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Mathematics Faculty: Publications since January 2015

List all publications in the database.    :chronological  alphabetical  combined listing:
%% Abel, Michael   
@article{fds317698,
   Title = {HOMFLY-PT 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: one-column 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 P-twists},
   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 Pfaffian-Grassmannian equivalence revisited},
   Journal = {Alg. Geom.},
   Volume = {2},
   Number = {3},
   Pages = {332-364},
   Year = {2015},
   url = {http://arxiv.org/abs/1401.3661},
   Key = {fds226939}
}


%% Agarwal, Pankaj K.   
@article{fds318110,
   Author = {Agarwal, PK and Aronov, B and Har-Peled, S and Phillips, JM and Yi, K and Zhang, W},
   Title = {Nearest-Neighbor Searching Under Uncertainty
             II},
   Journal = {ACM Transactions on Algorithms},
   Volume = {13},
   Number = {1},
   Pages = {1-25},
   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 = {Range-max queries on uncertain data},
   Journal = {Proceedings of the ACM SIGACT-SIGMOD-SIGART Symposium on
             Principles of Database Systems},
   Volume = {26-June-01-July-2016},
   Pages = {465-476},
   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
             d-dimensional query rectangle ρ, the expected maximum value
             or the most-likely maximum value in ρ can be computed
             quickly. The specific contributions of our paper include the
             following: (i) The first index of sub-quadratic size to
             achieve a sub-linear query time in any dimension d ≥ 1. It
             also provides a trade-off between query time and size of the
             index. (ii) A conditional lower bound for the most-likely
             range-max queries, based on the conjectured hardness of the
             set-intersection problem, which suggests that in the worst
             case the product (query time)2 x (index size) is
             Ω(n2/polylog(n)). (iii) A linear-size index for estimating
             the expected range-max 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 top-k values of the
             range-max.},
   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
             nearest-neighbor searching data structures},
   Journal = {Proceedings of the ACM SIGACT-SIGMOD-SIGART Symposium on
             Principles of Database Systems},
   Volume = {26-June-01-July-2016},
   Pages = {429-440},
   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 kd-trees, range trees, and BBD-trees 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 = {6.1-6.16},
   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
             double-struck 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 near-linear time for
             point sequences drawn from κ-packed or κ-bounded curves,
             and subquadratic time for backbone sequences. Roughly
             speaking, a curve is κ-packed if the length of its
             intersection with any ball of radius r is at most κ · r,
             and it is κ-bounded if the sub-curve 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 minimum-weight 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
             minimum-weight 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 = {311-325},
   Year = {2016},
   Month = {February},
   ISSN = {1041-4347},
   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 high-quality paths amid
             polygonal obstacles},
   Journal = {Proceedings of the Annual ACM-SIAM Symposium on Discrete
             Algorithms},
   Volume = {2},
   Pages = {1179-1192},
   Year = {2016},
   Month = {January},
   ISBN = {9781510819672},
   Abstract = {© Copyright (2016) by SIAM: Society for Industrial and
             Applied Mathematics.We study a path-planning 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
             polynomial-time 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 = {905-929},
   Year = {2015},
   Month = {December},
   ISSN = {0179-5376},
   url = {http://dx.doi.org/10.1007/s00454-015-9730-x},
   Doi = {10.1007/s00454-015-9730-x},
   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 = {871-904},
   Year = {2015},
   Month = {December},
   ISSN = {0179-5376},
   url = {http://dx.doi.org/10.1007/s00454-015-9729-3},
   Doi = {10.1007/s00454-015-9729-3},
   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 = {03-06-November-2015},
   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 piecewise-linear 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 sampling-based 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 = {796-811},
   Year = {2015},
   Month = {June},
   ISSN = {1868-8969},
   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 xy-monotone
             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 Gromov-Hausdorff distance for metric
             trees},
   Journal = {Lecture notes in computer science},
   Volume = {9472},
   Pages = {529-540},
   Year = {2015},
   Month = {January},
   ISSN = {0302-9743},
   url = {http://dx.doi.org/10.1007/978-3-662-48971-0_45},
   Abstract = {© Springer-Verlag Berlin Heidelberg 2015.The
             Gromov-Hausdorff distance is a natural way to measure
             distance between two metric spaces. We give the first proof
             of hardness and first non-trivial approximation algorithm
             for computing the Gromov-Hausdorff distance for geodesic
             metrics in trees. Specifically, we prove it is NP-hard to
             approximate the Gromov-Hausdorff 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 = {10.1007/978-3-662-48971-0_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 = {83-98},
   Year = {2015},
   ISSN = {0178-4617},
   url = {http://dx.doi.org/10.1007/s00453-013-9846-4},
   Abstract = {© 2013, Springer Science+Business Media New York.We present
             (single-pass) 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 sub-linear in n. For the
             problems of computing diameter, width and minimum enclosing
             ball of S, we obtain lower bounds on the worst-case
             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
             farthest-point 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/s00453-013-9846-4},
   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 = {3596-3622},
   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 = {1-15},
   Year = {2015},
   Month = {February},
   ISSN = {0393-0440},
   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 mean-field 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 non-Hermitian 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 Navier--Stokes Flow with an
             Exact Moving Boundary Using the Immersed Interface
             Method},
   Journal = {SIAM Journal on Numerical Analysis},
   Volume = {53},
   Number = {4},
   Pages = {2097-2111},
   Year = {2015},
   Month = {January},
   ISSN = {0036-1429},
   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 = {198-218},
   Year = {2016},
   Month = {January},
   ISSN = {1932-6157},
   url = {http://hdl.handle.net/10161/11157 Duke open
             access},
   Abstract = {New representations of tree-structured 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 = {10.1214/15-AOAS886},
   Key = {fds315426}
}

@article{fds311346,
   Author = {Paul Bendich and Ellen Gasparovic and John Harer and Christopher
             J. Tralie},
   Title = {Scaffoldings and Spines: Organizing High-Dimensional 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 = {Multi-scale local shape analysis and feature selection in
             machine learning applications},
   Journal = {Proceedings of the International Joint Conference on Neural
             Networks},
   Volume = {2015-September},
   Pages = {1-8},
   Year = {2015},
   Month = {September},
   url = {http://hdl.handle.net/10161/12014 Duke open
             access},
   Abstract = {© 2015 IEEE.We introduce a method called multi-scale 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 = {1173-1204},
   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 p-th 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
             continuously-varying 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 = {38-44},
   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 time-ordered 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 = {Feature-Aided 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 = {38-44},
   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 time-ordered 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 = {H-1 solutions of a class of fourth order nonlinear equations
             for image processing},
   Journal = {Discrete And Continuous Dynamical Systems},
   Volume = {10},
   Number = {1-2},
   Pages = {349 -- 366},
   Year = {2004},
   Key = {Greer04a}
}


%% 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 Vietoris--Rips
             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 $1 \le k \le d-1$ 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 Vietoris--Rips 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 d-dimensional torus, and
             show that there are, coarsely, two phase transitions. The
             first transition is analogous to the Erd\H{o}s-R\'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 = {3-4},
   Pages = {651-686},
   Year = {2015},
   url = {http://dx.doi.org/10.1007/s00440-014-0556-x},
   Doi = {10.1007/s00440-014-0556-x},
   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 = {933-948},
   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 society-wide 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 hands-on
             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 = {1457-1475},
   Publisher = {Springer Basel},
   Year = {2016},
   Month = {June},
   ISSN = {1424-0637},
   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
             quasi-local mass of spacelike 2-surfaces in the
             spacetime.},
   Doi = {10.1007/s00023-015-0420-2},
   Key = {fds300017}
}

