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Mathematics Faculty: Publications since January 2015

List all publications in the database.    :chronological  alphabetical  combined listing:
%% Abel, Michael   
@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{fds314402,
   Author = {A Yu and PK Agarwal and J Yang},
   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 = {PK Agarwal and K Fox and O Salzman},
   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 = {PK Agarwal and J Gao and LJ Guibas and H Kaplan and N Rubin and M
             Sharir},
   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 = {PK Agarwal and H Kaplan and N Rubin and M Sharir},
   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 = {W Zhang and PK Agarwal and S Mukherjee},
   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 = {PK Agarwal and T Mølhave and M Revsbæk and I Safa and Y Wang and J
             Yang},
   Title = {Maintaining Contour Trees of Dynamic Terrains},
   Journal = {Leibniz International Proceedings in Informatics,
             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 = {PK Agarwal and K Fox and A Nath and A Sidiropoulos and Y
             Wang},
   Title = {Computing the Gromov-Hausdorff distance for metric
             trees},
   Journal = {Lecture Notes in Computer Science (including subseries
             Lecture Notes in Artificial Intelligence and Lecture Notes
             in Bioinformatics)},
   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 = {PK Agarwal and R Sharathkumar},
   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}
}


%% Aspinwall, Paul S.   
@article{fds243265,
   Author = {PS Aspinwall},
   Title = {Exoflops in two dimensions},
   Journal = {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 = {PS Aspinwall and B Gaines},
   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 = {JT Beale},
   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 = {P Bendich and JS Marron and E Miller and A Pieloch and S
             Skwerer},
   Title = {Persistent homology analysis of brain artery
             trees},
   Journal = {The Annals of Applied Statistics},
   Volume = {10},
   Number = {1},
   Pages = {198-218},
   Year = {2016},
   Month = {March},
   ISSN = {1932-6157},
   url = {http://hdl.handle.net/10161/11157},
   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 = {P Bendich and E Gasparovic and J Harer and R Izmailov and L
             Ness},
   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},
   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 = {CJ Tralie and P Bendich},
   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{fds303060,
   Author = {LA Martinez-Medina and HL Bray and T Matos},
   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{fds303538,
   Author = {H Bray},
   Title = {A Family of Quasi-local Mass Functionals with Monotone
             Flows},
   Journal = {Proceedings of the 14th International Congress on
             Mathematical Physics},
   Editor = {JC Zambrini},
   Year = {2015},
   Month = {September},
   Key = {fds303538}
}

@article{fds287065,
   Author = {HL Bray and JL Jauregui},
   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 = {HL Bray and JL Jauregui},
   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 = {HL Bray and AR Parry},
   Title = {Modeling wave dark matter in dwarf spheroidal
             galaxies},
   Journal = {9TH BIENNIAL CONFERENCE ON CLASSICAL AND QUANTUM
             RELATIVISTIC DYNAMICS OF PARTICLES AND FIELDS (IARD
             2014)},
   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 = {WU Bajwa and MF Duarte and R Calderbank},
   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 = {A Harms and WU Bajwa and R Calderbank},
   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 = {M Nokleby and M Rodrigues and R Calderbank},
   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 = {L Wang and J Huang and X Yuan and K Krishnamurthy and J Greenberg and V
             Cevher, MRD Rodrigues and D Brady and R Calderbank and L
             Carin},
   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 = {A Harms and W Bajwa and R Calderbank},
   Title = {Efficient linear time-varying system identification using
             chirp waveforms},
   Journal = {Conference Record - 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{fds315774,
   Author = {I Daubechies and YG Wang and HT Wu},
   Title = {ConceFT: concentration of frequency and time via a
             multitapered synchrosqueezed transform.},
   Journal = {Philosophical transactions. Series A, Mathematical,
             physical, and engineering sciences},
   Volume = {374},
   Number = {2065},
   Pages = {20150193},
   Year = {2016},
   Month = {April},
   ISSN = {1364-503X},
   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.},
   Key = {fds315774}
}

