@article{11096, abstract = {As the gatekeepers of the eukaryotic cell nucleus, nuclear pore complexes (NPCs) mediate all molecular trafficking between the nucleoplasm and the cytoplasm. In recent years, transport-independent functions of NPC components, nucleoporins, have been identified including roles in chromatin organization and gene regulation. Here, we summarize our current view of the NPC as a dynamic hub for the integration of chromatin regulation and nuclear trafficking and discuss the functional interplay between nucleoporins and the nuclear genome.}, author = {Liang, Yun and HETZER, Martin W}, issn = {0955-0674}, journal = {Current Opinion in Cell Biology}, keywords = {Cell Biology}, number = {1}, pages = {65--70}, publisher = {Elsevier}, title = {{Functional interactions between nucleoporins and chromatin}}, doi = {10.1016/j.ceb.2010.09.008}, volume = {23}, year = {2011}, } @article{11100, abstract = {Eukaryotic cell function depends on the physical separation of nucleoplasmic and cytoplasmic components by the nuclear envelope (NE). Molecular communication between the two compartments involves active, signal-mediated trafficking, a function that is exclusively performed by nuclear pore complexes (NPCs). The individual NPC components and the mechanisms that are involved in nuclear trafficking are well documented and have become textbook knowledge. However, in addition to their roles as nuclear gatekeepers, NPC components-nucleoporins-have been shown to have critical roles in chromatin organization and gene regulation. These findings have sparked new enthusiasm to study the roles of this multiprotein complex in nuclear organization and explore novel functions that in some cases appear to go beyond a role in transport. Here, we discuss our present view of NPC biogenesis, which is tightly linked to proper cell cycle progression and cell differentiation. In addition, we summarize new data suggesting that NPCs represent dynamic hubs for the integration of gene regulation and nuclear transport processes.}, author = {Capelson, M. and Doucet, C. and HETZER, Martin W}, isbn = {9781936113071}, issn = {0091-7451}, journal = {Cold Spring Harbor Symposia on Quantitative Biology}, keywords = {Genetics, Molecular Biology, Biochemistry}, pages = {585--597}, publisher = {Cold Spring Harbor Laboratory Press}, title = {{Nuclear pore complexes: Guardians of the nuclear genome}}, doi = {10.1101/sqb.2010.75.059}, volume = {75}, year = {2011}, } @article{112, abstract = {Particle beams are important tools for probing atomic and molecular interactions. Here we demonstrate that particle beams also offer a unique opportunity to investigate interactions in macroscopic systems, such as granular media. Motivated by recent experiments on streams of grains that exhibit liquid-like breakup into droplets, we use molecular dynamics simulations to investigate the evolution of a dense stream of macroscopic spheres accelerating out of an opening at the bottom of a reservoir. We show how nanoscale details associated with energy dissipation during collisions modify the stream\'s macroscopic behavior. We find that inelastic collisions collimate the stream, while the presence of short-range attractive interactions drives structure formation. Parameterizing the collision dynamics by the coefficient of restitution (i.e., the ratio of relative velocities before and after impact) and the strength of the cohesive interaction, we map out a spectrum of behaviors that ranges from gaslike jets in which all grains drift apart to liquid-like streams that break into large droplets containing hundreds of grains. We also find a new, intermediate regime in which small aggregates form by capture from the gas phase, similar to what can be observed in molecular beams. Our results show that nearly all aspects of stream behavior are closely related to the velocity gradient associated with vertical free fall. Led by this observation, we propose a simple energy balance model to explain the droplet formation process. The qualitative as well as many quantitative features of the simulations and the model compare well with available experimental data and provide a first quantitative measure of the role of attractions in freely cooling granular streams.}, author = {Waitukaitis, Scott R and Grütjen, Helge and Royer, John and Jaeger, Heinrich}, journal = {Physical Review E}, number = {5}, publisher = {American Physical Society}, title = {{Droplet and cluster formation in freely falling granular streams}}, doi = {10.1103/PhysRevE.83.051302}, volume = {83}, year = {2011}, } @article{11673, abstract = {Given only the URL of a Web page, can we identify its topic? We study this problem in detail by exploring a large number of different feature sets and algorithms on several datasets. We also show that the inherent overlap between topics and the sparsity of the information in URLs makes this a very challenging problem. Web page classification without a page’s content is desirable when the content is not available at all, when a classification is needed before obtaining the content, or when classification speed is of utmost importance. For our experiments we used five different corpora comprising a total of about 3 million (URL, classification) pairs. We evaluated several techniques for feature generation and classification algorithms. The individual binary classifiers were then combined via boosting into metabinary classifiers. We achieve typical F-measure values between 80 and 85, and a typical precision of around 86. The precision can be pushed further over 90 while maintaining a typical level of recall between 30 and 40.