Mathematics Faculty: Publications since January 2015
List all publications in the database. :chronological alphabetical combined listing:
%% Abel, Michael
@article{fds300044,
Author = {M. Abel and M. Hogancamp},
Title = {Stable homology of torus links via categorified Young
symmetrizers II: onecolumn partitions},
Year = {2015},
Month = {October},
url = {http://arxiv.org/abs/1510.05330},
Key = {fds300044}
}
@article{fds300045,
Author = {M. Abel and L. Rozansky},
Title = {Virtual crossings and a filtration of the triply graded
homology of a link diagram},
Year = {2015},
Month = {February},
url = {http://arxiv.org/abs/1410.5892},
Key = {fds300045}
}
%% Addington, Nicolas
@article{fds226937,
Author = {N. Addington and W. Donovan and C. Meachan},
Title = {Mukai flops and Ptwists},
Year = {2015},
Month = {July},
url = {http://arxiv.org/abs/1507.02595},
Key = {fds226937}
}
@article{fds226938,
Author = {N. Addington and W. Donovan and C. Meachan},
Title = {Moduli spaces of torsion sheaves on K3 surfaces and derived
equivalences},
Year = {2015},
Month = {July},
url = {http://arxiv.org/abs/1507.02597},
Key = {fds226938}
}
@article{fds226939,
Author = {N. Addington and W. Donovan and E. Segal},
Title = {The PfaffianGrassmannian equivalence revisited},
Journal = {Alg. Geom.},
Volume = {2},
Number = {3},
Pages = {332364},
Year = {2015},
url = {http://arxiv.org/abs/1401.3661},
Key = {fds226939}
}
%% Agarwal, Pankaj K.
@article{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 = {905929},
Year = {2015},
Month = {December},
ISSN = {01795376},
url = {http://dx.doi.org/10.1007/s004540159730x},
Doi = {10.1007/s004540159730x},
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 = {871904},
Year = {2015},
Month = {December},
ISSN = {01795376},
url = {http://dx.doi.org/10.1007/s0045401597293},
Doi = {10.1007/s0045401597293},
Key = {fds235355}
}
@article{fds235346,
Author = {PK Agarwal and R Sharathkumar},
Title = {Streaming Algorithms for Extent Problems in High
Dimensions},
Journal = {Algorithmica},
Volume = {72},
Number = {1},
Pages = {8398},
Year = {2015},
ISSN = {01784617},
url = {http://dx.doi.org/10.1007/s0045301398464},
Abstract = {© 2013, Springer Science+Business Media New York.We present
(singlepass) streaming algorithms for maintaining extent
measures of a stream S of n points in $\mathbb{R} ^{d}$. We
focus on designing streaming algorithms whose working space
is polynomial in d (poly(d)) and sublinear in n. For the
problems of computing diameter, width and minimum enclosing
ball of S, we obtain lower bounds on the worstcase
approximation ratio of any streaming algorithm that uses
poly(d) space. On the positive side, we introduce the notion
of blurred ball cover and use it for answering approximate
farthestpoint queries and maintaining approximate minimum
enclosing ball and diameter of S. We describe a streaming
algorithm for maintaining a blurred ball cover whose working
space is linear in d and independent of n.},
Doi = {10.1007/s0045301398464},
Key = {fds235346}
}
%% Allman, Justin
@article{fds300039,
Author = {J. Allman},
Title = {An iterated residue perspective on stable Grothendieck
polynomials},
Year = {2015},
url = {http://arxiv.org/abs/1408.1911v2},
Abstract = {http://arxiv.org/abs/1408.1911v2},
Key = {fds300039}
}
%% 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 = {115},
Year = {2015},
Month = {February},
ISSN = {03930440},
url = {http://dx.doi.org/10.1016/j.geomphys.2014.09.012},
Doi = {10.1016/j.geomphys.2014.09.012},
Key = {fds243266}
}
%% Basak, Anirban
@article{fds300033,
Author = {A. Basak and A. Dembo},
Title = {Ferromagnetic Ising measures on large locally tree like
graphs},
Journal = {The Annals of Probability},
Year = {2015},
Month = {October},
url = {http://arxiv.org/abs/1205.4749},
Key = {fds300033}
}
@article{fds300030,
Author = {A. Basak and S. Mukherjee},
Title = {Universality of meanfield for the Potts
model},
Year = {2015},
Month = {August},
url = {http://arxiv.org/abs/1508.03949},
Key = {fds300030}
}
@article{fds300031,
Author = {A. Basak and M. Rudelson},
Title = {Invertibility of sparse nonHermitian matrices},
Year = {2015},
Month = {July},
url = {http://arxiv.org/abs/1507.03525},
Key = {fds300031}
}
@article{fds300034,
Author = {A. Basak and A. Bose and S. S. Mukherjee},
Title = {Limiting spectral distribution of a class of Hankel type
random matrices},
Journal = {Random Matrices: Theory and Applications},
Year = {2015},
Month = {April},
url = {http://arxiv.org/abs/1408.0874},
Key = {fds300034}
}
%% Beale, J. Thomas
@article{fds226858,
Author = {J. t. Beale and W. YIng and J. R. Wilson},
Title = {A simple method for computing singular or nearly singular
integrals on closed surfaces},
Journal = {Commun. Comput. Phys.},
Year = {2015},
Month = {August},
url = {http://www.math.duke.edu/faculty/beale/papers/bywcicp.pdf},
Key = {fds226858}
}
@article{fds243316,
Author = {JT Beale},
Title = {Uniform Error Estimates for NavierStokes Flow with an
Exact Moving Boundary Using the Immersed Interface
Method},
Journal = {SIAM Journal on Numerical Analysis},
Volume = {53},
Number = {4},
Pages = {20972111},
Year = {2015},
Month = {January},
ISSN = {00361429},
url = {http://www.math.duke.edu/faculty/beale/papers/nseiim.pdf},
Doi = {10.1137/151003441},
Key = {fds243316}
}
%% Bendich, Paul L
@article{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{fds226872,
Author = {Paul Bendich and J.S. Marron and Ezra Miller and Alex Pieloch and Sean Skwerer},
Title = {Persistent Homology Analysis of Brain Artery
Trees},
Journal = {Annals of Applied Statistics},
Year = {2015},
Abstract = {New representations of treestructured data objects, using
ideas from topological data analysis, enable improved
statistical analyses of a population of brain artery trees.
A number of representations of each data tree arise from
persistence diagrams that quantify branching and looping of
vessels at multiple scales. Novel approaches to the
statistical analysis, through various summaries of the
persistence diagrams, lead to heightened correlations with
covariates such as age and sex, relative to earlier analyses
of this data set. The correlation with age continues to be
significant even after controlling for correlations from
earlier significant summaries},
Key = {fds226872}
}
@article{fds226628,
Author = {Liz Munch and Paul Bendich and Kate Turner and Sayan Mukherjee and Jonathan Mattingly and John Harer},
Title = {Probabalistic Frechet Means and Statistics on
Vineyards},
Journal = {Electronic Journal of Statistics},
Volume = {9},
Pages = {11731204},
Year = {2015},
url = {http://arxiv.org/abs/1307.6530},
Abstract = {In order to use persistence diagrams as a true statistical
tool, it would be very useful to have a good notion of mean
and variance for a set of diagrams. In [21], Mileyko and his
collaborators made the rst study of the properties of the
Frechet mean in (Dp;Wp), the space of persistence diagrams
equipped with the pth Wasserstein metric. In particular,
they showed that the Frechet mean of a nite set of diagrams
always exists, but is not necessarily unique. As an
unfortunate consequence, one sees that the means of a
continuouslyvarying set of diagrams do not themselves vary
continuously, which presents obvious problems when trying to
extend the Frechet mean de nition to the realm of
vineyards. We x this problem by altering the original de
nition of Frechet mean so that it now becomes a probability
measure on the set of persistence diagrams; in a nutshell,
the mean of a set of diagrams will be a weighted sum of
atomic measures, where each atom is itself the (Frechet
mean) persistence diagram of a perturbation of the input
diagrams. We show that this new de nition de nes a (Holder)
continuous map, for each k, from (Dp)k ! P(Dp), and we
present several examples to show how it may become a useful
statistic on vineyards.},
Key = {fds226628}
}
@article{fds227232,
Author = {Christopher J Tralie and Paul Bendich},
Title = {Cover Song Identification with Timbral Shape},
Journal = {Proceedings of the 16th International Society for Music
Information Retrieval},
Pages = {3844},
Year = {2015},
url = {http://arxiv.org/abs/1507.05143},
Abstract = {We introduce a novel low level feature for identifying cover
songs which quantifies the relative changes in the smoothed
frequency spectrum of a song. Our key insight is that a
sliding window representation of a chunk of audio can be
viewed as a timeordered point cloud in high dimensions. For
corresponding chunks of audio between different versions of
the same song, these point clouds are approximately rotated,
translated, and scaled copies of each other. If we treat
MFCC embeddings as point clouds and cast the problem as a
relative shape sequence, we are able to correctly identify
42/80 cover songs in the “Covers 80” dataset. By
contrast, all other work to date on cover songs exclusively
relies on matching note sequences from Chroma derived
features.},
Key = {fds227232}
}
@article{fds226627,
Author = {David Rouse and Adam Watkins and David Porter and John Harer and Paul
Bendich, Nate Strawn and Elizabeth Munch and Jonathan DeSena and Jesse
Clarke, Jeff Gilbert and Sang Chin and Andrew
Newman},
Title = {FeatureAided Multiple Hypothesis Tracking Using Topological
and Statistical Behavior Classifiers},
Journal = {SPIE DSS 2015},
Volume = {9474},
Year = {2015},
Key = {fds226627}
}
@article{fds227130,
Author = {Paul Bendich and Ellen Gasparovic and John Harer and Rauf Ismailov and Linda Ness},
Title = {MultiScale Local Shape Analysis and Feature Selection in
Machine Learning Applications},
Journal = {Proceedings of the 2015 International Joint Conference on
Neural Networks},
Pages = {18},
Year = {2015},
url = {http://arxiv.org/abs/1410.3169},
Key = {fds227130}
}
%% Bertozzi, Andrea L
@booklet{Greer04a,
Author = {J. B. Greer and A. L. Bertozzi},
Title = {H1 solutions of a class of fourth order nonlinear equations
for image processing},
Journal = {Discrete And Continuous Dynamical Systems},
Volume = {10},
Number = {12},
Pages = {349  366},
Year = {2004},
Key = {Greer04a}
}
%% Bobrowski, Omer
@article{fds227054,
Author = {O. Bobrowski and S. Weinberger},
Title = {On the Vanishing of Homology in Random Čech
Complexes},
Year = {2015},
url = {http://arxiv.org/abs/1507.06945},
Key = {fds227054}
}
@article{fds227056,
Author = {O. Bobrowski and M. Kahle and P. Skraba},
Title = {Maximally Persistent Cycles in Random Geometric
Complexes},
Year = {2015},
url = {http://arxiv.org/abs/1509:04347},
Key = {fds227056}
}
@article{fds225071,
Author = {O. Bobrowski and S. Mukherjee},
Title = {The Topology of Probability Distributions on
Manifolds},
Journal = {Probability Theory and Related Fields},
Volume = {161},
Number = {34},
Pages = {651686},
Year = {2015},
url = {http://dx.doi.org/10.1007/s004400140556x},
Doi = {10.1007/s004400140556x},
Key = {fds225071}
}
@article{fds227050,
Author = {O. Bobrowski and S. Mukherjee and J. S. Taylor},
Title = {Topological Consistency via Kernel Estimation},
Journal = {Bernoulli},
Year = {2015},
url = {http://arxiv.org/abs/1407.5272},
Key = {fds227050}
}
%% Braley, Emily L.
@article{fds299955,
Author = {Lindsay D. Waldrop and Stephen C. Adolph and Cecilia G. Diniz
Behn and Emily Braley and Joshua A. Drew and Robert J. Full and Louis J.
