Mathematics Faculty: Publications since January 2015
List all publications in the database. :chronological alphabetical combined listing:
%% Abel, Michael
@article{fds317698,
Title = {HOMFLYPT homology for general link diagrams and braidlike
isotopy},
Year = {2016},
Month = {June},
url = {http://arxiv.org/abs/1607.00314},
Key = {fds317698}
}
@article{fds311722,
Author = {M. Abel and M. Hogancamp},
Title = {Stable homology of torus links via categorified Young
symmetrizers II: onecolumn partitions},
Year = {2016},
Month = {February},
url = {http://arxiv.org/abs/1510.05330},
Key = {fds311722}
}
@article{fds300045,
Author = {M. Abel and L. Rozansky},
Title = {Virtual crossings and a filtration of the triply graded
homology of a link diagram},
Year = {2015},
Month = {February},
url = {http://arxiv.org/abs/1410.5892},
Key = {fds300045}
}
%% Addington, Nicolas
@article{fds226937,
Author = {N. Addington and W. Donovan and C. Meachan},
Title = {Mukai flops and Ptwists},
Year = {2015},
Month = {July},
url = {http://arxiv.org/abs/1507.02595},
Key = {fds226937}
}
@article{fds226938,
Author = {N. Addington and W. Donovan and C. Meachan},
Title = {Moduli spaces of torsion sheaves on K3 surfaces and derived
equivalences},
Year = {2015},
Month = {July},
url = {http://arxiv.org/abs/1507.02597},
Key = {fds226938}
}
@article{fds226939,
Author = {N. Addington and W. Donovan and E. Segal},
Title = {The PfaffianGrassmannian equivalence revisited},
Journal = {Alg. Geom.},
Volume = {2},
Number = {3},
Pages = {332364},
Year = {2015},
url = {http://arxiv.org/abs/1401.3661},
Key = {fds226939}
}
%% Agarwal, Pankaj K.
@article{fds318110,
Author = {Agarwal, PK and Aronov, B and HarPeled, S and Phillips, JM and Yi, K and Zhang, W},
Title = {NearestNeighbor Searching Under Uncertainty
II},
Journal = {ACM Transactions on Algorithms},
Volume = {13},
Number = {1},
Pages = {125},
Year = {2016},
Month = {October},
url = {http://dx.doi.org/10.1145/2955098},
Doi = {10.1145/2955098},
Key = {fds318110}
}
@article{fds318111,
Author = {Agarwal, PK and Kumar, N and Sintos, S and Suri, S},
Title = {Rangemax queries on uncertain data},
Journal = {Proceedings of the ACM SIGACTSIGMODSIGART Symposium on
Principles of Database Systems},
Volume = {26June01July2016},
Pages = {465476},
Year = {2016},
Month = {June},
ISBN = {9781450341912},
url = {http://dx.doi.org/10.1145/2902251.2902281},
Abstract = {© 2016 ACM.Let P be a set of n uncertain points in ℝd,
where each point pi ∈ P is associated with a real value vi
and a probability αi ∈ (0,1] of existence, i.e., each pi
exists with an independent probability αi. We present
algorithms for building an index on P so that for a
ddimensional query rectangle ρ, the expected maximum value
or the mostlikely maximum value in ρ can be computed
quickly. The specific contributions of our paper include the
following: (i) The first index of subquadratic size to
achieve a sublinear query time in any dimension d ≥ 1. It
also provides a tradeoff between query time and size of the
index. (ii) A conditional lower bound for the mostlikely
rangemax queries, based on the conjectured hardness of the
setintersection problem, which suggests that in the worst
case the product (query time)2 x (index size) is
Ω(n2/polylog(n)). (iii) A linearsize index for estimating
the expected rangemax value within approximation factor 1/2
in O(logcn) time, for some constant c > 0; that is, if the
expected maximum value is μ then the query procedure
returns a value μ′ with μ/2 ≤ μ′ ≤ μ. (iv)
Extensions of our algorithm to more general uncertainty
models and for computing the topk values of the
rangemax.},
Doi = {10.1145/2902251.2902281},
Key = {fds318111}
}
@article{fds318112,
Author = {Agarwal, PK and Fox, K and Munagala, K and Nath, A},
Title = {Parallel algorithms for constructing range and
nearestneighbor searching data structures},
Journal = {Proceedings of the ACM SIGACTSIGMODSIGART Symposium on
Principles of Database Systems},
Volume = {26June01July2016},
Pages = {429440},
Year = {2016},
Month = {June},
ISBN = {9781450341912},
url = {http://dx.doi.org/10.1145/2902251.2902303},
Abstract = {© 2016 ACM.With the massive amounts of data available
today, it is common to store and process data using multiple
machines. Parallel programming platforms such as MapReduce
and its variants are popular frameworks for handling such
large data. We present the first provably efficient
algorithms to compute, store, and query data structures for
range queries and approximate nearest neighbor queries in a
popular parallel computing abstraction that captures the
salient features of MapReduce and other massively parallel
communication (MPC) models. In particular, we describe
algorithms for kdtrees, range trees, and BBDtrees that
only require O(1) rounds of communication for both
preprocessing and querying while staying competitive in
terms of running time and workload to their classical
counterparts. Our algorithms are randomized, but they can be
made deterministic at some increase in their running time
and workload while keeping the number of rounds of
communication to be constant.},
Doi = {10.1145/2902251.2902303},
Key = {fds318112}
}
@article{fds318113,
Author = {Agarwal, PK and Fox, K and Pan, J and Ying, R},
Title = {Approximating dynamic time warping and edit distance for a
pair of point sequences},
Journal = {LIPIcs},
Volume = {51},
Pages = {6.16.16},
Year = {2016},
Month = {June},
url = {http://dx.doi.org/10.4230/LIPIcs.SoCG.2016.6},
Abstract = {© Pankaj K. Agarwal, Kyle Fox, Jiangwei Pan, and Rex
Ying.We present the first subquadratic algorithms for
computing similarity between a pair of point sequences in
doublestruck Rd, for any fixed d > 1, using dynamic time
warping (DTW) and edit distance, assuming that the point
sequences are drawn from certain natural families of curves.
In particular, our algorithms compute (1 +
ε)approximations of DTW and ED in nearlinear time for
point sequences drawn from κpacked or κbounded curves,
and subquadratic time for backbone sequences. Roughly
speaking, a curve is κpacked if the length of its
intersection with any ball of radius r is at most κ · r,
and it is κbounded if the subcurve between two curve
points does not go too far from the two points compared to
the distance between the two points. In backbone sequences,
consecutive points are spaced at approximately equal
distances apart, and no two points lie very close together.
Recent results suggest that a subquadratic algorithm for DTW
or ED is unlikely for an arbitrary pair of point sequences
even for d = 1. The commonly used dynamic programming
algorithms for these distance measures reduce the problem to
computing a minimumweight path in a grid graph. Our
algorithms work by constructing a small set of rectangular
regions that cover the grid vertices. The weights of
vertices inside each rectangle are roughly the same, and we
develop efficient procedures to compute the approximate
minimumweight paths through these rectangles.},
Doi = {10.4230/LIPIcs.SoCG.2016.6},
Key = {fds318113}
}
@article{fds314402,
Author = {Yu, A and Agarwal, PK and Yang, J},
Title = {Top$k$
Preferences in High Dimensions},
Journal = {IEEE Transactions on Knowledge and Data Engineering},
Volume = {28},
Number = {2},
Pages = {311325},
Year = {2016},
Month = {February},
ISSN = {10414347},
url = {http://dx.doi.org/10.1109/TKDE.2015.2451630},
Doi = {10.1109/TKDE.2015.2451630},
Key = {fds314402}
}
@article{fds315094,
Author = {Agarwal, PK and Fox, K and Salzman, O},
Title = {An efficient algorithm for computing highquality paths amid
polygonal obstacles},
Journal = {Proceedings of the Annual ACMSIAM Symposium on Discrete
Algorithms},
Volume = {2},
Pages = {11791192},
Year = {2016},
Month = {January},
ISBN = {9781510819672},
Abstract = {© Copyright (2016) by SIAM: Society for Industrial and
Applied Mathematics.We study a pathplanning problem amid a
set 0 of obstacles in R2, in which we wish to compute a
short path between two points while also maintaining a high
clearance from 0; the clearance of a point is its distance
from a nearest obstacle in 0. Specifically, the problem asks
for a path minimizing the reciprocal of the clearance
integrated over the length of the path. We present the first
polynomialtime approximation scheme for this problem. Let n
be the total number of obstacle vertices and let ϵ ∈ (0,
1]. Our algorithm computes in time 0(n2/ϵ2 log n/ϵ) a path
of total cost at most (1 + ϵ) times the cost of the optimal
path.},
Key = {fds315094}
}
@article{fds235347,
Author = {Agarwal, PK and Gao, J and Guibas, LJ and Kaplan, H and Rubin, N and Sharir, M},
Title = {Stable Delaunay Graphs},
Journal = {Discrete & Computational Geometry},
Volume = {54},
Number = {4},
Pages = {905929},
Year = {2015},
Month = {December},
ISSN = {01795376},
url = {http://dx.doi.org/10.1007/s004540159730x},
Doi = {10.1007/s004540159730x},
Key = {fds235347}
}
@article{fds235355,
Author = {Agarwal, PK and Kaplan, H and Rubin, N and Sharir,
M},
Title = {Kinetic Voronoi Diagrams and Delaunay Triangulations under
Polygonal Distance Functions},
Journal = {Discrete & Computational Geometry},
Volume = {54},
Number = {4},
Pages = {871904},
Year = {2015},
Month = {December},
ISSN = {01795376},
url = {http://dx.doi.org/10.1007/s0045401597293},
Doi = {10.1007/s0045401597293},
Key = {fds235355}
}
@article{fds313238,
Author = {Zhang, W and Agarwal, PK and Mukherjee, S},
Title = {Contour trees of uncertain terrains},
Journal = {GIS: Proceedings of the ACM International Symposium on
Advances in Geographic Information Systems},
Volume = {0306November2015},
Year = {2015},
Month = {November},
ISBN = {9781450339674},
url = {http://dx.doi.org/10.1145/2820783.2820823},
Abstract = {We study contour trees of terrains, which encode the
topological changes of the level set of the height value ℓ
as we raise ℓ from ∞ to +∞ on the terrains, in the
presence of uncertainty in data. We assume that the terrain
is represented by a piecewiselinear height function over a
planar triangulation M, by specifying the height of each
vertex. We study the case when M is fixed and the
uncertainty lies in the height of each vertex in the
triangulation, which is described by a probability
distribution. We present efficient samplingbased Monte
Carlo methods for estimating, with high probability, (i) the
probability that two points lie on the same edge of the
contour tree, within additive error; (ii) the expected
distance of two points p; q and the probability that the
distance of p; q is at least ℓ on the contour tree, within
additive error, where the distance of p; q on a contour tree
is defined to be the difference between the maximum height
and the minimum height on the unique path from p to q on the
contour tree. The main technical contribution of the paper
is to prove that a small number of samples are sufficient to
estimate these quantities. We present two applications of
these algorithms, and also some experimental results to
demonstrate the effectiveness of our approach.},
Doi = {10.1145/2820783.2820823},
Key = {fds313238}
}
@article{fds313245,
Author = {Agarwal, PK and Mølhave, T and Revsbæk, M and Safa, I and Wang, Y and Yang, J},
Title = {Maintaining Contour Trees of Dynamic Terrains},
Journal = {LIPIcs},
Volume = {34},
Pages = {796811},
Year = {2015},
Month = {June},
ISSN = {18688969},
url = {http://dx.doi.org/10.4230/LIPIcs.SOCG.2015.796},
Abstract = {We study the problem of maintaining the contour tree T of a
terrain σ, represented as a triangulated xymonotone
surface, as the heights of its vertices vary continuously
with time. We characterize the combinatorial changes in T
and how they relate to topological changes in. We present a
kinetic data structure (KDS) for maintaining T efficiently.
It maintains certificates that fail, i.e., an event occurs,
only when the heights of two adjacent vertices become equal
or two saddle vertices appear on the same contour. Assuming
that the heights of two vertices of κ become equal only
O(1) times and these instances can be computed in O(1) time,
the KDS processes O(κ + n) events, where n is the number of
vertices in σ and κ; is the number of events at which the
combinatorial structure of T changes, and processes each
event in O(log n) time. The KDS can be extended to maintain
an augmented contour tree and a join/split
tree.},
Doi = {10.4230/LIPIcs.SOCG.2015.796},
Key = {fds313245}
}
@article{fds313246,
Author = {Agarwal, PK and Fox, K and Nath, A and Sidiropoulos, A and Wang,
Y},
Title = {Computing the GromovHausdorff distance for metric
trees},
Journal = {Lecture notes in computer science},
Volume = {9472},
Pages = {529540},
Year = {2015},
Month = {January},
ISSN = {03029743},
url = {http://dx.doi.org/10.1007/9783662489710_45},
Abstract = {© SpringerVerlag Berlin Heidelberg 2015.The
GromovHausdorff distance is a natural way to measure
distance between two metric spaces. We give the first proof
of hardness and first nontrivial approximation algorithm
for computing the GromovHausdorff distance for geodesic
metrics in trees. Specifically, we prove it is NPhard to
approximate the GromovHausdorff distance better than a
factor of 3. We complement this result by providing a
polynomial time O(min{n, √rn})approximation algorithm
where r is the ratio of the longest edge length in both
trees to the shortest edge length. For metric trees with
unit length edges, this yields an O(√ n)approximation
algorithm.},
Doi = {10.1007/9783662489710_45},
Key = {fds313246}
}
@article{fds235346,
Author = {Agarwal, PK and Sharathkumar, R},
Title = {Streaming Algorithms for Extent Problems in High
Dimensions},
Journal = {Algorithmica},
Volume = {72},
Number = {1},
Pages = {8398},
Year = {2015},
ISSN = {01784617},
url = {http://dx.doi.org/10.1007/s0045301398464},
Abstract = {© 2013, Springer Science+Business Media New York.We present
(singlepass) streaming algorithms for maintaining extent
measures of a stream S of n points in $\mathbb{R} ^{d}$. We
focus on designing streaming algorithms whose working space
is polynomial in d (poly(d)) and sublinear in n. For the
problems of computing diameter, width and minimum enclosing
ball of S, we obtain lower bounds on the worstcase
approximation ratio of any streaming algorithm that uses
poly(d) space. On the positive side, we introduce the notion
of blurred ball cover and use it for answering approximate
farthestpoint queries and maintaining approximate minimum
enclosing ball and diameter of S. We describe a streaming
algorithm for maintaining a blurred ball cover whose working
space is linear in d and independent of n.},
Doi = {10.1007/s0045301398464},
Key = {fds235346}
}
%% Allman, Justin
@article{fds300039,
Author = {J. Allman},
Title = {An iterated residue perspective on stable Grothendieck
polynomials},
Year = {2015},
url = {http://arxiv.org/abs/1408.1911v2},
Abstract = {http://arxiv.org/abs/1408.1911v2},
Key = {fds300039}
}
%% Arlotto, Alessandro
@article{fds319303,
Author = {Arlotto, A and Nguyen, VV and Steele, JM},
Title = {Optimal online selection of a monotone subsequence: a
central limit theorem},
Journal = {Stochastic Processes and their Applications},
Volume = {125},
Number = {9},
Pages = {35963622},
Year = {2015},
Month = {September},
url = {http://dx.doi.org/10.1016/j.spa.2015.03.009},
Doi = {10.1016/j.spa.2015.03.009},
Key = {fds319303}
}
%% Aspinwall, Paul S.
@article{fds243265,
Author = {Aspinwall, PS},
Title = {Exoflops in two dimensions},
Journal = {The Journal of High Energy Physics},
Volume = {2015},
Number = {7},
Year = {2015},
Month = {July},
url = {http://dx.doi.org/10.1007/JHEP07(2015)104},
Doi = {10.1007/JHEP07(2015)104},
Key = {fds243265}
}
@article{fds243266,
Author = {Aspinwall, PS and Gaines, B},
Title = {Rational curves and (0, 2)deformations},
Journal = {Journal of Geometry and Physics},
Volume = {88},
Pages = {115},
Year = {2015},
Month = {February},
ISSN = {03930440},
url = {http://dx.doi.org/10.1016/j.geomphys.2014.09.012},
Doi = {10.1016/j.geomphys.2014.09.012},
Key = {fds243266}
}
%% Basak, Anirban
@article{fds300033,
Author = {A. Basak and A. Dembo},
Title = {Ferromagnetic Ising measures on large locally tree like
graphs},
Journal = {The Annals of Probability},
Year = {2015},
Month = {October},
url = {http://arxiv.org/abs/1205.4749},
Key = {fds300033}
}
@article{fds300030,
Author = {A. Basak and S. Mukherjee},
Title = {Universality of meanfield for the Potts
model},
Year = {2015},
Month = {August},
url = {http://arxiv.org/abs/1508.03949},
Key = {fds300030}
}
@article{fds300031,
Author = {A. Basak and M. Rudelson},
Title = {Invertibility of sparse nonHermitian matrices},
Year = {2015},
Month = {July},
url = {http://arxiv.org/abs/1507.03525},
Key = {fds300031}
}
@article{fds300034,
Author = {A. Basak and A. Bose and S. S. Mukherjee},
Title = {Limiting spectral distribution of a class of Hankel type
random matrices},
Journal = {Random Matrices: Theory and Applications},
Year = {2015},
Month = {April},
url = {http://arxiv.org/abs/1408.0874},
Key = {fds300034}
}
%% Beale, J. Thomas
@article{fds226858,
Author = {J. t. Beale and W. YIng and J. R. Wilson},
Title = {A simple method for computing singular or nearly singular
integrals on closed surfaces},
Journal = {Commun. Comput. Phys.},
Year = {2015},
Month = {August},
url = {http://www.math.duke.edu/faculty/beale/papers/bywcicp.pdf},
Key = {fds226858}
}
@article{fds243316,
Author = {Beale, JT},
Title = {Uniform Error Estimates for NavierStokes Flow with an
Exact Moving Boundary Using the Immersed Interface
Method},
Journal = {SIAM Journal on Numerical Analysis},
Volume = {53},
Number = {4},
Pages = {20972111},
Year = {2015},
Month = {January},
ISSN = {00361429},
url = {http://www.math.duke.edu/faculty/beale/papers/nseiim.pdf},
Doi = {10.1137/151003441},
Key = {fds243316}
}
%% Bendich, Paul L
@article{fds315426,
Author = {Bendich, P and Marron, JS and Miller, E and Pieloch, A and Skwerer,
S},
Title = {Persistent Homology Analysis of Brain Artery
Trees.},
Journal = {The annals of applied statistics},
Volume = {10},
Number = {1},
Pages = {198218},
Year = {2016},
Month = {January},
ISSN = {19326157},
url = {http://hdl.handle.net/10161/11157 Duke open
access},
Abstract = {New representations of treestructured data objects, using
ideas from topological data analysis, enable improved
statistical analyses of a population of brain artery trees.
A number of representations of each data tree arise from
persistence diagrams that quantify branching and looping of
vessels at multiple scales. Novel approaches to the
statistical analysis, through various summaries of the
persistence diagrams, lead to heightened correlations with
covariates such as age and sex, relative to earlier analyses
of this data set. The correlation with age continues to be
significant even after controlling for correlations from
earlier significant summaries.},
Doi = {10.1214/15AOAS886},
Key = {fds315426}
}
@article{fds311346,
Author = {Paul Bendich and Ellen Gasparovic and John Harer and Christopher
J. Tralie},
Title = {Scaffoldings and Spines: Organizing HighDimensional Data
Using Cover Trees, Local Principal Component Analysis, and
Persistent Homology},
Year = {2016},
url = {http://arxiv.org/abs/1602.06245},
Key = {fds311346}
}
@article{fds315427,
Author = {Bendich, P and Gasparovic, E and Harer, J and Izmailov, R and Ness,
L},
Title = {Multiscale local shape analysis and feature selection in
machine learning applications},
Journal = {Proceedings of the International Joint Conference on Neural
Networks},
Volume = {2015September},
Pages = {18},
Year = {2015},
Month = {September},
url = {http://hdl.handle.net/10161/12014 Duke open
access},
Abstract = {© 2015 IEEE.We introduce a method called multiscale local
shape analysis for extracting features that describe the
local structure of points within a dataset. The method uses
both geometric and topological features at multiple levels
of granularity to capture diverse types of local information
for subsequent machine learning algorithms operating on the
dataset. Using synthetic and real dataset examples, we
demonstrate significant performance improvement of
classification algorithms constructed for these datasets
with correspondingly augmented features.},
Doi = {10.1109/IJCNN.2015.7280428},
Key = {fds315427}
}
@article{fds292867,
Author = {Paul Bendich and Peter Bubenik},
Title = {Stabilizing the output of persistent homology
computations},
Journal = {Proc. 2016 Symposium on Computational Geometry},
Year = {2015},
url = {http://arxiv.org/abs/1512.01700},
Key = {fds292867}
}
@article{fds227233,
Author = {Paul Bendich and Sang Chin and Jesse Clarke and Jonathan DeSena and John
Harer, Liz Munch and Andrew Newman and David Porter and David
Rouse, Nate Strawn and Adam Watkins.},
Title = {Topological and Statistical Behavior Classifiers for
Tracking Applications},
Journal = {IEEE Transactions on Aerospace and Electronic
Systems},
Year = {2015},
Key = {fds227233}
}
@article{fds226628,
Author = {Liz Munch and Paul Bendich and Kate Turner and Sayan Mukherjee and Jonathan Mattingly and John Harer},
Title = {Probabalistic Frechet Means and Statistics on
Vineyards},
Journal = {Electronic Journal of Statistics},
Volume = {9},
Pages = {11731204},
Year = {2015},
url = {http://arxiv.org/abs/1307.6530},
Abstract = {In order to use persistence diagrams as a true statistical
tool, it would be very useful to have a good notion of mean
and variance for a set of diagrams. In [21], Mileyko and his
collaborators made the rst study of the properties of the
Frechet mean in (Dp;Wp), the space of persistence diagrams
equipped with the pth Wasserstein metric. In particular,
they showed that the Frechet mean of a nite set of diagrams
always exists, but is not necessarily unique. As an
unfortunate consequence, one sees that the means of a
continuouslyvarying set of diagrams do not themselves vary
continuously, which presents obvious problems when trying to
extend the Frechet mean de nition to the realm of
vineyards. We x this problem by altering the original de
nition of Frechet mean so that it now becomes a probability
measure on the set of persistence diagrams; in a nutshell,
the mean of a set of diagrams will be a weighted sum of
atomic measures, where each atom is itself the (Frechet
mean) persistence diagram of a perturbation of the input
diagrams. We show that this new de nition de nes a (Holder)
continuous map, for each k, from (Dp)k ! P(Dp), and we
present several examples to show how it may become a useful
statistic on vineyards.},
Key = {fds226628}
}
@article{fds227232,
Author = {Christopher J Tralie and Paul Bendich},
Title = {Cover Song Identification with Timbral Shape},
Journal = {Proceedings of the 16th International Society for Music
Information Retrieval},
Pages = {3844},
Year = {2015},
url = {http://arxiv.org/abs/1507.05143},
Abstract = {We introduce a novel low level feature for identifying cover
songs which quantifies the relative changes in the smoothed
frequency spectrum of a song. Our key insight is that a
sliding window representation of a chunk of audio can be
viewed as a timeordered point cloud in high dimensions. For
corresponding chunks of audio between different versions of
the same song, these point clouds are approximately rotated,
translated, and scaled copies of each other. If we treat
MFCC embeddings as point clouds and cast the problem as a
relative shape sequence, we are able to correctly identify
42/80 cover songs in the “Covers 80” dataset. By
contrast, all other work to date on cover songs exclusively
relies on matching note sequences from Chroma derived
features.},
Key = {fds227232}
}
@article{fds226627,
Author = {David Rouse and Adam Watkins and David Porter and John Harer and Paul
Bendich, Nate Strawn and Elizabeth Munch and Jonathan DeSena and Jesse
Clarke, Jeff Gilbert and Sang Chin and Andrew
Newman},
Title = {FeatureAided Multiple Hypothesis Tracking Using Topological
and Statistical Behavior Classifiers},
Journal = {SPIE DSS 2015},
Volume = {9474},
Year = {2015},
Key = {fds226627}
}
@article{fds315425,
Author = {Tralie, CJ and Bendich, P},
Title = {Cover Song Identification with Timbral Shape
Sequences},
Journal = {Proc. of Int. Symp. on Music Inf. Retrieval},
Pages = {3844},
Year = {2015},
url = {http://arxiv.org/abs/1507.05143v1},
Abstract = {We introduce a novel low level feature for identifying cover
songs which quantifies the relative changes in the smoothed
frequency spectrum of a song. Our key insight is that a
sliding window representation of a chunk of audio can be
viewed as a timeordered point cloud in high dimensions. For
corresponding chunks of audio between different versions of
the same song, these point clouds are approximately rotated,
translated, and scaled copies of each other. If we treat
MFCC embeddings as point clouds and cast the problem as a
relative shape sequence, we are able to correctly identify
42/80 cover songs in the "Covers 80" dataset. By contrast,
all other work to date on cover songs exclusively relies on
matching note sequences from Chroma derived
features.},
Key = {fds315425}
}
%% Bertozzi, Andrea L
@booklet{Greer04a,
Author = {J. B. Greer and A. L. Bertozzi},
Title = {H1 solutions of a class of fourth order nonlinear equations
for image processing},
Journal = {Discrete And Continuous Dynamical Systems},
Volume = {10},
Number = {12},
Pages = {349  366},
Year = {2004},
Key = {Greer04a}
}
%% Bobrowski, Omer
@article{fds311845,
Author = {O Bobrowski and M Kahle and P Skraba},
Title = {Maximally Persistent Cycles in Random Geometric
Complexes},
Year = {2015},
Month = {September},
url = {http://arxiv.org/abs/1509.04347v2},
Abstract = {We initiate the study of persistent homology of random
geometric simplicial complexes. Our main interest is in
maximally persistent cycles of degree$k$ in persistent
homology, for a either the \cech or the VietorisRips
filtration built on a uniform Poisson process of intensity
$n$ in the unit cube $[0,1]^d$. This is a natural way of
measuring the largest "$k$dimensional hole" in a random
point set. This problem is in the intersection of geometric
probability and algebraic topology, and is naturally
motivated by a probabilistic view of topological inference.
We show that for all $d \ge 2$ and $1 \le k \le d1$ the
maximally persistent cycle has (multiplicative) persistence
of order $$ \Theta \left(\left(\frac{\log n}{\log \log n}
\right)^{1/k} \right),$$ with high probability,
characterizing its rate of growth as $n \to \infty$. The
implied constants depend on $k$, $d$, and on whether we
consider the VietorisRips or \cech filtration.},
Key = {fds311845}
}
@article{fds311846,
Author = {O Bobrowski and S Weinberger},
Title = {On the Vanishing of Homology in Random Čech
Complexes},
Year = {2015},
Month = {July},
url = {http://arxiv.org/abs/1507.06945v2},
Abstract = {We compute the homology of random \v{C}ech complexes over a
homogeneous Poisson process on the ddimensional torus, and
show that there are, coarsely, two phase transitions. The
first transition is analogous to the Erd\H{o}sR\'enyi phase
transition, where the \v{C}ech complex becomes connected.