}, author = {Baykan, Eda and Henzinger, Monika H and Marian, Ludmila and Weber, Ingmar}, issn = {1559-114X}, journal = {ACM Transactions on the Web}, keywords = {Topic classification, URL, ODP}, number = {3}, publisher = {Association for Computing Machinery}, title = {{A comprehensive study of features and algorithms for URL-based topic classification}}, doi = {10.1145/1993053.1993057}, volume = {5}, year = {2011}, } @article{11760, abstract = {We study a novel load balancing problem that arises in web search engines. The problem is a combination of an offline assignment problem, where files need to be (copied and) assigned to machines, and an online load balancing problem, where requests ask for specific files and need to be assigned to a corresponding machine, whose load is increased by this. We present simple deterministic algorithms for this problem and exhibit an interesting trade-off between the available space to make file copies and the obtainable makespan. We also give non-trivial lower bounds for a large class of deterministic algorithms and present a randomized algorithm that beats these bounds with high probability.}, author = {Dütting, Paul and Henzinger, Monika H and Weber, Ingmar}, issn = {0020-0190}, journal = {Information Processing Letters}, number = {4}, pages = {178--183}, publisher = {Elsevier}, title = {{Offline file assignments for online load balancing}}, doi = {10.1016/j.ipl.2010.11.022}, volume = {111}, year = {2011}, } @inproceedings{11796, abstract = {The design of truthful auctions that approximate the optimal expected revenue is a central problem in algorithmic mechanism design. 30 years after Myerson’s characterization of Bayesian optimal auctions in single-parameter domains [8], characterizing but also providing efficient mechanisms for multi-parameter domains still remains a very important unsolved problem. Our work improves upon recent results in this area, introducing new techniques for tackling the problem, while also combining and extending recently introduced tools. In particular we give the first approximation algorithms for Bayesian auctions with multiple heterogeneous items when bidders have additive valuations, budget constraints and general matroid feasibility constraints.}, author = {Henzinger, Monika H and Vidali, Angelina}, booktitle = {19th Annual European Symposium on Algorithms}, isbn = {9783642237188}, issn = {1611-3349}, location = {Saarbrücken, Germany}, pages = {192–202}, publisher = {Springer Nature}, title = {{Multi-parameter mechanism design under budget and matroid constraints}}, doi = {10.1007/978-3-642-23719-5_17}, volume = {6942}, year = {2011}, } @inproceedings{11864, abstract = {Auctions are widely used on the Web. Applications range from internet advertising to platforms such as eBay. In most of these applications the auctions in use are single/multi-item auctions with unit demand. The main drawback of standard mechanisms for this type of auctions, such as VCG and GSP, is the limited expressiveness that they offer to the bidders. The General Auction Mechanism (GAM) of [1] is taking a first step towards addressing the problem of limited expressiveness by computing a bidder optimal, envy free outcome for linear utility functions with identical slopes and a single discontinuity per bidder-item pair. We show that in many practical situations this does not suffice to adequately model the preferences of the bidders, and we overcome this problem by presenting the first mechanism for piece-wise linear utility functions with non-identical slopes and multiple discontinuities. Our mechanism runs in polynomial time. Like GAM it is incentive compatible for inputs that fulfill a certain non-degeneracy requirement, but our requirement is more general than the requirement of GAM. For discontinuous utility functions that are non-degenerate as well as for continuous utility functions the outcome of our mechanism is a competitive equilibrium. We also show how our mechanism can be used to compute approximately bidder optimal, envy free outcomes for a general class of continuous utility functions via piece-wise linear approximation. Finally, we prove hardness results for even more expressive settings.