Gross and John A. Jungck and Brynja Kohler and Jennifer C. Prairie and Blerta Shtylla and Laura A. Miller},
Title = {Using Active Learning to Teach Concepts and Methods in
Quantitative Biology},
Journal = {Integrative and Comparative Biology},
Volume = {55},
Number = {5},
Pages = {933948},
Publisher = {Oxford University Press},
Year = {2015},
url = {http://icb.oxfordjournals.org/content/55/5/933.full.pdf?keytype=ref&ijkey=nSisiIyjS2Dqt85},
Abstract = {This article provides a summary of the ideas discussed at
the 2015 Annual Meeting of the Society for Integrative and
Comparative Biology societywide symposium on Leading
Students and Faculty to Quantitative Biology through Active
Learning. It also includes a brief review of the recent
advancements in incorporating active learning approaches
into quantitative biology classrooms. We begin with an
overview of recent literature that shows that active
learning can improve students’ outcomes in Science,
Technology, Engineering and Math Education disciplines. We
then discuss how this approach can be particularly useful
when teaching topics in quantitative biology. Next, we
describe some of the recent initiatives to develop handson
activities in quantitative biology at both the graduate and
the undergraduate levels. Throughout the article we provide
resources for educators who wish to integrate active
learning and technology into their classrooms.},
Doi = {10.1093/icb/icv097},
Key = {fds299955}
}
%% Bray, Hubert
@article{fds303060,
Author = {LA MartinezMedina 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 = {025025},
Year = {2015},
Month = {December},
url = {http://arxiv.org/abs/1505.07154},
Doi = {10.1088/14757516/2015/12/025},
Key = {fds303060}
}
@article{fds303538,
Author = {H Bray},
Title = {A Family of Quasilocal 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 = {561575},
Year = {2015},
Month = {June},
ISSN = {0003889X},
url = {http://www.springer.com//0/c8d239381b86496b96d95ff26f1061eb},
Doi = {10.1007/s0001301507670},
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 = {285307},
Year = {2015},
Month = {April},
ISSN = {00103616},
url = {http://arxiv.org/abs/1310.8638},
Doi = {10.1007/s0022001421622},
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 = {17426588},
url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000358144800001&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
Doi = {10.1088/17426596/615/1/012001},
Key = {fds287070}
}
%% Bryant, Robert
@article{fds300229,
Author = {R. Bryant},
Title = {On the convex PfaffDarboux Theorem of Ekeland and
Nirenberg},
Year = {2015},
Month = {December},
url = {http://arxiv.org/abs/1512.07100},
Abstract = {The classical PfaffDarboux Theorem, which provides local
`normal forms' for 1forms on manifolds, has applications in
the theory of certain economic models. However, the normal
forms needed in these models come with an additional
requirement of convexity, which is not provided by the
classical proofs of the PfaffDarboux Theorem. (The
appropriate notion of `convexity' is a feature of the
economic model. In the simplest case, when the economic
model is formulated in a domain in nspace, convexity has
its usual meaning. In 2002, Ekeland and Nirenberg were able
to characterize necessary and sufficient conditions for a
given 1form to admit a convex local normal form (and to
show that some earlier attempts at this characterization had
been unsuccessful). In this article, after providing some
necessary background, I prove a strengthened and generalized
convex PfaffDarboux Theorem, one that covers the case of a
Legendrian foliation in which the notion of convexity is
defined in terms of a torsionfree affine connection on the
underlying manifold. (The main result in Ekeland and
Nirenberg's paper concerns the case in which the affine
connection is flat.)},
Key = {fds300229}
}
@article{fds300153,
Author = {R. Bryant},
Title = {On the conformal volume of 2tori},
Year = {2015},
Month = {July},
url = {http://arxiv.org/abs/1507.01485},
Keywords = {conformal volume},
Abstract = {This preprint provides a proof of a 1985 conjecture of
Montiel and Ros about the conformal volume of
tori.},
Key = {fds300153}
}
%% Calderbank, Robert
@article{fds235746,
Author = {WU Bajwa and MF Duarte and R Calderbank},
Title = {Conditioning of Random Block Subdictionaries With
Applications to BlockSparse Recovery and
Regression},
Journal = {IEEE Transactions on Information Theory},
Volume = {61},
Number = {7},
Pages = {40604079},
Year = {2015},
Month = {July},
ISSN = {00189448},
url = {http://dx.doi.org/10.1109/TIT.2015.2429632},
Doi = {10.1109/TIT.2015.2429632},
Key = {fds235746}
}
@article{fds235747,
Author = {A Harms and WU Bajwa and R Calderbank},
Title = {Identification of Linear TimeVarying Systems Through
Waveform Diversity},
Journal = {IEEE Transactions on Signal Processing},
Volume = {63},
Number = {8},
Pages = {20702084},
Year = {2015},
Month = {April},
ISSN = {1053587X},
url = {http://dx.doi.org/10.1109/TSP.2015.2407319},
Doi = {10.1109/TSP.2015.2407319},
Key = {fds235747}
}
@article{fds235748,
Author = {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 = {21332147},
Year = {2015},
Month = {April},
ISSN = {00189448},
url = {http://dx.doi.org/10.1109/TIT.2015.2407368},
Doi = {10.1109/TIT.2015.2407368},
Key = {fds235748}
}
@article{fds290773,
Author = {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 = {19231954},
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 timevarying system identification using
chirp waveforms},
Journal = {Conference Record  Asilomar Conference on Signals, Systems
and Computers},
Volume = {2015April},
Pages = {854858},
Year = {2015},
Month = {January},
ISBN = {9781479982974},
ISSN = {10586393},
url = {http://dx.doi.org/10.1109/ACSSC.2014.7094572},
Abstract = {© 2014 IEEE. Linear, timevarying (LTV) systems are
operators composed of time shifts, frequency shifts, and
complex amplitude scalings that act on continuous
finiteenergy waveforms. This paper builds upon a novel,
resourceefficient method previously proposed by the authors
for identifying the parametric description of such systems
from the sampled response to linear frequency modulated
(LFM) waveforms. If the LTV operator is probed with a
sufficiently diverse set of LFM pulses, more LFM pulses than
reflectors, then the system can be identified with high
accuracy. The accuracy is shown to be proportional to the
uncertainty in the estimated frequencies and confirmed with
numerical experiments.},
Doi = {10.1109/ACSSC.2014.7094572},
Key = {fds235744}
}
%% Chen, Ying
@article{fds300046,
Author = {Y. Chen and J. Shen},
Title = {Efficient, adaptive energy stable schemes for the
incompressible CahnHilliard NavierStokes phasefield
models},
Journal = {JCP},
Year = {2015},
Key = {fds300046}
}
%% Cornelis, Bruno I.
@article{fds299979,
Author = {Gabor Fodor and Bruno Cornelis and Rujie Yin and Ann Dooms and Ingrid
Daubechies},
Title = {Cradle removal in Xray images of panel paintings},
Journal = {Image Processing On Line (IPOL)},
Year = {2015},
Month = {December},
Key = {fds299979}
}
@article{fds299977,
Author = {A. Pizurica and L. Platisa and T. Ruzic and B. Cornelis and A. Dooms and M.
Martens, H. Dubois and B. Devolder and M. De Mey and I.
Daubechies},
Title = {Digital Image Processing of The Ghent Altarpiece: Supporting
the painting's study and conservation treatment},
Journal = {IEEE Signal Processing Magazine},
Volume = {32},
Number = {4},
Pages = {112  122},
Publisher = {IEEE},
Year = {2015},
Month = {July},
ISSN = {10535888},
Abstract = {Hanging in the Saint Bavo Cathedral in Ghent, Belgium, is
The Ghent Altarpiece, also known as The Adoration of the
Mystic Lamb (see Figure 1). According to an inscription on
the outer frames, it was painted by brothers Hubert and Jan
van Eyck for Joos Vijd and?his wife Elisabeth Borluut in
1432. It is one of the most admired and influential
paintings in the history of art and has given rise to many
intriguing questions that have been puzzling art historians
to date [11]. Moreover, the material history of the panels
is very complicated. They were hidden, dismantled, moved
away, stolen, and recovered during riots, fires and wars.
The recovery of the panels by the U.S. Army in the Nazi
hoards deep in the Altaussee salt mines has particularly
marked memories. One panel was stolen in 1934 and never
recovered. Besides varying conservation conditions, the
panels underwent numerous restoration treatments and were
even partially painted over.},
Key = {fds299977}
}
%% Curry, Justin
@article{UNKNOWN,
Author = {Curry, JustinMichael},
Title = {Topological data analysis and cosheaves},
Journal = {Japan Journal of Industrial and Applied Mathematics},
Volume = {32},
Number = {2},
Pages = {333371},
Publisher = {Springer Japan},
Year = {2015},
ISSN = {09167005},
url = {http://dx.doi.org/10.1007/s1316001501739},
Keywords = {Topological data analysis; Persistent homology; Sheaves and
cosheaves; Barcodes; ominimal topology; 55U99; 46M20;
32S60; 16G20; 6207; 03C64},
Language = {English},
Doi = {10.1007/s1316001501739},
Key = {UNKNOWN}
}
@article{UNKNOWN,
Author = {Curry, Justin and Ghrist, Robert and Nanda,
Vidit},
Title = {Discrete Morse Theory for Computing Cellular Sheaf
Cohomology},
Journal = {Foundations of Computational Mathematics},
Pages = {123},
Publisher = {Springer US},
Year = {2015},
ISSN = {16153375},
url = {http://dx.doi.org/10.1007/s1020801592668},
Keywords = {Cellular sheaf cohomology; Discrete Morse theory; 5504;
55N25; 55N30},
Language = {English},
Doi = {10.1007/s1020801592668},
Key = {UNKNOWN}
}
%% Daubechies, Ingrid
@article{fds287094,
Author = {I Daubechies and R Saab},
Title = {A Deterministic Analysis of Decimation for SigmaDelta
Quantization of Bandlimited Functions},
Journal = {IEEE Signal Processing Letters},
Volume = {22},
Number = {11},
Pages = {20932096},
Year = {2015},
Month = {November},
ISSN = {10709908},
url = {http://dx.doi.org/10.1109/LSP.2015.2459758},
Doi = {10.1109/LSP.2015.2459758},
Key = {fds287094}
}
@article{fds287095,
Author = {H Yang and J Lu and WP Brown and I Daubechies and L
Ying},
Title = {Quantitative Canvas Weave Analysis Using 2D Synchrosqueezed
Transforms: Application of timefrequency analysis to art
investigation},
Journal = {IEEE Signal Processing Magazine},
Volume = {32},
Number = {4},
Pages = {5563},
Year = {2015},
Month = {July},
ISSN = {10535888},
url = {http://dx.doi.org/10.1109/MSP.2015.2406882},
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 = {112122},
Year = {2015},
Month = {July},
ISSN = {10535888},
url = {http://dx.doi.org/10.1109/MSP.2015.2411753},
Doi = {10.1109/MSP.2015.2411753},
Key = {fds287096}
}
@article{fds287098,
Author = {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 = {249276},
Year = {2015},
Month = {January},
ISSN = {19328486},
url = {http://dx.doi.org/10.1002/ar.23084},
Abstract = {Threedimensional geometric morphometric (3DGM) methods for
placing landmarks on digitized bones have become
increasingly sophisticated in the last 20 years, including
greater degrees of automation. One aspect shared by all 3DGM
methods is that the researcher must designate initial
landmarks. Thus, researcher interpretations of homology and
correspondence are required for and influence
representations of shape. We present an algorithm allowing
fully automatic placement of correspondence points on
samples of 3D digital models representing bones of different
individuals/species, which can then be input into standard
3DGM software and analyzed with dimension reduction
techniques. We test this algorithm against several samples,
primarily a dataset of 106 primate calcanei represented by
1,024 correspondence points per bone. Results of our
automated analysis of these samples are compared to a
published study using a traditional 3DGM approach with 27
landmarks on each bone. Data were analyzed with
morphologika(2.5) and PAST. Our analyses returned strong
correlations between principal component scores, similar
variance partitioning among components, and similarities
between the shape spaces generated by the automatic and
traditional methods. While cluster analyses of both
automatically generated and traditional datasets produced
broadly similar patterns, there were also differences.
Overall these results suggest to us that automatic
quantifications can lead to shape spaces that are as
meaningful as those based on observer landmarks, thereby
presenting potential to save time in data collection,
increase completeness of morphological quantification,
eliminate observer error, and allow comparisons of shape
diversity between different types of bones. We provide an R
package for implementing this analysis.},
Doi = {10.1002/ar.23084},
Key = {fds287098}
}
@article{fds287099,
Author = {YG Wang and HT Wu and I Daubechies and Y Li and EH Estes and EZ
Soliman},
Title = {Automated J wave detection from digital 12lead
electrocardiogram.},
Journal = {Journal of electrocardiology},
Volume = {48},
Number = {1},
Pages = {2128},
Year = {2015},
Month = {January},
ISSN = {00220736},
url = {http://dx.doi.org/10.1016/j.jelectrocard.2014.10.006},
Abstract = {In this report we provide a method for automated detection
of J wave, defined as a notch or slur in the descending
slope of the terminal positive wave of the QRS complex,
using signal processing and functional data analysis
techniques. Two different sets of ECG tracings were selected
from the EPICARE ECG core laboratory, Wake Forest School of
Medicine, Winston Salem, NC. The first set was a training
set comprised of 100 ECGs of which 50 ECGs had Jwave and
the other 50 did not. The second set was a test set (n=116
ECGs) in which the Jwave status (present/absent) was only
known by the ECG Center staff. All ECGs were recorded using
GE MAC 1200 (GE Marquette, Milwaukee, Wisconsin) at 10mm/mV
calibration, speed of 25mm/s and 500HZ sampling rate. All
ECGs were initially inspected visually for technical errors
and inadequate quality, and then automatically processed
with the GE Marquette 12SL program 2001 version (GE
Marquette, Milwaukee, WI). We excluded ECG tracings with
major abnormalities or rhythm disorder. Confirmation of the
presence or absence of a J wave was done visually by the ECG
Center staff and verified once again by three of the
coauthors. There was no disagreement in the identification
of the J wave state. The signal processing and functional
data analysis techniques applied to the ECGs were conducted
at Duke University and the University of Toronto. In the
training set, the automated detection had sensitivity of
100% and specificity of 94%. For the test set, sensitivity
was 89% and specificity was 86%. In conclusion, test results
of the automated method we developed show a good J wave
detection accuracy, suggesting possible utility of this
approach for defining and detection of other complex ECG
waveforms.},
Doi = {10.1016/j.jelectrocard.2014.10.006},
Key = {fds287099}
}
@article{fds300272,
Author = {A. Pizurica and L. Platisa and T. Ruzic and B. Cornelis and A. Dooms and M.
Martens, H. Dubois and B. Devolder and M. De Mey and I.