@article{fds303060,
   Author = {Martinez-Medina, 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 = {025-025},
   Year = {2015},
   Month = {December},
   url = {http://arxiv.org/abs/1505.07154},
   Doi = {10.1088/1475-7516/2015/12/025},
   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 = {561-575},
   Year = {2015},
   Month = {June},
   ISSN = {0003-889X},
   url = {http://www.springer.com/-/0/c8d239381b86496b96d95ff26f1061eb},
   Doi = {10.1007/s00013-015-0767-0},
   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 = {285-307},
   Year = {2015},
   Month = {April},
   ISSN = {0010-3616},
   url = {http://arxiv.org/abs/1310.8638},
   Doi = {10.1007/s00220-014-2162-2},
   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 = {1742-6588},
   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 = {10.1088/1742-6596/615/1/012001},
   Key = {fds287070}
}


%% Bryant, Robert   
@article{fds300229,
   Author = {R. Bryant},
   Title = {On the convex Pfaff-Darboux Theorem of Ekeland and
             Nirenberg},
   Year = {2015},
   Month = {December},
   url = {http://arxiv.org/abs/1512.07100},
   Abstract = {The classical Pfaff-Darboux Theorem, which provides local
             `normal forms' for 1-forms 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 Pfaff-Darboux 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 n-space, convexity has
             its usual meaning. In 2002, Ekeland and Nirenberg were able
             to characterize necessary and sufficient conditions for a
             given 1-form 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 Pfaff-Darboux Theorem, one that covers the case of a
             Legendrian foliation in which the notion of convexity is
             defined in terms of a torsion-free 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 2-tori},
   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 Block-Sparse Recovery and
             Regression},
   Journal = {IEEE Transactions on Information Theory},
   Volume = {61},
   Number = {7},
   Pages = {4060-4079},
   Year = {2015},
   Month = {July},
   ISSN = {0018-9448},
   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 Time-Varying Systems Through
             Waveform Diversity},
   Journal = {IEEE Transactions on Signal Processing},
   Volume = {63},
   Number = {8},
   Pages = {2070-2084},
   Year = {2015},
   Month = {April},
   ISSN = {1053-587X},
   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 = {2133-2147},
   Year = {2015},
   Month = {April},
   ISSN = {0018-9448},
   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 = {1923-1954},
   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 time-varying system identification using
             chirp waveforms},
   Journal = {Conference Record of the Asilomar Conference on Signals,
             Systems and Computers},
   Volume = {2015-April},
   Pages = {854-858},
   Year = {2015},
   Month = {January},
   ISBN = {9781479982974},
   ISSN = {1058-6393},
   url = {http://dx.doi.org/10.1109/ACSSC.2014.7094572},
   Abstract = {© 2014 IEEE.Linear, time-varying (LTV) systems are
             operators composed of time shifts, frequency shifts, and
             complex amplitude scalings that act on continuous
             finite-energy waveforms. This paper builds upon a novel,
             resource-efficient 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 Cahn-Hilliard Navier-Stokes phase-field
             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 X-ray 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 = {1053-5888},
   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 = {333-371},
   Publisher = {Springer Japan},
   Year = {2015},
   ISSN = {0916-7005},
   url = {http://dx.doi.org/10.1007/s13160-015-0173-9},
   Keywords = {Topological data analysis; Persistent homology; Sheaves and
             cosheaves; Barcodes; o-minimal topology; 55U99; 46M20;
             32S60; 16G20; 62-07; 03C64},
   Language = {English},
   Doi = {10.1007/s13160-015-0173-9},
   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 = {1-23},
   Publisher = {Springer US},
   Year = {2015},
   ISSN = {1615-3375},
   url = {http://dx.doi.org/10.1007/s10208-015-9266-8},
   Keywords = {Cellular sheaf cohomology; Discrete Morse theory; 55-04;
             55N25; 55N30},
   Language = {English},
   Doi = {10.1007/s10208-015-9266-8},
   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 = {463-472},
   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
             computer-based 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 non-contact photoplethysmography
             (PPG). As technologies move from contact to non-contact 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
             non-contact sensors, on a beat-to-beat 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
             beat-to-beat heart rate pattern (i.e., heart rate
             variability).The adaptive harmonic model is applied to model
             the contact or non-contact PPG signals, and a new
             methodology, the Synchrosqueezing Transform (SST), is
             applied to extract IHR. The body sway rhythm inherited in
             the non-contact PPG signal is modeled and handled by the
             notion of wave-shape 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 non-contact 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 = {2016-May},
   Pages = {2299-2303},
   Year = {2016},
   Month = {May},
   ISBN = {9781479999880},
   ISSN = {1520-6149},
   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 high-level classiication output and the low-level
             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
             descriptor-based 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 = {1364-503X},
   url = {http://dx.doi.org/10.1098/rsta.2015.0193},
   Abstract = {A new method is proposed to determine the time-frequency
             content of time-dependent signals consisting of multiple
             oscillatory components, with time-varying 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 = {1364-503X},
   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 X-Ray Images of
             Paintings},
   Journal = {SIAM Journal on Imaging Sciences},
   Volume = {9},
   Number = {3},
   Pages = {1247-1272},
   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 Sigma-Delta
             Quantization of Bandlimited Functions},
   Journal = {IEEE Signal Processing Letters},
   Volume = {22},
   Number = {11},
   Pages = {2093-2096},
   Year = {2015},
   Month = {November},
   ISSN = {1070-9908},
   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 2-D Synchrosqueezed
             Transforms: Application of time-frequency analysis to art
             investigation},
   Journal = {IEEE Signal Processing Magazine},
   Volume = {32},
   Number = {4},
   Pages = {55-63},
   Year = {2015},
   Month = {July},
   ISSN = {1053-5888},
   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 = {112-122},
   Year = {2015},
   Month = {July},
   ISSN = {1053-5888},
   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 = {249-276},
   Year = {2015},
   Month = {January},
   ISSN = {1932-8486},
   url = {http://dx.doi.org/10.1002/ar.23084},
   Abstract = {Three-dimensional 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 12-lead
             electrocardiogram.},
   Journal = {Journal of Electrocardiology},
   Volume = {48},
   Number = {1},
   Pages = {21-28},
   Year = {2015},
   Month = {January},
   ISSN = {0022-0736},
   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 J-wave and
             the other 50 did not. The second set was a test set (n=116
             ECGs) in which the J-wave 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 12-SL 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 = {112-122},
   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 1-persistence 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/s12859-015-0645-6},
   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 shape-agnostic manner and
             with resistance to damping. The measurement is performed
             directly, without presupposing a particular pattern, by
             evaluating the circularity of a high-dimensional
             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/not-periodic classification, using synthetic data,
             SW1PerS outperforms all other algorithms in the low-noise
             regime. SW1PerS is shown to be the most shape-agnostic 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
             highly-ranked only by SW1PerS, contains evidently non-cosine
             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/s12859-015-0645-6},
   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 = {469-471},
   Editor = {Dolbow, J and Farhat, C and Harari, I and Lew, A},
   Year = {2015},
   Month = {November},
   ISSN = {0029-5981},
   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 B-spline finite elements
             with an efficient data transfer algorithm},
   Journal = {International Journal for Numerical Methods in
             Engineering},
   Volume = {102},
   Number = {3-4},
   Pages = {233-256},
   Editor = {de Borst, R and Farhat, C and Fish, J and Harari, I and Letallec, P and Perić, D},
   Year = {2015},
   Month = {April},
   ISSN = {0029-5981},
   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
             spline-based finite elements},
   Journal = {International Journal for Numerical Methods in
             Engineering},
   Volume = {104},
   Number = {7},
   Pages = {676-696},
   Editor = {Dolbow, J and Farhat, C and Harari, I and Lew, A},
   Year = {2015},
   ISSN = {0029-5981},
   url = {http://dx.doi.org/10.1002/nme.4766},
   Abstract = {© 2015 John Wiley & Sons, Ltd.The extended finite
             element method (X-FEM) has proven to be an accurate, robust
             method for solving embedded interface problems. With a few
             exceptions, the X-FEM has mostly been used in conjunction
             with piecewise-linear shape functions and an associated
             piecewise-linear geometrical representation of interfaces.
             In the current work, the use of spline-based 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 B-splines. 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 post-coital
             contraceptives: an update.},
   Journal = {Contraception},
   Volume = {91},
   Number = {4},
   Pages = {344-349},
   Year = {2015},
   Month = {April},
   ISSN = {0010-7824},
   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 12-22.
             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 post-coital 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 Ashley-Koch,
             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/s12864-014-1211-8},
   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 multi-tissue 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
             joint-tissue 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 cis-eQTLs are
             shared by both tissues. The power to detect shared eQTLs was
             improved by using an integrative statistical approach. The
             identified tissue-specific and shared eQTLs provide new
             insight into the genetic basis for CMI and related
             conditions.},
   Doi = {10.1186/s12864-014-1211-8},
   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 non-parametric Bayesian
             estimation},
   Journal = {Journal of the Royal Statistical Society: Series B
             (Statistical Methodology)},
   Volume = {77},
   Number = {1},
   Pages = {35-58},
   Year = {2015},
   Month = {January},
   ISSN = {1369-7412},
   url = {http://dx.doi.org/10.1111/rssb.12059},
   Abstract = {© 2014 Royal Statistical Society.Prior specification for
             non-parametric 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 non-parametric 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
             non-parametric conditional prior for the parameter given the
             functionals. Such priors can be easily constructed from
             standard non-parametric 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 non-parametric 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 non-parametric Bayesian
             estimation.},
   Journal = {Journal of the Royal Statistical Society: Series B
             (Statistical Methodology)},
   Volume = {77},
   Number = {1},
   Pages = {35-58},
   Year = {2015},
   Month = {January},
   ISSN = {1369-7412},
   url = {http://dx.doi.org/10.1111/rssb.12059},
   Abstract = {Prior specification for non-parametric 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
             non-parametric 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 non-parametric conditional
             prior for the parameter given the functionals. Such priors
             can be easily constructed from standard non-parametric 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 non-parametric
             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 mixed-scale density
             estimation},
   Journal = {Statistics and its Interface},
   Volume = {8},
   Number = {2},
   Pages = {195-201},
   Year = {2015},
   ISSN = {1938-7989},
   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 = {1369-1400},
   Year = {2016},
   Month = {April},
   ISSN = {0303-6812},
   url = {http://dx.doi.org/10.1007/s00285-015-0912-1},
   Doi = {10.1007/s00285-015-0912-1},
   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 = {3434-3464},
   Year = {2015},
   Month = {December},
   ISSN = {1050-5164},
   url = {http://dx.doi.org/10.1214/14-AAP1079},
   Doi = {10.1214/14-AAP1079},
   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 = {1934-1954},
   Year = {2015},
   Month = {October},
   ISSN = {0092-8240},
   url = {http://dx.doi.org/10.1007/s11538-015-0110-8},
   Doi = {10.1007/s11538-015-0110-8},
   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 = {1553-734X},
   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 chance-in
             form of the stochastic dynamics of basal stem cells-plays a
             critical role in the elimination of HPV-infected cell
             clones. In particular, we find that in immunocompetent
             adolescents with cervical HPV infections, the immune
             response may contribute less than 20% to virus clearance-the
             rest is taken care of by the stochastic proliferation
             dynamics in the basal layer. In HIV-negative 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 = {104-115},
   Year = {2015},
   Month = {February},
   ISSN = {1050-5164},
   url = {http://dx.doi.org/10.1214/13-AAP989},
   Doi = {10.1214/13-AAP989},
   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 3-manifolds},
   Journal = {Journal of the London Mathematical Society},
   Volume = {93},
   Number = {3},
   Pages = {785-810},
   Year = {2016},
   Month = {June},
   ISSN = {0024-6107},
   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 = {699-728},
   Year = {2016},
   Month = {January},
   ISSN = {0010-3616},
   url = {http://hdl.handle.net/10161/11700 Duke open
             access},
   Doi = {10.1007/s00220-015-2534-2},
   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 = {F967-F980},
   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 = {1932-6203},
   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. Three-dimensional digitization presents a way
             to re-introduce 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 Rankin-Selberg lifts},
   Journal = {Proceedings of the American Mathematical
             Society},
   Volume = {143},
   Number = {8},
   Pages = {3319-3329},
   Year = {2015},
   Month = {April},
   ISSN = {0002-9939},
   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 = {99-118},
   Year = {2015},
   ISSN = {0030-8730},
   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 = {5061-5069},
   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 L-functions 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 Littlewood-Richardson 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 = {99-118},
   Year = {2015},
   ISSN = {0030-8730},
   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 = {1550065-1550065},
   Year = {2016},
   Month = {August},
   ISSN = {0219-1997},
   url = {http://dx.doi.org/10.1142/S0219199715500650},
   Doi = {10.1142/S0219199715500650},
   Key = {fds287213}
}