The second transition is where all the other homology groups
are computed correctly (almost simultaneously). Our
calculations also suggest a finer measurement of scales,
where there is a further refinement to this picture and
separation between different homology groups.},
Key = {fds311846}
}
@article{fds225071,
Author = {O. Bobrowski and S. Mukherjee},
Title = {The Topology of Probability Distributions on
Manifolds},
Journal = {Probability Theory and Related Fields},
Volume = {161},
Number = {34},
Pages = {651686},
Year = {2015},
url = {http://dx.doi.org/10.1007/s004400140556x},
Doi = {10.1007/s004400140556x},
Key = {fds225071}
}
%% Braley, Emily L.
@article{fds299955,
Author = {Lindsay D. Waldrop and Stephen C. Adolph and Cecilia G. Diniz
Behn and Emily Braley and Joshua A. Drew and Robert J. Full and Louis J.
Gross and John A. Jungck and Brynja Kohler and Jennifer C. Prairie and Blerta Shtylla and Laura A. Miller},
Title = {Using Active Learning to Teach Concepts and Methods in
Quantitative Biology},
Journal = {Integrative and Comparative Biology},
Volume = {55},
Number = {5},
Pages = {933948},
Publisher = {Oxford University Press},
Year = {2015},
url = {http://icb.oxfordjournals.org/content/55/5/933.full.pdf?keytype=ref&ijkey=nSisiIyjS2Dqt85},
Abstract = {This article provides a summary of the ideas discussed at
the 2015 Annual Meeting of the Society for Integrative and
Comparative Biology societywide symposium on Leading
Students and Faculty to Quantitative Biology through Active
Learning. It also includes a brief review of the recent
advancements in incorporating active learning approaches
into quantitative biology classrooms. We begin with an
overview of recent literature that shows that active
learning can improve students’ outcomes in Science,
Technology, Engineering and Math Education disciplines. We
then discuss how this approach can be particularly useful
when teaching topics in quantitative biology. Next, we
describe some of the recent initiatives to develop handson
activities in quantitative biology at both the graduate and
the undergraduate levels. Throughout the article we provide
resources for educators who wish to integrate active
learning and technology into their classrooms.},
Doi = {10.1093/icb/icv097},
Key = {fds299955}
}
%% Bray, Hubert
@article{fds300017,
Author = {Bray, HL and Jauregui, JL and Mars, M},
Title = {Time Flat Surfaces and the Monotonicity of the Spacetime
Hawking Mass II},
Journal = {Annales Henri Poincaré},
Volume = {17},
Number = {6},
Pages = {14571475},
Publisher = {Springer Basel},
Year = {2016},
Month = {June},
ISSN = {14240637},
url = {http://arxiv.org/abs/1402.3287},
Abstract = {In this sequel paper we give a shorter, second proof of the
monotonicity of the Hawking mass for time flat surfaces
under spacelike uniformly area expanding flows in spacetimes
that satisfy the dominant energy condition. We also include
a third proof which builds on a known formula and describe a
class of sufficient conditions of divergence type for the
monotonicity of the Hawking mass. These flows of surfaces
may have connections to the problem in general relativity of
bounding the total mass of a spacetime from below by the
quasilocal mass of spacelike 2surfaces in the
spacetime.},
Doi = {10.1007/s0002301504202},
Key = {fds300017}
}
@article{fds303060,
Author = {MartinezMedina, LA and Bray, HL and Matos, T},
Title = {On wave dark matter in spiral and barred
galaxies},
Journal = {Journal of Cosmology and Astroparticle Physics},
Volume = {2015},
Number = {12},
Pages = {025025},
Year = {2015},
Month = {December},
url = {http://arxiv.org/abs/1505.07154},
Doi = {10.1088/14757516/2015/12/025},
Key = {fds303060}
}
@article{fds287065,
Author = {Bray, HL and Jauregui, JL},
Title = {On curves with nonnegative torsion},
Journal = {Archiv der Mathematik},
Volume = {104},
Number = {6},
Pages = {561575},
Year = {2015},
Month = {June},
ISSN = {0003889X},
url = {http://www.springer.com//0/c8d239381b86496b96d95ff26f1061eb},
Doi = {10.1007/s0001301507670},
Key = {fds287065}
}
@article{fds300016,
Author = {Bray, HL and Jauregui, JL},
Title = {Time Flat Surfaces and the Monotonicity of the Spacetime
Hawking Mass},
Journal = {Communications in Mathematical Physics},
Volume = {335},
Number = {1},
Pages = {285307},
Year = {2015},
Month = {April},
ISSN = {00103616},
url = {http://arxiv.org/abs/1310.8638},
Doi = {10.1007/s0022001421622},
Key = {fds300016}
}
@article{fds287070,
Author = {Bray, HL and Parry, AR},
Title = {Modeling wave dark matter in dwarf spheroidal
galaxies},
Journal = {Journal of Physics},
Volume = {615},
Year = {2015},
ISSN = {17426588},
url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000358144800001&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
Doi = {10.1088/17426596/615/1/012001},
Key = {fds287070}
}
%% Bryant, Robert
@article{fds300229,
Author = {R. Bryant},
Title = {On the convex PfaffDarboux Theorem of Ekeland and
Nirenberg},
Year = {2015},
Month = {December},
url = {http://arxiv.org/abs/1512.07100},
Abstract = {The classical PfaffDarboux Theorem, which provides local
`normal forms' for 1forms on manifolds, has applications in
the theory of certain economic models. However, the normal
forms needed in these models come with an additional
requirement of convexity, which is not provided by the
classical proofs of the PfaffDarboux Theorem. (The
appropriate notion of `convexity' is a feature of the
economic model. In the simplest case, when the economic
model is formulated in a domain in nspace, convexity has
its usual meaning. In 2002, Ekeland and Nirenberg were able
to characterize necessary and sufficient conditions for a
given 1form to admit a convex local normal form (and to
show that some earlier attempts at this characterization had
been unsuccessful). In this article, after providing some
necessary background, I prove a strengthened and generalized
convex PfaffDarboux Theorem, one that covers the case of a
Legendrian foliation in which the notion of convexity is
defined in terms of a torsionfree affine connection on the
underlying manifold. (The main result in Ekeland and
Nirenberg's paper concerns the case in which the affine
connection is flat.)},
Key = {fds300229}
}
@article{fds300153,
Author = {R. Bryant},
Title = {On the conformal volume of 2tori},
Year = {2015},
Month = {July},
url = {http://arxiv.org/abs/1507.01485},
Keywords = {conformal volume},
Abstract = {This preprint provides a proof of a 1985 conjecture of
Montiel and Ros about the conformal volume of
tori.},
Key = {fds300153}
}
%% Calderbank, Robert
@article{fds235746,
Author = {Bajwa, WU and Duarte, MF and Calderbank, R},
Title = {Conditioning of Random Block Subdictionaries With
Applications to BlockSparse Recovery and
Regression},
Journal = {IEEE Transactions on Information Theory},
Volume = {61},
Number = {7},
Pages = {40604079},
Year = {2015},
Month = {July},
ISSN = {00189448},
url = {http://dx.doi.org/10.1109/TIT.2015.2429632},
Doi = {10.1109/TIT.2015.2429632},
Key = {fds235746}
}
@article{fds235747,
Author = {Harms, A and Bajwa, WU and Calderbank, R},
Title = {Identification of Linear TimeVarying Systems Through
Waveform Diversity},
Journal = {IEEE Transactions on Signal Processing},
Volume = {63},
Number = {8},
Pages = {20702084},
Year = {2015},
Month = {April},
ISSN = {1053587X},
url = {http://dx.doi.org/10.1109/TSP.2015.2407319},
Doi = {10.1109/TSP.2015.2407319},
Key = {fds235747}
}
@article{fds235748,
Author = {Nokleby, M and Rodrigues, M and Calderbank, R},
Title = {Discrimination on the Grassmann Manifold: Fundamental Limits
of Subspace Classifiers},
Journal = {IEEE Transactions on Information Theory},
Volume = {61},
Number = {4},
Pages = {21332147},
Year = {2015},
Month = {April},
ISSN = {00189448},
url = {http://dx.doi.org/10.1109/TIT.2015.2407368},
Doi = {10.1109/TIT.2015.2407368},
Key = {fds235748}
}
@article{fds290773,
Author = {Wang, L and Huang, J and Yuan, X and Krishnamurthy, K and Greenberg, J and Cevher, V and Rodrigues, MRD and Brady, D and Calderbank, R and Carin,
L},
Title = {Signal Recovery and System Calibration from Multiple
Compressive Poisson Measurements},
Journal = {SIAM Journal on Imaging Sciences},
Volume = {8},
Number = {3},
Pages = {19231954},
Year = {2015},
Month = {January},
url = {http://dx.doi.org/10.1137/140998779},
Doi = {10.1137/140998779},
Key = {fds290773}
}
@article{fds235744,
Author = {Harms, A and Bajwa, W and Calderbank, R},
Title = {Efficient linear timevarying system identification using
chirp waveforms},
Journal = {Conference Record of the Asilomar Conference on Signals,
Systems and Computers},
Volume = {2015April},
Pages = {854858},
Year = {2015},
Month = {January},
ISBN = {9781479982974},
ISSN = {10586393},
url = {http://dx.doi.org/10.1109/ACSSC.2014.7094572},
Abstract = {© 2014 IEEE.Linear, timevarying (LTV) systems are
operators composed of time shifts, frequency shifts, and
complex amplitude scalings that act on continuous
finiteenergy waveforms. This paper builds upon a novel,
resourceefficient method previously proposed by the authors
for identifying the parametric description of such systems
from the sampled response to linear frequency modulated
(LFM) waveforms. If the LTV operator is probed with a
sufficiently diverse set of LFM pulses, more LFM pulses than
reflectors, then the system can be identified with high
accuracy. The accuracy is shown to be proportional to the
uncertainty in the estimated frequencies and confirmed with
numerical experiments.},
Doi = {10.1109/ACSSC.2014.7094572},
Key = {fds235744}
}
%% Chen, Ying
@article{fds300046,
Author = {Y. Chen and J. Shen},
Title = {Efficient, adaptive energy stable schemes for the
incompressible CahnHilliard NavierStokes phasefield
models},
Journal = {JCP},
Year = {2015},
Key = {fds300046}
}
%% Cornelis, Bruno I.
@article{fds299979,
Author = {Gabor Fodor and Bruno Cornelis and Rujie Yin and Ann Dooms and Ingrid
Daubechies},
Title = {Cradle removal in Xray images of panel paintings},
Journal = {Image Processing On Line (IPOL)},
Year = {2015},
Month = {December},
Key = {fds299979}
}
@article{fds299977,
Author = {A. Pizurica and L. Platisa and T. Ruzic and B. Cornelis and A. Dooms and M.
Martens, H. Dubois and B. Devolder and M. De Mey and I.
Daubechies},
Title = {Digital Image Processing of The Ghent Altarpiece: Supporting
the painting's study and conservation treatment},
Journal = {IEEE Signal Processing Magazine},
Volume = {32},
Number = {4},
Pages = {112  122},
Publisher = {IEEE},
Year = {2015},
Month = {July},
ISSN = {10535888},
Abstract = {Hanging in the Saint Bavo Cathedral in Ghent, Belgium, is
The Ghent Altarpiece, also known as The Adoration of the
Mystic Lamb (see Figure 1). According to an inscription on
the outer frames, it was painted by brothers Hubert and Jan
van Eyck for Joos Vijd and?his wife Elisabeth Borluut in
1432. It is one of the most admired and influential
paintings in the history of art and has given rise to many
intriguing questions that have been puzzling art historians
to date [11]. Moreover, the material history of the panels
is very complicated. They were hidden, dismantled, moved
away, stolen, and recovered during riots, fires and wars.
The recovery of the panels by the U.S. Army in the Nazi
hoards deep in the Altaussee salt mines has particularly
marked memories. One panel was stolen in 1934 and never
recovered. Besides varying conservation conditions, the
panels underwent numerous restoration treatments and were
even partially painted over.},
Key = {fds299977}
}
%% Curry, Justin
@article{UNKNOWN,
Author = {Curry, JustinMichael},
Title = {Topological data analysis and cosheaves},
Journal = {Japan Journal of Industrial and Applied Mathematics},
Volume = {32},
Number = {2},
Pages = {333371},
Publisher = {Springer Japan},
Year = {2015},
ISSN = {09167005},
url = {http://dx.doi.org/10.1007/s1316001501739},
Keywords = {Topological data analysis; Persistent homology; Sheaves and
cosheaves; Barcodes; ominimal topology; 55U99; 46M20;
32S60; 16G20; 6207; 03C64},
Language = {English},
Doi = {10.1007/s1316001501739},
Key = {UNKNOWN}
}
@article{UNKNOWN,
Author = {Curry, Justin and Ghrist, Robert and Nanda,
Vidit},
Title = {Discrete Morse Theory for Computing Cellular Sheaf
Cohomology},
Journal = {Foundations of Computational Mathematics},
Pages = {123},
Publisher = {Springer US},
Year = {2015},
ISSN = {16153375},
url = {http://dx.doi.org/10.1007/s1020801592668},
Keywords = {Cellular sheaf cohomology; Discrete Morse theory; 5504;
55N25; 55N30},
Language = {English},
Doi = {10.1007/s1020801592668},
Key = {UNKNOWN}
}
%% Daubechies, Ingrid
@article{fds318286,
Author = {Wu, HT and Lewis, GF and Davila, MI and Daubechies, I and Porges,
SW},
Title = {Optimizing Estimates of Instantaneous Heart Rate from Pulse
Wave Signals with the Synchrosqueezing Transform.},
Journal = {Methods of information in medicine},
Volume = {55},
Number = {5},
Pages = {463472},
Year = {2016},
Month = {October},
Abstract = {With recent advances in sensor and computer technologies,
the ability to monitor peripheral pulse activity is no
longer limited to the laboratory and clinic. Now inexpensive
sensors, which interface with smartphones or other
computerbased devices, are expanding into the consumer
market. When appropriate algorithms are applied, these new
technologies enable ambulatory monitoring of dynamic
physiological responses outside the clinic in a variety of
applications including monitoring fatigue, health, workload,
fitness, and rehabilitation. Several of these applications
rely upon measures derived from peripheral pulse waves
measured via contact or noncontact photoplethysmography
(PPG). As technologies move from contact to noncontact PPG,
there are new challenges. The technology necessary to
estimate average heart rate over a few seconds from a
noncontact PPG is available. However, a technology to
precisely measure instantaneous heat rate (IHR) from
noncontact sensors, on a beattobeat basis, is more
challenging.The objective of this paper is to develop an
algorithm with the ability to accurately monitor IHR from
peripheral pulse waves, which provides an opportunity to
measure the neural regulation of the heart from the
beattobeat heart rate pattern (i.e., heart rate
variability).The adaptive harmonic model is applied to model
the contact or noncontact PPG signals, and a new
methodology, the Synchrosqueezing Transform (SST), is
applied to extract IHR. The body sway rhythm inherited in
the noncontact PPG signal is modeled and handled by the
notion of waveshape function.The SST optimizes the
extraction of IHR from the PPG signals and the technique
functions well even during periods of poor signal to noise.
We contrast the contact and noncontact indices of PPG
derived heart rate with a criterion electrocardiogram (ECG).
ECG and PPG signals were monitored in 21 healthy subjects
performing tasks with different physical demands. The root
mean square error of IHR estimated by SST is significantly
better than commonly applied methods such as autoregressive
(AR) method. In the walking situation, while AR method
fails, SST still provides a reasonably good result.The SST
processed PPG data provided an accurate estimate of the ECG
derived IHR and consistently performed better than commonly
applied methods such as autoregressive method.},
Key = {fds318286}
}
@article{fds317216,
Author = {Yin, R and Monson, E and Honig, E and Daubechies, I and Maggioni,
M},
Title = {Object recognition in art drawings: Transfer of a neural
network},
Journal = {IEEE International Conference on Acoustics Speech and Signal
Processing},
Volume = {2016May},
Pages = {22992303},
Year = {2016},
Month = {May},
ISBN = {9781479999880},
ISSN = {15206149},
url = {http://dx.doi.org/10.1109/ICASSP.2016.7472087},
Abstract = {© 2016 IEEE.We consider the problem of recognizing objects
in collections of art works, in view of automatically
labeling, searching and organizing databases of art works.
To avoid manually labelling objects, we introduce a
framework for transferring a convolutional neural network
(CNN), trained on available large collections of labelled
natural images, to the context of drawings. We retrain both
the top and the bottom layer of the network, responsible for
the highlevel classiication output and the lowlevel
features detection respectively, by transforming natural
images into drawings. We apply this procedure to the
drawings in the Jan Brueghel Wiki, and show the transferred
CNN learns a discriminative metric on drawings and achieves
good recognition accuracy. We also discuss why standard
descriptorbased methods is problematic in the context of
drawings.},
Doi = {10.1109/ICASSP.2016.7472087},
Key = {fds317216}
}
@article{fds315774,
Author = {Daubechies, I and Wang, YG and Wu, HT},
Title = {ConceFT: concentration of frequency and time via a
multitapered synchrosqueezed transform.},
Journal = {Philosophical Transactions A},
Volume = {374},
Number = {2065},
Pages = {20150193},
Year = {2016},
Month = {April},
ISSN = {1364503X},
url = {http://dx.doi.org/10.1098/rsta.2015.0193},
Abstract = {A new method is proposed to determine the timefrequency
content of timedependent signals consisting of multiple
oscillatory components, with timevarying amplitudes and
instantaneous frequencies. Numerical experiments as well as
a theoretical analysis are presented to assess its
effectiveness.},
Doi = {10.1098/rsta.2015.0193},
Key = {fds315774}
}
@article{fds315775,
Author = {Huang, NE and Daubechies, I and Hou, TY},
Title = {Adaptive data analysis: theory and applications.},
Journal = {Philosophical Transactions A},
Volume = {374},
Number = {2065},
Pages = {20150207},
Year = {2016},
Month = {April},
ISSN = {1364503X},
url = {http://dx.doi.org/10.1098/rsta.2015.0207},
Doi = {10.1098/rsta.2015.0207},
Key = {fds315775}
}
@article{fds318287,
Author = {Yin, R and Cornelis, B and Fodor, G and Ocon, N and Dunson, D and Daubechies, I},
Title = {Removing Cradle Artifacts in XRay Images of
Paintings},
Journal = {SIAM Journal on Imaging Sciences},
Volume = {9},
Number = {3},
Pages = {12471272},
Year = {2016},
Month = {January},
url = {http://dx.doi.org/10.1137/15M1053554},
Doi = {10.1137/15M1053554},
Key = {fds318287}
}
@article{fds287094,
Author = {Daubechies, I and Saab, R},
Title = {A Deterministic Analysis of Decimation for SigmaDelta
Quantization of Bandlimited Functions},
Journal = {IEEE Signal Processing Letters},
Volume = {22},
Number = {11},
Pages = {20932096},
Year = {2015},
Month = {November},
ISSN = {10709908},
url = {http://dx.doi.org/10.1109/LSP.2015.2459758},
Doi = {10.1109/LSP.2015.2459758},
Key = {fds287094}
}
@article{fds287095,
Author = {Yang, H and Lu, J and Brown, WP and Daubechies, I and Ying,
L},
Title = {Quantitative Canvas Weave Analysis Using 2D Synchrosqueezed
Transforms: Application of timefrequency analysis to art
investigation},
Journal = {IEEE Signal Processing Magazine},
Volume = {32},
Number = {4},
Pages = {5563},
Year = {2015},
Month = {July},
ISSN = {10535888},
url = {http://hdl.handle.net/10161/12009 Duke open
access},
Doi = {10.1109/MSP.2015.2406882},
Key = {fds287095}
}
@article{fds287096,
Author = {Pizurica, A and Platisa, L and Ruzic, T and Cornelis, B and Dooms, A and Martens, M and Dubois, H and Devolder, B and De Mey and M and Daubechies,
I},
Title = {Digital Image Processing of The Ghent Altarpiece: Supporting
the painting's study and conservation treatment},
Journal = {IEEE Signal Processing Magazine},
Volume = {32},
Number = {4},
Pages = {112122},
Year = {2015},
Month = {July},
ISSN = {10535888},
url = {http://dx.doi.org/10.1109/MSP.2015.2411753},
Doi = {10.1109/MSP.2015.2411753},
Key = {fds287096}
}
@article{fds287098,
Author = {Boyer, DM and Puente, J and Gladman, JT and Glynn, C and Mukherjee, S and Yapuncich, GS and Daubechies, I},
Title = {A new fully automated approach for aligning and comparing
shapes.},
Journal = {The Anatomical Record : Advances in Integrative Anatomy and
Evolutionary Biology},
Volume = {298},
Number = {1},
Pages = {249276},
Year = {2015},
Month = {January},
ISSN = {19328486},
url = {http://dx.doi.org/10.1002/ar.23084},
Abstract = {Threedimensional geometric morphometric (3DGM) methods for
placing landmarks on digitized bones have become
increasingly sophisticated in the last 20 years, including
greater degrees of automation. One aspect shared by all 3DGM
methods is that the researcher must designate initial
landmarks. Thus, researcher interpretations of homology and
correspondence are required for and influence
representations of shape. We present an algorithm allowing
fully automatic placement of correspondence points on
samples of 3D digital models representing bones of different
individuals/species, which can then be input into standard
3DGM software and analyzed with dimension reduction
techniques. We test this algorithm against several samples,
primarily a dataset of 106 primate calcanei represented by
1,024 correspondence points per bone. Results of our
automated analysis of these samples are compared to a
published study using a traditional 3DGM approach with 27
landmarks on each bone. Data were analyzed with
morphologika(2.5) and PAST. Our analyses returned strong
correlations between principal component scores, similar
variance partitioning among components, and similarities
between the shape spaces generated by the automatic and
traditional methods. While cluster analyses of both
automatically generated and traditional datasets produced
broadly similar patterns, there were also differences.
Overall these results suggest to us that automatic
quantifications can lead to shape spaces that are as
meaningful as those based on observer landmarks, thereby
presenting potential to save time in data collection,
increase completeness of morphological quantification,
eliminate observer error, and allow comparisons of shape
diversity between different types of bones. We provide an R
package for implementing this analysis.},
Doi = {10.1002/ar.23084},
Key = {fds287098}
}
@article{fds287099,
Author = {Wang, YG and Wu, HT and Daubechies, I and Li, Y and Estes, EH and Soliman,
EZ},
Title = {Automated J wave detection from digital 12lead
electrocardiogram.},
Journal = {Journal of Electrocardiology},
Volume = {48},
Number = {1},
Pages = {2128},
Year = {2015},
Month = {January},
ISSN = {00220736},
url = {http://dx.doi.org/10.1016/j.jelectrocard.2014.10.006},
Abstract = {In this report we provide a method for automated detection
of J wave, defined as a notch or slur in the descending
slope of the terminal positive wave of the QRS complex,
using signal processing and functional data analysis
techniques. Two different sets of ECG tracings were selected
from the EPICARE ECG core laboratory, Wake Forest School of
Medicine, Winston Salem, NC. The first set was a training
set comprised of 100 ECGs of which 50 ECGs had Jwave and
the other 50 did not. The second set was a test set (n=116
ECGs) in which the Jwave status (present/absent) was only
known by the ECG Center staff. All ECGs were recorded using
GE MAC 1200 (GE Marquette, Milwaukee, Wisconsin) at 10mm/mV
calibration, speed of 25mm/s and 500HZ sampling rate. All
ECGs were initially inspected visually for technical errors
and inadequate quality, and then automatically processed
with the GE Marquette 12SL program 2001 version (GE
Marquette, Milwaukee, WI). We excluded ECG tracings with
major abnormalities or rhythm disorder. Confirmation of the
presence or absence of a J wave was done visually by the ECG
Center staff and verified once again by three of the
coauthors. There was no disagreement in the identification
of the J wave state. The signal processing and functional
data analysis techniques applied to the ECGs were conducted
at Duke University and the University of Toronto. In the
training set, the automated detection had sensitivity of
100% and specificity of 94%. For the test set, sensitivity
was 89% and specificity was 86%. In conclusion, test results
of the automated method we developed show a good J wave
detection accuracy, suggesting possible utility of this
approach for defining and detection of other complex ECG
waveforms.},
Doi = {10.1016/j.jelectrocard.2014.10.006},
Key = {fds287099}
}
@article{fds300272,
Author = {A. Pizurica and L. Platisa and T. Ruzic and B. Cornelis and A. Dooms and M.
Martens, H. Dubois and B. Devolder and M. De Mey and I.
Daubechies},
Title = {Digital Image Processing of The Ghent Altarpiece: Supporting
the painting's study and conservation treatment},
Journal = {IEEE Signal Processing Magazine},
Volume = {32},
Pages = {112122},
Publisher = {IEEE},
Year = {2015},
Key = {fds300272}
}
%% Deckard, Anastasia C
@article{fds292888,
Author = {Perea, JA and Deckard, A and Haase, SB and Harer,
J},
Title = {SW1PerS: Sliding windows and 1persistence scoring;
discovering periodicity in gene expression time series
data.},
Journal = {BMC Bioinformatics},
Volume = {16},
Pages = {257},
Year = {2015},
Month = {January},
url = {http://dx.doi.org/10.1186/s1285901506456},
Abstract = {Identifying periodically expressed genes across different
processes (e.g. the cell and metabolic cycles, circadian
rhythms, etc) is a central problem in computational biology.
Biological time series may contain (multiple) unknown signal
shapes of systemic relevance, imperfections like noise,
damping, and trending, or limited sampling density. While
there exist methods for detecting periodicity, their design
biases (e.g. toward a specific signal shape) can limit their
applicability in one or more of these situations.We present
in this paper a novel method, SW1PerS, for quantifying
periodicity in time series in a shapeagnostic manner and
with resistance to damping. The measurement is performed
directly, without presupposing a particular pattern, by
evaluating the circularity of a highdimensional
representation of the signal. SW1PerS is compared to other
algorithms using synthetic data and performance is
quantified under varying noise models, noise levels,
sampling densities, and signal shapes. Results on biological
data are also analyzed and compared.On the task of
periodic/notperiodic classification, using synthetic data,
SW1PerS outperforms all other algorithms in the lownoise
regime. SW1PerS is shown to be the most shapeagnostic of
the evaluated methods, and the only one to consistently
classify damped signals as highly periodic. On biological
data, and for several experiments, the lists of top 10%
genes ranked with SW1PerS recover up to 67% of those
generated with other popular algorithms. Moreover, the list
of genes from data on the Yeast metabolic cycle which are
highlyranked only by SW1PerS, contains evidently noncosine
patterns (e.g. ECM33, CDC9, SAM1,2 and MSH6) with highly
periodic expression profiles. In data from the Yeast cell
cycle SW1PerS identifies genes not preferred by other
algorithms, hence not previously reported as periodic, but
found in other experiments such as the universal growth rate
response of Slavov. These genes are BOP3, CDC10, YIL108W,
YER034W, MLP1, PAC2 and RTT101.In biological systems with
low noise, i.e. where periodic signals with interesting
shapes are more likely to occur, SW1PerS can be used as a
powerful tool in exploratory analyses. Indeed, by having an
initial set of periodic genes with a rich variety of signal
types, pattern/shape information can be included in the
study of systems and the generation of hypotheses regarding
the structure of gene regulatory networks.},
Doi = {10.1186/s1285901506456},
Key = {fds292888}
}
%% Dolbow, John E.