}, author = {Dütting, Paul and Henzinger, Monika H and Weber, Ingmar}, booktitle = {Proceedings of the 20th international conference on World wide web}, isbn = {978-145030632-4}, location = {Hyderabad, India}, pages = {127 -- 136}, publisher = {Association for Computing Machinery}, title = {{An expressive mechanism for auctions on the web}}, doi = {10.1145/1963405.1963427}, year = {2011}, } @article{2072, abstract = {Many species have morphologically and genetically differentiated sex chromosomes, such as the XY pair of mammals. Y chromosomes are often highly degenerated and carry few functional genes, so that XY males have only one copy of most Xlinked genes (whereas females have two). As a result, chromosome-wide mechanisms of dosage compensation, such as the mammalian X-inactivation, often evolve to reestablish expression balance. A similar phenomenon is expected in femaleheterogametic species, where ZW females should suffer from imbalances due to W-chromosome degeneration. However, no global dosage compensation mechanisms have been detected in the two independent ZW systems that have been studied systematically (birds and silkworm), leading to the suggestion that lack of global dosage compensation may be a general feature of female-heterogametic species. However, analyses of other independently evolved ZW systems are required to test if this is the case. In this study, we use published genomic and expression data to test for the presence of global dosage compensation in Schistosoma mansoni, a trematode parasite that causes schistosomiasis in humans. We find that Z-linked expression is reduced relative to autosomal expression in females but not males, consistent with incomplete or localized dosage compensation. This gives further support to the theory that female-heterogametic species may not require global mechanisms of dosage compensation.}, author = {Vicoso, Beatriz and Bachtrog, Doris}, journal = {Genome Biology and Evolution}, number = {1}, pages = {230 -- 235}, publisher = {Oxford University Press}, title = {{Lack of global dosage compensation in Schistosoma mansoni, a female-heterogametic parasite}}, doi = {10.1093/gbe/evr010}, volume = {3}, year = {2011}, } @inbook{2098, abstract = {This chapter presents a method for real-time animation of highly detailed facial expressions based on sparse motion captures data and a limited set of static example poses. The method for real-time animation of highly detailed facial expressions decomposes geometry into large-scale motion and fine-scale details, such as expression wrinkles. Both large- and fine-scale deformation algorithms run entirely on the GPU, and our implementation based on CUDA achieves an overall performance of about 30 fps. The face conveys the most relevant visual characteristics of human identity and expression. Hence, realistic facial animations or interactions with virtual avatars are important for storytelling and gameplay. However, current approaches are either computationally expensive, require very specialized capture hardware, or are extremely labor intensive. At runtime, given an arbitrary facial expression, the algorithm computes the skin strain from the relative distance between marker points and derives fine-scale corrections for the largescale deformation. During gameplay only the sparse set of marker-point positions is transmitted to the GPU. The face animation is entirely computed on the GPU where the resulting mesh can directly be used as input for the rendering stages. This data can be easily obtained by traditional capture hardware. The proposed in-game algorithm is fast. It also is easy to implement and maps well onto programmable GPUs.}, author = {Bernd Bickel and Lang, Manuel}, booktitle = {GPU Computing Gems Emerald Edition}, pages = {413 -- 426}, publisher = {Science Direct}, title = {{From sparse mocap to highly detailed facial animation}}, doi = {10.1016/B978-0-12-384988-5.00027-9}, year = {2011}, } @article{2099, abstract = {We present a new technique for passive and markerless facial performance capture based on anchor frames. Our method starts with high resolution per-frame geometry acquisition using state-of-theart stereo reconstruction, and proceeds to establish a single triangle mesh that is propagated through the entire performance. Leveraging the fact that facial performances often contain repetitive subsequences, we identify anchor frames as those which contain similar facial expressions to a manually chosen reference expression. Anchor frames are automatically computed over one or even multiple performances. We introduce a robust image-space tracking method that computes pixel matches directly from the reference frame to all anchor frames, and thereby to the remaining frames in the sequence via sequential matching. This allows us to propagate one reconstructed frame to an entire sequence in parallel, in contrast to previous sequential methods. Our anchored reconstruction approach also limits tracker drift and robustly handles occlusions and motion blur. The parallel tracking and mesh propagation offer low computation times. Our technique will even automatically match anchor frames across different sequences captured on different occasions, propagating a single mesh to all performances.