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Mathematics Faculty: Publications since January 2017

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

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

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

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

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

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

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

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


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

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

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

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


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


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


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


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


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

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

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


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

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


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

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


%% Daubechies, Ingrid   
@article{fds329931,
   Author = {Gao, T and Yapuncich, GS and Daubechies, I and Mukherjee, S and Boyer,
             DM},
   Title = {Development and Assessment of Fully Automated and Globally
             Transitive Geometric Morphometric Methods, With Application
             to a Biological Comparative Dataset With High Interspecific
             Variation.},
   Journal = {The Anatomical Record : Advances in Integrative Anatomy and
             Evolutionary Biology},
   Year = {2017},
   Month = {October},
   url = {http://dx.doi.org/10.1002/ar.23700},
   Abstract = {Automated geometric morphometric methods are promising tools
             for shape analysis in comparative biology, improving
             researchers' abilities to quantify variation extensively (by
             permitting more specimens to be analyzed) and intensively
             (by characterizing shapes with greater fidelity). Although
             use of these methods has increased, published automated
             methods have some notable limitations: pairwise
             correspondences are frequently inaccurate and pairwise
             mappings are not globally consistent (i.e., they lack
             transitivity across the full sample). Here, we reassess the
             accuracy of published automated methods-cPDist (Boyer et al.
             Proc Nat Acad Sci 108 (2011) 18221-18226) and auto3Dgm
             (Boyer et al.: Anat Rec 298 (2015a) 249-276)-and evaluate
             several modifications to these methods. We show that a
             substantial percentage of alignments and pairwise maps
             between specimens of dissimilar geometries were inaccurate
             in the study of Boyer et al. (Proc Nat Acad Sci 108 (2011)
             18221-18226), despite a taxonomically partitioned variance
             structure of continuous Procrustes distances. We show these
             inaccuracies are remedied using a globally informed
             methodology within a collection of shapes, rather than
             relying on pairwise comparisons (c.f. Boyer et al.: Anat Rec
             298 (2015a) 249-276). Unfortunately, while global
             information generally enhances maps between dissimilar
             objects, it can degrade the quality of correspondences
             between similar objects due to the accumulation of numerical
             error. We explore a number of approaches to mitigate this
             degradation, quantify their performance, and compare the
             generated pairwise maps (and the shape space characterized
             by these maps) to a "ground truth" obtained from landmarks
             manually collected by geometric morphometricians. Novel
             methods both improve the quality of the pairwise
             correspondences relative to cPDist and achieve a taxonomic
             distinctiveness comparable to auto3Dgm. Anat Rec, 2017. ©
             2017 Wiley Periodicals, Inc.},
   Doi = {10.1002/ar.23700},
   Key = {fds329931}
}

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

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

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

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

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


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

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

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


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

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

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

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

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

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

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

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

@article{fds329990,
   Author = {Ovaskainen, O and Tikhonov, G and Dunson, D and Grøtan, V and Engen, S and Sæther, B-E and Abrego, N},
   Title = {How are species interactions structured in species-rich
             communities? A new method for analysing time-series
             data},
   Journal = {Proceedings of the Royal Society of London: Biological
             Sciences},
   Volume = {284},
   Number = {1855},
   Pages = {20170768-20170768},
   Year = {2017},
   Month = {May},
   url = {http://dx.doi.org/10.1098/rspb.2017.0768},
   Doi = {10.1098/rspb.2017.0768},
   Key = {fds329990}
}

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

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

@article{fds329111,
   Author = {Durante, D and Paganin, S and Scarpa, B and Dunson,
             DB},
   Title = {Bayesian modelling of networks in complex business
             intelligence problems},
   Journal = {Journal of the Royal Statistical Society: Series C (Applied
             Statistics)},
   Volume = {66},
   Number = {3},
   Pages = {555-580},
   Year = {2017},
   Month = {April},
   url = {http://dx.doi.org/10.1111/rssc.12168},
   Doi = {10.1111/rssc.12168},
   Key = {fds329111}
}