@article{fds320224,
   Author = {Hain, R},
   Title = {The Hodge-de Rham theory of modular groups},
   Volume = {427},
   Pages = {422-514},
   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 = {Deligne-Beilinson 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 1-persistence 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/s12859-015-0645-6},
   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 shape-agnostic manner and
             with resistance to damping. The measurement is performed
             directly, without presupposing a particular pattern, by
             evaluating the circularity of a high-dimensional
             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/not-periodic classification, using synthetic data,
             SW1PerS outperforms all other algorithms in the low-noise
             regime. SW1PerS is shown to be the most shape-agnostic 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
             highly-ranked only by SW1PerS, contains evidently non-cosine
             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/s12859-015-0645-6},
   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 = {Feature-aided 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 J-G 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 channel-reservoir 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 = {0021-9606},
   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 finite-range 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 two-dimensional 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 one-dimensional systems, while predicting
             similar system dynamics and steady states as KMC methods. We
             then test the hierarchy on a two-dimensional model for the
             oxidation of CO on RuO2(110), showing that low-order
             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, J-G 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 = {2246-2267},
   Year = {2015},
   Month = {January},
   ISSN = {0036-1399},
   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 = {219-231},
   Year = {2015},
   ISSN = {0302-9743},
   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 multi-agent 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, J-G and Layton, AT},
   Title = {Fluid extraction across pumping and permeable walls in the
             viscous limit},
   Journal = {Physics of Fluids},
   Volume = {28},
   Number = {4},
   Pages = {041902-041902},
   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 contrast-enhanced quantitative susceptibility
             mapping with ultrashort echo time MRI for evaluating renal
             function.},
   Journal = {American Journal of Physiology: Renal Physiology},
   Volume = {310},
   Number = {2},
   Pages = {F174-F182},
   Year = {2016},
   Month = {January},
   url = {http://dx.doi.org/10.1152/ajprenal.00351.2015},
   Abstract = {Dynamic contrast-enhanced (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 17-wk course (3, 5, 7, 9, 13,
             17 wk of age). We conclude that the UTE-based 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 nitric-oxide-mediated vasodilation and oxidative
             Stress on renal medullary oxygenation: A modeling
             study},
   Journal = {Am J Physiol Renal Physiol},
   Volume = {310},
   Number = {F237-F247},
   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 Cohen-Wolkowiez, M and Chow, SC and Noveck,
             RJ},
   Title = {Intraarterial Microdosing: A Novel Drug Development
             Approach, Proof-of-Concept PET Study in Rats.},
   Journal = {Journal of nuclear medicine : official publication, Society
             of Nuclear Medicine},
   Volume = {56},
   Number = {11},
   Pages = {1793-1799},
   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 full-dose
             administration but with minimal systemic exposure. IAM could
             enable the safe, inexpensive, and early study of novel drugs
             at the first-in-human 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 60-min
             (18)F-FDG uptake PET imaging of ipsilateral and
             contralateral leg muscles (lateral gastrocnemius) and
             systemic muscles (spinotrapezius). The (18)F-FDG 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)F-FDG slope
             analysis found no difference between IAM and systemic
             full-dose 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, 0.023-0.058;
             P = 0.0052). The pharmacokinetics/pharmacodynamics data were
             used to identify model parameters that describe membrane
             insulin binding and glucose-insulin 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 whole-body 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 Cohen-Wolkowiez, M and Chow, S-C and Noveck, RJ},
   Title = {Intraarterial Microdosing: A Novel Drug Development
             Approach, Proof-of-Concept PET Study in Rats},
   Journal = {Journal of nuclear medicine : official publication, Society
             of Nuclear Medicine},
   Volume = {56},
   Number = {11},
   Pages = {1793-1799},
   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 = {F708-F719},
   Year = {2015},
   Month = {October},
   ISSN = {1931-857X},
   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: F34-F48, 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 pressure-induced increases in O(2)(-)
             production, O(2)(-)-mediated regulation of L-type 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, Y-N and Layton, AT and Hu, W-F and Lai,
             M-C},
   Title = {An Immersed Interface Method for Axisymmetric
             Electrohydrodynamic Simulations in Stokes
             flow},
   Journal = {Communications in computational physics},
   Volume = {18},
   Number = {02},
   Pages = {429-449},
   Year = {2015},
   Month = {August},
   ISSN = {1815-2406},
   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 Cohen-Wolkowiez, M and Chow, S and Noveck,
             RJ},
   Title = {INTRA-ARTERIAL MICRODOSING (IAM), A NOVEL DRUG DEVELOPMENT
             APPROACH, PROOF OF CONCEPT IN RATS},
   Journal = {Clinical Therapeutics},
   Volume = {37},
   Number = {8},
   Pages = {E40-E41},
   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 = {8-20},
   Year = {2015},
   Month = {June},
   ISSN = {0025-5564},
   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, acid-base, 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 = {F1343-F1357},
   Year = {2015},
   Month = {June},
   ISSN = {1931-857X},
   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
             S1-S2 segments, due to the greater contribution of the
             passive paracellular pathway to TNa in the former segment.
             Inhibition of NHE or Na-K-ATPase 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
             S1-S2 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 = {F951-F955},
   Year = {2015},
   Month = {May},
   ISSN = {1931-857X},
   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: 13-46, 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 = {F967-F980},
   Year = {2015},
   Month = {May},
   ISSN = {1931-857X},
   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
             hypertension-induced medullary hypoxia. Moreover, model
             predictions suggest that urine Po2 could serve as a
             biomarker for medullary hypoxia and a predictor of the risk
             for hospital-acquired acute kidney injury.},
   Doi = {10.1152/ajprenal.00600.2014},
   Key = {fds243615}
}