@article{fds315775,
   Author = {NE Huang and I Daubechies and TY Hou},
   Title = {Adaptive data analysis: theory and applications.},
   Journal = {Philosophical transactions. Series A, Mathematical,
             physical, and engineering sciences},
   Volume = {374},
   Number = {2065},
   Pages = {20150207},
   Year = {2016},
   Month = {April},
   ISSN = {1364-503X},
   Key = {fds315775}
}

@article{fds287094,
   Author = {I Daubechies and R Saab},
   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 = {H Yang and J Lu and WP Brown and I Daubechies and L
             Ying},
   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 = {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},
   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 = {DM Boyer and J Puente and JT Gladman and C Glynn and S Mukherjee and GS
             Yapuncich and I Daubechies},
   Title = {A new fully automated approach for aligning and comparing
             shapes.},
   Journal = {Anatomical record (Hoboken, N.J. : 2007)},
   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 = {YG Wang and HT Wu and I Daubechies and Y Li and EH Estes and EZ
             Soliman},
   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 = {JA Perea and A Deckard and SB Haase and J Harer},
   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{fds268258,
   Author = {W Jiang and C Annavarapu and JE Dolbow and I Harari},
   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 = {J Dolbow and C Farhat and I Harari and A
             Lew},
   Year = {2015},
   Month = {November},
   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}
}

@article{fds291309,
   Author = {J Dolbow and C Farhat and I Harari and A Lew},
   Title = {Special Issue: Advances in Embedded Interface
             Methods},
   Journal = {International Journal for Numerical Methods in
             Engineering},
   Volume = {104},
   Number = {7},
   Pages = {469-471},
   Editor = {J Dolbow and C Farhat and I Harari and A
             Lew},
   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 = {W Jiang and JE Dolbow},
   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 = {R de Borst and C Farhat and J Fish and I Harari and P
             Letallec and D Perić},
   Year = {2015},
   Month = {April},
   ISSN = {0029-5981},
   url = {http://dx.doi.org/10.1002/nme.4718},
   Doi = {10.1002/nme.4718},
   Key = {fds268257}
}


%% Dunson, David B.   
@article{fds257830,
   Author = {D Li and AJ Wilcox and DB Dunson},
   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 = {EF Lock and KL Soldano and ME Garrett and H Cope and CA Markunas and H
             Fuchs, G Grant and DB Dunson and SG Gregory and AE
             Ashley-Koch},
   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 = {J Chabout and A Sarkar and DB Dunson and ED Jarvis},
   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 = {DC Kessler and PD Hoff and DB Dunson},
   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 = {DC Kessler and PD Hoff and DB Dunson},
   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 = {A Canale and DB Dunson},
   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 = {R Durrett and J Foo and K Leder},
   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 = {R Durrett and Y Zhang},
   Title = {Coexistence of grass, saplings and trees in the
             Staver–Levin forest model},
   Journal = {The Annals of Applied Probability},
   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 = {A Talkington and R Durrett},
   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 = {MD Ryser and ER Myers and R Durrett},
   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},
   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 = {R Durrett and S Moseley},
   Title = {Spatial Moran models I. Stochastic tunneling in the neutral
             case},
   Journal = {The Annals of Applied Probability},
   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{fds311851,
   Author = {G Oliveira},
   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},
   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 = {JR Getz and J Klassen},
   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 = {JR Getz and H Hahn},
   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{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 = {JR Getz and H Hahn},
   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 = {D Arapura and A Dimca and R Hain},
   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{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}
}

@article{fds287214,
   Author = {R Hain},
   Title = {Genus 3 Mapping Class Groups are not Kähler},
   Journal = {Journal of Topology},
   Volume = {8},
   Number = {1},
   Pages = {213-246},
   Publisher = {Oxford University Press},
   Year = {2015},
   ISSN = {1753-8416},
   url = {http://arxiv.org/abs/1305.2052},
   Key = {fds287214}
}