@article{fds291309,
Author = {Dolbow, J and Farhat, C and Harari, I and Lew, A},
Title = {Special Issue: Advances in Embedded Interface
Methods},
Journal = {International Journal for Numerical Methods in
Engineering},
Volume = {104},
Number = {7},
Pages = {469471},
Editor = {Dolbow, J and Farhat, C and Harari, I and Lew, A},
Year = {2015},
Month = {November},
ISSN = {00295981},
url = {http://dx.doi.org/10.1002/nme.5116},
Doi = {10.1002/nme.5116},
Key = {fds291309}
}
@article{fds268257,
Author = {Jiang, W and Dolbow, JE},
Title = {Adaptive refinement of hierarchical Bspline finite elements
with an efficient data transfer algorithm},
Journal = {International Journal for Numerical Methods in
Engineering},
Volume = {102},
Number = {34},
Pages = {233256},
Editor = {de Borst, R and Farhat, C and Fish, J and Harari, I and Letallec, P and Perić, D},
Year = {2015},
Month = {April},
ISSN = {00295981},
url = {http://dx.doi.org/10.1002/nme.4718},
Doi = {10.1002/nme.4718},
Key = {fds268257}
}
@article{fds268258,
Author = {Jiang, W and Annavarapu, C and Dolbow, JE and Harari,
I},
Title = {A robust Nitsche's formulation for interface problems with
splinebased finite elements},
Journal = {International Journal for Numerical Methods in
Engineering},
Volume = {104},
Number = {7},
Pages = {676696},
Editor = {Dolbow, J and Farhat, C and Harari, I and Lew, A},
Year = {2015},
ISSN = {00295981},
url = {http://dx.doi.org/10.1002/nme.4766},
Abstract = {© 2015 John Wiley & Sons, Ltd.The extended finite
element method (XFEM) has proven to be an accurate, robust
method for solving embedded interface problems. With a few
exceptions, the XFEM has mostly been used in conjunction
with piecewiselinear shape functions and an associated
piecewiselinear geometrical representation of interfaces.
In the current work, the use of splinebased finite elements
is examined along with a Nitsche technique for enforcing
constraints on an embedded interface. To obtain optimal
rates of convergence, we employ a hierarchical local
refinement approach to improve the geometrical
representation of curved interfaces. We further propose a
novel weighting for the interfacial consistency terms
arising in the Nitsche variational form with Bsplines. A
qualitative dependence between the weights and the
stabilization parameters is established with additional
element level eigenvalue calculations. An important
consequence of this weighting is that the bulk as well as
the interfacial fields remain well behaved in the presence
of large heterogeneities as well as elements with
arbitrarily small volume fractions. We demonstrate the
accuracy and robustness of the proposed method through
several numerical examples.},
Doi = {10.1002/nme.4766},
Key = {fds268258}
}
%% Dunson, David B.
@article{fds257830,
Author = {Li, D and Wilcox, AJ and Dunson, DB},
Title = {Benchmark pregnancy rates and the assessment of postcoital
contraceptives: an update.},
Journal = {Contraception},
Volume = {91},
Number = {4},
Pages = {344349},
Year = {2015},
Month = {April},
ISSN = {00107824},
url = {http://dx.doi.org/10.1016/j.contraception.2015.01.002},
Abstract = {In 2001, we provided benchmark estimates of probability of
pregnancy given a single act of intercourse. Those
calculations assumed that intercourse and ovulation are
independent. Subsequent research has shown that this
assumption is not valid. We provide here an update of
previous benchmark estimates.We reanalyze earlier data from
two North Carolina studies that collected daily urine
samples and recorded daily intercourse for multiple
menstrual cycles. One study comprised 68 sexually active
women with either an intrauterine device or tubal ligation.
The second was of 221 women who planned to become pregnant
and had discontinued use of any birth control at enrollment.
Participants had no known fertility problems. New
statistical analyses were based on Monte Carlo simulations
and Bayesian methods.The probability that a single act of
intercourse occurs within a woman's fertile window is 25%,
compared with 20% in previous calculations. The probability
of pregnancy with intercourse on a given menstrual cycle day
is correspondingly higher than previously estimated, with
the largest increases occurring on menstrual days 1222.
These increases are, however, fairly small (for example, the
peak chance of conception on menstrual day 13 increased from
8.6% to 9.7%).Previous benchmark rates of pregnancy with one
act of intercourse were moderately underestimated due to a
mistaken assumption about the independence of intercourse
and ovulation.The chance of pregnancy with a single act of
unprotected intercourse is greater than previously
estimated. Previous benchmarks may underestimate the
efficacy of postcoital contraception.},
Doi = {10.1016/j.contraception.2015.01.002},
Key = {fds257830}
}
@article{fds257829,
Author = {Lock, EF and Soldano, KL and Garrett, ME and Cope, H and Markunas, CA and Fuchs, H and Grant, G and Dunson, DB and Gregory, SG and AshleyKoch,
AE},
Title = {Joint eQTL assessment of whole blood and dura mater tissue
from individuals with Chiari type I malformation.},
Journal = {BMC Genomics},
Volume = {16},
Pages = {11},
Year = {2015},
Month = {January},
url = {http://dx.doi.org/10.1186/s1286401412118},
Abstract = {Expression quantitative trait loci (eQTL) play an important
role in the regulation of gene expression. Gene expression
levels and eQTLs are expected to vary from tissue to tissue,
and therefore multitissue analyses are necessary to fully
understand complex genetic conditions in humans. Dura mater
tissue likely interacts with cranial bone growth and thus
may play a role in the etiology of Chiari Type I
Malformation (CMI) and related conditions, but it is often
inaccessible and its gene expression has not been well
studied. A genetic basis to CMI has been established;
however, the specific genetic risk factors are not well
characterized.We present an assessment of eQTLs for whole
blood and dura mater tissue from individuals with CMI. A
jointtissue analysis identified 239 eQTLs in either dura or
blood, with 79% of these eQTLs shared by both tissues.
Several identified eQTLs were novel and these implicate
genes involved in bone development (IPO8, XYLT1, and
PRKAR1A), and ribosomal pathways related to marrow and bone
dysfunction, as potential candidates in the development of
CMI.Despite strong overall heterogeneity in expression
levels between blood and dura, the majority of ciseQTLs are
shared by both tissues. The power to detect shared eQTLs was
improved by using an integrative statistical approach. The
identified tissuespecific and shared eQTLs provide new
insight into the genetic basis for CMI and related
conditions.},
Doi = {10.1186/s1286401412118},
Key = {fds257829}
}
@article{fds257827,
Author = {Chabout, J and Sarkar, A and Dunson, DB and Jarvis,
ED},
Title = {Male mice song syntax depends on social contexts and
influences female preferences.},
Journal = {Frontiers in Behavioral Neuroscience},
Volume = {9},
Pages = {76},
Year = {2015},
Month = {January},
url = {http://hdl.handle.net/10161/9544 Duke open
access},
Abstract = {In 2005, Holy and Guo advanced the idea that male mice
produce ultrasonic vocalizations (USV) with some features
similar to courtship songs of songbirds. Since then, studies
showed that male mice emit USV songs in different contexts
(sexual and other) and possess a multisyllabic repertoire.
Debate still exists for and against plasticity in their
vocalizations. But the use of a multisyllabic repertoire can
increase potential flexibility and information, in how
elements are organized and recombined, namely syntax. In
many bird species, modulating song syntax has ethological
relevance for sexual behavior and mate preferences. In this
study we exposed adult male mice to different social
contexts and developed a new approach of analyzing their
USVs based on songbird syntax analysis. We found that male
mice modify their syntax, including specific sequences,
length of sequence, repertoire composition, and spectral
features, according to stimulus and social context. Males
emit longer and simpler syllables and sequences when singing
to females, but more complex syllables and sequences in
response to fresh female urine. Playback experiments show
that the females prefer the complex songs over the simpler
ones. We propose the complex songs are to lure females in,
whereas the directed simpler sequences are used for direct
courtship. These results suggest that although mice have a
much more limited ability of song modification, they could
still be used as animal models for understanding some vocal
communication features that songbirds are used
for.},
Doi = {10.3389/fnbeh.2015.00076},
Key = {fds257827}
}
@article{fds257832,
Author = {Kessler, DC and Hoff, PD and Dunson, DB},
Title = {Marginally specified priors for nonparametric Bayesian
estimation},
Journal = {Journal of the Royal Statistical Society: Series B
(Statistical Methodology)},
Volume = {77},
Number = {1},
Pages = {3558},
Year = {2015},
Month = {January},
ISSN = {13697412},
url = {http://dx.doi.org/10.1111/rssb.12059},
Abstract = {© 2014 Royal Statistical Society.Prior specification for
nonparametric Bayesian inference involves the difficult
task of quantifying prior knowledge about a parameter of
high, often infinite, dimension. A statistician is unlikely
to have informed opinions about all aspects of such a
parameter but will have real information about functionals
of the parameter, such as the population mean or variance.
The paper proposes a new framework for nonparametric Bayes
inference in which the prior distribution for a possibly
infinite dimensional parameter is decomposed into two parts:
an informative prior on a finite set of functionals, and a
nonparametric conditional prior for the parameter given the
functionals. Such priors can be easily constructed from
standard nonparametric prior distributions in common use
and inherit the large support of the standard priors on
which they are based. Additionally, posterior approximations
under these informative priors can generally be made via
minor adjustments to existing Markov chain approximation
algorithms for standard nonparametric prior distributions.
We illustrate the use of such priors in the context of
multivariate density estimation using Dirichlet process
mixture models, and in the modelling of high dimensional
sparse contingency tables.},
Doi = {10.1111/rssb.12059},
Key = {fds257832}
}
@article{fds257849,
Author = {Kessler, DC and Hoff, PD and Dunson, DB},
Title = {Marginally specified priors for nonparametric Bayesian
estimation.},
Journal = {Journal of the Royal Statistical Society: Series B
(Statistical Methodology)},
Volume = {77},
Number = {1},
Pages = {3558},
Year = {2015},
Month = {January},
ISSN = {13697412},
url = {http://dx.doi.org/10.1111/rssb.12059},
Abstract = {Prior specification for nonparametric Bayesian inference
involves the difficult task of quantifying prior knowledge
about a parameter of high, often infinite, dimension. A
statistician is unlikely to have informed opinions about all
aspects of such a parameter but will have real information
about functionals of the parameter, such as the population
mean or variance. The paper proposes a new framework for
nonparametric Bayes inference in which the prior
distribution for a possibly infinite dimensional parameter
is decomposed into two parts: an informative prior on a
finite set of functionals, and a nonparametric conditional
prior for the parameter given the functionals. Such priors
can be easily constructed from standard nonparametric prior
distributions in common use and inherit the large support of
the standard priors on which they are based. Additionally,
posterior approximations under these informative priors can
generally be made via minor adjustments to existing Markov
chain approximation algorithms for standard nonparametric
prior distributions. We illustrate the use of such priors in
the context of multivariate density estimation using
Dirichlet process mixture models, and in the modelling of
high dimensional sparse contingency tables.},
Doi = {10.1111/rssb.12059},
Key = {fds257849}
}
@article{fds257828,
Author = {Canale, A and Dunson, DB},
Title = {Bayesian multivariate mixedscale density
estimation},
Journal = {Statistics and its Interface},
Volume = {8},
Number = {2},
Pages = {195201},
Year = {2015},
ISSN = {19387989},
url = {http://dx.doi.org/10.4310/SII.2015.v8.n2.a7},
Doi = {10.4310/SII.2015.v8.n2.a7},
Key = {fds257828}
}
%% Durrett, Richard T.
@article{fds243415,
Author = {Durrett, R and Foo, J and Leder, K},
Title = {Spatial Moran models, II: cancer initiation in spatially
structured tissue},
Journal = {Journal of Mathematical Biology},
Volume = {72},
Number = {5},
Pages = {13691400},
Year = {2016},
Month = {April},
ISSN = {03036812},
url = {http://dx.doi.org/10.1007/s0028501509121},
Doi = {10.1007/s0028501509121},
Key = {fds243415}
}
@article{fds243417,
Author = {Durrett, R and Zhang, Y},
Title = {Coexistence of grass, saplings and trees in the
Staver–Levin forest model},
Journal = {The annals of applied probability : an official journal of
the Institute of Mathematical Statistics},
Volume = {25},
Number = {6},
Pages = {34343464},
Year = {2015},
Month = {December},
ISSN = {10505164},
url = {http://dx.doi.org/10.1214/14AAP1079},
Doi = {10.1214/14AAP1079},
Key = {fds243417}
}
@article{fds302176,
Author = {Talkington, A and Durrett, R},
Title = {Estimating Tumor Growth Rates In Vivo},
Journal = {Bulletin of Mathematical Biology},
Volume = {77},
Number = {10},
Pages = {19341954},
Year = {2015},
Month = {October},
ISSN = {00928240},
url = {http://dx.doi.org/10.1007/s1153801501108},
Doi = {10.1007/s1153801501108},
Key = {fds302176}
}
@article{fds243418,
Author = {Ryser, MD and Myers, ER and Durrett, R},
Title = {HPV clearance and the neglected role of stochasticity.},
Journal = {PLoS computational biology},
Volume = {11},
Number = {3},
Pages = {e1004113},
Year = {2015},
Month = {March},
ISSN = {1553734X},
url = {http://hdl.handle.net/10161/9545 Duke open
access},
Abstract = {Clearance of anogenital and oropharyngeal HPV infections is
attributed primarily to a successful adaptive immune
response. To date, little attention has been paid to the
potential role of stochastic cell dynamics in the time it
takes to clear an HPV infection. In this study, we combine
mechanistic mathematical models at the cellular level with
epidemiological data at the population level to disentangle
the respective roles of immune capacity and cell dynamics in
the clearing mechanism. Our results suggest that chancein
form of the stochastic dynamics of basal stem cellsplays a
critical role in the elimination of HPVinfected cell
clones. In particular, we find that in immunocompetent
adolescents with cervical HPV infections, the immune
response may contribute less than 20% to virus clearancethe
rest is taken care of by the stochastic proliferation
dynamics in the basal layer. In HIVnegative individuals,
the contribution of the immune response may be
negligible.},
Doi = {10.1371/journal.pcbi.1004113},
Key = {fds243418}
}
@article{fds243416,
Author = {Durrett, R and Moseley, S},
Title = {Spatial Moran models I. Stochastic tunneling in the neutral
case},
Journal = {The annals of applied probability : an official journal of
the Institute of Mathematical Statistics},
Volume = {25},
Number = {1},
Pages = {104115},
Year = {2015},
Month = {February},
ISSN = {10505164},
url = {http://dx.doi.org/10.1214/13AAP989},
Doi = {10.1214/13AAP989},
Key = {fds243416}
}
@book{fds299418,
Author = {R.T. Durrett},
Title = {Branching process models of cancer},
Publisher = {Springer},
Year = {2015},
Key = {fds299418}
}
%% Fernandes de Oliveira, Goncalo M.
@article{fds316671,
Author = {Oliveira, G},
Title = {Monopoles on AC 3manifolds},
Journal = {Journal of the London Mathematical Society},
Volume = {93},
Number = {3},
Pages = {785810},
Year = {2016},
Month = {June},
ISSN = {00246107},
url = {http://jlms.oxfordjournals.org/content/early/2016/05/06/jlms.jdw017.abstract},
Doi = {10.1112/jlms/jdw017},
Key = {fds316671}
}
@article{fds311851,
Author = {Oliveira, G},
Title = {Calabi–Yau Monopoles for the Stenzel Metric},
Journal = {Communications in Mathematical Physics},
Volume = {341},
Number = {2},
Pages = {699728},
Year = {2016},
Month = {January},
ISSN = {00103616},
url = {http://hdl.handle.net/10161/11700 Duke open
access},
Doi = {10.1007/s0022001525342},
Key = {fds311851}
}
%% Fry, Brendan
@article{fds226007,
Author = {I Sgouralis and RG Evans and BS Gardiner and JA Smith and BC Fry and AT
Layton},
Title = {Renal hemodynamics, function, and oxygenation during cardiac
surgery performed on cardiopulmonary bypass: A modeling
study},
Journal = {Physiological Reports},
Volume = {3},
Pages = {e12260},
Year = {2015},
Key = {fds226007}
}
@article{fds226453,
Author = {BC Fry and A Edwards and AT Layton},
Title = {Impacts of nitric oxide and superoxide on renal medullary
oxygen transport and urine concentration},
Journal = {American Journal of Physiology  Renal Physiology},
Volume = {308},
Pages = {F967F980},
Year = {2015},
Key = {fds226453}
}
%% Gao, Tingran
@article{fds299988,
Author = {Tingran Gao and Gabriel S Yapuncich and Ingrid Daubechies and Doug M
Boyer},
Title = {Automated techniques for comparing shapes in a biological
comparative dataset with high interspecific variation:
tradeoffs, limitations, and progress},
Journal = {PLOS ONE},
Year = {2015},
Month = {December},
ISSN = {19326203},
Abstract = {During the development of evolutionary theory, foundational
principles were established through comparative anatomy.
However, comparative anatomy (in the form of high fidelity
geometric morphometric information) is currently a
relatively marginal source of evidence for evolutionary
biology. While it is conceivable that this shift reflects
the objectively low intrinsic information content of
anatomical variation, we believe such assessments are
premature. Instead, it seems that the relative difficulty of
studying comparative anatomy has led researchers to seek
other forms of data. Comparative datasets large enough to be
statistically powerful are rare, and the complexity of
anatomical shape variation foil even experienced
researchers' abilities to collect rich yet standardized
measurements. Threedimensional digitization presents a way
to reintroduce data from anatomical information by
increasing access to samples through virtual repositories
(extensive sampling) and by providing the potential for
automating aspects of shape comparison (intensive sampling).
In this paper, we reassess the accuracy and reliability of
some published automated methods and present updated
methodology. Ideally, these methods will promote wider
participation in anatomical studies and motivate other
research groups to focus on the problems of automated
quantification and comparison of anatomical
structures.},
Key = {fds299988}
}
%% Getz, Jayce R.
@article{fds292890,
Author = {Getz, JR and Klassen, J},
Title = {Isolating RankinSelberg lifts},
Journal = {Proceedings of the American Mathematical
Society},
Volume = {143},
Number = {8},
Pages = {33193329},
Year = {2015},
Month = {April},
ISSN = {00029939},
url = {http://dx.doi.org/10.1090/proc/12389},
Doi = {10.1090/proc/12389},
Key = {fds292890}
}
@article{fds226862,
Author = {J.R. Getz},
Title = {Nonabelian Fourier transforms for spherical
representations},
Year = {2015},
url = {arXiv:1506.09128},
Key = {fds226862}
}
@article{fds226899,
Author = {J.R. Getz and P. E. Herman},
Title = {A nonabelian trace formula},
Journal = {Research in the Mathematical Sciences},
Volume = {2},
Number = {1},
Year = {2015},
Abstract = {Let E/F be an extension of number fields with Gal(E/F)
simple and nonabelian. In a recent paper the first named
author suggested an approach to nonsolvable base change and
descent of automorphic representations of GL(2) along such
an extension. Motivated by this we prove a trace formula
whose spectral side is a weighted sum over cuspidal
automorphic representations of GL(2) over E that are
isomorphic to their Gal(E/F)conjugates.},
Key = {fds226899}
}
@article{fds292889,
Author = {Getz, JR and Hahn, H},
Title = {A general simple relative trace formula},
Journal = {Pacific Journal of Mathematics},
Volume = {277},
Number = {1},
Pages = {99118},
Year = {2015},
ISSN = {00308730},
url = {http://dx.doi.org/10.2140/pjm.2015.277.99},
Doi = {10.2140/pjm.2015.277.99},
Key = {fds292889}
}
%% Hahn, Heekyoung
@article{fds320109,
Author = {Hahn, H},
Title = {On tensor third $L$functions of automorphic representations
of $GL_n(\mathbb {A}_F)$},
Journal = {Proceedings of the American Mathematical
Society},
Volume = {144},
Number = {12},
Pages = {50615069},
Year = {2016},
Month = {May},
url = {http://dx.doi.org/10.1090/proc/13134},
Doi = {10.1090/proc/13134},
Key = {fds320109}
}
@article{fds305734,
Author = {H. Hahn},
Title = {On tensor thrid Lfunctions of automorphic representations
of GL_n(A_F)},
Journal = {Proc. Amer. Math. Soc.},
Year = {2016},
Key = {fds305734}
}
@article{fds227060,
Author = {H. Hahn},
Title = {On classical groups detected by the triple tensor product
and the LittlewoodRichardson semigroup},
Year = {2016},
Key = {fds227060}
}
@article{fds302444,
Author = {Getz, JR and Hahn, H},
Title = {A general simple relative trace formula},
Journal = {Pacific Journal of Mathematics},
Volume = {277},
Number = {1},
Pages = {99118},
Year = {2015},
ISSN = {00308730},
url = {http://dx.doi.org/10.2140/pjm.2015.277.99},
Doi = {10.2140/pjm.2015.277.99},
Key = {fds302444}
}
%% Hain, Richard
@article{fds287213,
Author = {Arapura, D and Dimca, A and Hain, R},
Title = {On the fundamental groups of normal varieties},
Journal = {Communications in Contemporary Mathematics},
Volume = {18},
Number = {04},
Pages = {15500651550065},
Year = {2016},
Month = {August},
ISSN = {02191997},
url = {http://dx.doi.org/10.1142/S0219199715500650},
Doi = {10.1142/S0219199715500650},
Key = {fds287213}
}
@article{fds320224,
Author = {Hain, R},
Title = {The Hodgede Rham theory of modular groups},
Volume = {427},
Pages = {422514},
Booktitle = {Recent Advances in Hodge Theory Period Domains, Algebraic
Cycles, and Arithmetic},
Publisher = {Cambridge University Press},
Editor = {Kerr, M and Pearlstein, G},
Year = {2016},
Month = {January},
ISBN = {110754629X},
url = {http://arxiv.org/abs/1403.6443v3},
Abstract = {This paper is an exposition of the completion of a modular
group with respect to its inclusion into SL_2(Q) and the
connection with the theory of modular forms and variations
of mixed Hodge structure over modular curves. Among the
goals of this paper are to give a context to Manin's
iterated Shimura integrals (iterated integrals of modular
forms) and to study relations in the "maximal Eisenstein
quotient" of the completion of SL_2(Z). In particular, we
use a computation of Terasoma to prove that Pollack's
quadratic relations in the derivation Lie algebra of a rank
two free Lie algebra lift to this Eisenstein quotient, and
are thus motivic. We also construct the normal functions
associated to Hecke eigen cusp forms.},
Key = {fds320224}
}
@article{fds299939,
Author = {R. Hain and Makoto Matsumoto},
Title = {Universal mixed elliptic motives},
Year = {2015},
Month = {December},
url = {http://arxiv.org/abs/1512.03975},
Key = {fds299939}
}
@article{fds299940,
Author = {Richard Hain},
Title = {DeligneBeilinson cohomology of affine groups},
Year = {2015},
Month = {July},
url = {http://arxiv.org/abs/1507.03144},
Key = {fds299940}
}
%% Harer, John
@article{fds243563,
Author = {Perea, JA and Deckard, A and Haase, SB and Harer,
J},
Title = {SW1PerS: Sliding windows and 1persistence scoring;
discovering periodicity in gene expression time series
data.},
Journal = {BMC Bioinformatics},
Volume = {16},
Pages = {257},
Year = {2015},
Month = {January},
url = {http://dx.doi.org/10.1186/s1285901506456},
Abstract = {Identifying periodically expressed genes across different
processes (e.g. the cell and metabolic cycles, circadian
rhythms, etc) is a central problem in computational biology.
Biological time series may contain (multiple) unknown signal
shapes of systemic relevance, imperfections like noise,
damping, and trending, or limited sampling density. While
there exist methods for detecting periodicity, their design
biases (e.g. toward a specific signal shape) can limit their
applicability in one or more of these situations.We present
in this paper a novel method, SW1PerS, for quantifying
periodicity in time series in a shapeagnostic manner and
with resistance to damping. The measurement is performed
directly, without presupposing a particular pattern, by
evaluating the circularity of a highdimensional
representation of the signal. SW1PerS is compared to other
algorithms using synthetic data and performance is
quantified under varying noise models, noise levels,
sampling densities, and signal shapes. Results on biological
data are also analyzed and compared.On the task of
periodic/notperiodic classification, using synthetic data,
SW1PerS outperforms all other algorithms in the lownoise
regime. SW1PerS is shown to be the most shapeagnostic of
the evaluated methods, and the only one to consistently
classify damped signals as highly periodic. On biological
data, and for several experiments, the lists of top 10%
genes ranked with SW1PerS recover up to 67% of those
generated with other popular algorithms. Moreover, the list
of genes from data on the Yeast metabolic cycle which are
highlyranked only by SW1PerS, contains evidently noncosine
patterns (e.g. ECM33, CDC9, SAM1,2 and MSH6) with highly
periodic expression profiles. In data from the Yeast cell
cycle SW1PerS identifies genes not preferred by other
algorithms, hence not previously reported as periodic, but
found in other experiments such as the universal growth rate
response of Slavov. These genes are BOP3, CDC10, YIL108W,
YER034W, MLP1, PAC2 and RTT101.In biological systems with
low noise, i.e. where periodic signals with interesting
shapes are more likely to occur, SW1PerS can be used as a
powerful tool in exploratory analyses. Indeed, by having an
initial set of periodic genes with a rich variety of signal
types, pattern/shape information can be included in the
study of systems and the generation of hypotheses regarding
the structure of gene regulatory networks.},
Doi = {10.1186/s1285901506456},
Key = {fds243563}
}
@article{fds300010,
Author = {David Rouse and Adam Watkins and David Porter and John Harer and Paul Bendich and Nate Strawn and Elizabeth Munch and Jonathan
DeSena and Jesse Clarke and Jeffrey Gilbert and Peter Chin and Andrew Newman},
Title = {Featureaided multiple hypothesis tracking using topological
and statistical behavior classifiers},
Journal = {Proc. SPIE 9474, Signal Processing, Sensor/Information
Fusion, and Target Recognition XXIV, 94740L},
Year = {2015},
ISSN = {10.1117/12.2179555},
Key = {fds300010}
}
@article{fds300009,
Author = {K. Mcgoff and X. Guo and A. Deckard and C. Kelliher and A. Leman and S.