@article{fds299957,
   Author = {Fields, B and Page, K},
   Title = {Preface},
   Volume = {2015-June},
   Year = {2015},
   Month = {January},
   ISBN = {9781450335638},
   Key = {fds299957}
}

@article{fds320185,
   Author = {Herschlag, G and Liu, J-G 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 = {2246-2267},
   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 Jian-Guo 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 = {978-0691150390},
   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 = {55-73},
   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 Jian-Guo 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 Cohen-Wolkowiez and Shein-Chung Chow and Robert J.
             Noveck},
   Title = {Intra-arterial 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 = {021902-021902},
   Year = {2015},
   Month = {February},
   ISSN = {1070-6631},
   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 super-resolution},
   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, Jian-Guo   
@article{fds318453,
   Author = {Huang, H and Liu, J-G},
   Title = {A note on Monge–Ampère Keller–Segel
             equation},
   Journal = {Applied Mathematics Letters},
   Volume = {61},
   Pages = {26-34},
   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, J-G and Huang, H},
   Title = {Well-posedness for the Keller-Segel equation with fractional
             Laplacian and the theory of propagation of
             chaos},
   Journal = {Kinetic and Related Models},
   Volume = {9},
   Number = {4},
   Pages = {715-748},
   Year = {2016},
   Month = {September},
   url = {http://dx.doi.org/10.3934/krm.2016013},
   Doi = {10.3934/krm.2016013},
   Key = {fds318454}
}

@article{fds318455,
   Author = {Liu, J-G and Cong, W},
   Title = {A degenerate $p$-Laplacian Keller-Segel model},
   Journal = {Kinetic and Related Models},
   Volume = {9},
   Number = {4},
   Pages = {687-714},
   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, J-G and Layton, AT},
   Title = {Fluid extraction across pumping and permeable walls in the
             viscous limit},
   Journal = {Physics of Fluids},
   Volume = {28},
   Number = {4},
   Pages = {041902-041902},
   Year = {2016},
   Month = {April},
   ISSN = {1070-6631},
   url = {http://dx.doi.org/10.1063/1.4946005},
   Doi = {10.1063/1.4946005},
   Key = {fds315797}
}

@article{fds300221,
   Author = {Liu, J-G and Wang, J},
   Title = {A Note on L ∞ $L^{\infty}$ -Bound and Uniqueness to a
             Degenerate Keller-Segel Model},
   Journal = {Acta Applicandae Mathematicae},
   Volume = {142},
   Number = {1},
   Pages = {173-188},
   Year = {2016},
   Month = {April},
   ISSN = {0167-8019},
   url = {http://dx.doi.org/10.1007/s10440-015-0022-5},
   Doi = {10.1007/s10440-015-0022-5},
   Key = {fds300221}
}

@article{fds318456,
   Author = {Liu, J-G and Pego, RL},
   Title = {On generating functions of Hausdorff moment
             sequences},
   Journal = {Transactions of the American Mathematical
             Society},
   Volume = {368},
   Number = {12},
   Pages = {8499-8518},
   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 diffusion-drift many particle systems in
             probability under a sobolev norm},
   Volume = {162},
   Series = {Proceedings of Particle Systems and Partial Differential
             Equations - III},
   Pages = {195-223},
   Publisher = {Springer},
   Year = {2016},
   Month = {January},
   ISBN = {9783319321424},
   url = {http://dx.doi.org/10.1007/978-3-319-32144-8_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 = {10.1007/978-3-319-32144-8_10},
   Key = {fds318457}
}

@article{fds300225,
   Author = {J.-G. Liu and J. Wang},
   Title = {Refined hyper-contractivity and uniqueness for the
             Keller-Segel equations},
   Journal = {Applied Math Letter},
   Volume = {52},
   Pages = {212-219},
   Year = {2016},
   Key = {fds300225}
}