Daubechies},
Title = {Digital Image Processing of The Ghent Altarpiece: Supporting
the painting's study and conservation treatment},
Journal = {IEEE Signal Processing Magazine},
Volume = {32},
Pages = {112122},
Publisher = {IEEE},
Year = {2015},
Key = {fds300272}
}
%% Deckard, Anastasia C
@article{fds292888,
Author = {JA Perea and A Deckard and SB Haase and J Harer},
Title = {SW1PerS: Sliding windows and 1persistence scoring;
discovering periodicity in gene expression time series
data.},
Journal = {BMC bioinformatics},
Volume = {16},
Pages = {257},
Year = {2015},
Month = {January},
url = {http://dx.doi.org/10.1186/s1285901506456},
Abstract = {Identifying periodically expressed genes across different
processes (e.g. the cell and metabolic cycles, circadian
rhythms, etc) is a central problem in computational biology.
Biological time series may contain (multiple) unknown signal
shapes of systemic relevance, imperfections like noise,
damping, and trending, or limited sampling density. While
there exist methods for detecting periodicity, their design
biases (e.g. toward a specific signal shape) can limit their
applicability in one or more of these situations.We present
in this paper a novel method, SW1PerS, for quantifying
periodicity in time series in a shapeagnostic manner and
with resistance to damping. The measurement is performed
directly, without presupposing a particular pattern, by
evaluating the circularity of a highdimensional
representation of the signal. SW1PerS is compared to other
algorithms using synthetic data and performance is
quantified under varying noise models, noise levels,
sampling densities, and signal shapes. Results on biological
data are also analyzed and compared.On the task of
periodic/notperiodic classification, using synthetic data,
SW1PerS outperforms all other algorithms in the lownoise
regime. SW1PerS is shown to be the most shapeagnostic of
the evaluated methods, and the only one to consistently
classify damped signals as highly periodic. On biological
data, and for several experiments, the lists of top 10%
genes ranked with SW1PerS recover up to 67% of those
generated with other popular algorithms. Moreover, the list
of genes from data on the Yeast metabolic cycle which are
highlyranked only by SW1PerS, contains evidently noncosine
patterns (e.g. ECM33, CDC9, SAM1,2 and MSH6) with highly
periodic expression profiles. In data from the Yeast cell
cycle SW1PerS identifies genes not preferred by other
algorithms, hence not previously reported as periodic, but
found in other experiments such as the universal growth rate
response of Slavov. These genes are BOP3, CDC10, YIL108W,
YER034W, MLP1, PAC2 and RTT101.In biological systems with
low noise, i.e. where periodic signals with interesting
shapes are more likely to occur, SW1PerS can be used as a
powerful tool in exploratory analyses. Indeed, by having an
initial set of periodic genes with a rich variety of signal
types, pattern/shape information can be included in the
study of systems and the generation of hypotheses regarding
the structure of gene regulatory networks.},
Doi = {10.1186/s1285901506456},
Key = {fds292888}
}
%% Dolbow, John E.
@article{fds268258,
Author = {W Jiang and C Annavarapu and JE Dolbow and I Harari},
Title = {A robust Nitsche's formulation for interface problems with
splinebased finite elements},
Journal = {International Journal for Numerical Methods in
Engineering},
Volume = {104},
Number = {7},
Pages = {676696},
Editor = {J Dolbow and C Farhat and I Harari and A
Lew},
Year = {2015},
Month = {November},
ISSN = {00295981},
url = {http://dx.doi.org/10.1002/nme.4766},
Abstract = {© 2015 John Wiley & Sons, Ltd.The extended finite
element method (XFEM) has proven to be an accurate, robust
method for solving embedded interface problems. With a few
exceptions, the XFEM has mostly been used in conjunction
with piecewiselinear shape functions and an associated
piecewiselinear geometrical representation of interfaces.
In the current work, the use of splinebased finite elements
is examined along with a Nitsche technique for enforcing
constraints on an embedded interface. To obtain optimal
rates of convergence, we employ a hierarchical local
refinement approach to improve the geometrical
representation of curved interfaces. We further propose a
novel weighting for the interfacial consistency terms
arising in the Nitsche variational form with Bsplines. A
qualitative dependence between the weights and the
stabilization parameters is established with additional
element level eigenvalue calculations. An important
consequence of this weighting is that the bulk as well as
the interfacial fields remain well behaved in the presence
of large heterogeneities as well as elements with
arbitrarily small volume fractions. We demonstrate the
accuracy and robustness of the proposed method through
several numerical examples.},
Doi = {10.1002/nme.4766},
Key = {fds268258}
}
@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 = {469471},
Editor = {J Dolbow and C Farhat and I Harari and A
Lew},
Year = {2015},
Month = {November},
ISSN = {00295981},
url = {http://dx.doi.org/10.1002/nme.5116},
Doi = {10.1002/nme.5116},
Key = {fds291309}
}
@article{fds268257,
Author = {W Jiang and JE Dolbow},
Title = {Adaptive refinement of hierarchical Bspline finite elements
with an efficient data transfer algorithm},
Journal = {International Journal for Numerical Methods in
Engineering},
Volume = {102},
Number = {34},
Pages = {233256},
Editor = {R de Borst and C Farhat and J Fish and I Harari and P
Letallec and D Perić},
Year = {2015},
Month = {April},
ISSN = {00295981},
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 postcoital
contraceptives: an update.},
Journal = {Contraception},
Volume = {91},
Number = {4},
Pages = {344349},
Year = {2015},
Month = {April},
ISSN = {00107824},
url = {http://dx.doi.org/10.1016/j.contraception.2015.01.002},
Abstract = {In 2001, we provided benchmark estimates of probability of
pregnancy given a single act of intercourse. Those
calculations assumed that intercourse and ovulation are
independent. Subsequent research has shown that this
assumption is not valid. We provide here an update of
previous benchmark estimates.We reanalyze earlier data from
two North Carolina studies that collected daily urine
samples and recorded daily intercourse for multiple
menstrual cycles. One study comprised 68 sexually active
women with either an intrauterine device or tubal ligation.
The second was of 221 women who planned to become pregnant
and had discontinued use of any birth control at enrollment.
Participants had no known fertility problems. New
statistical analyses were based on Monte Carlo simulations
and Bayesian methods.The probability that a single act of
intercourse occurs within a woman's fertile window is 25%,
compared with 20% in previous calculations. The probability
of pregnancy with intercourse on a given menstrual cycle day
is correspondingly higher than previously estimated, with
the largest increases occurring on menstrual days 1222.
These increases are, however, fairly small (for example, the
peak chance of conception on menstrual day 13 increased from
8.6% to 9.7%).Previous benchmark rates of pregnancy with one
act of intercourse were moderately underestimated due to a
mistaken assumption about the independence of intercourse
and ovulation.The chance of pregnancy with a single act of
unprotected intercourse is greater than previously
estimated. Previous benchmarks may underestimate the
efficacy of postcoital contraception.},
Doi = {10.1016/j.contraception.2015.01.002},
Key = {fds257830}
}
@article{fds257829,
Author = {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
AshleyKoch},
Title = {Joint eQTL assessment of whole blood and dura mater tissue
from individuals with Chiari type I malformation.},
Journal = {BMC genomics},
Volume = {16},
Pages = {11},
Year = {2015},
Month = {January},
url = {http://dx.doi.org/10.1186/s1286401412118},
Abstract = {Expression quantitative trait loci (eQTL) play an important
role in the regulation of gene expression. Gene expression
levels and eQTLs are expected to vary from tissue to tissue,
and therefore multitissue analyses are necessary to fully
understand complex genetic conditions in humans. Dura mater
tissue likely interacts with cranial bone growth and thus
may play a role in the etiology of Chiari Type I
Malformation (CMI) and related conditions, but it is often
inaccessible and its gene expression has not been well
studied. A genetic basis to CMI has been established;
however, the specific genetic risk factors are not well
characterized.We present an assessment of eQTLs for whole
blood and dura mater tissue from individuals with CMI. A
jointtissue analysis identified 239 eQTLs in either dura or
blood, with 79% of these eQTLs shared by both tissues.
Several identified eQTLs were novel and these implicate
genes involved in bone development (IPO8, XYLT1, and
PRKAR1A), and ribosomal pathways related to marrow and bone
dysfunction, as potential candidates in the development of
CMI.Despite strong overall heterogeneity in expression
levels between blood and dura, the majority of ciseQTLs are
shared by both tissues. The power to detect shared eQTLs was
improved by using an integrative statistical approach. The
identified tissuespecific and shared eQTLs provide new
insight into the genetic basis for CMI and related
conditions.},
Doi = {10.1186/s1286401412118},
Key = {fds257829}
}
@article{fds257827,
Author = {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},
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 nonparametric Bayesian
estimation},
Journal = {Journal of the Royal Statistical Society. Series B:
Statistical Methodology},
Volume = {77},
Number = {1},
Pages = {3558},
Year = {2015},
Month = {January},
ISSN = {13697412},
url = {http://dx.doi.org/10.1111/rssb.12059},
Abstract = {© 2014 Royal Statistical Society. Prior specification for
nonparametric Bayesian inference involves the difficult
task of quantifying prior knowledge about a parameter of
high, often infinite, dimension. A statistician is unlikely
to have informed opinions about all aspects of such a
parameter but will have real information about functionals
of the parameter, such as the population mean or variance.
The paper proposes a new framework for nonparametric Bayes
inference in which the prior distribution for a possibly
infinite dimensional parameter is decomposed into two parts:
an informative prior on a finite set of functionals, and a
nonparametric conditional prior for the parameter given the
functionals. Such priors can be easily constructed from
standard nonparametric prior distributions in common use
and inherit the large support of the standard priors on
which they are based. Additionally, posterior approximations
under these informative priors can generally be made via
minor adjustments to existing Markov chain approximation
algorithms for standard nonparametric prior distributions.
We illustrate the use of such priors in the context of
multivariate density estimation using Dirichlet process
mixture models, and in the modelling of high dimensional
sparse contingency tables.},
Doi = {10.1111/rssb.12059},
Key = {fds257832}
}
@article{fds257849,
Author = {DC Kessler and PD Hoff and DB Dunson},
Title = {Marginally specified priors for nonparametric Bayesian
estimation.},
Journal = {Journal of the Royal Statistical Society. Series B,
Statistical methodology},
Volume = {77},
Number = {1},
Pages = {3558},
Year = {2015},
Month = {January},
ISSN = {13697412},
url = {http://dx.doi.org/10.1111/rssb.12059},
Abstract = {Prior specification for nonparametric Bayesian inference
involves the difficult task of quantifying prior knowledge
about a parameter of high, often infinite, dimension. A
statistician is unlikely to have informed opinions about all
aspects of such a parameter but will have real information
about functionals of the parameter, such as the population
mean or variance. The paper proposes a new framework for
nonparametric Bayes inference in which the prior
distribution for a possibly infinite dimensional parameter
is decomposed into two parts: an informative prior on a
finite set of functionals, and a nonparametric conditional
prior for the parameter given the functionals. Such priors
can be easily constructed from standard nonparametric prior
distributions in common use and inherit the large support of
the standard priors on which they are based. Additionally,
posterior approximations under these informative priors can
generally be made via minor adjustments to existing Markov
chain approximation algorithms for standard nonparametric
prior distributions. We illustrate the use of such priors in
the context of multivariate density estimation using
Dirichlet process mixture models, and in the modelling of
high dimensional sparse contingency tables.},
Doi = {10.1111/rssb.12059},
Key = {fds257849}
}
@article{fds257828,
Author = {A Canale and DB Dunson},
Title = {Bayesian multivariate mixedscale density
estimation},
Journal = {Statistics and Its Interface},
Volume = {8},
Number = {2},
Pages = {195201},
Year = {2015},
ISSN = {19387989},
url = {http://dx.doi.org/10.4310/SII.2015.v8.n2.a7},
Doi = {10.4310/SII.2015.v8.n2.a7},
Key = {fds257828}
}
%% Durrett, Richard T.
@article{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 = {34343464},
Year = {2015},
Month = {December},
ISSN = {10505164},
url = {http://dx.doi.org/10.1214/14AAP1079},
Doi = {10.1214/14AAP1079},
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 = {19341954},
Year = {2015},
Month = {October},
ISSN = {00928240},
url = {http://dx.doi.org/10.1007/s1153801501108},
Doi = {10.1007/s1153801501108},
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 = {1553734X},
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 chancein
form of the stochastic dynamics of basal stem cellsplays a
critical role in the elimination of HPVinfected cell
clones. In particular, we find that in immunocompetent
adolescents with cervical HPV infections, the immune
response may contribute less than 20% to virus clearancethe
rest is taken care of by the stochastic proliferation
dynamics in the basal layer. In HIVnegative individuals,
the contribution of the immune response may be
negligible.},
Doi = {10.1371/journal.pcbi.1004113},
Key = {fds243418}
}
@article{fds243416,
Author = {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 = {104115},
Year = {2015},
Month = {February},
ISSN = {10505164},
url = {http://dx.doi.org/10.1214/13AAP989},
Doi = {10.1214/13AAP989},
Key = {fds243416}
}
@book{fds299418,
Author = {R.T. Durrett},
Title = {Branching process models of cancer},
Publisher = {Springer},
Year = {2015},
Key = {fds299418}
}
%% Fernandes de Oliveira, Goncalo M.