%% Harer, John   
@article{fds243563,
   Author = {JA Perea and A Deckard and SB Haase and J Harer},
   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{fds300012,
   Author = {G.J. Herschlag and S. Mitran and G. Lin},
   Title = {A consistent hierarchy of generalized kinetic equation
             approximations to the chemical master equation applied to
             surface catalysis},
   Journal = {J. Chem Phys},
   Volume = {142},
   Pages = {234703},
   Year = {2015},
   url = {http://arxiv.org/abs/1411.3696},
   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 di↵erential
             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 pre-
             dicting 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 e},
   Key = {fds300012}
}

@article{fds300011,
   Author = {G.J. Herschlag and J.-G. Liu and A.T. Layton},
   Title = {An exact solution for stokes flow in a channel with
             arbitrarily large wall permeability},
   Journal = {SIAM J. Appl. Math.},
   Volume = {75},
   Pages = {2246-2267},
   Year = {2015},
   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.},
   Key = {fds300011}
}

@article{fds300013,
   Author = {G.J. Herschlag and J.-G. Liu and A.T. Layton},
   Title = {Optimal reservoir conditions for fluid extraction through
             permeable walls in the viscous limit},
   Journal = {Phys. Flu.},
   Year = {2015},
   url = {http://arxiv.org/abs/1511.01469},
   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 = {fds300013}
}


%% 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 = {D Kraines and V Kraines},
   Title = {The threshold of cooperation among adaptive agents: Pavlov
             and the stag hunt},
   Journal = {Lecture Notes in Computer Science (including subseries
             Lecture Notes in Artificial Intelligence and Lecture Notes
             in Bioinformatics)},
   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{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{fds311144,
   Author = {Luke Xie and Anita Layton and Nian Wang and Peder Larson and Jeff Zhang and Vivian Lee and Chunlei Liu and G. Allan Johnson},
   Title = {Dynamic contrast-enhanced quantitative susceptibility
             mapping at ultrashort echo time for evaluating renal
             function},
   Journal = {Am J Physiol Renal Physiol},
   Volume = {310},
   Number = {F174-F182},
   Year = {2016},
   Key = {fds311144}
}

@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{fds300274,
   Author = {AT Layton and A Edwards},
   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 = {H Nganguia and Y-N Young and AT Layton and W-F Hu and M-C
             Lai},
   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{fds300276,
   Author = {I Sgouralis and AT Layton},
   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 = {AT Layton and V Vallon and A Edwards},
   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 = {AT Layton},
   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 = {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},
   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 = {B Fields and K Page},
   Title = {Preface},
   Journal = {scopus},
   Volume = {2015-June},
   Year = {2015},
   Month = {January},
   ISBN = {9781450335638},
   Key = {fds299957}
}

@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 = {L Li and SE Spagnolie},
   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{fds315797,
   Author = {G Herschlag and J-G Liu and AT Layton},
   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 = {J-G Liu and J Wang},
   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{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 = {Y Xue and C Wang and J-G Liu},
   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{fds300222,
   Author = {A Chertock and J-G Liu and T Pendleton},
   Title = {Elastic collisions among peakon solutions for the
             Camassa–Holm equation},
   Journal = {Applied Numerical Mathematics},
   Volume = {93},
   Pages = {30-46},
   Year = {2015},
   Month = {July},
   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{fds300223,
   Author = {P Degond and A Frouvelle and J-G Liu},
   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 = {April},
   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{fds246843,
   Author = {J Lu and JG Liu and D Margetis},
   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{fds313338,
   Author = {G Herschlag and J-G Liu and AT Layton},
   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{fds300226,
   Author = {J.-G. Liu and R.L. Pego},
   Title = {On generating functions of Hausdorff moment
             sequences},
   Journal = {Trans. Amer. Math. Soc.},
   Year = {2015},
   Key = {fds300226}
}

