á},
Title = {The Berry Connection of the Ginzburg–Landau
Vortices},
Journal = {Communications in Mathematical Physics},
Volume = {350},
Number = {1},
Pages = {105-128},
Year = {2017},
Month = {February},
url = {http://dx.doi.org/10.1007/s00220-016-2701-0},
Doi = {10.1007/s00220-016-2701-0},
Key = {fds331513}
}

@article{fds323660,
Author = {Jiang, T and Li, Y and Layton, AT and Wang, W and Sun, Y and Li, M and Zhou,
H and Yang, B},
Title = {Generation and phenotypic analysis of mice lacking all urea
transporters.},
Journal = {Kidney international},
Volume = {91},
Number = {2},
Pages = {338-351},
Year = {2017},
Month = {February},
url = {http://dx.doi.org/10.1016/j.kint.2016.09.017},
Abstract = {Urea transporters (UT) are a family of transmembrane
urea-selective channel proteins expressed in multiple
tissues and play an important role in the urine
concentrating mechanism of the mammalian kidney. UT
inhibitors have diuretic activity and could be developed as
novel diuretics. To determine if functional deficiency of
all UTs in all tissues causes physiological abnormality, we
established a novel mouse model in which all UTs were
knocked out by deleting an 87 kb of DNA fragment containing
most parts of Slc14a1 and Slc14a2 genes. Western blot
analysis and immunofluorescence confirmed that there is no
expression of urea transporter in these all-UT-knockout
mice. Daily urine output was nearly 3.5-fold higher, with
significantly lower urine osmolality in all-UT-knockout mice
than that in wild-type mice. All-UT-knockout mice were not
able to increase urinary urea concentration and osmolality
intake. A computational model that simulated UT-knockout
mouse models identified the individual contribution of each
UT in urine concentrating mechanism. Knocking out all UTs
also decreased the blood pressure and promoted the
maturation of the male reproductive system. Thus, functional
deficiency of all UTs caused a urea-selective
urine-concentrating defect with little physiological
abnormality in extrarenal organs.},
Doi = {10.1016/j.kint.2016.09.017},
Key = {fds323660}
}

@article{fds328439,
Author = {Watson, AB and Lu, J and Weinstein, MI},
Title = {Wavepackets in inhomogeneous periodic media: Effective
particle-field dynamics and Berry curvature},
Journal = {Journal of Mathematical Physics},
Volume = {58},
Number = {2},
Pages = {021503-021503},
Year = {2017},
Month = {February},
url = {http://dx.doi.org/10.1063/1.4976200},
Doi = {10.1063/1.4976200},
Key = {fds328439}
}

@article{fds326219,
Author = {Dunson, DB},
Title = {Toward Automated Prior Choice},
Journal = {Statistical science : a review journal of the Institute of
Mathematical Statistics},
Volume = {32},
Number = {1},
Pages = {41-43},
Year = {2017},
Month = {February},
url = {http://dx.doi.org/10.1214/16-STS607},
Doi = {10.1214/16-STS607},
Key = {fds326219}
}

@article{fds333226,
Author = {Abrego, N and Dunson, D and Halme, P and Salcedo, I and Ovaskainen,
O},
Title = {Wood-inhabiting fungi with tight associations with other
species have declined as a response to forest
management},
Journal = {Oikos},
Volume = {126},
Number = {2},
Year = {2017},
Month = {February},
url = {http://dx.doi.org/10.1111/oik.03674},
Doi = {10.1111/oik.03674},
Key = {fds333226}
}

@article{fds328817,
Author = {Herry, CL and Frasch, M and Seely, AJ and Wu, H-T},
Title = {Heart beat classification from single-lead ECG using the
synchrosqueezing transform.},
Journal = {Physiological Measurement},
Volume = {38},
Number = {2},
Pages = {171-187},
Year = {2017},
Month = {February},
url = {http://dx.doi.org/10.1088/1361-6579/aa5070},
Abstract = {The processing of ECG signal provides a wealth of
information on cardiac function and overall cardiovascular
health. While multi-lead ECG recordings are often necessary
for a proper assessment of cardiac rhythms, they are not
always available or practical, for example in fetal ECG
applications. Moreover, a wide range of small non-obtrusive
single-lead ECG ambulatory monitoring devices are now
available, from which heart rate variability (HRV) and other
health-related metrics are derived. Proper beat detection
and classification of abnormal rhythms is important for
reliable HRV assessment and can be challenging in
single-lead ECG monitoring devices. In this manuscript, we
modelled the heart rate signal as an adaptive non-harmonic
model and used the newly developed synchrosqueezing
transform (SST) to characterize ECG patterns. We show how
the proposed model can be used to enhance heart beat
detection and classification between normal and abnormal
rhythms. In particular, using the Massachusetts Institute of
Technology-Beth Israel Hospital (MIT-BIH) arrhythmia
database and the Association for the Advancement of Medical
Instrumentation (AAMI) beat classes, we trained and
validated a support vector machine (SVM) classifier on a
portion of the annotated beat database using the SST-derived
instantaneous phase, the R-peak amplitudes and R-peak to
R-peak interval durations, based on a single ECG lead. We
obtained sentivities and positive predictive values
comparable to other published algorithms using multiple
Doi = {10.1088/1361-6579/aa5070},
Key = {fds328817}
}

@article{fds329944,
Author = {Wu, H-K and Ko, Y-S and Lin, Y-S and Wu, H-T and Tsai, T-H and Chang,
H-H},
Title = {The correlation between pulse diagnosis and constitution
Journal = {Complementary Therapies in Medicine},
Volume = {30},
Pages = {107-112},
Year = {2017},
Month = {February},
url = {http://dx.doi.org/10.1016/j.ctim.2016.12.005},
Abstract = {Our study aimed to correlate pulse wave parameters such as
augmentation index (AI) and heart rate variability with
traditional Chinese medicine (TCM) constitution for
evaluating health status.Out of 177 subjects, 69 healthy
subjects were enrolled in the present study, and others were
excluded because of cardiovascular, liver, kidney, or other
diseases. Each subject was invited to complete pulse wave
examination and the Constitution in Chinese Medicine
Questionnaire. Independent Student's t-tests, Mann-Whitney
tests, and binary logistic regression analysis were used to
analyse the correlation between pulse wave parameters and
TCM constitution.Qi-deficient individuals had higher AI
(p=0.006) and lower diastolic blood pressure (p=0.011);
yang-deficient individuals had lower dP/dt max (p=0.030),
systolic blood pressure (p=0.020), and pulse pressure
(p=0.048); and damp-heat individuals had higher
subendocardial viability index (SEVI) scores (p=0.011). We
then categorized the phlegm dampness and yang-deficiency
individuals into the cold group and those with damp-heat and
yin-deficiency into the heat group. A comparison of the two
constitution groups showed higher AI in the cold group
(p=0.026). Binary logistic regression analysis demonstrated
that only AI was a determinant, as evidenced by the finding
that an increase of one unit in AI corresponded to an
increase of 5% in the odds ratio for individuals to have a
cold constitution (p=0.026).Individuals with qi-deficient
and cold constitutions had higher AI and lower SEVI,
potentially reflecting an increase in arterial stiffness.
This study can provide a basis for further investigation of
the physiological indicators of TCM constitutions in modern
medicine.},
Doi = {10.1016/j.ctim.2016.12.005},
Key = {fds329944}
}

@article{fds325388,
Author = {Deligiannis, N and Mota, JFC and Cornelis, B and Rodrigues, MRD and Daubechies, I},
Title = {Multi-Modal Dictionary Learning for Image Separation With
Application in Art Investigation},
Journal = {IEEE Transactions on Image Processing},
Volume = {26},
Number = {2},
Pages = {751-764},
Year = {2017},
Month = {February},
url = {http://dx.doi.org/10.1109/TIP.2016.2623484},
Doi = {10.1109/TIP.2016.2623484},
Key = {fds325388}
}

@article{fds325889,
Author = {Watson, AB and Lu, J and Weinstein, MI},
Title = {Wavepackets in inhomogeneous periodic media: Effective
particle-field dynamics and Berry curvature},
Journal = {Journal of Mathematical Physics},
Volume = {58},
Number = {2},
Pages = {021503-021503},
Year = {2017},
Month = {February},
url = {http://dx.doi.org/10.1063/1.4976200},
Doi = {10.1063/1.4976200},
Key = {fds325889}
}

@article{fds320926,
Author = {Niu, X and Luo, T and Lu, J and Xiang, Y},
Title = {Dislocation climb models from atomistic scheme to
dislocation dynamics},
Journal = {Journal of the Mechanics and Physics of Solids},
Volume = {99},
Pages = {242-258},
Year = {2017},
Month = {February},
url = {http://dx.doi.org/10.1016/j.jmps.2016.11.012},
Doi = {10.1016/j.jmps.2016.11.012},
Key = {fds320926}
}

@article{fds325701,
Author = {Liu, J-G and Wang, J},
Title = {Global existence for a thin film equation with subcritical
mass},
Journal = {Discrete and Continuous Dynamical Systems - Series
B},
Volume = {22},
Number = {4},
Pages = {1461-1492},
Year = {2017},
Month = {February},
url = {http://dx.doi.org/10.3934/dcdsb.2017070},
Doi = {10.3934/dcdsb.2017070},
Key = {fds325701}
}