@article{fds299985,
Author = {Goncalo Oliveira},
Title = {CalabiYau Monopoles for the Stenzel Metric},
Journal = {Communications in Mathematical Physics},
Year = {2015},
Key = {fds299985}
}
%% Fry, Brendan
@article{fds226007,
Author = {I Sgouralis and RG Evans and BS Gardiner and JA Smith and BC Fry and AT
Layton},
Title = {Renal hemodynamics, function, and oxygenation during cardiac
surgery performed on cardiopulmonary bypass: A modeling
study},
Journal = {Physiological Reports},
Volume = {3},
Pages = {e12260},
Year = {2015},
Key = {fds226007}
}
@article{fds226453,
Author = {BC Fry and A Edwards and AT Layton},
Title = {Impacts of nitric oxide and superoxide on renal medullary
oxygen transport and urine concentration},
Journal = {American Journal of Physiology  Renal Physiology},
Volume = {308},
Pages = {F967F980},
Year = {2015},
Key = {fds226453}
}
%% Gao, Tingran
@article{fds299988,
Author = {Tingran Gao and Gabriel S Yapuncich and Ingrid Daubechies and Doug M
Boyer},
Title = {Automated techniques for comparing shapes in a biological
comparative dataset with high interspecific variation:
tradeoffs, limitations, and progress},
Journal = {PLOS ONE},
Year = {2015},
Month = {December},
ISSN = {19326203},
Abstract = {During the development of evolutionary theory, foundational
principles were established through comparative anatomy.
However, comparative anatomy (in the form of high fidelity
geometric morphometric information) is currently a
relatively marginal source of evidence for evolutionary
biology. While it is conceivable that this shift reflects
the objectively low intrinsic information content of
anatomical variation, we believe such assessments are
premature. Instead, it seems that the relative difficulty of
studying comparative anatomy has led researchers to seek
other forms of data. Comparative datasets large enough to be
statistically powerful are rare, and the complexity of
anatomical shape variation foil even experienced
researchers' abilities to collect rich yet standardized
measurements. Threedimensional digitization presents a way
to reintroduce data from anatomical information by
increasing access to samples through virtual repositories
(extensive sampling) and by providing the potential for
automating aspects of shape comparison (intensive sampling).
In this paper, we reassess the accuracy and reliability of
some published automated methods and present updated
methodology. Ideally, these methods will promote wider
participation in anatomical studies and motivate other
research groups to focus on the problems of automated
quantification and comparison of anatomical
structures.},
Key = {fds299988}
}
%% Getz, Jayce R.
@article{fds292890,
Author = {JR Getz and J Klassen},
Title = {Isolating RankinSelberg lifts},
Journal = {Proceedings of the American Mathematical
Society},
Volume = {143},
Number = {8},
Pages = {33193329},
Year = {2015},
Month = {April},
ISSN = {00029939},
url = {http://dx.doi.org/10.1090/proc/12389},
Doi = {10.1090/proc/12389},
Key = {fds292890}
}
@article{fds226862,
Author = {J.R. Getz},
Title = {Nonabelian Fourier transforms for spherical
representations},
Year = {2015},
url = {arXiv:1506.09128},
Key = {fds226862}
}
@article{fds226899,
Author = {J.R. Getz and P. E. Herman},
Title = {A nonabelian trace formula},
Journal = {Research in the Mathematical Sciences},
Volume = {2},
Number = {1},
Year = {2015},
Abstract = {Let E/F be an extension of number fields with Gal(E/F)
simple and nonabelian. In a recent paper the first named
author suggested an approach to nonsolvable base change and
descent of automorphic representations of GL(2) along such
an extension. Motivated by this we prove a trace formula
whose spectral side is a weighted sum over cuspidal
automorphic representations of GL(2) over E that are
isomorphic to their Gal(E/F)conjugates.},
Key = {fds226899}
}
@article{fds292889,
Author = {JR Getz and H Hahn},
Title = {A general simple relative trace formula},
Journal = {Pacific Journal of Mathematics},
Volume = {277},
Number = {1},
Pages = {99118},
Year = {2015},
ISSN = {00308730},
url = {http://dx.doi.org/10.2140/pjm.2015.277.99},
Doi = {10.2140/pjm.2015.277.99},
Key = {fds292889}
}
%% Hahn, Heekyoung
@article{fds305734,
Author = {H. Hahn},
Title = {On tensor thrid Lfunctions of automorphic representations
of GL_n(A_F)},
Journal = {Proc. Amer. Math. Soc.},
Year = {2016},
Key = {fds305734}
}
@article{fds227060,
Author = {H. Hahn},
Title = {On classical groups detected by the triple tensor product
and the LittlewoodRichardson semigroup},
Year = {2016},
Key = {fds227060}
}
@article{fds302444,
Author = {JR Getz and H Hahn},
Title = {A general simple relative trace formula},
Journal = {Pacific Journal of Mathematics},
Volume = {277},
Number = {1},
Pages = {99118},
Year = {2015},
ISSN = {00308730},
url = {http://dx.doi.org/10.2140/pjm.2015.277.99},
Doi = {10.2140/pjm.2015.277.99},
Key = {fds302444}
}
%% Hain, Richard
@article{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{fds287213,
Author = {D Arapura and A Dimca and R Hain},
Title = {On the fundamental groups of normal varieties},
Journal = {Communications in Contemporary Mathematics},
Pages = {15500651550065},
Year = {2015},
Month = {August},
ISSN = {02191997},
url = {http://dx.doi.org/10.1142/S0219199715500650},
Doi = {10.1142/S0219199715500650},
Key = {fds287213}
}
@article{fds299940,
Author = {Richard Hain},
Title = {DeligneBeilinson 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 = {213246},
Publisher = {Oxford University Press},
Year = {2015},
ISSN = {17538416},
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 1persistence scoring;
discovering periodicity in gene expression time series
data.},
Journal = {BMC bioinformatics},
Volume = {16},
Pages = {257},
Year = {2015},
Month = {January},
url = {http://dx.doi.org/10.1186/s1285901506456},
Abstract = {Identifying periodically expressed genes across different
processes (e.g. the cell and metabolic cycles, circadian
rhythms, etc) is a central problem in computational biology.
Biological time series may contain (multiple) unknown signal
shapes of systemic relevance, imperfections like noise,
damping, and trending, or limited sampling density. While
there exist methods for detecting periodicity, their design
biases (e.g. toward a specific signal shape) can limit their
applicability in one or more of these situations.We present
in this paper a novel method, SW1PerS, for quantifying
periodicity in time series in a shapeagnostic manner and
with resistance to damping. The measurement is performed
directly, without presupposing a particular pattern, by
evaluating the circularity of a highdimensional
representation of the signal. SW1PerS is compared to other
algorithms using synthetic data and performance is
quantified under varying noise models, noise levels,
sampling densities, and signal shapes. Results on biological
data are also analyzed and compared.On the task of
periodic/notperiodic classification, using synthetic data,
SW1PerS outperforms all other algorithms in the lownoise
regime. SW1PerS is shown to be the most shapeagnostic of
the evaluated methods, and the only one to consistently
classify damped signals as highly periodic. On biological
data, and for several experiments, the lists of top 10%
genes ranked with SW1PerS recover up to 67% of those
generated with other popular algorithms. Moreover, the list
of genes from data on the Yeast metabolic cycle which are
highlyranked only by SW1PerS, contains evidently noncosine
patterns (e.g. ECM33, CDC9, SAM1,2 and MSH6) with highly
periodic expression profiles. In data from the Yeast cell
cycle SW1PerS identifies genes not preferred by other
algorithms, hence not previously reported as periodic, but
found in other experiments such as the universal growth rate
response of Slavov. These genes are BOP3, CDC10, YIL108W,
YER034W, MLP1, PAC2 and RTT101.In biological systems with
low noise, i.e. where periodic signals with interesting
shapes are more likely to occur, SW1PerS can be used as a
powerful tool in exploratory analyses. Indeed, by having an
initial set of periodic genes with a rich variety of signal
types, pattern/shape information can be included in the
study of systems and the generation of hypotheses regarding
the structure of gene regulatory networks.},
Doi = {10.1186/s1285901506456},
Key = {fds243563}
}
@article{fds300010,
Author = {David Rouse and Adam Watkins and David Porter and John Harer and Paul Bendich and Nate Strawn and Elizabeth Munch and Jonathan
DeSena and Jesse Clarke and Jeffrey Gilbert and Peter Chin and Andrew Newman},
Title = {Featureaided multiple hypothesis tracking using topological
and statistical behavior classifiers},
Journal = {Proc. SPIE 9474, Signal Processing, Sensor/Information
Fusion, and Target Recognition XXIV, 94740L},
Year = {2015},
ISSN = {10.1117/12.2179555},
Key = {fds300010}
}
@article{fds300009,
Author = {K. Mcgoff and X. Guo and A. Deckard and C. Kelliher and A. Leman and S.
Haase, J. Harer},
Title = {The Local Edge Machine: Inference of Dynamic Models of Gene
Regulation},
Journal = {Genome Biology},
Year = {2015},
Key = {fds300009}
}
%% Herschlag, Gregory J.
@article{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 finiterange 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 twodimensional numerical examples.
Lower levels within the hierarchy that consider shorter
spatial correlations are shown to be up to three orders of
magnitude faster than traditional kinetic Monte Carlo
methods (KMC) for onedimensional systems, while pre
dicting similar system dynamics and steady states as KMC
methods. We then test the hierarchy on a twodimensional
model for the oxidation of CO on RuO2(110), showing that
loworder truncations of the hierarchy 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 = {22462267},
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 channelreservoir barrier and
demonstrate that pumping can either enhance or impede fluid
extraction across channel walls. We find that associated
with each set of physical flow and pumping parameters, there
are optimal reservoir conditions that maximizes the amount
of material flowing from the channel into the
reservoir.},
Key = {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 = {219231},
Year = {2015},
ISSN = {03029743},
Abstract = {© 2015, Lecture Notes in Computer Science. All rights
reserved.Why is it that in an animal society, persistent
selfishness is quite rare yet in human society, even strict
laws and severe punishment do not eliminate selfish action
against the interests of the whole? Stochastic learning
agents called Pavlov strategies are used to model
interactions in the multiagent 2 × 2 Stag Hunt matrix
game, a close relative of the Prisoner’s Dilemma. Markov
chain methods and computer simulations establish a threshold
learning rate for the stability of cooperation. A society of
rapidly adapting agents may suffer strife and dissension
while another society with slower learning agents will enjoy
the benefits of virtually complete cooperation.},
Key = {fds296263}
}
%% Layton, Anita T.
@article{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 = {F708F719},
Year = {2015},
Month = {October},
ISSN = {1931857X},
url = {http://dx.doi.org/10.1152/ajprenal.00187.2015},
Abstract = {We expanded a published mathematical model of an afferent
arteriole smooth muscle cell in rat kidney (Edwards A,
Layton, AT. Am J Physiol Renal Physiol 306: F34F48, 2014)
to understand how nitric oxide (NO) and superoxide (O(2)())
modulate the arteriolar diameter and its myogenic response.
The present model includes the kinetics of NO and O(2)()
formation, diffusion, and reaction. Also included are the
effects of NO and its second messenger cGMP on cellular
Ca²⁺ uptake and efflux, Ca²⁺activated K⁺ currents,
and myosin light chain phosphatase activity. The model
considers as well pressureinduced increases in O(2)()
production, O(2)()mediated regulation of Ltype Ca²⁺
channel conductance, and increased O(2)() production in
spontaneous hypertensive rats (SHR). Our results indicate
that elevated O(2)() production in SHR is sufficient to
account for observed differences between normotensive and
hypertensive rats in the response of the afferent arteriole
to NO synthase inhibition, Tempol, and angiotensin II at
baseline perfusion pressures. In vitro, whether the myogenic
response is stronger in SHR remains uncertain. Our model
predicts that if mechanosensitive cation channels are not
modulated by O(2)(), then fractional changes in diameter
induced by pressure elevations should be smaller in SHR than
in normotensive rats. Our results also suggest that most NO
diffuses out of the smooth muscle cell without being
consumed, whereas most O(2)() is scavenged, by NO and
superoxide dismutase. Moreover, the predicted effects of
superoxide on arteriolar constriction are not predominantly
due to its scavenging of NO.},
Doi = {10.1152/ajprenal.00187.2015},
Key = {fds300274}
}
@article{fds300275,
Author = {H Nganguia and YN Young and AT Layton and WF Hu and MC
Lai},
Title = {An Immersed Interface Method for Axisymmetric
Electrohydrodynamic Simulations in Stokes
flow},
Journal = {Communications in Computational Physics},
Volume = {18},
Number = {02},
Pages = {429449},
Year = {2015},
Month = {August},
ISSN = {18152406},
url = {http://dx.doi.org/10.4208/cicp.171014.270315a},
Doi = {10.4208/cicp.171014.270315a},
Key = {fds300275}
}
@article{fds300276,
Author = {I Sgouralis and AT Layton},
Title = {Mathematical modeling of renal hemodynamics in physiology
and pathophysiology.},
Journal = {Mathematical biosciences},
Volume = {264},
Pages = {820},
Year = {2015},
Month = {June},
ISSN = {00255564},
url = {http://dx.doi.org/10.1016/j.mbs.2015.02.016},
Abstract = {In addition to the excretion of metabolic waste and toxin,
the kidney plays an indispensable role in regulating the
balance of water, electrolyte, acidbase, and blood
pressure. For the kidney to maintain proper functions,
hemodynamic control is crucial. In this review, we describe
representative mathematical models that have been developed
to better understand the kidney's autoregulatory processes.