@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}
}

@article{fds300228,
   Author = {J.-G. Liu and Y. Zhang},
   Title = {Convergence of diffusion-drift many particle systems in
             probability under a Sobolev norm},
   Series = {Proceedings of Particle Systems and Partial Differential
             Equations - III},
   Publisher = {Springer},
   Year = {2015},
   Key = {fds300228}
}


%% Lu, Jianfeng   
@article{fds311746,
   Author = {J. Lu and J Lu and B Wirth and H Yang},
   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 = {fds311746}
}

@article{fds311426,
   Author = {Bruno Cornelis and Haizhao Yang and Alex Goodfriend and Noelle Ocon and Jianfeng Lu and Ingrid Daubechies},
   Title = {Removal of canvas patterns in digital acquisitions of
             paintings},
   Year = {2016},
   Key = {fds311426}
}

@article{fds311425,
   Author = {J. Lu and Zhennan Zhou},
   Title = {Frozen Gaussian approximation with surface hopping for mixed
             quantum-classical dynamics: A mathematical justification of
             surface hopping algorithms},
   Year = {2016},
   url = {http://arxiv.org/abs/1602.06459},
   Key = {fds311425}
}

@article{fds243728,
   Author = {J Lu and V Moroz and CB Muratov},
   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 = {C Li and J Lu and W Yang},
   Title = {Gentlest ascent dynamics for calculating first excited state
             and exploring energy landscape of Kohn-Sham density
             functionals.},
   Journal = {The 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 = {H Yang and J Lu and WP Brown and I Daubechies and L
             Ying},
   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 = {Q Li and J Lu and W Sun},
   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 = {J Lu and CB Mendl},
   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 = {J Lu and JG Liu and D Margetis},
   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 = {J Lu and J Nolen},
   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 = {J Liu and J Lu and X Zhou},
   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 = {H Yang and J Lu and L Ying},
   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{fds300196,
   Author = {J. Lu and Zhennan Zhou},
   Title = {Bloch dynamics with second order Berry phase
             correction},
   Year = {2015},
   url = {http://arxiv.org/abs/1512.07357},
   Key = {fds300196}
}

@article{fds291823,
   Author = {J. Lu and Lexing Ying},
   Title = {Fast algorithm for periodic density fitting for Bloch
             waves},
   Year = {2015},
   url = {http://arxiv.org/abs/1512.00432},
   Key = {fds291823}
}

@article{fds290434,
   Author = {J. Lu and Lin Lin},
   Title = {Sharp decay estimates of discretized Green's functions for
             Schrodinger type operators},
   Year = {2015},
   url = {http://arxiv.org/abs/1511.07957},
   Key = {fds290434}
}

@article{fds227247,
   Author = {J. Lu and Lexing Ying},
   Title = {Sparsifying preconditioner for soliton calculations},
   Year = {2015},
   url = {http://arxiv.org/abs/1511.03756},
   Key = {fds227247}
}

@article{fds311745,
   Author = {J. Lu and Qin Li and Weiran Sun},
   Title = {Half-space kinetic equations with general boundary
             conditions},
   Journal = {Math. Comp.},
   Year = {2015},
   url = {http://arxiv.org/abs/1509.03225},
   Key = {fds311745}
}

@article{fds227008,
   Author = {J. Lu and Ricardo Delgadillo and Xu Yang},
   Title = {Gauge-invariant frozen Gaussian approximation method for the
             Schrodinger equation with periodic potentials},
   Year = {2015},
   url = {http://arxiv.org/abs/1509.05552},
   Key = {fds227008}
}

@article{fds226991,
   Author = {J. Lu and Felix Otto},
   Title = {An isoperimetric problem with Coulomb repulsion and
             attraction to a background nucleus},
   Year = {2015},
   url = {http://arxiv.org/abs/1508.07172},
   Key = {fds226991}
}

@article{fds226414,
   Author = {J. Lu and Jingrun Chen},
   Title = {Analysis of the divide-and-conquer method for electronic
             structure calculations},
   Journal = {Math. Comp.},
   Year = {2015},
   url = {http://arxiv.org/abs/1411.0066},
   Key = {fds226414}
}