Haase, J. Harer},
Title = {The Local Edge Machine: Inference of Dynamic Models of Gene
Regulation},
Journal = {Genome Biology},
Year = {2015},
Key = {fds300009}
}
%% Herschlag, Gregory J.
@article{fds316988,
Author = {G Herschlag and JG Liu and AT Layton},
Title = {Optimal reservoir conditions for fluid extraction through
permeable walls in the viscous limit},
Journal = {Phys. Flu.},
Year = {2015},
Month = {November},
url = {http://arxiv.org/abs/1511.01469v1},
Abstract = {In biological transport mechanisms such as insect
respiration and renal filtration, fluid travels along a
leaky channel allowing exchange with systems exterior the
the channel. The channels in these systems may undergo
peristaltic pumping which is thought to enhance the material
exchange. To date, little analytic work has been done to
study the effect of pumping on material extraction across
the channel walls. In this paper, we examine a fluid
extraction model in which fluid flowing through a leaky
channel is exchanged with fluid in a reservoir. The channel
walls are allowed to contract and expand uniformly,
simulating a pumping mechanism. In order to efficiently
determine solutions of the model, we derive a formal power
series solution for the Stokes equations in a finite channel
with uniformly contracting/expanding permeable walls. This
flow has been well studied in the case of weakly permeable
channel walls in which the normal velocity at the channel
walls is proportional to the wall velocity. In contrast we
do not assume weakly driven flow, but flow driven by
hydrostatic pressure, and we use Dacry's law to close our
system for normal wall velocity. We use our flow solution to
examine flux across the channelreservoir barrier and
demonstrate that pumping can either enhance or impede fluid
extraction across channel walls. We find that associated
with each set of physical flow and pumping parameters, there
are optimal reservoir conditions that maximizes the amount
of material flowing from the channel into the
reservoir.},
Key = {fds316988}
}
@article{fds316989,
Author = {Herschlag, GJ and Mitran, S and Lin, G},
Title = {A consistent hierarchy of generalized kinetic equation
approximations to the master equation applied to surface
catalysis.},
Journal = {Journal of Chemical Physics},
Volume = {142},
Number = {23},
Pages = {234703},
Year = {2015},
Month = {June},
ISSN = {00219606},
url = {http://hdl.handle.net/10161/12397 Duke open
access},
Abstract = {We develop a hierarchy of approximations to the master
equation for systems that exhibit translational invariance
and finiterange spatial correlation. Each approximation
within the hierarchy is a set of ordinary differential
equations that considers spatial correlations of varying
lattice distance; the assumption is that the full system
will have finite spatial correlations and thus the behavior
of the models within the hierarchy will approach that of the
full system. We provide evidence of this convergence in the
context of one and twodimensional numerical examples.
Lower levels within the hierarchy that consider shorter
spatial correlations are shown to be up to three orders of
magnitude faster than traditional kinetic Monte Carlo
methods (KMC) for onedimensional systems, while predicting
similar system dynamics and steady states as KMC methods. We
then test the hierarchy on a twodimensional model for the
oxidation of CO on RuO2(110), showing that loworder
truncations of the hierarchy efficiently capture the
essential system dynamics. By considering sequences of
models in the hierarchy that account for longer spatial
correlations, successive model predictions may be used to
establish empirical approximation of error estimates. The
hierarchy may be thought of as a class of generalized
phenomenological kinetic models since each element of the
hierarchy approximates the master equation and the lowest
level in the hierarchy is identical to a simple existing
phenomenological kinetic models.},
Doi = {10.1063/1.4922515},
Key = {fds316989}
}
@article{fds316991,
Author = {Herschlag, G and Liu, JG and Layton, AT},
Title = {An Exact Solution for Stokes Flow in a Channel with
Arbitrarily Large Wall Permeability},
Journal = {SIAM Journal on Applied Mathematics},
Volume = {75},
Number = {5},
Pages = {22462267},
Year = {2015},
Month = {January},
ISSN = {00361399},
url = {http://arxiv.org/abs/1411.3672},
Keywords = {filtration permeable boundaries Stokes flow},
Abstract = {We derive an exact solution for Stokes flow in a channel
with permeable walls. At the channel walls, the normal
component of the fluid velocity is described by Darcy’s
law, and the tangential component of the fluid velocity is
described by the no slip condition. The pressure exterior to
the channel is assumed to be constant. Although this problem
has been well studied, typical studies assume that the
permeability of the wall is small relative to other
nondimensional parameters; this work relaxes this assumption
and explores a regime in parameter space that has not yet
been well studied. A consequence of this relaxation is that
transverse velocity is no longer necessarily small when
compared with the axial velocity. We use our result to
explore how existing asymptotic theories break down in the
limit of large permeability for channels of small
length.},
Doi = {10.1137/140995854},
Key = {fds316991}
}
%% Hodel, Richard E.
@book{fds302140,
Author = {R.E. Hodel and Donald W. Loveland and Richard E. Hodel and S.G.
Sterrett},
Title = {Three Views of Logic: Mathematics, Philosophy, Computer
Science},
Year = {2016},
Key = {fds302140}
}
%% Kraines, David P.
@article{fds296263,
Author = {Kraines, D and Kraines, V},
Title = {The threshold of cooperation among adaptive agents: Pavlov
and the stag hunt},
Journal = {Lecture notes in computer science},
Volume = {1193},
Pages = {219231},
Year = {2015},
ISSN = {03029743},
Abstract = {© 2015, Lecture Notes in Computer Science. All rights
reserved.Why is it that in an animal society, persistent
selfishness is quite rare yet in human society, even strict
laws and severe punishment do not eliminate selfish action
against the interests of the whole? Stochastic learning
agents called Pavlov strategies are used to model
interactions in the multiagent 2 × 2 Stag Hunt matrix
game, a close relative of the Prisoner’s Dilemma. Markov
chain methods and computer simulations establish a threshold
learning rate for the stability of cooperation. A society of
rapidly adapting agents may suffer strife and dissension
while another society with slower learning agents will enjoy
the benefits of virtually complete cooperation.},
Key = {fds296263}
}
%% Layton, Anita T.
@article{fds320180,
Author = {Herschlag, G and Liu, JG and Layton, AT},
Title = {Fluid extraction across pumping and permeable walls in the
viscous limit},
Journal = {Physics of Fluids},
Volume = {28},
Number = {4},
Pages = {041902041902},
Year = {2016},
Month = {April},
url = {http://dx.doi.org/10.1063/1.4946005},
Doi = {10.1063/1.4946005},
Key = {fds320180}
}
@article{fds320181,
Author = {Xie, L and Layton, AT and Wang, N and Larson, PE and Zhang, JL and Lee, VS and Liu, C and Johnson, GA},
Title = {Dynamic contrastenhanced quantitative susceptibility
mapping with ultrashort echo time MRI for evaluating renal
function.},
Journal = {American Journal of Physiology: Renal Physiology},
Volume = {310},
Number = {2},
Pages = {F174F182},
Year = {2016},
Month = {January},
url = {http://dx.doi.org/10.1152/ajprenal.00351.2015},
Abstract = {Dynamic contrastenhanced (DCE) MRI can provide key insight
into renal function. DCE MRI is typically achieved through
an injection of a gadolinium (Gd)based contrast agent,
which has desirable T1 quenching and tracer kinetics.
However, significant T2* blooming effects and signal voids
can arise when Gd becomes very concentrated, especially in
the renal medulla and pelvis. One MRI sequence designed to
alleviate T2* effects is the ultrashort echo time (UTE)
sequence. In the present study, we observed T2* blooming in
the inner medulla of the mouse kidney, despite using UTE at
an echo time of 20 microseconds and a low dose of 0.03
mmol/kg Gd. We applied quantitative susceptibility mapping
(QSM) and resolved the signal void into a positive
susceptibility signal. The susceptibility values [in parts
per million (ppm)] were converted into molar concentrations
of Gd using a calibration curve. We determined the
concentrating mechanism (referred to as the concentrating
index) as a ratio of maximum Gd concentration in the inner
medulla to the renal artery. The concentrating index was
assessed longitudinally over a 17wk course (3, 5, 7, 9, 13,
17 wk of age). We conclude that the UTEbased DCE method is
limited in resolving extreme T2* content caused by the
kidney's strong concentrating mechanism. QSM was able to
resolve and confirm the source of the blooming effect to be
the large positive susceptibility of concentrated Gd. UTE
with QSM can complement traditional magnitude UTE and offer
a powerful tool to study renal pathophysiology.},
Doi = {10.1152/ajprenal.00351.2015},
Key = {fds320181}
}
@article{fds311143,
Author = {Brendan C. Fry and Aurelie Edwards and Anita T.
Layton},
Title = {Impact of nitricoxidemediated vasodilation and oxidative
Stress on renal medullary oxygenation: A modeling
study},
Journal = {Am J Physiol Renal Physiol},
Volume = {310},
Number = {F237F247},
Year = {2016},
Key = {fds311143}
}
@article{fds311142,
Author = {Runjing Liu and Anita T. Layton},
Title = {Modeling the effects of positive and negative feedback in
kidney blood flow control},
Journal = {Math Biosci, in press},
Year = {2016},
Key = {fds311142}
}
@article{fds305850,
Author = {Ying Chen and Brendan Fry and Anita T. Layton},
Title = {Modeling glucose metabolism in the kidney},
Journal = {Bull Math Biol, submitted},
Year = {2016},
Key = {fds305850}
}
@article{fds302902,
Author = {Ioannis Sgouralis and Roger G. Evans and Anita T.
Layton},
Title = {Renal medullary and Urinary Oxygen tension during
cardiopulmonary bypass in the rat},
Journal = {Math Med Biol, submitted},
Year = {2016},
Key = {fds302902}
}
@article{fds320182,
Author = {Burt, T and Rouse, DC and Lee, K and Wu, H and Layton, AT and Hawk, TC and Weitzel, DH and Chin, BB and CohenWolkowiez, M and Chow, SC and Noveck,
RJ},
Title = {Intraarterial Microdosing: A Novel Drug Development
Approach, ProofofConcept PET Study in Rats.},
Journal = {Journal of nuclear medicine : official publication, Society
of Nuclear Medicine},
Volume = {56},
Number = {11},
Pages = {17931799},
Year = {2015},
Month = {November},
url = {http://dx.doi.org/10.2967/jnumed.115.160986},
Abstract = {Intraarterial microdosing (IAM) is a novel drug development
approach combining intraarterial drug delivery and
microdosing. We aimed to demonstrate that IAM leads to
target exposure similar to that of systemic fulldose
administration but with minimal systemic exposure. IAM could
enable the safe, inexpensive, and early study of novel drugs
at the firstinhuman stage and the study of established
drugs in vulnerable populations.Insulin was administered
intraarterially (ipsilateral femoral artery) or systemically
to 8 CD IGS rats just before blood sampling or 60min
(18)FFDG uptake PET imaging of ipsilateral and
contralateral leg muscles (lateral gastrocnemius) and
systemic muscles (spinotrapezius). The (18)FFDG uptake
slope analysis was used to compare the interventions. Plasma
levels of insulin and glucose were compared using area under
the curve calculated by the linear trapezoidal method. A
physiologically based computational pharmacokinetics/pharmacodynamics
model was constructed to simulate the relationship between
the administered dose and response over time.(18)FFDG slope
analysis found no difference between IAM and systemic
fulldose slopes (0.0066 and 0.0061, respectively; 95%
confidence interval [CI], 0.024 to 0.029; P = 0.7895), but
IAM slope was statistically significantly greater than
systemic microdose (0.0018; 95% CI, 0.045 to 0.007; P =
0.0147) and sham intervention (0.0015; 95% CI, 0.0230.058;
P = 0.0052). The pharmacokinetics/pharmacodynamics data were
used to identify model parameters that describe membrane
insulin binding and glucoseinsulin dynamics.Target exposure
after IAM was similar to systemic full dose administration
but with minimal systemic effects. The computational
pharmacokinetics/pharmacodynamics model can be generalized
to predict wholebody response. Findings should be validated
in larger, controlled studies in animals and humans using a
range of targets and classes of drugs.},
Doi = {10.2967/jnumed.115.160986},
Key = {fds320182}
}
@article{fds320183,
Author = {Burt, T and Rouse, DC and Lee, K and Wu, H and Layton, AT and Hawk, TC and Weitzel, DH and Chin, BB and CohenWolkowiez, M and Chow, SC and Noveck, RJ},
Title = {Intraarterial Microdosing: A Novel Drug Development
Approach, ProofofConcept PET Study in Rats},
Journal = {Journal of nuclear medicine : official publication, Society
of Nuclear Medicine},
Volume = {56},
Number = {11},
Pages = {17931799},
Year = {2015},
Month = {November},
url = {http://dx.doi.org/10.2967/jnumed.115.160986},
Doi = {10.2967/jnumed.115.160986},
Key = {fds320183}
}
@article{fds300274,
Author = {Layton, AT and Edwards, A},
Title = {Predicted effects of nitric oxide and superoxide on the
vasoactivity of the afferent arteriole.},
Journal = {American Journal of Physiology: Renal Physiology},
Volume = {309},
Number = {8},
Pages = {F708F719},
Year = {2015},
Month = {October},
ISSN = {1931857X},
url = {http://dx.doi.org/10.1152/ajprenal.00187.2015},
Abstract = {We expanded a published mathematical model of an afferent
arteriole smooth muscle cell in rat kidney (Edwards A,
Layton, AT. Am J Physiol Renal Physiol 306: F34F48, 2014)
to understand how nitric oxide (NO) and superoxide (O(2)())
modulate the arteriolar diameter and its myogenic response.
The present model includes the kinetics of NO and O(2)()
formation, diffusion, and reaction. Also included are the
effects of NO and its second messenger cGMP on cellular
Ca²⁺ uptake and efflux, Ca²⁺activated K⁺ currents,
and myosin light chain phosphatase activity. The model
considers as well pressureinduced increases in O(2)()
production, O(2)()mediated regulation of Ltype Ca²⁺
channel conductance, and increased O(2)() production in
spontaneous hypertensive rats (SHR). Our results indicate
that elevated O(2)() production in SHR is sufficient to
account for observed differences between normotensive and
hypertensive rats in the response of the afferent arteriole
to NO synthase inhibition, Tempol, and angiotensin II at
baseline perfusion pressures. In vitro, whether the myogenic
response is stronger in SHR remains uncertain. Our model
predicts that if mechanosensitive cation channels are not
modulated by O(2)(), then fractional changes in diameter
induced by pressure elevations should be smaller in SHR than
in normotensive rats. Our results also suggest that most NO
diffuses out of the smooth muscle cell without being
consumed, whereas most O(2)() is scavenged, by NO and
superoxide dismutase. Moreover, the predicted effects of
superoxide on arteriolar constriction are not predominantly
due to its scavenging of NO.},
Doi = {10.1152/ajprenal.00187.2015},
Key = {fds300274}
}
@article{fds300275,
Author = {Nganguia, H and Young, YN and Layton, AT and Hu, WF and Lai,
MC},
Title = {An Immersed Interface Method for Axisymmetric
Electrohydrodynamic Simulations in Stokes
flow},
Journal = {Communications in computational physics},
Volume = {18},
Number = {02},
Pages = {429449},
Year = {2015},
Month = {August},
ISSN = {18152406},
url = {http://dx.doi.org/10.4208/cicp.171014.270315a},
Doi = {10.4208/cicp.171014.270315a},
Key = {fds300275}
}
@article{fds320184,
Author = {Burt, T and Wu, H and Layton, AT and Rouse, DC and Chin, BB and Hawk, TC and Weitzel, DH and CohenWolkowiez, M and Chow, S and Noveck,
RJ},
Title = {INTRAARTERIAL MICRODOSING (IAM), A NOVEL DRUG DEVELOPMENT
APPROACH, PROOF OF CONCEPT IN RATS},
Journal = {Clinical Therapeutics},
Volume = {37},
Number = {8},
Pages = {E40E41},
Year = {2015},
Month = {August},
Key = {fds320184}
}
@article{fds300276,
Author = {Sgouralis, I and Layton, AT},
Title = {Mathematical modeling of renal hemodynamics in physiology
and pathophysiology.},
Journal = {Mathematical Biosciences},
Volume = {264},
Pages = {820},
Year = {2015},
Month = {June},
ISSN = {00255564},
url = {http://dx.doi.org/10.1016/j.mbs.2015.02.016},
Abstract = {In addition to the excretion of metabolic waste and toxin,
the kidney plays an indispensable role in regulating the
balance of water, electrolyte, acidbase, and blood
pressure. For the kidney to maintain proper functions,
hemodynamic control is crucial. In this review, we describe
representative mathematical models that have been developed
to better understand the kidney's autoregulatory processes.
We consider mathematical models that simulate glomerular
filtration, and renal blood flow regulation by means of the
myogenic response and tubuloglomerular feedback. We discuss
the extent to which these modeling efforts have expanded the
understanding of renal functions in health and
disease.},
Doi = {10.1016/j.mbs.2015.02.016},
Key = {fds300276}
}
@article{fds311145,
Author = {Layton, AT and Vallon, V and Edwards, A},
Title = {Modeling oxygen consumption in the proximal tubule: effects
of NHE and SGLT2 inhibition.},
Journal = {American Journal of Physiology: Renal Physiology},
Volume = {308},
Number = {12},
Pages = {F1343F1357},
Year = {2015},
Month = {June},
ISSN = {1931857X},
url = {http://dx.doi.org/10.1152/ajprenal.00007.2015},
Abstract = {The objective of this study was to investigate how
physiological, pharmacological, and pathological conditions
that alter sodium reabsorption (TNa) in the proximal tubule
affect oxygen consumption (QO2 ) and Na(+) transport
efficiency (TNa/QO2 ). To do so, we expanded a mathematical
model of solute transport in the proximal tubule of the rat
kidney. The model represents compliant S1, S2, and S3
segments and accounts for their specific apical and
basolateral transporters. Sodium is reabsorbed
transcellularly, via apical Na(+)/H(+) exchangers (NHE) and
Na(+)glucose (SGLT) cotransporters, and paracellularly. Our
results suggest that TNa/QO2 is 80% higher in S3 than in
S1S2 segments, due to the greater contribution of the
passive paracellular pathway to TNa in the former segment.
Inhibition of NHE or NaKATPase reduced TNa and QO2 , as
well as Na(+) transport efficiency. SGLT2 inhibition also
reduced proximal tubular TNa but increased QO2 ; these
effects were relatively more pronounced in the S3 vs. the
S1S2 segments. Diabetes increased TNa and QO2 and reduced
TNa/QO2 , owing mostly to hyperfiltration. Since SGLT2
inhibition lowers diabetic hyperfiltration, the net effect
on TNa, QO2 , and Na(+) transport efficiency in the proximal
tubule will largely depend on the individual extent to which
glomerular filtration rate is lowered.},
Doi = {10.1152/ajprenal.00007.2015},
Key = {fds311145}
}
@article{fds243614,
Author = {Layton, AT},
Title = {Recent advances in renal hemodynamics: insights from bench
experiments and computer simulations.},
Journal = {American Journal of Physiology: Renal Physiology},
Volume = {308},
Number = {9},
Pages = {F951F955},
Year = {2015},
Month = {May},
ISSN = {1931857X},
url = {http://dx.doi.org/10.1152/ajprenal.00008.2015},
Abstract = {It has been long known that the kidney plays an essential
role in the control of body fluids and blood pressure and
that impairment of renal function may lead to the
development of diseases such as hypertension (Guyton AC,
Coleman TG, Granger Annu Rev Physiol 34: 1346, 1972). In
this review, we highlight recent advances in our
understanding of renal hemodynamics, obtained from
experimental and theoretical studies. Some of these studies
were published in response to a recent Call for Papers of
this journal: Renal Hemodynamics: Integrating with the
Nephron and Beyond.},
Doi = {10.1152/ajprenal.00008.2015},
Key = {fds243614}
}
@article{fds243615,
Author = {Fry, BC and Edwards, A and Layton, AT},
Title = {Impacts of nitric oxide and superoxide on renal medullary
oxygen transport and urine concentration.},
Journal = {American Journal of Physiology: Renal Physiology},
Volume = {308},
Number = {9},
Pages = {F967F980},
Year = {2015},
Month = {May},
ISSN = {1931857X},
url = {http://dx.doi.org/10.1152/ajprenal.00600.2014},
Abstract = {The goal of this study was to investigate the reciprocal
interactions among oxygen (O2), nitric oxide (NO), and
superoxide (O2 ()) and their effects on medullary
oxygenation and urinary output. To accomplish that goal, we
developed a detailed mathematical model of solute transport
in 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 simulations yield significant radial
gradients in interstitial fluid oxygen tension (Po2) and NO
and O2 () concentration in the OM and upper IM. In the deep
inner medulla, interstitial fluid concentrations become much
more homogeneous, as the radial organization of tubules and
vessels is not distinguishable. The model further predicts
that due to the nonlinear interactions among O2, NO, and O2
(), the effects of NO and O2 () on sodium transport,
osmolality, and medullary oxygenation cannot be gleaned by
considering each solute's effect in isolation. An additional
simulation suggests that a sufficiently large reduction in
tubular transport efficiency may be the key contributing
factor, more so than oxidative stress alone, to
hypertensioninduced medullary hypoxia. Moreover, model
predictions suggest that urine Po2 could serve as a
biomarker for medullary hypoxia and a predictor of the risk
for hospitalacquired acute kidney injury.},
Doi = {10.1152/ajprenal.00600.2014},
Key = {fds243615}
}
@article{fds299957,
Author = {Fields, B and Page, K},
Title = {Preface},
Volume = {2015June},
Year = {2015},
Month = {January},
ISBN = {9781450335638},
Key = {fds299957}
}
@article{fds320185,
Author = {Herschlag, G and Liu, JG and Layton, AT},
Title = {An Exact Solution for Stokes Flow in a Channel with
Arbitrarily Large Wall Permeability},
Journal = {SIAM Journal on Applied Mathematics},
Volume = {75},
Number = {5},
Pages = {22462267},
Year = {2015},
Month = {January},
url = {http://dx.doi.org/10.1137/140995854},
Doi = {10.1137/140995854},
Key = {fds320185}
}
@article{fds300035,
Author = {H. Nganguia and Y.N. Young and A. T. Layton and M.C. Lai and W.F.
Hu},
Title = {Electrohydrodynamics of a viscous drop with
inertia},
Journal = {Phys Rev E, submitted},
Year = {2015},
Key = {fds300035}
}
@article{fds302232,
Author = {Anita T. Layton and Volker Vallon and Aurelie
Edwards},
Title = {Predicted consequences of diabetes and SGLT inhibition on
transport and oxygen consumption along a rat
nephron},
Journal = {Am J Physiol Renal Physiol, in press},
Year = {2015},
Key = {fds302232}
}
@article{fds227194,
Author = {Gregory Herschlag and JianGuo Liu and Anita T.
Layton},
Title = {Optimal reservoir conditions for fluid extraction through
permeable walls in the viscous limit},
Journal = {Phys Fluids, submitted},
Year = {2015},
Key = {fds227194}
}
@article{fds303024,
Author = {Anita T. Layton and Aurelie Edwards},
Title = {Introduction to mathematical modeling of blood flow control
in the kidney},
Booktitle = {AWM proceedings for NIMBioS WS for Women in Mathematical
Biology},
Year = {2015},
Key = {fds303024}
}
@article{fds227201,
Author = {Veronica Ciocanel and Tracy L. Stepien and Aur´elie Edwards and Anita T. Layton},
Title = {Modeling autoregulation of the afferent arteriole of the rat
kidney},
Journal = {AWM proceedings for NIMBioS WS for Women in Mathematical
Biology, in press},
Year = {2015},
Key = {fds227201}
}
@article{fds227202,
Author = {Ioannis Sgouralis and Anita T. Layton},
Title = {Modeling blood flow and oxygenation in a diabetic rat
kidney},
Booktitle = {AWM proceedings for NIMBioS WS for Women in Mathematical
Biology, in press},
Year = {2015},
Key = {fds227202}
}
@article{fds226446,
Author = {Anita T. Layton},
Title = {Mathematical physiology},
Booktitle = {Princeton Companion to Applied Mathematics},
Editor = {Nicholas J. Higham},
Year = {2015},
ISBN = {9780691150390},
Key = {fds226446}
}
@article{fds226016,
Author = {Ioannis Sgouralis and Roger Evans and Bruce S. Gardiner and Julian A
Smith and Brendan C. Fry and Anita T. Layton},
Title = {Renal hemodynamics, function and oxygenation during cardiac
surgery performed on cardiopulmonary bypass: A modeling
study},
Journal = {Physiol Report},
Volume = {3},
Number = {1},
Year = {2015},
Key = {fds226016}
}
@article{fds226378,
Author = {Ashlee N. Ford Versypt and Elizabeth Makrides and Julia C.
Arciero and Laura Ellwein and Anita T. Layton},
Title = {Bifurcation Study of Blood Flow Control in the
Kidney},
Journal = {Math Biosci},
Volume = {263},
Pages = {169–179},
Year = {2015},
Key = {fds226378}
}
@article{fds226967,
Author = {Julia Arcerio and Laura Ellwein and Ashlee N. Ford Versypt and Elizabeth Makride and Anita T. Layton},
Title = {Modeling blood flow in the kidney},
Volume = {158},
Pages = {5573},
Booktitle = {The IMA Volumes in Mathematics and its Applications:
Applications of Dynamical Systems in Biology and
Medicine},
Year = {2015},
Key = {fds226967}
}
@article{fds227058,
Author = {Gregory J. Herschlag and JianGuo Liu and Anita T.
Layton},
Title = {An exact solution for Stokes flow in an infinite channel
with permeable walls},
Journal = {SIAM Appl Math, in press},
Year = {2015},
Key = {fds227058}
}
@article{fds226985,
Author = {Tal Burt and Douglas C. Rouse and Kihak Lee and Huali Wu and Anita T.
Layton and Thomas C. Hawk and Douglas H. Weitzel and Bennett B. Chin and Michael CohenWolkowiez and SheinChung Chow and Robert J.
Noveck},
Title = {Intraarterial microdosing (IAM), a novel drug development
approach,proof of concept in rodents},
Journal = {CPT: Pharmacometrics and Systems Pharmacology, in
press},
Year = {2015},
Key = {fds226985}
}
@article{fds226440,
Author = {Ioannis Sgouralis and Vasileios Maroulas and Anita T.