@article{fds300245,
Author = {Glatt-Holtz, N and Mattingly, JC and Richards,
G},
Title = {On Unique Ergodicity in Nonlinear Stochastic Partial
Differential Equations},
Journal = {Journal of Statistical Physics},
Volume = {166},
Number = {3-4},
Pages = {618-649},
Year = {2017},
Month = {February},
url = {http://arxiv.org/abs/1512.04126v1},
Abstract = {We illustrate how the notion of asymptotic coupling provides
a flexible and intuitive framework for proving the
uniqueness of invariant measures for a variety of stochastic
partial differential equations whose deterministic
counterpart possesses a finite number of determining modes.
Examples exhibiting parabolic and hyperbolic structure are
studied in detail. In the later situation we also present a
simple framework for establishing the existence of invariant
measures when the usual approach relying on the
Krylov-Bogolyubov procedure and compactness
fails.},
Doi = {10.1007/s10955-016-1605-x},
Key = {fds300245}
}

@article{fds323270,
Author = {Bobrowski, O and Mukherjee, S and Taylor, JE},
Title = {Topological consistency via kernel estimation},
Journal = {Bernoulli : official journal of the Bernoulli Society for
Mathematical Statistics and Probability},
Volume = {23},
Number = {1},
Pages = {288-328},
Year = {2017},
Month = {February},
url = {http://dx.doi.org/10.3150/15-BEJ744},
Doi = {10.3150/15-BEJ744},
Key = {fds323270}
}

@article{fds330626,
Author = {Wang, T and Rudin, C and Velez-Doshi, F and Liu, Y and Klampfl, E and Macneille, P},
Title = {Bayesian rule sets for interpretable classification},
Journal = {Proceedings / IEEE International Conference on Data Mining.
IEEE International Conference on Data Mining},
Pages = {1269-1274},
Year = {2017},
Month = {January},
ISBN = {9781509054725},
url = {http://dx.doi.org/10.1109/ICDM.2016.130},
Abstract = {© 2016 IEEE. A Rule Set model consists of a small number of
short rules for interpretable classification, where an
instance is classified as positive if it satisfies at least
one of the rules. The rule set provides reasons for
predictions, and also descriptions of a particular class. We
present a Bayesian framework for learning Rule Set models,
with prior parameters that the user can set to encourage the
model to have a desired size and shape in order to conform
with a domain-specific definition of interpretability. We
use an efficient inference approach for searching for the
MAP solution and provide theoretical bounds to reduce
computation. We apply Rule Set models to ten UCI data sets
and compare the performance with other interpretable and
non-interpretable models.},
Doi = {10.1109/ICDM.2016.130},
Key = {fds330626}
}

@article{fds324086,
Author = {Chen, J and Chang, Z and Qiu, Q and Li, X and Sapiro, G and Bronstein, A and Pietikäinen, M},
Title = {RealSense = real heart rate: Illumination invariant heart
rate estimation from videos},
Journal = {2016 6th International Conference on Image Processing
Theory, Tools and Applications, IPTA 2016},
Year = {2017},
Month = {January},
ISBN = {9781467389105},
url = {http://dx.doi.org/10.1109/IPTA.2016.7820970},
Abstract = {© 2016 IEEE. Recent studies validated the feasibility of
estimating heart rate from human faces in RGB video.
However, test subjects are often recorded under controlled
conditions, as illumination variations significantly affect
the RGB-based heart rate estimation accuracy. Intel
newly-announced low-cost RealSense 3D (RGBD) camera is
becoming ubiquitous in laptops and mobile devices starting
this year, opening the door to new and more robust computer
vision. RealSense cameras produce RGB images with extra
depth information inferred from a latent near-infrared (NIR)
channel. In this paper, we experimentally demonstrate, for
the first time, that heart rate can be reliably estimated
from RealSense near-infrared images. This enables
illumination invariant heart rate estimation, extending the
heart rate from video feasibility to low-light applications,
such as night driving. With the (coming) ubiquitous presence
of RealSense devices, the proposed method not only utilizes
its near-infrared channel, designed originally to be hidden
from consumers; but also exploits the associated depth
information for improved robustness to head
pose.},
Doi = {10.1109/IPTA.2016.7820970},
Key = {fds324086}
}

@article{fds330177,
Author = {Wu, Y and Agarwal, PK and Li, C and Yang, J and Yu, C},
Title = {Computational Fact Checking through Query
Perturbations},
Journal = {ACM Transactions on Database Systems},
Volume = {42},
Number = {1},
Pages = {1-41},
Year = {2017},
Month = {January},
url = {http://dx.doi.org/10.1145/2996453},
Doi = {10.1145/2996453},
Key = {fds330177}
}

@article{fds325508,
Author = {Sabag, O and Permuter, HH and Pfister, HD},
Title = {Single-letter bounds on the feedback capacity of unifilar
finite-state channels},
Journal = {2016 IEEE International Conference on the Science of
Electrical Engineering, ICSEE 2016},
Year = {2017},
Month = {January},
ISBN = {9781509021529},
url = {http://dx.doi.org/10.1109/ICSEE.2016.7806200},
Abstract = {© 2016 IEEE. Upper and lower bounds on the feedback
capacity of unifilar finite-state channels (FSCs) are
derived. The upper bound is derived using a new technique,
called the Q-contexts, which is based on a construction of a
directed graph that is used to quantize recursively the
receiver's output sequences to a finite set of contexts. For
any choice of Q-graph, the feedback capacity is bounded by a
single-letter expression, C fb ≤ sup I (X, S; Y |Q), where
the supremum is over P x|s,q and the distribution of (S, Q)
is their stationary distribution. The bound is tight for all
unifilar FSCs where feedback capacity is known: channels
where the state is a function of the outputs, the trapdoor
channel, Ising channels, the no-consecutive-ones
input-constrained erasure channel and for the memoryless
channel. The upper bound indicates that a single-letter
expression might exist for the capacity of finite-state
channels with or without feedback which are based on a
construction of auxiliary random variable with memory, such
as Q-graph, and not with i.i.d distribution. The lower bound
provides a sufficient condition for the optimality of the
upper bound, however, it is formulated such that independent
lower bounds on feedback capacity may be calculated. The
efficiency of these bounds is demonstrated by deriving a new
capacity result for the dicode erasure channel (DEC). The
upper bound also serves as a non-trivial bound on the
capacity of channels without feedback, a problem that is
still open.},
Doi = {10.1109/ICSEE.2016.7806200},
Key = {fds325508}
}

@article{fds328446,
Author = {Gounley, J and Draeger, EW and Randles, A},
Title = {Numerical simulation of a compound capsule in a constricted
microchannel.},
Journal = {Procedia Computer Science},
Volume = {108},
Pages = {175-184},
Year = {2017},
Month = {January},
url = {http://dx.doi.org/10.1016/j.procs.2017.05.209},
Abstract = {Simulations of the passage of eukaryotic cells through a
constricted channel aid in studying the properties of cancer
cells and their transport in the bloodstream. Compound
capsules, which explicitly model the outer cell membrane and
nuclear lamina, have the potential to improve computational
model fidelity. However, general simulations of compound
capsules transiting a constricted microchannel have not been
conducted and the influence of the compound capsule model on
computational performance is not well known. In this study,
we extend a parallel hemodynamics application to simulate
the fluid-structure interaction between compound capsules
and fluid. With this framework, we compare the deformation
of simple and compound capsules in constricted
microchannels, and explore how deformation depends on the
capillary number and on the volume fraction of the inner
membrane. The computational framework's parallel performance
in this setting is evaluated and future development lessons
are discussed.},
Doi = {10.1016/j.procs.2017.05.209},
Key = {fds328446}
}

@article{fds326839,
Author = {Laurence, TA and Ly, S and Fong, E and Shusteff, M and Randles, A and Gounley, J and Draeger, E},
Title = {Using stroboscopic flow imaging to validate large-scale
computational fluid dynamics simulations},
Journal = {Proceedings of SPIE},
Volume = {10076},
Year = {2017},
Month = {January},
ISBN = {9781510605930},
url = {http://dx.doi.org/10.1117/12.2253319},
computational modeling often requires direct validation
against experimental measurements. The work presented here
is motivated by taking a combined experimental and
computational approach to determine the ability of
large-scale computational fluid dynamics (CFD) simulations
to understand and predict the dynamics of circulating tumor
cells in clinically relevant environments. We use
stroboscopic light sheet fluorescence imaging to track the
paths and measure the velocities of fluorescent microspheres
throughout a human aorta model. Performed over complex
physiologicallyrealistic 3D geometries, large data sets are
acquired with microscopic resolution over macroscopic
distances.},
Doi = {10.1117/12.2253319},
Key = {fds326839}
}