@article{fds226438,
   Author = {J. Lu and Ricardo Delgadillo and Xu Yang},
   Title = {Frozen Gaussian approximation for high frequency wave
             propagation in periodic media},
   Year = {2015},
   url = {http://arxiv.org/abs/1504.08051},
   Key = {fds226438}
}

@article{fds305741,
   Author = {J. Lu and Rongjie Lai},
   Title = {Localized density matrix minimization and linear scaling
             algorithms},
   Journal = {J. Comput. Phys.},
   Year = {2015},
   url = {http://arxiv.org/abs/1506.01610},
   Key = {fds305741}
}

@article{fds226346,
   Author = {J. Lu and Xiantao Li},
   Title = {Traction boundary conditions for molecular static
             simulations},
   Year = {2015},
   url = {http://arxiv.org/abs/1503.03555},
   Key = {fds226346}
}

@article{fds243729,
   Author = {J Lu and L Ying},
   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 = {R Lai and J Lu and S Osher},
   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 = {J Lu and JL Marzuola},
   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}
}


%% Maggioni, Mauro   
@article{fds314792,
   Author = {M Maggioni and S Minsker and N Strawn},
   Title = {Multiscale dictionary learning: Non-asymptotic bounds and
             robustness},
   Journal = {Journal of Machine Learning Research},
   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 = {M Maggioni},
   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 = {M Maggioni and S Minsker and N Strawn},
   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}
}

@article{fds300143,
   Author = {Yi (Grace) Wang and Guangliang Chen and Mauro Maggioni},
   Title = {High-dimensional data-modeling techniques for detection of
             chemical plumes and anomalies in hyperspectral images and
             movies},
   Journal = {IEEE JSTARS},
   Year = {2015},
   Key = {fds300143}
}

@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{fds300245,
   Author = {NE Glatt-Holtz and JC Mattingly and G Richards},
   Title = {On Unique Ergodicity in Nonlinear Stochastic Partial
             Differential Equations},
   Journal = {arxiv},
   Year = {2015},
   Month = {December},
   url = {http://arxiv.org/abs/1512.04126v1},
   Abstract = {We illustrate how the notion of asymptotic coupling provides
             a flexible and intuitive framework for proving the
             uniqueness of invariant measures for a variety of stochastic
             partial differential equations whose deterministic
             counterpart possesses a finite number of determining modes.
             Examples exhibiting parabolic and hyperbolic structure are
             studied in detail. In the later situation we also present a
             simple framework for establishing the existence of invariant
             measures when the usual approach relying on the
             Krylov-Bogolyubov procedure and compactness
             fails.},
   Key = {fds300245}
}

@article{fds243880,
   Author = {J.C. Mattingly and Y Bakhtin and T Hurth and JC Mattingly},
   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{fds300244,
   Author = {JE Johndrow and JC Mattingly and S Mukherjee and D
             Dunson},
   Title = {Approximations of Markov Chains and Bayesian
             Inference},
   Journal = {arxiv},
   Year = {2015},
   Month = {August},
   url = {http://arxiv.org/abs/1508.03387v2},
   Abstract = {The Markov Chain Monte Carlo method is the dominant paradigm
             for posterior computation in Bayesian analysis. It has long
             been common to control computation time by making
             approximations to the Markov transition kernel.
             Comparatively little attention has been paid to convergence
             and estimation error in these approximating Markov Chains.
             We propose a framework for assessing when to use
             approximations in MCMC algorithms, and how much error in the
             transition kernel should be tolerated to obtain optimal
             estimation performance with respect to a specified
             discrepancy measure and computational budget. The results
             require only ergodicity of the exact kernel and control of
             the kernel approximation accuracy. The theoretical framework
             is applied to approximations based on random subsets of
             data, low-rank approximations of Gaussian processes, and a
             novel approximating Markov chain for discrete mixture
             models.},
   Key = {fds300244}
}