We consider mathematical models that simulate glomerular
filtration, and renal blood flow regulation by means of the
myogenic response and tubuloglomerular feedback. We discuss
the extent to which these modeling efforts have expanded the
understanding of renal functions in health and
disease.},
Doi = {10.1016/j.mbs.2015.02.016},
Key = {fds300276}
}
@article{fds243612,
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 = {F1343F1357},
Year = {2015},
Month = {June},
ISSN = {1931857X},
url = {http://dx.doi.org/10.1152/ajprenal.00007.2015},
Abstract = {The objective of this study was to investigate how
physiological, pharmacological, and pathological conditions
that alter sodium reabsorption (TNa) in the proximal tubule
affect oxygen consumption (QO2 ) and Na(+) transport
efficiency (TNa/QO2 ). To do so, we expanded a mathematical
model of solute transport in the proximal tubule of the rat
kidney. The model represents compliant S1, S2, and S3
segments and accounts for their specific apical and
basolateral transporters. Sodium is reabsorbed
transcellularly, via apical Na(+)/H(+) exchangers (NHE) and
Na(+)glucose (SGLT) cotransporters, and paracellularly. Our
results suggest that TNa/QO2 is 80% higher in S3 than in
S1S2 segments, due to the greater contribution of the
passive paracellular pathway to TNa in the former segment.
Inhibition of NHE or NaKATPase reduced TNa and QO2 , as
well as Na(+) transport efficiency. SGLT2 inhibition also
reduced proximal tubular TNa but increased QO2 ; these
effects were relatively more pronounced in the S3 vs. the
S1S2 segments. Diabetes increased TNa and QO2 and reduced
TNa/QO2 , owing mostly to hyperfiltration. Since SGLT2
inhibition lowers diabetic hyperfiltration, the net effect
on TNa, QO2 , and Na(+) transport efficiency in the proximal
tubule will largely depend on the individual extent to which
glomerular filtration rate is lowered.},
Doi = {10.1152/ajprenal.00007.2015},
Key = {fds243612}
}
@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 = {F951F955},
Year = {2015},
Month = {May},
ISSN = {1931857X},
url = {http://dx.doi.org/10.1152/ajprenal.00008.2015},
Abstract = {It has been long known that the kidney plays an essential
role in the control of body fluids and blood pressure and
that impairment of renal function may lead to the
development of diseases such as hypertension (Guyton AC,
Coleman TG, Granger Annu Rev Physiol 34: 1346, 1972). In
this review, we highlight recent advances in our
understanding of renal hemodynamics, obtained from
experimental and theoretical studies. Some of these studies
were published in response to a recent Call for Papers of
this journal: Renal Hemodynamics: Integrating with the
Nephron and Beyond.},
Doi = {10.1152/ajprenal.00008.2015},
Key = {fds243614}
}
@article{fds243615,
Author = {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 = {F967F980},
Year = {2015},
Month = {May},
ISSN = {1931857X},
url = {http://dx.doi.org/10.1152/ajprenal.00600.2014},
Abstract = {The goal of this study was to investigate the reciprocal
interactions among oxygen (O2), nitric oxide (NO), and
superoxide (O2 ()) and their effects on medullary
oxygenation and urinary output. To accomplish that goal, we
developed a detailed mathematical model of solute transport
in the renal medulla of the rat kidney. The model represents
the radial organization of the renal tubules and vessels,
which centers around the vascular bundles in the outer
medulla and around clusters of collecting ducts in the inner
medulla. Model simulations yield significant radial
gradients in interstitial fluid oxygen tension (Po2) and NO
and O2 () concentration in the OM and upper IM. In the deep
inner medulla, interstitial fluid concentrations become much
more homogeneous, as the radial organization of tubules and
vessels is not distinguishable. The model further predicts
that due to the nonlinear interactions among O2, NO, and O2
(), the effects of NO and O2 () on sodium transport,
osmolality, and medullary oxygenation cannot be gleaned by
considering each solute's effect in isolation. An additional
simulation suggests that a sufficiently large reduction in
tubular transport efficiency may be the key contributing
factor, more so than oxidative stress alone, to
hypertensioninduced medullary hypoxia. Moreover, model
predictions suggest that urine Po2 could serve as a
biomarker for medullary hypoxia and a predictor of the risk
for hospitalacquired acute kidney injury.},
Doi = {10.1152/ajprenal.00600.2014},
Key = {fds243615}
}
@article{fds299957,
Author = {B Fields and K Page},
Title = {Preface},
Journal = {scopus},
Volume = {2015June},
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{fds299383,
Author = {Runjing Liu and Anita T. Layton},
Title = {Modeling the effects of positive and negative feedback in
kidney blood flow control},
Journal = {Math Biosci, submitted},
Year = {2015},
Key = {fds299383}
}
@article{fds227194,
Author = {Gregory Herschlag and JianGuo Liu and Anita T.
Layton},
Title = {Optimal reservoir conditions for fluid extraction through
permeable walls in the viscous limit},
Journal = {Phys Fluids, submitted},
Year = {2015},
Key = {fds227194}
}
@article{fds227067,
Author = {Brendan C. Fry and Aurelie Edwards and Anita T.
Layton},
Title = {Impact of nitricoxidemediated vasodilation and Oxidative
Stress on renal medullary oxygenation: A modeling
study},
Journal = {Am J Physiol Renal Physiol, in press},
Year = {2015},
Key = {fds227067}
}
@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{fds227044,
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 contrastenhanced quantitative susceptibility
mapping at ultrashort echo time for evaluating renal
function},
Journal = {Am J Physiol Renal Physiol, in press},
Year = {2015},
Key = {fds227044}
}
@article{fds226446,
Author = {Anita T. Layton},
Title = {Mathematical physiology},
Booktitle = {Princeton Companion to Applied Mathematics},
Editor = {Nicholas J. Higham},
Year = {2015},
ISBN = {9780691150390},
Key = {fds226446}
}
@article{fds226016,
Author = {Ioannis Sgouralis and Roger Evans and Bruce S. Gardiner and Julian A
Smith and Brendan C. Fry and Anita T. Layton},
Title = {Renal hemodynamics, function and oxygenation during cardiac
surgery performed on cardiopulmonary bypass: A modeling
study},
Journal = {Physiol Report},
Volume = {3},
Number = {1},
Year = {2015},
Key = {fds226016}
}
@article{fds226378,
Author = {Ashlee N. Ford Versypt and Elizabeth Makrides and Julia C.
Arciero and Laura Ellwein and Anita T. Layton},
Title = {Bifurcation Study of Blood Flow Control in the
Kidney},
Journal = {Math Biosci},
Volume = {263},
Pages = {169–179},
Year = {2015},
Key = {fds226378}
}
@article{fds226967,
Author = {Julia Arcerio and Laura Ellwein and Ashlee N. Ford Versypt and Elizabeth Makride and Anita T. Layton},
Title = {Modeling blood flow in the kidney},
Volume = {158},
Pages = {5573},
Booktitle = {The IMA Volumes in Mathematics and its Applications:
Applications of Dynamical Systems in Biology and
Medicine},
Year = {2015},
Key = {fds226967}
}
@article{fds227058,
Author = {Gregory J. Herschlag and JianGuo Liu and Anita T.
Layton},
Title = {An exact solution for Stokes flow in an infinite channel
with permeable walls},
Journal = {SIAM Appl Math, in press},
Year = {2015},
Key = {fds227058}
}
@article{fds226985,
Author = {Tal Burt and Douglas C. Rouse and Kihak Lee and Huali Wu and Anita T.
Layton and Thomas C. Hawk and Douglas H. Weitzel and Bennett B. Chin and Michael CohenWolkowiez and SheinChung Chow and Robert J.
Noveck},
Title = {Intraarterial microdosing (IAM), a novel drug development
approach,proof of concept in rodents},
Journal = {CPT: Pharmacometrics and Systems Pharmacology, in
press},
Year = {2015},
Key = {fds226985}
}
@article{fds226440,
Author = {Ioannis Sgouralis and Vasileios Maroulas and Anita T.
Layton},
Title = {Transfer function analysis of dynamic blood flow control in
the rat kidney},
Journal = {Bull Math Biol, submitted},
Year = {2015},
Key = {fds226440}
}
@article{fds226368,
Author = {Anita T. Layton},
Title = {Tracking the distribution of a solute bolus in the rat
kidney},
Booktitle = {AWM proceedings for NIMBioS WS for Women in Mathematical
Biology, submitted},
Year = {2015},
Key = {fds226368}
}
%% Li, Lei
@article{fds302449,
Author = {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 = {021902021902},
Year = {2015},
Month = {February},
ISSN = {10706631},
url = {http://dx.doi.org/10.1063/1.4909516},
Doi = {10.1063/1.4909516},
Key = {fds302449}
}
%% Liao, Wenjing
@article{fds300127,
Author = {W. Liao},
Title = {MUSIC for multidimensional spectral estimation: stability
and superresolution},
Journal = {IEEE Transactions on Signal Processing},
Volume = {63},
Number = {23},
Year = {2015},
Month = {July},
Key = {fds300127}
}
%% Lipnowski, Michael
@article{fds227091,
Author = {M. Lipnowski},
Title = {Equivariant torsion and base change},
Journal = {Algebra and Number Theory},
Year = {2015},
url = {http://arxiv.org/abs/1312.2540},
Key = {fds227091}
}
@article{fds300040,
Author = {M. Lipnowski and J. Tsimerman},
Title = {How large is A_g(F_p)?},
Year = {2015},
url = {http://arxiv.org/abs/1511.02212},
Key = {fds300040}
}
@article{fds226181,
Author = {N. Bergeron and M. Lipnowski},
Title = {Twisted limit formula for torsion and cyclic base
change},
Year = {2015},
url = {http://arxiv.org/abs/1409.6749},
Key = {fds226181}
}
@article{fds226182,
Author = {J. Getz and H. Hahn and M. Lipnowski},
Title = {A relative Weyl law and spectral sparsity of distinguished
representations},
Year = {2015},
Key = {fds226182}
}
%% Liu, JianGuo
@article{fds300225,
Author = {J.G. Liu and J. Wang},
Title = {Refined hypercontractivity and uniqueness for the
KellerSegel equations},
Journal = {Applied Math Letter},
Volume = {52},
Pages = {212219},
Year = {2016},
Key = {fds300225}
}
@article{fds246842,
Author = {Y Xue and C Wang and JG Liu},
Title = {Simple Finite Element Numerical Simulation of Incompressible
Flow Over Nonrectangular Domains and the SuperConvergence
Analysis},
Journal = {Journal of Scientific Computing},
Volume = {65},
Number = {3},
Pages = {11891216},
Year = {2015},
Month = {December},
ISSN = {08857474},
url = {http://dx.doi.org/10.1007/s1091501500058},
Doi = {10.1007/s1091501500058},
Key = {fds246842}
}
@article{fds300222,
Author = {A Chertock and JG Liu and T Pendleton},
Title = {Elastic collisions among peakon solutions for the
Camassa–Holm equation},
Journal = {Applied Numerical Mathematics},
Volume = {93},
Pages = {3046},
Year = {2015},
Month = {July},
ISSN = {01689274},
url = {http://dx.doi.org/10.1016/j.apnum.2014.01.001},
Abstract = {© 2014 IMACS. The purpose of this paper is to study the
dynamics of the interaction among a special class of
solutions of the onedimensional CamassaHolm equation. The
equation yields soliton solutions whose identity is
preserved through nonlinear interactions. These solutions
are characterized by a discontinuity at the peak in the wave
shape and are thus called peakon solutions. We apply a
particle method to the CamassaHolm equation and show that
the nonlinear interaction among the peakon solutions
resembles an elastic collision, i.e., the total energy and
momentum of the system before the peakon interaction is
equal to the total energy and momentum of the system after
the collision. From this result, we provide several
numerical illustrations which support the analytical study,
as well as showcase the merits of using a particle method to
simulate solutions to the CamassaHolm equation under a wide
class of initial data.},
Doi = {10.1016/j.apnum.2014.01.001},
Key = {fds300222}
}
@article{fds300223,
Author = {P Degond and A Frouvelle and JG Liu},
Title = {Phase Transitions, Hysteresis, and Hyperbolicity for
SelfOrganized Alignment Dynamics},
Journal = {Archive for Rational Mechanics and Analysis},
Volume = {216},
Number = {1},
Pages = {63115},
Year = {2015},
Month = {April},
ISSN = {00039527},
url = {http://dx.doi.org/10.1007/s0020501408007},
Doi = {10.1007/s0020501408007},
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 = {15393755},
Abstract = {The BurtonCabreraFrank (BCF) model for the flow of line
defects (steps) on crystal surfaces has offered useful
insights into nanostructure evolution. This model has rested
on phenomenological grounds. Our goal is to show via scaling
arguments the emergence of the BCF theory for noninteracting
steps from a stochastic atomistic scheme of a kinetic
restricted solidonsolid model in one spatial dimension.