@article{fds330817,
Author = {Best, A and Dynes, P and Edelsbrunner, X and McDonald, B and Miller, SJ and Tor, K and Turnage-Butterbaugh, C and Weinstein,
M},
Title = {Benford Behavior of Generalized Zeckendorf
Decompositions},
Journal = {Springer Proceedings in Mathematics and Statistics},
Volume = {220},
Pages = {25-37},
Publisher = {Springer},
Year = {2017},
Month = {January},
url = {http://dx.doi.org/10.1007/978-3-319-68032-3_3},
Abstract = {© Springer International Publishing AG 2017. We prove
connections between Zeckendorf decompositions and
Benford’s law. Recall that if we define the Fibonacci
numbers by F 1 = 1, F 2 = 2, and F n+1 = F n + F n−1 ,
every positive integer can be written uniquely as a sum of
nonadjacent elements of this sequence; this is called the
Zeckendorf decomposition, and similar unique decompositions
exist for sequences arising from recurrence relations of the
form G n+1 = c 1 G n + … + c L G n+1−L with c i positive
and some other restrictions. Additionally, a set S ⊂ ℤ
is said to satisfy Benford’s law base 10 if the density of
the elements in S with leading digit d is (Formula
presented); in other words, smaller leading digits are more
likely to occur. We prove that as n → ∞ for a randomly
selected integer m in [0, G n+1 ) the distribution of the
leading digits of the summands in its generalized Zeckendorf
decomposition converges to Benford’s law almost surely.
Our results hold more generally: One obtains similar
theorems to those regarding the distribution of leading
digits when considering how often values in sets with
density are attained in the summands in the
decompositions.},
Doi = {10.1007/978-3-319-68032-3_3},
Key = {fds330817}
}

@article{fds325339,
Author = {Johndrow, JE and Bhattacharya, A and Dunson, DB},
Title = {TENSOR DECOMPOSITIONS AND SPARSE LOG-LINEAR
MODELS.},
Journal = {Annals of statistics},
Volume = {45},
Number = {1},
Pages = {1-38},
Year = {2017},
Month = {January},
url = {http://dx.doi.org/10.1214/15-aos1414},
Abstract = {Contingency table analysis routinely relies on log-linear
models, with latent structure analysis providing a common
alternative. Latent structure models lead to a reduced rank
tensor factorization of the probability mass function for
multivariate categorical data, while log-linear models
achieve dimensionality reduction through sparsity. Little is
known about the relationship between these notions of
dimensionality reduction in the two paradigms. We derive
several results relating the support of a log-linear model
to nonnegative ranks of the associated probability tensor.
Motivated by these findings, we propose a new collapsed
Tucker class of tensor decompositions, which bridge existing
PARAFAC and Tucker decompositions, providing a more flexible
framework for parsimoniously characterizing multivariate
categorical data. Taking a Bayesian approach to inference,
we illustrate empirical advantages of the new
decompositions.},
Doi = {10.1214/15-aos1414},
Key = {fds325339}
}

@article{fds326570,
Author = {Lin, L and St Thomas and B and Zhu, H and Dunson, DB},
Title = {Extrinsic local regression on manifold-valued
data.},
Journal = {Journal of the American Statistical Association},
Volume = {112},
Number = {519},
Pages = {1261-1273},
Year = {2017},
Month = {January},
url = {http://dx.doi.org/10.1080/01621459.2016.1208615},
Abstract = {We propose an extrinsic regression framework for modeling
data with manifold valued responses and Euclidean
predictors. Regression with manifold responses has wide
applications in shape analysis, neuroscience, medical
imaging and many other areas. Our approach embeds the
manifold where the responses lie onto a higher dimensional
Euclidean space, obtains a local regression estimate in that
space, and then projects this estimate back onto the image
of the manifold. Outside the regression setting both
intrinsic and extrinsic approaches have been proposed for
modeling i.i.d manifold-valued data. However, to our
knowledge our work is the first to take an extrinsic
approach to the regression problem. The proposed extrinsic
regression framework is general, computationally efficient
and theoretically appealing. Asymptotic distributions and
convergence rates of the extrinsic regression estimates are
derived and a large class of examples are considered
indicating the wide applicability of our
approach.},
Doi = {10.1080/01621459.2016.1208615},
Key = {fds326570}
}

@article{fds326840,
Author = {Gunalan, K and Chaturvedi, A and Howell, B and Duchin, Y and Lempka, SF and Patriat, R and Sapiro, G and Harel, N and McIntyre,
CC},
Title = {Creating and parameterizing patient-specific deep brain
stimulation pathway-activation models using the hyperdirect
pathway as an example.},
Journal = {PloS one},
Volume = {12},
Number = {4},
Pages = {e0176132},
Year = {2017},
Month = {January},
url = {http://dx.doi.org/10.1371/journal.pone.0176132},
Abstract = {Deep brain stimulation (DBS) is an established clinical
therapy and computational models have played an important
role in advancing the technology. Patient-specific DBS
models are now common tools in both academic and industrial
research, as well as clinical software systems. However, the
exact methodology for creating patient-specific DBS models
can vary substantially and important technical details are
often missing from published reports.Provide a detailed
description of the assembly workflow and parameterization of
a patient-specific DBS pathway-activation model (PAM) and
predict the response of the hyperdirect pathway to clinical
stimulation.Integration of multiple software tools (e.g.
COMSOL, MATLAB, FSL, NEURON, Python) enables the creation
and visualization of a DBS PAM. An example DBS PAM was
developed using 7T magnetic resonance imaging data from a
single unilaterally implanted patient with Parkinson's
disease (PD). This detailed description implements our best
computational practices and most elaborate parameterization
steps, as defined from over a decade of technical
evolution.Pathway recruitment curves and strength-duration
relationships highlight the non-linear response of axons to
changes in the DBS parameter settings.Parameterization of
patient-specific DBS models can be highly detailed and
constrained, thereby providing confidence in the simulation
predictions, but at the expense of time demanding technical
implementation steps. DBS PAMs represent new tools for
investigating possible correlations between brain pathway
activation patterns and clinical symptom
modulation.},
Doi = {10.1371/journal.pone.0176132},
Key = {fds326840}
}

@article{fds311606,
Author = {Cornelis, B and Yang, H and Goodfriend, A and Ocon, N and Lu, J and Daubechies, I},
Title = {Removal of Canvas Patterns in Digital Acquisitions of
Paintings.},
Journal = {IEEE Transactions on Image Processing},
Volume = {26},
Number = {1},
Pages = {160-171},
Publisher = {Institute of Electrical and Electronics Engineers
(IEEE)},
Year = {2017},
Month = {January},
ISSN = {1941-0042},
url = {http://hdl.handle.net/10161/11650 Duke open
access},
Abstract = {We address the removal of canvas artifacts from
high-resolution digital photographs and X-ray images of
paintings on canvas. Both imaging modalities are common
investigative tools in art history and art conservation.
Canvas artifacts manifest themselves very differently
according to the acquisition modality; they can hamper the
visual reading of the painting by art experts, for instance,
in preparing a restoration campaign. Computer-aided canvas
removal is desirable for restorers when the painting on
canvas they are preparing to restore has acquired over the
years a much more salient texture. We propose a new
algorithm that combines a cartoon-texture decomposition
method with adaptive multiscale thresholding in the
frequency domain to isolate and suppress the canvas
components. To illustrate the strength of the proposed
method, we provide various examples, for acquisitions in
both imaging modalities, for paintings with different types
of canvas and from different periods. The proposed algorithm
outperforms previous methods proposed for visual photographs
such as morphological component analysis and Wiener
filtering and it also works for the digital removal of
canvas artifacts in X-ray images.},
Doi = {10.1109/tip.2016.2621413},
Key = {fds311606}
}

@article{fds312767,
Author = {Lu, J and Yang, H},
Title = {Preconditioning Orbital Minimization Method for Planewave
Discretization},
Journal = {Multiscale Modeling & Simulation},
Volume = {15},
Number = {1},
Pages = {254-273},
Year = {2017},
Month = {January},
url = {http://hdl.handle.net/10161/11833 Duke open
access},
Abstract = {We present an efficient preconditioner for the orbital
minimization method when the Hamiltonian is discretized
using planewaves (i.e., pseudospectral method). This novel
preconditioner is based on an approximate Fermi operator
projection by pole expansion, combined with the sparsifying
preconditioner to efficiently evaluate the pole expansion
for a wide range of Hamiltonian operators. Numerical results
validate the performance of the new preconditioner for the
orbital minimization method, in particular, the iteration
number is reduced to $O(1)$ and often only a few iterations
are enough for convergence.},
Doi = {10.1137/16M1068670},
Key = {fds312767}
}

@article{fds315394,
Author = {Li, Y and Yang, H},
Title = {Interpolative Butterfly Factorization},
Journal = {SIAM Journal on Scientific Computing},
Volume = {39},
Number = {2},
Pages = {A503-A531},
Year = {2017},
Month = {January},
url = {http://arxiv.org/abs/1605.03616},
Doi = {10.1137/16M1074941},
Key = {fds315394}
}

@article{fds311604,
Author = {Yang, H},
Title = {Statistical analysis of synchrosqueezed transforms},
Journal = {Applied and Computational Harmonic Analysis},
Publisher = {Elsevier},
Year = {2017},
Month = {January},
ISSN = {1096-603X},
url = {http://hdl.handle.net/10161/11652 Duke open
access},
Doi = {10.1016/j.acha.2017.01.001},
Key = {fds311604}
}