@article{fds243882,
   Author = {DP Herzog and JC Mattingly},
   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{fds303549,
   Author = {S Luo and JC Mattingly},
   Title = {Scaling limits of a model for selection at two
             scales},
   Journal = {arxiv},
   Year = {2015},
   Month = {July},
   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}
}

@article{fds243883,
   Author = {S Huckemann and J Mattingly and E Miller and J
             Nolen},
   Title = {Sticky central limit theorems at isolated hyperbolic planar
             singularities},
   Journal = {Electronic Journal of Probability},
   Volume = {20},
   Year = {2015},
   Month = {January},
   url = {http://hdl.handle.net/10161/9516 Duke open
             access},
   Doi = {10.1214/EJP.v20-3887},
   Key = {fds243883}
}

@article{fds243884,
   Author = {DP Herzog and JC Mattingly},
   Title = {Noise-Induced Stabilization of Planar Flows
             II},
   Journal = {Electronic Journal of Probability},
   Volume = {20},
   Year = {2015},
   Month = {January},
   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{fds243881,
   Author = {SD Lawley and JC Mattingly and MC Reed},
   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}
}


%% 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{fds303556,
   Author = {P Bendich and JS Marron and E Miller and A Pieloch and S
             Skwerer},
   Title = {Persistent homology analysis of brain artery
             trees},
   Journal = {Annals of Applied Statistics},
   Pages = {19 pages},
   Year = {2015},
   Month = {December},
   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 = {E Miller},
   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 = {E Miller and M Owen and JS Provan},
   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{fds243886,
   Author = {S Huckemann and J Mattingly and E Miller and J
             Nolen},
   Title = {Sticky central limit theorems at isolated hyperbolic planar
             singularities},
   Journal = {Electronic Journal of Probability},
   Volume = {20},
   Year = {2015},
   Month = {January},
   url = {http://hdl.handle.net/10161/9516 Duke open
             access},
   Doi = {10.1214/EJP.v20-3887},
   Key = {fds243886}
}

@article{fds243885,
   Author = {C Berkesch Zamaere and S Griffeth and E Miller},
   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}
}


%% Motta, Francis C.   
@article{fds300018,
   Author = {F.C. Motta and D.A. Pearson and R.M. Bradley and P.D. Shipman},
   Title = {Producing nanodot arrays with improved hexagonal order by
             patterning surfaces before ion sputtering},
   Journal = {Physical Review E},
   Volume = {92},
   Number = {6},
   Year = {2015},
   Month = {December},
   url = {http://http://dx.doi.org/10.1103/PhysRevE.92.062401},
   Key = {fds300018}
}

@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{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{fds300019,
   Author = {F.C. Motta and B.D. Springer and P.D. Shipman},
   Title = {Optimally topologically transitive orbits in discrete
             dynamical systems},
   Journal = {The American Mathematical Monthly},
   Year = {2015},
   Month = {July},
   Key = {fds300019}
}

@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 = {R Lipshitz and L Ng and S Sarkar},
   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 = {T Ekholm and L Ng},
   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{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 = {J Nolen and J-M Roquejoffre and L Ryzhik},
   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 = {J Lu and J Nolen},
   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{fds287343,
   Author = {S Huckemann and J Mattingly and E Miller and J
             Nolen},
   Title = {Sticky central limit theorems at isolated hyperbolic planar
             singularities},
   Journal = {Electronic Journal of Probability},
   Volume = {20},
   Year = {2015},
   Month = {January},
   url = {http://hdl.handle.net/10161/9516},
   Doi = {10.1214/EJP.v20-3887},
   Key = {fds287343}
}

@article{fds290937,
   Author = {S Bhamidi and J Hannig and CY Lee and J Nolen},
   Title = {The importance sampling technique for understanding rare
             events in Erdős–Rényi random graphs},
   Journal = {Electronic Journal of Probability},
   Volume = {20},
   Year = {2015},
   Month = {January},
   url = {http://dx.doi.org/10.1214/EJP.v20-2696},
   Doi = {10.1214/EJP.v20-2696},
   Key = {fds290937}
}