Layton},
Title = {Transfer function analysis of dynamic blood flow control in
the rat kidney},
Journal = {Bull Math Biol, submitted},
Year = {2015},
Key = {fds226440}
}
@article{fds226368,
Author = {Anita T. Layton},
Title = {Tracking the distribution of a solute bolus in the rat
kidney},
Booktitle = {AWM proceedings for NIMBioS WS for Women in Mathematical
Biology, submitted},
Year = {2015},
Key = {fds226368}
}
%% Li, Lei
@article{fds302449,
Author = {Li, L and Spagnolie, SE},
Title = {Swimming and pumping by helical waves in viscous and
viscoelastic fluids},
Journal = {Physics of Fluids},
Volume = {27},
Number = {2},
Pages = {021902021902},
Year = {2015},
Month = {February},
ISSN = {10706631},
url = {http://dx.doi.org/10.1063/1.4909516},
Doi = {10.1063/1.4909516},
Key = {fds302449}
}
%% Liao, Wenjing
@article{fds300127,
Author = {W. Liao},
Title = {MUSIC for multidimensional spectral estimation: stability
and superresolution},
Journal = {IEEE Transactions on Signal Processing},
Volume = {63},
Number = {23},
Year = {2015},
Month = {July},
Key = {fds300127}
}
%% Lipnowski, Michael
@article{fds227091,
Author = {M. Lipnowski},
Title = {Equivariant torsion and base change},
Journal = {Algebra and Number Theory},
Year = {2015},
url = {http://arxiv.org/abs/1312.2540},
Key = {fds227091}
}
@article{fds300040,
Author = {M. Lipnowski and J. Tsimerman},
Title = {How large is A_g(F_p)?},
Year = {2015},
url = {http://arxiv.org/abs/1511.02212},
Key = {fds300040}
}
@article{fds226181,
Author = {N. Bergeron and M. Lipnowski},
Title = {Twisted limit formula for torsion and cyclic base
change},
Year = {2015},
url = {http://arxiv.org/abs/1409.6749},
Key = {fds226181}
}
@article{fds226182,
Author = {J. Getz and H. Hahn and M. Lipnowski},
Title = {A relative Weyl law and spectral sparsity of distinguished
representations},
Year = {2015},
Key = {fds226182}
}
%% Liu, JianGuo
@article{fds318453,
Author = {Huang, H and Liu, JG},
Title = {A note on Monge–Ampère Keller–Segel
equation},
Journal = {Applied Mathematics Letters},
Volume = {61},
Pages = {2634},
Year = {2016},
Month = {November},
url = {http://dx.doi.org/10.1016/j.aml.2016.05.003},
Doi = {10.1016/j.aml.2016.05.003},
Key = {fds318453}
}
@article{fds318454,
Author = {Liu, JG and Huang, H},
Title = {Wellposedness for the KellerSegel equation with fractional
Laplacian and the theory of propagation of
chaos},
Journal = {Kinetic and Related Models},
Volume = {9},
Number = {4},
Pages = {715748},
Year = {2016},
Month = {September},
url = {http://dx.doi.org/10.3934/krm.2016013},
Doi = {10.3934/krm.2016013},
Key = {fds318454}
}
@article{fds318455,
Author = {Liu, JG and Cong, W},
Title = {A degenerate $p$Laplacian KellerSegel model},
Journal = {Kinetic and Related Models},
Volume = {9},
Number = {4},
Pages = {687714},
Year = {2016},
Month = {September},
url = {http://dx.doi.org/10.3934/krm.2016012},
Doi = {10.3934/krm.2016012},
Key = {fds318455}
}
@article{fds315797,
Author = {Herschlag, G and Liu, JG and Layton, AT},
Title = {Fluid extraction across pumping and permeable walls in the
viscous limit},
Journal = {Physics of Fluids},
Volume = {28},
Number = {4},
Pages = {041902041902},
Year = {2016},
Month = {April},
ISSN = {10706631},
url = {http://dx.doi.org/10.1063/1.4946005},
Doi = {10.1063/1.4946005},
Key = {fds315797}
}
@article{fds300221,
Author = {Liu, JG and Wang, J},
Title = {A Note on L ∞ $L^{\infty}$ Bound and Uniqueness to a
Degenerate KellerSegel Model},
Journal = {Acta Applicandae Mathematicae},
Volume = {142},
Number = {1},
Pages = {173188},
Year = {2016},
Month = {April},
ISSN = {01678019},
url = {http://dx.doi.org/10.1007/s1044001500225},
Doi = {10.1007/s1044001500225},
Key = {fds300221}
}
@article{fds318456,
Author = {Liu, JG and Pego, RL},
Title = {On generating functions of Hausdorff moment
sequences},
Journal = {Transactions of the American Mathematical
Society},
Volume = {368},
Number = {12},
Pages = {84998518},
Year = {2016},
Month = {February},
url = {http://dx.doi.org/10.1090/tran/6618},
Doi = {10.1090/tran/6618},
Key = {fds318456}
}
@article{fds318457,
Author = {Liu, JG and Zhang, Y},
Title = {Convergence of diffusiondrift many particle systems in
probability under a sobolev norm},
Volume = {162},
Series = {Proceedings of Particle Systems and Partial Differential
Equations  III},
Pages = {195223},
Publisher = {Springer},
Year = {2016},
Month = {January},
ISBN = {9783319321424},
url = {http://dx.doi.org/10.1007/9783319321448_10},
Abstract = {© Springer International Publishing Switzerland 2016.In
this paperwedevelop a newmartingale method to showthe
convergence of the regularized empirical measure of many
particle systems in probability under a Sobolev norm to the
corresponding mean field PDE. Our method works well for the
simple case of Fokker Planck equation and we can estimate a
lower bound of the rate of convergence. This method can be
generalized to more complicated systems with
interactions.},
Doi = {10.1007/9783319321448_10},
Key = {fds318457}
}
@article{fds300225,
Author = {J.G. Liu and J. Wang},
Title = {Refined hypercontractivity and uniqueness for the
KellerSegel equations},
Journal = {Applied Math Letter},
Volume = {52},
Pages = {212219},
Year = {2016},
Key = {fds300225}
}
@article{fds246842,
Author = {Xue, Y and Wang, C and Liu, JG},
Title = {Simple Finite Element Numerical Simulation of Incompressible
Flow Over Nonrectangular Domains and the SuperConvergence
Analysis},
Journal = {Journal of Scientific Computing},
Volume = {65},
Number = {3},
Pages = {11891216},
Year = {2015},
Month = {December},
ISSN = {08857474},
url = {http://dx.doi.org/10.1007/s1091501500058},
Doi = {10.1007/s1091501500058},
Key = {fds246842}
}
@article{fds246843,
Author = {Lu, J and Liu, JG and Margetis, D},
Title = {Emergence of step flow from an atomistic scheme of epitaxial
growth in 1+1 dimensions.},
Journal = {Physical Review E  Statistical, Nonlinear, and Soft Matter
Physics},
Volume = {91},
Number = {3},
Pages = {032403},
Year = {2015},
Month = {March},
ISSN = {15393755},
url = {http://dx.doi.org/10.1103/PhysRevE.91.032403},
Abstract = {The BurtonCabreraFrank (BCF) model for the flow of line
defects (steps) on crystal surfaces has offered useful
insights into nanostructure evolution. This model has rested
on phenomenological grounds. Our goal is to show via scaling
arguments the emergence of the BCF theory for noninteracting
steps from a stochastic atomistic scheme of a kinetic
restricted solidonsolid model in one spatial dimension.
Our main assumptions are: adsorbed atoms (adatoms) form a
dilute system, and elastic effects of the crystal lattice
are absent. The step edge is treated as a front that
propagates via probabilistic rules for atom attachment and
detachment at the step. We formally derive a quasistatic
step flow description by averaging out the stochastic scheme
when terrace diffusion, adatom desorption, and deposition
from above are present.},
Doi = {10.1103/PhysRevE.91.032403},
Key = {fds246843}
}
@article{fds300223,
Author = {Degond, P and Frouvelle, A and Liu, JG},
Title = {Phase Transitions, Hysteresis, and Hyperbolicity for
SelfOrganized Alignment Dynamics},
Journal = {Archive for Rational Mechanics and Analysis},
Volume = {216},
Number = {1},
Pages = {63115},
Year = {2015},
Month = {January},
ISSN = {00039527},
url = {http://dx.doi.org/10.1007/s0020501408007},
Abstract = {© 2014, SpringerVerlag Berlin Heidelberg.We provide a
complete and rigorous description of phase transitions for
kinetic models of selfpropelled particles interacting
through alignment. These models exhibit a competition
between alignment and noise. Both the alignment frequency
and noise intensity depend on a measure of the local
alignment. We show that, in the spatially homogeneous case,
the phase transition features (number and nature of
equilibria, stability, convergence rate, phase diagram,
hysteresis) are totally encoded in how the ratio between the
alignment and noise intensities depend on the local
alignment. In the spatially inhomogeneous case, we derive
the macroscopic models associated to the stable equilibria
and classify their hyperbolicity according to the same
function.},
Doi = {10.1007/s0020501408007},
Key = {fds300223}
}
@article{fds300222,
Author = {Chertock, A and Liu, JG and Pendleton, T},
Title = {Elastic collisions among peakon solutions for the
CamassaHolm equation},
Journal = {Applied Numerical Mathematics},
Volume = {93},
Pages = {3046},
Year = {2015},
Month = {January},
ISSN = {01689274},
url = {http://dx.doi.org/10.1016/j.apnum.2014.01.001},
Abstract = {© 2014 IMACS.The purpose of this paper is to study the
dynamics of the interaction among a special class of
solutions of the onedimensional CamassaHolm equation. The
equation yields soliton solutions whose identity is
preserved through nonlinear interactions. These solutions
are characterized by a discontinuity at the peak in the wave
shape and are thus called peakon solutions. We apply a
particle method to the CamassaHolm equation and show that
the nonlinear interaction among the peakon solutions
resembles an elastic collision, i.e., the total energy and
momentum of the system before the peakon interaction is
equal to the total energy and momentum of the system after
the collision. From this result, we provide several
numerical illustrations which support the analytical study,
as well as showcase the merits of using a particle method to
simulate solutions to the CamassaHolm equation under a wide
class of initial data.},
Doi = {10.1016/j.apnum.2014.01.001},
Key = {fds300222}
}
@article{fds313338,
Author = {Herschlag, G and Liu, JG and Layton, AT},
Title = {An Exact Solution for Stokes Flow in a Channel with
Arbitrarily Large Wall Permeability},
Journal = {SIAM Journal on Applied Mathematics},
Volume = {75},
Number = {5},
Pages = {22462267},
Year = {2015},
Month = {January},
ISSN = {00361399},
url = {http://dx.doi.org/10.1137/140995854},
Doi = {10.1137/140995854},
Key = {fds313338}
}
@article{fds300227,
Author = {J.G. Liu and R. Yang},
Title = {A random particle blob method for the KellerSegel equation
and convergence analysis},
Journal = {Math. Comp.},
Year = {2015},
Key = {fds300227}
}
%% Lu, Jianfeng
@article{fds320186,
Author = {Yu, TQ and Lu, J and Abrams, CF and VandenEijnden,
E},
Title = {Multiscale implementation of infiniteswap replica exchange
molecular dynamics.},
Journal = {Proceedings of the National Academy of Sciences of
USA},
Volume = {113},
Number = {42},
Pages = {1174411749},
Year = {2016},
Month = {October},
Abstract = {Replica exchange molecular dynamics (REMD) is a popular
method to accelerate conformational sampling of complex
molecular systems. The idea is to run several replicas of
the system in parallel at different temperatures that are
swapped periodically. These swaps are typically attempted
every few MD steps and accepted or rejected according to a
MetropolisHastings criterion. This guarantees that the
joint distribution of the composite system of replicas is
the normalized sum of the symmetrized product of the
canonical distributions of these replicas at the different
temperatures. Here we propose a different implementation of
REMD in which (i) the swaps obey a continuoustime Markov
jump process implemented via Gillespie's stochastic
simulation algorithm (SSA), which also samples exactly the
aforementioned joint distribution and has the advantage of
being rejection free, and (ii) this REMDSSA is combined
with the heterogeneous multiscale method to accelerate the
rate of the swaps and reach the socalled infiniteswap
limit that is known to optimize sampling efficiency. The
method is easy to implement and can be trivially
parallelized. Here we illustrate its accuracy and efficiency
on the examples of alanine dipeptide in vacuum and
Cterminal βhairpin of protein G in explicit solvent. In
this latter example, our results indicate that the landscape
of the protein is a triple funnel with two folded structures
and one misfolded structure that are stabilized by
Hbonds.},
Key = {fds320186}
}
@article{fds320187,
Author = {Lu, J and Zhou, Z},
Title = {Improved sampling and validation of frozen Gaussian
approximation with surface hopping algorithm for
nonadiabatic dynamics.},
Journal = {Journal of Chemical Physics},
Volume = {145},
Number = {12},
Pages = {124109},
Year = {2016},
Month = {September},
url = {http://dx.doi.org/10.1063/1.4963107},
Abstract = {In the spirit of the fewest switches surface hopping, the
frozen Gaussian approximation with surface hopping (FGASH)
method samples a path integral representation of the
nonadiabatic dynamics in the semiclassical regime. An
improved sampling scheme is developed in this work for
FGASH based on birth and death branching processes. The
algorithm is validated for the standard test examples of
nonadiabatic dynamics.},
Doi = {10.1063/1.4963107},
Key = {fds320187}
}
@article{fds318293,
Author = {Li, X and Lu, J},
Title = {Traction boundary conditions for molecular static
simulations},
Journal = {Computer Methods in Applied Mechanics and
Engineering},
Volume = {308},
Pages = {310329},
Year = {2016},
Month = {August},
url = {http://dx.doi.org/10.1016/j.cma.2016.05.002},
Doi = {10.1016/j.cma.2016.05.002},
Key = {fds318293}
}
@article{fds318294,
Author = {Lin, L and Lu, J},
Title = {Decay estimates of discretized Green’s functions for
Schrödinger type operators},
Journal = {Science China Mathematics},
Volume = {59},
Number = {8},
Pages = {15611578},
Year = {2016},
Month = {August},
url = {http://dx.doi.org/10.1007/s1142501603114},
Doi = {10.1007/s1142501603114},
Key = {fds318294}
}
@article{fds318295,
Author = {Lai, R and Lu, J},
Title = {Localized density matrix minimization and linearscaling
algorithms},
Journal = {Journal of Computational Physics},
Volume = {315},
Pages = {194210},
Year = {2016},
Month = {June},
url = {http://dx.doi.org/10.1016/j.jcp.2016.02.076},
Doi = {10.1016/j.jcp.2016.02.076},
Key = {fds318295}
}
@article{fds318296,
Author = {Lu, J and Ying, L},
Title = {Sparsifying preconditioner for soliton calculations},
Journal = {Journal of Computational Physics},
Volume = {315},
Pages = {458466},
Year = {2016},
Month = {June},
url = {http://dx.doi.org/10.1016/j.jcp.2016.03.061},
Doi = {10.1016/j.jcp.2016.03.061},
Key = {fds318296}
}
@article{fds316401,
Author = {Lu, J and Wirth, B and Yang, H},
Title = {Combining 2D synchrosqueezed wave packet transform with
optimization for crystal image analysis},
Journal = {Journal of the Mechanics and Physics of Solids},
Volume = {89},
Pages = {194210},
Year = {2016},
Month = {April},
ISSN = {00225096},
url = {http://hdl.handle.net/10161/11296 Duke open
access},
Abstract = {© 2016 Elsevier Ltd. All rights reserved.We develop a
variational optimization method for crystal analysis in
atomic resolution images, which uses information from a 2D
synchrosqueezed transform (SST) as input. The
synchrosqueezed transform is applied to extract initial
information from atomic crystal images: crystal defects,
rotations and the gradient of elastic deformation. The
deformation gradient estimate is then improved outside the
identified defect region via a variational approach, to
obtain more robust results agreeing better with the physical
constraints. The variational model is optimized by a
nonlinear projected conjugate gradient method. Both examples
of images from computer simulations and imaging experiments
are analyzed, with results demonstrating the effectiveness
of the proposed method.},
Doi = {10.1016/j.jmps.2016.01.002},
Key = {fds316401}
}
@article{fds318297,
Author = {Chen, J and Lu, J},
Title = {Analysis of the divideandconquer method for electronic
structure calculations},
Journal = {Mathematics of Computation},
Volume = {85},
Number = {302},
Pages = {29192938},
Year = {2016},
Month = {January},
url = {http://dx.doi.org/10.1090/mcom/3066},
Doi = {10.1090/mcom/3066},
Key = {fds318297}
}
@article{fds320188,
Author = {Delgadillo, R and Lu, J and Yang, X},
Title = {GaugeInvariant Frozen Gaussian Approximation Method for the
Schrödinger Equation with Periodic Potentials},
Journal = {SIAM Journal on Scientific Computing},
Volume = {38},
Number = {4},
Pages = {A2440A2463},
Year = {2016},
Month = {January},
url = {http://dx.doi.org/10.1137/15M1040384},
Doi = {10.1137/15M1040384},
Key = {fds320188}
}
@article{fds243728,
Author = {Lu, J and Moroz, V and Muratov, CB},
Title = {OrbitalFree Density Functional Theory of OutofPlane
Charge Screening in Graphene},
Journal = {Journal of Nonlinear Science},
Volume = {25},
Number = {6},
Pages = {13911430},
Year = {2015},
Month = {December},
ISSN = {09388974},
url = {http://dx.doi.org/10.1007/s0033201592594},
Doi = {10.1007/s0033201592594},
Key = {fds243728}
}
@article{fds305048,
Author = {Li, C and Lu, J and Yang, W},
Title = {Gentlest ascent dynamics for calculating first excited state
and exploring energy landscape of KohnSham density
functionals.},
Journal = {Journal of Chemical Physics},
Volume = {143},
Number = {22},
Pages = {224110},
Year = {2015},
Month = {December},
ISSN = {00219606},
url = {http://dx.doi.org/10.1063/1.4936411},
Abstract = {We develop the gentlest ascent dynamics for KohnSham
density functional theory to search for the index1 saddle
points on the energy landscape of the KohnSham density
functionals. These stationary solutions correspond to
excited states in the ground state functionals. As shown by
various examples, the first excited states of many chemical
systems are given by these index1 saddle points. Our novel
approach provides an alternative, more robust way to obtain
these excited states, compared with the widely used ΔSCF
approach. The method can be easily generalized to target
higher index saddle points. Our results also reveal the
physical interest and relevance of studying the KohnSham
energy landscape.},
Doi = {10.1063/1.4936411},
Key = {fds305048}
}
@article{fds243731,
Author = {Yang, H and Lu, J and Brown, WP and Daubechies, I and Ying,
L},
Title = {Quantitative Canvas Weave Analysis Using 2D Synchrosqueezed
Transforms: Application of timefrequency analysis to art
investigation},
Journal = {IEEE Signal Processing Magazine},
Volume = {32},
Number = {4},
Pages = {5563},
Year = {2015},
Month = {July},
ISSN = {10535888},
url = {http://hdl.handle.net/10161/12009 Duke open
access},
Doi = {10.1109/MSP.2015.2406882},
Key = {fds243731}
}
@article{fds243732,
Author = {Li, Q and Lu, J and Sun, W},
Title = {Diffusion approximations and domain decomposition method of
linear transport equations: Asymptotics and
numerics},
Journal = {Journal of Computational Physics},
Volume = {292},
Pages = {141167},
Year = {2015},
Month = {July},
ISSN = {00219991},
url = {http://dx.doi.org/10.1016/j.jcp.2015.03.014},
Abstract = {© 2015 Elsevier Inc.In this paper we construct numerical
schemes to approximate linear transport equations with slab
geometry by diffusion equations. We treat both the case of
pure diffusive scaling and the case where kinetic and
diffusive scalings coexist. The diffusion equations and
their data are derived from asymptotic and layer analysis
which allows general scattering kernels and general data. We
apply the halfspace solver in [20] to resolve the boundary
layer equation and obtain the boundary data for the
diffusion equation. The algorithms are validated by
numerical experiments and also by error analysis for the
pure diffusive scaling case.},
Doi = {10.1016/j.jcp.2015.03.014},
Key = {fds243732}
}
@article{fds243733,
Author = {Lu, J and Mendl, CB},
Title = {Numerical scheme for a spatially inhomogeneous matrixvalued
quantum Boltzmann equation},
Journal = {Journal of Computational Physics},
Volume = {291},
Pages = {303316},
Year = {2015},
Month = {June},
ISSN = {00219991},
url = {http://dx.doi.org/10.1016/j.jcp.2015.03.020},
Doi = {10.1016/j.jcp.2015.03.020},
Key = {fds243733}
}
@article{fds243734,
Author = {Lu, J and Liu, JG and Margetis, D},
Title = {Emergence of step flow from an atomistic scheme of epitaxial
growth in 1+1 dimensions},
Journal = {Physical Review E  Statistical, Nonlinear, and Soft Matter
Physics},
Volume = {91},
Number = {3},
Pages = {032403},
Year = {2015},
Month = {March},
ISSN = {15393755},
url = {http://dx.doi.org/10.1103/PhysRevE.91.032403},
Abstract = {© 2015 American Physical Society.The BurtonCabreraFrank
(BCF) model for the flow of line defects (steps) on crystal
surfaces has offered useful insights into nanostructure
evolution. This model has rested on phenomenological
grounds. Our goal is to show via scaling arguments the
emergence of the BCF theory for noninteracting steps from a
stochastic atomistic scheme of a kinetic restricted
solidonsolid model in one spatial dimension. Our main
assumptions are: adsorbed atoms (adatoms) form a dilute
system, and elastic effects of the crystal lattice are
absent. The step edge is treated as a front that propagates
via probabilistic rules for atom attachment and detachment
at the step. We formally derive a quasistatic step flow
description by averaging out the stochastic scheme when
terrace diffusion, adatom desorption, and deposition from
above are present.},
Doi = {10.1103/PhysRevE.91.032403},
Key = {fds243734}
}
@article{fds243743,
Author = {Lu, J and Nolen, J},
Title = {Reactive trajectories and the transition path
process},
Journal = {Probability Theory and Related Fields},
Volume = {161},
Number = {12},
Pages = {195244},
Year = {2015},
Month = {February},
ISSN = {01788051},
url = {http://dx.doi.org/10.1007/s004400140547y},
Doi = {10.1007/s004400140547y},
Key = {fds243743}
}
@article{fds243736,
Author = {Liu, J and Lu, J and Zhou, X},
Title = {Efficient Rare Event Simulation for Failure Problems in
Random Media},
Journal = {SIAM Journal on Scientific Computing},
Volume = {37},
Number = {2},
Pages = {A609A624},
Year = {2015},
Month = {January},
ISSN = {10648275},
url = {http://dx.doi.org/10.1137/140965569},
Doi = {10.1137/140965569},
Key = {fds243736}
}
@article{fds305050,
Author = {Yang, H and Lu, J and Ying, L},
Title = {Crystal Image Analysis Using 2D Synchrosqueezed
Transforms},
Journal = {Multiscale Modeling & Simulation},
Volume = {13},
Number = {4},
Pages = {15421572},
Year = {2015},
Month = {January},
ISSN = {15403459},
url = {http://hdl.handle.net/10161/11648 Duke open
access},
Doi = {10.1137/140955872},
Key = {fds305050}
}
@article{fds243729,
Author = {Lu, J and Ying, L},
Title = {Compression of the electron repulsion integral tensor in
tensor hypercontraction format with cubic scaling
cost},
Journal = {Journal of Computational Physics},
Volume = {302},
Pages = {329335},
Year = {2015},
ISSN = {00219991},
url = {http://dx.doi.org/10.1016/j.jcp.2015.09.014},
Abstract = {© 2015 Elsevier Inc.Electron repulsion integral tensor has
ubiquitous applications in electronic structure
computations. In this work, we propose an algorithm which
compresses the electron repulsion tensor into the tensor
hypercontraction format with O(nN2logN) computational cost,
where N is the number of orbital functions and n is the
number of spatial grid points that the discretization of
each orbital function has. The algorithm is based on a novel
strategy of density fitting using a selection of a subset of
spatial grid points to approximate the pair products of
orbital functions on the whole domain.},
Doi = {10.1016/j.jcp.2015.09.014},
Key = {fds243729}
}
@article{fds243730,
Author = {Lai, R and Lu, J and Osher, S},
Title = {Density matrix minimization with ${\ell}_1$
regularization},
Journal = {Communications in Mathematical Sciences},
Volume = {13},
Number = {8},
Pages = {20972117},
Year = {2015},
ISSN = {15396746},
url = {http://dx.doi.org/10.4310/CMS.2015.v13.n8.a6},
Doi = {10.4310/CMS.2015.v13.n8.a6},
Key = {fds243730}
}
@article{fds243737,
Author = {Lu, J and Marzuola, JL},
Title = {Strang splitting methods for a quasilinear Schrödinger
equation: convergence, instability, and dynamics},
Journal = {Communications in Mathematical Sciences},
Volume = {13},
Number = {5},
Pages = {10511074},
Year = {2015},
ISSN = {15396746},
url = {http://dx.doi.org/10.4310/CMS.2015.v13.n5.a1},
Doi = {10.4310/CMS.2015.v13.n5.a1},
Key = {fds243737}
}
%% Ma, Ding
@article{fds318299,
Author = {Ma, D},
Title = {Inverse of some matrix related to double zeta values of odd
weight},
Journal = {Journal of Number Theory},
Volume = {166},
Pages = {166180},
Year = {2016},
Month = {September},
url = {http://dx.doi.org/10.1016/j.jnt.2016.02.007},
Doi = {10.1016/j.jnt.2016.02.007},
Key = {fds318299}
}
@article{fds318300,
Author = {Ma, D},
Title = {Period polynomial relations between formal double zeta
values of odd weight},
Journal = {Mathematische Annalen},
Volume = {365},
Number = {12},
Pages = {345362},
Year = {2016},
Month = {June},
url = {http://dx.doi.org/10.1007/s0020801513087},
Doi = {10.1007/s0020801513087},
Key = {fds318300}
}
%% Maggioni, Mauro
@article{fds318319,
Author = {Goetzmann, WN and Jones, PW and Maggioni, M and Walden,
J},
Title = {Beauty is in the bid of the beholder: An empirical basis for
style},
Journal = {Research in Economics},
Volume = {70},
Number = {3},
Pages = {388402},
Year = {2016},
Month = {September},
url = {http://dx.doi.org/10.1016/j.rie.2016.05.004},
Doi = {10.1016/j.rie.2016.05.004},
Key = {fds318319}
}
@article{fds316563,
Author = {Wang, Y and Chen, G and Maggioni, M},
Title = {HighDimensional Data Modeling Techniques for Detection of
Chemical Plumes and Anomalies in Hyperspectral Images and
Movies},
Journal = {IEEE Journal of Selected Topics in Applied Earth
Observations and Remote Sensing},
Volume = {9},
Number = {9},
Pages = {43164324},
Year = {2016},
Month = {September},
ISSN = {19391404},
url = {http://dx.doi.org/10.1109/JSTARS.2016.2539968},
Abstract = {We briefly review recent progress in techniques for modeling
and analyzing hyperspectral images and movies, in particular
for detecting plumes of both known and unknown chemicals.