@article{fds331926,
Author = {Coifman, RR and Steinerberger, S and Wu, HT},
Title = {Carrier frequencies, holomorphy. And unwinding},
Journal = {SIAM Journal on Mathematical Analysis},
Volume = {49},
Number = {6},
Pages = {4838-4864},
Year = {2017},
Month = {January},
url = {http://dx.doi.org/10.1137/16M1081087},
Abstract = {© 2017 Society for Industrial and Applied Mathematics. We
prove that functions of intrinsic-mode type (a classical
models for signals) behave essentially like holomorphic
functions: Adding a pure carrier frequency eint ensures that
the anti- holomorphic part is much smaller than the
holomorphic part lP-(f)||L 2 ≪||-P+(f)||L 2 . This enables
us to use techniques from complex analysis, in particular
the unwinding series. We study its stability and convergence
properties and show that the unwinding scries can provide a
high-resolution, noise- robust time-frequency
representation.},
Doi = {10.1137/16M1081087},
Key = {fds331926}
}

@article{fds328816,
Author = {Li, R and Frasch, MG and Wu, H-T},
Title = {Efficient Fetal-Maternal ECG Signal Separation from Two
Channel Maternal Abdominal ECG via Diffusion-Based Channel
Selection.},
Journal = {Frontiers in Physiology},
Volume = {8},
Pages = {277},
Year = {2017},
Month = {January},
url = {http://dx.doi.org/10.3389/fphys.2017.00277},
Abstract = {There is a need for affordable, widely deployable
maternal-fetal ECG monitors to improve maternal and fetal
health during pregnancy and delivery. Based on the
diffusion-based channel selection, here we present the
mathematical formalism and clinical validation of an
algorithm capable of accurate separation of maternal and
fetal ECG from a two channel signal acquired over maternal
abdomen. The proposed algorithm is the first algorithm, to
the best of the authors' knowledge, focusing on the fetal
ECG analysis based on two channel maternal abdominal ECG
signal, and we apply it to two publicly available databases,
the PhysioNet non-invasive fECG database (adfecgdb) and the
2013 PhysioNet/Computing in Cardiology Challenge (CinC2013),
to validate the algorithm. The state-of-the-art results are
achieved when compared with other available algorithms.
Particularly, the F1 score for the R peak detection achieves
99.3% for the adfecgdb and 87.93% for the CinC2013, and the
mean absolute error for the estimated R peak locations is
4.53 ms for the adfecgdb and 6.21 ms for the CinC2013. The
method has the potential to be applied to other fetal
cardiogenic signals, including cardiac doppler
signals.},
Doi = {10.3389/fphys.2017.00277},
Key = {fds328816}
}

@article{fds329942,
Author = {Frasch, MG and Boylan, GB and Wu, H-T and Devane,
D},
Title = {Commentary: Computerised interpretation of fetal heart rate
during labour (INFANT): a randomised controlled
trial.},
Journal = {Frontiers in Physiology},
Volume = {8},
Pages = {721},
Year = {2017},
Month = {January},
url = {http://dx.doi.org/10.3389/fphys.2017.00721},
Doi = {10.3389/fphys.2017.00721},
Key = {fds329942}
}

@article{fds329943,
Author = {Cicone, A and Wu, H-T},
Title = {How Nonlinear-Type Time-Frequency Analysis Can Help in
Sensing Instantaneous Heart Rate and Instantaneous
Respiratory Rate from Photoplethysmography in a Reliable
Way.},
Journal = {Frontiers in Physiology},
Volume = {8},
Pages = {701},
Year = {2017},
Month = {January},
url = {http://dx.doi.org/10.3389/fphys.2017.00701},
Abstract = {Despite the population of the noninvasive, economic,
comfortable, and easy-to-install photoplethysmography (PPG),
it is still lacking a mathematically rigorous and stable
algorithm which is able to simultaneously extract from a
single-channel PPG signal the instantaneous heart rate (IHR)
and the instantaneous respiratory rate (IRR). In this paper,
a novel algorithm called deppG is provided to tackle this
challenge. deppG is composed of two theoretically solid
nonlinear-type time-frequency analyses techniques, the
de-shape short time Fourier transform and the
synchrosqueezing transform, which allows us to extract the
instantaneous physiological information from the PPG signal
in a reliable way. To test its performance, in addition to
validating the algorithm by a simulated signal and
discussing the meaning of "instantaneous," the algorithm is
applied to two publicly available batch databases, the
Capnobase and the ICASSP 2015 signal processing cup. The
former contains PPG signals relative to spontaneous or
controlled breathing in static patients, and the latter is
made up of PPG signals collected from subjects doing intense
physical activities. The accuracies of the estimated IHR and
IRR are compared with the ones obtained by other methods,
and represent the state-of-the-art in this field of
research. The results suggest the potential of deppG to
extract instantaneous physiological information from a
signal acquired from widely available wearable devices, even
when a subject carries out intense physical
activities.},
Doi = {10.3389/fphys.2017.00701},
Key = {fds329943}
}

@article{fds329945,
Author = {Liu, W-T and Wu, H-T and Juang, J-N and Wisniewski, A and Lee, H-C and Wu,
D and Lo, Y-L},
Title = {Prediction of the severity of obstructive sleep apnea by
anthropometric features via support vector
machine.},
Journal = {PloS one},
Volume = {12},
Number = {5},
Pages = {e0176991},
Year = {2017},
Month = {January},
url = {http://dx.doi.org/10.1371/journal.pone.0176991},
Abstract = {To develop an applicable prediction for obstructive sleep
apnea (OSA) is still a challenge in clinical practice. We
apply a modern machine learning method, the support vector
machine to establish a predicting model for the severity of
OSA. The support vector machine was applied to build up a
prediction model based on three anthropometric features
(neck circumference, waist circumference, and body mass
index) and age on the first database. The established model
was then valided independently on the second database. The
anthropometric features and age were combined to generate
powerful predictors for OSA. Following the common practice,
we predict if a subject has the apnea-hypopnea index greater
then 15 or not as well as 30 or not. Dividing by genders and
age, for the AHI threhosld 15 (respectively 30), the cross
validation and testing accuracy for the prediction were
85.3% and 76.7% (respectively 83.7% and 75.5%) in young
female, while the negative likelihood ratio for the AHI
threhosld 15 (respectively 30) for the cross validation and
testing were 0.2 and 0.32 (respectively 0.06 and 0.1) in
young female. The more accurate results with lower negative
likelihood ratio in the younger patients, especially the
female subgroup, reflect the potential of the proposed model
for the screening purpose and the importance of approaching
by different genders and the effects of aging.},
Doi = {10.1371/journal.pone.0176991},
Key = {fds329945}
}

@article{fds328818,
Author = {Lin, Y-T and Wu, H-T},
Title = {ConceFT for Time-Varying Heart Rate Variability Analysis as
a Measure of Noxious Stimulation During General
Anesthesia.},
Journal = {IEEE Transactions on Biomedical Engineering},
Volume = {64},
Number = {1},
Pages = {145-154},
Year = {2017},
Month = {January},
url = {http://dx.doi.org/10.1109/tbme.2016.2549048},
Abstract = {Heart rate variability (HRV) offers a noninvasive way to
peek into the physiological status of the human body. When
this physiological status is dynamic, traditional HRV
indices calculated from power spectrum do not resolve the
dynamic situation due to the issue of nonstationarity.
Clinical anesthesia is a typically dynamic situation that
calls for time-varying HRV analysis. Concentration of
frequency and time (ConceFT) is a nonlinear time-frequency
(TF) analysis generalizing the multitaper technique and the
synchrosqueezing transform. The result is a sharp TF
representation capturing the dynamics inside HRV. Companion
indices of the commonly applied HRV indices, including
time-varying low-frequency power (tvLF), time-varying
high-frequency power, and time-varying low-high ratio, are
considered as measures of noxious stimulation.To evaluate
the feasibility of the proposed indices, we apply these
indices to study two different types of noxious stimulation,
the endotracheal intubation and surgical skin incision,
under general anesthesia. The performance was compared with
from electroencephalography.The results indicate that the
tvLF index performs best and outperforms not only the
traditional HRV index, but also the commonly used heart rate
reading.With the help of ConceFT, the proposed HRV indices
are potential to provide a better quantification of the
dynamic change of the autonomic nerve system.Our proposed
scheme of time-varying HRV analysis could contribute to the
clinical assessment of analgesia under general
anesthesia.},
Doi = {10.1109/tbme.2016.2549048},
Key = {fds328818}
}

@article{fds328819,
Author = {Wu, H-T},
Title = {Embedding Riemannian manifolds by the heat kernel of the
connection Laplacian},
Volume = {304},
Pages = {1055-1079},
Year = {2017},
Month = {January},
url = {http://dx.doi.org/10.1016/j.aim.2016.05.023},
Doi = {10.1016/j.aim.2016.05.023},
Key = {fds328819}
}