@article{fds326037,
   Author = {McKinney, M and Moffitt, AB and Gaulard, P and Travert, M and De Leval,
             L and Nicolae, A and Raffeld, M and Jaffe, ES and Pittaluga, S and Xi, L and Heavican, T and Iqbal, J and Belhadj, K and Delfau-Larue, MH and Fataccioli, V and Czader, MB and Lossos, IS and Chapman-Fredricks,
             JR and Richards, KL and Fedoriw, Y and Ondrejka, SL and Hsi, ED and Low, L and Weisenburger, D and Chan, WC and Mehta-Shah, N and Horwitz, S and Bernal-Mizrachi, L and Flowers, CR and Beaven, AW and Parihar, M and Baseggio, L and Parrens, M and Moreau, A and Sujobert, P and Pilichowska, M and Evens, AM and Chadburn, A et
             al.},
   Title = {The Genetic Basis of Hepatosplenic T-cell
             Lymphoma.},
   Journal = {Cancer Discovery},
   Volume = {7},
   Number = {4},
   Pages = {369-379},
   Year = {2017},
   Month = {April},
   url = {http://dx.doi.org/10.1158/2159-8290.cd-16-0330},
   Abstract = {Hepatosplenic T-cell lymphoma (HSTL) is a rare and lethal
             lymphoma; the genetic drivers of this disease are unknown.
             Through whole-exome sequencing of 68 HSTLs, we define
             recurrently mutated driver genes and copy-number alterations
             in the disease. Chromatin-modifying genes, including SETD2,
             INO80, and ARID1B, were commonly mutated in HSTL, affecting
             62% of cases. HSTLs manifest frequent mutations in STAT5B
             (31%), STAT3 (9%), and PIK3CD (9%), for which there
             currently exist potential targeted therapies. In addition,
             we noted less frequent events in EZH2, KRAS, and TP53SETD2
             was the most frequently silenced gene in HSTL. We
             experimentally demonstrated that SETD2 acts as a tumor
             suppressor gene. In addition, we found that mutations in
             STAT5B and PIK3CD activate critical signaling pathways
             important to cell survival in HSTL. Our work thus defines
             the genetic landscape of HSTL and implicates gene mutations
             linked to HSTL pathogenesis and potential treatment
             targets.Significance: We report the first systematic
             application of whole-exome sequencing to define the genetic
             basis of HSTL, a rare but lethal disease. Our work defines
             SETD2 as a tumor suppressor gene in HSTL and implicates
             genes including INO80 and PIK3CD in the disease. Cancer
             Discov; 7(4); 369-79. ©2017 AACR.See related commentary by
             Yoshida and Weinstock, p. 352This article is highlighted in
             the In This Issue feature, p. 339.},
   Doi = {10.1158/2159-8290.cd-16-0330},
   Key = {fds326037}
}

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

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

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

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

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


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

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

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

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

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

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


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


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


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


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


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


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

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

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


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

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


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

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

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

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

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

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

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

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


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


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

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

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


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

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

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

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


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

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

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

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

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

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

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

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

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

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

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

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

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

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


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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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


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


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


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

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

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

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

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

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

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

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

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


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

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

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

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

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


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

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

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


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

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

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


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


%% Ng, Lenhard L.   
@article{fds330520,
   Author = {Ekholm, T and Ng, L and Shende, V},
   Title = {A complete knot invariant from contact homology},
   Journal = {Inventiones mathematicae},
   Pages = {1-52},
   Year = {2017},
   Month = {October},
   url = {http://dx.doi.org/10.1007/s00222-017-0761-1},
   Abstract = {© 2017 Springer-Verlag GmbH Germany We construct an
             enhanced version of knot contact homology, and show that we
             can deduce from it the group ring of the knot group together
             with the peripheral subgroup. In particular, it completely
             determines a knot up to smooth isotopy. The enhancement
             consists of the (fully noncommutative) Legendrian contact
             homology associated to the union of the conormal torus of
             the knot and a disjoint cotangent fiber sphere, along with a
             product on a filtered part of this homology. As a corollary,
             we obtain a new, holomorphic-curve proof of a result of the
             third author that the Legendrian isotopy class of the
             conormal torus is a complete knot invariant.},
   Doi = {10.1007/s00222-017-0761-1},
   Key = {fds330520}
}