}, author = {Beeler, Thabo and Hahn, Fabian and Bradley, Derek J and Bernd Bickel and Beardsley, Paul A and Gotsman, Craig and Sumner, Robert W and Groß, Markus S}, journal = {ACM Transactions on Graphics}, number = {4}, publisher = {ACM}, title = {{High-quality passive facial performance capture using anchor frames}}, doi = {10.1145/2010324.1964970}, volume = {30}, year = {2011}, } @inproceedings{2100, abstract = {Acquiring panoramic images using stitching takes a lot of time and moving objects may cause ghosting. It is also difficult to obtain a full spherical panorama, because the downward picture cannot be captured while the camera is mounted on the tripod.}, author = {Pfeil, Jonas and Hildebrand, Kristian and Gremzow, Carsten and Bernd Bickel and Alexa, Marc}, publisher = {ACM}, title = {{Throwable panoramic ball camera}}, doi = {10.1145/2073370.2073373}, year = {2011}, } @inbook{2116, abstract = {Let P be the Ornstein-Uhlenbeck semigroup associated with the stochastic Cauchy problem dU(t)=AU(t)dt+dWH(t), where A is the generator of a C 0-semigroup S on a Banach space E, H is a Hilbert subspace of E, and W H is an H-cylindrical Brownian motion. Assuming that S restricts to a C 0-semigroup on H, we obtain L p -bounds for D H P(t). We show that if P is analytic, then the invariance assumption is fulfilled. As an application we determine the L p -domain of the generator of P explicitly in the case where S restricts to a C 0-semigroup on H which is similar to an analytic contraction semigroup. The results are applied to the 1D stochastic heat equation driven by additive space-time white noise.}, author = {Jan Maas and Van Neerven, Jan}, booktitle = {Parabolic Problems}, pages = {463 -- 477}, publisher = {Birkhäuser}, title = {{Gradient estimates and domain identification for analytic Ornstein-Uhlenbeck operators}}, doi = {10.1007/978-3-0348-0075-4_24}, volume = {80}, year = {2011}, } @article{2122, abstract = {We study, in L1(R̃n; γ) with respect to the gaussian measure, non- tangential maximal functions and conical square functions associ- ated with the Ornstein-Uhlenbeck operator by developing a set of techniques which allow us, to some extent, to compensate for the non-doubling character of the gaussian measure. The main result asserts that conical square functions can be controlled in L1-norm by non-tangential maximal functions. Along the way we prove a change of aperture result for the latter. This complements recent results on gaussian Hardy spaces due to Mauceri and Meda.}, author = {Jan Maas and van Neerven, Jan M and Portal, Pierre}, journal = {Publicacions Matemàtiques}, number = {2}, pages = {313 -- 341}, publisher = {Universitat Autònoma de Barcelona, Departament de Matemàtique}, title = {{Conical square functions and non-tangential maximal functions with respect to the Gaussian measure}}, doi = {10.5565/PUBLMAT_55211_03 }, volume = {55}, year = {2011}, } @article{2123, abstract = {We prove a Trotter product formula for gradient flows in metric spaces. This result is applied to establish convergence in the L 2-Wasserstein metric of the splitting method for some Fokker-Planck equations and porous medium type equations perturbed by a potential.}, author = {Clément, Philippe and Maas, Jan}, journal = {Journal of Evolution Equations}, number = {2}, pages = {405 -- 427}, publisher = {Birkhäuser}, title = {{A Trotter product formula for gradient flows in metric spaces}}, doi = {10.1007/s00028-010-0096-5}, volume = {11}, year = {2011}, } @article{2126, abstract = {Let K be an irreducible and reversible Markov kernel on a finite set X. We construct a metric W on the set of probability measures on X and show that with respect to this metric, the law of the continuous time Markov chain evolves as the gradient flow of the entropy. This result is a discrete counterpart of the Wasserstein gradient flow interpretation of the heat flow in Rn by Jordan, Kinderlehrer and Otto (1998). The metric W is similar to, but different from, the L2-Wasserstein metric, and is defined via a discrete variant of the Benamou–Brenier formula. }, author = {Jan Maas}, journal = {Journal of Functional Analysis}, number = {8}, pages = {2250 -- 2292}, publisher = {Academic Press}, title = {{Gradient flows of the entropy for finite Markov chains}}, doi = {10.1016/j.jfa.2011.06.009 }, volume = {261}, year = {2011}, } @unpublished{2138, abstract = {A (diatomic) shape resonance is a metastable state of a pair of colliding atoms quasi-bound by the centrifugal barrier imposed by the angular momentum involved in the collision. The temporary trapping of the atoms' scattering wavefunction corresponds to an enhanced atom pair density at low interatomic separations. This leads to larger overlap of the wavefunctions involved in a molecule formation process such as photoassociation, rendering the process more efficient. However, for an ensemble of atoms, the atom pair density will only be enhanced if the energy of the resonance comes close to the temperature of the atomic ensemble. Herein we explore the possibility of controlling the energy of a shape resonance by shifting it toward the temperature of atoms confined in a trap. The shifts are imparted by the interaction of non-resonant light with the anisotropic polarizability of the atom pair, which affects both the centrifugal barrier and the pair's rotational and vibrational levels. We find that at laser intensities of up to 5×109 W/cm2 the pair density is increased by one order of magnitude for 87Rb atoms at 100μK and by two orders of magnitude for 88Sr atoms at 20μK.