@article{22518, abstract = {Interannual variability of precipitation can directly or indirectly affect many hydrological, ecological, and biogeochemical processes that, in turn, influence climate. Despite the significant importance of the phenomenon, few studies have attempted to elucidate spatial patterns of this variability at the global scale. This study uses land gauge precipitation records of the Global Historical Climatology Network, version 2, as well as reanalysis data to provide an assessment of the spatial organization of characteristics of precipitation interannual variability. The coefficient of variation, skewness, and short- and long-range dependence of the precipitation variability are analyzed. Among the major inferences is that the coefficient of variation of annual precipitation shows a significant correlation with intra-annual seasonality. Specifically, subyearly precipitation anomalies occurring in locations with pronounced seasonality affect the total yearly amount, imposing a higher variability in the annual precipitation fluctuations. Furthermore, the study illustrates that a positive skewness of the distribution of annual precipitation is a robust property worldwide and its magnitude is related to the coefficient of variation. Additionally, annual precipitation exhibits very weak small-lag autocorrelation. Conversely, the intensity of long-memory–long-range dependence is significantly larger than zero, hinting that organized long-term variations are an important feature of the interannual variability of precipitation. }, author = {Fatichi, Simone and Ivanov, V. Yu. and Caporali, E.}, issn = {1520-0442}, journal = {Journal of Climate}, number = {16}, pages = {5512--5523}, publisher = {American Meteorological Society}, title = {{Investigating interannual variability of precipitation at the global scale: Is there a connection with seasonality?}}, doi = {10.1175/jcli-d-11-00356.1}, volume = {25}, year = {2012}, } @article{2263, abstract = {Nestin-cre transgenic mice have been widely used to direct recombination to neural stem cells (NSCs) and intermediate neural progenitor cells (NPCs). Here we report that a readily utilized, and the only commercially available, Nestin-cre line is insufficient for directing recombination in early embryonic NSCs and NPCs. Analysis of recombination efficiency in multiple cre-dependent reporters and a genetic mosaic line revealed consistent temporal and spatial patterns of recombination in NSCs and NPCs. For comparison we utilized a knock-in Emx1cre line and found robust recombination in NSCs and NPCs in ventricular and subventricular zones of the cerebral cortices as early as embryonic day 12.5. In addition we found that the rate of Nestin-cre driven recombination only reaches sufficiently high levels in NSCs and NPCs during late embryonic and early postnatal periods. These findings are important when commercially available cre lines are considered for directing recombination to embryonic NSCs and NPCs.}, author = {Liang, Huixuan and Hippenmeyer, Simon and Ghashghaei, H.}, journal = {Biology Open}, number = {12}, pages = {1200 -- 1203}, publisher = {Company of Biologists}, title = {{A Nestin-cre transgenic mouse is insufficient for recombination in early embryonic neural progenitors}}, doi = {10.1242/bio.20122287}, volume = {1}, year = {2012}, } @article{22538, abstract = {Numerous studies have explored the role of vegetation in controlling and mediating hydrological states and fluxes at the level of individual processes, which has led to improvements in our understanding of plot-scale dynamics. Relatively less effort has been directed toward spatially-explicit studies of vegetation-hydrology interactions at larger scales of a landscape. Only few continuous, process-oriented ecohydrological models had been proposed with structures of varying complexity. This study contributes to their further evolution and presents a novel ecohydrological model, Tethys-Chloris. The model synthesizes the state-of-the-art knowledge on individual processes and coupling mechanisms drawn from the disciplines of hydrology, plant physiology, and ecology. Specifically, the model reproduces all essential components of the hydrological cycle: it resolves the mass and energy budgets in the atmospheric surface layer at the hourly scale, while representing up to two layers of vegetation; it includes a module of snowpack evolution; it describes the saturated and unsaturated soil water dynamics, processes of runoff generation and flow routing. The component of vegetation dynamics parameterizes life cycle processes of different plant functional types, including photosynthesis, phenology, carbon allocation, and tissue turnover. This study presents a confirmation of the long-term, plot-scale model performance by simulating two types of ecosystems corresponding to different climate conditions. A consistent and highly satisfactory model skill in reproducing the energy and water budgets as well as physiological cycles of plants with minimum calibration overhead is demonstrated. Furthermore, these applications demonstrate that the model permits the identification of data types and observation frequencies crucial for appropriate evaluation of modeled dynamics. More importantly, through a synthesis of a wide array of process representations, the model ensures that climate, soil, vegetation, and topography collectively identify essential modes controlling ecohydrological systems, i.e., that satisfactory performance is a result of appropriate mimicking of internal processes.}, author = {Fatichi, Simone and Ivanov, V. Y. and Caporali, E.}, issn = {1942-2466}, journal = {Journal of Advances in Modeling Earth Systems}, number = {2}, publisher = {American Geophysical Union}, title = {{A mechanistic ecohydrological model to investigate complex interactions in cold and warm water‐controlled environments: 1. Theoretical framework and plot‐scale analysis}}, doi = {10.1029/2011ms000086}, volume = {4}, year = {2012}, } @article{2965, abstract = {Dieser Artikel soll die sechs verschiedenen Creative Commons Lizenzen erläutern und ihre Bedeutung im Rahmen des wissenschaftlichen Publizierens und des Open Access erklären (CC-BY, CC-BY-SA, CC-BY-NC, CC-BY-ND, CC-BYNC-SA, CC-BY-NC-ND).