@article{fds324089,
Author = {Cornelis, B and Yang, H and Goodfriend, A and Ocon, N and Lu, J and Daubechies, I},
Title = {Removal of Canvas Patterns in Digital Acquisitions of
Paintings.},
Journal = {IEEE Transactions on Image Processing},
Volume = {26},
Number = {1},
Pages = {160-171},
Year = {2017},
Month = {January},
url = {http://dx.doi.org/10.1109/tip.2016.2621413},
Abstract = {We address the removal of canvas artifacts from
high-resolution digital photographs and X-ray images of
paintings on canvas. Both imaging modalities are common
investigative tools in art history and art conservation.
Canvas artifacts manifest themselves very differently
according to the acquisition modality; they can hamper the
visual reading of the painting by art experts, for instance,
in preparing a restoration campaign. Computer-aided canvas
removal is desirable for restorers when the painting on
canvas they are preparing to restore has acquired over the
years a much more salient texture. We propose a new
algorithm that combines a cartoon-texture decomposition
method with adaptive multiscale thresholding in the
frequency domain to isolate and suppress the canvas
components. To illustrate the strength of the proposed
method, we provide various examples, for acquisitions in
both imaging modalities, for paintings with different types
of canvas and from different periods. The proposed algorithm
outperforms previous methods proposed for visual photographs
such as morphological component analysis and Wiener
filtering and it also works for the digital removal of
canvas artifacts in X-ray images.},
Doi = {10.1109/tip.2016.2621413},
Key = {fds324089}
}

@article{fds329099,
Author = {Voronin, S and Daubechies, I},
Title = {An iteratively reweighted least squares algorithm for sparse
regularization},
Volume = {693},
Pages = {391-411},
Booktitle = {Contemporary Mathematics},
Year = {2017},
Month = {January},
url = {http://dx.doi.org/10.1090/conm/693/13941},
Abstract = {© 2017 by the authors. We present a new algorithm and the
corresponding convergence analysis for the regularization of
linear inverse problems with sparsity constraints, applied
to a new generalized sparsity promoting functional. The
algorithm is based on the idea of iteratively reweighted
least squares, reducing the minimization at every iteration
step to that of a functional including only ℓ 2 -norms.
This amounts to smoothing of the absolute value function
that appears in the generalized sparsity promoting penalty
we consider, with the smoothing becoming iteratively less
pronounced. We demonstrate that the sequence of iterates of
our algorithm converges to a limit that minimizes the
original functional.},
Doi = {10.1090/conm/693/13941},
Key = {fds329099}
}

@article{fds327595,
Author = {Yin, R and Gao, T and Lu, YM and Daubechies, I},
Title = {A Tale of Two Bases: Local-Nonlocal Regularization on Image
Patches with Convolution Framelets},
Journal = {SIAM Journal on Imaging Sciences},
Volume = {10},
Number = {2},
Pages = {711-750},
Year = {2017},
Month = {January},
url = {http://dx.doi.org/10.1137/16M1091447},
Doi = {10.1137/16M1091447},
Key = {fds327595}
}

@article{fds330519,
Author = {Li, XH and Lu, J},
Title = {Quasi-nonlocal Coupling of Nonlocal Diffusions},
Journal = {SIAM Journal on Numerical Analysis},
Volume = {55},
Number = {5},
Pages = {2394-2415},
Year = {2017},
Month = {January},
url = {http://dx.doi.org/10.1137/16M1086443},
Doi = {10.1137/16M1086443},
Key = {fds330519}
}

@article{fds325890,
Author = {Lu, J and Yang, H},
Title = {Preconditioning Orbital Minimization Method for Planewave
Discretization},
Journal = {Multiscale Modeling & Simulation},
Volume = {15},
Number = {1},
Pages = {254-273},
Year = {2017},
Month = {January},
url = {http://dx.doi.org/10.1137/16M1068670},
Doi = {10.1137/16M1068670},
Key = {fds325890}
}

@article{fds333284,
Author = {Lin, L and Lu, J and Vanden-Eijnden, E},
Title = {A Mathematical Theory of Optimal Milestoning (with a Detour
via Exact Milestoning)},
Journal = {Communications on Pure & Applied Mathematics},
Year = {2017},
Month = {January},
url = {http://dx.doi.org/10.1002/cpa.21725},
Abstract = {© 2017 Wiley Periodicals, Inc. Milestoning is a
computational procedure that reduces the dynamics of complex
systems to memoryless jumps between intermediates, or
milestones, and only retains some information about the
probability of these jumps and the time lags between them.
Here we analyze a variant of this procedure, termed optimal
milestoning, which relies on a specific choice of milestones
to capture exactly some kinetic features of the original
dynamical system. In particular, we prove that optimal
milestoning permits the exact calculation of the mean first
passage times (MFPT) between any two milestones. In so
doing, we also analyze another variant of the method, called
exact milestoning, which also permits the exact calculation
of certain MFPTs, but at the price of retaining more
information about the original system's dynamics. Finally,
we discuss importance sampling strategies based on optimal
and exact milestoning that can be used to bypass the
simulation of the original system when estimating the
statistical quantities used in these methods.},
Doi = {10.1002/cpa.21725},
Key = {fds333284}
}

@article{fds323661,
Author = {Li, Q and Lu, J and Sun, W},
Title = {Validity and Regularization of Classical Half-Space
Equations},
Journal = {Journal of Statistical Physics},
Volume = {166},
Number = {2},
Pages = {398-433},
Year = {2017},
Month = {January},
url = {http://dx.doi.org/10.1007/s10955-016-1688-4},
Doi = {10.1007/s10955-016-1688-4},
Key = {fds323661}
}

@article{fds332173,
Author = {Li, Q and Lu, J},
Title = {An asymptotic preserving method for transport equations with
oscillatory scattering coefficients},
Journal = {Multiscale Modeling & Simulation},
Volume = {15},
Number = {4},
Pages = {1694-1718},
Year = {2017},
Month = {January},
url = {http://dx.doi.org/10.1137/16M109212X},
Abstract = {© 2017 Society for Industrial and Applied Mathematics. We
design a numerical scheme for transport equations with
oscillatory periodic scattering coefficients. The scheme is
asymptotic preserving in the diffusion limit as the Knudsen
number goes to zero. It also captures the homogenization
limit as the length scale of the scattering coefficient goes
to zero. The proposed method is based on the construction of
multiscale finite element basis and a Galerkin projection
based on the even-odd decomposition. The method is analyzed
in the asymptotic regime, as well as validated
numerically.},
Doi = {10.1137/16M109212X},
Key = {fds332173}
}

@article{fds327371,
Author = {Gao, Y and Liu, J-G and Lu, J},
Title = {Weak Solution of a Continuum Model For Vicinal Surface in
The Attachment-Detachment-Limited Regime},
Journal = {SIAM Journal on Mathematical Analysis},
Volume = {49},
Number = {3},
Pages = {1705-1731},
Year = {2017},
Month = {January},
url = {http://dx.doi.org/10.1137/16M1094543},
Abstract = {© 2017 Society for Industrial and Applied Mathematics. We
study in this work a continuum model derived from a
one-dimensional attachmentdetachment-limited type step flow
on a vicinal surface, u t = -u 2 (u 3 ) hhhh , where u,
considered as a function of step height h, is the step slope
of the surface. We formulate a notion of a weak solution to
this continuum model and prove the existence of a global
weak solution, which is positive almost everywhere. We also
study the long time behavior of the weak solution and prove
it converges to a constant solution as time goes to
infinity. The space-time Hölder continuity of the weak
solution is also discussed as a byproduct.},
Doi = {10.1137/16M1094543},
Key = {fds327371}
}

@article{fds325467,
Author = {Cornelis, B and Yang, H and Goodfriend, A and Ocon, N and Lu, J and Daubechies, I},
Title = {Removal of Canvas Patterns in Digital Acquisitions of
Paintings.},
Journal = {IEEE Transactions on Image Processing},
Volume = {26},
Number = {1},
Pages = {160-171},
Year = {2017},
Month = {January},
url = {http://dx.doi.org/10.1109/tip.2016.2621413},
Abstract = {We address the removal of canvas artifacts from
high-resolution digital photographs and X-ray images of
paintings on canvas. Both imaging modalities are common
investigative tools in art history and art conservation.
Canvas artifacts manifest themselves very differently
according to the acquisition modality; they can hamper the
visual reading of the painting by art experts, for instance,
in preparing a restoration campaign. Computer-aided canvas
removal is desirable for restorers when the painting on
canvas they are preparing to restore has acquired over the
years a much more salient texture. We propose a new
algorithm that combines a cartoon-texture decomposition
method with adaptive multiscale thresholding in the
frequency domain to isolate and suppress the canvas
components. To illustrate the strength of the proposed
method, we provide various examples, for acquisitions in
both imaging modalities, for paintings with different types
of canvas and from different periods. The proposed algorithm
outperforms previous methods proposed for visual photographs
such as morphological component analysis and Wiener
filtering and it also works for the digital removal of
canvas artifacts in X-ray images.},
Doi = {10.1109/tip.2016.2621413},
Key = {fds325467}
}

@article{fds329524,
Author = {Gao, Y and Liu, J-G and Lu, J},
Title = {Weak Solution of a Continuum Model For Vicinal Surface in
The Attachment-Detachment-Limited Regime},
Journal = {SIAM Journal on Mathematical Analysis},
Volume = {49},
Number = {3},
Pages = {1705-1731},
Year = {2017},
Month = {January},
url = {http://dx.doi.org/10.1137/16M1094543},
Doi = {10.1137/16M1094543},
Key = {fds329524}
}