}, author = {Ağanoğlu, Ruzin and Mikhail Lemeshko and Friedrich, Břetislav and González-Férez, Rosario and Koch, Christiane P}, booktitle = {Unknown}, publisher = {ArXiv}, title = {{Controlling a diatomic shape resonance with non-resonant light}}, year = {2011}, } @article{2198, abstract = {We show that dressing polar molecules with a far-off-resonant optical field leads to new types of intermolecular potentials, which undergo a crossover from the inverse power to oscillating behavior depending on the intermolecular distance, and whose parameters can be tuned by varying the laser intensity and wavelength. We present analytic expressions for the potential energy surfaces, thereby providing direct access to the parameters of an optical field required to design intermolecular interactions experimentally.}, author = {Mikhail Lemeshko}, journal = {Physical Review A - Atomic, Molecular, and Optical Physics}, number = {5}, publisher = {American Physical Society}, title = {{Shaping interactions between polar molecules with far-off-resonant light}}, doi = {10.1103/PhysRevA.83.051402}, volume = {83}, year = {2011}, } @article{2199, abstract = {By invoking supersymmetry, we found a condition under which the Stark-effect problem for a polar and polarizable molecule subject to nonresonant electric fields becomes exactly solvable for the family of stretched states. The analytic expressions for the wave function and eigenenergy and other expectation values allow one to readily reverse-engineer the problem of finding the values of the interaction parameters required for creating quantum states with preordained characteristics. The method also allows the construction of families of isospectral potentials, realizable with combined fields.}, author = {Mikhail Lemeshko and Mustafa, Mustafa K and Kais, Sabre and Friedrich, Břetislav}, journal = {Physical Review A - Atomic, Molecular, and Optical Physics}, number = {4}, publisher = {American Physical Society}, title = {{Supersymmetric factorization yields exact solutions to the molecular Stark-effect problem for "stretched" states}}, doi = {10.1103/PhysRevA.83.043415}, volume = {83}, year = {2011}, } @article{2200, abstract = {We made use of supersymmetric (SUSY) quantum mechanics to find the condition under which the Stark effect problem for a polar and polarizable closed-shell diatomic molecule subjected to collinear electrostatic and nonresonant radiative fields becomes exactly solvable. The condition Δω = ω2/4(m+1)2 connects values of the dimensionless parameters ω and Δω that characterize the strengths of the permanent and induced dipole interactions of the molecule with the respective fields. The exact solutions are obtained for the \J̃ = m, m; ω, Δω) family of 'stretched' states. The field-free and strong-field limits of the combined-fields problem were found to exhibit supersymmetry and shape invariance, which is indeed the reason why they are analytically solvable. By making use of the analytic form of the \J̃ = m,m; ω, Δω) wavefunctions, we obtained simple formulae for the expectation values of the space-fixed electric dipole moment, the alignment cosine and the angular momentum squared, and derived a 'sum rule' that combines the above expectation values into a formula for the eigenenergy. The analytic expressions for the characteristics of the strongly oriented and aligned states provide direct access to the values of the interaction parameters required for creating such states in the laboratory.}, author = {Mikhail Lemeshko and Mustafa, Mustafa K and Kais, Sabre and Friedrich, Břetislav}, journal = {New Journal of Physics}, publisher = {IOP Publishing Ltd.}, title = {{Supersymmetry identifies molecular Stark states whose eigenproperties can be obtained analytically}}, doi = {10.1088/1367-2630/13/6/063036}, volume = {13}, year = {2011}, } @misc{2312, abstract = {Soon, the genetic basis of most human Mendelian diseases will be solved. The next challenge will be to leverage this information to uncover basic mechanisms of disease and develop new therapies. To understand how this transformation is already beginning to unfold, we focus on the ciliopathies, a class of multi-organ diseases caused by disruption of the primary cilium. Through a convergence of data involving mutant gene discovery, proteomics, and cell biology, more than a dozen phenotypically distinguishable conditions are now united as ciliopathies. Sitting at the interface between simple and complex genetic conditions, these diseases provide clues to the future direction of human genetics.}, author = {Gaia Novarino and Akizu, Naiara and Gleeson, Joseph G}, booktitle = {Cell}, number = {1}, pages = {70 -- 79}, publisher = {Cell Press}, title = {{Modeling human disease in humans: The ciliopathies}}, doi = {10.1016/j.cell.2011.09.014}, volume = {147}, year = {2011}, }