@article{fds246842,
   Author = {Xue, Y and Wang, C and Liu, J-G},
   Title = {Simple Finite Element Numerical Simulation of Incompressible
             Flow Over Non-rectangular Domains and the Super-Convergence
             Analysis},
   Journal = {Journal of Scientific Computing},
   Volume = {65},
   Number = {3},
   Pages = {1189-1216},
   Year = {2015},
   Month = {December},
   ISSN = {0885-7474},
   url = {http://dx.doi.org/10.1007/s10915-015-0005-8},
   Doi = {10.1007/s10915-015-0005-8},
   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 = {1539-3755},
   url = {http://dx.doi.org/10.1103/PhysRevE.91.032403},
   Abstract = {The Burton-Cabrera-Frank (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 solid-on-solid 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
             Self-Organized Alignment Dynamics},
   Journal = {Archive for Rational Mechanics and Analysis},
   Volume = {216},
   Number = {1},
   Pages = {63-115},
   Year = {2015},
   Month = {January},
   ISSN = {0003-9527},
   url = {http://dx.doi.org/10.1007/s00205-014-0800-7},
   Abstract = {© 2014, Springer-Verlag Berlin Heidelberg.We provide a
             complete and rigorous description of phase transitions for
             kinetic models of self-propelled 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/s00205-014-0800-7},
   Key = {fds300223}
}

@article{fds300222,
   Author = {Chertock, A and Liu, JG and Pendleton, T},
   Title = {Elastic collisions among peakon solutions for the
             Camassa-Holm equation},
   Journal = {Applied Numerical Mathematics},
   Volume = {93},
   Pages = {30-46},
   Year = {2015},
   Month = {January},
   ISSN = {0168-9274},
   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 one-dimensional Camassa-Holm 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 Camassa-Holm 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 Camassa-Holm 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, J-G 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 = {2246-2267},
   Year = {2015},
   Month = {January},
   ISSN = {0036-1399},
   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 Keller-Segel 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 Vanden-Eijnden,
             E},
   Title = {Multiscale implementation of infinite-swap replica exchange
             molecular dynamics.},
   Journal = {Proceedings of the National Academy of Sciences of
             USA},
   Volume = {113},
   Number = {42},
   Pages = {11744-11749},
   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
             Metropolis-Hastings 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 continuous-time 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 REMD-SSA is combined
             with the heterogeneous multiscale method to accelerate the
             rate of the swaps and reach the so-called infinite-swap
             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
             C-terminal β-hairpin 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
             H-bonds.},
   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 (FGA-SH)
             method samples a path integral representation of the
             non-adiabatic dynamics in the semiclassical regime. An
             improved sampling scheme is developed in this work for
             FGA-SH based on birth and death branching processes. The
             algorithm is validated for the standard test examples of
             non-adiabatic 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 = {310-329},
   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 = {1561-1578},
   Year = {2016},
   Month = {August},
   url = {http://dx.doi.org/10.1007/s11425-016-0311-4},
   Doi = {10.1007/s11425-016-0311-4},
   Key = {fds318294}
}

@article{fds318295,
   Author = {Lai, R and Lu, J},
   Title = {Localized density matrix minimization and linear-scaling
             algorithms},
   Journal = {Journal of Computational Physics},
   Volume = {315},
   Pages = {194-210},
   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 = {458-466},
   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 = {194-210},
   Year = {2016},
   Month = {April},
   ISSN = {0022-5096},
   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 divide-and-conquer method for electronic
             structure calculations},
   Journal = {Mathematics of Computation},
   Volume = {85},
   Number = {302},
   Pages = {2919-2938},
   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 = {Gauge-Invariant Frozen Gaussian Approximation Method for the
             Schrödinger Equation with Periodic Potentials},
   Journal = {SIAM Journal on Scientific Computing},
   Volume = {38},
   Number = {4},
   Pages = {A2440-A2463},
   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 = {Orbital-Free Density Functional Theory of Out-of-Plane
             Charge Screening in Graphene},
   Journal = {Journal of Nonlinear Science},
   Volume = {25},
   Number = {6},
   Pages = {1391-1430},
   Year = {2015},
   Month = {December},
   ISSN = {0938-8974},
   url = {http://dx.doi.org/10.1007/s00332-015-9259-4},
   Doi = {10.1007/s00332-015-9259-4},
   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 Kohn-Sham density
             functionals.},
   Journal = {Journal of Chemical Physics},
   Volume = {143},
   Number = {22},
   Pages = {224110},
   Year = {2015},
   Month = {December},
   ISSN = {0021-9606},
   url = {http://dx.doi.org/10.1063/1.4936411},
   Abstract = {We develop the gentlest ascent dynamics for Kohn-Sham
             density functional theory to search for the index-1 saddle
             points on the energy landscape of the Kohn-Sham 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 index-1 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 Kohn-Sham
             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 2-D Synchrosqueezed
             Transforms: Application of time-frequency analysis to art
             investigation},
   Journal = {IEEE Signal Processing Magazine},
   Volume = {32},
   Number = {4},
   Pages = {55-63},
   Year = {2015},
   Month = {July},
   ISSN = {1053-5888},
   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 = {141-167},
   Year = {2015},
   Month = {July},
   ISSN = {0021-9991},
   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 half-space 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 matrix-valued
             quantum Boltzmann equation},
   Journal = {Journal of Computational Physics},
   Volume = {291},
   Pages = {303-316},
   Year = {2015},
   Month = {June},
   ISSN = {0021-9991},
   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 = {1539-3755},
   url = {http://dx.doi.org/10.1103/PhysRevE.91.032403},
   Abstract = {© 2015 American Physical Society.The Burton-Cabrera-Frank
             (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
             solid-on-solid 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 = {1-2},
   Pages = {195-244},
   Year = {2015},
   Month = {February},
   ISSN = {0178-8051},
   url = {http://dx.doi.org/10.1007/s00440-014-0547-y},
   Doi = {10.1007/s00440-014-0547-y},
   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 = {A609-A624},
   Year = {2015},
   Month = {January},
   ISSN = {1064-8275},
   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 = {1542-1572},
   Year = {2015},
   Month = {January},
   ISSN = {1540-3459},
   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 = {329-335},
   Year = {2015},
   ISSN = {0021-9991},
   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 = {2097-2117},
   Year = {2015},
   ISSN = {1539-6746},
   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 = {1051-1074},
   Year = {2015},
   ISSN = {1539-6746},
   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 = {166-180},
   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 = {1-2},
   Pages = {345-362},
   Year = {2016},
   Month = {June},
   url = {http://dx.doi.org/10.1007/s00208-015-1308-7},
   Doi = {10.1007/s00208-015-1308-7},
   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 = {388-402},
   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 = {High-Dimensional 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 = {4316-4324},
   Year = {2016},
   Month = {September},
   ISSN = {1939-1404},
   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 low-sampled complexity for
             intrinsically low-dimensional 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 state-of-the-art 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 = {2016-May},
   Pages = {2299-2303},
   Year = {2016},
   Month = {May},
   ISBN = {9781479999880},
   ISSN = {1520-6149},
   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 high-level classiication output and the low-level
             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
             descriptor-based 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: Non-asymptotic bounds and
             robustness},
   Journal = {Journal of machine learning research : JMLR},
   Volume = {17},
   Year = {2016},
   Month = {January},
   ISSN = {1532-4435},
   url = {http://arxiv.org/abs/1401.5833},
   Abstract = {© 2016 Mauro Maggioni, Stanislav Minsker, and Nate
             Strawn.High-dimensional datasets are well-approximated by
             low-dimensional structures. Over the past decade, this
             empirical observation motivated the investigation of
             detection, measurement, and modeling techniques to exploit
             these low-dimensional intrinsic structures, yielding
             numerous implications for high-dimensional statistics,
             machine learning, and signal processing. Manifold learning
             (where the low-dimensional structure is a manifold) and
             dictionary learning (where the low-dimensional 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 recently-introduced Geometric
             Multi-Resolution Analysis (GMRA) provides a robust,
             computationally eficient, multiscale procedure for
             simultaneously learning manifolds and dictionaries. In this
             work, we prove non-asymptotic probabilistic bounds on the
             approximation error of GMRA for a rich class of
             data-generating 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 low-dimensional
             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 = {1185-1188},
   Year = {2015},
   Month = {November},
   ISSN = {0002-9920},
   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 multi-resolution analysis for dictionary
             learning},
   Journal = {Proceedings of SPIE - The International Society for Optical
             Engineering},
   Volume = {9597},
   Year = {2015},
   Month = {January},
   ISBN = {9781628417630},
   ISSN = {0277-786X},
   url = {http://dx.doi.org/10.1117/12.2189594},
   Abstract = {© 2015 SPIE.We present an efficient algorithm and theory
             for Geometric Multi-Resolution 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 high-dimensional 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 high-dimensional
             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 = {Hyper-spectral Analysis of normal and malignant colon tissue
             microarray sections using a novel DMD system},
   Year = {2004},
   Key = {PathNIH2004}
}