}, author = {Danowski, Patrick}, journal = {Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare}, number = {2}, pages = {200 -- 212}, publisher = {Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare}, title = {{Kontext Open Access: Creative Commons}}, volume = {65}, year = {2012}, } @article{3262, abstract = {Living cells must control the reading out or "expression" of information encoded in their genomes, and this regulation often is mediated by transcription factors--proteins that bind to DNA and either enhance or repress the expression of nearby genes. But the expression of transcription factor proteins is itself regulated, and many transcription factors regulate their own expression in addition to responding to other input signals. Here we analyze the simplest of such self-regulatory circuits, asking how parameters can be chosen to optimize information transmission from inputs to outputs in the steady state. Some nonzero level of self-regulation is almost always optimal, with self-activation dominant when transcription factor concentrations are low and self-repression dominant when concentrations are high. In steady state the optimal self-activation is never strong enough to induce bistability, although there is a limit in which the optimal parameters are very close to the critical point.}, author = {Tkacik, Gasper and Walczak, Aleksandra and Bialek, William}, journal = {Physical Review E}, number = {4}, publisher = {American Physical Society}, title = {{Optimizing information flow in small genetic networks. III. A self-interacting gene}}, doi = {10.1103/PhysRevE.85.041903}, volume = {85}, year = {2012}, } @inproceedings{2936, abstract = {The notion of delays arises naturally in many computational models, such as, in the design of circuits, control systems, and dataflow languages. In this work, we introduce automata with delay blocks (ADBs), extending finite state automata with variable time delay blocks, for deferring individual transition output symbols, in a discrete-time setting. We show that the ADB languages strictly subsume the regular languages, and are incomparable in expressive power to the context-free languages. We show that ADBs are closed under union, concatenation and Kleene star, and under intersection with regular languages, but not closed under complementation and intersection with other ADB languages. We show that the emptiness and the membership problems are decidable in polynomial time for ADBs, whereas the universality problem is undecidable. Finally we consider the linear-time model checking problem, i.e., whether the language of an ADB is contained in a regular language, and show that the model checking problem is PSPACE-complete. Copyright 2012 ACM.}, author = {Chatterjee, Krishnendu and Henzinger, Thomas A and Prabhu, Vinayak}, booktitle = {Proceedings of the 10th ACM international conference on Embedded software}, location = {Tampere, Finland}, pages = {43 -- 52}, publisher = {ACM}, title = {{Finite automata with time delay blocks}}, doi = {10.1145/2380356.2380370}, year = {2012}, } @inproceedings{10907, abstract = {This paper presents a method to create a model of an articulated object using the planar motion in an initialization video. The model consists of rigid parts connected by points of articulation. The rigid parts are described by the positions of salient feature-points tracked throughout the video. Following a filtering step that identifies points that belong to different objects, rigid parts are found by a grouping process in a graph pyramid. Valid articulation points are selected by verifying multiple hypotheses for each pair of parts.}, author = {Artner, Nicole M. and Ion, Adrian and Kropatsch, Walter G.}, booktitle = {Graph-Based Representations in Pattern Recognition}, editor = {Jiang, Xiaoyi and Ferrer, Miquel and Torsello, Andrea}, isbn = {9783642208430}, issn = {1611-3349}, location = {Münster, Germany}, pages = {215--224}, publisher = {Springer}, title = {{Spatio-temporal extraction of articulated models in a graph pyramid}}, doi = {10.1007/978-3-642-20844-7_22}, volume = {6658}, year = {2011}, } @article{11094, abstract = {Nuclear pore complexes (NPCs) assemble at the end of mitosis during nuclear envelope (NE) reformation and into an intact NE as cells progress through interphase. Although recent studies have shown that NPC formation occurs by two different molecular mechanisms at two distinct cell cycle stages, little is known about the molecular players that mediate the fusion of the outer and inner nuclear membranes to form pores. In this paper, we provide evidence that the transmembrane nucleoporin (Nup), POM121, but not the Nup107–160 complex, is present at new pore assembly sites at a time that coincides with inner nuclear membrane (INM) and outer nuclear membrane (ONM) fusion. Overexpression of POM121 resulted in juxtaposition of the INM and ONM. Additionally, Sun1, an INM protein that is known to interact with the cytoskeleton, was specifically required for interphase assembly and localized with POM121 at forming pores. We propose a model in which POM121 and Sun1 interact transiently to promote early steps of interphase NPC assembly.}, author = {Talamas, Jessica A. and HETZER, Martin W}, issn = {1540-8140}, journal = {Journal of Cell Biology}, keywords = {Cell Biology}, number = {1}, pages = {27--37}, publisher = {Rockefeller University Press}, title = {{POM121 and Sun1 play a role in early steps of interphase NPC assembly}}, doi = {10.1083/jcb.201012154}, volume = {194}, year = {2011}, } @article{11095, author = {HETZER, Martin W and Cavalli, Giacomo}, issn = {0955-0674}, journal = {Current Opinion in Cell Biology}, keywords = {Cell Biology}, number = {3}, pages = {255--257}, publisher = {Elsevier}, title = {{Editorial overview}}, doi = {10.1016/j.ceb.2011.04.013}, volume = {23}, year = {2011}, } @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{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 = {Lemeshko, Mikhail and Mustafa, Mustafa 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}, } @article{22040, abstract = {We consider the defocusing nonlinear wave equation (mathematical formular) in the energy-supercritical regime p > 4. For even values of the power p, we show that blowup (or failure to scatter) must be accompanied by blowup of the critical Sobolev norm. An equivalent formulation is that solutions with bounded critical Sobolev norm are global and scatter. The impetus to consider this problem comes from recent work of Kenig and Merle who treated the case of spherically-symmetric solutions.}, author = {Killip, Rowan and Visan, Monica}, issn = {1088-6850}, journal = {Transactions of the American Mathematical Society}, number = {7}, pages = {3893--3893}, publisher = {American Mathematical Society}, title = {{The defocusing energy-supercritical nonlinear wave equation in three space dimensions}}, doi = {10.1090/s0002-9947-2011-05400-0}, volume = {363}, 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}, }