Our main assumptions are: adsorbed atoms (adatoms) form a
dilute system, and elastic effects of the crystal lattice
are absent. The step edge is treated as a front that
propagates via probabilistic rules for atom attachment and
detachment at the step. We formally derive a quasistatic
step flow description by averaging out the stochastic scheme
when terrace diffusion, adatom desorption, and deposition
from above are present.},
Key = {fds246843}
}
@article{fds300224,
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 Applied Math},
Volume = {75},
Pages = {22462267},
Year = {2015},
Key = {fds300224}
}
@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 KellerSegel equation
and convergence analysis},
Journal = {Math. Comp.},
Year = {2015},
Key = {fds300227}
}
@article{fds300228,
Author = {J.G. Liu and Y. Zhang},
Title = {Convergence of diffusiondrift 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{fds305049,
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},
Publisher = {Elsevier},
Editor = {K Bhattacharya},
Year = {2016},
Month = {January},
url = {http://hdl.handle.net/10161/11296},
Key = {fds305049}
}
@article{fds243728,
Author = {J Lu and V Moroz and CB Muratov},
Title = {OrbitalFree Density Functional Theory of OutofPlane
Charge Screening in Graphene},
Journal = {Journal of Nonlinear Science},
Volume = {25},
Number = {6},
Pages = {13911430},
Year = {2015},
Month = {December},
ISSN = {09388974},
url = {http://dx.doi.org/10.1007/s0033201592594},
Doi = {10.1007/s0033201592594},
Key = {fds243728}
}
@article{fds305048,
Author = {C Li and J Lu and W Yang},
Title = {Gentlest ascent dynamics for calculating first excited state
and exploring energy landscape of KohnSham density
functionals.},
Journal = {The Journal of chemical physics},
Volume = {143},
Number = {22},
Pages = {224110},
Year = {2015},
Month = {December},
ISSN = {00219606},
url = {http://dx.doi.org/10.1063/1.4936411},
Abstract = {We develop the gentlest ascent dynamics for KohnSham
density functional theory to search for the index1 saddle
points on the energy landscape of the KohnSham density
functionals. These stationary solutions correspond to
excited states in the ground state functionals. As shown by
various examples, the first excited states of many chemical
systems are given by these index1 saddle points. Our novel
approach provides an alternative, more robust way to obtain
these excited states, compared with the widely used ΔSCF
approach. The method can be easily generalized to target
higher index saddle points. Our results also reveal the
physical interest and relevance of studying the KohnSham
energy landscape.},
Doi = {10.1063/1.4936411},
Key = {fds305048}
}
@article{fds243731,
Author = {H Yang and J Lu and WP Brown and I Daubechies and L
Ying},
Title = {Quantitative Canvas Weave Analysis Using 2D Synchrosqueezed
Transforms: Application of timefrequency analysis to art
investigation},
Journal = {IEEE Signal Processing Magazine},
Volume = {32},
Number = {4},
Pages = {5563},
Year = {2015},
Month = {July},
ISSN = {10535888},
url = {http://dx.doi.org/10.1109/MSP.2015.2406882},
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 = {141167},
Year = {2015},
Month = {July},
ISSN = {00219991},
url = {http://dx.doi.org/10.1016/j.jcp.2015.03.014},
Abstract = {© 2015 Elsevier Inc. In this paper we construct numerical
schemes to approximate linear transport equations with slab
geometry by diffusion equations. We treat both the case of
pure diffusive scaling and the case where kinetic and
diffusive scalings coexist. The diffusion equations and
their data are derived from asymptotic and layer analysis
which allows general scattering kernels and general data. We
apply the halfspace solver in [20] to resolve the boundary
layer equation and obtain the boundary data for the
diffusion equation. The algorithms are validated by
numerical experiments and also by error analysis for the
pure diffusive scaling case.},
Doi = {10.1016/j.jcp.2015.03.014},
Key = {fds243732}
}
@article{fds243733,
Author = {J Lu and CB Mendl},
Title = {Numerical scheme for a spatially inhomogeneous matrixvalued
quantum Boltzmann equation},
Journal = {Journal of Computational Physics},
Volume = {291},
Pages = {303316},
Year = {2015},
Month = {June},
ISSN = {00219991},
url = {http://dx.doi.org/10.1016/j.jcp.2015.03.020},
Doi = {10.1016/j.jcp.2015.03.020},
Key = {fds243733}
}
@article{fds243734,
Author = {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 = {15393755},
url = {http://dx.doi.org/10.1103/PhysRevE.91.032403},
Abstract = {© 2015 American Physical Society. The BurtonCabreraFrank
(BCF) model for the flow of line defects (steps) on crystal
surfaces has offered useful insights into nanostructure
evolution. This model has rested on phenomenological
grounds. Our goal is to show via scaling arguments the
emergence of the BCF theory for noninteracting steps from a
stochastic atomistic scheme of a kinetic restricted
solidonsolid model in one spatial dimension. Our main
assumptions are: adsorbed atoms (adatoms) form a dilute
system, and elastic effects of the crystal lattice are
absent. The step edge is treated as a front that propagates
via probabilistic rules for atom attachment and detachment
at the step. We formally derive a quasistatic step flow
description by averaging out the stochastic scheme when
terrace diffusion, adatom desorption, and deposition from
above are present.},
Doi = {10.1103/PhysRevE.91.032403},
Key = {fds243734}
}
@article{fds243743,
Author = {J Lu and J Nolen},
Title = {Reactive trajectories and the transition path
process},
Journal = {Probability Theory and Related Fields},
Volume = {161},
Number = {12},
Pages = {195244},
Year = {2015},
Month = {February},
ISSN = {01788051},
url = {http://dx.doi.org/10.1007/s004400140547y},
Doi = {10.1007/s004400140547y},
Key = {fds243743}
}
@article{fds243736,
Author = {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 = {A609A624},
Year = {2015},
Month = {January},
ISSN = {10648275},
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 = {15421572},
Year = {2015},
Month = {January},
ISSN = {15403459},
url = {http://dx.doi.org/10.1137/140955872},
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{fds226997,
Author = {J. Lu and Qin Li and Weiran Sun},
Title = {Halfspace kinetic equations with general boundary
conditions},
Year = {2015},
url = {http://arxiv.org/abs/1509.03225},
Key = {fds226997}
}
@article{fds227008,
Author = {J. Lu and Ricardo Delgadillo and Xu Yang},
Title = {Gaugeinvariant 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 divideandconquer 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 = {329335},
Year = {2015},
ISSN = {00219991},
url = {http://dx.doi.org/10.1016/j.jcp.2015.09.014},
Abstract = {© 2015 Elsevier Inc.Electron repulsion integral tensor has
ubiquitous applications in electronic structure
computations. In this work, we propose an algorithm which
compresses the electron repulsion tensor into the tensor
hypercontraction format with O(nN2logN) computational cost,
where N is the number of orbital functions and n is the
number of spatial grid points that the discretization of
each orbital function has. The algorithm is based on a novel
strategy of density fitting using a selection of a subset of
spatial grid points to approximate the pair products of
orbital functions on the whole domain.},
Doi = {10.1016/j.jcp.2015.09.014},
Key = {fds243729}
}
@article{fds243730,
Author = {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 = {20972117},
Year = {2015},
ISSN = {15396746},
url = {http://dx.doi.org/10.4310/CMS.2015.v13.n8.a6},
Doi = {10.4310/CMS.2015.v13.n8.a6},
Key = {fds243730}
}
@article{fds243737,
Author = {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 = {10511074},
Year = {2015},
ISSN = {15396746},
url = {http://dx.doi.org/10.4310/CMS.2015.v13.n5.a1},
Doi = {10.4310/CMS.2015.v13.n5.a1},
Key = {fds243737}
}
%% Maggioni, Mauro
@article{fds290935,
Author = {M Maggioni},
Title = {Geometry of Data and Biology},
Journal = {Notices of the American Mathematical Society},
Volume = {62},
Number = {10},
Pages = {11851188},
Year = {2015},
Month = {November},
ISSN = {00029920},
url = {http://dx.doi.org/10.1090/noti1289},
Doi = {10.1090/noti1289},
Key = {fds290935}
}
@article{fds300136,
Author = {Mauro Maggioni and Stanislav Minsker and Nate Strawn},
Title = {Multiscale Dictionary Learning: NonAsymptotic Bounds and
Robustness},
Journal = {Jour. Mach. Lear. Res.},
Year = {2015},
url = {http://arxiv.org/abs/1401.5833},
Key = {fds300136}
}
@article{fds300137,
Author = {M. Crosskey and M. Maggioni},
Title = {ATLAS: A geometric approach to learning highdimensional
stochastic systems near manifolds},
Journal = {SIAM Journ. Mult. Model. Simul.},
Year = {2015},
Key = {fds300137}
}
@article{fds300142,
Author = {T. Tomita and J. Vogelstein and M. Maggioni},
Title = {Randomer Forests},
Year = {2015},
Key = {fds300142}
}
@article{fds300143,
Author = {Yi (Grace) Wang and Guangliang Chen and Mauro Maggioni},
Title = {Highdimensional datamodeling 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 = {Hyperspectral Analysis of normal and malignant colon tissue
microarray sections using a novel DMD system},
Year = {2004},
Key = {PathNIH2004}
}
@techreport{CMTech,
Author = {Ronald R Coifman and Mauro Maggioni},
Title = {Multiresolution Analysis associated to diffusion semigroups:
construction and fast algorithms},
Number = {YALE/DCS/TR1289},
Organization = {Dept. Comp. Sci., Yale University},
Institution = {Dept. Comp. Sci., Yale University},
Year = {2004},
Key = {CMTech}
}
%% Mattingly, Jonathan C.
@article{fds300245,
Author = {NE GlattHoltz 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
KrylovBogolyubov 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 = {37553787},
Year = {2015},
Month = {October},
ISSN = {09517715},
url = {http://hdl.handle.net/10161/9514},
Abstract = {This is a detailed analysis of invariant measures for
onedimensional dynamical systems with random switching. In
particular, we prove smoothness of the invariant densities
away from critical points and describe the asymptotics of
the invariant densities at critical points.},
Doi = {10.1088/09517715/28/11/3755},
Key = {fds243880}
}
@article{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, lowrank 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 = {28232845},
Year = {2015},
Month = {August},
ISSN = {09517715},
url = {http://hdl.handle.net/10161/9510},
Doi = {10.1088/09517715/28/8/2823},
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 fastreplicating virus strain outcompetes
slowerreplicating strains at the withinhost scale.
However, if the fastreplicating strain causes host
morbidity and is less frequently transmitted, it can be
outcompeted by slowerreplicating strains at the
betweenhost scale. Here we consider a stochastic
ballandurn process which models this type of phenomenon.
We prove the weak convergence of this process under two
natural scalings. The first scaling leads to a deterministic
nonlinear integropartial differential equation on the
interval $[0,1]$ with dependence on a single parameter,
$\lambda$. We show that the fixed points of this
differential equation are Beta distributions and that their
stability depends on $\lambda$ and the behavior of the
initial data around $1$. The second scaling leads to a
measurevalued FlemingViot process, an infinite dimensional
stochastic process that is frequently associated with a
population genetics.},
Key = {fds303549}
}
@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},
Doi = {10.1214/EJP.v203887},
Key = {fds243883}
}
@article{fds243884,
Author = {DP Herzog and JC Mattingly},
Title = {NoiseInduced Stabilization of Planar Flows
II},
Journal = {Electronic Journal of Probability},
Volume = {20},
Year = {2015},
Month = {January},
url = {http://hdl.handle.net/10161/9512},
Abstract = {© 2015 University of Washington. All rights reserved. We
continue the work started in Part I [6], showing how the
addition of noise can stabilize an otherwise unstable
system. The analysis makes use of nearly optimal Lyapunov
functions. In this continuation, we remove the main limiting
assumption of Part I by an inductive procedure as well as
establish a lower bound which shows that our construction is
radially sharp. We also prove a version of Peskir’s [7]
generalized Tanaka formula adapted to patching together
Lyapunov functions. This greatly simplifies the analysis
used in previous works.},
Doi = {10.1214/EJP.v204048},
Key = {fds243884}
}
@article{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 = {30353063},
Year = {2015},
Month = {January},
ISSN = {00361410},
url = {http://hdl.handle.net/10161/9517},
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 = {129},
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 = {18 pages},
Year = {2015},
Month = {December},
url = {http://arxiv.org/abs/1411.6652v1},
Abstract = {New representations of treestructured data objects, using
ideas from topological data analysis, enable improved
statistical analyses of a population of brain artery trees.