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


%% 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
             path-dependent 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 = {3755-3787},
   Year = {2015},
   Month = {October},
   ISSN = {0951-7715},
   url = {http://hdl.handle.net/10161/9514 Duke open
             access},
   Abstract = {This is a detailed analysis of invariant measures for
             one-dimensional 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 = {10.1088/0951-7715/28/11/3755},
   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 = {2823-2845},
   Year = {2015},
   Month = {August},
   ISSN = {0951-7715},
   url = {http://hdl.handle.net/10161/9510 Duke open
             access},
   Doi = {10.1088/0951-7715/28/8/2823},
   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 = {3035-3063},
   Year = {2015},
   Month = {January},
   ISSN = {0036-1410},
   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.v20-3887},
   Key = {fds243883}
}

@article{fds243884,
   Author = {Herzog, D and Mattingly, J},
   Title = {Noise-induced 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.v20-4048},
   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 fast-replicating virus strain outcompetes
             slower-replicating strains at the within-host scale.
             However, if the fast-replicating strain causes host
             morbidity and is less frequently transmitted, it can be
             outcompeted by slower-replicating strains at the
             between-host scale. Here we consider a stochastic
             ball-and-urn 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 integro-partial 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
             measure-valued Fleming-Viot 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 = {1-29},
   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 = {1319-1332},
   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 = {198-218},
   Year = {2016},
   Month = {January},
   url = {http://arxiv.org/abs/1411.6652v1},
   Abstract = {New representations of tree-structured 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 = {1178-1184},
   Year = {2015},
   Month = {November},
   ISSN = {0002-9920},
   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 = {51-91},
   Year = {2015},
   Month = {July},
   ISSN = {0196-8858},
   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 = {281-286},
   Year = {2015},
   ISSN = {0030-8730},
   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.v20-3887},
   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 = {115-115},
   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 = {52-55},
   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 = {1173-1204},
   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 p-th 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 continuously-varying 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 time-varying
             persistence diagrams, better known as vineyards.},
   Doi = {10.1214/15-EJS1030},
   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 Dai-Ichi
             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 multi-modal 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 = {475-513},
   Year = {2015},
   ISSN = {1663-487X},
   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 4-Manifold},
   Journal = {Journal of Differential Geometry},
   Volume = {101},
   Number = {1},
   Pages = {67-157},
   Year = {2015},
   ISSN = {0022-040X},
   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 1-handles to
             the 4-ball. In view of the surgery formula for symplectic
             homology [5], this gives a combinatorial description of the
             symplectic homology of any 4-dimensional 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 = {2304-2348},
   Year = {2016},
   Month = {December},
   ISSN = {0010-3640},
   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 = {439-476},
   Year = {2016},
   Month = {September},
   ISSN = {2194-0401},
   url = {http://arxiv.org/abs/1406.2186},
   Doi = {10.1007/s40072-015-0068-4},
   Key = {fds316661}
}

@article{fds318326,
   Author = {Nolen, JH and Roquejoffre, J-M and Ryzhik, L},
   Title = {Refined long time asymptotics for Fisher-KPP
             fronts},
   Year = {2016},
   Key = {fds318326}
}

@article{fds316662,
   Author = {Nolen, J and Roquejoffre, J-M and Ryzhik, L},
   Title = {Convergence to a single wave in the Fisher-KPP
             equation},
   Year = {2016},
   url = {http://arxiv.org/abs/1604.02994},
   Key = {fds316662}
}

@article{fds316609,
   Author = {Nolen, J and Mourrat, J-C},
   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 = {1050-5164},
   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 Erdős-Rényi random graphs},
   Journal = {Electronic Journal of Probability},
   Year = {2015},
   Month = {October},
   url = {http://ejp.ejpecp.org/article/view/2696},
   Doi = {10.1214/EJP.v20-2696},
   Key = {fds227095}
}

@article{fds287342,
   Author = {Nolen, J and Roquejoffre, J-M and Ryzhik, L},
   Title = {Power-Like Delay in Time Inhomogeneous Fisher-KPP
             Equations},
   Journal = {Communications in Partial Differential Equations},
   Volume = {40},
   Number = {3},
   Pages = {475-505},
   Year = {2015},
   Month = {March},
   ISSN = {0360-5302},
   url = {http://math.duke.edu/~nolen/preprints/bigdelay-draft.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 = {1-2},
   Pages = {195-244},
   Year = {2015},
   Month = {February},
   ISSN = {0178-8051},
   url = {http://dx.doi.org/10.1007/s00440-014-0547-y},
   Doi = {10.1007/s00440-014-0547-y},
   Key = {fds287345}
}