For detecting chemicals of known spectrum, we extend the
technique of using a single subspace for modeling the
background to a “mixture of subspaces” model to tackle
more complicated background. Furthermore, we use partial
least squares regression on a resampled training set to
boost performance. For the detection of unknown chemicals,
we view the problem as an anomaly detection problem and use
novel estimators with lowsampled complexity for
intrinsically lowdimensional data in high dimensions that
enable us to model the “normal” spectra and detect
anomalies. We apply these algorithms to benchmark datasets
made available by the Automated Target Detection program
cofunded by NSF, DTRA, and NGA, and compare, when
applicable, to current stateoftheart algorithms, with
favorable results.},
Doi = {10.1109/JSTARS.2016.2539968},
Key = {fds316563}
}
@article{fds317218,
Author = {Yin, R and Monson, E and Honig, E and Daubechies, I and Maggioni,
M},
Title = {Object recognition in art drawings: Transfer of a neural
network},
Journal = {IEEE International Conference on Acoustics Speech and Signal
Processing},
Volume = {2016May},
Pages = {22992303},
Year = {2016},
Month = {May},
ISBN = {9781479999880},
ISSN = {15206149},
url = {http://dx.doi.org/10.1109/ICASSP.2016.7472087},
Abstract = {© 2016 IEEE.We consider the problem of recognizing objects
in collections of art works, in view of automatically
labeling, searching and organizing databases of art works.
To avoid manually labelling objects, we introduce a
framework for transferring a convolutional neural network
(CNN), trained on available large collections of labelled
natural images, to the context of drawings. We retrain both
the top and the bottom layer of the network, responsible for
the highlevel classiication output and the lowlevel
features detection respectively, by transforming natural
images into drawings. We apply this procedure to the
drawings in the Jan Brueghel Wiki, and show the transferred
CNN learns a discriminative metric on drawings and achieves
good recognition accuracy. We also discuss why standard
descriptorbased methods is problematic in the context of
drawings.},
Doi = {10.1109/ICASSP.2016.7472087},
Key = {fds317218}
}
@article{fds314792,
Author = {Maggioni, M and Minsker, S and Strawn, N},
Title = {Multiscale dictionary learning: Nonasymptotic bounds and
robustness},
Journal = {Journal of machine learning research : JMLR},
Volume = {17},
Year = {2016},
Month = {January},
ISSN = {15324435},
url = {http://arxiv.org/abs/1401.5833},
Abstract = {© 2016 Mauro Maggioni, Stanislav Minsker, and Nate
Strawn.Highdimensional datasets are wellapproximated by
lowdimensional structures. Over the past decade, this
empirical observation motivated the investigation of
detection, measurement, and modeling techniques to exploit
these lowdimensional intrinsic structures, yielding
numerous implications for highdimensional statistics,
machine learning, and signal processing. Manifold learning
(where the lowdimensional structure is a manifold) and
dictionary learning (where the lowdimensional structure is
the set of sparse linear combinations of vectors from a
finite dictionary) are two prominent theoretical and
computational frameworks in this area. Despite their
ostensible distinction, the recentlyintroduced Geometric
MultiResolution Analysis (GMRA) provides a robust,
computationally eficient, multiscale procedure for
simultaneously learning manifolds and dictionaries. In this
work, we prove nonasymptotic probabilistic bounds on the
approximation error of GMRA for a rich class of
datagenerating statistical models that includes "noisy"
manifolds, thereby establishing the theoretical robustness
of the procedure and confirming empirical observations. In
particular, if a dataset aggregates near a lowdimensional
manifold, our results show that the approximation error of
the GMRA is completely independent of the ambient dimension.
Our work therefore establishes GMRA as a provably fast
algorithm for dictionary learning with approximation and
sparsity guarantees. We include several numerical
experiments confirming these theoretical results, and our
theoretical framework provides new tools for assessing the
behavior of manifold learning and dictionary learning
procedures on a large class of interesting
models.},
Key = {fds314792}
}
@article{fds290935,
Author = {Maggioni, M},
Title = {Geometry of Data and Biology},
Journal = {Notices of the American Mathematical Society},
Volume = {62},
Number = {10},
Pages = {11851188},
Year = {2015},
Month = {November},
ISSN = {00029920},
url = {http://dx.doi.org/10.1090/noti1289},
Doi = {10.1090/noti1289},
Key = {fds290935}
}
@article{fds313569,
Author = {Maggioni, M and Minsker, S and Strawn, N},
Title = {Geometric multiresolution analysis for dictionary
learning},
Journal = {Proceedings of SPIE  The International Society for Optical
Engineering},
Volume = {9597},
Year = {2015},
Month = {January},
ISBN = {9781628417630},
ISSN = {0277786X},
url = {http://dx.doi.org/10.1117/12.2189594},
Abstract = {© 2015 SPIE.We present an efficient algorithm and theory
for Geometric MultiResolution Analysis (GMRA), a procedure
for dictionary learning. Sparse dictionary learning provides
the necessary complexity reduction for the critical
applications of compression, regression, and classification
in highdimensional data analysis. As such, it is a critical
technique in data science and it is important to have
techniques that admit both efficient implementation and
strong theory for large classes of theoretical models. By
construction, GMRA is computationally efficient and in this
paper we describe how the GMRA correctly approximates a
large class of plausible models (namely, the noisy
manifolds).},
Doi = {10.1117/12.2189594},
Key = {fds313569}
}
@article{fds300137,
Author = {M. Crosskey and M. Maggioni},
Title = {ATLAS: A geometric approach to learning highdimensional
stochastic systems near manifolds},
Journal = {SIAM Journ. Mult. Model. Simul.},
Year = {2015},
Key = {fds300137}
}
@article{fds300142,
Author = {T. Tomita and J. Vogelstein and M. Maggioni},
Title = {Randomer Forests},
Year = {2015},
Key = {fds300142}
}
@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}
}
@misc{PathNIH2004,
Author = {GL Davis and Mauro Maggioni and FJ Warner and FB Geshwind and AC Coppi and RA DeVerse and RR Coifman},
Title = {Hyperspectral 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/TR1289},
Organization = {Dept. Comp. Sci., Yale University},
Institution = {Dept. Comp. Sci., Yale University},
Year = {2004},
Key = {CMTech}
}
%% Mattingly, Jonathan C.
@article{fds318321,
Author = {Hairer, M and Mattingly, J},
Title = {The strong Feller property for singular stochastic
PDEs},
Year = {2016},
Abstract = {We show that the Markov semigroups generated by a large
class of singular stochastic PDEs satisfy the strong Feller
property. These include for example the KPZ equation and the
dynamical $\Phi^4_3$ model. As a corollary, we prove that
the Brownian bridge measure is the unique invariant measure
for the KPZ equation with periodic boundary
conditions.},
Key = {fds318321}
}
@article{fds318322,
Author = {Tempkin, JOB and Koten, BV and Mattingly, JC and Dinner, AR and Weare,
J},
Title = {Trajectory stratification of stochastic dynamics},
Year = {2016},
Abstract = {We present a general mathematical framework for trajectory
stratification for simulating rare events. Trajectory
stratification involves decomposing trajectories of the
underlying process into fragments limited to restricted
regions of state space (strata), computing averages over the
distributions of the trajectory fragments within the strata
with minimal communication between them, and combining those
averages with appropriate weights to yield averages with
respect to the original underlying process. Our framework
reveals the full generality and flexibility of trajectory
stratification, and it illuminates a common mathematical
structure shared by existing algorithms for sampling rare
events. We demonstrate the power of the framework by
defining strata in terms of both points in time and
pathdependent variables for efficiently estimating averages
that were not previously tractable.},
Key = {fds318322}
}
@article{fds243880,
Author = {J.C. Mattingly and Bakhtin, Y and Hurth, T and Mattingly, JC},
Title = {Regularity of invariant densities for 1D systems with random
switching},
Journal = {Nonlinearity},
Volume = {28},
Number = {11},
Pages = {37553787},
Year = {2015},
Month = {October},
ISSN = {09517715},
url = {http://hdl.handle.net/10161/9514 Duke open
access},
Abstract = {This is a detailed analysis of invariant measures for
onedimensional dynamical systems with random switching. In
particular, we prove smoothness of the invariant densities
away from critical points and describe the asymptotics of
the invariant densities at critical points.},
Doi = {10.1088/09517715/28/11/3755},
Key = {fds243880}
}
@article{fds243882,
Author = {Herzog, DP and Mattingly, JC},
Title = {A practical criterion for positivity of transition
densities},
Journal = {Nonlinearity},
Volume = {28},
Number = {8},
Pages = {28232845},
Year = {2015},
Month = {August},
ISSN = {09517715},
url = {http://hdl.handle.net/10161/9510 Duke open
access},
Doi = {10.1088/09517715/28/8/2823},
Key = {fds243882}
}
@article{fds243881,
Author = {Lawley, SD and Mattingly, JC and Reed, MC},
Title = {Stochastic Switching in Infinite Dimensions with
Applications to Random Parabolic PDE},
Journal = {SIAM Journal on Mathematical Analysis},
Volume = {47},
Number = {4},
Pages = {30353063},
Year = {2015},
Month = {January},
ISSN = {00361410},
url = {http://hdl.handle.net/10161/9517 Duke open
access},
Doi = {10.1137/140976716},
Key = {fds243881}
}
@article{fds243883,
Author = {Huckemann, S and Mattingly, J and Miller, E and Nolen,
J},
Title = {Sticky central limit theorems at isolated hyperbolic planar
singularities},
Journal = {Electronic Journal of Probability},
Volume = {20},
Year = {2015},
url = {http://hdl.handle.net/10161/9516 Duke open
access},
Doi = {10.1214/EJP.v203887},
Key = {fds243883}
}
@article{fds243884,
Author = {Herzog, D and Mattingly, J},
Title = {Noiseinduced stabilization of planar flows
II},
Journal = {Electronic Journal of Probability},
Volume = {20},
Year = {2015},
url = {http://hdl.handle.net/10161/9512 Duke open
access},
Abstract = {© 2015 University of Washington. All rights reserved. We
continue the work started in Part I [6], showing how the
addition of noise can stabilize an otherwise unstable
system. The analysis makes use of nearly optimal Lyapunov
functions. In this continuation, we remove the main limiting
assumption of Part I by an inductive procedure as well as
establish a lower bound which shows that our construction is
radially sharp. We also prove a version of Peskir’s [7]
generalized Tanaka formula adapted to patching together
Lyapunov functions. This greatly simplifies the analysis
used in previous works.},
Doi = {10.1214/EJP.v204048},
Key = {fds243884}
}
@article{fds303549,
Author = {Luo, S and Mattingly, JC},
Title = {Scaling limits of a model for selection at two
scales},
Year = {2015},
url = {http://arxiv.org/abs/1507.00397v1},
Abstract = {The dynamics of a population undergoing selection is a
central topic in evolutionary biology. This question is
particularly intriguing in the case where selective forces
act in opposing directions at two population scales. For
example, a fastreplicating virus strain outcompetes
slowerreplicating strains at the withinhost scale.
However, if the fastreplicating strain causes host
morbidity and is less frequently transmitted, it can be
outcompeted by slowerreplicating strains at the
betweenhost scale. Here we consider a stochastic
ballandurn process which models this type of phenomenon.
We prove the weak convergence of this process under two
natural scalings. The first scaling leads to a deterministic
nonlinear integropartial differential equation on the
interval $[0,1]$ with dependence on a single parameter,
$\lambda$. We show that the fixed points of this
differential equation are Beta distributions and that their
stability depends on $\lambda$ and the behavior of the
initial data around $1$. The second scaling leads to a
measurevalued FlemingViot process, an infinite dimensional
stochastic process that is frequently associated with a
population genetics.},
Key = {fds303549}
}
%% McGoff, Kevin A
@article{fds225790,
Author = {K. McGoff and S. Mukherjee and A. Nobel and N. Pillai},
Title = {Consistency of maximum likelihood estimation for some
dynamical systems},
Journal = {Ann. Statist.},
Volume = {43},
Number = {1},
Pages = {129},
Year = {2015},
url = {http://arxiv.org/abs/1306.5603},
Key = {fds225790}
}
%% Miller, Ezra
@article{fds303557,
Author = {Kahle, T and Miller, E and O’Neill, C},
Title = {Irreducible decomposition of binomial ideals},
Journal = {Compositio Mathematica},
Volume = {152},
Number = {06},
Pages = {13191332},
Year = {2016},
Month = {June},
url = {http://arxiv.org/abs/1503.02607},
Abstract = {Building on coprincipal mesoprimary decomposition [Kahle and
Miller, 2014], we combinatorially construct an irreducible
decomposition of any given binomial ideal. In a parallel
manner, for congruences in commutative monoids we construct
decompositions that are direct combinatorial analogues of
binomial irreducible decompositions, and for binomial ideals
we construct decompositions into ideals that are as
irreducible as possible while remaining binomial. We provide
an example of a binomial ideal that is not an intersection
of irreducible binomial ideals, thus answering a question of
Eisenbud and Sturmfels [1996].},
Doi = {10.1112/S0010437X16007272},
Key = {fds303557}
}
@article{fds303556,
Author = {Bendich, P and Marron, JS and Miller, E and Pieloch, A and Skwerer,
S},
Title = {Persistent Homology Analysis of Brain Artery
Trees.},
Journal = {The annals of applied statistics},
Volume = {10},
Number = {1},
Pages = {198218},
Year = {2016},
Month = {January},
url = {http://arxiv.org/abs/1411.6652v1},
Abstract = {New representations of treestructured data objects, using
ideas from topological data analysis, enable improved
statistical analyses of a population of brain artery trees.
A number of representations of each data tree arise from
persistence diagrams that quantify branching and looping of
vessels at multiple scales. Novel approaches to the
statistical analysis, through various summaries of the
persistence diagrams, lead to heightened correlations with
covariates such as age and sex, relative to earlier analyses
of this data set. The correlation with age continues to be
significant even after controlling for correlations from
earlier significant summaries.},
Key = {fds303556}
}
@article{fds290936,
Author = {Miller, E},
Title = {Fruit Flies and Moduli: Interactions between Biology and
Mathematics},
Journal = {Notices of the American Mathematical Society},
Volume = {62},
Number = {10},
Pages = {11781184},
Year = {2015},
Month = {November},
ISSN = {00029920},
url = {http://dx.doi.org/10.1090/noti1290},
Doi = {10.1090/noti1290},
Key = {fds290936}
}
@article{fds243887,
Author = {Miller, E and Owen, M and Provan, JS},
Title = {Polyhedral computational geometry for averaging metric
phylogenetic trees},
Journal = {Advances in Applied Mathematics},
Volume = {68},
Pages = {5191},
Year = {2015},
Month = {July},
ISSN = {01968858},
url = {http://dx.doi.org/10.1016/j.aam.2015.04.002},
Doi = {10.1016/j.aam.2015.04.002},
Key = {fds243887}
}
@article{fds243885,
Author = {Berkesch Zamaere and C and Griffeth, S and Miller,
E},
Title = {Systems of parameters and holonomicity of A
hypergeometric systems},
Journal = {Pacific Journal of Mathematics},
Volume = {276},
Number = {2},
Pages = {281286},
Year = {2015},
ISSN = {00308730},
url = {http://dx.doi.org/10.2140/pjm.2015.276.281},
Doi = {10.2140/pjm.2015.276.281},
Key = {fds243885}
}
@article{fds243886,
Author = {Huckemann, S and Mattingly, J and Miller, E and Nolen,
J},
Title = {Sticky central limit theorems at isolated hyperbolic planar
singularities},
Journal = {Electronic Journal of Probability},
Volume = {20},
Year = {2015},
url = {http://hdl.handle.net/10161/9516 Duke open
access},
Doi = {10.1214/EJP.v203887},
Key = {fds243886}
}
%% Motta, Francis C.
@article{fds318324,
Author = {F.C. Motta and Francis C. Motta, and Patrick D. Shipman, and Bethany D.
Springer},
Title = {Optimally Topologically Transitive Orbits in Discrete
Dynamical Systems},
Journal = {American Mathematical Monthly},
Volume = {123},
Number = {2},
Pages = {115115},
Year = {2016},
url = {http://dx.doi.org/10.4169/amer.math.monthly.123.2.115},
Doi = {10.4169/amer.math.monthly.123.2.115},
Key = {fds318324}
}
@article{fds300026,
Author = {F.C. Motta and H. Adams and S. Chepushtanova and T. Emerson and E. Hanson and M. Kirby and R. Neville and C. Peterson and P.D. Shipman and L.
Ziegelmeier},
Title = {Persistent images: a stable vector representation of
persistent homology},
Year = {2015},
Month = {December},
Key = {fds300026}
}
@article{fds318325,
Author = {F.C. Motta and Pearson, DA and Bradley, RM and Motta, FC and Shipman,
PD},
Title = {Producing nanodot arrays with improved hexagonal order by
patterning surfaces before ion sputtering.},
Journal = {Physical Review E  Statistical, Nonlinear, and Soft Matter
Physics},
Volume = {92},
Number = {6},
Pages = {062401},
Year = {2015},
Month = {December},
url = {http://http://dx.doi.org/10.1103/PhysRevE.92.062401},
Abstract = {When the surface of a nominally flat binary material is
bombarded with a broad, normally incident ion beam,
disordered hexagonal arrays of nanodots can form. Shipman
and Bradley have derived equations of motion that govern the
coupled dynamics of the height and composition of such a
surface [Shipman and Bradley, Phys. Rev. B 84, 085420
(2011)]. We investigate the influence of initial conditions
on the hexagonal order yielded by integration of those
equations of motion. The initial conditions studied are
hexagonal and sinusoidal templates, straight scratches, and
nominally flat surfaces. Our simulations indicate that both
kinds of templates lead to marked improvements in the
hexagonal order if the initial wavelength is approximately
equal to or double the linearly selected wavelength.
Scratches enhance the hexagonal order in their vicinity if
their width is close to or less than the linearly selected
wavelength. Our results suggest that prepatterning a binary
material can dramatically increase the hexagonal order
achieved at large ion fluences.},
Doi = {10.1103/physreve.92.062401},
Key = {fds318325}
}
@article{fds300024,
Author = {F.C. Motta and H. Adams and M. Adamaszek},
Title = {Random cyclic dynamical systems},
Year = {2015},
Month = {November},
url = {http://arxiv.org/abs/1511.07832},
Key = {fds300024}
}
@article{fds300025,
Author = {F.C. Motta and S.R. Fassnacht and I. Oprea and P.D. Shipman and J. Kirkpatrick and G.
Borleske and D. Kamin},
Title = {Geometric methods to describe snow surface
roughness},
Journal = {35th Annual American Geophysical Union Hydrology
Days},
Year = {2015},
Month = {March},
url = {http://hydrologydays.colostate.edu/Papers_15/Fassnacht_paper.pdf},
Key = {fds300025}
}
@article{fds300014,
Author = {F.C. Motta and P.D. Shipman and B. D. Springer},
Title = {A Point of Tangency Between Combinatorics and Differential
Geometry},
Journal = {The American Mathematical Monthly},
Volume = {122},
Number = {1},
Pages = {5255},
Year = {2015},
Month = {January},
url = {http://dx.doi.org/10.4169/amer.math.monthly.122.01.52},
Key = {fds300014}
}
@article{fds300020,
Author = {F.C. Motta and P.D. Shipman},
Title = {Sharpening the defect of complex Hadamards with a
flow},
Year = {2015},
Key = {fds300020}
}
@article{fds300021,
Author = {F.C. Motta and P.D. Shipman and C. Burris},
Title = {An unoriented variation on de Bruijn sequences},
Year = {2015},
Key = {fds300021}
}
%% Mukherjee, Sayan
@article{fds258517,
Author = {E Munch and K Turner and P Bendich and S Mukherjee and J Mattingly and J
Harer},
Title = {Probabilistic Fréchet means for time varying persistence
diagrams},
Journal = {Electronic Journal of Statistics},
Volume = {9},
Number = {1},
Pages = {11731204},
Year = {2015},
url = {http://hdl.handle.net/10161/10051 Duke open
access},
Abstract = {In order to use persistence diagrams as a true statistical
tool, it would be very useful to have a good notion of mean
and variance for a set of diagrams. In 2011, Mileyko and his
collaborators made the first study of the properties of the
Fr\'echet mean in $(\mathcal{D}_p,W_p)$, the space of
persistence diagrams equipped with the pth Wasserstein
metric. In particular, they showed that the Fr\'echet mean
of a finite set of diagrams always exists, but is not
necessarily unique. The means of a continuouslyvarying set
of diagrams do not themselves (necessarily) vary
continuously, which presents obvious problems when trying to
extend the Fr\'echet mean definition to the realm of
vineyards. We fix this problem by altering the original
definition of Fr\'echet mean so that it now becomes a
probability measure on the set of persistence diagrams; in a
nutshell, the mean of a set of diagrams will be a weighted
sum of atomic measures, where each atom is itself a
persistence diagram determined using a perturbation of the
input diagrams. This definition gives for each $N$ a map
$(\mathcal{D}_p)^N \to \mathbb{P}(\mathcal{D}_p)$. We show
that this map is H\"older continuous on finite diagrams and
thus can be used to build a useful statistic on timevarying
persistence diagrams, better known as vineyards.},
Doi = {10.1214/15EJS1030},
Key = {fds258517}
}
%% Murphy, James
@article{fds292868,
Author = {Czaja, Wojciech and Benjamin Manning and Lance McLean and James M.
Murphy},
Title = {Fusion of aerial gamma ray survey and remote sensing data
for deeper understanding of radionucleotide fate after
radiological incidents: examples from the Fukushima DaiIchi
response},
Journal = {Journal of Radioanalytic and Nuclear Chemistry},
Year = {2015},
Key = {fds292868}
}
@article{fds292869,
Author = {Murphy, James M and Jacqueline Le Moigne and David J.
Harding},
Title = {Automatic image registration of multimodal remotely sensed
data with global shearlet features},
Journal = {IEEE Transactions on Geoscience and Remote
Sensing},
Year = {2015},
Key = {fds292869}
}
%% Ng, Lenhard L.
@article{fds299958,
Author = {C. Cornwell and L. Ng and S. Sivek},
Title = {Obstructions to Lagrangian concordance},
Journal = {Algebraic & Geometric Topology},
Year = {2015},
url = {http://arxiv.org/abs/1411.1364},
Key = {fds299958}
}
@article{fds299959,
Author = {L. Ng and D. Rutherford and V. Shende and S. Sivek and E.
Zaslow},
Title = {Augmentations are sheaves},
Year = {2015},
url = {http://arxiv.org/abs/1502.04939},
Key = {fds299959}
}
@article{fds299960,
Author = {L. Ng and D. Rutherford and V. Shende and S. Sivek},
Title = {The cardinality of the augmentation category of a Legendrian
link},
Year = {2015},
url = {http://arxiv.org/abs/1511.06724},
Key = {fds299960}
}
@article{fds243935,
Author = {Lipshitz, R and Ng, L and Sarkar, S},
Title = {On transverse invariants from Khovanov homology},
Journal = {Quantum Topology},
Volume = {6},
Number = {3},
Pages = {475513},
Year = {2015},
ISSN = {1663487X},
url = {http://dx.doi.org/10.4171/QT/69},
Doi = {10.4171/QT/69},
Key = {fds243935}
}
@article{fds243937,
Author = {Ekholm, T and Ng, L},
Title = {Legendrian contact homology in the boundary of a subcritical
weinstein 4Manifold},
Journal = {Journal of Differential Geometry},
Volume = {101},
Number = {1},
Pages = {67157},
Year = {2015},
ISSN = {0022040X},
Abstract = {We give a combinatorial description of the Legendrian
contact homology algebra associated to a Legendrian link in
S<sup>1</sup> × S<sup>2</sup> or
any connected sum #k(S<sup>1</sup>
×S<sup>2</sup>), viewed as the contact boundary
of the Weinstein manifold obtained by attaching 1handles to
the 4ball. In view of the surgery formula for symplectic
homology [5], this gives a combinatorial description of the
symplectic homology of any 4dimensional Weinstein manifold
(and of the linearized contact homology of its boundary). We
also study examples and discuss the invariance of the
Legendrian homology algebra under deformations, from both
the combinatorial and the analytical perspectives.},
Key = {fds243937}
}
%% Nolen, James H.
@article{fds316608,
Author = {Gloria, A and Nolen, J},
Title = {A Quantitative Central Limit Theorem for the Effective
Conductance on the Discrete Torus},
Journal = {Communications on Pure & Applied Mathematics},
Volume = {69},
Number = {12},
Pages = {23042348},
Year = {2016},
Month = {December},
ISSN = {00103640},
url = {http://dx.doi.org/10.1002/cpa.21614},
Doi = {10.1002/cpa.21614},
Key = {fds316608}
}
@article{fds316661,
Author = {Nolen, J},
Title = {Normal approximation for the net flux through a random
conductor},
Journal = {Stochastic Partial Differential Equations: Analysis and
Computations},
Volume = {4},
Number = {3},
Pages = {439476},
Year = {2016},
Month = {September},
ISSN = {21940401},
url = {http://arxiv.org/abs/1406.2186},
Doi = {10.1007/s4007201500684},
Key = {fds316661}
}
@article{fds318326,
Author = {Nolen, JH and Roquejoffre, JM and Ryzhik, L},
Title = {Refined long time asymptotics for FisherKPP
fronts},
Year = {2016},
Key = {fds318326}
}
@article{fds316662,
Author = {Nolen, J and Roquejoffre, JM and Ryzhik, L},
Title = {Convergence to a single wave in the FisherKPP
equation},
Year = {2016},
url = {http://arxiv.org/abs/1604.02994},
Key = {fds316662}
}
@article{fds316609,
Author = {Nolen, J and Mourrat, JC},
Title = {Scaling limit of the corrector in stochastic
homogenization},
Journal = {The annals of applied probability : an official journal of
the Institute of Mathematical Statistics},
Publisher = {Institute of Mathematical Statistics (IMS)},
Year = {2016},
ISSN = {10505164},
url = {http://arxiv.org/abs/1502.07440},
Key = {fds316609}
}
@article{fds227095,
Author = {S. Bhamidi and J. Hannig and C. Lee and J. Nolen},
Title = {The importance sampling technique for understanding rare
events in ErdősRényi random graphs},
Journal = {Electronic Journal of Probability},
Year = {2015},
Month = {October},
url = {http://ejp.ejpecp.org/article/view/2696},
Doi = {10.1214/EJP.v202696},
Key = {fds227095}
}
@article{fds287342,
Author = {Nolen, J and Roquejoffre, JM and Ryzhik, L},
Title = {PowerLike Delay in Time Inhomogeneous FisherKPP
Equations},
Journal = {Communications in Partial Differential Equations},
Volume = {40},
Number = {3},
Pages = {475505},
Year = {2015},
Month = {March},
ISSN = {03605302},
url = {http://math.duke.edu/~nolen/preprints/bigdelaydraft.pdf},
Doi = {10.1080/03605302.2014.972744},
Key = {fds287342}
}
@article{fds287345,
Author = {Lu, J and Nolen, J},
Title = {Reactive trajectories and the transition path
process},
Journal = {Probability Theory and Related Fields},
Volume = {161},
Number = {12},
Pages = {195244},
Year = {2015},
Month = {February},
ISSN = {01788051},
url = {http://dx.doi.org/10.1007/s004400140547y},
Doi = {10.1007/s004400140547y},
Key = {fds287345}
}
@article{fds299972,
Author = {J. Nolen and J.M. Roquejoffre and L. Ryzhik},
Title = {Refined long time asymptotics for the FisherKPP
equation},
Year = {2015},
url = {http://math.duke.edu/~nolen/preprints/kppbrezisv5.pdf},
Key = {fds299972}
}
@article{fds226519,
Author = {F. Hamel and J. Nolen and J.M. Roquejoffre and L.