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


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

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


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


%% 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}
}


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

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

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

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

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

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


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

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

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

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

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

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

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

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


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


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

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


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

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

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

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

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


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

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

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

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

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

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

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

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


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

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

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


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

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

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

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

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

@article{fds330624,
   Author = {Zeng, J and Ustun, B and Rudin, C},
   Title = {Interpretable classification models for recidivism
             prediction},
   Journal = {Journal of the Royal Statistical Society: Series A
             (Statistics in Society)},
   Volume = {180},
   Number = {3},
   Pages = {689-722},
   Year = {2017},
   Month = {June},
   url = {http://dx.doi.org/10.1111/rssa.12227},
   Doi = {10.1111/rssa.12227},
   Key = {fds330624}
}

@article{fds330625,
   Author = {Ustun, B and Adler, LA and Rudin, C and Faraone, SV and Spencer, TJ and Berglund, P and Gruber, MJ and Kessler, RC},
   Title = {The World Health Organization Adult Attention-Deficit/Hyperactivity
             Disorder Self-Report Screening Scale for
             DSM-5.},
   Journal = {JAMA Psychiatry},
   Volume = {74},
   Number = {5},
   Pages = {520-526},
   Year = {2017},
   Month = {May},
   url = {http://dx.doi.org/10.1001/jamapsychiatry.2017.0298},
   Abstract = {Recognition that adult attention-deficit/hyperactivity
             disorder (ADHD) is common, seriously impairing, and usually
             undiagnosed has led to the development of adult ADHD
             screening scales for use in community, workplace, and
             primary care settings. However, these scales are all
             calibrated to DSM-IV criteria, which are narrower than the
             recently developed DSM-5 criteria.To update for DSM-5
             criteria and improve the operating characteristics of the
             widely used World Health Organization Adult ADHD Self-Report
             Scale (ASRS) for screening.Probability subsamples of
             participants in 2 general population surveys (2001-2003
             household survey [n = 119] and 2004-2005 managed care
             subscriber survey [n = 218]) who completed the full
             29-question self-report ASRS, with both subsamples
             over-sampling ASRS-screened positives, were blindly
             administered a semistructured research diagnostic interview
             for DSM-5 adult ADHD. In 2016, the Risk-Calibrated
             Supersparse Linear Integer Model, a novel machine-learning
             algorithm designed to create screening scales with optimal
             integer weights and limited numbers of screening questions,
             was applied to the pooled data to create a DSM-5 version of
             the ASRS screening scale. The accuracy of the new scale was
             then confirmed in an independent 2011-2012 clinical sample
             of patients seeking evaluation at the New York University
             Langone Medical Center Adult ADHD Program (NYU Langone) and
             2015-2016 primary care controls (n = 300). Data analysis
             was conducted from April 4, 2016, to September 22, 2016.The
             sensitivity, specificity, area under the curve (AUC), and
             positive predictive value (PPV) of the revised ASRS.Of the
             total 637 participants, 44 (37.0%) household survey
             respondents, 51 (23.4%) managed care respondents, and 173
             (57.7%) NYU Langone respondents met DSM-5 criteria for adult
             ADHD in the semistructured diagnostic interview. Of the
             respondents who met DSM-5 criteria for adult ADHD, 123 were
             male (45.9%); mean (SD) age was 33.1 (11.4) years. A
             6-question screening scale was found to be optimal in
             distinguishing cases from noncases in the first 2 samples.
             Operating characteristics were excellent at the diagnostic
             threshold in the weighted (to the 8.2% DSM-5/Adult ADHD
             Clinical Diagnostic Scale population prevalence) data
             (sensitivity, 91.4%; specificity, 96.0%; AUC, 0.94; PPV,
             67.3%). Operating characteristics were similar despite a
             much higher prevalence (57.7%) when the scale was applied to
             the NYU Langone clinical sample (sensitivity, 91.9%;
             specificity, 74.0%; AUC, 0.83; PPV, 82.8%).The new ADHD
             screening scale is short, easily scored, detects the vast
             majority of general population cases at a threshold that
             also has high specificity and PPV, and could be used as a
             screening tool in specialty treatment settings.},
   Doi = {10.1001/jamapsychiatry.2017.0298},
   Key = {fds330625}
}