@article{fds299972,
   Author = {J. Nolen and J.-M. Roquejoffre and L. Ryzhik},
   Title = {Refined long time asymptotics for the Fisher-KPP
             equation},
   Year = {2015},
   url = {http://math.duke.edu/~nolen/preprints/kpp-brezis-v5.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.v20-3887},
   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.v20-2696},
   Doi = {10.1214/EJP.v20-2696},
   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 1-Persistence 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 ensemble-based spatially-coupled product
             codes},
   Volume = {2016-August},
   Pages = {2114-2118},
   Year = {2016},
   Month = {August},
   url = {http://dx.doi.org/10.1109/ISIT.2016.7541672},
   Abstract = {© 2016 IEEE.Several authors have proposed spatially-coupled
             (or convolutional-like) 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
             block-wise 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 spatially-coupled 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 = {Reed-muller codes achieve capacity on the quantum erasure
             channel},
   Volume = {2016-August},
   Pages = {1750-1754},
   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 error-correcting codes called stabilizer codes is
             known to contain capacity-achieving sequences for the
             quantum erasure channel, but no efficient method is known to
             construct these sequences. In this article, we explicitly
             describe a capacity-achieving code sequence for the quantum
             erasure channel. In particular, we show that
             Calderbank-Shor-Steane (CSS) stabilizer codes constructed
             from self-orthogonal binary linear codes are
             capacity-achieving on the quantum erasure channel if the
             binary linear codes are capacity-achieving on the binary
             erasure channel. Recently, Reed-Muller codes were shown to
             achieve capacity on classical erasure channels. Using this,
             we show that CSS codes constructed from binary Reed-Muller
             codes achieve the capacity of the quantum erasure channel.
             The capacity-achieving 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 bit-MAP and block-MAP decoding thresholds of
             reed-muller codes on BMS channels},
   Volume = {2016-August},
   Pages = {1755-1759},
   Year = {2016},
   Month = {August},
   url = {http://dx.doi.org/10.1109/ISIT.2016.7541600},
   Abstract = {© 2016 IEEE.The question whether RM codes are
             capacity-achieving is a long-standing 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
             doubly-transitive permutation groups, achieves capacity on
             the memoryless erasure channel under bit-MAP decoding. Thus,
             a natural question is what happens under block-MAP decoding.
             In [1], [2], by exploiting further symmetries of the code,
             the bit-MAP 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
             bit-MAP threshold to block-MAP 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 bit-MAP error probability decays
             as N-δ, for some δ > 0. Then, the block-MAP 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 capacity-achieving 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 = {Reed-Muller codes achieve capacity on erasure
             channels},
   Journal = {Proceedings of the Annual ACM Symposium on Theory of
             Computing},
   Volume = {19-21-June-2016},
   Pages = {658-669},
   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 near-optimal performance. An important consequence
             of this result is that a sequence of Reed-Muller 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 affine-invariant codes and, thus, to all
             extended primitive narrow-sense BCH codes. This is used to
             resolve, in the affirmative, the existence question for
             capacity-achieving 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 = {Hamidi-Sepehr, F and Chamberland, J-F and Pfister,
             HD},
   Title = {On the Performance of Block Codes Over Finite-State Channels
             in the Rare-Transition Regime},
   Journal = {IEEE Transactions on Communications},
   Volume = {63},
   Number = {11},
   Pages = {3974-3990},
   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 = {282-290},
   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
             error-correction in high-speed 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
             half-product 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 two-user
             symmetric Gaussian interference channels},
   Volume = {2015-June},
   Pages = {1711-1715},
   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 two-user symmetric Gaussian
             interference channel. A two-step approach is proposed for
             finding approximately optimal input distributions in the
             high signal-to-noise ratio (SNR) regime. First,
             approximately and precisely optimal input distributions are
             found for the Avestimehr-Diggavi-Tse (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 = {2015-June},
   Pages = {1287-1291},
   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
             low-complexity successive cancellation decoding, of any
             binary-input discrete memoryless channel. Arikan's
             construction is based on the Kronecker product of 2-by-2
             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 mixed-radix Cooley-Tukey
             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 = {Hamidi-Sepehr, F and Pfister, HD and Chamberland,
             J-F},
   Title = {Delay-Sensitive Communication Over Fading Channels: Queueing
             Behavior and Code Parameter Selection},
   Journal = {IEEE Transactions on Vehicular Technology},
   Volume = {64},
   Number = {9},
   Pages = {3957-3970},
   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 = {2015-June},
   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 = {Hamidi-Sepehr, F and Pfister, HD and Chamberland,
             J-F},
   Title = {Delay-Sensitive Communication Over Fading Channels: Queueing
             Behavior and Code Parameter Selection.},
   Journal = {IEEE Trans. Vehicular Technology},
   Volume = {64},
   Pages = {3957-3970},
   Year = {2015},
   url = {http://dx.doi.org/10.1109/TVT.2014.2365181},
   Doi = {10.1109/TVT.2014.2365181},
   Key = {fds319321}
}

@article{fds319322,
   Author = {Hamidi-Sepehr, F and Chamberland, J-F and Pfister,
             HD},
   Title = {On the Performance of Block Codes Over Finite-State Channels
             in the Rare-Transition Regime.},
   Journal = {IEEE Trans. Communications},
   Volume = {63},
   Pages = {3974-3990},
   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 = {5471-5473},
   Year = {2015},
   Month = {September},
   ISSN = {0002-9939},
   url = {http://dx.doi.org/10.1090/proc/12778},
   Doi = {10.1090/proc/12778},
   Key = {fds302459}
}

@article{fds302460,
   Author = {Heath-Brown, DR and Pierce, LB},
   Title = {Burgess bounds for short mixed character
             sums},
   Journal = {Journal of the London Mathematical Society},
   Volume = {91},
   Number = {3},
   Pages = {693-708},
   Year = {2015},
   Month = {June},
   ISSN = {0024-6107},
   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 = {751-770},
   Year = {2015},
   Month = {September},
   ISSN = {0550-3213},
   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 = {15-20-November-2015},
   Publisher = {ACM},
   Year = {2015},
   Month = {November},
   ISBN = {9781450337236},
   ISSN = {2167-4329},
   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 three-dimensional, high-resolution
             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 time-to-solution 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 = {70-75},
   Year = {2015},
   Month = {July},
   ISSN = {1877-7503},
   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 = {Lenard-Balescu Calculations and Classical Molecular Dynamics
             Simulations of Electrical and Thermal Conductivities of
             Hydrogen Plasmas},
   Journal = {Contributions to Plasma Physics},
   Volume = {55},
   Number = {2-3},
   Pages = {192-202},
   Year = {2015},
   Month = {February},
   ISSN = {0863-1042},
   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 = {16-31},
   Year = {2015},
   Month = {February},
   ISSN = {0743-7315},
   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 = {1172-1176},
   Year = {2015},
   Month = {November},
   ISSN = {0002-9920},
   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/s12918-015-0215-6},
   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 S-adenosylmethionine (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 long-range 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 long-range 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
             5-methyltetrahydrofolate (5 mTHF) to glycine-N-methyltransferase
             (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 long-range
             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
             S-adenosylhomocysteine also stabilizes reaction rates
             against changes in SAM.},
   Doi = {10.1186/s12918-015-0215-6},
   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 = {118-133},
   Year = {2015},
   Month = {July},
   ISSN = {0022-5193},
   url = {http://dx.doi.org/10.1016/j.jtbi.2015.04.006},
   Abstract = {Marked alterations in systemic glutamate-glutamine
             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 glutamate-glutamine
             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 24-h
             mark. We show that this rebound is achieved in part by the
             action of the cystine-glutamate 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
             rate-limiting 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/s12915-015-0189-2},
   Abstract = {Mathematical models are a useful tool for investigating a
             large number of questions in metabolism, genetics, and
             gene-environment 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, gene-environment interactions, and
             genotype-phenotype mapping, and how they can be used in
             precision and personalized medicine.},
   Doi = {10.1186/s12915-015-0189-2},
   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 = {3035-3063},
   Year = {2015},
   Month = {January},
   ISSN = {0036-1410},
   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 = {918-954},
   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 = {725-758},
   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 L2-Cohomology, 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 coverage-dependent marginal costs on optimal HPV
             vaccination strategies.},
   Journal = {Epidemics: the journal of infectious disease
             dynamics},
   Volume = {11},
   Pages = {32-47},
   Year = {2015},
   Month = {June},
   ISSN = {1755-4365},
   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 agent-based modeling
             framework to revisit the male vaccination debate in light of
             these new findings. Within this framework, we assess the
             impact of coverage-dependent 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 coverage-dependent, 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
             coverage-dependent 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 Borel-Serre and Satake
             Compactifications},
   Journal = {The Asian Journal of Mathematics},
   Volume = {19},
   Number = {3},
   Pages = {465-486},
   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>&thinsp;&isin;&thinsp;<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 Bruhat-Tits
             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
             Borel-Serre compactification of <nobr>&Gamma;&thinsp;\&thinsp;<i>X</i></nobr>,
             where &Gamma; is an <i>S</i>-arithmetic subgroup of
             <b>G</b>. In the case that &Gamma; is neat, we show that
             this fundamental group is isomorphic to <nobr>&Gamma;&thinsp;/&thinsp;<i>E</i>&Gamma;</nobr>,
             where <i>E</i>&Gamma; is the subgroup generated by the
             elements of &Gamma; 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 = {3293-3307},
   Year = {2015},
   Month = {November},
   ISSN = {1057-7149},
   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 = {40-42},
   Year = {2015},
   Month = {April},
   ISSN = {1740-9705},
   url = {http://dx.doi.org/10.1111/j.1740-9713.2015.00816.x},
   Doi = {10.1111/j.1740-9713.2015.00816.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 = {106-119},
   Year = {2015},
   Month = {January},
   ISSN = {1057-7149},
   url = {http://dx.doi.org/10.1109/tip.2014.2365720},
   Abstract = {Compressive sensing of signals drawn from a Gaussian mixture
             model (GMM) admits closed-form 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 low-rank covariance matrices, to gain
             computational speedup. We report extensive experimental
             results on image inpainting, compressive sensing of
             high-speed video, and compressive hyperspectral imaging (the
             latter two based on real compressive cameras). The results
             demonstrate that the proposed methods outperform
             state-of-the-art 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 high-field
             brain MRI},
   Journal = {Proceedings / IEEE International Symposium on Biomedical
             Imaging: from nano to macro. IEEE International Symposium on
             Biomedical Imaging},
   Volume = {2015-July},
   Pages = {1264-1267},
   Year = {2015},
   Month = {January},
   ISBN = {9781479923748},
   ISSN = {1945-7928},
   url = {http://dx.doi.org/10.1109/ISBI.2015.7164104},
   Abstract = {© 2015 IEEE.The subthalamic nucleus (STN) within the
             sub-cortical 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 pre-requisite process for reliable
             DBS direct targeting. While direct visualization of the STN
             is facilitated with advanced ultrahigh-field 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 low-field MRI, exploiting
             dependencies between the STN and its adjacent structures,
             learned from ultrahigh-field 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 low-field 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 = {978-3-319-45052-0},
   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 Larrain-Hubach and Mark
             Stern},
   Title = {Instantons on multi-Taub-NUT Spaces I: Asymptotic Form and
             Index Theorem},
   Journal = {arXiv:1608.00018},
   Year = {2016},
   Month = {August},
   Abstract = {We study finite action anti-self-dual Yang-Mills connections
             on the multi-Taub-NUT 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 multi-Taub-NUT 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 = {559-609},
   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 = {559-609},
   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}
}