@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{fds226709,
   Author = {A. Gloria and J. Nolen},
   Title = {A quantitative central limit theorem for the effective
             conductance on the discrete torus},
   Journal = {Communications on Pure and Applied Mathematics},
   Year = {2015},
   url = {http://arxiv.org/abs/1410.5734},
   Doi = {10.1002/cpa.21614},
   Key = {fds226709}
}

@article{fds291822,
   Author = {J. Nolen},
   Title = {Normal approximation for the net flux through a random
             conductor},
   Journal = {Stochastic Partial Differential Equations},
   Year = {2015},
   url = {http://arxiv.org/abs/1406.2186},
   Doi = {10.1007/s40072-015-0068-4},
   Key = {fds291822}
}

@article{fds226268,
   Author = {J.-C. Mourrat and J. Nolen},
   Title = {Scaling limit of the corrector in stochastic
             homogenization},
   Year = {2015},
   url = {http://arxiv.org/abs/1502.07440},
   Key = {fds226268}
}


%% 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}
}


%% Pierce, Lillian B.   
@article{fds302459,
   Author = {J Bober and E Carneiro and K Hughes and D Kosz and LB
             Pierce},
   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 = {DR Heath-Brown and LB Pierce},
   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 = {DR Morrison and M Ronen Plesser},
   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 = {M Bertolini and MR Plesser},
   Title = {Worldsheet instantons and (0,2) linear models},
   Journal = {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}
}


%% Reed, Michael C.   
@article{fds290938,
   Author = {MC Reed},
   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{fds244008,
   Author = {LM Bilinsky and MC Reed and HF Nijhout},
   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 = {HF Nijhout and JA Best and MC Reed},
   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 = {SD Lawley and JC Mattingly and MC Reed},
   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}
}

@article{fds290939,
   Author = {MC Reed and MV Gamble and MN Hall and HF Nijhout},
   Title = {Mathematical analysis of the regulation of competing
             methyltransferases.},
   Journal = {BMC systems biology},
   Volume = {9},
   Pages = {69},
   Year = {2015},
   Month = {January},
   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}
}


%% Robles, Colleen M   
@article{fds292860,
   Author = {Colleen Robles},
   Title = {Characteristic cohomology of the infinitesimal period
             relation},
   Journal = {Asian J. Math.},
   Year = {2015},
   url = {http://arxiv.org/abs/1310.8154},
   Key = {fds292860}
}

@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 = {MD Ryser and K McGoff and DP Herzog and DJ Sivakoff and ER
             Myers},
   Title = {Impact of coverage-dependent marginal costs on optimal HPV
             vaccination strategies.},
   Journal = {Epidemics},
   Volume = {11},
   Pages = {32-47},
   Year = {2015},
   Month = {June},
   ISSN = {1755-4365},
   url = {http://hdl.handle.net/10161/9500},
   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}
}


%% Stern, Mark A.   
@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 = {B Charbonneau and M Stern},
   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{fds299981,
   Author = {O. Barrett and F. W. K. Firk and S. J. Miller and C.
             Turnage-Butterbaugh},
   Title = {From Quantum Systems to L-Functions: Pair Correlation
             Statistics and Beyond},
   Booktitle = {Open Problems in Mathematics},
   Publisher = {Springer-Verlag},
   Editor = {John Nash Jr. and Michael Th. Rassias},
   Year = {2015},
   url = {http://arxiv.org/abs/1505.07481},
   Key = {fds299981}
}

@book{fds299983,
   Author = {X. Edelsbrunner and K. Huan and B. Mackall and J. Powell and C.
             Turnage-Butterbaugh and M. Weinstein},
   Title = {Benfordness of the Cauchy Distribution and
             Generalizations},
   Booktitle = {Theory and Applications of Benford's Law},
   Publisher = {Princeton University Press},
   Editor = {S. J. Miller},
   Year = {2015},
   Key = {fds299983}
}