A number of representations of each data tree arise from
persistence diagrams that quantify branching and looping of
vessels at multiple scales. Novel approaches to the
statistical analysis, through various summaries of the
persistence diagrams, lead to heightened correlations with
covariates such as age and sex, relative to earlier analyses
of this data set. The correlation with age continues to be
significant even after controlling for correlations from
earlier significant summaries},
Key = {fds303556}
}
@article{fds303557,
Author = {E Miller and T Kahle and C O'Neill},
Title = {Irreducible decomposition of binomial ideals},
Journal = {Compositio Mathematica},
Pages = {13 pages},
Year = {2015},
Month = {December},
url = {http://arxiv.org/abs/1503.02607},
Abstract = {Building on coprincipal mesoprimary decomposition [Kahle and
Miller, 2014], we combinatorially construct an irreducible
decomposition of any given binomial ideal. In a parallel
manner, for congruences in commutative monoids we construct
decompositions that are direct combinatorial analogues of
binomial irreducible decompositions, and for binomial ideals
we construct decompositions into ideals that are as
irreducible as possible while remaining binomial. We provide
an example of a binomial ideal that is not an intersection
of irreducible binomial ideals, thus answering a question of
Eisenbud and Sturmfels [1996].},
Key = {fds303557}
}
@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 = {11781184},
Year = {2015},
Month = {November},
ISSN = {00029920},
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 = {5191},
Year = {2015},
Month = {July},
ISSN = {01968858},
url = {http://dx.doi.org/10.1016/j.aam.2015.04.002},
Doi = {10.1016/j.aam.2015.04.002},
Key = {fds243887}
}
@article{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},
Doi = {10.1214/EJP.v203887},
Key = {fds243886}
}
@article{fds243885,
Author = {C Berkesch Zamaere and S Griffeth and E Miller},
Title = {Systems of parameters and holonomicity of hypergeometric
systems},
Journal = {Pacific Journal of Mathematics},
Volume = {276},
Number = {2},
Pages = {281286},
Year = {2015},
ISSN = {00308730},
url = {http://dx.doi.org/10.2140/pjm.2015.276.281},
Doi = {10.2140/pjm.2015.276.281},
Key = {fds243885}
}
%% 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 = {5255},
Year = {2015},
Month = {January},
url = {http://dx.doi.org/10.4169/amer.math.monthly.122.01.52},
Key = {fds300014}
}
@article{fds300020,
Author = {F.C. Motta and P.D. Shipman},
Title = {Sharpening the defect of complex Hadamards with a
flow},
Year = {2015},
Key = {fds300020}
}
@article{fds300021,
Author = {F.C. Motta and P.D. Shipman and C. Burris},
Title = {An unoriented variation on de Bruijn sequences},
Year = {2015},
Key = {fds300021}
}
%% Mukherjee, Sayan
@article{fds258517,
Author = {E Munch and K Turner and P Bendich and S Mukherjee and J Mattingly and J
Harer},
Title = {Probabilistic Fréchet means for time varying persistence
diagrams},
Journal = {Electronic Journal of Statistics},
Volume = {9},
Number = {1},
Pages = {11731204},
Year = {2015},
url = {http://hdl.handle.net/10161/10051},
Doi = {10.1214/15EJS1030},
Key = {fds258517}
}
%% Murphy, James
@article{fds292868,
Author = {Czaja, Wojciech and Benjamin Manning and Lance McLean and James M.
Murphy},
Title = {Fusion of aerial gamma ray survey and remote sensing data
for deeper understanding of radionucleotide fate after
radiological incidents: examples from the Fukushima DaiIchi
response},
Journal = {Journal of Radioanalytic and Nuclear Chemistry},
Year = {2015},
Key = {fds292868}
}
@article{fds292869,
Author = {Murphy, James M and Jacqueline Le Moigne and David J.
Harding},
Title = {Automatic image registration of multimodal remotely sensed
data with global shearlet features},
Journal = {IEEE Transactions on Geoscience and Remote
Sensing},
Year = {2015},
Key = {fds292869}
}
%% Ng, Lenhard L.
@article{fds299958,
Author = {C. Cornwell and L. Ng and S. Sivek},
Title = {Obstructions to Lagrangian concordance},
Journal = {Algebraic & Geometric Topology},
Year = {2015},
url = {http://arxiv.org/abs/1411.1364},
Key = {fds299958}
}
@article{fds299959,
Author = {L. Ng and D. Rutherford and V. Shende and S. Sivek and E.
Zaslow},
Title = {Augmentations are sheaves},
Year = {2015},
url = {http://arxiv.org/abs/1502.04939},
Key = {fds299959}
}
@article{fds299960,
Author = {L. Ng and D. Rutherford and V. Shende and S. Sivek},
Title = {The cardinality of the augmentation category of a Legendrian
link},
Year = {2015},
url = {http://arxiv.org/abs/1511.06724},
Key = {fds299960}
}
@article{fds243935,
Author = {R Lipshitz and L Ng and S Sarkar},
Title = {On transverse invariants from Khovanov homology},
Journal = {Quantum Topology},
Volume = {6},
Number = {3},
Pages = {475513},
Year = {2015},
ISSN = {1663487X},
url = {http://dx.doi.org/10.4171/QT/69},
Doi = {10.4171/QT/69},
Key = {fds243935}
}
@article{fds243937,
Author = {T Ekholm and L Ng},
Title = {Legendrian contact homology in the boundary of a subcritical
weinstein 4Manifold},
Journal = {Journal of Differential Geometry},
Volume = {101},
Number = {1},
Pages = {67157},
Year = {2015},
ISSN = {0022040X},
Abstract = {We give a combinatorial description of the Legendrian
contact homology algebra associated to a Legendrian link in
S<sup>1</sup> × S<sup>2</sup> or
any connected sum #k(S<sup>1</sup>
×S<sup>2</sup>), viewed as the contact boundary
of the Weinstein manifold obtained by attaching 1handles to
the 4ball. In view of the surgery formula for symplectic
homology [5], this gives a combinatorial description of the
symplectic homology of any 4dimensional Weinstein manifold
(and of the linearized contact homology of its boundary). We
also study examples and discuss the invariance of the
Legendrian homology algebra under deformations, from both
the combinatorial and the analytical perspectives.},
Key = {fds243937}
}
%% Nolen, James H.
@article{fds227095,
Author = {S. Bhamidi and J. Hannig and C. Lee and J. Nolen},
Title = {The importance sampling technique for understanding rare
events in ErdősRényi random graphs},
Journal = {Electronic Journal of Probability},
Year = {2015},
Month = {October},
url = {http://ejp.ejpecp.org/article/view/2696},
Doi = {10.1214/EJP.v202696},
Key = {fds227095}
}
@article{fds287342,
Author = {J Nolen and JM Roquejoffre and L Ryzhik},
Title = {PowerLike Delay in Time Inhomogeneous FisherKPP
Equations},
Journal = {Communications in Partial Differential Equations},
Volume = {40},
Number = {3},
Pages = {475505},
Year = {2015},
Month = {March},
ISSN = {03605302},
url = {http://math.duke.edu/~nolen/preprints/bigdelaydraft.pdf},
Doi = {10.1080/03605302.2014.972744},
Key = {fds287342}
}
@article{fds287345,
Author = {J Lu and J Nolen},
Title = {Reactive trajectories and the transition path
process},
Journal = {Probability Theory and Related Fields},
Volume = {161},
Number = {12},
Pages = {195244},
Year = {2015},
Month = {February},
ISSN = {01788051},
url = {http://dx.doi.org/10.1007/s004400140547y},
Doi = {10.1007/s004400140547y},
Key = {fds287345}
}
@article{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.v203887},
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.v202696},
Doi = {10.1214/EJP.v202696},
Key = {fds290937}
}
@article{fds299972,
Author = {J. Nolen and J.M. Roquejoffre and L. Ryzhik},
Title = {Refined long time asymptotics for the FisherKPP
equation},
Year = {2015},
url = {http://math.duke.edu/~nolen/preprints/kppbrezisv5.pdf},
Key = {fds299972}
}
@article{fds226519,
Author = {F. Hamel and J. Nolen and J.M. Roquejoffre and L.
Ryzhik},
Title = {The logarithmic delay of KPP fronts in a periodic
medium},
Journal = {Journal of the European Mathematical Society},
Year = {2015},
url = {http://arxiv.org/abs/1211.6173},
Key = {fds226519}
}
@article{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/s4007201500684},
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 1Persistence Scoring;
Discovering Periodicity in Gene Expression Time Series
Data},
Journal = {BMC Bioinformatics},
Year = {2015},
Month = {July},
Key = {fds226515}
}
%% Petters, Arlie O.
@book{fds15387,
Author = {A. O. Petters and M. C. Werner},
Title = {Gravitational Lensing and Black Holes},
Publisher = {Springer, in preparation},
Year = {2017},
Month = {Spring},
Key = {fds15387}
}
@book{fds51036,
Author = {A. O. Petters and X. Dong},
Title = {An Introduction to Mathematical Finance: Understanding and
Building Financial Intuition},
Series = {SUMAT},
Publisher = {Springer, in preparation},
Year = {2016},
Month = {Winter},
Key = {fds51036}
}
%% 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 = {54715473},
Year = {2015},
Month = {September},
ISSN = {00029939},
url = {http://dx.doi.org/10.1090/proc/12778},
Doi = {10.1090/proc/12778},
Key = {fds302459}
}
@article{fds302460,
Author = {DR HeathBrown and LB Pierce},
Title = {Burgess bounds for short mixed character
sums},
Journal = {Journal of the London Mathematical Society},
Volume = {91},
Number = {3},
Pages = {693708},
Year = {2015},
Month = {June},
ISSN = {00246107},
url = {http://dx.doi.org/10.1112/jlms/jdv009},
Doi = {10.1112/jlms/jdv009},
Key = {fds302460}
}
@misc{fds299989,
Author = {L.B. Pierce},
Title = {Recent Publications},
Year = {2015},
Key = {fds299989}
}
%% Plesser, M. Ronen
@article{fds248062,
Author = {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 = {751770},
Year = {2015},
Month = {September},
ISSN = {05503213},
url = {http://dx.doi.org/10.1016/j.nuclphysb.2015.05.030},
Doi = {10.1016/j.nuclphysb.2015.05.030},
Key = {fds248062}
}
@article{fds248063,
Author = {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 = {11721176},
Year = {2015},
Month = {November},
ISSN = {00029920},
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 = {118133},
Year = {2015},
Month = {July},
ISSN = {00225193},
url = {http://dx.doi.org/10.1016/j.jtbi.2015.04.006},
Abstract = {Marked alterations in systemic glutamateglutamine
metabolism characterize the catabolic state, in which there
is an increased breakdown and decreased synthesis of
skeletal muscle protein. Among these alterations are a
greatly increased net release of glutamine (Gln) from
skeletal muscle into blood plasma and a dramatic depletion
of intramuscular Gln. Understanding the catabolic state is
important because a number of pathological conditions with
very different etiologies are characterized by its presence;
these include major surgery, sepsis, trauma, and some
cancers. Acetaminophen (APAP) overdose is also accompanied
by dramatic changes in systemic glutamateglutamine
metabolism including large drops in liver glutathione (for
which glutamate is a precursor) and plasma Gln. We have
constructed a mathematical model of glutamate and glutamine
metabolism in rat which includes liver, blood plasma and
skeletal muscle. We show that for the normal rat, the model
solutions fit experimental data including the diurnal
variation in liver glutathione (GSH). We show that for the
rat chronically dosed with dexamethasone (an artificial
glucocorticoid which induces a catabolic state) the model
can be used to explain empirically observed facts such as
the linear decline in intramuscular Gln and the drop in
plasma glutamine. We show that for the Wistar rat undergoing
APAP overdose the model reproduces the experimentally
observed rebound of liver GSH to normal levels by the 24h
mark. We show that this rebound is achieved in part by the
action of the cystineglutamate antiporter, an amino acid
transporter not normally expressed in liver but induced
under conditions of oxidative stress. Finally, we explain
why supplementation with Gln, a Glu precursor, assists in
the preservation of liver GSH during APAP overdose despite
the fact that under normal conditions only Cys is
ratelimiting for GSH formation.},
Doi = {10.1016/j.jtbi.2015.04.006},
Key = {fds244008}
}
@article{fds244006,
Author = {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/s1291501501892},
Abstract = {Mathematical models are a useful tool for investigating a
large number of questions in metabolism, genetics, and
geneenvironment interactions. A model based on the
underlying biology and biochemistry is a platform for in
silico biological experimentation that can reveal the causal
chain of events that connect variation in one quantity to
variation in another. We discuss how we construct such
models, how we have used them to investigate homeostatic
mechanisms, geneenvironment interactions, and
genotypephenotype mapping, and how they can be used in
precision and personalized medicine.},
Doi = {10.1186/s1291501501892},
Key = {fds244006}
}
@article{fds244007,
Author = {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 = {30353063},
Year = {2015},
Month = {January},
ISSN = {00361410},
url = {http://hdl.handle.net/10161/9517},
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/s1291801502156},
Abstract = {Methyltransferase (MT) reactions, in which methyl groups are
attached to substrates, are fundamental to many aspects of
cell biology and human physiology. The universal methyl
donor for these reactions is Sadenosylmethionine (SAM) and
this presents the cell with an important regulatory problem.
If the flux along one pathway is changed then the SAM
concentration will change affecting all the other MT
pathways, so it is difficult for the cell to regulate the
pathways independently.We created a mathematical model,
based on the known biochemistry of the folate and methionine
cycles, to study the regulatory mechanisms that enable the
cell to overcome this difficulty. Some of the primary
mechanisms are longrange allosteric interactions by which
substrates in one part of the biochemical network affect the
activity of enzymes at distant locations in the network (not
distant in the cell). Because of these longrange allosteric
interactions, the dynamic behavior of the network is very
complicated, and so mathematical modeling is a useful tool
for investigating the effects of the regulatory mechanisms
and understanding the complicated underlying biochemistry
and cell biology.We study the allosteric binding of
5methyltetrahydrofolate (5 mTHF) to glycineNmethyltransferase
(GNMT) and explain why data in the literature implies that
when one molecule binds, GNMT retains half its activity.