%% Turnage-Butterbaugh, Caroline   
@book{fds320234,
   Author = {Mackall, B and Miller, SJ and Rapti, C and Turnage-Butterbaugh, C and Winsor, K},
   Title = {Some Results in the Theory of Low-lying Zeros},
   Booktitle = {Families of Automorphic Forms and the Trace
             Formula},
   Publisher = {Springer},
   Year = {2016},
   Month = {September},
   ISBN = {3319414240},
   Abstract = {Featuring the work of twenty-three internationally-recognized
             experts, this volume explores the trace formula, spectra of
             locally symmetric spaces, p-adic families, and other recent
             techniques from harmonic analysis and representation
             ...},
   Key = {fds320234}
}

@article{fds318339,
   Author = {Bui, HM and Heap, WP and Turnage-Butterbaugh, CL},
   Title = {GAPS BETWEEN ZEROS OF DEDEKIND ZETA-FUNCTIONS OF QUADRATIC
             NUMBER FIELDS. II},
   Journal = {Quarterly Journal of Mathematics},
   Volume = {67},
   Number = {3},
   Pages = {467-482},
   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 Turnage-Butterbaugh,
             C},
   Title = {From Quantum Systems to L-Functions: Pair Correlation
             Statistics and Beyond},
   Pages = {123-171},
   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 Turnage-Butterbaugh, 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 Turnage-Butterbaugh, 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 Turnage-Butterbaugh, CL and Winsor, K},
   Title = {Gaps between zeros of GL(2) L-functions},
   Journal = {Journal of Mathematical Analysis and Applications},
   Volume = {429},
   Number = {1},
   Pages = {204-232},
   Year = {2015},
   Month = {January},
   ISSN = {0022-247X},
   url = {http://dx.doi.org/10.1016/j.jmaa.2015.04.007},
   Abstract = {© 2015 Elsevier Inc.Let L(s, f) be an L-function associated
             to a primitive (holomorphic or Maass) cusp form f on GL(2)
             over Q. Combining mean-value 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 L-function 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. Turnage-Butterbaugh 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 Turnage-Butterbaugh,
             CL},
   Title = {Consecutive primes in tuples},
   Journal = {Acta Arithmetica},
   Volume = {167},
   Number = {3},
   Pages = {261-266},
   Year = {2015},
   ISSN = {0065-1036},
   url = {http://dx.doi.org/10.4064/aa167-3-4},
   Doi = {10.4064/aa167-3-4},
   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 = {257-288},
   Year = {2015},
   Month = {April},
   url = {http://dx.doi.org/10.2140/apde.2015.8.257},
   Abstract = {We consider the one-dimensional focusing (cubic) nonlinear
             Schrödinger equation (NLS) in the semiclassical limit with
             exponentially decaying complex-valued 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 = {1098-0121},
   url = {http://dx.doi.org/10.1103/PhysRevB.91.134503},
   Abstract = {Bose-Einstein condensates of exciton-polaritons 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 zero-velocity case. The
             soliton's far-field 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 Gross-Pitaevskii (GP) model. Within its regime of
             validity, we give a derivation of a single-mode 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 = {126-132},
   Year = {2016},
   Month = {May},
   ISSN = {0927-7757},
   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 = {36-59},
   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 = {55-64},
   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 self-similar 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 = {1539-3755},
   url = {http://dx.doi.org/10.1103/physreve.92.043016},
   Abstract = {The surface structure of converging thin fluid films
             displays self-similar 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
             surface-tension-driven 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 = {1-3},
   Year = {2015},
   Month = {October},
   ISSN = {0022-0833},
   url = {http://dx.doi.org/10.1007/s10665-014-9760-z},
   Doi = {10.1007/s10665-014-9760-z},
   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 = {978-3-319-23041-2},
   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 = {194-210},
   Publisher = {Elsevier},
   Editor = {Bhattacharya, K},
   Year = {2016},
   Month = {April},
   ISSN = {0022-5096},
   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 2-D Synchrosqueezed
             Transforms: Application of time-frequency analysis to art
             investigation},
   Journal = {IEEE Signal Processing Magazine},
   Volume = {32},
   Number = {4},
   Pages = {55-63},
   Year = {2015},
   Month = {July},
   ISSN = {1053-5888},
   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 X-radiographs.
             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 X-ray absorption,
             making the weave pattern stand out in X-ray images of the
             finished painting. To characterize this pattern, it is
             customary to visually inspect small areas within the
             X-radiograph 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 computer-assisted 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 = {33-66},
   Year = {2015},
   Month = {July},
   ISSN = {1063-5203},
   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 = {614-631},
   Year = {2015},
   Month = {January},
   ISSN = {1540-3459},
   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 = {714-732},
   Year = {2015},
   Month = {January},
   ISSN = {1540-3459},
   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 = {1542-1572},
   Year = {2015},
   Month = {January},
   ISSN = {1540-3459},
   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 semi-Lagrangian time splitting spectral method
             for the semi-classical Schrödinger equation with vector
             potentials using NUFFT},
   Journal = {Applied Numerical Mathematics},
   Volume = {111},
   Pages = {144-159},
   Year = {2017},
   Month = {January},
   url = {http://dx.doi.org/10.1016/j.apnum.2016.08.015},
   Doi = {10.1016/j.apnum.2016.08.015},
   Key = {fds318345}
}

@article{fds299987,
   Author = {Z. Zhou and Z. Ma and Y. Zhang.},
   Title = {A semi-Lagrangian time splitting method for the
             semi-classical Schrodinger equation with vector potentials
             using NUFFT},
   Year = {2015},
   Key = {fds299987}
}

 

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fax: 919.660.2821

Mathematics Department
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Durham, NC 27708-0320