@article{fds331396,
Author = {Liu, J-G and Wang, J},
Title = {A generalized Sz. Nagy inequality in higher dimensions and
the critical thin film equation},
Journal = {Nonlinearity},
Volume = {30},
Number = {1},
Pages = {35-60},
Year = {2017},
Month = {January},
url = {http://dx.doi.org/10.1088/0951-7715/30/1/35},
Doi = {10.1088/0951-7715/30/1/35},
Key = {fds331396}
}

@article{fds323838,
Author = {Degond, P and Liu, J-G and Merino-Aceituno, S and Tardiveau,
T},
Title = {Continuum dynamics of the intention field under weakly
cohesive social interaction},
Journal = {Mathematical Models & Methods in Applied
Sciences},
Volume = {27},
Number = {01},
Pages = {159-182},
Year = {2017},
Month = {January},
url = {http://dx.doi.org/10.1142/S021820251740005X},
Doi = {10.1142/S021820251740005X},
Key = {fds323838}
}

@article{fds329525,
Author = {Gao, Y and Liu, J-G},
Title = {Global Convergence of a Sticky Particle Method for the
Modified Camassa--Holm Equation},
Journal = {SIAM Journal on Mathematical Analysis},
Volume = {49},
Number = {2},
Pages = {1267-1294},
Year = {2017},
Month = {January},
url = {http://dx.doi.org/10.1137/16M1102069},
Doi = {10.1137/16M1102069},
Key = {fds329525}
}

@article{fds330536,
Author = {Liu, J-G and Xu, X},
Title = {Analytical Validation of a Continuum Model for the Evolution
of a Crystal Surface in Multiple Space Dimensions},
Journal = {SIAM Journal on Mathematical Analysis},
Volume = {49},
Number = {3},
Pages = {2220-2245},
Year = {2017},
Month = {January},
url = {http://dx.doi.org/10.1137/16M1098474},
Doi = {10.1137/16M1098474},
Key = {fds330536}
}

@article{fds328806,
Author = {Tomita, TM and Maggioni, M and Vogelstein, JT},
Title = {ROFLMAO: Robust oblique forests with linear MAtrix
operations},
Journal = {Proceedings of the 17th SIAM International Conference on
Data Mining, SDM 2017},
Pages = {498-506},
Year = {2017},
Month = {January},
ISBN = {9781611974874},
Abstract = {Copyright © by SIAM. Random Forest (RF) remains one of the
most widely used general purpose classification methods. Two
recent largescale empirical studies demonstrated it to be
the best overall classification method among a variety of
methods evaluated. One of its main limitations, however, is
that it is restricted to only axis-aligned recursive
partitions of the feature space. Consequently, RF is
particularly sensitive to the orientation of the data.
Several studies have proposed "oblique" decision forest
methods to address this limitation. However, these methods
either have a time and space complexity significantly
greater than RF, are sensitive to unit and scale, or
empirically do not perform as well as RF on real data. One
promising oblique method that was proposed alongside the
canonical RF method, called Forest-RC (F-RC), has not
received as much attention by the community. Despite it
being just as old as RF, virtually no studies exist
investigating its theoretical or empirical performance. In
this work, we demonstrate that F-RC empirically outperforms
RF and another recently proposed oblique method called
Random Rotation Random Forest, while approximately
maintaining the same computational complexity. Furthermore,
a variant of F-RC which rank transforms the data prior to
learning is especially invariant to affine transformations
and robust to data corruption. Open source code is
available.},
Key = {fds328806}
}

@article{fds325966,
Author = {Crosskey, M and Maggioni, M},
Title = {ATLAS: A Geometric Approach to Learning High-Dimensional
Stochastic Systems Near Manifolds},
Journal = {Multiscale Modeling & Simulation},
Volume = {15},
Number = {1},
Pages = {110-156},
Year = {2017},
Month = {January},
url = {http://dx.doi.org/10.1137/140970951},
Doi = {10.1137/140970951},
Key = {fds325966}
}

@article{fds330521,
Author = {Cieliebak, K and Ekholm, T and Latschev, J and Ng,
L},
Title = {Knot contact homology, string topology, and the cord
algebra},
Volume = {4},
Pages = {661-780},
Year = {2017},
Month = {January},
url = {http://dx.doi.org/10.5802/jep.55},
Abstract = {The conormal Lagrangian L K of a knot K in R 3 is the
submanifold of the cotangent bundle T ∗ R 3 consisting of
covectors along K that annihilate tangent vectors to K. By
intersecting with the unit cotangent bundle S ∗ R 3 , one
obtains the unit conormal Λ K , and the Legendrian contact
homology of Λ K is a knot invariant of K, known as knot
contact homology. We define a version of string topology for
strings in R 3 ∪ L K and prove that this is isomorphic in
degree 0 to knot contact homology. The string topology
perspective gives a topological derivation of the cord
algebra (also isomorphic to degree 0 knot contact homology)
and relates it to the knot group. Together with the
isomorphism this gives a new proof that knot contact
homology detects the unknot. Our techniques involve a
detailed analysis of certain moduli spaces of holomorphic
disks in T ∗ R 3 with boundary on R 3 ∪ L K
.},
Doi = {10.5802/jep.55},
Key = {fds330521}
}

@article{fds331366,
Author = {Agarwal, PK and Kumar, N and Sintos, S and Suri, S},
Title = {Range-max queries on uncertain data},
Journal = {Journal of Computer and System Sciences},
Year = {2017},
Month = {January},
url = {http://dx.doi.org/10.1016/j.jcss.2017.09.006},
Abstract = {© 2017. Let P be a set of n uncertain points in Rd, where
each point pi P is associated with a real value vi and
exists with probability αi (0,1] independently of the other
points. We present algorithms for building an index on P so
that for a d-dimensional query rectangle ρ, the expected
maximum value or the most-likely maximum value in ρ can be
computed quickly. Our main contributions include the
following: (i) The first index of sub-quadratic size to
achieve a sub-linear query time in any dimension. (ii) A
conditional lower bound for most-likely range-max queries,
based on the conjectured hardness of the set-intersection
problem. (iii) A near-linear-size index for estimating the
expected range-max value within approximation factor 1/2 in
O(polylog(n)) time. (iv) Extensions of our algorithm to more
general uncertainty models and for computing the top-k
values of the range-max.},
Doi = {10.1016/j.jcss.2017.09.006},
Key = {fds331366}
}

@article{fds330829,
Author = {Wu, Y and Gao, J and Agarwal, PK and Yang, J},
Title = {Finding diverse, high-value representatives on a surface of
Journal = {Proceedings of the VLDB Endowment International Conference
on Very Large Data Bases},
Volume = {10},
Number = {7},
Pages = {793-804},
Year = {2017},
Month = {January},
Abstract = {© 2017 VLDB Endowment. In many applications, the system
needs to selectively present a small subset of answers to
users. The set of all possible answers can be seen as an
elevation surface over a domain, where the elevation
measures the quality of each answer, and the dimensions of
the domain correspond to attributes of the answers with
which similarity between answers can be measured. This paper
considers the problem of finding a diverse set of k
high-quality representatives for such a surface. We show
that existing methods for diversified top-k and weighted
clustering problems are inadequate for this problem. We
propose k-DHR as a better formulation for the problem. We
show that k-DHR has a submodular and monotone objective
function, and we develop efficient algorithms for solving
k-DHR with provable guarantees. We conduct extensive
experiments to demonstrate the usefulness of the results
produced by k-DHR for applications in computational
lead-finding and fact-checking, as well as the efficiency
and effectiveness of our algorithms.},
Key = {fds330829}
}

@article{fds330830,
Author = {Garg, N and Sadiq, M and Agarwal, P},
Title = {GOASREP: Goal oriented approach for software requirements
elicitation and prioritization using analytic hierarchy
process},
Journal = {Advances in Intelligent Systems and Computing},
Volume = {516},
Pages = {281-287},
Year = {2017},
Month = {January},
ISBN = {9789811031557},
url = {http://dx.doi.org/10.1007/978-981-10-3156-4_28},
Abstract = {© Springer Nature Singapore Pte Ltd. 2017. Software
requirements elicitation is a valuable process for the
identification of software requirements according to the
need of different types of stake-holders. There are
different methods for the elicitation of software
requirements like traditional methods, group elicitation
methods, goal oriented methods, etc. Among these methods,
goal oriented methods have received much recognition by
software requirements engineering community. On the basis of
our literature review, we identify that “goal oriented
requirements elicitation processes do not support how to
select and prioritize the requirements using analytic
hierarchy process on the basis of the cost and effort
criteria”. Therefore, in-order to address this issue, we
proposed a method, i.e. GOASREP, for the elicitation of
software requirements using “goal oriented approach” and
the prioritization of the elicited requirements using
“analytic hierarchy process”. In the proposed method, we
used function point analysis approach for the estimation of
the cost of each requirement. COCOMO model has been applied
to estimate the effort of each requirement. Finally, the
usage of the GOASREP is explained using Institute
Examination System.},
Doi = {10.1007/978-981-10-3156-4_28},
Key = {fds330830}
}

@article{fds328966,
Author = {Li, Y and Yang, H},
Title = {Interpolative Butterfly Factorization},
Journal = {SIAM Journal on Scientific Computing},
Volume = {39},
Number = {2},
Pages = {A503-A531},
Year = {2017},
Month = {January},
url = {http://dx.doi.org/10.1137/16M1074941},
Doi = {10.1137/16M1074941},
Key = {fds328966}
}