Using the model, we quantify the effects of different
regulatory mechanisms and show how cell processes would be
different if the regulatory mechanisms were eliminated. In
addition, we use the model to interpret and understand data
from studies in the literature. Finally, we explain why a
full understanding of how competing MTs are regulated is
important for designing intervention strategies to improve
human health.We give strong computational evidence that once
bound GNMT retains half its activity. The longrange
allosteric interactions enable the cell to regulate the MT
reactions somewhat independently. The low K m values of many
MTs also play a role because the reactions then run near
saturation and changes in SAM have little effect. Finally,
the inhibition of the MTs by the product
Sadenosylhomocysteine also stabilizes reaction rates
against changes in SAM.},
Doi = {10.1186/s1291801502156},
Key = {fds290939}
}
%% 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 L2Cohomology, Johns Hopkins
U},
Year = {2015},
url = {http://arxiv.org/abs/1403.0646},
Key = {fds292861}
}
@article{fds292862,
Author = {Colleen Robles},
Title = {Classification of horizontal SL(2)s},
Journal = {Compositio Math.},
Year = {2015},
url = {http:/},
Key = {fds292862}
}
@article{fds292863,
Author = {M. Kerr and C. Robles},
Title = {Hodge theory and real orbits in flag varieties},
Year = {2015},
url = {http://arxiv.org/abs/1407.4507},
Key = {fds292863}
}
%% Ryser, Marc D.
@article{fds244097,
Author = {MD Ryser and K McGoff and DP Herzog and DJ Sivakoff and ER
Myers},
Title = {Impact of coveragedependent marginal costs on optimal HPV
vaccination strategies.},
Journal = {Epidemics},
Volume = {11},
Pages = {3247},
Year = {2015},
Month = {June},
ISSN = {17554365},
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 agentbased modeling
framework to revisit the male vaccination debate in light of
these new findings. Within this framework, we assess the
impact of coveragedependent marginal costs of vaccine
distribution on optimal immunization strategies against HPV.
Focusing on the two scenarios of ongoing and new vaccination
programs, we analyze different resource allocation policies
and their effects on overall disease burden. Our results
suggest that if the costs associated with vaccinating males
are relatively close to those associated with vaccinating
females, then coveragedependent, increasing marginal costs
may favor vaccination strategies that entail immunization of
both genders. In particular, this study emphasizes the
necessity for further empirical research on the nature of
coveragedependent vaccination costs.},
Doi = {10.1016/j.epidem.2015.01.003},
Key = {fds244097}
}
%% Saper, Leslie
@article{fds226574,
Author = {L. Ji and K. Murty and L. Saper and J. Scherk},
Title = {The Fundamental Group of Reductive BorelSerre and Satake
Compactifications},
Journal = {The Asian Journal of Mathematics},
Volume = {19},
Number = {3},
Pages = {465486},
Year = {2015},
url = {http://www.intlpress.com/site/pub/pages/journals/items/ajm/content/vols/0019/0003/a004/},
Abstract = {Let <b>G</b> be an almost simple, simply connected algebraic
group defined over a number field <i>k</i>, and let <i>S</i>
be a finite set of places of <i>k</i> including all infinite
places. Let <i>X</i> be the product over
<nobr><i>v</i> ∈ <i>S</i></nobr> of the
symmetric spaces associated to <b>G</b>(<i>k<sub>v</sub></i>),
when <i>v</i> is an infinite place, and the BruhatTits
buildings associated to <b>G</b>(<i>k<sub>v</sub></i>), when
<i>v</i> is a finite place. The main result of this paper is
to compute explicitly the fundamental group of the reductive
BorelSerre compactification of <nobr>Γ \ <i>X</i></nobr>,
where Γ is an <i>S</i>arithmetic subgroup of
<b>G</b>. In the case that Γ is neat, we show that
this fundamental group is isomorphic to <nobr>Γ / <i>E</i>Γ</nobr>,
where <i>E</i>Γ is the subgroup generated by the
elements of Γ belonging to unipotent radicals of
parabolic <i>k</i>subgroups. Analogous computations of the
fundamental group of the Satake compactifications are made.
It is noteworthy that calculations of the congruence
subgroup kernel <nobr><i>C</i>(<i>S</i>,<b>G</b>)</nobr>
yield similar results.},
Key = {fds226574}
}
%% 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 = {559609},
Year = {2015},
Key = {fds292866}
}
%% TurnageButterbaugh, Caroline
@book{fds299981,
Author = {O. Barrett and F. W. K. Firk and S. J. Miller and C.
TurnageButterbaugh},
Title = {From Quantum Systems to LFunctions: Pair Correlation
Statistics and Beyond},
Booktitle = {Open Problems in Mathematics},
Publisher = {SpringerVerlag},
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.
TurnageButterbaugh 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. TurnageButterbaugh 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
TurnageButterbaugh and K Winsor},
Title = {Gaps between zeros of GL(2) Lfunctions},
Journal = {Journal of Mathematical Analysis and Applications},
Volume = {429},
Number = {1},
Pages = {204232},
Year = {2015},
ISSN = {0022247X},
url = {http://dx.doi.org/10.1016/j.jmaa.2015.04.007},
Abstract = {© 2015 Elsevier Inc.Let L(s, f) be an Lfunction associated
to a primitive (holomorphic or Maass) cusp form f on GL(2)
over Q. Combining meanvalue estimates of Montgomery and
Vaughan with a method of Ramachandra, we prove a formula for
the mixed second moments of derivatives of L(1/2 + it, f)
and, via a method of Hall, use it to show that there are
infinitely many gaps between consecutive zeros of L(s, f)
along the critical line that are at least √3=1.732. . .
times the average spacing. Using general pair correlation
results due to Murty and Perelli in conjunction with a
technique of Montgomery, we also prove the existence of
small gaps between zeros of any primitive Lfunction of the
Selberg class. In particular, when f is a primitive
holomorphic cusp form on GL(2) over Q, we prove that there
are infinitely many gaps between consecutive zeros of L(s,
f) along the critical line that are at most 0.823 times the
average spacing.},
Doi = {10.1016/j.jmaa.2015.04.007},
Key = {fds302477}
}
@article{fds302479,
Author = {WD Banks and T Freiberg and CL TurnageButterbaugh},
Title = {Consecutive primes in tuples},
Journal = {Acta Arithmetica},
Volume = {167},
Number = {3},
Pages = {261266},
Year = {2015},
ISSN = {00651036},
url = {http://dx.doi.org/10.4064/aa16734},
Doi = {10.4064/aa16734},
Key = {fds302479}
}
%% Venakides, Stephanos
@article{fds226701,
Author = {Sergey Belov and Stephanos Venakides},
Title = {Smooth parametric dependence of asymptotics of the
semiclassical focusing NLS},
Journal = {Analysis & PDE},
Volume = {8},
Number = {2},
Pages = {257288},
Year = {2015},
Month = {April},
url = {http://dx.doi.org/10.2140/apde.2015.8.257},
Abstract = {We consider the onedimensional focusing (cubic) nonlinear
Schrödinger equation (NLS) in the semiclassical limit with
exponentially decaying complexvalued initial data, whose
phase is multiplied by a real parameter. We prove smooth
dependence of the asymptotic solution on the parameter.
Numerical results supporting our estimates of important
quantities are presented.},
Doi = {10.2140/apde.2015.8.257},
Key = {fds226701}
}
@article{fds244138,
Author = {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 = {10980121},
url = {http://dx.doi.org/10.1103/PhysRevB.91.134503},
Abstract = {BoseEinstein condensates of excitonpolaritons are
described by a Schrödinger system of two equations.
Nonlinearity due to exciton interactions gives rise to a
frequency band of dark soliton solutions, which are found
analytically for the lossless zerovelocity case. The
soliton's farfield value varies from zero to infinity as
the operating frequency varies across the band. For positive
detuning (photon frequency higher than exciton frequency),
the exciton wave function becomes discontinuous when the
operating frequency exceeds the exciton frequency. This
phenomenon lies outside the parameter regime of validity of
the GrossPitaevskii (GP) model. Within its regime of
validity, we give a derivation of a singlemode GP model
from the initial Schrödinger system and compare the
continuous polariton solitons and GP solitons using the
healing length notion.},
Doi = {10.1103/PhysRevB.91.134503},
Key = {fds244138}
}
%% Vigogna, Stefano
@article{fds300041,
Author = {E. De Vito and F. De Mari and S. Vigogna},
Title = {Geometric classiication of semidirect products in the
maximal parabolic subgroup of Sp(2,R)},
Journal = {Analysis and Applications},
Year = {2015},
Key = {fds300041}
}
@article{fds300042,
Author = {S. Dahlke and E. De Vito and F. De Mari and D. Labate and G. Steidl and G.
Teschke S. Vigogna},
Title = {Coorbit spaces with voice in a Fréchet space},
Journal = {Fourier Analysis and Applications},
Year = {2015},
Key = {fds300042}
}
@article{fds300043,
Author = {G. S. Alberti and S. Dahlke and F. De Mari and E. De Vito and S.
Vigogna},
Title = {Continuous and discrete frames generated by the evolution
flow of the Schrödinger equation},
Year = {2015},
Key = {fds300043}
}
%% Witelski, Thomas P.
@article{fds293132,
Author = {JA Dijksman and S Mukhopadhyay and C Gaebler and TP Witelski and RP
Behringer},
Title = {Obtaining selfsimilar scalings in focusing
flows.},
Journal = {Physical review. E, Statistical, nonlinear, and soft matter
physics},
Volume = {92},
Number = {4},
Pages = {043016},
Year = {2015},
Month = {October},
ISSN = {15393755},
url = {http://dx.doi.org/10.1103/physreve.92.043016},
Abstract = {The surface structure of converging thin fluid films
displays selfsimilar behavior, as was shown in the work by
Diez et al. [Q. Appl. Math. 210, 155 (1990)]. Extracting the
related similarity scaling exponents from either numerical
or experimental data is nontrivial. Here we provide two such
methods. We apply them to experimental and numerical data on
converging fluid films driven by both surface tension and
gravitational forcing. In the limit of pure gravitational
driving, we recover Diez' semianalytic result, but our
methods also allow us to explore the entire regime of mixed
capillary and gravitational driving, up to entirely
surfacetensiondriven flows. We find scaling forms of
smoothly varying exponents up to surprisingly small Bond
numbers. Our experimental results are in reasonable
agreement with our numerical simulations, which confirm
theoretically obtained relations between the scaling
exponents.},
Doi = {10.1103/physreve.92.043016},
Key = {fds293132}
}
@article{fds244178,
Author = {TP Witelski},
Title = {Preface to the special issue on “Thin films and fluid
interfaces”},
Journal = {Journal of Engineering Mathematics},
Volume = {94},
Number = {1},
Pages = {13},
Year = {2015},
Month = {October},
ISSN = {00220833},
url = {http://dx.doi.org/10.1007/s106650149760z},
Doi = {10.1007/s106650149760z},
Key = {fds244178}
}
@book{fds227199,
Author = {T.P. Witelski and M. Bowen},
Title = {Methods of Mathematical Modelling},
Series = {Springer Undergraduate Mathematics Series
(SUMS)},
Year = {2015},
ISBN = {9783319230412},
url = {http://www.springer.com/us/book/9783319230412},
Key = {fds227199}
}
%% Yang, Haizhao
@article{fds303562,
Author = {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},
Publisher = {Elsevier},
Editor = {K Bhattacharya},
Year = {2016},
Month = {January},
url = {http://hdl.handle.net/10161/11296},
Key = {fds303562}
}
@article{fds226959,
Author = {H Yang and J Lu and WP Brown and I Daubechies and L
Ying},
Title = {Quantitative Canvas Weave Analysis Using 2D Synchrosqueezed
Transforms: Application of timefrequency analysis to art
investigation},
Journal = {Signal Processing Magazine, IEEE},
Volume = {32},
Pages = {5563},
Year = {2015},
Month = {July},
ISSN = {10535888},
url = {http://dx.doi.org/10.1109/MSP.2015.2406882},
Abstract = {Quantitative canvas weave analysis has many applications in
art investigations of paintings, including dating,
forensics, and canvas rollmate identification.
Traditionally, canvas analysis is based on Xradiographs.
Prior to serving as a painting canvas, a piece of fabric is
coated with a priming agent; smoothing its surface makes
this layer thicker between and thinner right on top of weave
threads. These variations affect the Xray absorption,
making the weave pattern stand out in Xray images of the
finished painting. To characterize this pattern, it is
customary to visually inspect small areas within the
Xradiograph and count the number of horizontal and vertical
weave threads; averages of these then estimate the overall
canvas weave density. The tedium of this process typically
limits its practice to just a few sample regions of the
canvas. In addition, it does not capture more subtle
information beyond weave density, such as thread angles or
variations in the weave pattern. Signal processing
techniques applied to art investigation are now increasingly
used to develop computerassisted canvas weave analysis
tools.},
Doi = {10.1109/MSP.2015.2406882},
Key = {fds226959}
}
@article{fds226960,
Author = {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 = {3366},
Year = {2015},
Month = {July},
ISSN = {10635203},
url = {http://dx.doi.org/10.1016/j.acha.2014.08.004},
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},
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 = {614631},
Year = {2015},
Month = {January},
ISSN = {15403459},
url = {http://dx.doi.org/10.1137/140997658},
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 = {714732},
Year = {2015},
Month = {January},
ISSN = {15403459},
url = {http://dx.doi.org/10.1137/15M1007173},
Doi = {10.1137/15M1007173},
Key = {fds226963}
}
@article{fds292865,
Author = {Y. Li and H. Yang and L. Ying},
Title = {Multidimensional Butterfly Factorization},
Journal = {Applied and Computational Harmonic Analysis},
Year = {2015},
url = {http://arxiv.org/abs/1509.07925},
Key = {fds292865}
}
%% Zhou, Zhennan
@article{fds299987,
Author = {Z. Zhou and Z. Ma and Y. Zhang.},
Title = {A semiLagrangian time splitting method for the
semiclassical Schrodinger equation with vector potentials
using NUFFT},
Year = {2015},
Key = {fds299987}
}