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


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

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


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

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

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

@article{fds327666,
   Author = {Pisharady, PK and Sotiropoulos, SN and Duarte-Carvajalino, JM and Sapiro, G and Lenglet, C},
   Title = {Estimation of white matter fiber parameters from compressed
             multiresolution diffusion MRI using sparse Bayesian
             learning.},
   Journal = {NeuroImage},
   Year = {2017},
   Month = {June},
   url = {http://dx.doi.org/10.1016/j.neuroimage.2017.06.052},
   Abstract = {We present a sparse Bayesian unmixing algorithm BusineX:
             Bayesian Unmixing for Sparse Inference-based Estimation of
             Fiber Crossings (X), for estimation of white matter fiber
             parameters from compressed (under-sampled) diffusion MRI
             (dMRI) data. BusineX combines compressive sensing with
             linear unmixing and introduces sparsity to the previously
             proposed multiresolution data fusion algorithm RubiX,
             resulting in a method for improved reconstruction,
             especially from data with lower number of diffusion
             gradients. We formulate the estimation of fiber parameters
             as a sparse signal recovery problem and propose a linear
             unmixing framework with sparse Bayesian learning for the
             recovery of sparse signals, the fiber orientations and
             volume fractions. The data is modeled using a parametric
             spherical deconvolution approach and represented using a
             dictionary created with the exponential decay components
             along different possible diffusion directions. Volume
             fractions of fibers along these directions define the
             dictionary weights. The proposed sparse inference, which is
             based on the dictionary representation, considers the
             sparsity of fiber populations and exploits the spatial
             redundancy in data representation, thereby facilitating
             inference from under-sampled q-space. The algorithm improves
             parameter estimation from dMRI through data-dependent local
             learning of hyperparameters, at each voxel and for each
             possible fiber orientation, that moderate the strength of
             priors governing the parameter variances. Experimental
             results on synthetic and in-vivo data show improved accuracy
             with a lower uncertainty in fiber parameter estimates.
             BusineX resolves a higher number of second and third fiber
             crossings. For under-sampled data, the algorithm is also
             shown to produce more reliable estimates.},
   Doi = {10.1016/j.neuroimage.2017.06.052},
   Key = {fds327666}
}

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

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

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

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


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


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

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

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

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

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


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

@article{fds330816,
   Author = {Conrey, JB and Turnage-Butterbaugh, C},
   Title = {On r-gaps between zeros of the Riemann zeta-function},
   Journal = {(submitted)},
   Year = {2017},
   Key = {fds330816}
}

@article{fds330817,
   Author = {Best, A and Dynes, P and Edlesbrunner, X and McDonald, B and Miller, SJ and Turnage-Butterbaugh, C and Weinstein, M},
   Title = {Benford behavior of generalized Zeckendorf
             decompositions},
   Journal = {Combinatorial and Additive Number Theory II: CANT, New York,
             NY, USA 2015 and 2016},
   Publisher = {Springer},
   Year = {2017},
   Key = {fds330817}
}


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

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

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


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


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

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


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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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


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

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

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

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

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

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


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

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

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

 

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