@article{fds328558,
Author = {Lu, Y and Stuart, A and Weber, H},
Title = {Gaussian Approximations for Transition Paths in Brownian
Dynamics},
Journal = {SIAM Journal on Mathematical Analysis},
Volume = {49},
Number = {4},
Pages = {3005-3047},
Year = {2017},
Month = {January},
url = {http://dx.doi.org/10.1137/16M1071845},
Doi = {10.1137/16M1071845},
Key = {fds328558}
}

@article{fds318345,
Author = {Ma, Z and Zhang, Y and Zhou, Z},
Title = {An improved semi-Lagrangian time splitting spectral method
for the semi-classical Schrödinger equation with vector
potentials using NUFFT},
Journal = {Applied Numerical Mathematics},
Volume = {111},
Pages = {144-159},
Year = {2017},
Month = {January},
url = {http://dx.doi.org/10.1016/j.apnum.2016.08.015},
Doi = {10.1016/j.apnum.2016.08.015},
Key = {fds318345}
}

@article{fds322248,
Author = {Y. Gao and H. Ji and J. Liu and T. P. Witelski},
Title = {Global existence of solutions to a tear film model with
locally elevated evaporation rates},
Year = {2017},
url = {http://arxiv.org/abs/1701.00853},
Key = {fds322248}
}

@article{fds330523,
Author = {Pollack, A and Shah, S},
Title = {On the Rankin–Selberg integral of Kohnen and
Skoruppa},
Journal = {Mathematical Research Letters},
Volume = {24},
Number = {1},
Pages = {173-222},
Year = {2017},
url = {http://dx.doi.org/10.4310/MRL.2017.v24.n1.a8},
Doi = {10.4310/MRL.2017.v24.n1.a8},
Key = {fds330523}
}

@article{fds330335,
Author = {Pierce, LB and Turnage-Butterbaugh, CL and Wood,
MM},
Title = {An effective Chebotarev density theorem for families of
number fields, with an application to $\ell$-torsion in
class groups},
Journal = {(submitted)},
Year = {2017},
Abstract = {An effective Chebotarev density theorem for a fixed normal
extension $L/\mathbb{Q}$ provides an asymptotic, with an
explicit error term, for the number of primes of bounded
size with a prescribed splitting type in $L$. In many
applications one is most interested in the case where the
primes are small (with respect to the absolute discriminant
of $L$); this is well-known to be closely related to the
Generalized Riemann Hypothesis for the Dedekind zeta
function of $L$. In this work we prove a new effective
Chebotarev density theorem, independent of GRH, that
improves the previously known unconditional error term and
allows primes to be taken quite small (certainly as small as
an arbitrarily small power of the discriminant of $L$); this
theorem holds for the Galois closures of "almost all" number
fields that lie in an appropriate family of field
extensions. Such a family has fixed degree, fixed Galois
group of the Galois closure, and in certain cases a
ramification restriction on all tamely ramified primes in
each field; examples include totally ramified cyclic fields,
degree $n$ $S_n$-fields with square-free discriminant, and
degree $n$ $A_n$-fields. In all cases, our work is
independent of GRH; in some cases we assume the strong Artin
conjecture or hypotheses on counting number fields. The new
effective Chebotarev theorem is expected to have many
applications, of which we demonstrate two. First we prove
(for all integers $\ell \geq 1$) nontrivial bounds for
$\ell$-torsion in the class groups of "almost all" fields in
the families of fields we consider. This provides the first
nontrivial upper bounds for $\ell$-torsion, for all integers
$\ell \geq 1$, applicable to infinite families of fields of
arbitrarily large degree. Second, in answer to a question of
Ruppert, we prove that within each family, "almost all"
fields have a small generator.},
Key = {fds330335}
}

@article{fds325977,
Author = {Lin, L and Rao, V and Dunson, D},
Title = {Bayesian nonparametric inference on the Stiefel
manifold},
Journal = {Statistica Sinica},
Year = {2017},
url = {http://dx.doi.org/10.5705/ss.202016.0017},
Doi = {10.5705/ss.202016.0017},
Key = {fds325977}
}

@article{fds320425,
Author = {Hain, R},
Title = {Deligne-Beilinson Cohomology of Affine Groups},
Booktitle = {Hodge Theory and $L^2$-analysis},
Publisher = {International Press},
Editor = {Ji, L},
Year = {2017},
ISBN = {1571463518},
url = {http://arxiv.org/abs/1507.03144},
Abstract = {The goal of this paper is to develop the theory of
Deligne-Beilinson cohomology of affine groups with a mixed
Hodge structure. The motivation comes from Hodge theory and
the study of motives, where such groups appear. Several of
Francis Brown's period computations (arXiv:1407.5167) are
interpreted as elements of the DB cohomology of the relative
unipotent completion of $SL_2(Z)$ and their cup products.
The results in this paper are used in arXiv:1403.6443 where
they are used to prove that Pollack's quadratic relations
are motivic.},
Key = {fds320425}
}

@article{fds327403,
Author = {Jian, Y-Y and Pfister, HD and Narayanan, KR},
Title = {Approaching Capacity at High Rates with Iterative
Hard-Decision Decoding},
Journal = {IEEE Transactions on Information Theory},
Pages = {1-1},
Year = {2017},
url = {http://dx.doi.org/10.1109/TIT.2017.2717838},
Doi = {10.1109/TIT.2017.2717838},
Key = {fds327403}
}

@article{fds333681,
Author = {Häger, C and Pfister, HD},
Title = {Miscorrection-free Decoding of Staircase
Codes.},
Journal = {CoRR},
Volume = {abs/1709.06827},
Year = {2017},
Key = {fds333681}
}

@article{fds328056,
Author = {Fodor, G and Cornelis, B and Yin, R and Dooms, A and Daubechies,
I},
Title = {Cradle Removal in X-Ray Images of Panel Paintings},
Journal = {Image Processing On Line},
Volume = {7},
Pages = {23-42},
Year = {2017},
url = {http://dx.doi.org/10.5201/ipol.2017.174},
Doi = {10.5201/ipol.2017.174},
Key = {fds328056}
}

@article{fds329523,
Author = {Huang, H and Liu, J-G},
Title = {Discrete-in-time random particle blob method for the
Keller–Segel equation and convergence analysis},
Journal = {Communications in Mathematical Sciences},
Volume = {15},
Number = {7},
Pages = {1821-1842},
Year = {2017},
url = {http://dx.doi.org/10.4310/CMS.2017.v15.n7.a2},
Abstract = {© 2017 International Press. We establish an error estimate
of a discrete-in-time random particle blob method for the
Keller{Segel (KS) equation in ℝ d (d≥2). With a blob
size ε=N -1/d(d+1) log(N), we prove the convergence rate
between the solution to the KS equation and the empirical
measure of the random particle method under L 2 norm in
probability, where N is the number of the
particles.},
Doi = {10.4310/CMS.2017.v15.n7.a2},
Key = {fds329523}
}

@article{fds330537,
Author = {Degond, P and Herty, M and Liu, J-G},
Title = {Mean-field games and model predictive control},
Journal = {Communications in Mathematical Sciences},
Volume = {15},
Number = {5},
Pages = {1403-1422},
Year = {2017},
url = {http://dx.doi.org/10.4310/CMS.2017.v15.n5.a9},
Doi = {10.4310/CMS.2017.v15.n5.a9},
Key = {fds330537}
}

@article{fds333567,
Author = {Li, L and Liu, J-G},
Title = {A note on deconvolution with completely monotone sequences
and discrete fractional calculus},
Journal = {Quarterly of Applied Mathematics},
Pages = {1-1},
Year = {2017},
url = {http://dx.doi.org/10.1090/qam/1479},
Doi = {10.1090/qam/1479},
Key = {fds333567}
}

@article{fds333568,
Author = {Coquel, F and Jin, S and Liu, J-G and Wang, L},
Title = {Entropic sub-cell shock capturing schemes via Jin-Xin
relaxation and Glimm front sampling for scalar conservation
laws},
Journal = {Mathematics of Computation},
Pages = {1-1},
Year = {2017},
url = {http://dx.doi.org/10.1090/mcom/3253},
Doi = {10.1090/mcom/3253},
Key = {fds333568}
}

@article{fds333569,
Author = {Liu, J-G and Wang, L and Zhou, Z},
Title = {Positivity-preserving and asymptotic preserving method for
2D Keller-Segal equations},
Journal = {Mathematics of Computation},
Pages = {1-1},
Year = {2017},
url = {http://dx.doi.org/10.1090/mcom/3250},
Doi = {10.1090/mcom/3250},
Key = {fds333569}
}

@article{fds331594,
Author = {Li, L and Liu, J-G},
Title = {A note on deconvolution with completely monotone sequences
and discrete fractional calculus},
Journal = {Quarterly of Applied Mathematics},
Pages = {1-1},
Year = {2017},
url = {http://dx.doi.org/10.1090/qam/1479},
Doi = {10.1090/qam/1479},
Key = {fds331594}
}

@article{fds332376,
Author = {Ng, L and Rutherford, D and Shende, V and Sivek, S},
Title = {The cardinality of the augmentation category of a Legendrian
Journal = {Mathematical Research Letters},
Volume = {24},
Number = {6},
Pages = {1845-1874},
Year = {2017},
Key = {fds332376}
}