@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{fds302477,
   Author = {O Barrett and B McDonald and SJ Miller and P Ryan and CL
             Turnage-Butterbaugh and K Winsor},
   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},
   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{fds302479,
   Author = {WD Banks and T Freiberg and CL Turnage-Butterbaugh},
   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 = {S Komineas and SP Shipman and S Venakides},
   Title = {Continuous and discontinuous dark solitons in polariton
             condensates},
   Journal = {Physical Review B},
   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{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{fds311993,
   Author = {L.B. Smolka and C.K. McLaughlin and T.P. Witelski},
   Title = {Oil capture from a water surface by a falling
             sphere},
   Journal = {Colloids and Surfaces A},
   Volume = {497},
   Pages = {126-132},
   Year = {2016},
   Key = {fds311993}
}

@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 = {JA Dijksman and S Mukhopadhyay and C Gaebler and TP Witelski and RP
             Behringer},
   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 = {TP Witelski},
   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{fds315394,
   Author = {Y Li and H Yang},
   Title = {Interpolative Butterfly Factorization},
   Year = {2016},
   Month = {May},
   url = {http://arxiv.org/abs/1605.03616},
   Key = {fds315394}
}

@article{fds303562,
   Author = {J Lu and B Wirth and H Yang},
   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},
   Doi = {10.1016/j.jmps.2016.01.002},
   Key = {fds303562}
}

@article{fds312767,
   Author = {J Lu and H Yang},
   Title = {Preconditioning Orbital Minimization Method for Planewave
             Discretization},
   Year = {2016},
   Month = {March},
   url = {http://hdl.handle.net/10161/11833 Duke open
             access},
   Key = {fds312767}
}

@article{fds311606,
   Author = {B Cornelis and H Yang and A Goodfriend and N Ocon and J Lu and I
             Daubechies},
   Title = {Removal of Canvas Patterns in Digital Acquisitions of
             Paintings},
   Journal = {IEEE Transactions on Image Processing},
   Publisher = {Institute of Electrical and Electronics Engineers
             (IEEE)},
   Year = {2016},
   Month = {February},
   ISSN = {1941-0042},
   url = {http://hdl.handle.net/10161/11650 Duke open
             access},
   Key = {fds311606}
}

@article{fds311604,
   Author = {H Yang},
   Title = {Robustness Analysis of Synchrosqueezed Transforms},
   Journal = {Applied and Computational Harmonic Analysis},
   Publisher = {Elsevier},
   Year = {2016},
   Month = {February},
   ISSN = {1096-603X},
   url = {http://hdl.handle.net/10161/11652 Duke open
             access},
   Key = {fds311604}
}

@article{fds311605,
   Author = {Y Li and H Yang and L Ying},
   Title = {Multidimensional Butterfly Factorization},
   Journal = {Applied and Computational Harmonic Analysis},
   Publisher = {Elsevier},
   Year = {2016},
   Month = {February},
   ISSN = {1096-603X},
   url = {http://hdl.handle.net/10161/11651 Duke open
             access},
   Key = {fds311605}
}

@article{fds226959,
   Author = {H Yang and J Lu and WP Brown and I Daubechies and L
             Ying},
   Title = {Quantitative Canvas Weave Analysis Using 2-D Synchrosqueezed
             Transforms: Application of time-frequency analysis to art
             investigation},
   Journal = {Signal Processing Magazine, IEEE},
   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 = {H Yang},
   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 = {H Yang},
   Title = {Oscillatory data analysis and fast algorithms for integral
             operators},
   Journal = {manual},
   Editor = {L Ying and E Candes and L Ryzhik},
   Year = {2015},
   Month = {June},
   url = {http://hdl.handle.net/10161/11660 Duke open
             access},
   Key = {fds226958}
}

@article{fds226961,
   Author = {Y Li and H Yang and L Ying},
   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 = {Y Li and H Yang and ER Martin and KL Ho and L Ying},
   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 = {H Yang and J Lu and L Ying},
   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{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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