Ryzhik},
Title = {The logarithmic delay of KPP fronts in a periodic
medium},
Journal = {Journal of the European Mathematical Society},
Year = {2015},
url = {http://arxiv.org/abs/1211.6173},
Key = {fds226519}
}
@article{fds287343,
Author = {Huckemann, S and Mattingly, J and Miller, E and Nolen,
J},
Title = {Sticky central limit theorems at isolated hyperbolic planar
singularities},
Journal = {Electronic Journal of Probability},
Volume = {20},
Year = {2015},
url = {http://hdl.handle.net/10161/9516 Duke open
access},
Doi = {10.1214/EJP.v203887},
Key = {fds287343}
}
@article{fds290937,
Author = {Bhamidi, S and Hannig, J and Lee, CY and Nolen, J},
Title = {The importance sampling technique for understanding rare
events in Erdős–Rényi random graphs},
Journal = {Electronic Journal of Probability},
Volume = {20},
Year = {2015},
url = {http://dx.doi.org/10.1214/EJP.v202696},
Doi = {10.1214/EJP.v202696},
Key = {fds290937}
}
%% Perea, Jose A.
@article{fds226515,
Author = {Jose A. Perea and Anastasia Deckard and Steve B. Haase and John
Harer},
Title = {SW1PerS: Sliding Windows and 1Persistence Scoring;
Discovering Periodicity in Gene Expression Time Series
Data},
Journal = {BMC Bioinformatics},
Year = {2015},
Month = {July},
Key = {fds226515}
}
%% Petters, Arlie O.
@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}
}
@book{fds51036,
Author = {A. O. Petters and X. Dong},
Title = {An Introduction to Mathematical Finance: Understanding and
Building Financial Intuition},
Series = {SUMAT},
Publisher = {Springer, in preparation},
Year = {2016},
Month = {Winter},
Key = {fds51036}
}
%% Pfister, Henry
@article{fds319310,
Author = {Hager, C and Pfister, HD and Graell I Amat and A and Brannstrom,
F},
Title = {Deterministic and ensemblebased spatiallycoupled product
codes},
Volume = {2016August},
Pages = {21142118},
Year = {2016},
Month = {August},
url = {http://dx.doi.org/10.1109/ISIT.2016.7541672},
Abstract = {© 2016 IEEE.Several authors have proposed spatiallycoupled
(or convolutionallike) variants of product codes (PCs). In
this paper, we focus on a parametrized family of generalized
PCs that recovers some of these codes (e.g., staircase and
blockwise braided codes) as special cases and study the
iterative decoding performance over the binary erasure
channel. Even though our code construction is deterministic
(and not based on a randomized ensemble), we show that it is
still possible to rigorously derive the density evolution
(DE) equations that govern the asymptotic performance. The
obtained DE equations are then compared to those for a
related spatiallycoupled PC ensemble. In particular, we
show that there exists a family of (deterministic) braided
codes that follows the same DE equation as the ensemble, for
any spatial length and coupling width.},
Doi = {10.1109/ISIT.2016.7541672},
Key = {fds319310}
}
@article{fds319311,
Author = {Kumar, S and Calderbank, R and Pfister, HD},
Title = {Reedmuller codes achieve capacity on the quantum erasure
channel},
Volume = {2016August},
Pages = {17501754},
Year = {2016},
Month = {August},
url = {http://dx.doi.org/10.1109/ISIT.2016.7541599},
Abstract = {© 2016 IEEE.The quantum erasure channel is the simplest
example of a quantum communication channel and its
information capacity is known precisely. The subclass of
quantum errorcorrecting codes called stabilizer codes is
known to contain capacityachieving sequences for the
quantum erasure channel, but no efficient method is known to
construct these sequences. In this article, we explicitly
describe a capacityachieving code sequence for the quantum
erasure channel. In particular, we show that
CalderbankShorSteane (CSS) stabilizer codes constructed
from selforthogonal binary linear codes are
capacityachieving on the quantum erasure channel if the
binary linear codes are capacityachieving on the binary
erasure channel. Recently, ReedMuller codes were shown to
achieve capacity on classical erasure channels. Using this,
we show that CSS codes constructed from binary ReedMuller
codes achieve the capacity of the quantum erasure channel.
The capacityachieving nature of these CSS codes is also
explained from a GF(4) perspective.},
Doi = {10.1109/ISIT.2016.7541599},
Key = {fds319311}
}
@article{fds319312,
Author = {Kudekar, S and Kumar, S and Mondelli, M and Pfister, HD and Urbankez,
R},
Title = {Comparing the bitMAP and blockMAP decoding thresholds of
reedmuller codes on BMS channels},
Volume = {2016August},
Pages = {17551759},
Year = {2016},
Month = {August},
url = {http://dx.doi.org/10.1109/ISIT.2016.7541600},
Abstract = {© 2016 IEEE.The question whether RM codes are
capacityachieving is a longstanding open problem in coding
theory that was recently answered in the affirmative for
transmission over erasure channels [1], [2]. Remarkably, the
proof does not rely on specific properties of RM codes,
apart from their symmetry. Indeed, the main technical result
consists in showing that any sequence of linear codes, with
doublytransitive permutation groups, achieves capacity on
the memoryless erasure channel under bitMAP decoding. Thus,
a natural question is what happens under blockMAP decoding.
In [1], [2], by exploiting further symmetries of the code,
the bitMAP threshold was shown to be sharp enough so that
the block erasure probability also converges to 0. However,
this technique relies heavily on the fact that the
transmission is over an erasure channel. We present an
alternative approach to strengthen results regarding the
bitMAP threshold to blockMAP thresholds. This approach is
based on a careful analysis of the weight distribution of RM
codes. In particular, the flavor of the main result is the
following: assume that the bitMAP error probability decays
as Nδ, for some δ > 0. Then, the blockMAP error
probability also converges to 0. This technique applies to
transmission over any binary memoryless symmetric channel.
Thus, it can be thought of as a first step in extending the
proof that RM codes are capacityachieving to the general
case.},
Doi = {10.1109/ISIT.2016.7541600},
Key = {fds319312}
}
@article{fds319313,
Author = {Kudekar, S and Pfister, HD and Kumar, S and Şaşoǧlu, E and Mondelli,
M and Urbanke, R},
Title = {ReedMuller codes achieve capacity on erasure
channels},
Journal = {Proceedings of the Annual ACM Symposium on Theory of
Computing},
Volume = {1921June2016},
Pages = {658669},
Year = {2016},
Month = {June},
url = {http://dx.doi.org/10.1145/2897518.2897584},
Abstract = {© 2016 ACM.We introduce a new approach to proving that a
sequence of deterministic linear codes achieves capacity on
an erasure channel under maximum a posteriori decoding.
Rather than relying on the precise structure of the codes,
our method exploits code symmetry. In particular, the
technique applies to any sequence of linear codes where the
block lengths are strictly increasing, the code rates
converge, and the permutation group of each code is doubly
transitive. In a nutshell, we show that symmetry alone
implies nearoptimal performance. An important consequence
of this result is that a sequence of ReedMuller codes with
increasing block length and converging rate achieves
capacity. This possibility has been suggested previously in
the literature, but it has only been proven for cases where
the limiting code rate is 0 or 1. Moreover, these results
extend naturally to affineinvariant codes and, thus, to all
extended primitive narrowsense BCH codes. This is used to
resolve, in the affirmative, the existence question for
capacityachieving sequences of binary cyclic codes. The
primary tools used in the proofs are the sharp threshold
property for symmetric monotone boolean functions and the
area theorem for extrinsic information transfer (EXIT)
functions.},
Doi = {10.1145/2897518.2897584},
Key = {fds319313}
}
@article{fds319314,
Author = {HamidiSepehr, F and Chamberland, JF and Pfister,
HD},
Title = {On the Performance of Block Codes Over FiniteState Channels
in the RareTransition Regime},
Journal = {IEEE Transactions on Communications},
Volume = {63},
Number = {11},
Pages = {39743990},
Year = {2015},
Month = {November},
url = {http://dx.doi.org/10.1109/TCOMM.2015.2478794},
Doi = {10.1109/TCOMM.2015.2478794},
Key = {fds319314}
}
@article{fds319315,
Author = {Pfister, HD and Emmadi, SK and Narayanan, K},
Title = {Symmetric product codes},
Journal = {2015 Information Theory and Applications Workshop, ITA 2015
 Conference Proceedings},
Pages = {282290},
Year = {2015},
Month = {October},
ISBN = {9781479971954},
url = {http://dx.doi.org/10.1109/ITA.2015.7309002},
Abstract = {© 2015 IEEE.Product codes were introduced by Elias in 1954
and generalized by Tanner in 1981. Recently, a number of
generalized product codes have been proposed for forward
errorcorrection in highspeed optical communication. In
practice, these codes are decoded by iteratively decoding
each of the component codes. Symmetric product codes are a
subclass of generalized product codes that use symmetry to
reduce the block length of a product code while using the
same component code. One example of this subclass, dubbed
halfproduct codes, was introduced by Tanner in 1981 and
then generalized by Justesen in 2011. In this paper, we
discuss some initial results on symmetric product codes. Our
results show that: (i) these codes have a larger normalized
minimum distance than the product code from which they are
derived, (ii) some small constructions achieve the largest
minimum distance possible for a linear code, and (iii) they
can have better performance in both the waterfall region and
the error floor when compared to a product code of similar
length and rate.},
Doi = {10.1109/ITA.2015.7309002},
Key = {fds319315}
}
@article{fds319316,
Author = {Li, S and Huang, YC and Liu, T and Pfister, HD},
Title = {On the limits of treating interference as noise for twouser
symmetric Gaussian interference channels},
Volume = {2015June},
Pages = {17111715},
Year = {2015},
Month = {September},
ISBN = {9781467377041},
url = {http://dx.doi.org/10.1109/ISIT.2015.7282748},
Abstract = {© 2015 IEEE.The limits of treating interference as noise
are studied for the canonical twouser symmetric Gaussian
interference channel. A twostep approach is proposed for
finding approximately optimal input distributions in the
high signaltonoise ratio (SNR) regime. First,
approximately and precisely optimal input distributions are
found for the AvestimehrDiggaviTse (ADT) linear
deterministic model. These distributions are then
translated, systematically, into Gaussian models, which we
show can achieve the sum capacity to within O(log
log(SNR)).},
Doi = {10.1109/ISIT.2015.7282748},
Key = {fds319316}
}
@article{fds319317,
Author = {Rengaswamy, N and Pfister, HD},
Title = {Cyclic polar codes},
Volume = {2015June},
Pages = {12871291},
Year = {2015},
Month = {September},
ISBN = {9781467377041},
url = {http://dx.doi.org/10.1109/ISIT.2015.7282663},
Abstract = {© 2015 IEEE.Arikan introduced polar codes in 2009 and
proved that they achieve the symmetric capacity, under
lowcomplexity successive cancellation decoding, of any
binaryinput discrete memoryless channel. Arikan's
construction is based on the Kronecker product of 2by2
matrices and it was extended to larger matrices by
Şaşoǧlu et al. in 2010. In this paper, we construct
cyclic polar codes based on a mixedradix CooleyTukey
decomposition of the Galois field Fourier transform.
Ignoring the twiddle factors between stages, the derived
fast Fourier transform is essentially a Kronecker product of
small Fourier transform matrices. Thus, one can define a
successive cancellation decoder and observe that the
coordinate channels polarize. Choosing the locations of the
frozen symbols in the resulting polar code is identical to
choosing the locations of zeros in the Fourier transform of
the codewords and, thus, the code is cyclic.},
Doi = {10.1109/ISIT.2015.7282663},
Key = {fds319317}
}
@article{fds319318,
Author = {HamidiSepehr, F and Pfister, HD and Chamberland,
JF},
Title = {DelaySensitive Communication Over Fading Channels: Queueing
Behavior and Code Parameter Selection},
Journal = {IEEE Transactions on Vehicular Technology},
Volume = {64},
Number = {9},
Pages = {39573970},
Year = {2015},
Month = {September},
url = {http://dx.doi.org/10.1109/TVT.2014.2365181},
Doi = {10.1109/TVT.2014.2365181},
Key = {fds319318}
}
@article{fds319319,
Author = {Häger, C and i Amat, AG and Pfister, HD and Alvarado, A and Brännström, F and Agrell, E},
Title = {On parameter optimization for staircase codes},
Journal = {Optical Fiber Communication Conference, OFC
2015},
Year = {2015},
Month = {January},
ISBN = {9781557529374},
Abstract = {© OSA 2015.We discuss the optimization of staircase code
parameters based on density evolution. An extension of the
original code construction is proposed, leading to codes
with steeper waterfall performance.},
Key = {fds319319}
}
@article{fds319320,
Author = {Hager, C and Amat, AGI and Pfister, HD and Alvarado, A and Brannstrom,
F and Agrell, E},
Title = {On parameter optimization for staircase codes},
Journal = {Conference on Optical Fiber Communication, Technical Digest
Series},
Volume = {2015June},
Year = {2015},
Month = {January},
ISBN = {9781557529374},
Abstract = {© 2015 OSA.We discuss the optimization of staircase code
parameters based on density evolution. An extension of the
original code construction is proposed, leading to codes
with steeper waterfall performance.},
Key = {fds319320}
}
@article{fds319321,
Author = {HamidiSepehr, F and Pfister, HD and Chamberland,
JF},
Title = {DelaySensitive Communication Over Fading Channels: Queueing
Behavior and Code Parameter Selection.},
Journal = {IEEE Trans. Vehicular Technology},
Volume = {64},
Pages = {39573970},
Year = {2015},
url = {http://dx.doi.org/10.1109/TVT.2014.2365181},
Doi = {10.1109/TVT.2014.2365181},
Key = {fds319321}
}
@article{fds319322,
Author = {HamidiSepehr, F and Chamberland, JF and Pfister,
HD},
Title = {On the Performance of Block Codes Over FiniteState Channels
in the RareTransition Regime.},
Journal = {IEEE Trans. Communications},
Volume = {63},
Pages = {39743990},
Year = {2015},
url = {http://dx.doi.org/10.1109/TCOMM.2015.2478794},
Doi = {10.1109/TCOMM.2015.2478794},
Key = {fds319322}
}
%% Pierce, Lillian B.
@article{fds302459,
Author = {Bober, J and Carneiro, E and Hughes, K and Kosz, D and Pierce,
LB},
Title = {Corrigendum to “On a discrete version of Tanaka’s
theorem for maximal functions”},
Journal = {Proceedings of the American Mathematical
Society},
Volume = {143},
Number = {12},
Pages = {54715473},
Year = {2015},
Month = {September},
ISSN = {00029939},
url = {http://dx.doi.org/10.1090/proc/12778},
Doi = {10.1090/proc/12778},
Key = {fds302459}
}
@article{fds302460,
Author = {HeathBrown, DR and Pierce, LB},
Title = {Burgess bounds for short mixed character
sums},
Journal = {Journal of the London Mathematical Society},
Volume = {91},
Number = {3},
Pages = {693708},
Year = {2015},
Month = {June},
ISSN = {00246107},
url = {http://dx.doi.org/10.1112/jlms/jdv009},
Doi = {10.1112/jlms/jdv009},
Key = {fds302460}
}
@misc{fds299989,
Author = {L.B. Pierce},
Title = {Recent Publications},
Year = {2015},
Key = {fds299989}
}
%% Plesser, M. Ronen
@article{fds248062,
Author = {Morrison, DR and Ronen Plesser and M},
Title = {Special Lagrangian torus fibrations of complete intersection
Calabi–Yau manifolds: A geometric conjecture},
Journal = {Nuclear Physics B},
Volume = {898},
Pages = {751770},
Year = {2015},
Month = {September},
ISSN = {05503213},
url = {http://dx.doi.org/10.1016/j.nuclphysb.2015.05.030},
Doi = {10.1016/j.nuclphysb.2015.05.030},
Key = {fds248062}
}
@article{fds248063,
Author = {Bertolini, M and Plesser, MR},
Title = {Worldsheet instantons and (0,2) linear models},
Journal = {The Journal of High Energy Physics},
Volume = {2015},
Number = {8},
Year = {2015},
Month = {August},
url = {http://arxiv.org/abs/arXiv:1410.4541},
Abstract = {http://arxiv.org/abs/arXiv:1410.4541},
Doi = {10.1007/JHEP08(2015)081},
Key = {fds248063}
}
%% Randles, Amanda
@article{fds314524,
Author = {Randles, A and Draeger, EW and Oppelstrup, T and Krauss, L and Gunnels,
JA},
Title = {Massively parallel models of the human circulatory
system},
Journal = {International Conference for High Performance Computing,
Networking, Storage and Analysis, SC},
Volume = {1520November2015},
Publisher = {ACM},
Year = {2015},
Month = {November},
ISBN = {9781450337236},
ISSN = {21674329},
url = {http://dl.acm.org/citation.cfm?id=2807676},
Abstract = {© 2015 ACM.The potential impact of blood flow simulations
on the diagnosis and treatment of patients suffering from
vascular disease is tremendous. Empowering models of the
full arterial tree can provide insight into diseases such as
arterial hypertension and enables the study of the influence
of local factors on global hemodynamics. We present a new,
highly scalable implementation of the lattice Boltzmann
method which addresses key challenges such as multiscale
coupling, limited memory capacity and bandwidth, and robust
load balancing in complex geometries. We demonstrate the
strong scaling of a threedimensional, highresolution
simulation of hemodynamics in the systemic arterial tree on
1,572,864 cores of Blue Gene/Q. Faster calculation of flow
in full arterial networks enables unprecedented risk
stratification on a perpatient basis. In pursuit of this
goal, we have introduced computational advances that
significantly reduce timetosolution for biofluidic
simulations.},
Doi = {10.1145/2807591.2807676},
Key = {fds314524}
}
@article{fds314508,
Author = {Randles, A and Draeger, EW and Bailey, PE},
Title = {Massively parallel simulations of hemodynamics in the
primary large arteries of the human vasculature},
Journal = {Journal of Computational Science},
Volume = {9},
Pages = {7075},
Year = {2015},
Month = {July},
ISSN = {18777503},
url = {http://dx.doi.org/10.1016/j.jocs.2015.04.003},
Doi = {10.1016/j.jocs.2015.04.003},
Key = {fds314508}
}
@article{fds314509,
Author = {Whitley, HD and Scullard, CR and Benedict, LX and Castor, JI and Randles, A and Glosli, JN and Richards, DF and Desjarlais, MP and Graziani, FR},
Title = {LenardBalescu Calculations and Classical Molecular Dynamics
Simulations of Electrical and Thermal Conductivities of
Hydrogen Plasmas},
Journal = {Contributions to Plasma Physics},
Volume = {55},
Number = {23},
Pages = {192202},
Year = {2015},
Month = {February},
ISSN = {08631042},
url = {http://dx.doi.org/10.1002/ctpp.201400066},
Doi = {10.1002/ctpp.201400066},
Key = {fds314509}
}
@article{fds314510,
Author = {You, Y and Fu, H and Song, SL and Randles, A and Kerbyson, D and Marquez,
A and Yang, G and Hoisie, A},
Title = {Scaling Support Vector Machines on modern HPC
platforms},
Journal = {Journal of Parallel and Distributed Computing},
Volume = {76},
Pages = {1631},
Year = {2015},
Month = {February},
ISSN = {07437315},
url = {http://dx.doi.org/10.1016/j.jpdc.2014.09.005},
Doi = {10.1016/j.jpdc.2014.09.005},
Key = {fds314510}
}
%% Reed, Michael C.
@article{fds290938,
Author = {Reed, MC},
Title = {Mathematical Biology is Good for Mathematics},
Journal = {Notices of the American Mathematical Society},
Volume = {62},
Number = {10},
Pages = {11721176},
Year = {2015},
Month = {November},
ISSN = {00029920},
url = {http://dx.doi.org/10.1090/noti1288},
Doi = {10.1090/noti1288},
Key = {fds290938}
}
@article{fds290939,
Author = {Reed, MC and Gamble, MV and Hall, MN and Nijhout,
HF},
Title = {Mathematical analysis of the regulation of competing
methyltransferases.},
Journal = {BMC Systems Biology},
Volume = {9},
Pages = {69},
Year = {2015},
Month = {October},
url = {http://dx.doi.org/10.1186/s1291801502156},
Abstract = {Methyltransferase (MT) reactions, in which methyl groups are
attached to substrates, are fundamental to many aspects of
cell biology and human physiology. The universal methyl
donor for these reactions is Sadenosylmethionine (SAM) and
this presents the cell with an important regulatory problem.
If the flux along one pathway is changed then the SAM
concentration will change affecting all the other MT
pathways, so it is difficult for the cell to regulate the
pathways independently.We created a mathematical model,
based on the known biochemistry of the folate and methionine
cycles, to study the regulatory mechanisms that enable the
cell to overcome this difficulty. Some of the primary
mechanisms are longrange allosteric interactions by which
substrates in one part of the biochemical network affect the
activity of enzymes at distant locations in the network (not
distant in the cell). Because of these longrange allosteric
interactions, the dynamic behavior of the network is very
complicated, and so mathematical modeling is a useful tool
for investigating the effects of the regulatory mechanisms
and understanding the complicated underlying biochemistry
and cell biology.We study the allosteric binding of
5methyltetrahydrofolate (5 mTHF) to glycineNmethyltransferase
(GNMT) and explain why data in the literature implies that
when one molecule binds, GNMT retains half its activity.
Using the model, we quantify the effects of different
regulatory mechanisms and show how cell processes would be
different if the regulatory mechanisms were eliminated. In
addition, we use the model to interpret and understand data
from studies in the literature. Finally, we explain why a
full understanding of how competing MTs are regulated is
important for designing intervention strategies to improve
human health.We give strong computational evidence that once
bound GNMT retains half its activity. The longrange
allosteric interactions enable the cell to regulate the MT
reactions somewhat independently. The low K m values of many
MTs also play a role because the reactions then run near
saturation and changes in SAM have little effect. Finally,
the inhibition of the MTs by the product
Sadenosylhomocysteine also stabilizes reaction rates
against changes in SAM.},
Doi = {10.1186/s1291801502156},
Key = {fds290939}
}
@article{fds244008,
Author = {Bilinsky, LM and Reed, MC and Nijhout, HF},
Title = {The role of skeletal muscle in liver glutathione metabolism
during acetaminophen overdose.},
Journal = {Journal of Theoretical Biology},
Volume = {376},
Pages = {118133},
Year = {2015},
Month = {July},
ISSN = {00225193},
url = {http://dx.doi.org/10.1016/j.jtbi.2015.04.006},
Abstract = {Marked alterations in systemic glutamateglutamine
metabolism characterize the catabolic state, in which there
is an increased breakdown and decreased synthesis of
skeletal muscle protein. Among these alterations are a
greatly increased net release of glutamine (Gln) from
skeletal muscle into blood plasma and a dramatic depletion
of intramuscular Gln. Understanding the catabolic state is
important because a number of pathological conditions with
very different etiologies are characterized by its presence;
these include major surgery, sepsis, trauma, and some
cancers. Acetaminophen (APAP) overdose is also accompanied
by dramatic changes in systemic glutamateglutamine
metabolism including large drops in liver glutathione (for
which glutamate is a precursor) and plasma Gln. We have
constructed a mathematical model of glutamate and glutamine
metabolism in rat which includes liver, blood plasma and
skeletal muscle. We show that for the normal rat, the model
solutions fit experimental data including the diurnal
variation in liver glutathione (GSH). We show that for the
rat chronically dosed with dexamethasone (an artificial
glucocorticoid which induces a catabolic state) the model
can be used to explain empirically observed facts such as
the linear decline in intramuscular Gln and the drop in
plasma glutamine. We show that for the Wistar rat undergoing
APAP overdose the model reproduces the experimentally
observed rebound of liver GSH to normal levels by the 24h
mark. We show that this rebound is achieved in part by the
action of the cystineglutamate antiporter, an amino acid
transporter not normally expressed in liver but induced
under conditions of oxidative stress. Finally, we explain
why supplementation with Gln, a Glu precursor, assists in
the preservation of liver GSH during APAP overdose despite
the fact that under normal conditions only Cys is
ratelimiting for GSH formation.},
Doi = {10.1016/j.jtbi.2015.04.006},
Key = {fds244008}
}
@article{fds244006,
Author = {Nijhout, HF and Best, JA and Reed, MC},
Title = {Using mathematical models to understand metabolism, genes,
and disease.},
Journal = {BMC Biology},
Volume = {13},
Pages = {79},
Year = {2015},
Month = {January},
url = {http://dx.doi.org/10.1186/s1291501501892},
Abstract = {Mathematical models are a useful tool for investigating a
large number of questions in metabolism, genetics, and
geneenvironment interactions. A model based on the
underlying biology and biochemistry is a platform for in
silico biological experimentation that can reveal the causal
chain of events that connect variation in one quantity to
variation in another. We discuss how we construct such
models, how we have used them to investigate homeostatic
mechanisms, geneenvironment interactions, and
genotypephenotype mapping, and how they can be used in
precision and personalized medicine.},
Doi = {10.1186/s1291501501892},
Key = {fds244006}
}
@article{fds244007,
Author = {Lawley, SD and Mattingly, JC and Reed, MC},
Title = {Stochastic Switching in Infinite Dimensions with
Applications to Random Parabolic PDE},
Journal = {SIAM Journal on Mathematical Analysis},
Volume = {47},
Number = {4},
Pages = {30353063},
Year = {2015},
Month = {January},
ISSN = {00361410},
url = {http://hdl.handle.net/10161/9517 Duke open
access},
Doi = {10.1137/140976716},
Key = {fds244007}
}
%% Robles, Colleen M
@article{fds320189,
Author = {Robles, C},
Title = {Classification of horizontal s},
Journal = {Compositio Mathematica},
Volume = {152},
Number = {05},
Pages = {918954},
Year = {2016},
Month = {May},
url = {http://dx.doi.org/10.1112/S0010437X15007691},
Doi = {10.1112/S0010437X15007691},
Key = {fds320189}
}
@article{fds320190,
Author = {Robles, C},
Title = {Characteristic cohomology of the infinitesimal period
relation},
Journal = {Asian Journal of Mathematics},
Volume = {20},
Number = {4},
Pages = {725758},
Year = {2016},
url = {http://dx.doi.org/10.4310/AJM.2016.v20.n4.a7},
Doi = {10.4310/AJM.2016.v20.n4.a7},
Key = {fds320190}
}
@article{fds292861,
Author = {M. Green and P. Griffiths and C. Robles},
Title = {Extremal degenerations of polarized Hodge
structures},
Booktitle = {Proceedings of Hodge Theory and L2Cohomology, Johns Hopkins
U},
Year = {2015},
url = {http://arxiv.org/abs/1403.0646},
Key = {fds292861}
}
@article{fds292862,
Author = {Colleen Robles},
Title = {Classification of horizontal SL(2)s},
Journal = {Compositio Math.},
Year = {2015},
url = {http:/},
Key = {fds292862}
}
@article{fds292863,
Author = {M. Kerr and C. Robles},
Title = {Hodge theory and real orbits in flag varieties},
Year = {2015},
url = {http://arxiv.org/abs/1407.4507},
Key = {fds292863}
}
%% Ryser, Marc D.