@article{fds330203,
Author = {Pierce, LB and Turnage-Butterbaugh, CL and Wood,
MM},
Title = {An effective Chebotarev density theorem for families of
number fields, with an application to $\ell$-torsion in
class groups},
Journal = {(submitted)},
Year = {2017},
Abstract = {An effective Chebotarev density theorem for a fixed normal
extension $L/\mathbb{Q}$ provides an asymptotic, with an
explicit error term, for the number of primes of bounded
size with a prescribed splitting type in $L$. In many
applications one is most interested in the case where the
primes are small (with respect to the absolute discriminant
of $L$); this is well-known to be closely related to the
Generalized Riemann Hypothesis for the Dedekind zeta
function of $L$. In this work we prove a new effective
Chebotarev density theorem, independent of GRH, that
improves the previously known unconditional error term and
allows primes to be taken quite small (certainly as small as
an arbitrarily small power of the discriminant of $L$); this
theorem holds for the Galois closures of "almost all" number
fields that lie in an appropriate family of field
extensions. Such a family has fixed degree, fixed Galois
group of the Galois closure, and in certain cases a
ramification restriction on all tamely ramified primes in
each field; examples include totally ramified cyclic fields,
degree $n$ $S_n$-fields with square-free discriminant, and
degree $n$ $A_n$-fields. In all cases, our work is
independent of GRH; in some cases we assume the strong Artin
conjecture or hypotheses on counting number fields. The new
effective Chebotarev theorem is expected to have many
applications, of which we demonstrate two. First we prove
(for all integers $\ell \geq 1$) nontrivial bounds for
$\ell$-torsion in the class groups of "almost all" fields in
the families of fields we consider. This provides the first
nontrivial upper bounds for $\ell$-torsion, for all integers
$\ell \geq 1$, applicable to infinite families of fields of
arbitrarily large degree. Second, in answer to a question of
Ruppert, we prove that within each family, "almost all"
fields have a small generator.},
Key = {fds330203}
}

@article{fds320661,
Author = {Guo, S and Pierce, LB and Roos, J and Yung, P},
Title = {Polynomial Carleson operators along monomial curves in the
plane},
Journal = {Journal of Geometric Analysis},
Publisher = {SPRINGER-VERLAG},
Year = {2017},
Abstract = {We prove $L^p$ bounds for partial polynomial Carleson
operators along monomial curves $(t,t^m)$ in the plane
$\mathbb{R}^2$ with a phase polynomial consisting of a
single monomial. These operators are "partial" in the sense
that we consider linearizing stopping-time functions that
depend on only one of the two ambient variables. A
motivation for studying these partial operators is the
curious feature that, despite their apparent limitations,
for certain combinations of curve and phase, $L^2$ bounds
for partial operators along curves imply the full strength
of the $L^2$ bound for a one-dimensional Carleson operator,
and for a quadratic Carleson operator. Our methods, which
can at present only treat certain combinations of curves and
phases, in some cases adapt a $TT^*$ method to treat phases
involving fractional monomials, and in other cases use a
known vector-valued variant of the Carleson-Hunt
theorem.},
Key = {fds320661}
}

@article{fds320660,
Author = {Ellenberg, J and Pierce, LB and Wood, MM},
Title = {On ℓ-torsion in class groups of number
fields},
Journal = {Algebra and Number Theory},
Volume = {11},
Number = {8},
Pages = {1739-1778},
Year = {2017},
url = {http://dx.doi.org/10.2140/ant.2017.11.1739},
Abstract = {© 2017 Mathematical Sciences Publishers. For each integer
ℓ ≥ 1, we prove an unconditional upper bound on the size
of the ℓ-torsion subgroup of the class group, which holds
for all but a zerodensity set of field extensions of Q of
degree d, for any fixed d ε {2; 3; 4; 5} (with the
additional restriction in the case d D 4 that the field be
non-D 4 ). For sufficiently large ℓ (specified
explicitly), these results are as strong as a previously
known bound that is conditional on GRH. As part of our
argument, we develop a probabilistic “Chebyshev sieve,”
and give uniform, power-saving error terms for the
asymptotics of quartic (non-D 4 ) and quintic fields with
chosen splitting types at a finite set of
primes.},
Doi = {10.2140/ant.2017.11.1739},
Key = {fds320660}
}

@article{fds320463,
Author = {Reed, MC and Best, J and Nijhout, HF},
Title = {Mathematical models of neuromodulation and implications for
neurology and psychiatry},
Editor = {Erdi, P and Battacharya, B and Cochran, A},
Year = {2017},
Key = {fds320463}
}

@article{fds320468,
Author = {Reed, MC and Lawley, S and Nijhout, HF},
Title = {Spiracular fluttering increases oxygen uptake},
Year = {2017},
Key = {fds320468}
}

@article{fds321770,
Author = {Reed, MC and Best, J and Nijhout, HF},
Title = {Mathematical models of neuromodulation and implications for
neurology and psychiatry},
Booktitle = {Computational Neurology and Psychiatry},
Publisher = {SPRINGER},
Editor = {Erdi, P and Bhattacharya, B and Cochran, A},
Year = {2017},
Key = {fds321770}
}

@article{fds330704,
Author = {Thanacoody, HKR and Nijhout, HF and Reed, MC and Thomas,
S},
Title = {Mathematical modeling of the effect of different intravenous
acetylcysteine regimens on hepatic glutathione regeneration
and hepatocyte death following simulated acetaminophen
overdose},
Journal = {Clinical Toxicology},
Volume = {55},
Number = {7},
Pages = {753-753},
Year = {2017},
Key = {fds330704}
}

@article{fds330705,
Author = {Thanacoody, HKR and Nijhout, HF and Reed, MC and Thomas,
S},
Title = {Mathematical modeling of the effect of late administration
of a novel acetylcysteine regimen based on the SNAP trial on
hepatic glutathione regeneration and hepatocyte death
following simulated acetaminophen overdose},
Journal = {Clinical Toxicology},
Volume = {55},
Number = {7},
Pages = {753-754},
Year = {2017},
Key = {fds330705}
}

@article{fds320662,
Author = {Saper, L},
Title = {Perverse sheaves and the reductive Borel-Serre
compactification},
Volume = {39},
Pages = {555-581},
Booktitle = {Hodge Theory and L²-analysis},
Publisher = {International Press},
Editor = {Ji, L},
Year = {2017},
Abstract = {We briefly introduce the theory of perverse sheaves with
special attention to the topological situation where strata
can have odd dimension. This is part of a project to use
perverse sheaves on the topological reductive Borel-Serre
compactification of a Hermitian locally symmetric space as a
tool to study perverse sheaves on the Baily-Borel
compactification, a projective algebraic variety. We sketch
why the decomposition theorem holds for the natural map
between the reductive Borel-Serre and the Baily-Borel
compactifications. We demonstrate how to calculate
extensions of simple perverse sheaves on the reductive
Borel-Serre compactification and illustrate with the example
of Sp(4,R).},
Key = {fds320662}
}

@article{fds330393,
Author = {M.A. Stern},
Title = {"Nonlinear Harmonic Forms and Indefinite Bochner Formulas "
in Hodge Theory and L^2-Analysis},
Volume = {39},
Publisher = {Higher Education Press},
Year = {2017},
Key = {fds330393}
}

@article{fds333669,
Author = {Zhu, W and Qiu, Q and Huang, J and Calderbank, AR and Sapiro, G and Daubechies, I},
Title = {LDMNet: Low Dimensional Manifold Regularized Neural
Networks.},
Journal = {CoRR},
Volume = {abs/1711.06246},
Year = {2017},
Key = {fds333669}
}

@inproceedings{MM:EEG,
Author = {E Causevic and R~R Coifman and R Isenhart and A Jacquin and E~R John and M Maggioni and L~S Prichep and F~J
Warner},
Title = {{QEEG}-based classification with wavelet packets and
microstate features for triage applications in the
{ER}},
Year = {2005},
Key = {MM:EEG}
}

@booklet{Greer04a,
Author = {J. B. Greer and A. L. Bertozzi},
Title = {H-1 solutions of a class of fourth order nonlinear equations
for image processing},
Journal = {Discrete And Continuous Dynamical Systems},
Volume = {10},
Number = {1-2},
Pages = {349 -- 366},
Year = {2004},
Key = {Greer04a}
}

@misc{PathNIH2004,
Author = {GL Davis and Mauro Maggioni and FJ Warner and FB Geshwind and AC Coppi and RA DeVerse and RR Coifman},
Title = {Hyper-spectral Analysis of normal and malignant colon tissue
microarray sections using a novel DMD system},
Year = {2004},
Key = {PathNIH2004}
}

@techreport{CMTech,
Author = {Ronald R Coifman and Mauro Maggioni},
Title = {Multiresolution Analysis associated to diffusion semigroups:
construction and fast algorithms},
Number = {YALE/DCS/TR-1289},
Organization = {Dept. Comp. Sci., Yale University},
Institution = {Dept. Comp. Sci., Yale University},
Year = {2004},
Key = {CMTech}
}



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ph: 919.660.2800
fax: 919.660.2821

Mathematics Department
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