@article{fds244097,
Author = {Ryser, MD and McGoff, K and Herzog, DP and Sivakoff, DJ and Myers,
ER},
Title = {Impact of coveragedependent marginal costs on optimal HPV
vaccination strategies.},
Journal = {Epidemics: the journal of infectious disease
dynamics},
Volume = {11},
Pages = {3247},
Year = {2015},
Month = {June},
ISSN = {17554365},
url = {http://hdl.handle.net/10161/9500 Duke open
access},
Abstract = {The effectiveness of vaccinating males against the human
papillomavirus (HPV) remains a controversial subject. Many
existing studies conclude that increasing female coverage is
more effective than diverting resources into male
vaccination. Recently, several empirical studies on HPV
immunization have been published, providing evidence of the
fact that marginal vaccination costs increase with coverage.
In this study, we use a stochastic agentbased modeling
framework to revisit the male vaccination debate in light of
these new findings. Within this framework, we assess the
impact of coveragedependent marginal costs of vaccine
distribution on optimal immunization strategies against HPV.
Focusing on the two scenarios of ongoing and new vaccination
programs, we analyze different resource allocation policies
and their effects on overall disease burden. Our results
suggest that if the costs associated with vaccinating males
are relatively close to those associated with vaccinating
females, then coveragedependent, increasing marginal costs
may favor vaccination strategies that entail immunization of
both genders. In particular, this study emphasizes the
necessity for further empirical research on the nature of
coveragedependent vaccination costs.},
Doi = {10.1016/j.epidem.2015.01.003},
Key = {fds244097}
}
%% Saper, Leslie
@article{fds226574,
Author = {L. Ji and K. Murty and L. Saper and J. Scherk},
Title = {The Fundamental Group of Reductive BorelSerre and Satake
Compactifications},
Journal = {The Asian Journal of Mathematics},
Volume = {19},
Number = {3},
Pages = {465486},
Year = {2015},
url = {http://www.intlpress.com/site/pub/pages/journals/items/ajm/content/vols/0019/0003/a004/},
Abstract = {Let <b>G</b> be an almost simple, simply connected algebraic
group defined over a number field <i>k</i>, and let <i>S</i>
be a finite set of places of <i>k</i> including all infinite
places. Let <i>X</i> be the product over
<nobr><i>v</i> ∈ <i>S</i></nobr> of the
symmetric spaces associated to <b>G</b>(<i>k<sub>v</sub></i>),
when <i>v</i> is an infinite place, and the BruhatTits
buildings associated to <b>G</b>(<i>k<sub>v</sub></i>), when
<i>v</i> is a finite place. The main result of this paper is
to compute explicitly the fundamental group of the reductive
BorelSerre compactification of <nobr>Γ \ <i>X</i></nobr>,
where Γ is an <i>S</i>arithmetic subgroup of
<b>G</b>. In the case that Γ is neat, we show that
this fundamental group is isomorphic to <nobr>Γ / <i>E</i>Γ</nobr>,
where <i>E</i>Γ is the subgroup generated by the
elements of Γ belonging to unipotent radicals of
parabolic <i>k</i>subgroups. Analogous computations of the
fundamental group of the Satake compactifications are made.
It is noteworthy that calculations of the congruence
subgroup kernel <nobr><i>C</i>(<i>S</i>,<b>G</b>)</nobr>
yield similar results.},
Key = {fds226574}
}
%% Sapiro, Guillermo
@article{fds264703,
Author = {Delbracio, M and Sapiro, G},
Title = {Removing Camera Shake via Weighted Fourier Burst
Accumulation},
Journal = {IEEE Transactions on Image Processing},
Volume = {24},
Number = {11},
Pages = {32933307},
Year = {2015},
Month = {November},
ISSN = {10577149},
url = {http://dx.doi.org/10.1109/TIP.2015.2442914},
Doi = {10.1109/TIP.2015.2442914},
Key = {fds264703}
}
@article{fds264698,
Author = {Lucas, JE and Sapiro, G},
Title = {Cancer: What's luck got to do with it?},
Journal = {Significance},
Volume = {12},
Number = {2},
Pages = {4042},
Year = {2015},
Month = {April},
ISSN = {17409705},
url = {http://dx.doi.org/10.1111/j.17409713.2015.00816.x},
Doi = {10.1111/j.17409713.2015.00816.x},
Key = {fds264698}
}
@article{fds264706,
Author = {Yang, J and Liao, X and Yuan, X and Llull, P and Brady, DJ and Sapiro, G and Carin, L},
Title = {Compressive sensing by learning a Gaussian mixture model
from measurements.},
Journal = {IEEE Transactions on Image Processing},
Volume = {24},
Number = {1},
Pages = {106119},
Year = {2015},
Month = {January},
ISSN = {10577149},
url = {http://dx.doi.org/10.1109/tip.2014.2365720},
Abstract = {Compressive sensing of signals drawn from a Gaussian mixture
model (GMM) admits closedform minimum mean squared error
reconstruction from incomplete linear measurements. An
accurate GMM signal model is usually not available a priori,
because it is difficult to obtain training signals that
match the statistics of the signals being sensed. We propose
to solve that problem by learning the signal model in situ,
based directly on the compressive measurements of the
signals, without resorting to other signals to train a
model. A key feature of our method is that the signals being
sensed are treated as random variables and are integrated
out in the likelihood. We derive a maximum marginal
likelihood estimator (MMLE) that maximizes the likelihood of
the GMM of the underlying signals given only their linear
compressive measurements. We extend the MMLE to a GMM with
dominantly lowrank covariance matrices, to gain
computational speedup. We report extensive experimental
results on image inpainting, compressive sensing of
highspeed video, and compressive hyperspectral imaging (the
latter two based on real compressive cameras). The results
demonstrate that the proposed methods outperform
stateoftheart methods by significant margins.},
Doi = {10.1109/tip.2014.2365720},
Key = {fds264706}
}
@article{fds291305,
Author = {Kim, J and Duchin, Y and Sapiro, G and Vitek, J and Harel,
N},
Title = {Clinical subthalamic nucleus prediction from highfield
brain MRI},
Journal = {Proceedings / IEEE International Symposium on Biomedical
Imaging: from nano to macro. IEEE International Symposium on
Biomedical Imaging},
Volume = {2015July},
Pages = {12641267},
Year = {2015},
Month = {January},
ISBN = {9781479923748},
ISSN = {19457928},
url = {http://dx.doi.org/10.1109/ISBI.2015.7164104},
Abstract = {© 2015 IEEE.The subthalamic nucleus (STN) within the
subcortical region of the Basal ganglia is a crucial
targeting structure for Parkinson's Deep brain stimulation
(DBS) surgery. Volumetric segmentation of such small and
complex structure, which is elusive in clinical MRI
protocols, is thereby a prerequisite process for reliable
DBS direct targeting. While direct visualization of the STN
is facilitated with advanced ultrahighfield MR imaging (7
Tesla), such high fields are not always clinically
available. In this paper, we aim at the automatic prediction
of the STN region on clinical lowfield MRI, exploiting
dependencies between the STN and its adjacent structures,
learned from ultrahighfield MRI. We present a framework
based on a statistical shape model to learn such shape
relationship on high quality MR data sets. This allows for
an accurate prediction and visualization of the STN
structure, given detectable predictors on the lowfield MRI.
Experimental results on Parkinson's patients demonstrate
that the proposed approach enables accurate estimation of
the STN on clinical 1.5T MRI.},
Doi = {10.1109/ISBI.2015.7164104},
Key = {fds291305}
}
%% Smith, David A.
@article{fds317710,
Author = {James T. Fey and David A. Smith},
Title = {Algebra as Part of an Integrated High School
Curriculum},
Booktitle = {And the Rest is Just Algebra},
Publisher = {Springer},
Editor = {Sepideh Stewart},
Year = {2016},
Month = {October},
ISBN = {9783319450520},
Keywords = {integrated curriculum school algebra functions problem based
learning mathematical modeling applications},
Abstract = {Traditional high school mathematics curricula in the United
States devote two years almost exclusively to development of
student proficiency in the symbolic manipulations required
for solving algebraic equations and generating equivalent
algebraic expressions. However, recent design experiments
have shown that a focus on functions, mathematical modeling,
and computer algebra tools enables effective integration of
algebra with the other core strands of high school
mathematics.},
Key = {fds317710}
}
%% Stern, Mark A.
@article{fds317670,
Author = {Sergey A. Cherkis and Andres LarrainHubach and Mark
Stern},
Title = {Instantons on multiTaubNUT Spaces I: Asymptotic Form and
Index Theorem},
Journal = {arXiv:1608.00018},
Year = {2016},
Month = {August},
Abstract = {We study finite action antiselfdual YangMills connections
on the multiTaubNUT space. We establish the curvature and
the harmonic spinors decay rates and compute the index of
the associated Dirac operator. This is the first in a series
of papers proving the completeness of the bow construction
of instantons on multiTaubNUT spaces and exploring it in
detail.},
Key = {fds317670}
}
@article{fds292866,
Author = {M.A. Stern and B. Charbonneau},
Title = {Asymptotic Hodge Theory of Vector Bundles},
Journal = {Comm. in Anal. and Geom.},
Volume = {23},
Number = {3},
Pages = {559609},
Year = {2015},
Key = {fds292866}
}
@article{fds287402,
Author = {Charbonneau, B and Stern, M},
Title = {Asymptotic Hodge Theory of Vector Bundles},
Journal = {Geometry and Topology},
Volume = {23},
Number = {3},
Pages = {559609},
Year = {2015},
url = {http://xxx.lanl.gov/abs/1111.0591},
Abstract = {We introduce several families of filtrations on the space of
vector bundles over a smooth projective variety. These
filtrations are defined using the large k asymptotics of the
kernel of the Dolbeault Dirac operator on a bundle twisted
by the kth power of an ample line bundle. The filtrations
measure the failure of the bundle to admit a holomorphic
structure. We study compatibility under the Chern
isomorphism of these filtrations with the Hodge filtration
on cohomology.},
Key = {fds287402}
}
%% TurnageButterbaugh, Caroline
@book{fds320234,
Author = {Mackall, B and Miller, SJ and Rapti, C and TurnageButterbaugh, C and Winsor, K},
Title = {Some Results in the Theory of Lowlying Zeros},
Booktitle = {Families of Automorphic Forms and the Trace
Formula},
Publisher = {Springer},
Year = {2016},
Month = {September},
ISBN = {3319414240},
Abstract = {Featuring the work of twentythree internationallyrecognized
experts, this volume explores the trace formula, spectra of
locally symmetric spaces, padic families, and other recent
techniques from harmonic analysis and representation
...},
Key = {fds320234}
}
@article{fds318339,
Author = {Bui, HM and Heap, WP and TurnageButterbaugh, CL},
Title = {GAPS BETWEEN ZEROS OF DEDEKIND ZETAFUNCTIONS OF QUADRATIC
NUMBER FIELDS. II},
Journal = {Quarterly Journal of Mathematics},
Volume = {67},
Number = {3},
Pages = {467482},
Year = {2016},
Month = {September},
url = {http://dx.doi.org/10.1093/qmath/haw021},
Doi = {10.1093/qmath/haw021},
Key = {fds318339}
}
@book{fds318340,
Author = {Barret, O and Firk, F and Miller, SJ and TurnageButterbaugh,
C},
Title = {From Quantum Systems to LFunctions: Pair Correlation
Statistics and Beyond},
Pages = {123171},
Booktitle = {Open Problems in Mathematics},
Publisher = {Springer},
Editor = {John Nash Jr. and Michael Th. Rassias},
Year = {2016},
Month = {August},
ISBN = {3319321625},
url = {http://arxiv.org/abs/1505.07481},
Key = {fds318340}
}
@article{fds318341,
Author = {Best, A and Dynes, P and Edelsbrunner, X and McDonald, B and Miller, SJ and Tor, K and TurnageButterbaugh, C and Weinstein,
M},
Title = {Gaussian distribution of the number of summands in
generalized Zeckendorf decomposition in small
intervals},
Journal = {Integers},
Volume = {16},
Pages = {13 pages},
Year = {2016},
Key = {fds318341}
}
@book{fds320235,
Author = {Edelsbrunner, X and Huan, K and Mackall, B and Powell, J and TurnageButterbaugh, C and Weinstein, M},
Title = {Benfordness of the Cauchy Distribution and
Generalizations},
Booktitle = {Benford's Law Theory and Applications},
Publisher = {Princeton University Press},
Editor = {S. J. Miller},
Year = {2015},
Month = {June},
ISBN = {1400866596},
Abstract = {Emphasizing common challenges and techniques across the
disciplines, this accessible book shows how Benford’s law
can serve as a productive meeting ground for researchers and
practitioners in diverse fields.},
Key = {fds320235}
}
@article{fds302477,
Author = {Barrett, O and McDonald, B and Miller, SJ and Ryan, P and TurnageButterbaugh, CL and Winsor, K},
Title = {Gaps between zeros of GL(2) Lfunctions},
Journal = {Journal of Mathematical Analysis and Applications},
Volume = {429},
Number = {1},
Pages = {204232},
Year = {2015},
Month = {January},
ISSN = {0022247X},
url = {http://dx.doi.org/10.1016/j.jmaa.2015.04.007},
Abstract = {© 2015 Elsevier Inc.Let L(s, f) be an Lfunction associated
to a primitive (holomorphic or Maass) cusp form f on GL(2)
over Q. Combining meanvalue estimates of Montgomery and
Vaughan with a method of Ramachandra, we prove a formula for
the mixed second moments of derivatives of L(1/2 + it, f)
and, via a method of Hall, use it to show that there are
infinitely many gaps between consecutive zeros of L(s, f)
along the critical line that are at least √3=1.732. . .
times the average spacing. Using general pair correlation
results due to Murty and Perelli in conjunction with a
technique of Montgomery, we also prove the existence of
small gaps between zeros of any primitive Lfunction of the
Selberg class. In particular, when f is a primitive
holomorphic cusp form on GL(2) over Q, we prove that there
are infinitely many gaps between consecutive zeros of L(s,
f) along the critical line that are at most 0.823 times the
average spacing.},
Doi = {10.1016/j.jmaa.2015.04.007},
Key = {fds302477}
}
@article{fds299984,
Author = {A. Best and P. Dynes and X. Edelsbrunner and B. McDonald and S. J.
Miller and K. Tor and C. TurnageButterbaugh and M.
Weinstein},
Title = {Gaussian distribution of the number of summands in
generalized Zeckendorf decompositions},
Journal = {Integers},
Year = {2015},
Key = {fds299984}
}
@article{fds302479,
Author = {Banks, WD and Freiberg, T and TurnageButterbaugh,
CL},
Title = {Consecutive primes in tuples},
Journal = {Acta Arithmetica},
Volume = {167},
Number = {3},
Pages = {261266},
Year = {2015},
ISSN = {00651036},
url = {http://dx.doi.org/10.4064/aa16734},
Doi = {10.4064/aa16734},
Key = {fds302479}
}
%% Venakides, Stephanos
@article{fds226701,
Author = {Sergey Belov and Stephanos Venakides},
Title = {Smooth parametric dependence of asymptotics of the
semiclassical focusing NLS},
Journal = {Analysis & PDE},
Volume = {8},
Number = {2},
Pages = {257288},
Year = {2015},
Month = {April},
url = {http://dx.doi.org/10.2140/apde.2015.8.257},
Abstract = {We consider the onedimensional focusing (cubic) nonlinear
Schrödinger equation (NLS) in the semiclassical limit with
exponentially decaying complexvalued initial data, whose
phase is multiplied by a real parameter. We prove smooth
dependence of the asymptotic solution on the parameter.
Numerical results supporting our estimates of important
quantities are presented.},
Doi = {10.2140/apde.2015.8.257},
Key = {fds226701}
}
@article{fds244138,
Author = {Komineas, S and Shipman, SP and Venakides, S},
Title = {Continuous and discontinuous dark solitons in polariton
condensates},
Journal = {Physical Review B  Condensed Matter and Materials
Physics},
Volume = {91},
Number = {13},
Year = {2015},
Month = {April},
ISSN = {10980121},
url = {http://dx.doi.org/10.1103/PhysRevB.91.134503},
Abstract = {BoseEinstein condensates of excitonpolaritons are
described by a Schrödinger system of two equations.
Nonlinearity due to exciton interactions gives rise to a
frequency band of dark soliton solutions, which are found
analytically for the lossless zerovelocity case. The
soliton's farfield value varies from zero to infinity as
the operating frequency varies across the band. For positive
detuning (photon frequency higher than exciton frequency),
the exciton wave function becomes discontinuous when the
operating frequency exceeds the exciton frequency. This
phenomenon lies outside the parameter regime of validity of
the GrossPitaevskii (GP) model. Within its regime of
validity, we give a derivation of a singlemode GP model
from the initial Schrödinger system and compare the
continuous polariton solitons and GP solitons using the
healing length notion.},
Doi = {10.1103/PhysRevB.91.134503},
Key = {fds244138}
}
%% Vigogna, Stefano
@article{fds300041,
Author = {E. De Vito and F. De Mari and S. Vigogna},
Title = {Geometric classiication of semidirect products in the
maximal parabolic subgroup of Sp(2,R)},
Journal = {Analysis and Applications},
Year = {2015},
Key = {fds300041}
}
@article{fds300042,
Author = {S. Dahlke and E. De Vito and F. De Mari and D. Labate and G. Steidl and G.
Teschke S. Vigogna},
Title = {Coorbit spaces with voice in a Fréchet space},
Journal = {Fourier Analysis and Applications},
Year = {2015},
Key = {fds300042}
}
@article{fds300043,
Author = {G. S. Alberti and S. Dahlke and F. De Mari and E. De Vito and S.
Vigogna},
Title = {Continuous and discrete frames generated by the evolution
flow of the Schrödinger equation},
Year = {2015},
Key = {fds300043}
}
%% Witelski, Thomas P.
@article{fds317250,
Author = {Smolka, LB and McLaughlin, CK and Witelski, TP},
Title = {Oil capture from a water surface by a falling
sphere},
Journal = {Colloids and Surfaces A: Physicochemical and Engineering
Aspects},
Volume = {497},
Pages = {126132},
Year = {2016},
Month = {May},
ISSN = {09277757},
url = {http://dx.doi.org/10.1016/j.colsurfa.2016.02.026},
Doi = {10.1016/j.colsurfa.2016.02.026},
Key = {fds317250}
}
@article{fds313861,
Author = {P. Sanaei and G.W. Richardson and T. Witelski and L.J.
Cummings},
Title = {Flow and fouling in a pleated membrane filter},
Journal = {Journal of Fluid Mechanics},
Volume = {795},
Pages = {3659},
Year = {2016},
Key = {fds313861}
}
@article{fds310904,
Author = {C. George and L. N. Virgin and T.P. Witelski},
Title = {Experimental study of regular and chaotic transients in a
nonsmooth system},
Journal = {International Journal of Nonlinear Mechanics},
Volume = {81},
Pages = {5564},
Year = {2016},
url = {http://dx.doi.org/10.1016/j.ijnonlinmec.2015.12.006},
Doi = {10.1016/j.ijnonlinmec.2015.12.006},
Key = {fds310904}
}
@article{fds293132,
Author = {Dijksman, JA and Mukhopadhyay, S and Gaebler, C and Witelski, TP and Behringer, RP},
Title = {Obtaining selfsimilar scalings in focusing
flows.},
Journal = {Physical Review E  Statistical, Nonlinear, and Soft Matter
Physics},
Volume = {92},
Number = {4},
Pages = {043016},
Year = {2015},
Month = {October},
ISSN = {15393755},
url = {http://dx.doi.org/10.1103/physreve.92.043016},
Abstract = {The surface structure of converging thin fluid films
displays selfsimilar behavior, as was shown in the work by
Diez et al. [Q. Appl. Math. 210, 155 (1990)]. Extracting the
related similarity scaling exponents from either numerical
or experimental data is nontrivial. Here we provide two such
methods. We apply them to experimental and numerical data on
converging fluid films driven by both surface tension and
gravitational forcing. In the limit of pure gravitational
driving, we recover Diez' semianalytic result, but our
methods also allow us to explore the entire regime of mixed
capillary and gravitational driving, up to entirely
surfacetensiondriven flows. We find scaling forms of
smoothly varying exponents up to surprisingly small Bond
numbers. Our experimental results are in reasonable
agreement with our numerical simulations, which confirm
theoretically obtained relations between the scaling
exponents.},
Doi = {10.1103/physreve.92.043016},
Key = {fds293132}
}
@article{fds244178,
Author = {Witelski, TP},
Title = {Preface to the special issue on “Thin films and fluid
interfaces”},
Journal = {Journal of Engineering Mathematics},
Volume = {94},
Number = {1},
Pages = {13},
Year = {2015},
Month = {October},
ISSN = {00220833},
url = {http://dx.doi.org/10.1007/s106650149760z},
Doi = {10.1007/s106650149760z},
Key = {fds244178}
}
@book{fds227199,
Author = {T.P. Witelski and M. Bowen},
Title = {Methods of Mathematical Modelling},
Series = {Springer Undergraduate Mathematics Series
(SUMS)},
Year = {2015},
ISBN = {9783319230412},
url = {http://www.springer.com/us/book/9783319230412},
Key = {fds227199}
}
%% Yang, Haizhao
@article{fds303562,
Author = {Lu, J and Wirth, B and Yang, H},
Title = {Combining 2D synchrosqueezed wave packet transform with
optimization for crystal image analysis},
Journal = {Journal of the Mechanics and Physics of Solids},
Volume = {89},
Pages = {194210},
Publisher = {Elsevier},
Editor = {Bhattacharya, K},
Year = {2016},
Month = {April},
ISSN = {00225096},
url = {http://hdl.handle.net/10161/11296 Duke open
access},
Abstract = {© 2016 Elsevier Ltd. All rights reserved.We develop a
variational optimization method for crystal analysis in
atomic resolution images, which uses information from a 2D
synchrosqueezed transform (SST) as input. The
synchrosqueezed transform is applied to extract initial
information from atomic crystal images: crystal defects,
rotations and the gradient of elastic deformation. The
deformation gradient estimate is then improved outside the
identified defect region via a variational approach, to
obtain more robust results agreeing better with the physical
constraints. The variational model is optimized by a
nonlinear projected conjugate gradient method. Both examples
of images from computer simulations and imaging experiments
are analyzed, with results demonstrating the effectiveness
of the proposed method.},
Doi = {10.1016/j.jmps.2016.01.002},
Key = {fds303562}
}
@article{fds226959,
Author = {Yang, H and Lu, J and Brown, WP and Daubechies, I and Ying,
L},
Title = {Quantitative Canvas Weave Analysis Using 2D Synchrosqueezed
Transforms: Application of timefrequency analysis to art
investigation},
Journal = {IEEE Signal Processing Magazine},
Volume = {32},
Number = {4},
Pages = {5563},
Year = {2015},
Month = {July},
ISSN = {10535888},
url = {http://hdl.handle.net/10161/11649 Duke open
access},
Abstract = {Quantitative canvas weave analysis has many applications in
art investigations of paintings, including dating,
forensics, and canvas rollmate identification.
Traditionally, canvas analysis is based on Xradiographs.
Prior to serving as a painting canvas, a piece of fabric is
coated with a priming agent; smoothing its surface makes
this layer thicker between and thinner right on top of weave
threads. These variations affect the Xray absorption,
making the weave pattern stand out in Xray images of the
finished painting. To characterize this pattern, it is
customary to visually inspect small areas within the
Xradiograph and count the number of horizontal and vertical
weave threads; averages of these then estimate the overall
canvas weave density. The tedium of this process typically
limits its practice to just a few sample regions of the
canvas. In addition, it does not capture more subtle
information beyond weave density, such as thread angles or
variations in the weave pattern. Signal processing
techniques applied to art investigation are now increasingly
used to develop computerassisted canvas weave analysis
tools.},
Doi = {10.1109/MSP.2015.2406882},
Key = {fds226959}
}
@article{fds226960,
Author = {Yang, H},
Title = {Synchrosqueezed wave packet transforms and diffeomorphism
based spectral analysis for 1D general mode
decompositions},
Journal = {Applied and Computational Harmonic Analysis},
Volume = {39},
Number = {1},
Pages = {3366},
Year = {2015},
Month = {July},
ISSN = {10635203},
url = {http://hdl.handle.net/10161/11653 Duke open
access},
Doi = {10.1016/j.acha.2014.08.004},
Key = {fds226960}
}
@article{fds226958,
Author = {Yang, H},
Title = {Oscillatory data analysis and fast algorithms for integral
operators},
Editor = {Ying, L and Candes, E and Ryzhik, L},
Year = {2015},
Month = {June},
url = {http://hdl.handle.net/10161/11660 Duke open
access},
Key = {fds226958}
}
@article{fds226961,
Author = {Li, Y and Yang, H and Ying, L},
Title = {A Multiscale Butterfly Algorithm for Multidimensional
Fourier Integral Operators},
Journal = {Multiscale Modeling & Simulation},
Volume = {13},
Number = {2},
Pages = {614631},
Year = {2015},
Month = {January},
ISSN = {15403459},
url = {http://hdl.handle.net/10161/11655 Duke open
access},
Doi = {10.1137/140997658},
Key = {fds226961}
}
@article{fds226963,
Author = {Li, Y and Yang, H and Martin, ER and Ho, KL and Ying,
L},
Title = {Butterfly Factorization},
Journal = {Multiscale Modeling & Simulation},
Volume = {13},
Number = {2},
Pages = {714732},
Year = {2015},
Month = {January},
ISSN = {15403459},
url = {http://hdl.handle.net/10161/11654 Duke open
access},
Doi = {10.1137/15M1007173},
Key = {fds226963}
}
@article{fds311607,
Author = {Yang, H and Lu, J and Ying, L},
Title = {Crystal Image Analysis Using 2D Synchrosqueezed
Transforms},
Journal = {Multiscale Modeling & Simulation},
Volume = {13},
Number = {4},
Pages = {15421572},
Year = {2015},
Month = {January},
ISSN = {15403459},
url = {http://hdl.handle.net/10161/11648 Duke open
access},
Doi = {10.1137/140955872},
Key = {fds311607}
}
%% Zhou, Zhennan
@article{fds318345,
Author = {Ma, Z and Zhang, Y and Zhou, Z},
Title = {An improved semiLagrangian time splitting spectral method
for the semiclassical Schrödinger equation with vector
potentials using NUFFT},
Journal = {Applied Numerical Mathematics},
Volume = {111},
Pages = {144159},
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{fds299987,
Author = {Z. Zhou and Z. Ma and Y. Zhang.},
Title = {A semiLagrangian time splitting method for the
semiclassical Schrodinger equation with vector potentials
using NUFFT},
Year = {2015},
Key = {fds299987}
}
